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
GCA_004008355.1_ASM400835v1	CP025071	Bordetella parapertussis strain B149 chromosome, complete genome	1	1052473-1052559	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|CP025071.1_1056865_1057081_-	NA|263aa|up_9|CP025071.1_1032496_1033285_-	cd03293, ABC_NrtD_SsuB_transporters, ATP-binding cassette domain of the nitrate and sulfonate transporters	NA|145aa|up_8|CP025071.1_1034407_1034842_-	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|CP025071.1_1035896_1036823_-	pfam13468, Glyoxalase_3, Glyoxalase-like domain	NA|123aa|up_6|CP025071.1_1037109_1037478_+	COG3450, COG3450, Predicted enzyme of the cupin superfamily [General function prediction only]	NA|832aa|up_5|CP025071.1_1037577_1040073_+	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|CP025071.1_1040121_1040814_+	PRK10119, PRK10119, putative hydrolase; Provisional	NA|209aa|up_3|CP025071.1_1042268_1042895_+	cd01012, YcaC_related, YcaC related amidohydrolases; E	NA|659aa|up_2|CP025071.1_1042943_1044920_-	pfam16448, LapD_MoxY_N, LapD/MoxY periplasmic domain	NA|228aa|up_1|CP025071.1_1044935_1045619_-	COG3672, COG3672, Predicted transglutaminase-like cysteine proteinase [General    function prediction only]	NA|2216aa|up_0|CP025071.1_1045699_1052347_-	NF012211, tand_rpt_95, tandem-95 repeat protein	NA|222aa|down_0|CP025071.1_1052581_1053247_-	COG2197, CitB, Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]	NA|481aa|down_1|CP025071.1_1053268_1054711_-	TIGR01843, Hemolysin_secretion_protein_D_plasmid, type I secretion membrane fusion protein, HlyD family	NA|725aa|down_2|CP025071.1_1054713_1056888_-	TIGR03375, type_I_sec_LssB, type I secretion system ATPase, LssB family	NA|72aa|down_3|CP025071.1_1056865_1057081_-	NA	NA|490aa|down_4|CP025071.1_1057091_1058561_-	TIGR01844, Proteases_secretion_protein_PrtF, type I secretion outer membrane protein, TolC family	NA|431aa|down_5|CP025071.1_1058912_1060205_-	TIGR03862, flavo_PP4765, uncharacterized flavoprotein, PP_4765 family	csa3|109aa|down_6|CP025071.1_1060357_1060684_+	COG0640, ArsR, Predicted transcriptional regulators [Transcription]	NA|427aa|down_7|CP025071.1_1060680_1061961_+	PRK15445, PRK15445, arsenical efflux pump membrane protein ArsB	NA|322aa|down_8|CP025071.1_1062001_1062967_-	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|CP025071.1_1063010_1064147_-	pfam02515, CoA_transf_3, CoA-transferase family III
GCA_004008355.1_ASM400835v1	CP025071	Bordetella parapertussis strain B149 chromosome, complete genome	2	2198975-2199061	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|CP025071.1_2185622_2186378_-	PRK07023, PRK07023, SDR family oxidoreductase	NA|368aa|up_8|CP025071.1_2186407_2187512_-	PRK00578, prfB, peptide chain release factor 2; Validated	NA|567aa|up_7|CP025071.1_2187614_2189315_-	PRK11070, PRK11070, single-stranded-DNA-specific exonuclease RecJ	NA|326aa|up_6|CP025071.1_2189296_2190274_-	COG4255, COG4255, Uncharacterized protein conserved in bacteria [Function unknown]	NA|427aa|up_5|CP025071.1_2190283_2191564_+	TIGR02212, releasing_system_transmembrane_protein_lolC	NA|232aa|up_4|CP025071.1_2191556_2192252_+	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|CP025071.1_2192285_2193113_+	cd01310, TatD_DNAse, TatD like proteins;  E	NA|1077aa|up_2|CP025071.1_2193394_2196625_+	pfam03797, Autotransporter, Autotransporter beta-domain	NA|407aa|up_1|CP025071.1_2196745_2197966_-	COG3464, COG3464, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|255aa|up_0|CP025071.1_2198147_2198912_+	