assembly_id	genome_id	genome_def	crispr_array_locus_merge	crispr_array_location_merge	crispr_locus_id	crispr_pred_method	array_in_prot	prot_within_array_20000	prot_in_genome	crispr_type_by_cas_prot	consensus_repeat	repeat_length	self-targeting_spacer_number	self-targeting_target_number	spacer_location	protospacer_location	repeat_type	spacer_locus_num	spacer_num	correct_crispr_type	genome_cas_prots	unknown_protein_around_crispr	L10	L10_domain	L9	L9_domain	L8	L8_domain	L7	L7_domain	L6	L6_domain	L5	L5_domain	L4	L4_domain	L3	L3_domain	L2	L2_domain	L1	L1_domain	R1	R1_domain	R2	R2_domain	R3	R3_domain	R4	R4_domain	R5	R5_domain	R6	R6_domain	R7	R7_domain	R8	R8_domain	R9	R9_domain	R10	R10_domain
GCF_000599645.1_ASM59964v1	NZ_CP007391	Escherichia coli strain ST540 chromosome, complete genome	1	1093660-1094909	1,1,1	PILER-CR,CRISPRCasFinder,CRT	no		c2c9_V-U4,cas3,csa3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG	Orphan	GTGTTCCCCGCGCCAGCGGGGATAAACCG,GTGTTCCCCGCGCCAGCGGGGATAAACCG,GTGTTCCCCGCGCCAGCGGGGATAAACCG	29,29,29	0	0	NA	NA	I-E:I-E:I-E	19,20,20	20	Orphan	c2c9_V-U4,cas3,csa3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG	NA|47aa|up_1|NZ_CP007391.1_1092369_1092510_-,NA	NA|434aa|up_9|NZ_CP007391.1_1083066_1084368_+	PRK13168, rumA, 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD	NA|745aa|up_8|NZ_CP007391.1_1084415_1086650_+	PRK10872, relA, (p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional	NA|83aa|up_7|NZ_CP007391.1_1086727_1086976_+	PRK09798, PRK09798, MazF-MazE toxin-antitoxin system antitoxin MazE	NA|112aa|up_6|NZ_CP007391.1_1086975_1087311_+	PRK09907, PRK09907, endoribonuclease MazF	NA|264aa|up_5|NZ_CP007391.1_1087381_1088173_+	PRK09562, mazG, nucleoside triphosphate pyrophosphohydrolase; Reviewed	NA|546aa|up_4|NZ_CP007391.1_1088400_1090038_+	PRK05380, pyrG, CTP synthetase; Validated	NA|433aa|up_3|NZ_CP007391.1_1090125_1091424_+	PRK00077, eno, enolase; Provisional	NA|291aa|up_2|NZ_CP007391.1_1091483_1092356_-	COG1512, COG1512, Beta-propeller domains of methanol dehydrogenase type [General function prediction only]	NA|47aa|up_1|NZ_CP007391.1_1092369_1092510_-	NA	NA|224aa|up_0|NZ_CP007391.1_1092648_1093320_+	TIGR04322, organic_radical_activating_enzyme, putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE	NA|493aa|down_0|NZ_CP007391.1_1095547_1097026_-	cd07779, FGGY_ygcE_like, uncharacterized ygcE-like proteins	NA|426aa|down_1|NZ_CP007391.1_1097052_1098330_-	cd06174, MFS, Major Facilitator Superfamily	NA|262aa|down_2|NZ_CP007391.1_1098648_1099434_+	cd05347, Ga5DH-like_SDR_c, gluconate 5-dehydrogenase (Ga5DH)-like, classical (c) SDRs	NA|485aa|down_3|NZ_CP007391.1_1099503_1100958_+	COG0277, GlcD, FAD/FMN-containing dehydrogenases [Energy production and conversion]	NA|470aa|down_4|NZ_CP007391.1_1100979_1102389_+	cd17371, MFS_MucK, Cis,cis-muconate transport protein and similar proteins of the Major Facilitator Superfamily	NA|260aa|down_5|NZ_CP007391.1_1102366_1103146_+	COG2086, FixA, Electron transfer flavoprotein, beta subunit [Energy production and conversion]	NA|287aa|down_6|NZ_CP007391.1_1103142_1104003_+	COG2025, FixB, Electron transfer flavoprotein, alpha subunit [Energy production and conversion]	NA|192aa|down_7|NZ_CP007391.1_1104150_1104726_-	COG1954, GlpP, Glycerol-3-phosphate responsive antiterminator (mRNA-binding) [Transcription]	NA|87aa|down_8|NZ_CP007391.1_1104742_1105003_-	COG2440, FixX, Ferredoxin-like protein [Energy production and conversion]	NA|424aa|down_9|NZ_CP007391.1_1104993_1106265_-	PRK10015, PRK10015, oxidoreductase; Provisional
