I am attempting to trace carbons though a metabolic pathway. There are inconsistencies between atom numbering in the rPair reactions and molfile formats in the KEGG database

Ex: http://www.genome.jp/dbget-bin/www_bget?RP00079

Shows the reaction between Oxaloacetate (C00036) and (S)-Malate (C00149)  
http://rest.kegg.jp/get/C00036/mo l 
http://rest.kegg.jp/get/C00149/mol

Unfortunately the numbering of Oxaloacetate's molfile and the Entry1 in the rPair differ for no reason. However, (S)-Malate and Entry2 of the rPair are nearly identical.

How can I map the rPair to the molfile (specifically Oxaloacetate)
Simple to do with the Cactvs Cheminformatics Toolkit (version 3.428 and later, www,xemistry.com/academic ):

Tcl single-line script:

    molfile write RP00079.rxn [reaction create KEGG:RP00079]

Python single-line script:

    Molfile.Write('RP00079.rxn',Reaction('KEGG:RP00079'))

This writes out a standard MDL RXN file with full atom mapping. Structures and reaction/mapping data are extracted from the (dynamically downloaded) KEGG KCF data, not the Molfiles. Of course it is possible to do much more with the reaction data than just dumping it into a file with a few more script commands.

My experience is that it is highly advisable to use whenever possible the original data formats of sites - KCF for KEGG, ASN.1 for PubChem etc. Use tools which allow you to work with the original data. Any remote format conversion brings the risk of data loss and transformation weirdness which you cannot control, such as the atom scrambling in KEGG Molfile output.

---

    $RXN
    C00036_C00149
    WI    pycactvs 101920141408RP00079
    
      1  1
    $MOL
    Oxaloacetate
    WIpycactvs10191414082D 0   0.00000     0.00000C00036
    
     13 12  0  0  0  0  0  0  0  0999 V2000
       21.5736  -15.6638    0.0000 C   0  0  0  0  0  0  0  0  0  1  0  0
       22.9771  -15.6638    0.0000 C   0  0  0  0  0  0  0  0  0  2  0  0
       20.6530  -16.7130    0.0000 C   0  0  0  0  0  0  0  0  0  3  0  0
       21.0529  -14.4776    0.0000 O   0  0  0  0  0  0  0  0  0  4  0  0
       23.6787  -16.8742    0.0000 C   0  0  0  0  0  0  0  0  0  5  0  0
       19.2817  -16.4364    0.0000 O   0  0  0  0  0  0  0  0  0  6  0  0
       21.0402  -18.0393    0.0000 O   0  0  0  0  0  0  0  0  0  7  0  0
       22.9706  -18.0843    0.0000 O   0  0  0  0  0  0  0  0  0  8  0  0
       25.0057  -16.7976    0.0000 O   0  0  0  0  0  0  0  0  0  9  0  0
       23.7783  -15.3712    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
       22.8285  -14.8239    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
       19.0097  -15.6280    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
       22.1177  -18.0793    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
      1  2  1  0  0  0  0
      1  3  1  0  0  0  0
      1  4  2  0  0  0  0
      2  5  1  0  0  0  0
      3  6  1  0  0  0  0
      3  7  2  0  0  0  0
      5  8  1  0  0  0  0
      5  9  2  0  0  0  0
      2 10  1  0  0  0  0
      2 11  1  0  0  0  0
      6 12  1  0  0  0  0
      8 13  1  0  0  0  0
    A  001
    C5a
    A  002
    C1b
    A  003
    C6a
    A  004
    O5a
    A  005
    C6a
    A  006
    O6a
    A  007
    O6a
    A  008
    O6a
    A  009
    O6a
    M  END
    $MOL
    
    (S)-Malate
    WIpycactvs10191414082D 0   0.00000     0.00000C00149
    
     15 14  0  0  1  0  0  0  0  0999 V2000
       25.0942  -18.6205    0.0000 C   0  0  1  0  0  0  0  0  0  1  0  0
       26.2953  -19.3132    0.0000 C   0  0  0  0  0  0  0  0  0  2  0  0
       23.8998  -19.3132    0.0000 C   0  0  0  0  0  0  0  0  0  3  0  0
       25.0942  -17.2355    0.0000 O   0  0  0  0  0  0  0  0  0  4  0  0
       27.4897  -18.6205    0.0000 C   0  0  0  0  0  0  0  0  0  5  0  0
       22.7052  -18.6143    0.0000 O   0  0  0  0  0  0  0  0  0  7  0  0
       23.8360  -20.8303    0.0000 O   0  0  0  0  0  0  0  0  0  6  0  0
       28.6842  -19.3132    0.0000 O   0  0  0  0  0  0  0  0  0  8  0  0
       27.4834  -17.2355    0.0000 O   0  0  0  0  0  0  0  0  0  9  0  0
       24.3420  -18.1872    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
       25.7379  -19.9787    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
       26.8543  -19.9774    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
       25.8460  -16.8015    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
       22.7102  -17.7462    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
       28.6825  -20.1813    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
      1  2  1  0  0  0  0
      1  3  1  0  0  0  0
      1  4  1  1  0  0  0
      2  5  1  0  0  0  0
      3  6  1  0  0  0  0
      3  7  2  0  0  0  0
      5  8  1  0  0  0  0
      5  9  2  0  0  0  0
      1 10  1  0  0  0  0
      2 11  1  0  0  0  0
      2 12  1  0  0  0  0
      4 13  1  0  0  0  0
      6 14  1  0  0  0  0
      8 15  1  0  0  0  0
    A  001
    C1c
    A  002
    C1b
    A  003
    C6a
    A  004
    O1a
    A  005
    C6a
    A  006
    O6a
    A  007
    O6a
    A  008
    O6a
    A  009
    O6a
    M  END