PRK07024, PRK07024, SDR family oxidoreductase	NA|215aa|down_0|CP025071.1_2199092_2199737_-	pfam00300, His_Phos_1, Histidine phosphatase superfamily (branch 1)	NA|300aa|down_1|CP025071.1_2199747_2200647_-	COG0583, LysR, Transcriptional regulator [Transcription]	NA|362aa|down_2|CP025071.1_2200694_2201780_-	COG3842, PotA, ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]	NA|570aa|down_3|CP025071.1_2201776_2203486_-	COG1178, ThiP, ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]	NA|440aa|down_4|CP025071.1_2203562_2204882_-	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|CP025071.1_2205141_2206455_+	TIGR03616, Putative_pyrimidine_permease_RutG, pyrimidine utilization transport protein G	NA|546aa|down_6|CP025071.1_2206485_2208123_-	PRK15041, PRK15041, methyl-accepting chemotaxis protein	NA|159aa|down_7|CP025071.1_2208746_2209223_+	PRK00226, greA, transcription elongation factor GreA; Reviewed	NA|317aa|down_8|CP025071.1_2209524_2210475_-	pfam13011, LZ_Tnp_IS481, leucine-zipper of insertion element IS481	NA|201aa|down_9|CP025071.1_2210614_2211217_-	smart01103, CRS1_YhbY, Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly
GCA_004008355.1_ASM400835v1	CP025071	Bordetella parapertussis strain B149 chromosome, complete genome	3	3091586-3091682	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|117aa|up_1|CP025071.1_3088736_3089087_-,NA|139aa|down_2|CP025071.1_3094628_3095045_-	NA|425aa|up_9|CP025071.1_3078499_3079774_-	pfam06864, PAP_PilO, Pilin accessory protein (PilO)	NA|526aa|up_8|CP025071.1_3079777_3081355_-	TIGR02520, putative_Type_IV_pilus_protein, type IVB pilus formation outer membrane protein, R64 PilN family	NA|254aa|up_7|CP025071.1_3081351_3082113_-	cd06911, VirB9_CagX_TrbG, VirB9/CagX/TrbG, a component of the type IV secretion system	NA|452aa|up_6|CP025071.1_3082290_3083646_-	COG0154, GatA, Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]	NA|545aa|up_5|CP025071.1_3083642_3085277_-	COG1123, COG1123, ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]	NA|277aa|up_4|CP025071.1_3085269_3086100_-	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|CP025071.1_3086117_3087062_-	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|CP025071.1_3087114_3088689_-	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|117aa|up_1|CP025071.1_3088736_3089087_-	NA	NA|317aa|up_0|CP025071.1_3090561_3091512_+	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|CP025071.1_3091743_3092964_-	COG3464, COG3464, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|483aa|down_1|CP025071.1_3093151_3094600_+	PRK05932, PRK05932, RNA polymerase factor sigma-54; Reviewed	NA|139aa|down_2|CP025071.1_3094628_3095045_-	NA	NA|511aa|down_3|CP025071.1_3095302_3096835_+	TIGR02095, Glycogen_synthase, glycogen/starch synthase, ADP-glucose type	NA|732aa|down_4|CP025071.1_3103384_3105580_+	PRK05402, PRK05402, 1,4-alpha-glucan branching protein GlgB	NA|673aa|down_5|CP025071.1_3109452_3111471_+	PRK14507, PRK14507, malto-oligosyltrehalose synthase	NA|991aa|down_6|CP025071.1_3113999_3116972_-	PRK13557, PRK13557, histidine kinase; Provisional	NA|285aa|down_7|CP025071.1_3117072_3117927_-	PRK08176, pdxK, pyridoxine/pyridoxal/pyridoxamine kinase	NA|268aa|down_8|CP025071.1_3117923_3118727_-	cd00635, PLPDE_III_YBL036c_like, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins	NA|444aa|down_9|CP025071.1_3118786_3120118_+	PRK15481, PRK15481, transcriptional regulatory protein PtsJ; Provisional
