Table 3 Genes involved in the plant-bacteria relationship found in the Bacillus licheniformis GL174 genome

Chemotaxis and motility

Probable methyl-accepting chemotaxis protein BT9727_0469

TY90_12985 [C]

COG0840 Methyl-accepting chemotaxis protein

Chemotaxis protein CheY

TY90_15200

COG0784 FOG: CheY-like receiver

Flagellar motor switch phosphatase FliY

TY90_15195

COG1776 Chemotaxis protein CheC, inhibitor of MCP methylation

Motility protein B

TY90_17335

COG1360 Flagellar motor protein

Methyl-accepting chemotaxis protein tlpC

TY90_17020

COG0840 Methyl-accepting chemotaxis protein

Chemotaxis protein CheA

TY90_17615

COG0643 Chemotaxis protein histidine kinase and related kinases

Methyl-accepting chemotaxis protein mcpA

TY90_06200

COG0840 Methyl-accepting chemotaxis protein

Flagellar motor switch protein FliM

TY90_15190

COG1868 Flagellar motor switch protein

Probable methyl-accepting chemotaxis protein BT9727_0469

TY90_21790

COG5278 Predicted periplasmic ligand-binding sensor domain

Motility protein A

TY90_17330

COG1291 Flagellar motor component

Swarming motility protein swrAA

TY90_02805

na

Methyl-accepting chemotaxis protein mcpC

TY90_18510

COG0840 Methyl-accepting chemotaxis protein

Swarming motility protein swrB

TY90_17590

na

Methyl-accepting chemotaxis protein mcpA

TY90_06190

COG0840 Methyl-accepting chemotaxis protein

Chemotaxis protein CheV

TY90_18185

COG0835 Chemotaxis signal transduction protein

Methyl-accepting chemotaxis protein mcpB

TY90_00850

COG0840 Methyl-accepting chemotaxis protein

Chemotaxis protein CheW

TY90_17610

COG0835 Chemotaxis signal transduction protein

Chemotaxis protein methyltransferase

TY90_09925

COG1352 Methylase of chemotaxis methyl-accepting proteins

Chemotaxis response regulator protein-glutamate methylesterase

TY90_17620

COG2201 Chemotaxis response regulator containing a CheY-like receiver domain and a methylesterase domain

Flagellar motor switch protein FliG

TY90_15135

COG1536 Flagellar motor switch protein

Methyl-accepting chemotaxis protein tlpA

TY90_21795

COG0840 Methyl-accepting chemotaxis protein

Swarming motility protein swrAB

TY90_02810

COG0265 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain

Flagellar assembly factor FliW

TY90_02710

function unknown

Flagellar motor switch phosphatase FliY

TY90_15195

COG1776 Chemotaxis protein CheC, inhibitor of MCP methylation

Flagellar biosynthetic protein fliZ

TY90_15205

COG3190 Flagellar biogenesis protein

Flagellar biosynthetic protein fliR

TY90_15220

COG1684 Flagellar biosynthesis pathway, component FliR

Probable flagellar assembly protein fliH

TY90_15140

COG1317 Flagellar biosynthesis/type III secretory pathway protein

Flagellar biosynthetic protein fliP

TY90_15210

COG1338 Flagellar biosynthesis pathway, component FliP

Flagellar protein FliT

TY90_02740

na

Flagellar FliJ protein

TY90_15150

COG2882 Flagellar biosynthesis chaperone

Flagellar protein FliL

TY90_15185

COG1580 Flagellar basal body-associated protein

Flagellar motor switch protein FliG

TY90_15135

COG1536 Flagellar motor switch protein

Flagellar hook-basal body complex protein FliE

TY90_15125

COG1677 Flagellar hook-basal body protein

Flagellar biosynthetic protein FliQ

TY90_15215

COG1987 Flagellar biosynthesis pathway, component FliQ

Flagellar protein fliS

TY90_02735

COG1516 Flagellin-specific chaperone FliS

Plant wall degrading enzymes and plant colonization

Putative aminopeptidase ysdC

TY90_10480

COG1363 Cellulase M and related proteins

Putative aminopeptidase yhfE

TY90_04995

COG1363 Cellulase M and related proteins

Putative aminopeptidase ytoP

TY90_07450

COG1363 Cellulase M and related proteins

Endoglucanase

TY90_03065

COG2730 Endoglucanase

Endoglucanase B

TY90_17520

COG2730 Endoglucanase

Reducing end xylose-releasing exo-oligoxylanase

TY90_12415 [C]

