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_009909465.1_ASM990946v1	NZ_CP047658	Escherichia coli strain LD39-1 chromosome, complete genome	1	1052389-1053150	1,1,1	PILER-CR,CRISPRCasFinder,CRT	no		c2c9_V-U4,cas3,csa3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG,RT,WYL	Orphan	GAGTTCCCCGCGCCAGCGGGGATAAACCG,GAGTTCCCCGCGCCAGCGGGGATAAACCG,GAGTTCCCCGCGCCAGCGGGGATAAACCGN	29,29,30	0	0	NA	NA	I-E:I-E:I-E	11,11,12	12	Orphan	c2c9_V-U4,cas3,csa3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG,RT,WYL	NA,NA	NA|919aa|up_9|NZ_CP047658.1_1038982_1041739_-	PRK11107, PRK11107, hybrid sensory histidine kinase BarA; Provisional	NA|434aa|up_8|NZ_CP047658.1_1041795_1043097_+	PRK13168, rumA, 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD	NA|745aa|up_7|NZ_CP047658.1_1043144_1045379_+	PRK10872, relA, (p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional	NA|83aa|up_6|NZ_CP047658.1_1045456_1045705_+	PRK09798, PRK09798, MazF-MazE toxin-antitoxin system antitoxin MazE	NA|112aa|up_5|NZ_CP047658.1_1045704_1046040_+	PRK09907, PRK09907, endoribonuclease MazF	NA|264aa|up_4|NZ_CP047658.1_1046110_1046902_+	PRK09562, mazG, nucleoside triphosphate pyrophosphohydrolase; Reviewed	NA|546aa|up_3|NZ_CP047658.1_1047129_1048767_+	PRK05380, pyrG, CTP synthetase; Validated	NA|433aa|up_2|NZ_CP047658.1_1048854_1050153_+	PRK00077, eno, enolase; Provisional	NA|291aa|up_1|NZ_CP047658.1_1050212_1051085_-	COG1512, COG1512, Beta-propeller domains of methanol dehydrogenase type [General function prediction only]	NA|224aa|up_0|NZ_CP047658.1_1051378_1052050_+	TIGR04322, organic_radical_activating_enzyme, putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE	NA|371aa|down_0|NZ_CP047658.1_1053299_1054412_-	pfam01609, DDE_Tnp_1, Transposase DDE domain	NA|493aa|down_1|NZ_CP047658.1_1055748_1057227_-	cd07779, FGGY_ygcE_like, uncharacterized ygcE-like proteins	NA|426aa|down_2|NZ_CP047658.1_1057253_1058531_-	cd06174, MFS, Major Facilitator Superfamily	NA|262aa|down_3|NZ_CP047658.1_1058849_1059635_+	cd05347, Ga5DH-like_SDR_c, gluconate 5-dehydrogenase (Ga5DH)-like, classical (c) SDRs	NA|485aa|down_4|NZ_CP047658.1_1059704_1061159_+	COG0277, GlcD, FAD/FMN-containing dehydrogenases [Energy production and conversion]	NA|446aa|down_5|NZ_CP047658.1_1061252_1062590_+	cd17371, MFS_MucK, Cis,cis-muconate transport protein and similar proteins of the Major Facilitator Superfamily	NA|260aa|down_6|NZ_CP047658.1_1062567_1063347_+	COG2086, FixA, Electron transfer flavoprotein, beta subunit [Energy production and conversion]	NA|287aa|down_7|NZ_CP047658.1_1063343_1064204_+	COG2025, FixB, Electron transfer flavoprotein, alpha subunit [Energy production and conversion]	NA|192aa|down_8|NZ_CP047658.1_1064351_1064927_-	COG1954, GlpP, Glycerol-3-phosphate responsive antiterminator (mRNA-binding) [Transcription]	NA|87aa|down_9|NZ_CP047658.1_1064943_1065204_-	COG2440, FixX, Ferredoxin-like protein [Energy production and conversion]
GCF_009909465.1_ASM990946v1	NZ_CP047658	Escherichia coli strain LD39-1 chromosome, complete genome	2	1054472-1055110	2,2,2	CRISPRCasFinder,PILER-CR,CRT	no	cas3	c2c9_V-U4,cas3,csa3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG,RT,WYL	Unclear	GAGTTCCCCGCGCCAGCGGGGATAAACCG,GTTCCCCGCGCCAGCGGGGATAAACCG,GTTCCCCGCGCCAGCGGGGATAAACCG	29,27,27	0	0	NA	NA	I-E:I-E:I-E	10,10,10	10	Unclear	c2c9_V-U4,cas3,csa3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG,RT,WYL	NA,NA	NA|434aa|up_9|NZ_CP047658.1_1041795_1043097_+	PRK13168, rumA, 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD	NA|745aa|up_8|NZ_CP047658.1_1043144_1045379_+	PRK10872, relA, (p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional	NA|83aa|up_7|NZ_CP047658.1_1045456_1045705_+	PRK09798, PRK09798, MazF-MazE toxin-antitoxin system antitoxin MazE	NA|112aa|up_6|NZ_CP047658.1_1045704_1046040_+	PRK09907, PRK09907, endoribonuclease MazF	NA|264aa|up_5|NZ_CP047658.1_1046110_1046902_+	PRK09562, mazG, nucleoside triphosphate pyrophosphohydrolase; Reviewed	NA|546aa|up_4|NZ_CP047658.1_1047129_1048767_+	PRK05380, pyrG, CTP synthetase; Validated	NA|433aa|up_3|NZ_CP047658.1_1048854_1050153_+	PRK00077, eno, enolase; Provisional	NA|291aa|up_2|NZ_CP047658.1_1050212_1051085_-	COG1512, COG1512, Beta-propeller domains of methanol dehydrogenase type [General function prediction only]	NA|224aa|up_1|NZ_CP047658.1_1051378_1052050_+	TIGR04322, organic_radical_activating_enzyme, putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE	NA|371aa|up_0|NZ_CP047658.1_1053299_1054412_-	pfam01609, DDE_Tnp_1, Transposase DDE domain	NA|493aa|down_0|NZ_CP047658.1_1055748_1057227_-	cd07779, FGGY_ygcE_like, uncharacterized ygcE-like proteins	NA|426aa|down_1|NZ_CP047658.1_1057253_1058531_-	cd06174, MFS, Major Facilitator Superfamily	NA|262aa|down_2|NZ_CP047658.1_1058849_1059635_+	cd05347, Ga5DH-like_SDR_c, gluconate 5-dehydrogenase (Ga5DH)-like, classical (c) SDRs	NA|485aa|down_3|NZ_CP047658.1_1059704_1061159_+	COG0277, GlcD, FAD/FMN-containing dehydrogenases [Energy production and conversion]	NA|446aa|down_4|NZ_CP047658.1_1061252_1062590_+	cd17371, MFS_MucK, Cis,cis-muconate transport protein and similar proteins of the Major Facilitator Superfamily	NA|260aa|down_5|NZ_CP047658.1_1062567_1063347_+	COG2086, FixA, Electron transfer flavoprotein, beta subunit [Energy production and conversion]	NA|287aa|down_6|NZ_CP047658.1_1063343_1064204_+	COG2025, FixB, Electron transfer flavoprotein, alpha subunit [Energy production and conversion]	NA|192aa|down_7|NZ_CP047658.1_1064351_1064927_-	COG1954, GlpP, Glycerol-3-phosphate responsive antiterminator (mRNA-binding) [Transcription]	NA|87aa|down_8|NZ_CP047658.1_1064943_1065204_-	COG2440, FixX, Ferredoxin-like protein [Energy production and conversion]	NA|424aa|down_9|NZ_CP047658.1_1065194_1066466_-	PRK10015, PRK10015, oxidoreductase; Provisional
GCF_009909465.1_ASM990946v1	NZ_CP047658	Escherichia coli strain LD39-1 chromosome, complete genome	3	1080658-1080932	3,3,3	PILER-CR,CRISPRCasFinder,CRT	no	cas3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2	c2c9_V-U4,cas3,csa3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG,RT,WYL	Type I-E	GAGAGTTCCCCGCGCCAGCGGGGATAAACCGAT,GAGTTCCCCGCGCCAGCGGGGATAAACCG,GAGTTCCCCGCGCCAGCGGGGATAAACCG	33,29,29	0	0	NA	NA	I-E:I-E:I-E	2,4,4	4	TypeI-E	c2c9_V-U4,cas3,csa3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG,RT,WYL	NA,NA	NA|571aa|up_9|NZ_CP047658.1_1069023_1070736_+	PRK13504, PRK13504, NADPH-dependent assimilatory sulfite reductase hemoprotein subunit	NA|245aa|up_8|NZ_CP047658.1_1070810_1071545_+	PRK02090, PRK02090, phosphoadenylyl-sulfate reductase	cas3|889aa|up_7|NZ_CP047658.1_1071903_1074570_+	PRK09694, PRK09694, CRISPR-associated helicase/endonuclease Cas3	cas8e|503aa|up_6|NZ_CP047658.1_1074984_1076493_+	PRK09693, PRK09693, Cascade antiviral complex protein; Validated	cse2gr11|161aa|up_5|NZ_CP047658.1_1076485_1076968_+	cd09670, Cse2_I-E, CRISPR/Cas system-associated protein Cse2	cas7|364aa|up_4|NZ_CP047658.1_1076980_1078072_+	TIGR01869, CRISPR_system_Cascade_subunit_CasC, CRISPR-associated protein Cas7/Cse4/CasC, subtype I-E/ECOLI	cas5|225aa|up_3|NZ_CP047658.1_1078074_1078749_+	TIGR01868, hypothetical_protein, CRISPR-associated protein Cas5/CasD, subtype I-E/ECOLI	cas6e|200aa|up_2|NZ_CP047658.1_1078735_1079335_+	TIGR01907, CRISPR_system_Cascade_subunit_CasE, CRISPR-associated protein Cas6/Cse3/CasE, subtype I-E/ECOLI	cas1|306aa|up_1|NZ_CP047658.1_1079350_1080268_+	TIGR03638, cas1_ECOLI, CRISPR-associated endonuclease Cas1, subtype I-E/ECOLI	cas2|95aa|up_0|NZ_CP047658.1_1080269_1080554_+	PRK11558, PRK11558, putative ssRNA endonuclease; Provisional	NA|346aa|down_0|NZ_CP047658.1_1080952_1081990_-	PRK10199, PRK10199, alkaline phosphatase isozyme conversion aminopeptidase; Provisional	NA|303aa|down_1|NZ_CP047658.1_1082241_1083150_+	PRK05253, PRK05253, sulfate adenylyltransferase subunit CysD	NA|476aa|down_2|NZ_CP047658.1_1083151_1084579_+	PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional	NA|202aa|down_3|NZ_CP047658.1_1084578_1085184_+	PRK03846, PRK03846, adenylylsulfate kinase; Provisional	NA|108aa|down_4|NZ_CP047658.1_1085233_1085557_+	pfam12084, DUF3561, Protein of unknown function (DUF3561)	NA|104aa|down_5|NZ_CP047658.1_1085750_1086062_+	PRK00888, ftsB, cell division protein FtsB; Reviewed	NA|237aa|down_6|NZ_CP047658.1_1086080_1086791_+	PRK00155, ispD, D-ribitol-5-phosphate cytidylyltransferase	NA|160aa|down_7|NZ_CP047658.1_1086790_1087270_+	PRK00084, ispF, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; Reviewed	NA|350aa|down_8|NZ_CP047658.1_1087266_1088316_+	PRK00984, truD, tRNA pseudouridine synthase D; Reviewed	NA|254aa|down_9|NZ_CP047658.1_1088296_1089058_+	PRK00346, surE, 5'(3')-nucleotidase/polyphosphatase; Provisional
GCF_009909465.1_ASM990946v1	NZ_CP047658	Escherichia coli strain LD39-1 chromosome, complete genome	4	1573252-1573369	4	CRISPRCasFinder	no		c2c9_V-U4,cas3,csa3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG,RT,WYL	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,RT,WYL	NA,NA	NA|268aa|up_9|NZ_CP047658.1_1561887_1562691_+	PRK10128, PRK10128, 2-keto-3-deoxy-L-rhamnonate aldolase; Provisional	NA|301aa|up_8|NZ_CP047658.1_1562731_1563634_-	PRK09956, PRK09956, ISNCY family transposase	NA|397aa|up_7|NZ_CP047658.1_1563827_1565018_-	TIGR03379, glycerol3P_GlpC, glycerol-3-phosphate dehydrogenase, anaerobic, C subunit	NA|420aa|up_6|NZ_CP047658.1_1565014_1566274_-	COG3075, GlpB, Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]	NA|543aa|up_5|NZ_CP047658.1_1566263_1567892_-	PRK11101, glpA, anaerobic glycerol-3-phosphate dehydrogenase subunit A	NA|453aa|up_4|NZ_CP047658.1_1568164_1569523_+	PRK11273, glpT, glycerol-3-phosphate transporter	NA|359aa|up_3|NZ_CP047658.1_1569527_1570604_+	PRK11143, glpQ, glycerophosphodiester phosphodiesterase; Provisional	NA|217aa|up_2|NZ_CP047658.1_1571066_1571717_+	PRK09902, PRK09902, lipopolysaccharide kinase InaA	NA|85aa|up_1|NZ_CP047658.1_1571770_1572025_-	PRK10713, PRK10713, 2Fe-2S ferredoxin-like protein	NA|377aa|up_0|NZ_CP047658.1_1572024_1573155_-	PRK09101, nrdB, ribonucleotide-diphosphate reductase subunit beta; Reviewed	NA|762aa|down_0|NZ_CP047658.1_1573388_1575674_-	PRK09103, PRK09103, ribonucleoside-diphosphate reductase subunit alpha	NA|241aa|down_1|NZ_CP047658.1_1580249_1580972_-	PRK05134, PRK05134, bifunctional 2-polyprenyl-6-hydroxyphenol methylase/3-demethylubiquinol 3-O-methyltransferase UbiG	NA|876aa|down_2|NZ_CP047658.1_1581118_1583746_+	PRK05560, PRK05560, DNA gyrase subunit A; Validated	NA|563aa|down_3|NZ_CP047658.1_1583894_1585583_+	COG4685, COG4685, Uncharacterized protein conserved in bacteria [Function unknown]	NA|208aa|down_4|NZ_CP047658.1_1585579_1586203_+	COG3234, COG3234, Uncharacterized protein conserved in bacteria [Function unknown]	NA|1465aa|down_5|NZ_CP047658.1_1586346_1590741_+	COG2373, COG2373, Large extracellular alpha-helical protein [General function prediction only]	NA|550aa|down_6|NZ_CP047658.1_1590741_1592391_+	COG5445, COG5445, Predicted secreted protein [Function unknown]	NA|259aa|down_7|NZ_CP047658.1_1592395_1593172_+	COG4676, COG4676, Uncharacterized protein conserved in bacteria [Function unknown]	NA|395aa|down_8|NZ_CP047658.1_1593245_1594430_-	PRK05790, PRK05790, putative acyltransferase; Provisional	NA|441aa|down_9|NZ_CP047658.1_1594460_1595783_-	pfam02667, SCFA_trans, Short chain fatty acid transporter
GCF_009909465.1_ASM990946v1	NZ_CP047658	Escherichia coli strain LD39-1 chromosome, complete genome	5	2225564-2225687	5	CRISPRCasFinder	no	DEDDh	c2c9_V-U4,cas3,csa3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG,RT,WYL	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,RT,WYL	NA,NA|30aa|down_7|NZ_CP047658.1_2234583_2234673_+	NA|471aa|up_9|NZ_CP047658.1_2215018_2216431_-	PRK09206, PRK09206, pyruvate kinase PykF	NA|70aa|up_8|NZ_CP047658.1_2216987_2217197_+	PRK10292, PRK10292, fumarate hydratase FumD	NA|209aa|up_7|NZ_CP047658.1_2217651_2218278_+	PRK09898, PRK09898, ferredoxin-like protein	NA|701aa|up_6|NZ_CP047658.1_2218298_2220401_+	PRK09849, PRK09849, putative oxidoreductase; Provisional	NA|216aa|up_5|NZ_CP047658.1_2220404_2221052_+	PRK09947, PRK09947, YdhW family putative oxidoreductase system protein	NA|223aa|up_4|NZ_CP047658.1_2221115_2221784_+	TIGR03149, cyt_nit_nrfC, cytochrome c nitrite reductase, Fe-S protein	NA|262aa|up_3|NZ_CP047658.1_2221780_2222566_+	PRK15006, PRK15006, thiosulfate reductase cytochrome B subunit; Provisional	NA|271aa|up_2|NZ_CP047658.1_2222569_2223382_+	PRK09946, PRK09946, hypothetical protein; Provisional	NA|535aa|up_1|NZ_CP047658.1_2223393_2224998_-	PRK09897, PRK09897, FAD-NAD(P)-binding protein	NA|102aa|up_0|NZ_CP047658.1_2225123_2225429_-	PRK11118, PRK11118, putative monooxygenase; Provisional	NA|419aa|down_0|NZ_CP047658.1_2226001_2227258_+	PRK09945, PRK09945, hypothetical protein; Provisional	NA|458aa|down_1|NZ_CP047658.1_2227298_2228672_-	PRK01766, PRK01766, multidrug efflux protein; Reviewed	NA|214aa|down_2|NZ_CP047658.1_2228886_2229528_+	PRK13020, PRK13020, riboflavin synthase subunit alpha; Provisional	NA|383aa|down_3|NZ_CP047658.1_2229567_2230716_-	PRK11705, PRK11705, cyclopropane fatty acyl phospholipid synthase	NA|404aa|down_4|NZ_CP047658.1_2231006_2232218_-	PRK11043, PRK11043, Bcr/CflA family multidrug efflux MFS transporter	NA|311aa|down_5|NZ_CP047658.1_2232330_2233263_+	PRK11074, PRK11074, putative DNA-binding transcriptional regulator; Provisional	NA|342aa|down_6|NZ_CP047658.1_2233259_2234285_-	PRK10703, PRK10703, HTH-type transcriptional repressor PurR	NA|30aa|down_7|NZ_CP047658.1_2234583_2234673_+	NA	NA|390aa|down_8|NZ_CP047658.1_2234838_2236008_+	COG2814, AraJ, Arabinose efflux permease [Carbohydrate transport and metabolism]	NA|194aa|down_9|NZ_CP047658.1_2236153_2236735_-	PRK10543, PRK10543, superoxide dismutase [Fe]
GCF_009909465.1_ASM990946v1	NZ_CP047658	Escherichia coli strain LD39-1 chromosome, complete genome	6	2953241-2953332	6	CRISPRCasFinder	no		c2c9_V-U4,cas3,csa3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG,RT,WYL	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,RT,WYL	NA|70aa|up_9|NZ_CP047658.1_2942315_2942525_-,NA	NA|70aa|up_9|NZ_CP047658.1_2942315_2942525_-	NA	NA|1321aa|up_8|NZ_CP047658.1_2942579_2946542_+	PRK11809, putA, trifunctional transcriptional regulator/proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed	NA|213aa|up_7|NZ_CP047658.1_2946581_2947220_-	PRK15008, PRK15008, HTH-type transcriptional regulator RutR; Provisional	NA|364aa|up_6|NZ_CP047658.1_2947508_2948600_+	TIGR03612, RutA, pyrimidine utilization protein A	NA|231aa|up_5|NZ_CP047658.1_2948599_2949292_+	TIGR03614, RutB, pyrimidine utilization protein B	