Rv0121c Family assigned · medium
H37Rv Rv0121c · MTBC0 mtbc0_000132 ·
144 aa · 148074–148508 (-) ·
RefSeq NP_214635.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | TIGR03668 family PPOX class F420-dependent oxidoreductase |
| Revised (this work) | F420-dependent / PNPOx-class oxidoreductase (Pfam PNPOx_N PF01243; PGAP TIGR03668 PPOX-class F420-dependent oxidoreductase). Putative deazaflavin (F420)-dependent oxidoreductase, a redox chemistry characteristic of mycobacteria. |
Curated reference (UniProt)
| UniProt |
O07171
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Conserved protein |
UniProt still lists this protein as Conserved protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | PFAM pyridoxamine 5'-phosphate |
| Orthologous group | COG3576 |
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 | 0.688 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 3 missense, 1 nonsense, 1 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 1.03% of strains (1500) · 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 |
|---|---|---|---|---|
PNPOx_N | PF01243.28 | 1.2e-16 | 10–142 | Pyridoxamine 5'-phosphate oxidase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fusA2 (elongation factor G), medium confidence from genomic context alone (score 630 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0120c fusA2 |
elongation factor G | 629 | 630 ctx | neighborhood:558 |
Rv3079c hyp |
hypothetical protein | 612 | 597 ctx | cooccurence:591 |
Rv1875 hyp |
hypothetical protein | 940 | 559 ctx | cooccurence:552 textmining:870 |
Rv0122 hyp |
hypothetical protein | 533 | 533 ctx | neighborhood:532 |
Rv0123 hyp |
hypothetical protein | 533 | 533 ctx | neighborhood:532 |
Rv2125 hyp |
hypothetical protein | 511 | 511 | coexpression:447 |
Rv0953c |
oxidoreductase | 489 | 469 ctx | cooccurence:466 |
Rv3463 hyp |
hypothetical protein | 470 | 451 ctx | cooccurence:448 |
Rv2714 hyp |
hypothetical protein | 447 | 447 | coexpression:447 |
Rv3072c hyp |
hypothetical protein | 424 | 400 | |
Rv1240 mdh |
malate dehydrogenase | 400 | 400 | |
Rv2161c hyp |
hypothetical protein | 411 | 387 | |
Rv1155 |
pyridoxine/pyridoxamine 5'-phosphate oxidase | 894 | 219 | textmining:870 |
Rv3369 hyp |
hypothetical protein | 893 | 215 | textmining:870 |
Rv0132c fgd2 |
F420-dependent glucose-6-phosphate dehydrogenase | 423 | 192 |
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
- MTBC0 PGAP product: 'TIGR03668 family PPOX class F420-dependent oxidoreductase'
- Pfam: PNPOx_N PF01243 (E=1.2e-16)
ESM Atlas signal (exploratory)
Ancestral protein hash 449a9f213d8e03fddbfcfe1ab6b924bd ·
10 ESM-space neighbours (max similarity 0.902).
SAE features are orienting indices, not validated domains.
| # | Index | Activation | Interpretation |
|---|---|---|---|
| 1 | 8276 |
1.07 | Acidic/His catalytic loops |
| 2 | 3114 |
0.95 | Active-site rim β-loop elements |
| 3 | 733 |
0.93 | Aromatic cofactor-binding glycine loop |
| 4 | 9248 |
0.79 | Beta-sheet strand-turn motif |
| 5 | 5217 |
0.77 | Ligand-binding cleft rim module |
| 6 | 7714 |
0.69 | C-terminal cofactor-binding tails |
| 7 | 37 |
0.53 | Basic/aromatic ligand-binding patches |
| 8 | 14850 |
0.51 | Active site adjacent cofactor motifs |
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_214635.1)
- Domains: Pfam-A via hmmscan --cut_ga — PNPOx_N (PF01243.28)
- 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
COG3576 - Curated reference: UniProt O07171 (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 —
20 functional partner(s); context anchor
fusA2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000132|Rv0121c| MGEFDPKLRFAQSPVARLATSTPDGTPHLVPVVFALGARRPAEATGADVIYTAVDAKRKTTQRLRRLANLEHNPRASVLVDSYADDWTQLWWVRADGVAAIHRDGEVMRAAYRLLRAKYAQYQSVPLNGPVIAIAVQRWASWHA