Homework 5

due on 5/14

1.Please help Sho Ming to identify the gene and its protein sequence.

Ans: We used the similarity sequence search in NCBI to find the result. After BLAST search result suggested that the N.tabacum ltp1 gene for lipid transferase (emb|X62395|NTLTP1) has the highest score, 2976. Identities = 598/605 (98%), Positives = 598/605 (98%). The seven non-identical nucleotides are not different entirly but just can be substituted in all four types of nucleotides. The protein sequence required is 114 aa and is list here: 

             1 meiagkiacf vvlcmvvaap caeaitcgqv tsnlapclay lrntgplgrc
            51 cggvkalvns arttedrqia ctclksaaga isginlgkaa glpstcgvni
           101 pykispstdc skvq

2.How many nucleotide and protein sequence of Lycopersicon esculentum were know? Please find its class II small heat shock protein mRNA, complete cds.

Ans: Using the taxanomy browser in NCBI get the result. Its common name is tomato and its axonomy Id is 4081. There are 743 DNA sequences and 1020 protein sequences which have been known right now. The class II small heat shock protein (U72396) mRNA complete cds is listed: 

Sequence       738 nt, linear rna

             1 tacggctgcg agaagacgac agaaggggac tgcaattaca aatcaaacca
            51 aaattgacaa atttcacgca caaaatcaca atatccaaaa atttctcaat
           101 actgaaaatg gatttgaggt tgttgggtat cgataacaca ccactcttcc
           151 acactctcca ccatatgatg gaagctgccg gtgaagattc cgacaagtct
           201 gtcaatgcac catcaaggaa ctatgttcgt gatgctaagg ccatggctgc

           251 tacaccagcg gatgtgaagg agtatcctaa ttcgtatgtt tttgttgtgg
           301 atatgccagg gttgaaatct ggagatatca aagtgcaggt ggaagaagac
           351 aatgtgctgt tgattagtgg tgaaaggaag agggaagaag agaaagaagg
           401 tgcaaagttt attaggatgg agagaagggt tgggaaattc atgaggaagt
           451 ttagtctgcc agagaatgcg aatactgatg caatttctgc agtttgtcaa

           501 gatggagttc tgactgttac tgttcagaaa ttgcctcctc ctgagccaaa
           551 gaaacccaaa acaattgagg tgaaagttgc ttgaagttat ggactctgtt
           601 ttgatggttt gtggtatgat gtagtagaaa taaagttgta ggagtagtga
           651 acttttcctt tcatctttct gctatgtttt cacgtctgtt tgaatgttac
           701 aatagccatg ggtattgttt gttttgatgc caaaaaaa