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_002286135.1_ASM228613v1	NZ_CP016966	Bordetella pertussis strain E541, complete genome	1	250591-250675	1	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG	Orphan	GGTGCCTGTCCCCGCGGGGACAG	23	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG	NA,NA	NA|137aa|up_9|NZ_CP016966.1_238116_238527_+	TIGR02425, putative_gamma-carboxymuconolactone_decarboxylase, 4-carboxymuconolactone decarboxylase	NA|248aa|up_8|NZ_CP016966.1_239548_240292_-	COG1802, GntR, Transcriptional regulators [Transcription]	NA|348aa|up_7|NZ_CP016966.1_240335_241379_-	cd13602, PBP2_TRAP_BpDctp6_7, Substrate-binding domain of a pyroglutamic acid binding DctP subfamily of the tripartite ATP-independent periplasmic transporters; contains the type 2 periplasmic binding protein fold	NA|701aa|up_6|NZ_CP016966.1_241549_243652_+	TIGR00786, TRAP_transporter_permease_protein_SiaT, TRAP transporter, DctM subunit	NA|319aa|up_5|NZ_CP016966.1_245062_246019_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|164aa|up_4|NZ_CP016966.1_246037_246529_-	PRK14092, PRK14092, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase	NA|452aa|up_3|NZ_CP016966.1_246525_247881_-	TIGR01942, pcnB, poly(A) polymerase	NA|233aa|up_2|NZ_CP016966.1_247881_248580_-	cd02612, HAD_PGPPase, phosphatidylglycerol-phosphate phosphatase, similar to Escherichia coli K-12 phosphatidylglycerol-phosphate phosphatase C	NA|234aa|up_1|NZ_CP016966.1_248576_249278_-	PRK08903, PRK08903, DnaA regulatory inactivator Hda; Validated	NA|350aa|up_0|NZ_CP016966.1_249530_250580_+	PRK05385, PRK05385, phosphoribosylaminoimidazole synthetase; Provisional	NA|314aa|down_0|NZ_CP016966.1_250685_251627_-	PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed	NA|630aa|down_1|NZ_CP016966.1_251623_253513_-	PRK00095, mutL, DNA mismatch repair endonuclease MutL	NA|213aa|down_2|NZ_CP016966.1_253599_254238_+	PRK10847, PRK10847, DedA family protein	NA|462aa|down_3|NZ_CP016966.1_254380_255766_-	PRK10319, PRK10319, N-acetylmuramoyl-L-alanine amidase AmiA	NA|179aa|down_4|NZ_CP016966.1_255696_256233_-	COG0802, COG0802, Predicted ATPase or kinase [General function prediction only]	NA|464aa|down_5|NZ_CP016966.1_256384_257776_+	PRK00485, fumC, fumarate hydratase; Reviewed	NA|327aa|down_6|NZ_CP016966.1_257792_258773_-	COG0679, COG0679, Predicted permeases [General function prediction only]	NA|328aa|down_7|NZ_CP016966.1_258908_259892_+	cd13577, PBP2_BugE_Glu, Glutamate transporter of Bug (Bordetella uptake gene) protein family; contains the type 2 periplasmic binding fold	NA|300aa|down_8|NZ_CP016966.1_259956_260856_-	cd08415, PBP2_LysR_opines_like, The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the catabolism of opines and that of related regulators, contains the type 2 periplasmic binding fold	NA|585aa|down_9|NZ_CP016966.1_260962_262717_+	COG0405, Ggt, Gamma-glutamyltransferase [Amino acid transport and metabolism]
