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_009626835.1_ASM962683v1	NZ_CP043119	Bordetella parapertussis strain I143 chromosome, complete genome	1	1052541-1052627	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_CP043119.1_1056933_1057149_-	NA|263aa|up_9|NZ_CP043119.1_1032560_1033349_-	cd03293, ABC_NrtD_SsuB_transporters, ATP-binding cassette domain of the nitrate and sulfonate transporters	NA|145aa|up_8|NZ_CP043119.1_1034471_1034906_-	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_CP043119.1_1035964_1036891_-	pfam13468, Glyoxalase_3, Glyoxalase-like domain	NA|123aa|up_6|NZ_CP043119.1_1037177_1037546_+	COG3450, COG3450, Predicted enzyme of the cupin superfamily [General function prediction only]	NA|832aa|up_5|NZ_CP043119.1_1037645_1040141_+	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_CP043119.1_1040189_1040882_+	PRK10119, PRK10119, putative hydrolase; Provisional	NA|209aa|up_3|NZ_CP043119.1_1042336_1042963_+	cd01012, YcaC_related, YcaC related amidohydrolases; E	NA|659aa|up_2|NZ_CP043119.1_1043011_1044988_-	pfam16448, LapD_MoxY_N, LapD/MoxY periplasmic domain	NA|228aa|up_1|NZ_CP043119.1_1045003_1045687_-	COG3672, COG3672, Predicted transglutaminase-like cysteine proteinase [General    function prediction only]	NA|2216aa|up_0|NZ_CP043119.1_1045767_1052415_-	NF012211, tand_rpt_95, tandem-95 repeat protein	NA|222aa|down_0|NZ_CP043119.1_1052649_1053315_-	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_CP043119.1_1053336_1054779_-	TIGR01843, Hemolysin_secretion_protein_D_plasmid, type I secretion membrane fusion protein, HlyD family	NA|725aa|down_2|NZ_CP043119.1_1054781_1056956_-	TIGR03375, type_I_sec_LssB, type I secretion system ATPase, LssB family	NA|72aa|down_3|NZ_CP043119.1_1056933_1057149_-	NA	NA|490aa|down_4|NZ_CP043119.1_1057159_1058629_-	TIGR01844, Proteases_secretion_protein_PrtF, type I secretion outer membrane protein, TolC family	NA|431aa|down_5|NZ_CP043119.1_1058980_1060273_-	TIGR03862, flavo_PP4765, uncharacterized flavoprotein, PP_4765 family	csa3|109aa|down_6|NZ_CP043119.1_1060425_1060752_+	COG0640, ArsR, Predicted transcriptional regulators [Transcription]	NA|427aa|down_7|NZ_CP043119.1_1060748_1062029_+	PRK15445, PRK15445, arsenical efflux pump membrane protein ArsB	NA|322aa|down_8|NZ_CP043119.1_1062069_1063035_-	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_CP043119.1_1063078_1064215_-	pfam02515, CoA_transf_3, CoA-transferase family III
GCF_009626835.1_ASM962683v1	NZ_CP043119	Bordetella parapertussis strain I143 chromosome, complete genome	2	2199031-2199117	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_CP043119.1_2185678_2186434_-	PRK07023, PRK07023, SDR family oxidoreductase	NA|368aa|up_8|NZ_CP043119.1_2186463_2187568_-	PRK00578, prfB, peptide chain release factor 2; Validated	NA|567aa|up_7|NZ_CP043119.1_2187670_2189371_-	PRK11070, PRK11070, single-stranded-DNA-specific exonuclease RecJ	NA|326aa|up_6|NZ_CP043119.1_2189352_2190330_-	COG4255, COG4255, Uncharacterized protein conserved in bacteria [Function unknown]	NA|427aa|up_5|NZ_CP043119.1_2190339_2191620_+	TIGR02212, releasing_system_transmembrane_protein_lolC	NA|232aa|up_4|NZ_CP043119.1_2191612_2192308_+	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_CP043119.1_2192341_2193169_+	cd01310, TatD_DNAse, TatD like proteins;  E	NA|1077aa|up_2|NZ_CP043119.1_2193450_2196681_+	pfam03797, Autotransporter, Autotransporter beta-domain	NA|407aa|up_1|NZ_CP043119.1_2196801_2198022_-	COG3464, COG3464, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|255aa|up_0|NZ_CP043119.1_2198203_2198968_+	PRK07024, PRK07024, SDR family oxidoreductase	NA|215aa|down_0|NZ_CP043119.1_2199148_2199793_-	pfam00300, His_Phos_1, Histidine phosphatase superfamily (branch 1)	NA|300aa|down_1|NZ_CP043119.1_2199803_2200703_-	COG0583, LysR, Transcriptional regulator [Transcription]	NA|362aa|down_2|NZ_CP043119.1_2200750_2201836_-	COG3842, PotA, ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]	NA|570aa|down_3|NZ_CP043119.1_2201832_2203542_-	COG1178, ThiP, ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]	NA|440aa|down_4|NZ_CP043119.1_2203618_2204938_-	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_CP043119.1_2205197_2206511_+	TIGR03616, Putative_pyrimidine_permease_RutG, pyrimidine utilization transport protein G	NA|546aa|down_6|NZ_CP043119.1_2206541_2208179_-	PRK15041, PRK15041, methyl-accepting chemotaxis protein	NA|159aa|down_7|NZ_CP043119.1_2208802_2209279_+	PRK00226, greA, transcription elongation factor GreA; Reviewed	NA|317aa|down_8|NZ_CP043119.1_2209580_2210531_-	pfam13011, LZ_Tnp_IS481, leucine-zipper of insertion element IS481	NA|201aa|down_9|NZ_CP043119.1_2210670_2211273_-	smart01103, CRS1_YhbY, Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly
GCF_009626835.1_ASM962683v1	NZ_CP043119	Bordetella parapertussis strain I143 chromosome, complete genome	3	3091652-3091748	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_CP043119.1_3088802_3089162_-,NA|139aa|down_2|NZ_CP043119.1_3094694_3095111_-	NA|425aa|up_9|NZ_CP043119.1_3078565_3079840_-	pfam06864, PAP_PilO, Pilin accessory protein (PilO)	NA|526aa|up_8|NZ_CP043119.1_3079843_3081421_-	TIGR02520, putative_Type_IV_pilus_protein, type IVB pilus formation outer membrane protein, R64 PilN family	NA|254aa|up_7|NZ_CP043119.1_3081417_3082179_-	cd06911, VirB9_CagX_TrbG, VirB9/CagX/TrbG, a component of the type IV secretion system	NA|452aa|up_6|NZ_CP043119.1_3082356_3083712_-	COG0154, GatA, Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]	NA|545aa|up_5|NZ_CP043119.1_3083708_3085343_-	COG1123, COG1123, ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]	NA|277aa|up_4|NZ_CP043119.1_3085335_3086166_-	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_CP043119.1_3086183_3087128_-	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_CP043119.1_3087180_3088755_-	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_CP043119.1_3088802_3089162_-	NA	NA|317aa|up_0|NZ_CP043119.1_3090627_3091578_+	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_CP043119.1_3091809_3093030_-	COG3464, COG3464, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|483aa|down_1|NZ_CP043119.1_3093217_3094666_+	PRK05932, PRK05932, RNA polymerase factor sigma-54; Reviewed	NA|139aa|down_2|NZ_CP043119.1_3094694_3095111_-	NA	NA|511aa|down_3|NZ_CP043119.1_3095368_3096901_+	TIGR02095, Glycogen_synthase, glycogen/starch synthase, ADP-glucose type	NA|732aa|down_4|NZ_CP043119.1_3103450_3105646_+	PRK05402, PRK05402, 1,4-alpha-glucan branching protein GlgB	NA|673aa|down_5|NZ_CP043119.1_3109518_3111537_+	PRK14507, PRK14507, malto-oligosyltrehalose synthase	NA|991aa|down_6|NZ_CP043119.1_3114065_3117038_-	PRK13557, PRK13557, histidine kinase; Provisional	NA|285aa|down_7|NZ_CP043119.1_3117138_3117993_-	PRK08176, pdxK, pyridoxine/pyridoxal/pyridoxamine kinase	NA|268aa|down_8|NZ_CP043119.1_3117989_3118793_-	cd00635, PLPDE_III_YBL036c_like, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins	NA|444aa|down_9|NZ_CP043119.1_3118852_3120184_+	PRK15481, PRK15481, transcriptional regulatory protein PtsJ; Provisional
