Jason Lee, a student in the department of Life Sciences, got the mRNA from a plant.
¡@¡@ Here is the sequence:

¡@¡@¡@¡@¡@¡@¡@  ¡@1 atccactact tcatcataaa cctcacaact actattctat cttctcttct ctaattttca
¡@¡@¡@¡@¡@¡@¡@¡@61 taatcattaa gaatggaaat ggttaacaag attgcatgct ttgtgctttt atgcatggta
¡@¡@¡@¡@¡@¡@¡@ 121 gtggttgcac cccatgcaga ggcactaact tgtggtcaag ttacatctac cttggctcct
¡@¡@¡@¡@¡@¡@¡@ 181 tgtctccctt atctaatgaa tcgcggtcct ctcggaggct gttgtggtgg tgttaagggt
¡@¡@¡@¡@¡@¡@¡@ 241 cttttgggtc aagcccagac tacagtagac cgacagaccg catgcacttg cctaaaatca
¡@¡@¡@¡@¡@¡@¡@ 301 gctgcttctt cttttacagg ccttgatttg ggcaaagctg ctagtctccc tagcacttgt
¡@¡@¡@¡@¡@¡@¡@ 361 agtgtcaaca tcccttacaa gatcagcccc tctactgact gctctaaagt tcagtaaagc
¡@¡@¡@¡@¡@¡@¡@ 421 tgatcatcag aatttggttt catgaggaga attaagaata agatagatag cattgatctt
¡@¡@¡@¡@¡@¡@¡@ 481 gcttatggat cctttctttc tatgttgtat cagttgtcac tttctgtttt ttctgtgttt
¡@¡@¡@¡@¡@¡@¡@ 541 cctttaaatt ctcgtatgta gtcgagtctt gtatcgaaat ttgacgattg attatattgt
¡@¡@¡@¡@¡@¡@¡@ 601 atcagttgtt actttctgtt ttcctgtgtt tcttttaaaa tcgtatgtag tcgagtcttg
¡@¡@¡@¡@¡@¡@¡@ 661 tatcgaaatt tcccgattgg ctatgttgta ttaatctaat ctttgataat acacatctat
¡@¡@¡@¡@¡@¡@¡@ 721 cttatttggt

1. Please help him to translate the DNA sequence to protein sequence.

¡@¡@¡@¡@ I H Y F I I N L T T T I L S S L L Stop F S Stop S L R M E M V N K I A C F V L L C M V V V A P H A E A L T
¡@¡@¡@¡@   C G Q V T S T L A P C L P Y L M N R G P L G G C C G G V K G L L G Q A Q T T V D R Q T A C T C L K S
¡@¡@¡@        AAS S FT G L D L G K A A S L P S T C S V N I P Y K I S P S T D C S K V Q Stop S Stop S S E F G F M R R
¡@¡@¡@        I K N K I D SI D L A Y G S F L S M L Y Q L S L S V F S V F P L N S R M SStopS L V S K F D D Stop L Y C
¡@¡@¡@        I S C Y F L F S CV S F K I V C S R V L Y R N F P I G Y V V L I Stop S L I I H I Y L I W (5'3' Frame1)

2. Please help him to identify the complete cds of this gene. Use the graphic view to explain all the features
¡@of this gene.

¡@¡@¡@¡@¡@ The gene is " Lycopersicon pennellii lipid transfer protein 2 (LpLTP2) gene ".

