Rv3406 Resolved · high auto-curated
H37Rv Rv3406 · MTBC0 mtbc0_003620 ·
295 aa · 3850769–3851656 (+) ·
RefSeq NP_217923.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | dioxygenase |
|---|---|
| MTBC0 PGAP re-annotation | alpha-ketoglutarate-dependent sulfate ester dioxygenase |
| Revised (this work) | Alpha-ketoglutarate-dependent sulfate ester dioxygenase. Pfam: TauD (PF02668.23). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WKZ1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Alpha-ketoglutarate-dependent sulfate ester dioxygenase |
| EC (curated) |
EC 1.14.11.77
|
| Curated function | Alpha-ketoglutarate-dependent sulfate ester dioxygenase, which oxidizes medium-chain alkyl-sulfate esters. Shows preference for 2-ethylhexyl sulfate (2-EHS) in vitro, leading to the formation of succinate and 2-ethylhexanal. Has likely a role in sulfate scavenging in vivo..; FUNCTION: Also causes the inactivation of the 2-carboxyquinoxaline Ty38c (an antitubercular compound that inhibits DprE1) via oxidative decarboxylation, using Ty38c instead of alpha-ketoglutarate as a substrate. Is thus responsible for primary resistance of M.tuberculosis to Ty38c in vitro. Overexpression of Rv3406 causes . |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
Q Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| Preferred name | tauD |
| eggNOG description | taurine catabolism dioxygenase |
| Orthologous group | COG2175 |
| KEGG orthology |
K22303
|
| Gene Ontology (26) |
GO:0000907, GO:0000908, GO:0003674, GO:0003824, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005886, GO:0006790, GO:0008150, GO:0008152 +14 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 | 0.827 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 5 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 |
|---|---|---|---|---|
TauD | PF02668.23 | 6.1e-53 | 7–269 | Taurine catabolism dioxygenase TauD, TfdA family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3405c (HTH-type transcriptional regulator), high confidence from genomic context alone (score 786 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3405c |
HTH-type transcriptional regulator | 971 | 786 ctx | neighborhood:786 textmining:870 |
Rv3408 vapC47 |
ribonuclease VapC47 | 668 | 669 ctx | neighborhood:669 |
Rv3407 vapB47 |
antitoxin VapB47 | 668 | 669 ctx | neighborhood:669 |
Rv0147 |
aldehyde dehydrogenase | 629 | 506 | database:428 |
Rv0458 |
aldehyde dehydrogenase | 608 | 506 | database:428 |
Rv2858c aldC |
aldehyde dehydrogenase AldC | 525 | 506 | database:428 |
Rv0768 aldA |
aldehyde dehydrogenase AldA | 525 | 506 | database:428 |
Rv1187 rocA |
pyrroline-5-carboxylate dehydrogenase RocA | 525 | 506 | database:428 |
Rv3293 pcd |
piperideine-6-carboxylic acid dehydrogenase | 525 | 506 | database:428 |
Rv0223c |
aldehyde dehydrogenase | 525 | 506 | database:428 |
Rv0753c mmsA |
methylmalonate-semialdehyde dehydrogenase | 525 | 506 | database:428 |
Rv0234c gabD1 |
succinate-semialdehyde dehydrogenase | 525 | 506 | database:428 |
Rv1731 gabD2 |
succinate-semialdehyde dehydrogenase | 525 | 506 | database:428 |
Rv2383c mbtB |
phenyloxazoline synthase | 527 | 459 ctx | neighborhood:434 |
Rv2693c |
integral membrane protein | 470 | 436 | coexpression:404 |
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: dioxygenase
- MTBC0 PGAP product: alpha-ketoglutarate-dependent sulfate ester dioxygenase
- Pfam (hmmscan --cut_ga): TauD PF02668.23 (E=6e-53)
- (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_217923.1)
- Domains: Pfam-A via hmmscan --cut_ga — TauD (PF02668.23)
- 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
COG2175 - Curated reference: UniProt P9WKZ1 (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 —
25 functional partner(s); context anchor
Rv3405c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003620|Rv3406| MTDLITVKKLGSRIGAQIDGVRLGGDLDPAAVNEIRAALLAHKVVFFRGQHQLDDAEQLAFAGLLGTPIGHPAAIALADDAPIITPINSEFGKANRWHTDVTFAANYPAASVLRAVSLPSYGGSTLWANTAAAYAELPEPLKCLTENLWALHTNRYDYVTTKPLTAAQRAFRQVFEKPDFRTEHPVVRVHPETGERTLLAGDFVRSFVGLDSHESRVLFEVLQRRITMPENTIRWNWAPGDVAIWDNRATQHRAIDDYDDQHRLMHRVTLMGDVPVDVYGQASRVISGAPMEIAG