fbiA Resolved · high auto-curated
H37Rv Rv3261 · MTBC0 mtbc0_003469 ·
331 aa · 3662686–3663681 (+) ·
RefSeq NP_217778.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 2-phospho-L-lactate transferase |
|---|---|
| MTBC0 PGAP re-annotation | 2-phospho-L-lactate transferase |
| Revised (this work) | 2-phospho-L-lactate transferase. Pfam: CofD (PF01933.24). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WP81
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Phosphoenolpyruvate transferase |
| EC (curated) |
EC 2.7.8.28
|
| Curated function | Catalyzes the transfer of the phosphoenolpyruvate moiety from enoylpyruvoyl-2-diphospho-5'-guanosine (EPPG) to 7,8-didemethyl-8-hydroxy-5-deazariboflavin (FO) with the formation of dehydro coenzyme F420-0 and GMP. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
H Coenzyme transport and metabolism
|
|---|---|
| Preferred name | cofD |
| eggNOG description | Catalyzes the transfer of the 2-phospholactate moiety from lactyl (2) diphospho-(5')guanosine (LPPG) to 7,8-didemethyl- 8-hydroxy-5-deazariboflavin (FO) with the formation of the L- lactyl phosphodiester of 7,8-didemethyl-8-hydroxy-5- deazariboflavin (F420-0) and GMP |
| Orthologous group | COG0391 |
| EC number |
EC 2.7.8.28
|
| KEGG orthology |
K11212
|
| KEGG pathways |
map00680, map01120
|
| KEGG modules |
M00378
|
| Gene Ontology (16) |
GO:0003674, GO:0003824, GO:0006732, GO:0008150, GO:0008152, GO:0009058, GO:0009108, GO:0009987, GO:0016740, GO:0016772, GO:0016773, GO:0043743 +4 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 | 0.685 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 4 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 |
|---|---|---|---|---|
CofD | PF01933.24 | 2.6e-60 | 3–294 | 2-phospho-L-lactate transferase CofD |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fbiB (coenzyme F420:L-glutamate ligase), high confidence from genomic context alone (score 999 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3262 fbiB |
coenzyme F420:L-glutamate ligase | 999 | 999 ctx | neighborhood:882 cooccurence:773 coexpression:797 database:900 textmining:908 |
Rv2983 cofC |
2-phospho-L-lactate guanylyltransferase | 998 | 979 ctx | cooccurence:773 database:900 textmining:948 |
Rv1173 fbiC |
FO synthase | 997 | 975 ctx | cooccurence:727 database:900 textmining:893 |
Rv3547 ddn |
deazaflavin-dependent nitroreductase | 976 | 768 ctx | cooccurence:762 textmining:903 |
Rv0132c fgd2 |
F420-dependent glucose-6-phosphate dehydrogenase | 878 | 758 ctx | cooccurence:750 textmining:520 |
Rv3178 |
nitroreductase | 869 | 753 ctx | cooccurence:746 textmining:493 |
Rv1558 hyp |
hypothetical protein | 835 | 751 ctx | cooccurence:747 |
Rv3520c |
coenzyme F420-dependent oxidoreductase | 763 | 750 ctx | cooccurence:741 |
Rv1261c hyp |
hypothetical protein | 755 | 749 ctx | cooccurence:747 |
Rv0407 fgd1 |
F420-dependent glucose-6-phosphate dehydrogenase | 990 | 747 ctx | cooccurence:728 textmining:965 |
Rv2951c |
phthiodiolone/phenolphthiodiolone dimycocerosates ketoreductase | 760 | 747 ctx | cooccurence:737 |
Rv3093c |
oxidoreductase | 760 | 747 ctx | cooccurence:739 |
Rv0044c |
oxidoreductase | 742 | 729 ctx | cooccurence:718 |
Rv1855c |
oxidoreductase | 742 | 728 ctx | cooccurence:716 |
Rv3263 |
DNA methylase | 725 | 725 ctx | neighborhood:718 |
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: 2-phospho-L-lactate transferase
- MTBC0 PGAP product: 2-phospho-L-lactate transferase
- Pfam (hmmscan --cut_ga): CofD PF01933.24 (E=3e-60)
- (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_217778.1)
- Domains: Pfam-A via hmmscan --cut_ga — CofD (PF01933.24)
- 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
COG0391 - Curated reference: UniProt P9WP81 (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 —
56 functional partner(s); context anchor
fbiB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003469|Rv3261|fbiA MKVTVLAGGVGGARFLLGVQQLLGLGQFAANSAHSDADHQLSAVVNVGDDAWIHGLRVCPDLDTCMYTLGGGVDPQRGWGQRDETWHAMQELVRYGVQPDWFELGDRDLATHLVRTQMLQAGYPLSQITEALCDRWQPGARLLPATDDRCETHVVITDPVDESRKAIHFQEWWVRYRAQVPTHSFAFVGAEKSSAATEAIAALADADIIMLAPSNPVVSIGAILAVPGIRAALREATAPIVGYSPIIGEKPLRGMADTCLSVIGVDSTAAAVGRHYGARCATGILDCWLVHDGDHAEIDGVTVRSVPLLMTDPNATAEMVRAGCDLAGVVA