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_000195715.1_ASM19571v1	NC_002929	Bordetella pertussis Tohama I, complete genome	1	250749-250833	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|NC_002929.2_238274_238685_+	TIGR02425, putative_gamma-carboxymuconolactone_decarboxylase, 4-carboxymuconolactone decarboxylase	NA|248aa|up_8|NC_002929.2_239706_240450_-	COG1802, GntR, Transcriptional regulators [Transcription]	NA|348aa|up_7|NC_002929.2_240493_241537_-	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|NC_002929.2_241707_243810_+	TIGR00786, TRAP_transporter_permease_protein_SiaT, TRAP transporter, DctM subunit	NA|319aa|up_5|NC_002929.2_245220_246177_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|164aa|up_4|NC_002929.2_246195_246687_-	PRK14092, PRK14092, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase	NA|452aa|up_3|NC_002929.2_246683_248039_-	TIGR01942, pcnB, poly(A) polymerase	NA|233aa|up_2|NC_002929.2_248039_248738_-	cd02612, HAD_PGPPase, phosphatidylglycerol-phosphate phosphatase, similar to Escherichia coli K-12 phosphatidylglycerol-phosphate phosphatase C	NA|234aa|up_1|NC_002929.2_248734_249436_-	PRK08903, PRK08903, DnaA regulatory inactivator Hda; Validated	NA|350aa|up_0|NC_002929.2_249688_250738_+	PRK05385, PRK05385, phosphoribosylaminoimidazole synthetase; Provisional	NA|314aa|down_0|NC_002929.2_250843_251785_-	PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed	NA|630aa|down_1|NC_002929.2_251781_253671_-	PRK00095, mutL, DNA mismatch repair endonuclease MutL	NA|213aa|down_2|NC_002929.2_253757_254396_+	PRK10847, PRK10847, DedA family protein	NA|462aa|down_3|NC_002929.2_254538_255924_-	PRK10319, PRK10319, N-acetylmuramoyl-L-alanine amidase AmiA	NA|179aa|down_4|NC_002929.2_255854_256391_-	COG0802, COG0802, Predicted ATPase or kinase [General function prediction only]	NA|464aa|down_5|NC_002929.2_256542_257934_+	PRK00485, fumC, fumarate hydratase; Reviewed	NA|327aa|down_6|NC_002929.2_257950_258931_-	COG0679, COG0679, Predicted permeases [General function prediction only]	NA|328aa|down_7|NC_002929.2_259066_260050_+	cd13577, PBP2_BugE_Glu, Glutamate transporter of Bug (Bordetella uptake gene) protein family; contains the type 2 periplasmic binding fold	NA|300aa|down_8|NC_002929.2_260114_261014_-	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|NC_002929.2_261120_262875_+	COG0405, Ggt, Gamma-glutamyltransferase [Amino acid transport and metabolism]
GCF_000195715.1_ASM19571v1	NC_002929	Bordetella pertussis Tohama I, complete genome	2	410664-410757	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|NC_002929.2_398003_399062_-	cd04187, DPM1_like_bac, Bacterial DPM1_like enzymes are related to eukaryotic DPM1	NA|165aa|up_8|NC_002929.2_399191_399686_+	pfam00583, Acetyltransf_1, Acetyltransferase (GNAT) family	NA|326aa|up_7|NC_002929.2_399778_400756_+	pfam00665, rve, Integrase core domain	NA|402aa|up_6|NC_002929.2_400951_402157_+	TIGR00210, Sodium/glutamate_symport_carrier_protein, sodium--glutamate symport carrier (gltS)	NA|504aa|up_5|NC_002929.2_402153_403665_+	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|NC_002929.2_403680_404994_-	COG2031, AtoE, Short chain fatty acids transporter [Lipid metabolism]	NA|60aa|up_3|NC_002929.2_405184_405364_-	pfam04391, DUF533, Protein of unknown function (DUF533)	DEDDh|245aa|up_2|NC_002929.2_405773_406508_-	PRK05711, PRK05711, DNA polymerase III subunit epsilon; Provisional	NA|317aa|up_1|NC_002929.2_408952_409903_+	pfam00665, rve, Integrase core domain	NA|133aa|up_0|NC_002929.2_410034_410433_-	PRK00007, PRK00007, elongation factor G; Reviewed	NA|157aa|down_0|NC_002929.2_410843_411314_-	pfam00582, Usp, Universal stress protein family	NA|115aa|down_1|NC_002929.2_411402_411747_-	COG3453, COG3453, Uncharacterized protein conserved in bacteria [Function