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_001628735.1_ASM162873v1	NZ_CP011255	Bordetella pertussis strain I344 chromosome, complete genome	1	251601-251685	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|137aa|up_9|NZ_CP011255.1_239126_239537_+	TIGR02425, putative_gamma-carboxymuconolactone_decarboxylase, 4-carboxymuconolactone decarboxylase	NA|248aa|up_8|NZ_CP011255.1_240558_241302_-	COG1802, GntR, Transcriptional regulators [Transcription]	NA|348aa|up_7|NZ_CP011255.1_241345_242389_-	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_6|NZ_CP011255.1_242559_244662_+	TIGR00786, TRAP_transporter_permease_protein_SiaT, TRAP transporter, DctM subunit	NA|319aa|up_5|NZ_CP011255.1_246072_247029_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|164aa|up_4|NZ_CP011255.1_247047_247539_-	PRK14092, PRK14092, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase	NA|452aa|up_3|NZ_CP011255.1_247535_248891_-	TIGR01942, pcnB, poly(A) polymerase	NA|233aa|up_2|NZ_CP011255.1_248891_249590_-	cd02612, HAD_PGPPase, phosphatidylglycerol-phosphate phosphatase, similar to Escherichia coli K-12 phosphatidylglycerol-phosphate phosphatase C	NA|234aa|up_1|NZ_CP011255.1_249586_250288_-	PRK08903, PRK08903, DnaA regulatory inactivator Hda; Validated	NA|350aa|up_0|NZ_CP011255.1_250540_251590_+	PRK05385, PRK05385, phosphoribosylaminoimidazole synthetase; Provisional	NA|314aa|down_0|NZ_CP011255.1_251695_252637_-	PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed	NA|630aa|down_1|NZ_CP011255.1_252633_254523_-	PRK00095, mutL, DNA mismatch repair endonuclease MutL	NA|213aa|down_2|NZ_CP011255.1_254609_255248_+	PRK10847, PRK10847, DedA family protein	NA|462aa|down_3|NZ_CP011255.1_255390_256776_-	PRK10319, PRK10319, N-acetylmuramoyl-L-alanine amidase AmiA	NA|179aa|down_4|NZ_CP011255.1_256706_257243_-	COG0802, COG0802, Predicted ATPase or kinase [General function prediction only]	NA|464aa|down_5|NZ_CP011255.1_257394_258786_+	PRK00485, fumC, fumarate hydratase; Reviewed	NA|327aa|down_6|NZ_CP011255.1_258802_259783_-	COG0679, COG0679, Predicted permeases [General function prediction only]	NA|328aa|down_7|NZ_CP011255.1_259918_260902_+	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_CP011255.1_260966_261866_-	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_CP011255.1_261972_263727_+	COG0405, Ggt, Gamma-glutamyltransferase [Amino acid transport and metabolism]
GCF_001628735.1_ASM162873v1	NZ_CP011255	Bordetella pertussis strain I344 chromosome, complete genome	2	435129-435222	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_CP011255.1_422468_423527_-	cd04187, DPM1_like_bac, Bacterial DPM1_like enzymes are related to eukaryotic DPM1	NA|165aa|up_8|NZ_CP011255.1_423656_424151_+	pfam00583, Acetyltransf_1, Acetyltransferase (GNAT) family	NA|326aa|up_7|NZ_CP011255.1_424243_425221_+	pfam00665, rve, Integrase core domain	NA|402aa|up_6|NZ_CP011255.1_425416_426622_+	TIGR00210, Sodium/glutamate_symport_carrier_protein, sodium--glutamate symport carrier (gltS)	NA|504aa|up_5|NZ_CP011255.1_426618_428130_+	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_CP011255.1_428145_429459_-	COG2031, AtoE, Short chain fatty acids transporter [Lipid metabolism]	NA|60aa|up_3|NZ_CP011255.1_429649_429829_-	pfam04391, DUF533, Protein of unknown function (DUF533)	DEDDh|245aa|up_2|NZ_CP011255.1_430238_430973_-	PRK05711, PRK05711, DNA polymerase III subunit epsilon; Provisional	NA|317aa|up_1|NZ_CP011255.1_433417_434368_+	pfam00665, rve, Integrase core domain	NA|133aa|up_0|NZ_CP011255.1_434499_434898_-	PRK00007, PRK00007, elongation factor G; Reviewed	NA|157aa|down_0|NZ_CP011255.1_435308_435779_-	pfam00582, Usp, Universal stress protein family	NA|115aa|down_1|NZ_CP011255.1_435867_436212_-	COG3453, COG3453, Uncharacterized protein conserved in bacteria [Function unknown]	NA|467aa|down_2|NZ_CP011255.1_436311_437712_-	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_CP011255.1_439500_440019_-	COG1285, SapB, Uncharacterized membrane