¡@¡@¡@¡@¡@ [complete cds ]

¡@¡@¡@¡@¡@¡@¡@¡@ MEMVNKIACF VLLCMVVVAP HAEALTCGQV TSTLAPCLPY LMNRGPLGGC CGGVKGLLGQ
¡@¡@¡@¡@¡@¡@¡@¡  AQTTVDRQTA CTCLKSAASS FTGLDLGKAA SLPSTCSVNI PYKISPSTDC SKVQ

¡@¡@¡@¡@¡@¡@¡@¡@       ¡@¡@  1 atggaaatgg ttaacaagat tgcatgcttt gtgcttttat gcatggtagt ggttgcaccc
¡@¡@¡@¡@¡@¡@¡@¡@¡@¡@¡@¡ 61 catgcagagg cactaacttg tggtcaagtt acatctacct tggctccttg tctcccttat
¡@¡@¡@¡@¡@¡@¡@¡@¡@¡@¡@ 121 ctaatgaatc gcggtcctct cggaggctgt tgtggtggtg ttaagggtct tttgggtcaa
¡@¡@¡@¡@¡@¡@¡@¡@¡@¡@¡@ 181 gcccagacta cagtagaccg acagaccgca tgcacttgcc taaaatcagc tgcttcttct
¡@¡@¡@¡@¡@¡@¡@¡@¡@¡@¡@ 241 tttacaggcc ttgatttggg caaagctgct agtctcccta gcacttgtag tgtcaacatc
¡@¡@¡@¡@¡@¡@¡@¡@¡@¡@¡@ 301 ccttacaaga tcagcccctc tactgactgc tctaaagttc agta                 ¡@ Graphic view
¡@
3. After translation of this gene, please help him to do the protein sequence analysis  (including  pI, mol. wt.,
    secondary structure prediction, hydrophobic profile,  homology search, prosite scanning..........)
 

  • ¡@         PI : 8.36

    •                molecular weight : 11715.81
                   secondary  structure prediction :
                            alpha-helix / Deleage & Roux
                            
                            beta-sheet / Deleage & Roux
                   hydrophobic profile :
                   homology search :
                                                                                                                                                                            Score     E
           Sequences producing significant alignments: (top 10)                                                                                   (bits)  Value
           gi|1519357 (U66466) lipid transfer protein 2 [Lycopersicon pennellii                                                            197  2e-50
           gi|1519355  (U66465) lipid transfer protein 1 [Lycopersicon pennellii                                                            162  8e-40
           sp|P27056|NLT2_LYCES NONSPECIFIC LIPID-TRANSFER PROTEIN 2 PRECURSOR (LTP 2)      162  8e-40
           sp|Q03461|NLT2_TOBAC NONSPECIFIC LIPID-TRANSFER PROTEIN 2 PRECURSOR (LTP 2).   156  5e-38
           sp|Q42952|NLT1_TOBAC NONSPECIFIC LIPID-TRANSFER PROTEIN 1 PRECURSOR (LTP 1)    154  2e-37
           sp|P93224|NLT1_LYCES NONSPECIFIC LIPID-TRANSFER PROTEIN 1 PRECURSOR (LTP 1)      151  2e-36
           sp|Q39950|NLTP_HELAN NONSPECIFIC LIPID-TRANSFER PROTEIN PRECURSOR (LTP)          116  7e-26
           sp|P10976|NLTP_SPIOL NONSPECIFIC LIPID-TRANSFER PROTEIN PRECURSOR (LTP)             115  9e-26
           gb|AAD18029| (AF118131) lipid transfer protein LTP1 precursor [Capsicum annuum]                                113  5e-25
           gi|2829204 (AF044204) lipid transfer protein precursor [Gossypium hirsutum]                                             112  1e-24

                   prosite scanning :
                              [1] Casein kinase II phosphorylation site
                                         Number of matches: 2
                                           1      63-66 TTVD
                                           2      82-85 TGLD
                              [2] N-myristoylation site
                                         Number of matches: 6
                                           1      28-33 GQVTST
                                           2      48-53 GGCCGG
                                           3      49-54 GCCGGV
                                           4      52-57 GGVKGL
                                           5      59-64 GQAQTT
                                           6      83-88 GLDLGK
                              [3] Plant lipid transfer proteins signature
                                         92-113 LPSTCSVNIPYKISPSTDCSKV

        12/22/1999