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_001704255.1_ASM170425v1	NZ_CP016342	Bordetella parapertussis strain H904 chromosome, complete genome	1	1052540-1052626	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_CP016342.1_1056932_1057148_-	NA|263aa|up_9|NZ_CP016342.1_1032559_1033348_-	cd03293, ABC_NrtD_SsuB_transporters, ATP-binding cassette domain of the nitrate and sulfonate transporters	NA|145aa|up_8|NZ_CP016342.1_1034470_1034905_-	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_CP016342.1_1035963_1036890_-	pfam13468, Glyoxalase_3, Glyoxalase-like domain	NA|123aa|up_6|NZ_CP016342.1_1037176_1037545_+	COG3450, COG3450, Predicted enzyme of the cupin superfamily [General function prediction only]	NA|832aa|up_5|NZ_CP016342.1_1037644_1040140_+	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_CP016342.1_1040188_1040881_+	PRK10119, PRK10119, putative hydrolase; Provisional	NA|209aa|up_3|NZ_CP016342.1_1042335_1042962_+	cd01012, YcaC_related, YcaC related amidohydrolases; E	NA|659aa|up_2|NZ_CP016342.1_1043010_1044987_-	pfam16448, LapD_MoxY_N, LapD/MoxY periplasmic domain	NA|228aa|up_1|NZ_CP016342.1_1045002_1045686_-	COG3672, COG3672, Predicted transglutaminase-like cysteine proteinase [General    function prediction only]	NA|2216aa|up_0|NZ_CP016342.1_1045766_1052414_-	NF012211, tand_rpt_95, tandem-95 repeat protein	NA|222aa|down_0|NZ_CP016342.1_1052648_1053314_-	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_CP016342.1_1053335_1054778_-	TIGR01843, Hemolysin_secretion_protein_D_plasmid, type I secretion membrane fusion protein, HlyD family	NA|725aa|down_2|NZ_CP016342.1_1054780_1056955_-	TIGR03375, type_I_sec_LssB, type I secretion system ATPase, LssB family	NA|72aa|down_3|NZ_CP016342.1_1056932_1057148_-	NA	NA|490aa|down_4|NZ_CP016342.1_1057158_1058628_-	TIGR01844, Proteases_secretion_protein_PrtF, type I secretion outer membrane protein, TolC family	NA|431aa|down_5|NZ_CP016342.1_1058979_1060272_-	TIGR03862, flavo_PP4765, uncharacterized flavoprotein, PP_4765 family	csa3|109aa|down_6|NZ_CP016342.1_1060424_1060751_+	COG0640, ArsR, Predicted transcriptional regulators [Transcription]	NA|427aa|down_7|NZ_CP016342.1_1060747_1062028_+	PRK15445, PRK15445, arsenical efflux pump membrane protein ArsB	NA|322aa|down_8|NZ_CP016342.1_1062068_1063034_-	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_CP016342.1_1063077_1064214_-	pfam02515, CoA_transf_3, CoA-transferase family III
GCF_001704255.1_ASM170425v1	NZ_CP016342	Bordetella parapertussis strain H904 chromosome, complete genome	2	2198965-2199051	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_CP016342.1_2185612_2186368_-	PRK07023, PRK07023, SDR family oxidoreductase	NA|368aa|up_8|NZ_CP016342.1_2186397_2187502_-	PRK00578, prfB, peptide chain release factor 2; Validated	NA|567aa|up_7|NZ_CP016342.1_2187604_2189305_-	PRK11070, PRK11070, single-stranded-DNA-specific exonuclease RecJ	NA|326aa|up_6|NZ_CP016342.1_2189286_2190264_-	COG4255, COG4255, Uncharacterized protein conserved in bacteria [Function unknown]	NA|427aa|up_5|NZ_CP016342.1_2190273_2191554_+	TIGR02212, releasing_system_transmembrane_protein_lolC	NA|232aa|up_4|NZ_CP016342.1_2191546_2192242_+	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_CP016342.1_2192275_2193103_+	cd01310, TatD_DNAse, TatD like proteins;  E	NA|1077aa|up_2|NZ_CP016342.1_2193384_2196615_+	pfam03797, Autotransporter, Autotransporter beta-domain	NA|407aa|up_1|NZ_CP016342.1_2196735_2197956_-	