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_001686585.1_ASM168658v1	NZ_CP015769	Bordetella pertussis strain VA-145, complete genome	1	690086-690179	1	CRISPRCasFinder	no		csa3,cas3,DinG,DEDDh	Orphan	GTGCCTGTCCCCGCCGGGACAGGCAC	26	0	0	NA	NA	NA	1	1	Orphan	csa3,cas3,DinG,DEDDh	NA|132aa|up_9|NZ_CP015769.1_681065_681461_+,NA	NA|132aa|up_9|NZ_CP015769.1_681065_681461_+	NA	NA|131aa|up_8|NZ_CP015769.1_681457_681850_+	cd03441, R_hydratase_like, (R)-hydratase [(R)-specific enoyl-CoA hydratase]	NA|387aa|up_7|NZ_CP015769.1_681860_683021_+	cd01160, LCAD, Long chain acyl-CoA dehydrogenase	NA|324aa|up_6|NZ_CP015769.1_683058_684030_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|383aa|up_5|NZ_CP015769.1_684037_685186_+	pfam02515, CoA_transf_3, CoA-transferase family III	NA|297aa|up_4|NZ_CP015769.1_685182_686073_-	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|316aa|up_3|NZ_CP015769.1_686279_687227_+	cd00408, DHDPS-like, Dihydrodipicolinate synthase family	NA|317aa|up_2|NZ_CP015769.1_687325_688276_+	pfam00665, rve, Integrase core domain	NA|317aa|up_1|NZ_CP015769.1_688374_689325_+	pfam00665, rve, Integrase core domain	NA|133aa|up_0|NZ_CP015769.1_689456_689855_-	PRK00007, PRK00007, elongation factor G; Reviewed	NA|157aa|down_0|NZ_CP015769.1_690265_690736_-	pfam00582, Usp, Universal stress protein family	NA|115aa|down_1|NZ_CP015769.1_690824_691169_-	COG3453, COG3453, Uncharacterized protein conserved in bacteria [Function unknown]	NA|467aa|down_2|NZ_CP015769.1_691268_692669_-	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_CP015769.1_694457_694976_-	COG1285, SapB, Uncharacterized membrane protein [Function unknown]	NA|252aa|down_4|NZ_CP015769.1_695086_695842_+	COG0861, TerC, Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]	NA|411aa|down_5|NZ_CP015769.1_696037_697270_+	pfam02515, CoA_transf_3, CoA-transferase family III	NA|262aa|down_6|NZ_CP015769.1_697262_698048_+	PRK09245, PRK09245, crotonase/enoyl-CoA hydratase family protein	NA|324aa|down_7|NZ_CP015769.1_698114_699086_+	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_CP015769.1_699096_700074_-	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_CP015769.1_700199_701372_+	cd01152, ACAD_fadE6_17_26, Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26
GCF_001686585.1_ASM168658v1	NZ_CP015769	Bordetella pertussis strain VA-145, complete genome	2	1255452-1255546	2	CRISPRCasFinder	no		csa3,cas3,DinG,DEDDh	Orphan	TAAAAGGGCACCCGCAAGGGTGTCCTTTT	29	0	0	NA	NA	NA	1	1	Orphan	csa3,cas3,DinG,DEDDh	NA|127aa|up_2|NZ_CP015769.1_1253438_1253819_+,NA	NA|310aa|up_9|NZ_CP015769.1_1240968_1241898_+	COG2025, FixB, Electron transfer flavoprotein, alpha subunit [Energy production and conversion]	NA|609aa|up_8|NZ_CP015769.1_1242141_1243968_+	cd01153, ACAD_fadE5, Putative acyl-CoA dehydrogenases similar to fadE5	NA|214aa|up_7|NZ_CP015769.1_1244050_1244692_+	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_CP015769.1_1244881_1245916_+	COG1613, Sbp, ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]	NA|355aa|up_5|NZ_CP015769.1_1247752_1248817_+	cd03296, ABC_CysA_sulfate_importer, ATP-binding cassette domain of the sulfate transporter	NA|303aa|up_4|NZ_CP015769.1_1249614_1250523_+	PRK05253, PRK05253, sulfate adenylyltransferase subunit CysD	NA|425aa|up_3|NZ_CP015769.1_1252010_1253285_+	TIGR04470, hypothetical_protein_ALIPUT_00462, radical SAM mobile pair protein B	NA|127aa|up_2|NZ_CP015769.1_1253438_1253819_+	NA	NA|291aa|up_1|NZ_CP015769.1_1253826_1254699_-	TIGR03340, phn_DUF6, phosphonate utilization associated putative membrane protein	NA|127aa|up_0|NZ_CP015769.1_1255004_1255385_+	PRK05338, rplS, 50S ribosomal protein L19; Provisional	NA|242aa|down_0|NZ_CP015769.1_1255595_1256321_+	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_CP015769.1_1256416_1257367_-	pfam00665, rve, Integrase core domain	NA|350aa|down_2|NZ_CP015769.1_1257471_1258521_+	cd19094, AKR_Tas-like, Escherichia coli Tas protein and similar proteins	NA|339aa|down_3|NZ_CP015769.1_1258658_1259675_-	pfam02371, Transposase_20, Transposase IS116/IS110/IS902 family	NA|191aa|down_4|NZ_CP015769.1_1261183_1261756_-	COG3161, UbiC, 4-hydroxybenzoate synthetase (chorismate lyase) [Coenzyme metabolism]	NA|244aa|down_5|NZ_CP015769.1_1261815_1262547_+	COG1187, RsuA, 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]	NA|306aa|down_6|NZ_CP015769.1_1262598_1263516_-	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_7|NZ_CP015769.1_1264323_1267503_+	TIGR00915, Probable_aminoglycoside_efflux_pump, The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family	NA|461aa|down_8|NZ_CP015769.1_1267499_1268882_+	TIGR01845, Outer_membrane_protein_OprM, efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family	NA|84aa|down_9|NZ_CP015769.1_1268951_1269203_-	COG2261, COG2261, Predicted membrane protein [Function unknown]
GCF_001686585.1_ASM168658v1	NZ_CP015769	Bordetella pertussis strain VA-145, complete genome	3	2150834-2150961	3	CRISPRCasFinder	no		csa3,cas3,DinG,DEDDh	Orphan	AAAAAGCCCCCTCGGGGGGCAGCAAGCCCGCATAGCGGGCGCAGCG	46	0	0	NA	NA	NA	1	1	Orphan	csa3,cas3,DinG,DEDDh	NA,NA	NA|152aa|up_9|NZ_CP015769.1_2139742_2140198_+	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_CP015769.1_2140211_2141015_+	COG1024, CaiD, Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]	NA|144aa|up_7|NZ_CP015769.1_2141011_2141443_+	COG1545, COG1545, Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]	NA|386aa|up_6|NZ_CP015769.1_2141439_2142597_+	PRK06158, PRK06158, thiolase; Provisional	NA|259aa|up_5|NZ_CP015769.1_2142618_2143395_+	PRK05653, fabG, 3-oxoacyl-ACP reductase FabG	NA|239aa|up_4|NZ_CP015769.1_2145559_2146276_+	TIGR02429, 3-oxoadipate_CoA-transferase_subunit_A, 3-oxoacid CoA-transferase, A subunit	NA|214aa|up_3|NZ_CP015769.1_2146268_2146910_+	TIGR02428, 3-oxoadipate_CoA-transferase_subunit_B, 3-oxoacid CoA-transferase, B subunit	NA|244aa|up_2|NZ_CP015769.1_2146944_2147676_+	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_CP015769.1_2147693_2147906_+	