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_003713025.1_ASM371302v1	CP033428	Mycobacterium avium subsp. paratuberculosis strain MAPK_CN7/15 chromosome, complete genome	2	1284341-1284421	2	CRISPRCasFinder	no		csa3,DEDDh,cas4,WYL,cas3,DinG	Orphan	CCGCCCTACCCCGCTTCGCGGCG	23	0	0	NA	NA	NA	1	1	Orphan	csa3,DEDDh,cas4,WYL,cas3,DinG	NA,NA	NA|489aa|up_9|CP033428.1_1275261_1276728_+	pfam00823, PPE, PPE family	NA|113aa|up_8|CP033428.1_1276831_1277170_+	TIGR04529, hypothetical_protein, hemophore-related protein, Rv0203/Rv1174c family	NA|155aa|up_7|CP033428.1_1277203_1277668_-	pfam10756, bPH_6, Bacterial PH domain	NA|161aa|up_6|CP033428.1_1277664_1278147_-	PRK00061, ribH, 6,7-dimethyl-8-ribityllumazine synthase; Provisional	NA|426aa|up_5|CP033428.1_1278196_1279474_-	PRK09311, PRK09311, bifunctional 3,4-dihydroxy-2-butanone-4-phosphate synthase/GTP cyclohydrolase II	NA|200aa|up_4|CP033428.1_1279595_1280195_-	PRK09289, PRK09289, riboflavin synthase	NA|236aa|up_3|CP033428.1_1280313_1281021_+	pfam07161, LppX_LprAFG, LppX_LprAFG lipoprotein	NA|519aa|up_2|CP033428.1_1281017_1282574_+	TIGR00711, Uncharacterized_MFS-type_transporter_YhcA, drug resistance transporter, EmrB/QacA subfamily	NA|342aa|up_1|CP033428.1_1282570_1283596_-	TIGR00326, eubact_ribD, riboflavin biosynthesis protein RibD	NA|236aa|up_0|CP033428.1_1283592_1284300_-	PRK05581, PRK05581, ribulose-phosphate 3-epimerase; Validated	NA|316aa|down_0|CP033428.1_1285794_1286742_-	PRK00005, fmt, methionyl-tRNA formyltransferase; Reviewed	NA|275aa|down_1|CP033428.1_1286899_1287724_+	COG2226, UbiE, Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]	NA|162aa|down_2|CP033428.1_1287729_1288215_-	smart00347, HTH_MARR, helix_turn_helix multiple antibiotic resistance protein	NA|656aa|down_3|CP033428.1_1288342_1290310_-	PRK14873, PRK14873, primosomal protein N'	NA|264aa|down_4|CP033428.1_1290394_1291186_-	COG3714, COG3714, Predicted membrane protein [Function unknown]	NA|321aa|down_5|CP033428.1_1291184_1292147_+	pfam07859, Abhydrolase_3, alpha/beta hydrolase fold	NA|497aa|down_6|CP033428.1_1292192_1293683_+	COG2072, TrkA, Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]	NA|404aa|down_7|CP033428.1_1293832_1295044_-	PRK05250, PRK05250, S-adenosylmethionine synthetase; Validated	NA|421aa|down_8|CP033428.1_1295140_1296403_-	PRK05579, PRK05579, bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated	NA|109aa|down_9|CP033428.1_1296424_1296751_-	TIGR00690, DNA-directed_RNA_polymerase_subunit_omega, DNA-directed RNA polymerase, omega subunit
GCA_003713025.1_ASM371302v1	CP033428	Mycobacterium avium subsp. paratuberculosis strain MAPK_CN7/15 chromosome, complete genome	4	3501535-3501625	4	CRISPRCasFinder	no	DinG	csa3,DEDDh,cas4,WYL,cas3,DinG	Type IV-A	CCGCCGCGCTGCGGCGGGCATCGTCGCCGGGCT	33	0	0	NA	NA	NA	1	1	Orphan	csa3,DEDDh,cas4,WYL,cas3,DinG	NA,NA|153aa|down_3|CP033428.1_3505772_3506231_+,NA|96aa|down_4|CP033428.1_3506436_3506724_+,NA|71aa|down_7|CP033428.1_3509410_3509623_-	NA|336aa|up_9|CP033428.1_3490415_3491423_+	PRK13685, PRK13685, hypothetical protein; Provisional	