bioinfor 分析数据.docx

1、bioinfor 分析数据Cunninghamia lanceolataphenylalanine ammonia lyase (PAL2) mRNA, complete cdsGenBank: JQ904043.1GenBankGraphicsgb|JQ904043.1|:77-2305 Cunninghamia lanceolata phenylalanine ammonia lyase (PAL2) mRNA, complete cdsATGGCGGAGGTTGCAGCAGCAGAATATGATGATGCCCTAAACTGGTCGAAAGCCGCAGATTTGCTGAGAGGCAGCCA

2、TGTGAAGGAAGTGAAAAGCATGGTGGAAGAGTTCCATGGTATCAAGACTGTGTTTTTGGGAGGATCGAAGCTGAACATAGCCCAAGTTGCTGCAATCGCTCGCAGGCCCCAGGTGAAGGTTGTGCTCGATGAGAAAAGTGCCAAGAACAGAGTCGATGAAAGCTCAGATTGGGTTATCAATAATATTAGCAAAGGCACTGATACTTATGGAGTAACGACTGGATTTGGGGCCACTTCACACCGCAGAACGGATCAGACTTTCGAACTGCAGAAAGAATTGATCCGTTTCTTGAATGCTGG

3、AGTTTTAGGAGATGGAGTGAATTGTTTGTCTAGCTCTGCTACTAGGGCTGCCATGCTAGTAAGGACGAATACTCTGATGCAGGGCTACTCCGGTATTAGGTGGGAGATTTTGGATGCTCTGCAGAAATTAATAGATGCCCACATTACGCCTAAGTTGCCTCTGCGAGGGACTATTACTGCGTCTGGAGATCTGGTGCCTCTGTCCTACATTGCAGGGCTGCTTACTGGGAGGTCTAATTCTGTTGCTGTTGCGGAAGATGGGACTGAGATGAGTGCTGAGGAGGGTTTGAGATTGGCTGG

4、AGTTTCTAAGCCCTTTGAGCTCTATCCCAAGGAAGGCCTCGCCCTTGTCAATGGAACTGCTGTCGGTGCTGCGGTTGCTTGCACTGCTTGTTATGATGCTAATGTCTTGGTTGCTTTTGCAGAGGTTGCGTCTGCTATGTTTTGCGAGGTGATGCAGGGAAAACCAGAGTTCACAGATCCATTGACTCACAAGCTGAAGCACCATCCAGGCCAAATGGAAGCCGCAGCAGTGATGGAGTGGCTGCTAGAGGGGAGCTCGTACATGAAATCCGCAGCCAAGGTGCACGAAACAGATCCATT

5、AAAAAAGCCCAAGCAGGACCGCTACGCCTTACGGACCTCTCCACAGTGGCTGGGCCCCCAGATCGAAGTCATCCGCATGGCCACGCACGCTATAACCAGAGAAATCAATTCTGTCAATGACAATCCCCTCATAGATGTCGCCAGAGACAAAGCCCTACACGGCGGCAACTTTCAGGGCACACCAATTGGGGTTGCCATGGACAATGTTCGACTGGCATTGGCCGCCATTGCCAAGCTCATGTTCGCTCAGTTCTCAGAGCTCGTCAACGATTACTACAACAACGGCCTGCCGTCCAATCT

6、TTCCGGCGGAGTAAACCCTAGCCTGGATTACGGCCTCAAGGGCGCAGAGATCGCCATGGCCTCATATACTTCCGAAATACAGTATCTGGCAAACCCTGTAACAAACCATGTCCAGAGCGCAGAGCAGCACAACCAGGATGTAAACTCCCTGGGCCTGGTCTCTGCCAGAAAGACTGCAGAAGCCATTGAAATTCTCAAGCTCATGGTGTCCACATATCTGGTTGCCCTGTGTCAGGCTGTTGATCTTCGCCATCTAGAAGAAAACTTCCATGGCGGCATTAAACAGGCAGTTTGCCAGGC

7、AGCAAGAAAGACATTGTATTCAACAACAGGAGGCCTATTATTGCCCTCCAGATTCTGTGAAAAGGAGCTCTTGCAGGTCGTTGACAGGCTCCCTGTTTTCACCTACATAGAAGACGCTGCAGGGTCTTCTTCTCCATTAATGCTGCAGCTTCGCCAAGTGCTCGTAGACCAGGCCCTCAAATCACCAGACGAAAAGAGGGGTTTCCCTATAATTAACACAATCTCTCTGTTTGAACAAGAGCTCAGAAGAAAACTATCCATTGAGGTTCCACTCATACGCCAAAACTTTGAAGCTGGATG

