TABLE 2.

Predominant proteins detected in the outer membrane fractions that are not predicted to have an outer membrane locationa

Category or protein namebNCBI locus tag (NMB no.)No. of peptides in:Molecular mass (kDa)cpIcPSORTb locationdPredicted function (COGS)e
OMOMVLPS OM
Pyruvate dehydrogenase E1 component134124112499.55.8UEnergy production and conversion
Chaperonin (60 kDa)197222152457.44.9CPosttranslational modification, protein turnover, and chaperones
Glutamate dehydrogenase, NADP specific17101691248.56.2CAmino acid transport and metabolism
Glyceraldehyde-3-phosphate dehydrogenase2159146535.85.5CCarbohydrate transport and metabolism
ATP synthase F1 alpha subunit1936127355.35.5UEnergy production and conversion
Pyruvate dehydrogenase E2 component dihydrolipoamide acetyltransferase1342113455.25.4CEnergy production and conversion
DNA-directed RNA polymerase beta subunit01329832155.85.4CTranscription
Enolase128595846.14.8CCarbohydrate transport and metabolism
Bacterioferritin A120792517.94.8CInorganic ion transport and metabolism
GNA1946f194691731.25.2UInorganic ion transport and metabolism
ATP synthase F1 beta subunit193487550.45.0CEnergy production and conversion
Polyribonucleotide nucleotidyltransferase0758831376.45.4CTranslation
IMP dehydrogenase120183852.47.2CNucleotide transport and metabolism
Transketolase1457731271.65.6UCarbohydrate transport and metabolism
ATP synthase F1 gamma subunit193571332.59.3UEnergy production and conversion
Oligopeptidase A0214613876.05.2CAmino acid transport and metabolism
Translation elongation factor Tu0139610742.95.1CTranslation
Translation elongation factor Tu012466542.95.1CTranslation
Amino acid ABC transporter periplasmic amino acid binding protein161261527.05.1PAmino acid transport and metabolism
5-Methyltetrahydropteroyltriglutamate homocysteine methyltransferase094459685.05.4CAmino acid transport and metabolism
Conserved hypothetical protein010957050.19.3UUnknown
DNA-directed RNA polymerase beta subunit01335516153.77.3CTranscription
Alcohol dehydrogenase, propanol preferring0546531136.55.9CGeneral function prediction only
50S ribosomal protein L1012853724.19.9UTranslation
2-Oxoglutarate dehydrogenase E2 component dihydrolipoamide succinyltransferase095653641.55.2CMEnergy production and conversion
Thiol disulfide interchange protein DsbA029451725.45.4PPosttranslational modification, protein turnover, and chaperones
ATP phosphoribosyltransferase157951523.28.7CAmino acid transport and metabolism
Adhesin complex protein, putative209551513.39.8UNot in COGS
Spermidine putrescine ABC transporter periplasmic spermidine putrescine binding protein062351341.25.8PAmino acid transport and metabolism
Tryptophan synthase beta subunit069951243.26.6CAmino acid transport and metabolism
Hypothetical protein112648223.88.9UNot in COGS
Iron III ABC transporter periplasmic binding protein063445235.89.9PInorganic ion transport and metabolism
Carbamoyl phosphate synthase large subunit18554410117.35.2UAmino acid transport and metabolism
Pilin PilE001842218.19.4UCell motility
Spermidine putrescine ABC transporter periplasmic spermidine putrescine binding protein046242150.57.5PAmino acid transport and metabolism
2-Oxoglutarate dehydrogenase E3 component lipoamide dehydrogenase0957411050.16.2CEnergy production and conversion
Thiol disulfide interchange protein DsbA027841425.25.7UPosttranslational modification, protein turnover, and chaperones
Conserved hypothetical protein165241346.45.0UUnknown
Bacterioferritin B120640418.04.7CInorganic ion transport and metabolism
Conserved hypothetical protein159040411.57.5UUnknown
H.8 outer membrane protein153340218.54.7PEnergy production and conversion
Elongation factor G013838777.25.1CTranslation
DnaK protein055438468.74.9UPosttranslational modification, protein turnover, and chaperones
Valyl tRNA synthetase0174347106.65.3CTranslation
Acetate kinase151834442.46.1CEnergy production and conversion
Argininosuccinate lyase063733551.25.3CAmino acid transport and metabolism
Formate tetrahydrofolate ligase183933559.06.1CNucleotide transport and metabolism
Aldehyde dehydrogenase A1968321252.25.3CEnergy production and conversion
Hypothetical protein092832243.89.3PCell wall/membrane biogenesis
Thiol disulfide interchange protein DsbC055032228.68.7PPosttranslational modification, protein turnover, and chaperones
Delta-aminolevulinic acid dehydratase080131536.85.3CCoenzyme transport and metabolism
Ketol acid reductoisomerase157431436.45.9UAmino acid transport and metabolism
DNA-directed RNA polymerase alpha subunit016831336.15.0CTranscription
Glutamate ammonia ligase035931352.15.3CAmino acid transport and metabolism
Malate oxidoreductase, NAD067131345.45.1UEnergy production and conversion
Thiol disulfide interchange protein DsbD151931164.96.7CMPosttranslational modification, protein turnover, and chaperones
Hypothetical protein146830510.84.6UNot in COGS
RNA polymerase sigma factor RpoD153830373.84.9CTranscription
Host factor I074830310.88.8UGeneral function prediction only
Transsulfuration enzyme family protein160930241.96.7CAmino acid transport and metabolism
d-Lactate dehydrogenase099730063.46.7CEnergy production and conversion
ClpB protein147227495.15.5CPosttranslational modification, protein turnover, and chaperones
Ribonucleoside diphosphate reductase alpha subunit129124385.06.2CNucleotide transport and metabolism
