Non synonimous mutations found in sample: CIM5N

(1)

Non synonimous mutations found in sample: CIM5N

FILTERS: (ANN contains MODERATE OR HIGH)

1 CHROM POS ID REF ALT U00096 10439 . A G

G missense_variant MODERATE satP b0010 transcript AAC73121.1 Coding 1/1 c.56T>C p.Met19Thr 56/567 56/567 19/188

U00096 gene 9928-10494 - satP b0010 yaaH EcoGene:EG11512

U00096 CDS 9928-10494 - satP b0010 yaaH EcoGene:EG11512 1 11 succinate-acetate transporter AAC73121.1

SAMPLE QUAL FILTER DP RPB AF1 AC1 DP4 MQ FQ PV4 VDB IS FORMAT VALUES

RESULTS_MG1655

RESULTS_CIM5N 3.54 . 26 -1.444630e+00 0.4998 1 10,13,1,2 60 5.47 1,1,1,1 4.488797e-02 GT:PL:GQ 0/1:31,0,255:30

2 CHROM POS ID REF ALT U00096 23136 . C T

T missense_variant MODERATE ileS b0026 transcript AAC73137.1 Coding 1/1 c.746C>T p.Ala249Val 746/2817 746/2817 249/938 U00096 gene 22391-

25207

+ ileS b0026 JW0024 EcoGene:EG10492

U00096 CDS 22391- 25207

+ ileS b0026 JW0024 EcoGene:EG10492 enzyme; Aminoacyl tRNA synthetases, tRNA modification isoleucine tRNA synthetase; GO_component: GO:0005737 - cytoplasm; GO_process: GO:0006418 - tRNA aminoacylation for protein translation 1 11 isoleucyl-tRNA synthetase AAC73137.1 6.1.1.5

RESULTS_MG1655

RESULTS_CIM5N 222.0 . 46 1 2 0,0,30,16 60 -165 1.240177e-01 GT:PL:GQ 1/1:255,138,0:99

3 CHROM POS ID REF ALT U00096 59243 . A G

G missense_variant MODERATE yabP b4659 transcript b4659 Coding 1/1 c.770A>G p.Asn257Ser 770/806 770/806 257/267 WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS

U00096 gene 58474-59279 + yabP b4659 yabQ EcoGene:EG12610

U00096 CDS 58474-59052,59052-59279 + yabP b4659 yabQ EcoGene:EG12610 pseudogene, pentapeptide repeats-containing 1 11

RESULTS_MG1655

4 CHROM POS ID REF ALT U00096 88646 . G A

A missense_variant MODERATE cra b0080 transcript AAC73191.1 Coding 1/1 c.619G>A p.Asp207Asn 619/1005 619/1005 207/334 U00096 gene 88028-

89032

+ cra b0080 shl EcoGene:EG10338

U00096 CDS 88028- 89032

+ cra b0080 shl EcoGene:EG10338 regulator; Energy metabolism, carbon: Glycolysis transcriptional repressor of fru operon and others; GO_component: GO:0005737 - cytoplasm; GO_function: GO:0016563 - transcription activator activity;

GO_function: GO:0016564 - transcription repressor activity; GO_process: GO:0006096 - glycolysis; GO_process:

GO:0006350 - transcription 1 11 transcriptional repressor-activator for carbon metabolism AAC73191.1

RESULTS_MG1655

5 CHROM POS ID REF ALT U00096 89890 . T A

A missense_variant MODERATE mraZ b0081 transcript AAC73192.1 Coding 1/1 c.257T>A p.Met86Lys 257/459 257/459 86/152

U00096 gene 89634-90092 + mraZ b0081 yabB EcoGene:EG11084

U00096 CDS 89634-90092 + mraZ b0081 yabB EcoGene:EG11084 1 11 RsmH methytransferase inhibitor AAC73192.1

RESULTS_MG1655

(2)

6 CHROM POS ID REF ALT U00096 94873 . T A

A missense_variant MODERATE murF b0086 transcript AAC73197.1 Coding 1/1 c.224T>A p.Leu75Gln 224/1359 224/1359 75/452 U00096 gene 94650-

96008

+ murF b0086 mra EcoGene:EG10622

U00096 CDS 94650- 96008

+ murF b0086 mra EcoGene:EG10622 enzyme; Murein sacculus, peptidoglycan GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component: GO:0005737 - cytoplasm; GO_process: GO:0009252 - peptidoglycan biosynthetic process; GO_process: GO:0000270 - peptidoglycan metabolic process 1 11 UDP-N-acetylmuramoyl- tripeptide:D-alanyl-D- alanine ligase AAC73197.1 6.3.2.10 N-terminus verified by Edman degradation: PMID 2186811

RESULTS_MG1655

7 ^CHROM ^POS ^{ID REF ALT}

U00096 133484 . A G

G missense_variant MODERATE acnB b0118 transcript AAC73229.1 Coding 1/1 c.1870A>G p.Ile624Val 1870/2598 1870/2598 624/865 U00096 gene 131615-

134212

+ acnB b0118 yacJ EcoGene:EG12316

U00096 CDS 131615- 134212

+ acnB b0118 yacJ EcoGene:EG12316 enzyme; Energy metabolism, carbon: TCA cycle aconitate hydrase B; GO_process:

GO:0006099 - tricarboxylic acid cycle; GO_process: GO:0009060 - aerobic respiration; GO_process: GO:0009061 - anaerobic respiration 1 11 aconitate hydratase 2; aconitase B; 2-methyl-cis-aconitate hydratase AAC73229.1 4.2.1.99 N- terminus verified by Edman degradation: PMID 8932712,9298646,12473114

RESULTS_MG1655

8 ^CHROM ^POS ^{ID REF ALT}

U00096 157376 . C T

T missense_variant MODERATE folK b0142 transcript AAC73253.1 Coding 1/1 c.357G>A p.Met119Ile 357/480 357/480 119/159 U00096 gene 157253-

157732

- folK b0142 JW0138 EcoGene:EG11374

U00096 CDS 157253- 157732

- folK b0142 JW0138 EcoGene:EG11374 enzyme; Biosynthesis of cofactors, carriers: Folic acid 7,8-dihydro-6- hydroxymethylpterin- pyrophosphokinase; GO_process: GO:0046656 - folic acid biosynthetic process 1 11 2-amino-4- hydroxy-6-hydroxymethyldihyropteridine pyrophosphokinase AAC73253.1 2.7.6.3

RESULTS_MG1655

9 ^CHROM ^POS ^{ID REF ALT}

U00096 168654 . GA G

frameshift_variant HIGH fhuA b0150 transcript AAC73261.1 Coding 1/1 c.1172delA p.Asp391fs 1172/2244 1172/2244 391/747 U00096 gene 167484-

169727

+ fhuA b0150 tonA EcoGene:EG10302

U00096 CDS 167484- 169727

+ fhuA b0150 tonA EcoGene:EG10302 membrane; Outer membrane constituents outer membrane protein receptor for ferrichrome, colicin M, and phages T1, T5, and phi80; GO_component: GO:0009274 - peptidoglycan-based cell wall;

GO_component: GO:0009279 - cell outer membrane 1 11 ferrichrome outer membrane transporter AAC73261.1

RESULTS_MG1655

RESULTS_CIM5N 214.0 . 39 1 2 0,0,20,18 60 -149 5.634959e-02 37,0.948718 GT:PL:GQ 1/1:255,114,0:99

10 ^CHROM ^POS ^{ID REF ALT}

U00096 168655 . A T,G

T missense_variant MODERATE fhuA b0150 transcript AAC73261.1 Coding 1/1 c.1172A>T p.Asp391Val 1172/2244 1172/2244 391/747 G missense_variant MODERATE fhuA b0150 transcript AAC73261.1 Coding 1/1 c.1172A>G p.Asp391Gly 1172/2244 1172/2244 391/747