GCF_002286135.1_ASM228613v1	NZ_CP016966	Bordetella pertussis strain E541, complete genome	2	432034-432127	2	CRISPRCasFinder	no	DEDDh	DEDDh,csa3,cas3,DinG	Unclear	GTGCCTGTCCCCGCCGGGACAGGCAC	26	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG	NA,NA	NA|353aa|up_9|NZ_CP016966.1_419373_420432_-	cd04187, DPM1_like_bac, Bacterial DPM1_like enzymes are related to eukaryotic DPM1	NA|165aa|up_8|NZ_CP016966.1_420561_421056_+	pfam00583, Acetyltransf_1, Acetyltransferase (GNAT) family	NA|326aa|up_7|NZ_CP016966.1_421148_422126_+	pfam00665, rve, Integrase core domain	NA|402aa|up_6|NZ_CP016966.1_422321_423527_+	TIGR00210, Sodium/glutamate_symport_carrier_protein, sodium--glutamate symport carrier (gltS)	NA|504aa|up_5|NZ_CP016966.1_423523_425035_+	cd13520, PBP2_TAXI_TRAP, Substrate binding domain of TAXI proteins of the tripartite ATP-independent periplasmic transporters; the type 2 periplasmic binding protein fold	NA|438aa|up_4|NZ_CP016966.1_425050_426364_-	COG2031, AtoE, Short chain fatty acids transporter [Lipid metabolism]	NA|60aa|up_3|NZ_CP016966.1_426554_426734_-	pfam04391, DUF533, Protein of unknown function (DUF533)	DEDDh|245aa|up_2|NZ_CP016966.1_427143_427878_-	PRK05711, PRK05711, DNA polymerase III subunit epsilon; Provisional	NA|317aa|up_1|NZ_CP016966.1_430322_431273_+	pfam00665, rve, Integrase core domain	NA|133aa|up_0|NZ_CP016966.1_431404_431803_-	PRK00007, PRK00007, elongation factor G; Reviewed	NA|157aa|down_0|NZ_CP016966.1_432213_432684_-	pfam00582, Usp, Universal stress protein family	NA|115aa|down_1|NZ_CP016966.1_432772_433117_-	COG3453, COG3453, Uncharacterized protein conserved in bacteria [Function unknown]	NA|467aa|down_2|NZ_CP016966.1_433216_434617_-	COG1167, ARO8, Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]	NA|173aa|down_3|NZ_CP016966.1_436405_436924_-	COG1285, SapB, Uncharacterized membrane protein [Function unknown]	NA|252aa|down_4|NZ_CP016966.1_437034_437790_+	COG0861, TerC, Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]	NA|411aa|down_5|NZ_CP016966.1_437985_439218_+	pfam02515, CoA_transf_3, CoA-transferase family III	NA|262aa|down_6|NZ_CP016966.1_439210_439996_+	PRK09245, PRK09245, crotonase/enoyl-CoA hydratase family protein	NA|324aa|down_7|NZ_CP016966.1_440062_441034_+	cd07012, PBP2_Bug_TTT, Bug (Bordetella uptake gene) protein family of periplasmic solute-binding receptors; contains the type 2 periplasmic binding fold	NA|326aa|down_8|NZ_CP016966.1_441044_442022_-	cd08414, PBP2_LTTR_aromatics_like, The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold	NA|391aa|down_9|NZ_CP016966.1_442147_443320_+	cd01152, ACAD_fadE6_17_26, Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26
GCF_002286135.1_ASM228613v1	NZ_CP016966	Bordetella pertussis strain E541, complete genome	3	996352-996446	3	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG	Orphan	TAAAAGGGCACCCGCAAGGGTGTCCTTTT	29	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG	NA|127aa|up_2|NZ_CP016966.1_994338_994719_+,NA	NA|310aa|up_9|NZ_CP016966.1_981868_982798_+	COG2025, FixB, Electron transfer flavoprotein, alpha subunit [Energy production and conversion]	NA|609aa|up_8|NZ_CP016966.1_983041_984868_+	cd01153, ACAD_fadE5, Putative acyl-CoA dehydrogenases similar to fadE5	NA|214aa|up_7|NZ_CP016966.1_984950_985592_+	cd03016, PRX_1cys, Peroxiredoxin (PRX) family, 1-cys PRX subfamily; composed of PRXs containing only one conserved cysteine, which serves as the peroxidatic cysteine	NA|345aa|up_6|NZ_CP016966.1_985781_986816_+	COG1613, Sbp, ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]	NA|355aa|up_5|NZ_CP016966.1_988652_989717_+	cd03296, ABC_CysA_sulfate_importer, ATP-binding cassette domain of the sulfate transporter	NA|303aa|up_4|NZ_CP016966.1_990514_991423_+	PRK05253, PRK05253, sulfate