Comparative Genome Analysis and Development of Database System

Comparative Genome Analysis and Development of Database System
for Apple Mosaic Virus; RNA1, RNA2, RNA3
and
Apple Chlorotic Leaf Spot Virus strain P863

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Apple Mosaic Virus

Apple Chlorotic leaf Spot Virus

Genomes & Genes

Proteins & Domains

Identified ORFs

Results & Discussion

Acknowledgement

Contact us

Project Developed by;
Pankaj Kr. Agarwal
B.E. (Biotechnology)
Dept. of Biotechnology
SEC Sikar, Rajasthan.
INDIA

email:
pankajbt@gmail.com

Secondary Structure Results

Movement Protein secondary structure:

>Aclsv4.2 movement protein apple chlorotic leaf spot virus P863

MATMIRGHRLRIAEGDIPIAGVKSSRIYSDISPFKKASDLMIHWNEFVFKVMPEDIAGDGFRLASIPVIP
ccccccchhhhhcccccccccccccceecccccccccchhhhhhceeeeeeccccccccccccccccccc

SSEVQAVLRKRESTNYVHWGALSISIDALFRKNAGVSGWCYVYDNRWETFEQAMLQKFHFNLDSGSATLV
cchhhhhhhhccccceeeccccchhhhhhhhhccccceeeeeeccccchhhhhhhhhhhhccccccceee

TSPNFPVSLDDPGLSNSISVAVMFENLNFKFESYPISVRVGNMCRFFDSFLSSVKNKVDSNFLLEASNAD
ecccccccccccccccchhhhhhhhcccccccccceeeeecccceeeccccccccccccchhhhhhcccc

PLGVGAFGFEQDDQVSELFNYIQTVPTQAIKFREHEIPKGFLGMMGKKKIKSFEFASGSKGMERRKPNRG
ccccccccccccchhhhhhhhccccchhhhhhhhhcccchhhhhhcccccceeeeecccccccccccccc

KQIDRSFSQRAVPGFRSQNEKVEHQGLSTDSDFENFLRNKRGNKAGVKSTASEGSSVDNISSREFQFARQ
ccccccccccccccccccchhhhcccccccchhhhhhhhhcccccceeeeccccccccccchhhhhhhhh

NQAKEDGSSSEFAAQGGRKSKGISGRRKQTSSWKDRGNPGTDTGVHLREHSDPGNVRADGVSGPSGGSEI
hhhcccccchhhhhhccccccccceeeeceeeccccccccccceeeeeccccccceeeeeecccccccee

NGGSISPRVLQPEGSGQLDQSFQDYLFGPEHQQNDIPSGL
ccccccceeeccccccccchhhhhhcccccccccceeeec

Alpha helix     (Hh) :   114 is  24.78%

3₁₀ helix       (Gg) :     0 is   0.00%

Pi helix        (Ii) :     0 is   0.00%

Beta bridge     (Bb) :     0 is   0.00%

Extended strand (Ee) :    65 is  14.13%

Beta turn       (Tt) :     0 is   0.00%

Bend region     (Ss) :     0 is   0.00%

Random coil     (Cc) :   281 is  61.09%

Ambigous states (?)  :     0 is   0.00%

Other states : 0 is 0.00%

The secondary structures of Apple Leaf Chlorotic Leaf Spot Virus P863 movement protein showed that it contains 25% of α-helix, 14% β-sheets and 61% coils. So, the probable 3D structure of the movement protein of Apple Leaf Chlorotic Leaf Spot Virus P863 would be helical in shape.


>Apmvrna3.1 movement protein apple mosaic virus RNA3

MTTLGDKPSSDFEVGECSMEQFQQVSNDLHKLMLSAEMRNLPTKGCHVLRLRNMSKTKSLKLESKEQRGF
ccccccccccceeecccccccchhhhhhhhhhhhhhhhhccccccceeeeecccccchhhhhhhhhhhhh

IAKMADGLRRKFTEMLVGFFIIYVPLIQKTTSGLMTLKMIQSDTGERSDIITDFEASEAKVIMDRWGRSL
hhhhhhhhhhhhhhhhcceeeeeeccccccccchhhhhhhhccccccchhhhhhhhhhhhhhhhhhcchh

VAEAHLELLYSIVCTDIRPEAVVGELMVFWDETMSRRVVYSERGNPIVFPIMETQPSRYLKDKNLLMSMI
hhhhhhhhhhcccccccccceeeeeeeeeecccccceeeecccccceeeeeccccccchhhhhhhhhhhh

RGRIEVGAEGCDVAPMQLKVEPLGDKRQVLTIKPKEEPMKESKDIKIEEVSDGKHLKEQTKAVEMGDKLP
hceeeecccccccccccccccccccchhhhhhccccchhhhcccceeeeeccchhhhhhhhhhhhccccc

