bioinfor 分析数据

Cunninghamia lanceolata phenylalanine ammonia lyase (PAL2) mRNA, complete cds

GenBank: JQ904043.1

GenBank Graphics

>gb|JQ904043.1|:77-2305 Cunninghamia lanceolata phenylalanine ammonia lyase (PAL2) mRNA, complete cds 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-

TMHMM result

HELP 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 prob of N-in: 0.00386 WEBSEQUENCE TMHMM2.0 outside 1 742

ppmtogif: computing colormap... ppmtogif: 5 colors found

# plot in postscript, script for making the plot in gnuplot, data for plot

SignalP 4.1 Server - prediction results Technical University of Denmark # SignalP-4.1 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 NO

Name=Sequence SP='NO' D=0.290 D-cutoff=0.450 Networks=SignalP-noTM # data

# gnuplot script Please cite:

SignalP 4.0: discriminating signal peptides from transmembrane regions Petersen 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) 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% 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): 82 Total number of positively charged residues (Arg + Lys): 71 原子组成Atomic composition:

Carbon C 3571 Hydrogen H 5682 Nitrogen N 988 Oxygen O 1080 Sulfur S 31

分子式Formula: C3571H5682N988O1080S31 总原子数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 78685

Abs 0.1% (=1 g/l) 0.975, assuming all pairs of Cys residues form cystines Ext. coefficient 77810

Abs 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 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 be 38.35 This classifies the protein as stable.

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