GCA_004008355.1_ASM400835v1	CP025071	Bordetella parapertussis strain B149 chromosome, complete genome	4	3767544-3767625	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|CP025071.1_3763984_3764359_-,NA|81aa|down_4|CP025071.1_3771966_3772209_-	NA|321aa|up_9|CP025071.1_3757303_3758266_-	cd03789, GT9_LPS_heptosyltransferase, lipopolysaccharide heptosyltransferase and similar proteins	NA|419aa|up_8|CP025071.1_3758483_3759740_-	PRK07006, PRK07006, isocitrate dehydrogenase; Reviewed	NA|142aa|up_7|CP025071.1_3759942_3760368_+	pfam08897, DUF1841, Domain of unknown function (DUF1841)	NA|121aa|up_6|CP025071.1_3760418_3760781_-	COG2863, COG2863, Cytochrome c553 [Energy production and conversion]	NA|118aa|up_5|CP025071.1_3760793_3761147_-	COG2863, COG2863, Cytochrome c553 [Energy production and conversion]	NA|296aa|up_4|CP025071.1_3761307_3762195_+	COG0714, COG0714, MoxR-like ATPases [General function prediction only]	NA|391aa|up_3|CP025071.1_3762216_3763389_+	COG3825, COG3825, Uncharacterized protein conserved in bacteria [Function unknown]	NA|185aa|up_2|CP025071.1_3763392_3763947_-	COG1247, COG1247, Sortase and related acyltransferases [Cell envelope biogenesis, outer membrane]	NA|125aa|up_1|CP025071.1_3763984_3764359_-	NA	NA|917aa|up_0|CP025071.1_3764691_3767442_+	COG0612, PqqL, Predicted Zn-dependent peptidases [General function prediction only]	NA|378aa|down_0|CP025071.1_3767632_3768766_-	PRK10767, PRK10767, chaperone protein DnaJ; Provisional	NA|642aa|down_1|CP025071.1_3768866_3770792_-	PRK00290, dnaK, molecular chaperone DnaK; Provisional	NA|127aa|down_2|CP025071.1_3770882_3771263_-	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|CP025071.1_3771270_3771825_-	PRK14139, PRK14139, heat shock protein GrpE; Provisional	NA|81aa|down_4|CP025071.1_3771966_3772209_-	NA	NA|363aa|down_5|CP025071.1_3772290_3773379_-	PRK00035, hemH, ferrochelatase; Reviewed	NA|335aa|down_6|CP025071.1_3773436_3774441_-	PRK00082, hrcA, heat-inducible transcription repressor; Provisional	NA|300aa|down_7|CP025071.1_3774555_3775455_+	PRK02155, ppnK, NAD kinase	NA|554aa|down_8|CP025071.1_3775470_3777132_+	COG0497, RecN, ATPase involved in DNA repair [DNA replication, recombination, and repair]	NA|407aa|down_9|CP025071.1_3777164_3778385_-	COG3464, COG3464, Transposase and inactivated derivatives [DNA replication, recombination, and repair]
GCA_004008355.1_ASM400835v1	CP025071	Bordetella parapertussis strain B149 chromosome, complete genome	5	3920569-3920653	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|CP025071.1_3908529_3910284_-	COG0405, Ggt, Gamma-glutamyltransferase [Amino acid transport and metabolism]	NA|299aa|up_8|CP025071.1_3910390_3911287_+	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|CP025071.1_3911351_3912335_-	cd13577, PBP2_BugE_Glu, Glutamate transporter of Bug (Bordetella uptake gene) protein family; contains the type 2 periplasmic binding fold	NA|327aa|up_6|CP025071.1_3912470_3913451_+	COG0679, COG0679, Predicted permeases [General function prediction only]	NA|464aa|up_5|CP025071.1_3913467_3914859_-	PRK00485, fumC, fumarate hydratase; Reviewed	NA|179aa|up_4|CP025071.1_3915010_3915547_+	COG0802, COG0802, Predicted ATPase or kinase [General function prediction only]	NA|415aa|up_3|CP025071.1_3915618_3916863_+	PRK10319, PRK10319, N-acetylmuramoyl-L-alanine amidase AmiA	NA|213aa|up_2|CP025071.1_3917005_3917644_-	PRK10847, PRK10847, DedA family protein	NA|630aa|up_1|CP025071.1_3917730_3919620_+	PRK00095, mutL, DNA mismatch repair