bioinfor数据

1、Cunninghamia lanceolata phenylalanine ammonia lyase (PAL2) mRNA, complete cdsGenBank: JQ904043.1GenBank Graphics>gb|JQ904043.1|:77-2305 Cunninghamia lanceolata phenylalanine ammonia lyase (PAL2) mRNA, complete cdsATGGCGGAGGTTGCAGCAGCAGAATATGATGATGCCCTAAACTGGTCGAAAGCCGCAGATTTGCTGAGAGGCAG

2、CCATGTGAAGGAAGTGAAAAGCATGGTGGAAGAGTTCCATGGTATCAAGACTGTGTTTTTGGGAGGATCGAAGCTGAACATAGCCCAAGTTGCTGCAATCGCTCGCAGGCCCCAGGTGAAGGTTGTGCTCGATGAGAAAAGTGCCAAGAACAGAGTCGATGAAAGCTCAGATTGGGTTATCAATAATATTAGCAAAGGCACTGATACTTATGGAGTAACGACTGGATTTGGGGCCACTTCACACCGCAGAACGGATCAGACTTTCGAACTGCAGAAAGAATTGATCCGTTTCTTGAATGC

3、TGGAGTTTTAGGAGATGGAGTGAATTGTTTGTCTAGCTCTGCTACTAGGGCTGCCATGCTAGTAAGGACGAATACTCTGATGCAGGGCTACTCCGGTATTAGGTGGGAGATTTTGGATGCTCTGCAGAAATTAATAGATGCCCACATTACGCCTAAGTTGCCTCTGCGAGGGACTATTACTGCGTCTGGAGATCTGGTGCCTCTGTCCTACATTGCAGGGCTGCTTACTGGGAGGTCTAATTCTGTTGCTGTTGCGGAAGATGGGACTGAGATGAGTGCTGAGGAGGGTTTGAGATTGGC

4、TGGAGTTTCTAAGCCCTTTGAGCTCTATCCCAAGGAAGGCCTCGCCCTTGTCAATGGAACTGCTGTCGGTGCTGCGGTTGCTTGCACTGCTTGTTATGATGCTAATGTCTTGGTTGCTTTTGCAGAGGTTGCGTCTGCTATGTTTTGCGAGGTGATGCAGGGAAAACCAGAGTTCACAGATCCATTGACTCACAAGCTGAAGCACCATCCAGGCCAAATGGAAGCCGCAGCAGTGATGGAGTGGCTGCTAGAGGGGAGCTCGTACATGAAATCCGCAGCCAAGGTGCACGAAACAGATCC

5、ATTAAAAAAGCCCAAGCAGGACCGCTACGCCTTACGGACCTCTCCACAGTGGCTGGGCCCCCAGATCGAAGTCATCCGCATGGCCACGCACGCTATAACCAGAGAAATCAATTCTGTCAATGACAATCCCCTCATAGATGTCGCCAGAGACAAAGCCCTACACGGCGGCAACTTTCAGGGCACACCAATTGGGGTTGCCATGGACAATGTTCGACTGGCATTGGCCGCCATTGCCAAGCTCATGTTCGCTCAGTTCTCAGAGCTCGTCAACGATTACTACAACAACGGCCTGCCGTCCAA

6、TCTTTCCGGCGGAGTAAACCCTAGCCTGGATTACGGCCTCAAGGGCGCAGAGATCGCCATGGCCTCATATACTTCCGAAATACAGTATCTGGCAAACCCTGTAACAAACCATGTCCAGAGCGCAGAGCAGCACAACCAGGATGTAAACTCCCTGGGCCTGGTCTCTGCCAGAAAGACTGCAGAAGCCATTGAAATTCTCAAGCTCATGGTGTCCACATATCTGGTTGCCCTGTGTCAGGCTGTTGATCTTCGCCATCTAGAAGAAAACTTCCATGGCGGCATTAAACAGGCAGTTTGCCA

7、GGCAGCAAGAAAGACATTGTATTCAACAACAGGAGGCCTATTATTGCCCTCCAGATTCTGTGAAAAGGAGCTCTTGCAGGTCGTTGACAGGCTCCCTGTTTTCACCTACATAGAAGACGCTGCAGGGTCTTCTTCTCCATTAATGCTGCAGCTTCGCCAAGTGCTCGTAGACCAGGCCCTCAAATCACCAGACGAAAAGAGGGGTTTCCCTATAATTAACACAATCTCTCTGTTTGAACAAGAGCTCAGAAGAAAACTATCCATTGAGGTTCCACTCATACGCCAAAACTTTGAAGCTGG

