Rv2640c Family assigned · medium auto-curated
H37Rv Rv2640c · MTBC0 mtbc0_002810 ·
119 aa · 2989039–2989398 (-) ·
RefSeq NP_217156.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ArsR family transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | Rv2640c family ArsR-like transcriptional regulator |
| Revised (this work) | Rv2640c family ArsR-like transcriptional regulator. 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 |
I6Y1A7
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible transcriptional regulatory protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | arsR |
| eggNOG description | arsR family |
| 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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 0 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 | 2.2e-10 | 39–88 | Helix-turn-helix domain |
HTH_5 | PF01022.27 | 3.8e-15 | 41–89 | Bacterial regulatory protein, arsR family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: cadI (cadmium inducible protein CadI), high confidence from genomic context alone (score 812 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2641 cadI |
cadmium inducible protein CadI | 872 | 812 ctx | neighborhood:665 cooccurence:453 |
Rv2643 arsC |
arsenic-transport integral membrane protein ArsC | 851 | 802 ctx | neighborhood:687 |
Rv2642 |
ArsR family transcriptional regulator | 602 | 602 ctx | neighborhood:532 |
Rv2639c |
integral membrane protein | 564 | 549 ctx | neighborhood:542 |
Rv0576 |
transcriptional regulator | 505 | 505 ctx | cooccurence:458 |
Rv1994c cmtR |
HTH-type transcriptional regulator CmtR | 680 | 462 ctx | cooccurence:454 textmining:431 |
Rv2034 |
ArsR family HTH-type transcriptional repressor | 652 | 264 | textmining:547 |
Rv1353c |
HTH-type transcriptional regulator | 442 | 257 | |
Rv3173c |
TetR/Acr family transcriptional regulator | 569 | 227 | textmining:466 |
Rv1674c |
transcriptional regulator | 553 | 225 | textmining:448 |
Rv3167c |
TetR family transcriptional regulator | 425 | 202 | |
Rv3744 nmtR |
HTH-type transcriptional regulator NmtR | 590 | 83 | textmining:572 |
Rv0827c kmtR |
HTH-type transcriptional regulator KmtR | 450 | 78 | textmining:428 |
Rv0662c vapB7 |
antitoxin VapB7 | 416 | 52 | textmining:410 |
Rv1952 vapB14 |
antitoxin VapB14 | 439 | 41 | textmining:439 |
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: Rv2640c family ArsR-like transcriptional regulator
- Pfam (hmmscan --cut_ga): HTH_20 PF12840.14 (E=2e-10), HTH_5 PF01022.27 (E=4e-15)
- (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_217156.1)
- 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 I6Y1A7 (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 —
15 functional partner(s); context anchor
cadI - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002810|Rv2640c| MPKSLPVIDISAPVCCAPVAAGPMSDGDALAVALRLKALADPARVKIMSYLFSSPAGEQVSGQLAAALSLSDGTVSHHLAQLRKAGLVISDRRGMHVFHRVHPEALQALCTVLNPNCCA