GCF_000599645.1_ASM59964v1	NZ_CP007391	Escherichia coli strain ST540 chromosome, complete genome	2	1121719-1122235	2,2	CRISPRCasFinder,PILER-CR	no	cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2	c2c9_V-U4,cas3,csa3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG	Type I-E	GTGTTCCCCGCGCCAGCGGGGATAAACCG,GTTCCCCGCGTCAGCGGGGATAAACCG	29,27	0	0	NA	NA	I-E:I-E	8,8	8	TypeI-E	c2c9_V-U4,cas3,csa3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG	NA,NA	NA|245aa|up_9|NZ_CP007391.1_1110608_1111343_+	PRK02090, PRK02090, phosphoadenylyl-sulfate reductase	NA|100aa|up_8|NZ_CP007391.1_1113204_1113504_+	pfam01527, HTH_Tnp_1, Transposase	NA|289aa|up_7|NZ_CP007391.1_1113500_1114367_+	PHA02517, PHA02517, putative transposase OrfB; Reviewed	cas8e|503aa|up_6|NZ_CP007391.1_1116043_1117552_+	PRK09693, PRK09693, Cascade antiviral complex protein; Validated	cse2gr11|161aa|up_5|NZ_CP007391.1_1117544_1118027_+	cd09670, Cse2_I-E, CRISPR/Cas system-associated protein Cse2	cas7|364aa|up_4|NZ_CP007391.1_1118039_1119131_+	TIGR01869, CRISPR_system_Cascade_subunit_CasC, CRISPR-associated protein Cas7/Cse4/CasC, subtype I-E/ECOLI	cas5|225aa|up_3|NZ_CP007391.1_1119133_1119808_+	TIGR01868, hypothetical_protein, CRISPR-associated protein Cas5/CasD, subtype I-E/ECOLI	cas6e|200aa|up_2|NZ_CP007391.1_1119794_1120394_+	TIGR01907, CRISPR_system_Cascade_subunit_CasE, CRISPR-associated protein Cas6/Cse3/CasE, subtype I-E/ECOLI	cas1|306aa|up_1|NZ_CP007391.1_1120409_1121327_+	TIGR03638, cas1_ECOLI, CRISPR-associated endonuclease Cas1, subtype I-E/ECOLI	cas2|95aa|up_0|NZ_CP007391.1_1121328_1121613_+	PRK11558, PRK11558, putative ssRNA endonuclease; Provisional	NA|346aa|down_0|NZ_CP007391.1_1122316_1123354_-	PRK10199, PRK10199, alkaline phosphatase isozyme conversion aminopeptidase; Provisional	NA|303aa|down_1|NZ_CP007391.1_1123605_1124514_+	PRK05253, PRK05253, sulfate adenylyltransferase subunit CysD	NA|476aa|down_2|NZ_CP007391.1_1124515_1125943_+	PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional	NA|202aa|down_3|NZ_CP007391.1_1125942_1126548_+	PRK03846, PRK03846, adenylylsulfate kinase; Provisional	NA|108aa|down_4|NZ_CP007391.1_1126597_1126921_+	pfam12084, DUF3561, Protein of unknown function (DUF3561)	NA|104aa|down_5|NZ_CP007391.1_1127114_1127426_+	PRK00888, ftsB, cell division protein FtsB; Reviewed	NA|237aa|down_6|NZ_CP007391.1_1127444_1128155_+	PRK00155, ispD, D-ribitol-5-phosphate cytidylyltransferase	NA|160aa|down_7|NZ_CP007391.1_1128154_1128634_+	PRK00084, ispF, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; Reviewed	NA|350aa|down_8|NZ_CP007391.1_1128630_1129680_+	PRK00984, truD, tRNA pseudouridine synthase D; Reviewed	NA|254aa|down_9|NZ_CP007391.1_1129660_1130422_+	PRK00346, surE, 5'(3')-nucleotidase/polyphosphatase; Provisional
GCF_000599645.1_ASM59964v1	NZ_CP007391	Escherichia coli strain ST540 chromosome, complete genome	3	1660260-1660377	3	CRISPRCasFinder	no		c2c9_V-U4,cas3,csa3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG	Orphan	CCGAGCCGTAGGCCGGATAAGGCGTTCACGC	31	0	0	NA	NA	NA	1	1	Orphan	c2c9_V-U4,cas3,csa3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG	NA,NA	NA|268aa|up_9|NZ_CP007391.1_1648895_1649699_+	PRK10128, PRK10128, 2-keto-3-deoxy-L-rhamnonate aldolase; Provisional	NA|301aa|up_8|NZ_CP007391.1_1649739_1650642_-	PRK09956, PRK09956, ISNCY family transposase	NA|397aa|up_7|NZ_CP007391.1_1650835_1652026_-	TIGR03379, glycerol3P_GlpC, glycerol-3-phosphate dehydrogenase, anaerobic, C subunit	NA|420aa|up_6|NZ_CP007391.1_1652022_1653282_-	COG3075, GlpB, Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]	NA|543aa|up_5|NZ_CP007391.1_1653271_1654900_-	PRK11101, glpA, anaerobic glycerol-3-phosphate dehydrogenase subunit A	NA|453aa|up_4|NZ_CP007391.1_1655172_1656531_+	PRK11273, glpT, glycerol-3-phosphate transporter	NA|359aa|up_3|NZ_CP007391.1_1656535_1657612_+	PRK11143, glpQ, glycerophosphodiester