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_002442655.1_ASM244265v1	NZ_CP017160	Bordetella pertussis strain J223 chromosome, complete genome	1	250576-250660	1	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG	Orphan	GGTGCCTGTCCCCGCGGGGACAG	23	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG	NA,NA	NA|266aa|up_9|NZ_CP017160.1_236355_237153_-	cd08940, HBDH_SDR_c, d-3-hydroxybutyrate dehydrogenase (HBDH), classical (c) SDRs	NA|137aa|up_8|NZ_CP017160.1_238102_238513_+	TIGR02425, putative_gamma-carboxymuconolactone_decarboxylase, 4-carboxymuconolactone decarboxylase	NA|248aa|up_7|NZ_CP017160.1_239534_240278_-	COG1802, GntR, Transcriptional regulators [Transcription]	NA|348aa|up_6|NZ_CP017160.1_240321_241365_-	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_5|NZ_CP017160.1_241535_243638_+	TIGR00786, TRAP_transporter_permease_protein_SiaT, TRAP transporter, DctM subunit	NA|319aa|up_4|NZ_CP017160.1_245048_246005_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|164aa|up_3|NZ_CP017160.1_246023_246515_-	PRK14092, PRK14092, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase	NA|452aa|up_2|NZ_CP017160.1_246511_247867_-	TIGR01942, pcnB, poly(A) polymerase	NA|233aa|up_1|NZ_CP017160.1_247867_248566_-	cd02612, HAD_PGPPase, phosphatidylglycerol-phosphate phosphatase, similar to Escherichia coli K-12 phosphatidylglycerol-phosphate phosphatase C	NA|350aa|up_0|NZ_CP017160.1_249515_250565_+	PRK05385, PRK05385, phosphoribosylaminoimidazole synthetase; Provisional	NA|314aa|down_0|NZ_CP017160.1_250670_251612_-	PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed	NA|630aa|down_1|NZ_CP017160.1_251608_253498_-	PRK00095, mutL, DNA mismatch repair endonuclease MutL	NA|213aa|down_2|NZ_CP017160.1_253584_254223_+	PRK10847, PRK10847, DedA family protein	NA|462aa|down_3|NZ_CP017160.1_254365_255751_-	PRK10319, PRK10319, N-acetylmuramoyl-L-alanine amidase AmiA	NA|179aa|down_4|NZ_CP017160.1_255681_256218_-	COG0802, COG0802, Predicted ATPase or kinase [General function prediction only]	NA|464aa|down_5|NZ_CP017160.1_256369_257761_+	PRK00485, fumC, fumarate hydratase; Reviewed	NA|327aa|down_6|NZ_CP017160.1_257777_258758_-	COG0679, COG0679, Predicted permeases [General function prediction only]	NA|328aa|down_7|NZ_CP017160.1_258893_259877_+	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_CP017160.1_259941_260841_-	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_CP017160.1_260947_262702_+	COG0405, Ggt, Gamma-glutamyltransferase [Amino acid transport and metabolism]
GCF_002442655.1_ASM244265v1	NZ_CP017160	Bordetella pertussis strain J223 chromosome, complete genome	2	432015-432108	2	CRISPRCasFinder	no	DEDDh	DEDDh,csa3,cas3,DinG	Unclear	GTGCCTGTCCCCGCCGGGACAGGCAC	26	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG	NA,NA	NA|353aa|up_9|NZ_CP017160.1_419354_420413_-	cd04187, DPM1_like_bac, Bacterial DPM1_like enzymes are related to eukaryotic DPM1	NA|165aa|up_8|NZ_CP017160.1_420542_421037_+	pfam00583, Acetyltransf_1, Acetyltransferase (GNAT) family	NA|326aa|up_7|NZ_CP017160.1_421129_422107_+	pfam00665, rve, Integrase core domain	NA|402aa|up_6|NZ_CP017160.1_422302_423508_+	TIGR00210, Sodium/glutamate_symport_carrier_protein, sodium--glutamate symport carrier (gltS)	NA|504aa|up_5|NZ_CP017160.1_423504_425016_+	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_CP017160.1_425031_426345_-	COG2031, AtoE, Short chain fatty acids transporter [Lipid metabolism]	NA|60aa|up_3|NZ_CP017160.1_426535_426715_-	pfam04391, DUF533, Protein of unknown function (DUF533)	DEDDh|245aa|up_2|NZ_CP017160.1_427124_427859_-	PRK05711, PRK05711, DNA polymerase III subunit epsilon; Provisional	NA|317aa|up_1|NZ_CP017160.1_430303_431254_+	pfam00665, rve, Integrase core