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_009626335.1_ASM962633v1	NZ_CP043092	Bordetella parapertussis strain J280 chromosome, complete genome	1	1052546-1052632	1	CRISPRCasFinder	no	csa3	csa3,RT,DEDDh,cas3,DinG	Type I-A	CGTGGTGCCTGTCCCCGCGGGGAC	24	0	0	NA	NA	NA	1	1	Orphan	csa3,RT,DEDDh,cas3,DinG	NA,NA|72aa|down_3|NZ_CP043092.1_1056938_1057154_-	NA|263aa|up_9|NZ_CP043092.1_1032565_1033354_-	cd03293, ABC_NrtD_SsuB_transporters, ATP-binding cassette domain of the nitrate and sulfonate transporters	NA|145aa|up_8|NZ_CP043092.1_1034476_1034911_-	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	NA|309aa|up_7|NZ_CP043092.1_1035969_1036896_-	pfam13468, Glyoxalase_3, Glyoxalase-like domain	NA|123aa|up_6|NZ_CP043092.1_1037182_1037551_+	COG3450, COG3450, Predicted enzyme of the cupin superfamily [General function prediction only]	NA|832aa|up_5|NZ_CP043092.1_1037650_1040146_+	cd02094, P-type_ATPase_Cu-like, P-type heavy metal-transporting ATPase, similar to human copper-transporting ATPases, ATP7A and ATP7B	NA|231aa|up_4|NZ_CP043092.1_1040194_1040887_+	PRK10119, PRK10119, putative hydrolase; Provisional	NA|209aa|up_3|NZ_CP043092.1_1042341_1042968_+	cd01012, YcaC_related, YcaC related amidohydrolases; E	NA|659aa|up_2|NZ_CP043092.1_1043016_1044993_-	pfam16448, LapD_MoxY_N, LapD/MoxY periplasmic domain	NA|228aa|up_1|NZ_CP043092.1_1045008_1045692_-	COG3672, COG3672, Predicted transglutaminase-like cysteine proteinase [General    function prediction only]	NA|2216aa|up_0|NZ_CP043092.1_1045772_1052420_-	NF012211, tand_rpt_95, tandem-95 repeat protein	NA|222aa|down_0|NZ_CP043092.1_1052654_1053320_-	COG2197, CitB, Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]	NA|481aa|down_1|NZ_CP043092.1_1053341_1054784_-	TIGR01843, Hemolysin_secretion_protein_D_plasmid, type I secretion membrane fusion protein, HlyD family	NA|725aa|down_2|NZ_CP043092.1_1054786_1056961_-	TIGR03375, type_I_sec_LssB, type I secretion system ATPase, LssB family	NA|72aa|down_3|NZ_CP043092.1_1056938_1057154_-	NA	NA|490aa|down_4|NZ_CP043092.1_1057164_1058634_-	TIGR01844, Proteases_secretion_protein_PrtF, type I secretion outer membrane protein, TolC family	NA|431aa|down_5|NZ_CP043092.1_1058984_1060277_-	TIGR03862, flavo_PP4765, uncharacterized flavoprotein, PP_4765 family	csa3|109aa|down_6|NZ_CP043092.1_1060429_1060756_+	COG0640, ArsR, Predicted transcriptional regulators [Transcription]	NA|427aa|down_7|NZ_CP043092.1_1060752_1062033_+	PRK15445, PRK15445, arsenical efflux pump membrane protein ArsB	NA|322aa|down_8|NZ_CP043092.1_1062073_1063039_-	cd07012, PBP2_Bug_TTT, Bug (Bordetella uptake gene) protein family of periplasmic solute-binding receptors; contains the type 2 periplasmic binding fold	NA|379aa|down_9|NZ_CP043092.1_1063082_1064219_-	pfam02515, CoA_transf_3, CoA-transferase family III
