Fig 5A: Output from the AACompIdent tool where a protein from an E. coli 2-D
gel has been correctly identified by matching its amino acid composition,
estimated pI and MW against database entries for E. coli. Protein amino acid
composition was determined according to Wilkins et al. (8). The correct
protein identity, malate dehydrogenase, was the top-ranked protein in the
three lists, and showed a large score difference between the top and second
ranked proteins in the third list (where pI and MW windows are applied), and
also in the first list. See text for more details about the significance of
score patterns for identification confidence. In the second list, where the
amino acid composition of the query protein was matched against all entries
in the Swiss-Prot database without considering protein pI and MW, malate
dehydrogenase from four different species was ranked in the top four
positions. This illustrates that protein amino acid composition is
well-conserved across species boundaries. Note that the AACompIdent output
has been shortened for this figure.
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SEARCH VALUES:
Constellation 2
Calibration protein: OVAL_CHICK ( P01012 )
Species searched: ECOLI
Name given to unknown protein: coli147
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SpotNb coli147
==============
pI: 5.70 Range: ( 5.20, 6.20)
Mw: 34894 Range: ( 27915, 41873)
The closest Swiss-Prot entries for the species ECOLI:
Rank Score Protein (pI Mw) Description
=================================================
1 5 MDH_ECOLI 5.61 32337 MALATE DEHYDROGENASE (EC 1.1.1.37).
2 30 YHDH_ECOLI 5.63 34724 HYPOTHETICAL 34.7 KD PROTEIN IN MREB
3 31 K6P2_ECOLI 5.75 32388 6-PHOSPHOFRUCTOKINASE ISOZYME 2
4 33 ALKH_ECOLI 5.57 22284 4-HYDROXY-2-OXOGLUTARATE ALDOLASE
5 35 YEIN_ECOLI 5.37 32910 HYPOTHETICAL 32.9 KD PROTEIN IN NFO
The closest Swiss-Prot entries:
Rank Score Protein (pI Mw) Description
=================================================
1 4 MDH_SALTY 6.02 32451 MALATE DEHYDROGENASE (EC 1.1.1.37).
2 5 MDH_ECOLI 5.61 32337 MALATE DEHYDROGENASE (EC 1.1.1.37).
3 12 MDH_HAEIN 5.86 32542 MALATE DEHYDROGENASE (EC 1.1.1.37).
4 12 MDHM_EUCGU 5.64 33326 MALATE DEHYDROGENASE.
5 13 PUR2_CHICK 7.51 106543 PHOSPHORIBOSYLAMINE--GLYCINE LIGASE
The Swiss-Prot entries having pI and Mw values in the specified range:
Rank Score Protein (pI Mw) Description
=================================================
1 5 MDH_ECOLI 5.61 32337 MALATE DEHYDROGENASE (EC 1.1.1.37).
2 30 YHDH_ECOLI 5.63 34724 HYPOTHETICAL 34.7 KD PROTEIN IN MREB
3 31 K6P2_ECOLI 5.75 32388 6-PHOSPHOFRUCTOKINASE ISOZYME 2
4 35 YEIN_ECOLI 5.37 32910 HYPOTHETICAL 32.9 KD PROTEIN IN NFO
5 36 SUCC_ECOLI 5.37 41392 SUCCINYL-COA SYNTHETASE BETA CHAIN
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Last modified 22/Jan/2003 by ELG
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