bioinfor 分析数据.docx
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bioinfor 分析数据.docx
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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:
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