embA Resolved · high auto-curated
H37Rv Rv3794 · MTBC0 mtbc0_004022 ·
1094 aa · 4267354–4270638 (+) ·
RefSeq NP_218311.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | arabinosyltransferase A |
|---|---|
| MTBC0 PGAP re-annotation | arabinosyltransferase EmbA |
| Revised (this work) | Arabinosyltransferase EmbA. Pfam: Arabino_trans_N (PF17689.9), Arabinose_trans (PF04602.19), Arabino_trans_C (PF14896.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WNL9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable arabinosyltransferase A |
| EC (curated) |
EC 2.4.2.-
|
| Curated function | Arabinosyl transferase responsible for the polymerization of arabinose into the arabinan of arabinogalactan. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| Preferred name | embA |
| eggNOG description | Cell wall arabinan synthesis protein |
| Orthologous group | COG1807 |
| KEGG orthology |
K11385
|
| Gene Ontology (26) |
GO:0003674, GO:0003824, GO:0005575, GO:0005576, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0005887, GO:0008150, GO:0016020 +14 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 | 0.357 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 16 synonymous, 15 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 |
|---|---|---|---|---|
Arabino_trans_N | PF17689.9 | 2.7e-47 | 37–194 | Arabinosyltransferase concanavalin like domain |
Arabinose_trans | PF04602.19 | 7.4e-163 | 198–667 | Mycobacterial cell wall arabinan synthesis protein |
Arabino_trans_C | PF14896.13 | 5.2e-147 | 703–1091 | EmbC C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: embB (arabinosyltransferase B), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3795 embB |
arabinosyltransferase B | 999 | 1000 ctx | neighborhood:881 coexpression:798 experimental:999 database:900 |
Rv2244 acpM |
meromycolate extension acyl carrier protein | 986 | 986 | experimental:986 |
Rv3792 aftA |
arabinofuranosyltransferase | 997 | 959 ctx | neighborhood:669 cooccurence:760 database:500 textmining:931 |
Rv3791 dprE2 |
decaprenylphosphoryl-D-2-keto erythropentose reductase | 935 | 896 ctx | neighborhood:628 cooccurence:469 database:500 textmining:405 |
Rv2673 aftC |
alpha-(1->3)-arabinofuranosyltransferase | 952 | 884 ctx | cooccurence:768 database:500 textmining:604 |
Rv3789 |
GtrA family protein | 882 | 862 ctx | neighborhood:527 cooccurence:711 |
Rv3793 embC |
arabinosyltransferase C | 867 | 848 ctx | neighborhood:780 |
Rv3802c |
membrane protein | 807 | 808 ctx | cooccurence:773 |
Rv3805c aftB |
terminal beta-(1->2)-arabinofuranosyltransferase | 949 | 797 ctx | cooccurence:762 textmining:760 |
Rv3790 dprE1 |
decaprenylphosphoryl-beta-D-ribose oxidase | 872 | 791 ctx | neighborhood:601 cooccurence:455 textmining:413 |
Rv1476 |
membrane protein | 766 | 767 ctx | cooccurence:764 |
Rv3244c lpqB |
lipoprotein LpqB | 759 | 760 ctx | cooccurence:756 |
Rv0996 |
transmembrane protein | 745 | 746 ctx | cooccurence:744 |
Rv3438 hyp |
hypothetical protein | 742 | 743 ctx | cooccurence:735 |
Rv1610 |
membrane protein | 739 | 740 ctx | cooccurence:733 |
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: arabinosyltransferase A
- MTBC0 PGAP product: arabinosyltransferase EmbA
- Pfam (hmmscan --cut_ga): Arabino_trans_N PF17689.9 (E=3e-47), Arabinose_trans PF04602.19 (E=7e-163), Arabino_trans_C PF14896.13 (E=5e-147)
- (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_218311.1)
- Domains: Pfam-A via hmmscan --cut_ga — Arabino_trans_N (PF17689.9), Arabinose_trans (PF04602.19), Arabino_trans_C (PF14896.13)
- 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
COG1807 - Curated reference: UniProt P9WNL9 (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 —
125 functional partner(s); context anchor
embB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004022|Rv3794|embA MPHDGNERSHRIARLAAVVSGIAGLLLCGIVPLLPVNQTTATIFWPQGSTADGNITQITAPLVSGAPRALDISIPCSAIATLPANGGLVLSTLPAGGVDTGKAGLFVRANQDTVVVAFRDSVAAVAARSTIAAGGCSALHIWADTGGAGADFMGIPGGAGTLPPEKKPQVGGIFTDLKVGAQPGLSARVDIDTRFITTPGALKKAVMLLGVLAVLVAMVGLAALDRLSRGRTLRDWLTRYRPRVRVGFASRLADAAVIATLLLWHVIGATSSDDGYLLTVARVAPKAGYVANYYRYFGTTEAPFDWYTSVLAQLAAVSTAGVWMRLPATLAGIACWLIVSRFVLRRLGPGPGGLASNRVAVFTAGAVFLSAWLPFNNGLRPEPLIALGVLVTWVLVERSIALGRLAPAAVAIIVATLTATLAPQGLIALAPLLTGARAIAQRIRRRRATDGLLAPLAVLAAALSLITVVVFRDQTLATVAESARIKYKVGPTIAWYQDFLRYYFLTVESNVEGSMSRRFAVLVLLFCLFGVLFVLLRRGRVAGLASGPAWRLIGTTAVGLLLLTFTPTKWAVQFGAFAGLAGVLGAVTAFTFARIGLHSRRNLTLYVTALLFVLAWATSGINGWFYVGNYGVPWYDIQPVIASHPVTSMFLTLSILTGLLAAWYHFRMDYAGHTEVKDNRRNRILASTPLLVVAVIMVAGEVGSMAKAAVFRYPLYTTAKANLTALSTGLSSCAMADDVLAEPDPNAGMLQPVPGQAFGPDGPLGGISPVGFKPEGVGEDLKSDPVVSKPGLVNSDASPNKPNAAITDSAGTAGGKGPVGINGSHAALPFGLDPARTPVMGSYGENNLAATATSAWYQLPPRSPDRPLVVVSAAGAIWSYKEDGDFIYGQSLKLQWGVTGPDGRIQPLGQVFPIDIGPQPAWRNLRFPLAWAPPEADVARIVAYDPNLSPEQWFAFTPPRVPVLESLQRLIGSATPVLMDIATAANFPCQRPFSEHLGIAELPQYRILPDHKQTAASSNLWQSSSTGGPFLFTQALLRTSTIATYLRGDWYRDWGSVEQYHRLVPADQAPDAVVEEGVITVPGWGRPGPIRALP