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_002892745.1_ASM289274v1	NZ_CP019869	Bordetella pertussis strain J042 chromosome, complete genome	1	252846-252930	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_CP019869.1_240371_240782_+	TIGR02425, putative_gamma-carboxymuconolactone_decarboxylase, 4-carboxymuconolactone decarboxylase	NA|248aa|up_8|NZ_CP019869.1_241803_242547_-	COG1802, GntR, Transcriptional regulators [Transcription]	NA|348aa|up_7|NZ_CP019869.1_242590_243634_-	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_CP019869.1_243804_245907_+	TIGR00786, TRAP_transporter_permease_protein_SiaT, TRAP transporter, DctM subunit	NA|319aa|up_5|NZ_CP019869.1_247317_248274_+	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_CP019869.1_248292_248784_-	PRK14092, PRK14092, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase	NA|452aa|up_3|NZ_CP019869.1_248780_250136_-	TIGR01942, pcnB, poly(A) polymerase	NA|233aa|up_2|NZ_CP019869.1_250136_250835_-	cd02612, HAD_PGPPase, phosphatidylglycerol-phosphate phosphatase, similar to Escherichia coli K-12 phosphatidylglycerol-phosphate phosphatase C	NA|234aa|up_1|NZ_CP019869.1_250831_251533_-	PRK08903, PRK08903, DnaA regulatory inactivator Hda; Validated	NA|350aa|up_0|NZ_CP019869.1_251785_252835_+	PRK05385, PRK05385, phosphoribosylaminoimidazole synthetase; Provisional	NA|314aa|down_0|NZ_CP019869.1_252940_253882_-	PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed	NA|630aa|down_1|NZ_CP019869.1_253878_255768_-	PRK00095, mutL, DNA mismatch repair endonuclease MutL	NA|213aa|down_2|NZ_CP019869.1_255854_256493_+	PRK10847, PRK10847, DedA family protein	NA|462aa|down_3|NZ_CP019869.1_256635_258021_-	PRK10319, PRK10319, N-acetylmuramoyl-L-alanine amidase AmiA	NA|179aa|down_4|NZ_CP019869.1_257951_258488_-	COG0802, COG0802, Predicted ATPase or kinase [General function prediction only]	NA|464aa|down_5|NZ_CP019869.1_258639_260031_+	PRK00485, fumC, fumarate hydratase; Reviewed	NA|327aa|down_6|NZ_CP019869.1_260047_261028_-	COG0679, COG0679, Predicted permeases [General function prediction only]	NA|328aa|down_7|NZ_CP019869.1_261163_262147_+	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_CP019869.1_262211_263111_-	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_CP019869.1_263217_264972_+	COG0405, Ggt, Gamma-glutamyltransferase [Amino acid transport and metabolism]
GCF_002892745.1_ASM289274v1	NZ_CP019869	Bordetella pertussis strain J042 chromosome, complete genome	2	412761-412854	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_CP019869.1_400100_401159_-	cd04187, DPM1_like_bac, Bacterial DPM1_like enzymes are related to eukaryotic DPM1	NA|165aa|up_8|NZ_CP019869.1_401288_401783_+	pfam00583, Acetyltransf_1, Acetyltransferase (GNAT) family	NA|326aa|up_7|NZ_CP019869.1_401875_402853_+	pfam00665, rve, Integrase core domain	NA|402aa|up_6|NZ_CP019869.1_403048_404254_+	TIGR00210, Sodium/glutamate_symport_carrier_protein, sodium--glutamate symport carrier (gltS)	NA|504aa|up_5|NZ_CP019869.1_404250_405762_+	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_CP019869.1_405777_407091_-	COG2031, AtoE, Short chain fatty acids transporter [Lipid metabolism]	NA|60aa|up_3|NZ_CP019869.1_407281_407461_-	pfam04391, DUF533, Protein of unknown function (DUF533)	DEDDh|245aa|up_2|NZ_CP019869.1_407870_408605_-	PRK05711, PRK05711, DNA polymerase III subunit epsilon; Provisional	NA|317aa|up_1|NZ_CP019869.1_411049_412000_+	pfam00665, rve, Integrase core domain	NA|133aa|up_0|NZ_CP019869.1_412131_412530_-	