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_001900945.1_ASM190094v1	NZ_CP010235	Escherichia coli strain S40 chromosome, complete genome	1	776408-776525	1	CRISPRCasFinder	no		cas3,csa3,PD-DExK,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,c2c9_V-U4,DinG	Orphan	TGCCGGATGCGATGCTGGCGCACCTTATCCGGCCTACGGG	40	0	0	NA	NA	NA	1	1	Orphan	cas3,csa3,PD-DExK,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,c2c9_V-U4,DinG	NA,NA|55aa|down_0|NZ_CP010235.1_776598_776763_-	NA|115aa|up_9|NZ_CP010235.1_764129_764474_-	PRK11424, PRK11424, DNA-binding transcriptional activator TdcR; Provisional	NA|313aa|up_8|NZ_CP010235.1_764662_765601_+	PRK10341, PRK10341, transcriptional regulator TdcA	NA|330aa|up_7|NZ_CP010235.1_765699_766689_+	PRK08638, PRK08638, bifunctional threonine ammonia-lyase/L-serine ammonia-lyase TdcB	NA|444aa|up_6|NZ_CP010235.1_766710_768042_+	PRK13629, PRK13629, threonine/serine transporter TdcC; Provisional	NA|403aa|up_5|NZ_CP010235.1_768067_769276_+	PRK12379, PRK12379, propionate kinase	NA|765aa|up_4|NZ_CP010235.1_769309_771604_+	cd01678, PFL1, Pyruvate formate lyase 1	NA|130aa|up_3|NZ_CP010235.1_771617_772007_+	PRK11401, PRK11401, enamine/imine deaminase	NA|455aa|up_2|NZ_CP010235.1_772078_773443_+	PRK15040, PRK15040, L-serine ammonia-lyase	NA|444aa|up_1|NZ_CP010235.1_773717_775049_+	TIGR00814, membrane_transport_protein_YhjV, serine transporter	NA|437aa|up_0|NZ_CP010235.1_775076_776387_+	COG3681, COG3681, L-cysteine desulfidase [Amino acid transport and metabolism]	NA|55aa|down_0|NZ_CP010235.1_776598_776763_-	NA	NA|234aa|down_1|NZ_CP010235.1_776785_777487_-	COG1741, COG1741, Pirin-related protein [General function prediction only]	NA|299aa|down_2|NZ_CP010235.1_777591_778488_+	cd08431, PBP2_HupR, The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold	NA|119aa|down_3|NZ_CP010235.1_778538_778895_-	COG3152, COG3152, Predicted membrane protein [Function unknown]	NA|122aa|down_4|NZ_CP010235.1_779136_779502_-	COG3152, COG3152, Predicted membrane protein [Function unknown]	NA|329aa|down_5|NZ_CP010235.1_779794_780781_-	COG0435, ECM4, Predicted glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]	NA|131aa|down_6|NZ_CP010235.1_780850_781243_-	COG2259, COG2259, Predicted membrane protein [Function unknown]	NA|100aa|down_7|NZ_CP010235.1_781428_781728_-	pfam13997, YqjK, YqjK-like protein	NA|135aa|down_8|NZ_CP010235.1_781717_782122_-	COG5393, COG5393, Predicted membrane protein [Function unknown]	NA|102aa|down_9|NZ_CP010235.1_782124_782430_-	COG4575, ElaB, Uncharacterized conserved protein [Function unknown]
GCF_001900945.1_ASM190094v1	NZ_CP010235	Escherichia coli strain S40 chromosome, complete genome	2	1166737-1167009	1,2,1	PILER-CR,CRISPRCasFinder,CRT	no	cas3	cas3,csa3,PD-DExK,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,c2c9_V-U4,DinG	Unclear	GAGTTCCCCGCGCCAGCGGGGATAAACCG,GAGTTCCCCGCGCCAGCGGGGATAAACCG,GAGTTCCCCGCGCCAGCGGGGATAAACCG	29,29,29	0	0	NA	NA	I-E:I-E:I-E	4,4,4	4	Unclear	cas3,csa3,PD-DExK,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,c2c9_V-U4,DinG	NA|47aa|up_1|NZ_CP010235.1_1165446_1165587_-,NA	NA|434aa|up_9|NZ_CP010235.1_1156143_1157445_+	PRK13168, rumA, 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD	NA|745aa|up_8|NZ_CP010235.1_1157492_1159727_+	PRK10872, relA, (p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional	NA|83aa|up_7|NZ_CP010235.1_1159804_1160053_+	PRK09798, PRK09798, MazF-MazE toxin-antitoxin system antitoxin MazE	NA|112aa|up_6|NZ_CP010235.1_1160052_1160388_+	PRK09907, PRK09907, endoribonuclease MazF	NA|264aa|up_5|NZ_CP010235.1_1160458_1161250_+	PRK09562, mazG, nucleoside triphosphate pyrophosphohydrolase; Reviewed	NA|546aa|up_4|NZ_CP010235.1_1161477_1163115_+	PRK05380, pyrG, CTP synthetase; Validated	NA|433aa|up_3|NZ_CP010235.1_1163202_1164501_+	PRK00077, eno, enolase; Provisional	NA|291aa|up_2|NZ_CP010235.1_1164560_1165433_-	COG1512, COG1512, Beta-propeller domains of methanol dehydrogenase type [General function prediction only]	NA|47aa|up_1|NZ_CP010235.1_1165446_1165587_-	NA	NA|224aa|up_0|NZ_CP010235.1_1165725_1166397_+	TIGR04322, organic_radical_activating_enzyme, putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE	NA|519aa|down_0|NZ_CP010235.1_1167647_1169204_-	cd07779, FGGY_ygcE_like, uncharacterized ygcE-like proteins	NA|426aa|down_1|NZ_CP010235.1_1169230_1170508_-	cd06174, MFS, Major Facilitator Superfamily	NA|262aa|down_2|NZ_CP010235.1_1170826_1171612_+	cd05347, Ga5DH-like_SDR_c, gluconate 5-dehydrogenase (Ga5DH)-like, classical (c) SDRs	NA|485aa|down_3|NZ_CP010235.1_1171681_1173136_+	COG0277, GlcD, FAD/FMN-containing dehydrogenases [Energy production and conversion]	NA|470aa|down_4|NZ_CP010235.1_1173157_1174567_+	cd17371, MFS_MucK, Cis,cis-muconate transport protein and similar proteins of the Major Facilitator Superfamily	NA|260aa|down_5|NZ_CP010235.1_1174544_1175324_+	COG2086, FixA, Electron transfer flavoprotein, beta subunit [Energy production and conversion]	NA|287aa|down_6|NZ_CP010235.1_1175320_1176181_+	COG2025, FixB, Electron transfer flavoprotein, alpha subunit [Energy production and conversion]	NA|192aa|down_7|NZ_CP010235.1_1176328_1176904_-	COG1954, GlpP, Glycerol-3-phosphate responsive antiterminator (mRNA-binding) [Transcription]	NA|87aa|down_8|NZ_CP010235.1_1176920_1177181_-	COG2440, FixX, Ferredoxin-like protein [Energy production and conversion]	NA|424aa|down_9|NZ_CP010235.1_1177171_1178443_-	PRK10015, PRK10015, oxidoreductase; Provisional
GCF_001900945.1_ASM190094v1	NZ_CP010235	Escherichia coli strain S40 chromosome, complete genome	3	1192790-1194649	2,3,2	PILER-CR,CRISPRCasFinder,CRT	no	cas3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2	cas3,csa3,PD-DExK,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,c2c9_V-U4,DinG	Type I-E	GTGTTCCCCGCGCCAGCGGGGATAAACC,GTGTTCCCCGCGCCAGCGGGGATAAACCG,GTGTTCCCCGCGCCAGCGGGGATAAACCG	28,29,29	0	0	NA	NA	I-E:I-E:I-E	30,30,30	30	TypeI-E	cas3,csa3,PD-DExK,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,c2c9_V-U4,DinG	NA,NA	NA|245aa|up_9|NZ_CP010235.1_1182786_1183521_+	PRK02090, PRK02090, phosphoadenylyl-sulfate reductase	NA|51aa|up_8|NZ_CP010235.1_1183785_1183938_+	pfam01848, HOK_GEF, Hok/gef family	cas3|900aa|up_7|NZ_CP010235.1_1184131_1186831_+	COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense mechanisms]	cas8e|521aa|up_6|NZ_CP010235.1_1186928_1188491_+	TIGR02547, CRISPR_system_Cascade_subunit_CasA, CRISPR type I-E/ECOLI-associated protein CasA/Cse1	cse2gr11|180aa|up_5|NZ_CP010235.1_1188487_1189027_+	cd09731, Cse2_I-E, CRISPR/Cas system-associated protein Cse2	cas7|352aa|up_4|NZ_CP010235.1_1189038_1190094_+	TIGR01869, CRISPR_system_Cascade_subunit_CasC, CRISPR-associated protein Cas7/Cse4/CasC, subtype I-E/ECOLI	cas5|249aa|up_3|NZ_CP010235.1_1190104_1190851_+	cd09645, Cas5_I-E, CRISPR/Cas system-associated RAMP superfamily protein Cas5	cas6e|217aa|up_2|NZ_CP010235.1_1190832_1191483_+	TIGR01907, CRISPR_system_Cascade_subunit_CasE, CRISPR-associated protein Cas6/Cse3/CasE, subtype I-E/ECOLI	cas1|307aa|up_1|NZ_CP010235.1_1191479_1192400_+	TIGR03638, cas1_ECOLI, CRISPR-associated endonuclease Cas1, subtype I-E/ECOLI	cas2|98aa|up_0|NZ_CP010235.1_1192399_1192693_+	PRK11558, PRK11558, putative ssRNA endonuclease; Provisional	NA|346aa|down_0|NZ_CP010235.1_1194730_1195768_-	PRK10199, PRK10199, alkaline phosphatase isozyme conversion aminopeptidase; Provisional	NA|303aa|down_1|NZ_CP010235.1_1196019_1196928_+	PRK05253, PRK05253, sulfate adenylyltransferase subunit CysD	NA|476aa|down_2|NZ_CP010235.1_1196929_1198357_+	PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional	NA|202aa|down_3|NZ_CP010235.1_1198356_1198962_+	PRK03846, PRK03846, adenylylsulfate kinase; Provisional	NA|108aa|down_4|NZ_CP010235.1_1199011_1199335_+	pfam12084, DUF3561, Protein of unknown function (DUF3561)	NA|104aa|down_5|NZ_CP010235.1_1199528_1199840_+	PRK00888, ftsB, cell division protein FtsB; Reviewed	NA|237aa|down_6|NZ_CP010235.1_1199858_1200569_+	PRK00155, ispD, D-ribitol-5-phosphate cytidylyltransferase	NA|160aa|down_7|NZ_CP010235.1_1200568_1201048_+	PRK00084, ispF, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; Reviewed	NA|350aa|down_8|NZ_CP010235.1_1201044_1202094_+	PRK00984, truD, tRNA pseudouridine synthase D; Reviewed	NA|254aa|down_9|NZ_CP010235.1_1202074_1202836_+	PRK00346, surE, 5'(3')-nucleotidase/polyphosphatase; Provisional
GCF_001900945.1_ASM190094v1	NZ_CP010235	Escherichia coli strain S40 chromosome, complete genome	4	2382958-2383081	4	CRISPRCasFinder	no	DEDDh	cas3,csa3,PD-DExK,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,c2c9_V-U4,DinG	Unclear	CGACCCCCACCATGTCAAGGTGGTGCTCTAACCAACTGAGCTA	43	0	0	NA	NA	NA	1	1	Orphan	cas3,csa3,PD-DExK,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,c2c9_V-U4,DinG	NA,NA|30aa|down_7|NZ_CP010235.1_2391977_2392067_+	NA|471aa|up_9|NZ_CP010235.1_2372411_2373824_-	PRK09206, PRK09206, pyruvate kinase PykF	NA|70aa|up_8|NZ_CP010235.1_2374380_2374590_+	PRK10292, PRK10292, fumarate hydratase FumD	NA|209aa|up_7|NZ_CP010235.1_2375045_2375672_+	PRK09898, PRK09898, ferredoxin-like protein	NA|701aa|up_6|NZ_CP010235.1_2375692_2377795_+	PRK09849, PRK09849, putative oxidoreductase; Provisional	NA|213aa|up_5|NZ_CP010235.1_2377807_2378446_+	PRK09947, PRK09947, YdhW family putative oxidoreductase system protein	NA|223aa|up_4|NZ_CP010235.1_2378509_2379178_+	TIGR03149, cyt_nit_nrfC, cytochrome c nitrite reductase, Fe-S protein	NA|262aa|up_3|NZ_CP010235.1_2379174_2379960_+	PRK15006, PRK15006, thiosulfate reductase cytochrome B subunit; Provisional	NA|271aa|up_2|NZ_CP010235.1_2379963_2380776_+	PRK09946, PRK09946, hypothetical protein; Provisional	NA|535aa|up_1|NZ_CP010235.1_2380787_2382392_-	PRK09897, PRK09897, FAD-NAD(P)-binding protein	NA|102aa|up_0|NZ_CP010235.1_2382517_2382823_-	PRK11118, PRK11118, putative monooxygenase; Provisional	NA|419aa|down_0|NZ_CP010235.1_2383395_2384652_+	PRK09945, PRK09945, hypothetical protein; Provisional	NA|458aa|down_1|NZ_CP010235.1_2384692_2386066_-	PRK01766, PRK01766, multidrug efflux protein; Reviewed	NA|214aa|down_2|NZ_CP010235.1_2386280_2386922_+	PRK13020, PRK13020, riboflavin synthase subunit alpha; Provisional	NA|383aa|down_3|NZ_CP010235.1_2386961_2388110_-	PRK11705, PRK11705, cyclopropane fatty acyl phospholipid synthase	NA|404aa|down_4|NZ_CP010235.1_2388400_2389612_-	PRK11043, PRK11043, Bcr/CflA family multidrug efflux MFS transporter	NA|311aa|down_5|NZ_CP010235.1_2389724_2390657_+	PRK11074, PRK11074, putative DNA-binding transcriptional regulator; Provisional	NA|342aa|down_6|NZ_CP010235.1_2390653_2391679_-	PRK10703, PRK10703, HTH-type transcriptional repressor PurR	NA|30aa|down_7|NZ_CP010235.1_2391977_2392067_+	NA	NA|390aa|down_8|NZ_CP010235.1_2392232_2393402_+	COG2814, AraJ, Arabinose efflux permease [Carbohydrate transport and metabolism]	NA|194aa|down_9|NZ_CP010235.1_2393547_2394129_-	PRK10543, PRK10543, superoxide dismutase [Fe]
GCF_001900945.1_ASM190094v1	NZ_CP010235	Escherichia coli strain S40 chromosome, complete genome	5	3063597-3063688	5	CRISPRCasFinder	no		cas3,csa3,PD-DExK,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,c2c9_V-U4,DinG	Orphan	CCACCTTTTTTACCTGCTTCAGATGC	26	0	0	NA	NA	NA	1	1	Orphan	cas3,csa3,PD-DExK,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,c2c9_V-U4,DinG	NA|70aa|up_9|NZ_CP010235.1_3052847_3053057_-,NA|184aa|down_1|NZ_CP010235.1_3067091_3067643_+,NA|93aa|down_2|NZ_CP010235.1_3067644_3067923_+,NA|129aa|down_4|NZ_CP010235.1_3068197_3068584_+,NA|108aa|down_5|NZ_CP010235.1_3068722_3069046_+,NA|237aa|down_6|NZ_CP010235.1_3069529_3070240_+,NA|68aa|down_7|NZ_CP010235.1_3070264_3070468_+,NA|258aa|down_9|NZ_CP010235.1_3072829_3073603_+	NA|70aa|up_9|NZ_CP010235.1_3052847_3053057_-	NA	NA|1321aa|up_8|NZ_CP010235.1_3053111_3057074_+	PRK11809, putA, trifunctional transcriptional regulator/proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed	NA|213aa|up_7|NZ_CP010235.1_3057113_3057752_-	PRK15008, PRK15008, HTH-type transcriptional regulator RutR; Provisional	NA|364aa|up_6|NZ_CP010235.1_3058039_3059131_+	TIGR03612, RutA, pyrimidine utilization protein A	NA|231aa|up_5|NZ_CP010235.1_3059130_3059823_+	TIGR03614, RutB, pyrimidine utilization protein B	NA|129aa|up_4|NZ_CP010235.1_3059834_3060221_+	TIGR03610, RutC, pyrimidine utilization protein C	NA|267aa|up_3|NZ_CP010235.1_3060228_3061029_+	TIGR03611, RutD, pyrimidine utilization protein D	NA|197aa|up_2|NZ_CP010235.1_3061038_3061629_+	PRK05365, PRK05365, malonic semialdehyde reductase; Provisional	NA|165aa|up_1|NZ_CP010235.1_3061639_3062134_+	TIGR03615, flavoprotein_oxidoreductase, pyrimidine utilization flavin reductase protein F	NA|443aa|up_0|NZ_CP010235.1_3062154_3063483_+	TIGR03616, Putative_pyrimidine_permease_RutG, pyrimidine utilization transport protein G	NA|183aa|down_0|NZ_CP010235.1_3064660_3065209_+	cd03768, SR_ResInv, Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain	NA|184aa|down_1|NZ_CP010235.1_3067091_3067643_+	NA	NA|93aa|down_2|NZ_CP010235.1_3067644_3067923_+	NA	NA|91aa|down_3|NZ_CP010235.1_3067925_3068198_+	pfam13392, HNH_3, HNH endonuclease	NA|129aa|down_4|NZ_CP010235.1_3068197_3068584_+	NA	NA|108aa|down_5|NZ_CP010235.1_3068722_3069046_+	NA	NA|237aa|down_6|NZ_CP010235.1_3069529_3070240_+	NA	NA|68aa|down_7|NZ_CP010235.1_3070264_3070468_+	NA	NA|694aa|down_8|NZ_CP010235.1_3070584_3072666_+	TIGR02675, Mu-like_prophage_FluMu_protein_gp42, tape measure domain	NA|258aa|down_9|NZ_CP010235.1_3072829_3073603_+	NA
GCF_001900945.1_ASM190094v1	NZ_CP010235	Escherichia coli strain S40 chromosome, complete genome	6	3374073-3374218	6	CRISPRCasFinder	no		cas3,csa3,PD-DExK,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,c2c9_V-U4,DinG	Orphan	CGATTTGTAGGTCGGATAAGATGCGCAAGCATCGCATCCGACAATAAGTGCCG	53	0	0	NA	NA	NA	1	1	Orphan	cas3,csa3,PD-DExK,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,c2c9_V-U4,DinG	NA,NA	NA|330aa|up_9|NZ_CP010235.1_3361977_3362967_-	PRK00164, moaA, GTP 3',8-cyclase MoaA	NA|303aa|up_8|NZ_CP010235.1_3363363_3364272_+	TIGR01826, Putative_gluconeogenesis_factor, conserved hypothetical protein, cofD-related	NA|674aa|up_7|NZ_CP010235.1_3364463_3366485_-	PRK05298, PRK05298, excinuclease ABC subunit UvrB	NA|226aa|up_6|NZ_CP010235.1_3367063_3367741_-	PRK00090, bioD, ATP-dependent dethiobiotin synthetase BioD	NA|252aa|up_5|NZ_CP010235.1_3367733_3368489_-	PRK10258, PRK10258, biotin biosynthesis protein BioC; Provisional	NA|385aa|up_4|NZ_CP010235.1_3368475_3369630_-	PRK05958, PRK05958, 8-amino-7-oxononanoate synthase; Reviewed	NA|347aa|up_3|NZ_CP010235.1_3369626_3370667_-	PRK15108, PRK15108, biotin synthase; Provisional	NA|430aa|up_2|NZ_CP010235.1_3370753_3372043_+	PRK07986, PRK07986, adenosylmethionine--8-amino-7-oxononanoate transaminase; Validated	NA|159aa|up_1|NZ_CP010235.1_3372101_3372578_+	PRK10257, PRK10257, putative kinase inhibitor protein; Provisional	NA|428aa|up_0|NZ_CP010235.1_3372729_3374013_+	PRK10531, PRK10531, putative acyl-CoA thioester hydrolase	NA|754aa|down_0|NZ_CP010235.1_3374246_3376508_-	PRK11413, PRK11413, putative hydratase; Provisional	NA|478aa|down_1|NZ_CP010235.1_3376690_3378124_-	pfam00939, Na_sulph_symp, Sodium:sulfate symporter transmembrane region	NA|351aa|down_2|NZ_CP010235.1_3378199_3379252_-	NF033377, OMA_tautomer, 4-oxalomesaconate tautomerase	NA|318aa|down_3|NZ_CP010235.1_3379435_3380389_+	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_CP010235.1_3380429_3381425_-	PRK11028, PRK11028, 6-phosphogluconolactonase; Provisional	NA|273aa|down_5|NZ_CP010235.1_3381579_3382398_+	PRK10530, PRK10530, pyridoxal phosphate (PLP) phosphatase; Provisional	NA|353aa|down_6|NZ_CP010235.1_3382398_3383457_-	PRK11144, modC, molybdenum ABC transporter ATP-binding protein ModC	NA|230aa|down_7|NZ_CP010235.1_3383459_3384149_-	PRK09421, modB, molybdate ABC transporter permease subunit	NA|258aa|down_8|NZ_CP010235.1_3384148_3384922_-	PRK10677, modA, molybdate transporter periplasmic protein; Provisional	NA|50aa|down_9|NZ_CP010235.1_3385088_3385238_-	pfam10766, AcrZ, Multidrug efflux pump-associated protein AcrZ
GCF_001900945.1_ASM190094v1	NZ_CP010235	Escherichia coli strain S40 chromosome, complete genome	7	3638892-3639005	3	PILER-CR	no		cas3,csa3,PD-DExK,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,c2c9_V-U4,DinG	Orphan	TTTTTTTACCTGATTCGGGTAAA	23	0	0	NA	NA	NA	2	2	Orphan	cas3,csa3,PD-DExK,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,c2c9_V-U4,DinG	NA|34aa|up_7|NZ_CP010235.1_3633657_3633759_-,NA|261aa|up_6|NZ_CP010235.1_3633853_3634636_-,NA|36aa|up_3|NZ_CP010235.1_3636829_3636937_-,NA|101aa|up_1|NZ_CP010235.1_3637428_3637731_-,NA|288aa|down_3|NZ_CP010235.1_3641141_3642005_+	NA|57aa|up_9|NZ_CP010235.1_3633035_3633206_-	PRK09689, PRK09689, prophage protein NinE; Provisional	NA|152aa|up_8|NZ_CP010235.1_3633205_3633661_-	PRK09741, PRK09741, hypothetical protein; Provisional	NA|34aa|up_7|NZ_CP010235.1_3633657_3633759_-	NA	NA|261aa|up_6|NZ_CP010235.1_3633853_3634636_-	NA	NA|108aa|up_5|NZ_CP010235.1_3634810_3635134_-	pfam10548, P22_AR_C, P22AR C-terminal domain	NA|509aa|up_4|NZ_CP010235.1_3635245_3636772_-	cd00338, Ser_Recombinase, Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain	NA|36aa|up_3|NZ_CP010235.1_3636829_3636937_-	NA	NA|111aa|up_2|NZ_CP010235.1_3637028_3637361_-	PRK09541, emrE, EmrE family multidrug efflux SMR transporter	NA|101aa|up_1|NZ_CP010235.1_3637428_3637731_-	NA	NA|234aa|up_0|NZ_CP010235.1_3637727_3638429_-	pfam06992, Phage_lambda_P, Replication protein P	NA|180aa|down_0|NZ_CP010235.1_3639441_3639981_-	pfam06254, YdaT_toxin, Putative bacterial toxin ydaT	NA|77aa|down_1|NZ_CP010235.1_3640050_3640281_-	pfam15943, YdaS_antitoxin, Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT	NA|230aa|down_2|NZ_CP010235.1_3640385_3641075_+	COG2932, COG2932, Predicted transcriptional regulator [Transcription]	NA|288aa|down_3|NZ_CP010235.1_3641141_3642005_+	NA	NA|97aa|down_4|NZ_CP010235.1_3642398_3642689_+	PRK11354, kil, FtsZ inhibitor protein; Reviewed	NA|99aa|down_5|NZ_CP010235.1_3642764_3643061_+	pfam06064, Gam, Host-nuclease inhibitor protein Gam	NA|262aa|down_6|NZ_CP010235.1_3643066_3643852_+	TIGR01913, Uncharacterized_protein_UU154, phage recombination protein Bet	NA|227aa|down_7|NZ_CP010235.1_3643848_3644529_+	pfam09588, YqaJ, YqaJ-like viral recombinase domain	NA|54aa|down_8|NZ_CP010235.1_3644525_3644687_+	pfam07026, DUF1317, Protein of unknown function (DUF1317)	NA|186aa|down_9|NZ_CP010235.1_3644679_3645237_+	pfam05869, Dam, DNA N-6-adenine-methyltransferase (Dam)
GCF_001900945.1_ASM190094v1	NZ_CP010235	Escherichia coli strain S40 chromosome, complete genome	8	4319600-4319717	7	CRISPRCasFinder	no		cas3,csa3,PD-DExK,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,c2c9_V-U4,DinG	Orphan	TGCCGGATGCGATGCTGGCGCACCTTATCCGGCCTACGGG	40	0	0	NA	NA	NA	1	1	Orphan	cas3,csa3,PD-DExK,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,c2c9_V-U4,DinG	NA,NA|55aa|down_0|NZ_CP010235.1_4319790_4319955_-	NA|115aa|up_9|NZ_CP010235.1_4307321_4307666_-	PRK11424, PRK11424, DNA-binding transcriptional activator TdcR; Provisional	NA|313aa|up_8|NZ_CP010235.1_4307854_4308793_+	PRK10341, PRK10341, transcriptional regulator TdcA	NA|330aa|up_7|NZ_CP010235.1_4308891_4309881_+	PRK08638, PRK08638, bifunctional threonine ammonia-lyase/L-serine ammonia-lyase TdcB	NA|444aa|up_6|NZ_CP010235.1_4309902_4311234_+	PRK13629, PRK13629, threonine/serine transporter TdcC; Provisional	NA|403aa|up_5|NZ_CP010235.1_4311259_4312468_+	PRK12379, PRK12379, propionate kinase	NA|765aa|up_4|NZ_CP010235.1_4312501_4314796_+	cd01678, PFL1, Pyruvate formate lyase 1	NA|130aa|up_3|NZ_CP010235.1_4314809_4315199_+	PRK11401, PRK11401, enamine/imine deaminase	NA|455aa|up_2|NZ_CP010235.1_4315270_4316635_+	PRK15040, PRK15040, L-serine ammonia-lyase	NA|444aa|up_1|NZ_CP010235.1_4316909_4318241_+	TIGR00814, membrane_transport_protein_YhjV, serine transporter	NA|437aa|up_0|NZ_CP010235.1_4318268_4319579_+	COG3681, COG3681, L-cysteine desulfidase [Amino acid transport and metabolism]	NA|55aa|down_0|NZ_CP010235.1_4319790_4319955_-	NA	NA|234aa|down_1|NZ_CP010235.1_4319977_4320679_-	COG1741, COG1741, Pirin-related protein [General function prediction only]	NA|299aa|down_2|NZ_CP010235.1_4320783_4321680_+	cd08431, PBP2_HupR, The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold	NA|119aa|down_3|NZ_CP010235.1_4321730_4322087_-	COG3152, COG3152, Predicted membrane protein [Function unknown]	NA|122aa|down_4|NZ_CP010235.1_4322328_4322694_-	COG3152, COG3152, Predicted membrane protein [Function unknown]	NA|329aa|down_5|NZ_CP010235.1_4322986_4323973_-	COG0435, ECM4, Predicted glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]	NA|131aa|down_6|NZ_CP010235.1_4324042_4324435_-	COG2259, COG2259, Predicted membrane protein [Function unknown]	NA|100aa|down_7|NZ_CP010235.1_4324620_4324920_-	pfam13997, YqjK, YqjK-like protein	NA|135aa|down_8|NZ_CP010235.1_4324909_4325314_-	COG5393, COG5393, Predicted membrane protein [Function unknown]	NA|102aa|down_9|NZ_CP010235.1_4325316_4325622_-	COG4575, ElaB, Uncharacterized conserved protein [Function unknown]
GCF_001900945.1_ASM190094v1	NZ_CP010235	Escherichia coli strain S40 chromosome, complete genome	9	4490180-4490325	8	CRISPRCasFinder	no		cas3,csa3,PD-DExK,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,c2c9_V-U4,DinG	Orphan	CGATTTGTAGGTCGGATAAGATGCGCAAGCATCGCATCCGACAATAAGTGCCG	53	0	0	NA	NA	NA	1	1	Orphan	cas3,csa3,PD-DExK,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,c2c9_V-U4,DinG	NA,NA	NA|330aa|up_9|NZ_CP010235.1_4478084_4479074_-	PRK00164, moaA, GTP 3',8-cyclase MoaA	NA|303aa|up_8|NZ_CP010235.1_4479470_4480379_+	TIGR01826, Putative_gluconeogenesis_factor, conserved hypothetical protein, cofD-related	NA|674aa|up_7|NZ_CP010235.1_4480570_4482592_-	PRK05298, PRK05298, excinuclease ABC subunit UvrB	NA|226aa|up_6|NZ_CP010235.1_4483170_4483848_-	PRK00090, bioD, ATP-dependent dethiobiotin synthetase BioD	NA|252aa|up_5|NZ_CP010235.1_4483840_4484596_-	PRK10258, PRK10258, biotin biosynthesis protein BioC; Provisional	NA|385aa|up_4|NZ_CP010235.1_4484582_4485737_-	PRK05958, PRK05958, 8-amino-7-oxononanoate synthase; Reviewed	NA|347aa|up_3|NZ_CP010235.1_4485733_4486774_-	PRK15108, PRK15108, biotin synthase; Provisional	NA|430aa|up_2|NZ_CP010235.1_4486860_4488150_+	PRK07986, PRK07986, adenosylmethionine--8-amino-7-oxononanoate transaminase; Validated	NA|159aa|up_1|NZ_CP010235.1_4488208_4488685_+	PRK10257, PRK10257, putative kinase inhibitor protein; Provisional	NA|428aa|up_0|NZ_CP010235.1_4488836_4490120_+	PRK10531, PRK10531, putative acyl-CoA thioester hydrolase	NA|754aa|down_0|NZ_CP010235.1_4490353_4492615_-	PRK11413, PRK11413, putative hydratase; Provisional	NA|478aa|down_1|NZ_CP010235.1_4492797_4494231_-	pfam00939, Na_sulph_symp, Sodium:sulfate symporter transmembrane region	NA|351aa|down_2|NZ_CP010235.1_4494306_4495359_-	NF033377, OMA_tautomer, 4-oxalomesaconate tautomerase	NA|318aa|down_3|NZ_CP010235.1_4495542_4496496_+	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_CP010235.1_4496536_4497532_-	PRK11028, PRK11028, 6-phosphogluconolactonase; Provisional	NA|273aa|down_5|NZ_CP010235.1_4497686_4498505_+	