endonuclease MutL	NA|314aa|up_0|CP025071.1_3919616_3920558_+	PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed	NA|350aa|down_0|CP025071.1_3920663_3921713_-	PRK05385, PRK05385, phosphoribosylaminoimidazole synthetase; Provisional	NA|234aa|down_1|CP025071.1_3921965_3922667_+	PRK08903, PRK08903, DnaA regulatory inactivator Hda; Validated	NA|233aa|down_2|CP025071.1_3922663_3923362_+	cd02612, HAD_PGPPase, phosphatidylglycerol-phosphate phosphatase, similar to Escherichia coli K-12 phosphatidylglycerol-phosphate phosphatase C	NA|452aa|down_3|CP025071.1_3923362_3924718_+	TIGR01942, pcnB, poly(A) polymerase	NA|164aa|down_4|CP025071.1_3924714_3925206_+	PRK14092, PRK14092, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase	NA|319aa|down_5|CP025071.1_3925224_3926181_-	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|465aa|down_6|CP025071.1_3926207_3927602_-	pfam03972, MmgE_PrpD, MmgE/PrpD family	NA|701aa|down_7|CP025071.1_3927598_3929701_-	TIGR00786, TRAP_transporter_permease_protein_SiaT, TRAP transporter, DctM subunit	NA|347aa|down_8|CP025071.1_3929871_3930912_+	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|CP025071.1_3930955_3931699_+	COG1802, GntR, Transcriptional regulators [Transcription]
GCA_004008355.1_ASM400835v1	CP025071	Bordetella parapertussis strain B149 chromosome, complete genome	6	4131247-4131340	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|545aa|up_9|CP025071.1_4117989_4119624_+	cd05934, FACL_DitJ_like, Uncharacterized subfamily of fatty acid CoA ligase (FACL)	NA|398aa|up_8|CP025071.1_4119672_4120866_-	PRK06954, PRK06954, acetyl-CoA C-acetyltransferase	NA|343aa|up_7|CP025071.1_4120931_4121960_-	pfam00441, Acyl-CoA_dh_1, Acyl-CoA dehydrogenase, C-terminal domain	NA|391aa|up_6|CP025071.1_4121986_4123159_-	cd01152, ACAD_fadE6_17_26, Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26	NA|306aa|up_5|CP025071.1_4123344_4124262_+	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_4|CP025071.1_4124272_4125244_-	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_3|CP025071.1_4125310_4126096_-	PRK09245, PRK09245, crotonase/enoyl-CoA hydratase family protein	NA|252aa|up_2|CP025071.1_4127517_4128273_-	COG0861, TerC, Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]	NA|173aa|up_1|CP025071.1_4128383_4128902_+	COG1285, SapB, Uncharacterized membrane protein [Function unknown]	NA|706aa|up_0|CP025071.1_4128898_4131016_-	PRK00007, PRK00007, elongation factor G; Reviewed	NA|407aa|down_0|CP025071.1_4131377_4132598_-	COG3464, COG3464, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|157aa|down_1|CP025071.1_4132740_4133211_-	pfam00582, Usp, Universal stress protein family	NA|115aa|down_2|CP025071.1_4133299_4133644_-	COG3453, COG3453, Uncharacterized protein conserved in bacteria [Function unknown]	NA|467aa|down_3|CP025071.1_4133743_4135144_-	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|CP025071.1_4135332_4136247_+	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|CP025071.1_4136243_4136903_+	COG1280, RhtB, Putative threonine efflux protein [Amino acid transport and metabolism]	NA|308aa|down_6|CP025071.1_4136992_4137916_+	pfam12146, Hydrolase_4, Serine aminopeptidase, S33	NA|152aa|down_7|CP025071.1_4137921_4138377_-	COG4125, COG4125, Predicted membrane protein [Function unknown]	NA|368aa|down_8|CP025071.1_4138373_4139477_-	cd10807, YdjC_like_3, uncharacterized YdjC-like family proteins from bacteria	NA|103aa|down_9|CP025071.1_4139396_4139705_+	pfam04138, GtrA, GtrA-like protein
