escherichia coli genomes · 2020-06-11 · bacteria escherichia coli, goodall et al. (4), baba et...

Research Article for mBio

A pan-genome method to determine core regions of the Bacillus subtilis and

Escherichia coli genomes

Running Title

A pan-genome method for core region determination in bacteria

Authors

Granger Suttona, Gary B. Fogel

b, Bradley Abramson

a, Lauren Brinkac, Todd Michael

a, Enoch S.

Liub, Sterling Thomas

c#

a J. Craig Venter Institute

b Natural Selection, Inc.

c Noblis, Inc.

Corresponding author: Sterling Thomas, [email protected]

(which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. The copyright holder for this preprintthis version posted June 12, 2020. ; https://doi.org/10.1101/2020.06.11.147629doi: bioRxiv preprint

https://doi.org/10.1101/2020.06.11.147629

Abstract

Synthetic engineering of bacteria to produce industrial products is a burgeoning field of research

and application. In order to optimize genome design, designers need to understand which genes

are essential, which are optimal for growth, and locations in the genome that will be tolerated by

the organism when inserting engineered cassettes. We present a pan-genome based method for

the identification of core regions in a genome that are strongly conserved at the species level. We

show that these core regions are very likely to contain all or almost all essential genes. We assert

that synthetic engineers should avoid deleting or inserting into these core regions unless they

understand and are manipulating the function of the genes in that region. Similarly, if the

designer wishes to streamline the genome, non-core regions and in particular low penetrance

genes would be good targets for deletion. Care should be taken to remove entire cassettes with

similar penetrance of the genes within cassettes as they may harbor toxin/antitoxin genes which

need to be removed in tandem. The bioinformatic approach introduced here saves considerable

time and effort relative to knockout studies on single isolates of a given species and captures a

broad understanding of the conservation of genes that are core to a species.


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Importance

The pan-genome approach presented in this paper can be used to determine core regions of a

genome and has many possible applications. Synthetic engineering design can be informed by

which genes/regions are more conserved (core) versus less conserved. The level of conservation

of adjacent non-core genes tends to define cassettes of genes which may be part of a pathway or

system that can inform researchers about possible functional significance. The pattern of gene

presence across the different genomes of a species can inform the understanding of evolution and

horizontal gene acquisition. The approach saves considerable time and effort relative to

laboratory methods used to identify essential genes in species.


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Introduction

Over the last decade, considerable interest has been directed towards the determination of a

minimal bacterial cell, making use of a short genome consisting of only essential genes for

viability. The Mycoplasma mycoides JCVI-syn3.0 is a case example of synthetic engineering to

design and build a genome that contains a streamlined gene set essential for cell viability and cell

replication (1). However, the identification of “essential” genes - those genes that are critical for

cell viability and replication - takes considerable time and effort in a laboratory setting and is

usually determined with respect to one reference genome under one set of specific growth

conditions. For instance, Kobayashi et al. (2) and Koo et al. (3) experimentally and

computationally determined the minimal gene set in the gram-positive bacterium Bacillus

subtilis. Of the ~4,100 genes of the type strain, a total of 271 genes for Kobayashi and 257 genes

for Koo were shown to be essential. These essential genes were further categorized in terms of

cell metabolism and enzymatic capability. Additionally for the ~4400 genes in the gram-negative

bacteria Escherichia coli, Goodall et al. (4), Baba et al. (5), and Yamazaki et al. (6), it was

determined that 414 genes were essential to strain K-12.

Experimental studies to determine such essential genes are time consuming and often

restricted to a single environmental condition using a single strain of the species. In addition,

these approaches also knock out one gene at a time. As such, genes with multiple copies with

redundant functions are often not considered as essential following knockout, as their additional

copy is able to maintain cellular function. In other words, a viable organism would not result

from deleting all but the experimentally determined essential genes from the genome. Another

peculiarity of the single knockout essential genes is that pairs or cassettes of genes which can be


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removed and still have a viable organism are labeled essential because removal of just one gene

is lethal. For example, removing the methylation gene(s) without removing the restriction

digestion enzyme genes from the restriction mechanism results in cell death but the cell survives

if the entire system is removed. This is likewise true for toxin/antitoxin systems.

While it is possible to define “essential” genes relative to viability, another larger

question remains; which genes define a species? While specific phenotypes can vary across

strains, in general a species seems to require some minimal set of genes to not only survive in the

laboratory but to thrive in its natural environment. In contrast, some strains may have retained or

acquired some genes which improve survival for specific niches. Pan-genome analysis of large

sets of diverse strains from the same species provide the structure for determining what “core”

genes are present in all or almost all strains versus what genes are only present in a limited subset

of genomes. These core genes should determine the baseline phenotype (capabilities and traits)

of a species. We assert that truly essential genes should typically be a subset of core genes given

that core genes presumably confer fitness advantages that are not necessarily essential but have

been retained for a reason over evolutionary time. Previous pan-genome studies (7) have shown

that species tend to only tolerate the placement of noncore genes between what we call “core

regions” and not within those core regions. Here we define a pan-genome “core gene” as a gene

which is present in at least 95% of the strains of a species. A “core region” on the genome of a

given strain is the minimal region containing a set of adjacent core genes (and no noncore genes)

which are adjacent in all or almost all strains in a species. The reason an organism might

constrain a core region rather than just core genes is that the region may include regulatory

mechanisms such as operons, which allows for co-expression of multiple functionally associated

genes, or regulons which would be disrupted with the insertion of other genes. We believe that


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conservation of core regions in species indicates resistance to insertion of genes through

evolution or through human-mediated genetic engineering.

Here we present a pan-genome based calculation of core regions for B. subtilis spp.

subtilis and for E. coli. These core regions are compared to previous experimentally determined

essential genes from the literature. Our bioinformatics approach saves considerable time and

effort in determining core regions and can broaden our understanding of core genomic loci for

these specific species. The pan-genome approach outlined here provides a method to determine a

set of core regions and their associated metabolic functions which help define a bacterial

species/subspecies. This goes beyond determining which genes are essential for survival in a

defined laboratory setting and addresses what genes are conserved for a specific species. We

would expect that all truly essential genes for the species/subspecies would be a subset of the

core genes/regions since core genes would encompass genes responsible for providing a fitness

advantage in environmental conditions as well as being essential for viability. This approach

automates computational prediction of core genes/regions as an alternative to laborious

experimental methods to determine core genes through knockout studies. The proper

identification of core genes/regions will greatly improve the effectiveness of synthetic biology

and improve our understanding of prokaryotic diversity and phylogeny.


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Results

For B. subtlis, both Kobayashi et al. (2) and Koo et al. (3) used similar single knockout methods

to determine “essential” genes when grown in LB at 37ºC. Koo identified 257 essential genes

while Kobayashi identified 271 essential genes. The union of these two sets results in 305

essential genes (Table 1). The 305 genes were mapped to the pan genome graph (PGG) clusters

using the RefSeq genome NC_000964.3 (BioSample SAMEA3138188). Interestingly through

this mapping, 16 of the essential genes were not identified as core genes. We believe only 9 of

these 16 genes are truly essential. Gene wapI/yxxG (cluster 4769 present in 39 of 108 genomes)

is an antitoxin for the wapA toxin gene which is adjacent to it (present in 85 of 108 genomes) (8).

Gene rttF/yqcF (cluster 4590 present in 46 of 108 genomes) and gene rtbE/yxxD (cluster 4772

present in 53 of 108 genomes) are also the antitoxin of a cognate toxin-antitoxin pair (9). Gene

yezG (cluster 4411 present in 43 of 108 genomes) is also the toxin for a cognate toxin–antitoxin

pair (10). Gene sknR/yqaE (cluster 4643 present in 34 of 108 genomes) is part of a phage-like

region which, if removed would still allow B. subtilis to remain viable (11) possibly because it is

another antitoxin or similar mechanism. Genes bsuMA/ydiO (cluster 4838 present in 24 of 108

genomes) and bsuMB/ydiP (cluster 4839 present in 24 of 108 genomes) are part of a prophage

region of about 15 genes in 48 genomes which includes ydiR and ydiS which are type-2

restriction enzymes. These are not essential genes but they are essential if the restriction enzymes

are present (12).

Another 8 genes are involved in wall teichoic acid (WTA) biosynthesis: Genes tuaB

(cluster 4729 present in 85 of 108 genomes), mnaA/yvyH (cluster 4735 present in 84 of 108

genomes), tagH (cluster 4744 present in 84 of 108 genomes), tagG (cluster 4745 present in 35 of

108 genomes), tagF (cluster 4746 present in 35 of 108 genomes), tagD (cluster 4748 present in


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35 of 108 genomes), tagA (cluster 4749 present in 35 of 108 genomes) and tagB (cluster 4750

present in 35 of 108 genomes). The WTA genes are involved in production of anionic

glycopolymers required for consistent cell shape and division (13). The WTA genes are part of a

31 gene region which has been shown to be dispensable (14) but results in misformed cells with

poor growth properties. Gene rodA (cluster 3994 present in 97 of 108 genomes) appears to be the

exception as it is asserted to be essential for maintaining a rod shape and preventing spherical

cells which lyse (15). Kobayashi et al. (2) stated: “Ten essential genes are involved in cell shape

and division. Septum formation requires seven (ftsA, L, W, and Z, divIB and C, and pbpB; ref.

21), whereas cell shape requires three (rodA, and mreB and C).” Interestingly, genes ftsZ (cluster

1675 present in 105 of 108 genomes) and pbpB (cluster 1662 present in 107 of 108 genomes)

while considered core, using our 95% of genomes definition are the only core genes not present

in all 108 genomes. We investigated these 11 genes further to understand why essential genes did

not appear to be core genes. By examining the PGG we discovered that alternate genes with

homology to the essential genes had replaced the essential genes. Gene pbpB (cluster 1662 in

107 genomes) is replaced in the one remaining genome by cluster 7120 which is also annotated

as pbpB. Gene ftsZ (cluster 1675 in 105 genomes) is replaced in three genones by a four gene

insertion of clusters 8068, 8300, 8069, and 8070 where both 8068 and 8070 are annotated as ftsZ.

Gene rodA (cluster 3994 in 97 genomes) is replaced by either: cluster 8718 (2 genomes) or

clusters 10492, 6436, and 6437 (1 genome) or clusters 6436 and 6437 (8 genomes) where 8718

and 6436 are annotated as rodA. For B. subtilis spp. spizizenii strain W23, poly(ribitol phosphate)

is the main teichoic acid (16) and this was thought to distinguish spp. spizizenii from spp. subtilis

whose type strain 168 has poly(glycerol phosphate) as the main teichoic acid. Further study

found that the ribitol/glycerol distinction does not distinguish between spizizenii and subtilis


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subspecies (17) but rather either subspecies can contain one or the other. Our PGG confirms this

and in fact finds six distinct vairieties of the WTA region. For example the tagD gene (cluster

4748 in 35 genomes) has been replaced by mutlitple orthologs with the same annotation: cluster

3746 (23 genomes), cluster 5431 (43 genomes), cluster 6915 (2 genomes), cluster 7624 (3

genomes), and cluster 8731 (1 genome).

This shows that most essential genes in B. subtilis ssp. subtilis are encompassed by core

genes/regions. There are 258 core regions for B. subtilis (Table 2). The 289 essential genes

which are core genes are contained in only 63 of these regions. These 289 essential genes are not

evenly distributed in these 63 regions (e.g., 46 are in core region 3). Similarly, the 16 essential

genes in non-core regions (the regions between core regions) are contained in only 7 non-core

regions with 8 WTA genes in the non-core region between core regions 206 and 207. A table of

all B. subtilis genes is provided in Supplementary Table 1.

For E. coli, Goodall et al. (4) determined E. coli essential genes using an analysis of

transposon insertion events (TraDIS). The results of their study and two other studies, the Keio

collection (5) and the Profiling of the E. coli Chromosome (PEC) (6) were captured in Table S2

of Goodall et al. Of the 414 genes with overlap between these studies, the 248 essential genes in

common for all three studies are all core genes (Table 3). This set of 248 essential genes should

be the highest quality predictions as determined by all three studies and confirms our assertion

that essential genes should almost always be core genes. The next highest quality set of essential

gene predictions is the 45 essential genes where two of the three studies agree which 41 are core

genes: for Keio-PEC 15 of 16 are core genes, for TraDIS-Keio 8 of 11 are core genes, and for

TraDIS-PEC 18 of 18 are core genes (Table 3). The lowest quality set of essential gene

predictions is the 121 essential genes where only one study agrees which 89 are core genes: for


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Keio only 12 of 22 are core genes, for PEC only 18 of 18 are core genes, and for TraDIS only 59

of 81 are core genes (Table 3). One of the noncore essential genes present in two studies

(TraDIS-Keio), racR, is probably a toxin suppressor which is not essential in the absence of the

toxins. Bindal et al. (18) noted, “We further show that both YdaS and YdaT can act

independently as toxins and that RacR serves to counteract the toxicity by tightly downregulating

the expression of these toxins.” The racR gene is found in only 106 of the 971 genomes in the E.

coli PGG, whereas ydaS and ydaT are found in 106 and 150 genomes respectively, perhaps

arguing that ydaS is the key toxin gene. This recapitulates the pattern we observed in B. subtilis

where toxin suppressor genes are only essential in the presence of toxin genes. Similarly the dicA

gene (TraDIS-Keio) can be deleted if the dicB gene is also deleted. Kato et al. (19) noted: “The

dicA gene encoding a repressor of a cell division inhibitor was deleted in our study with the dicB,

the inhibitor gene.” There are 521 core regions for E. coli (Table 4). The 378 essential genes

which are core genes are contained in only 133 of these regions. These 378 essential genes are

not evenly distributed in these 133 regions (e.g., 27 are in core region 362). Similarly, the 36

essential genes in non-core regions (the regions between core regions) are contained in only 23

non-core regions with 4 in the non-core region between core regions 152 and 153. A table of all

E. coli genes is provided in Supplementary Table 3.


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Discussion

For the purpose of synthetic engineering, determining the set of core regions for a given species

is critical as changes to these regions should be expected to reduce fitness. Core regions indicate

parts of the genome that are conserved across evolution within a species. These regions are not

necessarily required for survival but presumably define the characteristic core genotype which

produces the core phenotype (lifestyle). Since most essential gene studies are carried out under

specific laboratory growth conditions, genes which would normally be essential for a species

across a diverse set of environmental conditions might not be discovered (e.g., due to fluctuating

temperatures). Correspondingly, genes required to out compete rival organisms through

increased fitness or to evade immune responses might not be found under laboratory conditions.

Core regions, therefore, should be a superset of essential genes in most cases but exceptions

might occur for genes which are not needed in a species’ natural niche but are required in a

laboratory setting. Another exception would be for genes which are essential for a particular

strain but not for other strains due to the presence of compensating non-core genes.

Verification of core genes or regions requires experimental studies on specific genomes.

However, it is cost prohibitive to do knockout studies on all strains of a pan-genome. One has to

carefully choose a single genome as a representative of the entire pan-genome for the purpose of

verifying the essentiality of core regions and/or the non-essentiality of noncore regions by

experimental validation. However, given the diversity of most bacterial species it is unlikely that

any one strain completely captures the capabilities of the species in all environmental conditions.

Further, while there are clearly core genes/regions associated with viability for a species, other

core regions probably contribute to a lesser degree to cell viability. For example, for the purpose

of synthetic engineering, changes in these locations may reduce fitness by slowing cell growth.


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The use of a PGG for identifying core regions of a bacterium is an automatable, low-cost,

rapid, and effective way to evaluate both gram-negative and gram-positive bacteria. This method

compliments and expands upon the experimental knockout approach by including environmental

diversity as a measure of what regions and genes are conserved across the species. The approach

also overcomes the limitations of knockout studies that are specific to the strains and conditions

used among other issues. Core region analysis should inform the design of synthetic engineering.

The B. subtilis WTA region provides a cautionary note for relying entirely upon core

regions to determine what is safe to remove. While most non-core regions involve cassettes of

genes which are entirely absent from som strains such as phage regions, sometimes orthologous

replacement possibly due to homologous recombination can have functionally equivalent genes

appearing to be non-core. A closer examination of the PGG can determine if a region is simply

missing from some strains versus being replaced in which case further study may be needed

before removal of the region. Of course in some cases the orthologous replacement does not need

to occur at the same location in the genome but that was the case for all instances in B. subtilis.


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Materials and Methods

For B. subtilis ssp. subtilis and E. coli we selected strains with complete genomes in RefSeq (20).

We restricted our analysis to complete genomes to ensure that missing genes due to incomplete

genome sequencing/assembly did not affect the approach or results. We limited our choice to

RefSeq for two reasons: RefSeq performs a series of quality checks to remove dubious genome

assemblies, and the initial pan-genome construction depends upon reasonably consistent

annotation which RefSeq provides. We extracted the genomes based on organism name: Bacillus

subtilis (we did not specify subspecies, since for many RefSeq genomes a subspecies is not

given) and Esherichia coli (we also specified Shigella since all Shigella species are actually

considered to be the same species as Escherichia coli) (21,22). For each pan-genome we then

compared the genomes using a fast Average Nucleotide Identity (ANI) estimate generated using

MASH (23). We used type strains and ANI to determine which of these genomes were actually

the desired organism. We also used ANI to remove very closely related strains to reduce

oversampling bias (for example for the B. subtilis type strain, 168, has at least 8 genomes in

RefSeq). We used GGRASP (24) to choose a single medoid sequence from any complete linkage

ANI cluster with a threshold of 0.01% or 1/10,000 base pair difference. The strain 168 medoid

genome is the Entrez reference genome for the B. subtilis type strain (GenBank sequence

AL009126.3, BioSample SAMEA3138188, Assembly ASM904v1/GCA_000009045.1) which

can be used to map the Kobayashi and Koo results.

Using this approach, for B. subtilis 143 genomes were downloaded from RefSeq. Of

these 132 genomes were determined to be B. subtilis spp. subtilis based on type strains and ANI.

The minimum ANI between any pair of the 132 B. subtilis spp. subtilis genomes was 97.28%


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whereas the maximum ANI of any of the 11 other genomes to the 132 genomes was 95.73%,

providing good separation between the other subspecies. The 132 genomes were reduced to 109

genomes after removing redundant strains. Finally we removed strain delta6 (BioSample

SAMN05150066) because it is known to have been engineered to remove multiple genes. Thus

we were left with 108 B. subtilis genomes (Supplemental Table 2). For E. coli (and Shigella) we

downloaded 1097 complete genomes from RefSeq. Of these, 1096 were determined using ANI

to actually be E. coli. The non E. coli genome was clearly mislabeled as its maximum ANI to

any other genome was 82.27%. The minimum pairwise ANI of any of the 1096 genomes was

95.53% which is not as tight as for B. subtilis spp. subtilis which is to be expected given that E.

coli is a species grouping not a subspecies grouping. One could arbitrarily try to choose a tighter

grouping around the K-12 reference genome but the pairwise ANI values of the other genomes

compared to the K-12 reference genome vary continuously from 96.22% to 100% with no

punctate break in the values. After removing redundancy 969 E. coli genomes remained. We

added back in two redundant genomes: The K-12 Entrez E. coli reference strain MG1655

(BioSample SAMN02604091) and the K-12 strain BW25113 (GenBank sequence accession

CP009273.1, GenBank Assembly accession ASM75055v1/GCA_000750555.1, GenBank

BioSample accession SAMN03013572) used by Goodall. By using a 95% threshold for the

number of genomes a gene must be in to be considered core, some small number of the 971

genomes (Supplemental Table 4) could be engineered to remove what are normally core genes

and not affect the assignment of core genes.

For B. subtilis ssp. subtilis and E. coli initial pan-genomes were based on the RefSeq

annotation of these genomes. The pan-genome was generated using the pan-genome pipeline at

the J. Craig Venter Institute (JCVI) at the nucleotide level using default parameters (25). This


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produced ortholog clusters using gene context (26) as well as a Pan-Genome Graph (PGG) (7).

The PGG has two main components: nodes representing genes, and edges representing the

sequence between genes and the order and orientation of the genes in the genomes. We updated

the code repository for the JCVI pan-genome pipeline with a script: iterate_pgg_graph.pl, which

calls pgg_annotate.pl for the genomes in the existing PGG in order to ensure consistent

annotation of the genomes and iterates until the PGG stabilizes. The script pgg_annotate.pl uses

an existing PGG to assign regions of a genome to nodes of the graph. This is done by blasting the

medoid sequence for the gene cluster the node represents against the genome and then uses

Needleman-Wunsch (27) to extend the alignment if needed. If there are conflicting blast matches

then the matches are resolved based on which matches are consistent with the structure of the

PGG which encapsulates gene context across the entire pan-genome. Once the nodes of the PGG

are mapped to each of the genomes in the pan-genome a new version of the PGG is intrinsic and

then explicitly extracted. This process is iterated to stability. This ensures that each genome is

consistently annotated so that genes missing from the original annotation of some genomes will

be consistently annotated across all genomes.

The original and refined PGG statistics for B. subtilis and E. coli are provided in Table 5.

The major goal of this reannotation and iteration until stabilization was to achieve consistent

annotation across all genomes in the PGG leading to a more comprehensive and cohesive PGG.

While the RefSeq annotations of these genomes tends to be highly consistent, many small genes

are often arbitrarily called from genome to genome and even some common longer genes can

occasionally be missed. There are three obvious points of improvement in the refined PGG for

both the cluster and edge stats: the number of size 1 clusters/edges significantly decreased due to

some dubious RefSeq gene calls being eliminated and some becoming shared with other


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genomes; the number of core clusters/edges significantly increased showing an improvement in

the consistency of annotation across all genomes; and the number of genes/edges in clusters/edge

instances greatly increased again indicating a much more consistent annotation.

Core regions were determined based on the PGG. Nodes in the PGG were orthologous

clusters of genes. Edges in the PGG represented adjacency of genes (contained in the clusters) in

the underlying genomes. The definition of which genes were or were not considered “core” was

determined relative to a threshold criterion. We used a criterion for core such that 95% or more

of the underlying genome had to contain the cluster or edge. Considering that we used only

complete genomes it might have been possible to use a 100% threshold. However, we opted for a

95% threshold based on prior experience and an abundance of caution to not under call core

genes/edges. Each core region began with a core cluster followed by a core edge (if possible –

otherwise the core region comprises a single cluster) to another core cluster and so on until a

core edge cannot be found to continue the core region. A core region is just a path in the

PGGwhich was then mapped onto any particular genome to determine the core region

coordinates. When the core threshold was below 100% any particular genome may be missing a

cluster (gene) or edge along this path which results in the path being broken into its remaining

constituent parts.

In order to compare core regions to experimentally determined essential genes we needed

a common base of reference. For each of the experimental studies, the genes are specified based

on a reference strain that was used for the experiments and has a complete genome in RefSeq.

For Kobayashi et al., only gene symbols/names were given which we mapped to Entrez GeneIDs

using Entrez search. GeneIDs with no matches were manually curated to estimate the best

matching gene symbol listed in the literature. For Koo, locus IDs were provided giving direct


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access to the gene coordinates for RefSeq accession NC_000964.3 (BioSample

SAMEA3138188, Assembly GCF_000009045.1). For Goodall, we used the data from three

studies in Table S2 from Goodall et al. Gene symbols/names again were all that was available

but these were consistent with the GenBank annotation downloadable in gff format for the K-12

BW25113 reference genome (GenBank accession CP009273.1) used by Goodall (BioSample

SAMN03013572). This gave us coordinates for all essential genes on RefSeq genomes which

were annotated with a PGG which produces a file with coordinates for clusters and edges

mapped to the genome. These coordinates allow us to affiliate essential genes to gene clusters.


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Acknowledgements

This research is based upon work supported [in part] by the Office of the Director of National

Intelligence (ODNI), Intelligence Advanced Research Projects Activity (IARPA) under Finding

Engineering Linked Indicators (FELIX) program contract #N6600118C-4506. The views and

conclusions contained herein are those of the authors and should not be interpreted as necessarily

representing the official policies, either expressed or implied, of ODNI, IARPA, or the U.S.

Government. The U.S. Government is authorized to reproduce and distribute reprints for

governmental purposes notwithstanding any copyright annotation therein.

The authors would like to thank Derren Barken for his assistance in table generation.


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References

1. Hutchison CA, Chuang RY, Noskov VN, Assad-Garcia N, Deerinck TJ, Ellisman MH,

Gill J, Kannan K, Karas BJ, Ma L, Pelletier JF, Qi ZQ, Richter RA, Strychalski EA, Sun

L, Suzuki Y, Tsvetanova B, Wise KS, Smith HO, Glass JI, Merryman C, Gibson DG,

Venter JC. 2016. Design and synthesis of a minimal bacterial genome. Science 351:

aad6253.

2. Kobayashi K, Ehrlich SD, Albertini A, Amati G, Andersen KK, Arnaud M, Asai K,

Ashikaga S, Aymerich S, Bessieres P, Boland F, Brignell SC, Bron S, Bunai K, Chapuis

J, Christiansen LC, Danchin A, Débarbouille M, Dervyn E, Deuerling E, Devine K,

Devine SK, Dreesen O, Errington J, Fillinger S, Foster SJ, Fujita Y, Galizzi A, Gardan R,

Eschevins C, Fukushima T, Haga K, Harwood CR, Hecker M, Hosoya D, Hullo MF,

Kakeshita H, Karamata D, Kasahara Y, Kawamura F, Koga K, Koski P, Kuwana R,

Imamura D, Ishimaru M, Ishikawa S, Ishio I, Le Coq D, Masson A, Mauël C, Meima R,

Mellado RP, Moir A, Moriya S, Nagakawa E, Nanamiya H, Nakai S, Nygaard P, Ogura

M, Ohanan T, O'Reilly M, O'Rourke M, Pragai Z, Pooley HM, Rapoport G, Rawlins JP,

Rivas LA, Rivolta C, Sadaie A, Sadaie Y, Sarvas M, Sato T, Saxild HH, Scanlan E,

Schumann W, Seegers JF, Sekiguchi J, Sekowska A, Séror SJ, Simon M, Stragier P,

Studer R, Takamatsu H, Tanaka T, Takeuchi M, Thomaides HB, Vagner V, van Dijl JM,

Watabe K, Wipat A, Yamamoto H, Yamamoto M, Yamamoto Y, Yamane K, Yata K,

Yoshida K, Yoshikawa H, Zuber U, Ogasawara N. 2003. Essential Bacillus subtilis

genes. Proc Natl Acad Sci U S A. 100: 4678-83.


https://doi.org/10.1101/2020.06.11.147629

3. Koo BM, Kritikos G, Farelli JD, Todor H, Tong K, Kimsey H, Wapinski I, Galardini M,

Cabal A, Peters JM, Hachmann AB, Rudner DZ, Allen KN, Typas A, Gross CA. 2017.

