hycE Family assigned · medium auto-curated
H37Rv Rv0087 · MTBC0 mtbc0_000097 ·
492 aa · 95577–97055 (+) ·
RefSeq NP_214601.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | formate hydrogenase HycE |
|---|---|
| MTBC0 PGAP re-annotation | NADH-quinone oxidoreductase subunit C |
| Revised (this work) | NADH-quinone oxidoreductase subunit C. Pfam: Complex1_30kDa (PF00329.26), NiFeSe_Hases (PF00374.25), Complex1_49kDa (PF00346.25). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
Q10884
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible formate hydrogenase HycE |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | hycE |
| eggNOG description | Respiratory-chain NADH dehydrogenase, 30 Kd subunit |
| Orthologous group | COG3261 |
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) pseudogene candidate
| pN/pS | 0.195 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 11 synonymous, 5 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 2.24% of strains (3248) · 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
Complex1_30kDa | PF00329.26 | 2.5e-16 | 11–120 | Respiratory-chain NADH dehydrogenase, 30 Kd subunit |
NiFeSe_Hases | PF00374.25 | 5.4e-08 | 181–247 | Nickel-dependent hydrogenase |
Complex1_49kDa | PF00346.25 | 8.4e-18 | 256–411 | Respiratory-chain NADH dehydrogenase, 49 Kd subunit |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0083 (oxidoreductase), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0083 |
oxidoreductase | 999 | 1000 ctx | neighborhood:884 cooccurence:774 coexpression:899 experimental:995 textmining:453 |
Rv0082 |
oxidoreductase | 999 | 1000 ctx | neighborhood:884 cooccurence:774 coexpression:926 experimental:999 textmining:835 |
Rv0086 hycQ |
hydrogenase HycQ | 999 | 1000 ctx | neighborhood:892 cooccurence:774 coexpression:925 experimental:995 textmining:850 |
Rv0084 hycD |
formate hydrogenlyase HycD | 999 | 1000 ctx | neighborhood:884 cooccurence:774 coexpression:580 experimental:999 textmining:763 |
Rv3153 nuoI |
NADH-quinone oxidoreductase subunit I | 999 | 1000 ctx | neighborhood:544 coexpression:434 experimental:999 textmining:545 |
Rv0085 hycP |
hydrogenase HycP | 999 | 996 ctx | neighborhood:892 cooccurence:774 coexpression:860 textmining:870 |
Rv1852 ureG |
urease accessory protein UreG | 995 | 992 | experimental:989 textmining:439 |
Rv3417c groEL1 |
chaperonin GroEL | 966 | 965 | experimental:965 |
Rv0440 groEL2 |
molecular chaperone GroEL | 966 | 965 | experimental:965 |
Rv0081 |
HTH-type transcriptional regulator | 948 | 897 ctx | neighborhood:874 textmining:516 |
Rv0088 |
polyketide cyclase/dehydrase | 673 | 673 ctx | neighborhood:658 |
Rv3146 nuoB |
NADH-quinone oxidoreductase subunit B | 661 | 638 ctx | cooccurence:514 |
Rv3156 nuoL |
NADH-quinone oxidoreductase subunit L | 741 | 623 ctx | neighborhood:544 |
Rv3152 nuoH |
NADH-quinone oxidoreductase subunit H | 725 | 616 ctx | neighborhood:544 |
Rv2467 pepN |
aminopeptidase PepN | 559 | 559 | experimental:558 |
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: formate hydrogenase HycE
- MTBC0 PGAP product: NADH-quinone oxidoreductase subunit C
- Pfam (hmmscan --cut_ga): Complex1_30kDa PF00329.26 (E=3e-16), NiFeSe_Hases PF00374.25 (E=5e-08), Complex1_49kDa PF00346.25 (E=8e-18)
- (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_214601.1)
- Domains: Pfam-A via hmmscan --cut_ga — Complex1_30kDa (PF00329.26), NiFeSe_Hases (PF00374.25), Complex1_49kDa (PF00346.25)
- 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
COG3261 - Curated reference: UniProt Q10884 (TrEMBL, unreviewed; 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 —
33 functional partner(s); context anchor
Rv0083 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000097|Rv0087|hycE MMSASWLRHRVSERGLIATAEQLWADSFRLALVAAHDDGDSLRVVYLFLAGYPDRRVELEYVVPADNPEIRSLAYLSFPAGRFEREMADLYGIRPVGHPKPRRLVRHAHWPDWHPMRTDAGPAPEFTDTGAFPFLAVEGPGVYEIPVGPVHAGLIEPGHFRFSVAGETIVRLKARLWFVHRGIEKLFHGRPATAAVDLAERISGDTSAAHALAHSLAIEDALGIELPHEVHRLRALIVELERLYNHAADLGALANDVGYSLANAHAQRIRENLLRRNAAVTGHRLLRGAIRAGGVALRALPDTDELAALAVDLAEVATLTLANSVVYDRFAGTAVLHPDDASALGCLGYVARASGLRSDARVEHPTIVLPITEIGAPDGDVLARYTVRRDEFAASAALAQHIVESHTGPIEYAATLHPVGAPSSGIGIVEGWRGTIVHRVEIDVDGRITRAKVVDPSWFNWPALPVAMADTIVPDFPLANKSFNQSYAGNDL