The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus

Abstract

Archaeoglobus fulgidus is the first sulphur-metabolizing organism to have its genome sequence determined. Its genome of 2,178,400 base pairs contains 2,436 open reading frames (ORFs). The information processing systems and the biosynthetic pathways for essential components (nucleotides, amino acids and cofactors) have extensive correlation with their counterparts in the archaeon Methanococcus jannaschii. The genomes of these two Archaea indicate dramatic differences in the way these organisms sense their environment, perform regulatory and transport functions, and gain energy. In contrast to M. jannaschii, A. fulgidus has fewer restriction-modification systems, and none of its genes appears to contain inteins. A quarter (651 ORFs) of the A. fulgidus genome encodes functionally uncharacterized yet conserved proteins, two-thirds of which are shared with M. jannaschii (428 ORFs). Another quarter of the genome encodes new proteins indicating substantial archaeal gene diversity.

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Nature © Macmillan Publishers Ltd 1998
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2 JULY 1998 101
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Acknowledgements. We thank D. McHugh, K. Stephens and J. D. Heath for initial subcloning,
purification and crystallization studies; R. Strong, K. Zhang and B. Scott for advice during the
crystallographic analysis; and the beamline staff at the Advanced Light Source (NLBL laboratories),
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NIH. K.E.F. was supported by an NIH training grant and the American Heart Associaiton. M.S.J. was
supported by an NSF fellowship and an NIH training grant.
Correspondence and requests for materials and coordinates should be addressed to B.L.S. (e-mail:
bstoddar@fred.fhcrc.org). Coordinates have been deposited in the Brookhaven Protein Data Bank
(accession nos lipp, 1a73, 1a74).
corrections
Emergence of symbiosis in
peptide self-replication
through a hypercyclic network
David H. Lee, Kay Severin, Yohei Yokobayashi
& M. Reza Ghadiri
Nature 390, 591–594 (1997)
..................................................................................................................................
Hypercycles are based on second-order (or higher) autocatalysis
and defined by two or more replicators that are connected by
another superimposed autocatalytic cycle. Our study describes a
mutualistic relationship between two replicators, each catalysing the
formation of the other, that are linked by a superimposed catalytic
cycle. Although the kinetic data suggest the intermediary of higher-
order species in the autocatalytic processes, the present system
should not be referred to as an example of a minimal hypercycle
in the absence of direct experimental evidence for the autocatalytic
cross-coupling between replicators.
M
The complete genome
sequence of the
hyperthermophilic,
sulphate-reducing archaeon
Archaeoglobus fulgidus
Hans-Peter Klenk, Rebecca A. Clayton, Jean-Francois Tomb,
Owen White, Karen E. Nelson, Karen A. Ketchum,
Robert J. Dodson, Michelle Gwinn, Erin K. Hickey,
Jeremy D. Peterson, Delwood L. Richardson,
Anthony R. Kerlavage, David E. Graham, Nikos C. Kyrpides,
Robert D. Fleischmann, John Quackenbush, Norman H. Lee,
Granger G. Sutton, Steven Gill, Ewen F. Kirkness,
Brian A. Dougherty, Keith McKenney, Mark D. Adams,
Brendan Loftus, Scott Peterson, Claudia I. Reich,
Leslie K. McNeil, Jonathan H. Badger, Anna Glodek,
Lixin Zhou, Ross Overbeek, Jeannine D. Gocayne,
Janice F. Weidman, Lisa McDonald, Teresa Utterback,
Matthew D. Cotton, Tracy Spriggs, Patricia Artiach,
Brian P. Kaine, Sean M. Sykes, Paul W. Sadow,
Kurt P. D’Andrea, Cheryl Bowman, Claire Fujii,
Stacey A. Garland, Tanya M. Mason, Gary J. Olsen,
Claire M. Fraser, Hamilton O. Smith, Carl R. Woese
& J. Craig Venter
Nature 390, 364–370 (1997)
..................................................................................................................................
The pathway for sulphate reduction is incorrect as published: in
Fig. 3 on page 367, adenylyl sulphate 3-phosphotransferase (cysC)is
not needed in the pathway as outlined, as adenylyl sulphate
reductase (aprAB) catalyses the first step in the reduction of adenylyl
sulphate. The correct sequence of reactions is: sulphate is first
activated to adenylyl sulphate, then reduced to sulphite and subse-
quently to sulphide. The enzymes catalysing these reactions are:
sulphate adenylyltransferase (sat), adenylylsulphate reductase
(aprAB), and sulphite reductase (dsrABD). We thank Jens-Dirk
Schwenn for bringing this error to our attention.
M

Nature © Macmillan Publishers Ltd 1997
The complete genome sequence of
the hyperthermophilic,
sulphate-reducing
archaeon Archaeoglobus fulgidus
Hans-Peter Klenk*, Rebecca A. Clayton*, Jean-Francois Tomb*, Owen White*, Karen E. Nelson*,
Karen A. Ketchum*, Robert J. Dodson*, Michelle Gwinn*, Erin K. Hickey*, Jeremy D. Peterson*,
Delwood L. Richardson*, Anthony R. Kerlavage*, David E. Graham
†
, Nikos C. Kyrpides
†
, Robert D. Fleischmann*,
John Quackenbush*, Norman H. Lee*, Granger G. Sutton*, Steven Gill*, Ewen F. Kirkness*, Brian A. Dougherty*,
Keith McKenney*, Mark D. Adams*, Brendan Loftus*, Scott Peterson*, Claudia I. Reich
†
, Leslie K. McNeil
†
,
Jonathan H. Badger
†
, Anna Glodek*, Lixin Zhou*, Ross Overbeek
‡
, Jeannine D. Gocayne*, Janice F. Weidman*,
Lisa McDonald*, Teresa Utterback*, Matthew D. Cotton*, Tracy Spriggs*, Patricia Artiach*, Brian P. Kaine
†
,
Sean M. Sykes*, Paul W. Sadow*, Kurt P. D’Andrea*, Cheryl Bowman*, Claire Fujii*, Stacey A. Garland*,
Tanya M. Mason*, Gary J. Olsen
†
, Claire M. Fraser*, Hamilton O. Smith*, Carl R. Woese
†
& J. Craig Venter*
* The Institute for Genomic Research (TIGR), Rockville, Maryland 20850, USA
†
Department of Microbiology, University of Illinois, Champaign-Urbana, Illinois 61801, USA
‡
Mathematics and Computer Science Division, Argonne National Laboratory, Illinois 60439, USA
........................................................................................................................................................................................................................................................
Archaeoglobus fulgidus is the first sulphur-metabolizing organism to have its genome sequence determined. Its
genome of 2,178,400 base pairs contains 2,436 open reading frames (ORFs). The information processing systems and
the biosynthetic pathways for essential components (nucleotides, amino acids and cofactors) have extensive
correlation with their counterparts in the archaeon Methanococcus jannaschii. The genomes of these two Archaea
indicate dramatic differences in the way these organisms sense their environment, perform regulatory and transport
functions, and gain energy. In contrast to M. jannaschii, A. fulgidus has fewer restriction–modification systems, and
none of its genes appears to contain inteins. A quarter (651 ORFs) of the A. fulgidus genome encodes functionally
uncharacterized yet conserved proteins, two-thirds of which are shared with M. jannaschii (428 ORFs). Another
quarter of the genome encodes new proteins indicating substantial archaeal gene diversity.
Biological sulphate reduction is part of the global sulphur cycle,
ubiquitous in the earth’s anaerobic environments, and is essential to
the basal workings of the biosphere. Growth by sulphate reduction
is restricted to relatively few groups of prokaryotes; all but one of
these are Eubacteria, the exception being the archaeal sulphate
reducers in the Archaeoglobales
1,2
. These organisms are unique in
that they are unrelated to other sulphate reducers, and because they
grow at extremely high temperatures
3
. The known Archaeoglobales
are strict anaerobes, most of which are hyperthermophilic marine
sulphate reducers found in hydrothermal environments
2,4
and in
subsurface oil fields
5
. High-temperature sulphate reduction by
Archaeoglobus species contributes to deep subsurface oil-well ‘sour-
ing’ by producing iron sulphide, which causes corrosion of iron and
steel in oil- and gas-processing systems
5
.
Archaeoglobus fulgidus VC-16 (refs 2, 4) is the type strain of the
Archaeoglobales. Cells are irregular spheres with a glycoprotein
envelope and monopolar flagella. Growth occurs between 60 and
95 8C, with optimum growth at 83 8C and a minimum division time
of 4 h. The organism grows organoheterotrophically using a variety
of carbon and energy sources, but can grow lithoautotrophically on
hydrogen, thiosulphate and carbon dioxide
6
. We sequenced the
genome of A. fulgidus strain VC-16 as an example of a sulphur-
metabolizing organism and to gain further insight into the Archaea
7,8
through genomic comparison with Methanococcus jannaschii
9
.
General features of the genome
The genome of A. fulgidus consists of a single, circular chromosome
of 2,178,400 base pairs (bp) with an average of 48.5% G+C content
(Fig. 1). There are three regions with low G+C content (,39%), two
rich in genes encoding enzymes for lipopolysaccharide (LPS)
biosynthesis, and two regions of high G+C content (.53%),
containing genes for large ribosomal RNAs, proteins involved in
haem biosynthesis (hemAB), and several transporters (Table 1).
Because the origins of replication in Archaea are not characterized,
we arbitrarily designated base pair one within a presumed non-
coding region upstream of one of three areas containing multiple
short repeat elements.
Open reading frames. Two independent coding analysis programs
and BLASTX
10
searches (see Methods) predicted 2,436 ORFs (Figs 1,
2, Tables 1, 2) covering 92.2% of the genome. The average size of the
A. fulgidus ORFs is 822 bp, similar to that of M. jannaschii (856 bp),
but smaller than that in the completely sequenced eubacterial
genomes (949 bp). All ORFs were searched against a non-redundant
protein database, resulting in 1,797 putative identifications that
were assigned biological roles within a classification system adapted
from ref. 11. Predicted start codons are 76% ATG, 22% GTG and 2%
TTG. Unlike M. jannaschii, where 18 inteins were found in coding
regions, no inteins were identified in A. fulgidus. Compared with M.
jannaschii, A. fulgidus contains a large number of gene duplications,
contributing to its larger genome size. The average protein relative
molecular mass (M
r
)inA. fulgidus is 29,753, ranging from 1,939
to 266,571, similar to that observed in other prokaryotes. The
isoelectric point (pI) of predicted proteins among sequenced
prokaryotes exhibits a bimodal distribution with peaks at pIs of
approximately 5.5 and 10.5. The exceptions to this are Mycoplasma
genitalium in which the distribution is skewed towards high pI
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articles
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1
100,000
200,000
300,000
400,000
500,000
600,000
700,000
800,000
900,000
1,000,000
1,100,000
1,200,000
1,300,000
1,400,000
1,500,000
1,600,000
1,700,000
1,800,000
1,900,000
2,000,000
2,100,000
Figure 1 Circular representation of the
A. fulgidus genome. The outer circle
shows predicted protein-coding regions
on the plus strand classified by function
according to the colour code in Fig. 2
(except for unknowns and hypotheticals,
which are in black). Second circle shows
predicted protein-coding regions on the
minus strand. Third and fourth circles
show IS elements (red) and other repeats
(green) on the plus and minus strand.
Fifth and sixth circles show tRNAs (blue),
rRNAs (red) and sRNAs (green) on the
plus and minus strand, respectively.
Table 1 Genome features
General
Chromosome size: 2,178,400 bp
Protein coding regions: 92.2%
Stable RNAs: 0.4%
...................................................................................................................................................................................................................................................................................................................................................................
Predicted protein coding sequences: 2,436 (1.1 per kb)
Identified by database match: 1,797
putative function assigned: 1,096
homologues of M. jannaschii ORFs: 916
conserved hypothetical proteins: 651
No database match: 639
Members of 242 paralogous families: 719
Members of 158 families with known functions: 475
...................................................................................................................................................................................................................................................................................................................................................................
Stable RNAs Coordinates
16S rRNA: 1,790,478–1,788,987
23S rRNA 1,788,751–1,785,820
5S rRNA: 81,144–81,021
7S RNA: 798,067–798,376
RNase P: 86,281–86,032
46 species of tRNA: no significant clusters
tRNAs with 15–62 bp introns: Asp
GUC
, Glu
UUC
, Leu
CAA
, Trp
CCA
, Tyr
GUA
...................................................................................................................................................................................................................................................................................................................................................................
Distinct G+C content regions Coordinates
HGC-1, .53% G+C 1,786,000–1,797,000
HGC-2, .53% G+C 2,158,000–2,159,000
LGC-1, ,39% G+C 281,000–284,000
LGC-2, ,39% G+C 544,000–550,000
LGC-3, ,39% G+C 1,175,000–1,177,000
...................................................................................................................................................................................................................................................................................................................................................................
Short, non-coding repeats Coordinates
SR-1A, CTTTCAATCCCATTTTGGTCTGATTTCAAC 147–4,213
SR-1B, CTTTCAATCCCATTTTGGTCTGATTTCAAC 398,368–401,590
SR-2, CTTTCAATCTCCATTTTCAGGGCCTCCCTTTCTTA 1,690,930–1,694,104
...................................................................................................................................................................................................................................................................................................................................................................
Long, coding repeats Length Copy number
LR-01 NADH-flavin oxidoreductase 1,886 bp 2 copies
LR-02 NifS, NifU + ORF 1,549 bp 2 copies
LR-03 ISA1214 putative transposase + ISORF2 1,214 bp 6 copies
LR-04 ISA1083 putative transposase + ISORF2 1,083 bp 3 copies
LR-05 type II secretion system protein 1,014 bp 4 copies
LR-06 ISA0963 putative transposase 963 bp 7 copies
LR-07 homologue of MJ0794 836 bp 3 copies
LR-08 conserved hypothetical protein 696 bp 2 copies
LR-09 conserved hypothetical protein 628 bp 2 copies
...................................................................................................................................................................................................................................................................................................................................................................

Nature © Macmillan Publishers Ltd 1997
(median, 9.8) and A. fulgidus where the skew is toward low pI
(median, 6.3).
Multigene families. In A. fulgidus 719 genes (30% of the total)
belong to 242 families with two or more members (Table 1). Of
these families, 157 contained genes with biological roles. Most of
these families contain genes assigned to the ‘energy metabolism’,
‘transport and binding proteins’, and ‘fatty acid and phospholipid
metabolism’ categories (Table 2). The superfamily of ATP-binding
subunits of ABC transporters is the largest, containing 40 members.
The importance of catabolic degradation and signal recognition
systems is reflected by the presence of two large superfamilies: acyl-
CoA ligases and signal-transducing histidine kinases. A. fulgidus
does not contain a homologue of the large 16-member family found
in M. jannaschii
9
.
Repetitive elements. Three regions of the A. fulgidus genome
contain short (,40 bp) direct repeats (Table 1). Two regions (SR-
1A and SR-1B) contain 48 and 60 copies, respectively, of an identical
30-bp repeat interspersed with unique sequences averaging 40 bp.
The third region (SR-2) contains 42 copies of a 37-bp repeat similar
in sequence to the SR-1 repeat and interspersed with unique
sequence averaging 41 bp. These repeated sequences are similar to
the short repeated sequences found in M. jannaschii.
Nine classes of long (.500 bp) repeated sequences with >95%
sequence identity were found (LR1-LR9; Table 1). LR-3 is a novel
element with 14-bp inverted repeats and two genes, one of which
has weak similarity to a transposase from Halobacterium salinarium.
One copy of LR-3 interrupts AF2090, a homologue of a large
M. jannaschii gene encoding a protein of unknown function. LR-4
and LR-6 encode putative transposases not identified in M. jan-
naschii that may represent IS elements. The remaining LR elements
are not similar to known IS elements.
Central intermediary and energy metabolism
Sulphur oxide reduction may be the dominant respiratory process
in anaerobic marine and freshwater environments, and is an
important aspect of the sulphur cycle in anaerobic ecosystems
12
.
In this pathway, sulphate (SO
2−
4
) is first activated to adenylylsulphate
(adenosine-59-phosphosulphate; APS), then reduced to sulphite
and subsequently to sulphide
1,13
(Fig. 3). The most important
enzyme in dissimilatory sulphate reduction, adenylylsulphate
reductase, reduces the activated sulphate to sulphite, releasing
AMP. In A. fulgidus, the APS reductase has a high degree of
similarity and identical physiological properties to APS reductases
in sulphate-reducing delta proteobacteria
14
. A desulphoviridin-type
sulphite reductase then adds six electrons to sulphite to produce
sulphide. As in the Eubacteria, three sulphite-reductase genes,
dsrABD, constitute an operon. The genes for adenylylsulphate
reductase and sulphate adenylyltransferase reside in a separate
operon. In A. fulgidus, sulphate can be replaced as an electron
acceptor by both thiosulphate (S
2
O
2−
3
) and sulphite (SO
2−
3
), but not
by elemental sulphur.
A. fulgidus VC-16 has been shown to use lactate, pyruvate,
methanol, ethanol, 1-propanol and formate as carbon and energy
sources
2
. Glucose has been described as a carbon source
1
, but neither
an uptake-transporter nor a catabolic pathway could be identified.
Although it has been reported that A. fulgidus is incapable of growth
on acetate
6
, multiple genes for acetyl-CoA synthetase (which con-
verts acetate to acetyl-CoA) were found. The organism may degrade
a variety of hydrocarbons and organic acids because of the presence
of 57 b-oxidation enzymes, at least one lipase, and a minimum of
five types of ferredoxin-dependent oxidoreductases (Fig. 3). The
predicted b-oxidation system is similar to those in Eubacteria and
mitochondria, and has not previously been described in the
Archaea. Escherichia coli requires both the fadD and fadL gene
products to import long-chain fatty acids across the cell envelope
into the cytosol
15
. A. fulgidus has 14 acyl-CoA ligases related to
FadD, but as expected given that it has no outer membrane, no
FadL. In E. coli, FadB has several metabolic functions, but in A.
fulgidus these functions seem to be distributed among separate
enzymes. For example, AF0435 encodes an orthologue of enoyl-
CoA hydratase and resembles the amino-terminal domain of FadB.
This gene is immediately upstream of a gene encoding an ortholo-
gue of 3-hydroxyacyl-CoA dehydrogenase that resembles the car-
boxy-terminal domain of FadB.
Acetyl-CoA is degraded by A. fulgidus through a C
1
-pathway, not
by the citric acid cycle or glyoxylate bypass
6,16,17
. This degradation is
catalysed through the carbon monoxide dehydrogenase (CODH)
pathway that consists of a five-subunit acetyl-CoA decarboxylase/
synthase complex (ACDS) and five enzymes that are typically
involved in methanogenesis
18
. In A. fulgidus, however, reverse
methanogenesis occurs, resulting in CO
2
production. All of the
enzymes and cofactors of methanogenesis from formylmethano-
furan to N
5
-methyltetrahydromethanopterin are used, but the
absence of methyl-CoM reductase eliminates the possibility of
methane production by conventional pathways. Production of
trace amounts of methane (,0.1 mmol ml
−1
)
19
is probably a result
of the reduction of N
5
-methyltetrahydromethanopterin to methane
and tetrahydromethanopterin by carbon monoxide (CO) dehydro-
genase.
A. fulgidus also contains genes suggesting it has a second CO
dehydrogenase system, homologous to that which enables
Rhodospirillum rubrum to grow without light using CO as its sole
energy source. Genes were detected for the nickel-containing CO
dehydrogenase (CooS), an iron–sulphur redox protein, and a
protein associated with the incorporation of nickel in CooS.