COG3464, COG3464, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|255aa|up_0|NZ_CP016342.1_2198137_2198902_+	PRK07024, PRK07024, SDR family oxidoreductase	NA|215aa|down_0|NZ_CP016342.1_2199082_2199727_-	pfam00300, His_Phos_1, Histidine phosphatase superfamily (branch 1)	NA|300aa|down_1|NZ_CP016342.1_2199737_2200637_-	COG0583, LysR, Transcriptional regulator [Transcription]	NA|362aa|down_2|NZ_CP016342.1_2200684_2201770_-	COG3842, PotA, ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]	NA|570aa|down_3|NZ_CP016342.1_2201766_2203476_-	COG1178, ThiP, ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]	NA|440aa|down_4|NZ_CP016342.1_2203552_2204872_-	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_CP016342.1_2205131_2206445_+	TIGR03616, Putative_pyrimidine_permease_RutG, pyrimidine utilization transport protein G	NA|546aa|down_6|NZ_CP016342.1_2206475_2208113_-	PRK15041, PRK15041, methyl-accepting chemotaxis protein	NA|159aa|down_7|NZ_CP016342.1_2208736_2209213_+	PRK00226, greA, transcription elongation factor GreA; Reviewed	NA|317aa|down_8|NZ_CP016342.1_2209514_2210465_-	pfam13011, LZ_Tnp_IS481, leucine-zipper of insertion element IS481	NA|201aa|down_9|NZ_CP016342.1_2210604_2211207_-	smart01103, CRS1_YhbY, Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly
GCF_001704255.1_ASM170425v1	NZ_CP016342	Bordetella parapertussis strain H904 chromosome, complete genome	3	3091576-3091672	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_CP016342.1_3088726_3089086_-,NA|139aa|down_2|NZ_CP016342.1_3094618_3095035_-	NA|425aa|up_9|NZ_CP016342.1_3078489_3079764_-	pfam06864, PAP_PilO, Pilin accessory protein (PilO)	NA|526aa|up_8|NZ_CP016342.1_3079767_3081345_-	TIGR02520, putative_Type_IV_pilus_protein, type IVB pilus formation outer membrane protein, R64 PilN family	NA|254aa|up_7|NZ_CP016342.1_3081341_3082103_-	cd06911, VirB9_CagX_TrbG, VirB9/CagX/TrbG, a component of the type IV secretion system	NA|452aa|up_6|NZ_CP016342.1_3082280_3083636_-	COG0154, GatA, Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]	NA|545aa|up_5|NZ_CP016342.1_3083632_3085267_-	COG1123, COG1123, ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]	NA|277aa|up_4|NZ_CP016342.1_3085259_3086090_-	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_CP016342.1_3086107_3087052_-	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_CP016342.1_3087104_3088679_-	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_CP016342.1_3088726_3089086_-	NA	NA|317aa|up_0|NZ_CP016342.1_3090551_3091502_+	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_CP016342.1_3091733_3092954_-	COG3464, COG3464, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|483aa|down_1|NZ_CP016342.1_3093141_3094590_+	PRK05932, PRK05932, RNA polymerase factor sigma-54; Reviewed	NA|139aa|down_2|NZ_CP016342.1_3094618_3095035_-	NA	NA|511aa|down_3|NZ_CP016342.1_3095292_3096825_+	TIGR02095, Glycogen_synthase, glycogen/starch synthase, ADP-glucose type	NA|732aa|down_4|NZ_CP016342.1_3103248_3105444_+	PRK05402, PRK05402, 1,4-alpha-glucan branching protein GlgB	NA|673aa|down_5|NZ_CP016342.1_3109316_3111335_+	PRK14507, PRK14507, malto-oligosyltrehalose synthase	NA|991aa|down_6|NZ_CP016342.1_3113863_3116836_-	PRK13557, PRK13557, histidine kinase; Provisional	NA|285aa|down_7|NZ_CP016342.1_3116936_3117791_-	PRK08176, pdxK, pyridoxine/pyridoxal/pyridoxamine kinase	NA|268aa|down_8|NZ_CP016342.1_3117787_3118591_-	cd00635, PLPDE_III_YBL036c_like, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins	NA|444aa|down_9|NZ_CP016342.1_3118650_3119982_+	PRK15481, PRK15481, transcriptional regulatory protein PtsJ; Provisional
GCF_001704255.1_ASM170425v1	NZ_CP016342	Bordetella parapertussis strain H904 chromosome, complete genome	4	3767417-3767498	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_CP016342.1_3763857_3764232_-,NA|81aa|down_4|NZ_CP016342.1_3771839_3772082_-	NA|321aa|up_9|NZ_CP016342.1_3757176_3758139_-	cd03789, GT9_LPS_heptosyltransferase, lipopolysaccharide heptosyltransferase and similar proteins	NA|419aa|up_8|NZ_CP016342.1_3758356_3759613_-	PRK07006, PRK07006, isocitrate dehydrogenase; Reviewed	NA|142aa|up_7|NZ_CP016342.1_3759815_3760241_+	pfam08897, DUF1841, Domain of unknown function (DUF1841)	NA|121aa|up_6|NZ_CP016342.1_3760291_3760654_-	COG2863, COG2863, Cytochrome c553 [Energy production and conversion]	NA|118aa|up_5|NZ_CP016342.1_3760666_3761020_-	COG2863, COG2863, Cytochrome c553 [Energy production and conversion]	NA|296aa|up_4|NZ_CP016342.1_3761180_3762068_+	COG0714, COG0714, MoxR-like ATPases [General function prediction only]	NA|391aa|up_3|NZ_CP016342.1_3762089_3763262_+	COG3825, COG3825, Uncharacterized protein conserved in bacteria [Function unknown]	NA|185aa|up_2|NZ_CP016342.1_3763265_3763820_-	COG1247, COG1247, Sortase and related acyltransferases [Cell envelope biogenesis, outer membrane]	NA|125aa|up_1|NZ_CP016342.1_3763857_3764232_-	NA	NA|917aa|up_0|NZ_CP016342.1_3764564_3767315_+	COG0612, PqqL, Predicted Zn-dependent peptidases [General function prediction only]	NA|378aa|down_0|NZ_CP016342.1_3767505_3768639_-	PRK10767, PRK10767, chaperone protein DnaJ; Provisional	NA|642aa|down_1|NZ_CP016342.1_3768739_3770665_-	PRK00290, dnaK, molecular chaperone DnaK; Provisional	NA|127aa|down_2|NZ_CP016342.1_3770755_3771136_-	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_CP016342.1_3771143_3771698_-	PRK14139, PRK14139, heat shock protein GrpE; Provisional	NA|81aa|down_4|NZ_CP016342.1_3771839_3772082_-	NA	NA|363aa|down_5|NZ_CP016342.1_3772163_3773252_-	PRK00035, hemH, ferrochelatase; Reviewed	NA|335aa|down_6|NZ_CP016342.1_3773309_3774314_-	PRK00082, hrcA, heat-inducible transcription repressor; Provisional	NA|300aa|down_7|NZ_CP016342.1_3774428_3775328_+	PRK02155, ppnK, NAD kinase	NA|554aa|down_8|NZ_CP016342.1_3775343_3777005_+	COG0497, RecN, ATPase involved in DNA repair [DNA replication, recombination, and repair]	NA|407aa|down_9|NZ_CP016342.1_3777037_3778258_-	COG3464, COG3464, Transposase and inactivated derivatives [DNA replication, recombination, and repair]
GCF_001704255.1_ASM170425v1	NZ_CP016342	Bordetella parapertussis strain H904 chromosome, complete genome	5	3920442-3920526	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_CP016342.1_3908402_3910157_-	COG0405, Ggt, Gamma-glutamyltransferase [Amino acid transport and metabolism]	NA|299aa|up_8|NZ_CP016342.1_3910263_3911160_+	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_CP016342.1_3911224_3912208_-	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_CP016342.1_3912343_3913324_+	COG0679, COG0679, Predicted permeases [General function prediction only]	NA|464aa|up_5|NZ_CP016342.1_3913340_3914732_-	PRK00485, fumC, fumarate hydratase; Reviewed	NA|179aa|up_4|NZ_CP016342.1_3914883_3915420_+	COG0802, COG0802, Predicted ATPase or kinase [General function prediction only]	NA|462aa|up_3|NZ_CP016342.1_3915350_3916736_+	PRK10319, PRK10319, N-acetylmuramoyl-L-alanine amidase AmiA	NA|213aa|up_2|NZ_CP016342.1_3916878_3917517_-	PRK10847, PRK10847, DedA family protein	NA|630aa|up_1|NZ_CP016342.1_3917603_3919493_+	PRK00095, mutL, DNA mismatch