Rv3300c Family assigned · medium auto-curated
H37Rv Rv3300c · MTBC0 mtbc0_003508 ·
305 aa · 3708063–3708980 (-) ·
RefSeq NP_217817.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | RluA family pseudouridine synthase |
| Revised (this work) | RluA family pseudouridine synthase. Pfam: PseudoU_synth_2 (PF00849.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O07166
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | RNA pseudouridylate synthase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | rluA |
| eggNOG description | pseudouridine synthase |
| Orthologous group | COG0564 |
| EC number |
EC 5.4.99.28, EC 5.4.99.29
|
| KEGG orthology |
K06177
|
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 | 3.874 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 10 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_2 | PF00849.28 | 1.4e-22 | 93–237 | RNA pseudouridylate synthase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: atsB (arylsulfatase AtsB), high confidence from genomic context alone (score 948 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3299c atsB |
arylsulfatase AtsB | 948 | 948 ctx | neighborhood:756 coexpression:796 |
Rv3301c phoY1 |
phosphate transport system transcriptional regulator PhoY | 943 | 843 ctx | neighborhood:792 textmining:656 |
Rv2420c rsfS hyp |
hypothetical protein | 843 | 829 | experimental:815 |
Rv2442c rplU |
50S ribosomal protein L21 | 826 | 826 | experimental:813 |
Rv3456c rplQ |
50S ribosomal protein L17 | 824 | 825 | experimental:813 |
Rv3443c rplM |
50S ribosomal protein L13 | 818 | 819 | experimental:806 |
Rv0723 rplO |
50S ribosomal protein L15 | 817 | 818 | experimental:806 |
Rv0640 rplK |
50S ribosomal protein L11 | 825 | 816 | experimental:809 |
Rv0701 rplC |
50S ribosomal protein L3 | 822 | 813 | experimental:804 |
Rv0714 rplN |
50S ribosomal protein L14 | 815 | 811 | experimental:803 |
Rv0715 rplX |
50S ribosomal protein L24 | 810 | 811 | experimental:803 |
Rv3302c glpD2 |
glycerol-3-phosphate dehydrogenase | 895 | 779 ctx | neighborhood:766 textmining:547 |
Rv3303c lpdA |
NAD(P)H quinone reductase LpdA | 870 | 779 ctx | neighborhood:759 textmining:437 |
Rv3262 fbiB |
coenzyme F420:L-glutamate ligase | 767 | 765 | coexpression:757 |
Rv1823 hyp |
hypothetical protein | 738 | 738 | coexpression:738 |
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: hypothetical protein
- MTBC0 PGAP product: RluA family pseudouridine synthase
- Pfam (hmmscan --cut_ga): PseudoU_synth_2 PF00849.28 (E=1e-22)
- (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_217817.1)
- Domains: Pfam-A via hmmscan --cut_ga — PseudoU_synth_2 (PF00849.28)
- 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
COG0564 - Curated reference: UniProt O07166 (TrEMBL, unreviewed; Predicted)
- 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 —
74 functional partner(s); context anchor
atsB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003508|Rv3300c| MALRPEDRLLSVHDVLGPVRVRLLGGSVLAELTARFGVAARAKVLAGEVVDDDGAVVDSGTVLPPGSVVHLYRDLPDEVPVPFDVPVLHQDADIVVVDKPHFLATMPRGRHVAQTALVRLRRELGLPELSPAHRLDRLTAGVLLFTTRREVRGSYQTMFARGLVRKTYLARAPVAPGLALPRLVRSRIVKRRGHLQAVCEPGVPNAETLVERIARDGLYRLTPTTGRTHQLRVHMAALGIPIMGDPLYPNVISVAAHDFSTPLQLLAQRIEFDDPLTGSHREFASTRTLTGATLPTWSAAADCRP