These represent elements of a system that could catalyse the
conversion of CO and H
2
O to CO
2
and H
2
.
In contrast to M. jannaschii, A. fulgidus contains genes representing
multiple catabolic pathways. Systems include CoA-SH-dependent
ferredoxin oxidoreductases specific for pyruvate, 2-ketoisovalerate,
2-ketoglutarate and indolepyruvate, as well as a 2-oxoacid with little
substrate specificity
20,21
. Four genes with similarity to the tungsten-
containing aldehyde ferredoxin oxidoreductase were also found
22
.
Biochemical pathways characteristic of eubacterial metabolism,
including the pentose-phosphate pathway, the Entner–Doudoroff
pathway, glycolysis and gluconeogenesis, are either completely
absent or only partly represented (Fig. 3). A. fulgidus does not
have typical eubacterial polysaccharide biosynthesis machinery, yet
it has been shown to produce a protein and carbohydrate-contain-
ing biofilm
23
. Nitrogen is obtained by importing inorganic mole-
cules or degrading amino acids (Fig. 3); neither a glutamate
dehydrogenase nor a relevant fix or nif gene is present.
The F
420
H
2
:quinone oxidoreductase complex
24
is recognized as
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366 NATURE
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Figure 2 Linear representation of the A. fulgidus genome illustrating the location
of each predicted protein-coding region, RNA gene, and repeat element in the
genome. Symbols for the transporters are as follows: AsO, arsenite; COH, sugar;
P
i
, phosphate; aa2, dipeptide; NH
+
4
, ammonium; a/o, arginine/lysine/ornithine; s/
p, spermidine/putrescine; glyc, glycerol; Cl
−
, chloride; Fe
2+
, iron(II); Fe
3+
, iron(III); I,
L, V, branched-chain amino acids; P, proline; pan, pantothenate; rib, ribose; lac,
lactate; Mg
2+
/Co
2+
, magnesium and cobalt; gln, glutamine; NO
3−
, nitrate; ox/for,
oxalate/formate; maln, malonic acid; Hg
2+
, mercury; phs, polysaccharide; SO
2−
4
,
sulphate; OCN
−
, cyanate; hex, hexuronate; phs, polysialic acid; K
+
, potassium
channel; H
+
/Na
+
, sodium/proton antiporter; Na
+
/Cl
−
, sodium- and chloride-
dependent transporter; P/G, osmoprotection protein; Cu
2+
, copper-transporting
ATPase; +?, cation-transporting ATPase; ?, ABC-transporter without known
function. Triplets associated with tRNAs represent the anticodon sequence.
Numbers associated with GES represent the number of membrane-spanning
domains (MSDs) according to Goldman, Engelman and Steiz scale as
determined by TopPred
39
. Genes whose identification is based on genes in
M. jannaschii are indicated by circles. Of the 236 proteins containing at least
one MSD,124 of these had two or more MSDs.
Q

Nature © Macmillan Publishers Ltd 1997
the main generator of proton-motive force. However, our analysis
indicates the presence of heterodisulphide reductase and several
molybdopterin-binding oxidoreductases, with polysulphide, nitrate,
dimethyl sulphoxide, and thiosulphate as potential substrates,
which might contribute to energizing the cell membrane. A. fulgidus
contains a large number of flavoproteins, iron–sulphur proteins
and iron-binding proteins that contribute to the general intra-
cellular flow of electrons (Fig. 3). Detoxification enzymes include a
peroxidase/catalase, an alkyl-hydroperoxide reductase, arsenate
reductase, and eight NADH oxidases, presumably catalysing the
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3
amt
nhe2
Na
+
H
+
hemUV
NH
4
+
3
feoB
trkAH
Fe
3+
Fe
2+
K
+
Na
+
H
+
napA
2
Mg
2+
corA
Cu
2+
cyanate
arsenite
NO
3
-
SO
4
2-
Pi
riboseglycerol
lactate
pantothenate
hexuronate polysialic acidoxalate
rbsAC
malate,
succinate,
malonic acid
glpF
lctPrfbABpanF
exuT
formate
oxlT
2 23
spermidine
putrescine
Ile, Leu, Val
Pro,
glycine-
betaine
di-peptides
Gln
Arg, Lys,
ornithine
Pro
potABCD
dppABCDF
proVWX
glnHP
cat
putP
4
3
2
pstABC
cysAT
nrtBC
arsB
cynX
mae1
Iron-sulfur proteins
Sulfate reduction
heterodisulfide, polysulfide,
nitrate, nitrite, and
thiosulfate reductases?
e-
e-
e-
e-
e-
e-
e-
e-
cytochromes
Quinone
Pool
e-
H+
H
+
F420H2
ATP
ADP, P
i
H
+
V
0
V
1
-ATPase
COO-H
+
COO-H
+
COO-H
+
ATP synthase
braCDEFG
copB
4
4
2
2
2
ENERGY PRODUCTION
Fatty Acid degradationSulfate reduction
dld
Lactate
Pyruvate
Acetyl-CoA
por
ABDG
lldD
Formate
CO2 +H2
pflD
Carbon monoxide dehydrogenase
Pathway
[CO]
CO2
cdh
CO2
CH
2
=H
4
MPT
CH
3
H
4
MPT
CH
4
?
Acetate
Ethanol
PEP
fadA
[3]
fadD
[9]
L,M /Fatty Acids
Acyl-CoA
Enoyl-CoA
3-hydroxyacyl-CoA
3-ketoacyl-CoA
fadE (acd)
[12]
fad
[5]
hbd
[10]
Acyl-CoA(-2)*
β-oxidation cycle
Dihdroxyacetone-P
glpK
Glycerol
glpA
3-P-Glycerate
2-P-Glycerate
eno
ppsA
acs
[6]
Suc-CoA
TCA
sucAB
Glutamate
gltB
Arginine
Urea
cycle
Ornithine
arginase
Aspartate
aspBC
acaB
[12]
Asparagine
Lysine
Threonine
Chorismate
Phenylalanine
Tryptophan
Branched chain amino acids
CH=H
4
MPT
CHO H
4
MPT
CHO MFR
Malate
Ox-acetate
mdhA
oadAB
BIOSYNTHETIC PATHWAYS DEGRADATIVE PATHWAYS
Heme/Cobalamin Biosynthesis pathway
UroporphyrinogenIII Precorrin2
Cobalamin
Siroheme
Glutamine
Pyrimidine Biosynthesis
HCO3-
Aspartate PRPP
2-oxoglutarate
korABDG
Ketoacids
vorABDG
Acetyl-CoA
Glutamate
aspB
[4]
aspC
ilvE
Valine
Leucine
Isoleucine
Aromatic
Amino Acids
iorAB
Biotin Biosynthesis
De novo
Purine Biosynthesis
Ribose-5-P PRPP Histidine
prsA
[2]
IMP Purines
(GTP)
?
Riboflavin
Folate Biosynthesis
Thiamine Biosynthesis
Thiamine diphosphate
3-P-adenylsulfate
Sulfate
Sulfide
Adenylsulfate
Sulfite
sat
aprAB
cysC
dsrABD
2-oxobutyrate
orAB
aliphatic
aromatic
aldehydes
aor
[4]
Serine Cysteine
Glycine
Proline
Entner-Doudoroff
G-6-P
G-3-P
Pentose shunt
Glucose
R-5-P
6-P-gluconate
UMP
?
CODH
CO
2
Rib1-5 P
Rubisco
?
CO
mcmA
Methylmalonyl-CoA*
Pyrimidines
Figure 3 An integrated view of metabolism and solute transport in A. fulgidus.
Biochemical pathways for energy production, biosynthesis of organic compounds,
and degradation of amino acids, aldehydes and acids are shown with the central
componentsofA. fulgidus metabolism,sulphate,lactate and acetyl-CoA highlighted.
Pathways or steps for which no enzymes were identified are represented by a red
arrow. A question mark is attached to pathways that could not be completely
elucidated. Macromolecular biosynthesis of RNA, DNA and ether lipids have
been omitted. Membrane-associated reactions that establish the proton-motive
force (PMF) and generate ATP (electron transport chain and V
1
V
0
-ATPase) are
linked to cytosolic pathways for energy production. The oxalate-formate
antiporters (oxlT ) may also contribute to the PMF by mediating electrogenic
anion exchange. Each gene product with a predicted function in ion or solute
transport is illustrated. Proteins are grouped by substrate specificity with
transporters for cations (green), anions (red), carbohydrates/organic alcohols/
acids (yellow), and amino acids/peptides/amines (blue) depicted. Ion-coupled
permeases are represented by ovals (mae1, exuT, panF, lctP, arsB, cynX,
napA/nhe2, amt, feoB, trkAH, cat and putP encode transporters for malate,
hexuronate, pantothenate, lactate, arsenite, cyanate, sodium, ammonium, iron
(II), potassium, arginine/lysine and proline, respectively). ATP-binding cassette
(ABC) transport systems are shown as composite figures of ovals, diamonds and
circles (proVWX, glnHPQ, dppABCDF, potABCD, braCDEFG, hemUV, nrtBC, cysAT,
pstABC, rbsAC,rfbAB correspond togene productsfor proline, glutamine,dipeptide,
spermidine/putrescine, branch-chain amino acids, iron (III), nitrate, sulphate,
phosphate, ribose and polysialic acid transport, respectively). All other porters
drawn as rectangles (glpF, glycerol uptake facilitator; copB, copper transporting
ATPase; corA, magnesium and cobalt transporter). Export and import of solutes is
designated by arrows. The number of paralogous genes encoding each protein is
indicated in brackets for cytoplasmic enzymes, or within the figure for transporters.
Abbreviations: acs, acetyl-CoA synthetase; aor, aldehyde ferredoxin oxidoreduc-
tase; aprAB, adenylylsulphate reductase; aspBC, aspartate aminotransferase; cdh,
acetyl-CoA decarbonylase/synthase complex; cysC, adenylylsulphate 3-phospho-
transferase; dld,
D-lactate dehydrogenase; dsrABD, sulphite reductase; eno,
enolase; fadA/acaB, 3-ketoacyl-CoA thiolase; fadD, long-chain-fatty-acid-CoA
ligase; fad, enoyl-CoA hydratase; fadE (acd), acyl-CoA dehydrogenase; glpA,
glycerol-3-phosphate dehydrogenase; glpK, glycerol kinase; gltB, glutamate
synthase; hbd, 3-hydroxyacyl-CoA dehydrogenase; ilvE, branched-chain amino-
acid aminotransferase; iorAB, indolepyruvate ferredoxin oxidoreductase; korABDG,
2-ketoglutarate ferredoxinoxidoreductase; lldD,
L-lactatedehydrogenase; mcmA,
methylmalonyl-CoA mutase; mdhA,
L-malate dehydrogenase; oadAB, oxaloacetate
decarboxylase; orAB, 2-oxoacid ferredoxin oxidoreductase; pflD, pyruvate
formate lysase 2; porABDG, pyruvate ferredoxin oxidoreductase; ppsA, phos-
phoenolpyruvate synthase; prsA, ribose-phosphate pyrophosphokinase; sucAB,
2-ketoglutarate dehydrogenase; sat, sulphate adenylyltransferase; TCA, tri-
carboxylic acid cycle; vorABDG, 2-ketoisovalerate ferredoxin oxidoreductase.

Nature © Macmillan Publishers Ltd 1997
four-electron reduction of molecular oxygen to water, with the
concurrent regeneration of NAD.
Transporters
A. fulgidus may synthesize several transporters for the import of
carbon-containing compounds, probably contributing to its ability
to switch from autotrophic to heterotrophic growth
5
. Both M.
jannaschii and A. fulgidus have branched-chain amino-acid ABC
transport systems and a transporter for the uptake of arginine and
lysine. A. fulgidus encodes proteins for dipeptide, spermidine/
putrescine, proline/glycine-betaine and glutamine uptake, as well
as transporters for sugars and acids, rather like the membrane
systems described in eubacterial heterotrophs. These compounds
provide the necessary substrates for numerous biosynthetic and
degradative pathways (Fig. 3).
Many A. fulgidus redox proteins are predicted to require iron.
Correspondingly, iron transporters have been identified for the
import of both oxidized (Fe
3+
) and reduced (Fe
2+
) forms of iron.
There are duplications in functional and regulatory genes in both
systems. The uptake of Fe
3+
may depend on haemin or a haemin-
like compound because A. fulgidus has orthologues to the eubac-
terial hem transport system proteins, HemU and HemV. A. fulgidus
may also use the regulatory protein Fur to modulate Fe
3+
transport;
this protein is not present in M. jannaschii. Fe
2+
uptake occurs
through a modified Feo system containing FeoB. This is the third
example of an isolated feoB gene: M. jannaschii and Helicobacter
pylori also appear to lack feoA, implying that FeoA is not essential
for iron transport in these organisms.
A complex suite of proteins regulates ionic homeostasis. Ten
distinct transporters facilitate the flux of the physiological ions K
+
,
Na
+
, NH
+
4
, Mg
2+
, Fe
2+
, Fe
3+
, NO
−
3
, SO
2−
4
and inorganic phosphate
(P
i
). Most of these transporters have homologues in M. jannaschii
and are therefore likely to be critical for nutrient acquisition during
autotrophic growth. A. fulgidus has additional ion transporters for
the elimination of toxic compounds including copper, cyanate and
arsenite. As in M. jannaschii, the A. fulgidus genome contains two
paralogous operons of cobalamin biosynthesis-cobalt transporters,
cbiMQO.
Sensory functions and regulation of gene expression
Consistent with its extensive energy-producing metabolism and
versatile system for carbon utilization, A. fulgidus has complex
sensory and regulatory networks. These networks contain over 55
proteins with presumed regulatory functions, including members
of the ArsR, AsnC and Sir2 families, as well as several iron-
dependent repressor proteins. There are at least 15 signal-transdu-
cing histidine kinases, but only nine response regulators; this
difference suggests there is a high degree of cross-talk between
kinases and regulators. Only four response regulators appear to be
in operons with histidine kinases, including those in the methyl-
directed chemotaxis system (Che), which lies adjacent to the
flagellar biosynthesis operon. Although rich in regulatory proteins,
A. fulgidus apparently lacks regulators for response to amino-acid
and carbon starvation as well as to DNA damage. Finally, A. fulgidus
contains a homologue of the mammalian mitochondrial benzo-
diazepine receptor, which functions as a sensor in signal-transduction
pathways
25
. These receptors have been previously identified only in
Proteobacteria and Cyanobacteria
25
.
Replication, repair and cell division
A. fulgidus possesses two family B DNA polymerases, both related to
the catalytic subunit of the eukaryal delta polymerase, as previously
observed in the Sulfolobales
26
. It also has a homologue of the
proofreading e subunit of E. coli Pol III, not previously observed
in the Archaea. The DNA repair system is more extensive than that
found in M. jannaschii, including a homologue of the eukaryal
Rad25, a 3-methyladenine DNA glycosylase, and exodeoxynuclease
III. As well as reverse gyrase, topoisomerase I (ref. 9), and topo-
isomerase VI (ref. 27), the genes for the first archaeal DNA gyrase
were identified.
A. fulgidus lacks a recognizable type II restriction-modification
system, but contains one type I system. In contrast, two type II and
three type I systems were identified in M. jannaschii. No homologue
of the M. jannaschii thermonuclease was identified.
The cell-division machinery is similar to that of M. jannaschii,
with orthologues of eubacterial fts and eukaryal cdc genes. However,
several cdc genes found in M. jannaschii, including homologues of
cdc23, cdc27, cdc47 and cdc54, appear to be absent in A. fulgidus.
Transcription and translation
A. fulgidus and M. jannaschii have transcriptional and translational
systems distinct from their eubacterial and eukaryal counterparts.
In both, the RNA polymerase contains the large universal subunits
and five smaller subunits found in both Archaea and eukaryotes.
Transcription initiation is a simplified version of the eukaryotic
mechanism
28,29
. However, A. fulgidus alone has a homologue of
eukaryotic TBP-interacting protein 49 not seen in M. jannaschii, but
apparently present in Sulfolobus solfactaricus.
Translation in A. fulgidus parallels M. jannaschii with a few
exceptions. The organism has only one rRNA operon with an Ala-
tRNA gene in the spacer and lacks a contiguous 5S rRNA gene.
Genes for 46 tRNAs were identified, five of which contain introns in
the anticodon region that are presumably removed by the intron
excision enzyme EndA. The gene for selenocysteine tRNA (SelC)
was not found, nor were the genes for SelA, SelB and SelD. With the
exception of Asp-tRNA
GTC
and Val-tRNA
CAC
, tRNA genes are not
linked in the A. fulgidus genome. The RNA component of the tRNA
maturation enzyme RNase P is present. Both A. fulgidus and M.
jannaschii appear to possess an enzyme that inserts the tRNA-
modified nucleoside archaeosine, but only A. fulgidus has the related
enzyme that inserts the modified base queuine.
Both A. fulgidus and M. jannaschii lack glutamine synthetase and
asparagine synthetase; the relevant tRNAs are presumably amino-
acylated with glutamic and aspartic acids, respectively. An enzymatic
in situ transamidation then converts the amino acid to its amide
form, as seen in other Archaea and in Gram-positive Eubacteria
30
.
Indeed, genes for the three subunits of the Glu-tRNA amidotrans-
ferase (gatABC) have been identified in A. fulgidus. The Lys
aminoacyl-tRNA synthetase in both organisms is a class I-type,
not a class II-type
31
. A. fulgidus possesses a normal tRNA synthetase
for both Cys and Ser, unlike M. jannaschii in which the former was
not identifiable and the latter was unusual
9
.
M. jannaschii has a single gene belonging to the TCP-1 chaper-
onin family, whereas A. fulgidus has two that encode subunits a and
b of the thermosome. Phylogenetic analysis of the archaeal TCP-1
family indicates that these A. fulgidus genes arose by a recent species-
specific gene duplication, as is the case for the two subunits of the
Thermoplasma acidophilum thermosome
32
and the Sulfolobus
shibatae rosettasome
33
. As in M. jannaschii, no dnaK gene was
identified.
Biosynthesis of essential components
Like most autotrophic microorganisms, A. fulgidus is able to
synthesize many essential compounds, including amino acids,
cofactors, carriers, purines and pyrimidines. Many of these biosyn-
thetic pathways show a high degree of conservation between A.
fulgidus and M. jannaschii. These two Archaea are similar in their
biosynthetic pathways for siroheme, cobalamin, molybdopterin,
riboflavin, thiamin and nictotinate, the role category with greatest
conservation between these two organisms being amino-acid bio-
synthesis. Of 78 A. fulgidus genes assigned to amino-acid bio-
synthetic pathways, at least 73 (94%) have homologues in M.
jannaschii. For both archaeal species, amino-acid biosynthetic
pathways resemble those of Bacillus subtilis more closely than
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those of E. coli. For example, in A. fulgidus and M. jannaschii,
tryptophan biosynthesis is accomplished by seven enzymes, TrpA,
B, C, D, E, F, G as in B. subtilis, rather than by five enzymes, TrpA, B,
C, D, E (including the bifunctional TrpC and TrpD) as found in E.
coli.
