Rv2621c Family assigned · medium auto-curated
H37Rv Rv2621c · MTBC0 mtbc0_002790 ·
224 aa · 2971446–2972120 (-) ·
RefSeq NP_217137.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | helix-turn-helix domain-containing protein |
| Revised (this work) | Helix-turn-helix domain-containing protein. Pfam: HTH_20 (PF12840.14). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6Y187
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 | COG2345 |
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 | 3.364 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 9 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.22% of strains (320) · 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_20 | PF12840.14 | 1.1e-08 | 17–58 | Helix-turn-helix domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2620c (transmembrane protein), high confidence from genomic context alone (score 920 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2620c |
transmembrane protein | 920 | 920 ctx | neighborhood:882 |
Rv2619c hyp |
hypothetical protein | 908 | 908 ctx | neighborhood:859 |
Rv3183 higA3 |
transcriptional regulator | 824 | 824 | coexpression:797 |
Rv3167c |
TetR family transcriptional regulator | 780 | 780 | coexpression:780 |
Rv0792c |
transcriptional regulator | 791 | 778 | coexpression:778 |
Rv1460 sufR |
transcriptional regulator | 761 | 761 | coexpression:761 |
Rv1776c |
transcriptional regulator | 811 | 759 | coexpression:759 |
Rv1674c |
transcriptional regulator | 741 | 741 | coexpression:739 |
Rv3060c |
GntR family transcriptional regulator | 746 | 734 | coexpression:734 |
Rv1359 |
transcriptional regulator | 734 | 734 | coexpression:734 |
Rv1985c lysG |
HTH-type transcriptional regulator | 733 | 733 | coexpression:733 |
Rv1167c |
transcriptional regulator | 733 | 733 | coexpression:733 |
Rv3263 |
DNA methylase | 730 | 730 | coexpression:730 |
Rv0038 hyp |
hypothetical protein | 703 | 703 | coexpression:703 |
Rv3855 ethR |
HTH-type transcriptional repressor EthR | 703 | 703 | coexpression:703 |
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: helix-turn-helix domain-containing protein
- Pfam (hmmscan --cut_ga): HTH_20 PF12840.14 (E=1e-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_217137.1)
- Domains: Pfam-A via hmmscan --cut_ga — HTH_20 (PF12840.14)
- 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
COG2345 - Curated reference: UniProt I6Y187 (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 —
39 functional partner(s); context anchor
Rv2620c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002790|Rv2621c| MGVSVIIRSLQEPVGRRRAVLRALCASRVPMSIAAIAGKLGVHPNTVRFHLDNLVADGQVERVEPGRGRPGRPPLMFRAVRRTDSTGTRRYRLLAEILASGLAAERDSRAMALSAGRAWGRQLEAPPAGADTEETIDHLVAVLDDLGFAPERRASNGRQQVGLRHCPFLELAETQAGVVCPVHLGIMRGALQTWGAPVTVDRLDAFVEPDLCLAHFTPLEGAIR