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_001605295.1_ASM160529v1	NZ_CP010964	Bordetella pertussis strain E476 chromosome, complete genome	1	252847-252931	1	CRISPRCasFinder	no		DEDDh,cas3,DinG,csa3	Orphan	GGTGCCTGTCCCCGCGGGGACAG	23	0	0	NA	NA	NA	1	1	Orphan	DEDDh,cas3,DinG,csa3	NA,NA	NA|137aa|up_9|NZ_CP010964.1_240372_240783_+	TIGR02425, putative_gamma-carboxymuconolactone_decarboxylase, 4-carboxymuconolactone decarboxylase	NA|248aa|up_8|NZ_CP010964.1_241804_242548_-	COG1802, GntR, Transcriptional regulators [Transcription]	NA|348aa|up_7|NZ_CP010964.1_242591_243635_-	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_CP010964.1_243805_245908_+	TIGR00786, TRAP_transporter_permease_protein_SiaT, TRAP transporter, DctM subunit	NA|319aa|up_5|NZ_CP010964.1_247318_248275_+	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_CP010964.1_248293_248785_-	PRK14092, PRK14092, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase	NA|452aa|up_3|NZ_CP010964.1_248781_250137_-	TIGR01942, pcnB, poly(A) polymerase	NA|233aa|up_2|NZ_CP010964.1_250137_250836_-	cd02612, HAD_PGPPase, phosphatidylglycerol-phosphate phosphatase, similar to Escherichia coli K-12 phosphatidylglycerol-phosphate phosphatase C	NA|234aa|up_1|NZ_CP010964.1_250832_251534_-	PRK08903, PRK08903, DnaA regulatory inactivator Hda; Validated	NA|350aa|up_0|NZ_CP010964.1_251786_252836_+	PRK05385, PRK05385, phosphoribosylaminoimidazole synthetase; Provisional	NA|314aa|down_0|NZ_CP010964.1_252941_253883_-	PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed	NA|630aa|down_1|NZ_CP010964.1_253879_255769_-	PRK00095, mutL, DNA mismatch repair endonuclease MutL	NA|213aa|down_2|NZ_CP010964.1_255855_256494_+	PRK10847, PRK10847, DedA family protein	NA|462aa|down_3|NZ_CP010964.1_256636_258022_-	PRK10319, PRK10319, N-acetylmuramoyl-L-alanine amidase AmiA	NA|179aa|down_4|NZ_CP010964.1_257952_258489_-	COG0802, COG0802, Predicted ATPase or kinase [General function prediction only]	NA|464aa|down_5|NZ_CP010964.1_258640_260032_+	PRK00485, fumC, fumarate hydratase; Reviewed	NA|327aa|down_6|NZ_CP010964.1_260048_261029_-	COG0679, COG0679, Predicted permeases [General function prediction only]	NA|328aa|down_7|NZ_CP010964.1_261164_262148_+	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_CP010964.1_262212_263112_-	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_CP010964.1_263218_264973_+	COG0405, Ggt, Gamma-glutamyltransferase [Amino acid transport and metabolism]
GCF_001605295.1_ASM160529v1	NZ_CP010964	Bordetella pertussis strain E476 chromosome, complete genome	2	412762-412855	2	CRISPRCasFinder	no	DEDDh	DEDDh,cas3,DinG,csa3	Unclear	GTGCCTGTCCCCGCCGGGACAGGCAC	26	0	0	NA	NA	NA	1	1	Orphan	DEDDh,cas3,DinG,csa3	NA,NA	NA|353aa|up_9|NZ_CP010964.1_400101_401160_-	cd04187, DPM1_like_bac, Bacterial DPM1_like enzymes are related to eukaryotic DPM1	NA|165aa|up_8|NZ_CP010964.1_401289_401784_+	pfam00583, Acetyltransf_1, Acetyltransferase (GNAT) family	NA|326aa|up_7|NZ_CP010964.1_401876_402854_+	pfam00665, rve, Integrase