No biotin biosynthetic genes were identified, yet biotin can be
detected in A. fulgidus cell extracts
34
, and several genes encode a
biotin-binding consensus sequence. Similarly, A. fulgidus lacks the
genes for pyridoxine biosynthesis although pyridoxine can be found
in cell extracts (albeit at lower levels than seen in E. coli and several
Archaea
34
). No gene encoding ferrochelatase, the terminal enzyme
in haem biosynthesis, has been identified, although A. fulgidus is
known to use cytochromes
34
. These cofactors may be obtained by
mechanisms that we have not recognized. Although all of the
enzymes required for pyrimidine biosynthesis appear to be present,
three enzymes in the purine pathway (GAR transformylase, AICAR
formyltransferase and the ATPase subunit of AIR carboxylase) have
not been identified, presumably because they exist as new isoforms.
The Archaea share a unique cell membrane composed of ether
lipids containing a glycerophosphate backbone with a 2,3-sn
stereochemistry
35
for which there are multiple biosynthetic
pathways
36
. In the case of Halobacterium cutirubrum, the backbone is
apparently obtained by enantiomeric inversion of sn-glycerol-3-
phosphate; in Sulfolobus acidocaldarius and Methanobacterium
thermoautotrophicum, sn-glycerol-1-phosphate dehydrogenase builds
the backbone from dihydroxyacetonephosphate. An orthologue of
sn-glycerol-1-phosphate dehydrogenase has been identified in
A. fulgidus, suggesting that the latter pathway is present.
Conclusions
Although A. fulgidus has been studied since its discovery ten years
ago
1
, the completed genome sequence provides a wealth of new
information about how this unusual organism exploits its environ-
ment. For example, its ability to reduce sulphur oxides has been well
characterized, but genome sequence data demonstrate that A.
fulgidus has a great diversity of electron transport systems, some
of unknown specificity. Similarly, A. fulgidus has been characterized
as a scavenger with numerous potential carbon sources, and its gene
complement reveals the extent of this capability. A. fulgidus appears
to obtain carbon from fatty acids through b-oxidation, from
degradation of amino acids, aldehydes and organic acids, and
perhaps from CO.
A. fulgidus has extensive gene duplication in comparison with
other fully sequenced prokaryotes. For example, in the fatty acid
and phospholipid metabolism category, there are 10 copies of 3-
hydroxyacyl-CoA dehydrogenase, 12 copies of 3-ketoacyl-CoA
thiolase, and 12 of acyl-CoA dehydrogenase. The duplicated pro-
teins are not identical, and their presence suggests considerable
metabolic differentiation, particularly with respect to the pathways
for decomposing and recycling carbon by scavenging fatty acids.
Other categories show similar, albeit less dramatic, gene redun-
dancy. For example, there are six copies of acetyl-CoA synthetase
and four aldehyde ferredoxin oxidoreductases for fermentation, as
well as four copies of aspartate aminotransferase for amino-acid
biosynthesis. These observations, together with the large number of
paralogous gene families, suggest that gene duplication has been an
important evolutionary mechanism for increasing physiological
diversity in the Archaeoglobales.
A comparison of two archaeal genomes is inadequate to assess the
diversity of the entire domain. Given this caveat, it is nevertheless
possible to draw some preliminary conclusions from the compar-
ison of M. jannaschii and A. fulgidus. A comparison of the gene
content of these Archaea reveals that gene conservation varies
significantly between role categories, with genes involved in tran-
scription, translation and replication highly conserved; approxi-
mately 80% of the A. fulgidus genes in these categories have
homologues in M. jannaschii. Biosynthetic pathways are also
highly conserved, with approximately 80% of the A. fulgidus
biosynthetic genes having homologues in M. jannaschii. In contrast,
only 35% of the A. fulgidus central intermediary metabolism genes
have homologues, reflecting their minimal metabolic overlap.
Over half of the A. fulgidus ORFs (1,290) have no assigned
biological role. Of these, 639 have no database match. The remain-
ing 651, designated ‘conserved hypothetical proteins’, have sequence
similarity to hypothetical proteins in other organisms, two-thirds
with apparent homologues in M. jannaschii. These shared hypothe-
tical proteins will probably add to our understanding of the genetic
repertoire of the Archaea. Analysis of the A. fulgidus and other
archaeal and eubacterial genomes will provide the information
necessary to begin to define a core set of archaeal genes, as well as
to better understand prokaryotic diversity.
M
. .. .. .. . . .. .. .. .. . . .. .. .. .. .. . . .. .. .. .. .. . . .. .. .. .. .. . . .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. ..
Methods
Whole-genome random sequencing procedure. The type strain, A. fulgidus
VC-16, was grown from a culture derived from a single cell isolated by optical
tweezers
37
and provided by K. O. Stetter (University of Regensburg). Cloning,
sequencing and assembly were essentially as described previously for genomes
sequenced by TIGR
9,38–40
. One small-insert and one medium-insert plasmid
library were generated by random mechanical shearing of genomic DNA. One
large-insert lambda (l) library was generated by partial Tsp509I digestion and
ligation to l-DASHII/EcoRI vector (Stratagene). In the initial random sequen-
cing phase, 6.7-fold sequence coverage was achieved with 27,150 sequences
from plasmid clones (average read length 500 bases) and 1,850 sequences from
l-clones. Both plasmid and l-sequences were jointly assembled using TIGR
assembler
41
, resulting in 152 contigs separated by sequence gaps and five groups
of contigs separated by physical gaps. Sequences from both ends of 560 l-clones
served as a genome scaffold, verifying the orientation, order and integrity and
the contigs. Sequence gaps were closed by editing the ends of sequence traces
and/or primer walking on plasmid or l-clones clones spanning the respective
gap. Physical gaps were closed by combinatorial polymerase chain reaction
(PCR) followed by sequencing of the PCR product. At the end of gap closure, 90
regions representing 0.33% of the genome had only single-sequence coverage.
These regions were confirmed with terminator reactions to ensure a minimum
of 2-fold sequence coverage for the whole genome. The final genome sequence
is based on 29,642 sequences, with a 6.8-fold sequence coverage. The linkage
between the terminal sequences of 2,101 clones from the small-insert plasmid
library (average size 1,419 bp) and 8,726 clones from the medium-insert
plasmid library (average size 2,954 bp) supported the genome scaffold
formed by the l-clones (average size 16,381 bp), with 96.9% of the genome
covered by l-clones. The reported sequence differs in 20 positions from the
14,389 bp of DNA in a total of 11 previously published A. fulgidus genes.
ORF prediction and gene family identification. Coding regions (ORFs) were
identified using a combination strategy based on two programs. Initial sets of
ORFs were derived with GeneSmith (H.O.S., unpublished), a program that
evaluates ORF length, separation and overlap between ORFs, and with
CRITICA (J.H.B. & G.J.O., unpublished), a coding region identification tool
using comparative analysis. The two largely overlapping sets of ORFs were
merged into one joint set containing all members of both initial sets. ORFs were
searched against a non-redundant protein database using BLASTX
10
and those
shorter than 30 codons ‘coding’ for proteins without a database match were
eliminated. Frameshifts were detected and corrected where appropriate as
described previously
40
. Remaining frameshifts are considered authentic and
corresponding regions were annotated as ‘authentic frameshift’. In total, 527
hidden Markov models, based upon conserved protein families (PFAM version
2.0), were searched with HMMER to determine ORF membership in families
and superfamilies
42
. Families of paralogous genes were constructed as described
previously
40
. TopPred
43
was used to identify membrane-spanning domains in
proteins.
Received 9 September; accepted 4 November 1997.
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Archaeoglobus fulgidus. Appl. Environ. Microbiol. 63, 3158–3163 (1997).
24. Kunow, J., Linder, D., Stetter, K. O. & Thauer, R. K. F
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: quinone oxidoreductase from
Archaeoglobus fulgidus—characterization of a membrane-bound mutlisubunit complex containing
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Acknowledgements. We thank M. Heaney, J. Scott and R. Shirley for software and database support;
V. Sapiro, B. Vincent, J. Meehan and D. Maas for computer system support; B. Cameron and D. J. Doyle
for editorial assistance: and K. O. Stetter for providing A. fulgidus VC-16. This work was supported by the
US Department of Energy.
Correspondence and requests for materials should be addressed to J.C.V. (e-mail: gaf@tigr.org). The
annotated genome sequence and the gene family alignments are available on the World-Wide Web
at http://www.tigr.org/tdb/mdb/afdb/afdb.html. The sequence has been deposited in GenBank with
accession number AE000782.
articles
370 NATURE
|
VOL 390
|
27 NOVEMBER 1997

Nature © Macmillan Publishers Ltd 1997
199
I,L,V
179 180
176
27120212
Fe3+
238
199 48
Fe3+
199
101
39 209
180
Fe3+
55
212
I,L,V
119
I,L,V
89
239
68
+?
117
199
63
74
116 60118 180
81
198
10
48
?
51
114
48
111
24168
105
I,L,V
164 56
205
198 198
83
92
91
92121
K+
11
148
77
237 26
100
110
122
H+/Na+
109 108
93
138
224
148
108
111184
106
241 105 234
106
1392811960
5
104 85
140308660117 9
Cu2+
198
116
110190
ox/for
14924
180
103 102 128 235 186 236
115
50
12
47
I,L,V
87161934848
158
77
NO3-
81123
199
NO3- NO3-
153
242
159
29142828
99
220 76 71
82
198
40 40
240
136
242
120 123
217
glutamine
maln
199
37
75
50
43 114
207
137
200 54 215
28142140
Co2+ Co2+
95
131813452
94 85
107
93
10 7
180
23
9
Mg2+/Co2+
9 9 9
107138
223
224
16
226 6 98
I,L,V
199
I,L,V
199
9
SO4
I,L,V
82
8
I,L,V
Hg2+
78
180
199
SO4
I,L,V
147 216 216
K+ K+
241 68
H+/Na+
153
157
241
159
137
1 230 89 150
9
46
180
NO3-NO3-
134
rib
199
32
rib
17
rib
88 59 180
99
87 22 45 86 86
219
206 85 84 60 212
83
I,L,V
199
28
4660211
229
I,L,V
199 82
I,L,V I,L,V
238
102
68
81 81 48 48
129
P
58 44 44 242 242
phs
NH4+
233 232
6
glutamine
P/G
80
P/G
80
P/G
71 195154
199
P/G ?
7338122
199
phs
199 78 77 44 68
122
76 71 75
11
?
199 74 14
121
glutamine
98
28
34
?
199 36
?
199
68
239
240
73
141
66
241
242 177
72 180
178
121
172
235
209
71
48
70
69
238
209 199 61 203
241
pan
97
139
196 217
24
OCN-
126
125
96
126 3 126 3126
95
6
126 126 66 65
12
125126
64 169 63 239 197
67
Co2+
?
199
?
67
199
126
pan
195461804448239
198
6
58
P
58
Pi
13
199 62
?
133 119 96
6712667
92
hex
12
217159153127
Fe2+
103
14314497
124
213 170 151 151
rib
199
7 68
ox/for
239 180 239 238 206 187 61 146 60
pan
12
58
91
149127199
phs
143144199118
1470
1383
1170
853
633
311
199
73
TCT
209
223
88
10
68
34
209217
199
rib
72
161161
100158
54
74
118
GACCATCTT
GGGGAATAA
GGCCCCTGG
227238221158180209481976123422064651091624260113145145241179199
1112161172
239 59 206
183
P
194
58 56 55 40 19
205
219 54
H+/Na+
53
216
52
209 240 51
10
146
50
175
49 184 35
69 180
242
163 48
129
130 68 47 201 184
235
?
199 181 217 12
209
45
44 43 20 13
?
124 156 90
183
109
70
57 42 42 214
6
135
21
21 132150
AsO
227
177
178 224
Pi
2
Pi
9
58
41
Pi
phs
41
Pi
199
Pi
40 40 217
202
I,L,V
199
I,L,V
199
67
239
I,L,V I,L,V I,L,V Fe3+ Fe3+
199
67
Fe3+
39
132435465768239
217
Cl-
38 104 231
glyc
31
90
155 180
101
37
180 36
113
?
136
199 34
180
33
180 194 154 33
6 9 10
32
124
?
135209
241 206
6
180 53 31 30
7
51
14 29
68146155156
28
9
1
11
168 167
10
157
10
158
27
26 192
153159160162163671261641651662
11
130
48159153180
141167168169170
68
1711738417417417517649
6
14 25
6
25 171 173 23
7
17
22 21 20 19
s/p
18
s/p
18
s/p
177178
199
a/o
228 17
179
18018124
RNaseP
7S
5S
23S 16S
TGC
182
GTA
TTTTGT
TAC
GGACGT
GGTGCAGCC
CTC
CGGCGA
184185
TCG
CGC
TTCCCG
159153162165
TCCCAA
GTGTGA
18618768
GCG
TTGCAG
CATGAG
CCT
4
TAG
GTT
188
GTCCACGCT
CAT
CTG
189
GAT
13179198
Na+/Cl-?
94161
199
??
190240180192179193
heme
184200201
195
239182
166
196197
202
203112204204204206207205241
2109
180
208
199210210211212185240
Replication, repair, restriction/modification
Transport
Central intermediary metabolism
Cellular processes
Cell envelope
Biosynthesis of cofactors, prosthetic groups, carriers
213214215
Amino acid biosynthesis
Other categories
Co2+
199
Co2+
217
Transcription
218218199
?
219
Translation
220221222
223
Regulatory functions
224152225
Energy metabolism
Fatty acid/Phospholipid metabolism
133182
Purines, pyrimidines, nucleosides and nucleotides
226228
a/o
198241
Unknown
Conserved hypothetical
1 kb
199
aa2
199
aa2aa2aa2aa2?
229230231232233
NH4+
234
Fe+++
232
233
NH4+
IS605
12362235236180
9
237
1822373217189188
212 115240
4
5678196
131
132
208923821618010
94
RNaseP
7S
11121422715
5S
1615222515179
9
222
16S
23S
CCA
Fe2+
89
lac
?
