Question

What is the predicted amino acid sequence encoded by Unknown_sequence_A? What process did you use to determine this?

Search for similar genes in other organisms. What other organisms have similar genes? Is there a similar gene in humans? How did you determine this?

Why might it be useful to use amino acid sequences to search for similar genes rather than DNA sequences directly?

>Unknown_sequence_A
ATGAGTTTTATTTTTAAATTTATTGCCACTTTTGTACGCAAAATGCTGGA
GCTGTTGCAATTTGGAGGGAAAACCCTTACGCACACGCTGAGTATTTATG
TAAAAACGAACACGGGCAAAACGCTGACCGTTAATCTGGAGCCCCAGTGG
GATATTAAAAACGTAAAGGAACTGGTGGCACCACAATTGGGACTTCAGCC
GGATGATCTAAAGATCATATTTGCCGGTAAGGAACTAAGCGATGCCACGA
CAATAGAGCAATGTGACTTGGGTCAGCAAAGCGTTTTGCATGCCATTCGT
TTGCGACCGCCCGTGCAGCGCCAGAAAATCCAGTCGGCCACTTTGGAGGA
GGAGGAACCTTCGCTTAGCGATGAAGCCTCCAAGCCTCTAAATGAAACTC
TGTTGGACTTGCAGCTGGAAAGCGAGGAGCGTCTGAATATAACCGATGAA
GAAAGAGTCCGTGCCAAAGCGCATTTCTTTGTACATTGCAGCCAATGCGA
TAAGCTGTGTAATGGCAAACTTCGGGTCCGCTGCGCTTTATGCAAGGGCG
GCGCCTTTACTGTCCATCGTGATCCGGAGTGTTGGGATGATGTCTTGAAG
TCGCGTAGAATTCCCGGTCATTGTGAAAGTCTGGAGGTGGCCTGCGTGGA
CAACGCGGCTGGCGATCCGCCCTTCGCTGAATTCTTCTTCAAGTGTGCTG
AGCATGTCTCCGGCGGGGAGAAGGATTTTGCGGCTCCATTGAATCTAATC
AAGAATAACATCAAGAATGTTCCTTGCCTGGCCTGCACGGATGTGAGTGA
TACCGTGTTGGTTTTCCCCTGCGCATCGCAGCACGTCACCTGTATCGACT
GCTTCCGCCATTATTGCCGTTCCCGTTTGGGCGAGCGTCAGTTTATGCCG
CATCCGGACTTCGGCTACACCTTGCCCTGTCCCGCAGGCTGCGAGCACTC
GTTCATCGAGGAGATTCATCACTTCAAGCTGTTGACACGCGAGGAGTACG
ATCGGTACCAGAGATTCGCCACCGAGGAGTATGTCCTACAGGCAGGTGGA
GTACTCTGCCCCCAGCCAGGATGCGGCATGGGCCTTTTGGTGGAGCCCGA
TTGTCGCAAGGTGACATGCCAGAACGGCTGTGGATACGTGTTCTGCCGCA
ATTGTCTGCAGGGCTACCATATCGGGGAGTGTCTGCCCGAGGGGACGGGC
GCCAGTGCCACAAACTCCTGCGAGTACACCGTGGACCCAAATCGAGCTGC
CGAGGCGCGATGGGATGAGGCCAGCAATGTCACCATCAAAGTCAGCACAA
AGCCCTGTCCAAAATGCAGAACCCCCACGGAGCGAGATGGCGGTTGCATG
CACATGGTCTGCACACGCGCTGGCTGCGGATTCGAGTGGTGCTGGGTCTG
CCAGACTGAGTGGACACGCGACTGCATGGGAGCCCACTGGTTCGGCTAA

Answer 1

Question

The predicted amino -acid sequence coded by the gene sequence is ubiquitin parkin protein.

