I am looking for the gene of a specific protein in a sequenced genome of Manduca sexta. The Genome (JHU_Msex_v1.0) should be available online and the protein i am looking for is protein kinas A (PKA), the analogous gene in Drosophila would be DC0. M. sexta PKA was characterized before so i assume knowing this, that it should be possible to somehow find the gene homologous to DC0 or PRKACA (vertebrate homolog) in the M. sexta genome, however i dont know how. Can anyone help me ? what program i need ?
If the genome has been annotated, you can likely find at least predicted genes/transcripts using NCBI Gene.
For example, this is the transcript predicted to be PKA https://www.ncbi.nlm.nih.gov/gene/?term=XM_030165592.2
You can then find the linked protein sequence in the transcript entry:
https://www.ncbi.nlm.nih.gov/protein/XP_030021452.1
The M. sexta genome is also available on the UCSC genome browser, which helps visualize homology with other organisms (i.e. D. melanogaster): https://genome.ucsc.edu/cgi-bin/hgTracks?db=hub_2790993_GCF_014839805.1&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=NC_051137.1%3A10146384%2D10157377&hgsid=1339887779_hUFhAZiDsqmTWUDn8AVpWwXAnFFx
If you need to find something that isn't already annotated/predicted you can use Protein BLAST to look for similar proteins in a specific organism using a known/presumed homolog from a better annotated organism.
https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome