Table list of genes found to be horizontally transferred between clades



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Table S3. List of genes found to be horizontally transferred between clades. Genes in close proximity to repeat regions or mobile elements and plasmid genes are denoted by * and &, respectively.


Lineages

Gene ID

Gene set


Distance from mobile element (bp)

Annotation

C-I, C-III



PAN002200

core




Uncharacterized protein involved in formation of periplasmic nitrate reductase

PAN003853

core




F0F1-type ATP synthase, epsilon subunit (mitochondrial delta subunit)

C-III, C-IV



PAN001208

core




Predicted membrane protein

PAN001547

core




Predicted periplasmic protein

PAN002200

core




Uncharacterized protein involved in formation of periplasmic nitrate reductase

PAN002260

core




Uncharacterized conserved protein

PAN002841

core




Uncharacterized protein conserved in bacteria

PAN002891*

core

33

Uncharacterized protein conserved in bacteria

PAN003250

core




Uncharacterized protein conserved in bacteria

PAN003274

core




Biotin carboxyl carrier protein

PAN003288

core




Factor for inversion stimulation Fis, transcriptional activator

PAN003317

core




DNA-directed RNA polymerase, alpha subunit/40 kD subunit

PAN003406

core




Shikimate kinase

PAN003878

core




Uncharacterized protein conserved in bacteria

PAN003889

core




Thiol-disulfide isomerase and thioredoxins

PAN004055*

core

30

Transcriptional regulator of met regulon

PAN004097&

core




Preprotein translocase subunit SecE

PAN004200

core




Predicted membrane protein

C-III, C-V



PAN001208

core




Predicted membrane protein

PAN001547

core




Predicted periplasmic protein

PAN002891*

core

33

Uncharacterized protein conserved in bacteria

PAN003250

core




Uncharacterized protein conserved in bacteria

PAN003274

core




Biotin carboxyl carrier protein

PAN003288

core




Factor for inversion stimulation Fis, transcriptional activator

PAN003317

core




DNA-directed RNA polymerase, alpha subunit/40 kD subunit

PAN003406

core




Shikimate kinase

PAN003878

core




Uncharacterized protein conserved in bacteria

PAN004055*

core

30

Transcriptional regulator of met regulon

PAN004097&

core




Preprotein translocase subunit SecE

C-IV, C-V




PAN000050*

core

17


Diadenosine tetraphosphatase and related serine/threonine protein phosphatases

PAN000490*

core

13

Predicted thioesterase

PAN000542

core




ABC-type uncharacterized transport system, ATPase component

PAN000550

core




Predicted ATPase

PAN000563

core




Malate/L-lactate dehydrogenases

PAN000599*

core

29

Phosphopantetheinyl transferase component of siderophore synthetase

PAN000607

core




ABC-type Fe3+-siderophore transport system, permease component

PAN000612

core




Isochorismate hydrolase

PAN000656

core




Rare lipoprotein B

PAN000667

core




Predicted metal-dependent hydrolase

PAN000669

core




2-methylthioadenine synthetase

PAN000690*

core

5

Flavodoxins

PAN000731

core




Biopolymer transport proteins

PAN000747*

core

19


ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA

PAN000755

core




3-carboxymuconate cyclase

PAN000886

core




Permeases of the major facilitator superfamily

PAN000931

core




3-hydroxymyristoyl/3-hydroxydecanoyl-(acyl carrier protein) dehydratases

PAN000949

core




Ni,Fe-hydrogenase I small subunit

PAN000968*

core

9

Uncharacterized component of anaerobic dehydrogenases

PAN000988*

core

211

High-affinity Fe2+/Pb2+ permease

PAN001000*

core

34

-

PAN001010

core




Predicted phosphatase homologous to the C-terminal domain of histone macroH2A1

PAN001022

core




Cytochrome B561

PAN001075

core




Transcriptional regulator

PAN001089

core




ABC-type spermidine/putrescine transport system, permease component I

PAN001237

core




Uncharacterized protein involved in cation transport

PAN001246

core




Nitrate reductase delta subunit

PAN001362

core




FOG: GGDEF domain

PAN001415

core




Sortase and related acyltransferases

PAN001438

core




Anaerobic dehydrogenases, typically selenocysteine-containing

PAN001473

core




NAD-dependent aldehyde dehydrogenases

PAN001509

core




Predicted permease

PAN001531

core




Adenosine deaminase

PAN001542

core




Predicted EndoIII-related endonuclease

PAN001592

core




-

PAN001595

core




Predicted permease

PAN001626

core




Threonyl-tRNA synthetase

PAN001634

core




Predicted phosphatase/phosphohexomutase

PAN001640

core




Alpha-galactosidases/6-phospho-beta-glucosidases, family 4 of glycosyl hydrolases

PAN001646*

core

46

NAD synthase

PAN001659

core




Uncharacterized conserved protein

PAN001754

core




Dihydroxyacid dehydratase/phosphogluconate dehydratase

PAN001784

core




FOG: CheY-like receiver

PAN001792

core




-

PAN001819

core




-

PAN001842

core




DNA-binding HTH domain-containing proteins

PAN002008

core




DNA gyrase inhibitor

PAN002010

core




Exonuclease I

PAN002061

core




Uridine kinase

PAN002130*

core

6

Uncharacterized membrane-associated protein

PAN002142*

core

60

ABC-type glucose/galactose transport system, permease component



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