Construction and Analysis of Two Genome-Scale Deletion Libraries for Bacillus subtilis.

Cell Syst. 4:291-305.

4. Goodall ECA, Robinson A, Johnston IG, Jabbari S, Turner KA, Cunningham AF, Lund

PA, Cole JA, Henderson IR. 2018. The Essential Genome of Escherichia coli K-12.

mBio. 20: e02096-17.

5. Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M,

Wanner BL, Mori H. 2006. Construction of Escherichia coli K-12 in-frame, single-gene

knockout mutants: the Keio collection. Mol Syst Biol. 2:2006.0008.

6. Yamazaki Y, Niki H, Kato J. 2008. Profiling of Escherichia coli Chromosome database.

Methods Mol Biol. 416:385–389.

7. Chan AP, Sutton G, DePew J, Krishnakumar R, Choi Y, Huang XZ, Beck E, Harkins

DM, Kim M, Lesho EP, Nikolich MP, Fouts DE. 2015. A novel method of consensus

pan-chromosome assembly and large-scale comparative analysis reveal the highly

flexible pan-genome of Acinetobacter baumannii. Genome Biol. 16:143.

8. Koskiniemi S, Lamoureux JG, Nikolakakis KC, t'Kint de Roodenbeke C, Kaplan MD,

Low DA, Hayes CS. 2013. Rhs proteins from diverse bacteria mediate intercellular

competition. Proc Natl Acad Sci U S A. 110:7032-7.

9. Holberger LE, Garza-Sánchez F, Lamoureux J, Low DA, Hayes CS. 2012. A novel

family of toxin/antitoxin proteins in Bacillus species. FEBS Lett. 586(2):132-6.

10. Brantl S, Müller P. 2019. Toxin-Antitoxin Systems in Bacillus subtilis. Toxins 11: pii:

E262.


https://doi.org/10.1101/2020.06.11.147629

11. Westers H, Dorenbos R, van Dijl JM, Kabel J, Flanagan T, Devine KM, Jude F, Seror SJ,

Beekman AC, Darmon E, Eschevins C, de Jong A, Bron S, Kuipers OP, Albertini AM,

Antelmann H, Hecker M, Zamboni N, Sauer U, Bruand C, Ehrlich DS, Alonso JC, Salas

M, Quax WJ. 2003. Genome engineering reveals large dispensable regions in Bacillus

subtilis. Mol Biol Evol. 20:2076-90.

12. Ohshima H, Matsuoka S, Asai K, Sadaie Y. 2002. Molecular organization of intrinsic

restriction and modification genes BsuM of Bacillus subtilis Marburg. J Bacteriol.

184:381-9.

13. Brown S, Santa Maria Jr, JP, Walker S. 2013. Wall teichoic acids of gram-positive

bacteria. Annu Rev Microbiol. 67:313-36.

14. D'Elia MA, Millar KE, Beveridge TJ, Brown ED. 2006. Wall teichoic acid polymers are

dispensable for cell viability in Bacillus subtilis. J Bacteriol. 188:8313-6.

15. Henriques AO, Glaser P, Piggot PJ, Moran CP Jr. 1998. Control of cell shape and

elongation by the rodA gene in Bacillus subtilis. Mol Microbiol. 28:235-47.

16. Lazarevic V. Abellan F-X, Möller SB, Karamata D, Mauël C. 2002. Comparison of

ribitol and glycerol teichoic acid genes in Bacillius subtilisW23 and 168: Identical

function, similar divergent organization, but different regulation. Microbiology. 148:815-

24.

17. Ahn S, Jun S, Ro H-J, Kim JH, Kim S. 2018. Complete genome of Bacillus subtilis

subsp. subtilis KCTC 3135T and variation in cell wall genes of B. subtilis strains. J

Microbiol Biotechnol. 28:1760-68.


https://doi.org/10.1101/2020.06.11.147629

18. Bindal G, Krishnamurthi R, Seshasayee ASN, Rath D. 2017. CRISPR-Cas-mediated gene

silencing reveals RacR to be a negative regulator of YdaS and YdaT toxins in

Escherichia coli K-12. mSphere. 2:e00483-17.

19. Kato J, Hashimoto M. Construction of consecutive deletions of the Escherichia coli

chromosome. 2007. Mol Syst Biol 3:132.

20. O'Leary NA, Wright MW, Brister JR, Ciufo S, Haddad D, McVeigh R, Rajput B,

Robbertse B, Smith-White B, Ako-Adjei D, Astashyn A, Badretdin A, Bao Y, Blinkova

O, Brover V, Chetvernin V, Choi J, Cox E, Ermolaeva O, Farrell CM, Goldfarb T, Gupta

T, Haft D, Hatcher E, Hlavina W, Joardar VS, Kodali VK, Li W, Maglott D, Masterson

P, McGarvey KM, Murphy MR, O'Neill K, Pujar S, Rangwala SH, Rausch D, Riddick

LD, Schoch C, Shkeda A, Storz SS, Sun H, Thibaud-Nissen F, Tolstoy I, Tully RE,

Vatsan AR, Wallin C, Webb D, Wu W, Landrum MJ, Kimchi A, Tatusova T, DiCuccio

M, Kitts P, Murphy TD, Pruitt KD. 2016. Reference sequence (RefSeq) database at

NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids

Res. 44:D733-45.

21. Lan R, Reeves PR. 2002. Escherichia coli in disguise: molecular origins of Shigella.

Microbes and Infection. 4: 1125-1132.

22. Meier-Kolthoff JP, Hahnke RL, Petersen J, Scheuner C, Michael V, Fiebig A, Rohde C,

Rohde M, Fartmann B, Goodwin LA, Chertkov O, Reddy T, Pati A, Ivanova NN,

Markowitz V, Kyrpides NC, Woyke T, Göker M, Klenk HP. 2014. Complete genome

sequence of DSM 30083(T), the type strain (U5/41(T)) of Escherichia coli, and a

proposal for delineating subspecies in microbial taxonomy. Stand Genomic Sci. 8:9:2.


https://doi.org/10.1101/2020.06.11.147629

23. Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, Phillippy

AM. 2016. Mash: fast genome and metagenome distance estimation using MinHash.

Genome Biol. 17:132.

24. Clarke TH, Brinkac LM, Sutton G, Fouts DE. 2018. GGRaSP: a R-package for selecting

representative genomes using Gaussian mixture models. Bioinformatics. 34:3032-3034.

25. Inman JM, Sutton GG, Beck E, Brinkac LM, Clarke TH, Fouts DE. 2019. Large-scale

comparative analysis of microbial pan-genomes using PanOCT. Bioinformatics. 35:1049-

1050.

26. Fouts DE, Brinkac L, Beck E, Inman J, Sutton G. 2012. PanOCT: automated clustering of

orthologs using conserved gene neighborhood for pan-genomic analysis of bacterial

strains and closely related species. Nucleic Acids Res. 40:e172.

27. Needleman SB, Wunsch CD. 1970. A general method applicable to the search for

similarities in the amino acid sequence of two proteins. J Mol Biol. 48:443-53.


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Table 1. The 305 B. subtilis genes deemed essential by either Kobayashi et al. or Koo et al. These genes are compared to the PGG

based annotation of core regions for the type strain genome used by Kobayashi et al. and Koo et al. (strain 168, GenBank sequence

AL009126.3, BioSample SAMEA3138188, Assembly ASM904v1/GCF_000009045.1). Columns 1-5 are the start, stop, strand,

cluster, and cluster size for the PGG annotation. Columns 6-11 are the gene type, start, stop, strand, locus tag, and gene symbol/name

for the GenBank annotation. Column 12 is a list of synonyms for B. subtilis genes associated with the Koo and Kobayashi genes.

Column 13 is the Koo et al. gene symbol/name. Columns 14-15 are the Kobayashi et al. gene symbol/name and evidence type (from

Supporting Table 4 “RB, reference to study with Bacillus subtilis; RO, reference to study with other bacteria; TW, this work; TW*,

inactivation failed but IPTG mutant could not be made”). Columns 16-17 are the GenBank protein product accession and name.

Column 18 is the PGG core or non-core region the gene is contained in.

PGG Start

PGG Stop PGG

Strand PGG

Cluster

PGG Cluster

Size

Genbank Type

Genbank Start

Genbank Stop

Strand Locus Tag GenBank

Gene Synonyms

Koo Gene

Kobayashi Gene

Kobayashi Evidence

Protein Product Protein Name Region

410 1750 + 2 108 gene 410 1750 + BSU_00010 dnaA dnaH dnaA dnaA RB NP_387882.1 chromosomal replication initiator informational ATPase

core 1

1939 3075 + 3 108 gene 1939 3075 + BSU_00020 dnaN dnaG dnaN dnaN RB NP_387883.1 DNA polymerase III (beta subunit) core 1

4867 6783 + 7 108 gene 4867 6783 + BSU_00060 gyrB novA gyrB gyrB RO NP_387887.1 DNA gyrase (subunit B) core 1

6994 9459 + 8 108 gene 6994 9459 + BSU_00070 gyrA cafB, nalA gyrA gyrA RO NP_387888.1 DNA gyrase (subunit A) core 1

15915 17381 + 15 108 gene 15915 17381 + BSU_00090 guaB gnaB

guaB TW NP_387890.1 inosine-monophosphate dehydrogenase

core 1


https://doi.org/10.1101/2020.06.11.147629

19062 19946 + 17 108 gene 19062 19946 + BSU_00110 pdxS yaaD

map TW* NP_387892.1

glutamine amidotransferase for pyridoxal phosphate synthesis; pyridoxal 5\'-phosphate synthase complex, synthase subunit

core 1

20880 22157 + 19 108 gene 20880 22157 + BSU_00130 serS

serS serS RO NP_387894.1 seryl-tRNA synthetase core 1

26814 28505 + 27 108 gene 26814 28505 + BSU_00190 dnaX dnaH dnaX dnaX TW NP_387900.2 DNA polymerase III subunit tau subunit

core 1

39159 39797 + 41 108 gene 39159 39797 + BSU_00280 tmk yaaP tmk tmk TW NP_387909.2 thymidylate kinase core 1

40665 41654 + 44 108 gene 40665 41654 + BSU_00310 holB yaaS holB holB TW NP_387912.1 DNA polymerase III clamp loader delta\' subunit

core 1

45633 47627 + 51 108 gene 45633 47627 + BSU_00380 metS metG metS metS RO NP_387919.1 methionyl-tRNA synthetase core 1

53516 54385 + 59 108 gene 53516 54385 + BSU_00460 ispE ipk, yabH ispE ispE TW NP_387927.1 4-(cytidine 5\'-diphospho)-2-C-methyl-D-erythritol kinase

core 1

56352 57722 + 63 108 gene 56352 57722 + BSU_00500 glmU tms, tms-

26 gcaD gcaD TW NP_387931.1

bifunctional glucosamine-1-phosphate N-acetyltransferase/UDP-N-acetylglucosamine pyrophosphorylase

core 1

57745 58698 + 64 108 gene 57745 58698 + BSU_00510 prs

prs prs TW NP_387932.1 phosphoribosylpyrophosphate synthetase

core 1

59504 60070 + 66 108 gene 59504 60070 + BSU_00530 pth

pth spoVC RB, TW NP_387934.1 peptidyl-tRNA hydrolase core 1

69168 69545 + 75 108 gene 69168 69545 + BSU_00620 divIC divIB, dds divIC divIC TW NP_387943.1 cell-division initiation protein core 1

74929 76347 + 82 108 gene 74929 76347 + BSU_00670 tilS

tilS yacA TW NP_387948.1 tRNA(ile2) lysidine synthetase core 1

85737 86594 + 92 108 gene 85737 86594 + BSU_00770 folP

sul

NP_387958.1 dihydropteroate synthase core 1

86587 86949 + 93 108 gene 86587 86949 + BSU_00780 folB folA, yacE folB hprT TW NP_387959.1 dihydroneopterin aldolase core 1

86946 87449 + 94 108 gene 86946 87449 + BSU_00790 folK

folK

NP_387960.1 7,8-dihydro-6-hydroxymethylpterin pyrophosphokinase

core 1

88727 90226 + 97 108 gene 88727 90226 + BSU_00820 lysS

lysS lysS TW NP_387963.1 lysyl-tRNA synthetase core 1


https://doi.org/10.1101/2020.06.11.147629

109789 110487 + 120 108 gene 109789 110487 + BSU_00900 ispD

ispD yacM TW NP_387971.1 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, nonmevalonate isoprenoid pathway

core 3

110480 110956 + 121 108 gene 110480 110956 + BSU_00910 ispF

ispF yacN TW NP_387972.1 2-C-methyl-D-erythritol-2,4-cyclodiphosphate synthase

core 3

111047 112498 + 122 108 gene 111047 112498 + BSU_00920 gltX

gltX gltX RO NP_387973.1 glutamyl-tRNA synthetase core 3

113450 114850 + 124 108 gene 113450 114850 + BSU_00940 cysS spnA cysS cysS RO NP_387975.1 dual cysteinyl-tRNA synthetase; cysteine persulfide synthase

core 3

117349 117498 + 129 108 gene 117349 117498 + BSU_00990 rpmGB rpmG, rpmG2

rpmGB RO NP_387980.1 ribosomal protein L33 core 3

117532 117711 + 130 108 gene 117532 117711 + BSU_01000 secE

secE secE RB NP_387981.1 preprotein translocase subunit core 3

119111 119809 + 133 108 gene 119111 119809 + BSU_01030 rplA

rplA RO NP_387984.2 ribosomal protein L1 (BL1) core 3

120061 120561 + 134 108 gene 120061 120561 + BSU_01040 rplJ

rplJ rplJ RO NP_387985.2 ribosomal protein L10 (BL5) core 3

120607 120978 + 135 108 gene 120607 120978 + BSU_01050 rplL

rplL rplL RO NP_387986.1 ribosomal protein L12 (BL9) core 3

121919 125500 + 137 108 gene 121919 125500 + BSU_01070 rpoB crsE, rfm rpoB rpoB RO NP_387988.2 RNA polymerase (beta subunit) core 3

125562 129161 + 138 108 gene 125562 129161 + BSU_01080 rpoC lpm, std rpoC rpoC TW NP_387989.2 RNA polymerase (beta\' subunit) core 3

129702 130118 + 140 108 gene 129702 130118 + BSU_01100 rpsL psL, fun,

strA rpsL rpsL RO NP_387991.2 ribosomal protein S12 (BS12) core 3

130160 130630 + 141 108 gene 130160 130630 + BSU_01110 rpsG

rpsG rpsG RO NP_387992.2 ribosomal protein S7 (BS7) core 3

130684 132762 + 142 108 gene 130684 132762 + BSU_01120 fusA fus fusA fusA TW NP_387993.2 elongation factor G core 3

132882 134072 + 143 108 gene 132882 134072 + BSU_01130 tufA tuf tufA tufA TW* NP_387994.1 elongation factor Tu core 3

135364 135672 + 145 108 gene 135364 135672 + BSU_01150 rpsJ tetA rpsJ rpsJ RO NP_387996.1 ribosomal protein S10 (BS13); transcription antitermination factor

core 3

135712 136341 + 146 108 gene 135712 136341 + BSU_01160 rplC

rplC rplC RO NP_387997.1 ribosomal protein L3 (BL3) core 3

136369 136992 + 147 108 gene 136369 136992 + BSU_01170 rplD

rplD rplD RO NP_387998.1 ribosomal protein L4 core 3

136992 137279 + 148 108 gene 136992 137279 + BSU_01180 rplW

rplW rplW RO NP_387999.2 ribosomal protein L23 core 3

137311 138144 + 149 108 gene 137311 138144 + BSU_01190 rplB

rplB rplB RO NP_388000.2 ribosomal protein L2 (BL2) core 3


https://doi.org/10.1101/2020.06.11.147629

138202 138480 + 150 108 gene 138202 138480 + BSU_01200 rpsS

rpsS rpsS RO NP_388001.1 ribosomal protein S19 (BS19) core 3

138497 138838 + 151 108 gene 138497 138838 + BSU_01210 rplV

rplV rplV RO NP_388002.1 ribosomal protein L22 (BL17) core 3

138842 139498 + 152 108 gene 138842 139498 + BSU_01220 rpsC

rpsC rpsC RO NP_388003.2 ribosomal protein S3 (BS3) core 3

139500 139934 + 153 108 gene 139500 139934 + BSU_01230 rplP

rplP rplP RO NP_388004.1 ribosomal protein L16 core 3

139924 140124 + 154 108 gene 139924 140124 + BSU_01240 rpmC

rpmC RO NP_388005.1 ribosomal protein L29 core 3

140147 140410 + 155 108 gene 140147 140410 + BSU_01250 rpsQ

rpsQ rpsQ RO NP_388006.1 ribosomal protein S17 (BS16) core 3

140451 140819 + 156 108 gene 140451 140819 + BSU_01260 rplNA

rplNA rplN RO NP_388007.1 ribosomal protein L14 core 3

140857 141168 + 157 108 gene 140857 141168 + BSU_01270 rplX

rplX rplX RO NP_388008.1 ribosomal protein L24 (BL23) core 3

141195 141734 + 158 108 gene 141195 141734 + BSU_01280 rplE

rplE rplE RO NP_388009.1 ribosomal protein L5 (BL6) core 3

141757 141942 + 159 108 gene 141757 141942 + BSU_01290 rpsNA rpsZ rpsNA rpsN RO NP_388010.1 ribosomal protein S14 core 3

141974 142372 + 160 108 gene 141974 142372 + BSU_01300 rpsH

rpsH rpsH RO NP_388011.2 ribosomal protein S8 (BS8) core 3

142402 142941 + 161 108 gene 142402 142941 + BSU_01310 rplF

rplF rplF RO NP_388012.1 ribosomal protein L6 (BL8) core 3

142974 143336 + 162 108 gene 142974 143336 + BSU_01320 rplR

rplR rplR RO NP_388013.2 ribosomal protein L18 core 3

143361 143861 + 163 108 gene 143361 143861 + BSU_01330 rpsE spcA rpsE rpsE RO NP_388014.1 ribosomal protein S5 core 3

143875 144054 + 164 108 gene 143875 144054 + BSU_01340 rpmD

rpmD rpmD RO NP_388015.1 ribosomal protein L30 (BL27) core 3

144085 144525 + 165 108 gene 144085 144525 + BSU_01350 rplO

rplO RO NP_388016.1 ribosomal protein L15 core 3

144527 145822 + 166 108 gene 144527 145822 + BSU_01360 secY

secY secY RB NP_388017.1 preprotein translocase subunit core 3

145877 146530 + 167 108 gene 145877 146530 + BSU_01370 adk

adk adk TW* NP_388018.1 adenylate kinase core 3

147585 147803 + 170 108 gene 147585 147803 + BSU_01390 infA

infA infA TW NP_388020.1 initiation factor IF-I core 3

147837 147950 + 171 108 gene 147837 147950 + BSU_01400 rpmJ

rpmJ RO NP_388021.1 ribosomal protein L36 (ribosomal protein B)

core 3

147973 148338 + 172 108 gene 147973 148338 + BSU_01410 rpsM

rpsM rpsM RO NP_388022.2 ribosomal protein S13 core 3

148359 148754 + 173 108 gene 148359 148754 + BSU_01420 rpsK

rpsK rpsK RO NP_388023.1 ribosomal protein S11 (BS11) core 3

148931 149875 + 174 108 gene 148931 149875 + BSU_01430 rpoA

rpoA rpoA RO NP_388024.1 RNA polymerase (alpha subunit) core 3

149953 150315 + 175 108 gene 149953 150315 + BSU_01440 rplQ

rplQ rplQ RO NP_388025.1 ribosomal protein L17 (BL15) core 3

153842 154279 + 180 108 gene 153842 154279 + BSU_01490 rplM

rplM rplM RO NP_388030.2 ribosomal protein L13 core 3

154300 154692 + 181 108 gene 154300 154692 + BSU_01500 rpsI

rpsI rpsI RO NP_388031.1 ribosomal protein S9 core 3

198497 199843 + 228 108 gene 198497 199843 + BSU_01770 glmM

glmM ybbT TW NP_388058.1 phosphoglucosamine mutase core 7


https://doi.org/10.1101/2020.06.11.147629

200277 202079 + 229 108 gene 200277 202079 + BSU_01780 glmS gcaA, ybxD glmS glmS TW NP_388059.1 L-glutamine-D-fructose-6-phosphate amidotransferase

core 7

338288 339106 + 358 108 gene 338288 339106 + BSU_03130 nadE outB nadE nadE RB NP_388195.1 ammonium-dependent NAD+ synthetase

core 19

340025 340585 + 360 108 gene 340025 340585 + BSU_03150 aroK aroI aroK

NP_388197.2 shikimate kinase core 19

508227 509312 + 510 108 gene 508248 509312 + BSU_04560 ddlA ddlA ddl ddl TW NP_388337.1 D-alanyl-D-alanine ligase A core 29

509384 510757 + 511 108 gene 509384 510757 + BSU_04570 murF ydbQ murF murF TW NP_388338.1 UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate-D-alanyl-D-alanine ligase

core 29

515710 516075 + 516 108 gene 515710 516075 + BSU_04620 acpS ydcB acpS acpS TW NP_388343.1 holo-acyl carrier protein synthase (phosphopantetheinyl transferase)

core 30

517372 518541 + 518 108 gene 517372 518541 + BSU_04640 alrA dal alrA alr TW NP_388345.1 D-alanine racemase core 30

641654 642130 + 670 108 gene 641654 642130 + BSU_05910 tsaE

ydiB TW NP_388472.1 tRNA(NNU) t(6)A37 threonylcarbamoyladenosine modification; ADP binding protein

core 45

642111 642800 + 671 108 gene 642111 642800 + BSU_05920 tsaB ydiC ydiC ydiC TW NP_388473.1

tRNA(NNU) t(6)A37 threonylcarbamoyladenosine modification; protease involved in TsaD function

core 45

643258 644298 + 673 108 gene 643258 644298 + BSU_05940 tsaD gcp, ydiE gcp gcp TW NP_388475.1

tRNA(NNU) t(6)A37 threonylcarbamoyladenosine modification; glycation binding protein

core 45

649903 650187 + 681 108 gene 649903 650187 + BSU_06020 groES mopB groES groES RB NP_388483.2 chaperonin small subunit core 46

650234 651868 + 682 108 gene 650234 651868 + BSU_06030 groEL mopA groEL groEL RB NP_388484.1 chaperonin large subunit core 46

655223 656506 + 4838 24 gene 655223 656506 + BSU_06060 bsuMA

ydiO ydiO RB, TW NP_388487.1 DNA-methyltransferase (cytosine-specific); prophage 3 region

non-core 46-

47


https://doi.org/10.1101/2020.06.11.147629

656528 657697 + 4839 24 gene 656528 657697 + BSU_06070 bsuMB

ydiP ydiP RB, TW NP_388488.1 DNA-methyltransferase (cytosine-specific); defective prophage 3

non-core 46-

47

719370 721589 + 738 108 gene 719370 721589 + BSU_06610 pcrA yerF pcrA pcrA RB, TW NP_388543.1 ATP-dependent DNA helicase core 50

721613 723619 + 739 108 gene 721613 723619 + BSU_06620 ligA lig, yerG ligA ligA TW NP_388544.1 DNA ligase (NAD-dependent) core 50

728732 729022 + 745 108 gene 728732 729022 + BSU_06670 gatC yedA, yerL gatC gatC RO NP_388549.1 glutamyl-tRNA(Gln) amidotransferase (subunit C)

core 51

729038 730495 + 746 108 gene 729038 730495 + BSU_06680 gatA yedB, yerM gatA gatA TW NP_388550.1 glutamyl-tRNA(Gln) amidotransferase (subunit A)

core 51

730509 731939 + 747 108 gene 730509 731939 + BSU_06690 gatB yerN gatB gatB TW NP_388551.2 glutamyl-tRNA(Gln) amidotransferase (subunit B)

core 51

736436 737347 + 750 108 gene 736436 737347 + BSU_06720 dagK dgkB

yerQ TW NP_388554.1 diacylglycerol kinase core 51

747079 747534 - 4411 43 gene 747079 747534 - BSU_06811 yezG yeeE yezG

YP_003097692.1 conserved hypothetical protein; HGT island

non-core 52-

53

970135 970617 + 976 108 gene 970135 970617 + BSU_08930 trmL ygaR

cspR TW NP_388774.2 tRNA (cytidine(34)-2\'-O)-methyltransferase

core 74

1028511 1029587 - 1054 108 gene 1028511 1029587 - BSU_09510 asiMA

yhdL yhdL TW NP_388832.1 negative regulator of the activity of sigma-M

core 77

1031395 1031994 + 1057 108 gene 1031395 1031994 + BSU_09540 plsC

plsC yhdO TW NP_388835.1 1-acylglycerol-phosphate (1-acyl-G3P) acyltransferase

core 77

1070364 1071242 - 1098 108 gene 1070364 1071242 - BSU_09950 prsA

prsA prsA TW NP_388876.1 molecular chaperone lipoprotein core 78

1209183 1210424 + 1230 108 gene 1209183 1210424 + BSU_11340 fabF yjaY fabF fabF TW* NP_389016.1 beta-ketoacyl-acyl carrier protein synthase II (involved in pimelate synthesis)

core 88

1218113 1219105 - 1238 108 gene 1218113 1219105 - BSU_11420 trpS

trpS trpS RO NP_389024.1 tryptophanyl-tRNA synthetase core 89


https://doi.org/10.1101/2020.06.11.147629

1237660 1238460 + 1260 108 gene 1237660 1238460 + BSU_11610 ppnKA nadF, yjbN ppnKA ppnK TW NP_389043.1 inorganic polyphosphate/ATP-NAD kinase (quinolate activated)

core 89

1321329 1321670 - 1381 108 gene 1321329 1321670 - BSU_12510 xre

xre

NP_389133.1 phage PBSX transcriptional regulator core 96

1396013 1397368 + 1468 108 gene 1396013 1397368 + BSU_13300 mgtE ykoK mgtE

NP_389213.1 magnesium transporter core 100

1471857 1473038 - 1541 108 gene 1471857 1473038 - BSU_14000 dapX uat patA

NP_389283.2 N-acetyl-L,L-diaminopimelate aminotransferase

core 103

1488973 1489683 + 1559 108 gene 1488973 1489683 + BSU_14180 dapH

dapH ykuQ TW NP_389301.2 tetrahydrodipicolinate N-acetyltransferase

core 104

1489753 1490877 + 1560 108 gene 1489753 1490877 + BSU_14190 dapI

dapL ykuR TW NP_389302.1 N-acetyl-diaminopimelate deacetylase

core 104

1523118 1524785 - 1595 108 gene 1523118 1524785 - BSU_14530 rnjA rnjA rnjA ykqC TW NP_389336.1 ribonuclease J1 core 106