Figure: Result of blastx

> > > Max Total Query E Per. Description Accession Score Score Cover value ident parkin, isoform B. (Drosophila melanogaster] 1001 1001 99% 0.0 100.00% NP_730600.1 S001679p (Drosophila melanogaster 999 999 99% 0.0 99.79% AAL13983.1 uncharacterized protein Dsimw501_GD12138, isoform A [Dr 998 998 99% 0.0 99.38% XP_016032785.1 E3 ubiquitin-protein ligase parkin (Drosophila sechellia 995 995 99% 0.0 99.17% XP_002040765.2 E3 ubiquitin-protein ligase parkin (Drosophila erectal 990 990 99% 0.0 98.55% XP_026833179.1 uncharacterized protein Ryak_GE22356, isoform D. (Drosopt 988 988 99% 0.0 98.13% XP_0020953682 PREDICTED: E3 ubiquitin-protein ligase parkin (Drosophila el 987 987 99% 0.0 98.13% XP_017080476.1 PREDICTED: E3 ubiquitin-protein ligase parkin isoform X1 [D 983 983 99% 0.0 97.72% XP_016934361.1 PREDICTED: E3 ubiquitin-protein ligase parkin isoform X1 (D 980 980 99% 0.0 97.30% XP_016955422.1 > >> > > SSSS 333 ✓ ✓ ✓ PREDICTED: E3 ubiquitin-protein ligase parkin (Drosophila rh 977 PREDICTED: E3 ubiquitin-protein ligase parkin. (Drosophila el 976 uncharacterized protein Dsimw501_GD12138, isoform B [Dr 974 PREDICTED: E3 ubiquitin-protein ligase parkin (Drosophilata 972 GM22162 (Drosophila sechellial 966 uncharacterized protein Dyak_GE22356, isoform B. (Drosopt 965 PREDICTED: E3 ubiquitin-protein ligase parkin isoform X2 D 959 PREDICTED: E3 ubiquitin-protein ligase parkin isoform X2 D 957 PREDICTED: E3 ubiquitin-protein ligase parkin (Drosophila fic 946 E3 ubiquitin-protein ligase parkin. (Drosophila serrata) 944 PREDICTED: E3 ubiquitin-protein ligase parkin (Drosophila ki 943 E3 ubiquitin-protein ligase parkin.(Drosophila ananassae) 938 PREDICTED: E3 ubiquitin-protein ligase parkin (Drosophila bi 937 E3 ubiquitin-protein ligase parkin (Drosophila obscura 928 E3 ubiquitin-protein ligase parkin (Scaptodrosophila lebanon 919 uncharacterized protein Dpse_GA10370 (Drosophila pseudo 918 E3 ubiquitin-protein ligase parkin (Drosophila persimilis 915 blast:E3 ubiquitin-protein ligase parkin (Drosophila guanche) 910 E3 ubiquitin-protein ligase parkin (Drosophila willistoni] 907 E3 ubiquitin-protein ligase parkin (Drosophila virilis 902 E3 ubiquitin-protein ligase, parkin isoform X1 [Drosophila no 901 uncharacterized protein Dmoj_GL12208. isoform A Drosoph 894 E3 ubiquitin-protein ligase parkin isoform X1 (Drosophila hy 892 E3 ubiquitin-protein ligase parkin isoform X1 (Drosophila na 892 PREDICTED: E3 ubiquitin-protein ligase parkin isoform X2D 887 uncharacterized protein Dyak_GE281 49 (Drosophila yakuba) 884 E3 ubiquitin-protein ligase parkin isoform X2 (Drosophila hy 879 E3 ubiquitin-protein ligase parkin isoform X3 (Drosophila hy 877 uncharacterized protein Dmoj_GI12208, isoform B. (Drosoph 876 PREDICTED: E3 ubiquitin-protein ligase parkin isoform X2 D 875 E3 ubiquitin-protein ligase parkin isoform X2 (Drosophila na 872 PREDICTED: E3 ubiquitin-protein ligase parkin isoform X1 ID 868 hypothetical protein AWZ03_009124 (Drosophila navojoa 866 GH16528 (Drosophila grimshawi 860 PREDICTED: E3 ubiquitin-protein ligase parkin (Musca dome 855 3 ubiquitin-protein Ligase parkin isoform X1.[Zeugodacus c 848 3 ubiquitin-protein ligase parkin (Lucilia cuprina 838 977 976 974 972 966 965 959 957 946 944 943 938 937 928 919 918 915 910 907 902 901 894 892 892 887 884 879 877 876 875 872 868 866 860 855 848 838 99% 99% 97% 99% 96% 97% 97% 97% 99% 99% 99% 99% 99% 99% 99% 99% 99% 99% 99% 99% 99% 99% 99% 99% 99% 89% 99% 99% 98% 98% 98% 97% 96% 96% 99% 99% 99% 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 96.89% XP_016984512.1 96.89% XP_0171217551 99.15% XP_016032786.1 96.69% XP_017015699.1 99.15% EDW44318.1 98.09% XP_015050783.1 97.45% XP_016934362.1 97.03% XP_016955423.1 95.85% XP_017048471.1 95.23% XP_020815963.1 95.85% XP_017038047.1 94,40% XP_001956965.2 94.19% XP_017096033.1 90.70% XP_022213694.1 89.12% XP_030373359.1 89.90% XP_001354063.3 89.48% XP_026848073.1 90.46% SPP85352.1 90.91% XP_002062135.2 91.08% XP_002048270.2 90.87% XP_030567643.1 90.46% XP_0020077612 90.25% XP_023163412.2 90.04% XP. 030242282.1 89.21% XP 017843327.1 97.93% XP_015045159.1 89.00% XP_023163413.2 89.00% XP_023163414.2 89.33% XP_015017729.1 89.33% XP_017861825.1 88.91% XP_030242283.1 88.79% XP_017843326.1 90.17% TDG44428.1 90.17% XP_001984548.1 82.99% XP_0051754802 79.44% XP_028895627.1 82.78% XP_0233032651 ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓ 333

I use "blastx" program of NCBI to known the amini-acid sequence. This program take nucleotide sequence as input sequence , translate this sequence into amino-acid and compare with all amino acid sequence present in the databases.

This protein is found in other organism too. Like chimps etc, D.melanogaster. Yes, this gene present in human too. This result is received by using tool "ncbi blastn".

It is useful to use amino acid sequences to search for similar genes rather than DNA sequences directly because more than 1 codon could be use for coding same amino acid( degenrate codon). Therefore , even though two sequences might not be similar at nucleotide level but similar at amino-acid sequence level.