From: Deep sequencing-based analysis of the anaerobic stimulon in Neisseria gonorrhoeae
Gene | ORF ID | Rep 1b | Rep 2 | Definitionc | Regulond |
---|---|---|---|---|---|
Small molecule biosynthesis | |||||
hda | NGO0187 | 4.1 | 4.1 | Histone deacetylase-like protein/acetoin utilization protein | Â |
pdxH | NGO0658 | 4.3 | 5.5 | Pyridoxamine 5-phosphate oxidase | MtrR |
mobA | NGO0754 | 3.5 | 4.6 | Molybdopterin-guanine dinucleotide biosynthesis protein | NsrR |
leu1 | NGO0848 | 6.6 | 4.5 | 2-isopropylmalate synthase | Â |
folA | NGO1694 | 3.8 | 2.8 | Dihydrofolate reductase | RpoH |
Transport and binding proteins | |||||
fHBP | NGO0033 | 3.5 | 4.2 | Factor H binding protein | Â |
hecA | NGO0706 | 3.2 | 4.9 | Filamentous hemagglutinin | Â |
bfrA | NGO0794 | 14.1 | 9.9 | Bacterioferritin A | Â |
bfrB | NGO0795 | 9.7 | 10.1 | Bacterioferritin B | MtrR |
pil | NGO1177 | 3.5 | 3.5 | Neisseria-specific type IV pilin-related protein | Â |
 | NGO1440 | 4.4 | 2.8 | ABC-type amino acid transporter, periplasmic protein |  |
lecA | NGO1981 | 5.0 | 3.9 | Adhesin protein | Lrp |
Energy metabolism/Oxidation-Reduction | |||||
cybP | NGO0805 | 3.2 | 2.8 | Nickel-dependent hydrogenase, b-type cytochrome subunit | Â |
npd | NGO1024 | 9.6 | 7.9 | 2-Nitropropane dioxygenase-like | MtrR |
aniA | NGO1276 | 28.4 | 28.0 | Nitrite reductase | NsrR, FNR |
eftD | NGO1396 | 5.2 | 5.1 | Electron transfer flavoprotein-ubiquinone oxidoreductase | Â |
Macromolecular biosynthesis | |||||
rl34 | NGO2182 | 3.0 | 3. 1 | 50S ribosomal protein L34 | Â |
Regulation | Â | Â | Â | Â | Â |
farR | NGO0058 | 4.0 | 3.7 | MarR family transcriptional regulator | Lrp, MtrR |
nmlR | NGO0602 | 7.2 | 7.6 | Transcriptional regulator nmlR | NmlR, FNR |
xre | NGO0797 | 3.2 | 3.4 | XRE family transcriptional regulator | Â |
marR | NGO1244 | 5.4 | 15.2 | MarR-family transcriptional regulator | RpoH, MtrR |
nosR a | NGO1401/1402 | 9.4 | 9.5 | Regulator of nitrous oxide reductase pseudogenes | FNR |
lexA | NGO1427 | 4.2 | 5.3 | LexA-family repressor | LexA |
arsR | NGO1562 | 6.1 | 2.2 | ArsR-family transcriptional regulator | Â |
Cell Structure | |||||
ompA | NGO1559 | 3.7 | 3.4 | Outer membrane protein | Â |
lpcA | NGO1986 | 4.2 | 6.1 | Phosphoheptose isomerase | Â |
Adaptation and stress response | |||||
grx3 | NGO0114 | 3.3 | 6.6 | Glutaredoxin 3 | Fur |
recN | NGO0318 | 4.7 | 5.5 | Repair protein RecN | Fur, LexA |
htpX | NGO0399 | 11.8 | 8.6 | Heat shock protein, Peptidase family M48 | Lrp |
dnrN | NGO0653 | 8.9 | 12.3 | Iron-sulfur cluster repair protein | NsrR, FNR |
 | NGO0757 | 2.6 | 4.1 | Putative periplasmic Cpx-family sensor kinase involved in P pilus formation |  |
hslR | NGO0822 | 2.7 | 5.0 | Heat shock protein HSP-15 | Â |
 | NGO1022 | 3.8 | 3.4 | DEDDh family exonuclease |  |
clpB | NGO1046 | 4.9 | 9.4 | Endopeptidase Clp ATP-binding chain B (HSP- F84.1) | RpoH, MtrR |
recX | NGO1053 | 3.6 | 2.8 | RecX-family regulator of RecA function | Â |
tehB | NGO1161 | 2.6 | 4.0 | Tellurite resistance protein | Â |
hsp33 | NGO1189 | 6.1 | 5.2 | Heat shock protein HSP-33 chaperonin | MtrR |
