生物信息学相关操作

本文格式为Word版，下载可任意编辑——生物信息学相关操作1

在地址栏填入/protparam/，跳转到如下：ProtParamtool

ProtParam(References/Documentation)isatoolwhichallowsthecomputationofvariousphysicalandchemicalparametersforagivenproteinstoredinSwiss-ProtorTrEMBLorforauserentered

sequence.Thecomputedparametersincludethemolecularweight,theoreticalpI,aminoacidcomposition,atomiccomposition,extinctioncoefficient,estimatedhalf-life,instabilityindex,aliphaticindexandgrandaverageofhydropathicity(GRAVY)(Disclaimer).

Pleasenotethatyoumayonlyfilloutoneofthefollowingfieldsatatime.

EnteraSwiss-Prot/TrEMBLaccessionnumber(AC)(forexampleP05130)orasequenceidentifier(ID)(forexampleKPC1_DROME):

Oryoucanpasteyourownsequenceintheboxbelow:

RESETComputeparameters在上方小框内填入p05130，点击computerparameters，跳转到如下：ProtParam

SelectionofendpointsonthesequenceKPC1_DROME(P05130)

ProteinkinaseC,brainisozyme(EC3)(PKC)(dPKC53E(BR))

Drosophilamelanogaster(Fruitfly).

Pleaseselectoneofthefollowingfeaturesbyclickingonapairofendpoints,andthecomputationwillbecarriedoutforthecorrespondingsequencefragment.Bydefault,thecompletesequenceisused.

Note:Onlythefeaturescorrespondingtosubsequencesofatleast5residuesarehighlighted.

FTCHAIN1-679ProteinkinaseC,brainisozyme.

FTDOMAIN191-278C2.

FTDOMAIN350-608Proteinkinase.

FTDOMAIN609-679AGC-kinaseC-terminal.FTZN_FING45-104Phorbol-ester/DAG-type1.FTZN_FING119-169Phorbol-ester/DAG-type2.FTNP_BIND356-364ATP(Bysimilarity).

Or,ifyouwishtoselectadifferentsequencefragment(atleast5aminoacidslong),youcanenterthedesiredendpointsonthe

sequencehere(bydefault,thecomputationwillbecarriedoutforthecompletesequence).N-terminal:C-terminal:ThesequenceKPC1_DROMEconsistsof679aminoacids.

RESETSUBMIT

默认状态下开启点击submit，为完整序列计算，显示如下：ProtParam

KPC1_DROME(P05130)

ProteinkinaseC,brainisozyme(EC3)(PKC)(dPKC53E(BR))

Drosophilamelanogaster(Fruitfly).

Thecomputationhasbeencarriedoutonthecompletesequence(679aminoacids).

Warning:Allcomputationresultsshownbelowdonottakeintoaccount

anyannotatedpost-translationalmodification.Referencesanddocumentationareavailable.

Pleasenotethemodifiedalgorithmforextinctioncoefficient.

Numberofaminoacids:679

Molecularweight:77694.9

TheoreticalpI:6.77

Aminoacidcomposition:Ala(A)284.1%Arg(R)263.8%Asn(N)294.3%Asp(D)527.7%Cys(C)233.4%Gln(Q)284.1%Glu(E)446.5%Gly(G)487.1%His(H)162.4%Ile(I)355.2%Leu(L)517.5%Lys(K)6810.0%Met(M)182.7%Phe(F)426.2%Pro(P)345.0%Ser(S)345.0%Thr(T)314.6%Trp(W)81.2%Tyr(Y)243.5%Val(V)405.9%Pyl(O)00.0%Sec(U)00.0%

(B)00.0%

CSVformat

(Z)00.0%(X)00.0%

Totalnumberofnegativelychargedresidues(Asp+Glu):96Totalnumberofpositivelychargedresidues(Arg+Lys):94

Atomiccomposition:

CarbonC3477HydrogenH5374NitrogenN922OxygenO1018SulfurS41

Formula:C3477H5374N922O1018S41

Totalnumberofatoms:10832

Extinctioncoefficients:

ExtinctioncoefficientsareinunitsofM-1cm-1,at280nmmeasuredinwater.

Ext.coefficient81135

Abs0.1%(=1g/l)1.044,assumingallpairsofCysresiduesformcystines

Ext.coefficient79760

Abs0.1%(=1g/l)1.027,assumingallCysresiduesarereduced

Estimatedhalf-life:

TheN-terminalofthesequenceconsideredisM(Met).

Theestimatedhalf-lifeis:30hours(mammalianreticulocytes,invitro).

>20hours(yeast,invivo).

>10hours(Escherichiacoli,invivo).

Instabilityindex:

Theinstabilityindex(II)iscomputedtobe37.98

Thisclassifiestheproteinasstable.

Aliphaticindex:70.60

Grandaverageofhydropathicity(GRAVY):-0.517

2

在地址栏填入/protscale/，跳转到如下：ProtScale

ProtScale[Reference/Documentation]allowsyoutocomputeandrepresenttheprofileproducedbyanyaminoacidscaleonaselectedprotein.

Anaminoacidscaleisdefinedbyanumericalvalueassignedtoeachtypeofaminoacid.Themostfrequentlyusedscalesarethehydrophobicityorhydrophilicityscalesandthesecondarystructureconformationalparametersscales,butmanyotherscalesexistwhicharebasedondifferentchemicalandphysicalpropertiesoftheaminoacids.Thisprogramprovides57predefinedscalesenteredfromtheliterature.

EnteraUniProtKB/Swiss-ProtorUniProtKB/TrEMBLaccessionnumber(AC)(e.g.P05130)orasequenceidentifier(ID)(e.g.KPC1_DROME):

Oryoucanpasteyourownsequenceintheboxbelow:Pleasechooseanaminoacidscalefromthefollow