bioinfor 分析数据.docx
《bioinfor 分析数据.docx》由会员分享，可在线阅读，更多相关《bioinfor 分析数据.docx（13页珍藏版）》请在冰豆网上搜索。
bioinfor分析数据
Cunninghamialanceolata phenylalanineammonialyase（PAL2）mRNA,completecds
GenBank:
JQ904043.1
GenBank Graphics
>gb|JQ904043.1|:
77-2305Cunninghamialanceolataphenylalanineammonialyase（PAL2）mRNA,completecds
ATGGCGGAGGTTGCAGCAGCAGAATATGATGATGCCCTAAACTGGTCGAAAGCCGCAGATTTGCTGAGAG
GCAGCCATGTGAAGGAAGTGAAAAGCATGGTGGAAGAGTTCCATGGTATCAAGACTGTGTTTTTGGGAGG
ATCGAAGCTGAACATAGCCCAAGTTGCTGCAATCGCTCGCAGGCCCCAGGTGAAGGTTGTGCTCGATGAG
AAAAGTGCCAAGAACAGAGTCGATGAAAGCTCAGATTGGGTTATCAATAATATTAGCAAAGGCACTGATA
CTTATGGAGTAACGACTGGATTTGGGGCCACTTCACACCGCAGAACGGATCAGACTTTCGAACTGCAGAA
AGAATTGATCCGTTTCTTGAATGCTGGAGTTTTAGGAGATGGAGTGAATTGTTTGTCTAGCTCTGCTACT
AGGGCTGCCATGCTAGTAAGGACGAATACTCTGATGCAGGGCTACTCCGGTATTAGGTGGGAGATTTTGG
ATGCTCTGCAGAAATTAATAGATGCCCACATTACGCCTAAGTTGCCTCTGCGAGGGACTATTACTGCGTC
TGGAGATCTGGTGCCTCTGTCCTACATTGCAGGGCTGCTTACTGGGAGGTCTAATTCTGTTGCTGTTGCG
GAAGATGGGACTGAGATGAGTGCTGAGGAGGGTTTGAGATTGGCTGGAGTTTCTAAGCCCTTTGAGCTCT
ATCCCAAGGAAGGCCTCGCCCTTGTCAATGGAACTGCTGTCGGTGCTGCGGTTGCTTGCACTGCTTGTTA
TGATGCTAATGTCTTGGTTGCTTTTGCAGAGGTTGCGTCTGCTATGTTTTGCGAGGTGATGCAGGGAAAA
CCAGAGTTCACAGATCCATTGACTCACAAGCTGAAGCACCATCCAGGCCAAATGGAAGCCGCAGCAGTGA
TGGAGTGGCTGCTAGAGGGGAGCTCGTACATGAAATCCGCAGCCAAGGTGCACGAAACAGATCCATTAAA
AAAGCCCAAGCAGGACCGCTACGCCTTACGGACCTCTCCACAGTGGCTGGGCCCCCAGATCGAAGTCATC
CGCATGGCCACGCACGCTATAACCAGAGAAATCAATTCTGTCAATGACAATCCCCTCATAGATGTCGCCA
GAGACAAAGCCCTACACGGCGGCAACTTTCAGGGCACACCAATTGGGGTTGCCATGGACAATGTTCGACT
GGCATTGGCCGCCATTGCCAAGCTCATGTTCGCTCAGTTCTCAGAGCTCGTCAACGATTACTACAACAAC
GGCCTGCCGTCCAATCTTTCCGGCGGAGTAAACCCTAGCCTGGATTACGGCCTCAAGGGCGCAGAGATCG
CCATGGCCTCATATACTTCCGAAATACAGTATCTGGCAAACCCTGTAACAAACCATGTCCAGAGCGCAGA
GCAGCACAACCAGGATGTAAACTCCCTGGGCCTGGTCTCTGCCAGAAAGACTGCAGAAGCCATTGAAATT
CTCAAGCTCATGGTGTCCACATATCTGGTTGCCCTGTGTCAGGCTGTTGATCTTCGCCATCTAGAAGAAA
ACTTCCATGGCGGCATTAAACAGGCAGTTTGCCAGGCAGCAAGAAAGACATTGTATTCAACAACAGGAGG
CCTATTATTGCCCTCCAGATTCTGTGAAAAGGAGCTCTTGCAGGTCGTTGACAGGCTCCCTGTTTTCACC
TACATAGAAGACGCTGCAGGGTCTTCTTCTCCATTAATGCTGCAGCTTCGCCAAGTGCTCGTAGACCAGG
CCCTCAAATCACCAGACGAAAAGAGGGGTTTCCCTATAATTAACACAATCTCTCTGTTTGAACAAGAGCT
CAGAAGAAAACTATCCATTGAGGTTCCACTCATACGCCAAAACTTTGAAGCTGGATGTTTTGAACATGTT
AACCAAATTCAGAGCTGCAGAACTTATCCTCTGTATAAATTTGTGCGAGGGGAGCTCGAAACGAGTTTGT
TGTGCGGGCCGACAGGAGGAACGCCAGGGGAGGATATTGAAAAAGTTTTTGCGGCCATTGGAGAAGGAAA
GCTGGAGAATTGTGTGATGGAATGCTTGGATGGATGGAATGAATCACCCGGCCCTTTTCTTCAACTCAAG
AAAAATAATCATGTCTGTGAAATAGTGAAATCTAACCATGCGTGCGGGTGGAGCTGGTCGCACCAGATTG
GAGGACAGCATCAGCAAATAAATGGAGGGAAGGGCTACTGGCTTCTCTCTATCATTTGA