 | NGO1245 | 4.0 | 8.5 | ABC-type multidrug transport system, ATPase/permease |  |
hit | NGO1273 | 2.3 | 5.5 | Protein Kinase C Interacting protein belonging to the ubiquitous HIT family of hydrolases that act on alpha-phosphates of ribonucleotides | Â |
nudH | NGO1334 | 3.3 | 3.3 | Nudix hydrolase, dinucleoside polyphosphate hydrolase | Â |
grpE | NGO1422 | 3.6 | 2.7 | Heat shock protein (HSP-70 cofactor; nucleotide exchange factor) | RpoH, MtrR |
erpA | NGO1426 | 2.8 | 2.6 | Putative iron-sulfur cluster insertion protein | RpoH, Lrp |
dnaK | NGO1429 | 2.7 | 3.4 | Heat shock protein, chaperone | RpoH |
 | NGO1566 | 3.4 | 3.1 | Nudix hydrolase, catalyzing the hydrolysis of nucleoside diphosphates |  |
ntrA | NGO1702 | 3.5 | 20.1 | Nitroreductase-like family containing uncharacterized proteins similar to nitroreductase | Â |
ccp | NGO1769 | 5.6 | 12.1 | Cytochrome c peroxidase | Â |
yhhF | NGO1860 | 3.7 | 4.1 | Probable DNA methylase | Â |
dnaJ | NGO1901 | 2.8 | 5.1 | Heat shock protein HSP-40 | RpoH |
Hypothetical or Unassigned | |||||
 | NGO0010 | 5.1 | 7.2 | Neisseria-specific protein, uncharacterized |  |
 | NGO0011 | 3.2 | 3.0 | Conserved hypothetical protein |  |
 | NGO0119 | 5.4 | 5.1 | Neisseria-specific protein, uncharacterized; possible ribonuclease |  |
 | NGO0165 | 3.2 | 5.9 | Neisseria-specific protein, uncharacterized |  |
 | NGO0569 | 3.8 | 2.1 | Conserved hypothetical protein (possible transcriptional regulator) |  |
 | NGO0570 | 3.5 | 3.4 | Possible DNA-binding CreA protein | RpoH |
 | NGO0618 | 3.3 | 2.7 | Neisseria-specific protein, uncharacterized |  |
 | DUF331 | 4.1 | 7.8 | Uncharacterized protein family DUF331; the function of this family is unknown |  |
 | NGO0802 | 3.7 | 4.0 | Hypothetical protein (possible Neisseria-specific protein) |  |
 | NGO0854 | 3.6 | 8.4 | Hypothetical protein |  |
 | NGO0895 | 6.4 | 4.6 | Neisseria-specific protein, uncharacterized |  |
 | NGO0896 | 4.1 | 5.0 | Hypothetical protein |  |
 | NGO0995 | 3.1 | 3.3 | Neisseria-specific protein, uncharacterized |  |
 | NGO1033 | 4.3 | 6.8 | Probable transglycosylase |  |
 | NGO1037 | 4.4 | 5.2 | Hypothetical protein |  |
 | NGO1191 | 3.5 | 2.7 | Neisseria-specific protein, uncharacterized |  |
 | NGO1277 | 6.6 | 7.0 | Conserved hypothetical protein (NirV) FGE- sulfatase super family. |  |
 | NGO1428 | 14.3 | 8.4 | Neisseria-specific protein, uncharacterized | LexA |
 | NGO1517 | 4.8 | 4.8 | Neisseria-specific protein, uncharacterized | NsrR |
 | NGO1793 | 6.4 | 4.3 | Conserved hypothetical protein (probable integral membrane protein) |  |
 | NGO1987 | 3.1 | 4.4 | Uncharacterized protein family UPF0102; the function of this family is unknown |  |
 | NGO2023 | 2.4 | 7.3 | Conserved hypothetical protein |  |
Small RNA fnrS c | Â | 24.9 | 17.8 | Probable small regulatory RNA | FNR |
Gene | ORF ID | Rep 1 | Rep 2 | Definition | Regulon |
Ngo Φ 1 phage | |||||
 | NGO0463 | 9.2 | 5.9 | Putative phage associated protein |  |
 | NGO0464 | 12.3 | 9.0 | Putative phage associated protein |  |
 | NGO0465 | 15.4 | 7.3 | Putative phage associated protein |  |
 | NGO0467 | 23.6 | 29.8 | Putative phage associated protein |  |