U00096 gene 167484- 169727

+ fhuA b0150 tonA EcoGene:EG10302

U00096 CDS 167484- 169727

+ fhuA b0150 tonA EcoGene:EG10302 membrane; Outer membrane constituents outer membrane protein receptor for ferrichrome, colicin M, and phages T1, T5, and phi80; GO_component: GO:0009274 - peptidoglycan-based cell wall;

GO_component: GO:0009279 - cell outer membrane 1 11 ferrichrome outer membrane transporter AAC73261.1

(3)

RESULTS_MG1655

RESULTS_CIM5N 35.8 . 3 1 2 0,0,1,2 60 -33 3.576709e-02 GT:PL:GQ 1/1:96,35,29,66,0,63:10

11 ^CHROM ^POS ^{ID REF ALT}

U00096 180462 . G A

A missense_variant MODERATE dgt b0160 transcript AAC73271.1 Coding 1/1 c.1226G>A p.Gly409Glu 1226/1518 1226/1518 409/505 U00096 gene 179237-

180754

+ dgt b0160 optA EcoGene:EG10225

U00096 CDS 179237- 180754

+ dgt b0160 optA EcoGene:EG10225 enzyme; Central intermediary metabolism: Nucleotide hydrolysis GO_component:

GO:0005737 - cytoplasm; GO_process: GO:0015949 - nucleobase, nucleoside and nucleotide interconversion 1 11 deoxyguanosine triphosphate triphosphohydrolase AAC73271.1 3.1.5.1

RESULTS_MG1655

RESULTS_CIM5N 3.54 . 23 -7.653838e-01 0.4998 1 10,9,0,3 60 5.47 0.22,0.28,1,0.0034 3.576709e-02 GT:PL:GQ 0/1:31,0,255:30

12 ^CHROM ^POS ^{ID REF ALT}

U00096 211168 . G A

A missense_variant MODERATE ldcC b0186 transcript AAC73297.1 Coding 1/1 c.1490G>A p.Gly497Glu 1490/2142 1490/2142 497/713 U00096 gene 209679-

211820

+ ldcC b0186 ldcH EcoGene:EG13219

U00096 CDS 209679- 211820

+ ldcC b0186 ldcH EcoGene:EG13219 enzyme; Energy metabolism, carbon: Pyruvate dehydrogenase GO_process:

GO:0006096 - glycolysis; GO_process: GO:0016052 - carbohydrate catabolic process 1 11 lysine decarboxylase 2, constitutive AAC73297.1 4.1.1.18 N-terminus verified by Edman degradation: PMID 9226257,9339543

RESULTS_MG1655

13 ^CHROM ^POS ^{ID REF ALT}

U00096 222219 . C A

A missense_variant MODERATE metN b0199 transcript AAC73310.1 Coding 1/1 c.427G>T p.Gly143Cys 427/1032 427/1032 143/343 U00096 gene 221614-

222645

- metN b0199 metD EcoGene:EG11621

U00096 CDS 221614- 222645

- metN b0199 metD EcoGene:EG11621 transport; Transport of small molecules: Amino acids, amines D- and L-methionine transport protein (ABC superfamily, atp_bind); GO_component: GO:0005737 - cytoplasm 1 11 DL-methionine transporter subunit AAC73310.1

RESULTS_MG1655

14 ^CHROM ^POS ^{ID REF ALT}

U00096 233614 . C T

T missense_variant MODERATE mltD b0211 transcript AAC73316.1 Coding 1/1 c.342G>A p.Met114Ile 342/1359 342/1359 114/452 U00096 gene 232597-

233955

- mltD b0211 yafG EcoGene:EG10246

U00096 CDS 232597- 233955

- mltD b0211 yafG EcoGene:EG10246 regulator; Energy metabolism, carbon: Anaerobic respiration GO_component:

GO:0005737 - cytoplasm; GO_function: GO:0016563 - transcription activator activity; GO_process: GO:0009061 - anaerobic respiration; GO_process: GO:0017004 - cytochrome complex assembly; GO_process: GO:0006350 - transcription 1 11 putative membrane-bound lytic murein transglycosylase D AAC73316.1 3.2.1.-

RESULTS_MG1655

15 ^CHROM ^POS ^{ID REF ALT}

U00096 236552 . C A

A missense_variant MODERATE dnaQ b0215 transcript AAC73320.1 Coding 1/1 c.486C>A p.His162Gln 486/732 486/732 162/243 U00096 gene 236067-

236798

+ dnaQ b0215 mutD EcoGene:EG10243

U00096 CDS 236067- + dnaQ b0215 mutD EcoGene:EG10243 enzyme; DNA - replication, repair, restriction/modification DNA polymerase III,

(4)

236798 epsilon subunit; GO_component: GO:0005737 - cytoplasm; GO_process: GO:0006261 - DNA-dependent DNA replication;

GO_process: GO:0006457 - protein folding 1 11 DNA polymerase III epsilon subunit AAC73320.1 2.7.7.7

RESULTS_MG1655

16 ^CHROM ^POS ^{ID REF ALT}

U00096 245180 . C A

A missense_variant MODERATE yafK b0224 transcript AAC73328.1 Coding 1/1 c.626G>T p.Arg209Leu 626/741 626/741 209/246

A downstream_gene_variant MODIFIER yafJ b0223 transcript AAC73327.1 Coding c.*768C>A 86

U00096 gene 245065-245805 - yafK b0224 JW0214 EcoGene:EG13148

U00096 CDS 245065-245805 - yafK b0224 JW0214 EcoGene:EG13148 1 11 L,D-transpeptidase-related protein AAC73328.1

RESULTS_MG1655

17 ^CHROM ^POS ^{ID REF ALT}

U00096 306370 . C T

T missense_variant MODERATE ecpD b0290 transcript AAC73393.1 Coding 1/1 c.448G>A p.Gly150Ser 448/1644 448/1644 150/547 U00096 gene 305174-

306817

- ecpD b0290 yagW EcoGene:EG13562

U00096 CDS 305174- 306817

- ecpD b0290 yagW EcoGene:EG13562 structural component; Surface structures putative receptor 1 11 polymerized tip adhesin of ECP fibers AAC73393.1

RESULTS_MG1655

18 ^CHROM ^POS ^ID ^REF ^ALT

U00096 309214 . ACCCC ACCC

frameshift_variant HIGH ecpC b0291 transcript AAC73394.1 Coding 1/1 c.115delG p.Gly39fs 115/2526 115/2526 39/841

downstream_gene_variant MODIFIER ecpB b0292 transcript AAC73395.1 Coding c.*669delG 140

U00096 gene 306807- 309332

- ecpC b0291 yagX EcoGene:EG13563

U00096 CDS 306807- 309332

- ecpC b0291 yagX EcoGene:EG13563 membrane; Outer membrane constituents putative enzyme 1 11 ECP production outer membrane protein AAC73394.1

RESULTS_MG1655

19 ^CHROM ^POS ^ID ^REF ^ALT

U00096 338643 . TGGG TGG

frameshift_variant HIGH yahG b0321 transcript AAC73424.1 Coding 1/1 c.322delG p.Glu108fs 322/1419 322/1419 108/472 U00096 gene 338325-339743 + yahG b0321 JW0313 EcoGene:EG13591

U00096 CDS 338325-339743 + yahG b0321 JW0313 EcoGene:EG13591 1 11 DUF1116 family protein AAC73424.1

RESULTS_MG1655

20 ^CHROM ^POS ^{ID REF ALT}

U00096 338644 . G T

T missense_variant MODERATE yahG b0321 transcript AAC73424.1 Coding 1/1 c.320G>T p.Trp107Leu 320/1419 320/1419 107/472