COG3405 Endoglucanase Y

Beta-glucosidase

TY90_12740

COG1472 Beta-glucosidase-related glycosidases

Trehalose-6-phosphate hydrolase

TY90_06865

COG0366 Glycosidases

Uncharacterized lipoprotein ybbD

TY90_09030

COG1472 Beta-glucosidase-related glycosidases

Oligo-1,6-glucosidase 1

TY90_14210

COG0366 Glycosidases

Intracellular maltogenic amylase

TY90_14180

COG0366 Glycosidases

Pullulanase

TY90_07415

COG1523 Type II secretory pathway, pullulanase PulA and related glycosidases

Alpha-amylase

TY90_16895

COG0366 Glycosidases

Arabinan endo-1,5-alpha-L-arabinosidase

TY90_10485

COG3507 Beta-xylosidase

Putative beta-xylosidase

TY90_13465 [C]

COG3507 Beta-xylosidase

Xylose isomerase

TY90_01590

COG2115 Xylose isomerase

Multiple sugar-binding periplasmic receptor ChvE

TY90_13115

COG4213 ABC-type xylose transport system, periplasmic component

Arabinan endo-1,5-alpha-L-arabinosidase

TY90_15525

COG3507 Beta-xylosidase

Uncharacterized protein yxiA

TY90_08160

COG3507 Beta-xylosidase

Ribose transport system permease protein rbsC

TY90_02405

COG1172 Ribose/xylose/arabinose/galactoside ABC-type transport systems, permease components

Xylose transport system permease protein xylH

TY90_13125

COG4214 ABC-type xylose transport system, permease component

D-xylose-binding periplasmic protein

TY90_09370

COG4213 ABC-type xylose transport system, periplasmic component

Iron nutrition and metabolism

Rhizobactin siderophore biosynthesis protein rhbE

TY90_18465

COG3486 Lysine/ornithine N-monooxygenase

Rhizobactin siderophore biosynthesis protein rhbD

TY90_18470

COG1670 Acetyltransferases, including N-acetylases of ribosomal proteins

Probable siderophore transport system permease protein yfiZ

TY90_07875

COG0609 ABC-type Fe3 + −siderophore transport system, permease component

Probable siderophore transport system permease protein yfhA

TY90_07870

COG0609 ABC-type Fe3 + −siderophore transport system, permease component

Rhizobactin siderophore biosynthesis protein rhbC

TY90_18475

na

Rhizobactin siderophore biosynthesis protein rhbF

TY90_18460

na

Probable siderophore-binding lipoprotein yfiY

TY90_07880

COG0614 ABC-type Fe3 + −hydroxamate transport system, periplasmic component

Probable siderophore-binding lipoprotein yfiY

TY90_08825

COG0614 ABC-type Fe3 + −hydroxamate transport system, periplasmic component

Ferrous iron transport protein B

TY90_15330

COG0370 Fe2+ transport system protein B

Iron(3+)-hydroxamate import system permease protein fhuG

TY90_12850

COG0609 ABC-type Fe3 + −siderophore transport system, permease component

Iron-uptake system permease protein feuC

TY90_02125

COG0609 ABC-type Fe3 + −siderophore transport system, permease component

Iron(3+)-hydroxamate-binding protein yxeB

TY90_11500

COG0614 ABC-type Fe3 + −hydroxamate transport system, periplasmic component

Iron(3+)-hydroxamate import ATP-binding protein FhuC

TY90_12855

COG1120 ABC-type cobalamin/Fe3 + −siderophores transport systems, ATPase components

