Rv1279 Family assigned · medium auto-curated
H37Rv Rv1279 · MTBC0 mtbc0_001369 ·
528 aa · 1439045–1440631 (+) ·
RefSeq NP_215795.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | GMC-type oxidoreductase |
|---|---|
| MTBC0 PGAP re-annotation | GMC family oxidoreductase N-terminal domain-containing protein |
| Revised (this work) | GMC family oxidoreductase N-terminal domain-containing protein. Pfam: GMC_oxred_N (PF00732.26), GMC_oxred_C (PF05199.20). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WMV5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized GMC-type oxidoreductase Rv1279 |
| EC (curated) |
EC 1.1.-.-
|
UniProt still lists this protein as Uncharacterized GMC-type oxidoreductase Rv1279; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| eggNOG description | Belongs to the GMC oxidoreductase family |
| Orthologous group | COG2303 |
| EC number |
EC 1.1.99.1
|
| KEGG orthology |
K00108
|
| KEGG pathways |
map00260, map01100
|
| KEGG modules |
M00555
|
| Gene Ontology (13) |
GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0016020, GO:0030312, GO:0044424, GO:0044444, GO:0044464 +1 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) pseudogene candidate
| pN/pS | 0.801 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 6 missense, 1 nonsense, 1 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 1.62% of strains (2353) · 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 |
|---|---|---|---|---|
GMC_oxred_N | PF00732.26 | 1.5e-60 | 6–298 | GMC oxidoreductase |
GMC_oxred_C | PF05199.20 | 1.9e-36 | 383–519 | GMC oxidoreductase |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1278 hyp |
hypothetical protein | 968 | 969 ctx | neighborhood:853 coexpression:796 |
Rv1277 hyp |
hypothetical protein | 889 | 889 ctx | neighborhood:853 |
Rv2350c plcB |
membrane-associated phospholipase B | 805 | 805 | database:800 |
Rv2349c plcC |
phospholipase C | 803 | 803 | database:800 |
Rv2351c plcA |
membrane-associated phospholipase A | 802 | 803 | database:800 |
Rv0437c psd |
phosphatidylserine decarboxylase | 808 | 801 | database:800 |
Rv1755c plcD |
Rv1755c, (MT1799, MTCY28.21c), len: 280 aa. Probable plcD, phospholipase C 4 (fragment) (see citations below),highly similar to C-terminus o | 800 | 801 | database:800 |
Rv2194 qcrC |
ubiquinol-cytochrome C reductase cytochrome subunit C | 785 | 775 | experimental:762 |
Rv2267c stf3 hyp |
hypothetical protein | 756 | 746 | experimental:411 database:583 |
Rv1691 hyp |
hypothetical protein | 756 | 746 | experimental:411 database:583 |
Rv3529c hyp |
hypothetical protein | 754 | 744 | experimental:411 database:583 |
Rv0832 PE_PGRS12 |
PE-PGRS family protein PE_PGRS12 | 739 | 729 | database:573 |
Rv2328 PE23 |
PE family protein PE23 | 739 | 729 | database:573 |
Rv3812 PE_PGRS62 |
PE-PGRS family protein PE_PGRS62 | 739 | 729 | database:573 |
Rv3036c TB22.2 hyp |
hypothetical protein | 739 | 729 | database:573 |
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: GMC-type oxidoreductase
- MTBC0 PGAP product: GMC family oxidoreductase N-terminal domain-containing protein
- Pfam (hmmscan --cut_ga): GMC_oxred_N PF00732.26 (E=2e-60), GMC_oxred_C PF05199.20 (E=2e-36)
- (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_215795.1)
- Domains: Pfam-A via hmmscan --cut_ga — GMC_oxred_N (PF00732.26), GMC_oxred_C (PF05199.20)
- 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
COG2303 - Curated reference: UniProt P9WMV5 (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 — 33 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001369|Rv1279| MDTQSDYVVVGTGSAGAVVASRLSTDPATTVVALEAGPRDKNRFIGVPAAFSKLFRSEIDWDYLTEPQPELDGREIYWPRGKVLGGSSSMNAMMWVRGFASDYDEWAARAGPRWSYADVLGYFRRIENVTAAWHFVSGDDSGVTGPLHISRQRSPRSVTAAWLAAARECGFAAARPNSPRPEGFCETVVTQRRGARFSTADAYLKPAMRRKNLRVLTGATATRVVIDGDRAVGVEYQSDGQTRIVYARREVVLCAGAVNSPQLLMLSGIGDRDHLAEHDIDTVYHAPEVGCNLLDHLVTVLGFDVEKDSLFAAEKPGQLISYLLRRRGMLTSNVGEAYGFVRSRPELKLPDLELIFAPAPFYDEALVPPAGHGVVFGPILVAPQSRGQITLRSADPHAKPVIEPRYLSDLGGVDRAAMMAGLRICARIAQARPLRDLLGSIARPRNSTELDEATLELALATCSHTLYHPMGTCRMGSDEASVVDPQLRVRGVDGLRVADASVMPSTVRGHTHAPSVLIGEKAADLIRS