hycP Family assigned · medium
H37Rv Rv0085 · MTBC0 mtbc0_000095 ·
220 aa · 93452–94114 (+) ·
RefSeq NP_214599.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hydrogenase HycP |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | Polytopic integral membrane protein with 7 predicted transmembrane helices (DeepTMHMM). RefSeq leaves it 'hydrogenase HycP'. A topological feature consistent with a membrane transporter/permease or membrane-embedded enzyme; the transported substrate and molecular function are undetermined. |
Curated reference (UniProt)
| UniProt |
P9WM75
SwissProt · reviewed
· Predicted
|
|---|---|
| UniProt name | Uncharacterized protein Rv0085 |
UniProt still lists this protein as Uncharacterized protein Rv0085; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | hycP |
| eggNOG description | Hydrogenase 4 membrane |
| Orthologous group | COG4237 |
| KEGG orthology |
K12140
|
| Gene Ontology (2) |
GO:0008150, GO:0040007
|
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 | 0.686 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 5 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: hycQ (hydrogenase HycQ), high confidence from genomic context alone (score 996 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0086 hycQ |
hydrogenase HycQ | 999 | 996 ctx | neighborhood:882 cooccurence:774 coexpression:860 textmining:826 |
Rv0087 hycE |
formate hydrogenase HycE | 999 | 996 ctx | neighborhood:892 cooccurence:774 coexpression:860 textmining:870 |
Rv0083 |
oxidoreductase | 996 | 996 ctx | neighborhood:874 cooccurence:774 coexpression:860 |
Rv0082 |
oxidoreductase | 994 | 994 ctx | neighborhood:874 cooccurence:736 coexpression:824 |
Rv0084 hycD |
formate hydrogenlyase HycD | 992 | 992 ctx | neighborhood:874 cooccurence:774 coexpression:731 |
Rv0081 |
HTH-type transcriptional regulator | 944 | 921 ctx | neighborhood:874 |
Rv0088 |
polyketide cyclase/dehydrase | 666 | 666 ctx | neighborhood:658 |
Rv0080 hyp |
hypothetical protein | 545 | 545 ctx | neighborhood:542 |
Rv0079 hyp |
hypothetical protein | 540 | 540 ctx | neighborhood:538 |
Rv0089 |
methyltransferase | 435 | 435 ctx | neighborhood:427 |
Rv1735c |
membrane protein | 553 | 54 | textmining:547 |
Rv1519 hyp |
hypothetical protein | 625 | 47 | textmining:623 |
Rv3126c hyp |
hypothetical protein | 549 | 44 | textmining:548 |
Rv2526 vapB17 |
antitoxin VapB17 | 439 | 41 | textmining:439 |
Rv0748 vapB31 |
antitoxin VapB31 | 438 | 41 | textmining:438 |
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
- DeepTMHMM: 7 transmembrane helices (type TM)
- Integral membrane topology (localisation feature, not a function)
- DeepTMHMM topology prediction (project 'Still unknown gene function', phase8, 2026-06-10). A topological feature, not a demonstrated molecular function.
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_214599.1)
- 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
COG4237 - Curated reference: UniProt P9WM75 (SwissProt, reviewed; 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 —
15 functional partner(s); context anchor
hycQ - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000095|Rv0085|hycP MSNANFSILVDFAAGGLVLASVLIVWRRDLRAIVRLLAWQGAALAAIPLLRGIRDNDRALIAVGIAVLALRALVLPWLLARAVGAEAAAQREATPLVNTASSLLITAGLTLTAFAITQPVVNLEPGVTINAVPAAFAVVLIALFVMTTRLHAVSQAAGFLMLDNGIAATAFLLTAGVPLIVELGASLDVLFAVIVIGVLTGRLRRIFGDADLDKLRELRD