8、ATGTTTTGAACATGTTAACCAAATTCAGAGCTGCAGAACTTATCCTCTGTATAAATTTGTGCGAGGGGAGCTCGAAACGAGTTTGTTGTGCGGGCCGACAGGAGGAACGCCAGGGGAGGATATTGAAAAAGTTTTTGCGGCCATTGGAGAAGGAAAGCTGGAGAATTGTGTGATGGAATGCTTGGATGGATGGAATGAATCACCCGGCCCTTTTCTTCAACTCAAGAAAAATAATCATGTCTGTGAAATAGTGAAATCTAACCATGCGTGCGGGTGGAGCTGGTCGCACCAGATTGGAGG

9、ACAGCATCAGCAAATAAATGGAGGGAAGGGCTACTGGCTTCTCTCTATCATTTGAClPAL2-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)MAEVAAAEYDDALNWSKAADLLRGSHVKEVKSMVEEFHGIKTVFLGGSKLNIAQVAAIARRPQV

10、KVVLDEKSAKNRVDESSDWVINNISKGTDTYGVTTGFGATSHRRTDQTFELQKELIRFLNAGVLGDGVNCLSSSATRAAMLVRTNTLMQGYSGIRWEILDALQKLIDAHITPKLPLRGTITASGDLVPLSYIAGLLTGRSNSVAVAEDGTEMSAEEGLRLAGVSKPFELYPKEGLALVNGTAVGAAVACTACYDANVLVAFAEVASAMFCEVMQGKPEFTDPLTHKLKHHPGQMEAAAVMEWLLEGSSYMKSAAKVHETDPLKKPKQDRYALRTSPQWLGPQIEVIRMATHAITREINSV

11、NDNPLIDVARDKALHGGNFQGTPIGVAMDNVRLALAAIAKLMFAQFSELVNDYYNNGLPSNLSGGVNPSLDYGLKGAEIAMASYTSEIQYLANPVTNHVQSAEQHNQDVNSLGLVSARKTAEAIEILKLMVSTYLVALCQAVDLRHLEENFHGGIKQAVCQAARKTLYSTTGGLLLPSRFCEKELLQVVDRLPVFTYIEDAAGSSSPLMLQLRQVLVDQALKSPDEKRGFPIINTISLFEQELRRKLSIEVPLIRQNFEAGCFEHVNQIQSCRTYPLYKFVRGELETSLLCGPTGGTPGE

12、DIEKVFAAIGEGKLENCVMECLDGWNESPGPFLQLKKNNHVCEIVKSNHACGWSWSHQIGGQHQQINGGKGYWLLSII-TMHMM resultHELP with 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

13、 prob of N-in: 0.00386WEBSEQUENCETMHMM2.0outside 1 742ppmtogif: computing colormap. ppmtogif: 5 colors found # plot in postscript, script for making the plot in gnuplot, data for plotSignalP 4.1 Server - prediction resultsTechnical University of Denmark # SignalP-4

14、.1 euk predictions>Sequence # Measure Position Value 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=SequenceSP='NO' D=0.290 D-cutoff=0.450 Networks=SignalP-noTM# data# gnuplot scriptPlease cite:Si

15、gnalP 4.0: discriminating signal peptides from transmembrane regionsPetersen 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.

16、7%Arg (R) 31 4.2%Asn (N) 35 4.7%Asp (D) 31 4.2%Cys (C) 14 1.9%Gln (Q) 33 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

17、%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 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

18、Total number of atoms: 11352消光数Extinction coefficients:Extinction coefficients 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

19、 are reduced半衰期Estimated half-life:The N-terminal of the sequence considered 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 b

20、e 38.35This classifies the protein as stable.脂肪系数Aliphatic index: 92.42总平均亲水性Grand 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

21、denominate the core region.Only scores above 500 are considered significant.Inside 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 ( 49

22、0) 508 ( 506) 367 498Outside to inside helices : 7 found from to score center 39 ( 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 corre

23、spondences 相关性列表Here is shown, which of the inside->outside helices correspond to which 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 o

24、f this orientation. 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-

25、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 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

26、 shown above or the prediction plot that is also created should be used for the topology assignment of unknown proteins.2 possible 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)