ClPAL2-qF1:
5’-TTACGCCTAAGTTGCCTCTGC-3’（60.1度）
ClPAL2-qR1:
5’-AGCCAATCTCAAACCCTCCTC-3’（59.8度）
ClPAL2-qF2:
5’-GCCTGCCGTCCAATCTTTCC-3’（64.1度）
ClPAL2-qR2:
5’-CATCCTGGTTGTGCTGCTCTGC-3’（65.3度）
MAEVAAAEYDDALNWSKAADLLRGSHVKEVKSMVEEFHGIKTVFLGGSKLNIAQVAAIARRPQVKVVLDEKSAKNRVDESSDWVINNISKGTDTYGVTTGFGATSHRRTDQTFELQKELIRFLNAGVLGDGVNCLSSSATRAAMLVRTNTLMQGYSGIRWEILDALQKLIDAHITPKLPLRGTITASGDLVPLSYIAGLLTGRSNSVAVAEDGTEMSAEEGLRLAGVSKPFELYPKEGLALVNGTAVGAAVACTACYDANVLVAFAEVASAMFCEVMQGKPEFTDPLTHKLKHHPGQMEAAAVMEWLLEGSSYMKSAAKVHETDPLKKPKQDRYALRTSPQWLGPQIEVIRMATHAITREINSVNDNPLIDVARDKALHGGNFQGTPIGVAMDNVRLALAAIAKLMFAQFSELVNDYYNNGLPSNLSGGVNPSLDYGLKGAEIAMASYTSEIQYLANPVTNHVQSAEQHNQDVNSLGLVSARKTAEAIEILKLMVSTYLVALCQAVDLRHLEENFHGGIKQAVCQAARKTLYSTTGGLLLPSRFCEKELLQVVDRLPVFTYIEDAAGSSSPLMLQLRQVLVDQALKSPDEKRGFPIINTISLFEQELRRKLSIEVPLIRQNFEAGCFEHVNQIQSCRTYPLYKFVRGELETSLLCGPTGGTPGEDIEKVFAAIGEGKLENCVMECLDGWNESPGPFLQLKKNNHVCEIVKSNHACGWSWSHQIGGQHQQINGGKGYWLLSII-
TMHMMresult
HELP withoutputformats
#WEBSEQUENCELength:
742
#WEBSEQUENCENumberofpredictedTMHs:
0
#WEBSEQUENCEExpnumberofAAsinTMHs:
0.09025
#WEBSEQUENCEExpnumber,first60AAs:
0.01558
#WEBSEQUENCETotalprobofN-in:
0.00386
WEBSEQUENCETMHMM2.0outside1742
ppmtogif:
computingcolormap...ppmtogif:
5colors
found
# plot inpostscript, script formakingtheplotingnuplot, data forplot
SignalP4.1Server-predictionresults
TechnicalUniversityofDenmark
#SignalP-4.1eukpredictions
>Sequence
#MeasurePositionValueCutoffsignalpeptide?
原始剪切位点得分max.C320.141
被结合得剪切位点的分数max.Y320.222
信号肽分数max.S190.469
meanS1-310.347
D1-310.2900.450NO
Name=SequenceSP='NO'D=0.290D-cutoff=0.450Networks=SignalP-noTM
#data
#gnuplotscript
Pleasecite:
SignalP4.0:
discriminatingsignalpeptidesfromtransmembraneregions
PetersenTN.,BrunakS.,vonHeijneG.&NielsenH.
NatureMethods,8:
785-786,2011
原始剪切位点得分
ProtParam
氨基酸数目Numberofaminoacids:
740
相对分子质量Molecularweight:
80730.2
理论PI值TheoreticalpI:
5.99
氨基酸组成Aminoacidcomposition:
Ala（A）729.7%
Arg（R）314.2%
Asn（N）354.7%
Asp（D）314.2%
Cys（C）141.9%
Gln（Q）334.5%
Glu（E）516.9%
Gly（G）598.0%
His（H）192.6%
Ile（I）364.9%
Leu（L）8010.8%
Lys（K）405.4%
Met（M）172.3%
Phe（F）223.0%
Pro（P）293.9%
Ser（S）506.8%
Thr（T）385.1%
Trp（W）91.2%
Tyr（Y）192.6%
Val（V）557.4%
Pyl（O）00.0%
Sec（U）00.0%
（B）00.0%
（Z）00.0%
（X）00.0%
正负电话残基数Totalnumberofnegativelychargedresidues（Asp+Glu）:
82
Totalnumberofpositivelychargedresidues（Arg+Lys）:
71
原子组成Atomiccomposition:
CarbonC3571
HydrogenH5682
NitrogenN988
OxygenO1080
SulfurS31
分子式Formula:
C3571H5682N988O1080S31
总原子数Totalnumberofatoms:
11352
消光数Extinctioncoefficients:
ExtinctioncoefficientsareinunitsofM-1cm-1,at280nmmeasuredinwater.