 | NGO0472 | 94.6 | 19.7 | Putative phage associated protein | FNR |
dnaB | NGO0485 | 6.1 | 4.2 | Replicative DNA helicase | Â |
 | NGO0488 | 4.2 | 10.0 | Putative phage associated protein |  |
 | NGO0489 | 10.2 | 16.9 | Phage Holliday junction resolvase (RusA-like) protein |  |
 | NGO0491 | 14.2 | 5.1 | Putative phage associated protein |  |
 | NGO0492 | 8.7 | 6.6 | Putative phage associated protein |  |
 | NGO0494 | 10.0 | 10.9 | Putative phage associated protein |  |
 | NGO0495 | 9.6 | 7.6 | Putative phage associated protein |  |
 | NGO0496 | 16.1 | 12.9 | Putative phage associated protein |  |
 | NGO0497 | 24.1 | 17.0 | Putative phage associated protein |  |
 | NGO0498 | 18.0 | 9.5 | Putative phage associated protein |  |
 | NGO0499 | 17.4 | 12.9 | Putative phage associated protein |  |
 | NGO0500 | 17.6 | 6.6 | Putative phage associated protein |  |
 | NGO0501 | 27.4 | 9.1 | Putative phage associated protein |  |
 | NGO0502 | 47.2 | 6.8 | Putative phage associated protein |  |
 | NGO0503 | 6.0 | 4.8 | Putative phage associated protein |  |
 | NGO0504 | 14.4 | 5.2 | Putative phage associated protein |  |
 | NGO0506 | 15.9 | 11.3 | Putative phage associated protein |  |
 | NGO0507 | 22.3 | 12.1 | Putative phage associated protein |  |
 | NGO0508 | 15.6 | 11.1 | Putative phage associated protein |  |
 | NGO0509 | 3.5 | 3.6 | Putative phage associated protein |  |
 | NGO0510 | 7.1 | 5.6 | Putative phage associated protein |  |
 | NGO0512 | 9.4 | 13.2 | Putative phage associated protein |  |
 | NGO0513 | 4.9 | 5.2 | Putative phage associated protein |  |
 | NGO0514 | 9.8 | 6.2 | Putative phage associated protein |  |
 | NGO0522 | 9.4 | 5.6 | Putative phage associated protein |  |
Ngo Φ2 phage | |||||
 | NGO1100 | 4.1 | 5.0 | Putative phage associated protein |  |
 | NGO1120 | 75.5 | 16.0 | Putative phage associated protein |  |
 | NGO1131 | 19.4 | 16.8 | Putative phage associated protein |  |
 | NGO1132 | 11.3 | 16.2 | Putative phage associated protein |  |
Ngo Φ3 phage | |||||
 | NGO1614 | 8.2 | 11.0 | Putative phage associated protein |  |
 | NGO1615 | 10.3 | 7.2 | Conserved hypothetical protein (type I restriction enzyme related) | FNR |
 | NGO1624 | 34.0 | 16.0 | Putative phage associated protein |  |
 | NGO1627 | 6.6 | 4.4 | Conserved hypothetical protein (probable phage origin) |  |
 | NGO1628 | 7.6 | 4.9 | Putative phage associated protein |  |
 | NGO1633 | 26.9 | 137.3 | Putative phage associated protein |  |
 | NGO1634 | 27.4 | 18.8 | Putative phage associated protein |  |
 | NGO1635 | 58.1 | 5.4 | Putative phage associated protein |  |
 | NGO1636 | 26.4 | 10.0 | Putative phage associated protein |  |
 | NGO1637 | 16.6 | 5.5 | Putative phage associated protein |  |
 | NGO1640 | 22.4 | 10.6 | Putative phage associated protein |  |
Ngo Φ5 phage | |||||
 | NGO0731 | 5.1 | 7.3 | Putative phage associated protein |  |
 | NGO0732 | 3.3 | 2.2 | Putative phage associated protein |  |
Gene | ID | Rep 1 | Rep 2 | Definition | Regulon |
Small molecule biosynthesis | |||||
cysK | NGO0340 | -2.8 | -6.7 | Cysteine synthase | FNR |