1528326 1529441 + 1601 108 gene 1528326 1529441 + BSU_14580 pdhA aceA

pdhA RB NP_389341.1 pyruvate dehydrogenase (E1 alpha subunit)

core 106

1552412 1552693 + 1629 108 gene 1552412 1552693 + BSU_14840 ylaN

ylaN ylaN TW NP_389367.1 conserved hypothetical protein core 108

1552899 1554110 + 1630 108 gene 1552899 1554110 + BSU_14850 ftsW ylaO ftsW ftsW TW NP_389368.1 cell-division protein; transporter of lipid-linked cell wall precursors

core 108

1570078 1570563 + 1647 108 gene 1570078 1570563 + BSU_15020 coaD ylbI coaD

NP_389385.1 phosphopantetheine adenylyltransferase

core 109

1575804 1575983 + 1654 108 gene 1575804 1575983 + BSU_15080 rpmF

rpmF RO NP_389391.1 ribosomal protein L32 core 110

1581597 1581950 + 1661 108 gene 1581597 1581950 + BSU_15150 ftsL yllD, ylxB ftsL ftsL RB NP_389398.1 cell-division protein core 110

1581947 1584097 + 1662 107 gene 1581947 1584097 + BSU_15160 pbpB

pbpB pbpB RB NP_389399.2 penicillin-binding protein 2B core 110

1586330 1587814 + 1664 108 gene 1586330 1587814 + BSU_15180 murE

murE murE RO NP_389401.1 UDP-N-acetylmuramoylalanyl-D-glutamate-2, 6-diaminopimelate ligase

core 110

1587926 1588900 + 1665 108 gene 1587926 1588900 + BSU_15190 mraY

mraY mraY RO NP_389402.2 phospho-N-acetylmuramoyl-pentapeptide undecaprenyl phosphate (C55P) transferase

core 110


https://doi.org/10.1101/2020.06.11.147629

1588901 1590256 + 1666 108 gene 1588901 1590256 + BSU_15200 murD

murD murD RB NP_389403.1 UDP-N-acetylmuramoylalanyl-D-glutamate ligase

core 110

1591540 1592631 + 1668 108 gene 1591540 1592631 + BSU_15220 murG

murG murG RB NP_389405.2

UDP-N-acetylglucosamine-N-acetylmuramyl-(pentapeptide)pyrophosphoryl-undecaprenol N-acetylglucosamine transferase

core 110

1592663 1593574 + 1669 108 gene 1592663 1593574 + BSU_15230 murB ylxC murB murB RB NP_389406.1 UDP-N-acetylenolpyruvoylglucosamine reductase

core 110

1593704 1594495 + 1670 108 gene 1593704 1594495 + BSU_15240 divIB dds divIB divIB RB NP_389407.1 cell-division initiation protein core 110

1596474 1597796 + 1674 108 gene 1596474 1597796 + BSU_15280 ftsA

ftsA ftsA RB NP_389411.2 cell-division protein essential for Z-ring assembly

core 110

1597832 1598980 + 1675 105 gene 1597832 1598980 + BSU_15290 ftsZ

ftsZ ftsZ RB NP_389412.2 cell-division initiation protein core 110

1613357 1616122 + 1689 108 gene 1613357 1616122 + BSU_15430 ileS

ileS ileS RO NP_389426.2 isoleucyl-tRNA synthetase core 110

1641949 1642563 + 1714 108 gene 1641949 1642563 + BSU_15680 gmk yloD gmk gmk TW NP_389450.2 guanylate kinase core 111

1642851 1644071 + 1716 108 gene 1642851 1644071 + BSU_15700 coaBC yloI coaBC

NP_389452.1

coenzyme A biosynthesis bifunctional protein CoaBC; phosphopantothenoylcysteine synthetase/decarboxylase

core 111

1644068 1646485 + 1717 108 gene 1644068 1646485 + BSU_15710 priA yloJ priA priA RB, TW NP_389453.1 primosomal replication factor Y (primosomal protein N\')

core 111

1646999 1647952 + 1719 108 gene 1646999 1647952 + BSU_15730 fmt yloL

fmt TW NP_389455.1 methionyl-tRNA formyltransferase core 111

1653103 1653999 + 1724 108 gene 1653103 1653999 + BSU_15780 rsgA cpgA, engC

yloQ TW NP_389460.1 GTPase involved in ribosome biogenesis

core 111

1655599 1655787 - 1728 108 gene 1655599 1655787 - BSU_15820 rpmB yloT

rpmB RO NP_389464.1 ribosomal protein L28 core 111

1662547 1663548 + 1735 108 gene 1662547 1663548 + BSU_15890 plsX ylpD plsX plsX TW NP_389471.1 phosphate:acyl-ACP acyltransferase core 111

1663567 1664520 + 1736 108 gene 1663567 1664520 + BSU_15900 fabD ylpE fabD fabD TW NP_389472.1 malonyl CoA:acyl carrier protein transacylase

core 111


https://doi.org/10.1101/2020.06.11.147629

1664513 1665253 + 1737 108 gene 1664513 1665253 + BSU_15910 fabG ylpF fabG fabG TW NP_389473.1 beta-ketoacyl-acyl carrier protein reductase

core 111

1665337 1665570 + 1738 108 gene 1665337 1665570 + BSU_15920 acpA acpP acpA acpA RO NP_389474.1 acyl carrier protein core 111

1665710 1666459 + 1739 108 gene 1665710 1666459 + BSU_15930 rnc

rnc, rncS rnc rnc RB NP_389475.1 ribonuclease III

core 111

1666560 1670120 + 1740 108 gene 1666560 1670120 + BSU_15940 smc ylqA smc smc RB, TW NP_389476.2 chromosome condensation and segregation SMC ATPase

core 111

1670140 1671129 + 1741 108 gene 1670140 1671129 + BSU_15950 ftsY srb ftsY ftsY RB NP_389477.1 signal recognition particle (docking protein)

core 111

1672174 1673514 + 1744 108 gene 1672174 1673514 + BSU_15980 ffh

ffh ffh RB NP_389480.1 signal recognition particle-like (SRP) GTPase

core 112

1673620 1673892 + 1745 108 gene 1673620 1673892 + BSU_15990 rpsP

rpsP rpsP RO NP_389481.1 ribosomal protein S16 (BS17) core 112

1675171 1675902 + 1749 108 gene 1675171 1675902 + BSU_16030 trmD

trmD trmD TW NP_389485.1 tRNA(m1G37)methyltransferase core 112

1676042 1676389 + 1750 108 gene 1676042 1676389 + BSU_16040 rplS

rplS rplS RO NP_389486.2 ribosomal protein L19 core 112

1676532 1677380 + 1751 108 gene 1676532 1677380 + BSU_16050 rbgA

rbgA ylqF RB, TW NP_389487.1 ribosome biogenesis GTPase A core 112

1683661 1685736 + 1758 108 gene 1683661 1685736 + BSU_16120 topA topI

topA TW NP_389494.1 DNA topoisomerase I core 112

1717933 1718673 + 1796 108 gene 1717933 1718673 + BSU_16490 rpsB

rpsB rpsB RO NP_389531.1 ribosomal protein S2 core 112

1718775 1719656 + 1797 108 gene 1718775 1719656 + BSU_16500 tsf

tsf tsf TW NP_389532.1 elongation factor Ts core 112

1719802 1720524 + 1798 108 gene 1719802 1720524 + BSU_16510 pyrH smbA pyrH

NP_389533.2 uridylate kinase core 112

1720526 1721083 + 1799 108 gene 1720526 1721083 + BSU_16520 frr

frr frr TW NP_389534.1 ribosome recycling factor core 112

1721214 1721996 + 1800 108 gene 1721214 1721996 + BSU_16530 uppS yluA uppS

NP_389535.1 undecaprenyl pyrophosphate synthase

core 112

1722000 1722809 + 1801 108 gene 1722000 1722809 + BSU_16540 cdsA

cdsA cdsA TW NP_389536.1 phosphatidate cytidylyltransferase (CDP-diglyceride synthase)

core 112

1722871 1724022 + 1802 108 gene 1722871 1724022 + BSU_16550 dxr yluB dxr dxr TW NP_389537.2 1-deoxy-D-xylulose-5-phosphate reductoisomerase

core 112

1725330 1727024 + 1804 108 gene 1725330 1727024 + BSU_16570 proS

proS proS RO NP_389539.1 prolyl-tRNA synthetase core 112

1727133 1731446 + 1805 108 gene 1727133 1731446 + BSU_16580 polC dnaF, mutI polC polC RB, TW NP_389540.1 DNA polymerase III (alpha subunit) core 112


https://doi.org/10.1101/2020.06.11.147629

1732281 1733396 + 1807 108 gene 1732281 1733396 + BSU_16600 nusA

nusA nusA RB NP_389542.1 transcription translation coupling factor involved in Rho-dependent transcription termination

core 113

1734009 1736159 + 1810 108 gene 1734009 1736159 + BSU_16630 infB

infB infB TW NP_389545.1 initiation factor IF-2 core 113

1737834 1738784 + 1814 108 gene 1737834 1738784 + BSU_16670 ribC

ribC

NP_389549.1 bifunctional riboflavin kinase FAD synthase

core 113

1738941 1739210 + 1815 108 gene 1738941 1739210 + BSU_16680 rpsO

rpsO rpsO RO NP_389550.1 ribosomal protein S15 (BS18) core 113

1745991 1747031 + 1822 108 gene 1745991 1747031 + BSU_16750 asd

asd asd TW NP_389557.1 aspartate-semialdehyde dehydrogenase

core 113

1747123 1748337 + 1823 108 gene 1747123 1748337 + BSU_16760 dapG lssD dapG

NP_389558.2 aspartokinase I (alpha and beta subunits)

core 113

1748368 1749240 + 1824 108 gene 1748368 1749240 + BSU_16770 dapA

dapA dapA TW NP_389559.1 4-hydroxy-tetrahydrodipicolinate synthase

core 113

1762623 1763204 + 1837 108 gene 1762623 1763204 + BSU_16920 pgsA ymfN pgsA pgsA TW NP_389574.2 CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase

core 113

1767310 1768872 + 1841 108 gene 1767310 1768872 + BSU_16960 rny

ymdA TW NP_389578.1 endoribonuclease Y core 113

1868617 1869009 + 1884 108 gene 1868617 1869009 + BSU_17370 nrdI

nrdI ymaA TW NP_389619.1 co-factor of ribonucleotide diphosphate reductase

core 115

1868969 1871071 + 1885 108 gene 1868969 1871071 + BSU_17380 nrdE nrdA nrdE nrdE RB NP_389620.1 ribonucleoside-diphosphate reductase (major subunit)

core 115

1871089 1872078 + 1886 108 gene 1871089 1872078 + BSU_17390 nrdF

nrdF nrdF RB NP_389621.1 ribonucleoside-diphosphate reductase (minor subunit)

core 115

1919861 1921864 + 1996 108 gene 1919861 1921864 + BSU_17890 tktA

tkt TW NP_389672.1 transketolase core 127

1922549 1922767 + 1998 108 gene 1922549 1922767 + BSU_17910 yneF yoxG yneF

NP_389674.1 putative acyltransferase core 127

1931920 1932501 - 2015 108 gene 1931920 1932501 - BSU_18070 plsY

plsY yneS TW NP_389689.1 acylphosphate:glycerol-3-phosphate O-acyltransferase

core 128

1933477 1935444 + 2017 108 gene 1933477 1935444 + BSU_18090 parE grlB parE parE RB NP_389691.2 subunit B of DNA topoisomerase IV (ATP-dependent)

core 128


https://doi.org/10.1101/2020.06.11.147629

1935448 1937868 + 2018 108 gene 1935448 1937868 + BSU_18100 parC grlA parC parC RB NP_389692.2 subunit A of DNA topoisomerase IV (ATP-dependent)

core 128

2107505 2108758 - 2115 108 gene 2107505 2108758 - BSU_19360 odhB citM

odhB TW NP_389818.2 2-oxoglutarate dehydrogenase complex (dihydrolipoamide transsuccinylase, E2 subunit)

core 137

2296603 2297109 - 2181 108 gene 2296603 2297109 - BSU_21810 dfrA

dfrA dfrA TW NP_390064.1 dihydrofolate reductase core 140

2345433 2346131 - 2240 108 gene 2345433 2346131 - BSU_22350 dnaD

dnaD dnaD RB NP_390116.1 DNA-remodelling primosomal protein

core 142

2346224 2347516 - 2241 108 gene 2346224 2347516 - BSU_22360 asnS

asnS RO NP_390117.1 asparaginyl-tRNA synthetase core 142

2354918 2355895 - 2249 108 gene 2354918 2355895 - BSU_22440 birA

birA birA TW NP_390125.1 biotin acetyl-CoA-carboxylase ligase and biotin regulon repressor (BirA-biotinoyl-5\'-AMP)

core 142

2355880 2357073 - 2250 108 gene 2355880 2357073 - BSU_22450 cca papS, ypjI cca cca TW NP_390126.1 tRNA nucleotidyltransferase core 142

2359340 2360143 - 2254 108 gene 2359340 2360143 - BSU_22490 dapB

dapB dapB TW NP_390130.1 (4S)-4-hydroxy-2,3,4, 5-tetrahydro-(2S)-dipicolinic acid (HTPA) dehydratase reductase

core 142

2367954 2369240 - 2265 108 gene 2367954 2369240 - BSU_22600 aroA

aroE

NP_390141.1

3-phosphoshikimate 1-carboxyvinyltransferase (5-enolpyruvoylshikimate-3-phosphate synthase)

core 142

2379100 2380272 - 2276 108 gene 2379100 2380272 - BSU_22710 aroF aroF aroF

NP_390152.3 chorismate synthase core 142

2381919 2382965 - 2279 108 gene 2381919 2382965 - BSU_22740 hepT gerC3, gerCC, hepB

hepT RB NP_390155.1

heptaprenyl diphosphate synthase component II

core 142

2383615 2384370 - 2281 108 gene 2383615 2384370 - BSU_22760 hepS gerC1, gerCA, hepA

hepS RB NP_390157.1

heptaprenyl diphosphate synthase component I

core 142

2384783 2385355 - 2283 108 gene 2384783 2385355 - BSU_22780 folEA folE, mtrA folEA

NP_390159.1 GTP cyclohydrolase I core 142


https://doi.org/10.1101/2020.06.11.147629

2385543 2385821 - 2284 108 gene 2385543 2385821 - BSU_22790 hbs hupA,

dbpA, hbsU hbs hbs RB NP_390160.1

non-specific DNA-binding protein HBsu

core 142

2389151 2390188 - 2288 108 gene 2389151 2390188 - BSU_22830 gpsA glyC

gpsA RB NP_390164.1 NADPH-dependent glycerol-3-phosphate dehydrogenase

core 142

2390206 2391516 - 2289 108 gene 2390206 2391516 - BSU_22840 der

engA yphC RB, TW NP_390165.1 GTPase essential for ribosome 50S subunit assembly (maturation of the 50S subunit central protoberance)

core 142

2396045 2396719 - 2296 108 gene 2396045 2396719 - BSU_22890 cmk jofC, ypfC, cmk cmk RB NP_390170.1 cytidylate kinase core 143

2417984 2419159 - 2319 108 gene 2417984 2419159 - BSU_23130 resC ypxC

resC RB NP_390194.2 factor required for cytochrome c synthesis

core 143

2419179 2420807 - 2320 108 gene 2419179 2420807 - BSU_23140 resB ypxB

resB RB NP_390195.1 factor required for cytochrome c synthesis

core 143

2420804 2421343 - 2321 108 gene 2420804 2421343 - BSU_23150 resA ypxA

resA RB NP_390196.2 extracytoplasmic thioredoxin involved in cytochrome c maturation (lipoprotein)

core 143

2425248 2425841 - 2327 108 gene 2425248 2425841 - BSU_23210 spcB

ypuH RB, TW NP_390202.1 chromosome condensation and segregation factor

core 143

2425831 2426586 - 2328 108 gene 2425831 2426586 - BSU_23220 scpA

scpA ypuG RB, TW NP_390203.1 chromosome condensation and partitioning factor

core 143

2478006 2478929 - 2411 108 gene 2478006 2478929 - BSU_23840 rnz

rnz yqjK TW NP_390265.1 ribonuclease Z core 146

2523713 2525614 - 2456 108 gene 2523713 2525614 - BSU_24270 dxs yqiE dxs dxs TW NP_390307.1 1-deoxyxylulose-5-phosphate synthase

core 146

2525789 2526679 - 2457 108 gene 2525789 2526679 - BSU_24280 ispA

yqiD TW NP_390308.2 farnesyl diphosphate synthase core 146

2528404 2529255 - 2460 108 gene 2528404 2529255 - BSU_24310 folD yqiA

folD TW NP_390311.1

methylenetetrahydrofolate dehydrogenase; methenyltetrahydrofolate cyclohydrolase

core 146

2530354 2531706 - 2463 108 gene 2530354 2531706 - BSU_24340 accC

accC1, yqhX

accC accC TW NP_390314.2 acetyl-CoA carboxylase subunit (biotin carboxylase subunit)

core 146


https://doi.org/10.1101/2020.06.11.147629

2531718 2532197 - 2464 108 gene 2531718 2532197 - BSU_24350 accB fabE, yqhW accB accB TW NP_390315.1 acetyl-CoA carboxylase subunit (biotin carboxyl carrier subunit)

core 146

2574408 2574557 - 2522 108 gene 2574408 2574557 - BSU_24900 rpmGA rpmG1

rpmGA RO NP_570908.2 ribosomal protein L33 core 148

2589123 2590256 + 2538 108 gene 2589123 2590256 + BSU_25070 ispG yqfY ispG yqfY TW NP_390386.1

4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase)

core 150

2596535 2597479 + 2547 108 gene 2596535 2597479 + BSU_25160 ispH

ispH yqfP TW NP_390395.2 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase

core 150

2600214 2601329 - 2551 108 gene 2600214 2601329 - BSU_25200 sigA rpoD sigA sigA TW NP_390399.2 RNA polymerase major sigma-43 factor (sigma-A)

core 150

2601528 2603339 - 2552 108 gene 2601528 2603339 - BSU_25210 dnaG dnaE dnaG dnaG RB NP_390400.2 DNA primase core 150

2605730 2607769 - 2556 108 gene 2605730 2607769 - BSU_25260 glyS yqfK glyS glyS RO NP_390404.2 glycyl-tRNA synthetase (beta subunit)

core 150

2607762 2608649 - 2557 108 gene 2607762 2608649 - BSU_25270 glyQ yqfJ glyQ glyQ RO NP_390405.1 glycyl-tRNA synthetase (alpha subunit)

core 150

2610041 2610946 - 2560 108 gene 2610041 2610946 - BSU_25290 era bex, yqfH era era RB, TW NP_390407.1 maturation of 16S RNA and assembly of 30S ribosomal subunit GTPase

core 150

2620371 2620544 - 2572 108 gene 2620371 2620544 - BSU_25410 rpsU yqeX

rpsU RO NP_390419.1 ribosomal protein S21 core 150

2635815 2636081 + 2586 108 gene 2635815 2636081 + BSU_25550 rpsT yqeO

rpsT RO NP_390433.2 ribosomal protein S20 (BS20) core 150

2636096 2637139 - 2587 108 gene 2636096 2637139 - BSU_25560 holA

holA yqeN TW NP_390434.1 DNA polymerase clamp loader delta subunit

core 150

2643765 2644334 - 2597 108 gene 2643765 2644334 - BSU_25640 nadD

nadD yqeJ TW NP_390442.1 nicotinate-nucleotide adenylyltransferase

core 150

2644346 2644636 - 2598 108 gene 2644346 2644636 - BSU_25650 yqeI

yqeI TW NP_390443.1 50S RNA-binding protein core 150

2645490 2646590 - 2600 108 gene 2645490 2646590 - BSU_25670 rgpH

yqeH RB, TW NP_390445.1 potassium-dependent GTPase involved in ribosome 30S assembly

core 150


https://doi.org/10.1101/2020.06.11.147629

2646594 2647112 - 2601 108 gene 2646594 2647112 - BSU_25680 yqeG

yqeG

NP_390446.1 phosphatase (active on GMP and Glc-6-P)

core 150

2662712 2663290 + 4590 46 gene 2662712 2663290 + BSU_25870 rttF

yqcF

NP_390464.1 antitoxin factor of ribonuclease toxin RttG; skin element

non-core

150-151

2698893 2699243 + 4643 34 gene 2698893 2699243 + BSU_26350 sknR

yqaE

NP_390512.1 skin element; transcriptional repressor of yqaF-yqaN operon (Xre family)

non-core

150-151

2798174 2800810 - 2726 108 gene 2798174 2800810 - BSU_27410 alaS

alaS alaS RO NP_390618.1 alanyl-tRNA synthetase core 162

2809413 2810528 - 2737 108 gene 2809413 2810528 - BSU_27500 mnmA yrrA trmU trmU TW NP_390627.3 tRNA-specific 2-thiouridylase core 163

2810559 2811698 - 2738 108 gene 2810559 2811698 - BSU_27510 iscSA

iscS yrvO TW NP_390629.2 cysteine desulfurase involved in U34 tRNA thiolation

core 163

2814743 2816521 - 2743 108 gene 2814743 2816521 - BSU_27550 aspS

aspS aspS RO NP_390633.1 aspartyl-tRNA synthetase, promiscuous (also recognizes tRNAasn)

core 163

2816535 2817809 - 2744 108 gene 2816535 2817809 - BSU_27560 hisS

hisS hisS TW NP_390634.1 histidyl-tRNA synthetase core 163

2852661 2853947 - 2782 108 gene 2852661 2853947 - BSU_27920 obgE

obg obg RB, TW NP_390670.1 ppGpp-binding GTPase involved in cell portioning, DNA repair and ribosome assembly

core 165

2854880 2855164 - 2785 108 gene 2854880 2855164 - BSU_27940 rpmA

rpmA rpmA RO NP_390672.1 ribosomal protein L27 (BL24) core 165

2855177 2855515 - 2786 108 gene 2855177 2855515 - BSU_27950 rppA

ysxB

NP_390673.2 ribosomal protein L27 specific N-terminal end cysteine protease

core 165

2855518 2855826 - 2787 108 gene 2855518 2855826 - BSU_27960 rplU

rplU rplU RO NP_390674.1 ribosomal protein L21 (BL20) core 165

2859317 2859835 - 2792 108 gene 2859317 2859835 - BSU_28010 mreD rodB mreD

NP_390679.1 cell-shape determining protein core 165

2859832 2860704 - 2793 108 gene 2859832 2860704 - BSU_28020 mreC

mreC mreC TW NP_390680.2 cell-shape determining protein core 165

2860735 2861748 - 2794 108 gene 2860735 2861748 - BSU_28030 mreB

mreB mreB TW NP_390681.2 cell-shape determining protein core 165

2865312 2866604 - 2799 108 gene 2865312 2866604 - BSU_28080 folC

folC

NP_390686.1 folyl-polyglutamate synthase core 165

2866664 2869306 - 2800 108 gene 2866664 2869306 - BSU_28090 valS

valS valS RO NP_390687.2 valyl-tRNA synthetase core 165


https://doi.org/10.1101/2020.06.11.147629

2879882 2880469 - 2811 108 gene 2879882 2880469 - BSU_28190 engB

ysxC ysxC RB, TW NP_390697.1 GTPase involved in ribosome 50S subunit assembly (maturation of the central 50S protuberance)

core 165

2903217 2904035 - 2841 108 gene 2903217 2904035 - BSU_28390 rcmE glr, murI racE

NP_390717.2 glutamate racemase core 168

2913024 2913338 - 2851 108 gene 2913024 2913338 - BSU_28500 trxA trx trxA trxA TW NP_390728.1 thioredoxin core 168

2927008 2929422 - 2864 108 gene 2927008 2929422 - BSU_28630 pheT

pheT pheT RO NP_390741.1 phenylalanyl-tRNA synthetase (beta subunit)

core 168

2929438 2930472 - 2865 108 gene 2929438 2930472 - BSU_28640 pheS

pheS pheS RO NP_390742.1 phenylalanyl-tRNA synthetase (alpha subunit)

core 168

2952224 2952583 - 2886 108 gene 2952224 2952583 - BSU_28850 rplT

rplT rplT RO NP_390763.1 ribosomal protein L20 core 168

2952615 2952815 - 2887 108 gene 2952615 2952815 - BSU_28860 rpmI

rpmI RO NP_390764.1 ribosomal protein L35 core 168

2952828 2953349 - 2888 108 gene 2952828 2953349 - BSU_28870 infC

infC infC TW* NP_390765.1 initiation factor IF-3 core 168

2963185 2964120 - 2898 108 gene 2963185 2964120 - BSU_28980 dnaI ytxA dnaI dnaI RB NP_390776.1 helicase loader core 168

2964148 2965566 - 2899 108 gene 2964148 2965566 - BSU_28990 dnaB

dnaB dnaB RB NP_390777.1 helicase loading protein; replication initiation membrane attachment protein

core 168

2970922 2971515 - 2906 108 gene 2970922 2971515 - BSU_29060 coaE

coaE ytaG TW NP_390784.1 dephosphocoenzyme A kinase core 168

2986588 2987547 - 2919 108 gene 2986588 2987547 - BSU_29190 pfkA pfk

pfkA TW NP_390797.1 6-phosphofructokinase core 169

2987731 2988708 - 2920 108 gene 2987731 2988708 - BSU_29200 accA

accA accA TW NP_390798.1 acetyl-CoA carboxylase (carboxyltransferase alpha subunit)

core 169

2988693 2989565 - 2921 108 gene 2988693 2989565 - BSU_29210 accD yttI accD accD TW NP_390799.2 acetyl-CoA carboxylase (carboxyltransferase beta subunit)

core 169

2991269 2994616 - 2923 108 gene 2991269 2994616 - BSU_29230 dnaEC

dnaE dnaE RB, TW NP_390801.1 DNA polymerase III (alpha subunit), DnaE3

core 169

3035730 3036332 + 2958 108 gene 3035730 3036332 + BSU_29660 rpsD

rpsD rpsD RO NP_390844.1 ribosomal protein S4 (BS4) core 170

3036603 3037871 - 2959 108 gene 3036603 3037871 - BSU_29670 tyrS tyrS1 tyrS tyrS TW* NP_390845.1 tyrosyl-tRNA synthetase core 170

3048177 3049475 - 2971 108 gene 3048177 3049475 - BSU_29790 murC ytxF murC murC TW NP_390857.1 UDP-N-acetyl muramate-alanine ligase

core 170

3102629 3105043 - 3021 108 gene 3102629 3105043 - BSU_30320 leuS

leuS leuS RO NP_390910.1 leucyl-tRNA synthetase core 170


https://doi.org/10.1101/2020.06.11.147629

3127825 3129027 - 3045 108 gene 3127825 3129027 - BSU_30550 metK metE metK metK TW NP_390933.1 S-adenosylmethionine synthetase core 173

