glnA3 Family assigned · medium auto-curated
H37Rv Rv1878 · MTBC0 mtbc0_001992 ·
450 aa · 2146061–2147413 (+) ·
RefSeq NP_216394.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | glutamine synthetase GlnA |
|---|---|
| MTBC0 PGAP re-annotation | glutamine synthetase family protein |
| Revised (this work) | Glutamine synthetase family protein. Pfam: Gln-synt_C (PF00120.30). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O07752
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable glutamine synthetase GlnA3 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | glnA3 |
| eggNOG description | glutamine synthetase |
| Orthologous group | COG0174 |
| EC number |
EC 6.3.1.2
|
| KEGG orthology |
K01915
|
| KEGG pathways |
map00220, map00250, map00630, map00910, map01100, map01120, map01230, map02020, map04217, map04724, map04727
|
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 | 0.177 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 2 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 |
|---|---|---|---|---|
Gln-synt_C | PF00120.30 | 9.2e-65 | 112–432 | Glutamine synthetase, catalytic domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: gltB (glutamate synthase large subunit), high confidence from genomic context alone (score 970 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1879 hyp |
hypothetical protein | 998 | 995 ctx | neighborhood:881 fusion:862 cooccurence:697 textmining:654 |
Rv3859c gltB |
glutamate synthase large subunit | 985 | 970 ctx | neighborhood:456 coexpression:497 database:900 textmining:519 |
Rv3436c glmS |
glucosamine--fructose-6-phosphate aminotransferase | 923 | 916 | database:900 |
Rv3858c gltD |
glutamate synthase small subunit | 916 | 913 | database:900 |
Rv1383 carA |
carbamoyl-phosphate synthase small subunit | 914 | 909 | database:900 |
Rv1384 carB |
carbamoyl-phosphate synthase large subunit | 914 | 906 | database:900 |
Rv3432c gadB |
glutamate decarboxylase GadB | 911 | 906 | database:900 |
Rv1187 rocA |
pyrroline-5-carboxylate dehydrogenase RocA | 909 | 906 | database:900 |
Rv0252 nirB |
nitrite reductase large subunit NirB | 933 | 904 | database:900 |
Rv0808 purF |
amidophosphoribosyltransferase | 911 | 904 | database:900 |
Rv0253 nirD |
nitrite reductase small subunit NirD | 907 | 902 | database:900 |
Rv0788 purQ |
phosphoribosylformylglycinamidine synthase | 906 | 901 | database:900 |
Rv2476c gdh |
NAD-dependent glutamate dehydrogenase | 938 | 900 | database:900 textmining:409 |
Rv2222c glnA2 |
glutamine synthetase | 869 | 858 | database:800 |
Rv2220 glnA1 |
glutamine synthetase | 886 | 853 | 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: glutamine synthetase GlnA
- MTBC0 PGAP product: glutamine synthetase family protein
- Pfam (hmmscan --cut_ga): Gln-synt_C PF00120.30 (E=9e-65)
- (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_216394.1)
- Domains: Pfam-A via hmmscan --cut_ga — Gln-synt_C (PF00120.30)
- 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
COG0174 - Curated reference: UniProt O07752 (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 —
63 functional partner(s); context anchor
gltB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001992|Rv1878|glnA3 MTATPLAAAAIAQLEAEGVDTVIGTVVNPAGLTQAKTVPIRRTNTFANPGLGASPVWHTFCIDQCSIAFTADISVVGDQRLRIDLSALRIIGDGLAWAPAGFFEQDGTPVPACSRGTLSRIEAALADAGIDAVIGHEVEFLLVDADGQRLPSTLWAQYGVAGVLEHEAFVRDVNAAATAAGIAIEQFHPEYGANQFEISLAPQPPVAAADQLVLTRLIIGRTARRHGLRVSLSPAPFAGSIGSGAHQHFSLTMSEGMLFSGGTGAAGMTSAGEAAVAGVLRGLPDAQGILCGSIVSGLRMRPGNWAGIYACWGTENREAAVRFVKGGAGSAYGGNVEVKVVDPSANPYLASAAILGLALDGMKTKAVLPSETTVDPTQLSDVDRDRAGILRLAADQADAIAVLDSSKLLRCILGDPVVDAVVAVRQLEHERYGDLDPAQLADKFRMAWSV