phosphodiesterase; Provisional	NA|217aa|up_2|NZ_CP007391.1_1658074_1658725_+	PRK09902, PRK09902, lipopolysaccharide kinase InaA	NA|85aa|up_1|NZ_CP007391.1_1658778_1659033_-	PRK10713, PRK10713, 2Fe-2S ferredoxin-like protein	NA|377aa|up_0|NZ_CP007391.1_1659032_1660163_-	PRK09101, nrdB, ribonucleotide-diphosphate reductase subunit beta; Reviewed	NA|762aa|down_0|NZ_CP007391.1_1660396_1662682_-	PRK09103, PRK09103, ribonucleoside-diphosphate reductase subunit alpha	NA|1245aa|down_1|NZ_CP007391.1_1663377_1667112_+	PRK09752, PRK09752, AIDA-I family autotransporter YfaL	NA|241aa|down_2|NZ_CP007391.1_1667239_1667962_-	PRK05134, PRK05134, bifunctional 2-polyprenyl-6-hydroxyphenol methylase/3-demethylubiquinol 3-O-methyltransferase UbiG	NA|876aa|down_3|NZ_CP007391.1_1668108_1670736_+	PRK05560, PRK05560, DNA gyrase subunit A; Validated	NA|563aa|down_4|NZ_CP007391.1_1670884_1672573_+	COG4685, COG4685, Uncharacterized protein conserved in bacteria [Function unknown]	NA|208aa|down_5|NZ_CP007391.1_1672569_1673193_+	COG3234, COG3234, Uncharacterized protein conserved in bacteria [Function unknown]	NA|1465aa|down_6|NZ_CP007391.1_1673336_1677731_+	COG2373, COG2373, Large extracellular alpha-helical protein [General function prediction only]	NA|550aa|down_7|NZ_CP007391.1_1677731_1679381_+	COG5445, COG5445, Predicted secreted protein [Function unknown]	NA|259aa|down_8|NZ_CP007391.1_1679385_1680162_+	COG4676, COG4676, Uncharacterized protein conserved in bacteria [Function unknown]	NA|950aa|down_9|NZ_CP007391.1_1680436_1683286_+	PRK10841, PRK10841, two-component system sensor histidine kinase RcsC
GCF_000599645.1_ASM59964v1	NZ_CP007391	Escherichia coli strain ST540 chromosome, complete genome	4	2231672-2231795	4	CRISPRCasFinder	no	DEDDh	c2c9_V-U4,cas3,csa3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG	Unclear	CGACCCCCACCATGTCAAGGTGGTGCTCTAACCAACTGAGCTA	43	0	0	NA	NA	NA	1	1	Orphan	c2c9_V-U4,cas3,csa3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG	NA,NA|30aa|down_7|NZ_CP007391.1_2240691_2240781_+	NA|471aa|up_9|NZ_CP007391.1_2221126_2222539_-	PRK09206, PRK09206, pyruvate kinase PykF	NA|70aa|up_8|NZ_CP007391.1_2223095_2223305_+	PRK10292, PRK10292, fumarate hydratase FumD	NA|209aa|up_7|NZ_CP007391.1_2223759_2224386_+	PRK09898, PRK09898, ferredoxin-like protein	NA|701aa|up_6|NZ_CP007391.1_2224406_2226509_+	PRK09849, PRK09849, putative oxidoreductase; Provisional	NA|213aa|up_5|NZ_CP007391.1_2226521_2227160_+	PRK09947, PRK09947, YdhW family putative oxidoreductase system protein	NA|223aa|up_4|NZ_CP007391.1_2227223_2227892_+	TIGR03149, cyt_nit_nrfC, cytochrome c nitrite reductase, Fe-S protein	NA|262aa|up_3|NZ_CP007391.1_2227888_2228674_+	PRK15006, PRK15006, thiosulfate reductase cytochrome B subunit; Provisional	NA|271aa|up_2|NZ_CP007391.1_2228677_2229490_+	PRK09946, PRK09946, hypothetical protein; Provisional	NA|535aa|up_1|NZ_CP007391.1_2229501_2231106_-	PRK09897, PRK09897, FAD-NAD(P)-binding protein	NA|102aa|up_0|NZ_CP007391.1_2231231_2231537_-	PRK11118, PRK11118, putative monooxygenase; Provisional	NA|419aa|down_0|NZ_CP007391.1_2232109_2233366_+	PRK09945, PRK09945, hypothetical protein; Provisional	NA|458aa|down_1|NZ_CP007391.1_2233406_2234780_-	PRK01766, PRK01766, multidrug efflux protein; Reviewed	NA|214aa|down_2|NZ_CP007391.1_2234994_2235636_+	PRK13020, PRK13020, riboflavin synthase subunit alpha; Provisional	NA|383aa|down_3|NZ_CP007391.1_2235675_2236824_-	PRK11705, PRK11705, cyclopropane fatty acyl phospholipid synthase	NA|404aa|down_4|NZ_CP007391.1_2237114_2238326_-	PRK11043, PRK11043, Bcr/CflA family multidrug efflux MFS transporter	NA|311aa|down_5|NZ_CP007391.1_2238438_2239371_+	PRK11074, PRK11074, putative DNA-binding transcriptional regulator; Provisional	NA|342aa|down_6|NZ_CP007391.1_2239367_2240393_-	PRK10703, PRK10703, HTH-type transcriptional repressor PurR	NA|30aa|down_7|NZ_CP007391.1_2240691_2240781_+	NA	NA|390aa|down_8|NZ_CP007391.1_2240946_2242116_+	COG2814, AraJ, Arabinose efflux permease [Carbohydrate transport and metabolism]	NA|194aa|down_9|NZ_CP007391.1_2242350_2242932_-	PRK10543, PRK10543, superoxide dismutase [Fe]
