thiO Resolved · high auto-curated
H37Rv Rv0415 · MTBC0 mtbc0_000435 ·
340 aa · 504513–505535 (+) ·
RefSeq NP_214929.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | thiamine biosynthesis oxidoreductase ThiO |
|---|---|
| MTBC0 PGAP re-annotation | glycine oxidase ThiO |
| Revised (this work) | Glycine oxidase ThiO. Pfam: DAO (PF01266.31). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P96261
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | glycine oxidase |
| EC (curated) |
EC 1.4.3.19
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | thiO |
| eggNOG description | Glycine oxidase |
| Orthologous group | COG0665 |
| EC number |
EC 1.4.3.19
|
| KEGG orthology |
K03153
|
| KEGG pathways |
map00730, map01100
|
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 | 0.458 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 6 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 |
|---|---|---|---|---|
DAO | PF01266.31 | 3.7e-55 | 10–329 | FAD dependent oxidoreductase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: thiG (thiazole synthase), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0417 thiG |
thiazole synthase | 999 | 1000 ctx | neighborhood:881 fusion:838 cooccurence:709 coexpression:461 database:900 textmining:949 |
Rv0416 thiS |
sulfur carrier protein ThiS | 986 | 929 ctx | neighborhood:881 coexpression:430 textmining:817 |
Rv0414c thiE |
thiamine-phosphate synthase | 888 | 873 ctx | neighborhood:776 cooccurence:412 |
Rv0331 |
dehydrogenase/reductase | 853 | 834 | experimental:821 |
Rv2211c gcvT |
aminomethyltransferase | 844 | 823 | experimental:773 |
Rv3671c marP |
serine protease | 627 | 622 | database:549 |
Rv3339c icd1 |
isocitrate dehydrogenase | 619 | 599 | database:576 |
Rv1872c lldD2 |
L-lactate dehydrogenase | 614 | 590 | database:551 |
Rv0694 mftD |
mycofactocin system heme/flavin oxidoreductase MftD | 613 | 589 | database:551 |
Rv0125 pepA |
serine protease PepA | 568 | 563 | database:549 |
Rv1223 htrA |
serine protease HtrA | 567 | 562 | database:549 |
Rv0983 pepD |
serine protease PepD | 567 | 562 | database:549 |
Rv1043c hyp |
hypothetical protein | 564 | 559 | database:549 |
Rv3672c hyp |
hypothetical protein | 562 | 546 | database:524 |
Rv2609c |
membrane protein | 559 | 543 | database:524 |
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: thiamine biosynthesis oxidoreductase ThiO
- MTBC0 PGAP product: glycine oxidase ThiO
- Pfam (hmmscan --cut_ga): DAO PF01266.31 (E=4e-55)
- (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_214929.1)
- Domains: Pfam-A via hmmscan --cut_ga — DAO (PF01266.31)
- 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
COG0665 - Curated reference: UniProt P96261 (TrEMBL, unreviewed; 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 —
89 functional partner(s); context anchor
thiG - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000435|Rv0415|thiO MASDLHTGSLAVIGGGVIGLSVARRAAQAGWPVRVHRSDERGASWVAGGMLAPHSEGWPGEERLLRLGLQSLRLWREGSFLDGLGPQLVTAHESLVVAVDRADVADLRTVADWLSAQGHPVIWESAARDVEPLLAQGIRHGFRAPTELAVDNRALLDALCRDCERLGVRWSSQVSSLSDVDAHTVVIANGIDAPALWPGLPIRPVKGEVLRLRWRPGCMPLPQRVIRARVRGRQVYLVPRSDGVVVGATQYEHGRDTAPVVSGVRDLLDDACTVLPALGEYELAECEAGLRPMTPDNLPLVQRLDSRTLVAAGHGRSGFLLAPWTAEQIVSELVSVGAAS