Table 3

Genes with reduced expression in LPS-deficient A. baumannii strain 19606R

Gene identifieraGene nameProtein descriptionFold change in expressionCOG categorySignal peptidecPredicted locationd
HMPREF0010_01583Hypothetical−∞b
HMPREF0010_01592Hypothetical−∞
HMPREF0010_03584Hypothetical−17.1
HMPREF0010_03084Hypothetical−16.0
HMPREF0010_01874Lysine export protein−13.0ECM
HMPREF0010_02378Hypothetical−12.1
HMPREF0010_03583Hypothetical−12.1
HMPREF0010_01580Hypothetical−11.3Cyt
HMPREF0010_00379Hypothetical−11.3SpII
HMPREF0010_02377Hypothetical−11.3Cyt
HMPREF0010_02379Hypothetical−10.6
HMPREF0010_00669Hypothetical−9.8
HMPREF0010_01582Hypothetical−9.8
HMPREF0010_03594Hypothetical−9.2
HMPREF0010_03083Hypothetical−9.2
HMPREF0010_03161Hypothetical−8.6Cyt
HMPREF0010_00517fhaBPutative filamentous hemagglutinin−8.6OM
HMPREF0010_02398Hypothetical−8.6Cyt
HMPREF0010_01993pilRPutative response regulator, PilR−8.0TCyt
HMPREF0010_03596Fis-like DNA binding protein−8.0K
HMPREF0010_01126Hypothetical−8.0SpI
HMPREF0010_00670Metallo-β-lactamase−7.0RCyt
HMPREF0010_02504Sulfate transporter−7.0PPer
HMPREF0010_03593Hypothetical−7.0Cyt
HMPREF0010_02381Hypothetical−7.0SCyt
HMPREF0010_00518Hypothetical−6.5SCyt
HMPREF0010_00006antBPutative antirepressor protein, AntB−6.5K
HMPREF0010_03013Hypothetical−6.5SpII
HMPREF0010_02376Exonuclease−6.5
HMPREF0010_03014Hypothetical−6.1SSpI
HMPREF0010_00516Haemolysin secretion/activation protein−6.1USpIOM
HMPREF0010_02388Hypothetical−6.1
HMPREF0010_01123assCType VI secretion effector−6.1U
HMPREF0010_03431hutUUrocanate hydratase−6.1E
HMPREF0010_01153Hypothetical−6.1CM
HMPREF0010_00933Periplasmic binding protein-dependent ATP binding cassette−6.1PCyt
HMPREF0010_03012csgGCurli assembly/production protein−6.1M
HMPREF0010_01584Hypothetical−6.1SpI
HMPREF0010_02380Hypothetical−6.1
HMPREF0010_01347Putative transporter−5.7MCM
HMPREF0010_02923Hypothetical−5.7
HMPREF0010_03591Hypothetical−5.3S
HMPREF0010_01344Hypothetical−5.3SpIOM
HMPREF0010_00985Putative homoserine lactone efflux protein−5.3ECM
HMPREF0010_03597Hypothetical−5.3Cyt
HMPREF0010_03595DNA-dependent helicase−4.9LCyt
HMPREF0010_00281Benzoate membrane transport protein−4.9QCM
HMPREF0010_03087Hypothetical−4.9SpI
HMPREF0010_01125assAType VI secretion protein−4.9UCyt
HMPREF0010_02387Hypothetical−4.9Cyt
HMPREF0010_00598fimBPili-associated assembly protein−4.6NSpIPer
HMPREF0010_03432hutHHistidine ammonia-lyase−4.6E
HMPREF0010_01124assBType VI secretion protein−4.6U
HMPREF0010_01122assDType VI secretion associated lysozyme−4.6UCyt
HMPREF0010_02316Hypothetical−4.6SpI
HMPREF0010_03592Hypothetical−4.6Cyt
HMPREF0010_03238dadXAlanine racemase−4.6MCyt
HMPREF0010_03635actPATPase−4.3PCM
HMPREF0010_03534Acetate permease−4.3RSpICM