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_CP015769.1_2148476_2149427_+	pfam00665, rve, Integrase core domain	NA|243aa|down_0|NZ_CP015769.1_2150984_2151713_-	PRK00215, PRK00215, transcriptional repressor LexA	NA|401aa|down_1|NZ_CP015769.1_2151763_2152966_-	PRK09257, PRK09257, aromatic amino acid transaminase	NA|679aa|down_2|NZ_CP015769.1_2153043_2155080_+	PRK05298, PRK05298, excinuclease ABC subunit UvrB	NA|164aa|down_3|NZ_CP015769.1_2155332_2155824_+	cd16343, LMWPTP, Low molecular weight protein tyrosine phosphatase	NA|171aa|down_4|NZ_CP015769.1_2156039_2156552_+	TIGR02010, Putative_HTH-type_transcriptional_regulator, iron-sulfur cluster assembly transcription factor IscR	NA|404aa|down_5|NZ_CP015769.1_2156569_2157781_+	PRK14012, PRK14012, IscS subfamily cysteine desulfurase	NA|137aa|down_6|NZ_CP015769.1_2157818_2158229_+	PRK11325, PRK11325, scaffold protein; Provisional	NA|108aa|down_7|NZ_CP015769.1_2158230_2158554_+	TIGR02011, Protein_yfhF	NA|171aa|down_8|NZ_CP015769.1_2158556_2159069_+	PRK03578, hscB, Fe-S protein assembly co-chaperone HscB	NA|621aa|down_9|NZ_CP015769.1_2159198_2161061_+	PRK05183, hscA, chaperone protein HscA; Provisional
GCF_001686585.1_ASM168658v1	NZ_CP015769	Bordetella pertussis strain VA-145, complete genome	4	3697920-3698029	4	CRISPRCasFinder	no		csa3,cas3,DinG,DEDDh	Orphan	TTGACTGCCAAGACGGTATCTGTCCCC	27	0	0	NA	NA	NA	1	1	Orphan	csa3,cas3,DinG,DEDDh	NA|138aa|up_8|NZ_CP015769.1_3684219_3684633_-,NA	NA|317aa|up_9|NZ_CP015769.1_3683282_3684233_-	pfam00665, rve, Integrase core domain	NA|138aa|up_8|NZ_CP015769.1_3684219_3684633_-	NA	NA|993aa|up_7|NZ_CP015769.1_3684586_3687565_+	pfam17936, Big_6, Bacterial Ig domain	NA|293aa|up_6|NZ_CP015769.1_3688491_3689370_+	pfam00487, FA_desaturase, Fatty acid desaturase	NA|317aa|up_5|NZ_CP015769.1_3691318_3692269_+	pfam00665, rve, Integrase core domain	NA|156aa|up_4|NZ_CP015769.1_3692265_3692733_-	PRK00203, rnhA, ribonuclease H; Reviewed	NA|257aa|up_3|NZ_CP015769.1_3692775_3693546_-	pfam08241, Methyltransf_11, Methyltransferase domain	NA|267aa|up_2|NZ_CP015769.1_3693566_3694367_+	TIGR03413, GSH_gloB, hydroxyacylglutathione hydrolase	NA|470aa|up_1|NZ_CP015769.1_3694377_3695787_+	PRK10783, mltD, membrane-bound lytic murein transglycosylase D; Provisional	NA|262aa|up_0|NZ_CP015769.1_3695881_3696667_+	PRK06997, PRK06997, enoyl-[acyl-carrier-protein] reductase FabI	NA|131aa|down_0|NZ_CP015769.1_3698030_3698423_-	COG1765, COG1765, Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]	NA|227aa|down_1|NZ_CP015769.1_3698560_3699241_+	pfam04391, DUF533, Protein of unknown function (DUF533)	NA|333aa|down_2|NZ_CP015769.1_3699245_3700244_-	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_CP015769.1_3700312_3701263_-	pfam00665, rve, Integrase core domain	NA|234aa|down_4|NZ_CP015769.1_3702767_3703469_+	PRK09468, ompR, osmolarity response regulator; Provisional	NA|475aa|down_5|NZ_CP015769.1_3703468_3704893_+	PRK09467, envZ, osmolarity sensor protein; Provisional	NA|447aa|down_6|NZ_CP015769.1_3705962_3707303_-	pfam01654, Cyt_bd_oxida_I, Cytochrome bd terminal oxidase subunit I	NA|588aa|down_7|NZ_CP015769.1_3707418_3709182_+	PRK05347, PRK05347, glutaminyl-tRNA synthetase; Provisional	NA|293aa|down_8|NZ_CP015769.1_3709293_3710172_+	PRK00030, minC, septum site-determining protein MinC	NA|272aa|down_9|NZ_CP015769.1_3710284_3711100_+	COG2894, MinD, Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]
