生物信息学相关操作.doc

生物信息学相关操作 - 教育文库 1 在地址栏填入://web.expasy.org/protparam/，跳转到如下： ProtParam tool ProtParam (References / Documentation) is a tool which allows the putation of various physical and chemical parameters for a given protein stored in Swiss-Prot or TrEMBL or for a user entered sequence. The puted parameters include the molecular weight, theoretical pI, amino acid position, atomic position, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity (GRAVY) (Disclaimer). Please note that you may only fill out one of the following fields at a time. Enter a Swiss-Prot/TrEMBL accession number (AC) (for exle P05130) or a sequence identifier (ID) (for exle KPC1_DROME): Or you can paste your own sequence in the box below: RESET pute parameters 在上方小框内填入p05130，点击puter parameters，跳转到如下： ProtParam Protein kinase C, brain isozyme (EC 2.7.11.13) (PKC) (dPKC53E(BR)) Drosophila melanogaster (Fruit fly). Note: Only the features corresponding to subsequences of at least 5 residues are highlighted. FT CHAIN 1-679 Protein kinase C, brain isozyme. FT DOMAIN 191-278 C2. FT DOMAIN 350-608 Protein kinase. FT DOMAIN 609-679 AGC-kinase C-terminal. FT ZN_FING 45-104 Phorbol-ester/DAG-type 1. FT ZN_FING 119-169 Phorbol-ester/DAG-type 2. FT NP_BIND 356-364 ATP (By similarity). sequence here (by default, the putation will be carried out for the plete sequence). N-terminal: C-terminal: The sequence KPC1_DROME consists of 679 amino acids. RESET SUBMIT 默认状态下翻开点击submit，为完好序列计算，显示如下： ProtParam KPC1_DROME (P05130) Protein kinase C, brain isozyme (EC 2.7.11.13) (PKC) (dPKC53E(BR)) Drosophila melanogaster (Fruit fly). The putation has been carried out on the plete sequence (679 amino acids). Warning: All putation results shown below do not take into account any annotated post-translational modification. References and documentation are available. Please note the modified algorithm for extinction coefficient. Number of amino acids: 679 Molecular weight: 77694.9 Theoretical pI: 6.77 Amino acid position: Ala (A) 28 4.1% Arg (R) 26 3.8% Asn (N) 29 4.3% Asp (D) 52 7.7% Cys (C) 23 3.4% Gln (Q) 28 4.1% Glu (E) 44 6.5% Gly (G) 48 7.1% His (H) 16 2.4% Ile (I) 35 5.2% Leu (L) 51 7.5% Lys (K) 68 10.0% Met (M) 18 2.7% Phe (F) 42 6.2% Pro (P) 34 5.0% Ser (S) 34 5.0% Thr (T) 31 4.6% Trp (W) 8 1.2% Tyr (Y) 24 3.5% Val (V) 40 5.9% Pyl (O) 0 0.0% Sec (U) 0 0.0% (B) 0 0.0% CSV format (Z) 0 0.0% (X) 0 0.0% Total number of negatively charged residues (Asp + Glu): 96 Total number of positively charged residues (Arg + Lys): 94 Atomic position: Carbon C 3477 Hydrogen H 5374 Nitrogen N 922 Oxygen O 8 Sulfur S 41 Formula: C3477H5374N922O8S41 Total number of atoms: 10832 Extinction coefficients: Extinction coefficients are in units of M-1 cm-1, at 280 nm measured in water. Ext. coefficient 81135 Abs 0.1% (=1 g/l) 1.044, assuming all pairs of Cys residues form cystines Ext. coefficient 79760 Abs 0.1% (=1 g/l) 1.027, assuming all Cys residues are reduced 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). Instability index: The instability index (II) is puted to be 37.98 This classifies the protein as stable. Aliphatic index: 70.60 Grand average of hydropathicity (GRAVY): -0.517 2 在地址栏填入://web.expasy.org/protscale/，跳转到如下： ProtScale ProtScale [Reference / Documentation] allows you to pute and represent the profile produced by any amino acid scale on a selected protein. An amino acid scale is defined by a numerical value assigned to each type of amino acid. The most frequently used scales are the hydrophobicity or hydrophilicity scales and the secondary structure conformational parameters scales, but many other scales exist which are based on different chemical and physical properties of the amino acids. This program provides 57 predefined scales entered from the literature. Enter a UniProtKB/Swiss-Prot or UniProtKB/TrEMBL accession number (AC) (e.g. P05130) or a sequence identifier (ID) (e.g. KPC1_DROME): Or you can paste your own sequence in the box below: Please choose an amino acid scale from the following list. To display information about a scale (author, reference, amino acid scale values) you can click on its name. Molecular weight Bulkiness Polarity / Grantham Number of codon(s) Polarity / Zimmerman Refractivity 第 页 共 页。