U00096 gene 338325-339743 + yahG b0321 JW0313 EcoGene:EG13591

U00096 CDS 338325-339743 + yahG b0321 JW0313 EcoGene:EG13591 1 11 DUF1116 family protein AAC73424.1

RESULTS_MG1655

RESULTS_CIM5N 24.0 . 6 -1.427508e+00 0.5 1 0,4,1,1 60 27 0.33,0.32,1,0.038 7.520000e-02 GT:PL:GQ 0/1:54,0,99:57

(5)

21 ^CHROM ^POS ^{ID REF ALT}

U00096 349262 . C T

T missense_variant MODERATE prpB b0331 transcript AAC73434.1 Coding 1/1 c.581C>T p.Ala194Val 581/891 581/891 194/296 U00096 gene 348682-

349572

+ prpB b0331 yahQ EcoGene:EG13601

U00096 CDS 348682- 349572

+ prpB b0331 yahQ EcoGene:EG13601 putative enzyme; Not classified putative phosphonomutase 2; GO_component:

GO:0005737 - cytoplasm; GO_process: GO:0019395 - fatty acid oxidation 1 11 2-methylisocitrate lyase AAC73434.1 4.1.3.30

RESULTS_MG1655

RESULTS_CIM5N 222.0 . 51 -1.385918e-01 1 2 0,1,28,21 60 -139 0.44,0.33,1,0.14 2.622671e-01 GT:PL:GQ 1/1:255,112,0:99

22 ^CHROM ^POS ^{ID REF ALT}

U00096 353381 . G A

A missense_variant MODERATE prpE b0335 transcript AAC73438.1 Coding 1/1 c.676G>A p.Val226Met 676/1887 676/1887 226/628 U00096 gene 352706-

354592

+ prpE b0335 yahU EcoGene:EG13604

U00096 CDS 352706- 354592

+ prpE b0335 yahU EcoGene:EG13604 putative enzyme; Not classified putative propionyl-CoA synthetase; GO_component:

GO:0005737 - cytoplasm; GO_process: GO:0019395 - fatty acid oxidation 1 11 propionate--CoA ligase AAC73438.1

RESULTS_MG1655

23 ^CHROM ^POS ^{ID REF ALT}

U00096 370289 . C A

A missense_variant MODERATE mhpB b0348 transcript AAC73451.1 Coding 1/1 c.13C>A p.Leu5Ile 13/945 13/945 5/314

A downstream_gene_variant MODIFIER mhpA b0347 transcript AAC73450.1 Coding c.*1665C>A 14

U00096 gene 370277- 371221

+ mhpB b0348 JW0339 EcoGene:EG20274

U00096 CDS 370277- 371221

+ mhpB b0348 JW0339 EcoGene:EG20274 enzyme; Degradation of small molecules: Carbon compounds GO_process:

GO:0019395 - fatty acid oxidation 1 11 2,3-dihydroxyphenylpropionate 1,2-dioxygenase AAC73451.1 1.13.11.- N-terminus verified by Edman degradation: PMID 8399388

RESULTS_MG1655

RESULTS_CIM5N 225.0 . 51 1.160584e+00 0.5 1 19,8,11,13 60 225 0.094,1,1,0.09 1.344785e-01 GT:PL:GQ 0/1:255,0,255:99

24 ^CHROM ^POS ^{ID REF ALT}

U00096 370877 . G A

A missense_variant MODERATE mhpB b0348 transcript AAC73451.1 Coding 1/1 c.601G>A p.Gly201Arg 601/945 601/945 201/314 U00096 gene 370277-

371221

+ mhpB b0348 JW0339 EcoGene:EG20274

U00096 CDS 370277- 371221

+ mhpB b0348 JW0339 EcoGene:EG20274 enzyme; Degradation of small molecules: Carbon compounds GO_process:

GO:0019395 - fatty acid oxidation 1 11 2,3-dihydroxyphenylpropionate 1,2-dioxygenase AAC73451.1 1.13.11.- N-terminus verified by Edman degradation: PMID 8399388

RESULTS_MG1655

25 ^CHROM ^POS ^{ID REF ALT}

U00096 397213 . A T

T missense_variant MODERATE sbmA b0377 transcript AAC73480.1 Coding 1/1 c.575A>T p.Gln192Leu 575/1221 575/1221 192/406 U00096 gene 396639-

397859

+ sbmA b0377 JW0368 EcoGene:EG10928

U00096 CDS 396639- 397859

+ sbmA b0377 JW0368 EcoGene:EG10928 putative membrane; Drug/analog sensitivity sensitivity to microcin B17, possibly envelop protein; GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component: GO:0019866 - organelle inner membrane; GO_process: GO:0042493 - response to drug 1 11 peptide antibiotic transporter AAC73480.1

RESULTS_MG1655

(6)

26 ^CHROM ^POS ^{ID REF ALT}

U00096 402171 . T A

A missense_variant MODERATE phoA b0383 transcript AAC73486.2 Coding 1/1 c.425T>A p.Leu142Gln 425/1416 425/1416 142/471 U00096 gene 401747-

403162

+ phoA b0383 psiA EcoGene:EG10727

U00096 CDS 401747- 403162

+ phoA b0383 psiA EcoGene:EG10727 enzyme; Central intermediary metabolism: Phosphorus compounds alkaline phosphatase; start codon corrected; GO_component: GO:0042597 - periplasmic space; GO_process: GO:0006793 - phosphorus metabolic process 1 11 bacterial alkaline phosphatase AAC73486.2 3.1.3.1

RESULTS_MG1655

27 ^CHROM ^POS ^{ID REF ALT}

U00096 403320 . G T

T missense_variant MODERATE psiF b0384 transcript AAC73487.2 Coding 1/1 c.40G>T p.Val14Phe 40/321 40/321 14/106

T downstream_gene_variant MODIFIER phoA b0383 transcript AAC73486.2 Coding c.*1416G>T 158

U00096 gene 403281- 403601

+ psiF b0384 JW5054 EcoGene:EG11401

U00096 CDS 403281- 403601

+ psiF b0384 JW5054 EcoGene:EG11401 phenotype; Central intermediary metabolism: Phosphorus compounds induced by phosphate starvation; GO_process: GO:0006793 - phosphorus metabolic process; GO_process: GO:0042594 - response to starvation 1 11 PsiF family protein AAC73487.2

RESULTS_MG1655

28 ^CHROM ^POS ^{ID REF ALT}

U00096 408831 . C T

T missense_variant MODERATE ykiA b0392 transcript b0392 Coding 1/1 c.223C>T p.Pro75Ser 223/342 223/342 75/113 WARNING_TRANSCRIPT_NO_START_CODON

U00096 gene 408609-408950 + ykiA b0392 JW0383 EcoGene:EG14282

U00096 CDS 408609-408950 + ykiA b0392 JW0383 EcoGene:EG14282 pseudogene 1 11

RESULTS_MG1655

RESULTS_CIM5N 218.0 . 23 2.154101e-01 0.5 1 9,2,6,6 59 171 0.19,0.35,1,1 1.534248e-01 GT:PL:GQ 0/1:248,0,198:99

29 ^CHROM ^POS ^{ID REF ALT}

U00096 411916 . A C

C missense_variant MODERATE araJ b0396 transcript AAC73499.1 Coding 1/1 c.566T>G p.Leu189Arg 566/1185 566/1185 189/394 U00096 gene 411297-

412481

- araJ b0396 JW0386 EcoGene:EG10060

U00096 CDS 411297- 412481

- araJ b0396 JW0386 EcoGene:EG10060 transport; Degradation of small molecules: Carbon compounds involved in either transport or processing of arabinose polymers; GO_component: GO:0009274 - peptidoglycan-based cell wall;

