TABLE 2.
Genes identified via SCOTS
| Class | Clone(s) | Gene and/or possible functiona | % Identity/ % similarityb | Spanc | Reference(s)d | GenBank accession no. |
|---|---|---|---|---|---|---|
| Secreted | H7 | ApxIVA var3 RTX toxin (A. pleuropneumoniae) | 33 | AAD01905 | ||
| Cell surface | B5 | Autotransporter adhesin, similar to Hsf in H. influenzae (A. pleuropneumoniae) | 29, 39, 41 | ZP_00204542 | ||
| E4 | flpD, fimbria-like protein (H. ducreyi); flp genes are essential for microcolony formation in H. ducreyi | 65/66 | 188 | 12, 31, 37 | NP_873737 | |
| B9 | Outer membrane protein similar to immunogenic protein PomA of P. multocida (A. pleuropneumoniae) | 13, 42 | E47068 | |||
| F4 | Outer membrane protein of unknown function (A. pleuropneumoniae) | ZP_00135264 | ||||
| Metabolism | A7 | guaA GMP synthase (A. pleuropneumoniae), linked to virulence in various organisms, including P. multocida | 12, 27, 32, 34 | ZP_00134556 | ||
| A8 | Diadenosine tetraphosphatase similar to ApaH in S. enterica serovar Typhimurium (A. pleuropneumoniae); linked to virulence in H. parasuis and serovar Typhimurium | 21, 24 | ZP_00134055 | |||
| A9 | fuc1, l-fucose isomerase (H. influenzae); in Bacteroides thetaiotaomicron, the l-fucose metabolic pathway is coordinated with the production of fucosylated glycans in enterocytes | 76/78 | 222 | 22, 25 | P44779 | |
| C2 | ptsB, sucrose-specific phosphotransferase EII component (P. multocida); linked to virulence in serovar Typhimurium, S. aureus, and H. influenzae | 83/85 | 216 | 28 | NP_246785 | |
| H3 | Sugar phosphate permease (A. pleuropneumoniae) | ZP_00135166 | ||||
| C7 | Oxygen-sensitive ribonucleoside-triphosphate reductase (A. pleuropneumoniae) | ZP_00134686 | ||||
| D2 | Thiol:disulfide interchange protein, similar to DsbA in H. influenzae (A. pleuropneumoniae); essential for virulence factor expression in P. aeruginosa | 17, 34 | ZP_00134426 | |||
| D3 | 3-Polyprenyl-4-hydroxybenzoate decarboxylase (A. pleuropneumoniae) | ZP_00134932 | ||||
| G6 | Ribosomal protein RpS19 (H. influenzae) | 100/100 | 90 | P44385 | ||
| E12 | Biotin-(acetyl-coenzyme A carboxylase) ligase (A. pleuropneumoniae) | ZP_00134488 | ||||
| F12 | Dethiobiotin synthetase (A. pleuropneumoniae) | ZP_00135280 | ||||
| F11 | NADH ubiquinone oxidoreductase subunit 5 (A. pleuropneumoniae) | 34 | ZP_00135039 | |||
| G8 | SAM-dependent methyltransferase (A. pleuropneumoniae) | 34 | ZP_00134291 | |||
| A4 | Uncharacterized conserved protein involved in oxidation of intracellular sulfur (A. pleuropneumoniae) | ZP_00133817 | ||||
| A11 | Transposase (A. pleuropneumoniae) | ZP_00134532 | ||||
| D1 | 3-Oxoacyl-(acyl-carrier protein) reductase (H. influenzae) | 78/82 | 238 | P43713 | ||
| D4 | Predicted GTPase (A. pleuropneumoniae) | ZP_00134954 | ||||
| G11 | ATPase (A. pleuropneumoniae) | ZP_00134371 | ||||
| E9 | Restriction-modification system (ALXA and HSDM, M . haemolytica); M. haemolytica AlxA activates leukotoxin transcription in E. coli | 81/81 | 156 | 20 | P95510 | |
| F8 | Molybdopterin biosynthesis protein (H. ducreyi) | 84/86 | 174 | 34 | AAP95073 | |
| H6 | Leucyl-tRNA synthetase (A. pleuropneumoniae) | ZP_00133841 | ||||
| F9 | Predicted hydrolase of alkaline phosphatase superfamily (A. pleuropneumoniae) | ZP_00134565 | ||||
| Regulatory | A3 | rpoB, RNA polymerase subunit (H. ducreyi) | 91/94 | 207 | AAP96608 | |
| B2 | Cell shape-determining protein, similar to MreC (A. pleuropneumoniae) | ZP_00134717 | ||||
| A10 | Signal recognition particle protein (H. influenzae) | 88/93 | 243 | P44518 | ||
| H5 | Molecular chaperone (A. pleuropneumoniae) | ZP_00134922 | ||||
| H4 | Putative transcriptional regulator (A. pleuropneumoniae) | ZP_00134590 | ||||
| Stress | C9 | tufA, elongation factor (EF) Tu (H. ducreyi); EF-Tu acts as a fibronectin binding protein in M. pneumoniae, linked to virulence in K. pneumoniae | 100/100 | 135 | 9, 40 | NP_872680 |
| Transport | A5 | apaA, putative ABC transporter, immunogenic (A. pleuropneumoniae) | 30 | AF109148 | ||
| H1 | dmsA, dimethyl sulfoxide reductase, catalytic subunit (A. pleuropneumoniae); deletion mutants are attenuated | 2 | AY138463 | |||
| C4 | hgbA, hemoglobin-binding protein (A. pleuropneumoniae); enables iron uptake from hemoglobin | 5, 38 | AAO33396 | |||
| G1 | Na+/H+ antiporter (A. pleuropneumoniae); essential for in vivo survival in S. agalactiae | 27 | ZP_00134319 | |||
| E1 | Predicted metal-binding protein (A. pleuropneumoniae) | ZP_00135073 | ||||
| E7 | Membrane components of Kef-type potassium transport systems (A. pleuropneumoniae) | ZP_00134994 | ||||
| F1 | Anaerobic C4-dicarboxylate transporter (A. pleuropneumoniae) | 34 | ZP_00134386 | |||
| F2 | tbpA, transferrin receptor; small subunit (A. pleuropneumoniae); upregulated and essential in vivo | 1 | CAA90896 | |||
| F5 | ATPase; cation transport (A. pleuropneumoniae) | ZP_00135075 | ||||
| G10 | Di- and tricarboxylate transporters (A. pleuropneumoniae) | ZP_00135062 | ||||
| Unknown | B8 | Hypothetical protein PA2218 (P. aeruginosa) | 76/83 | 162 | Q01609 | |
| G7, F7e | A. pleuropneumoniae; no homology to known genes |
a
Genes with highest similarity to SCOTS sequences, obtained from public databases, source organism in parentheses, genes names given where available. SAM, S-adenosylmethionine.
b
Identity/similarity percentages apply to amino acids.
c
Span means the number of nucleotides over which similarity was detected.
d
Publications reporting the isolation of identical or similar sequences.
e
Sequences have not been submitted as these are partial open reading frames only.