NA|328aa|up_8|CP033428.1_3491441_3492425_-	PRK13685, PRK13685, hypothetical protein; Provisional	NA|438aa|up_7|CP033428.1_3492457_3493771_-	PLN03142, PLN03142, Probable chromatin-remodeling complex ATPase chain; Provisional	NA|258aa|up_6|CP033428.1_3494790_3495564_+	PRK00129, upp, uracil phosphoribosyltransferase; Reviewed	NA|527aa|up_5|CP033428.1_3495415_3496996_-	cd05799, PGM2, This CD includes PGM2 (phosphoglucomutase 2) and PGM2L1 (phosphoglucomutase 2-like 1)	NA|272aa|up_4|CP033428.1_3497000_3497816_-	PRK08202, PRK08202, purine nucleoside phosphorylase; Provisional	NA|219aa|up_3|CP033428.1_3497914_3498571_+	pfam01083, Cutinase, Cutinase	NA|401aa|up_2|CP033428.1_3498616_3499819_+	cd05672, M20_ACY1L2-like, M20 Peptidase aminoacylase 1-like protein 2-like, amidohydrolase subfamily	NA|393aa|up_1|CP033428.1_3499815_3500994_+	cd08014, M20_Acy1-like, M20 Peptidase aminoacylase 1 subfamily	NA|156aa|up_0|CP033428.1_3501016_3501484_-	pfam13772, AIG2_2, AIG2-like family	NA|472aa|down_0|CP033428.1_3501637_3503053_+	PRK07845, PRK07845, flavoprotein disulfide reductase; Reviewed	NA|585aa|down_1|CP033428.1_3503109_3504864_+	COG0578, GlpA, Glycerol-3-phosphate dehydrogenase [Energy production and conversion]	NA|291aa|down_2|CP033428.1_3504860_3505733_+	cd02558, PSRA_1, Pseudouridine synthase, a subgroup of the RluA family	NA|153aa|down_3|CP033428.1_3505772_3506231_+	NA	NA|96aa|down_4|CP033428.1_3506436_3506724_+	NA	NA|378aa|down_5|CP033428.1_3506955_3508089_+	pfam00823, PPE, PPE family	NA|379aa|down_6|CP033428.1_3508198_3509335_+	pfam00823, PPE, PPE family	NA|71aa|down_7|CP033428.1_3509410_3509623_-	NA	NA|118aa|down_8|CP033428.1_3509708_3510062_-	pfam05305, DUF732, Protein of unknown function (DUF732)	NA|306aa|down_9|CP033428.1_3510253_3511171_+	COG3509, LpqC, Poly(3-hydroxybutyrate) depolymerase [Secondary metabolites biosynthesis, transport, and catabolism]
GCA_003713025.1_ASM371302v1	CP033428	Mycobacterium avium subsp. paratuberculosis strain MAPK_CN7/15 chromosome, complete genome	5	4027708-4027788	5	CRISPRCasFinder	no		csa3,DEDDh,cas4,WYL,cas3,DinG	Orphan	GCCGCCGAAGGCGGGTAGCTGGA	23	0	0	NA	NA	NA	1	1	Orphan	csa3,DEDDh,cas4,WYL,cas3,DinG	NA|80aa|up_3|CP033428.1_4023686_4023926_-,NA	NA|141aa|up_9|CP033428.1_4018762_4019185_-	smart00347, HTH_MARR, helix_turn_helix multiple antibiotic resistance protein	NA|138aa|up_8|CP033428.1_4019303_4019717_+	pfam06150, ChaB, ChaB	NA|280aa|up_7|CP033428.1_4019807_4020647_-	cd05355, SDR_c1, classical (c) SDR, subgroup 1	NA|191aa|up_6|CP033428.1_4021192_4021765_+	pfam09167, DUF1942, Domain of unknown function (DUF1942)	NA|313aa|up_5|CP033428.1_4021860_4022799_+	cd07987, LPLAT_MGAT-like, Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: MGAT-like	NA|232aa|up_4|CP033428.1_4022822_4023518_-	COG0745, OmpR, Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]	NA|80aa|up_3|CP033428.1_4023686_4023926_-	NA	NA|266aa|up_2|CP033428.1_4024257_4025055_+	cd04254, AAK_UMPK-PyrH-Ec, UMP kinase (UMPK)-Ec, the microbial/chloroplast uridine monophosphate kinase (uridylate kinase) enzyme that catalyzes UMP phosphorylation