GO_component: GO:0019866 - organelle inner membrane; GO_process: GO:0016052 - carbohydrate catabolic process 1 11 L-arabinose-inducible putative transporter, MFS family AAC73499.1

RESULTS_MG1655

RESULTS_CIM5N 225.0 . 24 1.788854e+00 0.5 1 5,4,4,11 60 164 0.21,1,1,1 1.552565e-01 GT:PL:GQ 0/1:255,0,191:99

30 ^CHROM ^POS ^{ID REF ALT}

U00096 412396 . A G

G missense_variant MODERATE araJ b0396 transcript AAC73499.1 Coding 1/1 c.86T>C p.Leu29Pro 86/1185 86/1185 29/394 U00096 gene 411297-

412481

- araJ b0396 JW0386 EcoGene:EG10060

U00096 CDS 411297- 412481

- araJ b0396 JW0386 EcoGene:EG10060 transport; Degradation of small molecules: Carbon compounds involved in either transport or processing of arabinose polymers; GO_component: GO:0009274 - peptidoglycan-based cell wall;

GO_component: GO:0019866 - organelle inner membrane; GO_process: GO:0016052 - carbohydrate catabolic process 1 11 L-arabinose-inducible putative transporter, MFS family AAC73499.1

(7)

RESULTS_MG1655

31 ^CHROM ^POS ^{ID REF ALT}

U00096 414600 . C T

T stop_gained HIGH sbcC b0397 transcript AAC73500.1 Coding 1/1 c.1154G>A p.Trp385* 1154/3147 1154/3147 385/1048 U00096 gene 412607-

415753

- sbcC b0397 rmuA EcoGene:EG10927

U00096 CDS 412607- 415753

- sbcC b0397 rmuA EcoGene:EG10927 enzyme; Degradation of DNA ATP-dependent dsDNA exonuclease; GO_component:

GO:0005737 - cytoplasm; GO_process: GO:0006308 - DNA catabolic process 1 11 exonuclease, dsDNA, ATP-dependent AAC73500.1 N-terminus verified by Edman degradation: PMID 9242643

RESULTS_MG1655

32 ^CHROM ^POS ^{ID REF ALT}

U00096 415362 . T C

C missense_variant MODERATE sbcC b0397 transcript AAC73500.1 Coding 1/1 c.392A>G p.Asp131Gly 392/3147 392/3147 131/1048 U00096 gene 412607-

415753

- sbcC b0397 rmuA EcoGene:EG10927

U00096 CDS 412607- 415753

- sbcC b0397 rmuA EcoGene:EG10927 enzyme; Degradation of DNA ATP-dependent dsDNA exonuclease; GO_component:

GO:0005737 - cytoplasm; GO_process: GO:0006308 - DNA catabolic process 1 11 exonuclease, dsDNA, ATP-dependent AAC73500.1 N-terminus verified by Edman degradation: PMID 9242643

RESULTS_MG1655

33 ^CHROM ^POS ^{ID REF ALT}

U00096 435821 . A T

T missense_variant MODERATE thiL b0417 transcript AAC73520.1 Coding 1/1 c.188A>T p.Asp63Val 188/978 188/978 63/325 U00096 gene 435634-

436611

+ thiL b0417 JW0407 EcoGene:EG20227

U00096 CDS 435634- 436611

+ thiL b0417 JW0407 EcoGene:EG20227 enzyme; Biosynthesis of cofactors, carriers: Thiamine GO_process: GO:0009228 - thiamin biosynthetic process 1 11 thiamine monophosphate kinase AAC73520.1 2.7.4.16

RESULTS_MG1655

34 ^CHROM ^POS ^{ID REF ALT}

U00096 447488 . T C

C missense_variant MODERATE cyoE b0428 transcript AAC73531.1 Coding 1/1 c.218A>G p.Asn73Ser 218/891 218/891 73/296 U00096 gene 446815-

447705

- cyoE b0428 JW0418 EcoGene:EG10182

U00096 CDS 446815- 447705

- cyoE b0428 JW0418 EcoGene:EG10182 enzyme; Energy metabolism, carbon: Aerobic respiration protoheme IX farnesyltransferase (haeme O biosynthesis); GO_component: GO:0009274 - peptidoglycan-based cell wall;

GO_component: GO:0019866 - organelle inner membrane; GO_process: GO:0009060 - aerobic respiration 1 11 protoheme IX farnesyltransferase AAC73531.1 2.5.1.-

RESULTS_MG1655

35 ^CHROM ^POS ^{ID REF ALT}

U00096 448089 . CAAA CAA

frameshift_variant HIGH cyoC b0430 transcript AAC73533.1 Coding 1/1 c.569delT p.Val190fs 569/615 569/615 190/204

upstream_gene_variant MODIFIER cyoD b0429 transcript AAC73532.1 Coding c.-1delT 46

U00096 gene 448046- 448660

- cyoC b0430 JW0420 EcoGene:EG10180

U00096 CDS 448046- - cyoC b0430 JW0420 EcoGene:EG10180 enzyme; Energy metabolism, carbon: Aerobic respiration GO_component:

(8)

448660 GO:0009274 - peptidoglycan-based cell wall; GO_component: GO:0019866 - organelle inner membrane; GO_process:

GO:0009060 - aerobic respiration 1 11 cytochrome o ubiquinol oxidase subunit III AAC73533.1 1.10.3.-

RESULTS_MG1655

36 ^CHROM ^POS ^{ID REF ALT}

U00096 453654 . C G

G missense_variant MODERATE yajG b0434 transcript AAC73537.2 Coding 1/1 c.514G>C p.Asp172His 514/579 514/579 172/192

G upstream_gene_variant MODIFIER ampG b0433 transcript AAC73536.1 Coding c.-1G>C 109

U00096 gene 453589- 454167

- yajG b0434 JW0424 EcoGene:EG12182

U00096 CDS 453589- 454167

- yajG b0434 JW0424 EcoGene:EG12182 putative enzyme; Not classified putative polymerase/proteinase 1 11 putative lipoprotein AAC73537.2

RESULTS_MG1655

37 ^CHROM ^POS ^{ID REF ALT}

U00096 471299 . C T

T stop_gained HIGH mdlB b0449 transcript AAC73552.1 Coding 1/1 c.664C>T p.Gln222* 664/1782 664/1782 222/593 U00096 gene 470636-

472417

+ mdlB b0449 mdl EcoGene:EG14374

U00096 CDS 470636- 472417

+ mdlB b0449 mdl EcoGene:EG14374 GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component:

GO:0019866 - organelle inner membrane 1 11 putative multidrug ABC transporter ATPase AAC73552.1

RESULTS_MG1655

38 ^CHROM ^POS ^{ID REF ALT}

U00096 475050 . G A

A stop_gained HIGH tesB b0452 transcript AAC73555.1 Coding 1/1 c.112C>T p.Gln38* 112/861 112/861 38/286

U00096 gene 474301- 475161

- tesB b0452 JW0442 EcoGene:EG10995

U00096 CDS 474301- 475161

- tesB b0452 JW0442 EcoGene:EG10995 enzyme; Fatty acid and phosphatidic acid biosynthesis 1 11 acyl-CoA thioesterase 2 AAC73555.1 3.1.2.-

RESULTS_MG1655

39 ^CHROM ^POS ^{ID REF ALT}

U00096 475469 . C T

T missense_variant MODERATE ybaY b0453 transcript AAC73556.1 Coding 1/1 c.91C>T p.Pro31Ser 91/573 91/573 31/190 U00096 gene 475379-

475951

+ ybaY b0453 JW0443 EcoGene:EG13253

U00096 CDS 475379- 475951

+ ybaY b0453 JW0443 EcoGene:EG13253 phenotype; Not classified glycoprotein/polysaccharide metabolism; GO_process:

