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

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 No^a	Annotation and/or Homologue Proteins	KPN^b	Knexus NCBInr	PeptIdent Swiss-prot/ TrEMBL		Mascot NCBInr Score^d		Mascot kpn Score^d
			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

^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.

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