GCF_000599645.1_ASM59964v1	NZ_CP007391	Escherichia coli strain ST540 chromosome, complete genome	5	2883115-2883206	5	CRISPRCasFinder	no		c2c9_V-U4,cas3,csa3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG	Orphan	CCACCTTTTTTACCTGCTTCAGATGC	26	0	0	NA	NA	NA	1	1	Orphan	c2c9_V-U4,cas3,csa3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG	NA|70aa|up_9|NZ_CP007391.1_2872192_2872402_-,NA	NA|70aa|up_9|NZ_CP007391.1_2872192_2872402_-	NA	NA|1321aa|up_8|NZ_CP007391.1_2872456_2876419_+	PRK11809, putA, trifunctional transcriptional regulator/proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed	NA|213aa|up_7|NZ_CP007391.1_2876457_2877096_-	PRK15008, PRK15008, HTH-type transcriptional regulator RutR; Provisional	NA|364aa|up_6|NZ_CP007391.1_2877383_2878475_+	TIGR03612, RutA, pyrimidine utilization protein A	NA|231aa|up_5|NZ_CP007391.1_2878474_2879167_+	TIGR03614, RutB, pyrimidine utilization protein B	NA|129aa|up_4|NZ_CP007391.1_2879178_2879565_+	TIGR03610, RutC, pyrimidine utilization protein C	NA|267aa|up_3|NZ_CP007391.1_2879572_2880373_+	TIGR03611, RutD, pyrimidine utilization protein D	NA|197aa|up_2|NZ_CP007391.1_2880382_2880973_+	PRK05365, PRK05365, malonic semialdehyde reductase; Provisional	NA|165aa|up_1|NZ_CP007391.1_2880983_2881478_+	TIGR03615, flavoprotein_oxidoreductase, pyrimidine utilization flavin reductase protein F	NA|443aa|up_0|NZ_CP007391.1_2881498_2882827_+	TIGR03616, Putative_pyrimidine_permease_RutG, pyrimidine utilization transport protein G	NA|199aa|down_0|NZ_CP007391.1_2883629_2884226_+	PRK03767, PRK03767, NAD(P)H:quinone oxidoreductase; Provisional	NA|76aa|down_1|NZ_CP007391.1_2884246_2884474_+	PRK10174, PRK10174, hypothetical protein; Provisional	NA|414aa|down_2|NZ_CP007391.1_2884511_2885753_-	PRK10173, PRK10173, glucose-1-phosphatase/inositol phosphatase; Provisional	NA|417aa|down_3|NZ_CP007391.1_2886047_2887298_-	PRK09784, PRK09784, YccE family protein	NA|307aa|down_4|NZ_CP007391.1_2887557_2888478_+	PRK10266, PRK10266, curved DNA-binding protein	NA|102aa|down_5|NZ_CP007391.1_2888477_2888783_+	PRK10265, PRK10265, chaperone modulator CbpM	NA|200aa|down_6|NZ_CP007391.1_2888934_2889534_-	PRK04976, torD, chaperone protein TorD; Validated	NA|849aa|down_7|NZ_CP007391.1_2889530_2892077_-	PRK15102, PRK15102, trimethylamine-N-oxide reductase TorA	NA|391aa|down_8|NZ_CP007391.1_2892076_2893249_-	PRK15032, PRK15032, pentaheme c-type cytochrome TorC	NA|231aa|down_9|NZ_CP007391.1_2893378_2894071_+	PRK10766, PRK10766, two-component system response regulator TorR
GCF_000599645.1_ASM59964v1	NZ_CP007391	Escherichia coli strain ST540 chromosome, complete genome	6	3025473-3025678	6,2,3	CRISPRCasFinder,CRT,PILER-CR	no		c2c9_V-U4,cas3,csa3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG	Orphan	TTTCTAAGCTGCCTGTACGGCAGTGAAC,TTTCTAAGCTGCCTGTACGGCAGTGAAC,TTTCTAAGCTGCCTGTACGGCAGTGAACG	28,28,29	0	0	NA	NA	I-F:I-F:I-F	3,3,2	3	Orphan	c2c9_V-U4,cas3,csa3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG	NA,NA	NA|431aa|up_9|NZ_CP007391.1_3010596_3011889_-	PRK05431, PRK05431, seryl-tRNA synthetase; Provisional	NA|448aa|up_8|NZ_CP007391.1_3011979_3013323_-	PRK13342, PRK13342, recombination factor protein RarA; Reviewed	NA|204aa|up_7|NZ_CP007391.1_3013333_3013945_-	TIGR00547, Outer-membrane_lipoprotein_carrier_protein, periplasmic