Table 1.
List of genes identified as potentially being phase variable in N. gonorrhoeae – excluding the opa and pilC genes.
| XNG# † | TRACT ‡ | CANDIDACY * | FUNCTIONAL ROLE | GENE | ANNOTATED FUNCTION |
| XNG0023 | GGGGCGG - | L | Other | prolyl oligopeptidase family protein | |
| XNG0060 | C(G)6 - | S | Surface sugar biosynthesis | wbpC / pglI | putative LPS biosynthesis or pilin glycosylation protein |
| XNG0075 | (C)7 - | L | Hypothetical protein | hypothetical protein | |
| XNG0080 | (C)10 - | S | Hypothetical protein | pglH | pilin glycosylation protein |
| XNG0081 | A(C)7 - | S | Surface sugar biosynthesis | pglG | pilin glycosylation protein |
| XNG0112 | (A)6 p | S | Hypothetical protein | hypothetical protein | |
| XNG0115 | (C)4 - | L | Other | cvaA | putative colicin V secretion protein |
| XNG0158 | (C)5 degenerate | L | Hypothetical protein | hypothetical protein | |
| XNG0188 | AA(C)5 - | L | Other | potD-2 | spermidine/putrescine ABC transporter, |
| XNG0189 | (CAAACAC)4 - | K | Surface sugar biosynthesis | pglE | pilin glycosylation protein |
| XNG0245 | degenerate | S | Iron acquisition | lbpA | lactoferrin-binding protein A |
| XNG0388 | (G)7 + | S | R-M Systems | hsdS|| | type I restriction enzyme S protein |
| XNG0412 | (G)7 + | S | Hypothetical protein | hypothetical protein | |
| XNG0470 | (G)7 + | S | Hypothetical protein | hypothetical protein †† | |
| XNG0473 | (T)9 + | S | Hypothetical protein | hypothetical protein | |
| XNG0503a | (C)6A(C)9 + | S | Hypothetical protein | hypothetical protein | |
| XNG0508 | AACCGGCAAACA - | L / M | Hypothetical protein | hypothetical protein | |
| XNG0520 | (CCCAA)12 - | S | R-M Systems | type III restriction system methylase | |
| XNG0552 | (C)5 degenerate | L | Hypothetical protein | hypothetical protein | |
| XNG0608 | CCACACCC - | M | Other | nifS | aminotransferase |
| XNG0610 | (G)7 - | L | Other | lldD | L-lactate dehydrogenase |
| XNG0612 | (GCCA)37 - | S | R-M Systems | putative restriction system methylase | |
| XNG0644 | (A)9 - | L | R-M Systems | modification methylase NlaIV | |
| XNG0663 | CCCCTCC + | L | Hypothetical protein | hypothetical protein | |
| XNG0703 | (C)7 - | L | Other | dnaX | DNA polymerase III, subunits gamma and tau |
| XNG0714 | GGAAGG - | L | Other | mobA | molybdopterin-guanine dinucleotide biosynthesis |
| XNG0832 | (T)11C(G)6 p | K | Surface associated proteins | porA | outer membrane protein |
| XNG0887 | (AAGC)4 - | S | Hypothetical protein | hypothetical protein | |
| XNG0905 | (AAGC)3 + | S | Surface associated proteins | virG | AIDA related protein |
| XNG0954 | (C)7 - | L | Other | ppx | exopolyphosphatase |
| XNG0973 | (C)6 - | L | Hypothetical protein | hypothetical protein | |
| XNG0986 | (C)6 degenerate | S | Other | aspA | putative serotype-1-specific antigen |
| XNG1000 | (G)7 + | S | Hypothetical protein | hypothetical protein | |
| XNG1041 | piv-Nm1B inserted | S | Surface sugar biosynthesis | putative glycosyl transferase | |
| XNG1207a | (G)8 + | S | Hypothetical protein | hypothetical protein ** | |
| XNG1216 | GGCGGCCAA | K | Iron acquisition | hmbR | hemoglobin receptor |
| XNG1268 | (AT)5 - | L | Other | fixP | cytochrome c oxidase, subunit III |