core domain	NA|402aa|up_6|NZ_CP010964.1_403049_404255_+	TIGR00210, Sodium/glutamate_symport_carrier_protein, sodium--glutamate symport carrier (gltS)	NA|504aa|up_5|NZ_CP010964.1_404251_405763_+	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_CP010964.1_405778_407092_-	COG2031, AtoE, Short chain fatty acids transporter [Lipid metabolism]	NA|60aa|up_3|NZ_CP010964.1_407282_407462_-	pfam04391, DUF533, Protein of unknown function (DUF533)	DEDDh|245aa|up_2|NZ_CP010964.1_407871_408606_-	PRK05711, PRK05711, DNA polymerase III subunit epsilon; Provisional	NA|317aa|up_1|NZ_CP010964.1_411050_412001_+	pfam00665, rve, Integrase core domain	NA|133aa|up_0|NZ_CP010964.1_412132_412531_-	PRK00007, PRK00007, elongation factor G; Reviewed	NA|157aa|down_0|NZ_CP010964.1_412941_413412_-	pfam00582, Usp, Universal stress protein family	NA|115aa|down_1|NZ_CP010964.1_413500_413845_-	COG3453, COG3453, Uncharacterized protein conserved in bacteria [Function unknown]	NA|467aa|down_2|NZ_CP010964.1_413944_415345_-	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_CP010964.1_417133_417652_-	COG1285, SapB, Uncharacterized membrane protein [Function unknown]	NA|252aa|down_4|NZ_CP010964.1_417762_418518_+	COG0861, TerC, Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]	NA|411aa|down_5|NZ_CP010964.1_418713_419946_+	pfam02515, CoA_transf_3, CoA-transferase family III	NA|262aa|down_6|NZ_CP010964.1_419938_420724_+	PRK09245, PRK09245, crotonase/enoyl-CoA hydratase family protein	NA|324aa|down_7|NZ_CP010964.1_420790_421762_+	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_CP010964.1_421772_422750_-	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_CP010964.1_422875_424048_+	cd01152, ACAD_fadE6_17_26, Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26
GCF_001605295.1_ASM160529v1	NZ_CP010964	Bordetella pertussis strain E476 chromosome, complete genome	3	1018839-1018933	3	CRISPRCasFinder	no		DEDDh,cas3,DinG,csa3	Orphan	TAAAAGGGCACCCGCAAGGGTGTCCTTTT	29	0	0	NA	NA	NA	1	1	Orphan	DEDDh,cas3,DinG,csa3	NA|127aa|up_2|NZ_CP010964.1_1016825_1017206_+,NA	NA|310aa|up_9|NZ_CP010964.1_1004349_1005279_+	COG2025, FixB, Electron transfer flavoprotein, alpha subunit [Energy production and conversion]	NA|609aa|up_8|NZ_CP010964.1_1005522_1007349_+	cd01153, ACAD_fadE5, Putative acyl-CoA dehydrogenases similar to fadE5	NA|214aa|up_7|NZ_CP010964.1_1007431_1008073_+	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|334aa|up_6|NZ_CP010964.1_1008295_1009297_+	COG1613, Sbp, ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]	NA|355aa|up_5|NZ_CP010964.1_1011139_1012204_+	cd03296, ABC_CysA_sulfate_importer, ATP-binding cassette domain of the sulfate transporter	NA|303aa|up_4|NZ_CP010964.1_1013001_1013910_+	PRK05253, PRK05253, sulfate adenylyltransferase subunit CysD	NA|425aa|up_3|NZ_CP010964.1_1015397_1016672_+	TIGR04470, hypothetical_protein_ALIPUT_00462, radical SAM mobile pair protein B	NA|127aa|up_2|NZ_CP010964.1_1016825_1017206_+	NA	NA|291aa|up_1|NZ_CP010964.1_1017213_1018086_-	