repair endonuclease MutL	NA|314aa|up_0|NZ_CP016342.1_3919489_3920431_+	PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed	NA|350aa|down_0|NZ_CP016342.1_3920536_3921586_-	PRK05385, PRK05385, phosphoribosylaminoimidazole synthetase; Provisional	NA|234aa|down_1|NZ_CP016342.1_3921838_3922540_+	PRK08903, PRK08903, DnaA regulatory inactivator Hda; Validated	NA|233aa|down_2|NZ_CP016342.1_3922536_3923235_+	cd02612, HAD_PGPPase, phosphatidylglycerol-phosphate phosphatase, similar to Escherichia coli K-12 phosphatidylglycerol-phosphate phosphatase C	NA|452aa|down_3|NZ_CP016342.1_3923235_3924591_+	TIGR01942, pcnB, poly(A) polymerase	NA|164aa|down_4|NZ_CP016342.1_3924587_3925079_+	PRK14092, PRK14092, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase	NA|319aa|down_5|NZ_CP016342.1_3925097_3926054_-	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_CP016342.1_3926080_3927475_-	pfam03972, MmgE_PrpD, MmgE/PrpD family	NA|701aa|down_7|NZ_CP016342.1_3927471_3929574_-	TIGR00786, TRAP_transporter_permease_protein_SiaT, TRAP transporter, DctM subunit	NA|347aa|down_8|NZ_CP016342.1_3929744_3930785_+	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_CP016342.1_3930828_3931572_+	COG1802, GntR, Transcriptional regulators [Transcription]
GCF_001704255.1_ASM170425v1	NZ_CP016342	Bordetella parapertussis strain H904 chromosome, complete genome	6	4131134-4131227	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_CP016342.1_4119559_4120753_-	PRK06954, PRK06954, acetyl-CoA C-acetyltransferase	NA|343aa|up_8|NZ_CP016342.1_4120818_4121847_-	pfam00441, Acyl-CoA_dh_1, Acyl-CoA dehydrogenase, C-terminal domain	NA|391aa|up_7|NZ_CP016342.1_4121873_4123046_-	cd01152, ACAD_fadE6_17_26, Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26	NA|306aa|up_6|NZ_CP016342.1_4123231_4124149_+	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_CP016342.1_4124159_4125131_-	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_CP016342.1_4125197_4125983_-	PRK09245, PRK09245, crotonase/enoyl-CoA hydratase family protein	NA|410aa|up_3|NZ_CP016342.1_4125979_4127209_-	pfam02515, CoA_transf_3, CoA-transferase family III	NA|252aa|up_2|NZ_CP016342.1_4127404_4128160_-	COG0861, TerC, Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]	NA|173aa|up_1|NZ_CP016342.1_4128270_4128789_+	COG1285, SapB, Uncharacterized membrane protein [Function unknown]	NA|706aa|up_0|NZ_CP016342.1_4128785_4130903_-	PRK00007, PRK00007, elongation factor G; Reviewed	NA|407aa|down_0|NZ_CP016342.1_4131264_4132485_-	COG3464, COG3464, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|157aa|down_1|NZ_CP016342.1_4132627_4133098_-	pfam00582, Usp, Universal stress protein family	NA|115aa|down_2|NZ_CP016342.1_4133186_4133531_-	COG3453, COG3453, Uncharacterized protein conserved in bacteria [Function unknown]	NA|482aa|down_3|NZ_CP016342.1_4133630_4135076_-	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_CP016342.1_4135219_4136134_+	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_CP016342.1_4136130_4136790_+	COG1280, RhtB, Putative threonine efflux protein [Amino acid transport and metabolism]	NA|308aa|down_6|NZ_CP016342.1_4136879_4137803_+	pfam12146, Hydrolase_4, Serine aminopeptidase, S33	NA|152aa|down_7|NZ_CP016342.1_4137808_4138264_-	COG4125, COG4125, Predicted membrane protein [Function unknown]	NA|368aa|down_8|NZ_CP016342.1_4138260_4139364_-	cd10807, YdjC_like_3, uncharacterized YdjC-like family proteins from bacteria	NA|91aa|down_9|NZ_CP016342.1_4139319_4139592_+	pfam04138, GtrA, GtrA-like protein
