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_011492885.1_ASM1149288v1	NZ_CP049353	Escherichia coli strain T28R chromosome, complete genome	1	944459-945524	1,1,1	CRISPRCasFinder,CRT,PILER-CR	no	cas3	cas3,csa3,PD-DExK,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG,RT,c2c9_V-U4	Unclear	GTGTTCCCCGCGCCAGCGGGGATAAACCG,GTGTTCCCCGCGCCAGCGGGGATAAACCG,GTGTTCCCCGCGCCAGCGGGGATAAACCG	29,29,29	2	2	944488-944519|944549-944580	NZ_CP049353.1_1293145-1293176|NZ_CP049353.1_1293145-1293176	I-E:I-E:I-E	17,17,14	17	Unclear	cas3,csa3,PD-DExK,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG,RT,c2c9_V-U4	NA|47aa|up_1|NZ_CP049353.1_943168_943309_-,NA	NA|434aa|up_9|NZ_CP049353.1_933865_935167_+	PRK13168, rumA, 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD	NA|745aa|up_8|NZ_CP049353.1_935214_937449_+	PRK10872, relA, (p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional	NA|83aa|up_7|NZ_CP049353.1_937526_937775_+	PRK09798, PRK09798, MazF-MazE toxin-antitoxin system antitoxin MazE	NA|112aa|up_6|NZ_CP049353.1_937774_938110_+	PRK09907, PRK09907, endoribonuclease MazF	NA|264aa|up_5|NZ_CP049353.1_938180_938972_+	PRK09562, mazG, nucleoside triphosphate pyrophosphohydrolase; Reviewed	NA|546aa|up_4|NZ_CP049353.1_939199_940837_+	PRK05380, pyrG, CTP synthetase; Validated	NA|433aa|up_3|NZ_CP049353.1_940924_942223_+	PRK00077, eno, enolase; Provisional	NA|291aa|up_2|NZ_CP049353.1_942282_943155_-	COG1512, COG1512, Beta-propeller domains of methanol dehydrogenase type [General function prediction only]	NA|47aa|up_1|NZ_CP049353.1_943168_943309_-	NA	NA|224aa|up_0|NZ_CP049353.1_943447_944119_+	TIGR04322, organic_radical_activating_enzyme, putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE	NA|493aa|down_0|NZ_CP049353.1_946162_947641_-	cd07779, FGGY_ygcE_like, uncharacterized ygcE-like proteins	NA|426aa|down_1|NZ_CP049353.1_947667_948945_-	cd06174, MFS, Major Facilitator Superfamily	NA|262aa|down_2|NZ_CP049353.1_949263_950049_+	cd05347, Ga5DH-like_SDR_c, gluconate 5-dehydrogenase (Ga5DH)-like, classical (c) SDRs	NA|485aa|down_3|NZ_CP049353.1_950118_951573_+	COG0277, GlcD, FAD/FMN-containing dehydrogenases [Energy production and conversion]	NA|470aa|down_4|NZ_CP049353.1_951594_953004_+	cd17371, MFS_MucK, Cis,cis-muconate transport protein and similar proteins of the Major Facilitator Superfamily	NA|260aa|down_5|NZ_CP049353.1_952981_953761_+	COG2086, FixA, Electron transfer flavoprotein, beta subunit [Energy production and conversion]	NA|298aa|down_6|NZ_CP049353.1_953724_954618_+	COG2025, FixB, Electron transfer flavoprotein, alpha subunit [Energy production and conversion]	NA|192aa|down_7|NZ_CP049353.1_954765_955341_-	COG1954, GlpP, Glycerol-3-phosphate responsive antiterminator (mRNA-binding) [Transcription]	NA|87aa|down_8|NZ_CP049353.1_955357_955618_-	COG2440, FixX, Ferredoxin-like protein [Energy production and conversion]	NA|424aa|down_9|NZ_CP049353.1_955608_956880_-	PRK10015, PRK10015, oxidoreductase; Provisional
GCF_011492885.1_ASM1149288v1	NZ_CP049353	Escherichia coli strain T28R chromosome, complete genome	2	971729-972245	2,2,2	CRISPRCasFinder,CRT,PILER-CR	no	cas3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2	cas3,csa3,PD-DExK,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG,RT,c2c9_V-U4	Type I-E	GTGTTCCCCGCGCCAGCGGGGATAAACCG,GNGTTCCCCGCGTCAGCGGGGATAAACCG,GTTCCCCGCGTCAGCGGGGATAAACCG	29,29,27	0	0	NA	NA	I-E:I-E:I-E	8,8,8	8	TypeI-E	cas3,csa3,PD-DExK,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG,RT,c2c9_V-U4	NA,NA	NA|245aa|up_9|NZ_CP049353.1_961223_961958_+	PRK02090, PRK02090, phosphoadenylyl-sulfate reductase	NA|51aa|up_8|NZ_CP049353.1_962222_962375_+	