gltB Family assigned · medium auto-curated
H37Rv Rv3859c · MTBC0 mtbc0_004092 ·
1527 aa · 4355608–4360191 (-) ·
RefSeq NP_218376.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | glutamate synthase large subunit |
|---|---|
| MTBC0 PGAP re-annotation | glutamate synthase large subunit |
| Revised (this work) | Glutamate synthase large subunit. Pfam: GATase_2 (PF00310.27), Glu_syn_central (PF04898.21), Glu_synthase (PF01645.24), GXGXG (PF01493.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P96218
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Glutamate synthase [NADPH] large chain |
| EC (curated) |
EC 1.4.1.13
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | gltB |
| eggNOG description | glutamate synthase |
| Orthologous group | COG0067 |
| EC number |
EC 1.4.1.13, EC 1.4.1.14, EC 1.4.7.1
|
| KEGG orthology |
K00265, K00284
|
| KEGG pathways |
map00250, map00630, map00910, map01100, map01110, map01120, map01130, map01230
|
| Gene Ontology (50) |
GO:0003674, GO:0003824, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0006082, GO:0006520, GO:0006536, GO:0006537 +38 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 | 0.31 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 14 synonymous, 13 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 |
|---|---|---|---|---|
GATase_2 | PF00310.27 | 1.9e-178 | 18–439 | Glutamine amidotransferases class-II |
Glu_syn_central | PF04898.21 | 8.6e-113 | 466–757 | Glutamate synthase central domain |
Glu_synthase | PF01645.24 | 3.7e-146 | 821–1189 | Conserved region in glutamate synthase |
GXGXG | PF01493.26 | 1.5e-101 | 1249–1498 | GXGXG motif |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: gltD (glutamate synthase small subunit), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3858c gltD |
glutamate synthase small subunit | 999 | 1000 ctx | neighborhood:881 fusion:900 cooccurence:774 coexpression:999 experimental:999 database:900 textmining:711 |
Rv3106 fprA |
NADPH-ferredoxin reductase FprA | 999 | 1000 ctx | neighborhood:455 coexpression:999 experimental:999 textmining:519 |
Rv1175c fadH |
NADPH dependent 2,4-dienoyl-CoA reductase FadH | 999 | 1000 ctx | neighborhood:544 coexpression:999 experimental:999 textmining:670 |
Rv0886 fprB |
ferredoxin/ferredoxin--NADP reductase | 999 | 1000 ctx | neighborhood:544 coexpression:999 experimental:999 textmining:621 |
Rv1384 carB |
carbamoyl-phosphate synthase large subunit | 991 | 971 ctx | neighborhood:544 coexpression:407 database:900 textmining:730 |
Rv2220 glnA1 |
glutamine synthetase | 989 | 970 ctx | neighborhood:456 coexpression:501 database:900 textmining:659 |
Rv2860c glnA4 |
glutamine synthetase | 985 | 970 ctx | neighborhood:456 coexpression:499 database:900 textmining:519 |
Rv1878 glnA3 |
glutamine synthetase GlnA | 985 | 970 ctx | neighborhood:456 coexpression:497 database:900 textmining:519 |
Rv2222c glnA2 |