domain	NA|133aa|up_0|NZ_CP017160.1_431385_431784_-	PRK00007, PRK00007, elongation factor G; Reviewed	NA|157aa|down_0|NZ_CP017160.1_432194_432665_-	pfam00582, Usp, Universal stress protein family	NA|115aa|down_1|NZ_CP017160.1_432753_433098_-	COG3453, COG3453, Uncharacterized protein conserved in bacteria [Function unknown]	NA|467aa|down_2|NZ_CP017160.1_433197_434598_-	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_CP017160.1_436386_436905_-	COG1285, SapB, Uncharacterized membrane protein [Function unknown]	NA|411aa|down_4|NZ_CP017160.1_437965_439198_+	pfam02515, CoA_transf_3, CoA-transferase family III	NA|262aa|down_5|NZ_CP017160.1_439190_439976_+	PRK09245, PRK09245, crotonase/enoyl-CoA hydratase family protein	NA|324aa|down_6|NZ_CP017160.1_440042_441014_+	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_7|NZ_CP017160.1_441024_442002_-	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_8|NZ_CP017160.1_442127_443300_+	cd01152, ACAD_fadE6_17_26, Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26	NA|343aa|down_9|NZ_CP017160.1_443326_444355_+	pfam00441, Acyl-CoA_dh_1, Acyl-CoA dehydrogenase, C-terminal domain
GCF_002442655.1_ASM244265v1	NZ_CP017160	Bordetella pertussis strain J223 chromosome, complete genome	3	996298-996392	3	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG	Orphan	TAAAAGGGCACCCGCAAGGGTGTCCTTTT	29	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG	NA|127aa|up_2|NZ_CP017160.1_994284_994665_+,NA	NA|310aa|up_9|NZ_CP017160.1_981814_982744_+	COG2025, FixB, Electron transfer flavoprotein, alpha subunit [Energy production and conversion]	NA|609aa|up_8|NZ_CP017160.1_982987_984814_+	cd01153, ACAD_fadE5, Putative acyl-CoA dehydrogenases similar to fadE5	NA|214aa|up_7|NZ_CP017160.1_984896_985538_+	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_CP017160.1_985727_986762_+	COG1613, Sbp, ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]	NA|355aa|up_5|NZ_CP017160.1_988598_989663_+	cd03296, ABC_CysA_sulfate_importer, ATP-binding cassette domain of the sulfate transporter	NA|303aa|up_4|NZ_CP017160.1_990460_991369_+	PRK05253, PRK05253, sulfate adenylyltransferase subunit CysD	NA|425aa|up_3|NZ_CP017160.1_992856_994131_+	TIGR04470, hypothetical_protein_ALIPUT_00462, radical SAM mobile pair protein B	NA|127aa|up_2|NZ_CP017160.1_994284_994665_+	NA	NA|291aa|up_1|NZ_CP017160.1_994672_995545_-	TIGR03340, phn_DUF6, phosphonate utilization associated putative membrane protein	NA|127aa|up_0|NZ_CP017160.1_995850_996231_+	PRK05338, rplS, 50S ribosomal protein L19; Provisional	NA|242aa|down_0|NZ_CP017160.1_996441_997167_+	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_CP017160.1_997262_998213_-	pfam00665, rve, Integrase core domain	NA|350aa|down_2|NZ_CP017160.1_998317_999367_+	cd19094, AKR_Tas-like, Escherichia coli Tas protein and similar proteins	NA|339aa|down_3|NZ_CP017160.1_999504_1000521_-	pfam02371, Transposase_20, Transposase IS116/IS110/IS902 family	NA|191aa|down_4|NZ_CP017160.1_1002029_1002602_-	COG3161, UbiC, 4-hydroxybenzoate synthetase (chorismate lyase) [Coenzyme metabolism]	NA|244aa|down_5|NZ_CP017160.1_1002661_1003393_+	COG1187, RsuA, 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]	NA|306aa|down_6|NZ_CP017160.1_1003444_1004362_-	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_CP017160.1_1005169_1008349_+	TIGR00915, Probable_aminoglycoside_efflux_pump, The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family	NA|461aa|down_8|NZ_CP017160.1_1008345_1009728_+	TIGR01845, Outer_membrane_protein_OprM, efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family	NA|84aa|down_9|NZ_CP017160.1_1009797_1010049_-	COG2261, COG2261, Predicted membrane protein [Function unknown]