GO:0042158 - lipoprotein biosynthetic process; GO_process: GO:0009101 - glycoprotein biosynthetic process 1 11 outer membrane lipoprotein AAC73556.1

RESULTS_MG1655

40 ^CHROM ^POS ^{ID REF ALT}

U00096 511741 . C T

T missense_variant MODERATE glsA b0485 transcript AAC73587.1 Coding 1/1 c.101C>T p.Ala34Val 101/933 101/933 34/310 U00096 gene 511641-

512573

+ glsA b0485 ybaS EcoGene:EG13247

U00096 CDS 511641- + glsA b0485 ybaS EcoGene:EG13247 enzyme; l-glutamine catabolism putative glutaminase; GO_process: GO:0009063 -

(9)

512573 cellular amino acid catabolic process 1 11 glutaminase 1 AAC73587.1

RESULTS_MG1655

41 ^CHROM ^POS ^{ID REF ALT}

U00096 514719 . C T

T stop_gained HIGH ybbJ b0488 transcript AAC73590.2 Coding 1/1 c.141G>A p.Trp47* 141/459 141/459 47/152

T downstream_gene_variant MODIFIER qmcA b0489 transcript AAC73591.1 Coding c.*918G>A 137

U00096 gene 514401- 514859

- ybbJ b0488 JW5065 EcoGene:EG13257

U00096 CDS 514401- 514859

- ybbJ b0488 JW5065 EcoGene:EG13257 1 11 inner membrane protein; stimulator of the QmcA suppressor of ftsH- htpX AAC73590.2

RESULTS_MG1655

42 ^CHROM ^POS ^{ID REF ALT}

U00096 551066 . G T

T missense_variant MODERATE ybcF b0521 transcript AAC73623.1 Coding 1/1 c.628G>T p.Ala210Ser 628/894 628/894 210/297 U00096 gene 550439-

551332

+ ybcF b0521 JW0510 EcoGene:EG12384

U00096 CDS 550439- 551332

+ ybcF b0521 JW0510 EcoGene:EG12384 putative enzyme; Purine nitrogen catabolism putative carbamate kinase;

GO_process: GO:0006526 - arginine biosynthetic process; GO_process: GO:0006221 - pyrimidine nucleotide biosynthetic process 1 11 putative carbonate kinase AAC73623.1

RESULTS_MG1655

43 ^CHROM ^POS ^{ID REF ALT}

U00096 558633 . A G

G missense_variant MODERATE sfmA b0530 transcript AAC73632.2 Coding 1/1 c.422A>G p.Asn141Ser 422/543 422/543 141/180 U00096 gene 558212-

558754

+ sfmA b0530 JW0519 EcoGene:EG13881

U00096 CDS 558212- 558754

+ sfmA b0530 JW0519 EcoGene:EG13881 putative structural component; Surface structures putative fimbrial-like protein;

GO_component: GO:0009289 - pilus 1 11 FimA homolog, function unknown AAC73632.2

RESULTS_MG1655

44 ^CHROM ^POS ^{ID REF ALT}

U00096 602184 . G A

A missense_variant MODERATE pheP b0576 transcript AAC73677.1 Coding 1/1 c.226G>A p.Glu76Lys 226/1377 226/1377 76/458 U00096 gene 601959-

603335

+ pheP b0576 JW0565 EcoGene:EG10708

U00096 CDS 601959- 603335

+ pheP b0576 JW0565 EcoGene:EG10708 transport; Transport of small molecules: Amino acids, amines phenylalanine- specific transport system; GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component: GO:0019866 - organelle inner membrane; GO_process: GO:0009094 - L-phenylalanine biosynthetic process; GO_process: GO:0009063 - cellular amino acid catabolic process 1 11 phenylalanine transporter AAC73677.1

RESULTS_MG1655

45 ^CHROM ^POS ^{ID REF ALT}

U00096 616329 . G T

T missense_variant MODERATE entF b0586 transcript AAC73687.1 Coding 1/1 c.2173G>T p.Ala725Ser 2173/3882 2173/3882 725/1293 U00096 gene 614157-

618038

+ entF b0586 JW0578 EcoGene:EG10264

(10)

U00096 CDS 614157- 618038

+ entF b0586 JW0578 EcoGene:EG10264 enzyme; Biosynthesis of cofactors, carriers: Enterochelin ATP-dependent serine activating enzyme (may be part of enterobactin synthase as component F); GO_component: GO:0005737 - cytoplasm;

GO_process: GO:0009239 - enterobactin biosynthetic process; GO_process: GO:0015937 - coenzyme A biosynthetic process; GO_process: GO:0019184 - nonribosomal peptide biosynthetic process; GO_process: GO:0006826 - iron ion transport 1 11 enterobactin synthase multienzyme complex component, ATP-dependent AAC73687.1 2.7.7.- N-terminus verified by Edman degradation: PMID 1826089,2974033

RESULTS_MG1655

46 ^CHROM ^POS ^{ID REF ALT}

U00096 620329 . A C

C missense_variant MODERATE fepG b0589 transcript AAC73690.1 Coding 1/1 c.860T>G p.Leu287Arg 860/993 860/993 287/330

C upstream_gene_variant MODIFIER fepC b0588 transcript AAC73689.1 Coding c.-1T>G 130

U00096 gene 620196- 621188

- fepG b0589 JW0581 EcoGene:EG10298

U00096 CDS 620196- 621188

- fepG b0589 JW0581 EcoGene:EG10298 transport; Transport of small molecules: Cations ferric enterobactin transport protein; membrane component of ABC superfamily; GO_component: GO:0009274 - peptidoglycan-based cell wall;

GO_component: GO:0019866 - organelle inner membrane; GO_process: GO:0006826 - iron ion transport 1 11 iron- enterobactin ABC transporter permease AAC73690.1

RESULTS_MG1655

47 ^CHROM ^POS ^{ID REF ALT}

U00096 633737 . G A

A missense_variant MODERATE ybdL b0600 transcript AAC73701.1 Coding 1/1 c.152G>A p.Arg51Gln 152/1161 152/1161 51/386 U00096 gene 633586-

634746

+ ybdL b0600 JW0593 EcoGene:EG13531

U00096 CDS 633586- 634746

+ ybdL b0600 JW0593 EcoGene:EG13531 putative enzyme; Not classified PLP-dependent methionine aminotransferase;

GO_process: GO:0008152 - metabolic process 1 11 methionine aminotransferase, PLP-dependent AAC73701.1 2.6.1.-

RESULTS_MG1655

RESULTS_CIM5N 81.0 . 43 1.357608e+00 0.5 1 24,11,2,6 60 84 0.042,1,1,0.24 1.171281e-01 GT:PL:GQ 0/1:111,0,255:99

48 ^CHROM ^POS ^{ID REF ALT}

U00096 643214 . A T

T missense_variant MODERATE ybdR b0608 transcript AAC73709.1 Coding 1/1 c.1127A>T p.Lys376Ile 1127/1239 1127/1239 376/412 U00096 gene 642088-

643326

+ ybdR b0608 JW0601 EcoGene:EG13537

U00096 CDS 642088- 643326

+ ybdR b0608 JW0601 EcoGene:EG13537 putative enzyme; Not classified putative oxidoreductase 1 11 putative Zn- dependent NAD(P)-binding oxidoreductase AAC73709.1

RESULTS_MG1655

49 ^CHROM ^POS ^{ID REF ALT}

U00096 645865 . C T

T missense_variant MODERATE citT b0612 transcript AAC73713.1 Coding 1/1 c.716G>A p.Cys239Tyr 716/1464 716/1464 239/487 U00096 gene 645117-