GCF_009626835.1_ASM962683v1	NZ_CP043119	Bordetella parapertussis strain I143 chromosome, complete genome	4	3767592-3767673	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_CP043119.1_3764032_3764407_-,NA|81aa|down_4|NZ_CP043119.1_3772014_3772257_-	NA|321aa|up_9|NZ_CP043119.1_3757351_3758314_-	cd03789, GT9_LPS_heptosyltransferase, lipopolysaccharide heptosyltransferase and similar proteins	NA|419aa|up_8|NZ_CP043119.1_3758531_3759788_-	PRK07006, PRK07006, isocitrate dehydrogenase; Reviewed	NA|142aa|up_7|NZ_CP043119.1_3759990_3760416_+	pfam08897, DUF1841, Domain of unknown function (DUF1841)	NA|121aa|up_6|NZ_CP043119.1_3760466_3760829_-	COG2863, COG2863, Cytochrome c553 [Energy production and conversion]	NA|118aa|up_5|NZ_CP043119.1_3760841_3761195_-	COG2863, COG2863, Cytochrome c553 [Energy production and conversion]	NA|296aa|up_4|NZ_CP043119.1_3761355_3762243_+	COG0714, COG0714, MoxR-like ATPases [General function prediction only]	NA|391aa|up_3|NZ_CP043119.1_3762264_3763437_+	COG3825, COG3825, Uncharacterized protein conserved in bacteria [Function unknown]	NA|185aa|up_2|NZ_CP043119.1_3763440_3763995_-	COG1247, COG1247, Sortase and related acyltransferases [Cell envelope biogenesis, outer membrane]	NA|125aa|up_1|NZ_CP043119.1_3764032_3764407_-	NA	NA|917aa|up_0|NZ_CP043119.1_3764739_3767490_+	COG0612, PqqL, Predicted Zn-dependent peptidases [General function prediction only]	NA|378aa|down_0|NZ_CP043119.1_3767680_3768814_-	PRK10767, PRK10767, chaperone protein DnaJ; Provisional	NA|642aa|down_1|NZ_CP043119.1_3768914_3770840_-	PRK00290, dnaK, molecular chaperone DnaK; Provisional	NA|127aa|down_2|NZ_CP043119.1_3770930_3771311_-	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_CP043119.1_3771318_3771873_-	PRK14139, PRK14139, heat shock protein GrpE; Provisional	NA|81aa|down_4|NZ_CP043119.1_3772014_3772257_-	NA	NA|363aa|down_5|NZ_CP043119.1_3772338_3773427_-	PRK00035, hemH, ferrochelatase; Reviewed	NA|335aa|down_6|NZ_CP043119.1_3773484_3774489_-	PRK00082, hrcA, heat-inducible transcription repressor; Provisional	NA|300aa|down_7|NZ_CP043119.1_3774603_3775503_+	PRK02155, ppnK, NAD kinase	NA|554aa|down_8|NZ_CP043119.1_3775518_3777180_+	COG0497, RecN, ATPase involved in DNA repair [DNA replication, recombination, and repair]	NA|407aa|down_9|NZ_CP043119.1_3777212_3778433_-	COG3464, COG3464, Transposase and inactivated derivatives [DNA replication, recombination, and repair]
GCF_009626835.1_ASM962683v1	NZ_CP043119	Bordetella parapertussis strain I143 chromosome, complete genome	5	3920617-3920701	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_CP043119.1_3908577_3910332_-	COG0405, Ggt, Gamma-glutamyltransferase [Amino acid transport and metabolism]	NA|299aa|up_8|NZ_CP043119.1_3910438_3911335_+	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_CP043119.1_3911399_3912383_-	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_CP043119.1_3912518_3913499_+	COG0679, COG0679, Predicted permeases [General function prediction only]	NA|464aa|up_5|NZ_CP043119.1_3913515_3914907_-	PRK00485, fumC, fumarate hydratase; Reviewed	NA|179aa|up_4|NZ_CP043119.1_3915058_3915595_+	COG0802, COG0802, Predicted ATPase or kinase [General function prediction only]	NA|462aa|up_3|NZ_CP043119.1_3915525_3916911_+	PRK10319, PRK10319, N-acetylmuramoyl-L-alanine amidase AmiA	NA|213aa|up_2|NZ_CP043119.1_3917053_3917692_-	PRK10847, PRK10847, DedA family protein	NA|630aa|up_1|NZ_CP043119.1_3917778_3919668_+	PRK00095, mutL, DNA mismatch repair endonuclease MutL	NA|314aa|up_0|NZ_CP043119.1_3919664_3920606_+	PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed	NA|350aa|down_0|NZ_CP043119.1_3920711_3921761_-	PRK05385, PRK05385, phosphoribosylaminoimidazole synthetase; Provisional	NA|234aa|down_1|NZ_CP043119.1_3922013_3922715_+	PRK08903, PRK08903, DnaA regulatory inactivator Hda; Validated	NA|233aa|down_2|NZ_CP043119.1_3922711_3923410_+	cd02612, HAD_PGPPase, phosphatidylglycerol-phosphate phosphatase, similar to Escherichia coli K-12 phosphatidylglycerol-phosphate phosphatase C	NA|452aa|down_3|NZ_CP043119.1_3923410_3924766_+	TIGR01942, pcnB, poly(A) polymerase	NA|164aa|down_4|NZ_CP043119.1_3924762_3925254_+	PRK14092, PRK14092, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase	NA|319aa|down_5|NZ_CP043119.1_3925272_3926229_-	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_CP043119.1_3926255_3927650_-	pfam03972, MmgE_PrpD, MmgE/PrpD family	NA|701aa|down_7|NZ_CP043119.1_3927646_3929749_-	TIGR00786, TRAP_transporter_permease_protein_SiaT, TRAP transporter, DctM subunit	NA|347aa|down_8|NZ_CP043119.1_3929919_3930960_+	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_CP043119.1_3931003_3931747_+	COG1802, GntR, Transcriptional regulators [Transcription]
GCF_009626835.1_ASM962683v1	NZ_CP043119	Bordetella parapertussis strain I143 chromosome, complete genome	6	4131308-4131401	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_CP043119.1_4119733_4120927_-	PRK06954, PRK06954, acetyl-CoA C-acetyltransferase	NA|343aa|up_8|NZ_CP043119.1_4120992_4122021_-	pfam00441, Acyl-CoA_dh_1, Acyl-CoA dehydrogenase, C-terminal domain	NA|391aa|up_7|NZ_CP043119.1_4122047_4123220_-	cd01152, ACAD_fadE6_17_26, Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26	NA|306aa|up_6|NZ_CP043119.1_4123405_4124323_+	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_CP043119.1_4124333_4125305_-	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_CP043119.1_4125371_4126157_-	PRK09245, PRK09245, crotonase/enoyl-CoA hydratase family protein	NA|410aa|up_3|NZ_CP043119.1_4126153_4127383_-	pfam02515, CoA_transf_3, CoA-transferase family III	NA|252aa|up_2|NZ_CP043119.1_4127578_4128334_-	COG0861, TerC, Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]	NA|173aa|up_1|NZ_CP043119.1_4128444_4128963_+	COG1285, SapB, Uncharacterized membrane protein [Function unknown]	NA|706aa|up_0|NZ_CP043119.1_4128959_4131077_-	PRK00007, PRK00007, elongation factor G; Reviewed	NA|407aa|down_0|NZ_CP043119.1_4131438_4132659_-	COG3464, COG3464, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|157aa|down_1|NZ_CP043119.1_4132801_4133272_-	pfam00582, Usp, Universal stress protein family	NA|115aa|down_2|NZ_CP043119.1_4133360_4133705_-	COG3453, COG3453, Uncharacterized protein conserved in bacteria [Function unknown]	NA|482aa|down_3|NZ_CP043119.1_4133804_4135250_-	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_CP043119.1_4135393_4136308_+	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_CP043119.1_4136304_4136964_+	COG1280, RhtB, Putative threonine efflux protein [Amino acid transport and metabolism]	NA|308aa|down_6|NZ_CP043119.1_4137053_4137977_+	pfam12146, Hydrolase_4, Serine aminopeptidase, S33	NA|152aa|down_7|NZ_CP043119.1_4137982_4138438_-	COG4125, COG4125, Predicted membrane protein [Function unknown]	NA|368aa|down_8|NZ_CP043119.1_4138434_4139538_-	cd10807, YdjC_like_3, uncharacterized YdjC-like family proteins from bacteria	NA|91aa|down_9|NZ_CP043119.1_4139493_4139766_+	pfam04138, GtrA, GtrA-like protein