GCF_002442655.1_ASM244265v1	NZ_CP017160	Bordetella pertussis strain J223 chromosome, complete genome	4	1147794-1147927	4	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG	Orphan	CCCCCTTGGGGGCAGCAAGCCCGCACAGCGGGCGCAGCGTGGGGGCCTTTT	51	1	3	1147845-1147876|1147845-1147876|1147845-1147876	NZ_CP017160.1_1355685-1355654|NZ_CP017160.1_1820724-1820755|NZ_CP017160.1_1997915-1997884	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG	NA|101aa|up_8|NZ_CP017160.1_1134773_1135076_-,NA	NA|622aa|up_9|NZ_CP017160.1_1132201_1134067_+	cd05907, VL_LC_FACS_like, Long-chain fatty acid CoA synthetases and Bubblegum-like very long-chain fatty acid CoA synthetases	NA|101aa|up_8|NZ_CP017160.1_1134773_1135076_-	NA	NA|252aa|up_7|NZ_CP017160.1_1136644_1137400_-	PRK07023, PRK07023, SDR family oxidoreductase	NA|368aa|up_6|NZ_CP017160.1_1137429_1138534_-	PRK00578, prfB, peptide chain release factor 2; Validated	NA|567aa|up_5|NZ_CP017160.1_1138636_1140337_-	PRK11070, PRK11070, single-stranded-DNA-specific exonuclease RecJ	NA|326aa|up_4|NZ_CP017160.1_1140318_1141296_-	COG4255, COG4255, Uncharacterized protein conserved in bacteria [Function unknown]	NA|427aa|up_3|NZ_CP017160.1_1141305_1142586_+	TIGR02212, releasing_system_transmembrane_protein_lolC	NA|232aa|up_2|NZ_CP017160.1_1142578_1143274_+	cd03255, ABC_MJ0796_LolCDE_FtsE, ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein	NA|276aa|up_1|NZ_CP017160.1_1143307_1144135_+	cd01310, TatD_DNAse, TatD like proteins;  E	NA|1077aa|up_0|NZ_CP017160.1_1144416_1147647_+	pfam03797, Autotransporter, Autotransporter beta-domain	NA|1309aa|down_0|NZ_CP017160.1_1148381_1152308_+	pfam11924, IAT_beta, Inverse autotransporter, beta-domain	NA|599aa|down_1|NZ_CP017160.1_1154207_1156004_+	COG2333, ComEC, Predicted hydrolase (metallo-beta-lactamase superfamily) [General function prediction only]	NA|323aa|down_2|NZ_CP017160.1_1156003_1156972_+	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|282aa|down_3|NZ_CP017160.1_1157041_1157887_+	COG0613, COG0613, Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]	NA|185aa|down_4|NZ_CP017160.1_1157954_1158509_+	PRK01885, greB, transcription elongation factor GreB; Reviewed	NA|317aa|down_5|NZ_CP017160.1_1158555_1159506_-	pfam00665, rve, Integrase core domain	NA|211aa|down_6|NZ_CP017160.1_1159604_1160237_-	pfam16970, FimA, Type-1 fimbrial protein, A	NA|761aa|down_7|NZ_CP017160.1_1160401_1162684_-	PRK07232, PRK07232, bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed	NA|899aa|down_8|NZ_CP017160.1_1162838_1165535_-	PRK13012, PRK13012, 2-oxoacid dehydrogenase subunit E1; Provisional	NA|163aa|down_9|NZ_CP017160.1_1165660_1166149_+	COG1522, Lrp, Transcriptional regulators [Transcription]
GCF_002442655.1_ASM244265v1	NZ_CP017160	Bordetella pertussis strain J223 chromosome, complete genome	5	1820749-1820876	5	CRISPRCasFinder	no	csa3	DEDDh,csa3,cas3,DinG	Type I-A	AAAAAGCCCCCTCGGGGGGCAGCAAGCCCGCATAGCGGGCGCAGCG	46	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG	NA|79aa|up_2|NZ_CP017160.1_1816957_1817194_+,NA	NA|112aa|up_9|NZ_CP017160.1_1808304_1808640_-	cd03441, R_hydratase_like, (R)-hydratase [(R)-specific enoyl-CoA hydratase]	NA|150aa|up_8|NZ_CP017160.1_1808646_1809096_-	cd03443, PaaI_thioesterase, PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria	csa3|100aa|up_7|NZ_CP017160.1_1809303_1809603_+	COG0640, ArsR, Predicted transcriptional regulators [Transcription]	NA|213aa|up_6|NZ_CP017160.1_1810770_1811409_-	pfam13994, PgaD, PgaD-like protein	NA|420aa|up_5|NZ_CP017160.1_1811389_1812649_-	PRK11204, PRK11204, N-glycosyltransferase; Provisional	NA|702aa|up_4|NZ_CP017160.1_1812652_1814758_-	TIGR03938, hypothetical_protein_Pcar_2791, poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB	NA|662aa|up_3|NZ_CP017160.1_1814763_1816749_-	