Methodology Report

Vaxign: The First Web-Based Vaccine Design Program for Reverse Vaccinology and Applications for Vaccine Development

Table 4

Conserved UPEC outer membrane proteins predicted by Vaxign.

#Protein RefSeqSymbolAdhesinTMHNot in K-12Micro-arrayProte-omicsProtein Name

Iron ion binding and iron/siderophore transporter activity

1NP_752820.1ybiL0.8571Catecholate siderophore receptor fiu precursor (TonB-dependent receptor fiu) (Ferric iron uptake protein)
2NP_754328.1c24360.4730putative pesticin receptor precursor (tonB-dependent receptor)
3NP_754406.1c25180.830XTonB dependent receptor
4NP_752238c02940.830XTonB dependent receptor
5NP_753164.1iroN0.6720++Siderophore receptor iron
6NP_752600.1fepA0.7920+ferrienterobactin receptor (TonB-dependent receptor)
7NP_752135.1fhuA0.7460++ferrichrome outer membrane transporter
8NP_754374.1Hma (c2482)0.7720X++outer membrane heme acquisition protein
9NP_756170chuA0.8460X++Outer membrane heme/hemoglobin receptor
10NP_753551.1prrA0.5890XPutative TonB-dependent outer membrane receptor
11NP_753179c12650.7770XOuter membrane heme/ hemoglobin receptor
12NP_753125c12060.7940XOuter membrane heme/haemoglobin receptor
13NP_755646c37750.790Xputative iron compound receptor
14NP_753820.1yddB0.7650hypothetical protein c1924 (tonB-dependent receptor family)

Fimbrial biogenesis outer membrane usher protein

15NP_757244.1fimD0.7441+Outer membrane usher protein fimD precursor
16NP_757034papC_20.6741XPapC protein
17NP_755465papC0.6660XPapC protein
18NP_754524.1yehB00Outer membrane usher protein yehB precursor
19NP_752120.1htrE0.6430Putative outer membrane usher protein
20NP_753830.1c19340.8561Outer membrane usher protein fimD precursor
21NP_754765.1yfcU0.5630XFimbrial export usher family protein
22NP_753156.1focD0.8540F1C fimbrial usher
23NP_756076.1ycbS0.5591Outer membrane usher protein ycbS precursor
24NP_753159focH0.9170XF1C putative fimbrial adhesin precursor

Porin and ion transport

25NP_753469.1nmpC0.7881X+Outer membrane porin protein nmpC precursor
26NP_754644.1ompC0.6880+Outer membrane porin protein C
27NP_756858.1lamB0.8060+maltoporin
28NP_752996.1ompF0.6140+Outer membrane protein F (Porin family)
29NP_754240.1c23480.7590XOuter membrane porin protein nmpC precursor
30NP_752325.1phoE0.7290Outer membrane phosphoporin protein E
31NP_753724.1ompN0.7510Outer membrane protein N precursor
32NP_754275.1c23830.5970XOuter membrane protein N precursor
33NP_754771.1fadL0.8710+Long-chain fatty acid outer membrane transporter
34NP_756025.1hofQ0.1860+Outer membrane porin HofQ

Other transport proteins

35NP_756748.1c48940.810XNucleoside-specific channel-forming protein tsx precursor
36NP_756500.1c46420.6940Putative outer membrane Protein yieC
37NP_753669.1c17650.4370Partial putative outer membrane channel protein
38NP_752455.1tsx0.8330+Nucleoside-specific channel-forming protein tsx precursor

Lipoproteins

39NP_756849.1yjbH0.6510Lipoprotein yjbH precursor
40NP_755008.1yfiB0.5640Putative outer membrane lipoprotein
41NP_756936.1yjcP0.1850Putative outer membrane efflux protein MdtP
42NP_752589.1cusC0.5160Copper/silver efflux system outer membrane protein CusC
43NP_754925.1yfhM0.2240Lipoprotein yfhM precursor
44NP_756232.1yiaD0.5263+Putative outer membrane lipoprotein

Other outer membrane proteins

45NP_752286.1c03450.9871XShlA/HecA/FhaA exofamily protein
46NP_752352eaeH0.9041XPutative adhesin
47NP_753126c12070.7020XHypothetical protein
48NP_753493c15850.5260XPutative tail component of prophage
49NP_754912c30300.711XSinI-like protein
50NP_756286c44240.990XPutative adhesin
51NP_752116.1yadC0.811Putative fimbrial-like adhesin protein
52NP_752162.1yaeT0.6370++Outer membrane protein assembly factor YaeT
53NP_752163.1hlpA0.5870Periplasmic chaperone
54NP_752339.1yagX0.5710Hypothetical protein c0402
55NP_752642.1crcA0.7391Palmitoyl transferase for Lipid A
56NP_752830.1ompX0.8181++Outer membrane protein X
57NP_753262.1flgK0.840Flagellar hook-associated protein FlgK
58NP_753627.1ompW0.8480+Outer membrane protein W
59NP_753695.1ompG0.6180Outer membrane protein G precursor
60NP_754014.1ydiY0.7080Hypothetical protein c2120
61NP_754081.1yeaF0.8520++MltA-interacting protein precursor
62NP_754523.1yehA0.8470Hypothetical protein c2635
63NP_754661.1yfaL0.9490Adhesin
64NP_755530.1c36550.9620+Antigen 43 precursor
65NP_756601.1pldA0.7560Phospholipase A
66NP_754578.1cirA0.510Colicin I receptor
67NP_755652.2tolC00+Outer membrane channel protein
68NP_752583.1ompT00++Outer membrane protease
69NP_756783.1btuB00+Vitamin B12/cobalamin outer membrane transporter
70NP_754246.1fliF0.2132Flagellar MS-ring protein
71NP_755960.1yheF0.2390General secretion pathway protein D precursor
72NP_752585.1nfrA0.2980Bacteriophage N4 receptor, outer membrane subunit
73NP_753902.1uidC0.3041Putative outer membrane porin protein
74NP_754656.1c27700.3480Hypothetical protein c2770
75NP_757165.1ytfM0.40Hypothetical protein c5318
76NP_753730.1ydbH0.4011Hypothetical protein c1828
77NP_756204.1yhjL0.4080Cellulose synthase subunit BcsC
78NP_751977.1c00210.4181Hypothetical protein c0021
79NP_757166.1ytfN0.4261Hypothetical protein c5319
80NP_754559.2yohG0.4270+Multidrug resistance outer membrane protein MdtQ
81NP_756598.1c47390.430Hypothetical protein c4739
82NP_753585.1ychP0.4350Hypothetical protein c1680
83NP_754913.1c30310.4480SinH-like protein
84NP_752491.1ybaU0.4641Peptidyl-prolyl cis-trans isomerase (rotamase D)
85NP_755264.1c33890.2823XHypothetical protein

Note: The protein RefSeq numbers are from UPEC strain CFT073. All 85 proteins are conserved across total four UPEC genomes. This table also shows the adhesin probability, number of transmembrane helixes, and absence in nonpathogenic K-12 MG1655. TMH, transmembrane alpha helix prediction. Microarray, transcriptomic mRNA results ( + for up-regulation in vivo). Proteomics, protein expression results ( + for up-regulation in urine or in vivo).