HMPREF0010_03007Hypothetical−4.3SCM
HMPREF0010_02929Hypothetical−4.3
HMPREF0010_01346Tartrate dehydrogenase−4.3ECyt
HMPREF0010_01404ggtγ-Glutamyltranspeptidase−4.0ESpIIPer
HMPREF0010_01579Hypothetical−4.0Cyt
HMPREF0010_01116assJType VI-associated OmpA-like lipoprotein−4.0MSpIOM
HMPREF0010_02809Response regulator receiver protein−4.0TCyt
HMPREF0010_02843Hypothetical−4.0
HMPREF0010_02390Hypothetical−4.0R
HMPREF0010_03598Hypothetical−4.0Cyt
HMPREF0010_00007Hypothetical−4.0SpII
HMPREF0010_03239dadAD-amino acid dehydrogenase−3.7ESpI
HMPREF0010_01789calBSuccinic semialdehyde dehydrogenase−3.7CCyt
HMPREF0010_03533Hypothetical−3.7S
HMPREF0010_03604Hypothetical−3.7
HMPREF0010_03298Hypothetical−3.7
HMPREF0010_01111assOType VI secretion protein−3.7U
HMPREF0010_02865Hypothetical−3.7SpI
HMPREF0010_03590Hypothetical−3.7
HMPREF0010_03236cycAd-alanine/d-serine/glycine permease−3.7ECM
HMPREF0010_03763Metallo-β-lactamase−3.5RSpI
HMPREF0010_01439Hypothetical−3.5
HMPREF0010_01114assLProtein disaggregation chaperone−3.5OCyt
HMPREF0010_02375Hypothetical−3.5Cyt
HMPREF0010_03695Hypothetical−3.5SpI
HMPREF0010_01210Multicopper oxidase−3.2QPer
HMPREF0010_00597fimAFimbrial protein−3.2NSpIExt
HMPREF0010_00403cydBCytochrome oxidase subunit II−3.2CCM
HMPREF0010_01013Indolepyruvate ferredoxin oxidoreductase−3.2C
HMPREF0010_01121assEVasA-like type VI secretion protein−3.2UCyt
HMPREF0010_01119assGHypothetical−3.2CM
HMPREF0010_01118assHIcmF-like type VI secretion protein−3.2UCM
HMPREF0010_01428Hypothetical−3.0Cyt
HMPREF0010_03448Hypothetical−3.0CM
HMPREF0010_00402Hypothetical−3.0SSpI
HMPREF0010_00404cydABacterial cytochrome ubiquinol oxidase−3.0CCM
HMPREF0010_01112assNType VI secretion protein−2.8U
HMPREF0010_02666Hypothetical−2.8Ext
HMPREF0010_02523Glutamate synthase−2.8ECyt
HMPREF0010_01649Hypothetical−2.6SpII
HMPREF0010_03251vgrGVgrG-like type VI secretion protein−2.6SOM
HMPREF0010_00401Cyd operon protein−2.6SCM
HMPREF0010_02596Hypothetical−2.6SpII
HMPREF0010_02999hsdMDNA methylase−2.5V
HMPREF0010_02847Toluene catabolism−2.5ISpIOM
HMPREF0010_02245Ferredoxin reductase−2.5C
HMPREF0010_03163Hypothetical−2.5Cyt
  • a Genes were considered to be differentially expressed if they displayed at least a 1.5-fold difference in gene expression at a confidence level of 95%.

  • b The minus infinity symbol (−∞) indicates a gene where replicate samples from 19606R had zero read counts across the total gene length.

  • c Presence of signal peptide (signal peptidase I [spI] or signal peptidase II [spII] cleavage sites) as predicted by SignalP (7) and LipoP (20).

  • d Cellular localization predicted using PSORTB (17). Localization abbreviations: Cyt, cytoplasmic; CM, cytoplasmic membrane; Per, periplasmic; OM, outer membrane; Ext, extracellular.