2338
2339
2340 23412342
2343
23442345 2346
2347
2348
2349
2350 2351
2352
23532354 2355 2356
2357
2358 2359
2360
2361 2362 2363 2364
2365
2366
2367
2368 2369 2370 2371 2372
2373
2374
2375
2376 2377 2378
2379
2380
2381
2382 2383 2384 2385 2386 2387 2388 2389-N 2390 23922393
2394
2395
2396
2397 2398 2399 2400
2401
2402 2403 24042405 2406 2407 2408 2409 2410 2411 2412 2413 2414
2415
2416 2417 2418
2419
2420 2421 2422 2423
2424
2425 2426
2427
2428 2429 2430 2431 2432
2433
2434
2435
2436
23s rRNA
5s/16s rRNAs
tRNA
7S RNA
RNaseP
CAG
Paralogous gene family
DNA repeat
Insertion element
Transporter
GES region
LP-8A
Methanococcus homologue
Authentic frameshift
2389-C
2391
1898 1899
1900
1901
2005
2006
2007
2008
2110 2111 2112
22292230
2231
2232
1897
1902
1903
1904
1905
1906
1907
1908
1909
1910
1911
1912
1913
1914
1915
1916
1917
1918
1919 1920 1921 1922 1923
1924
1925
1926
1927 1928 1929 1930 1931 1932
1933
1934 1935 1936 1937 1938
1939
1940 1941 1942
1943
1944
1945
1946
1947
1948
1949
1950
1951
1952 1953 1954 1955 1956 1957
1958
1959 1960 1961 1962 1963 1965
1964
1966
1967
1968 1969 1970 1971 1972
1973
1974
1975
1976 19771978
1979
1980 1981
1982
1983
1984
1985 1986 1987 1988 1989 1990
1991
1992 1993
1994
1995 1996
1997
1998 1999
2000
2001
2002
2003 2004 2005
2009 2010 2011
2012
2013 2014 2015 2016
2017
2018 2019 2021
2020
2022
2023
2024 2025
2026
2027 2028 2029 2030
2031
2032 2033 2034
2035
2036 2037 2038
2039
2040 2041 2042 2043 2044
2045
2046 2048
2047
2049 2050
2051
2052
2053
2054
2055
2056 2057 2058
2059
2060 2061
2062
2063
2064
2065 20662067206820692070 2071 2072 2073 2074 2075 2076 2077
2078
2079 2080 2081 20822083 2084 2085
2086
2087
2088
2089 2090-N
2091
2092 2090-C 2093 20942095 2096
2097
2098 2099 2100
2101
2102 2103 2104
2105
2106
2107
2108 2109
2113 2114
2115
2117
2116
2118 2119 2120 2121 2122 2123 2124
2125
2126 2127 2128
2129
2130 2131 2132 2133 21342135 2136 2137
2138
2139
2140
2141
2142
21432144
2145
2146 2147 2148
2149
2150 2151 2152 2153 2154 2155
2156
21572158
2159
21602161 2162
2163
2164 2165
2166
2167 2168
2169
2170 2171 2172 2173 2174 2175 2176 2178
2177
2179
2180
2181 2182 2183 2184
2185
2186 2187 2188 2189
2190
2191 2192 21932194 2195 2196
2197
2198
2199
2200 2201 2202
2203
2204 2205 2206 2207 2208 2209 2210 2211 22122213 2214 2215 2216 2217 22182219 2220 2221 2222 2223 2224 2225 2226
2227
2228 2229
2233 2234 2235 2236 2237 2238 2239
2240
2241
2242
2243 2244 2245 2246 2247
2248
2249 2250
2251
2252 2253 2254 2255
2256
2257 2258 2259
2260
2261 22622263 2264
2265
2266
2267
2268
2269
2270 2271 2272 2273 2274 2275 2276
2277
2278
2279
2280 2281 2282 2283 2284 2285 2286
2287
2288
2289
2290 2291 2292
2293
2294 2295 2296
2297
2298 2299
2300
2301 2302
2303
2304 23052306
2307
2308 2309 2310 2311
2312
2313
2314
2315
2316
2317
2318
2319 2320 2321
2322
2323
2324
23252326 2327 2328
2329
2330
2331
2332
2333
2334 2335 2336 2337 2338
ISA1214-6
LR-5B
285000
380000
475000
570000
665000
760000
855000
950000
1140000
1425000
1520000
1615000
1710000
1805000
1995000
2090000
190000
1045000
1235000
1330000
1900000
95000 nt
1
99
100
101 102
214 215
312
421 422 423
519
520
521 522
634
745 746
747
854 855 856
953
954
955
1043 1044 1045
1171
1172
1173 1174
1278
1279
1280
1384 1386
1385
1387
1471
1587 1588
1695 1696 1697
1698
1699
1799
1800
1801
SR-1A
213
420
2 3 4 5 6 7 8
9
10 11 12 13 14 15 16 17 18 19 20 21
22
23 24 25 26 27 28 29 30 31 32 33
34
35 36
37
38
39
40 41
42
43
44
45 46 47 48 49 50
51
52
53
54 55 5657 58
59
60 61
62
63 64
65
66 67 68 69
70
71 72 73 74 75
76
77 78 79 80 81 82 83 85
84
86
87
88 89 90
91
92
93
94 95 96 97 98 99
103 104
105
106
107
108 109 110 111 112 113 114
115
116
117
118 119 120 121
122
123 124 125126
127
128 129
130
131 132 133
134
135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 152
151
153 154 155 156 157 158
159
160
161
162 163 164
165
166
167
168 169 170 171
172
173
174
175 176 177 178
179
180 181 182
183
184 185 186
187
188 189 190 191192 193 194195 196 197 198 199 200
201
202 203 204
205
206 207 208 209
210
211 212 213
216
217
218
219 220 221
222
223 224
225
226 227
228
229
230
231 232 233
234
235 236
237
238 239
240
241 242
243
244 245 246 247
248
249
250
251 252 253 254 255 256 257
258
259 260 261 262 264
263
265 266 267 268269 270 271 272 273 274 275 276 277 278 279 280281 282 283
284
285 286 287 288 289
290
291 292 293 294 295
296
297298
299
300 301 302
303
304 305 306 307 308 309
310
311
313 314
315
316
317
318 319 320 321
322
323 324 325 327
326
328 329 330
331
332 333
334
335 336 337 339
338
340 341
342
343 344 345 346 347 348
349
350 351 352 353
354
355 356 357
358
359
360
361 362
363
364 365 366 367 368 369 370 371
372
373 374 375 376 377 378 379 380 381 382
383
384 385
386
387 388
389
390
391
392
393
394 395 396 397 398
399
400 401 402 403
404
405
406
407
408
409 410 411
412
413
414
415
416
417 418
419
420
424
425 426 427
428
429 430 431
432
433 434 435 436 437 438 439 440 441
442
443 444
445
446
447
448
449
450 451
452
453 454 455 456 457
458
459
460
461
462
463 464
465
466 467
468
469
470
471 472 473 474 475
476
477 478
479
480 481 482 483 484
485
486 487
488
489 490 491 492
493
494 495 496 497 498 499 500
501
502
503
504 505
506
507 508
509
510 511 512 513
514
515 516 517 518 519
523
524
525 526
527
528 529 530 531 532
533
534 535 536
537
538 539 540
541
542 543 544 545 546 547 548 549
550
551 552 553
554
555556 557 558 559 560 561
562
563 564 565 566 567 568 569 570 571 572
573
574
575
576 577
578
579 580
581
582
583
584 585 586
587
588 589 590
591
592 593 594 595 596 597
598
599 600
601
602 603
604
605
606
607 608 609 610 611 612
613
614 615
616
617 618619 620 621 622 623
624
625
626
627 628
629
630
631
632 633
635
636
637 638
639
640
641
642 643644 645 646 647
648
649 650 651
652
653 654 655 656
657
658
659
660 661 662 663 664 665 666 667
668
669
670
671 672 673 674 675
676
677 678 679 680 681 682 683
684
685
686
687 688 689 690 691
692
693 695
694
696 697698
699
700 701
702
703 704 705 707
706
708
709
710 711
712
713 714
715
716
717
718 719 720
721
722
723
724
725
726
727
728
729
730
731
732 733
734
735 736 737 738
739
741
740
742 743 745744
748 749
750
751
752
753 754 755 756 757 758
759
760
761
762
763
764765766 767
768
769
770
771 772
773
774
775
776 777 778 779 780 781 782
783
784 785
786
787
788
789
790
791
792
793
794
795 796 797
798
799
800
802
801
803
804
805 806 808
807
809
810
811 812 813 814 815
816
817 818 819
820
821 822
823
824
825
826 827 828 829
830
831 832 833 834 836
835
837 838
839
840 841 842 843
844
845 846 847 848
849
850 852
851
853
857 858
859
860 861 862
863
864 865 866
867
868
869
870 871 872 873 874875 876 877 878 879 880
881
882
883
884 885 886 887
888
889
890
891 892 893 894 895 896 897 898 899 900 901
902
903
904
905
906
907 908 909 910
911
912 913 914
915
916 917
918
919 920 921 922 923 924 926
925
927 928
929
930
931
932 933
934
935
936
937 938 939 940 941
942
943 944
945
946 947
948
949 950
951
952 953
956
957 958
959
960
961
962
963
964 965 966 967 968 969 970 971 972 973 974 975 976 977
978
979
980
981
982
983
984
985
986
987 988 989 990 991 992 993 994
995
996 997 998
999
1000 1001 1002 1003 1004
1005
1006 1007 1008 1009 1010 1011
1012
1013
1014
1015
1016
1017
1018
1019 1020 1021 1022 1023 1024 1025 1026 1027 1028 1029 1030
1031
1032
1033
1034 1035 1036 1037
1038
1039
1040
1041 10421043
1046
1047
1048 1049 1050 1051
1052
1053 1054 1055 1056
1057
1058 1059 1060 1061
1062
1063 1064 1065 1066 10671068
1069
1070 1071 1072 1073
1074
1075
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1078
10791080
1081
10821083
1084
10851086
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1095 1096 1097 1098 1099 1100
1101
11021103 1104
1105
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1108 1109
1110
1111 1112
1113
1114
1115
11161117 1118 1119 1120 1121 1122 1123
1124
1125
1126
11271128
1129
11301131 1132
1133
1134 1135 1136
1137
1138 1139 1140 1141 1142 1143 1144 1145 1146 1147 1148 1149 1150
1151
1152
1153
1154 1155 1156 1157 1158
1159
116011611162 1163 1164
1165
1166 1167 1168 1169 1170
1175 1176 1177 1178 1179
1180
1181
1182
1183 1184
1185
1186 1187
1188
1189 1190 1191 1192 1193 1194 1195 1196 1197 1198
1199
1200 1201
1202
1203 1204 1205 1206
1207
1208 1209 1210 1211 1212 1213 1214 1215 1216
1217
1218
1219
1220 1221 1222
1223
1224 1225
1226
1227
1228
1229 1230
1231
1232
1233
1234
1235
1236 1237 1238 1239 1240 1241
1242
1243 1244 1245
1246
1247
1248
1249 1250 1251 1252 1253 1254 1255 1256 1257
1258
1259 1260 1261 1262 1263 1264 1265 1266 1267 1268 12691270
1271
1272
1273
1274
1275
1276 12771278
1282
1281
12831284 1285 1286 1287 1288
1289
1290 1291 1292
1293
1294 1295 1296 1297 1298 1299 1300
1301
130213031304 1305 1306 1307
1308
1309 1310 1311 1312 1313
1314
1315 1316 1317
1318
1319 1320 1321 1323
1322
1324 1325
1326
1327 1328
1329
1330
1331
1332
1333
1334 1336
1335
1337 1338 1339 1340 1341
1342
1343 1344 1345 1346
1347
1348
1349
1350 1351
1352
1353 1354 1355 1356 1357
1358
1359
1360
1361 1362
1363
1364 1365 1366 1367 1368
1369
1370
1371
1372
1373
1374
1375
1376
1377
1378
1379
1380
1381
13821383
1388 1389
1390
1391 1392
1393
1394
1395
1396 1397
1398
1399 1400
1401
1402 1403 14041405 1406 1407
1408
1409 1410 1411 1412
1413
1414
1415
1416
1417
1418 1419 1420 1421 1422 1423 1424
1425
1426
1427
1428 1429 14301431
1432
1433 1434 1435
1436
1437 1438
1439
1440
1441
1442 1443 1444
1445
1446
1447
1448 1449
1450
1451 1452 1453 1454 1455 1456 1457 1458 1459 1460 1461 1462
1463
1464 1465 1466 1467 1468
1469
1470
1472
1473
1474
1475
1476 14771478
1479
1480
1481
1482 1483
1484
1485 1486 1487 1488 1489 1490 1491 1492 1493 1494 1495
1496
1497
1498
1499 1500 1501 1502
1503
1504 1505 1506 1507 1508 1509 1510 1511
1512
1513 1514 1515
1516
1517 1518
1519
1520 1521 1522
1523
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1526 1527 1528 1529
1530
1531 1532
1533
153415351536 1537 1538 1539
1540
1541 1542 1543
1544
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1546
1547 15481549 1550
1551
1552 1553 1554 1555 1556 1557 1558 1559 1560 1561 1562 1563
1564
1565 1566 1567 1568
1569
1570 1571 1572 1573 1574 1575 157615771578 1579 1580 1581 1582 1583 1584 1585
1586
1589
1590
1591
1592
1593
1594
1595 1596 15971598 1599
1600
1601
1602
1603
1604
1605 1606
1607
1608 1609 1610
1611
1612 1613
1614
1615
1616
16171618
1619
1620
1621
1622
1623
1624 1625 16261627 1628 1629
1630
1631 1632 1633 1634 1635
1636
1637 1638 1639 1640 1641 1642 1643 1644
1645
1646
1647
1648 1649
1650
1651 1652
1653
1654 1655 1656
1657
1658 1659 1660 1661 16621663 1664 1665
1666
1667 1668 1669 1670 1671 1672 1673 1674 1675 1676
1677
1678 1679 1680
1681
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1684 1685 1686 1687 1688 1689
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1693 1694 1695
1700
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1703 1704 1705 1706 1707
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17131714 1715 1716 171717181719 1720 1721 1722 1723 1724 1725 1727
1726
1728 1729
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1731 1732 1734
1733
1735 1736
1737
1738
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1740
1741
1743
1742
1744 1745 1746
1747
1748 1749
1750
1751 1752
1753
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1756 1757 1758 1760
1759
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1762
1763 1764
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1766 1767 1768 1769
1770
1771 1772 1773 1774 1775 1776 1777 1778 1779 1780 1781
1782
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1785 1786
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1790 1791 17921793 1794 1795 1796 1797 1798
1802 1803 1804
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1806 180718081809 1810
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1812 1813 1814 1815
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1821 1822 1823
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1846 18471848 1849 1850
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1852 1853 1854 1855 1856 1857
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1859 1860 1861
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1865 1866
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1868 1869 1870
1871
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1876 1877
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1879 1880 1881 1882 1883 1885
1884
1886 1887 1888
1889
189018911892 1893 1894 1895 1896 1897
ISA1214-2
ISA1214-3
ISA1214-4ISA1214-5
LR-1A
LR-1B
LR-2A
LR-2B
LR-5A
LR-6A
LR-6B
LR-7A
LR-7B
LR-7C
LR-7D
LR-7E
LR-7F
LR-8A
LR-8B
LR-9A
LR-9B
LR-9C
SR-1B
SR-2

Nature © Macmillan Publishers Ltd 1997
AMINO ACID BIOSYNTHESIS
General
AF0906 hydantoin utilization protein A (hyuA) 27.4%
Aromatic amino acid family
AF0228 3-dehydroquinate dehydratase (aroD) 36.8%
AF1497 5-enolpyruvylshikimate 3-phosphate synthase (aroA) 41.5%
AF1603 anthranilate synthase component I (trpE) 43.7%
AF1604 anthranilate synthase component II (trpD) 43.8%
AF1602 anthranilate synthase component II (trpG) 50.0%
AF0227 chorismate mutase/prephenate dehydratase (pheA) 32.2%
AF0670 chorismate synthase (aroC) 55.3%
AF1601 phosphoribosyl anthranilate isomerase (trpF) 37.1%
AF2327 shikimate 5-dehydrogenase (aroE) 43.1%
AF0343 tryptophan repressor binding protein (wrbA) 46.6%
AF1599 tryptophan synthase, subunit alpha (trpA) 39.5%
AF1240 tryptophan synthase, subunit beta (trpB-1) 39.4%
AF1600 tryptophan synthase, subunit beta (trpB-2) 64.1%
Aspartate family
AF2112 5 -methyltetrahydropteroyltriglutamate-
homocysteine methyltransferase (metE) 28.1%
AF0882 asparaginase (asnA) 45.9%
AF1439 asparagine synthetase (asnB) 36.9%
AF2366 aspartate aminotransferase (aspB-1) 42.3%
AF2129 aspartate aminotransferase (aspB-2) 45.4%
AF1623 aspartate aminotransferase (aspB-3) 39.4%
AF0409 aspartate aminotransferase (aspB-4) 45.2%
AF1417 aspartate aminotransferase (aspC) 46.2%
AF0700 aspartate kinase (lysC) 49.1%
AF1422 aspartate racemase 48.0%
AF1506 aspartate-semialdehyde dehydrogenase (asd) 60.9%
AF0800 diaminopimelate decarboxylase (lysA) 45.6%
AF0747 diaminopimelate epimerase (dapF) 45.8%
AF0909 dihydrodipicolinate reductase (dapB) 48.6%
AF0910 dihydrodipicolinate synthase (dapA) 51.0%
AF0935 homoserine dehydrogenase (hom) 47.9%
AF0886 S-adenosylhomocysteinase hydrolase (ahcY-1) 31.7%
AF2000 S-adenosylhomocysteinase hydrolase (ahcY-2) 67.3%
AF0051 succinyl-diaminopimelate desuccinylase (dapE-1) 30.5%
AF0904 succinyl-diaminopimelate desuccinylase (dapE-2) 43.8%
AF0551 threonine synthase (thrC-1) 40.5%
AF1316 threonine synthase (thrC-2) 61.0%
Glutamate family
AF1280 acetylglutamate kinase (argB) 56.1%
AF2288 acetylglutamate kinase, putative 29.0%
AF0080 acetylornithine aminotransferase (argD-1) 48.3%
AF1815 acetylornithine aminotransferase (argD-2) 36.2%
AF0522 acetylornithine deacetylase (argE) 29.4%
AF0883 argininosuccinate lyase (argH) 42.2%
AF2252 argininosuccinate synthetase (argG) 62.0%
AF1147 glutamate N-acetyltransferase (argJ) 47.8%
AF0953 glutamate synthase (gltB) 57.9%
AF0949 glutamine synthetase (glnA) 43.3%
AF2071 N-acetyl-gamma-glutamyl-phosphate
reductase (argC) 53.3%
AF1255 ornithine carbamoyltransferase (argF) 51.7%
Pyruvate family
AF0957 2-isopropylmalate synthase (leuA-1) 53.5%
AF0219 2-isopropylmalate synthase (leuA-2) 53.9%
