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Supplementary Table 2. Evaluation of Phenotypes with their significantly correlated Pfam families by the Šidák correction method
Phenotype
Description
Anaerobic
Organisms which do not grow in
the presence of oxygen
Bacillus or
coccobacillu
s
Bacterial colony with Bacilli
predominate with -highly
pleomorphic and inconclusive
morphology.
Catalase
To test for catalase activity, the
bacteria to be tested are mixed
with Hydrogen Peroxide.
Catalase is an enzyme that
catalyzes the breakdown of
hydrogen peroxide to oxygen and
water.
Coccus
A bacterium having a spherical or
spheroidal shape.
Coccus pairs or
chains
The predominant forms are cocci
in chains or pairs.
Summary of Results
Only one prediction was highly significant according to
Bonferroni and also found to be correct in our
evaluation: PF02915.6 Rubrerythrin (Rr). According to
the PFAM entry, this protein domain is found in
anaerobic sulphate-reducing bacteria. According to
Karlin et al. “the anaerobic delta genomes encode
multiple copies of the anaerobic detoxification protein
rubrerythrin that can neutralize hydrogen peroxide.”
Additionally, Putz et al have identified rubrerythrin in
the anaerobic organelles (hydrogenosomes) of
parasitic flagellate Trichomonas vaginalis.
Only one prediction was highly significant according to
Bonferroni and also found to be incorrect in our
evaluation: PF02388 - FemAB family negatively
correlated with bacillus.
According to the PFAM and PubMed entries, this
protein domain involved in Staphylococcal species which are bacilli.
The PFAM family PF00199 (catalase) was perfectly
matched to the phenotype associated with catalase
activity (p<0.019). The remainder of the predictions
could be related to catalase via metabolism (catalytic
activity). This is to be expected, as catalase breaks
down the cytotoxic hydrogen peroxide byproduct of the
electron transport chain. Another group of predictions
relate histidine biosynthesis activity with catalase.
There is anecdotal evidence that histidine biosynthesis
and catalase activity are related in a variety of
metabolic processes with over 300 publications in
PubMed.
Since only negatively correlated Pfam families are
identified, which means that the 'coccus' phenotype is
associated with the absence of these Pfam families. It
suggests that the functions of these Pfam families are
not involved in the phenotype.
Since only negatively correlated Pfam families are
identified, which means that this phenotype is
associated with the absence of these Pfam families. It
suggests that the functions of these Pfam families are
Reference
(s)
Num.
corre
lated
Pfam
Num.
positi
vely
correl
ated
Pfam
Num.
anticorrel
ated
Pfam
60
Corroborated
Pfams out of a
set of 100
reviewed Pfam
[1,2]
1
1
0
PF02915.6 [3]
[4,5]
1
0
1
[6]
15
15
0
N/A
10
0
10
N/A
6
0
6
PF00180.7 [7]
PF00199.8 (#)
not involved in the phenotype.
predominate
ColistinPolymyxin
susceptible
This is a particular susceptibility
to the antibiotic colistin
(polymyxin E), which are active
against gram-negative bacteria.
Curved
bacilli
Curved, comma or 'gull wing'
rods. Does not include helical or
spirochete forms
There are 27 significant Pfam families predicted for this
phenotype, and 14 of them are also found in the
predicted Pfam families for ‘gram negative,’ such as
'Lipid-A-disaccharide synthetase', and
‘Phosphatidylglycerophosphatase A' that are involved
in the lipopolysaccharide biosynthesis.
There is only one PFAM family predicted for this
phenotype. In PFAM this family includes functionally
uncharacterized proteins from such pathogenic
bacteria as Helicobacter pylori, Campylobacter jejuni,
and Vibrio cholerae, of which all are 'curved bacilli'.
[8,9]
27
27
0
N/A
1
1
0
PF03968.3 [10]
PF04453.4 [10]
PF04972.3 [11]
D-Mannitol
* Results from this
class are explained
in more detail in the
section Results
and Discussion
Organisms which grow in the
medium containing only DMannitol
There are two Pfam families predicted. Both seem to
be involved in mannitol metabolism.
[12,13]
2
2
0
Organisms which grow both in
the presence and absence of air
All the three Pfam families are involved in the
phosphotransferase system pathway, which is a major
carbohydrate transport system in bacteria.
[14-17]
3
3
0
PF02302.6 [18]
PF00358.7 [18]
PF04215.2 [17]
63
PF04279.4 [26]
PF02321.6 [27]
PF00529.8 [24]
PF00593.10 [28]
PF07715.1 [29]
PF04413.3 [30]
PF07660.2 [31]
PF02684.5 [8]
PF04613.2 [32]
PF03331.3 [33]
PF03279.3 [34]
PF02348.6 [35]
PF06293.3 [36]
Facultative
* Results from this
class are explained
in more detail in the
section Results
and Discussion
Gram
negative *
Results from this
class are explained
in more detail in the
section Results
and Discussion
Gram-negative forms
predominate
Gram
positive
Gram-positive forms predominate
Growth on
MacConkey agar is used for the
As discussed in more detail in the paper, the most
significant predicted Pfam families for the Gram
negative are classified as lipopolysaccharide
biosynthesis, lipopolysaccharide metabolism and lipid
A biosynthesis, which are characteristics of Gram
negative bacteria.