8、TTTTGAACATGTTAACCAAATTCAGAGCTGCAGAACTTATCCTCTGTATAAATTTGTGCGAGGGGAGCTCGAAACGAGTTTGTTGTGCGGGCCGACAGGAGGAACGCCAGGGGAGGATATTGAAAAAGTTTTTGCGGCCATTGGAGAAGGAAAGCTGGAGAATTGTGTGATGGAATGCTTGGATGGATGGAATGAATCACCCGGCCCTTTTCTTCAACTCAAGAAAAATAATCATGTCTGTGAAATAGTGAAATCTAACCATGCGTGCGGGTGGAGCTGGTCGCACCAGATTGGAGGACA

9、GCATCAGCAAATAAATGGAGGGAAGGGCTACTGGCTTCTCTCTATCATTTGAClPAL2-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)MAEVAAAEYDDALNWSKAADLLRGSHVKEVKSMVEEFHGIKTVFLGGSKLNIAQVAAIARRPQVKVVLD

10、EKSAKNRVDESSDWVINNISKGTDTYGVTTGFGATSHRRTDQTFELQKELIRFLNAGVLGDGVNCLSSSATRAAMLVRTNTLMQGYSGIRWEILDALQKLIDAHITPKLPLRGTITASGDLVPLSYIAGLLTGRSNSVAVAEDGTEMSAEEGLRLAGVSKPFELYPKEGLALVNGTAVGAAVACTACYDANVLVAFAEVASAMFCEVMQGKPEFTDPLTHKLKHHPGQMEAAAVMEWLLEGSSYMKSAAKVHETDPLKKPKQDRYALRTSPQWLGPQIEVIRMATHAITREINSVNDNPL

11、IDVARDKALHGGNFQGTPIGVAMDNVRLALAAIAKLMFAQFSELVNDYYNNGLPSNLSGGVNPSLDYGLKGAEIAMASYTSEIQYLANPVTNHVQSAEQHNQDVNSLGLVSARKTAEAIEILKLMVSTYLVALCQAVDLRHLEENFHGGIKQAVCQAARKTLYSTTGGLLLPSRFCEKELLQVVDRLPVFTYIEDAAGSSSPLMLQLRQVLVDQALKSPDEKRGFPIINTISLFEQELRRKLSIEVPLIRQNFEAGCFEHVNQIQSCRTYPLYKFVRGELETSLLCGPTGGTPGEDIEKV

12、FAAIGEGKLENCVMECLDGWNESPGPFLQLKKNNHVCEIVKSNHACGWSWSHQIGGQHQQINGGKGYWLLSII-TMHMM resultHELPwith output formats# WEBSEQUENCE Length: 742# WEBSEQUENCE Number of predicted TMHs: 0# WEBSEQUENCE Exp number of AAs in TMHs: 0.09025# WEBSEQUENCE Exp number, first 60 AAs: 0.01558# WEBSEQUENCE Total prob of N-

13、in: 0.00386WEBSEQUENCE TMHMM2.0 outside 1 742ppmtogif: computing colormap. ppmtogif: 5 colors found#plotin postscript,scriptfor making the plot in gnuplot,datafor plotSignalP 4.1 Server - prediction resultsTechnical University of Denmark # SignalP-4.1 euk predictionsSequence # Measure Position Value

14、 Cutoff signal peptide?原始剪切位点得分 max. C 32 0.141被结合得剪切位点的分数max. Y 32 0.222信号肽分数max. S 19 0.469 mean S 1-31 0.347 D 1-31 0.290 0.450 NOName=Sequence SP=NO D=0.290 D-cutoff=0.450 Networks=SignalP-noTM# data# gnuplot scriptPlease cite:SignalP 4.0: discriminating signal peptides from transmembrane region

15、sPetersen TN., Brunak S., von Heijne G. & Nielsen H.Nature Methods, 8:785-786, 2011原始剪切位点得分ProtParam氨基酸数目Number of amino acids: 740相对分子质量Molecular weight: 80730.2理论PI值Theoretical pI: 5.99氨基酸组成Amino acid composition: Ala (A) 72 9.7%Arg (R) 31 4.2%Asn (N) 35 4.7%Asp (D) 31 4.2%Cys (C) 14 1.9%Gln (Q) 3

16、3 4.5%Glu (E) 51 6.9%Gly (G) 59 8.0%His (H) 19 2.6%Ile (I) 36 4.9%Leu (L) 80 10.8%Lys (K) 40 5.4%Met (M) 17 2.3%Phe (F) 22 3.0%Pro (P) 29 3.9%Ser (S) 50 6.8%Thr (T) 38 5.1%Trp (W) 9 1.2%Tyr (Y) 19 2.6%Val (V) 55 7.4%Pyl (O) 0 0.0%Sec (U) 0 0.0% (B) 0 0.0% (Z) 0 0.0% (X) 0 0.0%正负电话残基数Total number of

