nagA Resolved · high auto-curated
H37Rv Rv3332 · MTBC0 mtbc0_003545 ·
383 aa · 3744580–3745731 (+) ·
RefSeq NP_217849.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | N-acetylglucosamine-6-phosphate deacetylase NagA |
|---|---|
| MTBC0 PGAP re-annotation | N-acetylglucosamine-6-phosphate deacetylase |
| Revised (this work) | N-acetylglucosamine-6-phosphate deacetylase. Pfam: Amidohydro_1 (PF01979.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53382
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | N-acetylglucosamine-6-phosphate deacetylase |
| EC (curated) |
EC 3.5.1.25
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| Preferred name | nagA |
| eggNOG description | Belongs to the metallo-dependent hydrolases superfamily. NagA family |
| Orthologous group | COG1820 |
| EC number |
EC 3.5.1.25
|
| KEGG orthology |
K01443
|
| KEGG pathways |
map00520, map01130
|
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 | 0.774 · 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 |
|---|---|---|---|---|
Amidohydro_1 | PF01979.27 | 1.7e-39 | 48–379 | Amidohydrolase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: sugI (sugar-transport integral membrane protein SugI), high confidence from genomic context alone (score 980 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3331 sugI |
sugar-transport integral membrane protein SugI | 996 | 980 ctx | neighborhood:882 coexpression:810 textmining:811 |
Rv3436c glmS |
glucosamine--fructose-6-phosphate aminotransferase | 987 | 908 | database:900 textmining:870 |
Rv3441c mrsA |
phosphoglucosamine mutase | 981 | 901 | database:900 textmining:823 |
Rv1445c devB |
6-phosphogluconolactonase | 847 | 827 | coexpression:692 experimental:431 |
Rv0669c |
neutral ceramidase | 845 | 824 | coexpression:687 experimental:431 |
Rv3242c hyp |
hypothetical protein | 785 | 786 | coexpression:772 |
Rv0792c |
transcriptional regulator | 749 | 718 ctx | cooccurence:418 coexpression:462 |
Rv3330 dacB1 |
penicillin-binding protein DacB | 938 | 705 ctx | neighborhood:659 textmining:801 |
Rv1321 nucS |
endonuclease NucS | 617 | 618 ctx | fusion:549 |
Rv3329 |
aminotransferase | 929 | 480 ctx | neighborhood:477 textmining:870 |
Rv2584c apt |
adenine phosphoribosyltransferase | 464 | 464 | |
Rv0237 lpqI |
lipoprotein LpqI | 897 | 424 | textmining:830 |
Rv2703 sigA |
RNA polymerase sigma factor SigA | 422 | 408 | coexpression:408 |
Rv2710 sigB |
RNA polymerase sigma factor SigB | 422 | 408 | coexpression:408 |
Rv2894c xerC |
tyrosine recombinase XerC | 402 | 403 | coexpression:403 |
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: N-acetylglucosamine-6-phosphate deacetylase NagA
- MTBC0 PGAP product: N-acetylglucosamine-6-phosphate deacetylase
- Pfam (hmmscan --cut_ga): Amidohydro_1 PF01979.27 (E=2e-39)
- (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_217849.1)
- Domains: Pfam-A via hmmscan --cut_ga — Amidohydro_1 (PF01979.27)
- 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
COG1820 - Curated reference: UniProt O53382 (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 —
23 functional partner(s); context anchor
sugI - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003545|Rv3332|nagA MTVLGADAVVIDGRICRPGWVHTADGRILSGGAGAPPMPADAEFPDAIVVPGFVDMHVHGGGGASFADGNAADIARAAEFHLRHGTTTTLASLVTAGPAELLSAVGALAEATRDGVVAGIHLEGPWLSPARCGAHDHTRMRAPDPAEIESVLAAADGAVRMVTLAPELPGSDAAIRRFRDAEVVVAVGHTDATYTQTRHAIDLGATVGTHLFNAMPPLDHRAPGPVLALLCDPRVTVEIIADGVHVHPAVVHAVIEAVGPDRVAVVTDAIAAAGCGDGAFRLGTMPIEVESSVARVAGASTLAGSTTTMDQLFRTVAGLGSKSDSAGDVALAAAVQVTSATPARALGLTGVGRLAAGYAANLVVLDRDLRVTAVMVNDDWRVG