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Table 2 Clusters of 4 or more consecutive genes with a best match outside the Firmicutes5.

From: Evolutionary relationships of Fusobacterium nucleatum based on phylogenetic analysis and comparative genomics

# 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
  1. 1 "Split" indicates a cluster separated by a long intergenic spacer, the two parts of the cluster generally coding for different functions.
  2. 2 Range of sequence similarity among the genes from each cluster compared to their BLAST top hits.
  3. 3 Representative species with similar gene order.
  4. 4 An "orphan" gene is defined as an ORF with an unknown function and no BLAST similarity in the current database. Short orphans (<500 bp) are likely to be pseudogene remnants or other non-functional regions (Mira et al. 2002, Davies et al. 2004).
  5. 5 Only protein coding genes are included in the analysis.