646580

- citT b0612 ybdS EcoGene:EG13538

U00096 CDS 645117- 646580

- citT b0612 ybdS EcoGene:EG13538 putative membrane; Not classified GO_component: GO:0009274 - peptidoglycan- based cell wall; GO_component: GO:0019866 - organelle inner membrane; GO_process: GO:0016052 - carbohydrate catabolic process 1 11 citrate/succinate antiporter; citrate carrier AAC73713.1

RESULTS_MG1655

50 ^CHROM ^POS ^{ID REF ALT}

U00096 649472 . G A

(11)

A stop_gained HIGH citF b0615 transcript AAC73716.1 Coding 1/1 c.100C>T p.Gln34* 100/1533 100/1533 34/510

A downstream_gene_variant MODIFIER citE b0616 transcript AAC73717.2 Coding c.*909C>T 110

U00096 gene 648039- 649571

- citF b0615 ybdV EcoGene:EG13541

U00096 CDS 648039- 649571

- citF b0615 ybdV EcoGene:EG13541 enzyme; Central intermediary metabolism: Pool, multipurpose conversions citrate lyase alpha chain; GO_component: GO:0005737 - cytoplasm 1 11 citrate lyase, citrate-ACP transferase (alpha) subunit AAC73716.1 4.1.3.6

RESULTS_MG1655

51 ^CHROM ^POS ^{ID REF ALT}

U00096 651373 . G A

A missense_variant MODERATE citC b0618 transcript AAC73719.2 Coding 1/1 c.484C>T p.Arg162Cys 484/1059 484/1059 162/352 U00096 gene 650798-

651856

- citC b0618 ybeO EcoGene:EG13645

U00096 CDS 650798- 651856

- citC b0618 ybeO EcoGene:EG13645 enzyme; Central intermediary metabolism: Pool, multipurpose conversions citrate lyase synthetase (citrate (pro-3S)-lyase ligase; GO_component: GO:0005737 - cytoplasm; GO_process: GO:0006464 - protein modification process 1 11 citrate lyase ligase; [citrate [pro-3S]-lyase] ligase AAC73719.2 6.2.1.22

RESULTS_MG1655

52 ^CHROM ^POS ^{ID REF ALT}

U00096 670290 . C T

T missense_variant MODERATE nadD b0639 transcript AAC73740.1 Coding 1/1 c.283G>A p.Glu95Lys 283/642 283/642 95/213 U00096 gene 669931-

670572

- nadD b0639 ybeN EcoGene:EG13241

U00096 CDS 669931- 670572

- nadD b0639 ybeN EcoGene:EG13241 GO_process: GO:0009435 - NAD biosynthetic process 1 11 nicotinic acid mononucleotide adenylyltransferase, NAD(P)-dependent AAC73740.1 2.7.7.18

RESULTS_MG1655

RESULTS_CIM5N 225.0 . 38 6.591248e-01 0.5 1 11,10,7,9 59 225 0.74,1,0.13,1 1.244642e-01 GT:PL:GQ 0/1:255,0,255:99

53 ^CHROM ^POS ^{ID REF ALT}

U00096 693279 . G A

A missense_variant MODERATE ybeZ b0660 transcript AAC73761.2 Coding 1/1 c.100C>T p.Arg34Cys 100/1041 100/1041 34/346 U00096 gene 692338-

693378

- ybeZ b0660 phoL EcoGene:EG13656

U00096 CDS 692338- 693378

- ybeZ b0660 phoL EcoGene:EG13656 putative ATP-binding protein in pho regulon 1 11 heat shock protein, putative NTPase; PhoH-like protein AAC73761.2

RESULTS_MG1655

54 ^CHROM ^POS ^{ID REF ALT}

U00096 713562 . C T

T missense_variant MODERATE pgm b0688 transcript AAC73782.1 Coding 1/1 c.5C>T p.Ala2Val 5/1641 5/1641 2/546

T downstream_gene_variant MODIFIER seqA b0687 transcript AAC73781.1 Coding c.*546C>T 30

U00096 gene 713558- 715198

+ pgm b0688 pgmA EcoGene:EG12144

U00096 CDS 713558- 715198

+ pgm b0688 pgmA EcoGene:EG12144 enzyme; Degradation of small molecules: Carbon compounds GO_component:

GO:0005737 - cytoplasm; GO_process: GO:0016052 - carbohydrate catabolic process; GO_process: GO:0006006 - glucose metabolic process 1 11 phosphoglucomutase AAC73782.1 5.4.2.2

RESULTS_MG1655

55 ^CHROM ^POS ^ID ^REF ^ALT

(12)

U00096 725399 . GCCC GCC

frameshift_variant HIGH kdpB b0697 transcript AAC73791.1 Coding 1/1 c.1635delG p.Ala545fs 1635/2049 1635/2049 545/682 U00096 gene 724988-

727036

- kdpB b0697 kac EcoGene:EG10514

U00096 CDS 724988- 727036

- kdpB b0697 kac EcoGene:EG10514 enzyme; Transport of small molecules: Cations ATPase of high-affinity potassium transport system, B chain; GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component: GO:0019866 - organelle inner membrane; GO_function: GO:0015662 - ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism 1 11 potassium translocating ATPase, subunit B AAC73791.1 3.6.3.12

RESULTS_MG1655

56 ^CHROM ^POS ^{ID REF ALT}

U00096 725400 . C G

G missense_variant MODERATE kdpB b0697 transcript AAC73791.1 Coding 1/1 c.1637G>C p.Gly546Ala 1637/2049 1637/2049 546/682 U00096 gene 724988-

727036

- kdpB b0697 kac EcoGene:EG10514

U00096 CDS 724988- 727036

- kdpB b0697 kac EcoGene:EG10514 enzyme; Transport of small molecules: Cations ATPase of high-affinity potassium transport system, B chain; GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component: GO:0019866 - organelle inner membrane; GO_function: GO:0015662 - ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism 1 11 potassium translocating ATPase, subunit B AAC73791.1 3.6.3.12

RESULTS_MG1655

RESULTS_CIM5N 21.0 . 7 -1.534291e+00 0.5 1 4,1,1,1 60 24 1,0.38,1,1 7.840000e-02 GT:PL:GQ 0/1:51,0,131:54

57 ^CHROM ^POS ^{ID REF ALT}

U00096 734251 . C T

T missense_variant MODERATE rhsO b0703 transcript b0703 Coding 1/1 c.119C>T p.Ala40Val 119/1521 119/1521 40/506 WARNING_TRANSCRIPT_NO_START_CODON T downstream_gene_variant MODIFIER ybfB b0702 transcript AAC73796.1 Coding c.*327C>T 149

U00096 gene 734133-735653 + rhsO b0703 ybfO EcoGene:EG13661

U00096 CDS 734133-735653 + rhsO b0703 ybfO EcoGene:EG13661 pseudogene, Rhs family 1 11

RESULTS_MG1655

58 ^CHROM ^POS ^{ID REF ALT}

U00096 740678 . C T

T missense_variant MODERATE phr b0708 transcript AAC73802.1 Coding 1/1 c.1172C>T p.Thr391Ile 1172/1419 1172/1419 391/472 U00096 gene 739507-

740925

+ phr b0708 phrB EcoGene:EG10736

U00096 CDS 739507- 740925

+ phr b0708 phrB EcoGene:EG10736 enzyme; DNA - replication, repair, restriction/modification deoxyribodipyrimidine photolyase (photoreactivation); GO_component: GO:0005737 - cytoplasm; GO_process: GO:0006281 - DNA repair 1 11 deoxyribodipyrimidine photolyase, FAD-binding AAC73802.1 4.1.99.3

RESULTS_MG1655

59 ^CHROM ^POS ^{ID REF ALT}

U00096 741686 . T C

C missense_variant MODERATE dtpD b0709 transcript AAC73803.1 Coding 1/1 c.871A>G p.Ile291Val 871/1482 871/1482 291/493 U00096 gene 741075-

