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Seq 206-1 detailed analysis

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    Detailed analysis of Seq 206-1:

    1. Sequence from Fgenesh(F):

    >FGENESH:   1   3 exon (s)  49302  -  50387   182 aa, chain -
    MKAILIDGRPVRSAVTRYHLKRLGIIVQVVNNLSAVAKAFPGQNGATVSREKATILFIES
    DFWRPETDVQLLNHLRENKNHKDKYGSIFDIVMCKPIRASTIASSIQPLLRVVMPERRDN
    QNRPSFLRSLLVGKNILVVDDNKVNLRVAAAALKKYGANVVVLKVARMLSVYFNPHIDLM
    HV

    blastp result from F.png

    blastp from F-2.png

    It matches to the histidine kinase [Zea mays], and also matches to the putative histidine kinase 1 [Oryza sativa Japonica Group] with the e-value of 7e-64.

    Then blast the sequence of the Oryza sativa Japonica Group, get the following results:

    rice of F-1.png

    rice of F-2.png

    By using rice sequence to blast again, we found it matches to the Ricinus communis, Populus trichocarpa, Lotus japonicas, Betula pendula and so on, whose   e-values are all 0.

    At last, compare the repeated sequence of the original sequence to the rice sequence using BlastX, and get the following results:

    compare result from F.png

    The e-value is good (1e-99). It can be assumed as Hypothetical Histidine Kinase.

     

    2. The sequence from the GeneMark(G):

    >Sun Nov 21 16:23:28 EST 2010_1|GeneMark.hmm|gene 1|265_aa
    MAILYCTRASGLGMEIVPTVAFALAPRERASCAMAPAAGNHKHGKDGRVESTTNGVFNTL
    SGFEAADRQNSWQYFKMLLSDKESLLDDLEGENSDQSDSDHVTLAISIEDTGVGIPLQAQ
    DRVFTPFMQADSSTSRNYGGTGIGLSISKCLAELMGGQISFVSRPFVGSTFTFSATLKRS
    YKDTSVDSSRSFAVTRYHLKRLGIIVQVVNNLSAVAKAFPGQNGATVSREKATILFIESD
    FWRPETDVQLLNHLRENKNRQLSDG

    It also matches to histidine kinase [Zea mays], and strongly matches to Oryza sativa Japonica Group. So we assume it is the hypothetical Histidine Kinase.

    And we found some conserved domains in this area. Please see the pictures below:

    blastp from G-1.png

    The conserved domain is Htpase_c super family, Histidine kinase-like ATPases; this family includes several ATP-binding proteins, for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins. It has G-X-G motif.

    motif from G.png

    3. Compare with Maize EST

    Input sequence from 48302  to  51387 compare with maize ETS.

    206-1 compare with maize EST.bmp

    4. Further analysis by using Interproscan,

    for 206-1 finding motif.bmp

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