udgA Family assigned · medium auto-curated
H37Rv Rv0322 · MTBC0 mtbc0_000343 ·
443 aa · 392583–393914 (+) ·
RefSeq NP_214836.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | UDP-glucose 6-dehydrogenase UdgA |
|---|---|
| MTBC0 PGAP re-annotation | UDP-glucose/GDP-mannose dehydrogenase family protein |
| Revised (this work) | UDP-glucose/GDP-mannose dehydrogenase family protein. Pfam: UDPG_MGDP_dh_N (PF03721.21), UDPG_MGDP_dh (PF00984.25), UDPG_MGDP_dh_C (PF03720.23). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O07248
TrEMBL · unreviewed
· Inferred from homology
|
|---|---|
| UniProt name | UDP-glucose 6-dehydrogenase |
| EC (curated) |
EC 1.1.1.22
|
| Curated function | Catalyzes the conversion of UDP-glucose into UDP-glucuronate, one of the precursors of teichuronic acid. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| Preferred name | ugd |
| eggNOG description | Belongs to the UDP-glucose GDP-mannose dehydrogenase family |
| Orthologous group | COG1004 |
| EC number |
EC 1.1.1.22
|
| KEGG orthology |
K00012
|
| KEGG pathways |
map00040, map00053, map00520, map01100
|
| KEGG modules |
M00014, M00129, M00361, M00362
|
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 | 0.719 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 3 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.26% of strains (372) · 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 |
|---|---|---|---|---|
UDPG_MGDP_dh_N | PF03721.21 | 6.3e-62 | 1–181 | UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain |
UDPG_MGDP_dh | PF00984.25 | 4.6e-31 | 204–297 | UDP-glucose/GDP-mannose dehydrogenase family, central domain |
UDPG_MGDP_dh_C | PF03720.23 | 2.3e-29 | 322–422 | UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rmlA (glucose-1-phosphate thymidylyltransferase), high confidence from genomic context alone (score 932 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3634c galE1 |
UDP-glucose 4-epimerase | 969 | 967 | coexpression:412 database:900 |
Rv0993 galU |
UTP--glucose-1-phosphate uridylyltransferase | 973 | 963 | coexpression:463 database:900 |
Rv3468c |
dTDP-glucose 4,6-dehydratase | 960 | 958 | coexpression:415 database:900 |
Rv0501 galE2 |
UDP-glucose 4-epimerase GalE | 950 | 948 | coexpression:414 database:900 |
Rv0334 rmlA |
glucose-1-phosphate thymidylyltransferase | 958 | 932 ctx | neighborhood:544 coexpression:857 textmining:417 |
Rv3809c glf |
UDP-galactopyranose mutase | 876 | 869 | coexpression:858 |
Rv3465 rmlC |
dTDP-4-dehydrorhamnose 3,5-epimerase | 899 | 868 | coexpression:857 |
Rv1510 hyp |
hypothetical protein | 895 | 868 | coexpression:857 |
Rv0618 galTa |
Rv0618, (MTCY19H5.03c), len: 231 aa (probable partial CDS). Probable galTa, first part of galactose-1-phosphate uridylyltransferase, highly | 829 | 823 | database:800 |
Rv3784 |
dTDP-glucose 4,6-dehydratase | 838 | 788 | coexpression:704 |
Rv3630 |
integral membrane protein | 804 | 778 | coexpression:733 |
Rv3464 rmlB |
dTDP-glucose 4,6-dehydratase | 822 | 735 | coexpression:704 |
Rv0321 dcd |
deoxycytidine triphosphate deaminase | 612 | 611 ctx | neighborhood:611 |
Rv0112 gca |
GDP-mannose 4,6-dehydratase | 617 | 596 | coexpression:412 |
Rv0557 mgtA |
GDP-mannose-dependent alpha-mannosyltransferase | 824 | 583 | coexpression:442 textmining:596 |
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: UDP-glucose 6-dehydrogenase UdgA
- MTBC0 PGAP product: UDP-glucose/GDP-mannose dehydrogenase family protein
- Pfam (hmmscan --cut_ga): UDPG_MGDP_dh_N PF03721.21 (E=6e-62), UDPG_MGDP_dh PF00984.25 (E=5e-31), UDPG_MGDP_dh_C PF03720.23 (E=2e-29)
- (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_214836.1)
- Domains: Pfam-A via hmmscan --cut_ga — UDPG_MGDP_dh_N (PF03721.21), UDPG_MGDP_dh (PF00984.25), UDPG_MGDP_dh_C (PF03720.23)
- 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
COG1004 - Curated reference: UniProt O07248 (TrEMBL, unreviewed; Inferred from homology)
- 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 —
56 functional partner(s); context anchor
rmlA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000343|Rv0322|udgA MRCSVFGTGYLGATHAVGMAQLGHEVVGVDIDPGKVAKLAGGDIPFYEPGLRKLLTDNLAAGRLRFTTDYDMAADFADVHFLGVGTPQKIGEYGADLRHVHAVIDALVPRLVRASILVGKSTVPVGTAAELGHRAGALAPRGVDVEIAWNPEFLREGFAVHDTLNPDRIVLGVQDDSTRAEVAVRELYAPLLAAGVPFLVTDLQTAELVKVSANAFLATKISFINAISEVCEAAGADVSQLADALGYDPRIGRQCLNAGLGFGGGCLPKDIRAFMARAGELGADQALTFLREVDSINMRRRTKMVELATTACGGSLLGANIAVLGAAFKPESDDVRDSPALNVAGQLQLNGATVHVYDPKALDNAHRLFPTLNYAVSVAEACERADAVLVLTEWREFIDLEPADLANRVRARVIVDGRNCLDVTRWRRAGWRVFRLGVPRLGH