TIGR03340, phn_DUF6, phosphonate utilization associated putative membrane protein	NA|127aa|up_0|NZ_CP010964.1_1018391_1018772_+	PRK05338, rplS, 50S ribosomal protein L19; Provisional	NA|242aa|down_0|NZ_CP010964.1_1018982_1019708_+	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|350aa|down_1|NZ_CP010964.1_1019809_1020859_+	cd19094, AKR_Tas-like, Escherichia coli Tas protein and similar proteins	NA|339aa|down_2|NZ_CP010964.1_1020996_1022013_-	pfam02371, Transposase_20, Transposase IS116/IS110/IS902 family	NA|191aa|down_3|NZ_CP010964.1_1023521_1024094_-	COG3161, UbiC, 4-hydroxybenzoate synthetase (chorismate lyase) [Coenzyme metabolism]	NA|244aa|down_4|NZ_CP010964.1_1024153_1024885_+	COG1187, RsuA, 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]	NA|306aa|down_5|NZ_CP010964.1_1024936_1025854_-	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_CP010964.1_1026661_1029841_+	TIGR00915, Probable_aminoglycoside_efflux_pump, The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family	NA|461aa|down_7|NZ_CP010964.1_1029837_1031220_+	TIGR01845, Outer_membrane_protein_OprM, efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family	NA|84aa|down_8|NZ_CP010964.1_1031289_1031541_-	COG2261, COG2261, Predicted membrane protein [Function unknown]	NA|205aa|down_9|NZ_CP010964.1_1031686_1032301_-	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_001605295.1_ASM160529v1	NZ_CP010964	Bordetella pertussis strain E476 chromosome, complete genome	4	1893435-1893562	4	CRISPRCasFinder	no		DEDDh,cas3,DinG,csa3	Orphan	AAAAAGCCCCCTCGGGGGGCAGCAAGCCCGCATAGCGGGCGCAGCG	46	0	0	NA	NA	NA	1	1	Orphan	DEDDh,cas3,DinG,csa3	NA,NA	NA|134aa|up_9|NZ_CP010964.1_1882397_1882799_+	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_CP010964.1_1882812_1883616_+	COG1024, CaiD, Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]	NA|144aa|up_7|NZ_CP010964.1_1883612_1884044_+	COG1545, COG1545, Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]	NA|386aa|up_6|NZ_CP010964.1_1884040_1885198_+	PRK06158, PRK06158, thiolase; Provisional	NA|259aa|up_5|NZ_CP010964.1_1885219_1885996_+	PRK05653, fabG, 3-oxoacyl-ACP reductase FabG	NA|223aa|up_4|NZ_CP010964.1_1888208_1888877_+	TIGR02429, 3-oxoadipate_CoA-transferase_subunit_A, 3-oxoacid CoA-transferase, A subunit	NA|214aa|up_3|NZ_CP010964.1_1888869_1889511_+	TIGR02428, 3-oxoadipate_CoA-transferase_subunit_B, 3-oxoacid CoA-transferase, B subunit	NA|244aa|up_2|NZ_CP010964.1_1889545_1890277_+	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_CP010964.1_1890294_1890507_+	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_CP010964.1_1891077_1892028_+	pfam00665, rve, Integrase core domain	NA|217aa|down_0|NZ_CP010964.1_1893585_1894236_-	PRK00215, PRK00215, transcriptional repressor LexA	NA|401aa|down_1|NZ_CP010964.1_1894364_1895567_-	PRK09257, PRK09257, aromatic amino acid transaminase	NA|679aa|down_2|NZ_CP010964.1_1895644_1897681_+	PRK05298, PRK05298, excinuclease ABC subunit UvrB	NA|164aa|down_3|NZ_CP010964.1_1897933_1898425_+	cd16343, LMWPTP, Low