GCF_009626335.1_ASM962633v1	NZ_CP043092	Bordetella parapertussis strain J280 chromosome, complete genome	2	2199056-2199142	2	CRISPRCasFinder	no		csa3,RT,DEDDh,cas3,DinG	Orphan	AGTGTGCCTGTCCCCGCAGGGACAG	25	0	0	NA	NA	NA	1	1	Orphan	csa3,RT,DEDDh,cas3,DinG	NA,NA	NA|252aa|up_9|NZ_CP043092.1_2185703_2186459_-	PRK07023, PRK07023, SDR family oxidoreductase	NA|368aa|up_8|NZ_CP043092.1_2186488_2187593_-	PRK00578, prfB, peptide chain release factor 2; Validated	NA|567aa|up_7|NZ_CP043092.1_2187695_2189396_-	PRK11070, PRK11070, single-stranded-DNA-specific exonuclease RecJ	NA|326aa|up_6|NZ_CP043092.1_2189377_2190355_-	COG4255, COG4255, Uncharacterized protein conserved in bacteria [Function unknown]	NA|427aa|up_5|NZ_CP043092.1_2190364_2191645_+	TIGR02212, releasing_system_transmembrane_protein_lolC	NA|232aa|up_4|NZ_CP043092.1_2191637_2192333_+	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_3|NZ_CP043092.1_2192366_2193194_+	cd01310, TatD_DNAse, TatD like proteins;  E	NA|1077aa|up_2|NZ_CP043092.1_2193475_2196706_+	pfam03797, Autotransporter, Autotransporter beta-domain	NA|407aa|up_1|NZ_CP043092.1_2196826_2198047_-	COG3464, COG3464, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|255aa|up_0|NZ_CP043092.1_2198228_2198993_+	PRK07024, PRK07024, SDR family oxidoreductase	NA|215aa|down_0|NZ_CP043092.1_2199173_2199818_-	pfam00300, His_Phos_1, Histidine phosphatase superfamily (branch 1)	NA|300aa|down_1|NZ_CP043092.1_2199828_2200728_-	COG0583, LysR, Transcriptional regulator [Transcription]	NA|362aa|down_2|NZ_CP043092.1_2200775_2201861_-	COG3842, PotA, ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]	NA|570aa|down_3|NZ_CP043092.1_2201857_2203567_-	COG1178, ThiP, ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]	NA|440aa|down_4|NZ_CP043092.1_2203643_2204963_-	cd13518, PBP2_Fe3_thiamine_like, Substrate binding domain of iron and thiamine transporters-like, a member of the type 2 periplasmic binding fold superfamily	NA|438aa|down_5|NZ_CP043092.1_2205222_2206536_+	TIGR03616, Putative_pyrimidine_permease_RutG, pyrimidine utilization transport protein G	NA|546aa|down_6|NZ_CP043092.1_2206566_2208204_-	PRK15041, PRK15041, methyl-accepting chemotaxis protein	NA|159aa|down_7|NZ_CP043092.1_2208827_2209304_+	PRK00226, greA, transcription elongation factor GreA; Reviewed	NA|317aa|down_8|NZ_CP043092.1_2209605_2210556_-	pfam13011, LZ_Tnp_IS481, leucine-zipper of insertion element IS481	NA|201aa|down_9|NZ_CP043092.1_2210695_2211298_-	smart01103, CRS1_YhbY, Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly
GCF_009626335.1_ASM962633v1	NZ_CP043092	Bordetella parapertussis strain J280 chromosome, complete genome	3	3091663-3091759	3	CRISPRCasFinder	no		csa3,RT,DEDDh,cas3,DinG	Orphan	GTGCCTGTCCCGGCGGGGACAGGCACCC	28	0	0	NA	NA	NA	1	1	Orphan	csa3,RT,DEDDh,cas3,DinG	NA|120aa|up_1|NZ_CP043092.1_3088813_3089173_-,NA|139aa|down_2|NZ_CP043092.1_3094705_3095122_-	NA|425aa|up_9|NZ_CP043092.1_3078576_3079851_-	pfam06864, PAP_PilO, Pilin accessory protein (PilO)	NA|526aa|up_8|NZ_CP043092.1_3079854_3081432_-	TIGR02520, putative_Type_IV_pilus_protein, type IVB pilus formation outer membrane protein, R64 PilN family	NA|254aa|up_7|NZ_CP043092.1_3081428_3082190_-	cd06911, VirB9_CagX_TrbG, VirB9/CagX/TrbG, a component of the type IV secretion system	NA|452aa|up_6|NZ_CP043092.1_3082367_3083723_-	COG0154, GatA, Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]	