Here is the sequence of very conserved yeast protein. You would like to find it's plant homolog.
>Scsec19 GGGATTGTAGATGTAGTTTCAACACGTCGGCTGATTTATCCCGATTTTGTTAGTAGAAAAGGTTCTACTT CATTCTTGCTTGAGACGTCGTCCCATCAAATTTCTAACATAGTCTTTTTTCAAGGAAGGATATTTTTCAA AGCAGGACTGCAATTAGTCTTTTCCTTTTCTTTACTCCCCTTCCATCATAACTGTTAGTGAATAACCACT TATATAGCATAACACAATGGATCAAGAAACAATAGACACTGACTACGACGTGATTGTCTTAGGTACCGGT ATTACCGAATGTATCTTATCTGGTTTACTCTCTGTAGATGGAAAAAAGGTATTACATATTGACAAGCAAG ACCATTATGGTGGCGAAGCTGCTTCTGTGACCTTATCTCAATTGTATGAAAAATTTAAACAAAATCCGAT CAGTAAAGAGGAACGGGAGTCCAAGTTTGGTAAAGATAGAGATTGGAATGTCGACTTAATTCCTAAATTC CTGATGGCCAATGGTGAGCTGACAAATATTTTAATACATACCGATGTGACCAGATATGTCGATTTCAAGC AAGTTTCTGGCTCCTACGTTTTTAAGCAAGGCAAAATTTACAAAGTGCCAGCTAATGAAATAGAAGCCAT TTCATCGCCATTGATGGGTATTTTTGAAAAACGTAGAATGAAGAAATTTTTAGAATGGATTAGCTCTTAC AAAGAAGATGACTTGTCCACTCATCAAGGATTAGACTTAGACAAGAATACCATGGATGAAGTGTATTATA AATTTGGGTTAGGCAATTCTACCAAAGAATTCATCGGTCATGCAATGGCTTTATGGACCAATGATGACTA CTTACAACAACCTGCTAGGCCATCGTTTGAGAGGATTTTGTTATATTGCCAAAGTGTTGCCCGTTACGGT AAATCACCTTATTTGTATCCTATGTATGGGTTAGGCGAACTTCCACAAGGATTTGCTCGTTTGTCGGCTA TTTACGGTGGTACTTACATGCTAGACACTCCAATTGATGAAGTATTGTATAAAAAAGACACAGGAAAATT TGAAGGGGTCAAGACTAAGCTGGGAACTTTCAAGGCCCCATTGGTTATTGCTGATCCAACTTATTTTCCC GAAAAATGTAAATCTACTGGTCAAAGAGTTATTAGAGCCATCTGTATTCTTAACCATCCAGTTCCGAACA CCAGTAACGCGGATTCTTTACAAATTATTATCCCACAAAGCCAACTGGGAAGGAAAAGCGATATATACGT TGCGATTGTTTCAGATGCGCATAACGTTTGCTCCAAGGGTCACTATTTAGCAATTATTTCTACAATCATT GAAACTGATAAACCACATATAGAATTAGAGCCTGCTTTCAAACTTCTGGGACCAATCGAAGAAAAATTCA TGGGAATTGCCGAATTATTTGAACCAAGAGAAGACGGCTCTAAGGATAACATTTACTTATCCAGATCATA CGACGCATCCTCTCATTTCGAATCCATGACTGACGATGTTAAAGATATTTACTTCAGAGTAACAGGCCAC CCATTAGTTCTAAAACAAAGACAAGAACAAGAAAAGCAGTAAATTCATACCTTTACGACTAAAGCAGCAA TTGGAGGGTAAACTTATTTTTTCC
Compare two sequences using BLATSP or FASTA program. Use three different similarity matrices and different fap penalties. Summarize somehow what was the effect on results.