PRK00007, PRK00007, elongation factor G; Reviewed	NA|157aa|down_0|NZ_CP019869.1_412940_413411_-	pfam00582, Usp, Universal stress protein family	NA|115aa|down_1|NZ_CP019869.1_413499_413844_-	COG3453, COG3453, Uncharacterized protein conserved in bacteria [Function unknown]	NA|467aa|down_2|NZ_CP019869.1_413943_415344_-	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_CP019869.1_417132_417651_-	COG1285, SapB, Uncharacterized membrane protein [Function unknown]	NA|252aa|down_4|NZ_CP019869.1_417761_418517_+	COG0861, TerC, Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]	NA|411aa|down_5|NZ_CP019869.1_418712_419945_+	pfam02515, CoA_transf_3, CoA-transferase family III	NA|262aa|down_6|NZ_CP019869.1_419937_420723_+	PRK09245, PRK09245, crotonase/enoyl-CoA hydratase family protein	NA|324aa|down_7|NZ_CP019869.1_420789_421761_+	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_CP019869.1_421771_422749_-	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_CP019869.1_422874_424047_+	cd01152, ACAD_fadE6_17_26, Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26
GCF_002892745.1_ASM289274v1	NZ_CP019869	Bordetella pertussis strain J042 chromosome, complete genome	3	1075330-1075424	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_CP019869.1_1073316_1073697_+,NA	NA|310aa|up_9|NZ_CP019869.1_1060840_1061770_+	COG2025, FixB, Electron transfer flavoprotein, alpha subunit [Energy production and conversion]	NA|609aa|up_8|NZ_CP019869.1_1062013_1063840_+	cd01153, ACAD_fadE5, Putative acyl-CoA dehydrogenases similar to fadE5	NA|214aa|up_7|NZ_CP019869.1_1063922_1064564_+	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_CP019869.1_1064786_1065788_+	COG1613, Sbp, ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]	NA|355aa|up_5|NZ_CP019869.1_1067630_1068695_+	cd03296, ABC_CysA_sulfate_importer, ATP-binding cassette domain of the sulfate transporter	NA|303aa|up_4|NZ_CP019869.1_1069492_1070401_+	PRK05253, PRK05253, sulfate adenylyltransferase subunit CysD	NA|425aa|up_3|NZ_CP019869.1_1071888_1073163_+	TIGR04470, hypothetical_protein_ALIPUT_00462, radical SAM mobile pair protein B	NA|127aa|up_2|NZ_CP019869.1_1073316_1073697_+	NA	NA|291aa|up_1|NZ_CP019869.1_1073704_1074577_-	TIGR03340, phn_DUF6, phosphonate utilization associated putative membrane protein	NA|127aa|up_0|NZ_CP019869.1_1074882_1075263_+	PRK05338, rplS, 50S ribosomal protein L19; Provisional	NA|242aa|down_0|NZ_CP019869.1_1075473_1076199_+	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_CP019869.1_1076300_1077350_+	cd19094, AKR_Tas-like, Escherichia coli Tas protein and similar proteins	NA|339aa|down_2|NZ_CP019869.1_1077487_1078504_-	pfam02371, Transposase_20, Transposase IS116/IS110/IS902 family	NA|191aa|down_3|NZ_CP019869.1_1080012_1080585_-	COG3161, UbiC, 4-hydroxybenzoate synthetase (chorismate lyase) [Coenzyme metabolism]	NA|244aa|down_4|NZ_CP019869.1_1080644_1081376_+	COG1187, RsuA, 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]	NA|306aa|down_5|NZ_CP019869.1_1081427_1082345_-	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_CP019869.1_1083152_1086332_+	TIGR00915, Probable_aminoglycoside_efflux_pump, The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family	NA|461aa|down_7|NZ_CP019869.1_1086328_1087711_+	TIGR01845, Outer_membrane_protein_OprM, efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family	NA|84aa|down_8|NZ_CP019869.1_1087780_1088032_-	COG2261, COG2261, Predicted membrane protein [Function unknown]	NA|205aa|down_9|NZ_CP019869.1_1088177_1088792_-	