Compared to the 'Gram positive', the positive
correlated Pfam families (86 total) for the 'Gram
negative' have a good correlation with the negative
correlated Pfam families (24 total) for the 'Gram
positive', of which 22 Pfam families are shared. On the
other hand, there are 51 shared Pfam families between
positively correlated 'Gram positive' Pfam families and
negatively correlated 'Gram negative' Pfam families.
Some of the top 10 Pfam families are found in the
literature to be associated with 'Gram-positive' bacteria.
Since this test is used to distinguish lactose fermenting
[19-25]
149
86
[15,37]
110
86
24
PF04918.2 [38]
PF04203.3 [39]
PF02684.5 [8]
PF04613.2 [32]
PF03331.3 [40]
PF03279.3 [34]
PF02321.6 [27]
[15,37,41]
111
110
1
PF00593.10 [42]
MacConkey
agar
Growth on
ordinary
blood agar
Indole
L-Arabinose
isolation of gram-negative enteric
bacteria and the differentiation of
lactose fermenting from lactose
non-fermenting gram-negative
bacteria. It has also become
common to use the media to
differentiate bacteria by their
abilities to ferment sugars other
than lactose. In these cases
lactose is replaced in the medium
by another sugar. It also inhibits
growth of gram-positive bacteria.
This describes a growth
phenotype on a general purpose
non-selective medium used
commonly for cultures. Enriched
with whole blood, it is used to
isolate certain microorganisms
and detect hemolytic activity.
Indole is a component of the
amino acid tryptophan, which
some bacteria are able to
metabolize using the enzyme
tryptophanase. Indole is tested to
determine tryptophan
metabolism.
This conventional biochemical
testing consists on measuring the
anaerobic acid production of the
bacterial isolate in presence of a
medium containing L_Arabinose
and no other sugars.
gram-negative bacteria, it shares a number of
predictions with the 'Gram negative' phenotype. There
are 26 positively correlated Pfam families shared
between them. 7 out of top 10 most significant
correlated Pfam families have unknown function, which
may be of interest for further exploration.
PF07715.1 [29]
There was only one association with this phenotype
and its relationship to the phenotype could not be
established in the literature.
N/A
1
1
0
The results associated to this phenotype were in the
lower portion of our set near the statistical significance
threshold. There was no clear pattern of association
between the associated Pfam families and the
phenotype.
N/A
5
5
0
The predicted PFAM family L-arabinose isomerase is a
perfect match with the L-Arabinose phenotype.
N/A
1
1
0
This phenotype indicates the
ability of the organisms to move,
typically using flagella or cilia.
The most significant PFAM families associated with
this are involved in flagellar motility and chemotaxis.
More details are descried in the paper.
[43-59]
18
18
0
PF00460.8 (#)
PF00669.8 (#)
PF01584.8 [60]
PF01514.7 [61]
PF00771.7 [62]
PF02154.5 (#)
PF00700.8 (#)
PF00813.7 [63]
PF01052.8 [64]
PF01311.8 [65]
PF01312.8 [66]
PF00015.10 (#)
PF03963.3 (#)
PF03705.5 [67]
PF01739.8 [67]
PF01313.7 [53]
ONPG is a lactose analog used
to test for beta galactosidase
The PFAM family found to be associated with this
phenotype includes beta galacosidase, which facilitates
[68-73]
1
1
0
PF00703.9 [74]
Motile
Results from this
class are explained
in more detail in the
section Results
and Discussion
and in Tables 4A
and 4B
ONPG (beta
galactosidas
e)
Oxidase
activity.
the hydrolysis of ONPG.
Proteins with oxidase activity
participate in a
reduction/oxidation reaction
where atmospheric oxygen is the
electron acceptor
The two Pfam families PF02630.4 and PF00033.8, are
a mitochondrion-associated cytochrome c oxidase
assembly factor and a component of respiratory chain
complex III (which has oxidoreductase activity),
respectively. Both are directly associated to oxidase
activity.
Spore
formation
This phenotype includes proteins
involved in the development of
spores.
Except for two Pfam families that have unknown
functions, the remaining 9 PFAM families, constituted
of proteins involved in spore development as well as
structure, are found to be directly related to this
phenotype.
Strictly
aerobic
This phenotype describes the
ability of organisms to grow only
in the presence of air.
Only a single Pfam prediction was found for this
phenotype: "Bacterial signaling protein N terminal
repeat." According to Galperin et al. it is found
exclusively in aerobic or facultative aerobic bacteria.
Urea
hydrolysis
This phenotype describes an
organism’s ability to perform the
breakdown of Urea by the
enzyme Urease to form ammonia
and carbamine acid.
The two Pfam families found significantly associated to
this phenotype form some of the subdomains of the
Urease enzyme, which is involved in urea hydrolysis.
[75-78]
2
2
0
PF02630.4 [79]
PF06898.1 (#)
PF03323.3 (#)
PF03419.3 (#)
PF03862.3 (#)
PF05504.1 (#)
PF05580.2 [84]
PF05582.2 [85]
PF07451.1 (#)
PF07454.1 (#)
[70,80-86]
11
11
0
[87]
1
1
0
[88-92]
2
2
0
PF02814.5 (#)
PF05194.2 (#)
Legend: # denotes self-evident relationships
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