NA|129aa|up_4|NZ_CP047658.1_2949303_2949690_+	TIGR03610, RutC, pyrimidine utilization protein C	NA|267aa|up_3|NZ_CP047658.1_2949697_2950498_+	TIGR03611, RutD, pyrimidine utilization protein D	NA|197aa|up_2|NZ_CP047658.1_2950507_2951098_+	PRK05365, PRK05365, malonic semialdehyde reductase; Provisional	NA|165aa|up_1|NZ_CP047658.1_2951108_2951603_+	TIGR03615, flavoprotein_oxidoreductase, pyrimidine utilization flavin reductase protein F	NA|443aa|up_0|NZ_CP047658.1_2951623_2952952_+	TIGR03616, Putative_pyrimidine_permease_RutG, pyrimidine utilization transport protein G	NA|199aa|down_0|NZ_CP047658.1_2953755_2954352_+	PRK03767, PRK03767, NAD(P)H:quinone oxidoreductase; Provisional	NA|76aa|down_1|NZ_CP047658.1_2954372_2954600_+	PRK10174, PRK10174, hypothetical protein; Provisional	NA|414aa|down_2|NZ_CP047658.1_2954819_2956061_-	PRK10173, PRK10173, glucose-1-phosphatase/inositol phosphatase; Provisional	NA|419aa|down_3|NZ_CP047658.1_2956353_2957610_-	PRK09784, PRK09784, YccE family protein	NA|307aa|down_4|NZ_CP047658.1_2957870_2958791_+	PRK10266, PRK10266, curved DNA-binding protein	NA|102aa|down_5|NZ_CP047658.1_2958790_2959096_+	PRK10265, PRK10265, chaperone modulator CbpM	NA|200aa|down_6|NZ_CP047658.1_2959247_2959847_-	PRK04976, torD, chaperone protein TorD; Validated	NA|849aa|down_7|NZ_CP047658.1_2959843_2962390_-	PRK15102, PRK15102, trimethylamine-N-oxide reductase TorA	NA|391aa|down_8|NZ_CP047658.1_2962389_2963562_-	PRK15032, PRK15032, pentaheme c-type cytochrome TorC	NA|231aa|down_9|NZ_CP047658.1_2963691_2964384_+	PRK10766, PRK10766, two-component system response regulator TorR
GCF_009909465.1_ASM990946v1	NZ_CP047658	Escherichia coli strain LD39-1 chromosome, complete genome	7	3095024-3095229	7,4,4	CRISPRCasFinder,CRT,PILER-CR	no		c2c9_V-U4,cas3,csa3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG,RT,WYL	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,RT,WYL	NA,NA	NA|431aa|up_9|NZ_CP047658.1_3080147_3081440_-	PRK05431, PRK05431, seryl-tRNA synthetase; Provisional	NA|448aa|up_8|NZ_CP047658.1_3081530_3082874_-	PRK13342, PRK13342, recombination factor protein RarA; Reviewed	NA|204aa|up_7|NZ_CP047658.1_3082884_3083496_-	TIGR00547, Outer-membrane_lipoprotein_carrier_protein, periplasmic chaperone LolA	NA|1330aa|up_6|NZ_CP047658.1_3083650_3087640_-	PRK10263, PRK10263, DNA translocase FtsK; Provisional	NA|165aa|up_5|NZ_CP047658.1_3087774_3088269_-	PRK11169, PRK11169, leucine-responsive transcriptional regulator Lrp	NA|322aa|up_4|NZ_CP047658.1_3088813_3089779_+	PRK10262, PRK10262, thioredoxin reductase; Provisional	NA|589aa|up_3|NZ_CP047658.1_3089901_3091668_+	PRK11174, PRK11174, cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed	NA|574aa|up_2|NZ_CP047658.1_3091668_3093390_+	PRK11160, PRK11160, cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed	NA|235aa|up_1|NZ_CP047658.1_3093431_3094136_+	PRK00301, aat, leucyl/phenylalanyl-tRNA--protein transferase; Reviewed	NA|73aa|up_0|NZ_CP047658.1_3094420_3094639_+	PRK00276, infA, translation initiation factor IF-1; Validated	NA|759aa|down_0|NZ_CP047658.1_3095437_3097714_-	PRK11034, clpA, ATP-dependent Clp protease ATP-binding subunit; Provisional	NA|107aa|down_1|NZ_CP047658.1_3097744_3098065_-	PRK00033, clpS, ATP-dependent Clp protease adaptor protein ClpS; Reviewed	NA|75aa|down_2|NZ_CP047658.1_3098387_3098612_+	PRK09937, PRK09937, cold shock-like protein CspD	NA|649aa|down_3|NZ_CP047658.1_3098684_3100631_-	PRK10535, PRK10535, macrolide ABC transporter ATP-binding protein/permease MacB	NA|372aa|down_4|NZ_CP047658.1_3100627_3101743_-	PRK11578, PRK11578, macrolide transporter subunit MacA; Provisional	NA|319aa|down_5|NZ_CP047658.1_3101893_3102850_+	