742556

- dtpD b0709 ybgH EcoGene:EG13304

U00096 CDS 741075- 742556

- dtpD b0709 ybgH EcoGene:EG13304 transport; Not classified putative transport protein; GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component: GO:0019866 - organelle inner membrane; GO_process: GO:0009063 - cellular amino acid catabolic process 1 11 dipeptide and tripeptide permease D AAC73803.1

RESULTS_MG1655

RESULTS_CIM5N 104.0 . 46 1.276885e-01 0.5 1 18,18,3,6 60 107 0.47,1,1,0.25 1.305702e-01 GT:PL:GQ 0/1:134,0,255:99

(13)

60 ^CHROM U00096 747445 . ^POS ^{ID REF ALT} G T

T missense_variant MODERATE abrB b0715 transcript AAC73809.2 Coding 1/1 c.325C>A p.Pro109Thr 325/1047 325/1047 109/348 U00096 gene 746723-

747769

- abrB b0715 ybgN EcoGene:EG13310

U00096 CDS 746723- 747769

- abrB b0715 ybgN EcoGene:EG13310 putative transport; Not classified putative transport protein; GO_component:

GO:0009274 - peptidoglycan-based cell wall; GO_component: GO:0019866 - organelle inner membrane 1 11 regulator of aidB expression; inner membrane protein AAC73809.2

RESULTS_MG1655

61 ^CHROM ^POS ^{ID REF ALT}

U00096 751218 . C T

T missense_variant MODERATE ybgQ b0718 transcript AAC73812.2 Coding 1/1 c.952G>A p.Glu318Lys 952/2448 952/2448 318/815 U00096 gene 749722-

752169

- ybgQ b0718 JW5099 EcoGene:EG13313

U00096 CDS 749722- 752169

- ybgQ b0718 JW5099 EcoGene:EG13313 putative membrane; Not classified GO_component: GO:0009274 -

peptidoglycan-based cell wall; GO_component: GO:0009279 - cell outer membrane 1 11 putative outer membrane protein AAC73812.2

RESULTS_MG1655

62 ^CHROM ^POS ^{ID REF ALT}

U00096 776966 . A G

G missense_variant MODERATE tolA b0739 transcript AAC73833.1 Coding 1/1 c.625A>G p.Lys209Glu 625/1266 625/1266 209/421 U00096 gene 776342-

777607

+ tolA b0739 lky EcoGene:EG11007

U00096 CDS 776342- 777607

+ tolA b0739 lky EcoGene:EG11007 membrane; Colicin-related functions membrane spanning protein, required for outer membrane integrity; GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component: GO:0019866 - organelle inner membrane 1 11 membrane anchored protein in TolA-TolQ-TolR complex AAC73833.1

RESULTS_MG1655

63 ^CHROM ^POS ^{ID REF ALT}

U00096 793746 . C T

T missense_variant MODERATE modF b0760 transcript AAC73847.1 Coding 1/1 c.43G>A p.Asp15Asn 43/1473 43/1473 15/490

T downstream_gene_variant MODIFIER modE b0761 transcript AAC73848.1 Coding c.*789G>A 110

U00096 gene 792316- 793788

- modF b0760 phrA EcoGene:EG11677

U00096 CDS 792316- 793788

- modF b0760 phrA EcoGene:EG11677 transport; Transport of small molecules: Anions ATP-binding component of molybdate transport system; GO_component: GO:0005737 - cytoplasm; GO_function: GO:0042888 - molybdenum ion transmembrane transporter activity; GO_process: GO:0006777 - Mo-molybdopterin cofactor biosynthetic process 1 11 molybdate ABC transporter ATPase AAC73847.1

RESULTS_MG1655

64 ^CHROM ^POS ^{ID REF ALT}

U00096 812748 . C T

T missense_variant MODERATE bioD b0778 transcript AAC73865.1 Coding 1/1 c.479C>T p.Ala160Val 479/678 479/678 160/225 U00096 gene 812270-

812947

+ bioD b0778 JW0761 EcoGene:EG10120

U00096 CDS 812270- 812947

+ bioD b0778 JW0761 EcoGene:EG10120 enzyme; Biosynthesis of cofactors, carriers: Biotin GO_process: GO:0009102 - biotin biosynthetic process 1 11 dethiobiotin synthetase AAC73865.1 6.3.3.3

RESULTS_MG1655

(14)

65 ^CHROM ^POS ^{ID REF ALT}

U00096 825538 . C T

T missense_variant MODERATE ybhR b0792 transcript AAC73879.1 Coding 1/1 c.571G>A p.Val191Ile 571/1107 571/1107 191/368 U00096 gene 825002-

826108

- ybhR b0792 JW5803 EcoGene:EG13674

U00096 CDS 825002- 826108

- ybhR b0792 JW5803 EcoGene:EG13674 GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component:

GO:0019866 - organelle inner membrane 1 11 putative ABC transporter permease AAC73879.1

RESULTS_MG1655

66 ^CHROM ^POS ^{ID REF ALT}

U00096 829147 . G A

A stop_gained HIGH ybhG b0795 transcript AAC73882.1 Coding 1/1 c.826C>T p.Gln276* 826/999 826/999 276/332

A upstream_gene_variant MODIFIER ybhF b0794 transcript AAC73881.2 Coding c.-1C>T 166

U00096 gene 828974- 829972

- ybhG b0795 JW0779 EcoGene:EG13315

U00096 CDS 828974- 829972

- ybhG b0795 JW0779 EcoGene:EG13315 putative membrane; Not classified putative membrane protein; GO_component:

GO:0009274 - peptidoglycan-based cell wall; GO_component: GO:0009279 - cell outer membrane 1 11 putative membrane fusion protein (MFP) component of efflux pump, membrane anchor AAC73882.1

RESULTS_MG1655

67 ^CHROM ^POS ^{ID REF ALT}

U00096 830043 . C A

A stop_gained HIGH ybiH b0796 transcript AAC73883.2 Coding 1/1 c.601G>T p.Glu201* 601/672 601/672 201/223

A upstream_gene_variant MODIFIER ybhG b0795 transcript AAC73882.1 Coding c.-1G>T 71

U00096 gene 829972- 830643

- ybiH b0796 JW0780 EcoGene:EG12406

U00096 CDS 829972- 830643

- ybiH b0796 JW0780 EcoGene:EG12406 putative regulator; Not classified putative transcriptional regulator;

GO_component: GO:0005737 - cytoplasm; GO_function: GO:0016564 - transcription repressor activity; GO_process:

GO:0006350 - transcription 1 11 DUF1956 domain-containing tetR family putative transcriptional regulator AAC73883.2

RESULTS_MG1655

68 ^CHROM ^POS ^{ID REF ALT}

U00096 895153 . G A

A missense_variant MODERATE potG b0855 transcript AAC73942.2 Coding 1/1 c.163G>A p.Gly55Ser 163/1134 163/1134 55/377 U00096 gene 894991-

896124

+ potG b0855 JW5818 EcoGene:EG11630

U00096 CDS 894991- 896124

+ potG b0855 JW5818 EcoGene:EG11630 transport; Transport of small molecules: Amino acids, amines ATP-binding component of putrescine transport system; GO_component: GO:0005737 - cytoplasm; GO_process: GO:0006596 - polyamine biosynthetic process; GO_process: GO:0009310 - amine catabolic process; GO_process: GO:0015847 - putrescine transport 1 11 putrescine ABC transporter ATPase AAC73942.2

RESULTS_MG1655

69 ^CHROM ^POS ^{ID REF ALT}

U00096 900090 . A T

T missense_variant MODERATE artJ b0860 transcript AAC73947.1 Coding 1/1 c.486T>A p.Asp162Glu 486/732 486/732 162/243

