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


1 "Split" indicates a cluster separated by a long intergenic spacer, the two parts of the cluster generally coding for different functions.

2 Range of sequence similarity among the genes from each cluster compared to their BLAST top hits.

3 Representative species with similar gene order.

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 Only protein coding genes are included in the analysis.

Mira et al. BMC Evolutionary Biology 2004 4:50   doi:10.1186/1471-2148-4-50

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