glfT2 Resolved · high auto-curated
H37Rv Rv3808c · MTBC0 mtbc0_004036 ·
637 aa · 4294476–4296389 (-) ·
RefSeq NP_218325.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | galactofuranosyl transferase GlfT |
|---|---|
| MTBC0 PGAP re-annotation | galactofuranosyl transferase GlfT2 |
| Revised (this work) | Galactofuranosyl transferase GlfT2. Pfam: Glft2_N (PF17994.8), Glyco_tranf_2_3 (PF13641.13), GlfT2_domain3 (PF19320.5). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53585
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Galactofuranosyltransferase GlfT2 |
| EC (curated) |
EC 2.4.1.288
|
| Curated function | Involved in the galactan polymerization of the arabinogalactan (AG) region of the mycolylarabinogalactan-peptidoglycan (mAGP) complex, an essential component of the mycobacteria cell wall. Thus, successively transfers approximately 28 galactofuranosyl (Galf) residues from UDP-galactofuranose (UDP-Galf) onto the galactofuranosyl-galactofuranosyl-rhamnosyl-GlcNAc-diphospho-decaprenol (Galf-Galf-Rha-GlcNAc-PP-C50) acceptor produced by GlfT1, with alternating 1->5 and 1->6 links, forming a galactan domain with approximately 30 galactofuranosyl residues. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | glfT |
| eggNOG description | transferase |
| Orthologous group | COG1216 |
| EC number |
EC 2.4.1.288
|
| KEGG orthology |
K16650
|
| CAZy family |
GT2
|
| Gene Ontology (78) |
GO:0000271, GO:0003674, GO:0003824, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0005975, GO:0005976, GO:0006139 +66 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 | 0.481 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 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 |
|---|---|---|---|---|
Glft2_N | PF17994.8 | 4.7e-61 | 9–152 | Galactofuranosyltransferase 2 N-terminal |
Glyco_tranf_2_3 | PF13641.13 | 9.4e-19 | 161–418 | Glycosyltransferase like family 2 |
GlfT2_domain3 | PF19320.5 | 3.2e-84 | 435–626 | Galactofuranosyltransferase-2, domain 3 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: glfT1 (galactofuranosyl transferase GlfT), high confidence from genomic context alone (score 980 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3782 glfT1 |
galactofuranosyl transferase GlfT | 998 | 980 ctx | cooccurence:770 database:900 textmining:934 |
Rv3809c glf |
UDP-galactopyranose mutase | 991 | 976 ctx | neighborhood:881 cooccurence:762 textmining:676 |
Rv3806c ubiA |
decaprenyl-phosphate phosphoribosyltransferase | 970 | 963 ctx | neighborhood:843 coexpression:772 |
Rv3807c |
decaprenylphosphoryl-5-phosphoribose phosphatase | 898 | 860 ctx | neighborhood:843 |
Rv3805c aftB |
terminal beta-(1->2)-arabinofuranosyltransferase | 857 | 832 ctx | neighborhood:756 |
Rv1836c hyp |
hypothetical protein | 739 | 740 | coexpression:740 |
Rv3792 aftA |
arabinofuranosyltransferase | 876 | 618 | database:500 textmining:691 |
Rv3783 rfbD |
O-antigen/lipopolysaccharide ABC transporter permease RfbD | 924 | 613 | textmining:813 |
Rv3802c |
membrane protein | 617 | 597 | |
Rv2518c ldtB |
L,D-transpeptidase LdtB | 521 | 522 ctx | cooccurence:520 |
Rv3794 embA |
arabinosyltransferase A | 681 | 476 ctx | cooccurence:450 textmining:416 |
Rv3810 pirG |
cell surface protein | 471 | 471 ctx | neighborhood:459 |
Rv3804c fbpA |
diacylglycerol acyltransferase/mycolyltransferase Ag85A | 470 | 470 | |
Rv3811 hyp |
hypothetical protein | 466 | 466 | |
Rv3795 embB |
arabinosyltransferase B | 570 | 465 ctx | cooccurence:445 |
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: galactofuranosyl transferase GlfT
- MTBC0 PGAP product: galactofuranosyl transferase GlfT2
- Pfam (hmmscan --cut_ga): Glft2_N PF17994.8 (E=5e-61), Glyco_tranf_2_3 PF13641.13 (E=9e-19), GlfT2_domain3 PF19320.5 (E=3e-84)
- (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_218325.1)
- Domains: Pfam-A via hmmscan --cut_ga — Glft2_N (PF17994.8), Glyco_tranf_2_3 (PF13641.13), GlfT2_domain3 (PF19320.5)
- 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
COG1216 - Curated reference: UniProt O53585 (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 —
35 functional partner(s); context anchor
glfT1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004036|Rv3808c|glfT2 MSELAASLLSRVILPRPGEPLDVRKLYLEESTTNARRAHAPTRTSLQIGAESEVSFATYFNAFPASYWRRWTTCKSVVLRVQVTGAGRVDVYRTKATGARIFVEGHDFTGTEDQPAAVETEVVLQPFEDGGWVWFDITTDTAVTLHSGGWYATSPAPGTANIAVGIPTFNRPADCVNALRELTADPLVDQVIGAVIVPDQGERKVRDHPDFPAAAARLGSRLSIHDQPNLGGSGGYSRVMYEALKNTDCQQILFMDDDIRLEPDSILRVLAMHRFAKAPMLVGGQMLNLQEPSHLHIMGEVVDRSIFMWTAAPHAEYDHDFAEYPLNDNNSRSKLLHRRIDVDYNGWWTCMIPRQVAEELGQPLPLFIKWDDADYGLRAAEHGYPTVTLPGAAIWHMAWSDKDDAIDWQAYFHLRNRLVVAAMHWDGPKAQVIGLVRSHLKATLKHLACLEYSTVAIQNKAIDDFLAGPEHIFSILESALPQVHRIRKSYPDAVVLPAASELPPPLHKNKAMKPPVNPLVIGYRLARGIMHNLTAANPQHHRRPEFNVPTQDARWFLLCTVDGATVTTADGCGVVYRQRDRAKMFALLWQSLRRQRQLLKRFEEMRRIYRDALPTLSSKQKWETALLPAANQEPEHG