cobQ2 Resolved · high auto-curated
H37Rv Rv3713 · MTBC0 mtbc0_003936 ·
231 aa · 4182348–4183043 (+) ·
RefSeq NP_218230.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | cobyric acid synthase CobQ |
|---|---|
| MTBC0 PGAP re-annotation | type 1 glutamine amidotransferase |
| Revised (this work) | Type 1 glutamine amidotransferase. Pfam: GATase_3 (PF07685.21). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6XI14
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Lipid II isoglutaminyl synthase |
| EC (curated) |
EC 3.5.1.2, EC 6.3.5.13
|
| Curated function | The lipid II isoglutaminyl synthase complex catalyzes the formation of alpha-D-isoglutamine in the cell wall lipid II stem peptide. The GatD subunit catalyzes the hydrolysis of glutamine to glutamate and ammonia. The resulting ammonia molecule is channeled to the active site of MurT. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | cobQ2 |
| eggNOG description | glutamine amidotransferase |
| Orthologous group | COG3442 |
| KEGG orthology |
K07009
|
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 | 0.158 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 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 |
|---|---|---|---|---|
GATase_3 | PF07685.21 | 3.1e-35 | 3–197 | CobB/CobQ-like glutamine amidotransferase domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3712 (ligase), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3712 |
ligase | 999 | 1000 ctx | neighborhood:882 fusion:872 cooccurence:774 experimental:817 database:900 textmining:907 |
Rv2153c murG |
UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol-N-acetylglucosamine transferase | 907 | 902 | database:900 |
Rv2158c murE |
UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase | 922 | 853 | experimental:817 textmining:494 |
Rv3711c dnaQ |
DNA polymerase III subunit epsilon | 885 | 742 ctx | neighborhood:739 textmining:574 |
Rv1391 dfp |
bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate--cysteine ligase | 415 | 405 | coexpression:405 |
Rv2208 cobS |
adenosylcobinamide-GDP ribazoletransferase | 617 | 97 | textmining:594 |
Rv2157c murF |
UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | 550 | 87 | textmining:528 |
Rv0255c cobQ1 |
cobyric acid synthase | 701 | 85 | textmining:688 |
Rv0254c cobU |
bifunctional cobinamide kinase/cobinamide phosphate guanylyltransferase | 679 | 77 | textmining:667 |
Rv2065 cobH |
precorrin-8X methylmutase | 807 | 63 | textmining:803 |
Rv2677c hemY |
protoporphyrinogen oxidase | 519 | 60 | textmining:510 |
Rv2228c |
multifunctional RNASE H/alpha-ribazole phosphatase/acid phosphatase | 658 | 54 | textmining:654 |
Rv2152c murC |
UDP-N-acetylmuramate--alanine ligase | 480 | 53 | textmining:473 |
Rv3714c hyp |
hypothetical protein | 810 | 51 | textmining:809 |
Rv2392 cysH |
phosphoadenosine phosphosulfate reductase | 514 | 50 | textmining:510 |
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: cobyric acid synthase CobQ
- MTBC0 PGAP product: type 1 glutamine amidotransferase
- Pfam (hmmscan --cut_ga): GATase_3 PF07685.21 (E=3e-35)
- (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_218230.1)
- Domains: Pfam-A via hmmscan --cut_ga — GATase_3 (PF07685.21)
- 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
COG3442 - Curated reference: UniProt I6XI14 (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 —
19 functional partner(s); context anchor
Rv3712 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003936|Rv3713|cobQ2 MVRIGLVLPDVMGTYGDGGNAVVLRQRLLLRGIAAEIVEITLADPVPDSLDLYTLGGAEDYAQRLATRHLRRYPGLQRAAGRGAPVLAICAAIQVLGHWYETSSGDRVDGVGLLDVTTSPQDARTIGELVSKPLLAGLTQPLTGFENHRGGTVLGPGTSPLGAVVKGAGNRAGDGFDGAVAGSVVATYMHGPCLARNPELADLLLSKVVGELAPLDLPEVDLLRRERLSAR