Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|
| MTBC0 PGAP re-annotation | nitronate monooxygenase family protein |
|---|
| Revised (this work) | Nitronate monooxygenase (NMO) family protein; FMN-dependent oxidoreductase of the NMO / 2-nitropropane dioxygenase class. Pfam confirms a tandem NMO (PF03060) + FMN_dh (PF01070) architecture. The precise physiological substrate in M. tuberculosis is not experimentally established. |
|---|
Curated reference (UniProt)
| UniProt |
P71591
TrEMBL · unreviewed
· Predicted
|
|---|
| UniProt name | Nitronate monooxygenase |
|---|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|
| eggNOG description | 2-nitropropane dioxygenase |
|---|
| Orthologous group | COG2070 |
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| EC number |
EC 1.13.12.16
|
|---|
| KEGG orthology |
K00459
|
|---|
| KEGG pathways |
map00910
|
|---|
| Gene Ontology (148) |
GO:0000166, GO:0001775, GO:0002252, GO:0002263, GO:0002274, GO:0002275, GO:0002283, GO:0002366, GO:0002376, GO:0002443, GO:0002444, GO:0002446 +136 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 |
1.19 · relaxed/neutral
|
|---|
| Polymorphic sites (≥ 0.1% of strains) |
3 synonymous, 8 missense, 2 nonsense, 2 frameshift
|
|---|
| Disruption |
4 distinct premature-stop/frameshift site(s); most common in
4.65% of strains
(6751) · convergent
|
|---|
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 |
|---|
NMO | PF03060.22 |
9.4e-30 | 80–308 |
Nitronate monooxygenase |
FMN_dh | PF01070.25 |
3.6e-07 | 117–203 |
FMN-dependent dehydrogenase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner:
whiB5 (transcriptional regulator WhiB5),
medium confidence from genomic context alone
(score 521 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) |
|---|
Rv2781c |
oxidoreductase |
929 |
930 |
database:900 |
Rv0267 narU |
nitrite extrusion protein NarU |
908 |
908 |
database:900 |
Rv0261c narK3 |
nitrate/nitrite transporter |
908 |
908 |
database:900 |
Rv1737c narK2 |
nitrate/nitrite transporter |
908 |
908 |
database:900 |
Rv2329c narK1 |
nitrate/nitrite transporter |
908 |
908 |
database:900 |
Rv1164 narI |
nitrate reductase subunit gamma |
902 |
903 |
database:900 |
Rv1162 narH |
nitrate reductase subunit beta |
901 |
902 |
database:900 |
Rv1161 narG |
nitrate reductase subunit alpha |
900 |
901 |
database:900 |
Rv1736c narX |
nitrate reductase-like protein NarX |
900 |
901 |
database:900 |
Rv0252 nirB |
nitrite reductase large subunit NirB |
906 |
900 |
database:900 |
Rv0253 nirD |
nitrite reductase small subunit NirD |
900 |
900 |
database:900 |
Rv2524c fas |
fatty acid synthase |
780 |
746 |
coexpression:710 |
Rv0022c whiB5 |
transcriptional regulator WhiB5 |
521 |
521 ctx |
neighborhood:516 |
Rv2048c pks12 |
polyketide synthase |
574 |
502 |
|
Rv1527c pks5 |
polyketide synthase |
574 |
501 |
|
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: 'nitronate monooxygenase family protein' (was 'hypothetical protein')
- Pfam (hmmscan --cut_ga): NMO PF03060 (E=9.4e-30) + FMN_dh PF01070 (E=3.6e-07) -- the FMN_dh domain was not in the PGAP label
- Family assignment is domain/homology based; no Mtb-specific functional study found in tbmonitor (2021-2026)
ESM Atlas signal (exploratory)
Ancestral protein hash d606df771774fdb2f4035dac38bca96a ·
10 ESM-space neighbours (max similarity 0.889).
SAE features are orienting indices, not validated domains.
| # | Index | Activation | Interpretation |
|---|
| 1 | 12964 |
1.33 |
Active-site phosphate/metal-binding loops |
| 2 | 11055 |
1.11 |
N-terminal active-site lid loops |
| 3 | 8967 |
0.96 |
TIM-barrel and flavoprotein cores |
| 4 | 13561 |
0.96 |
TIM-barrel alpha/beta catalytic core |
| 5 | 12705 |
0.86 |
Nucleotide and sugar-phosphate TIM-barrels |
| 6 | 13701 |
0.83 |
C-terminal accessory binding extensions |
| 7 | 136 |
0.75 |
Gly/Thr-rich phosphate-binding loop |
| 8 | 11842 |
0.75 |
Glycine-rich phosphate-binding loops |
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_214535.1)
- Domains: Pfam-A via hmmscan --cut_ga — NMO (PF03060.22), FMN_dh (PF01070.25)
- 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
COG2070
- Curated reference: UniProt
P71591
(TrEMBL, unreviewed; 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 —
33 functional partner(s); context anchor
whiB5
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000026|Rv0021c|
MVLSTAFSQMFGIDYPIVSAPMDLIAGGELAAAVSGAGGLGLIGGGYGDRDWLARQFDLAAGAPVGCGFITWSLARQPQLLDLALQYEPVAVMLSFGDPAVFADAIKSAGTRLVCQIQNRTQAERALQVGADVLVAQGTEAGGHGHGPRSTLTLVPEIVDLVTARGTDIPVIAAGGIADGRGLAAALMLGAAGVLVGTRFYATVEALSTPQARDPLLAATGDDMCRTTIYDQLRRYPWPQGHTMSVLSNALTDQFEDTELDILHREEAMARYWRAVAARDYSIANVTAGQAAGLVNAVLPAADVITGMAQQAARTLTAMRAV
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