hesB | NGO0632 | -3.8 | -4.0 | Iron-sulfur cluster biosynthesis | Â |
iscU | NGO0633 | -4.8 | -5.3 | Iron-sulfur cluster assembly scaffold protein | Â |
iscS | NGO0636 | -4.8 | -5.6 | Cysteine desulferase | Â |
hisD | NGO1240 | -3.3 | -3.2 | Histidinol dehydrogenase | Â |
pgsA | NGO1247 | -3.8 | -7.1 | CDP-alcohol phosphatidyltransferase | Â |
asd | NGO1997 | -3.3 | -5.0 | Aspartate-semialdehyde dehydrogenase | Â |
Transport and binding proteins | |||||
gluP | NGO0142 | -3.1 | -4.3 | Glucose/galactose transporter | Â |
nhaC | NGO0143 | -2.8 | -3.3 | Na+/H+ antiporter (NhaC) | Â |
amtB | NGO0198 | -3.7 | -5.3 | Ammonium Transporter Family | Â |
fbp | NGO0217 | -4.8 | -5.6 | ABC-type iron transporter, periplasmic binding protein | Fur, Lrp |
oxiA | NGO0372 | -6.7 | -20.0 | Bacterial extracellular solute-binding protein | FarR |
 | NGO0373 | -3.7 | -11.1 | ABC-type arginine transport system, permease component | FarR |
glnQ | NGO0374 | -2.9 | -11.1 | ABC-type amino acid transporter, ATP-binding protein | FarR, FNR |
citT | NGO0377 | -5.6 | -9.1 | Di- and tri-carboxylate transporters (inorganic ion transport) | Â |
cysA | NGO0445 | -5.6 | -9.1 | ABC-type sulfate transporter, ATP-binding protein | Lrp |
sbp | NGO0877 | -4.8 | -25.0 | ABC-related sulfate-binding protein | Â |
 | NGO1290 | -3.8 | -3.3 | Putative sodium/alanine symport protein |  |
hemO | NGO1318 | -7.1 | -12.5 | Heme oxygenase/iron starvation protein | Fur |
lldP | NGO1361 | -9.1 | -8.3 | L-lactate permease (partial only) | Â |
exbD | NGO1377 | -3.4 | -3.6 | Membrane bound biopolymer transport protein ExbD/TolR | Â |
exbB | NGO1378 | -3.1 | -5.0 | Transport protein | Â |
lctP | NGO1449 | -4.0 | -14.3 | L-lactate permease | Â |
potF | NGO1494 | -7.7 | -20.0 | ABC-type spermidine/putrescine transporter, solute binding protein | MtrR |
putP | NGO1552 | -5.6 | -11.1 | Sodium/proline symport protein | Â |
ompU | NGO1688 | -2.6 | -3.7 | Putative iron uptake protein | FNR |
yaaJ | NGO1787 | -3.3 | -4.3 | Sodium/alanine symport protein | Â |
 | NGO1807 | -2.7 | -3.8 | Amino-acid symport protein |  |
gltS | NGO1890 | -3.1 | -5.0 | Sodium/glutamate symport protein | MtrR |
 | NGO1954 | -3.6 | -6.3 | Di- and tri-peptide permease, PRT2 |  |
sstT | NGO1957 | -4.5 | -11.1 | Sodium/serine symport protein | Â |
glnM | NGO2011 | -6.7 | -12.5 | ABC-type amino acid transport system, permease component | MtrR, FarR |
glnP | NGO2012 | -10.0 | -10.0 | ABC-type amino acid transport system, permease component | FarR |
glnQ | NGO2013 | -6.3 | -11.1 | ABC-type amino acid transporter, ATP-binding protein | MtrR, FarR |
apaA | NGO2014 | -6.3 | -16.7 | Bacterial extracellular solute-binding proteins, family 3 | MtrR, FarR |
 | NGO2016 | -3.6 | -3.3 | Predicted permease |  |
 | NGO2096 | -6.3 | -12.5 | SNF family sodium-dependent transporter |  |
Energy metabolism/Oxidation-Reduction | |||||
 | NGO0108 | -4.0 | -5.9 | NADPH-dependent FMN reductase | Fur, Lrp |
lldD | NGO0639 | -7.1 | -11.1 | L-lactate dehydrogenase | Â |
eda | NGO0713 | -3.0 | -5.6 | KHG-KDPG bifunctional aldolase | Â |
rpeC | NGO0758 | -4.8 | -3.8 | Ribulose-phosphate 3-epimerase | Â |