NA|545aa|up_5|NZ_CP043092.1_3083719_3085354_-	COG1123, COG1123, ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]	NA|277aa|up_4|NZ_CP043092.1_3085346_3086177_-	COG1173, DppC, ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]	NA|315aa|up_3|NZ_CP043092.1_3086194_3087139_-	COG0601, DppB, ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]	NA|525aa|up_2|NZ_CP043092.1_3087191_3088766_-	cd08502, PBP2_NikA_DppA_OppA_like_16, The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold	NA|120aa|up_1|NZ_CP043092.1_3088813_3089173_-	NA	NA|317aa|up_0|NZ_CP043092.1_3090638_3091589_+	cd08440, PBP2_LTTR_like_4, TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold	NA|407aa|down_0|NZ_CP043092.1_3091820_3093041_-	COG3464, COG3464, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|483aa|down_1|NZ_CP043092.1_3093228_3094677_+	PRK05932, PRK05932, RNA polymerase factor sigma-54; Reviewed	NA|139aa|down_2|NZ_CP043092.1_3094705_3095122_-	NA	NA|511aa|down_3|NZ_CP043092.1_3095379_3096912_+	TIGR02095, Glycogen_synthase, glycogen/starch synthase, ADP-glucose type	NA|732aa|down_4|NZ_CP043092.1_3103461_3105657_+	PRK05402, PRK05402, 1,4-alpha-glucan branching protein GlgB	NA|673aa|down_5|NZ_CP043092.1_3109529_3111548_+	PRK14507, PRK14507, malto-oligosyltrehalose synthase	NA|991aa|down_6|NZ_CP043092.1_3114076_3117049_-	PRK13557, PRK13557, histidine kinase; Provisional	NA|285aa|down_7|NZ_CP043092.1_3117149_3118004_-	PRK08176, pdxK, pyridoxine/pyridoxal/pyridoxamine kinase	NA|268aa|down_8|NZ_CP043092.1_3118000_3118804_-	cd00635, PLPDE_III_YBL036c_like, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins	NA|444aa|down_9|NZ_CP043092.1_3118863_3120195_+	PRK15481, PRK15481, transcriptional regulatory protein PtsJ; Provisional
GCF_009626335.1_ASM962633v1	NZ_CP043092	Bordetella parapertussis strain J280 chromosome, complete genome	4	3767629-3767710	4	CRISPRCasFinder	no		csa3,RT,DEDDh,cas3,DinG	Orphan	CTGTCCCCGCCGGGACAGGCACC	23	0	0	NA	NA	NA	1	1	Orphan	csa3,RT,DEDDh,cas3,DinG	NA|125aa|up_1|NZ_CP043092.1_3764069_3764444_-,NA|81aa|down_4|NZ_CP043092.1_3772051_3772294_-	NA|321aa|up_9|NZ_CP043092.1_3757388_3758351_-	cd03789, GT9_LPS_heptosyltransferase, lipopolysaccharide heptosyltransferase and similar proteins	NA|419aa|up_8|NZ_CP043092.1_3758568_3759825_-	PRK07006, PRK07006, isocitrate dehydrogenase; Reviewed	NA|142aa|up_7|NZ_CP043092.1_3760027_3760453_+	pfam08897, DUF1841, Domain of unknown function (DUF1841)	NA|121aa|up_6|NZ_CP043092.1_3760503_3760866_-	COG2863, COG2863, Cytochrome c553 [Energy production and conversion]	NA|118aa|up_5|NZ_CP043092.1_3760878_3761232_-	COG2863, COG2863, Cytochrome c553 [Energy production and conversion]	NA|296aa|up_4|NZ_CP043092.1_3761392_3762280_+	COG0714, COG0714, MoxR-like ATPases [General function prediction only]	NA|391aa|up_3|NZ_CP043092.1_3762301_3763474_+	COG3825, COG3825, Uncharacterized protein conserved in bacteria [Function unknown]	NA|185aa|up_2|NZ_CP043092.1_3763477_3764032_-	COG1247, COG1247, Sortase and related acyltransferases [Cell envelope biogenesis, outer membrane]	NA|125aa|up_1|NZ_CP043092.1_3764069_3764444_-	NA	NA|917aa|up_0|NZ_CP043092.1_3764776_3767527_+	