trpB Family assigned · medium auto-curated
H37Rv Rv1612 · MTBC0 - ·
410 aa · 1811127–1812359 (+) ·
RefSeq NP_216128.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | tryptophan synthase subunit beta |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Tryptophan synthase subunit beta. Pfam: PALP (PF00291.32). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P9WFX9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Tryptophan synthase beta chain |
| EC (curated) |
EC 4.2.1.20
|
| Curated function | The beta subunit is responsible for the synthesis of L-tryptophan from indole and L-serine. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | trpB |
| eggNOG description | The beta subunit is responsible for the synthesis of L- tryptophan from indole and L-serine |
| Orthologous group | COG0133 |
| EC number |
EC 4.2.1.20
|
| KEGG orthology |
K01696
|
| KEGG pathways |
map00260, map00400, map01100, map01110, map01130, map01230
|
| KEGG modules |
M00023
|
| Gene Ontology (57) |
GO:0000162, GO:0003674, GO:0003824, GO:0004834, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0006082, GO:0006520, GO:0006568, GO:0006576 +45 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 | 0.253 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 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 |
|---|---|---|---|---|
PALP | PF00291.32 | 6.4e-48 | 66–391 | Pyridoxal-phosphate dependent enzyme |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: trpA (tryptophan synthase subunit alpha), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1613 trpA |
tryptophan synthase subunit alpha | 999 | 1000 ctx | neighborhood:882 fusion:900 cooccurence:774 coexpression:979 experimental:999 database:900 textmining:843 |
Rv1611 trpC |
indole-3-glycerol phosphate synthase | 999 | 1000 ctx | neighborhood:793 fusion:856 cooccurence:774 coexpression:794 database:900 textmining:569 |
Rv1614 lgt |
prolipoprotein diacylglyceryl transferase | 993 | 994 ctx | neighborhood:882 coexpression:948 |
Rv1609 trpE |
anthranilate synthase component I | 992 | 975 ctx | neighborhood:721 cooccurence:728 coexpression:700 textmining:719 |
Rv2192c trpD |
anthranilate phosphoribosyltransferase | 991 | 973 ctx | cooccurence:772 coexpression:858 textmining:696 |
Rv0013 trpG |
anthranilate synthase component II | 975 | 965 ctx | cooccurence:708 coexpression:857 |
Rv1559 ilvA |
threonine dehydratase IlvA | 949 | 934 | database:900 |
Rv2386c mbtI |
salicylate synthase | 953 | 925 ctx | cooccurence:737 coexpression:691 textmining:411 |
Rv3042c serB2 |
phosphoserine phosphatase SerB | 928 | 924 | database:900 |
Rv1077 cbs |
cystathionine beta-synthase | 909 | 904 | database:900 |
Rv1093 glyA1 |
serine hydroxymethyltransferase | 912 | 901 | database:900 |
Rv0069c sdaA |
L-serine dehydratase | 904 | 901 | database:900 |
Rv0436c pssA |
CDP-diacylglycerol--serine O-phosphatidyltransferase | 900 | 901 | database:900 |
Rv0070c glyA2 |
serine hydroxymethyltransferase | 912 | 900 | database:900 |
Rv1005c pabB |
para-aminobenzoate synthase component I | 898 | 888 ctx | cooccurence:637 coexpression:692 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): tryptophan synthase subunit beta
- Pfam (hmmscan --cut_ga): PALP PF00291.32 (E=6e-48)
- (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_216128.1)
- Domains: Pfam-A via hmmscan --cut_ga — PALP (PF00291.32)
- 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
COG0133 - Curated reference: UniProt P9WFX9 (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 —
70 functional partner(s); context anchor
trpA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1612|trpB MSAAIAEPTSHDPDSGGHFGGPSGWGGRYVPEALMAVIEEVTAAYQKERVSQDFLDDLDRLQANYAGRPSPLYEATRLSQHAGSARIFLKREDLNHTGSHKINNVLGQALLARRMGKTRVIAETGAGQHGVATATACALLGLDCVIYMGGIDTARQALNVARMRLLGAEVVAVQTGSKTLKDAINEAFRDWVANADNTYYCFGTAAGPHPFPTMVRDFQRIIGMEARVQIQGQAGRLPDAVVACVGGGSNAIGIFHAFLDDPGVRLVGFEAAGDGVETGRHAATFTAGSPGAFHGSFSYLLQDEDGQTIESHSISAGLDYPGVGPEHAWLKEAGRVDYRPITDSEAMDAFGLLCRMEGIIPAIESAHAVAGALKLGVELGRGAVIVVNLSGRGDKDVETAAKWFGLLGND