molecular weight protein tyrosine phosphatase	NA|171aa|down_4|NZ_CP010964.1_1898640_1899153_+	TIGR02010, Putative_HTH-type_transcriptional_regulator, iron-sulfur cluster assembly transcription factor IscR	NA|404aa|down_5|NZ_CP010964.1_1899170_1900382_+	PRK14012, PRK14012, IscS subfamily cysteine desulfurase	NA|137aa|down_6|NZ_CP010964.1_1900419_1900830_+	PRK11325, PRK11325, scaffold protein; Provisional	NA|108aa|down_7|NZ_CP010964.1_1900831_1901155_+	TIGR02011, Protein_yfhF	NA|171aa|down_8|NZ_CP010964.1_1901157_1901670_+	PRK03578, hscB, Fe-S protein assembly co-chaperone HscB	NA|621aa|down_9|NZ_CP010964.1_1901799_1903662_+	PRK05183, hscA, chaperone protein HscA; Provisional
GCF_001605295.1_ASM160529v1	NZ_CP010964	Bordetella pertussis strain E476 chromosome, complete genome	5	3443645-3443754	5	CRISPRCasFinder	no		DEDDh,cas3,DinG,csa3	Orphan	TTGACTGCCAAGACGGTATCTGTCCCC	27	0	0	NA	NA	NA	1	1	Orphan	DEDDh,cas3,DinG,csa3	NA,NA	NA|363aa|up_9|NZ_CP010964.1_3427922_3429011_+	cd08948, 5beta-POR_like_SDR_a, progesterone 5-beta-reductase-like proteins (5beta-POR), atypical (a) SDRs	NA|317aa|up_8|NZ_CP010964.1_3429007_3429958_-	pfam00665, rve, Integrase core domain	NA|993aa|up_7|NZ_CP010964.1_3430311_3433290_+	pfam17936, Big_6, Bacterial Ig domain	NA|293aa|up_6|NZ_CP010964.1_3434216_3435095_+	pfam00487, FA_desaturase, Fatty acid desaturase	NA|317aa|up_5|NZ_CP010964.1_3437043_3437994_+	pfam00665, rve, Integrase core domain	NA|156aa|up_4|NZ_CP010964.1_3437990_3438458_-	PRK00203, rnhA, ribonuclease H; Reviewed	NA|257aa|up_3|NZ_CP010964.1_3438500_3439271_-	pfam08241, Methyltransf_11, Methyltransferase domain	NA|267aa|up_2|NZ_CP010964.1_3439291_3440092_+	TIGR03413, GSH_gloB, hydroxyacylglutathione hydrolase	NA|470aa|up_1|NZ_CP010964.1_3440102_3441512_+	PRK10783, mltD, membrane-bound lytic murein transglycosylase D; Provisional	NA|262aa|up_0|NZ_CP010964.1_3441606_3442392_+	PRK06997, PRK06997, enoyl-[acyl-carrier-protein] reductase FabI	NA|131aa|down_0|NZ_CP010964.1_3443755_3444148_-	COG1765, COG1765, Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]	NA|227aa|down_1|NZ_CP010964.1_3444285_3444966_+	pfam04391, DUF533, Protein of unknown function (DUF533)	NA|324aa|down_2|NZ_CP010964.1_3444970_3445942_-	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_CP010964.1_3446037_3446988_-	pfam00665, rve, Integrase core domain	NA|234aa|down_4|NZ_CP010964.1_3448492_3449194_+	PRK09468, ompR, osmolarity response regulator; Provisional	NA|475aa|down_5|NZ_CP010964.1_3449193_3450618_+	PRK09467, envZ, osmolarity sensor protein; Provisional	NA|352aa|down_6|NZ_CP010964.1_3450634_3451690_-	pfam02322, Cyt_bd_oxida_II, Cytochrome bd terminal oxidase subunit II	NA|447aa|down_7|NZ_CP010964.1_3451686_3453027_-	pfam01654, Cyt_bd_oxida_I, Cytochrome bd terminal oxidase subunit I	NA|588aa|down_8|NZ_CP010964.1_3453142_3454906_+	PRK05347, PRK05347, glutaminyl-tRNA synthetase; Provisional	NA|293aa|down_9|NZ_CP010964.1_3455017_3455896_+	PRK00030, minC, septum site-determining protein MinC