chaperone LolA	NA|1330aa|up_6|NZ_CP007391.1_3014099_3018089_-	PRK10263, PRK10263, DNA translocase FtsK; Provisional	NA|165aa|up_5|NZ_CP007391.1_3018223_3018718_-	PRK11169, PRK11169, leucine-responsive transcriptional regulator Lrp	NA|322aa|up_4|NZ_CP007391.1_3019262_3020228_+	PRK10262, PRK10262, thioredoxin reductase; Provisional	NA|589aa|up_3|NZ_CP007391.1_3020350_3022117_+	PRK11174, PRK11174, cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed	NA|574aa|up_2|NZ_CP007391.1_3022117_3023839_+	PRK11160, PRK11160, cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed	NA|235aa|up_1|NZ_CP007391.1_3023880_3024585_+	PRK00301, aat, leucyl/phenylalanyl-tRNA--protein transferase; Reviewed	NA|73aa|up_0|NZ_CP007391.1_3024869_3025088_+	PRK00276, infA, translation initiation factor IF-1; Validated	NA|759aa|down_0|NZ_CP007391.1_3025888_3028165_-	PRK11034, clpA, ATP-dependent Clp protease ATP-binding subunit; Provisional	NA|107aa|down_1|NZ_CP007391.1_3028195_3028516_-	PRK00033, clpS, ATP-dependent Clp protease adaptor protein ClpS; Reviewed	NA|75aa|down_2|NZ_CP007391.1_3028838_3029063_+	PRK09937, PRK09937, cold shock-like protein CspD	NA|649aa|down_3|NZ_CP007391.1_3029135_3031082_-	PRK10535, PRK10535, macrolide ABC transporter ATP-binding protein/permease MacB	NA|372aa|down_4|NZ_CP007391.1_3031078_3032194_-	PRK11578, PRK11578, macrolide transporter subunit MacA; Provisional	NA|319aa|down_5|NZ_CP007391.1_3032344_3033301_+	COG2990, VirK, Uncharacterized protein conserved in bacteria [Function unknown]	NA|553aa|down_6|NZ_CP007391.1_3033297_3034956_-	COG3593, COG3593, Predicted ATP-dependent endonuclease of the OLD family [DNA replication, recombination, and repair]	NA|300aa|down_7|NZ_CP007391.1_3036533_3037433_+	COG2431, COG2431, Predicted membrane protein [Function unknown]	NA|551aa|down_8|NZ_CP007391.1_3037576_3039229_+	PRK05290, PRK05290, hybrid cluster protein; Provisional	NA|323aa|down_9|NZ_CP007391.1_3039240_3040209_+	PRK10684, PRK10684, HCP oxidoreductase, NADH-dependent; Provisional
GCF_000599645.1_ASM59964v1	NZ_CP007391	Escherichia coli strain ST540 chromosome, complete genome	7	3190968-3191112	7	CRISPRCasFinder	no		c2c9_V-U4,cas3,csa3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG	Orphan	GTAGGTCGGATAAGATGCGCAAGCATCGCATCCGACAATAAGTGCCGGATGC	52	0	0	NA	NA	NA	1	1	Orphan	c2c9_V-U4,cas3,csa3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG	NA|147aa|up_8|NZ_CP007391.1_3186060_3186501_+,NA|79aa|up_7|NZ_CP007391.1_3186497_3186734_+,NA|106aa|up_6|NZ_CP007391.1_3186730_3187048_+,NA|56aa|up_3|NZ_CP007391.1_3188010_3188178_+,NA	NA|55aa|up_9|NZ_CP007391.1_3185899_3186064_+	pfam10930, DUF2737, Protein of unknown function (DUF2737)	NA|147aa|up_8|NZ_CP007391.1_3186060_3186501_+	NA	NA|79aa|up_7|NZ_CP007391.1_3186497_3186734_+	NA	NA|106aa|up_6|NZ_CP007391.1_3186730_3187048_+	NA	NA|180aa|up_5|NZ_CP007391.1_3187034_3187574_+	pfam04448, DUF551, Protein of unknown function (DUF551)	NA|93aa|up_4|NZ_CP007391.1_3187573_3187852_+	pfam15944, DUF4752, Domain of unknown function (DUF4752)	NA|56aa|up_3|NZ_CP007391.1_3188010_3188178_+	NA	NA|73aa|up_2|NZ_CP007391.1_3188217_3188436_+	pfam07825, Exc, Excisionase-like protein	NA|357aa|up_1|NZ_CP007391.1_3188413_3189484_+	cd00800, INT_Lambda_C, C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase	NA|428aa|up_0|NZ_CP007391.1_3189618_3190902_+	PRK10531, PRK10531, putative acyl-CoA thioester hydrolase	NA|754aa|down_0|NZ_CP007391.1_3191135_3193397_-	PRK11413, PRK11413, putative hydratase; Provisional	NA|478aa|down_1|NZ_CP007391.1_3193579_3195013_-	pfam00939, Na_sulph_symp, Sodium:sulfate symporter transmembrane region	NA|351aa|down_2|NZ_CP007391.1_3195088_3196141_-	NF033377, OMA_tautomer, 4-oxalomesaconate