3146238 3147353 - 3068 108 gene 3146238 3147353 - BSU_30780 menC ytfD menC menC TW NP_390956.1 O-succinylbenzoate-CoA synthase core 173

3147350 3148810 - 3069 108 gene 3147350 3148810 - BSU_30790 menE

menE menE TW NP_390957.1 O-succinylbenzoic acid-CoA ligase core 173

3148901 3149716 - 3070 108 gene 3148901 3149716 - BSU_30800 menB

menB menB TW NP_390958.1 dihydroxynapthoic acid synthetase core 173

3149751 3150575 - 3071 108 gene 3149751 3150575 - BSU_30810 menH

ytfB, ytxM

menH RB NP_390959.1 2-succinyl-6-hydroxy-2, 4-cyclohexadiene-1-carboxylate synthase

core 173

3150563 3152305 - 3072 108 gene 3150563 3152305 - BSU_30820 menD

menD menD TW NP_390960.1

2-oxoglutarate decarboxylase and 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase

core 173

3246598 3249003 + 3180 108 gene 3246598 3249003 + BSU_31600 mrpA ntrA, shaA,

yufT mrpA mrpA TW NP_391038.2

sodium transporter component of a Na+/H+ antiporter

core 177

3248996 3249427 + 3181 108 gene 3248996 3249427 + BSU_31610 mrpB yufU mrpB mrpB TW NP_391039.1 Na+/H+ antiporter complex core 177

3249427 3249768 + 3182 108 gene 3249427 3249768 + BSU_31620 mrpC yufV mrpC mrpC TW NP_391040.2 component of Na+/H+ antiporter core 177

3249761 3251242 + 3183 108 gene 3249761 3251242 + BSU_31630 mrpD yufD mrpD mrpD TW NP_391041.3 proton transporter component of Na+/H+ antiporter

core 177

3251248 3251724 + 3184 108 gene 3251248 3251724 + BSU_31640 mrpE

mrpE

YP_054591.2 non essential component of Na+/H+ antiporter

core 177

3251724 3252008 + 3185 108 gene 3251724 3252008 + BSU_31650 mrpF yufC mrpF mrpF TW NP_391043.2 efflux transporter for Na+ and cholate

core 177

3251992 3252366 + 3186 108 gene 3251992 3252366 + BSU_31660 mrpG yufB mrpG

NP_391044.1 non essential component of Na+/H+ antiporter

core 177

3259403 3260875 - 3196 108 gene 3259403 3260875 - BSU_31750 pncB

pncB yueK TW NP_391053.1 nicotinate phosphoribosyltransferase

core 178


https://doi.org/10.1101/2020.06.11.147629

3301586 3302584 + 3231 108 gene 3301586 3302584 + BSU_32110 trxBB

yumC yumC TW NP_391091.2 ferredoxin-NADP+ reductase (flavodoxin)

core 179

3306040 3306894 - 3259 108 gene 3306040 3306894 - BSU_32170 dapF yutL dapF dapF TW NP_391097.1 diaminopimelate epimerase core 180

3355593 3356990 - 3312 108 gene 3355593 3356990 - BSU_32670 sufB

sufB yurU TW NP_391146.1 FeS cluster formation scaffold protein

core 185

3357011 3357454 - 3313 108 gene 3357011 3357454 - BSU_32680 sufU nifU iscU yurV TW NP_391147.1 iron-sulfur cluster assembly sulfur-transfer protein (Zn(2+)-dependent)

core 185

3357444 3358664 - 3314 108 gene 3357444 3358664 - BSU_32690 sufS yurW sufS csd TW NP_391148.1 cysteine desulfurase core 185

3358664 3359977 - 3315 108 gene 3358664 3359977 - BSU_32700 sufD

sufD yurX TW NP_391149.1 Fe-S cluster assembly protein SufD core 185

3359995 3360780 - 3316 108 gene 3359995 3360780 - BSU_32710 sufC

sufC yurY TW NP_391150.1 sulfur mobilizing ABC protein, ATPase

core 185

3476555 3477847 - 3499 108 gene 3476555 3477847 - BSU_33900 eno

eno eno TW NP_391270.1 enolase core 193

3477877 3479412 - 3500 108 gene 3477877 3479412 - BSU_33910 pgm gpmI pgm pgm TW NP_391271.1 phosphoglycerate mutase core 193

3479405 3480166 - 3501 108 gene 3479405 3480166 - BSU_33920 tpiA tpi

tpiA TW NP_391272.1 triose phosphate isomerase core 193

3480197 3481381 - 3502 108 gene 3480197 3481381 - BSU_33930 pgk

pgk TW NP_391273.1 phosphoglycerate kinase core 193

3481698 3482705 - 3503 108 gene 3481698 3482705 - BSU_33940 gapA gap gapA

NP_391274.1 glyceraldehyde-3-phosphate dehydrogenase (NAD-dependent, glycolytic)

core 193

3533419 3534102 - 3555 108 gene 3533419 3534102 - BSU_34430 racX

racE TW NP_391323.1 promiscuous aminoacid racemase (prefers arginine, lysine and ornithine)

core 196

3573207 3574157 - 3642 108 gene 3573207 3574157 - BSU_34790 trxB yvcH trxB trxB TW NP_391359.1 thioredoxin reductase core 199

3627139 3628240 - 3689 108 gene 3627139 3628240 - BSU_35290 prfB

prfB prfB TW NP_391409.1 peptide chain release factor 2 core 203

3628310 3630835 - 3690 108 gene 3628310 3630835 - BSU_35300 secA div+ secA secA RB NP_391410.1 translocase binding subunit (ATPase) core 203

3648654 3649730 - 3721 108 gene 3648654 3649730 - BSU_35530 tagO yvhI tagO tagO TW NP_391433.1 UDP-N-acetylglucosamine:undecaprenyl-P N-acetylglucosaminyl-1-P transferase

core 206


https://doi.org/10.1101/2020.06.11.147629

3656752 3658203 - 4729 85 gene 3656752 3658203 - BSU_35600 tuaB yvhB tuaB

NP_391440.1 putative exporter involved in biosynthesis of teichuronic acid

non-core

206-207

3664241 3665383 - 4735 84 gene 3664241 3665383 - BSU_35660 mnaA

mnaA yvyH TW NP_391446.1 UDP-N-acetylmannosamine 2-epimerase

non-core

206-207

3673564 3675147 - 4744 84 gene 3673564 3675147 - BSU_35700 tagH

tagH tagH RB NP_391451.1 ATP-binding teichoic acid precursor transporter component

non-core

206-207

3675167 3675994 - 4745 35 gene 3675167 3675994 - BSU_35710 tagG

tagG tagG RB NP_391452.1 teichoic acid precursors permease non-core

206-207

3676159 3678399 - 4746 35 gene 3676159 3678399 - BSU_35720 tagF rodC, tag3 tagF tagF TW NP_391453.1

CDP-glycerol:polyglycerol phosphate glycero-phosphotransferase (poly(glycerol phosphate) polymerase)

non-core

206-207

3680581 3680970 - 4748 35 gene 3680581 3680970 - BSU_35740 tagD

tagD tagD TW NP_391455.1 glycerol-3-phosphate cytidylyltransferase

non-core

206-207

3681370 3682140 + 4749 35 gene 3681370 3682140 + BSU_35750 tagA

tagA tagA TW NP_391456.1

N-acetylmannosamine (ManNAc) C4 hydroxyl of a membrane-anchored N-acetylglucosaminyl diphospholipid (GlcNAc-pp-undecaprenyl, lipid I) glycosyltransferase

non-core

206-207

3682173 3683318 + 4750 35 gene 3682173 3683318 + BSU_35760 tagB tagF, rodC,

tag3 tagB tagB TW NP_391457.1

teichoic acid primase, CDP-glycerol:N-acetyl-beta-d-mannosaminyl-1, 4-N-acetyl-d-glucosaminyldiphosphoundecaprenyl glycerophosphotransferase

non-core

206-207

3740206 3740547 - 3807 108 gene 3740206 3740547 - BSU_36310 ssbB ywpH

ssb RO NP_391512.2 single-strand DNA-binding protein core 214

3743732 3744157 - 3814 108 gene 3743732 3744157 - BSU_36370 fabZ ywpB fabZ

NP_391518.2 beta-hydroxyacyl core 215


https://doi.org/10.1101/2020.06.11.147629

3747254 3748255 - 3818 108 gene 3747254 3748255 - BSU_36410 mbl

mbl

NP_391522.2 MreB-like morphogen core 215

3777949 3779259 - 3857 108 gene 3777949 3779259 - BSU_36760 murAA murA murAA murAA TW NP_391557.1 UDP-N-acetylglucosamine 1-carboxyvinyltransferase

core 217

3789190 3790437 - 3871 108 gene 3789190 3790437 - BSU_36900 glyA glyC, ipc-

34d glyA TW NP_391571.1 serine hydroxymethyltransferase

core 217

3792969 3794009 - 3876 108 gene 3792969 3794009 - BSU_36950 tsaC ipc-29d

ywlC TW NP_391576.1

tRNA(NNU) t(6)A37 threonylcarbamoyladenosine modification; threonine-dependent ADP-forming ATPase

core 217

3797085 3798155 - 3882 108 gene 3797085 3798155 - BSU_37010 prfA

prfA prfA TW NP_391582.1 peptide chain release factor 1 core 217

3803081 3803281 - 3888 108 gene 3803081 3803281 - BSU_37070 rpmEA

rpmE RO NP_391588.1 ribosomal protein L31 core 217

3808512 3809369 - 3894 108 gene 3808512 3809369 - BSU_37120 fbaA fba, fba1,

tsr fbaA TW NP_391593.1 fructose-1,6-bisphosphate aldolase

core 217

3810693 3812300 - 3897 108 gene 3810693 3812300 - BSU_37150 pyrG ctrA pyrG pyrG TW NP_391596.1 CTP synthetase core 218

3833650 3835320 - 3916 108 gene 3833650 3835320 - BSU_37330 argS

argS argS RO NP_391614.1 arginyl-tRNA synthetase core 219

3912332 3913513 - 3994 97 gene 3912332 3913513 - BSU_38120 rodA ywcF, ipa-

42d rodA rodA RB NP_391691.1

glycosyltransferase involved in extension of the lateral walls of the cell

non-core

224-225

3950726 3951661 - 4034 108 gene 3950726 3951661 - BSU_38490 menA ywaB, ipa-

6d menA menA TW NP_391728.1

1,4-dihydroxy-2-naphthoate octaprenyltransferase

core 229

3969999 3970319 - 4056 108 gene 3969999 3970319 - BSU_38690 yxlC

yxlC

NP_391748.1 sigma-Y antisigma factor core 229

4023054 4023482 - 4769 39 gene 4023054 4023482 - BSU_39220 wapI N17H yxxG

NP_391801.1 antitoxin of WapA tRNase non-core

234-235

4036344 4036787 - 4772 53 gene 4036344 4036787 - BSU_39290 rtbE N17A yxxD

NP_391808.1 antitoxin factor of the RttD-RttE toxin-antitoxin system

non-core

236-237

4151853 4153688 - 4257 108 gene 4151853 4153688 - BSU_40400 walK

walK yycG RB, TW NP_391920.1 two-component sensor histidine kinase

core 250

4153696 4154403 - 4258 108 gene 4153696 4154403 - BSU_40410 walR

walR yycF RB, TW NP_391921.1 two-component response regulator core 250

4157471 4158835 - 4265 108 gene 4157471 4158835 - BSU_40440 dnaC

dnaC dnaC RB NP_391924.2 replicative DNA helicase core 250

4163197 4163646 - 4271 108 gene 4163197 4163646 - BSU_40500 rplI

rplI RO NP_391930.1 ribosomal protein L9 core 250


https://doi.org/10.1101/2020.06.11.147629

4168204 4169133 + 4277 108 gene 4168204 4169133 + BSU_40550 ppaC

ppaC ppaC TW NP_391935.1 inorganic pyrophosphatase (Mn2+-dependent)

core 251

4198603 4198842 - 4303 108 gene 4198603 4198842 - BSU_40890 rpsR

rpsR rpsR RO NP_391969.2 ribosomal protein S18 core 257

4198886 4199404 - 4304 108 gene 4198886 4199404 - BSU_40900 ssbA

ssbA

NP_391970.1 single-strand DNA-binding protein core 257

4199445 4199732 - 4305 108 gene 4199445 4199732 - BSU_40910 rpsF

rpsF RO NP_391971.1 ribosomal protein S6 (BS9) core 257

4214753 4215103 - 4320 108 gene 4214753 4215103 - BSU_41050 rnpA

rnpA rnpA RO NP_391985.1 protein component of ribonuclease P (RNase P) (substrate specificity)

core 258

4215255 4215389 - 4321 108 gene 4215255 4215389 - BSU_41060 rpmH

rpmH RO NP_391986.1 ribosomal protein L34 core 258


https://doi.org/10.1101/2020.06.11.147629

Table 2. The 258 B. subtilis core regions identified through the pan-genome graph.

Core Region Start Stop Length (bp)

1 410 92089 91680

2 92253 95352 3100

3 98109 165706 67598

4 165830 165902 73

5 166253 166328 76

6 166501 168053 1553

7 177083 202079 24997

8 205409 210946 5538

9 222971 227954 4984

10 228066 238129 10064

11 241917 243661 1745

12 243892 250053 6162

13 252514 282897 30384

14 283003 317603 34601

15 317725 318927 1203

16 319180 320352 1173

17 320421 327377 6957

18 327618 332396 4779

19 335329 340585 5257

20 340613 364142 23530

21 365170 365754 585

22 365841 369217 3377

23 369773 370105 333

24 370259 406007 35749

25 406131 435989 29859

26 436036 455738 19703

27 455771 478741 22971

28 488314 490554 2241

29 490777 514764 23988

30 515016 524249 9234

31 525743 529419 3677

32 559264 560612 1349

33 561514 566101 4588

34 568345 569949 1605

35 570371 575562 5192

36 579541 582479 2939

37 582536 585037 2502

38 585155 587336 2182


https://doi.org/10.1101/2020.06.11.147629

39 587744 591891 4148

40 593407 599067 5661

41 599107 600105 999

42 601019 602427 1409

43 603012 604576 1565

44 604736 631811 27076

45 632774 648704 15931

46 648742 651868 3127

47 664775 680873 16099

48 680907 694281 13375

49 694425 696998 2574

50 697157 724825 27669

51 724987 737347 12361

52 737603 738982 1380

53 749562 749763 202

54 750959 753131 2173

55 753817 754401 585

56 755907 764765 8859

57 764781 770113 5333

58 772142 788636 16495

59 791462 795867 4406

60 796001 813818 17818

61 814384 817243 2860

62 827993 844645 16653

63 850367 860263 9897

64 860303 875055 14753

65 875178 878051 2874

66 879002 886173 7172

67 888143 893798 5656

68 893904 898867 4964

69 905010 909125 4116

70 909198 911928 2731

71 913924 928658 14735

72 928803 953294 24492

73 953373 957667 4295

74 959311 988377 29067

75 988417 988872 456

76 989712 1013851 24140

77 1013958 1050234 36277

78 1050443 1092728 42286

79 1092770 1108704 15935

80 1108736 1125153 16418

81 1125123 1135225 10103


https://doi.org/10.1101/2020.06.11.147629

82 1135255 1149935 14681

83 1150206 1156473 6268

84 1156504 1159081 2578

85 1160776 1169849 9074

86 1178218 1182395 4178

87 1187700 1204420 16721

88 1204506 1213449 8944

89 1217326 1250504 33179

90 1252177 1262861 10685

91 1268275 1268592 318

92 1270426 1276291 5866

93 1276337 1289101 12765

94 1290018 1313615 23598

95 1313840 1314304 465

96 1315869 1334247 18379

97 1339632 1343227 3596

98 1345631 1382430 36800

99 1382677 1383147 471

100 1383320 1417416 34097

101 1417561 1441788 24228

102 1447251 1466599 19349

103 1466638 1478836 12199

104 1482248 1494362 12115

105 1494403 1514963 20561

106 1514997 1534239 19243

107 1534279 1538692 4414

108 1538770 1557631 18862

109 1558034 1573790 15757

110 1575051 1616122 41072

111 1616267 1671129 54863

112 1671166 1731446 60281

113 1731457 1780220 48764

114 1780404 1782523 2120

115 1860014 1879759 19746

116 1879787 1880377 591

117 1887352 1888743 1392

118 1888774 1895165 6392

119 1896424 1899125 2702

120 1899589 1900514 926

121 1901117 1901377 261

122 1901429 1903058 1630

123 1903511 1904749 1239

124 1905370 1906207 838


https://doi.org/10.1101/2020.06.11.147629

125 1906272 1906706 435

126 1907013 1907201 189

127 1910167 1924962 14796

128 1924993 1942455 17463

129 1942714 1957360 14647

130 1958027 1960087 2061

131 1998340 2003182 4843

132 2003276 2015681 12406

133 2017886 2021144 3259

134 2021223 2022467 1245

135 2073658 2075779 2122

136 2079096 2085980 6885

137 2086070 2128421 42352

138 2128464 2139457 10994

139 2140898 2151256 10359

140 2287097 2297109 10013

141 2297984 2330022 32039

142 2330075 2393559 63485

143 2393602 2433522 39921

144 2435012 2435224 213

145 2435833 2476859 41027

146 2476969 2532197 55229

147 2532353 2564883 32531

148 2564923 2581617 16695

149 2584035 2587573 3539

150 2588701 2653340 64640

151 2701362 2701754 393

152 2716035 2718802 2768

153 2718959 2724827 5869

154 2727160 2730226 3067

155 2732747 2732881 135

156 2732980 2739105 6126

157 2739486 2740193 708

158 2741357 2743889 2533

159 2747984 2751651 3668

160 2752167 2773222 21056

161 2773783 2784652 10870

162 2784688 2805313 20626

163 2805348 2832367 27020

164 2832424 2840925 8502

165 2841307 2897432 56126

166 2898292 2898929 638

167 2898931 2899752 822


https://doi.org/10.1101/2020.06.11.147629

168 2899816 2982269 82454

169 2982603 2998620 16018

170 3009915 3106995 97081

171 3107232 3109360 2129

172 3109397 3115974 6578

173 3117976 3183195 65220

174 3183201 3188048 4848

175 3188173 3208154 19982

176 3210445 3213829 3385

177 3214372 3253448 39077

178 3257092 3266655 9564

179 3269914 3305261 35348

180 3305599 3308231 2633

181 3308368 3318002 9635

182 3318029 3334990 16962

183 3335414 3344979 9566

184 3345013 3354487 9475

185 3355593 3382499 26907

186 3382633 3419421 36789

187 3419656 3436651 16996

188 3436849 3440961 4113

189 3441121 3450788 9668

190 3450709 3457941 7233

191 3459848 3464067 4220

192 3467564 3474070 6507

193 3476555 3488042 11488

194 3487974 3495701 7728

195 3495876 3499257 3382

196 3499541 3535473 35933

197 3536012 3542691 6680

198 3545889 3568135 22247

199 3568527 3580038 11512

200 3582936 3591268 8333

201 3591288 3601909 10622

202 3606762 3609221 2460

203 3610064 3630835 20772

204 3631003 3634754 3752

205 3636046 3647406 11361

206 3648654 3651068 2415

207 3684826 3688547 3722

208 3691372 3693906 2535

209 3695363 3696223 861

210 3696257 3714679 18423


https://doi.org/10.1101/2020.06.11.147629

211 3716009 3722541 6533

212 3724420 3725136 717

213 3727427 3727687 261

214 3728511 3741592 13082

215 3742351 3750677 8327

216 3750768 3761700 10933

217 3761987 3810611 48625

218 3810693 3819178 8486

219 3833650 3845998 12349

220 3847853 3851893 4041

221 3852186 3856447 4262

222 3856639 3874180 17542

223 3874332 3899182 24851

224 3900963 3912226 11264

225 3914009 3926399 12391

226 3926682 3937515 10834

227 3938310 3949922 11613

228 3949952 3950584 633

229 3950726 3973278 22553

230 3973364 3982915 9552

231 3983187 3984026 840

232 3984132 3989084 4953

233 3989948 3990967 1020

234 3992671 4018656 25986

235 4030710 4031645 936

236 4031797 4033755 1959

237 4038513 4039159 647

238 4039466 4040875 1410

239 4049009 4062143 13135

240 4062543 4084383 21841

241 4084799 4086540 1742

242 4088002 4092666 4665

243 4106245 4121056 14812

244 4121166 4123903 2738

245 4128119 4130044 1926

246 4134436 4139537 5102

247 4140260 4141474 1215

248 4141711 4145506 3796

249 4145747 4147132 1386

250 4147419 4165622 18204

251 4166815 4171359 4545

252 4176900 4178145 1246

253 4183445 4185681 2237


https://doi.org/10.1101/2020.06.11.147629

254 4186092 4187174 1083

255 4191198 4195744 4547

256 4196350 4196730 381

257 4197780 4205517 7738

258 4205556 4215389 9834


https://doi.org/10.1101/2020.06.11.147629

Table 3. The 414 E. coli genes deemed essential by Goodall et al., Baba et al., or Yamazaki et al. These genes are compared to the

PGG based annotation of core regions for the K-12 BW25113 strain used by Goodall (GenBank sequence CP009273.1, Assembly

ASM75055v1/GCA_000750555.1, BioSample SAMN03013572). Columns 1-5 are the start, stop, strand, cluster, and cluster size for

the PGG annotation. Columns 6-11 are the gene type, start, stop, strand, locus tag, and gene symbol/name for the GenBank annotation.

Column 12 is a list of gene synonyms for the gene from GenBank. Columns 13-21 are from Goodall et al.: 13-15 from Table S1

(normal essentiality), 16-18 from Table S4 (essentiality after outgrowth), 19-20 from Table S3 (outlier discrepancies), and 21 from

Table S2 (comparison of data sets). Column 22 is the PGG core or non-core region the gene is contained in.

PGG Start PGG Stop PGG

Strand PGG

Cluster

PGG Cluster

Size Type Start End Strand Locus Tag

Gene GenBank

Synonyms Insertion

Index Score Log Likelihood

Ratio Class

Insertion Index Score2

Log Likelihood

Ratio3 Class4

Venn group

Cause of discrepancy

TraDIS/Keio/PEC

Region

428911 430014 + 9603 957 gene 428911 430014 + BW25113_0414 ribD ECK0408, JW0404,

ribG, ybaE

0.008152174

-17.08601447 Essential 0.004528986 -9.88843503 Essential

All 3 core 39

1258333 1258956 - 4835 963 gene 1258333 1258956 - BW25113_1209 lolB

ECK1197, hemM,

JW1200, ychC

0.004807692

-20.77735583 Essential 0.001602564 -

13.58320673

Essential

All 3 core 136

2523606 2524592 - 14903 963 gene 2523606 2524592 - BW25113_2412 zipA ECK2407, JW2404

0.011144883

-14.84018637 Essential 0.006079027 -

8.681451304

Essential

All 3 core 279

431090 432067 + 9600 965 gene 431090 432067 + BW25113_0417 thiL ECK0411, JW0407

0.005112474

-20.35269783 Essential 0.00204499 -

12.77045808

Essential

All 3 core 39

3982448 3983188 - 7451 965 gene 3982448 3983188 - BW25113_3804 hemD ECK3798, JW3776

0.025641026

-8.469391606 Essential 0.012145749 -

5.305270251

Essential

All 3 core 421

487548 489479 + 9544 966 gene 487548 489479 + BW25113_0470 dnaX dnaZ,

ECK0464, JW0459

0.005175983

-20.26726714 Essential 0.001552795 -

13.68672073

Essential

All 3 core 44

1253385 1253969 - 4840 968 gene 1253385 1253969 - BW25113_1204 pth

asuA, ECK1192, JW1195,

rap

0.017094017

-11.65807531 Essential 0.005128205 -

9.391156882

Essential

All 3 core 136

1260468 1261550 + 4833 968 gene 1260468 1261550 + BW25113_1211 prfA

ECK1199, JW1202,

sueB, uar, ups

0.005540166

-19.7959005 Essential 0.001846722 -

13.11337585

Essential

All 3 core 136

3596110 3597603 - 161 968 gene 3596110 3597603 - BW25113_3464 ftsY ECK3448, JW3429

0.002008032

-26.71851386 Essential 0.004016064 -

10.35463768

Essential

All 3 core 374

661772 663673 - 9389 969 gene 661772 663673 - BW25113_0635 mrdA ECK0628, JW0630,

pbpA

0.005257624


All 3 core 66


https://doi.org/10.1101/2020.06.11.147629

1256384 1257331 - 4837 969 gene 1256384 1257331 - BW25113_1207 prs

dnaR, ECK1195, JW1198,

prsA

0.003164557

-23.64112411 Essential 0 -

173.5517401

Essential

All 3 core 136

1257482 1258333 - 4836 969 gene 1257482 1258333 - BW25113_1208 ispE

ECK1196, ipk,

JW1199, ychB

0.003521127

-22.91372984 Essential 0 -

173.5517401

Essential

All 3 core 136

1259170 1260426 + 4834 969 gene 1259170 1260426 + BW25113_1210 hemA ECK1198,

gtrA, JW1201

0.005568815

-19.760084 Essential 0.000795545 -

15.81493049

Essential

All 3 core 136

1261550 1262383 + 4832 969 gene 1261550 1262383 + BW25113_1212 prmC ECK1200,

hemK, JW1203

0.002398082

-25.52115633 Essential 0 -

173.5517401

Essential

All 3 core 136

1263621 1264475 + 4829 969 gene 1263621 1264475 + BW25113_1215 kdsA ECK1203, JW1206

0.002339181

-25.68914942 Essential 0.002339181 -

12.31119701

Essential

All 3 core 136

4161985 4163013 + 7623 969 gene 4161985 4163013 + BW25113_3972 murB ECK3964, JW3940,

yijB

0.009718173

-15.83087441 Essential 0.002915452 -

11.53777194

Essential

All 3 core 454

4163010 4163975 + 7624 969 gene 4163010 4163975 + BW25113_3973 birA bioR, dhbB, ECK3965, JW3941

0.031055901


All 3 core 454

4167286 4167669 + 7633 969 gene 4167286 4167669 + BW25113_3981 secE ECK3972, JW3944,

mbrC, prlG

0.010416667


All 3 core 454

4167671 4168216 + 7634 969 gene 4167671 4168216 + BW25113_3982 nusG ECK3973, JW3945

0.014652015

-12.82250177 Essential 0.010989011 -

5.855559211

Essential

All 3 core 454

4169924 4170421 + 7638 969 gene 4169924 4170421 + BW25113_3985 rplJ ECK3976, JW3948