NGNISG
cceeec

Alpha helix     (Hh) :   119 is  41.61

3₁₀ helix       (Gg) :     0 is   0.00%

Pi helix        (Ii) :     0 is   0.00%

Beta bridge     (Bb) :     0 is   0.00%

Extended strand (Ee) :    45 is  15.73%

Beta turn       (Tt) :     0 is   0.00%

Bend region     (Ss) :     0 is   0.00%

Random coil     (Cc) :   122 is  42.66%

Ambigous states (?)  :     0 is   0.00%

Other states         :     0 is   0.00%

The secondary structures of Apple Mosaic Virus RNA3 movement protein showed that it contains 41% of α-helix, 15% β-sheets and 42% coils. So, the probable 3D structure of the movement protein of Apple Mosaic Virus RNA3 would be helical in shape.

Coat Protein secondary structure:

>Apmvrna3.2 coat protein apple mosaic virus RNA3

MVCKYCNHTHPGSCAGCKWCHSTNRFAPPKRAVARQANPNKGKIPVSVSRAGRSIRRGGQLGRLGARMLS
ccccccccccccccccccccccccccccchhhhhhhccccccccceeeecccchhhhcchhhhhhhhhhh

RKFLKGHRVLSSREVTATVEGRFVNIDFADVFRDLLEKDLKVYTFIIRVNSLSSNGWIGLVEDYDESNPK
hhhhccceeeccccceeecccceeccchhhhhhhhhhhhhceeeeeeeeeecccccceeeeecccccccc

GPNPMDRKGFKKDQPRGGMWEAPPNTTFDDFVRKFRLVLEFKTNFAAGAKVFMRDLYVITSELPPVQIPT
cccccccccccecccccccccccccccccchhhhhhhhhhhhhhhhhhhhhhhhhhhhcccccccccccc

NVLLIDEDLLEL
chhhhhcceeec

Alpha helix     (Hh) :    72 is  32.43%

3₁₀ helix       (Gg) :     0 is   0.00%

Pi helix        (Ii) :     0 is   0.00%

Beta bridge     (Bb) :     0 is   0.00%

Extended strand (Ee) :    31 is  13.96%

Beta turn       (Tt) :     0 is   0.00%

Bend region     (Ss) :     0 is   0.00%

Random coil     (Cc) :   119 is  53.60%

Ambigous states (?)  :     0 is   0.00%

Other states         :     0 is   0.00%

The secondary structures of Apple Mosaic Virus RNA3 coat protein showed that it contains 32% of α-helix, 14% β-sheets and 54% coils. So, the probable 3D structure of the movement protein of Apple Mosaic Virus RNA3 would be helical in shape.

>Aclsv4.3 coat protein apple chlorotic leaf spot virus P863

MRRLNIKAYQQTAISRIFSETRGVIKLELNPLLQKGHQLITFLQENFSLLDRTRRRRMAAVLNLQLKVDA
cccccccchhhhhhhhhhhhccchhhhhhchhhhcccchhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh

SLKAFLGAENRPLHGKTGATLEQILESIFANIAIQGTSEQTEFLDLVVEVKSMEDQSVLGSYNLKEVVNL
hhhhhhccccccccccccchhhhhhhhhhhhhhcccccchhhhhhhhhhhcccccccccccccchhhhhh

IKAFKTTSSDPNINKMTFRQVCEAFAPEARNGLVKLKYKGVFTNLFTTMPEVGSKYPELMFDFNKGLNMF
hhccccccccccccchhhhhhhhhccchhhhhhhhhcccceeeeeeecccccccccchhhhhhccccchh

IMNKAQQKVITNMNRRLLQTEFAKSENEAKLSSVSTDLCI
Hhhhchhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhceec


Alpha  helix     (Hh) :   154 is  61.60%

3₁₀ helix       (Gg) :     0 is   0.00%

Pi helix        (Ii) :     0 is   0.00%

Beta bridge     (Bb) :     0 is   0.00%

Extended strand (Ee) :     9 is   3.60%

Beta turn       (Tt) :     0 is   0.00%

Bend region     (Ss) :     0 is   0.00%

Random coil     (Cc) :    87 is  34.80%

Ambigous states (?)  :     0 is   0.00%

Other states         :     0 is   0.00%

The secondary structures of Apple Leaf Chlorotic Leaf Spot Virus P863 coat protein showed that it contains 61% of α-helix, 4% β-sheets and 35% coils. So, the probable 3D structure of the movement protein of Apple Chlorotic Leaf Spot Virus P863 would be helical in shape.