tautomerase	NA|318aa|down_3|NZ_CP007391.1_3196324_3197278_+	cd08440, PBP2_LTTR_like_4, TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold	NA|332aa|down_4|NZ_CP007391.1_3197318_3198314_-	PRK11028, PRK11028, 6-phosphogluconolactonase; Provisional	NA|273aa|down_5|NZ_CP007391.1_3198468_3199287_+	PRK10530, PRK10530, pyridoxal phosphate (PLP) phosphatase; Provisional	NA|353aa|down_6|NZ_CP007391.1_3199287_3200346_-	PRK11144, modC, molybdenum ABC transporter ATP-binding protein ModC	NA|230aa|down_7|NZ_CP007391.1_3200348_3201038_-	PRK09421, modB, molybdate ABC transporter permease subunit	NA|258aa|down_8|NZ_CP007391.1_3201037_3201811_-	PRK10677, modA, molybdate transporter periplasmic protein; Provisional	NA|50aa|down_9|NZ_CP007391.1_3201977_3202127_-	pfam10766, AcrZ, Multidrug efflux pump-associated protein AcrZ
GCF_000599645.1_ASM59964v1	NZ_CP007391	Escherichia coli strain ST540 chromosome, complete genome	8	3428877-3428973	8	CRISPRCasFinder	no		c2c9_V-U4,cas3,csa3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG	Orphan	TTGTAGGCCTGATAAGATGCGTCAAGC	27	0	0	NA	NA	NA	1	1	Orphan	c2c9_V-U4,cas3,csa3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG	NA,NA	NA|231aa|up_9|NZ_CP007391.1_3420672_3421365_-	PRK15195, PRK15195, molecular chaperone FimC	NA|181aa|up_8|NZ_CP007391.1_3421584_3422127_-	PRK15194, PRK15194, type 1 fimbrial protein subunit FimA	NA|289aa|up_7|NZ_CP007391.1_3422597_3423464_+	PRK10792, PRK10792, bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD	NA|71aa|up_6|NZ_CP007391.1_3423465_3423678_+	PRK11507, PRK11507, ribosome-associated protein YbcJ	NA|174aa|up_5|NZ_CP007391.1_3423785_3424307_+	COG1988, COG1988, Predicted membrane-bound metal-dependent hydrolases [General function prediction only]	NA|462aa|up_4|NZ_CP007391.1_3424342_3425728_-	PRK00260, cysS, cysteinyl-tRNA synthetase; Validated	NA|165aa|up_3|NZ_CP007391.1_3425901_3426396_+	PRK10791, PRK10791, peptidylprolyl isomerase B	NA|241aa|up_2|NZ_CP007391.1_3426398_3427121_+	PRK05340, PRK05340, UDP-2,3-diacylglucosamine hydrolase; Provisional	NA|170aa|up_1|NZ_CP007391.1_3427238_3427748_+	COG0041, PurE, Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase [Nucleotide transport and metabolism]	NA|356aa|up_0|NZ_CP007391.1_3427744_3428812_+	PRK06019, PRK06019, phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed	NA|298aa|down_0|NZ_CP007391.1_3429016_3429910_-	PRK09411, PRK09411, carbamate kinase; Reviewed	NA|272aa|down_1|NZ_CP007391.1_3429906_3430722_-	pfam11392, DUF2877, Protein of unknown function (DUF2877)	NA|420aa|down_2|NZ_CP007391.1_3430732_3431992_-	pfam06545, DUF1116, Protein of unknown function (DUF1116)	NA|556aa|down_3|NZ_CP007391.1_3432001_3433669_-	PRK06091, PRK06091, membrane protein FdrA; Validated	NA|350aa|down_4|NZ_CP007391.1_3433985_3435035_+	PRK15025, PRK15025, ureidoglycolate dehydrogenase; Provisional	NA|412aa|down_5|NZ_CP007391.1_3435056_3436292_+	TIGR03176, AllC, allantoate amidohydrolase	NA|262aa|down_6|NZ_CP007391.1_3436302_3437088_+	TIGR03214, ura-cupin, putative allantoin catabolism protein	NA|382aa|down_7|NZ_CP007391.1_3437315_3438461_-	PRK09932, PRK09932, glycerate 3-kinase	NA|434aa|down_8|NZ_CP007391.1_3438482_3439784_-	PRK11412, PRK11412, uracil/xanthine transporter	NA|454aa|down_9|NZ_CP007391.1_3439840_3441202_-	PRK08044, PRK08044, allantoinase AllB