unknown]	NA|467aa|down_2|NC_002929.2_411846_413247_-	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|NC_002929.2_415035_415554_-	COG1285, SapB, Uncharacterized membrane protein [Function unknown]	NA|252aa|down_4|NC_002929.2_415664_416420_+	COG0861, TerC, Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]	NA|411aa|down_5|NC_002929.2_416615_417848_+	pfam02515, CoA_transf_3, CoA-transferase family III	NA|262aa|down_6|NC_002929.2_417840_418626_+	PRK09245, PRK09245, crotonase/enoyl-CoA hydratase family protein	NA|324aa|down_7|NC_002929.2_418692_419664_+	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|NC_002929.2_419674_420652_-	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|NC_002929.2_420777_421950_+	cd01152, ACAD_fadE6_17_26, Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26
GCF_000195715.1_ASM19571v1	NC_002929	Bordetella pertussis Tohama I, complete genome	3	1014639-1014733	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|NC_002929.2_1012625_1013006_+,NA	NA|310aa|up_9|NC_002929.2_1000149_1001079_+	COG2025, FixB, Electron transfer flavoprotein, alpha subunit [Energy production and conversion]	NA|609aa|up_8|NC_002929.2_1001322_1003149_+	cd01153, ACAD_fadE5, Putative acyl-CoA dehydrogenases similar to fadE5	NA|214aa|up_7|NC_002929.2_1003231_1003873_+	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|NC_002929.2_1004095_1005097_+	COG1613, Sbp, ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]	NA|355aa|up_5|NC_002929.2_1006939_1008004_+	cd03296, ABC_CysA_sulfate_importer, ATP-binding cassette domain of the sulfate transporter	NA|303aa|up_4|NC_002929.2_1008801_1009710_+	PRK05253, PRK05253, sulfate adenylyltransferase subunit CysD	NA|425aa|up_3|NC_002929.2_1011197_1012472_+	TIGR04470, hypothetical_protein_ALIPUT_00462, radical SAM mobile pair protein B	NA|127aa|up_2|NC_002929.2_1012625_1013006_+	NA	NA|291aa|up_1|NC_002929.2_1013013_1013886_-	TIGR03340, phn_DUF6, phosphonate utilization associated putative membrane protein	NA|127aa|up_0|NC_002929.2_1014191_1014572_+	PRK05338, rplS, 50S ribosomal protein L19; Provisional	NA|242aa|down_0|NC_002929.2_1014782_1015508_+	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|NC_002929.2_1015609_1016659_+	cd19094, AKR_Tas-like, Escherichia coli Tas protein and similar proteins	NA|339aa|down_2|NC_002929.2_1016796_1017813_-	pfam02371, Transposase_20, Transposase IS116/IS110/IS902 family	NA|191aa|down_3|NC_002929.2_1019321_1019894_-	COG3161, UbiC, 4-hydroxybenzoate synthetase (chorismate lyase) [Coenzyme metabolism]	NA|244aa|down_4|NC_002929.2_1019953_1020685_+	COG1187, RsuA, 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]	NA|306aa|down_5|NC_002929.2_1020736_1021654_-	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|NC_002929.2_1022461_1025641_+	TIGR00915, Probable_aminoglycoside_efflux_pump, The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family	NA|461aa|down_7|NC_002929.2_1025637_1027020_+	TIGR01845, Outer_membrane_protein_OprM, efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family	NA|84aa|down_8|NC_002929.2_1027089_1027341_-	COG2261, COG2261, Predicted membrane protein [Function unknown]	NA|205aa|down_9|NC_002929.2_1027486_1028101_-	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_000195715.1_ASM19571v1	NC_002929	Bordetella pertussis Tohama I, complete genome	4	1883991-1884118	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|NC_002929.2_1872953_1873355_+	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|NC_002929.2_1873368_1874172_+	COG1024, CaiD, Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]	NA|144aa|up_7|NC_002929.2_1874168_1874600_+	COG1545, COG1545, Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]	NA|386aa|up_6|NC_002929.2_1874596_1875754_+	PRK06158, PRK06158, thiolase; Provisional	NA|259aa|up_5|NC_002929.2_1875775_1876552_+	