glf Resolved · high auto-curated
H37Rv Rv3809c · MTBC0 mtbc0_004037 ·
399 aa · 4296386–4297585 (-) ·
RefSeq NP_218326.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | UDP-galactopyranose mutase |
|---|---|
| MTBC0 PGAP re-annotation | UDP-galactopyranose mutase |
| Revised (this work) | UDP-galactopyranose mutase. Pfam: NAD_binding_8 (PF13450.13), Amino_oxidase (PF01593.31), GLF (PF03275.20). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WIQ1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | UDP-galactopyranose mutase |
| EC (curated) |
EC 5.4.99.9
|
| Curated function | Catalyzes the interconversion through a 2-keto intermediate of uridine diphosphogalactopyranose (UDP-GalP) into uridine diphosphogalactofuranose (UDP-GalF) which is a key building block for cell wall construction in Mycobacterium tuberculosis. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| Preferred name | glf |
| eggNOG description | UDP-galactopyranose mutase |
| Orthologous group | COG0562 |
| EC number |
EC 5.4.99.9
|
| KEGG orthology |
K01854
|
| KEGG pathways |
map00052, map00520
|
| Gene Ontology (21) |
GO:0003674, GO:0003824, GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0008150, GO:0008767, GO:0009273, GO:0009987, GO:0016020, GO:0016853 +9 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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 0 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 |
|---|---|---|---|---|
NAD_binding_8 | PF13450.13 | 3.3e-20 | 12–81 | NAD(P)-binding Rossmann-like domain |
Amino_oxidase | PF01593.31 | 3.6e-06 | 19–95 | Flavin containing amine oxidoreductase |
GLF | PF03275.20 | 7.2e-82 | 156–366 | UDP-galactopyranose mutase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: glfT2 (galactofuranosyl transferase GlfT), high confidence from genomic context alone (score 976 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3808c glfT2 |
galactofuranosyl transferase GlfT | 991 | 976 ctx | neighborhood:881 cooccurence:762 textmining:676 |
Rv0501 galE2 |
UDP-glucose 4-epimerase GalE | 969 | 928 | database:900 textmining:589 |
Rv3634c galE1 |
UDP-glucose 4-epimerase | 969 | 927 | database:900 textmining:600 |
Rv3468c |
dTDP-glucose 4,6-dehydratase | 969 | 926 | database:900 textmining:598 |
Rv0618 galTa |
Rv0618, (MTCY19H5.03c), len: 231 aa (probable partial CDS). Probable galTa, first part of galactose-1-phosphate uridylyltransferase, highly | 909 | 904 | database:900 |
Rv3782 glfT1 |
galactofuranosyl transferase GlfT | 962 | 901 ctx | cooccurence:744 database:500 textmining:637 |
Rv0334 rmlA |
glucose-1-phosphate thymidylyltransferase | 910 | 870 | coexpression:859 |
Rv0322 udgA |
UDP-glucose 6-dehydrogenase UdgA | 876 | 869 | coexpression:858 |
Rv1510 hyp |
hypothetical protein | 882 | 868 | coexpression:857 |
Rv3465 rmlC |
dTDP-4-dehydrorhamnose 3,5-epimerase | 911 | 864 | coexpression:853 |
Rv3806c ubiA |
decaprenyl-phosphate phosphoribosyltransferase | 880 | 847 ctx | neighborhood:843 |
Rv3807c |
decaprenylphosphoryl-5-phosphoribose phosphatase | 878 | 845 ctx | neighborhood:843 |
Rv3805c aftB |
terminal beta-(1->2)-arabinofuranosyltransferase | 763 | 763 ctx | neighborhood:756 |
Rv3783 rfbD |
O-antigen/lipopolysaccharide ABC transporter permease RfbD | 885 | 762 | coexpression:667 textmining:539 |
Rv3630 |
integral membrane protein | 772 | 746 | coexpression:731 |
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-galactopyranose mutase
- MTBC0 PGAP product: UDP-galactopyranose mutase
- Pfam (hmmscan --cut_ga): NAD_binding_8 PF13450.13 (E=3e-20), Amino_oxidase PF01593.31 (E=4e-06), GLF PF03275.20 (E=7e-82)
- (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_218326.1)
- Domains: Pfam-A via hmmscan --cut_ga — NAD_binding_8 (PF13450.13), Amino_oxidase (PF01593.31), GLF (PF03275.20)
- 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
COG0562 - Curated reference: UniProt P9WIQ1 (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 —
40 functional partner(s); context anchor
glfT2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004037|Rv3809c|glf MQPMTARFDLFVVGSGFFGLTIAERVATQLDKRVLVLERRPHIGGNAYSEAEPQTGIEVHKYGAHLFHTSNKRVWDYVRQFTDFTDYRHRVFAMHNGQAYQFPMGLGLVSQFFGKYFTPEQARQLIAEQAAEIDTADAQNLEEKAISLIGRPLYEAFVKGYTAKQWQTDPKELPAANITRLPVRYTFDNRYFSDTYEGLPTDGYTAWLQNMAADHRIEVRLNTDWFDVRGQLRPGSPAAPVVYTGPLDRYFDYAEGRLGWRTLDFEVEVLPIGDFQGTAVMNYNDLDVPYTRIHEFRHFHPERDYPTDKTVIMREYSRFAEDDDEPYYPINTEADRALLATYRARAKSETASSKVLFGGRLGTYQYLDMHMAIASALNMYDNVLAPHLRDGVPLLQDGA