protein [Function unknown]	NA|252aa|down_4|NZ_CP011255.1_440129_440885_+	COG0861, TerC, Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]	NA|411aa|down_5|NZ_CP011255.1_441080_442313_+	pfam02515, CoA_transf_3, CoA-transferase family III	NA|262aa|down_6|NZ_CP011255.1_442305_443091_+	PRK09245, PRK09245, crotonase/enoyl-CoA hydratase family protein	NA|324aa|down_7|NZ_CP011255.1_443157_444129_+	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_8|NZ_CP011255.1_444139_445117_-	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_9|NZ_CP011255.1_445242_446415_+	cd01152, ACAD_fadE6_17_26, Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26
GCF_001628735.1_ASM162873v1	NZ_CP011255	Bordetella pertussis strain I344 chromosome, complete genome	3	1553898-1554025	3	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG	Orphan	AAAAAGCCCCCTCGGGGGGCAGCAAGCCCGCATAGCGGGCGCAGCG	46	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG	NA,NA	NA|134aa|up_9|NZ_CP011255.1_1542860_1543262_+	cd03450, NodN, NodN (nodulation factor N) contains a single hot dog fold similar to those of the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit	NA|268aa|up_8|NZ_CP011255.1_1543275_1544079_+	COG1024, CaiD, Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]	NA|144aa|up_7|NZ_CP011255.1_1544075_1544507_+	COG1545, COG1545, Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]	NA|386aa|up_6|NZ_CP011255.1_1544503_1545661_+	PRK06158, PRK06158, thiolase; Provisional	NA|259aa|up_5|NZ_CP011255.1_1545682_1546459_+	PRK05653, fabG, 3-oxoacyl-ACP reductase FabG	NA|223aa|up_4|NZ_CP011255.1_1548671_1549340_+	TIGR02429, 3-oxoadipate_CoA-transferase_subunit_A, 3-oxoacid CoA-transferase, A subunit	NA|214aa|up_3|NZ_CP011255.1_1549332_1549974_+	TIGR02428, 3-oxoadipate_CoA-transferase_subunit_B, 3-oxoacid CoA-transferase, B subunit	NA|244aa|up_2|NZ_CP011255.1_1550008_1550740_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|71aa|up_1|NZ_CP011255.1_1550757_1550970_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|317aa|up_0|NZ_CP011255.1_1551540_1552491_+	pfam00665, rve, Integrase core domain	NA|217aa|down_0|NZ_CP011255.1_1554048_1554699_-	PRK00215, PRK00215, transcriptional repressor LexA	NA|401aa|down_1|NZ_CP011255.1_1554827_1556030_-	PRK09257, PRK09257, aromatic amino acid transaminase	NA|679aa|down_2|NZ_CP011255.1_1556107_1558144_+	PRK05298, PRK05298, excinuclease ABC subunit UvrB	NA|164aa|down_3|NZ_CP011255.1_1558396_1558888_+	cd16343, LMWPTP, Low molecular weight protein tyrosine phosphatase	NA|171aa|down_4|NZ_CP011255.1_1559103_1559616_+	TIGR02010, Putative_HTH-type_transcriptional_regulator, iron-sulfur cluster assembly transcription factor IscR	NA|404aa|down_5|NZ_CP011255.1_1559633_1560845_+	PRK14012, PRK14012, IscS subfamily cysteine desulfurase	NA|137aa|down_6|NZ_CP011255.1_1560882_1561293_+	PRK11325, PRK11325, scaffold protein; Provisional	NA|108aa|down_7|NZ_CP011255.1_1561294_1561618_+	TIGR02011, Protein_yfhF	NA|171aa|down_8|NZ_CP011255.1_1561620_1562133_+	PRK03578, hscB, Fe-S protein assembly co-chaperone HscB	NA|621aa|down_9|NZ_CP011255.1_1562262_1564125_+	PRK05183, hscA, chaperone protein HscA; Provisional
GCF_001628735.1_ASM162873v1	NZ_CP011255	Bordetella pertussis strain I344 chromosome, complete genome	4	2649516-2649632	4	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG	Orphan	TTTTTTGCCTTGGGGCGGCCCGGCGGCAAAAAAA	34	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG	NA,NA	NA|163aa|up_9|NZ_CP011255.1_2631237_2631726_-	COG1522, Lrp, Transcriptional regulators [Transcription]	NA|899aa|up_8|NZ_CP011255.1_2631851_2634548_+	PRK13012, PRK13012, 2-oxoacid dehydrogenase subunit E1; Provisional	NA|761aa|up_7|NZ_CP011255.1_2634702_2636985_+	PRK07232, PRK07232, bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed	NA|208aa|up_6|NZ_CP011255.1_2637161_2637785_+	pfam16970, FimA, Type-1 fimbrial protein, A	NA|317aa|up_5|NZ_CP011255.1_2637883_2638834_+	pfam00665, rve, Integrase core domain	NA|185aa|up_4|NZ_CP011255.1_2638880_2639435_-	