Table 2 Clusters of 4 or more consecutive genes with a best match outside the Firmicutes5.
# | Putative function | Observations1 | Sequence similarity2 | Genes | Sinteny3 |
|---|---|---|---|---|---|
1 | Transposase + 4 hypothetical proteins of similar sequence | Flanked by 3 short orphans4 One of proteins is a short ORF | 24–32 | FN1511 to FN1515 |  |
2 | KDO (LPS core synthesis) + endonuclease and DNA pol III | Includes a short orphan | 31–58 | FN1561 to FN1576 |  |
3 | Peptide ABC transporter | It includes two long (>1500 bp) hypothetical proteins | 30–56 | FN1650 to FN1656 |  |
4 | sysnthesis of LPS (O chain) + phosphatidylcholine synthesis | Split by a hypothetical protein and 3 short ORFs | 37–61 | FN1661 to FN1668 |  |
5 | carbohydrate trasnport-pot operon (periplasmic binding prot dependent transport) | Split by long spacer | 22–55 | FN1792 to FN1800 | Thermotoga maritima |
6 | periplasmic binding protein dependent cation (Mn2+, Zn2+) transport | posibly Co2+ Flanked by transposase and archaeal best-match ORF | 24–56 | FN1807 to FN1814 | Pseudomonas putida |
7 | DNA pol III gamma and tau subunits and TonB OM export system | Flanked by hypothetical orphans | 25–36 | FN1830 to FN1834 | Helicobacter pylori |
8 | Periplasmic amilase and ribose ABC trasnporter | Short orphan in the middle | 23–32 | FN1893 to FN1897 |  |
9 | LPS synthesis and/or decoration and outer membarne stabilization | Flanked by 3528 bp hypothet. protein with eukaryotic best-match followed by long spacer | 25–77 | FN1908 to FN1911 | Geobacter sulfurreducens |
10 | capsule biosynthesis | Includes 2 short ORFs (possible HIPA pseudogenes) | 23–46 | FN1997 to FN2003 | Bordetella bronchiseptica Yersinia pestis |
11 | Slow porin homologous to OmpA (Bacteroides) or Opr (Pseudomonas) | Split by a long spacer with some homology to membrane proteins. Includes 2 short ORF | 23–49 | FN2056 to FN2062 |  |
12 | Hypothetical exported 24-amino acid repeat protein | Includes 4 short ORFs (one of them with homology to subunit δ of DNA Polym. III) | 34–45 | FN2110 to FN2122 |  |
13 | 24 aa repeat protein like in cluster 23 | Protein match to Helycobacter hepaticus | 31–53 | FN0023 to FN0028 |  |
14 | Endonuclease + 3 genes implicated in porfirinic siderophore synthesis | Flanked by short orphan | 24–65 | FN0185 to FN0188 | Haemophilus influenzae |
15 | DNA helicase + peptide transporters | High gene order conservation in an archaeal species | 28–42 | FN0191 to FN0197 | Methanosarcina acetivorans |
16 | Sugar ABC transporter | Short spacers/overlapping genes | 31–48 | FN0217 to FN0220 | Escherichia coli |
17 | Large cluster of hemolysin/ hemagglutinin containing hemagglutinin FhaB | Largest bacterial protein. Some degraded hemolysin copies found throughout genome | 23–26 | FN0290 to FN0293 | Escherichia coli |
18 | ABC iron/haemin transporter with periplasmic binding protein | Flanked by long spacer | 27–47 | FN0300 to FN0303 | Methanosarcina acetivorans |
19 | Periplasmic binding protein dependent iron transport system | Physically linked to other iron transport genes of Gram positive and Archaeal match | 34–49 | FN0309 to FN0312 | Bordetella bronchiseptica |
20 | NA+/H+ antiporter + 3 genes of unknown function | Split by a tRNA gene. Includes 2 short orphans | 33–53 | FN0350 to FN0354 | Treponema denticola |
21 | Two clusters of genes implicated in drug efflux (detoxification) extrusion out of OM | Flanked by two orphans of 402 and 618 bp | 21–37 | FN0515 to FN0519 | Vibrio cholerae |
22 | Mixed functions cluster |  | 30–44 | FN0524 to FN0527 |  |
23 | LPS synthesis and/or decoration and outer membarne stabilization | Includes recA and recX proteins with best match to Caulobacter and Vibrio | 29–100 | FN0538 to FN0548 | Haemophilus ducreyi |
24 | Structural lipoprotein with release and mureine anchoring components | Flanked by short ORF | 30–46 | FN0579 to FN0582 | Helicobacter hepaticus |
25 | Membrane-related functions + Fe-S oxidoreductase | Includes a short hypothetical protein with biased codon use | 32–55 | FN0734 to FN0739 |  |
26 | Haemin uptake with periplasmic binding protein iron acquisition | Haemin genes tightly-linked, probable operon | 24–59 | FN0766 to FN0771 | Campylobacter jejuni |
27 | Biotin biosynthesis | Most spacers are short, possible cotranscription | 31–55 | FN0846 to FN0852 | Campylobacter jejuni |
28 | Hydrolase + protease + aromatic compound synthesis | Mixed function cluster | 30–47 | FN0869 to FN0873 |  |
29 | Iron ABC transporter | Flanked by a short orphan with biased codon usage | 45–71 | FN0879 to FN0882 | Treponema denticola |
30 | Membrane proteins | 1st and 2nd genes probably permeases | 22–37 | FN1030 to FN1033 | Photorhabdus luminescens |
31 | Lipase B componet of type II secretion system + 24 aa repeat protein+ bacterioferritin | All proteins of short length | 26–34 | FN1075 to FN1079 |  |
32 | KDO (cetodeoxyoctulonic acid biosynthetic operon) | KDO is a component of LPS core in Fusobacterium and many Gram negatives. | 31–100 | FN1221 to FN1224 |  |
33 | Eps synthesis + EpsF (secretion of proteins/large biomolecules) | Possible tandem duplication | 30–47 | FN1242 to FN1245 | Ralstonia solanacearum |
34 | LOS choline decoration + Ton B (biopolymer transport through Outer Membrane) | Includes a short ORF (a degraded copy of a biopolymer transporter) | 29–40 | FN1306 to FN1312 | Pseudomonas aeruginosa |
35 | ABC transporter system | Flanked by short orphan followed by a transposase | 30–69 | FN1346 to FN1355 | Treponema denticola |
36 | ABC amino acid transport system | liv G-M operon; biased and homogeneous codon usage | 50–62 | FN1428 to FN1431 | Bifidobacterium longum |