Rv1711 Resolved · high auto-curated
H37Rv Rv1711 · MTBC0 mtbc0_001821 ·
254 aa · 1950853–1951617 (+) ·
RefSeq NP_216227.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | RNA pseudouridine synthase |
|---|---|
| MTBC0 PGAP re-annotation | pseudouridine synthase |
| Revised (this work) | Pseudouridine synthase. Pfam: S4 (PF01479.31), 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 |
P9WHQ1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized RNA pseudouridine synthase Rv1711 |
| EC (curated) |
EC 5.4.99.-
|
UniProt still lists this protein as Uncharacterized RNA pseudouridine synthase Rv1711; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | rluB |
| eggNOG description | Belongs to the pseudouridine synthase RsuA family |
| Orthologous group | COG1187 |
| EC number |
EC 5.4.99.19, EC 5.4.99.22
|
| KEGG orthology |
K06178, K06183
|
| Gene Ontology (45) |
GO:0000154, GO:0000455, GO:0001522, GO:0003674, GO:0003824, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0006139, GO:0006364 +33 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 | 0.488 · purifying |
|---|---|
| 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 |
|---|---|---|---|---|
S4 | PF01479.31 | 3.3e-13 | 15–57 | S4 domain |
PseudoU_synth_2 | PF00849.28 | 2.1e-23 | 76–211 | RNA pseudouridylate synthase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: cmk (cytidylate kinase), high confidence from genomic context alone (score 995 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1712 cmk |
cytidylate kinase | 997 | 995 ctx | neighborhood:882 fusion:592 coexpression:886 textmining:489 |
Rv1713 engA |
GTPase Der | 995 | 993 ctx | neighborhood:881 cooccurence:704 coexpression:810 |
Rv1710 scpB |
segregation and condensation protein ScpB | 988 | 977 ctx | neighborhood:881 coexpression:814 textmining:509 |
Rv1709 scpA |
segregation and condensation protein ScpA | 964 | 932 ctx | neighborhood:881 coexpression:451 textmining:505 |
Rv1708 |
initiation inhibitor protein | 886 | 887 ctx | neighborhood:881 |
Rv0427c xthA |
exodeoxyribonuclease III protein XthA | 814 | 815 | coexpression:805 |
Rv1707 |
transmembrane protein | 743 | 744 ctx | neighborhood:744 |
Rv1714 |
oxidoreductase | 601 | 601 ctx | neighborhood:520 |
Rv1703c |
methyltransferase | 562 | 563 ctx | neighborhood:544 |
Rv1715 fadB3 |
3-hydroxybutyryl-CoA dehydrogenase FadB | 540 | 540 ctx | neighborhood:519 |
Rv2364c era |
GTPase Era | 546 | 517 ctx | cooccurence:431 |
Rv1716 hyp |
hypothetical protein | 511 | 511 ctx | neighborhood:489 |
Rv1717 hyp |
hypothetical protein | 488 | 488 ctx | neighborhood:476 |
Rv1420 uvrC |
excinuclease ABC subunit UvrC | 481 | 481 ctx | cooccurence:442 |
Rv2440c obg |
GTPase Obg | 518 | 477 ctx | cooccurence:410 |
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: RNA pseudouridine synthase
- MTBC0 PGAP product: pseudouridine synthase
- Pfam (hmmscan --cut_ga): S4 PF01479.31 (E=3e-13), PseudoU_synth_2 PF00849.28 (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_216227.1)
- Domains: Pfam-A via hmmscan --cut_ga — S4 (PF01479.31), 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
COG1187 - Curated reference: UniProt P9WHQ1 (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 —
29 functional partner(s); context anchor
cmk - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001821|Rv1711| MMAEPEESREPRGIRLQKVLSQAGIASRRAAEKMIVDGRVEVDGHVVTELGTRVDPQVAVVRVDGARVVLDDSLVYLALNKPRGMHSTMSDDRGRPCIGDLIERKVRGTKKLFHVGRLDADTEGLMLLTNDGELAHRLMHPSHEVPKTYLATVTGSVPRGLGRTLRAGIELDDGPAFVDDFAVVDAIPGKTLVRVTLHEGRNRIVRRLLAAAGFPVEALVRTDIGAVSLGKQRPGSVRALRSNEIGQLYQAVGL