homework7

Homework 7

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.

114 AA; 11716 MW; EA5981F6 CRC32
MEMVNKIACF VLLCMVVVAP HAEALTCGQV TSTLAPCLPY LMNRGPLGGC CGGVKGLLGQAQTTVDRQTA CTCLKSAASS FTGLDLGKAA SLPSTCSVNI PYKISPSTDC SKVQ
http://www.expasy.ch/cgi-bin/get-sprot-entry?VIRT14887

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

gi|1519357 (U66466) lipid transfer protein 2 [Lycopersicon penne... 197 2e-50

http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=gb|U66466.1|&form=6&db=s&Dopt=g

1 gtaatccagc taagaacgtc agaagtaaaa caaacttgtc gtaaaatatt taatttgaag
61 ttgtatttaa atcttaatta ttttttttta aagctatact cacatcattt caattattct
121 ttttgtaaaa gtatctctag agcttcataa tttttttttt aaaaatcttc gatcaaactg
181 ttagagtagg taaaagtctc acattgatgg ggaaatagac tgattatttg cttataagga
241 tgtggacaat actcctctca tataatagca tttaagatta aattagacct aaataacata
301 ttttagcatg atattagagt tatattcatt cttgtttgaa cttccgatcc acatctcaat
361 tggatctaca taaaaaaggg atattaaagt aagtaaaagc cctacattaa tcgaggaatc
421 tacttatacg aactttggtg ataaaaaaaa agactcctac acgtaagatg ttagaactag
481 ctaccacatg actttagagc cagcataata atgtacacca tcaaaatgct ttaaattttc
541 aacctaacaa ccaactacct ctctcactcc tccattggcc atctactcca aatttccctc
601 tataaaaaca ctcaaccaaa acacatttct tctcatccac tacttcatca taaacctcac
661 aactactatt ctatcttctc ttctctaatt ttcataatca ttaagaatgg aaatggttaa
721 caagattgca tgctttgtgc ttttatgcat ggtagtggtt gcaccccatg cagaggcact
781 aacttgtggt caagttacat ctaccttggc tccttgtctc ccttatctaa tgaatcgcgg
841 tcctctcgga ggctgttgtg gtggtgttaa gggtcttttg ggtcaagccc agactacagt
901 agaccgacag accgcatgca cttgcctaaa atcagctgct tcttctttta caggccttga
961 tttgggcaaa gctgctagtc tccctagcac ttgtagtgtc aacatccctt acaagatcag
1021 cccctctact gactgctcta agtatgttaa tttttcatct tttttgacct ataacaacac
1081 ctaactcttc gtattaatcc tagtacgaaa aataaagtaa caaaaaaatg atatgtgcta
1141 gcacattgtc acaatatgac atgcaagtgt gtttggtttt ctcaaaaaat aagtggattt
1201 tttatttata ttttagtgtt aagaaatatt agtttaaaaa tatttatata tgtaattata
1261 aagaaaaaag atactattat agttagtaca ttatgttttt gttatcatta tcattattat
1321 tattattaat gttggttttg ttcattgtta atgcagagtt cagtaaagct gatcatcaga
1381 atttggtttc atgaggagaa ttaagaataa gatagatagc attgatcttg cttatggatc
1441 ctttctttct atgttgtatc agttgtcact ttctgttttt tctgtgtttc ctttaaattc
1501 tcgtatgtag tcgagtcttg tatcgaaatt tgacgattga ttatattgta tcagttgtta
1561 ctttctgttt tcctgtgttt cttttaaaat cgtatgtagt cgagtcttgt atcgaaattt
1621 cccgattggc tatgttgtat taatctaatc tttgataata cacatctatc ttatttggta
1681 tatgtactct ctcgtctatt caatattttt ggtctacttt tactagggtt tttttaatat
1741 gcattacaca tatatatcaa attcgagtaa tatatagtat acgctattgt gtgctcattc
1801 atctaggtac ctcctttttc taaccacttc ttacacgtac aatgctaatt attg

graphic view

3.After translation of this gene, please help him to do the protein sequence analysis

a.Molecular weight: 11715.81

b.Theoretical pI: 8.36

c.secondary structure prediction,

d.hydrophobic profile,

MIN: -1.54444444444444
MAX: 3.51111111111111

e.homology search,

f.prosite scanning
[1] PDOC00006 PS00006 CK2_PHOSPHO_SITE
Casein kinase II phosphorylation site

Number of matches: 2
      1      63-66 TTVD
      2      82-85 TGLD

[2] PDOC00008 PS00008 MYRISTYL
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] PDOC00516 PS00597 PLANT_LTP
Plant lipid transfer proteins signature
            92-113 LPSTCSVNIPYKISPSTDCSKV