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_001605215.1_ASM160521v1	NZ_CP010845	Bordetella pertussis strain H561 chromosome, complete genome	1	250590-250674	1	CRISPRCasFinder	no		csa3,cas3,DinG,DEDDh	Orphan	GGTGCCTGTCCCCGCGGGGACAG	23	0	0	NA	NA	NA	1	1	Orphan	csa3,cas3,DinG,DEDDh	NA,NA	NA|137aa|up_9|NZ_CP010845.1_238115_238526_+	TIGR02425, putative_gamma-carboxymuconolactone_decarboxylase, 4-carboxymuconolactone decarboxylase	NA|248aa|up_8|NZ_CP010845.1_239547_240291_-	COG1802, GntR, Transcriptional regulators [Transcription]	NA|348aa|up_7|NZ_CP010845.1_240334_241378_-	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_CP010845.1_241548_243651_+	TIGR00786, TRAP_transporter_permease_protein_SiaT, TRAP transporter, DctM subunit	NA|319aa|up_5|NZ_CP010845.1_245061_246018_+	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_CP010845.1_246036_246528_-	PRK14092, PRK14092, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase	NA|452aa|up_3|NZ_CP010845.1_246524_247880_-	TIGR01942, pcnB, poly(A) polymerase	NA|233aa|up_2|NZ_CP010845.1_247880_248579_-	cd02612, HAD_PGPPase, phosphatidylglycerol-phosphate phosphatase, similar to Escherichia coli K-12 phosphatidylglycerol-phosphate phosphatase C	NA|234aa|up_1|NZ_CP010845.1_248575_249277_-	PRK08903, PRK08903, DnaA regulatory inactivator Hda; Validated	NA|350aa|up_0|NZ_CP010845.1_249529_250579_+	PRK05385, PRK05385, phosphoribosylaminoimidazole synthetase; Provisional	NA|314aa|down_0|NZ_CP010845.1_250684_251626_-	PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed	NA|630aa|down_1|NZ_CP010845.1_251622_253512_-	PRK00095, mutL, DNA mismatch repair endonuclease MutL	NA|213aa|down_2|NZ_CP010845.1_253598_254237_+	PRK10847, PRK10847, DedA family protein	NA|462aa|down_3|NZ_CP010845.1_254379_255765_-	PRK10319, PRK10319, N-acetylmuramoyl-L-alanine amidase AmiA	NA|179aa|down_4|NZ_CP010845.1_255695_256232_-	COG0802, COG0802, Predicted ATPase or kinase [General function prediction only]	NA|464aa|down_5|NZ_CP010845.1_256383_257775_+	PRK00485, fumC, fumarate hydratase; Reviewed	NA|327aa|down_6|NZ_CP010845.1_257791_258772_-	COG0679, COG0679, Predicted permeases [General function prediction only]	NA|328aa|down_7|NZ_CP010845.1_258907_259891_+	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_CP010845.1_259955_260855_-	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_CP010845.1_260961_262716_+	COG0405, Ggt, Gamma-glutamyltransferase [Amino acid transport and metabolism]
GCF_001605215.1_ASM160521v1	NZ_CP010845	Bordetella pertussis strain H561 chromosome, complete genome	2	479402-479495	2	CRISPRCasFinder	no		csa3,cas3,DinG,DEDDh	Orphan	GTGCCTGTCCCCGCCGGGACAGGCAC	26	0	0	NA	NA	NA	1	1	Orphan	csa3,cas3,DinG,DEDDh	NA|132aa|up_8|NZ_CP010845.1_471430_471826_+,NA	NA|134aa|up_9|NZ_CP010845.1_471032_471434_+	COG1545, COG1545, Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]	NA|132aa|up_8|NZ_CP010845.1_471430_471826_+	NA	NA|131aa|up_7|NZ_CP010845.1_471822_472215_+	cd03441, R_hydratase_like, (R)-hydratase [(R)-specific enoyl-CoA hydratase]	NA|387aa|up_6|NZ_CP010845.1_472225_473386_+	cd01160, LCAD, Long chain acyl-CoA dehydrogenase	NA|324aa|up_5|NZ_CP010845.1_473423_474395_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|383aa|up_4|NZ_CP010845.1_474402_475551_+	pfam02515, CoA_transf_3, CoA-transferase family III	NA|297aa|up_3|NZ_CP010845.1_475547_476438_-	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_2|NZ_CP010845.1_476644_477592_+	cd00408, DHDPS-like, Dihydrodipicolinate synthase family	NA|317aa|up_1|NZ_CP010845.1_477690_478641_+	pfam00665, rve, Integrase core domain	NA|133aa|up_0|NZ_CP010845.1_478772_479171_-	PRK00007, PRK00007, elongation factor G; Reviewed	NA|157aa|down_0|NZ_CP010845.1_479581_480052_-	pfam00582, Usp, Universal stress protein family	NA|115aa|down_1|NZ_CP010845.1_480140_480485_-	COG3453, COG3453, Uncharacterized protein conserved in bacteria [Function unknown]	NA|467aa|down_2|NZ_CP010845.1_480584_481985_-	