COG0612, PqqL, Predicted Zn-dependent peptidases [General function prediction only]	NA|378aa|down_0|NZ_CP043092.1_3767717_3768851_-	PRK10767, PRK10767, chaperone protein DnaJ; Provisional	NA|642aa|down_1|NZ_CP043092.1_3768951_3770877_-	PRK00290, dnaK, molecular chaperone DnaK; Provisional	NA|127aa|down_2|NZ_CP043092.1_3770967_3771348_-	cd02947, TRX_family, TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a TRX domain; and Group II, which are composed of fusion proteins of TRX and additional domains	NA|185aa|down_3|NZ_CP043092.1_3771355_3771910_-	PRK14139, PRK14139, heat shock protein GrpE; Provisional	NA|81aa|down_4|NZ_CP043092.1_3772051_3772294_-	NA	NA|363aa|down_5|NZ_CP043092.1_3772375_3773464_-	PRK00035, hemH, ferrochelatase; Reviewed	NA|335aa|down_6|NZ_CP043092.1_3773521_3774526_-	PRK00082, hrcA, heat-inducible transcription repressor; Provisional	NA|300aa|down_7|NZ_CP043092.1_3774640_3775540_+	PRK02155, ppnK, NAD kinase	NA|554aa|down_8|NZ_CP043092.1_3775555_3777217_+	COG0497, RecN, ATPase involved in DNA repair [DNA replication, recombination, and repair]	NA|407aa|down_9|NZ_CP043092.1_3777249_3778470_-	COG3464, COG3464, Transposase and inactivated derivatives [DNA replication, recombination, and repair]
GCF_009626335.1_ASM962633v1	NZ_CP043092	Bordetella parapertussis strain J280 chromosome, complete genome	5	3920654-3920738	5	CRISPRCasFinder	no		csa3,RT,DEDDh,cas3,DinG	Orphan	CTGTCCCCGCGGGGACAGGCACC	23	0	0	NA	NA	NA	1	1	Orphan	csa3,RT,DEDDh,cas3,DinG	NA,NA	NA|585aa|up_9|NZ_CP043092.1_3908614_3910369_-	COG0405, Ggt, Gamma-glutamyltransferase [Amino acid transport and metabolism]	NA|299aa|up_8|NZ_CP043092.1_3910475_3911372_+	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_CP043092.1_3911436_3912420_-	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_CP043092.1_3912555_3913536_+	COG0679, COG0679, Predicted permeases [General function prediction only]	NA|464aa|up_5|NZ_CP043092.1_3913552_3914944_-	PRK00485, fumC, fumarate hydratase; Reviewed	NA|179aa|up_4|NZ_CP043092.1_3915095_3915632_+	COG0802, COG0802, Predicted ATPase or kinase [General function prediction only]	NA|462aa|up_3|NZ_CP043092.1_3915562_3916948_+	PRK10319, PRK10319, N-acetylmuramoyl-L-alanine amidase AmiA	NA|213aa|up_2|NZ_CP043092.1_3917090_3917729_-	PRK10847, PRK10847, DedA family protein	NA|630aa|up_1|NZ_CP043092.1_3917815_3919705_+	PRK00095, mutL, DNA mismatch repair endonuclease MutL	NA|314aa|up_0|NZ_CP043092.1_3919701_3920643_+	PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed	NA|350aa|down_0|NZ_CP043092.1_3920748_3921798_-	PRK05385, PRK05385, phosphoribosylaminoimidazole synthetase; Provisional	NA|234aa|down_1|NZ_CP043092.1_3922050_3922752_+	PRK08903, PRK08903, DnaA regulatory inactivator Hda; Validated	NA|233aa|down_2|NZ_CP043092.1_3922748_3923447_+	cd02612, HAD_PGPPase, phosphatidylglycerol-phosphate phosphatase, similar to Escherichia coli K-12 phosphatidylglycerol-phosphate phosphatase C	NA|452aa|down_3|NZ_CP043092.1_3923447_3924803_+	TIGR01942, pcnB, poly(A) polymerase	NA|164aa|down_4|NZ_CP043092.1_3924799_3925291_+	