adenylyltransferase subunit CysD	NA|425aa|up_3|NZ_CP016966.1_992910_994185_+	TIGR04470, hypothetical_protein_ALIPUT_00462, radical SAM mobile pair protein B	NA|127aa|up_2|NZ_CP016966.1_994338_994719_+	NA	NA|291aa|up_1|NZ_CP016966.1_994726_995599_-	TIGR03340, phn_DUF6, phosphonate utilization associated putative membrane protein	NA|127aa|up_0|NZ_CP016966.1_995904_996285_+	PRK05338, rplS, 50S ribosomal protein L19; Provisional	NA|242aa|down_0|NZ_CP016966.1_996495_997221_+	cd03426, CoAse, Coenzyme A pyrophosphatase (CoAse), a member of the Nudix hydrolase superfamily, functions to catalyze the elimination of oxidized inactive CoA, which can inhibit CoA-utilizing enzymes	NA|317aa|down_1|NZ_CP016966.1_997316_998267_-	pfam00665, rve, Integrase core domain	NA|350aa|down_2|NZ_CP016966.1_998371_999421_+	cd19094, AKR_Tas-like, Escherichia coli Tas protein and similar proteins	NA|339aa|down_3|NZ_CP016966.1_999558_1000575_-	pfam02371, Transposase_20, Transposase IS116/IS110/IS902 family	NA|191aa|down_4|NZ_CP016966.1_1002083_1002656_-	COG3161, UbiC, 4-hydroxybenzoate synthetase (chorismate lyase) [Coenzyme metabolism]	NA|306aa|down_5|NZ_CP016966.1_1003498_1004416_-	cd08422, PBP2_CrgA_like, The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain	NA|1060aa|down_6|NZ_CP016966.1_1005223_1008403_+	TIGR00915, Probable_aminoglycoside_efflux_pump, The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family	NA|461aa|down_7|NZ_CP016966.1_1008399_1009782_+	TIGR01845, Outer_membrane_protein_OprM, efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family	NA|84aa|down_8|NZ_CP016966.1_1009851_1010103_-	COG2261, COG2261, Predicted membrane protein [Function unknown]	NA|217aa|down_9|NZ_CP016966.1_1010248_1010899_-	cd02968, SCO, SCO (an acronym for Synthesis of Cytochrome c Oxidase) family; composed of proteins similar to Sco1, a membrane-anchored protein possessing a soluble domain with a TRX fold
GCF_002286135.1_ASM228613v1	NZ_CP016966	Bordetella pertussis strain E541, complete genome	4	1893830-1893957	4	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG	Orphan	AAAAAGCCCCCTCGGGGGGCAGCAAGCCCGCATAGCGGGCGCAGCG	46	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG	NA,NA	NA|152aa|up_9|NZ_CP016966.1_1882738_1883194_+	cd03450, NodN, NodN (nodulation factor N) contains a single hot dog fold similar to those of the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit	NA|268aa|up_8|NZ_CP016966.1_1883207_1884011_+	COG1024, CaiD, Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]	NA|144aa|up_7|NZ_CP016966.1_1884007_1884439_+	COG1545, COG1545, Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]	NA|386aa|up_6|NZ_CP016966.1_1884435_1885593_+	PRK06158, PRK06158, thiolase; Provisional	NA|259aa|up_5|NZ_CP016966.1_1885614_1886391_+	PRK05653, fabG, 3-oxoacyl-ACP reductase FabG	NA|239aa|up_4|NZ_CP016966.1_1888555_1889272_+	TIGR02429, 3-oxoadipate_CoA-transferase_subunit_A, 3-oxoacid CoA-transferase, A subunit	NA|214aa|up_3|NZ_CP016966.1_1889264_1889906_+	TIGR02428, 3-oxoadipate_CoA-transferase_subunit_B, 3-oxoacid CoA-transferase, B subunit	NA|244aa|up_2|NZ_CP016966.1_1889940_1890672_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|71aa|up_1|NZ_CP016966.1_1890689_1890902_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|317aa|up_0|NZ_CP016966.1_1891472_1892423_+	pfam00665, rve, Integrase core