AF2199 3-isopropylmalate dehydratase, large subunit (leuC) 49.3%
AF0629 3-isopropylmalate dehydratase, small subunit (leuD-1) 56.4%
AF1761 3-isopropylmalate dehydratase, small subunit (leuD-2) 57.1%
AF0628 3-isopropylmalate dehydrogenase (leuB) 59.2%
AF1720 acetolactate synthase, large subunit (ilvB-1) 57.5%
AF1780 acetolactate synthase, large subunit (ilvB-2) 32.1%
AF2015 acetolactate synthase, large subunit (ilvB-3) 34.1%
AF2100 acetolactate synthase, large subunit (ilvB-4) 38.4%
AF1719 acetolactate synthase, small subunit (ilvN) 60.4%
AF1672 acetolactate synthase, small subunit, putative 29.7%
AF0933 branched-chain amino acid aminotransferase (ilvE) 59.0%
AF1014 dihydroxy-acid dehydratase (ilvD) 54.5%
AF1985 ketol-acid reductoisomerase (ilvC) 61.8%
Serine family
AF0813 phosphoglycerate dehydrogenase (serA) 48.8%
AF2138 phosphoserine phosphatase (serB) 50.7%
AF0273 sarcosine oxidase, subunit alpha (soxA) 31.1%
AF0274 sarcosine oxidase, subunit beta (soxB) 26.5%
AF0852 serine hydroxymethyltransferase (glyA) 56.1%
Histidine family
AF0590 ATP phosphoribosyltransferase (hisG) 31.6%
AF0212 histidinol dehydrogenase (hisD) 51.6%
AF2002 histidinol-phosphate aminotransferase (hisC-1) 39.8%
AF2024 histidinol-phosphate aminotransferase (hisC-2) 36.8%
AF0985 imidazoleglycerol-phosphate
dehydrogenase/histidinol-phosphatase (hisB) 42.2%
AF0819 imidazoleglycerol-phosphate synthase,
cyclase subunit (hisF) 67.0%
AF2265 imidazoleglycerol-phosphate synthase,
subunit H (hisH) 44.4%
AF0509 imidazoleglycerol-phosphate synthase,
subunit H, putative 43.2%
AF1950 phosphoribosyl-AMP cyclohydrolase/
phosphoribosyl-ATP pyrophosphohydrolase (hisIE) 59.6%
AF0713 phosphoribosylformimino-5-aminoimidazole
carboxamide ribotide isomerase (hisA-1) 37.5%
AF0986 phosphoribosylformimino-5-aminoimidazole
carboxamide ribotide isomerase (hisA-2) 42.2%
BIOSYNTHESIS OF COFACTORS, PROSTHETIC GROUPS, AND CARRIERS
General
AF1855 2,3-dihydroxybenzoate-AMP ligase (entE) 27.2%
AF1070 coenzyme F390 synthetase (ftsA-1) 30.3%
AF1671 coenzyme F390 synthetase (ftsA-2) 31.9%
AF2013 coenzyme F390 synthetase (ftsA-3) 30.4%
AF2151 isochorismatase (entB) 31.2%
Folic acid
AF1414 dihydropteroate synthase 40.8%
Heme and porphyrin
AF1648 bacteriochlorophyll synthase, 33 kDa subunit 27.9%
AF0464 bacteriochlorophyll synthase, 43 kDa subunit (chlP-1) 29.7%
AF1023 bacteriochlorophyll synthase, 43 kDa subunit (chlP-2) 31.2%
AF1637 bacteriochlorophyll synthase, 43 kDa subunit (chlP-3) 27.0%
AF0037 cobalamin (5’-phosphate) synthase (cobS-1) 33.9%
AF2323 cobalamin (5’-phosphate) synthase (cobS-2) 34.4%
AF0725 cobalamin biosynthesis precorrin methylase (cbiG) 30.7%
AF0727 cobalamin biosynthesis precorrin-2 methyltransferase
(cbiL) 31.5%
AF0726 cobalamin biosynthesis precorrin-3 methylase (cbiF) 49.2%
AF0724 cobalamin biosynthesis precorrin-3 methylase (cbiH) 49.0%
AF0722 cobalamin biosynthesis precorrin-6Y methylase (cbiE) 32.4%
AF0732 cobalamin biosynthesis precorrin-8W
decarboxylase (cbiT) 30.8%
AF1336 cobalamin biosynthesis protein (cbiB) 38.4%
AF0723 cobalamin biosynthesis protein (cbiD) 36.3%
AF0728 cobalamin biosynthesis protein (cbiM-1) 51.4%
AF1843 cobalamin biosynthesis protein (cbiM-2) 41.2%
AF0731 cobalt transport ATP-binding protein (cbiO-1) 47.2%
AF1841 cobalt transport ATP-binding protein (cbiO-2) 41.1%
AF0729 cobalt transport protein (cbiN) 56.0%
AF0730 cobalt transport protein (cbiQ-1) 32.6%
AF1842 cobalt transport protein (cbiQ-2) 30.3%
AF1338 cobyric acid synthase (cbiP) 44.5%
AF2229 cobyrinic acid a,c-diamide synthase (cbiA) 42.3%
AF1241 glutamate-1-semialdehyde aminotransferase (hemL) 54.3%
AF1975 glutamyl-tRNA reductase (hemA) 42.7%
AF1594 heme biosynthesis protein (nirH) 25.2%
AF1125 heme biosynthesis protein (nirJ-1) 38.7%
AF2009 heme biosynthesis protein (nirJ-2) 31.8%
AF1593 heme d1 biosynthesis protein (nirD) 29.4%
AF1311 oxygen-independent coproporphyrinogen III
oxidase, putative 27.1%
AF1242 porphobilinogen deaminase (hemC) 46.3%
AF1974 porphobilinogen synthase (hemB) 60.4%
AF1784 protoporphyrinogen oxidase (hemK) 33.5%
AF0422 uroporphyrin-III C-methyltransferase (cysG-1) 41.7%
AF1243 uroporphyrin-III C-methyltransferase (cysG-2) 52.5%
AF0116 uroporphyrinogen III synthase (hemD) 27.4%
Menaquinone and ubiquinone
AF2176 4-hydroxybenzoate octaprenyltransferase (ubiA) 41.6%
AF0404 4-hydroxybenzoate octaprenyltransferase, putative 30.6%
AF2413 coenzyme PQQ synthesis protein (pqqE) 30.5%
AF1191 dihydroxynaphthoic acid synthase (menB) 54.6%
AF1551 octaprenyl-diphosphate synthase (ispB) 33.2%
AF0140 ubiquinone/menaquinone biosynthesis
methyltransferase (ubiE) 31.0%
Molybdopterin
AF2006 molybdenum cofactor biosynthesis protein (moaA) 47.8%
AF0265 molybdenum cofactor biosynthesis protein (moaB) 44.4%
AF2150 molybdenum cofactor biosynthesis protein (moaC) 62.0%
AF0931 molybdenum cofactor biosynthesis protein (moeA-1) 50.8%
AF0930 molybdenum cofactor biosynthesis protein (moeA-2) 44.8%
AF0161 molybdenum cofactor biosynthesis protein (moeA-3) 30.5%
AF0531 molybdenum cofactor biosynthesis protein (moeB) 44.0%
AF1022 molybdenum-pterin-binding protein (mopB) 39.3%
AF1624 molybdopterin converting factor, subunit 1 (moaD) 36.6%
AF2179 molybdopterin converting factor, subunit 2 (moaE) 33.3%
AF2005 molybdopterin-guanine dinucleotide biosynthesis
protein A (mobA) 33.2%
AF2253 molybdopterin-guanine dinucleotide biosynthesis
protein B (mobB) 40.0%
Pantothenate
AF1645 pantothenate metabolism flavoprotein (dfp) 42.4%
Riboflavin
AF0484 GTP cyclohydrolase II (ribA-1) 44.5%
AF2107 GTP cyclohydrolase II (ribA-2) 47.1%
AF1416 riboflavin synthase (ribC) 53.3%
AF2128 riboflavin synthase, subunit beta (ribE) 75.9%
AF2007 riboflavin-specific deaminase (ribG) 43.7%
Thiamine
AF2075 hydroxyethylthiazole kinase (thiM) 33.6%
AF2208 hydroxymethylpyrimidine phosphate kinase (thiD) 35.5%
AF1695 thiamine biosynthesis protein (apbA) 36.9%
AF2412 thiamine biosynthesis protein (thiC) 60.2%
AF0553 thiamine biosynthesis protein (thiF) 38.1%
AF0088 thiamine biosynthesis protein, putative 28.2%
AF0702 thiamine biosynthetic enzyme (thi1) 50.0%
AF0733 thiamine monophosphate kinase (thiL) 30.4%
AF2074 thiamine phosphate pyrophosphorylase (thiE) 45.5%
Pyridine nucleotides
AF1000 NH(3)-dependent NAD+ synthetase (nadE) 52.0%
AF1839 nicotinate-nucleotide pyrophosphorylase (nadC) 43.2%
AF1837 quinolinate synthetase (nadA), authentic frameshift 53.9%
CELL ENVELOPE
Membranes, lipoproteins, and porins
AF1420 membrane protein 51.8%
AF1354 membrane protein, putative 32.8%
Surface polysaccharides, lipopolysaccharides and antigens
AF0324 dTDP-glucose 4,6-dehydratase (rfbB) 50.0%
AF0043 first mannosyl transferase (wbaZ-1) 30.0%
AF0606 first mannosyl transferase (wbaZ-2) 29.0%
AF1728 galactosyltransferase 26.9%
AF0044 GDP-D-mannose dehydratase (gmd-1),
authentic frameshift 40.7%
AF1142 glucose-1-phosphate cytidylyltransferase (rfbF) 38.6%
AF0242 glucose-1-phosphate thymidylyltransferase (graD-1) 27.7%
AF0325 glucose-1-phosphate thymidylyltransferase (graD-2) 45.2%
AF0321 glycosyl transferase 30.7%
AF0387 glycosyltransferase, putative 33.8%
AF0467 immunogenic protein (bcsp31-1) 34.7%
AF0635 immunogenic protein (bcsp31-2) 44.3%
AF0988 immunogenic protein (bcsp31-3) 28.3%
AF0602 LPS biosynthesis protein, putative 29.6%
AF0617 LPS biosynthesis protein, putative 29.0%
AF0607 LPS glycosyltransferase, putative 29.7%
AF0326 mannose-1-phosphate guanylyltransferase
(rfbM), authentic frameshift 42.4%
AF1097 mannose-6-phosphate isomerase/mannose-1-
phosphate guanylyl transferase (manC) 43.1%
AF0035 mannosephosphate isomerase, putative 31.3%
AF0045 mannosyltransferase A (mtfA) 38.7%
AF0311 O-antigen biosynthesis protein (rfbC), authentic
frameshift 30.6%
AF0458 phosphomannomutase (pmm) 39.5%
AF0595 polysaccharide biosynthesis protein, putative 24.1%
AF0322 rhamnosyl transferase (rfbQ) 27.5%
AF0323 spore coat polysaccharide biosynthesis protein
(spsK-2), authentic frameshift 36.3%
AF0620 succinoglycan biosynthesis protein (exoM) 24.8%
AF0361 UDP-glucose 4-epimerase (galE-1) 38.6%
AF2016 UDP-glucose 4-epimerase (galE-2) 30.0%
AF0302 UDP-glucose dehydrogenase (ugd-1) 43.8%
AF0596 UDP-glucose dehydrogenase (ugd-2) 44.1%
Surface structures
AF1054 flagellin (flaB1-1) 30.0%
AF1055 flagellin (flaB1-2) 31.1%
AF0275 surface layer protein B (slgB-1) 30.8%
AF1413 surface layer protein B (slgB-2) 29.9%
CELLULAR PROCESSES
General
AF1040 chemotaxis histidine kinase (cheA) 41.9%
AF1035 chemotaxis histidine kinase, putative 25.3%
AF1036 chemotaxis histidine kinase, putative 30.4%
AF1037 chemotaxis protein methyltransferase (cheR) 33.2%
AF1042 chemotaxis response regulator (cheY) 62.9%
AF1034 methyl-accepting chemotaxis protein (tlpC-1) 27.5%
AF1045 methyl-accepting chemotaxis protein (tlpC-2) 29.6%
AF1041 protein-glutamate methylesterase (cheB) 43.3%
AF1032 purine NTPase, putative 32.2%
AF1044 purine-binding chemotaxis protein (cheW) 40.4%
Cell division
AF0517 cell division control protein 21 (cdc21) 32.8%
AF1297 cell division control protein 48, AAA family (cdc48-1) 69.1%
AF2098 cell division control protein 48, AAA family (cdc48-2) 62.0%
AF0244 cell division control protein 6, putative 27.5%
AF1285 cell division control protein, AAA family, putative 49.3%
AF0696 cell division inhibitor (minD-1) 55.0%
AF1937 cell division inhibitor (minD-2) 32.8%
AF2051 cell division protein (ftsJ) 40.8%
AF0535 cell division protein (ftsZ-1) 60.4%
AF0570 cell division protein (ftsZ-2) 61.4%
AF0837 cell division protein pelota (pelA) 41.7%
AF1215 cell division protein, putative 32.8%
AF0238 centromere/microtubule-binding protein (cbf5) 58.8%
AF1558 chromosome segregation protein (smc1) 32.8%
AF1822 serine/threonine phosphatase (ppa) 31.9%
Chaperones
AF1296 small heat shock protein (hsp20-1) 52.3%
AF1971 small heat shock protein (hsp20-2) 38.1%
AF2238 thermosome, subunit alpha (thsA) 70.6%
AF1451 thermosome, subunit beta (thsB) 68.2%
Chromosome-associated protein
AF0337 archaeal histone A1 (hpyA1-1) 64.6%
AF1493 archaeal histone A1 (hpyA1-2) 69.7%
Detoxification
AF2173 2-nitropropane dioxygenase (ncd2) 39.7%
AF0270 alkyl hydroperoxide reductase 73.5%
AF1361 arsenate reductase (arsC) 30.5%
AF0550 N-ethylammeline chlorohydrolase (trzA-1) 45.9%
AF0997 N-ethylammeline chlorohydrolase (trzA-2) 44.5%
AF0254 NADH oxidase (noxA-1) 35.1%
AF0395 NADH oxidase (noxA-2) 35.5%
AF0400 NADH oxidase (noxA-3) 40.8%
AF0951 NADH oxidase (noxA-4) 36.7%
AF1858 NADH oxidase (noxA-5) 34.0%
AF0455 NADH oxidase (noxB-1) 43.3%
AF1262 NADH oxidase (noxB-2) 42.9%
AF0226 NADH oxidase (noxC) 38.4%
AF0515 NADH oxidase, putative 25.5%
AF2233 peroxidase / catalase (perA) 62.9%
Protein and peptide secretion
AF1902 protein translocase, subunit SEC61 alpha (secY) 50.0%
AF0536 protein translocase, subunit SEC61 gamma (secE) 25.0%
AF2062 signal recognition particle receptor (dpa) 54.8%
AF1258 signal recognition particle, subunit SRP19 (srp19) 36.6%
AF0622 signal recognition particle, subunit SRP54 (srp54) 51.2%
AF1791 signal sequence peptidase (sec11) 36.3%
AF1657 signal sequence peptidase (spc21) 47.0%
AF1655 signal sequence peptidase, putative 34.5%
AF0338 type II secretion system protein (gspE-1) 38.5%
AF0659 type II secretion system protein (gspE-2) 38.2%
AF0996 type II secretion system protein (gspE-3) 41.7%
AF1049 type II secretion system protein (gspE-4) 46.5%
CENTRAL INTERMEDIARY METABOLISM
Degradation of polysaccharides
AF1207 2-deoxy-D-gluconate 3-dehydrogenase (kduD) 45.3%
AF1795 endoglucanase (celM) 55.4%
Phosphorus compounds
AF0756 exopolyphosphatase (ppx1) 55.1%
Polyamine biosynthesis
AF0646 agmatinase (speB) 33.3%
AF2334 spermidine synthase (speE) 37.1%
Polysaccharides - (cytoplasmic)
AF0599 dolichol phosphate mannose synthase, putative 32.1%
Sulfur metabolism
AF0288 adenylylsulfate 3-phosphotransferase (cysC) 52.0%
AF1670 adenylylsulfate reductase, subunit A (aprA) 96.0%
AF1669 adenylylsulfate reductase, subunit B (aprB) 97.3%
AF1667 sulfate adenylyltransferase (sat) 28.4%
AF2228 sulfite reductase, desulfoviridin-type subunit
gamma (dsvC) 41.3%
AF0423 sulfite reductase, subunit alpha (dsrA) 100.0%
AF0424 sulfite reductase, subunit beta (dsrB) 100.0%
AF0425 sulfite reductase, subunit gamma (dsrD) 97.4%
Other
AF1706 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid
hydrolase (pcbD) 29.4%
AF0675 2-hydroxy-6-oxohepta-2,4-dienoate hydrolase (todF) 26.3%
AF0091 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase
(hpcE-1) 44.5%
AF2225 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase
(hpcE-2) 66.0%
AF0333 4-hydroxyphenylacetate-3-hydroxylase (hpaA-1) 22.4%
AF0885 4-hydroxyphenylacetate-3-hydroxylase (hpaA-2) 26.0%
AF1027 4-hydroxyphenylacetate-3-hydroxylase (hpaA-3) 21.0%
AF0669 4-oxalocrotonate tautomerase, putative 31.9%
AF0808 glycolate oxidase subunit (glcD) 32.0%
AF2216 methylmalonyl-CoA decarboxylase, biotin carboxyl
carrier subunit (mmdC) 36.2%
AF2217 methylmalonyl-CoA decarboxylase, subunit alpha
(mmdA) 62.5%
AF1288 methylmalonyl-CoA mutase, subunit alpha (mutB),
authentic frameshift 46.1%
AF2219 methylmalonyl-CoA mutase, subunit alpha,
C-terminus (mcmA2) 48.7%
AF2215 methylmalonyl-CoA mutase, subunit alpha,
N-terminus (mcmA1) 51.2%
AF2099 muconate cycloisomerase II (clcB) 24.9%
AF1425 phosphonopyruvate decarboxylase (bcpC-1) 35.0%
AF1751 phosphonopyruvate decarboxylase (bcpC-2) 48.6%
ENERGY METABOLISM
Amino acids and amines
AF1958 2-hydroxyglutaryl-CoA dehydratase, subunit alpha
(hgdA) 30.5%
Table 2 . List of
A. fulgidus
genes with putative identification. Gene numbers correspond to those in Fig. 2. Percentages
represent per cent identities.

Nature © Macmillan Publishers Ltd 1997
AF1957 2-hydroxyglutaryl-CoA dehydratase,
subunit beta (hgdB) 24.4%
AF0130 acetylpolyamine aminohydrolase (aphA) 38.7%
AF2290 acetylpolyamine aminohydrolase, putative 33.3%
AF0991 glutaryl-CoA dehydrogenase (gcdH) 48.7%
AF1323 group II decarboxylase 28.0%
AF2004 group II decarboxylase 46.1%
AF2295 group II decarboxylase 30.5%
AF1665 ornithine cyclodeaminase (arcB) 35.3%
Anaerobic
AF1145 4-hydroxybutyrate CoA transferase (cat2-1) 46.5%
AF1854 4-hydroxybutyrate CoA transferase (cat2-2) 47.5%
AF0866 glycerol kinase (glpK) 33.8%
AF1328 glycerol-3-phosphate dehydrogenase (glpA) 27.8%
AF0871 glycerol-3-phosphate dehydrogenase (NAD(P)+)
(gpsA) 36.3%
AF0020 L-carnitine dehydratase (caiB-1) 33.3%
AF0990 L-carnitine dehydratase (caiB-2) 31.2%
ATP-proton motive force interconversion
AF1158 ATP synthase, subunit E, putative 47.1%
AF1166 H+-transporting ATP synthase, subunit A (atpA) 67.0%
AF1167 H+-transporting ATP synthase, subunit B (atpB) 72.6%
AF1164 H+-transporting ATP synthase, subunit C (atpC) 37.5%
AF1168 H+-transporting ATP synthase, subunit D (atpD) 47.1%
AF1163 H+-transporting ATP synthase, subunit E (atpE) 36.3%
AF1165 H+-transporting ATP synthase, subunit F (atpF) 45.0%
AF1159 H+-transporting ATP synthase, subunit I (atpI) 30.1%
AF1160 H+-transporting ATP synthase, subunit K (atpK-1) 46.3%
AF1162 H+-transporting ATP synthase, subunit K (atpK-2) 46.3%
Electron transport
AF2036 cytochrome C oxidase folding protein (coxD) 33.3%
AF0144 cytochrome C oxidase, subunit II (cbaB) 34.2%
AF0142 cytochrome C oxidase, subunit II, putative 38.0%
AF0190 cytochrome C oxidase, subunit II, putative 31.7%
AF1057 cytochrome C-type biogenesis protein (ccdA) 30.7%
