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

From: Biocontrol traits of Bacillus licheniformis GL174, a culturable endophyte of Vitis vinifera cv. Glera

Category Protein name Sequence ID COG definition
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