Homework #4

1. 1).Search Results from "blastn" (Only the sequence with the highest homology was selected here.):

    LOCUS       NTLTP1       2075 bp    DNA             PLN       05-MAY-1995
             NID         g19882
             KEYWORDS    lipid transferase; Ltp1 gene; non-specific lipid transferase.
             SOURCE      common tobacco.
             ORGANISM  Nicotiana tabacum
                               Eukaryotae; mitochondrial eukaryotes; Viridiplantae;
                               Charophyta/Embryophyta group; Embryophyta; Magnoliophyta;
                               Magnoliopsida; Solananae; Solanales; Solanaceae; Nicotiana

2).from "blastx":
    LOCUS       100346        114 aa                              12-APR-1995
             DEFINITION  lipid transfer protein - common tobacco.
             ACCESSION   100346
             PID         g100346
             DBSOURCE    PIR: locus S22168
                     summary: #length 114 #molecular-weight 11523 #checksum 189.
                     genetic: #introns 112/2.
                     superfamily: phospholipid transfer protein.
                     PIR dates: 20-Feb-1995 #sequence_revision 20-Feb-1995 
#text_change
               12-Apr-1995.
            KEYWORDS    .
            SOURCE      common tobacco.
            ORGANISM  Nicotiana tabacum
                    Eukaryotae; mitochondrial eukaryotes; Viridiplantae;
                    Charophyta/Embryophyta group; Embryophyta; Magnoliophyta;
                    Magnoliopsida; Solananae; Solanales; Solanaceae; Nicotiana.

3). Protein Sequence:
  >gi|100346|pir||S22168 lipid transfer protein - common tobacco
  
        MEIAGKIACFVVLCMVVAAPCAEAITCGQVTSNLAPCLAYLRNTGPLGRCCGGVKALV
        NSARTTEDRQIACTCLKSAAGAISGINLGKAAGLPSTCGVNIPYKISPSTDCSKVQ
2. Trp Repressor Gene Sequence:

Definition     E.coli trpR gene coding for the trp operon repressor protein.
GenBank        Name:  ECOTRPR,   Accession:  J01715
NCBI           Seq ID: 148059
Comment        [3]  revises [1].
               [2] experimentally determined the promoter region for trpR by
               determining which restriction sites are protected in the
               presence of the TrpR protein and RNA polymerase. The trpR
               promoter region is highly homologous to the trp and aroH
               promoter regions, which are also controlled by the trpR gene
               product.
Updated        Sep 22, 1986
Citation       REF [4]

               G. Bogosian (1990).  no plans to publish. Unpublished
Coding region                                     148059:  385..711
Coding region  label:  orf-173.                   148059:  765..1178
Coding region  label:  orf-121.                   148059:  813..1178
Coding region  label:  orf-101.                   148059:  873..1178

Sequence       1289 nt, linear ds dna
       1 ggatccggaa acgaatatca acattggcac cagttacctg caatatgttt
             51 atcagcagtt tggcaataat cgtattttct cctcagcagc ttataacgcc
           101 ggactagggc gggtgcgaac ctggcttggc aacagcgccg ggcgtatcga
           151 cgcagtggca tttgtcgaga gtattccatt ctccgagacg cgcggttatg
           201 tgaagaacgt gctggcttat gacgcttact accgctattt catgggggat

           251 aaaccgacgt tgatgagcgc cacggaatgg ggacgtcgtt actgatccgc
           301 acgtttatga tatgctatcg tactctttag cgagtacaac cgggggaggc
           351 attttgcttc ccccgctaac aatggcgaca tattatggcc caacaatcac
           401 cctattcagc agcgatggca gaacagcgtc accaggagtg gttacgtttt
           451 gtcgacctgc ttaagaatgc ctaccaaaac gatctccatt taccgttgtt

           501 aaacctgatg ctgacgccag atgagcgcga agcgttgggg actcgcgtgc
           551 gtattgtcga agagctgttg cgcggcgaaa tgagccagcg tgagttaaaa
           601 aatgaactcg gcgcaggcat cgcgacgatt acgcgtggat ctaacagcct
           651 gaaagccgcg cccgtcgagc tgcgccagtg gctggaagag gtgttgctga
           701 aaagcgattg attttgtagg cctgataaga cgtggcgcat caggcatcgt

           751 gcaccgaatg ccggatgcgg cgtgaaggcc ttatccgtcc tacaaatacc
           801 cgtaatttca atatgtttgg taggcatgat aagacgcggc agcgtcgcat
           851 caggcgctta atacacggca ttatgaaacg gactcagcgc caggatcacc
           901 gcctggtgat agacgctggc gcgagtgagt ttcccggcgg taaacacgcc
           951 gatcgcccct tccttacgac cgatctcatc aataccggta taacgcgaca

          1001 tcacgggacc aagcgcctca ccttcacgca ctttttccag aatcaccgca
          1051 ggcaacggca aagtagccga acgcgcctcg ccgcgctggc tggcgttttc
          1101 aatcaccacc caactgaaag tgctgtcacc atcgatgcca gcttcaatcg
          1151 ccacccaaaa atcagcctct ggaagtaaac ggcgggcatt ggctacccga
          1201 tttcgtgcgc cagcgcgcgt ttcctcactg ccaaagggct gttccggtac

          1251 accgctctcg acggcaacgg atgcaatatg gcaggatcc

3. 1). We have known 679 nucleotide sequences, and 832 protein sequences of Lycopersicon esculentum so far.
  2). Views:     
  
 Links:  
1622944        ---------------------------------------------------

Definition     Lycopersicon esculentum class II small heat shock protein Le-
                             HSP18.6 mRNA, complete cds.
GenBank        Name:  LEU72396,   Accession:  U72396
NCBI           Seq ID: 1622944
Updated        Oct 21, 1996
Citation       REF [1]

               D.K. Kadyrzhanova, K.E. Vlachonasios, P. Ververidis & D.R.
               Dilley (1996).  A heat-treatment chilling tolerance related
               cDNA from tomato fruit encoding a small heat-shock protein
               class II. Unpublished
Citation       REF [2]

               Data Submission: D.K. Kadyrzhanova, K.E. Vlachonasios, P.
               Ververidis & D.R. Dilley (1996).
Created        Oct 23, 1996
Coding region  Comments:  heat treatment/chilling 1622944:  81..584
               tolerance related protein from tomato fruit.
Sequence       738 nt, linear rna

              1 tacggctgcg agaagacgac agaaggggac tgcaattaca aatcaaacca
            51 aaattgacaa atttcacgca caaaatctca atgtccaaaa 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 aggggagaag agaaagaagg
           401 tgcaaagttt attaggatgg agagaagggt tgggaaattc atgaggaagt
           451 ttagtctgcc agagaatgcg aatactgatg caatttctgc agtttgtcaa

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