search

arpcard / rgi

Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.
Other
319 stars 76 forks source link

[BUG] Salmonella sequence with best hit to Ecoli soxR instead of Salmonella soxR #220

Closed kalilamali closed 10 months ago

kalilamali commented 1 year ago

Salmonella isolate gives a Best_Hit_ARO to Escherichia coli soxR with mutation conferring antibiotic resistance instead of Salmonella soxR with mutation conferring antibiotic resistance despite blastp showing a perfect match to Salmonella soxR sequence.

Web portal - RGI 6.0.1, CARD 3.2.6

This is the predicted protein:

Predicted_Protein MEKKSPRLKALLTPGEVAKRSGVAVSALHFYESKGLITSIRNSGNQRRYKRDVLRYVAIIKIAQRIGIPL ATIGDAFGILPEGHTLSAKEWKQLSSQWREELDRRIHTLVALRDELDGCIGCGCLSRSDCPLRNPGDRLG EHGTGARLLEDD

image image

github-actions[bot] commented 10 months ago

Issue is stale and will be closed in 7 days unless there is new activity