PRK14092, PRK14092, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase	NA|319aa|down_5|NZ_CP043092.1_3925309_3926266_-	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|465aa|down_6|NZ_CP043092.1_3926292_3927687_-	pfam03972, MmgE_PrpD, MmgE/PrpD family	NA|701aa|down_7|NZ_CP043092.1_3927683_3929786_-	TIGR00786, TRAP_transporter_permease_protein_SiaT, TRAP transporter, DctM subunit	NA|347aa|down_8|NZ_CP043092.1_3929956_3930997_+	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_9|NZ_CP043092.1_3931040_3931784_+	COG1802, GntR, Transcriptional regulators [Transcription]
GCF_009626335.1_ASM962633v1	NZ_CP043092	Bordetella parapertussis strain J280 chromosome, complete genome	6	4131346-4131439	6	CRISPRCasFinder	no	DEDDh	csa3,RT,DEDDh,cas3,DinG	Unclear	GTGCCTGTCCCCGCCGGGACAGGCAC	26	0	0	NA	NA	NA	1	1	Orphan	csa3,RT,DEDDh,cas3,DinG	NA,NA	NA|398aa|up_9|NZ_CP043092.1_4119771_4120965_-	PRK06954, PRK06954, acetyl-CoA C-acetyltransferase	NA|343aa|up_8|NZ_CP043092.1_4121030_4122059_-	pfam00441, Acyl-CoA_dh_1, Acyl-CoA dehydrogenase, C-terminal domain	NA|391aa|up_7|NZ_CP043092.1_4122085_4123258_-	cd01152, ACAD_fadE6_17_26, Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26	NA|306aa|up_6|NZ_CP043092.1_4123443_4124361_+	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|324aa|up_5|NZ_CP043092.1_4124371_4125343_-	cd07012, PBP2_Bug_TTT, Bug (Bordetella uptake gene) protein family of periplasmic solute-binding receptors; contains the type 2 periplasmic binding fold	NA|262aa|up_4|NZ_CP043092.1_4125409_4126195_-	PRK09245, PRK09245, crotonase/enoyl-CoA hydratase family protein	NA|410aa|up_3|NZ_CP043092.1_4126191_4127421_-	pfam02515, CoA_transf_3, CoA-transferase family III	NA|252aa|up_2|NZ_CP043092.1_4127616_4128372_-	COG0861, TerC, Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]	NA|173aa|up_1|NZ_CP043092.1_4128482_4129001_+	COG1285, SapB, Uncharacterized membrane protein [Function unknown]	NA|706aa|up_0|NZ_CP043092.1_4128997_4131115_-	PRK00007, PRK00007, elongation factor G; Reviewed	NA|407aa|down_0|NZ_CP043092.1_4131476_4132697_-	COG3464, COG3464, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|157aa|down_1|NZ_CP043092.1_4132839_4133310_-	pfam00582, Usp, Universal stress protein family	NA|115aa|down_2|NZ_CP043092.1_4133398_4133743_-	COG3453, COG3453, Uncharacterized protein conserved in bacteria [Function unknown]	NA|482aa|down_3|NZ_CP043092.1_4133842_4135288_-	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|305aa|down_4|NZ_CP043092.1_4135431_4136346_+	COG0697, RhaT, Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]	NA|220aa|down_5|NZ_CP043092.1_4136342_4137002_+	COG1280, RhtB, Putative threonine efflux protein [Amino acid transport and metabolism]	NA|308aa|down_6|NZ_CP043092.1_4137091_4138015_+	pfam12146, Hydrolase_4, Serine aminopeptidase, S33	NA|152aa|down_7|NZ_CP043092.1_4138020_4138476_-	COG4125, COG4125, Predicted membrane protein [Function unknown]	NA|368aa|down_8|NZ_CP043092.1_4138472_4139576_-	cd10807, YdjC_like_3, uncharacterized YdjC-like family proteins from bacteria	NA|91aa|down_9|NZ_CP043092.1_4139531_4139804_+	pfam04138, GtrA, GtrA-like protein