Sequences:
>gi_13397640 unknown protein, Brassica napus MSSAPSPGTGSPPSPPSNSTTTTPPPASAPPPTTPSSPPPPSTIPTSPPPSSRSTPSAPPPSPPTPSTPG SPPPLPQPSPPAPTTPGSPPAPVTPPTRNPPPSVPGPPSNPSREGGSPRPPSSPSPPSPSSDGLSTGVVV GIAIGGVALLVIVTLICLLCKKKRRRDEEDAYYVPPPPPPGPKAGGPYGGQQQQWRQQNATPPSDHVVTS LPPPPKAPSPPRQPPPPPPPPFMSSSGGSDYSDRPVLPPPSPGLVLGFSKSTFTYEELARATNGFSEANL LGQGGFGYVHKGVLPSGKEVAVKQLKVGSGQGEREFQAEVEIISRVHHRHLVSLVGYCIAGAKRLLVYEF VPNNNLELHLHGEGRPTMEWSTRLKIALGSAKGLSYLHEDCNPKIIHRDIKASNILIDFKFEAKVADFGL AKIASDTNTHVSTRVMGTFGYLAPEYAASGKLTEKSDVFSFGVVLLELITGRRPVDANNVYVDDSLVDWA RPLLNRASEQGDFEGLADAKMNNGYDREEMARMVACAAACVRHSARRRPRMSQIVRALEGNVSLSDLNEG MRPGQSNVYSSYGGSTDYDSSQYNEDMKKFRKMALGTQEYNATGEYSNPTSDYGLYPSGSSSEGQTTREM EMGKIKRTGQGYSGPSL >gi_1345852_sp_P41242|MATK_MOUSE Megakaryocyte-associated tyrosine-protein kinase MARRSSRVSWLAFEGWESRDLPRVSPRLFGAWHPAPAAARMPTRWAPGTQCMTKCENSRPKPGELAFRKG DMVTILEACEDKSWYRAKHHGSGQEGLLAAAALRHGEALSTDPKLSLMPWFHGKISGQEAIQQLQPPEDG LFLVRESARHPGDYVLCVSFGRDVIHYRVLHRDGHLTIDEAVCFCNLMDMVEHYTKDKGAICTKLVKPRR KQGAKSAEEELAKAGWLLDLQHLTLGAQIGEGEFGAVLQGEYLGQKVAVKNIKCDVTAQAFLDETAVMTK LQHRNLVRLLGVILHHGLYIVMEHVSKGNLVNFLRTRGRALVSTSQLLQFALHVAEGMEYLESKKLVHRD LAARNILVSEDLVAKVSDFGLAKAERKGLDSSRLPVKWTAPEALKNGRFSSKSDVWSFGVLLWEVFSYGR APYPKMSLKEVSEAVEKGYRMEPPDGCPGSVHTLMGSCWEAEPARRPPFRKIVEKLGRELRSVGVSAPAG GQEAEGSAPTRSQDP
You got DNA sequence from sequencing facility, DNA encode bacterial gene. Sequencing servis marked your sequence as probably errorneous, you have to expect erros and frameshifts.
>rc-m2-30 TGCCCTGCGCCGCGCTATTCGACGCCATCATGGACTGCCTGAAGGAGCATGGCGAGGTGCGCACCATTCG CGTGGCTGCGGCGGACGTGAACGGGGTGGCAACGGGTAAGCGCATACCCGCACGTTTCGCAAGCAAGGTT TTTTCCGAGGGAACACGGTAACCGTTCTCGGTGATGAACCTCGACATCTGGGGCGAGGACATCGAGGAAA GTCCGCTGGTTTTTGAAACCGGCCTCTGCGATGGCCTGTTGCGCGCGACCGAGAGGCCCTTCATGCCGAT GCCCTGGCTCGACCCACCGACGGCGCTACTGCCGATCTGGATGTATCACATGGATGGCCGCCCCTATTCG GCCCTCCACGGCAGGCGCTGGCGGCGGTCAAGGACCGCTACACCGTAAAGGGCCTGACGGGCGTGGTGGC GACGGAACTTGAAGCTGCTGTGATCGACGACAGCGGCACGATTCTGCGCGTGCCGCCCTCGCCCCGTTCC GGCAAGCGCCGCACCGGGCCCGAAATCCTGTCGCTGCGTTCGCTTGACGCCTTTGACGGCTTCTTCACCG CGCTTTACGCGGCCTGCGAGGTGATGGACATTCCGGCAGATATGGCGATTTCCGAAACCGCCTCGGGGCA GTTCGAGATCAACCTGATGCAGTAGGCCGATCCGCGGAAGTCCGCCGATGACACCTGGCTGTTCAAGATG CTGGTCAAGGGTCTGGCGCGGCAGCACGGCTATGCCGCCTCGCCCATGGCGAAACCCAATGATCTGTGGT CGGGCAACGGGATGCGCGGGCATTTCTCGACCCTCGATCAGAACGGCGAAAACATCTTCAACCTGGGCAC CGAAAAGGGCTCGGATGCGTTGCTGTCCGCGGTGGCGGGCTATCTGGCGGCGCTGCCGGGACCGACGCTG ATCTTTGCGGTGGTTCAGAACAGCTACACCCAGCAGGTGCCCAATGCCCGTGTGTCTACGCGAATTGTCT GGGCCTATGAGAACCGCGCGGGGTTTTTGCGGATCCCGTCTTCGGGGCACGCGGCGCGGCGGATCGAGCA GTCGGGTGGCGTGGGGCGACGTGAACCCCTATCTGATAATCGCCGCTAGCCTTGGTGCGGCGCTGGTCGG GCTCGTAGACAAAATGGTCCCCGACGAGCCGATCGTCGACAACGCTGATGCGAAATATCTGCCGCACCCG CCCGCAACGTGGAAACTCGAGATAACCCTGTTCGACAGCTGCCCGCTGATCAAGCGCATCTTTGTAGAAG AGCTGATCGAGAACTCCCTGATGACCAAGCGTTAGGAGATCCACTACATGGCGGCGCTGTCCGAAGAGTA GCAGACCGAGCTTTACCTCGCCATCGTCGCCCTGCGTGATCGCGTACCGACTime-stamp: <2024-11-06 13:47:18 (hpaces)>