AF2192 cytochrome C-type biogenesis protein (nrfE) 36.1%
AF2296 cytochrome oxidase, subunit I (cydA-1) 22.9%
AF2297 cytochrome oxidase, subunit I (cydA-2) 31.5%
AF2046 cytochrome oxidase, subunit I, putative 25.1%
AF0528 cytochrome-c3 hydrogenase, subunit gamma 39.3%
AF0833 desulfoferrodoxin (dfx) 63.0%
AF0344 desulfoferrodoxin, putative 47.3%
AF0287 electron transfer flavoprotein, subunit alpha (etfA) 39.7%
AF0286 electron transfer flavoprotein, subunit beta (etfB) 38.8%
AF1380 F420-nonreducing hydrogenase (vhtA) 34.8%
AF1371 F420-nonreducing hydrogenase (vhtD-1) 30.9%
AF1378 F420-nonreducing hydrogenase (vhtD-2) 33.1%
AF1381 F420-nonreducing hydrogenase (vhtG) 46.1%
AF1824 F420H2:quinone oxidoreductase, 11.2 kDa subunit,
putative 24.1%
AF1823 F420H2:quinone oxidoreductase, 16.5 kDa subunit,
putative 25.7%
AF1832 F420H2:quinone oxidoreductase, 32 kDa subunit
(nuoI) 95.5%
AF1833 F420H2:quinone oxidoreductase, 39 kDa
subunit, putative 33.6%
AF1829 F420H2:quinone oxidoreductase, 39.7 kDa
subunit, putative 43.8%
AF1831 F420H2:quinone oxidoreductase, 41.2 kDa subunit,
putative 34.8%
AF1827 F420H2:quinone oxidoreductase, 43.2 kDa subunit,
putative 26.9%
AF1830 F420H2:quinone oxidoreductase, 45 kDa subunit
(nuoD) 80.0%
AF1825 F420H2:quinone oxidoreductase, 53.9 kDa subunit
(nuoM) 32.1%
AF1826 F420H2:quinone oxidoreductase, 72.4 kDa
subunit (nuoL) 33.2%
AF0156 ferredoxin (fdx-1) 45.3%
AF0166 ferredoxin (fdx-2) 49.2%
AF0355 ferredoxin (fdx-3) 53.2%
AF0427 ferredoxin (fdx-4) 56.1%
AF0923 ferredoxin (fdx-5) 56.9%
AF1010 ferredoxin (fdx-6) 44.4%
AF1239 ferredoxin (fdx-7) 29.0%
AF2142 ferredoxin (fdx-8) 38.0%
AF0164 ferredoxin-nitrite reductase (nirA) 29.7%
AF2332 flavodoxin, putative 30.3%
AF0167 flavoprotein (fprA-1) 33.2%
AF1520 flavoprotein (fprA-2) 47.2%
AF0557 flavoprotein reductase 26.2%
AF1463 fumarate reductase, flavoprotein subunit (fdrA) 27.0%
AF1536 glutaredoxin (grx-1) 34.3%
AF2145 glutaredoxin (grx-2) 38.8%
AF0663 heterodisulfide reductase, subunit A (hdrA-1) 42.2%
AF1377 heterodisulfide reductase, subunit A (hdrA-2) 46.8%
AF0662 heterodisulfide reductase, subunit A/
methylviologen reducing hydrogenase, subunit delta 34.2%
AF1238 heterodisulfide reductase, subunit A/methylviologen
reducing hydrogenase, subunit delta 53.7%
AF1375 heterodisulfide reductase, subunit B (hdrB) 36.0%
AF0271 heterodisulfide reductase, subunit B, putative 35.3%
AF1376 heterodisulfide reductase, subunit C (hdrC) 33.3%
AF0502 heterodisulfide reductase, subunit D, putative 33.8%
AF0809 heterodisulfide reductase, subunit D, putative 100.0%
AF0661 heterodisulfide reductase, subunit E, putative 23.8%
AF0755 heterodisulfide reductase, subunits E and D, putative 31.8%
AF0506 iron-sulfur binding reductase 38.5%
AF1773 iron-sulfur binding reductase 33.3%
AF1998 iron-sulfur binding reductase 29.6%
AF0627 iron-sulfur cluster binding protein 45.5%
AF0688 iron-sulfur cluster binding protein 44.8%
AF1153 iron-sulfur cluster binding protein 27.9%
AF1185 iron-sulfur cluster binding protein 36.7%
AF1263 iron-sulfur cluster binding protein 42.1%
AF2380 iron-sulfur cluster binding protein 35.3%
AF2381 iron-sulfur cluster binding protein 34.4%
AF2409 iron-sulfur cluster binding protein 28.2%
AF0076 iron-sulfur cluster binding protein 32.7%
AF1461 iron-sulfur cluster binding protein, putative 51.0%
AF1436 iron-sulfur flavoprotein (isf-1) 35.7%
AF1519 iron-sulfur flavoprotein (isf-2) 56.6%
AF1896 iron-sulfur flavoprotein (isf-3) 37.1%
AF1372 methylviologen-reducing hydrogenase,
subunit alpha (vhuA) 39.4%
AF1374 methylviologen-reducing hydrogenase,
subunit delta (vhuD) 41.7%
AF1373 methylviologen-reducing hydrogenase,
subunit gamma (vhuG) 38.6%
AF0157 molybdopterin oxidoreductase, iron-sulfur binding
subunit 38.6%
AF0174 molybdopterin oxidoreductase, membrane subunit 26.0%
AF0175 molybdopterin oxidoreductase, iron-sulfur binding
subunit 42.0%
AF0176 molybdopterin oxidoreductase, molybdopterin
binding subunit 32.6%
AF0499 molybdopterin oxidoreductase, iron-sulfur binding
subunit 41.5%
AF0500 molybdopterin oxidoreductase, membrane subunit 27.9%
AF1202 molybdopterin oxidoreductase, iron-sulfur
binding subunit 35.5%
AF1203 molybdopterin oxidoreductase, molybdopterin binding
subunit 30.1%
AF2384 molybdopterin oxidoreductase, molybdopterin binding
subunit 34.6%
AF2385 molybdopterin oxidoreductase, iron-sulfur binding
subunit 46.9%
AF2386 molybdopterin oxidoreductase, membrane subunit 30.3%
AF0159 molybdopterin oxidoreductase, molybdopterin
binding subunit, putative 30.9%
AF2267 NAD(P)H-flavin oxidoreductase 31.4%
AF0131 NAD(P)H-flavin oxidoreductase, putative 28.2%
AF2352 NADH dehydrogenase, subunit 1, putative 28.9%
AF1828 NADH dehydrogenase, subunit 3 24.3%
AF0248 NADH-dependent flavin oxidoreductase 36.7%
AF0342 nigerythrin, putative 33.3%
AF0546 nitrate reductase, gamma subunit (narI) 30.1%
AF0501 nitrate reductase, gamma subunit, putative 29.3%
AF1126 P450 cytochrome, putative 30.5%
AF0463 polyferredoxin (mvhB), authentic frameshift 32.2%
AF1379 quinone-reactive Ni/Fe-hydrogenase B-type
cytochrome subunit (hydC) 29.0%
AF0173 reductase, assembly protein 30.0%
AF0547 reductase, iron-sulfur binding subunit 28.3%
AF0867 reductase, putative 33.3%
AF0880 rubredoxin (rd-1) 69.2%
AF1349 rubredoxin (rd-2) 67.9%
AF0832 rubrerythrin (rr1) 45.7%
AF0831 rubrerythrin (rr2) 63.7%
AF1640 rubrerythrin (rr3) 37.8%
AF2312 rubrerythrin (rr4) 41.4%
AF0711 thioredoxin (trx-1) 28.4%
AF0769 thioredoxin (trx-2) 38.5%
AF1284 thioredoxin (trx-3) 52.9%
AF2144 thioredoxin (trx-4) 48.9%
AF1339 ubiquinol-cytochrome C reductase complex,
subunit VI requiring protein 60.9%
Fermentation
AF1779 2-hydroxyacid dehydrogenase, putative 37.6%
AF0469 2-ketoglutarate ferredoxin oxidoreductase,
subunit alpha (korA) 52.3%
AF0468 2-ketoglutarate ferredoxin oxidoreductase,
subunit beta (korB) 51.2%
AF0470 2-ketoglutarate ferredoxin oxidoreductase,
subunit delta (korD) 47.2%
AF0471 2-ketoglutarate ferredoxin oxidoreductase,
subunit gamma (korG) 40.0%
AF2053 2-ketoisovalerate ferredoxin oxidoreductase,
subunit alpha (vorA) 41.2%
AF2052 2-ketoisovalerate ferredoxin oxidoreductase,
subunit beta (vorB) 42.7%
AF2054 2-ketoisovalerate ferredoxin oxidoreductase,
subunit delta (vorD) 51.5%
AF2055 2-ketoisovalerate ferredoxin oxidoreductase,
subunit gamma (vorG) 45.2%
AF0749 2-oxoacid ferredoxin oxidoreductase,
subunit alpha (orA) 33.7%
AF0750 2-oxoacid ferredoxin oxidoreductase,
subunit beta (orB) 49.2%
AF1286 acetoin utilization protein, putative 35.1%
AF0197 acetyl-CoA synthetase (acs-1) 27.1%
AF0366 acetyl-CoA synthetase (acs-2) 47.3%
AF0677 acetyl-CoA synthetase (acs-3) 40.9%
AF0975 acetyl-CoA synthetase (acs-4) 42.3%
AF0976 acetyl-CoA synthetase (acs-5) 36.2%
AF1287 acetyl-CoA synthetase (acs-6) 34.3%
AF0024 alcohol dehydrogenase, iron-containing 36.2%
AF0339 alcohol dehydrogenase, iron-containing 37.4%
AF2019 alcohol dehydrogenase, iron-containing 35.7%
AF2389-C acetyl-CoA synthetase, putative 64.8%
AF2389-N acetyl-CoA synthetase, putative 59.3%
AF2101 alcohol dehydrogenase, zinc-dependent 34.8%
AF0023 aldehyde ferredoxin oxidoreductase (aor-1) 41.1%
AF0077 aldehyde ferredoxin oxidoreductase (aor-2) 32.6%
AF0340 aldehyde ferredoxin oxidoreductase (aor-3) 38.4%
AF2281 aldehyde ferredoxin oxidoreductase (aor-4) 53.0%
AF0006 corrinoid methyltransferase protein (mtaC-1) 30.7%
AF0011 corrinoid methyltransferase protein (mtaC-2) 29.5%
AF0394 D-lactate dehydrogenase, cytochrome-type (dld) 31.9%
AF0560 formate dehydrogenase (fdhD1), authentic frameshift 32.9%
AF1199 glutaconate CoA-transferase, subunit A (gctA) 31.9%
AF1198 glutaconate CoA-transferase, subunit B (gctB),
authentic frameshift 37.0%
AF1489 indolepyruvate ferredoxin oxidoreductase,
subunit alpha (iorA) 48.1%
AF2030 indolepyruvate ferredoxin oxidoreductase,
subunit beta (iorB) 41.1%
AF0807 L-lactate dehydrogenase, cytochrome-type (lldD) 39.4%
AF0855 L-malate dehydrogenase, NAD+-dependent (mdhA) 40.1%
AF2085 oxaloacetate decarboxylase, biotin carboxyl carrier
subunit, putative 38.7%
AF2084 oxaloacetate decarboxylase, sodium ion pump subunit
(oadB) 59.8%
AF1252 oxaloacetate decarboxylase, subunit alpha (oadA) 63.3%
AF1701 pyruvate ferredoxin oxidoreductase,
subunit alpha (porA) 50.3%
AF1702 pyruvate ferredoxin oxidoreductase,
subunit beta (porB) 50.7%
AF1700 pyruvate ferredoxin oxidoreductase, subunit delta
(porD) 53.1%
AF1699 pyruvate ferredoxin oxidoreductase, subunit gamma
(porG) 50.8%
Gluconeogenesis
AF0710 phosphoenolpyruvate synthase (ppsA) 61.4%
Glycolysis
AF1146 3-phosphoglycerate kinase (pgk) 48.8%
AF1132 enolase (eno) 53.9%
AF1732 glyceraldehyde 3-phosphate dehydrogenase (gap) 56.6%
AF1304 triosephosphate isomerase (tpiA) 56.4%
Pentose phosphate pathway
AF0943 ribose 5-phosphate isomerase (rpi) 48.9%
Sugars
AF0356 carbohydrate kinase, pfkB family 31.3%
AF0401 carbohydrate kinase, pfkB family 34.1%
AF1324 carbohydrate kinase, FGGY family 27.1%
AF1752 carbohydrate kinase, FGGY family 29.3%
AF0861 D-arabino 3-hexulose 6-phosphate formaldehyde
lyase (hps-1) 30.6%
AF1305 D-arabino 3-hexulose 6-phosphate
formaldehyde lyase (hps-2) 44.2%
AF0480 fuculose-1-phosphate aldolase (fucA) 31.8%
TCA cycle
AF1963 aconitase (acn) 57.1%
AF1340 citrate synthase (citZ) 50.3%
AF1098 fumarase (fum-1) 49.1%
AF1099 fumarase (fum-2) 53.4%
AF0647 isocitrate dehydrogenase, NADP (icd) 57.2%
AF1727 malate oxidoreductase (mae) 52.3%
AF0681 succinate dehydrogenase, flavoprotein subunit A
(sdhA) 48.2%
AF0682 succinate dehydrogenase, iron-sulfur subunit B (sdhB) 51.3%
AF0683 succinate dehydrogenase, subunit C (sdhC) 36.6%
AF0684 succinate dehydrogenase, subunit D (sdhD) 25.9%
AF1539 succinyl-CoA synthetase, alpha subunit (sucD-1) 56.9%
AF2185 succinyl-CoA synthetase, alpha subunit (sucD-2) 63.5%
AF1540 succinyl-CoA synthetase, beta subunit (sucC-1) 51.3%
AF2186 succinyl-CoA synthetase, beta subunit (sucC-2) 49.6%
FATTY ACID AND PHOSPHOLIPID METABOLISM
General
AF1736 3-hydroxy-3-methylglutaryl-coenzyme A reductase
(mvaA) 57.1%
AF0017 3-hydroxyacyl-CoA dehydrogenase (hbd-1) 41.1%
AF0285 3-hydroxyacyl-CoA dehydrogenase (hbd-2) 55.8%
AF0434 3-hydroxyacyl-CoA dehydrogenase (hbd-3) 40.7%
AF1025 3-hydroxyacyl-CoA dehydrogenase (hbd-4) 45.6%
AF1122 3-hydroxyacyl-CoA dehydrogenase (hbd-5) 45.2%
AF1177 3-hydroxyacyl-CoA dehydrogenase (hbd-6) 35.8%
AF1190 3-hydroxyacyl-CoA dehydrogenase (hbd-7) 46.5%
AF1206 3-hydroxyacyl-CoA dehydrogenase (hbd-8) 36.3%
AF2017 3-hydroxyacyl-CoA dehydrogenase (hbd-9) 35.4%
AF2273 3-hydroxyacyl-CoA dehydrogenase (hbd-10) 39.4%
AF0018 3-ketoacyl-CoA thiolase (acaB-1) 41.0%
AF0034 3-ketoacyl-CoA thiolase (acaB-2) 38.3%
AF0133 3-ketoacyl-CoA thiolase (acaB-3) 32.3%
AF0134 3-ketoacyl-CoA thiolase (acaB-4) 32.5%
AF0201 3-ketoacyl-CoA thiolase (acaB-5) 26.9%
AF0202 3-ketoacyl-CoA thiolase (acaB-6) 33.5%
AF0283 3-ketoacyl-CoA thiolase (acaB-7) 42.0%
AF0438 3-ketoacyl-CoA thiolase (acaB-8) 42.4%
AF0967 3-ketoacyl-CoA thiolase (acaB-9) 33.7%
AF0968 3-ketoacyl-CoA thiolase (acaB-10) 28.0%
AF1291 3-ketoacyl-CoA thiolase (acaB-11) 40.1%
AF2416 3-ketoacyl-CoA thiolase (acaB-12) 49.9%
AF1028 3-ketoacyl-CoA thiolase (fadA-1) 38.8%
AF1197 3-ketoacyl-CoA thiolase (fadA-2) 47.2%
AF2243 3-ketoacyl-CoA thiolase (fadA-3) 40.3%
AF0033 acyl carrier protein synthase (acaA-1) 28.6%
AF2415 acyl carrier protein synthase (acaA-2) 58.7%
AF0199 acyl-CoA dehydrogenase (acd-1) 35.9%
AF0436 acyl-CoA dehydrogenase (acd-2) 44.1%
AF0498 acyl-coA dehydrogenase (acd-3) 22.9%
AF0671 acyl-CoA dehydrogenase (acd-4) 37.9%
AF0845 acyl-CoA dehydrogenase (acd-5) 44.6%
AF0964 acyl-CoA dehydrogenase (acd-6) 35.8%
AF1026 acyl-CoA dehydrogenase (acd-7) 42.6%
AF1141 acyl-CoA dehydrogenase (acd-8) 43.2%
AF1293 acyl-CoA dehydrogenase (acd-9) 45.8%
AF2057 acyl-CoA dehydrogenase (acd-10) 44.6%
AF2244 acyl-CoA dehydrogenase (acd-11) 42.6%
AF2275 acyl-CoA dehydrogenase (acd-12) 38.9%
AF1175 acyl-CoA dehydrogenase, short chain-specific (acdS) 30.1%
AF0818 acylphosphatase (acyP) 36.8%
AF0868 alkyldihydroxyacetonephosphate synthase 33.6%
AF2286 bifunctional short chain isoprenyl diphosphate
synthase (idsA) 42.7%
AF0220 biotin carboxylase (acc) 59.1%
AF0865 carboxylesterase (est-1) 27.1%
AF1537 carboxylesterase (est-2) 29.0%
AF2336 carboxylesterase (est-3) 30.4%
AF1716 carboxylesterase (estA) 40.4%
AF1744 CDP-diacylglycerol—glycerol-3-phosphate 3-
phosphatidyltransferase (pgsA-2) 26.7%
AF1143 CDP-diacylglycerol—glycerol-3-phosphate-3-
phosphatidyltransferase (pgsA-1) 27.0%
AF2044 CDP-diacylglycerol—serine O-phosphatidyltransferase
(pssA) 36.6%
AF0435 enoyl-CoA hydratase (fad-1) 47.6%
AF0685 enoyl-CoA hydratase (fad-2) 39.9%
AF0963 enoyl-CoA hydratase (fad-3) 48.6%
AF1641 enoyl-CoA hydratase (fad-4) 41.7%
AF2429 enoyl-CoA hydratase (fad-5) 34.7%
AF1763 lipase, putative 33.5%
AF0089 long-chain-fatty-acid—CoA ligase (fadD-1) 31.9%
AF0200 long-chain-fatty-acid—CoA ligase (fadD-2) 34.8%
AF0687 long-chain-fatty-acid—CoA ligase (fadD-3) 31.1%
AF0840 long-chain-fatty-acid—CoA ligase (fadD-4) 38.1%
AF1029 long-chain-fatty-acid—CoA ligase (fadD-5) 37.8%
AF1510 long-chain-fatty-acid—CoA ligase (fadD-6) 36.0%
AF1772 long-chain-fatty-acid—CoA ligase (fadD-7) 38.7%
AF1932 long-chain-fatty-acid—CoA ligase (fadD-8) 31.0%
AF2368 long-chain-fatty-acid—CoA ligase (fadD-9) 38.7%
AF1753 lysophospholipase 33.5%
AF0196 medium-chain acyl-CoA ligase (alkK-1) 34.6%
AF0262 medium-chain acyl-CoA ligase (alkK-2) 38.6%
AF0672 medium-chain acyl-CoA ligase (alkK-3) 31.0%
AF1261 medium-chain acyl-CoA ligase (alkK-4) 42.7%
AF2033 medium-chain acyl-CoA ligase (alkK-5) 33.5%
AF2289 mevalonate kinase (mvk) 40.6%
AF1794 myo-inositol-1-phosphate synthase (ino1) 32.2%
AF2045 phosphatidylserine decarboxylase (psd2) 42.5%
AF1674 sn-glycerol-1-phosphate dehydrogenase (gldA) 44.0%
AUTOTROPHIC METABOLISM
General
AF1100 acetyl-CoA decarbonylase/synthase, subunit alpha
(cdhA-1) 50.4%
AF2397 acetyl-CoA decarbonylase/synthase, subunit alpha
(cdhA-2) 54.0%
AF0379 acetyl-CoA decarbonylase/synthase, subunit beta
(cdhC) 62.7%
AF0377 acetyl-CoA decarbonylase/synthase, subunit delta
(cdhD) 57.4%
AF1101 acetyl-CoA decarbonylase/synthase, subunit epsilon
(cdhB-1) 40.0%
AF2398 acetyl-CoA decarbonylase/synthase, subunit epsilon
(cdhB-2) 38.9%
AF0376 acetyl-CoA decarbonylase/synthase,
subunit gamma (cdhE) 55.4%
AF1849 carbon monoxide dehydrogenase, catalytic subunit
(cooS) 39.9%
AF0950 carbon monoxide dehydrogenase, iron sulfur subunit
(cooF) 38.9%
AF1535 ferredoxin-thioredoxin reductase, catalytic subunit
(ftrB) 38.6%
AF2073 formylmethanofuran:tetrahydromethanopterin
formyltransferase (ftr-1) 46.0%
AF2207 formylmethanofuran:tetrahydromethanopterin
formyltransferase (ftr-2) 68.4%

Nature © Macmillan Publishers Ltd 1997
AF1935 N5,N10-methenyltetrahydromethanopterin
cyclohydrolase (mch) 97.3%
AF0714 N5,N10-methylenetetrahydromethanopterin
dehydrogenase (mtd) 61.8%
AF1066 N5,N10-methylenetetrahydromethanopterin reductase
(mer-1) 59.1%
AF1196 N5,N10-methylenetetrahydromethanopterin reductase
(mer-2) 37.4%
AF0009 N5-methyltetrahydromethanopterin:coenzyme M
methyltransferase (mtr) 42.1%
AF1587 ribulose bisphosphate carboxylase, large subunit
(rbcL-1) 40.6%
AF1638 ribulose bisphosphate carboxylase, large subunit
(rbcL-2) 44.9%
AF1930 tungsten formylmethanofuran dehydrogenase,
subunit A (fwdA) 48.9%
AF1650 tungsten formylmethanofuran dehydrogenase,
subunit B (fwdB-1) 37.0%