Ext.coefficient78685
Abs0.1%（=1g/l）0.975,assumingallpairsofCysresiduesformcystines
Ext.coefficient77810
Abs0.1%（=1g/l）0.964,assumingallCysresiduesarereduced
半衰期Estimatedhalf-life:
TheN-terminalofthesequenceconsideredisM（Met）.
Theestimatedhalf-lifeis:
30hours（mammalianreticulocytes,invitro）.
>20hours（yeast,invivo）.
>10hours（Escherichiacoli,invivo）.
不稳定系数Instabilityindex:
Theinstabilityindex（II）iscomputedtobe38.35
Thisclassifiestheproteinasstable.
脂肪系数Aliphaticindex:
92.42
总平均亲水性Grandaverageofhydropathicity（GRAVY）:
-0.129
TMpredoutput
Sequence:
MAE...SII,length:
742
Predictionparameters:
TM-helixlengthbetween17and33
1.）Possibletransmembranehelices可能的跨膜结构区
Thesequencepositionsinbracketsdenominatethecoreregion.
Onlyscoresabove500areconsideredsignificant.
Insidetooutsidehelices:
6found
From位置toscorecenter片段中间位置
122（125）146（143）739135
184（184）202（202）513192
241（241）266（257）1226249
259（261）277（277）807269
397（397）414（414）253405
490（490）508（506）367498
Outsidetoinsidehelices:
7found
fromtoscorecenter
39（39）58（58）11447
125（125）146（146）472135
182（182）201（199）440190
238（238）255（255）951247
241（247）266（266）901256
388（388）410（408）177398
490（490）508（506）303498
2.）Tableofcorrespondences相关性列表
Hereisshown,whichoftheinside->outsidehelicescorrespondtowhichoftheoutside->insidehelices.
Helicesshowninbracketsareconsideredinsignificant.
A"+"-symbolindicatesapreferenceofthisorientation.
A"++"-symbolindicatesastrongpreferenceofthisorientation.
inside->outside|outside->inside
|（39-58（20）114++）
122-146（25）739++|（125-146（22）472）
184-202（19）513|（182-201（20）440）
241-266（26）1226++|238-255（18）951
259-277（19）807|241-266（26）901+
（397-414（18）253）|（388-410（23）177）
（490-508（19）367）|（490-508（19）303）
3.）Suggestedmodelsfortransmembranetopology建议的跨膜拓扑模型
Thesesuggestionsarepurelyspeculativeandshouldbeusedwithextremecautionsincetheyarebasedontheassumptionthatalltransmembraneheliceshavebeenfound.
Inmostcases,theCorrespondenceTableshownaboveorthepredictionplotthatisalsocreatedshouldbeusedforthetopologyassignmentofunknownproteins.
2possiblemodelsconsidered,onlysignificantTM-segmentsused
***themodelsdifferinthenumberofTM-helices!
***
最优拓扑结构----->STRONGLYpreferedmodel:
N-terminusinside
3strongtransmembranehelices,totalscore:
2497
#fromtolengthscoreorientation
1122146（25）739i-o
2238255（18）951o-i
3259277（19）807i-o
------>alternativemodel
2strongtransmembranehelices,totalscore:
1758
#fromtolengthscoreorientation
1238255（18）951o-i
2259277（19）807i-o
每一位置计算分值
Interproscan
ProtScale
所用氨基酸标度信息
singthescale Hphob./Kyte&Doolittle,theindividualvaluesforthe20aminoacidsare:
Ala:
1.800Arg:
-4.500Asn:
-3.500Asp:
-3.500Cys:
2.500Gln:
-3.500
Glu:
-3.500Gly:
-0.400His:
-3.200Ile:
4.500Leu:
3.800Lys:
-3.900
Met:
1.900Phe:
2.800Pro:
-1.600Ser:
-0.800Thr:
-0.700Trp:
-0.900
Tyr:
-1.300Val:
4.200:
-3.500:
-3.500:
-0.490
分析所用参数信息
Weightsforwindowpositions1,..,9,using linearweightvariationmodel:
123456789
1.001.001.001.001.001.001.001.001.00
edgecenteredge
以0为界，上面的正值表示疏水性，负值表示亲水性
TheresultsofyourProtScalequeryareavailableinthefollowingformats:
升级会员 