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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

From: Protein identification from two-dimensional gel electrophoresis analysis of Klebsiella pneumoniae by combined use of mass spectrometry data and raw genome sequences

Spot Noa Annotation and/or Homologue Proteins KPNb Knexus NCBInr PeptIdent Swiss-prot/ TrEMBL   Mascot NCBInr Scored   Mascot kpn Scored  
    Z(%) c Score d SC e (%) Score d SC e (%) Score d SC e (%)
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   
  1. aRefers to the proteins labelled in Figure 1 b 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.