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_002892745.1_ASM289274v1	NZ_CP019869	Bordetella pertussis strain J042 chromosome, complete genome	4	1205894-1206026	4	CRISPRCasFinder	no		DEDDh,cas3,DinG,csa3	Orphan	AAAAGGCCCCCACGCTGCGCCCGCTGTGCGGGCTTGCTGCCCCCAAGGGGG	51	1	3	1205945-1205975|1205945-1205975|1205945-1205975	NZ_CP019869.1_1950973-1950943|NZ_CP019869.1_2276420-2276390|NZ_CP019869.1_2773793-2773763	NA	1	1	Orphan	DEDDh,cas3,DinG,csa3	NA,NA|101aa|down_9|NZ_CP019869.1_1218745_1219048_+	NA|329aa|up_9|NZ_CP019869.1_1193755_1194742_-	PRK05231, PRK05231, homoserine kinase; Provisional	NA|338aa|up_8|NZ_CP019869.1_1194881_1195895_+	PRK11815, PRK11815, tRNA dihydrouridine(20/20a) synthase DusA	NA|317aa|up_7|NZ_CP019869.1_1195891_1196842_-	pfam00665, rve, Integrase core domain	NA|153aa|up_6|NZ_CP019869.1_1196954_1197413_-	cd04623, CBS_pair_bac_euk, Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains present in bacteria and eukaryotes	NA|438aa|up_5|NZ_CP019869.1_1197449_1198763_-	PRK04214, rbn, ribonuclease BN/unknown domain fusion protein; Reviewed	NA|124aa|up_4|NZ_CP019869.1_1198780_1199152_+	pfam09842, DUF2069, Predicted membrane protein (DUF2069)	NA|488aa|up_3|NZ_CP019869.1_1199148_1200612_+	PRK00029, PRK00029, YdiU family protein	NA|243aa|up_2|NZ_CP019869.1_1200752_1201481_+	COG0745, OmpR, Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]	NA|950aa|up_1|NZ_CP019869.1_1201462_1204312_-	cd01948, EAL, EAL domain	NA|317aa|up_0|NZ_CP019869.1_1204524_1205475_+	pfam00665, rve, Integrase core domain	NA|1077aa|down_0|NZ_CP019869.1_1206173_1209404_-	pfam03797, Autotransporter, Autotransporter beta-domain	NA|276aa|down_1|NZ_CP019869.1_1209685_1210513_-	cd01310, TatD_DNAse, TatD like proteins;  E	NA|232aa|down_2|NZ_CP019869.1_1210546_1211242_-	cd03255, ABC_MJ0796_LolCDE_FtsE, ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein	NA|427aa|down_3|NZ_CP019869.1_1211234_1212515_-	TIGR02212, releasing_system_transmembrane_protein_lolC	NA|326aa|down_4|NZ_CP019869.1_1212524_1213502_+	COG4255, COG4255, Uncharacterized protein conserved in bacteria [Function unknown]	NA|567aa|down_5|NZ_CP019869.1_1213483_1215184_+	PRK11070, PRK11070, single-stranded-DNA-specific exonuclease RecJ	NA|368aa|down_6|NZ_CP019869.1_1215286_1216391_+	PRK00578, prfB, peptide chain release factor 2; Validated	NA|252aa|down_7|NZ_CP019869.1_1216420_1217176_+	PRK07023, PRK07023, SDR family oxidoreductase	NA|507aa|down_8|NZ_CP019869.1_1217182_1218703_+	PRK00484, lysS, lysyl-tRNA synthetase; Reviewed	NA|101aa|down_9|NZ_CP019869.1_1218745_1219048_+	NA
GCF_002892745.1_ASM289274v1	NZ_CP019869	Bordetella pertussis strain J042 chromosome, complete genome	5	1950968-1951095	5	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_CP019869.1_1939930_1940332_+	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_CP019869.1_1940345_1941149_+	COG1024, CaiD, Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]	NA|144aa|up_7|NZ_CP019869.1_1941145_1941577_+	COG1545, COG1545, Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]	NA|386aa|up_6|NZ_CP019869.1_1941573_1942731_+	PRK06158, PRK06158, thiolase; Provisional	NA|259aa|up_5|NZ_CP019869.1_1942752_1943529_+	PRK05653, fabG, 3-oxoacyl-ACP reductase FabG	NA|223aa|up_4|NZ_CP019869.1_1945741_1946410_+	TIGR02429, 3-oxoadipate_CoA-transferase_subunit_A, 3-oxoacid CoA-transferase, A subunit	NA|214aa|up_3|NZ_CP019869.1_1946402_1947044_+	TIGR02428, 3-oxoadipate_CoA-transferase_subunit_B, 3-oxoacid CoA-transferase, B subunit	NA|244aa|up_2|NZ_CP019869.1_1947078_1947810_+	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_CP019869.1_1947827_1948040_+	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_CP019869.1_1948610_1949561_+	pfam00665, rve, Integrase core domain	NA|217aa|down_0|NZ_CP019869.1_1951118_1951769_-	PRK00215, PRK00215, transcriptional repressor LexA	NA|401aa|down_1|NZ_CP019869.1_1951897_1953100_-	PRK09257, PRK09257, aromatic amino acid transaminase	NA|679aa|down_2|NZ_CP019869.1_1953177_1955214_+	PRK05298, PRK05298, excinuclease ABC subunit UvrB	NA|164aa|down_3|NZ_CP019869.1_1955466_1955958_+	cd16343, LMWPTP, Low molecular weight protein tyrosine phosphatase	NA|171aa|down_4|NZ_CP019869.1_1956173_1956686_+	TIGR02010, Putative_HTH-type_transcriptional_regulator, iron-sulfur cluster assembly transcription factor IscR	NA|404aa|down_5|NZ_CP019869.1_1956703_1957915_+	PRK14012, PRK14012, IscS subfamily cysteine desulfurase	NA|137aa|down_6|NZ_CP019869.1_1957952_1958363_+	PRK11325, PRK11325, scaffold protein; Provisional	NA|108aa|down_7|NZ_CP019869.1_1958364_1958688_+	TIGR02011, Protein_yfhF	NA|171aa|down_8|NZ_CP019869.1_1958690_1959203_+	PRK03578, hscB, Fe-S protein assembly co-chaperone HscB	NA|621aa|down_9|NZ_CP019869.1_1959332_1961195_+	PRK05183, hscA, chaperone protein HscA; Provisional
GCF_002892745.1_ASM289274v1	NZ_CP019869	Bordetella pertussis strain J042 chromosome, complete genome	6	3502217-3502326	6	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_CP019869.1_3486494_3487583_+	cd08948, 5beta-POR_like_SDR_a, progesterone 5-beta-reductase-like proteins (5beta-POR), atypical (a) SDRs	NA|317aa|up_8|NZ_CP019869.1_3487579_3488530_-	pfam00665, rve, Integrase core domain	NA|993aa|up_7|NZ_CP019869.1_3488883_3491862_+	pfam17936, Big_6, Bacterial Ig domain	NA|293aa|up_6|NZ_CP019869.1_3492788_3493667_+	pfam00487, FA_desaturase, Fatty acid desaturase	NA|317aa|up_5|NZ_CP019869.1_3495615_3496566_+	pfam00665, rve, Integrase core domain	NA|156aa|up_4|NZ_CP019869.1_3496562_3497030_-	PRK00203, rnhA, ribonuclease H; Reviewed	NA|257aa|up_3|NZ_CP019869.1_3497072_3497843_-	pfam08241, Methyltransf_11, Methyltransferase domain	NA|267aa|up_2|NZ_CP019869.1_3497863_3498664_+	TIGR03413, GSH_gloB, hydroxyacylglutathione hydrolase	NA|470aa|up_1|NZ_CP019869.1_3498674_3500084_+	PRK10783, mltD, membrane-bound lytic murein transglycosylase D; Provisional	NA|262aa|up_0|NZ_CP019869.1_3500178_3500964_+	PRK06997, PRK06997, enoyl-[acyl-carrier-protein] reductase FabI	NA|131aa|down_0|NZ_CP019869.1_3502327_3502720_-	COG1765, COG1765, Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]	NA|227aa|down_1|NZ_CP019869.1_3502857_3503538_+	pfam04391, DUF533, Protein of unknown function (DUF533)	NA|324aa|down_2|NZ_CP019869.1_3503542_3504514_-	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_CP019869.1_3504609_3505560_-	pfam00665, rve, Integrase core domain	NA|234aa|down_4|NZ_CP019869.1_3507064_3507766_+	PRK09468, ompR, osmolarity response regulator; Provisional	NA|475aa|down_5|NZ_CP019869.1_3507765_3509190_+	PRK09467, envZ, osmolarity sensor protein; Provisional	NA|352aa|down_6|NZ_CP019869.1_3509206_3510262_-	pfam02322, Cyt_bd_oxida_II, Cytochrome bd terminal oxidase subunit II	NA|447aa|down_7|NZ_CP019869.1_3510258_3511599_-	pfam01654, Cyt_bd_oxida_I, Cytochrome bd terminal oxidase subunit I	NA|588aa|down_8|NZ_CP019869.1_3511714_3513478_+	PRK05347, PRK05347, glutaminyl-tRNA synthetase; Provisional	NA|293aa|down_9|NZ_CP019869.1_3513589_3514468_+	PRK00030, minC, septum site-determining protein MinC