fdx | NGO0825 | -5.3 | -5.3 | Ferredoxin | Â |
cisY | NGO0918 | -3.6 | -3.8 | Type II citrate synthase | Lrp |
sdhB | NGO0920 | -2.9 | -4.2 | Succinate dehydrogenase, iron-sulfur protein | Lrp |
sdhA | NGO0921 | -3.7 | -3.4 | Succinate dehydrogenase, flavoprotein subunit | Lrp |
sdhD | NGO0922 | -2.9 | -3.4 | Succinate dehydrogenase, membrane anchor protein | Â |
sdhC | NGO0923 | -1.8 | -4.2 | Succinate dehydrogenase, cytochrome b556 chain | Â |
fumC | NG01029 | -2.9 | -6.3 | Fumarate hydratase | Fur, MtrR |
gpmA | NGO1258 | -4.0 | -5.6 | Phosphoglyceromutase | Lrp |
nqrA | NGO1413 | -4.0 | -7.7 | Na(+)-translocating NADH-quinone reductase subunit A | Â |
nqrB | NGO1414 | -5.0 | -8.3 | Na(+)-translocating NADH-quinone reductase subunit B | Â |
nqrC | NGO1415 | -4.2 | -8.3 | Na(+)-translocating NADH-quinone reductase subunit C | Â |
nqrD | NGO1416 | -3.8 | -16.7 | Na(+)-translocating NADH-quinone reductase subunit D | Â |
nqrE | NGO1417 | -4.3 | -12.5 | Na(+)-translocating NADH-quinone reductase subunit E | Â |
nqrF | NGO1418 | -3.7 | -9.1 | Na(+)-translocating NADH-quinone reductase subunit F | MtrR |
dadA | NGO1808 | -3.6 | -5.3 | D-amino acid dehydrogenase small subunit | Â |
mqo | NGO1980 | -3.7 | -5.0 | Malate:quinone oxidoreductase | Â |
Macromolecular biosynthesis | |||||
greB | NGO0262 | -3.7 | -5.3 | Transcription elongation factor | Â |
parC | NGO1259 | -3.8 | -2.9 | DNA topoisomerase IV subunit A | Â |
 | NGO1261 | -6.3 | -7.1 | S-adenosylmethionine-dependent methyltransferase |  |
rplP | NGO1831.1 | -3.2 | -6.3 | 50S ribosomal protein L16 | Lrp |
rpsC | NGO1832 | -3.2 | -7.7 | 30S ribosomal protein S3 | Lrp |
rplV | NGO1833 | -2.9 | -10.0 | 50S ribosomal protein L22 | Â |
rpsS | NGO1834 | -2.8 | -12.5 | 30S ribosomal protein S19 | Â |
rplD | NGO1837 | -2.2 | -7.1 | 50S ribosomal protein L4 | Â |
rspJ | NGO1841 | -2.7 | -7.1 | 30S ribosomal protein S10 | Lrp |
rpoC | NGO1850 | -3.3 | -5.0 | DNA-directed RNA polymerase subunit beta' | Â |
rpoB | NGO1851 | -2.1 | -4.5 | DNA-directed RNA polymerase subunit beta | Â |
Cell Structure | |||||
nspA | NGO0233 | -3.1 | -3.7 | Outer membrane protein (Probable Opa protein) | Â |
GNA2132 | NGO1958 | -5.3 | -8.3 | Predicted lipoprotein GNA2132 | Â |
lgtG | NGO2072 | -7.7 | -6.3 | Probable lipooligosaccharide glycosyl transferase G | Â |
Adaptation and stress response | |||||
cspA | NGO0410 | -3.8 | -3.3 | Cold shock protein | Â |
trxB | NGO0580 | -2.6 | -4.8 | Thioredoxin reductase | NmlR |
trx1 | NGO0652 | -5.3 | -6.3 | Thioredoxin I | Fur |
cstA | NGO1064 | -3.8 | -12.5 | Putative carbon starvation protein | Â |
mtrF | NGO1368 | -7.7 | -25.0 | Antibiotic resistance efflux pump component | MtrR, FarR |
sspB | NGO2131 | -4.5 | -3.6 | Protease specificity-enhancing factor | Â |
Hypothetical or unassigned | |||||
 | NGO0554 | -4.5 | -5.0 | Hypothetical protein | Fur |
 | NGO0635 | -4.8 | -3.6 | Hypothetical protein |  |
 | NGO1065 | -4.8 | -7.7 | Hypothetical protein |  |
 | NGO2097 | -3.7 | -3.1 | Conserved hypothetical protein |  |
Small RNA | |||||
nrrF e | Â | -4.8 | -7.7 | Fur-repressed small regulatory RNA | Fur |