truB Resolved · high auto-curated
H37Rv Rv2793c · MTBC0 mtbc0_002972 ·
298 aa · 3124779–3125675 (-) ·
RefSeq NP_217309.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | tRNA pseudouridine synthase B |
|---|---|
| MTBC0 PGAP re-annotation | tRNA pseudouridine(55) synthase TruB |
| Revised (this work) | TRNA pseudouridine(55) synthase TruB. Pfam: TruB_N (PF01509.24), TruB_C_2 (PF16198.11), TruB_C (PF09142.18). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WHP7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | tRNA pseudouridine synthase B |
| EC (curated) |
EC 5.4.99.25
|
| Curated function | Responsible for synthesis of pseudouridine from uracil-55 in the psi GC loop of transfer RNAs. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | truB |
| eggNOG description | Responsible for synthesis of pseudouridine from uracil- 55 in the psi GC loop of transfer RNAs |
| Orthologous group | COG0130 |
| EC number |
EC 5.4.99.25
|
| KEGG orthology |
K03177
|
| Gene Ontology (39) |
GO:0001522, GO:0003674, GO:0003824, GO:0005575, GO:0005618, GO:0005623, GO:0006139, GO:0006396, GO:0006399, GO:0006400, GO:0006725, GO:0006807 +27 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 | 0.264 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 10 synonymous, 7 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 |
|---|---|---|---|---|
TruB_N | PF01509.24 | 6.6e-52 | 27–179 | TruB family pseudouridylate synthase (N terminal domain) |
TruB_C_2 | PF16198.11 | 4.3e-12 | 180–220 | tRNA pseudouridylate synthase B C-terminal domain |
TruB_C | PF09142.18 | 1.9e-23 | 236–291 | tRNA Pseudouridine synthase II, C terminal |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pptT (4'-phosphopantetheinyl transferase), high confidence from genomic context alone (score 906 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3396c guaA |
GMP synthase | 937 | 928 | coexpression:923 |
Rv2839c infB |
translation initiation factor IF-2 | 965 | 919 | coexpression:814 experimental:435 textmining:590 |
Rv2794c pptT |
4'-phosphopantetheinyl transferase | 906 | 906 ctx | neighborhood:882 |
Rv2795c hyp |
hypothetical protein | 887 | 887 ctx | neighborhood:882 |
Rv2838c rbfA |
ribosome-binding factor RbfA | 967 | 876 | coexpression:853 textmining:745 |
Rv1407 fmu |
16S rRNA m5C967 methyltransferase | 923 | 876 | coexpression:811 textmining:413 |
Rv2841c nusA |
transcription termination/antitermination protein NusA | 818 | 819 | coexpression:788 |
Rv2786c ribF |
bifunctional riboflavin kinase /FMN adenylyltransferase | 944 | 810 ctx | fusion:614 coexpression:412 textmining:720 |
Rv1630 rpsA |
30S ribosomal protein S1 | 835 | 808 | coexpression:647 experimental:436 |
Rv2785c rpsO |
30S ribosomal protein S15 | 900 | 774 | coexpression:682 textmining:578 |
Rv0208c trmB |
tRNA (guanine-N(7)-)-methyltransferase | 817 | 758 | coexpression:648 |
Rv2907c rimM |
16S rRNA processing protein RimM | 820 | 752 | coexpression:678 |
Rv0668 rpoC |
DNA-directed RNA polymerase subunit beta' | 777 | 745 | coexpression:672 |
Rv2783c gpsI |
bifunctional guanosine pentaphosphate synthetase/polyribonucleotide nucleotidyltransferase | 802 | 722 | coexpression:654 |
Rv0722 rpmD |
50S ribosomal protein L30 | 729 | 719 | coexpression:652 |
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: tRNA pseudouridine synthase B
- MTBC0 PGAP product: tRNA pseudouridine(55) synthase TruB
- Pfam (hmmscan --cut_ga): TruB_N PF01509.24 (E=7e-52), TruB_C_2 PF16198.11 (E=4e-12), TruB_C PF09142.18 (E=2e-23)
- (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_217309.1)
- Domains: Pfam-A via hmmscan --cut_ga — TruB_N (PF01509.24), TruB_C_2 (PF16198.11), TruB_C (PF09142.18)
- 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
COG0130 - Curated reference: UniProt P9WHP7 (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 —
148 functional partner(s); context anchor
pptT - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002972|Rv2793c|truB MSATGPGIVVIDKPAGMTSHDVVGRCRRIFATRRVGHAGTLDPMATGVLVIGIERATKILGLLTAAPKSYAATIRLGQTTSTEDAEGQVLQSVPAKHLTIEAIDAAMERLRGEIRQVPSSVSAIKVGGRRAYRLARQGRSVQLEARPIRIDRFELLAARRRDQLIDIDVEIDCSSGTYIRALARDLGDALGVGGHVTALRRTRVGRFELDQARSLDDLAERPALSLSLDEACLLMFARRDLTAAEASAAANGRSLPAVGIDGVYAACDADGRVIALLRDEGSRTRSVAVLRPATMHPG