EMBOSS: findkm

Program findkm

Function

Find Km and Vmax for an enzyme reaction by a Hanes/Woolf plot

Description

Takes a file of enzymatic data and plots Michaelis Menten and Hanes Woolf plots of the data. From these ot calculates the Michaelis Menten constant (Km) and the maximum velocity (Vmax) of the reaction.

Usage

Here is a sample session with findkm. 

%findkm
Calculates Km and Vmax for an enzyme reaction.
Enter name of file containing data: enztest.dat   
Display on device [xwin]:

Command line arguments 

   Mandatory qualifiers:
  [-infile]            infile     Enter name of file containing data
  [-outfile]           outfile    Output file name
   -graphlb            xygraph    Graph type

   Optional qualifiers: (none)
   Advanced qualifiers:
   -[no]plot           bool       S/V vs S

   General qualifiers:
  -help                bool       report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose

Mandatory qualifiers Allowed values Default
[-infile]
(Parameter 1)		 Enter name of file containing data Input file Required
[-outfile]
(Parameter 2)		 Output file name Output file <sequence>.findkm
-graphlb Graph type EMBOSS has a list of known devices, including postscript, ps, hpgl, hp7470, hp7580, meta, colourps, cps, xwindows, x11, tektronics, tekt, tek4107t, tek, none, null, text, data, xterm, png EMBOSS_GRAPHICS value, or x11
Optional qualifiers Allowed values Default
(none)
Advanced qualifiers Allowed values Default
-[no]plot S/V vs S Yes/No Yes

Input file format

The input file is a file of enzymatic data, [S] against V, Substrate concentration against reaction velocity.

The data for the example run are shown below: 


  0.10   2
  0.20   4
  0.50   9
  1.00  17
  2.00  29
  5.00  50
 10.00  67
 20.00  80
 50.00  91
100.00  95

Output file format

Here is a sample output from the example above, together with the plots: 

---Hanes Woolf Plot Calculations---
Slope of best fit line is a = 0.01
Coefficient in Eqn of line y = ma +b is b = 0.05
Where line cuts x axis = (-0.20, 0)
Where line cuts y axis = (0, 0.05)
Limit-point of graph for plot = (103.00, 1.08)

Vmax = 99.70, Km = 4.894612
Click here for the graphical output

Data files

See Input File Format

Notes

References

  1. Voet & Voet (1993) 'Biochemistry'
  2. Dawes 'Quantitative Problems in Biochemistry' 5th Edition.
  3. Manuel G. Claros, Francisco M. Canovas 'Lines&Kinetics: a graphic tool to deal with linear regressions and enzyme kinetics.' EMBnet.news vol 5.1 http://www.uk.embnet.org/embnet.news/vol5_1/kinetics.html
  4. Cornish-Bowden (1996) 'Fundamentals of Enzyme kinetics' Portland Press, London.

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Program nameDescription

Author(s)

This application was written by Sinead O'Leary (soleary@hgmp.mrc.ac.uk)

This application was modified for inclusion in EMBOSS by David Martin (david.martin@biotek.uio.no) at the Norwegian EMBnet node.

History

Completed November 1999

Modified May 2000

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments