dusB Resolved · high auto-curated
H37Rv Rv0823c · MTBC0 mtbc0_000872 ·
389 aa · 919544–920713 (-) ·
RefSeq NP_215338.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | tRNA-dihydrouridine synthase |
|---|---|
| MTBC0 PGAP re-annotation | tRNA dihydrouridine synthase DusB |
| Revised (this work) | TRNA dihydrouridine synthase DusB. Pfam: Dus (PF01207.24). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WNS7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable tRNA-dihydrouridine synthase |
| EC (curated) |
EC 1.3.1.-
|
| Curated function | Catalyzes the synthesis of 5,6-dihydrouridine (D), a modified base found in the D-loop of most tRNAs, via the reduction of the C5-C6 double bond in target uridines. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | dus |
| eggNOG description | Catalyzes the synthesis of 5,6-dihydrouridine (D), a modified base found in the D-loop of most tRNAs, via the reduction of the C5-C6 double bond in target uridines |
| Orthologous group | COG0042 |
| Gene Ontology (11) |
GO:0008150, GO:0010565, GO:0019216, GO:0019217, GO:0019222, GO:0031323, GO:0050789, GO:0050794, GO:0062012, GO:0065007, GO:0080090
|
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 | 0.94 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 8 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.18% of strains (260) · clonal |
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 |
|---|---|---|---|---|
Dus | PF01207.24 | 1.0e-96 | 26–333 | Dihydrouridine synthase (Dus) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: desA1 (acyl-ACP desaturase DesA), high confidence from genomic context alone (score 956 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0824c desA1 |
acyl-ACP desaturase DesA | 979 | 956 ctx | neighborhood:781 coexpression:806 textmining:560 |
Rv3282 hyp |
hypothetical protein | 776 | 776 ctx | cooccurence:745 |
Rv1094 desA2 |
acyl-ACP desaturase DesA | 874 | 769 | coexpression:755 textmining:479 |
Rv1177 fdxC |
ferredoxin FdxC | 767 | 767 | coexpression:767 |
Rv0825c hyp |
hypothetical protein | 691 | 691 ctx | neighborhood:690 |
Rv2992c gltS |
glutamate--tRNA ligase | 709 | 682 | database:589 |
Rv2845c proS |
proline--tRNA ligase | 698 | 679 | database:647 |
Rv0822c hyp |
hypothetical protein | 673 | 673 ctx | neighborhood:569 |
Rv3602c panC |
pantothenate synthetase | 669 | 669 | coexpression:646 |
Rv0826 hyp |
hypothetical protein | 656 | 656 ctx | neighborhood:655 |
Rv0208c trmB |
tRNA (guanine-N(7)-)-methyltransferase | 657 | 579 | |
Rv3455c truA |
tRNA pseudouridine synthase A | 614 | 496 | coexpression:407 |
Rv1407 fmu |
16S rRNA m5C967 methyltransferase | 629 | 492 | |
Rv0821c phoY2 |
phosphate-transport system transcriptional regulator PhoY2 | 473 | 453 ctx | neighborhood:448 |
Rv2444c rne |
ribonuclease E | 448 | 448 |
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-dihydrouridine synthase
- MTBC0 PGAP product: tRNA dihydrouridine synthase DusB
- Pfam (hmmscan --cut_ga): Dus PF01207.24 (E=1e-96)
- (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_215338.1)
- Domains: Pfam-A via hmmscan --cut_ga — Dus (PF01207.24)
- 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
COG0042 - Curated reference: UniProt P9WNS7 (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 —
66 functional partner(s); context anchor
desA1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000872|Rv0823c|dusB MSRRRAIQPSPALRIGPIELASPVVLAPMAGVTNVAFRALCRQLEQSKVGTVSGLYVCEMVTARALIERHPVTMHMTTFSADESPRSLQLYTVDPDTTYAAARMIAGEGLADHIDMNFGCPVPKVTKRGGGAALPFKRRLFGQIVAAAVRATEGTDIPVTVKFRIGIDDAHHTHLDAGRIAEAEGAAAVALHARTAAQRYSGTADWEQIARLKQHVRTIPVLGNGDIYDAGDALAMMSTTGCDGVVIGRGCLGRPWLFAELSAAFTGSPAPTPPTLGEVADIIRRHGTLLAAHFGEDKGMRDIRKHIAWYLHGFPAGSALRRALAMVKTFDELDCLLDRLDGTVPFPDSATGARGRQGSPARVALPDGWLTDPDDCRVPEGADAMGSGG