glutamine synthetase | 985 | 970 ctx | neighborhood:456 coexpression:500 database:900 textmining:519 |
Rv3575c |
LacI family transcriptional regulator | 976 | 963 | experimental:963 |
Rv3436c glmS |
glucosamine--fructose-6-phosphate aminotransferase | 981 | 958 ctx | neighborhood:544 database:900 textmining:589 |
Rv0808 purF |
amidophosphoribosyltransferase | 965 | 953 ctx | neighborhood:544 database:900 |
Rv1383 carA |
carbamoyl-phosphate synthase small subunit | 954 | 953 ctx | neighborhood:544 database:900 |
Rv1187 rocA |
pyrroline-5-carboxylate dehydrogenase RocA | 940 | 917 | database:900 |
Rv0788 purQ |
phosphoribosylformylglycinamidine synthase | 903 | 904 | database:900 |
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 large subunit
- MTBC0 PGAP product: glutamate synthase large subunit
- Pfam (hmmscan --cut_ga): GATase_2 PF00310.27 (E=2e-178), Glu_syn_central PF04898.21 (E=9e-113), Glu_synthase PF01645.24 (E=4e-146), GXGXG PF01493.26 (E=2e-101)
- (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_218376.1)
- Domains: Pfam-A via hmmscan --cut_ga — GATase_2 (PF00310.27), Glu_syn_central (PF04898.21), Glu_synthase (PF01645.24), GXGXG (PF01493.26)
- 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
COG0067 - Curated reference: UniProt P96218 (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 —
449 functional partner(s); context anchor
gltD - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004092|Rv3859c|gltB MTPKRVGLYNPAFEHDSCGVAMVVDMHGRRSRDIVDKAITALLNLEHRGAQGAEPRSGDGAGILIQVPDEFLREAVDFELPAPGSYATGIAFLPQSSKDAAAACAAVQKIAEAEGLQVLGWRSVPTDDSSLGALSRDAMPTFRQVFLAGASGMALERRCYVVRKRAEHELGTKGPGQDGPGRETVYFPSLSGQTLVYKGMLTTPQLKAFYLDLQDERLTSALGIVHSRFSTNTFPSWPLAHPFRRIAHNGEINTVTGNENWMRAREALIKTDIFGSAADVEKLFPICTPGASDTARFDEVLELLHLGGRSLAHAVLMMIPEAWERHESMDPARRAFYQYHASLMEPWDGPASMTFTDGTVVGAVLDRNGLRPSRIWVTDDGLVVMASEAGVLDLHPSTVVRRMRLQPGRMFLVDTAQGRIVSDEEIKADLAAEHPYQEWLDNGLVPLDELPEGKDVRMPHHRIVMRQLAFGYTYEELNLLVAPMARLGAEPIGSMGTDTPVAVLSQRPRMLYDYFHQLFAQVTNPPLDAIREEVVTSLQGTTGGERDLLNPDENSCHQIVLPQPILRNHELAKLVSLDPNDKVNGRPHGLRSKVIRCLYRVSEGGAGLAAALEEVRGAAAAAIADGARIIILSDRESDEEMAPIPSLLAVAGVHHHLVRERTRTQVGLVVESGDAREVHHMAALVGFGAAAINPYLVFESIEDMLDRGVIEGIDRTAALNNYIKAAGKGVLKVMSKMGISTLASYTGAQLFQAVGISEQVLDEYFTGLTCPTGGITLDDIAADVAARHRLAYLDRPDERAHRELEVGGEYQWRREGEYHLFNPETVFKLQHSTRTGQYKIFKEYTRLVDDQSERMASLRGLLKFRTGVRPPVPLDEVEPASEIVKRFSTGAMSYGSISAEAHETLAIAMNRLGARSNCGEGGEDVKRFDRDPNGDWRRSAIKQVASARFGVTSHYLTNCTDLQIKMAQGAKPGEGGQLPGHKVYPWVAEVRHSTPGVGLISPPPHHDIYSIEDLAQLIHDLKNANPSARVHVKLVSENGVGTVAAGVSKAHADVVLISGHDGGTGATPLTSMKHAGAPWELGLAETQQTLLLNGLRDRIVVQVDGQLKTGRDVMIATLLGAEEFGFATAPLVVAGCIMMRVCHLDTCPVGVATQNPLLRERFTGKPEFVENFFMFIAEEVREYLAQLGFRTVNEAVGQAGALDTTLARAHWKAHKLDLAPVLHEPESAFMNQDLYCSSRQDHGLDKALDQQLIVMSREALDSGKPVRFSTTIGNVNRTVGTMLGHELTKAYGGQGLPDGTIDITFDGSAGNSFGAFVPKGITLRVYGDANDYVGKGLSGGRIVVRPSDDAPQDYVAEDNIIGGNVILFGATSGEVYLRGVVGERFAVRNSGAHAVVEGVGDHGCEYMTGGRVVILGRTGRNFAAGMSGGVAYVYDPDGELPANLNSEMVELETLDEDDADWLHGTIQVHVDATDSAVGQRILSDWSGQQRHFVKVMPRDYKRVLQAIALAERDGVDVDKAIMAAAHG