gltD Family assigned · medium auto-curated
H37Rv Rv3858c · MTBC0 mtbc0_004091 ·
488 aa · 4354149–4355615 (-) ·
RefSeq NP_218375.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | glutamate synthase small subunit |
|---|---|
| MTBC0 PGAP re-annotation | glutamate synthase subunit beta |
| Revised (this work) | Glutamate synthase subunit beta. Pfam: Fer4_20 (PF14691.12), Pyr_redox_2 (PF07992.21), FAD_binding_3 (PF01494.26), Pyr_redox (PF00070.34), FAD_oxidored (PF12831.14), DAO (PF01266.31), FAD_binding_2 (PF00890.31), NAD_binding_8 (PF13450.13), Amino_oxidase (PF01593.31). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WN19
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Glutamate synthase [NADPH] small chain |
| EC (curated) |
EC 1.4.1.13
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | gltD |
| eggNOG description | glutamate synthase |
| Orthologous group | COG0493 |
| EC number |
EC 1.4.1.13, EC 1.4.1.14
|
| KEGG orthology |
K00266
|
| KEGG pathways |
map00250, map00910, map01100, map01110, map01120, map01130, map01230
|
| Gene Ontology (13) |
GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0008150, GO:0016020, GO:0040007, GO:0044424, GO:0044444, GO:0044464 +1 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 | 0.335 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 6 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 |
|---|---|---|---|---|
Fer4_20 | PF14691.12 | 4.9e-25 | 25–132 | Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster |
Pyr_redox_2 | PF07992.21 | 4.1e-26 | 146–459 | Pyridine nucleotide-disulphide oxidoreductase |
FAD_binding_3 | PF01494.26 | 3.5e-05 | 146–177 | FAD binding domain |
Pyr_redox | PF00070.34 | 1.4e-05 | 147–180 | Pyridine nucleotide-disulphide oxidoreductase |
FAD_oxidored | PF12831.14 | 2.4e-07 | 147–183 | FAD dependent oxidoreductase |
DAO | PF01266.31 | 1.2e-06 | 147–180 | FAD dependent oxidoreductase |
FAD_binding_2 | PF00890.31 | 1.2e-05 | 147–181 | FAD binding domain |
NAD_binding_8 | PF13450.13 | 1.8e-10 | 149–183 | NAD(P)-binding Rossmann-like domain |
Amino_oxidase | PF01593.31 | 3.7e-09 | 155–184 | Flavin containing amine oxidoreductase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: gltB (glutamate synthase large subunit), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3859c gltB |
glutamate synthase large subunit | 999 | 1000 ctx | neighborhood:881 fusion:900 cooccurence:774 coexpression:999 experimental:999 database:900 textmining:711 |
Rv1937 |
oxygenase | 992 | 989 | experimental:973 database:568 |
Rv2220 glnA1 |
glutamine synthetase | 953 | 916 | database:900 textmining:467 |
Rv2860c glnA4 |
glutamine synthetase | 917 | 913 | database:900 |
Rv2222c glnA2 |
glutamine synthetase | 917 | 913 | database:900 |
Rv1878 glnA3 |
glutamine synthetase GlnA | 916 | 913 | database:900 |
Rv1187 rocA |
pyrroline-5-carboxylate dehydrogenase RocA | 915 | 911 | database:900 |
Rv1384 carB |
carbamoyl-phosphate synthase large subunit | 930 | 907 | database:900 |
Rv0808 purF |
amidophosphoribosyltransferase | 913 | 905 | database:900 |
Rv2476c gdh |
NAD-dependent glutamate dehydrogenase | 910 | 905 | database:900 |
Rv3436c glmS |
glucosamine--fructose-6-phosphate aminotransferase | 916 | 904 | database:900 |
Rv1383 carA |
carbamoyl-phosphate synthase small subunit | 907 | 904 | database:900 |
Rv0788 purQ |
phosphoribosylformylglycinamidine synthase | 900 | 901 | database:900 |
Rv3432c gadB |
glutamate decarboxylase GadB | 900 | 900 | database:900 |
Rv2455c korA |
2-oxoglutarate oxidoreductase subunit KorA | 851 | 829 | 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: glutamate synthase small subunit
- MTBC0 PGAP product: glutamate synthase subunit beta
- Pfam (hmmscan --cut_ga): Fer4_20 PF14691.12 (E=5e-25), Pyr_redox_2 PF07992.21 (E=4e-26), FAD_binding_3 PF01494.26 (E=3e-05), Pyr_redox PF00070.34 (E=1e-05), FAD_oxidored PF12831.14 (E=2e-07), DAO PF01266.31 (E=1e-06), FAD_binding_2 PF00890.31 (E=1e-05), NAD_binding_8 PF13450.13 (E=2e-10), Amino_oxidase PF01593.31 (E=4e-09)
- (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_218375.1)
- Domains: Pfam-A via hmmscan --cut_ga — Fer4_20 (PF14691.12), Pyr_redox_2 (PF07992.21), FAD_binding_3 (PF01494.26), Pyr_redox (PF00070.34), FAD_oxidored (PF12831.14), DAO (PF01266.31), FAD_binding_2 (PF00890.31), NAD_binding_8 (PF13450.13), Amino_oxidase (PF01593.31)
- 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
COG0493 - Curated reference: UniProt P9WN19 (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 —
86 functional partner(s); context anchor
gltB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004091|Rv3858c|gltD MADPGGFLKYTHRKLPKRRPVPLRLRDWREVYEEFDNESLRQQATRCMDCGIPFCHNGCPLGNLIPEWNDLVRRGRWRDAIERLHATNNFPDFTGRLCPAPCEPACVLGINQDPVTIKQIELEIIDKAFDEGWVQPRPPRKLTGQTVAVVGSGPAGLAAAQQLTRAGHTVTVFEREDRIGGLLRYGIPEFKMEKRHLDRRLDQMRSEGTEFRPGVNVGVDISAEKLRADFDAVVLAGGATAWRELPIPGRELEGVHQAMEFLPWANRVQEGDDVLDEDGQPPITAKGKKVVIIGGGDTGADCLGTVHRQGAIAVHQFEIMPRPPDARAESTPWPTYPLMYRVSAAHEEGGERVFSVNTEAFVGTDGRVSALRAHEVTMLDGKFVKVEGSDFELEADLVLLAMGFVGPERAGLLTDLGVKFTERGNVARGDDFDTSVPGVFVAGDMGRGQSLIVWAIAEGRAAAAAVDRYLMGSSALPAPVKPTAAPLQ