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_CP010845.1_483773_484292_-	COG1285, SapB, Uncharacterized membrane protein [Function unknown]	NA|252aa|down_4|NZ_CP010845.1_484402_485158_+	COG0861, TerC, Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]	NA|411aa|down_5|NZ_CP010845.1_485353_486586_+	pfam02515, CoA_transf_3, CoA-transferase family III	NA|262aa|down_6|NZ_CP010845.1_486578_487364_+	PRK09245, PRK09245, crotonase/enoyl-CoA hydratase family protein	NA|324aa|down_7|NZ_CP010845.1_487430_488402_+	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_CP010845.1_488412_489390_-	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_CP010845.1_489515_490688_+	cd01152, ACAD_fadE6_17_26, Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26
GCF_001605215.1_ASM160521v1	NZ_CP010845	Bordetella pertussis strain H561 chromosome, complete genome	3	1043719-1043813	3	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_CP010845.1_1041705_1042086_+,NA	NA|310aa|up_9|NZ_CP010845.1_1029235_1030165_+	COG2025, FixB, Electron transfer flavoprotein, alpha subunit [Energy production and conversion]	NA|609aa|up_8|NZ_CP010845.1_1030408_1032235_+	cd01153, ACAD_fadE5, Putative acyl-CoA dehydrogenases similar to fadE5	NA|214aa|up_7|NZ_CP010845.1_1032317_1032959_+	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_CP010845.1_1033181_1034183_+	COG1613, Sbp, ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]	NA|355aa|up_5|NZ_CP010845.1_1036019_1037084_+	cd03296, ABC_CysA_sulfate_importer, ATP-binding cassette domain of the sulfate transporter	NA|303aa|up_4|NZ_CP010845.1_1037881_1038790_+	PRK05253, PRK05253, sulfate adenylyltransferase subunit CysD	NA|425aa|up_3|NZ_CP010845.1_1040277_1041552_+	TIGR04470, hypothetical_protein_ALIPUT_00462, radical SAM mobile pair protein B	NA|127aa|up_2|NZ_CP010845.1_1041705_1042086_+	NA	NA|291aa|up_1|NZ_CP010845.1_1042093_1042966_-	TIGR03340, phn_DUF6, phosphonate utilization associated putative membrane protein	NA|127aa|up_0|NZ_CP010845.1_1043271_1043652_+	PRK05338, rplS, 50S ribosomal protein L19; Provisional	NA|242aa|down_0|NZ_CP010845.1_1043862_1044588_+	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_CP010845.1_1044683_1045634_-	pfam00665, rve, Integrase core domain	NA|350aa|down_2|NZ_CP010845.1_1045738_1046788_+	cd19094, AKR_Tas-like, Escherichia coli Tas protein and similar proteins	NA|339aa|down_3|NZ_CP010845.1_1046925_1047942_-	pfam02371, Transposase_20, Transposase IS116/IS110/IS902 family	NA|191aa|down_4|NZ_CP010845.1_1049450_1050023_-	COG3161, UbiC, 4-hydroxybenzoate synthetase (chorismate lyase) [Coenzyme metabolism]	NA|244aa|down_5|NZ_CP010845.1_1050082_1050814_+	COG1187, RsuA, 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]	NA|306aa|down_6|NZ_CP010845.1_1050865_1051783_-	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_CP010845.1_1052590_1055770_+	TIGR00915, Probable_aminoglycoside_efflux_pump, The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family	NA|461aa|down_8|NZ_CP010845.1_1055766_1057149_+	TIGR01845, Outer_membrane_protein_OprM, efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family	NA|84aa|down_9|NZ_CP010845.1_1057218_1057470_-	COG2261, COG2261, Predicted membrane protein [Function unknown]
GCF_001605215.1_ASM160521v1	NZ_CP010845	Bordetella pertussis strain H561 chromosome, complete genome	4	1939097-1939224	4	CRISPRCasFinder	no		csa3,cas3,DinG,DEDDh	Orphan	AAAAAGCCCCCTCGGGGGGCAGCAAGCCCGCATAGCGGGCGCAGCG	46	0	0	NA	NA	NA	1	1	Orphan	csa3,cas3,DinG,DEDDh	NA,NA	NA|134aa|up_9|NZ_CP010845.1_1928059_1928461_+	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_CP010845.1_1928474_1929278_+	COG1024, CaiD, Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]	NA|144aa|up_7|NZ_CP010845.1_1929274_1929706_+	COG1545, COG1545, Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]	NA|386aa|up_6|NZ_CP010845.1_1929702_1930860_+	PRK06158, PRK06158, thiolase; Provisional	NA|259aa|up_5|NZ_CP010845.1_1930881_1931658_+	