domain	NA|243aa|down_0|NZ_CP016966.1_1893980_1894709_-	PRK00215, PRK00215, transcriptional repressor LexA	NA|401aa|down_1|NZ_CP016966.1_1894759_1895962_-	PRK09257, PRK09257, aromatic amino acid transaminase	NA|679aa|down_2|NZ_CP016966.1_1896039_1898076_+	PRK05298, PRK05298, excinuclease ABC subunit UvrB	NA|164aa|down_3|NZ_CP016966.1_1898328_1898820_+	cd16343, LMWPTP, Low molecular weight protein tyrosine phosphatase	NA|171aa|down_4|NZ_CP016966.1_1899035_1899548_+	TIGR02010, Putative_HTH-type_transcriptional_regulator, iron-sulfur cluster assembly transcription factor IscR	NA|404aa|down_5|NZ_CP016966.1_1899565_1900777_+	PRK14012, PRK14012, IscS subfamily cysteine desulfurase	NA|137aa|down_6|NZ_CP016966.1_1900814_1901225_+	PRK11325, PRK11325, scaffold protein; Provisional	NA|108aa|down_7|NZ_CP016966.1_1901226_1901550_+	TIGR02011, Protein_yfhF	NA|171aa|down_8|NZ_CP016966.1_1901552_1902065_+	PRK03578, hscB, Fe-S protein assembly co-chaperone HscB	NA|621aa|down_9|NZ_CP016966.1_1902194_1904057_+	PRK05183, hscA, chaperone protein HscA; Provisional
GCF_002286135.1_ASM228613v1	NZ_CP016966	Bordetella pertussis strain E541, complete genome	5	3430395-3430504	5	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG	Orphan	TTGACTGCCAAGACGGTATCTGTCCCC	27	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG	NA|138aa|up_8|NZ_CP016966.1_3416694_3417108_-,NA	NA|317aa|up_9|NZ_CP016966.1_3415757_3416708_-	pfam00665, rve, Integrase core domain	NA|138aa|up_8|NZ_CP016966.1_3416694_3417108_-	NA	NA|993aa|up_7|NZ_CP016966.1_3417061_3420040_+	pfam17936, Big_6, Bacterial Ig domain	NA|293aa|up_6|NZ_CP016966.1_3420966_3421845_+	pfam00487, FA_desaturase, Fatty acid desaturase	NA|317aa|up_5|NZ_CP016966.1_3423793_3424744_+	pfam00665, rve, Integrase core domain	NA|156aa|up_4|NZ_CP016966.1_3424740_3425208_-	PRK00203, rnhA, ribonuclease H; Reviewed	NA|257aa|up_3|NZ_CP016966.1_3425250_3426021_-	pfam08241, Methyltransf_11, Methyltransferase domain	NA|267aa|up_2|NZ_CP016966.1_3426041_3426842_+	TIGR03413, GSH_gloB, hydroxyacylglutathione hydrolase	NA|470aa|up_1|NZ_CP016966.1_3426852_3428262_+	PRK10783, mltD, membrane-bound lytic murein transglycosylase D; Provisional	NA|262aa|up_0|NZ_CP016966.1_3428356_3429142_+	PRK06997, PRK06997, enoyl-[acyl-carrier-protein] reductase FabI	NA|131aa|down_0|NZ_CP016966.1_3430505_3430898_-	COG1765, COG1765, Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]	NA|227aa|down_1|NZ_CP016966.1_3431035_3431716_+	pfam04391, DUF533, Protein of unknown function (DUF533)	NA|333aa|down_2|NZ_CP016966.1_3431720_3432719_-	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|317aa|down_3|NZ_CP016966.1_3432787_3433738_-	pfam00665, rve, Integrase core domain	NA|234aa|down_4|NZ_CP016966.1_3435242_3435944_+	PRK09468, ompR, osmolarity response regulator; Provisional	NA|475aa|down_5|NZ_CP016966.1_3435943_3437368_+	PRK09467, envZ, osmolarity sensor protein; Provisional	NA|447aa|down_6|NZ_CP016966.1_3438437_3439778_-	pfam01654, Cyt_bd_oxida_I, Cytochrome bd terminal oxidase subunit I	NA|588aa|down_7|NZ_CP016966.1_3439893_3441657_+	PRK05347, PRK05347, glutaminyl-tRNA synthetase; Provisional	NA|293aa|down_8|NZ_CP016966.1_3441768_3442647_+	PRK00030, minC, septum site-determining protein MinC	NA|272aa|down_9|NZ_CP016966.1_3442759_3443575_+	COG2894, MinD, Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]