U00096 gene 899844- 900575

- artJ b0860 JW0844 EcoGene:EG11628

U00096 CDS 899844- - artJ b0860 JW0844 EcoGene:EG11628 transport; Transport of small molecules: Amino acids, amines arginine 3rd

(15)

900575 transport system periplasmic binding protein; GO_component: GO:0042597 - periplasmic space; GO_process:

GO:0006526 - arginine biosynthetic process 1 11 arginine ABC transporter periplasmic binding protein AAC73947.1

RESULTS_MG1655

70 ^CHROM ^POS ^{ID REF ALT}

U00096 913087 . C T

T missense_variant MODERATE hcp b0873 transcript AAC73960.2 Coding 1/1 c.728G>A p.Cys243Tyr 728/1653 728/1653 243/550 U00096 gene 912162-

913814

- hcp b0873 ybjW EcoGene:EG13692

U00096 CDS 912162- 913814

- hcp b0873 ybjW EcoGene:EG13692 orf; Not classified 1 11 hybrid-cluster [4Fe-2S-2O] subunit of anaerobic terminal reductases AAC73960.2

RESULTS_MG1655

71 ^CHROM ^POS ^{ID REF ALT}

U00096 937762 . G A

A missense_variant MODERATE lolA b0891 transcript AAC73977.2 Coding 1/1 c.391G>A p.Gly131Ser 391/612 391/612 131/203 U00096 gene 937372-

937983

+ lolA b0891 yzzV EcoGene:EG12684

U00096 CDS 937372- 937983

+ lolA b0891 yzzV EcoGene:EG12684 transport; Protein, peptide secretion periplasmic protein effects translocation of lipoproteins from inner membrane to outer; GO_component: GO:0042597 - periplasmic space 1 11 lipoprotein chaperone AAC73977.2

RESULTS_MG1655

72 ^CHROM ^POS ^{ID REF ALT}

U00096 943523 . G T

T missense_variant MODERATE dmsB b0895 transcript AAC73981.1 Coding 1/1 c.110G>T p.Arg37Leu 110/618 110/618 37/205

T downstream_gene_variant MODIFIER dmsA b0894 transcript AAC73980.2 Coding c.*2445G>T 120

U00096 gene 943414- 944031

+ dmsB b0895 JW0878 EcoGene:EG10233

U00096 CDS 943414- 944031

+ dmsB b0895 JW0878 EcoGene:EG10233 enzyme; Energy metabolism, carbon: Anaerobic respiration anaerobic dimethyl sulfoxide reductase subunit B; GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component:

GO:0019866 - organelle inner membrane; GO_process: GO:0009061 - anaerobic respiration 1 11 dimethyl sulfoxide reductase, anaerobic, subunit B AAC73981.1 1.8.99.-

RESULTS_MG1655

73 ^CHROM ^POS ^{ID REF ALT}

U00096 954462 . T C

C missense_variant MODERATE focA b0904 transcript AAC73990.1 Coding 1/1 c.5A>G p.Lys2Arg 5/858 5/858 2/285 U00096 gene 953609-

954466

- focA b0904 ycaE EcoGene:EG11258

U00096 CDS 953609- 954466

- focA b0904 ycaE EcoGene:EG11258 putative transport; Degradation of small molecules: Carbon compounds probable formate transporter (formate channel 1); GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component:

GO:0019866 - organelle inner membrane; GO_process: GO:0016052 - carbohydrate catabolic process 1 11 formate channel AAC73990.1

RESULTS_MG1655

RESULTS_CIM5N 13.2 . 10 1.436141e+00 0.5 1 3,5,1,1 60 16.1 1,3.2e-05,1,1 7.680000e-02 GT:PL:GQ 0/1:43,0,205:46

74 ^CHROM ^POS ^{ID REF ALT}

U00096 974632 . C A

A missense_variant MODERATE mukF b0922 transcript AAC74008.1 Coding 1/1 c.314C>A p.Pro105Gln 314/1323 314/1323 105/440

(16)

U00096 gene 974319- 975641

+ mukF b0922 kicB EcoGene:EG12165

U00096 CDS 974319- 975641

+ mukF b0922 kicB EcoGene:EG12165 factor; Cell killing mukF protein (killing factor KICB) 1 11 chromosome condensin MukBEF, kleisin-like subunit, binds calcium AAC74008.1

RESULTS_MG1655

75 ^CHROM ^POS ^{ID REF ALT}

U00096 1008814 . C T

T missense_variant MODERATE rlmL b0948 transcript AAC74034.1 Coding 1/1 c.971C>T p.Ala324Val 971/2109 971/2109 324/702 U00096 gene 1007844-

1009952

+ rlmL b0948 ycbY EcoGene:EG13717

U00096 CDS 1007844- 1009952

+ rlmL b0948 ycbY EcoGene:EG13717 enzyme; rRNA modification putative oxidoreductase 1 11 23S rRNA m(2)G2445 and m(7)G2069 methyltransferases, SAM-dependent AAC74034.1

RESULTS_MG1655

76 ^CHROM ^POS ^{ID REF ALT}

U00096 1032971 . C T

T missense_variant MODERATE hyaA b0972 transcript AAC74057.1 Coding 1/1 c.833C>T p.Thr278Ile 833/1119 833/1119 278/372 U00096 gene 1032139-

1033257

+ hyaA b0972 JW0954 EcoGene:EG10468

U00096 CDS 1032139- 1033257

+ hyaA b0972 JW0954 EcoGene:EG10468 enzyme; Energy metabolism, carbon: Aerobic respiration hydrogenase-1 small subunit; GO_component: GO:0019866 - organelle inner membrane; GO_process: GO:0009060 - aerobic respiration;

GO_process: GO:0009061 - anaerobic respiration 1 11 hydrogenase 1, small subunit AAC74057.1 1.12.99.6

RESULTS_MG1655

77 ^CHROM ^POS ^{ID REF ALT}

U00096 1047811 . C T

T missense_variant MODERATE gfcD b0984 transcript AAC74069.1 Coding 1/1 c.135G>A p.Met45Ile 135/2097 135/2097 45/698

T downstream_gene_variant MODIFIER gfcC b0985 transcript AAC74070.1 Coding c.*747G>A 134

U00096 gene 1045849- 1047945

- gfcD b0984 ymcA EcoGene:EG13729

U00096 CDS 1045849- 1047945

- gfcD b0984 ymcA EcoGene:EG13729 1 11 putative O-antigen capsule production periplasmic protein AAC74069.1

RESULTS_MG1655

78 ^CHROM ^POS ^{ID REF ALT}

U00096 1061195 . C T

T missense_variant MODERATE torA b0997 transcript AAC74082.1 Coding 1/1 c.1940C>T p.Pro647Leu 1940/2547 1940/2547 647/848 U00096 gene 1059256-

1061802

+ torA b0997 JW0982 EcoGene:EG11814

U00096 CDS 1059256- 1061802

+ torA b0997 JW0982 EcoGene:EG11814 enzyme; Energy metabolism, carbon: Anaerobic respiration trimethylamine N- oxide reductase subunit; GO_component: GO:0042597 - periplasmic space; GO_process: GO:0009061 - anaerobic respiration 1 11 trimethylamine N-oxide (TMAO) reductase I, catalytic subunit AAC74082.1 1.6.6.9

RESULTS_MG1655

79 ^CHROM ^POS ^{ID REF ALT}

U00096 1069647 . A G

G missense_variant MODERATE rutG b1006 transcript AAC74091.2 Coding 1/1 c.193T>C p.Ser65Pro 193/1329 193/1329 65/442

Non synonimous mutations found in sample: CIM5N