0.006024096


All 3 core 454

4170488 4170853 + 7639 969 gene 4170488 4170853 + BW25113_3986 rplL ECK3977, JW3949

0 -172.1619602 Essential 0 -

173.5517401

Essential

All 3 core 454

4171173 4175201 + 7640 969 gene 4171173 4175201 + BW25113_3987 rpoB

ECK3978, ftsR, groN, JW3950,

mbrD, nitB, rif, ron,

sdgB, stl, stv, tabD,

tabG

0.001737404

-27.69214838 Essential 0.001489203 -

13.82339514

Essential

All 3 core 454

4175278 4179501 + 7641 969 gene 4175278 4179501 + BW25113_3988 rpoC ECK3979, JW3951,

tabB

0.010179924

-15.49644362 Essential 0.00686553 -

8.150154164

Essential

All 3 core 454

384209 385183 - 3382 970 gene 384209 385183 - BW25113_0369 hemB ECK0366, JW0361,

ncf

0.012307692

-14.11477855 Essential 0.009230769 -

6.757137001

Essential

All 3 core 35

548674 549396 - 9489 970 gene 548674 549396 - BW25113_0524 lpxH ECK0517, JW0513,

ybbF

0.006915629


All 3 core 53

550067 551452 + 9487 970 gene 550067 551452 + BW25113_0526 cysS ECK0519, JW0515

0 -172.1619602 Essential 0 -

173.5517401

Essential

All 3 core 53

552331 553197 - 9484 970 gene 552331 553197 - BW25113_0529 folD ads,

ECK0522, JW0518

0.017301038

-11.56617533 Essential 0.005767013 -

8.905185288

Essential

All 3 core 53

660657 661769 - 9390 970 gene 660657 661769 - BW25113_0634 mrdB ECK0627, JW0629,

rodA

0.004492363

-21.24478909 Essential 0.000898473 -

15.43549285

Essential

All 3 core 66

665387 666028 - 9385 970 gene 665387 666028 - BW25113_0639 nadD

ECK0632, fusB,

JW0634, ybeN

0.014018692

-13.15232618 Essential 0.007788162 -

7.575652432

Essential

All 3 core 66


https://doi.org/10.1101/2020.06.11.147629

666030 667061 - 9384 970 gene 666030 667061 - BW25113_0640 holA ECK0633, JW0635

0.014534884

-12.88253731 Essential 0.010658915 -

6.018275232

Essential

All 3 core 66

667061 667642 - 9383 970 gene 667061 667642 - BW25113_0641 lptE ECK0634, JW0636,

rlpB

0.010309278


All 3 core 66

667657 670239 - 9382 970 gene 667657 670239 - BW25113_0642 leuS ECK0635, JW0637

0.001935734

-26.96535804 Essential 0.000387147 -

18.01638909

Essential

All 3 core 66

684799 686337 - 9367 970 gene 684799 686337 - BW25113_0657 lnt cutE,

ECK0649, JW0654

0.012995452


All 3 core 68

701549 703213 + 9347 970 gene 701549 703213 + BW25113_0680 glnS ECK0668, JW0666

0.004804805


All 3 core 71

706391 706921 - 9342 970 gene 706391 706921 - BW25113_0684 fldA ECK0672, JW0671

0.005649718

-19.65987986 Essential 0 -

173.5517401

Essential

All 3 core 72

1123295 1124830 + 4959 970 gene 1123295 1124830 + BW25113_1069 murJ

ECK1054, JW1056,

mviN, mviS, yceN

0.00390625 -22.2042982 Essential 0.001302083 -14.2584822 Essential

All 3 core 126

1145184 1146113 + 4936 970 gene 1145184 1146113 + BW25113_1092 fabD ECK1078, JW1078,

tfpA

0.007526882

-17.65096927 Essential 0.002150538 -

12.59952381

Essential

All 3 core 127

1146126 1146860 + 4935 970 gene 1146126 1146860 + BW25113_1093 fabG ECK1079, JW1079

0 -172.1619602 Essential 0 -

173.5517401

Essential

All 3 core 127

1147071 1147307 + 4934 970 gene 1147071 1147307 + BW25113_1094 acpP ECK1080, JW1080

0.004219409

-21.67561417 Essential 0 -

173.5517401

Essential

All 3 core 127

1150580 1151221 + 4930 970 gene 1150580 1151221 + BW25113_1098 tmk ECK1084, JW1084,

ycfG

0.004672897

-20.97345916 Essential 0.007788162 -

7.575652432

Essential

All 3 core 127

1151218 1152222 + 4929 970 gene 1151218 1152222 + BW25113_1099 holB ECK1085, JW1085

0.011940299

-14.3370201 Essential 0.005970149 -

8.758604546

Essential

All 3 core 127

1170883 1172082 + 4911 970 gene 1170883 1172082 + BW25113_1116 lolC ECK1102, JW5161,

ycfU

0.000833333

-32.60579817 Essential 0 -

173.5517401

Essential

All 3 core 128

1172075 1172776 + 4910 970 gene 1172075 1172776 + BW25113_1117 lolD ECK1103, JW5162,

ycfV

0.002849003

-24.3546829 Essential 0.001424501 -

13.96794772

Essential

All 3 core 128

1172776 1174020 + 4909 970 gene 1172776 1174020 + BW25113_1118 lolE ECK1104, JW1104,

ycfW

0.003212851

-23.53807484 Essential 0.002409639 -

12.20857368

Essential

All 3 core 128

1325305 1327902 + 4764 970 gene 1325305 1327902 + BW25113_1274 topA

asuA, ECK1268, JW1266,

supX

0.01308699 -13.6624738 Essential 0.003464203 -

10.91044744

Essential

All 3 core 143

1332827 1333417 - 4758 970 gene 1332827 1333417 - BW25113_1277 ribA ECK1272, JW1269

0.001692047

-27.86982087 Essential 0.001692047 -

13.40409226

Essential

All 3 core 145

1344508 1345296 - 4745 970 gene 1344508 1345296 - BW25113_1288 fabI

ECK1283, envM, gts, JW1281,

qmeA

0.001267427

-29.80636683 Essential 0 -

173.5517401

Essential

All 3 core 145

1884829 1885524 - 11026 970 gene 1884829 1885524 - BW25113_1807 tsaB ECK1805, JW1796, rpf, yeaZ

0.005747126

-19.54102957 Essential 0.001436782 -

13.94006168

Essential

All 3 core 206

3519828 3521963 + 231 970 gene 3519828 3521963 + BW25113_3398 yrfF

ECK3385, igaA,

JW3361, mucM, umoB

0.030430712

-7.052653118 Essential 0.012640449 -

5.078368995

Essential

All 3 core 364


https://doi.org/10.1101/2020.06.11.147629

3593289 3594143 - 164 970 gene 3593289 3594143 - BW25113_3461 rpoH

ECK3445, fam, hin,

htpR, JW3426

0.010526316

-15.2545729 Essential 0.003508772 -

10.86308191

Essential

All 3 core 374

3806091 3807311 + 7277 970 gene 3806091 3807311 + BW25113_3639 dfp coaBC,

ECK3629, JW5642

0.008190008

-17.05314352 Essential 0.004095004 -

10.28005412

Essential

All 3 core 398

4476035 4477135 + 6561 970 gene 4476035 4477135 + BW25113_4261 lptF ECK4254, JW4218,

yjgP

0.009082652


All 3 core 506

4477135 4478217 + 6560 970 gene 4477135 4478217 + BW25113_4262 lptG ECK4255, JW5760,

yjgQ

0.011080332

-14.88243706 Essential 0.006463527 -

8.416292755

Essential

All 3 core 506

21407 22348 + 14167 971 gene 21407 22348 + BW25113_0025 ribF ECK0026, JW0023,

yaaC

0.005307856

-20.0930286 Essential 0.003184713 -

11.21906678

Essential

All 3 core 6

25207 25701 + 14165 971 gene 25207 25701 + BW25113_0027 lspA ECK0028, JW0025

0.012121212

-14.22682379 Essential 0.006060606 -

8.694437804

Essential

All 3 core 6

26277 27227 + 14163 971 gene 26277 27227 + BW25113_0029 ispH ECK0030, JW0027, lytB, yaaE

0.008412198

-16.86290727 Essential 0.001051525 -

14.94049774

Essential

All 3 core 6

28374 29195 + 14161 971 gene 28374 29195 + BW25113_0031 dapB ECK0032, JW0029

0.001216545


All 3 core 7

49823 50302 + 14143 971 gene 49823 50302 + BW25113_0048 folA ECK0049, JW0047,

tmrA

0.004166667

-21.76194665 Essential 0 -

173.5517401

Essential

All 3 core 8

54755 57109 - 14137 971 gene 54755 57109 - BW25113_0054 lptD

ECK0055, imp,

JW0053, ostA, yabG

0.007218684

-17.94579327 Essential 0.003397028 -

10.98275811

Essential

All 3 core 9

87519 87884 + 14107 971 gene 87519 87884 + BW25113_0083 ftsL ECK0084, JW0081,

mraR, yabD

0.040983607

-4.457809192 Essential 0.027322404 0.44230867

7 Unclear

All 3 core 14

87900 89666 + 14106 971 gene 87900 89666 + BW25113_0084 ftsI ECK0085, JW0082,

pbpB, sep

0.007923033

-17.28819005 Essential 0.004527448 -

9.889772102

Essential

All 3 core 14

89653 91140 + 14105 971 gene 89653 91140 + BW25113_0085 murE ECK0086, JW0083

0.004032258

-21.98681522 Essential 0.000672043 -

16.33678495

Essential

All 3 core 14

91137 92495 + 14104 971 gene 91137 92495 + BW25113_0086 murF ECK0087, JW0084,

mra

0.006622517

-18.55131361 Essential 0.004415011 -

9.988451416

Essential

All 3 core 14

92489 93571 + 14103 971 gene 92489 93571 + BW25113_0087 mraY ECK0088, JW0085,

murX

0.005540166

-19.7959005 Essential 0.002770083 -

11.71996304

Essential

All 3 core 14

93574 94890 + 14102 971 gene 93574 94890 + BW25113_0088 murD ECK0089, JW0086

0.006074412

-19.15526311 Essential 0.004555809 -

9.865170395

Essential

All 3 core 14

94890 96134 + 14101 971 gene 94890 96134 + BW25113_0089 ftsW ECK0090, JW0087

0.018473896


All 3 core 14

96131 97198 + 14100 971 gene 96131 97198 + BW25113_0090 murG ECK0091, JW0088

0.003745318

-22.49213431 Essential 0.002808989 -

11.67044482

Essential

All 3 core 14

97252 98727 + 14099 971 gene 97252 98727 + BW25113_0091 murC ECK0092, JW0089

0.005420054

-19.94800949 Essential 0.003387534 -

10.99306934

Essential

All 3 core 14

99642 100472 + 14097 971 gene 99642 100472 + BW25113_0093 ftsQ ECK0094, JW0091

0.018050542

-11.24122024 Essential 0.014440433 -

4.288329169

Essential

All 3 core 14


https://doi.org/10.1101/2020.06.11.147629

100469 101731 + 14096 971 gene 100469 101731 + BW25113_0094 ftsA divA,

ECK0095, JW0092

0.006334125

-18.86292727 Essential 0.002375297 -

12.25827109

Essential

All 3 core 14

101792 102943 + 14095 971 gene 101792 102943 + BW25113_0095 ftsZ ECK0096, JW0093, sfiB, sulB

0.001736111


All 3 core 14

103044 103961 + 14094 971 gene 103044 103961 + BW25113_0096 lpxC

asmB, ECK0097,

envA, JW0094

0.013071895

-13.67100273 Essential 0.002178649 -

12.55521848

Essential

All 3 core 14

104766 107471 + 14092 971 gene 104766 107471 + BW25113_0098 secA

azi, ECK0099, JW0096, pea, prlD

0.015151515

-12.57114779 Essential 0.00849963 -

7.161402532

Essential

All 3 core 14

138495 139157 - 14063 971 gene 138495 139157 - BW25113_0126 can ECK0125, JW0122,

yadF

0.010558069

-15.23276688 Essential 0.004524887 -

9.891999277

Essential

All 3 core 18

170089 171369 - 14032 971 gene 170089 171369 - BW25113_0154 hemL

ECK0153, gsa,

JW0150, popC

0.010928962

-14.9823987 Essential 0.004683841 -

9.755502708

Essential

All 3 core 23

173097 173441 + 14030 971 gene 173097 173441 + BW25113_0156 erpA ECK0155, JW0152,

yadR

0.014492754

-12.90423574 Essential 0.011594203 -

5.563999989

Essential

All 3 core 23

181610 182434 - 14020 971 gene 181610 182434 - BW25113_0166 dapD ECK0164, JW0161,

ssa

0.008484848

-16.80171855 Essential 0.006060606 -

8.694437804

Essential

All 3 core 24

185199 185993 - 14018 971 gene 185199 185993 - BW25113_0168 map ECK0166, JW0163,

pepM

0.021383648

-9.922770224 Essential 0.00754717 -

7.721307883

Essential

All 3 core 24

186361 187086 + 14016 971 gene 186361 187086 + BW25113_0169 rpsB ECK0168, JW0164

0.002754821

-24.58263598 Essential 0.00137741 -

14.07692838

Essential

All 3 core 24

187344 188195 + 14014 971 gene 187344 188195 + BW25113_0170 tsf ECK0169, JW0165

0.003521127

-22.91372984 Essential 0.001173709 -

14.59119381

Essential

All 3 core 25

188342 189067 + 14013 971 gene 188342 189067 + BW25113_0171 pyrH ECK0170, JW0166,

smbA, umk

0.005509642

-19.83425577 Essential 0 -

173.5517401

Essential

All 3 core 25

189359 189916 + 14012 971 gene 189359 189916 + BW25113_0172 frr ECK0171,

JW0167, rrf 0.01254480

3 -13.97449934 Essential 0.001792115

-13.2134730

4 Essential

All 3 core 25

190008 191204 + 14011 971 gene 190008 191204 + BW25113_0173 dxr

ECK0172, ispC,

JW0168, yaeM

0.006683375

-18.48719616 Essential 0.003341688 -

11.04318803

Essential

All 3 core 25

191393 192151 + 14010 971 gene 191390 192151 + BW25113_0174 ispU

ECK0173, JW0169,

rth, uppS, yaeS

0.00656168 -18.61596728 Essential 0.005249344 -

9.295821533

Essential

All 3 core 25

192164 193021 + 14009 971 gene 192164 193021 + BW25113_0175 cdsA ECK0174, JW5810

0.005827506

-19.44438964 Essential 0.004662005 -

9.774048393

Essential

All 3 core 25

194415 196847 + 14007 971 gene 194415 196847 + BW25113_0177 bamA

ecfK, ECK0176, JW0172, omp85,

yaeT, yzzN, yzzY

0.003288122

-23.38042638 Essential 0 -

173.5517401

Essential

All 3 core 25

197458 198483 + 14005 971 gene 197458 198483 + BW25113_0179 lpxD

ECK0178, firA,

JW0174, omsA, ssc

0.002923977

-24.17841327 Essential 0.001949318 -

12.93213012

Essential

All 3 core 25

198588 199043 + 14004 971 gene 198588 199043 + BW25113_0180 fabZ

ECK0179, JW0175,

sabA, sefA, sfhC, yaeA

0.006578947

-18.59755968 Essential 0.002192982 -

12.53281706

Essential

All 3 core 25


https://doi.org/10.1101/2020.06.11.147629

199047 199835 + 14003 971 gene 199047 199835 + BW25113_0181 lpxA ECK0180, JW0176

0.002534854

-25.14614224 Essential 0.001267427 -

14.34524008

Essential

All 3 core 25

199835 200983 + 14002 971 gene 199835 200983 + BW25113_0182 lpxB ECK0181, JW0177,

pgsB

0.006962576

-18.19992375 Essential 0.003481288 -

10.89223376

Essential

All 3 core 25

201613 205095 + 14000 971 gene 201613 205095 + BW25113_0184 dnaE ECK0183, JW0179,

polC, sdgC

0.002296871

-25.81239972 Essential 0.000861326 -

15.56748841

Essential

All 3 core 25

205108 206067 + 13999 971 gene 205108 206067 + BW25113_0185 accA ECK0184, JW0180

0.00625 -18.95635603 Essential 0 -

173.5517401

Essential

All 3 core 25

208818 210116 + 13996 971 gene 208818 210116 + BW25113_0188 tilS ECK0187, JW0183,

mesJ, yaeN

0.018475751

-11.06200112 Essential 0.005388761 -

9.188029383

Essential

All 3 core 25

213544 215262 - 13989 971 gene 213544 215262 - BW25113_0194 proS drpA,

ECK0194, JW0190

0.006399069

-18.79160058 Essential 0.002326934 -

12.32930183

Essential

All 3 core 26

430103 430573 + 9602 971 gene 430103 430573 + BW25113_0415 ribE ECK0409, JW0405,

ribH, ybaF 0 -172.1619602 Essential 0

-173.551740

1 Essential

All 3 core 39

433771 435633 - 9597 971 gene 433771 435633 - BW25113_0420 dxs ECK0414, JW0410,

yajP

0.002147075

-26.26739609 Essential 0.001610306 -

13.56736282

Essential

All 3 core 41

435658 436557 - 9596 971 gene 435658 436557 - BW25113_0421 ispA ECK0415, JW0411

0.006666667

-18.50474397 Essential 0.004444444 -

9.962440011

Essential

All 3 core 41

492631 493275 + 9539 971 gene 492631 493275 + BW25113_0474 adk

dnaW, ECK0468, JW0463,

plsA

0.003100775


All 3 core 44

493511 494473 + 9538 971 gene 493511 494473 + BW25113_0475 hemH ECK0469, JW0464,

popA, visA

0.007268951

-17.89691102 Essential 0.003115265 -

11.29911028

Essential

All 3 core 44

921681 921899 - 5153 971 gene 921681 921899 - BW25113_0884 infA bypA1,

ECK0875, JW0867

0.00456621 -21.1325582 Essential 0.00456621 -

9.856176602

Essential

All 3 core 100

932828 933439 + 5145 971 gene 932828 933439 + BW25113_0891 lolA ECK0882, JW0874, lplA, yzzV

0.003267974

-23.42227814 Essential 0.003267974 -

11.12493505

Essential

All 3 core 100

934884 936176 + 5143 971 gene 934884 936176 + BW25113_0893 serS ECK0884, JW0876

0.004640371

-21.02159143 Essential 0.000773395 -

15.90260584

Essential

All 3 core 100

957451 959124 + 5125 971 gene 957451 959124 + BW25113_0911 rpsA ECK0902, JW0894,

ssyF

0.015531661

-12.38469926 Essential 0.002389486 -

12.23766447

Essential

All 3 core 105

962077 963825 + 5122 971 gene 962077 963825 + BW25113_0914 msbA ECK0905, JW0897

0.001143511

-30.49428949 Essential 0.000571755 -

16.83269407

Essential

All 3 core 105

963822 964808 + 5121 971 gene 963822 964808 + BW25113_0915 lpxK ECK0906, JW0898,

ycaH

0.005065856

-20.41605543 Essential 0.003039514 -

11.38808183

Essential

All 3 core 105

966308 967054 + 5118 971 gene 966308 967054 + BW25113_0918 kdsB ECK0909, JW0901

0 -172.1619602 Essential 0.001338688 -

14.16909828

Essential

All 3 core 105

969775 971097 + 5114 971 gene 969775 971097 + BW25113_0922 mukF ECK0913, JW0905,

kicB

0.003779289

-22.43039243 Essential 0.001511716 -

13.77442102

Essential

All 3 core 105

971078 971782 + 5113 971 gene 971078 971782 + BW25113_0923 mukE ECK0914, JW0906,

kicA, ycbA

0.008510638

-16.78011426 Essential 0.004255319 -

10.13189554

Essential

All 3 core 105


https://doi.org/10.1101/2020.06.11.147629

971782 976242 + 5112 971 gene 971782 976242 + BW25113_0924 mukB ECK0915, JW0907

0.00403497 -21.98220695 Essential 0.00044833 -

17.57279517

Essential

All 3 core 105

983041 984441 - 5105 971 gene 983041 984441 - BW25113_0930 asnS ECK0921, JW0913, lcs, tss

0.001427552

-29.0098859 Essential 0 -

173.5517401

Essential

All 3 core 106

1011408 1011926 - 5080 971 gene 1011408 1011926 - BW25113_0954 fabA ECK0945, JW0937

0.009633911

-15.89347357 Essential 0.003853565 -

10.51178503

Essential

All 3 core 107

1710205 1711479 - 11205 971 gene 1710205 1711479 - BW25113_1637 tyrS ECK1633, JW1629

0 -172.1619602 Essential 0 -

173.5517401

Essential

All 3 core 183

1736858 1737499 - 11178 971 gene 1736858 1737499 - BW25113_1662 ribC ECK1658, JW1654,

ribE

0.018691589

-10.97237971 Essential 0.00623053 -

8.575650382

Essential

All 3 core 185

1789814 1792201 - 11124 971 gene 1789814 1792201 - BW25113_1713 pheT ECK1711, JW1703

0.001675042

-27.93764461 Essential 0.000837521 -

15.65491372

Essential

All 3 core 193

1792216 1793199 - 11123 971 gene 1792216 1793199 - BW25113_1714 pheS ECK1712, JW5277, phe-act

0.00101626 -31.28221971 Essential 0 -

173.5517401

Essential

All 3 core 193

1793650 1794006 - 11122 971 gene 1793650 1794006 - BW25113_1716 rplT ECK1714, JW1706,

pdzA 0 -172.1619602 Essential 0

-173.551740

1 Essential

All 3 core 194

1794353 1794895 - 11120 971 gene 1794353 1794895 - BW25113_1718 infC

ECK1716, fit,

JW5829, srjA

0 -172.1619602 Essential 0 -

173.5517401

Essential

All 3 core 194

1794899 1796827 - 11119 971 gene 1794899 1796827 - BW25113_1719 thrS ECK1717, JW1709

0.002073613

-26.50204125 Essential 0.001036807 -

14.98507717

Essential

All 3 core 194

1816715 1817542 + 11098 971 gene 1816715 1817542 + BW25113_1740 nadE

ECK1738, efg,

JW1729, ntrL

0.002415459

-25.47236625 Essential 0 -

173.5517401

Essential

All 3 core 198

1857028 1858023 + 11056 971 gene 1857028 1858023 + BW25113_1779 gapA ECK1777, JW1768

0.002008032

-26.71851386 Essential 0 -

173.5517401

Essential

All 3 core 201

1943007 1944779 - 10961 971 gene 1943007 1944779 - BW25113_1866 aspS ECK1867,

JW1855, tls 0.00564015

8 -19.67164917 Essential 0.002256063 -12.4356925 Essential

All 3 core 211

1954319 1956052 + 10950 971 gene 1954319 1956052 + BW25113_1876 argS ECK1877, JW1865,

lov

0.001153403

-30.43672668 Essential 0 -

173.5517401

Essential

All 3 core 214

1985750 1986298 - 10915 971 gene 1985750 1986298 - BW25113_1912 pgsA ECK1911, JW1897

0 -172.1619602 Essential 0 -

173.5517401

Essential

All 3 core 220

2187779 2189812 + 13297 971 gene 2187779 2189812 + BW25113_2114 metG ECK2107, JW2101

0.016715831

-11.82848048 Essential 0.006882989 -

8.138832319

Essential

All 3 core 245

2236463 2237131 - 13256 971 gene 2236463 2237131 - BW25113_2153 folE ECK2146, JW2140

0.004484305

-21.25714257 Essential 0 -

173.5517401

Essential

All 3 core 252

2330272 2332899 - 13173 971 gene 2330272 2332899 - BW25113_2231 gyrA

ECK2223, hisW,

JW2225, nalA, nfxA, norA, parD

0.005707763

-19.58882502 Essential 0.003424658 -

10.95287954

Essential

All 3 core 258

2338344 2340629 + 13169 971 gene 2338344 2340629 + BW25113_2234 nrdA dnaF,

ECK2226, JW2228

0.000874891

-32.28141399 Essential 0 -

173.5517401

Essential

All 3 core 259

2340863 2341993 + 13168 971 gene 2340863 2341993 + BW25113_2235 nrdB ECK2227,

ftsB, JW2229

0.000884173

-32.21105382 Essential 0.000884173 -

15.48568898

Essential

All 3 core 259


https://doi.org/10.1101/2020.06.11.147629

2425153 2426421 - 13088 971 gene 2425153 2426421 - BW25113_2315 folC dedC,

ECK2309, JW2312

0.011032309

-14.91401514 Essential 0.001576044 -

13.63800212

Essential

All 3 core 267

2426491 2427405 - 13087 971 gene 2426491 2427405 - BW25113_2316 accD

dedB, ECK2310, JW2313,

usg

0.009836066

-15.74412319 Essential 0.005464481 -

9.130314146

Essential

All 3 core 267

2433864 2435084 - 13079 971 gene 2433864 2435084 - BW25113_2323 fabB ECK2317,

fabC, JW2320

0 -172.1619602 Essential 0.000819001 -

15.72456071

Essential

All 3 core 269

2512736 2514151 - 14913 971 gene 2512736 2514151 - BW25113_2400 gltX ECK2394, JW2395

0.007768362


All 3 core 277

2521520 2523535 - 14904 971 gene 2521520 2523535 - BW25113_2411 ligA

dnaL, ECK2406, JW2403, lig, lop, pdeC

0.002480159

-25.29367742 Essential 0.001984127 -

12.87252593

Essential

All 3 core 279

2584966 2586093 + 14852 971 gene 2584966 2586093 + BW25113_2472 dapE ECK2467, JW2456,

msgB

0.007978723

-17.23855666 Essential 0.005319149 -

9.241599155

Essential

All 3 core 283

2592241 2593119 - 14845 971 gene 2592241 2593119 - BW25113_2478 dapA ECK2474, JW2463

0.004550626

-21.15609645 Essential 0.004550626 -

9.869657857

Essential

All 3 core 284

2629243 2630715 - 14809 971 gene 2629243 2630715 - BW25113_2511 der

ECK2507, engA,

JW5403, yfgK

0.000678887

-33.9708671 Essential 0 -

173.5517401

Essential

All 3 core 287

2632660 2633934 - 14806 971 gene 2632660 2633934 - BW25113_2514 hisS ECK2510, JW2498

