hrp1 Resolved · high auto-curated
H37Rv Rv2626c · MTBC0 mtbc0_002795 ·
143 aa · 2976124–2976555 (-) ·
RefSeq NP_217142.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypoxic response protein |
|---|---|
| MTBC0 PGAP re-annotation | hypoxic response protein Hrp1 |
| Revised (this work) | Hypoxic response protein Hrp1. Pfam: CBS (PF00571.34). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WJA3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Hypoxic response protein 1 |
| Curated function | Unlike some other CBS-domain containing proteins does not seem to bind AMP. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | CBS domain |
| Orthologous group | COG0517 |
| Gene Ontology (40) |
GO:0001666, GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0006950, GO:0008150, GO:0009605, GO:0009607 +28 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 | 0.103 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 1 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 |
|---|---|---|---|---|
CBS | PF00571.34 | 1.0e-12 | 4–55 | CBS domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rip3 (zinc metalloprotease Rip3), high confidence from genomic context alone (score 920 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2625c rip3 |
zinc metalloprotease Rip3 | 920 | 920 ctx | neighborhood:609 coexpression:805 |
Rv2624c |
universal stress protein | 920 | 908 ctx | neighborhood:586 coexpression:788 |
Rv2030c hyp |
hypothetical protein | 939 | 901 | coexpression:860 textmining:412 |
Rv2031c hspX |
alpha-crystallin | 950 | 863 | coexpression:859 textmining:654 |
Rv2623 TB31.7 |
universal stress protein | 949 | 862 | coexpression:860 textmining:648 |
Rv1733c |
transmembrane protein | 950 | 861 | coexpression:860 textmining:659 |
Rv2032 acg |
NAD(P)H nitroreductase | 929 | 861 | coexpression:860 textmining:513 |
Rv2627c hyp |
hypothetical protein | 860 | 861 | coexpression:860 |
Rv1996 |
universal stress protein | 870 | 856 | coexpression:853 |
Rv1737c narK2 |
nitrate/nitrite transporter | 906 | 853 | coexpression:853 |
Rv3134c |
universal stress protein | 881 | 851 | coexpression:848 |
Rv3127 hyp |
hypothetical protein | 863 | 840 | coexpression:839 |
Rv2007c fdxA |
ferredoxin | 902 | 834 | coexpression:834 textmining:434 |
Rv1997 ctpF |
cation transporter ATPase F | 860 | 830 | coexpression:804 |
Rv3131 |
NAD(P)H nitroreductase | 893 | 818 | coexpression:817 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: hypoxic response protein
- MTBC0 PGAP product: hypoxic response protein Hrp1
- Pfam (hmmscan --cut_ga): CBS PF00571.34 (E=1e-12)
- (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_217142.1)
- Domains: Pfam-A via hmmscan --cut_ga — CBS (PF00571.34)
- 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
COG0517 - Curated reference: UniProt P9WJA3 (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 —
39 functional partner(s); context anchor
rip3 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002795|Rv2626c|hrp1 MTTARDIMNAGVTCVGEHETLTAAAQYMREHDIGALPICGDDDRLHGMLTDRDIVIKGLAAGLDPNTATAGELARDSIYYVDANASIQEMLNVMEEHQVRRVPVISEHRLVGIVTEADIARHLPEHAIVQFVKAICSPMALAS