hns Family assigned · low auto-curated
H37Rv Rv3852 · MTBC0 mtbc0_004085 ·
134 aa · 4349184–4349588 (+) ·
RefSeq NP_218369.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | histone-like protein Hns |
|---|---|
| MTBC0 PGAP re-annotation | histone-like protein Hns |
| Revised (this work) | Histone-like protein Hns. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6YHB0
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Histone-like protein Rv3852 |
| Curated function | Binds DNA in vitro. It has been proposed that Rv3852 plays a role in nucleoid organization and may function as an anchorage to tether the DNA to the membrane. However, it was later shown that it has no influence on nucleoid shape or compaction. It plays no role in virulence and only a minor role in the control of transcription, and does not appear to function as a typical nucleoid-associated protein..; FUNCTION: Interacts with Wag31, an important cell shape and cell wall integrity determinant, and facilitates the localization of Wag31 to the cell poles and the cell wall, thus enabling nascent . |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Preferred name | hns |
|---|---|
| Orthologous group | 2AVD4 |
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 | 0.365 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 1 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.61% of strains (884) · 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rraA (RNase E regulator RraA), high confidence from genomic context alone (score 879 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3853 rraA |
RNase E regulator RraA | 879 | 879 ctx | neighborhood:861 |
Rv3850 hyp |
hypothetical protein | 764 | 764 ctx | neighborhood:763 |
Rv3851 |
membrane protein | 562 | 562 ctx | neighborhood:558 |
Rv3849 espR |
ESX-1 transcriptional regulator EspR | 618 | 461 ctx | neighborhood:455 |
Rv3597c lsr2 |
iron-regulated H-NS-like protein | 644 | 53 | textmining:640 |
Rv2986c hupB |
DNA-binding protein HU | 553 | 50 | textmining:549 |
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: histone-like protein Hns
- MTBC0 PGAP product: histone-like protein Hns
- (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_218369.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
2AVD4 - Curated reference: UniProt I6YHB0 (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 —
6 functional partner(s); context anchor
rraA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004085|Rv3852|hns MPDPQDRPDSEPSDASTPPAKKLPAKKAAKKAPARKTPAKKAPAKKTPAKGAKSAPPKPAEAPVSLQQRIETNGQLAAAAKDAAAQAKSTVEGANDALARNASVPAPSHSPVPLIVAVTLSLLALLLIRQLRRR