Rv3183 Family assigned · medium auto-curated
H37Rv Rv3183 · MTBC0 mtbc0_003384 ·
109 aa · 3575563–3575892 (+) ·
RefSeq NP_217699.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | XRE family transcriptional regulator |
| Revised (this work) | XRE family transcriptional regulator. Pfam: HTH_37 (PF13744.13), HTH_31 (PF13560.13), HTH_3 (PF01381.29). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53333
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative antitoxin HigA3 |
| Curated function | Putative antitoxin component of a type II toxin-antitoxin (TA) system. Its cognate toxin would be HigB3. |
UniProt still lists this protein as Putative antitoxin HigA3; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | Helix-turn-helix 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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 0 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.17% of strains (246) · 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_37 | PF13744.13 | 5.4e-07 | 37–98 | Helix-turn-helix domain |
HTH_31 | PF13560.13 | 1.4e-06 | 37–91 | Helix-turn-helix domain |
HTH_3 | PF01381.29 | 5.2e-08 | 41–95 | Helix-turn-helix |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3182 higB3 hyp |
hypothetical protein | 991 | 972 ctx | neighborhood:882 cooccurence:771 textmining:701 |
Rv0691c mftR |
mycofactocin biosynthesis transcriptional regulator MftR | 882 | 882 | coexpression:850 |
Rv3263 |
DNA methylase | 859 | 859 | coexpression:859 |
Rv3066 |
DeoR family transcriptional regulator | 857 | 857 | coexpression:833 |
Rv3840 |
transcriptional regulator | 848 | 848 | coexpression:848 |
Rv1776c |
transcriptional regulator | 845 | 845 | coexpression:845 |
Rv1985c lysG |
HTH-type transcriptional regulator | 850 | 844 | coexpression:844 |
Rv3736 |
AraC/XylS family transcriptional regulator | 846 | 841 | coexpression:841 |
Rv3167c |
TetR family transcriptional regulator | 836 | 836 | coexpression:836 |
Rv1725c hyp |
hypothetical protein | 842 | 835 | coexpression:835 |
Rv0339c iniR |
transcriptional regulator | 840 | 835 | coexpression:812 |
Rv0212c nadR |
transcriptional regulator NadR | 833 | 833 | coexpression:810 |
Rv1674c |
transcriptional regulator | 838 | 832 | coexpression:832 |
Rv3055 |
TetR family transcriptional regulator | 824 | 825 | coexpression:800 |
Rv2621c |
transcriptional regulator | 824 | 824 | coexpression:797 |
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: transcriptional regulator
- MTBC0 PGAP product: XRE family transcriptional regulator
- Pfam (hmmscan --cut_ga): HTH_37 PF13744.13 (E=5e-07), HTH_31 PF13560.13 (E=1e-06), HTH_3 PF01381.29 (E=5e-08)
- (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_217699.1)
- Domains: Pfam-A via hmmscan --cut_ga — HTH_37 (PF13744.13), HTH_31 (PF13560.13), HTH_3 (PF01381.29)
- 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
COG1396 - Curated reference: UniProt O53333 (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 — 99 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003384|Rv3183| MTMARNWRDIRADAVAQGRVDLQRAAVAREEMRDAVLAHRLAEIRKALGHARQADVAALMGVSQARVSKLESGDLSHTELGTLQAYVAALGGHLRIVAEFGENTVELTA