PRK01885, greB, transcription elongation factor GreB; Reviewed	NA|282aa|up_3|NZ_CP011255.1_2639502_2640348_-	COG0613, COG0613, Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]	NA|323aa|up_2|NZ_CP011255.1_2640417_2641386_-	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|288aa|up_1|NZ_CP011255.1_2641385_2642249_-	COG2333, ComEC, Predicted hydrolase (metallo-beta-lactamase superfamily) [General function prediction only]	NA|1309aa|up_0|NZ_CP011255.1_2645081_2649008_-	pfam11924, IAT_beta, Inverse autotransporter, beta-domain	NA|1077aa|down_0|NZ_CP011255.1_2649743_2652974_-	pfam03797, Autotransporter, Autotransporter beta-domain	NA|276aa|down_1|NZ_CP011255.1_2653255_2654083_-	cd01310, TatD_DNAse, TatD like proteins;  E	NA|232aa|down_2|NZ_CP011255.1_2654116_2654812_-	cd03255, ABC_MJ0796_LolCDE_FtsE, ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein	NA|427aa|down_3|NZ_CP011255.1_2654804_2656085_-	TIGR02212, releasing_system_transmembrane_protein_lolC	NA|326aa|down_4|NZ_CP011255.1_2656094_2657072_+	COG4255, COG4255, Uncharacterized protein conserved in bacteria [Function unknown]	NA|567aa|down_5|NZ_CP011255.1_2657053_2658754_+	PRK11070, PRK11070, single-stranded-DNA-specific exonuclease RecJ	NA|368aa|down_6|NZ_CP011255.1_2658856_2659961_+	PRK00578, prfB, peptide chain release factor 2; Validated	NA|252aa|down_7|NZ_CP011255.1_2659990_2660746_+	PRK07023, PRK07023, SDR family oxidoreductase	NA|507aa|down_8|NZ_CP011255.1_2660752_2662273_+	PRK00484, lysS, lysyl-tRNA synthetase; Reviewed	NA|211aa|down_9|NZ_CP011255.1_2662600_2663233_-	pfam17932, TetR_C_24, Tetracyclin repressor-like, C-terminal domain
GCF_001628735.1_ASM162873v1	NZ_CP011255	Bordetella pertussis strain I344 chromosome, complete genome	5	3435056-3435165	5	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG	Orphan	TTGACTGCCAAGACGGTATCTGTCCCC	27	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG	NA,NA	NA|363aa|up_9|NZ_CP011255.1_3419333_3420422_+	cd08948, 5beta-POR_like_SDR_a, progesterone 5-beta-reductase-like proteins (5beta-POR), atypical (a) SDRs	NA|317aa|up_8|NZ_CP011255.1_3420418_3421369_-	pfam00665, rve, Integrase core domain	NA|993aa|up_7|NZ_CP011255.1_3421722_3424701_+	pfam17936, Big_6, Bacterial Ig domain	NA|293aa|up_6|NZ_CP011255.1_3425627_3426506_+	pfam00487, FA_desaturase, Fatty acid desaturase	NA|317aa|up_5|NZ_CP011255.1_3428454_3429405_+	pfam00665, rve, Integrase core domain	NA|156aa|up_4|NZ_CP011255.1_3429401_3429869_-	PRK00203, rnhA, ribonuclease H; Reviewed	NA|257aa|up_3|NZ_CP011255.1_3429911_3430682_-	pfam08241, Methyltransf_11, Methyltransferase domain	NA|267aa|up_2|NZ_CP011255.1_3430702_3431503_+	TIGR03413, GSH_gloB, hydroxyacylglutathione hydrolase	NA|470aa|up_1|NZ_CP011255.1_3431513_3432923_+	PRK10783, mltD, membrane-bound lytic murein transglycosylase D; Provisional	NA|262aa|up_0|NZ_CP011255.1_3433017_3433803_+	PRK06997, PRK06997, enoyl-[acyl-carrier-protein] reductase FabI	NA|131aa|down_0|NZ_CP011255.1_3435166_3435559_-	COG1765, COG1765, Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]	NA|227aa|down_1|NZ_CP011255.1_3435696_3436377_+	pfam04391, DUF533, Protein of unknown function (DUF533)	NA|324aa|down_2|NZ_CP011255.1_3436381_3437353_-	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_CP011255.1_3437448_3438399_-	pfam00665, rve, Integrase core domain	NA|234aa|down_4|NZ_CP011255.1_3439903_3440605_+	PRK09468, ompR, osmolarity response regulator; Provisional	NA|475aa|down_5|NZ_CP011255.1_3440604_3442029_+	PRK09467, envZ, osmolarity sensor protein; Provisional	NA|352aa|down_6|NZ_CP011255.1_3442045_3443101_-	pfam02322, Cyt_bd_oxida_II, Cytochrome bd terminal oxidase subunit II	NA|447aa|down_7|NZ_CP011255.1_3443097_3444438_-	pfam01654, Cyt_bd_oxida_I, Cytochrome bd terminal oxidase subunit I	NA|588aa|down_8|NZ_CP011255.1_3444553_3446317_+	PRK05347, PRK05347, glutaminyl-tRNA synthetase; Provisional	NA|293aa|down_9|NZ_CP011255.1_3446428_3447307_+	PRK00030, minC, septum site-determining protein MinC
