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Table 1 List of predicted genes involved in bacterial endophytic behavior [38] in Serratia sp. LCN16 genome. Burkholderia phytofirmans PsJN (CP001052-54) was used as reference genome for orthologous search in Serratia sp. LCN16, Serratia proteamaculans 568 (Spro568, NC_009832) and S. liquefaciens ATCC 27592 (CP006252). The description presented is based on KEGG annotation [69]

From: The genome and genetics of a high oxidative stress tolerant Serratia sp. LCN16 isolated from the plant parasitic nematode Bursaphelenchus xylophilus

Gene Function Description Gene Identification Orthologous genes
Number Copies Name PsJN Spro568 ATCC 27592
Transporter Arabinose operon regulatory LCN16_02277 1 araC Bphyt_0033 Spro_1385 M495_06380
Lysine exporter protein LCN16_04024 1   Bphyt_0034 - M495_06375
High-affinity branched-chain amino acid transport LCN16_00248 1 livF Bphyt_3906 Spro_0232 M495_01020
High-affinity branched-chain amino acid transport LCN16_00245 1 livH Bphyt_3908 Spro_3202 M495_01005
NAD(P) transhydrogenase subunit beta LCN16_02610 1 pntB Bphyt_4261 Spro_2584 M495_12845
ABC transporter related LCN16_02535 1 malk_1 Bphyt_4584 Spro_4470 M495_22510
Metabolite:H+ symporter (MHS) family LCN16_03836 1 citA Bphyt_5520 Spro_3179 M495_10135
Extracellular solute-binding protein LCN16_01236 1 modA Bphyt_5521 Spro_3180 -
Gluconate 2-dehydrogenase LCN16_02150 1   Bphyt_4638 Spro_2138 M495_10390
Gluconate 2-dehydrogenase LCN16_02151 1   Bphyt_4639 Spro_2137 M495_10385
Gluconate 2-dehydrogenase LCN16_02152 1   Bphyt_4640 Spro_2136 M495_10380
Secretion and delivery system TypeVI secretion protein - 0 - Bphyt_4913 Spro_3003 -
TypeVI secretion protein - 0 - Bphyt_4914 Spro_3004 -
TypeVI secretion protein - 0 - Bphyt_4919 Spro_3013 M495_03685
RND family efflux transporter MFP subunit LCN16_01039 1 acrA Bphyt_6992 Spro_1127 M495_04880
Plant polymer degradation/modification Alpha/beta hydrolase family protein LCN16_01434 1   Bphyt_6134 Spro_0990 M495_12205
Alpha/alpha-trehalase - 0   Bphyt_5350 - -
Cupin LCN16_02559 2   Bphyt_2288 - -
Peptidase M48 Ste24p LCN16_04051 1 loiP Bphyt_3335 Spro_3955 M495_20655
Transcriptional regulator HTH-type transcriptional regulator LrpC LCN16_01418 1 lrpC Bphyt_0434 Spro_1462 M495_06820
Regulator protein FrmR LCN16_01244 1 frmR Bphyt_0109 - -
AraC family transcriptional regulator LCN16_02277 1 araC Bphyt_2287 Spro_2540 M495_12625
Transcriptional regulatory protein LCN16_03523 1 ompR Bphyt_4604 Spro_4621 M495_23305
Transcriptional regulatory, DeoR family LCN16_01600 1 deoR Bphyt_4951 Spro_2259 M495_11240
Transcriptional regulatory, LysR family LCN16_02297 1 ampR Bphyt_5523 Spro_3181 M495_17720
LrgB family operon - 0   Bphyt_5345 Spro_1569 M495_07365
Flavoprotein WrbA LCN16_01736 1 wrbA Bphyt_6351 Spro_1813 M495_08400
Detoxification Glutathione S-transferase LCN16_01390 7 gst Bphyt_1366 Spro_3320 M495_17060
Short-chain dehydrogenase LCN16_02779 1   Bphyt_1098 Spro_1971 M495_09250
S-(hydroxymethyl)-gluthathione dehydrogenase LCN16_01515 1 frmA Bphyt_5114 Spro_1557 M495_07305
2-hydropantoate 2-reductase LCN16_00995 1 panE Bphyt_5159 Spro_3174 -
Redox potential maintenance Acetoacetyl-coa reductase LCN16_01349 1 phbB Bphyt_5655 Spro_3465 M495_17855
Acetaldehyde dehydrogenase LCN16_02742 1 adhE Bphyt_1467 Spro_3026 M495_05210
Carbonate dehydratase LCN16_00514 1 cynT Bphyt_2146 Spro_1534 M495_07235
Aldehyde dehydrogenase LCN16_02563 3 gabD Bphyt_4023 Spro_4305 M495_21680
Malate/L-lactate dehydrogenase LCN16_02031 1 ybiC Bphyt_5456 Spro_2010 M495_09840
3-hydroxyisobutyrate dehydrogenase LCN16_01348 1 garR Bphyt_5931 Spro_1492 M495_07025
Others Amino-acid metabolite efflux pump LCN16_01419 1 eamA Bphyt_0435 Spro_1463 M495_06825
2-isopropylmalate synthase LCN16_00673 2 leuA Bphyt_0573 Spro_1875 M495_00910
Diaminopimelate decarboxylase LCN16_03946 1 lysA Bphyt_7089 Spro_3836 M495_20025