COG2990, VirK, Uncharacterized protein conserved in bacteria [Function unknown]	NA|553aa|down_6|NZ_CP047658.1_3102846_3104505_-	COG3593, COG3593, Predicted ATP-dependent endonuclease of the OLD family [DNA replication, recombination, and repair]	NA|232aa|down_7|NZ_CP047658.1_3104929_3105625_+	PRK05420, PRK05420, aquaporin Z; Provisional	NA|300aa|down_8|NZ_CP047658.1_3106119_3107019_+	COG2431, COG2431, Predicted membrane protein [Function unknown]	NA|551aa|down_9|NZ_CP047658.1_3107162_3108815_+	PRK05290, PRK05290, hybrid cluster protein; Provisional
GCF_009909465.1_ASM990946v1	NZ_CP047658	Escherichia coli strain LD39-1 chromosome, complete genome	8	3215302-3215446	8	CRISPRCasFinder	no		c2c9_V-U4,cas3,csa3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG,RT,WYL	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,RT,WYL	NA,NA	NA|330aa|up_9|NZ_CP047658.1_3203200_3204190_-	PRK00164, moaA, GTP 3',8-cyclase MoaA	NA|303aa|up_8|NZ_CP047658.1_3204586_3205495_+	TIGR01826, Putative_gluconeogenesis_factor, conserved hypothetical protein, cofD-related	NA|674aa|up_7|NZ_CP047658.1_3205686_3207708_-	PRK05298, PRK05298, excinuclease ABC subunit UvrB	NA|226aa|up_6|NZ_CP047658.1_3208286_3208964_-	PRK00090, bioD, ATP-dependent dethiobiotin synthetase BioD	NA|252aa|up_5|NZ_CP047658.1_3208956_3209712_-	PRK10258, PRK10258, biotin biosynthesis protein BioC; Provisional	NA|385aa|up_4|NZ_CP047658.1_3209698_3210853_-	PRK05958, PRK05958, 8-amino-7-oxononanoate synthase; Reviewed	NA|347aa|up_3|NZ_CP047658.1_3210849_3211890_-	PRK15108, PRK15108, biotin synthase; Provisional	NA|430aa|up_2|NZ_CP047658.1_3211976_3213266_+	PRK07986, PRK07986, adenosylmethionine--8-amino-7-oxononanoate transaminase; Validated	NA|159aa|up_1|NZ_CP047658.1_3213324_3213801_+	PRK10257, PRK10257, putative kinase inhibitor protein; Provisional	NA|428aa|up_0|NZ_CP047658.1_3213952_3215236_+	PRK10531, PRK10531, putative acyl-CoA thioester hydrolase	NA|754aa|down_0|NZ_CP047658.1_3215469_3217731_-	PRK11413, PRK11413, putative hydratase; Provisional	NA|478aa|down_1|NZ_CP047658.1_3217913_3219347_-	pfam00939, Na_sulph_symp, Sodium:sulfate symporter transmembrane region	NA|351aa|down_2|NZ_CP047658.1_3219422_3220475_-	NF033377, OMA_tautomer, 4-oxalomesaconate tautomerase	NA|318aa|down_3|NZ_CP047658.1_3220658_3221612_+	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_CP047658.1_3221652_3222648_-	PRK11028, PRK11028, 6-phosphogluconolactonase; Provisional	NA|273aa|down_5|NZ_CP047658.1_3222802_3223621_+	PRK10530, PRK10530, pyridoxal phosphate (PLP) phosphatase; Provisional	NA|353aa|down_6|NZ_CP047658.1_3223621_3224680_-	PRK11144, modC, molybdenum ABC transporter ATP-binding protein ModC	NA|230aa|down_7|NZ_CP047658.1_3224682_3225372_-	PRK09421, modB, molybdate ABC transporter permease subunit	NA|258aa|down_8|NZ_CP047658.1_3225371_3226145_-	PRK10677, modA, molybdate transporter periplasmic protein; Provisional	NA|50aa|down_9|NZ_CP047658.1_3226311_3226461_-	pfam10766, AcrZ, Multidrug efflux pump-associated protein AcrZ
GCF_009909465.1_ASM990946v1	NZ_CP047658	Escherichia coli strain LD39-1 chromosome, complete genome	9	3593793-3593937	9	CRISPRCasFinder	no		c2c9_V-U4,cas3,csa3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG,RT,WYL	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,RT,WYL	NA,NA|28aa|down_2|NZ_CP047658.1_3595982_3596066_-	NA|357aa|up_9|NZ_CP047658.1_3578934_3580005_-	PRK00147, queA, S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional	NA|194aa|up_8|NZ_CP047658.1_3580097_3580679_+	PRK10045, PRK10045, ACP phosphodiesterase	NA|606aa|up_7|NZ_CP047658.1_3580683_3582501_-	PRK10785, PRK10785, maltodextrin glucosidase; Provisional	