Rv2642 Family assigned · medium auto-curated
H37Rv Rv2642 · MTBC0 mtbc0_002812 ·
126 aa · 2990094–2990474 (+) ·
RefSeq NP_217158.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ArsR family 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). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P71941
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Possible transcriptional regulatory protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | Transcriptional regulator |
| Orthologous group | COG0640 |
| KEGG orthology |
K03892
|
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 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 | 7.1e-10 | 38–90 | Helix-turn-helix domain |
HTH_5 | PF01022.27 | 1.8e-17 | 40–88 | Bacterial regulatory protein, arsR family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: arsC (arsenic-transport integral membrane protein ArsC), high confidence from genomic context alone (score 940 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2643 arsC |
arsenic-transport integral membrane protein ArsC | 954 | 940 ctx | neighborhood:882 |
Rv1674c |
transcriptional regulator | 816 | 811 | coexpression:777 |
Rv1931c |
transcriptional regulator | 788 | 788 | coexpression:738 |
Rv0494 |
HTH-type transcriptional regulator | 788 | 781 | coexpression:780 |
Rv3167c |
TetR family transcriptional regulator | 764 | 756 | coexpression:756 |
Rv1460 sufR |
transcriptional regulator | 766 | 754 | coexpression:754 |
Rv2641 cadI |
cadmium inducible protein CadI | 762 | 753 ctx | neighborhood:703 |
Rv3183 higA3 |
transcriptional regulator | 746 | 739 | coexpression:739 |
Rv0767c |
HTH-type transcriptional regulator | 743 | 735 | coexpression:735 |
Rv1985c lysG |
HTH-type transcriptional regulator | 743 | 733 | coexpression:733 |
Rv1167c |
transcriptional regulator | 666 | 654 | coexpression:654 |
Rv0653c |
transcriptional regulator | 666 | 654 | coexpression:654 |
Rv0792c |
transcriptional regulator | 618 | 615 | coexpression:615 |
Rv2640c |
ArsR family transcriptional regulator | 602 | 602 ctx | neighborhood:532 |
Rv2358 smtB |
HTH-type transcriptional regulator SmtB | 565 | 566 ctx | cooccurence:564 |
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: ArsR family transcriptional regulator
- MTBC0 PGAP product: metalloregulator ArsR/SmtB family transcription factor
- Pfam (hmmscan --cut_ga): HTH_20 PF12840.14 (E=7e-10), HTH_5 PF01022.27 (E=2e-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_217158.1)
- Domains: Pfam-A via hmmscan --cut_ga — HTH_20 (PF12840.14), HTH_5 (PF01022.27)
- 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
COG0640 - Curated reference: UniProt P71941 (TrEMBL, unreviewed; Predicted)
- 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
arsC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002812|Rv2642| MSNLHPLPEVASCVVAPLVREPLNPPAAAEMAARFKALADPVRLQLLSSVASRAGGEACVCDISAGVEVSQPTISHHLKVLRDAGLLTSRRRASWVYYAVVPEALTVLSNLLSVHADAAPALGAPA