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Table 2 Summary of selected SSH sequences

From: Use of suppression subtractive hybridisation to extend our knowledge of genome diversity in Campylobacter jejuni

SSH

Length (bp)

Best BLASTX match/comments [GenBank accession number]

%ID

Length (AA)

E-value

  

Best match with another genus

   

629-D8

1116

extracellular solute-binding protein, family 1/ABC transporter (Rhodopseudomonas palustris BisB5) [ABE40377]

38

234

3e-36

629-D9

>502

phosphodiesterase (Delftia acidovorans) [AAN52089]

42

107

7e-16

  

Best match with C. jejuni (<80% identity)

   

670-H5

116

Outer membrane lipoprotein MapA CJE1173 (C. jejuni RM1221) [AAW35499]

70

31

4e-4

670-2

365

conserved hypothetical protein CJE0262 (C. jejuni RM1221) [AAW34855]

76

75

2e-27

1967-D4

272

flagellar hook subunit protein (C. jejuni NCTC 11168) [CAB73715]

60

86

3e-18

1967-F11

369

Putative membrane protein CJE0032 (C. jejuni RM1221) [AAW34630]

56

107

6e-20

629-E2

1001

putative periplasmic protein (C. jejuni 81–176) [EAQ73077]

52

209

1e-36

961-E7

750

capsular polysaccharide biosynthesis protein CJE1602 (C. jejuni RM1221) [AAW36035]

29

240

3e-17

961-HG5

160

putative sugar transferase, capsule-related (C. jejuni 176.83) [CAI39731]

47

51

9e-6

961-D5

385

putative glycosyltransferase, LOS-related (C. jejuni ATCC 43446) [AAX33825]

52

126

4e-31

  

Metabolism using alternative terminal electron acceptors

   

1967-H9

382

anaerobic dimethyl sulfoxide reductase chain B, DmsB, Cju35 (C. jejuni 81–176) [ABF83738]

100

109

8e-62

1967-C2

310

probable pyridine nucleotide-disulfide oxidoreductase YkgC (C. jejuni 84-25) [EAQ95476]

100

102

1e-51

629-C10

1213

cytochrome C biogenesis protein, Cju05 (C. jejuni 81–176) [ABF61591]; gamma-glutamyl transpeptidase, Cju06 (C. jejuni 81–176) [ABF61592]

100 100

211 118

e-108 1e-92

  

Other SSH sequences used in the distribution analysis

   

1967-A5

364

serine protease, subtilase family (C. jejuni 81–176) [AEQ72903]

100

120

8e-32

961-A9

678

dTDP-glucose pyrophosphorylase (C. jejuni subsp. doylei 269.97) [EAU03120]

96

154

3e-74

670-D7

466

putative nickase, cpp17, plasmid pTet/pCC31 – related (C. jejuni HB93-13) [EAQ59637]

99

155

5e-77

  1. SSH sequences matching outside the genus Campylobacter, sharing less than 80% identity in BLASTX searches with Campylobacter proteins, or used in distribution analysis, were included in the table. A full list of SSH sequences is included in Additional file 1. %ID; % protein sequence identity
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BMC Genomics

ISSN: 1471-2164

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