Iron(3+)-hydroxamate-binding protein yxeB

TY90_15350

COG0614 ABC-type Fe3 + −hydroxamate transport system, periplasmic component

Iron(3+)-hydroxamate-binding protein fhuD

TY90_13845

COG0614 ABC-type Fe3 + −hydroxamate transport system, periplasmic component

Iron-uptake system-binding protein

TY90_02115

COG0614 ABC-type Fe3 + −hydroxamate transport system, periplasmic component

Phosphate nutrition and metabolism

Phosphate-binding protein pstS

TY90_12210

COG0226 ABC-type phosphate transport system, periplasmic component

Phosphate import ATP-binding protein PstB 1

TY90_12230

COG1117 ABC-type phosphate transport system, ATPase component

Sulfate permease CysP

TY90_14565

COG0306 Phosphate/sulphate permeases

Probable low-affinity inorganic phosphate transporter

TY90_10295

COG0306 Phosphate/sulphate permeases

Probable ABC transporter permease protein yqgI

TY90_12220

COG0581 ABC-type phosphate transport system, permease component

Phosphate import ATP-binding protein PstB 2

TY90_12225

COG1117 ABC-type phosphate transport system, ATPase component

Probable ABC transporter permease protein yqgH

TY90_12215

COG0573 ABC-type phosphate transport system, permease component

Uncharacterized protein yqeW

TY90_11930

COG1283 Na+/phosphate symporter

UPF0111 protein ykaA

TY90_10290

COG1392 Phosphate transport regulator (distant homolog of PhoU)

Alkaline phosphatase 3

TY90_20965

COG1785 Alkaline phosphatase

Probable manganese-dependent inorganic pyrophosphatase

TY90_02230

COG1227 Inorganic pyrophosphatase/exopolyphosphatase

Uncharacterized protein ypjD

TY90_17920

COG1694 Predicted pyrophosphatase

MazG Nucleotide Pyrophosphohydrolase

TY90_20180

COG1694 Predicted pyrophosphatase

Bifunctional oligoribonuclease and PAP phosphatase nrnA

TY90_16540

COG0618 Exopolyphosphatase-related proteins

Uncharacterized protein YhcW

TY90_11780

COG0637 Predicted phosphatase/phosphohexomutase

Putative beta-phosphoglucomutase

TY90_14215

COG0637 Predicted phosphatase/phosphohexomutase

Uncharacterized protein yvdC

TY90_08560

COG1694 Predicted pyrophosphatase

Pyrophosphatase ppaX

TY90_02900

COG0546 Predicted phosphatases

3-phytase

TY90_13145

na

Nitrogen uptake and metabolism

NifU-like protein

TY90_07755

COG0822 NifU homolog involved in Fe-S cluster formation

Putative ammonium transporter sll0108

TY90_15930 [C]

COG0004 Ammonia permease

Assimilatory nitrate reductase electron transfer subunit

TY90_04420

COG1251 NAD(P)H-nitrite reductase

Nitrite reductase [NAD(P)H]

TY90_04410

COG1251 NAD(P)H-nitrite reductase

Nitrate transporter

TY90_20435

COG2223 Nitrate/nitrite transporter

Assimilatory nitrite reductase [NAD(P)H] small subunit

TY90_04405

COG2146 Ferredoxin subunits of nitrite reductase and ring-hydroxylating dioxygenases

Uncharacterized transporter ywcJ

TY90_01155

COG2116 Formate/nitrite family of transporters

Uncharacterized transporter yrhG

TY90_11795

COG2116 Formate/nitrite family of transporters

Nitrate reductase beta chain

TY90_03135

COG1140 Nitrate reductase beta subunit

Nitrate reductase gamma chain

TY90_03145

COG2181 Nitrate reductase gamma subunit

Probable nitrate reductase molybdenum cofactor assembly chaperone NarJ

TY90_03140

COG2180 Nitrate reductase delta subunit

Uncharacterized ABC transporter permease protein ytlD

TY90_07125

COG0600 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component

Nitrate transporter

TY90_20435

COG2223 Nitrate/nitrite transporter

Putative aliphatic sulfonates transport permease protein ssuC

TY90_11560

COG0600 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component

Aliphatic sulfonates import ATP-binding protein SsuB

TY90_11550

COG1116 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component

Uncharacterized ABC transporter ATP-binding protein YtlC

TY90_07130

COG1116 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component

Putative aliphatic sulfonates-binding protein

TY90_1155

COG0715 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components

Antibiotics and secondary metabolites production and transport, biocontrol-related genes

