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Table 3 rLogFC values for genes upregulated in human urine. BLAST results of hypothetical proteins are represented in parentheses

From: DFI-seq identification of environment-specific gene expression in uropathogenic Escherichia coli

Genes upregulated during growth in human urine compared to LB Protein Number of genes in operon rLogFC
ybdL Aminotransferase 1 2.453653
ybdH Hypothetical protein (oxidoreductase) 1 2.351791
metE 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase 1 2.285647
metR DNA-binding transcriptional dual regulator for metE and MetH 1 2.236911
yjaB Hypothetical protein (acetyltransferase) 1 2.137446
metA Homoserine O-succinyltransferase 1 2.033752
argC ;
argB
N-acetyl-gamma-glutamyl-phosphate reductase;
Acetylglutamate kinase
2 2.026239
metF 5,10-methylenetetrahydrofolate reductase 1 2.010415
argE Acetylornithine deacetylase 1 1.957286
ilvY IlvY DNA-binding transcriptional dual regulator 1 1.947862
argD bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase 1 1.91199
yibI Hypothetical protein 1 1.905502
artJ Arginine-binding periplasmic protein 2 1 1.808872
argG Argininosuccinate synthase 1 1.797071
ilvG ;
ilvM
Acetolacetate synthase 2 catalytic subunit; acetolactate synthase 2 regulatory subunit 2 1.752627
yifB ;
UTI89_C4323
predicted ATP-dependent protease;
hypothetical protein
2 1.711417
ydcX Hypothetical protein (membrane protein) 1 1.634447
UTI89_C2996;
UTI89_C2997;
UTI89_C2998;
yfdN1;
UTI89_C3000
bacteriophage V crossover junction endodeoxyribonuclease;
hypothetical protein;
bacteriophage V DNA adenine methylase;
hypothetical protein;
hypothetical protein
5 1.618326
Crl DNA-binding transcriptional regulator Crl 1 1.554786
potF putrescine ABC transporter substrate-binding protein 1 1.529378
metJ transcriptional repressor protein MetJ 1 1.513308
yibH Hypothetical protein (membrane protein) 1 1.511398
UTI89_C2260 Hypothetical protein 1 1.503588
UTI89_C0254 ;
UTI89_C0255;
UTI89_C0256
Hypothetical protein;
Hypothetical protein (peptidase C39);
Hypothetical protein
3 1.502547