GCF_001686585.1_ASM168658v1	NZ_CP015769	Bordetella pertussis strain VA-145, complete genome	5	4072403-4072487	5	CRISPRCasFinder	no		csa3,cas3,DinG,DEDDh	Orphan	CTGTCCCCGCGGGGACAGGCACC	23	0	0	NA	NA	NA	1	1	Orphan	csa3,cas3,DinG,DEDDh	NA,NA	NA|585aa|up_9|NZ_CP015769.1_4060360_4062115_-	COG0405, Ggt, Gamma-glutamyltransferase [Amino acid transport and metabolism]	NA|300aa|up_8|NZ_CP015769.1_4062221_4063121_+	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|328aa|up_7|NZ_CP015769.1_4063185_4064169_-	cd13577, PBP2_BugE_Glu, Glutamate transporter of Bug (Bordetella uptake gene) protein family; contains the type 2 periplasmic binding fold	NA|327aa|up_6|NZ_CP015769.1_4064304_4065285_+	COG0679, COG0679, Predicted permeases [General function prediction only]	NA|464aa|up_5|NZ_CP015769.1_4065301_4066693_-	PRK00485, fumC, fumarate hydratase; Reviewed	NA|179aa|up_4|NZ_CP015769.1_4066844_4067381_+	COG0802, COG0802, Predicted ATPase or kinase [General function prediction only]	NA|462aa|up_3|NZ_CP015769.1_4067311_4068697_+	PRK10319, PRK10319, N-acetylmuramoyl-L-alanine amidase AmiA	NA|213aa|up_2|NZ_CP015769.1_4068839_4069478_-	PRK10847, PRK10847, DedA family protein	NA|630aa|up_1|NZ_CP015769.1_4069564_4071454_+	PRK00095, mutL, DNA mismatch repair endonuclease MutL	NA|314aa|up_0|NZ_CP015769.1_4071450_4072392_+	PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed	NA|350aa|down_0|NZ_CP015769.1_4072497_4073547_-	PRK05385, PRK05385, phosphoribosylaminoimidazole synthetase; Provisional	NA|234aa|down_1|NZ_CP015769.1_4073799_4074501_+	PRK08903, PRK08903, DnaA regulatory inactivator Hda; Validated	NA|233aa|down_2|NZ_CP015769.1_4074497_4075196_+	cd02612, HAD_PGPPase, phosphatidylglycerol-phosphate phosphatase, similar to Escherichia coli K-12 phosphatidylglycerol-phosphate phosphatase C	NA|452aa|down_3|NZ_CP015769.1_4075196_4076552_+	TIGR01942, pcnB, poly(A) polymerase	NA|164aa|down_4|NZ_CP015769.1_4076548_4077040_+	PRK14092, PRK14092, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase	NA|319aa|down_5|NZ_CP015769.1_4077058_4078015_-	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|701aa|down_6|NZ_CP015769.1_4079425_4081528_-	TIGR00786, TRAP_transporter_permease_protein_SiaT, TRAP transporter, DctM subunit	NA|348aa|down_7|NZ_CP015769.1_4081698_4082742_+	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|248aa|down_8|NZ_CP015769.1_4082785_4083529_+	COG1802, GntR, Transcriptional regulators [Transcription]	NA|137aa|down_9|NZ_CP015769.1_4084550_4084961_-	TIGR02425, putative_gamma-carboxymuconolactone_decarboxylase, 4-carboxymuconolactone decarboxylase