GCF_000599645.1_ASM59964v1	NZ_CP007391	Escherichia coli strain ST540 chromosome, complete genome	9	3562539-3562683	9	CRISPRCasFinder	no		c2c9_V-U4,cas3,csa3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG	Orphan	TTTTGTAGGCCTGATAAGACGCGACAAGCGTCGCATCAGGCAT	43	0	0	NA	NA	NA	1	1	Orphan	c2c9_V-U4,cas3,csa3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG	NA,NA|28aa|down_2|NZ_CP007391.1_3564728_3564812_-	NA|357aa|up_9|NZ_CP007391.1_3547680_3548751_-	PRK00147, queA, S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional	NA|194aa|up_8|NZ_CP007391.1_3548843_3549425_+	PRK10045, PRK10045, ACP phosphodiesterase	NA|606aa|up_7|NZ_CP007391.1_3549429_3551247_-	PRK10785, PRK10785, maltodextrin glucosidase; Provisional	NA|458aa|up_6|NZ_CP007391.1_3551402_3552776_-	PRK10580, proY, putative proline-specific permease; Provisional	NA|440aa|up_5|NZ_CP007391.1_3552851_3554171_-	PRK15433, PRK15433, branched-chain amino acid transporter carrier protein BrnQ	NA|432aa|up_4|NZ_CP007391.1_3554577_3555873_-	PRK11006, phoR, phosphate regulon sensor histidine kinase PhoR	NA|230aa|up_3|NZ_CP007391.1_3555930_3556620_-	PRK10161, PRK10161, phosphate response regulator transcription factor PhoB	NA|401aa|up_2|NZ_CP007391.1_3556809_3558012_+	PRK10966, PRK10966, exonuclease subunit SbcD; Provisional	NA|1048aa|up_1|NZ_CP007391.1_3558008_3561152_+	PRK10246, PRK10246, exonuclease subunit SbcC; Provisional	NA|395aa|up_0|NZ_CP007391.1_3561277_3562462_+	PRK10091, PRK10091, MFS transport protein AraJ; Provisional	NA|303aa|down_0|NZ_CP007391.1_3562706_3563615_-	PRK09557, PRK09557, fructokinase; Reviewed	NA|304aa|down_1|NZ_CP007391.1_3563739_3564651_+	COG2974, RdgC, DNA recombination-dependent growth factor C [DNA replication, recombination, and repair]	NA|28aa|down_2|NZ_CP007391.1_3564728_3564812_-	NA	NA|95aa|down_3|NZ_CP007391.1_3565298_3565583_-	PRK10579, PRK10579, pyrimidine/purine nucleoside phosphorylase	NA|226aa|down_4|NZ_CP007391.1_3565654_3566332_-	PRK10481, PRK10481, hypothetical protein; Provisional	NA|64aa|down_5|NZ_CP007391.1_3566589_3566781_-	PRK10380, PRK10380, hypothetical protein; Provisional	NA|175aa|down_6|NZ_CP007391.1_3566830_3567355_-	PRK03731, aroL, shikimate kinase AroL	NA|155aa|down_7|NZ_CP007391.1_3567531_3567996_-	PRK00124, PRK00124, YaiI/YqxD family protein	NA|270aa|down_8|NZ_CP007391.1_3568115_3568925_+	PRK11880, PRK11880, pyrroline-5-carboxylate reductase; Reviewed	NA|372aa|down_9|NZ_CP007391.1_3568941_3570057_-	PRK10245, adrA, diguanylate cyclase AdrA; Provisional
GCF_000599645.1_ASM59964v1	NZ_CP007391	Escherichia coli strain ST540 chromosome, complete genome	10	3964513-3964642	10	CRISPRCasFinder	no		c2c9_V-U4,cas3,csa3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG	Orphan	GCTGGAGAGCAACCGTAGGCCGGATAAGATGCGCCAGCAT	40	0	0	NA	NA	NA	1	1	Orphan	c2c9_V-U4,cas3,csa3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG	NA,NA	NA|177aa|up_9|NZ_CP007391.1_3950698_3951229_-	PRK00871, PRK00871, glutathione-regulated potassium-efflux system oxidoreductase KefF	NA|453aa|up_8|NZ_CP007391.1_3951310_3952669_-	cd17316, MFS_SV2_like, Metazoan Synaptic vesicle glycoprotein 2 (SV2) and related small molecule transporters of the Major Facilitator Superfamily	NA|96aa|up_7|NZ_CP007391.1_3952727_3953015_-	PRK15449, PRK15449, ferredoxin-like protein FixX; Provisional	NA|429aa|up_6|NZ_CP007391.1_3953011_3954298_-	PRK10157, PRK10157, putative oxidoreductase FixC; Provisional	NA|314aa|up_5|NZ_CP007391.1_3954348_3955290_-	PRK03363, fixB, electron transfer flavoprotein subunit alpha/FixB family protein	NA|381aa|up_4|NZ_CP007391.1_3958869_3960012_+	PRK03354, PRK03354, crotonobetainyl-CoA dehydrogenase; Validated	NA|406aa|up_3|NZ_CP007391.1_3960140_3961358_+	PRK03525, PRK03525, L-carnitine CoA-transferase	NA|518aa|up_2|NZ_CP007391.1_3961431_3962985_+	PRK08008, caiC, putative crotonobetaine/carnitine-CoA ligase; Validated	NA|262aa|up_1|NZ_CP007391.1_3963093_3963879_+	PRK03580, PRK03580, crotonobetainyl-CoA hydratase	NA|197aa|up_0|NZ_CP007391.1_3963884_3964475_+	PRK13627, PRK13627, carnitine operon protein CaiE; Provisional	