pfam01848, HOK_GEF, Hok/gef family	cas3|899aa|up_7|NZ_CP049353.1_962438_965135_-	PRK09694, PRK09694, CRISPR-associated helicase/endonuclease Cas3	cas8e|521aa|up_6|NZ_CP049353.1_965745_967308_+	TIGR02547, CRISPR_system_Cascade_subunit_CasA, CRISPR type I-E/ECOLI-associated protein CasA/Cse1	cse2gr11|201aa|up_5|NZ_CP049353.1_967297_967900_+	TIGR02548, CRISPR_system_Cascade_subunit_CasB, CRISPR type I-E/ECOLI-associated protein CasB/Cse2	cas7|353aa|up_4|NZ_CP049353.1_967922_968981_+	pfam09344, Cas_CT1975, CT1975-like protein	cas5|242aa|up_3|NZ_CP049353.1_968990_969716_+	cd09756, Cas5_I-E, CRISPR/Cas system-associated RAMP superfamily protein Cas5	cas6e|236aa|up_2|NZ_CP049353.1_969715_970423_+	cd09664, Cas6_I-E, CRISPR/Cas system-associated RAMP superfamily protein Cas6e	cas1|306aa|up_1|NZ_CP049353.1_970419_971337_+	TIGR03638, cas1_ECOLI, CRISPR-associated endonuclease Cas1, subtype I-E/ECOLI	cas2|95aa|up_0|NZ_CP049353.1_971338_971623_+	PRK11558, PRK11558, putative ssRNA endonuclease; Provisional	NA|346aa|down_0|NZ_CP049353.1_972327_973365_-	PRK10199, PRK10199, alkaline phosphatase isozyme conversion aminopeptidase; Provisional	NA|303aa|down_1|NZ_CP049353.1_973616_974525_+	PRK05253, PRK05253, sulfate adenylyltransferase subunit CysD	NA|476aa|down_2|NZ_CP049353.1_974526_975954_+	PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional	NA|202aa|down_3|NZ_CP049353.1_975953_976559_+	PRK03846, PRK03846, adenylylsulfate kinase; Provisional	NA|108aa|down_4|NZ_CP049353.1_976608_976932_+	pfam12084, DUF3561, Protein of unknown function (DUF3561)	NA|104aa|down_5|NZ_CP049353.1_977125_977437_+	PRK00888, ftsB, cell division protein FtsB; Reviewed	NA|237aa|down_6|NZ_CP049353.1_977455_978166_+	PRK00155, ispD, D-ribitol-5-phosphate cytidylyltransferase	NA|160aa|down_7|NZ_CP049353.1_978165_978645_+	PRK00084, ispF, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; Reviewed	NA|350aa|down_8|NZ_CP049353.1_978641_979691_+	PRK00984, truD, tRNA pseudouridine synthase D; Reviewed	NA|254aa|down_9|NZ_CP049353.1_979671_980433_+	PRK00346, surE, 5'(3')-nucleotidase/polyphosphatase; Provisional
GCF_011492885.1_ASM1149288v1	NZ_CP049353	Escherichia coli strain T28R chromosome, complete genome	3	1534697-1534814	3	CRISPRCasFinder	no		cas3,csa3,PD-DExK,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG,RT,c2c9_V-U4	Orphan	CCGAGCCGTAGGCCGGATAAGGCGTTCACGC	31	0	0	NA	NA	NA	1	1	Orphan	cas3,csa3,PD-DExK,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG,RT,c2c9_V-U4	NA,NA	NA|332aa|up_9|NZ_CP049353.1_1522748_1523744_-	PRK09956, PRK09956, ISNCY family transposase	NA|397aa|up_8|NZ_CP049353.1_1523936_1525127_-	TIGR03379, glycerol3P_GlpC, glycerol-3-phosphate dehydrogenase, anaerobic, C subunit	NA|420aa|up_7|NZ_CP049353.1_1525123_1526383_-	COG3075, GlpB, Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]	NA|543aa|up_6|NZ_CP049353.1_1526372_1528001_-	PRK11101, glpA, anaerobic glycerol-3-phosphate dehydrogenase subunit A	NA|453aa|up_5|NZ_CP049353.1_1528273_1529632_+	PRK11273, glpT, glycerol-3-phosphate transporter	NA|359aa|up_4|NZ_CP049353.1_1529636_1530713_+	PRK11143, glpQ, glycerophosphodiester phosphodiesterase; Provisional	NA|410aa|up_3|NZ_CP049353.1_1530907_1532136_+	PRK09409, PRK09409, IS2 transposase TnpB; Reviewed	NA|217aa|up_2|NZ_CP049353.1_1532511_1533162_+	PRK09902, PRK09902, lipopolysaccharide kinase InaA	NA|85aa|up_1|NZ_CP049353.1_1533215_1533470_-	PRK10713, PRK10713, 2Fe-2S ferredoxin-like protein	NA|377aa|up_0|NZ_CP049353.1_1533469_1534600_-	PRK09101, nrdB, ribonucleotide-diphosphate reductase subunit beta; Reviewed	NA|762aa|down_0|NZ_CP049353.1_1534833_1537119_-	PRK09103, PRK09103, ribonucleoside-diphosphate reductase subunit alpha	NA|1251aa|down_1|NZ_CP049353.1_1538590_1542343_+	PRK09752, PRK09752, AIDA-I family autotransporter YfaL	NA|241aa|down_2|NZ_CP049353.1_1542470_1543193_-	PRK05134, PRK05134, bifunctional 2-polyprenyl-6-hydroxyphenol methylase/3-demethylubiquinol 3-O-methyltransferase UbiG	NA|876aa|down_3|NZ_CP049353.1_1543339_1545967_+	PRK05560, PRK05560, DNA gyrase subunit A; Validated	NA|563aa|down_4|NZ_CP049353.1_1546115_1547804_+	COG4685, COG4685, Uncharacterized protein conserved in bacteria [Function unknown]	NA|208aa|down_5|NZ_CP049353.1_1547800_1548424_+	COG3234, COG3234, Uncharacterized protein conserved in bacteria [Function unknown]	NA|1465aa|down_6|NZ_CP049353.1_1548567_1552962_+	COG2373, COG2373, Large extracellular alpha-helical protein [General function prediction only]	NA|496aa|down_7|NZ_CP049353.1_1552962_1554450_+	COG5445, COG5445, Predicted secreted protein [Function unknown]	NA|259aa|down_8|NZ_CP049353.1_1554454_1555231_+	COG4676, COG4676, Uncharacterized protein conserved in bacteria [Function unknown]	NA|395aa|down_9|NZ_CP049353.1_1555304_1556489_-	PRK05790, PRK05790, putative acyltransferase; Provisional
GCF_011492885.1_ASM1149288v1	NZ_CP049353	Escherichia coli strain T28R chromosome, complete genome	4	2171775-2171898	4	CRISPRCasFinder	no	DEDDh	cas3,csa3,PD-DExK,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG,RT,c2c9_V-U4	Unclear	CGACCCCCACCATGTCAAGGTGGTGCTCTAACCAACTGAGCTA	43	0	0	NA	NA	NA	1	1	Orphan	cas3,csa3,PD-DExK,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG,RT,c2c9_V-U4	NA,NA|30aa|down_7|NZ_CP049353.1_2180794_2180884_+	NA|471aa|up_9|NZ_CP049353.1_2161229_2162642_-	PRK09206, PRK09206, pyruvate kinase PykF	NA|70aa|up_8|NZ_CP049353.1_2163198_2163408_+	PRK10292, PRK10292, fumarate hydratase FumD	NA|209aa|up_7|NZ_CP049353.1_2163862_2164489_+	PRK09898, PRK09898, ferredoxin-like protein	NA|701aa|up_6|NZ_CP049353.1_2164509_2166612_+	PRK09849, PRK09849, putative oxidoreductase; Provisional	NA|213aa|up_5|NZ_CP049353.1_2166624_2167263_+	PRK09947, PRK09947, YdhW family putative oxidoreductase system protein	NA|223aa|up_4|NZ_CP049353.1_2167326_2167995_+	TIGR03149, cyt_nit_nrfC, cytochrome c nitrite reductase, Fe-S protein	NA|262aa|up_3|NZ_CP049353.1_2167991_2168777_+	PRK15006, PRK15006, thiosulfate reductase cytochrome B subunit; Provisional	NA|271aa|up_2|NZ_CP049353.1_2168780_2169593_+	PRK09946, PRK09946, hypothetical protein; Provisional	NA|535aa|up_1|NZ_CP049353.1_2169604_2171209_-	PRK09897, PRK09897, FAD-NAD(P)-binding protein	NA|102aa|up_0|NZ_CP049353.1_2171334_2171640_-	PRK11118, PRK11118, putative monooxygenase; Provisional	NA|419aa|down_0|NZ_CP049353.1_2172212_2173469_+	PRK09945, PRK09945, hypothetical protein; Provisional	NA|458aa|down_1|NZ_CP049353.1_2173509_2174883_-	PRK01766, PRK01766, multidrug efflux protein; Reviewed	NA|214aa|down_2|NZ_CP049353.1_2175097_2175739_+	PRK13020, PRK13020, riboflavin synthase subunit alpha; Provisional	NA|383aa|down_3|NZ_CP049353.1_2175778_2176927_-	PRK11705, PRK11705, cyclopropane fatty acyl phospholipid synthase	NA|404aa|down_4|NZ_CP049353.1_2177217_2178429_-	PRK11043, PRK11043, Bcr/CflA family multidrug efflux MFS transporter	NA|311aa|down_5|NZ_CP049353.1_2178541_2179474_+	PRK11074, PRK11074, putative DNA-binding transcriptional regulator; Provisional	NA|342aa|down_6|NZ_CP049353.1_2179470_2180496_-	PRK10703, PRK10703, HTH-type transcriptional repressor PurR	NA|30aa|down_7|NZ_CP049353.1_2180794_2180884_+	NA	NA|390aa|down_8|NZ_CP049353.1_2181049_2182219_+	COG2814, AraJ, Arabinose efflux permease [Carbohydrate transport and metabolism]	NA|194aa|down_9|NZ_CP049353.1_2182453_2183035_-	PRK10543, PRK10543, superoxide dismutase [Fe]
