Rv0474 Family assigned · medium auto-curated
H37Rv Rv0474 · MTBC0 mtbc0_000499 ·
140 aa · 568386–568808 (+) ·
RefSeq NP_214988.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | HTH-type transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | helix-turn-helix transcriptional regulator |
| Revised (this work) | Helix-turn-helix transcriptional regulator. Pfam: 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 |
P9WMH9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized HTH-type transcriptional regulator Rv0474 |
UniProt still lists this protein as Uncharacterized HTH-type transcriptional regulator Rv0474; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | transcriptional |
| Orthologous group | COG1396 |
| Gene Ontology (11) |
GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0030312, GO:0044424, GO:0044444, GO:0044464, GO:0071944
|
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 | 0.128 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 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_31 | PF13560.13 | 1.4e-11 | 22–78 | Helix-turn-helix domain |
HTH_3 | PF01381.29 | 5.2e-15 | 26–79 | Helix-turn-helix |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: hbhA (heparin binding hemagglutinin HbhA), high confidence from genomic context alone (score 720 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2185c TB16.3 hyp |
hypothetical protein | 772 | 764 ctx | cooccurence:763 |
Rv0854 hyp |
hypothetical protein | 763 | 755 ctx | cooccurence:754 |
Rv0857 hyp |
hypothetical protein | 752 | 753 ctx | cooccurence:749 |
Rv0475 hbhA |
heparin binding hemagglutinin HbhA | 720 | 720 ctx | neighborhood:711 |
Rv0476 |
transmembrane protein | 709 | 709 ctx | neighborhood:661 |
Rv0487 hyp |
hypothetical protein | 687 | 688 ctx | cooccurence:682 |
Rv3197 |
ABC transporter ATP-binding protein | 677 | 678 ctx | cooccurence:673 |
Rv0502 hyp |
hypothetical protein | 676 | 677 ctx | cooccurence:672 |
Rv0477 hyp |
hypothetical protein | 671 | 668 ctx | neighborhood:661 |
Rv3679 |
anion transporter ATPase | 665 | 665 ctx | cooccurence:663 |
Rv0478 deoC |
2-deoxyribose-5-phosphate aldolase | 655 | 655 ctx | neighborhood:647 |
Rv0473 |
transmembrane protein | 634 | 634 ctx | neighborhood:632 |
Rv3916c hyp |
hypothetical protein | 602 | 603 ctx | cooccurence:597 |
Rv3680 |
anion transporter ATPase | 546 | 547 ctx | cooccurence:542 |
Rv3233c |
Rv3233c, (MTCY20B11.08c), len: 196 aa. Possible triacylglycerol synthase (See Daniel et al., 2004), similar to C-terminus of Q9RIU8|SCM11.13 | 506 | 507 ctx | cooccurence:501 |
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: HTH-type transcriptional regulator
- MTBC0 PGAP product: helix-turn-helix transcriptional regulator
- Pfam (hmmscan --cut_ga): HTH_31 PF13560.13 (E=1e-11), HTH_3 PF01381.29 (E=5e-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_214988.1)
- Domains: Pfam-A via hmmscan --cut_ga — 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 P9WMH9 (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 —
25 functional partner(s); context anchor
hbhA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000499|Rv0474| MSSEEKLAAKVSTKASDVASDIGSFIRSQRETAHVSMRQLAERSGVSNPYLSQVERGLRKPSADVLSQIAKALRVSAEVLYVRAGILEPSETSQVRDAIITDTAITERQKQILLDIYASFTHQNEATREECPSDPTPTDD