0.007843137

-17.35996883 Essential 0.004705882 -

9.736847507

Essential

All 3 core 287

2634045 2635163 - 14805 971 gene 2634045 2635163 - BW25113_2515 ispG ECK2511,

gcpE, JW2499

0.004468275

-21.28178126 Essential 0.002680965 -

11.83559533

Essential

All 3 core 287

2656801 2657604 + 14787 971 gene 2656801 2657604 + BW25113_2533 suhB ECK2530, JW2517,

ssyA

0.016169154

-12.08083279 Essential 0.008706468 -

7.044988333

Essential

All 3 core 289

2693977 2694357 - 14754 971 gene 2693977 2694357 - BW25113_2563 acpS dpj,

ECK2561, JW2547

0.002624672

-24.91048841 Essential 0.002624672 -

11.91029244

Essential

All 3 core 293

2695840 2696745 - 14751 971 gene 2695840 2696745 - BW25113_2566 era ECK2564, JW2550,

sdgE

0.005518764

-19.82277225 Essential 0.003311258 -

11.07675766

Essential

All 3 core 293

2697694 2698668 - 14748 971 gene 2697694 2698668 - BW25113_2568 lepB ECK2566, JW2552,

lep

0.021538462

-9.865876328 Essential 0.01025641 -

6.220506973

Essential

All 3 core 293

2716086 2717441 + 14730 971 gene 2716086 2717441 + BW25113_2585 pssA ECK2583, JW2569,

pss

0.003687316

-22.59881556 Essential 0.002949853 -

11.49575145

Essential

All 3 core 294

2729505 2730242 + 14719 971 gene 2729505 2730242 + BW25113_2595 bamD

ecfD, ECK2593, JW2577,

yfiO

0.013550136

-13.40497064 Essential 0.006775068 -

8.209122806

Essential

All 3 core 296

2737542 2737889 - 14708 971 gene 2737542 2737889 - BW25113_2606 rplS ECK2603, JW2587

0.025862069

-8.399510111 Essential 0.00862069 -

7.093061258

Essential

All 3 core 298

2737931 2738698 - 14707 971 gene 2737931 2738698 - BW25113_2607 trmD ECK2604, JW2588

0.0078125 -17.38767452 Essential 0.00390625 -

10.46028479

Essential

All 3 core 298

2739296 2739544 - 14705 971 gene 2739296 2739544 - BW25113_2609 rpsP ECK2606, JW2590

0.008032129

-17.19126165 Essential 0.008032129 -

7.431057811

Essential

All 3 core 298

2739793 2741154 - 14704 971 gene 2739793 2741154 - BW25113_2610 ffh ECK2607, JW5414

0.01174743 -14.45617269 Essential 0.008076358 -

7.405138551

Essential

All 3 core 298


https://doi.org/10.1101/2020.06.11.147629

2743474 2744067 - 14701 971 gene 2743474 2744067 - BW25113_2614 grpE ECK2610, JW2594

0.035353535

-5.769005313 Essential 0.023569024 -0.82460818 Unclear

All 3 core 299

2744190 2745068 + 14699 971 gene 2744190 2745068 + BW25113_2615 nadK ECK2611, JW2596, yfjB, yfjE

0.001137656

-30.52859315 Essential 0.001137656 -

14.69063643

Essential

All 3 core 299

2812320 2812505 - 12413 971 gene 2812320 2812505 - BW25113_2696 csrA ECK2691, JW2666,

zfiA

0.037634409

-5.220254659 Essential 0.005376344 -

9.197548656

Essential

All 3 core 304

2864660 2865139 - 12363 971 gene 2864660 2865139 - BW25113_2746 ispF ECK2741, JW2716,

ygbB

0.002083333

-26.47053041 Essential 0 -

173.5517401

Essential

All 3 core 309

2865139 2865849 - 12362 971 gene 2865139 2865849 - BW25113_2747 ispD ECK2742, JW2717,

ygbP

0.012658228

-13.90823625 Essential 0.011251758 -

5.727940492

Essential

All 3 core 309

2865868 2866179 - 12361 971 gene 2865868 2866179 - BW25113_2748 ftsB ECK2743, JW2718,

ygbQ

0.019230769

-10.7523091 Essential 0.025641026 -

0.117358534

Unclear

All 3 core 309

2900002 2901300 - 12328 971 gene 2900002 2901300 - BW25113_2779 eno ECK2773, JW2750

0.008468052

-16.81582141 Essential 0.006158584 -

8.625671968

Essential

All 3 core 313

2901388 2903025 - 12327 971 gene 2901388 2903025 - BW25113_2780 pyrG ECK2774, JW2751

0.002442002


All 3 core 313

2958521 2959396 - 12278 971 gene 2958521 2959396 - BW25113_2828 lgt ECK2824, JW2796,

umpA

0.012557078

-13.96730234 Essential 0.007990868 -

7.455317852

Essential

All 3 core 316

3063524 3064603 - 12165 971 gene 3063524 3064603 - BW25113_2925 fbaA

ald, ECK2921, fba, fda, JW2892

0.007407407

-17.7638918 Essential 0 -

173.5517401

Essential

All 3 core 322

3064818 3065981 - 12164 971 gene 3064818 3065981 - BW25113_2926 pgk ECK2922, JW2893

0.009450172

-16.03174237 Essential 0.006013746 -

8.727595751

Essential

All 3 core 322

3080065 3081219 + 12148 971 gene 3080065 3081219 + BW25113_2942 metK ECK2937, JW2909,

metX

0.008658009

-16.65781583 Essential 0.005194805 -

9.338545704

Essential

All 3 core 329

3086859 3087275 + 12141 971 gene 3086859 3087275 + BW25113_2949 yqgF ECK2944, JW2916

0.026378897

-8.237989554 Essential 0.009592326 -

6.564215265

Essential

All 3 core 329

3156103 3156840 - 622 971 gene 3156103 3156840 - BW25113_3018 plsC ECK3009, JW2986,

parF

0.004065041

-21.93130923 Essential 0.006775068 -

8.209122806

Essential

All 3 core 333

3166863 3168755 - 610 971 gene 3166863 3168755 - BW25113_3030 parE ECK3021, JW2998,

nfxD 0.00792393 -17.28738803 Essential 0.003169572

-11.2363968

6 Essential

All 3 core 336

3195250 3196488 + 584 971 gene 3195250 3196488 + BW25113_3056 cca ECK3046, JW3028

0.020177563

-10.37828348 Essential 0.012106538 -

5.323457847

Essential

All 3 core 340

3202889 3203902 - 575 971 gene 3202889 3203902 - BW25113_3064 tsaD

ECK3054, gcp,

JW3036, ygjD

0.006903353

-18.25994026 Essential 0.003944773 -

10.42296633

Essential

All 3 core 340

3306701 3309373 - 464 971 gene 3306701 3309373 - BW25113_3168 infB

ECK3157, gicD,

JW3137, ssyG

0.011597456


All 3 core 352

3309398 3310885 - 463 971 gene 3309398 3310885 - BW25113_3169 nusA ECK3158, JW3138

0.016801075

-11.78978054 Essential 0.014112903 -

4.428329564

Essential

All 3 core 352

3318360 3320294 - 454 971 gene 3318360 3320294 - BW25113_3178 ftsH

ECK3167, hflB,

JW3145, mrsC, std,

tolZ

0.042377261

-4.154008379 Essential 0.009302326 -

6.718609156

Essential

All 3 core 353


https://doi.org/10.1101/2020.06.11.147629

3323941 3325113 - 449 971 gene 3323941 3325113 - BW25113_3183 obgE

cgtA, ECK3172, JW3150,

obg, yhbZ

0.028985507

-7.460166058 Essential 0.011935209 -

5.403290225

Essential

All 3 core 353

3326221 3326478 - 447 971 gene 3326221 3326478 - BW25113_3185 rpmA ECK3174, JW3152,

rpz

0.003875969

-22.25757105 Essential 0.003875969 -

10.48981876

Essential

All 3 core 353

3326499 3326810 - 446 971 gene 3326499 3326810 - BW25113_3186 rplU ECK3175, JW3153

0.006410256

-18.7793833 Essential 0.006410256 -

8.452381285

Essential

All 3 core 353

3327069 3328040 + 445 971 gene 3327069 3328040 + BW25113_3187 ispB

cel, ECK3176, JW3154,

yhbD

0.011316872

-14.72869052 Essential 0.005144033 -

9.378609131

Essential

All 3 core 353

3328594 3329853 - 443 971 gene 3328594 3329853 - BW25113_3189 murA

ECK3178, JW3156,

mrbA, murZ

0.001587302

-28.29874364 Essential 0.000793651 -

15.82233677

Essential

All 3 core 353

3336739 3337296 + 432 971 gene 3336739 3337296 + BW25113_3200 lptA ECK3189, JW3167,

yhbN

0.021505376


All 3 core 353

3371174 3371566 - 405 971 gene 3371174 3371566 - BW25113_3230 rpsI ECK3219, JW3199

0.010178117

-15.49772501 Essential 0 -

173.5517401

Essential

All 3 core 355

3371582 3372010 - 404 971 gene 3371582 3372010 - BW25113_3231 rplM ECK3220, JW3200

0 -172.1619602 Essential 0 -

173.5517401

Essential

All 3 core 355

3391746 3392234 - 387 971 gene 3391746 3392234 - BW25113_3249 mreD ECK3237, JW3218

0.028629857

-7.562911402 Essential 0.016359918 -

3.496147861

Unclear

All 3 core 356

3392234 3393337 - 386 971 gene 3392234 3393337 - BW25113_3250 mreC ECK3238, JW3219

0.031702899

-6.706333794 Essential 0.023550725 -

0.830949693

Unclear

All 3 core 356

3393403 3394446 - 385 971 gene 3393403 3394446 - BW25113_3251 mreB

ECK3239, envB,

JW3220, mon, rodY

0.006704981

-18.46456543 Essential 0.003831418 -

10.53359668

Essential

All 3 core 356

3398795 3399265 + 379 971 gene 3398795 3399265 + BW25113_3255 accB ECK3242,

fabE, JW3223

0.006369427

-18.82407043 Essential 0.002123142 -

12.64318399

Essential

All 3 core 356

3399276 3400625 + 378 971 gene 3399276 3400625 + BW25113_3256 accC ECK3243,

fabG, JW3224

0.002962963

-24.08848745 Essential 0.000740741 -

16.03628564

Essential

All 3 core 356

3424202 3424774 - 350 971 gene 3424202 3424774 - BW25113_3282 tsaC ECK3269, JW3243,

rimN, yrdC 0.02443281 -8.860280933 Essential 0.008726003

-7.03408022

3 Essential

All 3 core 361

3427049 3427558 + 346 971 gene 3427049 3427558 + BW25113_3287 def ECK3273,

fms, JW3248

0.029411765

-7.338332519 Essential 0.009803922 -

6.453263176

Essential

All 3 core 361

3427573 3428520 + 345 971 gene 3427573 3428520 + BW25113_3288 fmt ECK3274, JW3249,

yhdD

0.021097046

-10.0290149 Essential 0.012658228 -

5.070300127

Essential

All 3 core 361

3432975 3433358 - 338 971 gene 3432975 3433358 - BW25113_3294 rplQ ECK3281, JW3256

0.002604167

-24.96358498 Essential 0 -

173.5517401

Essential

All 3 core 362

3433399 3434388 - 337 971 gene 3433399 3434388 - BW25113_3295 rpoA

ECK3282, JW3257, pez, phs,

sez

0.004040404

-21.97298241 Essential 0.003030303 -

11.39902274

Essential

All 3 core 362

3434414 3435034 - 336 971 gene 3434414 3435034 - BW25113_3296 rpsD ECK3283, JW3258,

ramA, sud 0 -172.1619602 Essential 0

-173.551740

1 Essential

All 3 core 362

3435068 3435457 - 335 971 gene 3435068 3435457 - BW25113_3297 rpsK ECK3284, JW3259

0 -172.1619602 Essential 0 -

173.5517401

Essential

All 3 core 362


https://doi.org/10.1101/2020.06.11.147629

3435474 3435830 - 334 971 gene 3435474 3435830 - BW25113_3298 rpsM ECK3285, JW3260

0 -172.1619602 Essential 0 -

173.5517401

Essential

All 3 core 362

3436125 3437456 - 332 971 gene 3436125 3437456 - BW25113_3300 secY ECK3287, JW3262,

prlA

0.000750751

-33.30101992 Essential 0.000750751 -

15.99472356

Essential

All 3 core 362

3437464 3437898 - 331 971 gene 3437464 3437898 - BW25113_3301 rplO ECK3288, JW3263

0 -172.1619602 Essential 0 -

173.5517401

Essential

All 3 core 362

3437902 3438081 - 330 971 gene 3437902 3438081 - BW25113_3302 rpmD ECK3289, JW3264

0 -172.1619602 Essential 0 -

173.5517401

Essential

All 3 core 362

3438085 3438588 - 329 971 gene 3438085 3438588 - BW25113_3303 rpsE

ECK3290, eps,

JW3265, spc, spcA

0 -172.1619602 Essential 0 -

173.5517401

Essential

All 3 core 362

3438603 3438956 - 328 971 gene 3438603 3438956 - BW25113_3304 rplR ECK3291, JW3266

0 -172.1619602 Essential 0 -

173.5517401

Essential

All 3 core 362

3438966 3439499 - 327 971 gene 3438966 3439499 - BW25113_3305 rplF ECK3292, JW3267

0 -172.1619602 Essential 0 -

173.5517401

Essential

All 3 core 362

3439512 3439904 - 326 971 gene 3439512 3439904 - BW25113_3306 rpsH ECK3293, JW3268

0.002544529

-25.12036917 Essential 0 -

173.5517401

Essential

All 3 core 362

3439938 3440243 - 325 971 gene 3439938 3440243 - BW25113_3307 rpsN ECK3294, JW3269

0 -172.1619602 Essential 0 -

173.5517401

Essential

All 3 core 362

3440258 3440797 - 324 971 gene 3440258 3440797 - BW25113_3308 rplE ECK3295, JW3270

0.001851852

-27.26337251 Essential 0.003703704 -

10.66132336

Essential

All 3 core 362

3440812 3441126 - 323 971 gene 3440812 3441126 - BW25113_3309 rplX ECK3296, JW3271

0 -172.1619602 Essential 0 -

173.5517401

Essential

All 3 core 362

3441137 3441508 - 322 971 gene 3441137 3441508 - BW25113_3310 rplN ECK3297, JW3272

0 -172.1619602 Essential 0.002688172 -

11.82612657

Essential

All 3 core 362

3441673 3441927 - 321 971 gene 3441673 3441927 - BW25113_3311 rpsQ ECK3298, JW3273,

neaA

0.003921569

-22.17749955 Essential 0.003921569 -

10.44541096

Essential

All 3 core 362

3441927 3442118 - 320 971 gene 3441927 3442118 - BW25113_3312 rpmC ECK3299, JW3274

0.005208333

-20.22413515 Essential 0.005208333 -

9.327918422

Essential

All 3 core 362

3442118 3442528 - 319 971 gene 3442118 3442528 - BW25113_3313 rplP ECK3300, JW3275

0.00729927 -17.86758046 Essential 0 -

173.5517401

Essential

All 3 core 362

3442541 3443242 - 318 971 gene 3442541 3443242 - BW25113_3314 rpsC ECK3301, JW3276

0.004273504

-21.58814052 Essential 0.001424501 -

13.96794772

Essential

All 3 core 362

3443260 3443592 - 317 971 gene 3443260 3443592 - BW25113_3315 rplV ECK3302,

eryB, JW3277

0.012012012

-14.2931597 Essential 0.006006006 -

8.733089593

Essential

All 3 core 362

3443607 3443885 - 316 971 gene 3443607 3443885 - BW25113_3316 rpsS ECK3303, JW3278

0.003584229

-22.79249401 Essential 0 -

173.5517401

Essential

All 3 core 362

3443902 3444723 - 315 971 gene 3443902 3444723 - BW25113_3317 rplB ECK3304, JW3279

0.00486618 -20.69390119 Essential 0.003649635 -

10.71643421

Essential

All 3 core 362

3444741 3445043 - 314 971 gene 3444741 3445043 - BW25113_3318 rplW ECK3305, JW3280

0.00330033 -23.35518875 Essential 0.00330033 -

11.08887333

Essential

All 3 core 362


https://doi.org/10.1101/2020.06.11.147629

3445040 3445645 - 313 971 gene 3445040 3445645 - BW25113_3319 rplD ECK3306,

eryA, JW3281

0.00330033 -23.35518875 Essential 0 -

173.5517401

Essential

All 3 core 362

3445656 3446285 - 312 971 gene 3445656 3446285 - BW25113_3320 rplC ECK3307, JW3282

0.004761905

-20.84336986 Essential 0 -

173.5517401

Essential

All 3 core 362

3446318 3446629 - 311 971 gene 3446318 3446629 - BW25113_3321 rpsJ ECK3308, JW3283,

nusE

0.006410256

-18.7793833 Essential 0 -

173.5517401

Essential

All 3 core 362

3464759 3466873 - 292 971 gene 3464759 3466873 - BW25113_3340 fusA ECK3327, far, fus, JW3302

0.005200946

-20.23396158 Essential 0.00141844 -

13.98179026

Essential

All 3 core 363

3466970 3467440 - 291 971 gene 3466901 3467440 - BW25113_3341 rpsG ECK3328, JW3303

0.024074074

-8.979386506 Essential 0.014814815 -

4.130145373

Essential

All 3 core 363

3467537 3467911 - 290 971 gene 3467537 3467911 - BW25113_3342 rpsL

asuB, ECK3329, JW3304,

strA

0.008 -17.21967899 Essential 0.002666667 -

11.85444324

Essential

All 3 core 363

3505993 3506997 - 245 971 gene 3505993 3506997 - BW25113_3384 trpS ECK3371, JW3347

0.00199005 -26.77908321 Essential 0 -

173.5517401

Essential

All 3 core 364

3567135 3568238 - 191 971 gene 3567135 3568238 - BW25113_3433 asd

dap, ECK3419,

hom, JW3396

0.002717391


All 3 core 369

3717767 3718678 - 54 971 gene 3717767 3718678 - BW25113_3560 glyQ

cfcA, ECK3548,

glyS, JW3531

0.001096491

-30.77482494 Essential 0.003289474 -

11.10094099

Essential

All 3 core 389

3776002 3777021 - 7247 971 gene 3776002 3777021 - BW25113_3608 gpsA ECK3598, JW3583

0.011764706


All 3 core 395

3801900 3803177 + 7271 971 gene 3801900 3803177 + BW25113_3633 waaA ECK3623, JW3608,

kdtA

0.009389671

-16.07781367 Essential 0.003912363 -

10.45434405

Essential

All 3 core 398

3803185 3803664 + 7272 971 gene 3803185 3803664 + BW25113_3634 coaD ECK3624, JW3609,

kdtB, yicA 0.00625 -18.95635603 Essential 0.004166667

-10.2132903

5 Essential

All 3 core 398

3804798 3805034 - 7275 971 gene 3804798 3805034 - BW25113_3637 rpmB ECK3627, JW3612

0.004219409

-21.67561417 Essential 0 -

173.5517401

Essential

All 3 core 398

3807292 3807747 + 7278 971 gene 3807292 3807747 + BW25113_3640 dut

dnaS, ECK3630, JW3615,

sof

0.010964912

-14.95854446 Essential 0.013157895 -

4.845836117

Essential

All 3 core 398

3814788 3815411 + 7287 971 gene 3814788 3815411 + BW25113_3648 gmk ECK3638, JW3623,

spoR

0.003205128

-23.55445252 Essential 0.003205128 -

11.19580493

Essential

All 3 core 400

3871065 3873479 - 7344 971 gene 3871065 3873479 - BW25113_3699 gyrB

acrB, Cou, ECK3691,

himB, hisU, hopA,

JW5625, nalC, parA, pcbA, pcpA

0.004554865

-21.14968616 Essential 0.001656315 -

13.47458181

Essential

All 3 core 410

3874581 3875681 - 7346 971 gene 3874581 3875681 - BW25113_3701 dnaN ECK3693, JW3678

0.005449591

-19.91030829 Essential 0.002724796 -

11.77833211

Essential

All 3 core 410

3875686 3877089 - 7347 971 gene 3875686 3877089 - BW25113_3702 dnaA ECK3694,

hsm-2, JW3679

0.003561254

-22.83639392 Essential 0.000712251 -

16.15755739

Essential

All 3 core 410

3877696 3877836 + 7349 971 gene 3877696 3877836 + BW25113_3703 rpmH ECK3695, JW3680,

rimA, ssaF 0 -172.1619602 Essential 0

-173.551740

1 Essential

All 3 core 411


https://doi.org/10.1101/2020.06.11.147629

3877853 3878212 + 7350 971 gene 3877853 3878212 + BW25113_3704 rnpA ECK3696, JW3681

0.044444444

-3.71643435 Essential 0.027777778 0.59191535 Unclear

All 3 core 411

3878436 3880082 + 7352 971 gene 3878436 3880082 + BW25113_3705 yidC ECK3698, JW3683

0.009107468

-16.29639683 Essential 0.004857316 -

9.610383003

Essential

All 3 core 411

3905199 3907028 - 7376 971 gene 3905199 3907028 - BW25113_3729 glmS ECK3722, JW3707

0.031147541

-6.856153186 Essential 0.00273224 -

11.76868287

Essential

All 3 core 414

3907190 3908560 - 7377 971 gene 3907190 3908560 - BW25113_3730 glmU ECK3723, JW3708, tms, yieA

0.010211524

-15.47406887 Essential 0.005105762 -

9.408996618

Essential

All 3 core 414

3983185 3984126 - 7452 971 gene 3983185 3984126 - BW25113_3805 hemC ECK3799, JW5932,

popE

0.012738854

-13.86145793 Essential 0.005307856 -

9.250336637

Essential

All 3 core 421

4027968 4028513 + 7496 971 gene 4027968 4028513 + BW25113_3850 hemG ECK3842, JW3827,

yihB

0.003663004

-22.64401575 Essential 0.009157509 -

6.796764258

Essential

All 3 core 427

4043493 4044125 - 7511 971 gene 4043493 4044125 - BW25113_3865 yihA ECK3857,

engB, JW5930

0.023696682

-9.106272554 Essential 0.006319115 -

8.514596152

Essential

All 3 core 432

4155356 4156213 + 7618 971 gene 4155356 4156213 + BW25113_3967 murI

dga, ECK3959,

glr, JW5550,

yijA

0.006993007

-18.16927168 Essential 0.003496503 -

10.87607306

Essential

All 3 core 449

4242944 4243816 + 7699 971 gene 4242944 4243816 + BW25113_4040 ubiA

cyr, ECK4032, JW4000,

sdgG

0.017182131

-11.61884284 Essential 0.005727377 -

8.934202357

Essential

All 3 core 469

4243971 4246394 - 7700 971 gene 4243971 4246394 - BW25113_4041 plsB ECK4033, JW4001

0.012788779

-13.83262504 Essential 0.008663366 -

7.069108257

Essential

All 3 core 469

4247043 4247651 + 7702 971 gene 4247043 4247651 + BW25113_4043 lexA

ECK4035, exrA,

JW4003, spr, tsl, umuA

0.02134647 -9.936484521 Essential 0.014778325 -4.14547925 Essential

All 3 core 469

4254242 4255657 + 7711 971 gene 4254242 4255657 + BW25113_4052 dnaB

ECK4044, groP, grpA,

grpD, JW4012

0.011299435

-14.73992408 Essential 0.005649718 -

8.991464372

Essential

All 3 core 471

4264053 4264589 + 1249 971 gene 4264053 4264589 + BW25113_4059 ssb

ECK4051, exrB,

JW4020, lexC

0.001862197

-27.22590934 Essential 0 -

173.5517401

Essential

All 3 core 473

4360505 4360798 + 1343 971 gene 4360505 4360798 + BW25113_4142 groS

ECK4136, groES,

JW4102, mopB, TabB

0.010204082

-15.47933255 Essential 0 -

173.5517401

Essential

All 3 core 486

4379209 4380177 - 1361 971 gene 4379209 4380177 - BW25113_4160 psd ECK4156, JW4121

0.035087719

-5.834683906 Essential 0.025799794 -

0.063996442

Unclear

All 3 core 491

4381421 4381966 + 1363 971 gene 4381421 4381966 + BW25113_4162 orn ECK4158, JW5740,

yjeR

0.014652015

-12.82250177 Essential 0.003663004 -

10.70274847

Essential

All 3 core 491

4385402 4385863 + 1370 971 gene 4385402 4385863 + BW25113_4168 tsaE ECK4164, JW4126,

yjeE

0.015151515

-12.57114779 Essential 0.006493506 -

8.396071181

Essential

All 3 core 492

4415656 4415883 + 1404 971 gene 4415656 4415883 + BW25113_4202 rpsR ECK4198, JW4160

0.030701754

-6.977931647 Essential 0.013157895 -

4.845836117

Essential

All 3 core 495

4438939 4439469 - 7908 971 gene 4438939 4439469 - BW25113_4226 ppa ECK4222, JW4185

0.003766478

-22.45361297 Essential 0.001883239 -

13.04787805

Essential

All 3 core 499


https://doi.org/10.1101/2020.06.11.147629

4470799 4473654 - 6564 971 gene 4470799 4473654 - BW25113_4258 valS ECK4251, JW4215, val-act

0.00245098 -25.37369246 Essential 0.0017507 -

13.29119485

Essential

All 3 core 506

4590055 4590792 - 14235 971 gene 4590055 4590792 - BW25113_4361 dnaC dnaD,

ECK4351, JW4325

0.008130081


All 3 core 514

153740 154219 - 14045 778 gene 153740 154219 - BW25113_0142 folK ECK0141, JW0138

0.079166667

2.160389125 Unclear 0.022916667 -

1.051794567

Unclear KP Conditionally essential

Keio-PEC non-core 20-

21

928680 932669 + 5146 944 gene 928680 932669 + BW25113_0890 ftsK dinH,

ECK0881, JW0873

0.117293233

7.020558521 Non-

essential 0.029573935

1.174571987

Unclear KP

Genes containing a transposon free region

Keio-PEC core 100

4112308 4113267 - 7581 968 gene 4112308 4113267 - BW25113_3933 ftsN ECK3925, JW3904,

msgA

0.207291667

16.12149011 Non-


32.43494447

Non-essential

KP


Keio-PEC core 441

1136638 1139823 - 4944 970 gene 1136638 1139823 - BW25113_1084 rne

ams, ECK1069,

hmp1, JW1071,

smbB

0.064030132

-0.140424844 Unclear 0.023226616 -

0.943565344

Unclear KP


Keio-PEC core 127

1139958 1140278 + 4943 970 gene 1139958 1140278 + BW25113_1085 yceQ ECK1070, JW5154