PRK05653, fabG, 3-oxoacyl-ACP reductase FabG	NA|223aa|up_4|NZ_CP010845.1_1933870_1934539_+	TIGR02429, 3-oxoadipate_CoA-transferase_subunit_A, 3-oxoacid CoA-transferase, A subunit	NA|214aa|up_3|NZ_CP010845.1_1934531_1935173_+	TIGR02428, 3-oxoadipate_CoA-transferase_subunit_B, 3-oxoacid CoA-transferase, B subunit	NA|244aa|up_2|NZ_CP010845.1_1935207_1935939_+	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_CP010845.1_1935956_1936169_+	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_CP010845.1_1936739_1937690_+	pfam00665, rve, Integrase core domain	NA|217aa|down_0|NZ_CP010845.1_1939247_1939898_-	PRK00215, PRK00215, transcriptional repressor LexA	NA|401aa|down_1|NZ_CP010845.1_1940026_1941229_-	PRK09257, PRK09257, aromatic amino acid transaminase	NA|679aa|down_2|NZ_CP010845.1_1941306_1943343_+	PRK05298, PRK05298, excinuclease ABC subunit UvrB	NA|164aa|down_3|NZ_CP010845.1_1943595_1944087_+	cd16343, LMWPTP, Low molecular weight protein tyrosine phosphatase	NA|171aa|down_4|NZ_CP010845.1_1944302_1944815_+	TIGR02010, Putative_HTH-type_transcriptional_regulator, iron-sulfur cluster assembly transcription factor IscR	NA|404aa|down_5|NZ_CP010845.1_1944832_1946044_+	PRK14012, PRK14012, IscS subfamily cysteine desulfurase	NA|137aa|down_6|NZ_CP010845.1_1946081_1946492_+	PRK11325, PRK11325, scaffold protein; Provisional	NA|108aa|down_7|NZ_CP010845.1_1946493_1946817_+	TIGR02011, Protein_yfhF	NA|171aa|down_8|NZ_CP010845.1_1946819_1947332_+	PRK03578, hscB, Fe-S protein assembly co-chaperone HscB	NA|621aa|down_9|NZ_CP010845.1_1947461_1949324_+	PRK05183, hscA, chaperone protein HscA; Provisional
GCF_001605215.1_ASM160521v1	NZ_CP010845	Bordetella pertussis strain H561 chromosome, complete genome	5	3446474-3446583	5	CRISPRCasFinder	no		csa3,cas3,DinG,DEDDh	Orphan	TTGACTGCCAAGACGGTATCTGTCCCC	27	0	0	NA	NA	NA	1	1	Orphan	csa3,cas3,DinG,DEDDh	NA,NA	NA|363aa|up_9|NZ_CP010845.1_3430751_3431840_+	cd08948, 5beta-POR_like_SDR_a, progesterone 5-beta-reductase-like proteins (5beta-POR), atypical (a) SDRs	NA|317aa|up_8|NZ_CP010845.1_3431836_3432787_-	pfam00665, rve, Integrase core domain	NA|993aa|up_7|NZ_CP010845.1_3433140_3436119_+	pfam17936, Big_6, Bacterial Ig domain	NA|293aa|up_6|NZ_CP010845.1_3437045_3437924_+	pfam00487, FA_desaturase, Fatty acid desaturase	NA|317aa|up_5|NZ_CP010845.1_3439872_3440823_+	pfam00665, rve, Integrase core domain	NA|156aa|up_4|NZ_CP010845.1_3440819_3441287_-	PRK00203, rnhA, ribonuclease H; Reviewed	NA|257aa|up_3|NZ_CP010845.1_3441329_3442100_-	pfam08241, Methyltransf_11, Methyltransferase domain	NA|267aa|up_2|NZ_CP010845.1_3442120_3442921_+	TIGR03413, GSH_gloB, hydroxyacylglutathione hydrolase	NA|470aa|up_1|NZ_CP010845.1_3442931_3444341_+	PRK10783, mltD, membrane-bound lytic murein transglycosylase D; Provisional	NA|262aa|up_0|NZ_CP010845.1_3444435_3445221_+	PRK06997, PRK06997, enoyl-[acyl-carrier-protein] reductase FabI	NA|131aa|down_0|NZ_CP010845.1_3446584_3446977_-	COG1765, COG1765, Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]	NA|227aa|down_1|NZ_CP010845.1_3447114_3447795_+	pfam04391, DUF533, Protein of unknown function (DUF533)	NA|324aa|down_2|NZ_CP010845.1_3447799_3448771_-	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_CP010845.1_3448866_3449817_-	pfam00665, rve, Integrase core domain	NA|234aa|down_4|NZ_CP010845.1_3451321_3452023_+	PRK09468, ompR, osmolarity response regulator; Provisional	NA|475aa|down_5|NZ_CP010845.1_3452022_3453447_+	PRK09467, envZ, osmolarity sensor protein; Provisional	NA|447aa|down_6|NZ_CP010845.1_3454516_3455857_-	pfam01654, Cyt_bd_oxida_I, Cytochrome bd terminal oxidase subunit I	NA|588aa|down_7|NZ_CP010845.1_3455972_3457736_+	PRK05347, PRK05347, glutaminyl-tRNA synthetase; Provisional	NA|293aa|down_8|NZ_CP010845.1_3457847_3458726_+	PRK00030, minC, septum site-determining protein MinC	NA|272aa|down_9|NZ_CP010845.1_3458838_3459654_+	COG2894, MinD, Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]