GCF_011492885.1_ASM1149288v1	NZ_CP049353	Escherichia coli strain T28R chromosome, complete genome	5	2808060-2808151	5	CRISPRCasFinder	no		cas3,csa3,PD-DExK,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG,RT,c2c9_V-U4	Orphan	CCACCTTTTTTACCTGCTTCAGATGC	26	0	0	NA	NA	NA	1	1	Orphan	cas3,csa3,PD-DExK,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG,RT,c2c9_V-U4	NA|70aa|up_9|NZ_CP049353.1_2797135_2797345_-,NA	NA|70aa|up_9|NZ_CP049353.1_2797135_2797345_-	NA	NA|1321aa|up_8|NZ_CP049353.1_2797399_2801362_+	PRK11809, putA, trifunctional transcriptional regulator/proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed	NA|213aa|up_7|NZ_CP049353.1_2801401_2802040_-	PRK15008, PRK15008, HTH-type transcriptional regulator RutR; Provisional	NA|364aa|up_6|NZ_CP049353.1_2802327_2803419_+	TIGR03612, RutA, pyrimidine utilization protein A	NA|231aa|up_5|NZ_CP049353.1_2803418_2804111_+	TIGR03614, RutB, pyrimidine utilization protein B	NA|129aa|up_4|NZ_CP049353.1_2804122_2804509_+	TIGR03610, RutC, pyrimidine utilization protein C	NA|267aa|up_3|NZ_CP049353.1_2804516_2805317_+	TIGR03611, RutD, pyrimidine utilization protein D	NA|197aa|up_2|NZ_CP049353.1_2805326_2805917_+	PRK05365, PRK05365, malonic semialdehyde reductase; Provisional	NA|165aa|up_1|NZ_CP049353.1_2805927_2806422_+	TIGR03615, flavoprotein_oxidoreductase, pyrimidine utilization flavin reductase protein F	NA|443aa|up_0|NZ_CP049353.1_2806442_2807771_+	TIGR03616, Putative_pyrimidine_permease_RutG, pyrimidine utilization transport protein G	NA|199aa|down_0|NZ_CP049353.1_2808574_2809171_+	PRK03767, PRK03767, NAD(P)H:quinone oxidoreductase; Provisional	NA|76aa|down_1|NZ_CP049353.1_2809191_2809419_+	PRK10174, PRK10174, hypothetical protein; Provisional	NA|414aa|down_2|NZ_CP049353.1_2809456_2810698_-	PRK10173, PRK10173, glucose-1-phosphatase/inositol phosphatase; Provisional	NA|307aa|down_3|NZ_CP049353.1_2813283_2814204_+	PRK10266, PRK10266, curved DNA-binding protein	NA|102aa|down_4|NZ_CP049353.1_2814203_2814509_+	PRK10265, PRK10265, chaperone modulator CbpM	NA|200aa|down_5|NZ_CP049353.1_2814660_2815260_-	PRK04976, torD, chaperone protein TorD; Validated	NA|849aa|down_6|NZ_CP049353.1_2815256_2817803_-	PRK15102, PRK15102, trimethylamine-N-oxide reductase TorA	NA|391aa|down_7|NZ_CP049353.1_2817802_2818975_-	PRK15032, PRK15032, pentaheme c-type cytochrome TorC	NA|231aa|down_8|NZ_CP049353.1_2819104_2819797_+	PRK10766, PRK10766, two-component system response regulator TorR	NA|343aa|down_9|NZ_CP049353.1_2819769_2820798_-	PRK10936, PRK10936, TMAO reductase system periplasmic protein TorT; Provisional
GCF_011492885.1_ASM1149288v1	NZ_CP049353	Escherichia coli strain T28R chromosome, complete genome	6	2950435-2950640	6,3,3	CRISPRCasFinder,CRT,PILER-CR	no		cas3,csa3,PD-DExK,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG,RT,c2c9_V-U4	Orphan	TTTCTAAGCTGCCTGTACGGCAGTGAAC,TTTCTAAGCTGCCTGTACGGCAGTGAAC,TTTCTAAGCTGCCTGTACGGCAGTGAACG	28,28,29	0	0	NA	NA	I-F:I-F:I-F	3,3,2	3	Orphan	cas3,csa3,PD-DExK,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG,RT,c2c9_V-U4	NA,NA	NA|431aa|up_9|NZ_CP049353.1_2935558_2936851_-	PRK05431, PRK05431, seryl-tRNA synthetase; Provisional	NA|448aa|up_8|NZ_CP049353.1_2936941_2938285_-	PRK13342, PRK13342, recombination factor protein RarA; Reviewed	NA|204aa|up_7|NZ_CP049353.1_2938295_2938907_-	TIGR00547, Outer-membrane_lipoprotein_carrier_protein, periplasmic chaperone LolA	NA|1330aa|up_6|NZ_CP049353.1_2939061_2943051_-	PRK10263, PRK10263, DNA translocase FtsK; Provisional	NA|165aa|up_5|NZ_CP049353.1_2943185_2943680_-	PRK11169, PRK11169, leucine-responsive transcriptional regulator Lrp	NA|322aa|up_4|NZ_CP049353.1_2944224_2945190_+	PRK10262, PRK10262, thioredoxin reductase; Provisional	NA|589aa|up_3|NZ_CP049353.1_2945312_2947079_+	PRK11174, PRK11174, cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed	NA|574aa|up_2|NZ_CP049353.1_2947079_2948801_+	PRK11160, PRK11160, cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed	NA|235aa|up_1|NZ_CP049353.1_2948842_2949547_+	PRK00301, aat, leucyl/phenylalanyl-tRNA--protein transferase; Reviewed	NA|73aa|up_0|NZ_CP049353.1_2949831_2950050_+	PRK00276, infA, translation initiation factor IF-1; Validated	NA|759aa|down_0|NZ_CP049353.1_2950850_2953127_-	PRK11034, clpA, ATP-dependent Clp protease ATP-binding subunit; Provisional	NA|107aa|down_1|NZ_CP049353.1_2953157_2953478_-	PRK00033, clpS, ATP-dependent Clp protease adaptor protein ClpS; Reviewed	NA|75aa|down_2|NZ_CP049353.1_2953800_2954025_+	PRK09937, PRK09937, cold shock-like protein CspD	NA|649aa|down_3|NZ_CP049353.1_2954097_2956044_-	PRK10535, PRK10535, macrolide ABC transporter ATP-binding protein/permease MacB	NA|372aa|down_4|NZ_CP049353.1_2956040_2957156_-	PRK11578, PRK11578, macrolide transporter subunit MacA; Provisional	NA|317aa|down_5|NZ_CP049353.1_2957312_2958263_+	COG2990, VirK, Uncharacterized protein conserved in bacteria [Function unknown]	NA|553aa|down_6|NZ_CP049353.1_2958259_2959918_-	COG3593, COG3593, Predicted ATP-dependent endonuclease of the OLD family [DNA replication, recombination, and repair]	NA|232aa|down_7|NZ_CP049353.1_2960342_2961038_+	PRK05420, PRK05420, aquaporin Z; Provisional	NA|300aa|down_8|NZ_CP049353.1_2961532_2962432_+	COG2431, COG2431, Predicted membrane protein [Function unknown]	NA|551aa|down_9|NZ_CP049353.1_2962575_2964228_+	PRK05290, PRK05290, hybrid cluster protein; Provisional
GCF_011492885.1_ASM1149288v1	NZ_CP049353	Escherichia coli strain T28R chromosome, complete genome	7	3114329-3114473	7	CRISPRCasFinder	no		cas3,csa3,PD-DExK,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG,RT,c2c9_V-U4	Orphan	GTAGGTCGGATAAGATGCGCAAGCATCGCATCCGACAATAAGTGCCGGATGC	52	0	0	NA	NA	NA	1	1	Orphan	cas3,csa3,PD-DExK,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG,RT,c2c9_V-U4	NA|47aa|up_6|NZ_CP049353.1_3108370_3108511_-,NA|56aa|up_3|NZ_CP049353.1_3111371_3111539_+,NA	NA|320aa|up_9|NZ_CP049353.1_3106075_3107035_-	COG3272, COG3272, Uncharacterized conserved protein [Function unknown]	NA|175aa|up_8|NZ_CP049353.1_3107227_3107752_+	PRK10477, PRK10477, outer membrane lipoprotein Blc; Provisional	NA|126aa|up_7|NZ_CP049353.1_3107907_3108285_-	pfam06530, Phage_antitermQ, Phage antitermination protein Q	NA|47aa|up_6|NZ_CP049353.1_3108370_3108511_-	NA	NA|121aa|up_5|NZ_CP049353.1_3108507_3108870_-	PRK09786, PRK09786, endodeoxyribonuclease RUS; Reviewed	NA|410aa|up_4|NZ_CP049353.1_3110024_3111253_-	PRK09409, PRK09409, IS2 transposase TnpB; Reviewed	NA|56aa|up_3|NZ_CP049353.1_3111371_3111539_+	NA	NA|73aa|up_2|NZ_CP049353.1_3111578_3111797_+	pfam07825, Exc, Excisionase-like protein	NA|357aa|up_1|NZ_CP049353.1_3111774_3112845_+	cd00800, INT_Lambda_C, C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase	NA|428aa|up_0|NZ_CP049353.1_3112979_3114263_+	PRK10531, PRK10531, putative acyl-CoA thioester hydrolase	NA|478aa|down_0|NZ_CP049353.1_3116940_3118374_-	pfam00939, Na_sulph_symp, Sodium:sulfate symporter transmembrane region	NA|351aa|down_1|NZ_CP049353.1_3118449_3119502_-	NF033377, OMA_tautomer, 4-oxalomesaconate tautomerase	NA|318aa|down_2|NZ_CP049353.1_3119685_3120639_+	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_3|NZ_CP049353.1_3120679_3121675_-	PRK11028, PRK11028, 6-phosphogluconolactonase; Provisional	NA|273aa|down_4|NZ_CP049353.1_3121829_3122648_+	PRK10530, PRK10530, pyridoxal phosphate (PLP) phosphatase; Provisional	NA|353aa|down_5|NZ_CP049353.1_3122648_3123707_-	PRK11144, modC, molybdenum ABC transporter ATP-binding protein ModC	NA|230aa|down_6|NZ_CP049353.1_3123709_3124399_-	PRK09421, modB, molybdate ABC transporter permease subunit	NA|258aa|down_7|NZ_CP049353.1_3124398_3125172_-	PRK10677, modA, molybdate transporter periplasmic protein; Provisional	NA|50aa|down_8|NZ_CP049353.1_3125337_3125487_-	pfam10766, AcrZ, Multidrug efflux pump-associated protein AcrZ	NA|263aa|down_9|NZ_CP049353.1_3125615_3126404_+	PRK10676, PRK10676, DNA-binding transcriptional regulator ModE; Provisional
GCF_011492885.1_ASM1149288v1	NZ_CP049353	Escherichia coli strain T28R chromosome, complete genome	8	3347511-3347607	8	CRISPRCasFinder	no		cas3,csa3,PD-DExK,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG,RT,c2c9_V-U4	Orphan	TTGTAGGCCTGATAAGATGCGTCAAGC	27	0	0	NA	NA	NA	1	1	Orphan	cas3,csa3,PD-DExK,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG,RT,c2c9_V-U4	NA,NA	NA|207aa|up_9|NZ_CP049353.1_3338037_3338658_+	PRK09935, PRK09935, fimbriae biosynthesis transcriptional regulator FimZ	NA|181aa|up_8|NZ_CP049353.1_3339442_3339985_-	PRK15194, PRK15194, type 1 fimbrial protein subunit FimA	NA|289aa|up_7|NZ_CP049353.1_3341231_3342098_+	PRK10792, PRK10792, bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD	NA|71aa|up_6|NZ_CP049353.1_3342099_3342312_+	PRK11507, PRK11507, ribosome-associated protein YbcJ	NA|174aa|up_5|NZ_CP049353.1_3342419_3342941_+	COG1988, COG1988, Predicted membrane-bound metal-dependent hydrolases [General function prediction only]	NA|462aa|up_4|NZ_CP049353.1_3342976_3344362_-	PRK00260, cysS, cysteinyl-tRNA synthetase; Validated	NA|165aa|up_3|NZ_CP049353.1_3344535_3345030_+	PRK10791, PRK10791, peptidylprolyl isomerase B	NA|241aa|up_2|NZ_CP049353.1_3345032_3345755_+	PRK05340, PRK05340, UDP-2,3-diacylglucosamine hydrolase; Provisional	NA|170aa|up_1|NZ_CP049353.1_3345872_3346382_+	COG0041, PurE, Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase [Nucleotide transport and metabolism]	NA|356aa|up_0|NZ_CP049353.1_3346378_3347446_+	PRK06019, PRK06019, phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed	NA|298aa|down_0|NZ_CP049353.1_3347640_3348534_-	PRK09411, PRK09411, carbamate kinase; Reviewed	NA|272aa|down_1|NZ_CP049353.1_3348530_3349346_-	pfam11392, DUF2877, Protein of unknown function (DUF2877)	NA|420aa|down_2|NZ_CP049353.1_3349356_3350616_-	pfam06545, DUF1116, Protein of unknown function (DUF1116)	NA|556aa|down_3|NZ_CP049353.1_3350625_3352293_-	PRK06091, PRK06091, membrane protein FdrA; Validated	NA|350aa|down_4|NZ_CP049353.1_3352608_3353658_+	PRK15025, PRK15025, ureidoglycolate dehydrogenase; Provisional	NA|412aa|down_5|NZ_CP049353.1_3353679_3354915_+	TIGR03176, AllC, allantoate amidohydrolase	NA|262aa|down_6|NZ_CP049353.1_3354925_3355711_+	TIGR03214, ura-cupin, putative allantoin catabolism protein	NA|382aa|down_7|NZ_CP049353.1_3355938_3357084_-	PRK09932, PRK09932, glycerate 3-kinase	NA|434aa|down_8|NZ_CP049353.1_3357105_3358407_-	PRK11412, PRK11412, uracil/xanthine transporter	NA|454aa|down_9|NZ_CP049353.1_3358463_3359825_-	PRK08044, PRK08044, allantoinase AllB
GCF_011492885.1_ASM1149288v1	NZ_CP049353	Escherichia coli strain T28R chromosome, complete genome	9	3846990-3847125	4	PILER-CR	no		cas3,csa3,PD-DExK,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG,RT,c2c9_V-U4	Orphan	TGAATCACCAATATTGAAAA	20	0	0	NA	NA	NA	2	2	Orphan	cas3,csa3,PD-DExK,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG,RT,c2c9_V-U4	NA,NA	NA|126aa|up_9|NZ_CP049353.1_3837696_3838074_+	PRK05461, apaG, CO2+/MG2+ efflux protein ApaG; Reviewed	NA|281aa|up_8|NZ_CP049353.1_3838080_3838923_+	TIGR00668, Bis5'-nucleosyl-tetraphosphatase_symmetrical, bis(5'-nucleosyl)-tetraphosphatase (symmetrical)	NA|160aa|up_7|NZ_CP049353.1_3839000_3839480_-	PRK10769, folA, type 3 dihydrofolate reductase	NA|621aa|up_6|NZ_CP049353.1_3839671_3841534_-	PRK03562, PRK03562, glutathione-regulated potassium-efflux system protein KefC; Provisional	NA|177aa|up_5|NZ_CP049353.1_3841526_3842057_-	PRK00871, PRK00871, glutathione-regulated potassium-efflux system oxidoreductase KefF	NA|444aa|up_4|NZ_CP049353.1_3842164_3843496_-	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_CP049353.1_3843554_3843842_-	PRK15449, PRK15449, ferredoxin-like protein FixX; Provisional	NA|429aa|up_2|NZ_CP049353.1_3843838_3845125_-	PRK10157, PRK10157, putative oxidoreductase FixC; Provisional	NA|314aa|up_1|NZ_CP049353.1_3845175_3846117_-	PRK03363, fixB, electron transfer flavoprotein subunit alpha/FixB family protein	NA|257aa|up_0|NZ_CP049353.1_3846131_3846902_-	PRK03359, PRK03359, putative electron transfer flavoprotein FixA; Reviewed	NA|505aa|down_0|NZ_CP049353.1_3847374_3848889_+	PRK03356, PRK03356, L-carnitine/gamma-butyrobetaine antiport BCCT transporter	NA|381aa|down_1|NZ_CP049353.1_3848919_3850062_+	PRK03354, PRK03354, crotonobetainyl-CoA dehydrogenase; Validated	NA|406aa|down_2|NZ_CP049353.1_3850190_3851408_+	PRK03525, PRK03525, L-carnitine CoA-transferase	NA|518aa|down_3|NZ_CP049353.1_3851481_3853035_+	PRK08008, caiC, putative crotonobetaine/carnitine-CoA ligase; Validated	NA|262aa|down_4|NZ_CP049353.1_3853143_3853929_+	PRK03580, PRK03580, crotonobetainyl-CoA hydratase	NA|197aa|down_5|NZ_CP049353.1_3853934_3854525_+	PRK13627, PRK13627, carnitine operon protein CaiE; Provisional	NA|132aa|down_6|NZ_CP049353.1_3854733_3855129_-	PRK11476, PRK11476, carnitine metabolism transcriptional regulator CaiF	NA|1074aa|down_7|NZ_CP049353.1_3855390_3858612_-	PRK05294, carB, carbamoyl-phosphate synthase large subunit	NA|383aa|down_8|NZ_CP049353.1_3858629_3859778_-	PRK12564, PRK12564, carbamoyl-phosphate synthase small subunit	NA|274aa|down_9|NZ_CP049353.1_3860233_3861055_-	COG0289, DapB, Dihydrodipicolinate reductase [Amino acid transport and metabolism]
GCF_011492885.1_ASM1149288v1	NZ_CP049353	Escherichia coli strain T28R chromosome, complete genome	10	3854563-3854704	9	CRISPRCasFinder	no		cas3,csa3,PD-DExK,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG,RT,c2c9_V-U4	Orphan	GCTGGAGAGCAACCGTAGGCCGGATAAGATGCGCCAGCATCGCATCCGGCGA	52	0	0	NA	NA	NA	1	1	Orphan	cas3,csa3,PD-DExK,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG,RT,c2c9_V-U4	NA,NA	NA|96aa|up_9|NZ_CP049353.1_3843554_3843842_-	PRK15449, PRK15449, ferredoxin-like protein FixX; Provisional	NA|429aa|up_8|NZ_CP049353.1_3843838_3845125_-	PRK10157, PRK10157, putative oxidoreductase FixC; Provisional	NA|314aa|up_7|NZ_CP049353.1_3845175_3846117_-	PRK03363, fixB, electron transfer flavoprotein subunit alpha/FixB family protein	NA|257aa|up_6|NZ_CP049353.1_3846131_3846902_-	PRK03359, PRK03359, putative electron transfer flavoprotein FixA; Reviewed	NA|505aa|up_5|NZ_CP049353.1_3847374_3848889_+	PRK03356, PRK03356, L-carnitine/gamma-butyrobetaine antiport BCCT transporter	NA|381aa|up_4|NZ_CP049353.1_3848919_3850062_+	PRK03354, PRK03354, crotonobetainyl-CoA dehydrogenase; Validated	NA|406aa|up_3|NZ_CP049353.1_3850190_3851408_+	PRK03525, PRK03525, L-carnitine CoA-transferase	NA|518aa|up_2|NZ_CP049353.1_3851481_3853035_+	PRK08008, caiC, putative crotonobetaine/carnitine-CoA ligase; Validated	NA|262aa|up_1|NZ_CP049353.1_3853143_3853929_+	PRK03580, PRK03580, crotonobetainyl-CoA hydratase	NA|197aa|up_0|NZ_CP049353.1_3853934_3854525_+	PRK13627, PRK13627, carnitine operon protein CaiE; Provisional	NA|132aa|down_0|NZ_CP049353.1_3854733_3855129_-	PRK11476, PRK11476, carnitine metabolism transcriptional regulator CaiF	NA|1074aa|down_1|NZ_CP049353.1_3855390_3858612_-	PRK05294, carB, carbamoyl-phosphate synthase large subunit	NA|383aa|down_2|NZ_CP049353.1_3858629_3859778_-	PRK12564, PRK12564, carbamoyl-phosphate synthase small subunit	NA|274aa|down_3|NZ_CP049353.1_3860233_3861055_-	COG0289, DapB, Dihydrodipicolinate reductase [Amino acid transport and metabolism]	NA|305aa|down_4|NZ_CP049353.1_3861221_3862136_-	PRK10768, PRK10768, ribonucleoside hydrolase RihC; Provisional	NA|317aa|down_5|NZ_CP049353.1_3862201_3863152_-	PRK01045, ispH, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed	NA|150aa|down_6|NZ_CP049353.1_3863153_3863603_-	PRK15095, PRK15095, FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional	NA|165aa|down_7|NZ_CP049353.1_3863727_3864222_-	PRK00376, lspA, lipoprotein signal peptidase	NA|939aa|down_8|NZ_CP049353.1_3864221_3867038_-	PRK05743, ileS, isoleucyl-tRNA synthetase; Reviewed	NA|314aa|down_9|NZ_CP049353.1_3867080_3868022_-	PRK05627, PRK05627, bifunctional riboflavin kinase/FAD synthetase
GCF_011492885.1_ASM1149288v1	NZ_CP049354	Escherichia coli strain T28R plasmid pT28R-1, complete sequence	1	160385-160542	1	PILER-CR	no			Orphan	CCGTACCCGGTATAGTGGAT	20	0	0	NA	NA	NA	2	2	Orphan	cas3,csa3,PD-DExK,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DEDDh,DinG,RT,c2c9_V-U4	NA|259aa|up_9|NZ_CP049354.1_151493_152270_+,NA|114aa|up_8|NZ_CP049354.1_152458_152800_+,NA|88aa|up_7|NZ_CP049354.1_152900_153164_+,NA|235aa|up_6|NZ_CP049354.1_153391_154096_+,NA|140aa|up_5|NZ_CP049354.1_154128_154548_-,NA|172aa|down_0|NZ_CP049354.1_160731_161247_-,NA|59aa|down_2|NZ_CP049354.1_164799_164976_-,NA|386aa|down_4|NZ_CP049354.1_166930_168088_-,NA|274aa|down_6|NZ_CP049354.1_169286_170108_-,NA|268aa|down_7|NZ_CP049354.1_171724_172528_-,NA|67aa|down_9|NZ_CP049354.1_175199_175400_-	NA|259aa|up_9|NZ_CP049354.1_151493_152270_+	NA	NA|114aa|up_8|NZ_CP049354.1_152458_152800_+	NA	NA|88aa|up_7|NZ_CP049354.1_152900_153164_+	NA	NA|235aa|up_6|NZ_CP049354.1_153391_154096_+	NA	NA|140aa|up_5|NZ_CP049354.1_154128_154548_-	NA	NA|795aa|up_4|NZ_CP049354.1_154635_157020_-	pfam13750, Big_3_3, Bacterial Ig-like domain (group 3)	NA|201aa|up_3|NZ_CP049354.1_157270_157873_+	pfam13752, DUF4165, Domain of unknown function (DUF4165)	NA|79aa|up_2|NZ_CP049354.1_157884_158121_+	pfam12245, Big_3_2, Bacterial Ig-like domain (group 3)	NA|199aa|up_1|NZ_CP049354.1_158276_158873_+	pfam13750, Big_3_3, Bacterial Ig-like domain (group 3)	NA|294aa|up_0|NZ_CP049354.1_159264_160146_+	pfam16441, DUF5038, Domain of unknown function (DUF5038)	NA|172aa|down_0|NZ_CP049354.1_160731_161247_-	NA	NA|819aa|down_1|NZ_CP049354.1_161897_164354_-	pfam13750, Big_3_3, Bacterial Ig-like domain (group 3)	NA|59aa|down_2|NZ_CP049354.1_164799_164976_-	NA	NA|559aa|down_3|NZ_CP049354.1_164990_166667_-	pfam13708, DUF4942, Domain of unknown function (DUF4942)	NA|386aa|down_4|NZ_CP049354.1_166930_168088_-	NA	NA|275aa|down_5|NZ_CP049354.1_168447_169272_+	TIGR00571, DNA_adenine_methylase, DNA adenine methylase (dam)	NA|274aa|down_6|NZ_CP049354.1_169286_170108_-	NA	NA|268aa|down_7|NZ_CP049354.1_171724_172528_-	NA	NA|105aa|down_8|NZ_CP049354.1_174218_174533_+	pfam12840, HTH_20, Helix-turn-helix domain	NA|67aa|down_9|NZ_CP049354.1_175199_175400_-	NA