PRK05653, fabG, 3-oxoacyl-ACP reductase FabG	NA|223aa|up_4|NC_002929.2_1878764_1879433_+	TIGR02429, 3-oxoadipate_CoA-transferase_subunit_A, 3-oxoacid CoA-transferase, A subunit	NA|214aa|up_3|NC_002929.2_1879425_1880067_+	TIGR02428, 3-oxoadipate_CoA-transferase_subunit_B, 3-oxoacid CoA-transferase, B subunit	NA|244aa|up_2|NC_002929.2_1880101_1880833_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|71aa|up_1|NC_002929.2_1880850_1881063_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|317aa|up_0|NC_002929.2_1881633_1882584_+	pfam00665, rve, Integrase core domain	NA|217aa|down_0|NC_002929.2_1884141_1884792_-	PRK00215, PRK00215, transcriptional repressor LexA	NA|401aa|down_1|NC_002929.2_1884920_1886123_-	PRK09257, PRK09257, aromatic amino acid transaminase	NA|679aa|down_2|NC_002929.2_1886200_1888237_+	PRK05298, PRK05298, excinuclease ABC subunit UvrB	NA|164aa|down_3|NC_002929.2_1888489_1888981_+	cd16343, LMWPTP, Low molecular weight protein tyrosine phosphatase	NA|171aa|down_4|NC_002929.2_1889196_1889709_+	TIGR02010, Putative_HTH-type_transcriptional_regulator, iron-sulfur cluster assembly transcription factor IscR	NA|404aa|down_5|NC_002929.2_1889726_1890938_+	PRK14012, PRK14012, IscS subfamily cysteine desulfurase	NA|137aa|down_6|NC_002929.2_1890975_1891386_+	PRK11325, PRK11325, scaffold protein; Provisional	NA|108aa|down_7|NC_002929.2_1891387_1891711_+	TIGR02011, Protein_yfhF	NA|171aa|down_8|NC_002929.2_1891713_1892226_+	PRK03578, hscB, Fe-S protein assembly co-chaperone HscB	NA|621aa|down_9|NC_002929.2_1892355_1894218_+	PRK05183, hscA, chaperone protein HscA; Provisional
GCF_000195715.1_ASM19571v1	NC_002929	Bordetella pertussis Tohama I, complete genome	5	3428955-3429064	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|NC_002929.2_3413232_3414321_+	cd08948, 5beta-POR_like_SDR_a, progesterone 5-beta-reductase-like proteins (5beta-POR), atypical (a) SDRs	NA|317aa|up_8|NC_002929.2_3414317_3415268_-	pfam00665, rve, Integrase core domain	NA|993aa|up_7|NC_002929.2_3415621_3418600_+	pfam17936, Big_6, Bacterial Ig domain	NA|293aa|up_6|NC_002929.2_3419526_3420405_+	pfam00487, FA_desaturase, Fatty acid desaturase	NA|317aa|up_5|NC_002929.2_3422353_3423304_+	pfam00665, rve, Integrase core domain	NA|156aa|up_4|NC_002929.2_3423300_3423768_-	PRK00203, rnhA, ribonuclease H; Reviewed	NA|257aa|up_3|NC_002929.2_3423810_3424581_-	pfam08241, Methyltransf_11, Methyltransferase domain	NA|267aa|up_2|NC_002929.2_3424601_3425402_+	TIGR03413, GSH_gloB, hydroxyacylglutathione hydrolase	NA|470aa|up_1|NC_002929.2_3425412_3426822_+	PRK10783, mltD, membrane-bound lytic murein transglycosylase D; Provisional	NA|262aa|up_0|NC_002929.2_3426916_3427702_+	PRK06997, PRK06997, enoyl-[acyl-carrier-protein] reductase FabI	NA|131aa|down_0|NC_002929.2_3429065_3429458_-	COG1765, COG1765, Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]	NA|227aa|down_1|NC_002929.2_3429595_3430276_+	pfam04391, DUF533, Protein of unknown function (DUF533)	NA|324aa|down_2|NC_002929.2_3430280_3431252_-	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|317aa|down_3|NC_002929.2_3431347_3432298_-	pfam00665, rve, Integrase core domain	NA|234aa|down_4|NC_002929.2_3433802_3434504_+	PRK09468, ompR, osmolarity response regulator; Provisional	NA|475aa|down_5|NC_002929.2_3434503_3435928_+	PRK09467, envZ, osmolarity sensor protein; Provisional	NA|352aa|down_6|NC_002929.2_3435944_3437000_-	pfam02322, Cyt_bd_oxida_II, Cytochrome bd terminal oxidase subunit II	NA|447aa|down_7|NC_002929.2_3436996_3438337_-	pfam01654, Cyt_bd_oxida_I, Cytochrome bd terminal oxidase subunit I	NA|588aa|down_8|NC_002929.2_3438452_3440216_+	PRK05347, PRK05347, glutaminyl-tRNA synthetase; Provisional	NA|293aa|down_9|NC_002929.2_3440327_3441206_+	PRK00030, minC, septum site-determining protein MinC