0.090342679

3.696304238 Non-


8.077358051

Non-essential

KP Polar

insertions Keio-PEC core 127

104192 104704 + 14093 971 gene 104192 104704 + BW25113_0097 secM ECK0098, JW5007,

srrA, yacA

0.087719298

3.34589178 Unclear 0.048732943 6.89464588

5 Non-

essential KP


Keio-PEC core 14

193033 194385 + 14008 971 gene 193033 194385 + BW25113_0176 rseP

ecfE, ECK0175, JW0171,

yaeL

0.057649667

-1.212948026 Unclear 0.002217295 -

12.49510308

Essential KP Conditionally essential

Keio-PEC core 25

423103 424950 + 9609 971 gene 423103 424950 + BW25113_0408 secD ECK0402, JW0398

0.056818182

-1.358330908 Unclear 0.013528139 -

4.682257928

Essential KP Errors in library

construction Keio-PEC core 38

424961 425932 + 9608 971 gene 424961 425932 + BW25113_0409 secF ECK0403, JW0399

0.085390947

3.029940696 Unclear 0.018518519 -

2.653380889

Unclear KP Errors in library


2277855 2279615 + 13214 971 gene 2277855 2279615 + BW25113_2188 yejM ECK2182, JW2176,

yejN

0.093696763

4.136233447 Non-


2.413233184

Unclear KP


Keio-PEC core 254

3177172 3177825 - 599 971 gene 3177172 3177825 - BW25113_3041 ribB

ECK3032, htrP,

JW3009, luxH

0.051987768

-2.23234331 Unclear 0.042813456 5.20005766

4 Non-

essential KP


Keio-PEC core 338

3336195 3336770 + 433 971 gene 3336195 3336770 + BW25113_3199 lptC ECK3188, JW3166,

yrbK

0.071180556

0.983663531 Unclear 0.050347222 7.34877528

7 Non-

essential KP


Keio-PEC core 353

3375559 3376626 + 400 971 gene 3375559 3376626 + BW25113_3235 degS ECK3224,

hhoB, htrH, JW3204

0.143258427

9.882280933 Non-


-5.73557023

2 Essential KP

Conditionally essential

Keio-PEC core 355

3594388 3595446 - 163 971 gene 3594388 3595446 - BW25113_3462 ftsX ECK3446,

ftsS, JW3427

0.134088763

8.901244327 Non-


5.925306016

Non-essential

KP


Keio-PEC core 374

3595439 3596107 - 162 971 gene 3595439 3596107 - BW25113_3463 ftsE ECK3447, JW3428

0.144992526

10.06464909 Non-


7.062228789

Non-essential

KP Errors in library


3815760 3817868 + 7289 971 gene 3815760 3817868 + BW25113_3650 spoT ECK3640, JW3625

0.100521574

5.005815705 Non-


8.380473806

Non-essential

KP


Keio-PEC core 400

1197715 1198389 - 24944 47 gene 1197715 1198389 - BW25113_1145 cohE ECK1131, JW1131,

ymfK 0 -172.1619602 Essential 0

-173.551740

1 Essential KT Unclear TraDIS-Keio

non-core 131-132

1414022 1414498 - 4312 106 gene 1414022 1414498 - BW25113_1356 racR

cohR, ECK1354, JW1351,

ydaR

0.012578616

-13.95468959 Essential 0.008385744 -

7.226236375

Essential KT Unclear TraDIS-Keio non-core 152-153


https://doi.org/10.1101/2020.06.11.147629

1642191 1642598 + 8268 128 gene 1642191 1642598 + BW25113_1570 dicA ECK1564,

ftsT, JW1562

0 -172.1619602 Essential 0 -

173.5517401

Essential KT Errors in library

construction TraDIS-Keio

non-core 179-180

766914 768482 + 9289 971 gene 766914 768482 + BW25113_0733 cydA ECK0721, JW0722

0.019120459

-10.79690017 Essential 0.008285532 -

7.283732415


construction TraDIS-Keio core 77

922930 924651 - 5151 971 gene 922930 924651 - BW25113_0886 cydC

ECK0877, JW0869,

mdrA, mdrH,

surB, ycaB

0.036585366

-5.469436285 Essential 0.019163763 -

2.409660146

Unclear KT Errors in library


1186072 1187442 - 4898 971 gene 1186072 1187442 - BW25113_1131 purB ade,

ECK1117, JW1117

0.012399708

-14.0600538 Essential 0.001458789 -13.8906244 Essential KT Conditionally essential

TraDIS-Keio core 131

2690713 2691249 - 14761 971 gene 2690713 2691216 - BW25113_2559 tadA ECK2557, JW2543,

yfhC

0.029761905

-7.239296387 Essential 0.003968254 -

10.40035699



2702796 2703371 - 14743 971 gene 2702796 2703371 - BW25113_2573 rpoE ECK2571, JW2557,

sigE

0.027777778

-7.813274253 Essential 0.003472222 -

10.90188985



3971961 3973313 + 7441 971 gene 3971961 3973313 + BW25113_3793 wzyE ECK3786, JW3769,

rffT

0.012564671

-13.96285363 Essential 0.009608278 -

6.555801775

Essential KT Unclear TraDIS-Keio core 419

4013586 4015226 + 7483 971 gene 4013586 4015226 + BW25113_3835 ubiB

aarF, ECK3829, JW3812,

yigQ, yigR, yigS

0.006093845

-19.13298299 Essential 0.002437538 -

12.16863919

Essential KT Conditionally essential


4018348 4019841 + 7489 971 gene 4018348 4019841 + BW25113_3843 ubiD ECK3835, JW3819, yigC, yigY

0.022088353

-9.666521984 Essential 0.008701473 -

7.047779847

Essential KT Conditionally essential


4164004 4164954 - 7625 969 gene 4164004 4164954 - BW25113_3974 coaA

ECK3966, JW3942, panK, rts,

ts-9

0.016824395

-11.77922323 Essential 0.009463722 -6.63234268 Essential PT Errors in library

construction TraDIS-PEC core 454

22391 25207 + 14166 971 gene 22391 25207 + BW25113_0026 ileS ECK0027,

ilvS, JW0024

0.002484913

-25.28072825 Essential 0.00141995 -

13.97833663

Essential PT Errors in library


109086 109706 - 14088 971 gene 109086 109706 - BW25113_0103 coaE ECK0103, JW0100,

yacE

0.020933977

-10.09000813 Essential 0.009661836 -

6.527612863



430593 431012 + 9601 971 gene 430593 431012 + BW25113_0416 nusB

ECK0410, groNB,

JW0406, ssaD, ssyB

0.038095238

-5.112435103 Essential 0.014285714 -

4.354270567

Essential PT Polar

insertions TraDIS-PEC core 39

2611434 2612180 - 14827 971 gene 2611434 2612135 - BW25113_2496 hda

ECK2492, idaB,

JW5397, yfgE

0.012820513

-13.81435035 Essential 0.004273504 -

10.11535818



2812740 2815370 - 12412 971 gene 2812740 2815370 - BW25113_2697 alaS

act, ala-act, ECK2692, JW2667,

lovB

0.000760167

-33.21801291 Essential 0 -

173.5517401



3028543 3029641 - 12201 971 gene 3028543 3029641 - BW25113_2891 prfB ECK2886, JW5847,

supK 0.00273224 -24.63841954 Essential 0.000910747

-15.3930014

4 Essential PT

Errors in library


3157074 3159332 - 621 971 gene 3157074 3159332 - BW25113_3019 parC ECK3010, JW2987

0.008410801

-16.86408869 Essential 0.003098716 -

11.31839661



3197580 3197948 - 582 971 gene 3197580 3197948 - BW25113_3058 folB ECK3048, JW3030,

ygiG

0.029810298

-7.225681066 Essential 0.002710027 -11.7975412 Essential PT Conditionally essential

TraDIS-PEC core 340

3204466 3206211 + 572 971 gene 3204466 3206211 + BW25113_3066 dnaG

dnaP, ECK3056, JW3038,

parB, sdgA

0.001718213

-27.76675924 Essential 0.001145475 -

14.66882613



3206406 3208247 + 570 971 gene 3206406 3208247 + BW25113_3067 rpoD alt,

ECK3057, JW3039

0.001628664

-28.12612808 Essential 0.000542888 -

16.99093748




https://doi.org/10.1101/2020.06.11.147629

3316092 3317429 - 456 971 gene 3316092 3317429 - BW25113_3176 glmM ECK3165, JW3143,

mrsA, yhbF

0.007473842

-17.70089145 Essential 0.004484305 -

9.927417451



3337303 3338028 + 431 971 gene 3337303 3338028 + BW25113_3201 lptB ECK3190, JW3168,

yhbG

0.002754821

-24.58263598 Essential 0.002754821 -

11.73954498



3715688 3717757 - 55 971 gene 3715688 3717757 - BW25113_3559 glyS ECK3547, gly-act, JW3530

0.001932367

-26.97707354 Essential 0.000966184 -

15.20751537



3959777 3961036 + 7429 971 gene 3959777 3961036 + BW25113_3783 rho

ECK3775, hdf,

JW3756, nitA, nusD, psuA, rnsC, sbaA, sun, tabC, tsu

0.004761905

-20.84336986 Essential 0.002380952 -

12.25004589



4360842 4362488 + 1344 971 gene 4360842 4362488 + BW25113_4143 groL

ECK4137, groEL,

JW4103, mopA

0.00667881 -18.4919865 Essential 0.004250152 -

10.13660413



4380274 4381326 - 1362 971 gene 4380274 4381326 - BW25113_4161 rsgA

ECK4157, engC,

JW4122, yjeQ

0.024691358

-8.775325975 Essential 0.008547009 -

7.134586068



4590795 4591334 - 14234 971 gene 4590795 4591334 - BW25113_4362 dnaT ECK4352, JW4326

0.009259259

-16.17806066 Essential 0.005555556 -

9.061639178

Essential PT Unclear TraDIS-PEC core 514

281106 282488 + 9093 58 gene 281106 282488 + BW25113_0270 yagG ECK0271, JW0263

0.23065799 18.21291061 Non-


33.65567835

Non-essential

K Unclear Keio only non-core 34-

35

235587 235865 + 1554 72 pseudogene 235593 235865 + BW25113_4503 yafF ECK0219, JW0208

0.326007326

26.15277505 Non-


49.30848265

Non-essential

K


Keio only non-core 29-

30

3791599 3792672 - 6615 153 gene 3791599 3792672 - BW25113_3623 waaU ECK3613, JW3598,

rfaK, waaK

0.227188082

17.90698672 Non-


34.90938304

Non-essential

K


Keio only non-core 397-398

3161210 3161605 - 619 330 gene 3161210 3161605 - BW25113_3021 mqsA ECK3012, JW2989,

ygiT

0.138888889

9.418401974 Non-


19.37214231

Non-essential

K


Keio only non-core 333-334

1642880 1643050 + 11630 354 gene 1642922 1643050 + BW25113_1572 ydfB ECK1566, JW1564

0.07751938 1.923662732 Unclear 0.031007752 1.63185417

7 Unclear K Unclear Keio only

non-core 179-180

4296687 4297616 - 1280 500 gene 4296687 4297616 - BW25113_4084 alsK ECK4077, JW5724,

yjcT 0.31827957 25.53607274

Non-essential

0.232258065 52.2423655

8 Non-

essential K

Errors in library

construction Keio only

non-core 479-480

4438264 4438515 + 7910 547 gene 4438264 4438515 + BW25113_4224 chpS

chpBI, ECK4220, JW5750,

yjfB

0.226190476

17.8187494 Non-


38.59767553

Non-essential

K Anti-Toxin Keio only non-core 498-499

2082943 2083194 - 13394 735 gene 2082943 2083194 - BW25113_2017 yefM ECK2012, JW5835

0.075396825

1.61421362 Unclear 0.027777778 0.59191535 Unclear K Anti-Toxin Keio only non-core 234-235

2904450 2904698 - 12324 818 gene 2904450 2904698 - BW25113_2783 mazE

chpAI, chpR,

ECK2777, JW2754,

tasA

0.192771084

14.7804794 Non-


21.49872632

Non-essential

K Anti-Toxin Keio only non-core 313-314

604915 605535 - 9446 889 gene 604915 605535 - BW25113_0583 entD ECK0575, JW5085

0.164251208

12.03105967 Non-


23.16781243

Non-essential

K Errors in library

construction Keio only

non-core 57-58

3883596 3884843 + 7356 946 gene 3883596 3884843 + BW25113_3709 tnaB

ECK3702, JW5619, JW5622,

tnaP, trpP

0.525641026

41.14469998 Non-


104.2756867

Non-essential

K Errors in library

construction Keio only core 412

1764872 1765228 + 11150 958 gene 1764872 1765228 + BW25113_1689 ydiL ECK1687, JW1679

0.294117647

23.58178253 Non-


31.63615187

Non-essential

K Unclear Keio only core 186


https://doi.org/10.1101/2020.06.11.147629

3683628 3685967 - 86 963 gene 3683628 3685967 - BW25113_3532 bcsB ECK3517, JW3500,

yhjN

0.288461538

23.11810449 Non-


49.68220353

Non-essential

K Errors in library


3253080 3253469 - 522 966 gene 3253080 3253469 - BW25113_3113 tdcF ECK3102, JW5521,

yhaR 0.21025641 16.3911441

Non-essential

0.151282051 32.9965409

7 Non-

essential K Unclear Keio only core 349

1219735 1220001 - 4875 969 gene 1219735 1220001 - BW25113_1174 minE ECK1162, JW1163,

minB

0.048689139

-2.861471825 Unclear 0.041198502 4.72859772

7 Non-

essential K

Errors in library


1220005 1220817 - 4874 969 gene 1220005 1220817 - BW25113_1175 minD ECK1163, JW1164,

minB

0.166051661

12.20988517 Non-


19.67802331

Non-essential

K Errors in library


3295848 3296726 + 474 969 gene 3295848 3296726 + BW25113_3159 yhbV ECK3147, JW5530

0.253697383

20.2082008 Non-


45.49939363

Non-essential

K Unclear Keio only core 351

3285834 3286694 - 487 970 gene 3285834 3286694 - BW25113_3146 rsmI ECK3134, JW3115,

yraL

0.205574913

15.964729 Non-


32.08283433

Non-essential

K Errors in library


2696742 2697422 - 14750 971 gene 2696742 2697422 - BW25113_2567 rnc ECK2565, JW2551,

ranA

0.067547724

0.421826829 Unclear 0.019089574 -

2.437509338

Unclear K Polar

insertions Keio only core 293

3330322 3330615 - 441 971 gene 3330322 3330615 - BW25113_3191 mlaB ECK3180, JW5535,

yrbB

0.336734694

27.0027312 Non-

essential 0.261904762 59.1806718

Non-essential

K Errors in library


3602577 3603242 + 154 971 gene 3602577 3603242 + BW25113_3471 yhhQ ECK3455, JW3436

0.243243243

19.31024275 Non-


36.33809299

Non-essential

K Errors in library


4012984 4013589 + 7482 971 gene 4012984 4013589 + BW25113_3834 ubiJ ECK3828, JW3811,

yigP

0.156765677

11.27885212 Non-

essential 0.118811881 25.0749831

Non-essential

K Polar

insertions Keio only core 427

692419 692503 - 9356 967 tRNA 692419 692503 - BW25113_0672 leuW tRNA-Leu

P

RNA genes not

considered in our

analysis

PEC only core 68

4165316 4165391 + 7628 969 tRNA 4165316 4165391 + BW25113_3976 thrU tRNA-Thr

P

RNA genes not

considered in our

analysis

PEC only core 454

4165601 4165675 + 7630 969 tRNA 4165601 4165675 + BW25113_3978 glyT tRNA-Gly

P

RNA genes not

considered in our

analysis

PEC only core 454

560179 560255 + 9477 970 tRNA 560179 560255 + BW25113_0536 argU tRNA-Arg

P

RNA genes not

considered in our

analysis

PEC only core 54

1027081 1027168 - 5062 970 tRNA 1027081 1027168 - BW25113_0971 serT tRNA-Ser

P

RNA genes not

considered in our

analysis

PEC only core 108

4040326 4043112 + 7510 970 gene 4040326 4043112 + BW25113_3863 polA ECK3855, JW3835,

resA

0.095801938

4.407982507 Non-


6.608498825

Non-essential

P


PEC only core 432

471912 472008 + 9561 971 SRP_RNA 471904 472017 + BW25113_0455 ffs

4.5S sRNA component

of Signal Recognition Particle

(SRP)

P

RNA genes not

considered in our

analysis

PEC only core 44

1985296 1985382 - 10918 971 tRNA 1985296 1985382 - BW25113_1909 leuZ tRNA-Leu

P

RNA genes not

considered in our

analysis

PEC only core 220

1985395 1985468 - 10917 971 tRNA 1985395 1985468 - BW25113_1910 cysT tRNA-Cys

P

RNA genes not

considered in our

analysis

PEC only core 220


https://doi.org/10.1101/2020.06.11.147629

2811912 2812004 - 12414 971 tRNA 2811912 2812004 - BW25113_2695 serV tRNA-Ser

P

RNA genes not

considered in our

analysis

PEC only core 304

3315431 3315517 - 458 971 tRNA 3315431 3315517 - BW25113_3174 leuU tRNA-Leu

P

RNA genes not

considered in our

analysis

PEC only core 353

3335632 3336198 + 434 971 gene 3335632 3336198 + BW25113_3198 kdsC ECK3187, JW3165, yrbI, yrbJ

0.132275132

8.703671917 Non-


17.84678784

Non-essential

P Polar

insertions PEC only core 353

3940317 3940392 + 7408 971 tRNA 3940317 3940392 + BW25113_3761 trpT tRNA-Trp

P

RNA genes not

considered in our

analysis

PEC only core 418

3975735 3975811 + 7444 971 tRNA 3975735 3975811 + BW25113_3796 argX tRNA-Arg

P

RNA genes not

considered in our

analysis

PEC only core 419

3975870 3975945 + 7445 971 tRNA 3975869 3975945 + BW25113_3797 hisR tRNA-His

P

RNA genes not

considered in our

analysis

PEC only core 419

3976095 3976171 + 7447 971 tRNA 3976095 3976171 + BW25113_3799 proM tRNA-Pro

P

RNA genes not

considered in our

analysis

PEC only core 419

4114540 4116738 - 7583 971 gene 4114540 4116738 - BW25113_3935 priA ECK3927, JW3906,

srgA

0.090950432

3.776675641 Non-


-0.48490891

4 Unclear P

Errors in library

construction PEC only core 442

4365516 4366082 + 1348 971 gene 4365516 4366082 + BW25113_4147 efp ECK4141, JW4107

0.074074074

1.418735065 Unclear 0.012345679 -

5.213005676

Essential P Errors in library

construction PEC only core 488

2557882 2558691 + 17731 32 gene 2557882 2558691 + BW25113_2450 yffS ECK2445 0.02962963 -7.276601225 Essential 0.024691358 -

0.438938723

Unclear

TraDIS only non-core 282-283

1192989 1193693 - 17523 44 gene 1192989 1193693 - BW25113_1138 ymfE ECK1124, JW5166

0.018439716

-11.07705114 Essential 0.004255319 -

10.13189554

Essential


1524179 1524350 + 9732 68 gene 1524179 1524661 + BW25113_1457 ydcD ECK1451, JW1452

0.028985507

-7.460166058 Essential 0.00621118 -

8.589064978

Essential


1414622 1414918 + 4313 106 gene 1414622 1414918 + BW25113_1357 ydaS ECK1355, JW1352

0.03030303 -7.088034047 Essential 0.013468013 -

4.708669777

Essential


2005030 2005832 - 4291 143 pseudogene 2004704 2005832 - BW25113_4495 yedN

ECK1932, JW1918, JW5912,

yedM

0.040888889

-4.478728525 Essential 0.008888889 -

6.943692285

Essential


1631304 1631714 + 7818 202 gene 1631304 1631714 + BW25113_1549 ydfO ECK1543, JW5252

0.02919708 -7.399517805 Essential 0.01459854 -

4.221291329

Essential


1459422 1459487 - 8167 207 gene 1459422 1459487 - BW25113_4674 ynbG ECK4489 0 -172.1619602 Essential 0 -

173.5517401

Essential


1639890 1640129 - 8263 247 gene 1639890 1640129 - BW25113_1564 relB ECK1558,

JW1556, RC 0.01666666

7 -11.85087856 Essential 0.0125

-5.14231587

8 Essential

TraDIS only

non-core 179-180

1412095 1412265 - 4306 257 gene 1412095 1412265 - BW25113_4526 ydaE ECK1349, JW1346

0.029239766

-7.387323963 Essential 0 -

173.5517401

Essential


1429215 1429265 - 74732 411 pseudogene 1429215 1429265 - BW25113_4638 ttcC ECK4447 0.01960784

3 -10.60151157 Essential 0

-173.551740

1 Essential

TraDIS only

non-core 152-153


https://doi.org/10.1101/2020.06.11.147629

234744 235223 - 13965 534 gene 234744 235223 - BW25113_4586 ykfM ECK4397 0.02083333

3 -10.12785226 Essential 0.010416667

-6.13946696

1 Essential

TraDIS only

non-core 29-30

2988673 2988882 - 7873 585 pseudogene 2988673 2989379 - BW25113_2858 ygeN ECK2855, JW5459,

ygeM

0.025423729

-8.538567963 Essential 0.012711864 -

5.045992785

Essential


2984627 2985118 + 12254 627 gene 2984627 2985118 + BW25113_2851 ygeG ECK2849, JW2819

0.044715447

-3.660160022 Essential 0.036585366 3.35572773

1 Unclear

TraDIS only

non-core 316-317

2983913 2984402 + 12255 629 pseudogene 2983913 2984402 + BW25113_2850 ygeF ECK2848, JW2818

0.022357724

-9.570374812 Essential 0.010162602 -

6.268275126

Essential


2983178 2983258 - 12257 641 gene 2983178 2983258 - BW25113_4683 yqeL ECK4498 0.02469135

8 -8.775325975 Essential 0.061728395

10.47446051

Non-essential


1521197 1521409 + 1832 680 gene 1521197 1521409 + BW25113_1455 yncH ECK1449, JW5235

0.014084507

-13.1174424 Essential 0.004694836 -

9.746188617

Essential


1207136 1207459 - 4892 683 gene 1207136 1207459 - BW25113_1160 iraM

ECK1147, elb1, elbA, JW1147,

ycgW

0.043209877

-3.975952967 Essential 0.021604938 -

1.515945912

Unclear


2898916 2899056 + 12330 685 gene 2898916 2899056 + BW25113_4682 yqcG ECK4497 0.02836879

4 -7.638979344 Essential 0.021276596

-1.63377036

9 Unclear

TraDIS only

non-core 312-313

1586433 1586699 - 1885 767 gene 1586433 1586699 - BW25113_1508 hipB ECK1501, JW1501

0.02247191 -9.529909302 Essential 0.003745318 -

10.61933383

Essential


1539995 1540285 - 1848 809 pseudogene 1540007 1540285 - BW25113_1472 yddL ECK1466, JW1468

0.039426523



4258457 4258979 - 7817 828 gene 4258737 4258940 - BW25113_4621 yjbS ECK4429 0.01960784

3 -10.60151157 Essential 0.009803922

-6.45326317

6 Essential

TraDIS only

non-core 472-473

3227087 3227503 - 553 836 gene 3227087 3227503 - BW25113_3082 higA ECK3072, JW3053,

ygjM

0.040767386

-4.505615563 Essential 0.009592326 -

6.564215265

Essential


1578019 1578216 - 1876 963 gene 1578019 1578216 - BW25113_1500 safA ECK4475,

yneN 0.03535353

5 -5.769005313 Essential 0.005050505

-9.45316228

5 Essential

TraDIS only core 171

1111118 1112038 - 4974 967 gene 1111118 1112038 - BW25113_1054 lpxL

ECK1039, htrB,

JW1041, waaM

0.007600434

-17.58228345 Essential 0.004343105 -

10.05254968

Essential


122182 124074 + 14075 968 gene 122182 124074 + BW25113_0115 aceF ECK0114, JW0111

0.04437401 -3.731100261 Essential 0.01320655 -

4.824210081

Essential

TraDIS only core 16

4168375 4168803 + 7635 969 gene 4168375 4168803 + BW25113_3983 rplK ECK3974, JW3946,

relC

0.009324009

-16.12812595 Essential 0.004662005 -

9.774048393

Essential


4168807 4169511 + 7636 969 gene 4168807 4169511 + BW25113_3984 rplA ECK3975, JW3947,

rpy

0.031205674

-6.840373332 Essential 0.012765957 -

5.021531178

Essential


4187644 4188708 + 7651 969 gene 4187644 4188708 + BW25113_3997 hemE ECK3989,

hemC, JW3961

0.011267606

-14.76047015 Essential 0.005633803 -

9.003267203

Essential


654707 655672 - 9398 970 gene 654707 655672 - BW25113_0628 lipA ECK0621,

JW0623, lip 0.01138716

4 -14.68356459 Essential 0.005175983

-9.35336491

5 Essential

TraDIS only core 65

687330 687797 - 9365 970 gene 687330 687797 - BW25113_0659 ybeY ECK0651, JW0656

0.027777778

-7.813274253 Essential 0.008547009 -

7.134586068

Essential

TraDIS only core 68


https://doi.org/10.1101/2020.06.11.147629

1142823 1142996 + 4939 970 gene 1142823 1142996 + BW25113_1089 rpmF ECK1075, JW1075

0.022988506



1144215 1145168 + 4937 970 gene 1144215 1145168 + BW25113_1091 fabH ECK1077, JW1077

0.012578616

-13.95468959 Essential 0.002096436 -

12.68621415

Essential


1305346 1306065 + 4788 970 gene 1305346 1306065 + BW25113_1252 tonB

ECK1246, exbA,

JW5195, T1rec

0.040277778

-4.614558523 Essential 0.015277778 -

3.937113272

Essential


1317295 1317339 - 4774 970 gene 1317295 1317339 - BW25113_1265 trpL ECK1259, JW1257,

trpEE

0.044444444

-3.71643435 Essential 0.022222222 -

1.296252231

Unclear


1334500 1334808 + 4756 970 gene 1334500 1334808 + BW25113_1279 yciS ECK1274, JW1271

0.038834951

-4.941379755 Essential 0.012944984 -

4.940945513

Essential


1341053 1341157 + 4748 970 gene 1341053 1341157 + BW25113_4672 ymiB ECK4487 0.00952381 -15.97603279 Essential 0.028571429 0.85079032

2 Unclear


1940372 1940437 - 10966 970 gene 1940372 1940437 - BW25113_4677 yobI ECK4492 0.03030303 -7.088034047 Essential 0.03030303 1.40792025