AF1929 tungsten formylmethanofuran dehydrogenase,
subunit B (fwdB-2) 49.4%
AF1931 tungsten formylmethanofuran dehydrogenase,
subunit C (fwdC) 44.1%
AF1651 tungsten formylmethanofuran dehydrogenase,
subunit D (fwdD-1) 32.6%
AF1928 tungsten formylmethanofuran dehydrogenase,
subunit D (fwdD-2) 52.6%
AF0177 tungsten formylmethanofuran dehydrogenase,
subunit E (fwdE) 29.7%
AF1644 tungsten formylmethanofuran dehydrogenase,
subunit F (fwdF) 38.2%
AF1649 tungsten formylmethanofuran dehydrogenase,
subunit G (fwdG) 45.6%
PURINES, PYRIMIDINES, NUCLEOSIDES, AND NUCLEOTIDES
2’-Deoxyribonucleotide metabolism
AF1108 deoxycytidine triphosphate deaminase, putative 38.1%
AF1664 ribonucleotide reductase (nrd) 59.7%
AF1554 thioredoxin reductase (trxB) 45.2%
AF2047 thymidylate synthase, putative 33.1%
Nucleotide and nucleoside interconversions
AF0876 5’-nucleotidase (nt5) 30.9%
AF0676 adenylate kinase (adk) 56.1%
AF1900 cytidylate kinase (cmk) 48.6%
AF0767 nucleoside diphosphate kinase (ndk) 56.4%
AF0061 thymidylate kinase (tmk) 34.9%
AF1308 thymidylate kinase, putative 26.3%
AF2042 uridylate kinase (pyrH) 53.6%
Purine ribonucleotide biosynthesis
AF2242 adenylosuccinate lyase (purB) 52.3%
AF0841 adenylosuccinate synthetase (purA) 70.8%
AF0873 amidophosphoribosyltransferase (purF) 55.8%
AF0253 GMP synthase (guaA-1) 59.8%
AF1320 GMP synthase (guaA-2) 49.4%
AF1811 inosine monophosphate cyclohydrolase 38.3%
AF0847 inosine monophosphate dehydrogenase (guaB-1) 41.6%
AF2118 inosine monophosphate dehydrogenase (guaB-2) 31.9%
AF1259 inosine monophosphate dehydrogenase, putative 51.6%
AF1157 phosphoribosylamine—glycine ligase (purD) 40.9%
AF1271 phosphoribosylaminoimidazole carboxylase (purE) 42.8%
AF1272 phosphoribosylaminoimidazolesuccinocarboxamide
synthase (purC) 34.7%
AF1693 phosphoribosylformylglycinamidine cyclo-ligase
(purM) 53.8%
AF1260 phosphoribosylformylglycinamidine synthase I (purQ) 40.9%
AF1940 phosphoribosylformylglycinamidine synthase II (purL) 41.5%
AF0589 ribose-phosphate pyrophosphokinase (prsA-1) 35.0%
AF1419 ribose-phosphate pyrophosphokinase (prsA-2) 41.1%
Pyrimidine ribonucleotide biosynthesis
AF0106 aspartate carbamoyltransferase, catalytic
subunit (pyrB) 60.7%
AF0107 aspartate carbamoyltransferase, regulatory
subunit (pyrI) 48.2%
AF1274 carbamoyl-phosphate synthase, large subunit (carB) 65.1%
AF1273 carbamoyl-phosphate synthase, small subunit (carA) 55.2%
AF0252 CTP synthase (pyrG) 58.3%
AF2250 dihydroorotase (pyrC) 37.2%
AF0745 dihydroorotase dehydrogenase (pyrD) 44.8%
AF1741 orotate phosphoribosyl transferase (pyrE) 49.0%
AF0386 orotate phosphoribosyl transferase, putative 39.0%
Salvage of nucleosides and nucleotides
AF0240 adenine deaminase (adeC) 39.5%
AF1764 dCMP deaminase, putative 39.0%
AF1788 methylthioadenosine phosphorylase (mtaP) 40.0%
AF1341 thymidine phosphorylase (deoA-1) 46.7%
AF1342 thymidine phosphorylase (deoA-2) 40.7%
AF0239 xanthine-guanine phosphoribosyltransferase (gptA-1) 25.7%
AF1789 xanthine-guanine phosphoribosyltransferase (gptA-2) 28.2%
REGULATORY FUNCTIONS
AF1959 (R)-hydroxyglutaryl-CoA dehydratase activator (hgdC) 51.2%
AF0168 arsenical resistance operon repressor, putative 36.7%
AF2204 arylsulfatase regulatory protein, putative 29.9%
AF0074 biotin operon repressor/biotin—[acetyl CoA
carboxylase] ligase (birA) 36.6%
AF1724 dinitrogenase reductase activating glycohydrolase
(draG) 37.9%
AF2232 ferric uptake regulation protein (fur) 25.8%
AF1785 iron-dependent repressor 42.0%
AF2395 iron-dependent repressor 40.0%
AF0245 iron-dependent repressor (desR) 28.2%
AF1984 iron-dependent repressor (troR) 28.3%
AF2430 lacZ expression regulatory protein (icc) 29.6%
AF1622 leucine responsive regulatory protein (lrp) 29.1%
AF0673 mercuric resistance operon regulatory protein (merR) 37.6%
AF2425 methanol dehydrogenase regulatory protein (moxR) 48.3%
AF1475 mitochondrial benzodiazepine receptor/sensory
transduction protein 38.4%
AF0198 monoamine oxidase regulatory protein, putative 41.7%
AF1933 monoamine oxidase regulatory protein, putative 38.9%
AF0978 nitrogen regulatory protein P-II (glnB-1) 61.7%
AF1747 nitrogen regulatory protein P-II (glnB-2) 58.0%
AF1750 nitrogen regulatory protein P-II (glnB-3) 60.7%
AF0331 pheromone shutdown protein (traB) 40.5%
AF1797 phosphate regulatory protein, putative 30.7%
AF0521 protease synthase and sporulation regulator Pai1,
putative 52.4%
AF1627 repressor protein 59.1%
AF1793 repressor protein 54.5%
AF0449 response regulator 38.1%
AF1063 response regulator 36.3%
AF1256 response regulator 42.5%
AF1384 response regulator 44.7%
AF1473 response regulator 32.5%
AF1898 response regulator 48.7%
AF2249 response regulator 44.8%
AF2419 response regulator 37.9%
AF0004 RNase L inhibitor 54.5%
AF0021 signal-transducing histidine kinase 26.1%
AF0208 signal-transducing histidine kinase 27.9%
AF0450 signal-transducing histidine kinase 32.4%
AF0770 signal-transducing histidine kinase 26.9%
AF0893 signal-transducing histidine kinase 28.7%
AF1184 signal-transducing histidine kinase 29.8%
AF1452 signal-transducing histidine kinase 28.5%
AF1467 signal-transducing histidine kinase 37.4%
AF1472 signal-transducing histidine kinase 30.4%
AF1483 signal-transducing histidine kinase 27.7%
AF1515 signal-transducing histidine kinase 32.0%
AF1639 signal-transducing histidine kinase 29.9%
AF1721 signal-transducing histidine kinase 34.5%
AF2109 signal-transducing histidine kinase 31.6%
AF0881 signal-transducing histidine kinase,
authentic frameshift 26.5%
AF0277 signal-transducing histidine kinase, putative 29.8%
AF0410 signal-transducing histidine kinase, putative 27.1%
AF0448 signal-transducing histidine kinase, putative 26.1%
AF1620 signal-transducing histidine kinase, putative 26.2%
AF2032 signal-transducing histidine kinase, putative 22.5%
AF2420 signal-transducing histidine kinase, putative 28.4%
AF0442 succinoglycan biosynthesis regulator (exsB) 37.2%
AF1516 sugar fermentation stimulation protein (sfsA) 31.0%
AF1270 transcriptional regulatory protein, ArsR family 35.4%
AF1544 transcriptional regulatory protein, ArsR family 32.3%
AF1853 transcriptional regulatory protein, ArsR family 34.9%
AF2136 transcriptional regulatory protein, ArsR family 39.8%
AF0439 transcriptional regulatory protein, AsnC family 29.8%
AF0474 transcriptional regulatory protein, AsnC family 51.0%
AF0584 transcriptional regulatory protein, AsnC family 35.3%
AF1121 transcriptional regulatory protein, AsnC family 35.8%
AF1148 transcriptional regulatory protein, AsnC family 32.6%
AF1404 transcriptional regulatory protein, AsnC family 45.1%
AF1448 transcriptional regulatory protein, AsnC family 30.6%
AF1723 transcriptional regulatory protein, AsnC family 46.4%
AF1743 transcriptional regulatory protein, AsnC family 34.9%
AF2127 transcriptional regulatory protein, LysR family 30.8%
AF0114 transcriptional regulatory protein, putative 35.6%
AF1968 transcriptional regulatory protein, Rok family 32.9%
AF0112 transcriptional regulatory protein, Sir2 family 38.9%
AF1676 transcriptional regulatory protein, Sir2 family 40.6%
AF1817 transcriptional regulatory protein, TetR family 24.5%
AF0363 transcriptional repressor (cinR) 27.5%
REPLICATION
DNA replication, restriction, modification, recombination, and repair
AF2117 3-methyladenine DNA glycosylase (alkA) 30.0%
AF2060 activator 1, replication factor C, 35 KDa subunit 66.3%
AF1195 activator 1, replication factor C, 53 KDa subunit 43.7%
AF0465 DNA gyrase, subunit A (gyrA) 48.4%
AF0530 DNA gyrase, subunit B (gyrB) 58.4%
AF1388 DNA helicase, putative 46.8%
AF1960 DNA helicase, putative 32.7%
AF0623 DNA ligase (lig) 44.4%
AF1725 DNA ligase, putative 32.7%
AF0497 DNA polymerase B1 (polB) 45.1%
AF0693 DNA polymerase B2 (boxA), authentic frameshift 32.3%
AF0972 DNA polymerase III, subunit epsilon (dnaQ) 31.9%
AF2277 DNA polymerase, bacteriophage-type 36.9%
AF0742 DNA primase, putative 26.8%
AF0264 DNA repair protein RAD2 (rad2) 44.4%
AF0358 DNA repair protein RAD25 32.5%
AF1031 DNA repair protein RAD32 (rad32) 37.6%
AF0993 DNA repair protein RAD51 (radA) 59.3%
AF2096 DNA repair protein REC 40.0%
AF2418 DNA repair protein, putative 28.9%
AF1806 DNA topoisomerase I (topA) 36.2%
AF0940 DNA topoisomerase VI, subunit A (top6A) 39.8%
AF0652 DNA topoisomerase VI, subunit B (top6B) 43.9%
AF1692 endonuclease III (nth) 44.3%
AF0580 exodeoxyribonuclease III (xthA) 41.3%
AF2314 methylated-DNA-protein-cysteine
methyltransferase (ogt) 55.3%
AF1409 modification methylase, type III R/M system 31.4%
AF1234 mutator protein MutT (mutT) 63.6%
AF2200 mutator protein MutT, putative 42.0%
AF0335 proliferating-cell nuclear antigen (pol30) 33.7%
AF0694 replication control protein A, putative 30.2%
AF1024 reverse gyrase (top-RG) 40.7%
AF0621 ribonuclease HII (rnhB) 39.3%
AF1715 type I restriction-modification enzyme, M subunit,
authentic frameshift 63.0%
AF1708 type I restriction-modification enzyme, R subunit 38.2%
AF1710 type I restriction-modification enzyme, S subunit 33.0%
TRANSCRIPTION
DNA-dependent RNA polymerase
AF1888 DNA-directed RNA polymerase, subunit A’ (rpoA1) 63.6%
AF1889 DNA-directed RNA polymerase, subunit A’’ (rpoA2) 55.7%
AF1887 DNA-directed RNA polymerase, subunit B’ (rpoB1) 65.3%
AF1886 DNA-directed RNA polymerase, subunit B’’ (rpoB2) 57.1%
AF2282 DNA-directed RNA polymerase, subunit D (rpoD) 34.6%
AF1117 DNA-directed RNA polymerase, subunit E’ (rpoE1) 48.4%
AF1116 DNA-directed RNA polymerase, subunit E’’ (rpoE2) 40.0%
AF1885 DNA-directed RNA polymerase, subunit H (rpoH) 59.5%
AF1131 DNA-directed RNA polymerase, subunit K (rpoK) 61.5%
AF0207 DNA-directed RNA polymerase, subunit L (rpoL) 42.0%
AF1130 DNA-directed RNA polymerase, subunit N (rpoN) 58.8%
Transcription factors
AF1813 TBP-interacting protein TIP49 45.7%
AF1299 transcription initiation factor IIB 60.4%
AF0373 transcription initiation factor IID 59.4%
AF0757 transcription initiation factor IIE, subunit alpha, putative23.5%
AF1891 transcription termination-antitermination factor NusA,
putative 48.9%
AF1235 transcription-associated protein TFIIS 59.0%
RNA processing
AF1783 dimethyladenosine transferase (ksgA) 44.7%
AF2087 fibrillarin (fib) 49.3%
AF0482 mRNA 3’-end processing factor, putative 55.5%
AF0532 mRNA 3’-end processing factor, putative 39.1%
AF2361 mRNA 3’-end processing factor, putative 30.5%
AF2399 rRNA methylase, putative 36.4%
AF0362 snRNP, putative 32.0%
AF0875 snRNP, putative 35.7%
TRANSLATION
Amino acyl tRNA synthetases
AF2255 alanyl-tRNA synthetase (alaS) 47.1%
AF0894 arginyl-tRNA synthetase (argS) 48.8%
AF0920 aspartyl-tRNA synthetase (aspS) 62.5%
AF0411 cysteinyl-tRNA synthetase (cysS) 46.1%
AF0260 glutamyl-tRNA synthetase (gltX) 44.9%
AF0916 glycyl-tRNA synthetase (glyS) 51.2%
AF1642 histidyl-tRNA synthetase (hisS) 46.0%
AF0633 isoleucyl-tRNA synthetase (ileS) 48.9%
AF2421 leucyl-tRNA synthetase (leuS) 49.7%
AF1216 lysyl-tRNA synthetase (lysS) 43.6%
AF1453 methionyl-tRNA synthetase (metS) 45.2%
AF1955 phenylalanyl-tRNA synthetase, subunit alpha (pheS) 44.4%
AF1424 phenylalanyl-tRNA synthetase, subunit beta (pheT) 42.6%
AF1609 prolyl-tRNA synthetase (proS) 56.8%
AF2035 seryl-tRNA synthetase (serS) 45.4%
AF0548 threonyl-tRNA synthetase (thrS) 46.9%
AF1694 tryptophanyl-tRNA synthetase (trpS) 52.4%
AF0776 tyrosyl-tRNA synthetase (tyrS) 57.6%
AF2224 valyl-tRNA synthetase (valS) 54.5%
Degradation of proteins, peptides, and glycopeptides
AF1976 26S protease regulatory subunit 4 66.0%
AF1653 alkaline serine protease (aprM) 44.5%
AF0578 aminopeptidase, putative 27.8%
AF0364 ATP-dependent protease La (lon) 36.6%
AF1946 cysteine proteinase, putative 36.2%
AF1281 intracellular protease (pfpI) 56.0%
AF1112 O-sialoglycoprotein endopeptidase (gcp) 57.6%
AF0665 O-sialoglycoprotein endopeptidase, putative 35.6%
AF2086 protease inhibitor, putative 37.0%
AF0490 proteasome, subunit alpha (psmA) 60.8%
AF0481 proteasome, subunit beta (psmB) 58.3%
AF2034 X-pro aminopeptidase (pepQ) 34.6%
Protein modification
AF0656 antibiotic maturation protein (pmbA) 32.7%
AF0378 CODH nickel-insertion accessory protein (cooC-1) 35.7%
AF1685 CODH nickel-insertion accessory protein (cooC-2) 47.4%
AF1615 cofactor modifying protein (cmo) 27.2%
AF2195 deoxyhypusine synthase (dys1-1) 32.6%
AF2300 deoxyhypusine synthase (dys1-2) 34.9%
AF0381 diphthine synthase (dph5) 40.8%
AF2324 fmu and fmv protein 40.0%
AF1367 hydrogenase expression/formation protein (hypA) 40.4%
AF1368 hydrogenase expression/formation protein (hypB) 54.4%
AF1369 hydrogenase expression/formation protein (hypC) 40.5%
AF1370 hydrogenase expression/formation protein (hypD) 46.0%
AF1365 hydrogenase expression/formation protein (hypE) 51.5%
AF1366 hydrogenase expression/formation regulatory
protein (hypF) 45.1%
AF0036 L-isoaspartyl protein carboxyl methyltransferase
(pcm-1) 60.7%
AF2322 L-isoaspartyl protein carboxyl methyltransferase
(pcm-2) 59.3%
AF1840 methionyl aminopeptidase (map) 48.6%
AF1989 peptidyl-prolyl cis-trans isomerase (slyD) 34.4%
AF0853 proliferating-cell nucleolar antigen P120, putative 35.7%
AF2039 proliferating-cell nucleolar antigen P120, putative 44.2%
AF1449 pyruvate formate-lyase 2 (pflD) 37.8%
AF1450 pyruvate formate-lyase 2 activating enzyme (pflC) 38.8%
AF0117 pyruvate formate-lyase activating enzyme (act-1) 25.5%
AF0918 pyruvate formate-lyase activating enzyme (act-2) 42.3%
AF1330 pyruvate formate-lyase activating enzyme (act-3) 45.8%
AF2278 pyruvate formate-lyase activating enzyme (act-4) 42.5%
AF1961 pyruvate formate-lyase activating enzyme (pflX) 50.2%
AF0380 transmembrane oligosaccharyl transferase, putative 27.8%
AF0329 transmembrane oligosaccharyl transferase, putative 29.3%
Ribosomal proteins: synthesis and modification
AF1490 LSU ribosomal protein L1P (rpl1P) 48.6%
AF1922 LSU ribosomal protein L2P (rpl2P) 60.4%
AF1925 LSU ribosomal protein L3P (rpl3P) 56.5%
AF1924 LSU ribosomal protein L4P (rpl4P) 56.4%
AF1912 LSU ribosomal protein L5P (rpl5P) 51.7%
AF1909 LSU ribosomal protein L6P (rpl6P) 53.7%
AF0764 LSU ribosomal protein L7AE (rpl7AE) 60.7%
AF1491 LSU ribosomal protein L10E (rpl10E) 45.6%
AF0538 LSU ribosomal protein L11P (rpl11P) 67.8%
AF1492 LSU ribosomal protein L12A (rpl12A) 76.0%
AF1128 LSU ribosomal protein L13P (rpl13P) 47.4%
AF1915 LSU ribosomal protein L14P (rpl14P) 66.7%
AF2319 LSU ribosomal protein L15E (rpl15E) 70.3%
AF1903 LSU ribosomal protein L15P (rpl15P) 53.8%
AF1127 LSU ribosomal protein L18E (rpl18E) 53.8%
AF1906 LSU ribosomal protein L18P (rpl18P) 57.8%
AF1907 LSU ribosomal protein L19E (rpl19E) 55.5%
AF1529 LSU ribosomal protein L21E (rpl21E) 53.2%
AF1920 LSU ribosomal protein L22P (rpl22P) 55.2%
AF1923 LSU ribosomal protein L23P (rpl23P) 55.6%
AF0537 LSU ribosomal protein L24A (rpl24A) 51.4%
AF0766 LSU ribosomal protein L24E (rpl24E) 66.1%
AF1914 LSU ribosomal protein L24P (rpl24P) 57.8%
AF1918 LSU ribosomal protein L29P (rpl29P) 44.6%
AF1890 LSU ribosomal protein L30E (rpl30E) 41.7%
AF1904 LSU ribosomal protein L30P (rpl30P) 55.9%
AF2066 LSU ribosomal protein L31E (rpl31E) 50.6%
AF1908 LSU ribosomal protein L32E (rpl32E) 51.2%
AF0057 LSU ribosomal protein L37AE (rpl37AE) 47.6%
AF0874 LSU ribosomal protein L37E (rpl37E) 57.9%
AF2067 LSU ribosomal protein L39E (rpl39E) 56.9%
AF1430 LSU ribosomal protein L40E (rpl40E) 73.3%
AF1333 LSU ribosomal protein L44E (rpl44E) 46.8%
AF2064 LSU ribosomal protein LXA (rplXA) 53.8%
