argC Resolved · high auto-curated
H37Rv Rv1652 · MTBC0 mtbc0_001761 ·
352 aa · 1877618–1878676 (+) ·
RefSeq NP_216168.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | N-acetyl-gamma-glutamyl-phoshate reductase |
|---|---|
| MTBC0 PGAP re-annotation | N-acetyl-gamma-glutamyl-phosphate reductase |
| Revised (this work) | N-acetyl-gamma-glutamyl-phosphate reductase. Pfam: Semialdhyde_dh (PF01118.31), Semialdhyde_dhC_1 (PF22698.2), Semialdhyde_dhC (PF02774.24). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WPZ9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | N-acetyl-gamma-glutamyl-phosphate reductase |
| EC (curated) |
EC 1.2.1.38
|
| Curated function | Catalyzes the NADPH-dependent reduction of N-acetyl-5-glutamyl phosphate to yield N-acetyl-L-glutamate 5-semialdehyde. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | argC |
| eggNOG description | Catalyzes the NADPH-dependent reduction of N-acetyl-5- glutamyl phosphate to yield N-acetyl-L-glutamate 5-semialdehyde |
| Orthologous group | COG0002 |
| EC number |
EC 1.2.1.38
|
| KEGG orthology |
K00145
|
| KEGG pathways |
map00220, map01100, map01110, map01130, map01210, map01230
|
| KEGG modules |
M00028, M00845
|
| Gene Ontology (15) |
GO:0000166, GO:0003674, GO:0005488, GO:0008150, GO:0036094, GO:0040007, GO:0043167, GO:0043168, GO:0048037, GO:0050661, GO:0050662, GO:0070401 +3 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 | 0.127 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 15 synonymous, 5 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 |
|---|---|---|---|---|
Semialdhyde_dh | PF01118.31 | 1.6e-18 | 11–140 | Semialdehyde dehydrogenase, NAD binding domain |
Semialdhyde_dhC_1 | PF22698.2 | 6.9e-51 | 158–320 | Semialdehyde dehydrogenase, dimerisation domain |
Semialdhyde_dhC | PF02774.24 | 2.7e-29 | 167–323 | Semialdehyde dehydrogenase, dimerisation domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: argD (acetylornithine aminotransferase), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1655 argD |
acetylornithine aminotransferase | 999 | 1000 ctx | neighborhood:881 cooccurence:669 coexpression:937 database:900 textmining:925 |
Rv1654 argB |
acetylglutamate kinase | 999 | 1000 ctx | neighborhood:882 fusion:611 cooccurence:764 coexpression:973 database:900 textmining:923 |
Rv1653 argJ |
bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase | 999 | 999 ctx | neighborhood:881 cooccurence:736 coexpression:984 textmining:876 |
Rv1656 argF |
ornithine carbamoyltransferase | 999 | 995 ctx | neighborhood:835 coexpression:961 textmining:895 |
Rv1657 argR |
arginine repressor | 997 | 986 ctx | neighborhood:881 coexpression:888 textmining:811 |
Rv1658 argG |
argininosuccinate synthase | 995 | 984 ctx | neighborhood:812 coexpression:901 textmining:759 |
Rv1659 argH |
argininosuccinate lyase | 996 | 977 ctx | neighborhood:783 coexpression:868 textmining:844 |
Rv1213 glgC |
glucose-1-phosphate adenylyltransferase | 833 | 783 | coexpression:765 |
Rv2321c rocD2 |
Rv2321c, (MTCY3G12.13), len: 181 aa. Probable rocD2,ornithine aminotransferase, highly similar to C-terminal region of other ornithine amino | 834 | 767 | coexpression:678 |
Rv2322c rocD1 |
Rv2322c, (MTCY3G12.12), len: 221 aa. Probable rocD1,ornithine aminotransferase, highly similar to N-terminal region of other ornithine amino | 812 | 736 | coexpression:678 |
Rv1384 carB |
carbamoyl-phosphate synthase large subunit | 820 | 642 | coexpression:612 textmining:519 |
Rv1202 dapE |
succinyl-diaminopimelate desuccinylase DapE | 656 | 620 | |
Rv3859c gltB |
glutamate synthase large subunit | 712 | 604 ctx | neighborhood:544 |
Rv1647 |
adenylate cyclase | 546 | 547 ctx | neighborhood:544 |
Rv1650 pheT |
phenylalanine--tRNA ligase subunit beta | 546 | 547 ctx | neighborhood:544 |
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-acetyl-gamma-glutamyl-phoshate reductase
- MTBC0 PGAP product: N-acetyl-gamma-glutamyl-phosphate reductase
- Pfam (hmmscan --cut_ga): Semialdhyde_dh PF01118.31 (E=2e-18), Semialdhyde_dhC_1 PF22698.2 (E=7e-51), Semialdhyde_dhC PF02774.24 (E=3e-29)
- (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_216168.1)
- Domains: Pfam-A via hmmscan --cut_ga — Semialdhyde_dh (PF01118.31), Semialdhyde_dhC_1 (PF22698.2), Semialdhyde_dhC (PF02774.24)
- 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
COG0002 - Curated reference: UniProt P9WPZ9 (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 —
41 functional partner(s); context anchor
argD - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001761|Rv1652|argC MQNRQVANATKVAVAGASGYAGGEILRLLLGHPAYADGRLRIGALTAATSAGSTLGEHHPHLTPLAHRVVEPTEAAVLGGHDAVFLALPHGHSAVLAQQLSPETLIIDCGADFRLTDAAVWERFYGSSHAGSWPYGLPELPGARDQLRGTRRIAVPGCYPTAALLALFPALAADLIEPAVTVVAVSGTSGAGRAATTDLLGAEVIGSARAYNIAGVHRHTPEIAQGLRAVTDRDVSVSFTPVLIPASRGILATCTARTRSPLSQLRAAYEKAYHAEPFIYLMPEGQLPRTGAVIGSNAAHIAVAVDEDAQTFVAIAAIDNLVKGTAGAAVQSMNLALGWPETDGLSVVGVAP