8 Unclear


2135115 2135696 - 13344 970 gene 2135115 2135696 - BW25113_2065 dcd

dus, ECK2059, JW2050,

paxA

0.030927835

-6.915999887 Essential 0 -

173.5517401

Essential


4012215 4012970 + 7481 970 gene 4012215 4012970 + BW25113_3833 ubiE

ECK3827, JW5581, menG,

menH, yigO

0.044973545

-3.606791384 Essential 0.007936508 -

7.487399067

Essential


20815 21078 - 14169 971 gene 20815 21078 - BW25113_0023 rpsT ECK0024, JW0022,

sup 0 -172.1619602 Essential 0

-173.551740

1 Essential

TraDIS only core 6

124399 125823 + 14074 971 gene 124399 125823 + BW25113_0116 lpd

dhl, ECK0115, JW0112,

lpdA

0.008421053

-16.855423 Essential 0.002105263 -

12.67193958

Essential

TraDIS only core 16

754162 756963 + 9297 971 gene 754162 756963 + BW25113_0726 sucA ECK0714,

JW0715, lys 0.03604568

2 -5.599728351 Essential 0.015346181

-3.90882489

5 Essential

TraDIS only core 75

756978 758195 + 9296 971 gene 756978 758195 + BW25113_0727 sucB ECK0715, JW0716

0.031198686

-6.842268967 Essential 0.013957307 -

4.495386645

Essential

TraDIS only core 75

768498 769637 + 9288 971 gene 768498 769637 + BW25113_0734 cydB ECK0722, JW0723

0.028947368

-7.471136099 Essential 0.005263158 -

9.285050544

Essential

TraDIS only core 77

769652 769765 + 9287 971 gene 769652 769765 + BW25113_4515 cydX ECK0723, JW0724,

ybgT

0.043859649

-3.83871021 Essential 0.026315789 0.10867049

8 Unclear

TraDIS only core 77

924652 926418 - 5150 971 gene 924652 926418 - BW25113_0887 cydD ECK0878,

htrD, JW0870

0.042444822



966129 966311 + 5119 971 gene 966129 966311 + BW25113_0917 ycaR ECK0908, JW0900

0.038251366

-5.076126751 Essential 0.043715847 5.46165912 Non-

essential TraDIS only core 105

1025795 1026124 - 5064 971 gene 1025795 1026124 - BW25113_0969 tusE ECK0960, JW0952,

yccK

0.036363636

-5.522790325 Essential 0.009090909 -

6.832951723

Essential


1188123 1189229 - 4896 971 gene 1188123 1189229 - BW25113_1133 mnmA

asuE, ECK1119, JW1119,

trmU, ycfB

0.029810298



1711608 1712264 - 11204 971 gene 1711608 1712264 - BW25113_1638 pdxH ECK1634, JW1630

0.02891933 -7.47920808 Essential 0.00152207 -

13.75211663

Essential



https://doi.org/10.1101/2020.06.11.147629

1719938 1720177 - 11194 971 gene 1719938 1720177 - BW25113_1648 ydhL ECK1644, JW5827

0.041666667

-4.307985423 Essential 0.020833333 -

1.793945138

Unclear


1722604 1723251 + 11190 971 gene 1722604 1723251 + BW25113_1652 rnt ECK1648, JW1644

0.026234568



1789510 1789809 - 11125 971 gene 1789510 1789809 - BW25113_1712 ihfA ECK1710, hid, himA,

JW1702

0.036666667

-5.449934172 Essential 0.01 -

6.351668274

Essential


1793389 1793523 - 7195 971 gene 1793483 1793527 - BW25113_1715 pheM ECK1713, JW1705,

phtL 0 -172.1619602 Essential 0

-173.551740

1 Essential


1794059 1794256 - 11121 971 gene 1794059 1794256 - BW25113_1717 rpmI ECK1715, JW1707

0.02020202 -10.36882094 Essential 0.01010101 -

6.299774025

Essential


2275996 2276280 + 13217 971 gene 2275996 2276280 + BW25113_2185 rplY ECK2179, JW2173

0.007017544

-18.14464769 Essential 0.007017544 -

8.052201423

Essential


2333046 2333768 + 13172 971 gene 2333046 2333768 + BW25113_2232 ubiG ECK2224, JW2226,

pufX, yfaB

0.017980636



2421536 2422105 - 13092 971 gene 2421536 2422105 - BW25113_2311 ubiX dedF,

ECK2305, JW2308

0.01754386 -11.45958812 Essential 0.005263158 -

9.285050544

Essential


2527425 2529152 + 14899 971 gene 2527425 2529152 + BW25113_2416 ptsI ctr,

ECK2411, JW2409

0.03587963 -5.640113382 Essential 0.008101852 -

7.390238446

Essential


2624317 2625894 - 14813 971 gene 2624317 2625894 - BW25113_2507 guaA ECK2503, JW2491

0.031685678

-6.71094865 Essential 0.001267427 -

14.34524008

Essential


2650107 2650442 - 14795 971 gene 2650107 2650442 - BW25113_2525 fdx ECK2522, JW2509

0.041666667

-4.307985423 Essential 0.017857143 -

2.906891943

Unclear


2650444 2652294 - 14794 971 gene 2650444 2652294 - BW25113_2526 hscA ECK2523,

hsc, JW2510

0.03619665 -5.563133723 Essential 0.015667207 -

3.776832573

Essential


2653262 2653648 - 14791 971 gene 2653262 2653648 - BW25113_2529 iscU

ECK2526, hsm-5,

JW2513, miaC, nifU,

yfhN

0.010335917

-15.38660276 Essential 0.005167959 -

9.359694254

Essential


2653676 2654890 - 14790 971 gene 2653676 2654890 - BW25113_2530 iscS

ECK2527, JW2514,

nuvC, yfhO, yzzO

0.012345679

-14.09214201 Essential 0.003292181 -

11.09792888

Essential


2677613 2678866 - 14769 971 gene 2677613 2678866 - BW25113_2551 glyA ECK2548, JW2535

0.002392344

-25.53734318 Essential 0.003189793 -

11.21326718

Essential


2728390 2729370 - 14720 971 gene 2728390 2729370 - BW25113_2594 rluD ECK2592, JW2576, sfhB, yfiI

0.023445464

-9.191663545 Essential 0.013251784 -

4.804140289

Essential


2738729 2739277 - 14706 971 gene 2738729 2739277 - BW25113_2608 rimM ECK2605, JW5413,

yfjA

0.010928962

-14.9823987 Essential 0.003642987 -

10.72325433

Essential


2957720 2958514 - 12279 971 gene 2957720 2958514 - BW25113_2827 thyA ECK2823, JW2795

0 -172.1619602 Essential 0 -

173.5517401

Essential


3027016 3028533 - 12202 971 gene 3027016 3028533 - BW25113_2890 lysS

asuD, ECK2885,

herC, JW2858

0.011857708

-14.38782943 Essential 0.001976285 -

12.88587409

Essential


3034672 3035652 + 12194 971 gene 3034672 3035652 + BW25113_2898 ygfZ ECK2893, JW2866,

yzzW

0.033639144

-6.199428634 Essential 0.02038736 -

1.956438484

Unclear



https://doi.org/10.1101/2020.06.11.147629

3045699 3046877 - 12185 971 gene 3045699 3046877 - BW25113_2907 ubiH

acd, ECK2902, JW2875,

visB

0.03307888 -6.343734547 Essential 0.005089059 -

9.422310407

Essential


3073003 3074994 - 12155 971 gene 3073003 3074994 - BW25113_2935 tktA ECK2930, JW5478,

tkt

0.041164659

-4.417920388 Essential 0.019076305 -

2.442494934

Unclear


3204140 3204355 + 573 971 gene 3204140 3204355 + BW25113_3065 rpsU ECK3055, JW3037

0.013888889

-13.22155404 Essential 0.00462963 -

9.801663538

Essential


3304774 3305043 - 467 971 gene 3304774 3305043 - BW25113_3165 rpsO ECK3154, JW3134,

secC 0.02962963 -7.276601225 Essential 0.011111111

-5.79605046

1 Essential


3306136 3306537 - 465 971 gene 3306136 3306537 - BW25113_3167 rbfA

ECK3156, JW3136, sdr-43, yhbB

0.042288557

-4.173126561 Essential 0.019900498 -

2.135433705

Unclear


3317422 3318270 - 455 971 gene 3317422 3318270 - BW25113_3177 folP dhpS,

ECK3166, JW3144

0.041224971

-4.404661108 Essential 0.00942285 -

6.654107084

Essential


3507741 3508418 - 243 971 gene 3507741 3508418 - BW25113_3386 rpe

dod, ECK3373, JW3349,

yhfD

0.03539823 -5.757998822 Essential 0.013274336 -

4.794147004

Essential


3988122 3988946 + 7458 971 gene 3988122 3988946 + BW25113_3809 dapF ECK3804, JW5592

0.04 -4.676800152 Essential 0.029090909 1.01900286

9 Unclear


4414935 4415330 + 1402 971 gene 4414935 4415330 + BW25113_4200 rpsF ECK4196, JW4158,

sdgH

0.002525253

-25.17181345 Essential 0 -

173.5517401

Essential


4415337 4415651 + 1403 971 gene 4415337 4415651 + BW25113_4201 priB ECK4197, JW4159

0.031746032

-6.694783646 Essential 0.00952381 -

6.600444847

Essential


4597620 4598033 + 14223 971 gene 4597620 4598033 + BW25113_4372 holD ECK4363, JW4334

0.024154589




https://doi.org/10.1101/2020.06.11.147629

Table 4. The 521 E. coli core regions identified through the pan-genome graph.

Core Region Start Stop Length (bp)

1 337 5237 4901

2 5683 9893 4211

3 9928 15298 5371

4 16751 16960 210

5 17325 18655 1331

6 20815 28207 7393

7 28374 39115 10742

8 39244 50302 11059

9 50380 58179 7800

10 59687 66546 6860

11 66477 67752 1276

12 67838 72097 4260

13 72131 73786 1656

14 75335 113586 38252

15 113596 118038 4443

16 118579 125823 7245

17 127869 130699 2831

18 130875 143343 12469

19 143455 144357 903

20 144431 146088 1658

21 154216 161021 6806

22 161217 163751 2535

23 166265 180582 14318

24 181610 187086 5477

25 187344 212466 25123

26 212666 220198 7533

27 220258 222062 1805

28 222237 225166 2930

29 225245 233494 8250

30 235906 242292 6387

31 244845 246584 1740

32 247385 248440 1056

33 249196 249648 453

34 250746 258657 7912

35 380688 385435 4748

36 390586 403917 13332

37 404403 419788 15386

38 419793 425932 6140

39 426061 432563 6503

40 432617 433591 975


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41 433771 442122 8352

42 442271 447066 4796

43 447110 447302 193

44 447526 502022 54497

45 502059 503536 1478

46 504331 509324 4994

47 509449 509856 408

48 509857 518286 8430

49 525588 531153 5566

50 543813 545072 1260

51 545083 546788 1706

52 546983 548643 1661

53 548674 553197 4524

54 560179 560255 77

55 588766 592919 4154

56 594170 600880 6711

57 601721 602839 1119

58 605480 613494 8015

59 613710 619966 6257

60 620341 630832 10492

61 630805 632025 1221

62 633160 637323 4164

63 639013 647312 8300

64 650039 651792 1754

65 652013 655884 3872

66 657093 670956 13864

67 678933 683203 4271

68 684799 692826 8028

69 692969 694633 1665

70 695030 701346 6317

71 701549 703213 1665

72 703790 710654 6865

73 716512 724796 8285

74 734457 743225 8769

75 748641 758195 9555

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77 766914 776374 9461

78 777033 777108 76

79 777224 793887 16664

80 794042 796031 1990

81 798959 802737 3779

82 802795 803365 571

83 803424 811003 7580


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84 811195 816044 4850

85 816998 827692 10695

86 828526 832892 4367

87 833121 836987 3867

88 837006 853011 16006

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92 872166 883415 11250

93 883435 895101 11667

94 895300 899190 3891

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97 911716 918270 6555

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99 921274 921358 85

100 921340 936176 14837

101 936415 940352 3938

102 940387 942475 2089

103 945796 946536 741

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106 979975 992968 12994

107 1000224 1026874 26651

108 1027081 1037371 10291

109 1046419 1046631 213

110 1046917 1051634 4718

111 1051717 1059231 7515

112 1061041 1063164 2124

113 1063368 1063604 237

114 1065316 1067615 2300

115 1067627 1074602 6976

116 1074761 1076269 1509

117 1076812 1080103 3292

118 1080448 1081512 1065

119 1093021 1096243 3223

120 1096307 1097140 834

121 1097167 1098652 1486

122 1098868 1099304 437

123 1099407 1100358 952

124 1100417 1108862 8446

125 1110976 1114502 3527

126 1114763 1136442 21680


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127 1136638 1162845 26208

128 1163055 1175797 12743

129 1177161 1179076 1916

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131 1183772 1191829 8058

132 1219409 1222928 3520

133 1223170 1224985 1816

134 1226052 1235405 9354

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138 1282994 1289600 6607

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148 1377220 1384983 7764

149 1386248 1387147 900

150 1387484 1390179 2696

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152 1400236 1406205 5970

153 1429442 1431150 1709

154 1431517 1436000 4484

155 1436111 1439947 3837

156 1476512 1481220 4709

157 1483970 1486107 2138

158 1488405 1497382 8978

159 1509019 1511259 2241

160 1511356 1513284 1929

161 1515220 1517322 2103

162 1517356 1520237 2882

163 1533107 1538317 5211

164 1540545 1546248 5704

165 1546655 1546939 285

166 1547085 1550017 2933

167 1550882 1551313 432

168 1561761 1566678 4918

169 1573890 1575047 1158


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170 1575099 1576781 1683

171 1577183 1580743 3561

172 1581077 1581991 915

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174 1605164 1606111 948

175 1606223 1608960 2738

176 1611285 1613165 1881

177 1613377 1614464 1088

178 1616903 1617171 269

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181 1651004 1652127 1124

182 1657247 1669204 11958

183 1669229 1723251 54023

184 1728011 1728358 348

185 1728692 1762942 34251

186 1763331 1766542 3212

187 1766769 1769701 2933

188 1772647 1773558 912

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190 1774658 1778934 4277

191 1778991 1783738 4748

192 1783870 1789409 5540

193 1789510 1793199 3690

194 1793389 1796827 3439

195 1799219 1806582 7364

196 1807678 1810385 2708

197 1810643 1812757 2115

198 1812862 1837971 25110

199 1839256 1844950 5695

200 1845117 1846785 1669

201 1855959 1863099 7141

202 1863212 1864495 1284

203 1866118 1866285 168

204 1867831 1873512 5682

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207 1888330 1916569 28240

208 1916570 1917480 911

209 1917622 1933348 15727

210 1933479 1938456 4978

211 1938603 1944779 6177

212 1946523 1948670 2148


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213 1948835 1951264 2430

214 1951289 1956052 4764

215 1956837 1960448 3612

216 1960650 1963621 2972

217 1965287 1972101 6815

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220 1985296 1995270 9975

221 1998784 2003347 4564

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223 2016374 2017159 786

224 2017449 2025798 8350

225 2029316 2034599 5284

226 2034856 2035506 651

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232 2074862 2076028 1167

233 2076237 2077664 1428

234 2079185 2082609 3425

235 2083280 2083462 183

236 2083543 2090706 7164

237 2131383 2132966 1584

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239 2145192 2146609 1418

240 2147497 2159002 11506

241 2159149 2160678 1530

242 2161470 2163092 1623

243 2170991 2178911 7921

244 2179003 2180777 1775

245 2186272 2189812 3541

246 2199174 2204579 5406

247 2204704 2208123 3420

248 2209136 2212036 2901

249 2213171 2222544 9374

250 2222917 2223864 948

251 2224103 2227318 3216

252 2227512 2245176 17665

253 2247724 2249493 1770

254 2253198 2279766 26569

255 2283690 2305013 21324


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256 2306509 2313355 6847

257 2320846 2327881 7036

258 2328435 2333768 5334

259 2338344 2342951 4608

260 2343414 2351282 7869

261 2355910 2367017 11108

262 2367127 2374506 7380

263 2375087 2376004 918

264 2380413 2380916 504

265 2383527 2416080 32554

266 2417215 2424242 7028

267 2424501 2427405 2905

268 2428303 2431330 3028

269 2431310 2437249 5940

270 2437370 2441919 4550

271 2449806 2454749 4944

272 2457731 2459712 1982

273 2459788 2459862 75

274 2472681 2491774 19094

275 2492150 2507723 15574

276 2509122 2512290 3169

277 2512736 2514485 1750

278 2514612 2514687 76

279 2519289 2531070 11782

280 2532031 2537982 5952

281 2539132 2541456 2325

282 2543005 2550656 7652

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284 2590264 2594307 4044

285 2608179 2624224 16046

286 2624317 2628961 4645

287 2629243 2638223 8981

288 2638372 2646698 8327

289 2647215 2661205 13991

290 2666627 2666720 94

291 2666705 2667127 423

292 2667175 2692966 25792

293 2693022 2707589 14568

294 2707798 2719199 11402

295 2719430 2724917 5488

296 2724959 2730242 5284

297 2730272 2735752 5481

298 2735742 2743419 7678


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299 2743474 2749314 5841

300 2782344 2793834 11491

301 2793879 2807513 13635

302 2807577 2810862 3286

303 2811143 2811219 77

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308 2849812 2853013 3202

309 2859918 2866388 6471

310 2866746 2870977 4232

311 2880669 2885938 5270

312 2898106 2898777 672

313 2900002 2904044 4043

314 2904776 2927047 22272

315 2928943 2940932 11990

316 2941116 2980435 39320

317 2992343 2997327 4985

318 3024593 3038460 13868

319 3039527 3050308 10782

320 3050321 3052684 2364

321 3053112 3054216 1105

322 3059636 3067105 7470

323 3068045 3068554 510

324 3069538 3070815 1278

325 3070830 3072218 1389

326 3072246 3072689 444

327 3073003 3076030 3028

328 3076236 3077156 921

329 3077294 3091762 14469

330 3091917 3103800 11884

331 3129667 3132952 3286

332 3133075 3154505 21431

333 3154616 3159519 4904

334 3162108 3165192 3085

335 3165889 3166815 927

336 3166863 3174940 8078

337 3174978 3176682 1705

338 3177172 3178077 906

339 3185098 3185562 465

340 3188323 3209032 20710

341 3209086 3209850 765


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342 3210138 3219530 9393

343 3219593 3227042 7450

344 3227976 3232904 4929

345 3233303 3239881 6579

346 3240011 3246028 6018

347 3246677 3250010 3334

348 3250038 3251369 1332

349 3251405 3260957 9553

350 3263575 3270212 6638

351 3285834 3297814 11981

352 3297932 3313339 15408

353 3315431 3353975 38545

354 3362373 3367848 5476

355 3369638 3385387 15750

356 3385817 3400625 14809

357 3400734 3406159 5426

358 3412196 3413425 1230

359 3413493 3416553 3061

360 3416784 3417144 361

361 3420568 3432489 11922

362 3432975 3446629 13655

363 3463504 3492974 29471

364 3505993 3524011 18019

365 3524074 3527799 3726

366 3527875 3536553 8679

367 3537433 3549149 11717

368 3553207 3556878 3672

369 3557494 3569024 11531

370 3569081 3572086 3006

371 3572310 3574986 2677

372 3578441 3585685 7245

373 3586084 3591727 5644

374 3591915 3606274 14360

375 3606329 3612349 6021

376 3619039 3623962 4924

377 3629568 3641148 11581

378 3643597 3644022 426

379 3647165 3648573 1409

380 3648615 3658328 9714

381 3659540 3662548 3009

382 3662952 3678978 16027

383 3682515 3689545 7031

384 3689818 3693447 3630


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385 3693456 3699150 5695

386 3699458 3701677 2220

387 3701808 3703835 2028

388 3704159 3713960 9802

389 3715688 3720721 5034

390 3720767 3724125 3359

391 3724491 3734942 10452

392 3750036 3755315 5280

393 3763603 3764739 1137

394 3764742 3770387 5646

395 3770759 3782420 11662

396 3782407 3785911 3505

397 3787347 3789335 1989

398 3801900 3808450 6551

399 3808487 3810899 2413

400 3812234 3820651 8418

401 3820820 3825526 4707

402 3825579 3829676 4098

403 3833909 3835099 1191

404 3835310 3844086 8777

405 3844162 3846348 2187

406 3847282 3849667 2386

407 3857972 3863801 5830

408 3868681 3868776 96

409 3869500 3870834 1335

410 3871065 3877089 6025

411 3877383 3881552 4170

412 3881795 3890186 8392

413 3900213 3904885 4673

414 3905199 3918993 13795

415 3919372 3927130 7759

416 3927138 3934687 7550

417 3937055 3939984 2930

418 3940062 3953173 13112

419 3954037 3977554 23518

420 3979792 3979963 172

421 3980046 3987419 7374

422 3987882 3993505 5624

423 3993652 3995736 2085

424 3996648 4001737 5090

425 4001799 4008674 6876

426 4008714 4010552 1839

427 4010452 4028513 18062


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428 4028891 4030577 1687

429 4030870 4033800 2931

430 4033879 4033994 116

431 4034266 4037404 3139

432 4037559 4049699 12141

433 4049985 4053590 3606

434 4068913 4071798 2886

435 4072657 4072869 213

436 4073659 4080209 6551

437 4086484 4086798 315

438 4087279 4096315 9037

439 4096397 4098442 2046

440 4098597 4108688 10092

441 4108773 4114384 5612

442 4114540 4117153 2614

443 4117214 4117822 609

444 4118006 4122195 4190

445 4122223 4143026 20804

446 4143624 4148151 4528

447 4148201 4150718 2518

448 4151052 4153502 2451

449 4155356 4156527 1172

450 4156587 4158140 1554

451 4158300 4158375 76

452 4158560 4161489 2930

453 4161567 4161682 116

454 4161985 4179501 17517

455 4180663 4188708 8046

456 4188718 4191747 3030

457 4193248 4197599 4352

458 4199702 4199777 76

459 4199962 4202892 2931

460 4202970 4203085 116

461 4203608 4208341 4734

462 4208524 4210260 1737

463 4212732 4217439 4708

464 4217659 4220070 2412

465 4220282 4221559 1278

466 4221812 4230127 8316

467 4230253 4230663 411

468 4232554 4240402 7849

469 4242328 4249049 6722

470 4251597 4254159 2563


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471 4254242 4256789 2548

472 4257042 4258235 1194

473 4259342 4264589 5248

474 4264688 4266985 2298

475 4266988 4271557 4570

476 4273181 4275141 1961

477 4275341 4285722 10382

478 4286253 4286942 690

479 4287036 4294220 7185

480 4311514 4312239 726

481 4313153 4315558 2406

482 4316216 4323767 7552

483 4325511 4331445 5935

484 4331728 4333083 1356

485 4334746 4341479 6734

486 4352368 4362979 10612

487 4363182 4364179 998

488 4364446 4366516 2071

489 4366692 4373437 6746

490 4373656 4375158 1503

491 4375864 4382252 6389

492 4382400 4399823 17424

493 4399794 4399868 75

494 4402204 4414204 12001

495 4414333 4416374 2042

496 4418752 4421093 2342

497 4421138 4427312 6175

498 4428525 4438253 9729

499 4438939 4440735 1797

500 4440875 4449128 8254

501 4449285 4449672 388

502 4449717 4450181 465

503 4450339 4460138 9800

504 4460344 4462350 2007

505 4468290 4468706 417

506 4470799 4479880 9082

507 4485007 4486306 1300

508 4541193 4545166 3974

509 4547195 4549343 2149

510 4549814 4550497 684

511 4550527 4551301 775

512 4577726 4581096 3371

513 4581474 4583129 1656


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514 4586967 4592675 5709

515 4593294 4595857 2564

516 4596132 4599254 3123

517 4599231 4604077 4847

518 4604497 4611419 6923

519 4612918 4618364 5447

520 4618672 4620339 1668

521 4620550 4631445 10896


https://doi.org/10.1101/2020.06.11.147629

Table 5. Pan-genome graph statistics for B. subtilis and E. coli.

PGG Statistic B. subtilis

original PGG B. subtilis

refined PGG E. coli

original PGG E. coli

refined PGG

Size 1 clusters 4434 3231 87423 27273

Shared (size>1) clusters) 8174 8204 68970 48129

# of genes in shared clusters 463311 487562 5039502 5610683

Core clusters 3558 3778 2968 3631

Size 1 edges 7282 5479 153199 67566

Shared edges 9755 9433 99284 67248

Edge instances in shared edges 460452 485177 4970823 5567497

Core edges 3230 3520 2218 3124


https://doi.org/10.1101/2020.06.11.147629

Supplementary Table 1. All B. subtilis genes compared to the PGG based annotation of core

regions for the type strain genome used by Kobayashi et al and Koo et al. (strain 168, GenBank

sequence AL009126.3, BioSample SAMEA3138188, Assembly

ASM904v1/GCF_000009045.1). Columns 1-5 are the start, stop, strand, cluster, and cluster size

for the PGG annotation. Columns 6-11 are the gene type, start, stop, strand, locus tag, and gene

symbol/name for the GenBank annotation. Column 12 is the Koo et al. gene symbol/name.

Columns 13-14 are the Kobayashi et al. gene symbol/name and evidence type (from Supporting

Table 4 “RB, reference to study with Bacillus subtilis ; RO, reference to study with other

bacteria; TW, this work; TW*, inactivation failed but IPTG mutant could not be made”).

Columns 15-16 are the GenBank protein product accession and name. Column 17 is the PGG

core or non-core region the gene is contained in.

Supplementary Table 2. The 108 B. subtilis genomes used in the study. Data is from GenBank

RefSeq: BioSample ID, Assembly ID, GenBank Species, GenBank Strain, Genome SIaze, and

whether the genome is a type strain.

Supplementary Table 3. All E. coli genes compared to the PGG based annotation of core

regions for the K-12 BW25113 strain used by Goodall (GenBank sequence CP009273.1,

Assembly ASM75055v1/GCA_000750555.1, BioSample SAMN03013572). Columns 1-5 are

the start, stop, strand, cluster, and cluster size for the PGG annotation. Columns 6-11 are the

gene type, start, stop, strand, locus tag, and gene symbol/name for the GenBank annotation.

Column 12 is a list of gene synonyms for the gene from GenBank. Columns 13-21 are from

Goodall et al.: 13-15 from Table S1 (normal essentiality), 16-18 from Table S4 (essentiality after


https://doi.org/10.1101/2020.06.11.147629

outgrowth), 19-20 from Table S3 (outlier discrepancies), and 21 from Table S2 (comparison of

data sets). Column 22 is the PGG core or non-core region the gene is contained in.

Supplementary Table 4. The 971 E. coli genomes used in the study. Data is from GenBank

RefSeq: BioSample ID, Assembly ID, GenBank Species, GenBank Strain, Genome SIaze, and

whether the genome is a type strain.


https://doi.org/10.1101/2020.06.11.147629

escherichia coli genomes · 2020-06-11 · bacteria escherichia coli, goodall et al. (4), baba et...

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