Rv2324 Family assigned · medium auto-curated
H37Rv Rv2324 · MTBC0 mtbc0_002472 ·
148 aa · 2621083–2621529 (+) ·
RefSeq NP_216840.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | AsnC family transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | Lrp/AsnC family transcriptional regulator |
| Revised (this work) | Lrp/AsnC family transcriptional regulator. Pfam: HTH_AsnC-type (PF13404.13), HTH_24 (PF13412.13), 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.
Curated reference (UniProt)
| UniProt |
P71888
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | HTH-type transcriptional regulator Rv2324 |
| Curated function | Transcriptional regulator involved in growth, DNA replication and damage control. Plays a crucial role in regulating survival and growth of M.tuberculosis. Could function as a global regulator in both the latent/persistent and active phases of growth. Binds to its own promoter region and to promoters of multiple metabolic genes, such as serB2, lat, ald and roc operon. In vitro, interacts with intrinsically curved and non-curved DNA molecules, and with both supercoiled and linear DNA, with higher affinity for supercoiled DNA. Binds to DNA recombination, replication and repair intermediates. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | transcriptional |
| 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 | 0.653 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 2 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 |
|---|---|---|---|---|
HTH_AsnC-type | PF13404.13 | 3.5e-15 | 4–44 | AsnC-type helix-turn-helix domain |
HTH_24 | PF13412.13 | 1.9e-14 | 4–51 | Winged helix-turn-helix DNA-binding |
AsnC_trans_reg | PF01037.29 | 4.0e-17 | 68–147 | Lrp/AsnC ligand binding domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2319c (universal stress protein), medium confidence from genomic context alone (score 615 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2323c hyp |
hypothetical protein | 943 | 710 ctx | neighborhood:618 textmining:813 |
Rv1725c hyp |
hypothetical protein | 692 | 690 | coexpression:690 |
Rv2621c |
transcriptional regulator | 656 | 655 | coexpression:655 |
Rv2319c |
universal stress protein | 713 | 615 ctx | neighborhood:613 |
Rv2320c rocE |
cationic amino acid transporter permease RocE | 650 | 613 ctx | neighborhood:606 |
Rv2322c rocD1 |
Rv2322c, (MTCY3G12.12), len: 221 aa. Probable rocD1,ornithine aminotransferase, highly similar to N-terminal region of other ornithine amino | 597 | 594 ctx | neighborhood:590 |
Rv2321c rocD2 |
Rv2321c, (MTCY3G12.13), len: 181 aa. Probable rocD2,ornithine aminotransferase, highly similar to C-terminal region of other ornithine amino | 684 | 593 ctx | neighborhood:590 |
Rv3291c lrpA |
transcriptional regulator LrpA | 531 | 532 | coexpression:415 |
Rv1985c lysG |
HTH-type transcriptional regulator | 502 | 474 | coexpression:474 |
Rv3183 higA3 |
transcriptional regulator | 463 | 441 | coexpression:441 |
Rv3167c |
TetR family transcriptional regulator | 426 | 409 | coexpression:409 |
Rv0339c iniR |
transcriptional regulator | 425 | 404 | |
Rv3736 |
AraC/XylS family transcriptional regulator | 434 | 402 | |
Rv3066 |
DeoR family transcriptional regulator | 554 | 398 | |
Rv0792c |
transcriptional regulator | 414 | 386 |
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: AsnC family transcriptional regulator
- MTBC0 PGAP product: Lrp/AsnC family transcriptional regulator
- Pfam (hmmscan --cut_ga): HTH_AsnC-type PF13404.13 (E=4e-15), HTH_24 PF13412.13 (E=2e-14), AsnC_trans_reg PF01037.29 (E=4e-17)
- (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_216840.1)
- Domains: Pfam-A via hmmscan --cut_ga — HTH_AsnC-type (PF13404.13), HTH_24 (PF13412.13), 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 P71888 (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 —
26 functional partner(s); context anchor
Rv2319c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002472|Rv2324| MDRLDDTDERILAELAEHARATFAEIGHKVSLSAPAVKRRVDRMLESGVIKGFTTVVDRNALGWNTEAYVQIFCHGRIAPDQLRAAWVNIPEVVSAATVTGTSDAILHVLAHDMRHLEAALERIRSSADVERSESTVVLSNLIDRMPP