findkm

 

Function

Find Km and Vmax for an enzyme reaction

Description

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

Usage

Here is a sample session with findkm 


% findkm -graph cps 
Find Km and Vmax for an enzyme reaction
Enter name of file containing data: enztest.dat
Output file [enztest.findkm]: 

Created findkm.ps

Go to the input files for this example
Go to the output files for this example

Command line arguments 

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

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

   Associated qualifiers:

   "-outfile" associated qualifiers
   -odirectory2         string     Output directory

   "-graphlb" associated qualifiers
   -gprompt             boolean    Graph prompting
   -gtitle              string     Graph title
   -gsubtitle           string     Graph subtitle
   -gxtitle             string     Graph x axis title
   -gytitle             string     Graph y axis title
   -goutfile            string     Output file for non interactive displays
   -gdirectory          string     Output directory

   General qualifiers:
   -auto                boolean    Turn off prompts
   -stdout              boolean    Write standard output
   -filter              boolean    Read standard input, write standard output
   -options             boolean    Prompt for standard and additional values
   -debug               boolean    Write debug output to program.dbg
   -verbose             boolean    Report some/full command line options
   -help                boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning             boolean    Report warnings
   -error               boolean    Report errors
   -fatal               boolean    Report fatal errors
   -die                 boolean    Report deaths

Standard (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, xml EMBOSS_GRAPHICS value, or x11
Additional (Optional) qualifiers Allowed values Default
(none)
Advanced (Unprompted) qualifiers Allowed values Default
-[no]plot S/V vs S Boolean value Yes/No Yes

Input file format

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

Input files for usage example

File: enztest.dat

  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

Output files for usage example

File: enztest.findkm

---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

Graphics File: findkm.ps

[findkm results]

Data files

None.

Notes

None.

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

None.

Diagnostic Error Messages

None.

Exit status

It exits with a status of 0.

Known bugs

None.

See also

Program nameDescription

Author(s)

Sinead O'Leary (current e-mail address unknown)
while she was at:
HGMP-RC, Genome Campus, Hinxton, Cambridge CB10 1SB, UK

This application was modified by David Martin (dmartin © rfcgr.mrc.ac.uk)

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

None