nadB Resolved · high auto-curated
H37Rv Rv1595 · MTBC0 mtbc0_001701 ·
527 aa · 1807769–1809352 (+) ·
RefSeq NP_216111.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | L-aspartate oxidase |
|---|---|
| MTBC0 PGAP re-annotation | L-aspartate oxidase |
| Revised (this work) | L-aspartate oxidase. Pfam: FAD_binding_2 (PF00890.31), Succ_DH_flav_C (PF02910.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WJJ9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | L-aspartate oxidase |
| EC (curated) |
EC 1.4.3.16
|
| Curated function | Catalyzes the oxidation of L-aspartate to iminoaspartate, the first step in the de novo biosynthesis of NAD(+). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
H Coenzyme transport and metabolism
|
|---|---|
| Preferred name | nadB |
| eggNOG description | Catalyzes the oxidation of L-aspartate to iminoaspartate |
| Orthologous group | COG0029 |
| EC number |
EC 1.4.3.16
|
| KEGG orthology |
K00278
|
| KEGG pathways |
map00250, map00760, map01100
|
| KEGG modules |
M00115
|
| Gene Ontology (2) |
GO:0008150, GO:0040007
|
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 | 0.744 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 10 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 |
|---|---|---|---|---|
FAD_binding_2 | PF00890.31 | 3.1e-88 | 11–381 | FAD binding domain |
Succ_DH_flav_C | PF02910.26 | 1.6e-06 | 426–498 | Fumarate reductase flavoprotein C-term |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: nadA (quinolinate synthetase A), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1594 nadA |
quinolinate synthetase A | 999 | 1000 ctx | neighborhood:881 cooccurence:769 coexpression:966 experimental:446 database:900 textmining:944 |
Rv1596 nadC |
nicotinate-nucleotide pyrophosphatase | 999 | 1000 ctx | neighborhood:881 fusion:869 cooccurence:767 coexpression:947 textmining:965 |
Rv1538c ansA |
L-aparaginase | 918 | 905 | database:900 |
Rv1380 pyrB |
aspartate carbamoyltransferase | 909 | 902 | database:900 |
Rv0357c purA |
adenylosuccinate synthetase | 913 | 901 | database:900 |
Rv1658 argG |
argininosuccinate synthase | 913 | 901 | database:900 |
Rv2201 asnB |
asparagine synthetase | 903 | 900 | database:900 |
Rv3601c panD |
aspartate 1-decarboxylase | 845 | 830 | database:800 |
Rv1593c hyp |
hypothetical protein | 832 | 825 ctx | neighborhood:788 |
Rv3709c ask |
aspartokinase | 824 | 815 | database:800 |
Rv2455c korA |
2-oxoglutarate oxidoreductase subunit KorA | 826 | 812 | database:800 |
Rv0066c icd2 |
isocitrate dehydrogenase | 809 | 809 | database:800 |
Rv1240 mdh |
malate dehydrogenase | 835 | 808 | database:800 |
Rv0211 pckA |
phosphoenolpyruvate carboxykinase | 817 | 807 | database:800 |
Rv3432c gadB |
glutamate decarboxylase GadB | 806 | 806 | database:800 |
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: L-aspartate oxidase
- MTBC0 PGAP product: L-aspartate oxidase
- Pfam (hmmscan --cut_ga): FAD_binding_2 PF00890.31 (E=3e-88), Succ_DH_flav_C PF02910.26 (E=2e-06)
- (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_216111.1)
- Domains: Pfam-A via hmmscan --cut_ga — FAD_binding_2 (PF00890.31), Succ_DH_flav_C (PF02910.26)
- 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
COG0029 - Curated reference: UniProt P9WJJ9 (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 —
42 functional partner(s); context anchor
nadA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001701|Rv1595|nadB MAGPAWRDAADVVVIGTGVAGLAAALAADRAGRSVVVLSKAAQTHVTATHYAQGGIAVVLPDNDDSVDAHVADTLAAGAGLCDPDAVYSIVADGYRAVTDLVGAGARLDESVPGRWALTREGGHSRRRIVHAGGDATGAEVQRALQDAAGMLDIRTGHVALRVLHDGTAVTGLLVVRPDGCGIISAPSVILATGGLGHLYSATTNPAGSTGDGIALGLWAGVAVSDLEFIQFHPTMLFAGRAGGRRPLITEAIRGEGAILVDRQGNSITAGVHPMGDLAPRDVVAAAIDARLKATGDPCVYLDARGIEGFASRFPTVTASCRAAGIDPVRQPIPVVPGAHYSCGGIVTDVYGQTELLGLYAAGEVARTGLHGANRLASNSLLEGLVVGGRAGKAAAAHAAAAGRSRATSSATWPEPISYTALDRGDLQRAMSRDASMYRAAAGLHRLCDSLSGAQVRDVACRRDFEDVALTLVAQSVTAAALARTESRGCHHRAEYPCTVPEQARSIVVRGADDANAVCVQALVAVC