PRK10530, PRK10530, pyridoxal phosphate (PLP) phosphatase; Provisional	NA|353aa|down_6|NZ_CP010235.1_4498505_4499564_-	PRK11144, modC, molybdenum ABC transporter ATP-binding protein ModC	NA|230aa|down_7|NZ_CP010235.1_4499566_4500256_-	PRK09421, modB, molybdate ABC transporter permease subunit	NA|258aa|down_8|NZ_CP010235.1_4500255_4501029_-	PRK10677, modA, molybdate transporter periplasmic protein; Provisional	NA|50aa|down_9|NZ_CP010235.1_4501195_4501345_-	pfam10766, AcrZ, Multidrug efflux pump-associated protein AcrZ
GCF_001900945.1_ASM190094v1	NZ_CP010235	Escherichia coli strain S40 chromosome, complete genome	10	4782743-4782875	4	PILER-CR	no		cas3,csa3,PD-DExK,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,c2c9_V-U4,DinG	Orphan	ATCACCAATATTGAAAA	17	0	0	NA	NA	NA	2	2	Orphan	cas3,csa3,PD-DExK,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,c2c9_V-U4,DinG	NA,NA	NA|126aa|up_9|NZ_CP010235.1_4773447_4773825_+	PRK05461, apaG, CO2+/MG2+ efflux protein ApaG; Reviewed	NA|281aa|up_8|NZ_CP010235.1_4773831_4774674_+	TIGR00668, Bis5'-nucleosyl-tetraphosphatase_symmetrical, bis(5'-nucleosyl)-tetraphosphatase (symmetrical)	NA|160aa|up_7|NZ_CP010235.1_4774751_4775231_-	PRK10769, folA, type 3 dihydrofolate reductase	NA|621aa|up_6|NZ_CP010235.1_4775422_4777285_-	PRK03562, PRK03562, glutathione-regulated potassium-efflux system protein KefC; Provisional	NA|177aa|up_5|NZ_CP010235.1_4777277_4777808_-	PRK00871, PRK00871, glutathione-regulated potassium-efflux system oxidoreductase KefF	NA|444aa|up_4|NZ_CP010235.1_4777915_4779247_-	cd17316, MFS_SV2_like, Metazoan Synaptic vesicle glycoprotein 2 (SV2) and related small molecule transporters of the Major Facilitator Superfamily	NA|96aa|up_3|NZ_CP010235.1_4779304_4779592_-	PRK15449, PRK15449, ferredoxin-like protein FixX; Provisional	NA|429aa|up_2|NZ_CP010235.1_4779588_4780875_-	PRK10157, PRK10157, putative oxidoreductase FixC; Provisional	NA|314aa|up_1|NZ_CP010235.1_4780925_4781867_-	PRK03363, fixB, electron transfer flavoprotein subunit alpha/FixB family protein	NA|257aa|up_0|NZ_CP010235.1_4781881_4782652_-	PRK03359, PRK03359, putative electron transfer flavoprotein FixA; Reviewed	NA|505aa|down_0|NZ_CP010235.1_4783125_4784640_+	PRK03356, PRK03356, L-carnitine/gamma-butyrobetaine antiport BCCT transporter	NA|381aa|down_1|NZ_CP010235.1_4784670_4785813_+	PRK03354, PRK03354, crotonobetainyl-CoA dehydrogenase; Validated	NA|406aa|down_2|NZ_CP010235.1_4785941_4787159_+	PRK03525, PRK03525, L-carnitine CoA-transferase	NA|518aa|down_3|NZ_CP010235.1_4787232_4788786_+	PRK08008, caiC, putative crotonobetaine/carnitine-CoA ligase; Validated	NA|262aa|down_4|NZ_CP010235.1_4788894_4789680_+	PRK03580, PRK03580, crotonobetainyl-CoA hydratase	NA|197aa|down_5|NZ_CP010235.1_4789685_4790276_+	PRK13627, PRK13627, carnitine operon protein CaiE; Provisional	NA|132aa|down_6|NZ_CP010235.1_4790361_4790757_-	PRK11476, PRK11476, carnitine metabolism transcriptional regulator CaiF	NA|1074aa|down_7|NZ_CP010235.1_4791017_4794239_-	PRK05294, carB, carbamoyl-phosphate synthase large subunit	NA|383aa|down_8|NZ_CP010235.1_4794256_4795405_-	PRK12564, PRK12564, carbamoyl-phosphate synthase small subunit	NA|274aa|down_9|NZ_CP010235.1_4795860_4796682_-	COG0289, DapB, Dihydrodipicolinate reductase [Amino acid transport and metabolism]
