snzP Family assigned · medium auto-curated
H37Rv Rv2606c · MTBC0 mtbc0_002774 ·
299 aa · 2956724–2957623 (-) ·
RefSeq NP_217122.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | pyridoxine biosynthesis protein |
|---|---|
| MTBC0 PGAP re-annotation | pyridoxal 5'-phosphate synthase lyase subunit PdxS |
| Revised (this work) | Pyridoxal 5'-phosphate synthase lyase subunit PdxS. Pfam: SOR_SNZ (PF01680.24). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WII9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Pyridoxal 5'-phosphate synthase subunit PdxS |
| EC (curated) |
EC 4.3.3.6
|
| Curated function | Catalyzes the formation of pyridoxal 5'-phosphate from ribose 5-phosphate (RBP), glyceraldehyde 3-phosphate (G3P) and ammonia. The ammonia is provided by the PdxT subunit. Can also use ribulose 5-phosphate and dihydroxyacetone phosphate as substrates, resulting from enzyme-catalyzed isomerization of RBP and G3P, respectively. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
H Coenzyme transport and metabolism
|
|---|---|
| Preferred name | pdxS |
| eggNOG description | Catalyzes the formation of pyridoxal 5'-phosphate from ribose 5-phosphate (RBP), glyceraldehyde 3-phosphate (G3P) and ammonia. The ammonia is provided by the PdxT subunit. Can also use ribulose 5-phosphate and dihydroxyacetone phosphate as substrates, resulting from enzyme-catalyzed isomerization of RBP and G3P, respectively |
| Orthologous group | COG0214 |
| EC number |
EC 4.3.3.6
|
| KEGG orthology |
K06215
|
| KEGG pathways |
map00750
|
| Gene Ontology (56) |
GO:0003674, GO:0003824, GO:0005575, GO:0005623, GO:0005886, GO:0006081, GO:0006725, GO:0006732, GO:0006766, GO:0006767, GO:0006793, GO:0006796 +44 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 | 1.32 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 4 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 |
|---|---|---|---|---|
SOR_SNZ | PF01680.24 | 3.7e-106 | 12–217 | SOR/SNZ family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: snoP (glutamine amidotransferase SnoP), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2604c snoP |
glutamine amidotransferase SnoP | 999 | 1000 ctx | neighborhood:822 cooccurence:774 coexpression:855 experimental:928 database:900 textmining:948 |
Rv2607 pdxH |
pyridoxine/pyridoxamine 5'-phosphate oxidase | 988 | 953 ctx | neighborhood:550 database:900 textmining:757 |
Rv2605c tesB2 |
acyl-CoA thioesterase II | 980 | 860 ctx | neighborhood:823 textmining:870 |
Rv1449c tkt |
transketolase | 830 | 824 | database:800 |
Rv1448c tal |
transaldolase | 826 | 818 | database:800 |
Rv1017c prsA |
ribose-phosphate pyrophosphokinase | 815 | 816 | database:800 |
Rv2465c rpiB |
ribose-5-phosphate isomerase B | 804 | 804 | database:800 |
Rv3068c pgmA |
phosphoglucomutase PgmA | 800 | 801 | database:800 |
Rv2436 rbsK |
ribokinase RbsK | 819 | 800 | database:800 |
Rv1436 gap |
glyceraldehyde 3-phosphate dehydrogenase | 810 | 782 ctx | fusion:757 |
Rv2603c |
transcriptional regulator | 846 | 747 ctx | neighborhood:735 textmining:418 |
Rv1295 thrC |
threonine synthase | 724 | 661 | coexpression:655 |
Rv2614c thrS |
threonine--tRNA ligase | 563 | 563 ctx | neighborhood:544 |
Rv2613c |
AP-4-A phosphorylase | 557 | 558 ctx | neighborhood:544 |
Rv2610c pimA |
alpha-(1-2)-phosphatidylinositol mannosyltransferase | 527 | 515 ctx | neighborhood: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: pyridoxine biosynthesis protein
- MTBC0 PGAP product: pyridoxal 5'-phosphate synthase lyase subunit PdxS
- Pfam (hmmscan --cut_ga): SOR_SNZ PF01680.24 (E=4e-106)
- (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_217122.1)
- Domains: Pfam-A via hmmscan --cut_ga — SOR_SNZ (PF01680.24)
- 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
COG0214 - Curated reference: UniProt P9WII9 (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 —
28 functional partner(s); context anchor
snoP - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002774|Rv2606c|snzP MDPAGNPATGTARVKRGMAEMLKGGVIMDVVTPEQARIAEGAGAVAVMALERVPADIRAQGGVSRMSDPDMIEGIIAAVTIPVMAKVRIGHFVEAQILQTLGVDYIDESEVLTPADYAHHIDKWNFTVPFVCGATNLGEALRRISEGAAMIRSKGEAGTGDVSNATTHMRAIGGEIRRLTSMSEDELFVAAKELQAPYELVAEVARAGKLPVTLFTAGGIATPADAAMMMQLGAEGVFVGSGIFKSGAPEHRAAAIVKATTFFDDPDVLAKVSRGLGEAMVGINVDEIAVGHRLAQRGW