hupB Family assigned · medium auto-curated
H37Rv Rv2986c · MTBC0 mtbc0_003171 ·
214 aa · 3364485–3365129 (-) ·
RefSeq NP_217502.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | DNA-binding protein HU |
|---|---|
| MTBC0 PGAP re-annotation | DNA-binding protein HupB |
| Revised (this work) | DNA-binding protein HupB. Pfam: Bac_DNA_binding (PF00216.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WMK7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | DNA-binding protein HupB |
| EC (curated) |
EC 1.16.3.1
|
| Curated function | A nucleoid-associated protein (NAP) that probably plays a role in chromosome compactation. Binds DNA non-specifically, with greater affinity for supercoiled than linear DNA, binds well to nicked DNA, gapped and cruciform DNA. Has a preference for A:T rich DNA. Required for activation of the mtbB operon. Binds the mtbB promoter in the presence of iron, binding is seen with as little as 25 uM Fe(2+) and increases with increasing Fe(2+). RNase E and HupB jointly contribute to cellular adaptation to changing growth conditions and survival during antibiotic treatment and in the host. Plays a role i. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | hup |
| eggNOG description | Histone-like DNA-binding protein which is capable of wrapping DNA to stabilize it, and thus to prevent its denaturation under extreme environmental conditions |
| Orthologous group | COG0776 |
| KEGG orthology |
K03530
|
| Gene Ontology (117) |
GO:0000976, GO:0001067, GO:0001130, GO:0001216, GO:0003674, GO:0003676, GO:0003677, GO:0003684, GO:0003690, GO:0003700, GO:0005488, GO:0005575 +105 more
|
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, 3 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 |
|---|---|---|---|---|
Bac_DNA_binding | PF00216.27 | 7.2e-27 | 1–89 | Bacterial DNA-binding protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pheT (phenylalanine--tRNA ligase subunit beta), medium confidence from genomic context alone (score 672 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2785c rpsO |
30S ribosomal protein S15 | 742 | 714 | coexpression:649 |
Rv2412 rpsT |
30S ribosomal protein S20 | 730 | 699 | coexpression:674 |
Rv1650 pheT |
phenylalanine--tRNA ligase subunit beta | 701 | 672 ctx | neighborhood:544 |
Rv2904c rplS |
50S ribosomal protein L19 | 594 | 594 | coexpression:581 |
Rv0685 tuf |
elongation factor Tu | 649 | 565 | coexpression:484 |
Rv2987c leuD |
3-isopropylmalate dehydratase small subunit | 554 | 555 ctx | neighborhood:548 |
Rv3648c cspA |
cold shock protein A | 585 | 537 | |
Rv2988c leuC |
3-isopropylmalate dehydratase large subunit | 516 | 516 ctx | neighborhood:511 |
Rv0652 rplL |
50S ribosomal protein L7/L12 | 521 | 494 | coexpression:494 |
Rv0979A rpmF |
50S ribosomal protein L32 | 555 | 490 | coexpression:448 |
Rv2841c nusA |
transcription termination/antitermination protein NusA | 489 | 490 | |
Rv1307 atpH |
ATP synthase subunit b/delta | 498 | 471 | coexpression:470 |
Rv2817c cas1 |
CRISPR-associated endonuclease Cas1 | 470 | 471 | experimental:465 |
Rv2442c rplU |
50S ribosomal protein L21 | 512 | 463 | coexpression:460 |
Rv3920c hyp |
hypothetical protein | 461 | 461 | coexpression:443 |
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: DNA-binding protein HU
- MTBC0 PGAP product: DNA-binding protein HupB
- Pfam (hmmscan --cut_ga): Bac_DNA_binding PF00216.27 (E=7e-27)
- (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_217502.1)
- Domains: Pfam-A via hmmscan --cut_ga — Bac_DNA_binding (PF00216.27)
- 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
COG0776 - Curated reference: UniProt P9WMK7 (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 —
63 functional partner(s); context anchor
pheT - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003171|Rv2986c|hupB MNKAELIDVLTQKLGSDRRQATAAVENVVDTIVRAVHKGDSVTITGFGVFEQRRRAARVARNPRTGETVKVKPTSVPAFRPGAQFKAVVSGAQRLPAEGPAVKRGVGASAAKKVAKKAPAKKATKAAKKAATKAPARKAATKAPAKKAATKAPAKKAVKATKSPAKKVTKAVKKTAVKASVRKAATKAPAKKAAAKRPATKAPAKKATARRGRK