NA|132aa|down_0|NZ_CP007391.1_3964683_3965079_-	PRK11476, PRK11476, carnitine metabolism transcriptional regulator CaiF	NA|1074aa|down_1|NZ_CP007391.1_3965340_3968562_-	PRK05294, carB, carbamoyl-phosphate synthase large subunit	NA|383aa|down_2|NZ_CP007391.1_3968579_3969728_-	PRK12564, PRK12564, carbamoyl-phosphate synthase small subunit	NA|274aa|down_3|NZ_CP007391.1_3970183_3971005_-	COG0289, DapB, Dihydrodipicolinate reductase [Amino acid transport and metabolism]	NA|305aa|down_4|NZ_CP007391.1_3971171_3972086_-	PRK10768, PRK10768, ribonucleoside hydrolase RihC; Provisional	NA|317aa|down_5|NZ_CP007391.1_3972151_3973102_-	PRK01045, ispH, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed	NA|150aa|down_6|NZ_CP007391.1_3973103_3973553_-	PRK15095, PRK15095, FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional	NA|165aa|down_7|NZ_CP007391.1_3973677_3974172_-	PRK00376, lspA, lipoprotein signal peptidase	NA|939aa|down_8|NZ_CP007391.1_3974171_3976988_-	PRK05743, ileS, isoleucyl-tRNA synthetase; Reviewed	NA|314aa|down_9|NZ_CP007391.1_3977030_3977972_-	PRK05627, PRK05627, bifunctional riboflavin kinase/FAD synthetase
GCF_000599645.1_ASM59964v1	NZ_CP007391	Escherichia coli strain ST540 chromosome, complete genome	11	4262090-4262239	11	CRISPRCasFinder	no		c2c9_V-U4,cas3,csa3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG	Orphan	TGAACGCCTTATCCGACCTACACAGCACTGAACTCGTAGGCCTGATAAGACGCG	54	0	0	NA	NA	NA	1	1	Orphan	c2c9_V-U4,cas3,csa3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG	NA|191aa|up_6|NZ_CP007391.1_4253021_4253594_+,NA|528aa|down_6|NZ_CP007391.1_4269435_4271019_-	NA|256aa|up_9|NZ_CP007391.1_4249854_4250622_+	PRK11231, fecE, Fe(3+) dicitrate ABC transporter ATP-binding protein FecE	NA|86aa|up_8|NZ_CP007391.1_4251179_4251437_-	COG2085, COG2085, Predicted dinucleotide-binding enzymes [General function prediction only]	NA|117aa|up_7|NZ_CP007391.1_4252570_4252921_-	COG2963, COG2963, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|191aa|up_6|NZ_CP007391.1_4253021_4253594_+	NA	NA|275aa|up_5|NZ_CP007391.1_4253642_4254467_-	pfam18863, AbiJ_NTD4, AbiJ N-terminal domain 4	NA|340aa|up_4|NZ_CP007391.1_4255280_4256300_+	cd05283, CAD1, Cinnamyl alcohol dehydrogenases (CAD)	NA|501aa|up_3|NZ_CP007391.1_4256429_4257932_+	pfam05872, DUF853, Bacterial protein of unknown function (DUF853)	NA|361aa|up_2|NZ_CP007391.1_4258092_4259175_-	PRK15071, PRK15071, lipopolysaccharide ABC transporter permease; Provisional	NA|367aa|up_1|NZ_CP007391.1_4259174_4260275_-	PRK15120, PRK15120, lipopolysaccharide ABC transporter permease LptF; Provisional	NA|504aa|up_0|NZ_CP007391.1_4260541_4262053_+	PRK00913, PRK00913, multifunctional aminopeptidase A; Provisional	NA|148aa|down_0|NZ_CP007391.1_4262406_4262850_+	PRK05728, PRK05728, DNA polymerase III subunit chi; Validated	NA|952aa|down_1|NZ_CP007391.1_4262849_4265705_+	PRK05729, valS, valyl-tRNA synthetase; Reviewed	NA|399aa|down_2|NZ_CP007391.1_4265758_4266955_-	COG4269, COG4269, Predicted membrane protein [Function unknown]	NA|168aa|down_3|NZ_CP007391.1_4267147_4267651_+	pfam00583, Acetyltransf_1, Acetyltransferase (GNAT) family	NA|139aa|down_4|NZ_CP007391.1_4267696_4268113_-	PRK11191, PRK11191, ribonuclease E inhibitor RraB	NA|335aa|down_5|NZ_CP007391.1_4268274_4269279_+	PRK03515, PRK03515, ornithine carbamoyltransferase subunit I; Provisional	NA|528aa|down_6|NZ_CP007391.1_4269435_4271019_-	NA	NA|151aa|down_7|NZ_CP007391.1_4271141_4271594_-	COG2731, EbgC, Beta-galactosidase, beta subunit [Carbohydrate transport and metabolism]	NA|198aa|down_8|NZ_CP007391.1_4271738_4272332_-	COG1309, AcrR, Transcriptional regulator [Transcription]	NA|238aa|down_9|NZ_CP007391.1_4272402_4273116_+	PRK12742, PRK12742, SDR family oxidoreductase
