truA Resolved · high auto-curated
H37Rv Rv3455c · MTBC0 - ·
256 aa · 3876052–3876822 (-) ·
RefSeq NP_217972.3
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | tRNA pseudouridine synthase A |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | TRNA pseudouridine synthase A. Pfam: PseudoU_synth_1 (PF01416.26). |
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 |
P9WHP9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | tRNA pseudouridine synthase A |
| EC (curated) |
EC 5.4.99.12
|
| Curated function | Formation of pseudouridine at positions 38, 39 and 40 in the anticodon stem and loop of transfer RNAs. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | truA |
| eggNOG description | Formation of pseudouridine at positions 38, 39 and 40 in the anticodon stem and loop of transfer RNAs |
| Orthologous group | COG0101 |
| EC number |
EC 5.4.99.12
|
| KEGG orthology |
K06173
|
| Gene Ontology (38) |
GO:0001522, GO:0003674, GO:0003824, GO:0005575, GO:0005618, GO:0005623, GO:0006139, GO:0006396, GO:0006399, GO:0006400, GO:0006725, GO:0006807 +26 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 | 0.503 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 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 |
|---|---|---|---|---|
PseudoU_synth_1 | PF01416.26 | 8.3e-25 | 137–238 | tRNA pseudouridine synthase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rpoA (DNA-directed RNA polymerase subunit alpha), high confidence from genomic context alone (score 988 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3457c rpoA |
DNA-directed RNA polymerase subunit alpha | 993 | 988 ctx | neighborhood:766 coexpression:949 textmining:492 |
Rv3456c rplQ |
50S ribosomal protein L17 | 989 | 988 ctx | neighborhood:796 coexpression:943 |
Rv3458c rpsD |
30S ribosomal protein S4 | 843 | 835 ctx | neighborhood:684 coexpression:434 |
Rv3459c rpsK |
30S ribosomal protein S11 | 760 | 745 ctx | neighborhood:684 |
Rv3460c rpsM |
30S ribosomal protein S13 | 734 | 723 ctx | neighborhood:684 |
Rv2793c truB |
tRNA pseudouridine synthase B | 861 | 676 | coexpression:433 textmining:591 |
Rv3462c infA |
translation initiation factor IF-1 | 707 | 665 ctx | neighborhood:580 |
Rv2367c ybeY |
endoribonuclease | 666 | 658 | experimental:561 |
Rv2325c hyp |
hypothetical protein | 653 | 596 | coexpression:563 |
Rv0710 rpsQ |
30S ribosomal protein S17 | 608 | 586 | experimental:446 |
Rv0722 rpmD |
50S ribosomal protein L30 | 575 | 575 | coexpression:484 |
Rv0208c trmB |
tRNA (guanine-N(7)-)-methyltransferase | 657 | 550 | coexpression:400 |
Rv3116 moeB2 |
molybdenum cofactor biosynthesis protein MoeB | 594 | 542 | experimental:519 |
Rv3206c moeB1 |
adenylyltransferase/sulfurtransferase MoeZ | 593 | 541 | experimental:519 |
Rv0422c thiD |
hydroxymethylpyrimidine/phosphomethylpyrimidine kinase | 539 | 539 | coexpression:501 |
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): tRNA pseudouridine synthase A
- Pfam (hmmscan --cut_ga): PseudoU_synth_1 PF01416.26 (E=8e-25)
- (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_217972.3)
- Domains: Pfam-A via hmmscan --cut_ga — PseudoU_synth_1 (PF01416.26)
- 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
COG0101 - Curated reference: UniProt P9WHP9 (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 —
101 functional partner(s); context anchor
rpoA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3455c|truA MGQRTVAGDLDAALTTIFRTPVRLRAAGRTDAGVHASGQVAHVDVPADALPNAYPRAGHVGDPEFLPLLRRLGRFLPADVRILDITRAPAGFDARFSALRRHYVYRLSTAPYGVEPQQARYITAWPRELDLDAMTAASRDLMGLHDFAAFCRHREGATTIRDLQRLDWSRAGTLVTAHVTADAFCWSMVRSLVGALLAVGEHRRATTWCRELLTATGRSSDFAVAPAHGLTLIQVDYPPDDQLASRNLVTRDVRSG