Rv1674c Family assigned · medium auto-curated
H37Rv Rv1674c · MTBC0 mtbc0_001781 ·
218 aa · 1911275–1911931 (-) ·
RefSeq NP_216190.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | metalloregulator ArsR/SmtB family transcription factor |
| Revised (this work) | Metalloregulator ArsR/SmtB family transcription factor. Pfam: HTH_20 (PF12840.14), HTH_5 (PF01022.27), Rhodanese (PF00581.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53921
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable transcriptional regulatory protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | Rhodanese-like domain |
| Orthologous group | COG0607 |
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 | 0.737 · 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_20 | PF12840.14 | 3.0e-06 | 19–68 | Helix-turn-helix domain |
HTH_5 | PF01022.27 | 3.1e-07 | 24–67 | Bacterial regulatory protein, arsR family |
Rhodanese | PF00581.26 | 2.4e-16 | 120–210 | Rhodanese-like domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: cmr (HTH-type transcriptional regulator Cmr), high confidence from genomic context alone (score 903 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1675c cmr |
HTH-type transcriptional regulator Cmr | 918 | 903 ctx | neighborhood:420 coexpression:839 |
Rv1931c |
transcriptional regulator | 864 | 864 | coexpression:862 |
Rv3167c |
TetR family transcriptional regulator | 866 | 861 | coexpression:861 |
Rv0494 |
HTH-type transcriptional regulator | 866 | 861 | coexpression:859 |
Rv1267c embR |
transcriptional regulator EmbR | 860 | 860 | coexpression:860 |
Rv0212c nadR |
transcriptional regulator NadR | 860 | 860 | coexpression:860 |
Rv3840 |
transcriptional regulator | 860 | 860 | coexpression:860 |
Rv0691c mftR |
mycofactocin biosynthesis transcriptional regulator MftR | 863 | 858 | coexpression:858 |
Rv3830c |
TetR family transcriptional regulator | 859 | 854 | coexpression:854 |
Rv3736 |
AraC/XylS family transcriptional regulator | 859 | 851 | coexpression:848 |
Rv1359 |
transcriptional regulator | 850 | 850 | coexpression:850 |
Rv3082c virS |
HTH-type transcriptional regulator VirS | 853 | 845 | coexpression:841 |
Rv3124 moaR1 |
transcriptional regulator MoaR | 845 | 845 | coexpression:845 |
Rv0194 |
multidrug ABC transporter ATPase/permease | 850 | 844 | coexpression:772 |
Rv1151c cobB |
NAD-dependent protein deacylase | 841 | 841 | coexpression:836 |
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: metalloregulator ArsR/SmtB family transcription factor
- Pfam (hmmscan --cut_ga): HTH_20 PF12840.14 (E=3e-06), HTH_5 PF01022.27 (E=3e-07), Rhodanese PF00581.26 (E=2e-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_216190.1)
- Domains: Pfam-A via hmmscan --cut_ga — HTH_20 (PF12840.14), HTH_5 (PF01022.27), Rhodanese (PF00581.26)
- 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
COG0607 - Curated reference: UniProt O53921 (TrEMBL, unreviewed; 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 —
131 functional partner(s); context anchor
cmr - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001781|Rv1674c| MSGAKKLIFEQFALVGQALSSGHRLELLDLLVQGERSVDALARASGLTFANASQHLLQLRRAGLVTSRRDGKRVIYALSDPQVWDVVRAVRAVAERNLASVGSLVRQYYTDRDSLEPISRDELQARVAAGSVLVLDVRPAMEYAAGHLPGAVSIPLDELAERLDELPSGIDIVACCRGPYCVYAYDALELLRPNGFSARRLDGGFSEWLAADLPVVRT