TIGR03939, PGA_TPR_OMP, poly-beta-1,6 N-acetyl-D-glucosamine export porin PgaA	NA|79aa|up_2|NZ_CP017160.1_1816957_1817194_+	NA	NA|162aa|up_1|NZ_CP017160.1_1817538_1818024_+	COG1846, MarR, Transcriptional regulators [Transcription]	NA|317aa|up_0|NZ_CP017160.1_1818391_1819342_+	pfam00665, rve, Integrase core domain	NA|217aa|down_0|NZ_CP017160.1_1820899_1821550_-	PRK00215, PRK00215, transcriptional repressor LexA	NA|401aa|down_1|NZ_CP017160.1_1821678_1822881_-	PRK09257, PRK09257, aromatic amino acid transaminase	NA|679aa|down_2|NZ_CP017160.1_1822958_1824995_+	PRK05298, PRK05298, excinuclease ABC subunit UvrB	NA|164aa|down_3|NZ_CP017160.1_1825247_1825739_+	cd16343, LMWPTP, Low molecular weight protein tyrosine phosphatase	NA|171aa|down_4|NZ_CP017160.1_1825954_1826467_+	TIGR02010, Putative_HTH-type_transcriptional_regulator, iron-sulfur cluster assembly transcription factor IscR	NA|404aa|down_5|NZ_CP017160.1_1826484_1827696_+	PRK14012, PRK14012, IscS subfamily cysteine desulfurase	NA|137aa|down_6|NZ_CP017160.1_1827733_1828144_+	PRK11325, PRK11325, scaffold protein; Provisional	NA|108aa|down_7|NZ_CP017160.1_1828145_1828469_+	TIGR02011, Protein_yfhF	NA|171aa|down_8|NZ_CP017160.1_1828471_1828984_+	PRK03578, hscB, Fe-S protein assembly co-chaperone HscB	NA|621aa|down_9|NZ_CP017160.1_1829113_1830976_+	PRK05183, hscA, chaperone protein HscA; Provisional
GCF_002442655.1_ASM244265v1	NZ_CP017160	Bordetella pertussis strain J223 chromosome, complete genome	6	3433339-3433448	6	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG	Orphan	TTGACTGCCAAGACGGTATCTGTCCCC	27	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG	NA,NA	NA|288aa|up_9|NZ_CP017160.1_3416718_3417582_+	PLN02864, PLN02864, enoyl-CoA hydratase	NA|363aa|up_8|NZ_CP017160.1_3417617_3418706_+	cd08948, 5beta-POR_like_SDR_a, progesterone 5-beta-reductase-like proteins (5beta-POR), atypical (a) SDRs	NA|993aa|up_7|NZ_CP017160.1_3420005_3422984_+	pfam17936, Big_6, Bacterial Ig domain	NA|293aa|up_6|NZ_CP017160.1_3423910_3424789_+	pfam00487, FA_desaturase, Fatty acid desaturase	NA|317aa|up_5|NZ_CP017160.1_3426737_3427688_+	pfam00665, rve, Integrase core domain	NA|156aa|up_4|NZ_CP017160.1_3427684_3428152_-	PRK00203, rnhA, ribonuclease H; Reviewed	NA|257aa|up_3|NZ_CP017160.1_3428194_3428965_-	pfam08241, Methyltransf_11, Methyltransferase domain	NA|267aa|up_2|NZ_CP017160.1_3428985_3429786_+	TIGR03413, GSH_gloB, hydroxyacylglutathione hydrolase	NA|470aa|up_1|NZ_CP017160.1_3429796_3431206_+	PRK10783, mltD, membrane-bound lytic murein transglycosylase D; Provisional	NA|262aa|up_0|NZ_CP017160.1_3431300_3432086_+	PRK06997, PRK06997, enoyl-[acyl-carrier-protein] reductase FabI	NA|131aa|down_0|NZ_CP017160.1_3433449_3433842_-	COG1765, COG1765, Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]	NA|227aa|down_1|NZ_CP017160.1_3433979_3434660_+	pfam04391, DUF533, Protein of unknown function (DUF533)	NA|324aa|down_2|NZ_CP017160.1_3434664_3435636_-	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_CP017160.1_3435731_3436682_-	pfam00665, rve, Integrase core domain	NA|234aa|down_4|NZ_CP017160.1_3438186_3438888_+	PRK09468, ompR, osmolarity response regulator; Provisional	NA|475aa|down_5|NZ_CP017160.1_3438887_3440312_+	PRK09467, envZ, osmolarity sensor protein; Provisional	NA|447aa|down_6|NZ_CP017160.1_3441381_3442722_-	pfam01654, Cyt_bd_oxida_I, Cytochrome bd terminal oxidase subunit I	NA|588aa|down_7|NZ_CP017160.1_3442837_3444601_+	PRK05347, PRK05347, glutaminyl-tRNA synthetase; Provisional	NA|293aa|down_8|NZ_CP017160.1_3444712_3445591_+	PRK00030, minC, septum site-determining protein MinC	NA|272aa|down_9|NZ_CP017160.1_3445703_3446519_+	COG2894, MinD, Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]