AF0739 ribosomal protein S18 alanine acetyltransferase 38.5%
AF2303 ribosomal protein S6 modification protein (rimK) 32.2%
AF1133 SSU ribosomal protein S2P (rps2P) 58.3%
AF1919 SSU ribosomal protein S3P (rps3P) 50.0%
AF1913 SSU ribosomal protein S4E (rps4E) 48.9%
AF2284 SSU ribosomal protein S4P (rps4P) 59.1%
AF1905 SSU ribosomal protein S5P (rps5P) 60.0%
AF0511 SSU ribosomal protein S6E (rps6E) 50.8%
AF1893 SSU ribosomal protein S7P (rps7P) 59.6%
AF2152 SSU ribosomal protein S8E (rps8E) 61.6%
AF1910 SSU ribosomal protein S8P (rps8E) 64.6%
AF1129 SSU ribosomal protein S9P (rps9P) 59.5%
AF0938 SSU ribosomal protein S10P (rps10P) 71.0%
AF2283 SSU ribosomal protein S11P (rps11P) 71.1%
AF1892 SSU ribosomal protein S12P (rps12P) 74.1%
AF2285 SSU ribosomal protein S13P (rps13P) 52.1%
AF1911 SSU ribosomal protein S14P (rps14P) 61.5%
AF0801 SSU ribosomal protein S15P (rps15P) 62.0%
AF0911 SSU ribosomal protein S17E (rps17E) 52.6%
AF1916 SSU ribosomal protein S17P (rps17P) 59.0%
AF2069 SSU ribosomal protein S19E (rps19E) 64.2%
AF1921 SSU ribosomal protein S19P (rps19P) 60.9%
AF1114 SSU ribosomal protein S24E (rps24E) 40.2%
AF1113 SSU ribosomal protein S27AE (rps27AE) 60.0%
AF1334 SSU ribosomal protein S27E (rps27E) 49.0%
AF0765 SSU ribosomal protein S28E (rps28E) 55.6%
AF2320 SSU ribosomal protein S3AE (rps3AE) 38.9%
tRNA modification
AF0588 archaeosine tRNA-ribosyltransferase (tgtA) 52.0%
AF1954 Glu-tRNA amidotransferase, subunit A (gatA-1) 38.6%
AF2329 Glu-tRNA amidotransferase, subunit A (gatA-2) 53.5%
AF1440 Glu-tRNA amidotransferase, subunit B (gatB-1) 54.7%
AF2116 Glu-tRNA amidotransferase, subunit B (gatB-2) 46.4%

Nature © Macmillan Publishers Ltd 1997
AF2328 Glu-tRNA amidotransferase, subunit C (gatC) 35.1%
AF0815 N2,N2-dimethylguanosine tRNA methyltransferase
(trm1) 38.2%
AF1730 pseudouridylate synthase I (truA) 37.4%
AF1485 queuine tRNA-ribosyltransferase (tgtB) 44.1%
AF0493 ribonuclease PH (rph) 30.8%
AF0900 tRNA intron endonuclease (endA) 41.8%
AF2156 tRNA nucleotidyltransferase (cca) 43.9%
Translation factors
AF2350 ATP-dependent RNA helicase HepA, putative 31.5%
AF2254 ATP-dependent RNA helicase, DEAD-family (deaD) 52.2%
AF0071 ATP-dependent RNA helicase, putative 29.6%
AF1458 ATP-dependent RNA helicase, putative 48.1%
AF2406 ATP-dependent RNA helicase, putative 35.2%
AF1149 large helicase-related protein (lhr-1) 34.5%
AF2177 large helicase-related protein (lhr-2), authentic
frameshift 56.0%
AF1220 peptide chain release factor eRF, subunit 1 51.2%
AF2245 SKI2-family helicase, authentic frameshift 45.7%
AF0937 translation elongation factor EF-1, subunit alpha (tuf) 74.4%
AF0574 translation elongation factor EF-1, subunit beta 31.3%
AF1894 translation elongation factor EF-2 (fus) 62.5%
AF0777 translation initiation factor eIF-1A (eif1A) 57.5%
AF0527 translation initiation factor eIF-2, subunit alpha (eif2A) 51.1%
AF2326 translation initiation factor eIF-2, subunit beta, putative 45.5%
AF0592 translation initiation factor eIF-2,
subunit gamma (eif2G) 64.4%
AF0370 translation initiation factor eIF-2B, subunit
delta (eif2BD) 53.3%
AF2037 translation initiation factor eIF-2B, subunit
delta (eif2BD) 57.9%
AF0645 translation initiation factor eIF-5A (eif5A) 50.4%
AF0768 translation initiation factor IF-2 (infB) 52.2%
TRANSPORT AND BINDING PROTEINS
General
AF0393 ABC transporter, ATP-binding protein 34.5%
AF0984 ABC transporter, ATP-binding protein 35.2%
AF1006 ABC transporter, ATP-binding protein 35.1%
AF1018 ABC transporter, ATP-binding protein 57.7%
AF1021 ABC transporter, ATP-binding protein 37.8%
AF1136 ABC transporter, ATP-binding protein 39.3%
AF1139 ABC transporter, ATP-binding protein 38.2%
AF1300 ABC transporter, ATP-binding protein 34.1%
AF1469 ABC transporter, ATP-binding protein 43.5%
AF1819 ABC transporter, ATP-binding protein 51.1%
AF1982 ABC transporter, ATP-binding protein 41.3%
AF2364 ABC transporter, ATP-binding protein 53.5%
AF1005 ABC transporter, ATP-binding protein, putative 28.7%
AF1064 ABC transporter, ATP-binding protein, putative 36.0%
AF1983 ABC transporter, periplasmic binding protein 25.4%
AF1981 ABC transporter, permease protein 29.9%
AF1995 sodium- and chloride-dependent transporter 52.5%
Amino acids, peptides and amines
AF1766 amino-acid ABC transporter, periplasmic
binding protein/protein kinase 27.4%
AF0222 branched-chain amino acid ABC transporter,
ATP-binding protein (braF-1) 42.7%
AF0822 branched-chain amino acid ABC transporter,
ATP-binding protein (braF-2) 44.7%
AF0959 branched-chain amino acid ABC transporter, ATP-
binding protein (braF-3) 37.6%
AF1390 branched-chain amino acid ABC transporter,
ATP-binding protein (braF-4) 59.7%
AF0221 branched-chain amino acid ABC transporter,
ATP-binding protein (braG-1) 48.2%
AF0823 branched-chain amino acid ABC transporter,
ATP-binding protein (braG-2) 42.9%
AF0958 branched-chain amino acid ABC transporter,
ATP-binding protein (braG-3) 34.1%
AF1389 branched-chain amino acid ABC transporter, ATP-
binding protein (braG-4) 64.6%
AF0223 branched-chain amino acid ABC transporter,
periplasmic binding protein (braC-1) 34.3%
AF0827 branched-chain amino acid ABC transporter,
periplasmic binding protein (braC-2) 26.8%
AF0962 branched-chain amino acid ABC transporter,
periplasmic binding protein (braC-3) 25.6%
AF1391 branched-chain amino acid ABC transporter,
periplasmic binding protein (braC-4) 50.1%
AF0224 branched-chain amino acid ABC transporter,
permease protein (braD-1) 25.4%
AF0825 branched-chain amino acid ABC transporter,
permease protein (braD-2) 30.8%
AF0961 branched-chain amino acid ABC transporter,
permease protein (braD-3) 23.9%
AF1392 branched-chain amino acid ABC transporter,
permease protein (braD-4) 65.4%
AF0225 branched-chain amino acid ABC transporter,
permease protein (braE-1) 28.7%
AF0824 branched-chain amino acid ABC transporter,
permease protein (braE-2) 31.3%
AF0960 branched-chain amino acid ABC transporter,
permease protein (braE-3) 30.1%
AF1393 branched-chain amino acid ABC transporter,
permease protein (braE-4) 60.5%
AF1612 cationic amino acid transporter (cat-1) 29.5%
AF1774 cationic amino acid transporter (cat-2) 38.0%
AF1770 dipeptide ABC transporter, ATP-binding protein (dppD) 47.8%
AF1771 dipeptide ABC transporter, ATP-binding protein (dppF) 43.1%
AF1767 dipeptide ABC transporter, dipeptide-binding
protein (dppA) 33.1%
AF1768 dipeptide ABC transporter, permease protein (dppB) 39.3%
AF1769 dipeptide ABC transporter, permease protein (dppC) 40.8%
AF0680 glutamine ABC transporter, ATP-binding protein (glnQ) 63.8%
AF0231 glutamine ABC transporter, periplasmic glutamine-
binding protein (glnH) 38.0%
AF0232 glutamine ABC transporter, permease protein (glnP) 39.3%
AF0981 osmoprotection protein (proV) 39.0%
AF0979 osmoprotection protein (proW-1) 32.8%
AF0980 osmoprotection protein (proW-2) 36.8%
AF0982 osmoprotection protein (proX) 28.7%
AF0015 proline permease (putP-1) 26.2%
AF0969 proline permease (putP-2) 27.4%
AF1222 proline permease (putP-3) 27.0%
AF1608 spermidine/putrescine ABC transporter, ATP-
binding protein (potA) 50.2%
AF1605 spermidine/putrescine ABC transporter, periplasmic
spermidine/putrescine-binding protein (potD),
authentic frameshift 31.0%
AF1607 spermidine/putrescine ABC transporter, permease
protein (potB) 38.0%
AF1606 spermidine/putrescine ABC transporter, permease
protein (potC) 38.7%
Anions
AF2308 arsenite transport protein (arsB) 27.3%
AF1415 chloride channel, putative 27.3%
AF0025 cyanate transport protein (cynX) 24.5%
AF0087 nitrate ABC transporter, ATP-binding protein (nrtC-1) 47.4%
AF0638 nitrate ABC transporter, ATP-binding protein (nrtC-2) 55.5%
AF0640 nitrate ABC transporter, ATP-binding protein, putative 32.5%
AF0086 nitrate ABC transporter, permease protein (nrtB-1) 35.4%
AF0639 nitrate ABC transporter, permease protein (nrtB-2) 37.4%
AF1359 phosphate ABC transporter, ATP-binding
protein (pstB) 66.0%
AF1356 phosphate ABC transporter, periplasmic phosphate-
binding protein (phoX) 25.1%
AF1358 phosphate ABC transporter, permease protein (pstA) 34.1%
AF1357 phosphate ABC transporter, permease protein (pstC) 33.7%
AF1360 phosphate ABC transporter, regulatory protein (phoU) 26.9%
AF0791 phosphate permease, putative 31.1%
AF1798 phosphate permease, putative 52.9%
AF0092 sulfate ABC transporter, ATP-binding protein (cysA) 54.2%
AF0093 sulfate ABC transporter, permease protein (cysT) 44.1%
Carbohydrates, organic alcohols, and acids
AF0347 C4-dicarboxylate transporter (mae1) 24.5%
AF1426 glycerol uptake facilitator, MIP channel (glpF) 36.2%
AF0013 hexuronate transporter (exuT) 25.1%
AF0806 L-lactate permease (lctP) 31.7%
AF0008 oxalate/formate antiporter (oxlT-1) 25.7%
AF0367 oxalate/formate antiporter (oxlT-2) 33.2%
AF1069 pantothenate permease (panF-1) 28.9%
AF1205 pantothenate permease (panF-2) 24.8%
AF0237 pantothenate permease (panF-3) 25.1%
AF0041 polysaccharide ABC transporter, ATP-binding
protein (rfbB-1) 42.5%
AF0290 polysaccharide ABC transporter, ATP-binding protein
(rfbB-2) 43.9%
AF0042 polysaccharide ABC transporter, permease protein
(rfbA-1) 27.5%
AF0289 polysaccharide ABC transporter, permease protein
(rfbA-2) 28.5%
AF0887 ribose ABC transporter, ATP-binding protein (rbsA-1) 33.3%
AF1170 ribose ABC transporter, ATP-binding protein (rbsA-2) 27.9%
AF0888 ribose ABC transporter, permease protein (rbsC-1) 24.1%
AF0889 ribose ABC transporter, permease protein (rbsC-2) 31.2%
AF2014 sugar transporter, putative 26.0%
Cations
AF0977 ammonium transporter (amt-1) 44.3%
AF1746 ammonium transporter (amt-2) 49.0%
AF1749 ammonium transporter (amt-3) 41.5%
AF0473 cation-transporting ATPase, P-type (pacS) 44.0%
AF0152 copper-transporting ATPase, P-type (copB) 44.5%
AF0246 iron (II) transporter (feoB-1) 33.3%
AF2394 iron (II) transporter (feoB-2) 48.0%
AF0561 iron (II) transporter (feoB-3), authentic frameshift 29.4%
AF0430 iron (III) ABC transporter, ATP-binding protein (hemV-1) 50.4%
AF0432 iron (III) ABC transporter, ATP-binding protein (hemV-2) 58.7%
AF1401 iron (III) ABC transporter, ATP-binding protein (hemV-3) 35.2%
AF1397 iron (III) ABC transporter, periplasmic hemin-binding protein
(hemT), authentic frameshift 28.2%
AF0431 iron (III) ABC transporter, permease protein (hemU-1) 36.2%
AF1402 iron (III) ABC transporter, permease protein (hemU-2) 35.2%
AF0786 magnesium and cobalt transporter (corA) 40.1%
AF0346 mercuric transport protein periplasmic
component (merP) 35.2%
AF0217 Na+/H+ antiporter (napA-1) 28.2%
AF1245 Na+/H+ antiporter (napA-2) 28.4%
AF0846 Na+/H+ antiporter (nhe2) 33.1%
AF0715 potassium channel, putative 39.5%
AF1673 potassium channel, putative 36.3%
AF2197 potassium channel, putative 24.6%
AF0218 TRK potassium uptake system protein (trkA-1) 30.2%
AF0838 TRK potassium uptake system protein (trkA-2) 42.9%
AF0839 TRK potassium uptake system protein (trkH) 39.8%
Other
AF0834 ferritin, putative 39.8%
AF1980 heme exporter protein C (helC) 29.0%
AF1144 multidrug resistance protein 29.2%
AF1325 multidrug resistance protein 29.9%
AF2258 multidrug resistance protein 31.3%
OTHER CATEGORIES
Adaptations and atypical conditions
AF0508 ethylene-inducible protein 74.5%
AF0235 heat shock protein (htpX) 32.9%
AF0942 surE stationary-phase survival protein (surE) 50.2%
AF1996 virulence associated protein C (vapC-1) 50.0%
AF1690 virulence associated protein C (vapC-2) 30.0%
Drug and analog sensitivity
AF1884 daunorubicin resistance ATP-binding protein (drrA) 47.1%
AF1883 daunorubicin resistance membrane protein (drrB) 27.0%
AF0487 penicillin G acylase 31.7%
AF1214 phenylacrylic acid decarboxylase (pad1) 43.2%
AF2194 rRNA (adenine-N6)-methyltransferase, putative 29.2%
AF1696 small multidrug export protein (qacE) 39.0%
Transposon-related functions
AF0120 insertion sequence ISH S1, authentic frameshift 34.5%
AF0193 ISA0963-1, putative transposase, authentic frameshift 34.3%
AF0309 ISA0963-2, putative transposase 33.5%
AF1310 ISA0963-3, putative transposase 33.5%
AF1383 ISA0963-4, putative transposase 33.5%
AF1410 ISA0963-5, putative transposase 33.5%
AF1705 ISA0963-6, putative transposase 33.5%
AF1836 ISA0963-7, putative transposase, authentic frameshift 20.0%
AF0678 ISA1083-1, ISORF2 33.6%
AF0679 ISA1083-1, putative transposase 37.2%
AF1351 ISA1083-2, ISORF2 30.8%
AF1352 ISA1083-2, putative transposase 31.5%
AF2140 ISA1083-3, ISORF2 30.8%
AF2139 ISA1083-3, putative transposase 31.5%
AF0278 ISA1214-1, ISORF2 27.7%
AF0279 ISA1214-1, putative transposase 33.3%
AF0305 ISA1214-2, ISORF2 27.7%
AF0306 ISA1214-2, putative transposase 33.3%
AF0641 ISA1214-3, ISORF2 26.5%
AF0642 ISA1214-3, putative transposase 33.3%
AF0857 ISA1214-4, ISORF2 27.7%
AF0858 ISA1214-4, putative transposase 33.3%
AF2091 ISA1214-5, ISORF2 26.5%
AF2092 ISA1214-5, putative transposase 33.3%
AF2223 ISA1214-6, ISORF2 26.5%
AF2222 ISA1214-6, putative transposase 25.6%
AF0138 transposase IS240-A 43.3%
AF0895 transposase IS240-A 46.2%
AF2390 transposase, authentic frameshift 24.0%
AF0137 transposase, putative 29.6%
AF1628 transposase, putative 32.8%
UNKNOWN
AF0477 AAA superfamily ATPase 35.0%
AF0513 allene oxide synthase, putative 39.5%
AF0478 ATP-binding protein PhnP (phnP) 30.9%
AF1775 atrazine chlorohydrolase, putative 34.4%
AF0973 bile acid-inducible operon protein F (baiF-1) 30.8%
AF0974 bile acid-inducible operon protein F (baiF-2) 29.9%
AF1315 bile acid-inducible operon protein F (baiF-3) 31.3%
AF2063 c-myc binding protein, putative 21.7%
AF1992 calcium-binding protein, putative 31.2%
AF2287 carotenoid biosynthetic gene ERWCRTS, putative 49.4%
AF0512 chloroplast inner envelope membrane protein 42.5%
AF2251 competence-damage protein, putative 28.0%
AF0090 dehydrase 34.1%
AF1498 dehydrase, putative 29.4%
AF1518 DNA/pantothenate metabolism flavoprotein, putative 51.4%
AF0039 dolichol-P-glucose synthetase, putative 33.7%
AF0328 dolichol-P-glucose synthetase, putative 39.0%
AF0581 dolichol-P-glucose synthetase, putative 27.5%
AF0569 DR-beta chain MHC class II 37.7%
AF0383 endonuclease III, putative 47.1%
AF1150 erpK protein, putative 54.9%
AF2372 extragenic suppressor (suhB) 37.0%
AF1418 glycerol-3-phosphate cytidyltransferase (taqD) 56.6%
AF0744 GTP-binding protein 33.4%
AF1181 GTP-binding protein 36.3%
AF1364 GTP-binding protein 57.5%
AF2146 GTP-binding protein 65.9%
AF0428 GTP-binding protein, GTP1/OBG-family 43.9%
AF2237 HAM1 protein 31.4%
AF2211 HIT family protein (hit) 29.6%
AF0216 L-isoaspartyl protein carboxyl methyltransferase
PimT, putative 35.5%
AF2313 maoC protein (maoC) 43.0%
AF0429 methyltransferase 43.8%
AF0186 nifS protein, class-V aminotransferase (nifS-1) 46.1%
AF0564 nifS protein, class-V aminotransferase (nifS-2) 45.1%
AF0185 nifU protein (nifU-1) 55.6%
AF0565 nifU protein (nifU-2) 55.6%
AF0632 nifU protein (nifU-3) 47.4%
AF1781 nodulation protein NfeD (nfeD) 33.4%
AF2269 nucleotide-binding protein 48.7%
AF2382 nucleotide-binding protein 49.1%
AF0374 p-nitrophenyl phosphatase (pho2) 31.7%
AF1978 periplasmic divalent cation tolerance protein (cutA) 31.3%
AF1652 prepro-subtilisin sendai, putative 35.6%
AF2021 rod shape-determining protein (mreB) 26.6%
AF1778 stage V sporulation protein (spoVG) 43.9%
AF1970 TPR domain-containing protein 29.0%
AF2202 tryptophan-specific permease, putative 25.2%
AF0816 vtpJ-therm, putative 42.1%
AF1679 vtpJ-therm, putative 45.1%