snoP Family assigned · medium auto-curated
H37Rv Rv2604c · MTBC0 mtbc0_002772 ·
198 aa · 2955246–2955842 (-) ·
RefSeq NP_217120.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | glutamine amidotransferase SnoP |
|---|---|
| MTBC0 PGAP re-annotation | pyridoxal 5'-phosphate synthase glutaminase subunit PdxT |
| Revised (this work) | Pyridoxal 5'-phosphate synthase glutaminase subunit PdxT. Pfam: SNO (PF01174.26), 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 |
P9WII7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Pyridoxal 5'-phosphate synthase subunit PdxT |
| EC (curated) |
EC 3.5.1.2, EC 4.3.3.6
|
| Curated function | Catalyzes the hydrolysis of glutamine to glutamate and ammonia as part of the biosynthesis of pyridoxal 5'-phosphate. The resulting ammonia molecule is channeled to the active site of PdxS. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
H Coenzyme transport and metabolism
|
|---|---|
| Preferred name | pdxT |
| eggNOG description | Catalyzes the hydrolysis of glutamine to glutamate and ammonia as part of the biosynthesis of pyridoxal 5'-phosphate. The resulting ammonia molecule is channeled to the active site of PdxS |
| Orthologous group | COG0311 |
| EC number |
EC 4.3.3.6
|
| KEGG orthology |
K08681
|
| KEGG pathways |
map00750
|
| Gene Ontology (73) |
GO:0003674, GO:0003824, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0006081, GO:0006725, GO:0006732, GO:0006766, GO:0006767 +61 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 | 0.559 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 3 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 |
|---|---|---|---|---|
SNO | PF01174.26 | 8.9e-59 | 8–194 | SNO glutamine amidotransferase family |
GATase_3 | PF07685.21 | 1.1e-07 | 19–96 | CobB/CobQ-like glutamine amidotransferase domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: snzP (pyridoxine biosynthesis protein), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2606c snzP |
pyridoxine biosynthesis protein | 999 | 1000 ctx | neighborhood:822 cooccurence:774 coexpression:855 experimental:928 database:900 textmining:948 |
Rv2607 pdxH |
pyridoxine/pyridoxamine 5'-phosphate oxidase | 994 | 947 ctx | neighborhood:496 database:900 textmining:898 |
Rv2605c tesB2 |
acyl-CoA thioesterase II | 984 | 884 ctx | neighborhood:882 textmining:870 |
Rv1448c tal |
transaldolase | 816 | 817 | database:800 |
Rv1449c tkt |
transketolase | 801 | 801 | database:800 |
Rv1017c prsA |
ribose-phosphate pyrophosphokinase | 801 | 801 | database:800 |
Rv2436 rbsK |
ribokinase RbsK | 819 | 800 | database:800 |
Rv3068c pgmA |
phosphoglucomutase PgmA | 800 | 800 | database:800 |
Rv2465c rpiB |
ribose-5-phosphate isomerase B | 800 | 800 | database:800 |
Rv2603c |
transcriptional regulator | 854 | 760 ctx | neighborhood:757 textmining:418 |
Rv2613c |
AP-4-A phosphorylase | 550 | 551 ctx | neighborhood:544 |
Rv2614c thrS |
threonine--tRNA ligase | 547 | 548 ctx | neighborhood:544 |
Rv3581c ispF |
2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | 426 | 427 | coexpression:420 |
Rv3396c guaA |
GMP synthase | 544 | 131 | textmining:497 |
Rv1850 ureC |
urease subunit alpha | 517 | 46 | textmining:515 |
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 amidotransferase SnoP
- MTBC0 PGAP product: pyridoxal 5'-phosphate synthase glutaminase subunit PdxT
- Pfam (hmmscan --cut_ga): SNO PF01174.26 (E=9e-59), GATase_3 PF07685.21 (E=1e-07)
- (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_217120.1)
- Domains: Pfam-A via hmmscan --cut_ga — SNO (PF01174.26), 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
COG0311 - Curated reference: UniProt P9WII7 (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 —
20 functional partner(s); context anchor
snzP - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002772|Rv2604c|snoP MSVPRVGVLALQGDTREHLAALRECGAEPMTVRRRDELDAVDALVIPGGESTTMSHLLLDLDLLGPLRARLADGLPAYGSCAGMILLASEILDAGAAGRQALPLRAMNMTVRRNAFGSQVDSFEGDIEFAGLDDPVRAVFIRAPWVERVGDGVQVLARAAGHIVAVRQGAVLATAFHPEMTGDRRIHQLFVDIVTSAA