Obtain protein transmembrane-domains and topology information
get_protein_tm_topology.RdGiven a set of UniProt IDs, this function queries UniProt to obtain the information regarding transmembrane domains (TMDs) and topology and then parses this information to define additional columns describining the TMDs and topology
Examples
uniprotIDs <- c('O76024', 'Q03135', 'Q96T23')
get_protein_tm_topology(uniprotIDs)
#> UniprotID Length Intramembrane
#> 1 O76024 890
#> 2 Q03135 178 INTRAMEM 105..125; /note=Helical; /evidence=ECO:0000255
#> 3 Q96T23 1441
#> Transmembrane
#> 1 TRANSMEM 314..334; /note=Helical; /evidence=ECO:0000255; TRANSMEM 340..360; /note=Helical; /evidence=ECO:0000255; TRANSMEM 402..422; /note=Helical; /evidence=ECO:0000255; TRANSMEM 427..447; /note=Helical; /evidence=ECO:0000255; TRANSMEM 465..485; /note=Helical; /evidence=ECO:0000255; TRANSMEM 496..516; /note=Helical; /evidence=ECO:0000255; TRANSMEM 529..549; /note=Helical; /evidence=ECO:0000255; TRANSMEM 563..583; /note=Helical; /evidence=ECO:0000255; TRANSMEM 589..609; /note=Helical; /evidence=ECO:0000255; TRANSMEM 632..652; /note=Helical; /evidence=ECO:0000255; TRANSMEM 870..890; /note=Helical; /evidence=ECO:0000255
#> 2
#> 3
#> Topological.domain
#> 1 TOPO_DOM 653..869; /note=Lumenal; /evidence=ECO:0000255
#> 2 TOPO_DOM 2..104; /note=Cytoplasmic; /evidence=ECO:0000255; TOPO_DOM 126..178; /note=Cytoplasmic; /evidence=ECO:0000255
#> 3
#> n_tms tm_start
#> 1 11 314;340;402;427;465;496;529;563;589;632;870
#> 2 0 <NA>
#> 3 0 <NA>
#> tm_end tm_length
#> 1 334;360;422;447;485;516;549;583;609;652;890 20;20;20;20;20;20;20;20;20;20;20
#> 2 <NA> <NA>
#> 3 <NA> <NA>
#> tm_types
#> 1 Helical;Helical;Helical;Helical;Helical;Helical;Helical;Helical;Helical;Helical;Helical
#> 2 <NA>
#> 3 <NA>
#> tm_types_set topology n_term c_term topology_start
#> 1 Helical Lumenal Lumenal Lumenal 653
#> 2 <NA> Cytoplasmic;Cytoplasmic Cytoplasmic Cytoplasmic 2;126
#> 3 <NA> <NA> <NA> <NA> <NA>
#> topology_end topology_length
#> 1 869 216
#> 2 104;178 102;52
#> 3 <NA> <NA>