Table 2

Compare cross-species identification using public protein databases with identification using the specific protein database ProtKpn for the identification of protein of dha regulon of Klebsiella pneumoniae
Spot Noa
 Annotation and/or Homologue Proteins
 KPNb
 Knexus
NCBInr
 PeptIdent
Swiss-prot/
TrEMBL
Mascot
NCBInr
Scored
Mascot
kpn
Scored



Z(%)c
 Scored
 SCe (%)
 Scored
 SCe (%)
 Scored
 SCe (%)
5
 Glycerol dehydrogenase (EC 1.1.1.6) (GLDH) P45511_GLDA_CITFR
 862
 n.i.
 n.i.
 -
 n.i.
 -
 121
 39
39

n.i.
 n.i.
 -
 n.i.
 -
 136
 34
97
 Dihydroxyacetone kinase (EC 2.7.1.29) sp| P45510| DAK_CITFR
 332
 n.i.
 0.19
 9.4
 n.i.
 -
 131
 31
42
 Dehydroxyacetone kinase II, subunit 1 (EC 2.7.1.121) P76015_YCGT_ECOLI
 863
 n.i.
 n.i.
 -
 n.i.
 -
 102
 42
114

n.i.
 n.i.
 -
 n.i.
 -
 89
 29
18
 Dihydroxyacetone kinase II, subunit 2 (EC 2.7.1.121) P76014_YCGS_ECOLI
 864
 n.i.
 n.i.
 -
 n.i.
 -
 152
 77
153

n.i.
 n.i.
 -
 n.i.
 -
 103
 60
33
 Glycerol dehydratase beta subunit (EC 4.2.1.30) tr| O08505 [Klebsiella pneumoniae]
 855
 91
 n.i.
 -
 n.i.
 -
 71
 46
62
 glycerol dehydratase small subunit (EC 4.2.1.30) tr| Q59475
 854
 98
 n.i.
 -
 94
 52
 96
 52
12
 1,3-propanediol dehydrogenase (EC 1.1.1.202) Q59477_DHAT_KLEPN
 858
 n.i
 0.31
 34.1
 94
 34
 105
 36
35

99
 0.35
 54.0
 182
 54
 175
 48
36

91
 0.18
 37.0
 75
 36
 63
 26
103

n.i.
 0.25
 31.8
 114
 38
 114
 38
107

99
 0.42
 35.9
 158
 41
 184
 41
6
 Hypothetical oxidoreductase yqhD (EC 1.1.-.-) Q46856_YQHD_ECOLI
 3405
 n.i.
 0.1916
 15.5
 n.i.
 -
 199
 40
40

n.i.
 n.i.
 -
 n.i.
 -
 130
 29
117

n.i.
 n.i.
 -
 n.i.
 -
 119
 37
129
 Putative glycerol dehydrogenasetr| Q8ZR27
 2195




74
 42
151
 orfY, unknown function gi| 940439| (U30903) [Klebsiella pneumoniae]
 857
 84
 n.i
 -
 81
 48

aRefers to the proteins labelled in Figure 1b Protein access numbers in the ProtKpn database cKnexus uses ProFound as search program. Profound calculates the probability that a candidate in a database search is the protein being analysed., A Z score is estimated as an indicator of the quality of the search result, when the search result is compared against an estimated random match population. Z score is the distance to the population mean in unit of standard deviation. It also corresponds to the percentile of the search in the random match population. d Using Peptident score is the number of peptides that match the theoretical peptides from a database entry divided by the total number of peptide masses specified for the search. Using Mascot score is -10*Log(P), where P is the probability that the observed match is a random event. If there is also a superscript number beside the score, it represents the position of this protein in the protein candidate list. Otherwise, it is the top one. eSC: Sequence coverage, defined as the ratio of the portion of protein sequence covered by matched peptides to the whole length of protein sequence.

Wang et al. Proteome Science 2003 1:6   doi:10.1186/1477-5956-1-6