| XNG1281 | G(A)7 - | S | Hypothetical protein | hypothetical protein | |
| XNG1341 | (CAAG)20 | S | Surface associated proteins | adhesin | |
| XNG1356 | CCCTGCACC p | M | Other | pntA | NAD(P) transhydrogenase alpha subunit |
| XNG1384 | TCCGCCC - | L | Other | amiC | N-acetylmuramoyl-L-alanine amidase |
| XNG1423 | TGTGGGGG - | S | Other | dca | competence-associated protein |
| XNG1460 | (C)7 - | L | Hypothetical protein | hypothetical protein | |
| XNG1511 | (G)8 + | S | Hypothetical protein | hypothetical protein | |
| XNG1563 | (AAGC)3 + | S | Surface associated proteins | vapA | virulence associated protein |
| XNG1577 | (G)8 + | S | Hypothetical protein | hypothetical protein ** | |
| XNG1589 | (C)4TCC - | L | Other | dinG | probable ATP-dependent helicase |
| XNG1644 | (G)11 - | K | Surface sugar biosynthesis | pgtA | pilin glycosylation protein |
| XNG1733 | (G)8 - | M | Hypothetical protein | hypothetical protein | |
| XNG1740 | (C)7 - | L | Other | rplK | 50S ribosomal protein L11 |
| XNG1788 | (G)8 + | M | Hypothetical protein | hypothetical protein ** | |
| XNG1834 | (C)8 - | M | Hypothetical protein | hypothetical protein | |
| XNG1856 | (TA)5 - | L | Hypothetical protein | hypothetical protein | |
| XNG1858 | (G)5 - | L | Surface associated proteins | mafA-3 | putative adhesin |
| XNG1868 | (C)7 + | L | Other | map | methionine aminopeptidase |
| XNG1934 | (A)9 p | S | Other | putative lipoprotein | |
| XNG1942/41 | (C)6 + | S | Other | putative hydrolase | |
| XNG1968 | (C)11 - | K | Surface sugar biosynthesis | lgtG | lipopolysaccharide glycosyl transferase |
| XNG1989 | (C)13 p | K | Iron acquisition | frpB / fetA | iron-regulated outer membrane protein |
| XNG2004 | (G)9 + | K | Iron acquisition | hpuA | hemoglobin-haptoglobin utilization protein |
| XNG2045 | (G)11 + | K | Surface sugar biosynthesis | lgtA | acto-N-neotetraose biosynthesis glycosyl transferase |
| XNG2047 | (G)14 + | K | Surface sugar biosynthesis | lgtC | LPS biosynthesis protein |
| XNG2048 | (G)14 - | K | Surface sugar biosynthesis | lgtD | LPS biosynthesis protein |
| XNG2061 | (TTCC)3 - | L | Other | plsX | fatty acid-phospholipid synthesis protein |
† CDS designation numbers come from our own annotation of the N. gonorrhoeae strain FA1090 genome sequence.
‡ The known or potential phase variable repeat tract from N. gonorrhoeae strain FA1090. The equivalent sequence is identified for genes without a repeat tract that are phase variable candidates from the meningococci. Following the sequence a - or + signifies if the CDS is in-frame or frame-shifted, respectively. Repeats in promoter or predicted promoter locations are indicated with a p. Degenerate indicates a gene with multiple frame-shifts or in-frame termination conditions.
* The predicted likelihood of phase variability. K indicates a known phase variable gene; S indicates a strong candidate for phase variation; M indicates a moderate candidate; L indicates a low candidate. See text for details of these thresholds.
†† XNG0470 is a homologue of XNG1014, and XNG1513 which have a (G)6 and are not frame-shifted.
** XNG1207a, XNG1577, and XNG1788 are homologues of each other.