17、negatively charged residues (Asp + Glu): 82Total number of positively charged residues (Arg + Lys): 71原子组成Atomic composition:Carbon C 3571Hydrogen H 5682Nitrogen N 988Oxygen O 1080Sulfur S 31分子式Formula: C3571H5682N988O1080S31总原子数Total number of atoms: 11352消光数Extinction coefficients:Extinction coeff

18、icients are in units of M-1 cm-1, at 280 nm measured in water.Ext. coefficient 78685Abs 0.1% (=1 g/l) 0.975, assuming all pairs of Cys residues form cystinesExt. coefficient 77810Abs 0.1% (=1 g/l) 0.964, assuming all Cys residues are reduced半衰期Estimated half-life:The N-terminal of the sequence consi

19、dered is M (Met).The estimated half-life is: 30 hours (mammalian reticulocytes, in vitro).20 hours (yeast, in vivo).10 hours (Escherichia coli, in vivo).不稳定系数Instability index:The instability index (II) is computed to be 38.35This classifies the protein as stable.脂肪系数Aliphatic index: 92.42总平均亲水性Gran

20、d average of hydropathicity (GRAVY): -0.129TMpred outputSequence: MAE.SII, length: 742Prediction parameters: TM-helix length between 17 and 331.) Possible transmembrane helices可能的跨膜结构区The sequence positions in brackets denominate the core region.Only scores above 500 are considered significant.Insid

21、e to outside helices : 6 found From位置to score center片段中间位置 122 ( 125) 146 ( 143) 739 135 184 ( 184) 202 ( 202) 513 192 241 ( 241) 266 ( 257) 1226 249 259 ( 261) 277 ( 277) 807 269 397 ( 397) 414 ( 414) 253 405 490 ( 490) 508 ( 506) 367 498Outside to inside helices : 7 found from to score center 39 (

22、 39) 58 ( 58) 114 47 125 ( 125) 146 ( 146) 472 135 182 ( 182) 201 ( 199) 440 190 238 ( 238) 255 ( 255) 951 247 241 ( 247) 266 ( 266) 901 256 388 ( 388) 410 ( 408) 177 398 490 ( 490) 508 ( 506) 303 4982.) Table of correspondences相关性列表Here is shown, which of the inside-outside helices correspond to wh

23、ich of the outside-inside helices.Helices shown in brackets are considered insignificant.A +-symbol indicates a preference of this orientation.A +-symbol indicates a strong preference of this orientation. inside-outside | outside-inside |( 39- 58 (20) 114 + ) 122- 146 (25) 739 + |( 125- 146 (22) 472

24、 ) 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.) Suggested models for transmembrane topology建议的跨膜拓扑模型These suggestions are purely

25、speculative and should be used with extreme caution since they are based on the assumption that all transmembrane helices have been found.In most cases, the Correspondence Table shown above or the prediction plot that is also created should be used for the topology assignment of unknown proteins.2 p

26、ossible models considered, only significant TM-segments used* the models differ in the number of TM-helices ! *最优拓扑结构- STRONGLY prefered model: N-terminus inside 3 strong transmembrane helices, total score : 2497 # from to length score orientation 1 122 146 (25) 739 i-o 2 238 255 (18) 951 o-i 3 259

27、277 (19) 807 i-o- alternative model 2 strong transmembrane helices, total score : 1758 # from to length score orientation 1 238 255 (18) 951 o-i 2 259 277 (19) 807 i-o每一位置计算分值InterproscanProtScale所用氨基酸标度信息sing the scaleHphob. / Kyte & Doolittle, the individual values for the 20 amino acids are:Ala:

28、1.800 Arg: -4.500 Asn: -3.500 Asp: -3.500 Cys: 2.500 Gln: -3.500 Glu: -3.500 Gly: -0.400 His: -3.200 Ile: 4.500 Leu: 3.800 Lys: -3.900 Met: 1.900 Phe: 2.800 Pro: -1.600 Ser: -0.800 Thr: -0.700 Trp: -0.900 Tyr: -1.300 Val: 4.200 : -3.500 : -3.500 : -0.490 分析所用参数信息Weights for window positions 1,.,9, usinglinear weight variation model: 1 2 3 4 5 6 7 8 9 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 edge center edge以0为界，上面的正值表示疏水性，负值表示亲水性The results of your ProtScale query are available in the following formats: