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Table 2 Sequenced inserts, gene name and protein product. UTI89 genome coordinates of identified inserts, and position relative to proximal genes. Colony identifiers are ordered in accordance to sequence start and end sites. Colonies marked in bold were used for GFP expression analysis. Differential fluorescence is reported as GFP fluorescence fold change of select UTI89/pMWLib clones grown in human urine versus LB

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

Gene Protein Gene start Insert sequence start Insert sequence end Colony ID Fold change in mean GFP signal
argA N-acetylglutamate synthase 3139678 3139160 3139678 8, 57 13.5
3139113 3139736 45
argC N-acetyl-gamma-glutamyl-phosphate reductase 4439034 4438574 4439108 60 8.2
4438733 4439183 84  
argE Acetylornithine deacetylase 4438919 4439100 4438541 4, 93 14.1
4439305 4438787 42
argG Argininosuccinate synthase 3538472 3538296 3538904 51 4.3
3538143 3538627 82
artJ Arginine-binding periplasmic protein 2 861650 862067 861578 16 7.9
asnA asparagine synthetase A 4188023 4187539 4188150 1, 24, 38, 46, 49, 86 1.4
asnB asparagine synthetase B 674199 674321 673791 30 Lower in urine
674541 673908 35
674162 673571 72
manZ PTS system mannose-specific transporter subunit IID 1930575 1930463 1930677 35 Lower in urine
ecnA entericidin A 4648116 4647814 4648373 17 2.1
ecnB entericidin B 4648352
ilvC Ketol-acid reductoisomerase 4218632 4218651 4219116 20 4.5
4218333 4218799 83
ilvG Acetolacetate synthase 2 catalytic subunit 4211428 4210930 4211421 7, 10 13.8
metA Homoserine O-succinyltransferase 4462506 4462367 4462876 2 2.4
4462142 4462760 9, 11
4462396 4462910 34, 52, 53, 66, 73, 79, 90
4462388 4463001 81
metC Cystathionine beta-lyase 3362694 3362313 3362827 76 2.7
metE 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase 4277928 4277452 4277904 6, 26, 67 25.4
4277357 4277878 13, 44, 58, 87
4277611 4278191 74
metF 5,10-methylenetetrahydrofolate reductase 4416931 4416691 4417181 18, 23, 31 42.5
potF putrescine ABC transporter substrate-binding protein 854834 854439 855001 5 2.4
854460 855009 43
serA D-3-phosphoglycerate dehydrogenase 3236056 3236446 3236125 41 3.9
yaiM hypothetical protein 395196 395661 395108
UTI89_C1129 outer membrane heme/hemoglobin receptor 1122532 1122106 1122627 91 Lower in urine
UTI89_C4885 hypothetical protein 4787503 4787381 4787460
yajB ACP phosphodieterase 439176 439346 438767 25 Lower in urine
ybdH hypothetical protein 617328 617543 617035 3, 15, 36, 54, 69, 85, 88, 92 9.5
617447 617035 89
617636 617023 21, 50, 56, 77
617691 617083 28, 78
617543 617107 61
ybdL aminotransferase 617488 617206 617798 33, 37, 47 5.0
617323 617815 62
yeaR Hypothetical protein 1912199 1912872 1912250 65 6.6
yibI Hypothetical protein 4027446 4027775 4027295 19, 70, 75 5.6
4027590 4027356 68
Unannotated gene    48649 49106 12, 14, 22, 27, 32, 39, 40, 48, 55, 59, 64, 71, 80, 94, 95 Non-fluorescent
48681 49177 63
Opposite strand of yagV    315403 315898 29 Could not be cultivated in urine