Use jbrowse-plugin-protein3d with pre-defined UniProt ID

[abjanssen]

Hello,

Maybe the plugin is still too much work in progress for this but, I am interested in using the jbrowse-plugin-protein3d plugin for our Streptococcus pneumoniae genome browser (https://pneumobrowse2.veeninglab.com/). However, I can't seem to get the plugin to recognize the uniprot IDs that I already have in my gff file

From what I can see in the code of the plugin, it looks for "uniprot" in the gene' info, but even if I have that exact name as a field in my gene info, it doesn't seem to pick it up. For example, the information of a gene in the gff looks like this

EF3030_1	prokka	gene	66	1202	.	-	.	ID=KANOAJAN_00001_gene;Name=dnaN;gene=dnaN;locus_tag=KANOAJAN_00001;uniprot=B2IQZ0;amino_acid_seq=MIHFSINKNLFLQALNTTKRAISSKNAIPILSTIKIDVTNEGITLIGSNGQISIENFISQKNEDAGLLITSLGSILLEASFFINVVSSLPDVTLDFKEIEQNQIVLTSGKSEITLKGKDSEQYPRIQEISASTPLILETKLLKKIINETAFAASTQESRPILTGVHFVLSQHKELKTVATDSHRLSQKKLTLEKNSDDFDVVIPSRSLREFSAVFTDDIETVEIFFANNQILFRSENISFYTRLLEGNYPDTDRLIPTDFNTTITFNVVNLRQSMERARLLSSATQNGTVKLEIKDGVVSAHVHSPEVGKVNEEIDTDQVTGEDLTISFNPTYLIDSLKALNSEKVTISFISAVRPFTLVPADTDEDFMQLITPVRTN;conservation_pb=%5B%7B%22Locus tag%22%3A%22KKBGAPLG_00001 + KKBGAPLG_02273%22%2C%22Genome%22%3A%224954-98%22%7D%2C%7B%22Locus tag%22%3A%22BPAJBCOI_02146%22%2C%22Genome%22%3A%22BHN418%22%7D%2C%7B%22Locus tag%22%3A%22GCCANGDB_02450%22%2C%22Genome%22%3A%22BM6001%22%7D%2C%7B%22Locus tag%22%3A%22SPV_0002%22%2C%22Genome%22%3A%22D39V%22%7D%2C%7B%22Locus tag%22%3A%22PBPDCFME_00021%22%2C%22Genome%22%3A%22DCC1476%22%7D%2C%7B%22Locus tag%22%3A%22LGIMAHCD_00001 + LGIMAHCD_02222%22%2C%22Genome%22%3A%22DP1322%22%7D%2C%7B%22Locus tag%22%3A%22KANOAJAN_00001%22%2C%22Genome%22%3A%22EF3030%22%7D%2C%7B%22Locus tag%22%3A%22LBPJGIKI_00002%22%2C%22Genome%22%3A%22GM17%22%7D%2C%7B%22Locus tag%22%3A%22NPLHCJEM_02289%22%2C%22Genome%22%3A%22LILPNEUHC 19F%22%7D%2C%7B%22Locus tag%22%3A%22MBKLHCAH_00077%22%2C%22Genome%22%3A%22M264-3%22%7D%2C%7B%22Locus tag%22%3A%22OIJFJHOI_02293 + OIJFJHOI_00001%22%2C%22Genome%22%3A%22PJ755/1%22%7D%2C%7B%22Locus tag%22%3A%22JMFOCFNE_01144%22%2C%22Genome%22%3A%22R1501%22%7D%2C%7B%22Locus tag%22%3A%22EGPCNNKB_00030%22%2C%22Genome%22%3A%22SN36255%22%7D%2C%7B%22Locus tag%22%3A%22AGAIBJGL_00002%22%2C%22Genome%22%3A%22SN75752%22%7D%2C%7B%22Locus tag%22%3A%22JDJMKJEM_00002%22%2C%22Genome%22%3A%22SP264%22%7D%2C%7B%22Locus tag%22%3A%22AKFHGGLM_00001 + AKFHGGLM_02343%22%2C%22Genome%22%3A%22Spn1439-106%22%7D%2C%7B%22Locus tag%22%3A%22HLJICIJH_00001%22%2C%22Genome%22%3A%22TIGR4%22%7D%2C%7B%22Locus tag%22%3A%22EOOINEPP_00020%22%2C%22Genome%22%3A%22TL7/1993%22%7D%2C%7B%22Locus tag%22%3A%22EDBIKKDI_02207%22%2C%22Genome%22%3A%22TW31%22%7D%5D 
EF3030_1	Prodigal:002006	CDS	66	1202	.	-	0	ID=KANOAJAN_00001;Parent=KANOAJAN_00001_gene;eC_number=2.7.7.7;Name=dnaN;gene=dnaN;inference=ab initio prediction:Prodigal:002006;locus_tag=KANOAJAN_00001;product=DNA polymerase III beta subunit;protein_id=EF3030_00001

Could you give me some pointers on how to adapt my annotation fields in my gff files to get this plugin to pick up on the uniprot code to use?

Thanks!

[cmdcolin]

This is actually a good use case. It seems obvious but I did not have the ability to read a uniprot ID from the GFF file, I will add this and let you know

[cmdcolin]

I added this feature in jbrowse-plugin-protein3d v0.0.15

PR here GMOD/jbrowse-plugin-protein3d#22

It tries to pick up the uniprot= on the gene feature and use it in the "Launch protein view" dialog

[abjanssen]

This works great, thank you very much!