50S ribosomal protein L4014324023.210.2UTranslation
50S ribosomal protein L10013023017.68.6UTranslation
Succinyl-coenzyme A synthetase beta subunit095922641.35.1CEnergy production and conversion
Isoleucyl tRNA synthetase1833225104.15.6CTranslation
Glucose-6-phosphate isomerase138822462.06.4CCarbohydrate transport and metabolism
Enoyl acyl carrier protein reductase033621627.76.1CLipid transport and metabolism
Lipoprotein, putative020421413.99.1UTranslation
50S ribosomal protein L3014221322.710.4CTranslation
Threonyl tRNA synthetase072021372.66.2CTranslation
Peptidyl prolyl cis,trans-isomerase079121316.85.1CPosttranslational modification, protein turnover, and chaperones
Acetolactate synthase III large subunit157721362.86.2UAmino acid transport and metabolism
Conserved hypothetical protein179621320.98.9UGeneral function prediction only
Gamma-glutamyltranspeptidase105721365.06.3PAmino acid transport and metabolism
Single-strand binding protein146020419.46.0UReplication, recombination, and repair
Aspartate carbamoyltransferase regulatory subunit010720316.99.3CNucleotide transport and metabolism
DNA binding protein HU beta12302039.39.8UReplication, recombination, and repair
Amino acid ABC transporter periplasmic amino acid binding protein078720328.86.2PAmino acid transport and metabolism
Argininosuccinate synthase212918349.65.2UAmino acid transport and metabolism
Hemolysin, putative209113521.710.0UGeneral function prediction only
Leucyl tRNA synthetase189713298.05.2UNot in COGS
50S ribosomal protein L19058913113.810.7CTranslation
30S ribosomal protein S1130113061.15.0CTranslation
Carboxy terminal peptidase133213053.29.4UCell wall/membrane biogenesis
Citrate synthase095411848.16.7CEnergy production and conversion
Pyruvate dehydrogenase E3 component lipoamide dehydrogenase134411861.85.1CEnergy production and conversion
Conserved hypothetical protein107311542.04.6UAmino acid transport and metabolism
Proline dehydrogenase0401114129.96.4CAmino acid transport and metabolism
Phosphoenolpyruvate synthase061811387.15.1CCarbohydrate transport and metabolism
Rare lipoprotein B, putative070711317.66.5UCell wall/membrane biogenesis
Conserved hypothetical protein031710518.15.9CGeneral function prediction only
Alcohol dehydrogenase, zinc containing060410537.95.7UAmino acid transport and metabolism
2,3,4,5-Tetrahydropyridine-2-carboxylate N-succinyltransferase033510429.45.5CAmino acid transport and metabolism
Hypothetical protein047810423.65.0UNot in COGS
Phosphoribosylaminoimidazole carboxylase catalytic subunit143910417.15.5UNucleotide transport and metabolism
Polypeptide deformylase011010319.15.8CTranslation
Cysteine synthase076310332.86.4UAmino acid transport and metabolism
Phosphate acetyltransferase Pta, putative063108252.24.8UGeneral function prediction only
Trigger factor131304148.34.7UPosttranslational modification, protein turnover, and chaperones
Soluble lytic murein transglycosylase, putative194904067.79.5PCell wall/membrane biogenesis
Peroxiredoxin two-family protein glutaredoxin094603126.94.8UPosttranslational modification, protein turnover, and chaperones
Membrane fusion protein171603042.89.2CMCell wall/membrane biogenesis
Glyceraldehyde-3-phosphate dehydrogenase020701338.98.6CCarbohydrate transport and metabolism
Chorismate synthase168001339.46.5CAmino acid transport and metabolism
Adenylosuccinate lyase028401350.45.9UNucleotide transport and metabolism
2-Oxoglutarate dehydrogenase E1 component0955008105.06.6CEnergy production and conversion
Glutamate dehydrogenase, NAD specific147600446.25.3CAmino acid transport and metabolism
DNA topoisomerase I011800387.08.2CReplication, recombination, and repair
AspAg102900350.75.4CAmino acid transport and metabolism
Phosphoenolpyruvate carboxylase2061003101.16.8CEnergy production and conversion
Conserved hypothetical protein165300310.45.0USignal transduction mechanisms
Cytochrome c5167700328.76.2UEnergy production and conversion
  • a Proteins which were detected on the basis of three or more peptide matches and which were predicted by PSORTb to have locations other than the outer membrane.

  • b The protein name is the name in the annotation of the MC58 genome located at http://www.tigr.org/ unless indicated otherwise.

  • c The theoretical molecular mass and pI values were calculated using the ProteinLynx Global Server Package (version 2.05).

  • d Subcellular location predicted by PSORTb. C, cytoplasmic; P, periplasmic; CM, cytoplasmic membrane; U, unattributed. Similar results were obtained in an analysis of a second independent preparation of each fraction. Proteins detected with only one or two peptide matches are included in the full complement of proteins detected, which is available in the supplemental material.

  • e Predicted functional categories were derived from the Clusters of Orthologous Groups of proteins (COGS) database (located at http://www.ncbi.nlm.nih.gov/sutils/). Similar results were obtained in an analysis of a second independent preparation of each fraction.

  • f The name in the annotation of the MC58 genome located at http://www.tigr.org/ differs from the published name used in the text. See reference 33.

  • g The name in the annotation of the MC58 genome located at http://www.tigr.org/ differs from the published name used in the text. See reference 52.