Surfactin synthase thioesterase subunit

TY90_12925

COG3208 Predicted thioesterase involved in non-ribosomal peptide biosynthesis

Surfactin synthase subunit 2

TY90_21750

COG1020 Non-ribosomal peptide synthetase modules and related proteins

Putative phosphoenolpyruvate synthase

TY90_00915

COG3319 Thioesterase domains of type I polyketide synthases or non-ribosomal peptide synthetases

Surfactin synthase subunit 2

TY90_21285

COG1020 Non-ribosomal peptide synthetase modules and related proteins

D-alanine--poly(phosphoribitol) ligase subunit 1

TY90_01430

COG1020 Non-ribosomal peptide synthetase modules and related proteins

Putative phosphoenolpyruvate synthase

TY90_16790

COG3319 Thioesterase domains of type I polyketide synthases or non-ribosomal peptide synthetases

Surfactin synthase subunit 1

TY90_17065

COG1020 Non-ribosomal peptide synthetase modules and related proteins

Surfactin synthase subunit 3

TY90_12920

COG1020 Non-ribosomal peptide synthetase modules and related proteins

Putative phosphoenolpyruvate synthase

TY90_00550

COG3319 Thioesterase domains of type I polyketide synthases or non-ribosomal peptide synthetases

lantibiotic ABC transporter ATP-binding protein

TY90_19070

COG1131 ABC-type multidrug transport system, ATPase component

lantibiotic ABC transporter ATP-binding protein

TY90_19920

COG1131 ABC-type multidrug transport system, ATPase component

lantibiotic immunity protein

TY90_01250

na

lantibiotic immunity protein

TY90_01260

na

lantibiotic lichenicidin A1

TY90_01200

na

lantibiotic lichenicidin A2

TY90_01205

na

lantibiotic-modifying protein

TY90_01195

na

lantibiotic-modifying protein

TY90_01210

na

LanY

TY90_01235

na

bacteriocin biosynthesis protein SagD

TY90_04705

COG1944 Uncharacterized conserved protein

bacteriocin maturation protein

TY90_04710

na

chitinase

TY90_20245

COG3979 Uncharacterized protein contain chitin-binding domain type 3

chitinase

TY90_20250

COG3325 Chitinase

Spermidine/putrescine transport system permease protein PotC

TY90_17055

COG1177 ABC-type spermidine/putrescine transport system, permease component II

Spermidine/putrescine import ATP-binding protein PotA

TY90_17045

COG3839 ABC-type sugar transport systems, ATPase components

Spermidine/putrescine-binding periplasmic protein 2

TY90_17040

COG0687 Spermidine/putrescine-binding periplasmic protein

Spermidine synthase

TY90_01960

COG0421 Spermidine synthase

acetoin dehydrogenase

TY90_13415

COG3284 Transcriptional activator \of acetoin/glycerol metabolism

acetoin dehydrogenase

TY90_20060

na

acetoin reductase

TY90_03165

COG1028 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)

acetoin utilization protein AcuB

TY90_20055

COG0517 FOG: CBS domain

acetoin:2,2 C6-dichlorophenolindophenol oxidoreductase subunit alpha

TY90_13395

COG1071 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, alpha subunit

acetolactate synthase

TY90_02385

COG0028 Thiamine pyrophosphate-requiring enzymes [acetolactate synthase, pyruvate dehydrogenase (cytochrome), glyoxylate carboligase, phosphonopyruvate decarboxylase]

acetolactate synthase

TY90_05725

COG0440 Acetolactate synthase, small (regulatory) subunit

acetolactate synthase catalytic subunit

TY90_05730

COG0440 Acetolactate synthase, small (regulatory) subunit

Oxidative stress response

Catalase X

TY90_01280

COG0753 Catalase

Probable manganese catalase

TY90_03405

COG3546 Mn-containing catalase

Glutathione peroxidase homolog BsaA

TY90_00120

COG0386 Glutathione peroxidase