NA|458aa|up_6|NZ_CP047658.1_3582656_3584030_-	PRK10580, proY, putative proline-specific permease; Provisional	NA|440aa|up_5|NZ_CP047658.1_3584105_3585425_-	PRK15433, PRK15433, branched-chain amino acid transporter carrier protein BrnQ	NA|432aa|up_4|NZ_CP047658.1_3585831_3587127_-	PRK11006, phoR, phosphate regulon sensor histidine kinase PhoR	NA|230aa|up_3|NZ_CP047658.1_3587184_3587874_-	PRK10161, PRK10161, phosphate response regulator transcription factor PhoB	NA|401aa|up_2|NZ_CP047658.1_3588063_3589266_+	PRK10966, PRK10966, exonuclease subunit SbcD; Provisional	NA|1048aa|up_1|NZ_CP047658.1_3589262_3592406_+	PRK10246, PRK10246, exonuclease subunit SbcC; Provisional	NA|395aa|up_0|NZ_CP047658.1_3592531_3593716_+	PRK10091, PRK10091, MFS transport protein AraJ; Provisional	NA|303aa|down_0|NZ_CP047658.1_3593960_3594869_-	PRK09557, PRK09557, fructokinase; Reviewed	NA|304aa|down_1|NZ_CP047658.1_3594993_3595905_+	COG2974, RdgC, DNA recombination-dependent growth factor C [DNA replication, recombination, and repair]	NA|28aa|down_2|NZ_CP047658.1_3595982_3596066_-	NA	NA|95aa|down_3|NZ_CP047658.1_3596551_3596836_-	PRK10579, PRK10579, pyrimidine/purine nucleoside phosphorylase	NA|226aa|down_4|NZ_CP047658.1_3596907_3597585_-	PRK10481, PRK10481, hypothetical protein; Provisional	NA|64aa|down_5|NZ_CP047658.1_3597842_3598034_-	PRK10380, PRK10380, hypothetical protein; Provisional	NA|175aa|down_6|NZ_CP047658.1_3598083_3598608_-	PRK03731, aroL, shikimate kinase AroL	NA|155aa|down_7|NZ_CP047658.1_3598784_3599249_-	PRK00124, PRK00124, YaiI/YqxD family protein	NA|270aa|down_8|NZ_CP047658.1_3599368_3600178_+	PRK11880, PRK11880, pyrroline-5-carboxylate reductase; Reviewed	NA|372aa|down_9|NZ_CP047658.1_3600194_3601310_-	PRK10245, adrA, diguanylate cyclase AdrA; Provisional
GCF_009909465.1_ASM990946v1	NZ_CP047658	Escherichia coli strain LD39-1 chromosome, complete genome	10	3781418-3781514	10	CRISPRCasFinder	no	DEDDh	c2c9_V-U4,cas3,csa3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG,RT,WYL	Unclear	GCCAGCGTCGCATCAGGCATCCGCGCA	27	0	0	NA	NA	NA	1	1	Orphan	c2c9_V-U4,cas3,csa3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG,RT,WYL	NA,NA	NA|549aa|up_9|NZ_CP047658.1_3771692_3773339_-	PRK07193, fliF, flagellar MS-ring protein; Reviewed	NA|114aa|up_8|NZ_CP047658.1_3773343_3773685_-	pfam02049, FliE, Flagellar hook-basal body complex protein FliE	NA|329aa|up_7|NZ_CP047658.1_3773699_3774686_-	COG2204, AtoC, Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]	NA|284aa|up_6|NZ_CP047658.1_3775072_3775924_+	pfam01052, FliMN_C, Type III flagellar switch regulator (C-ring) FliN C-term	NA|124aa|up_5|NZ_CP047658.1_3775916_3776288_+	TIGR02480, Flagellar_motor_switch_protein_FliN, flagellar motor switch protein FliN	NA|251aa|up_4|NZ_CP047658.1_3776284_3777037_+	PRK05699, fliP, flagellar biosynthesis protein FliP; Reviewed	NA|91aa|up_3|NZ_CP047658.1_3777039_3777312_+	COG1987, FliQ, Flagellar biosynthesis pathway, component FliQ [Cell motility and secretion / Intracellular trafficking and secretion]	NA|261aa|up_2|NZ_CP047658.1_3777313_3778096_+	COG1684, FliR, Flagellar biosynthesis pathway, component FliR [Cell motility and secretion / Intracellular trafficking and secretion]	NA|380aa|up_1|NZ_CP047658.1_3778085_3779225_+	PRK05702, flhB, flagellar type III secretion system protein FlhB	NA|698aa|up_0|NZ_CP047658.1_3779208_3781302_+	COG1298, FlhA, Flagellar biosynthesis pathway, component FlhA [Cell motility and secretion / Intracellular trafficking and secretion]	NA|166aa|down_0|NZ_CP047658.1_3781517_3782015_-	COG1943, COG1943, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|258aa|down_1|NZ_CP047658.1_3782190_3782964_-	