aftD Family assigned · medium auto-curated
H37Rv Rv0236c · MTBC0 mtbc0_000251 ·
1400 aa · 283030–287232 (-) ·
RefSeq NP_214750.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | alpha-(1->3)-arabinofuranosyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | DUF3367 domain-containing protein |
| Revised (this work) | DUF3367 domain-containing protein. Pfam: GT-C_AftD (PF11847.14), CBM_AftD (PF24607.2). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P96419
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Alpha-(1->3)-arabinofuranosyltransferase |
| EC (curated) |
EC 2.4.2.47
|
| Curated function | Involved in the biosynthesis of the arabinogalactan (AG) region of the mycolylarabinogalactan-peptidoglycan (mAGP) complex, an essential component of the mycobacterial cell wall. Catalyzes the addition of an arabinofuranosyl (Araf) residue from the sugar donor decaprenyl-phospho-arabinose (DPA) on the C-3 of an alpha-(1->5)-linked Araf from the arabinan backbone of AG. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| Preferred name | aftD |
| eggNOG description | capsule organization |
| Orthologous group | COG4981 |
| KEGG orthology |
K16648
|
| Gene Ontology (8) |
GO:0005575, GO:0005623, GO:0005886, GO:0008150, GO:0016020, GO:0040007, GO:0044464, GO:0071944
|
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 | 0.642 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 15 synonymous, 24 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 |
|---|---|---|---|---|
GT-C_AftD | PF11847.14 | 2.4e-277 | 16–692 | Alpha-(1->3)-arabinofuranosyltransferase, N-terminal GT-C domain |
CBM_AftD | PF24607.2 | 1.1e-66 | 942–1090 | Arabinofuranosyltransferase D, third carbohydrate binding module |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: aftC (alpha-(1->3)-arabinofuranosyltransferase), high confidence from genomic context alone (score 956 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2673 aftC |
alpha-(1->3)-arabinofuranosyltransferase | 996 | 956 ctx | cooccurence:580 database:900 textmining:931 |
Rv0224c |
methyltransferase | 807 | 800 ctx | cooccurence:653 |
Rv0226c |
transmembrane protein | 977 | 799 ctx | cooccurence:764 textmining:895 |
Rv2378c mbtG |
L-lysine N6-monooxygenase | 749 | 750 ctx | cooccurence:746 |
Rv0955 |
integral membrane protein | 762 | 741 ctx | cooccurence:735 |
Rv0227c |
membrane protein | 851 | 740 ctx | cooccurence:720 textmining:452 |
Rv0235c |
transmembrane protein | 734 | 734 ctx | neighborhood:730 |
Rv1159 pimE |
polyprenol-phosphate-mannose-dependent alpha-(1-2)-phosphatidylinositol pentamannoside mannosyltransferase | 806 | 729 ctx | cooccurence:711 |
Rv0236A hyp |
hypothetical protein | 729 | 729 ctx | neighborhood:728 |
Rv2181 |
alpha-(1-2)-phosphatidylinositol mannoside mannosyltransferase | 887 | 700 ctx | cooccurence:532 textmining:639 |
Rv0204c |
transmembrane protein | 739 | 666 ctx | cooccurence:616 |
Rv0225 hyp |
hypothetical protein | 667 | 649 ctx | cooccurence:627 |
Rv0804 hyp |
hypothetical protein | 621 | 621 ctx | cooccurence:620 |
Rv0234c gabD1 |
succinate-semialdehyde dehydrogenase | 748 | 616 ctx | neighborhood:614 |
Rv1863c |
integral membrane protein | 596 | 596 ctx | cooccurence:585 |
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: alpha-(1->3)-arabinofuranosyltransferase
- MTBC0 PGAP product: DUF3367 domain-containing protein
- Pfam (hmmscan --cut_ga): GT-C_AftD PF11847.14 (E=2e-277), CBM_AftD PF24607.2 (E=1e-66)
- (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_214750.1)
- Domains: Pfam-A via hmmscan --cut_ga — GT-C_AftD (PF11847.14), CBM_AftD (PF24607.2)
- 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
COG4981 - Curated reference: UniProt P96419 (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 —
65 functional partner(s); context anchor
aftC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000251|Rv0236c|aftD MAPLSRKWLPVVGAVALALTFAQSPGQVSPDTKLDLTANPLRFLARATNLWNSDLPFGQAQNQAYGYLFPHGTFFVIGHLLGVPGWVTQRLWWAVLLTVGFWGLLRVAEALGVGGPSSRVVGAVAFALSPRVLTTLGSISSETLPMMLAPWVLLPTILALRGTSGRSVRALAAQAGLAVALMGAVNAIATLAGCLPAVIWWACHRPNRLWWRYTAWWLLAMALATLWWVMALTQLHGVSPPFLDFIESSGVTTQWSSLVEVLRGTDSWTPFVAPNATAGAPLVTGSAAILGTCLVAAAGLAGLTSPAMPARGRLVTMLLVGVVLLAVGHRGGLASPVAHPVQAFLDAAGTPLRNVHKVGPVIRLPLVLGLAQLLSRVPLPGSAPRPAWLRAFAHPERDKRVAVAVVALTALMVSTSLAWTGRVAPPGTFGALPQYWQEAADWLRTHHAATPTPGRVLVVPGAPFATQVWGTSHDEPLQVLGDGPWGVRDSIPLTPPQTIRALDSVQRLFAAGRPSAGLADTLARQGISYVLVRNDLDPETSRSARPILLHRSIAGSPGLAKLAEFGAPVGPDPLAGFVNDSGLRPRYPAIEIYRVSAPANPGAPYFAATDQLARVDGGPEVLLRLDERRRLQGQPPLGPVLMTADARAAGLPVPQVAVTDTPVARETDYGRVDHHSSAIRAPGDARHTYNRVPDYPVPGAEPVVGGWTGGRITVSSSSADATAMPDVAPASAPAAAVDGDPATAWVSNALQAAVGQWLQVDFDRPVTNAVVTLTPSATAVGAQVRRILIETVNGSTTLRFDEAGKPLTAALPYGETPWVRFTAAATDDGSAGVQFGITDLAITQYDASGFAHPVQLRHTVLVPGPPPGSAIAGWDLGSELLGRPGCAPGPDGVRCAASMALAPEEPANLSRTLTVPRPVSVTPMVWVRPRQGPKLADLIAAPSTTRASGDSDLVDILGSAYAAADGDPATAWTAPQRVVQHKTPPTLTLTLPRPTVVTGLRLAASRSMLPAHPTVVAINLGDGPQVRQLQVGELTTLWLHPRVTDTVSVSLLDWDDVIDRNALGFDQLKPPGLAEVVVLGAGGAPIAPADAARNRARALTVDCDHGPVVAVAGRFVHTSIRTTVGALLDGEPVAALPCEREPIALPAGQQELLISPGAAFVVDGAQLSTPGAGLSSATVTSAETGAWGPTHREVRVPESATSRVLVVPESINSGWVARTSTGARLTPIAVNGWQQAWVVPAGNPGTITLTFAPNSLYRASLAIGLALLPLLALLAFWRTGRRQLADRPTPPWRPGAWAAAGVLAAGAVIASIAGVMVMGTALGVRYALRRRERLRDRVTVGLAAGGLILAGAALSRHPWRSVDGYAGNWASVQLLALISVSVVAASVVATSESRGQDRMQ