COG0791, Spr, Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]	NA|87aa|down_2|NZ_CP047658.1_3783149_3783410_+	COG3077, RelB, DNA-damage-inducible protein J [DNA replication, recombination, and repair]	NA|93aa|down_3|NZ_CP047658.1_3783412_3783691_+	COG3041, COG3041, Uncharacterized protein conserved in bacteria [Function unknown]	NA|247aa|down_4|NZ_CP047658.1_3783846_3784587_+	COG3034, COG3034, Uncharacterized protein conserved in bacteria [Function unknown]	NA|256aa|down_5|NZ_CP047658.1_3784557_3785325_-	pfam13230, GATase_4, Glutamine amidotransferases class-II	NA|193aa|down_6|NZ_CP047658.1_3785530_3786109_-	PRK00414, gmhA, D-sedoheptulose 7-phosphate isomerase	NA|815aa|down_7|NZ_CP047658.1_3786348_3788793_+	PRK09463, fadE, acyl-CoA dehydrogenase; Reviewed	NA|158aa|down_8|NZ_CP047658.1_3788835_3789309_-	PRK09993, PRK09993, C-lysozyme inhibitor; Provisional	NA|257aa|down_9|NZ_CP047658.1_3789462_3790233_+	PRK10438, PRK10438, C-N hydrolase family amidase; Provisional
GCF_009909465.1_ASM990946v1	NZ_CP047658	Escherichia coli strain LD39-1 chromosome, complete genome	11	3901002-3901133	11	CRISPRCasFinder	no		c2c9_V-U4,cas3,csa3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG,RT,WYL	Orphan	AATGCAGACTAACCCGCAGATCCAGCAGCGAAGAGA	36	0	0	NA	NA	NA	1	1	Orphan	c2c9_V-U4,cas3,csa3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG,RT,WYL	NA,NA	NA|309aa|up_9|NZ_CP047658.1_3887116_3888043_-	COG1131, CcmA, ABC-type multidrug transport system, ATPase component [Defense mechanisms]	NA|221aa|up_8|NZ_CP047658.1_3888151_3888814_+	PRK10437, PRK10437, carbonic anhydrase; Provisional	NA|179aa|up_7|NZ_CP047658.1_3888854_3889391_-	PRK15423, PRK15423, hypoxanthine phosphoribosyltransferase; Provisional	NA|797aa|up_6|NZ_CP047658.1_3889596_3891987_+	TIGR03074, PQQ_membr_DH, membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family	NA|517aa|up_5|NZ_CP047658.1_3892188_3893739_-	PRK10965, PRK10965, multicopper oxidase; Provisional	NA|116aa|up_4|NZ_CP047658.1_3893904_3894252_+	pfam09691, T2SS_PulS_OutS, Type II secretion system pilotin lipoprotein (PulS_OutS)	NA|289aa|up_3|NZ_CP047658.1_3894357_3895224_+	PRK00811, PRK00811, polyamine aminopropyltransferase	NA|265aa|up_2|NZ_CP047658.1_3895239_3896034_+	PRK05462, PRK05462, adenosylmethionine decarboxylase	NA|121aa|up_1|NZ_CP047658.1_3896070_3896433_-	PRK05248, PRK05248, hypothetical protein; Provisional	NA|866aa|up_0|NZ_CP047658.1_3896607_3899205_-	PRK09238, PRK09238, bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase; Validated	NA|475aa|down_0|NZ_CP047658.1_3901483_3902908_-	PRK06467, PRK06467, dihydrolipoamide dehydrogenase; Reviewed	NA|631aa|down_1|NZ_CP047658.1_3903232_3905125_-	PRK11854, aceF, pyruvate dehydrogenase dihydrolipoyltransacetylase; Validated	NA|888aa|down_2|NZ_CP047658.1_3905139_3907803_-	PRK09405, aceE, pyruvate dehydrogenase subunit E1; Reviewed	NA|255aa|down_3|NZ_CP047658.1_3907963_3908728_-	PRK09464, pdhR, pyruvate dehydrogenase complex transcriptional repressor PdhR	NA|457aa|down_4|NZ_CP047658.1_3909271_3910642_+	PRK10238, PRK10238, aromatic amino acid transporter AroP	NA|285aa|down_5|NZ_CP047658.1_3910684_3911539_-	pfam17113, AmpE, Regulatory signalling modulator protein AmpE	NA|184aa|down_6|NZ_CP047658.1_3911535_3912087_-	PRK11789, PRK11789, 1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD	NA|298aa|down_7|NZ_CP047658.1_3912174_3913068_+	PRK09016, PRK09016, carboxylating nicotinate-nucleotide diphosphorylase	NA|147aa|down_8|NZ_CP047658.1_3913270_3913711_+	PRK10574, PRK10574, putative major pilin subunit; Provisional	NA|462aa|down_9|NZ_CP047658.1_3913720_3915106_+	PRK10436, PRK10436, hypothetical protein; Provisional