and plays a key role in pyrimidine nucleotide biosynthesis; regulation of this process is via feed-back control and via gene repression of carbamoyl phosphate synthetase (the first enzyme of the pyrimidine biosynthesis pathway)	NA|186aa|up_1|CP033428.1_4025070_4025628_+	PRK00083, frr, ribosome recycling factor; Reviewed	NA|312aa|up_0|CP033428.1_4025660_4026596_+	pfam01148, CTP_transf_1, Cytidylyltransferase family	NA|168aa|down_0|CP033428.1_4027855_4028359_+	cd03011, TlpA_like_ScsD_MtbDsbE, TlpA-like family, suppressor for copper sensitivity D protein (ScsD) and actinobacterial DsbE homolog subfamily; composed of ScsD, the DsbE homolog of Mycobacterium tuberculosis (MtbDsbE) and similar proteins, all containing a redox-active CXXC motif	NA|85aa|down_1|CP033428.1_4029218_4029473_-	pfam10939, DUF2631, Protein of unknown function (DUF2631)	NA|420aa|down_2|CP033428.1_4029558_4030818_+	PRK05447, PRK05447, 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional	NA|408aa|down_3|CP033428.1_4030837_4032061_+	pfam02163, Peptidase_M50, Peptidase family M50	NA|389aa|down_4|CP033428.1_4032093_4033260_+	PRK00366, ispG, flavodoxin-dependent (E)-4-hydroxy-3-methylbut-2-enyl-diphosphate synthase	NA|285aa|down_5|CP033428.1_4033308_4034163_+	COG3393, COG3393, Predicted acetyltransferase [General function prediction only]	NA|606aa|down_6|CP033428.1_4034291_4036109_+	COG0768, FtsI, Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]	NA|196aa|down_7|CP033428.1_4036154_4036742_+	pfam08044, DUF1707, Domain of unknown function (DUF1707)	NA|498aa|down_8|CP033428.1_4037634_4039128_+	PRK00784, PRK00784, cobyric acid synthase	NA|184aa|down_9|CP033428.1_4039257_4039809_+	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]
GCA_003713025.1_ASM371302v1	CP033428	Mycobacterium avium subsp. paratuberculosis strain MAPK_CN7/15 chromosome, complete genome	6	4181169-4181249	6	CRISPRCasFinder	no		csa3,DEDDh,cas4,WYL,cas3,DinG	Orphan	CGCTAATGGCGGTGACCCGCTGCGCC	26	1	1	4181195-4181223	CP033428.1_3446434-3446406	NA	1	1	Orphan	csa3,DEDDh,cas4,WYL,cas3,DinG	NA,NA|176aa|down_5|CP033428.1_4186539_4187067_-	NA|642aa|up_9|CP033428.1_4170902_4172828_+	PRK05444, PRK05444, 1-deoxy-D-xylulose-5-phosphate synthase; Provisional	NA|429aa|up_8|CP033428.1_4172872_4174159_-	COG0349, Rnd, Ribonuclease D [Translation, ribosomal structure and biogenesis]	NA|206aa|up_7|CP033428.1_4174160_4174778_-	pfam11452, DUF3000, Protein of unknown function (DUF3000)	NA|274aa|up_6|CP033428.1_4174905_4175727_-	PRK07327, PRK07327, enoyl-CoA hydratase/isomerase family protein	NA|358aa|up_5|CP033428.1_4175774_4176848_+	PRK00115, hemE, uroporphyrinogen decarboxylase; Validated	NA|452aa|up_4|CP033428.1_4176844_4178200_+	PRK11883, PRK11883, protoporphyrinogen oxidase; Reviewed	NA|232aa|up_3|CP033428.1_4178205_4178901_+	COG3253, ywfI, Predicted heme peroxidase involved in anaerobic stress response [General function prediction only]	NA|251aa|up_2|CP033428.1_4178897_4179650_+	pfam13649, Methyltransf_25, Methyltransferase domain	NA|283aa|up_1|CP033428.1_4179716_4180565_-	pfam18741, MTES_1575, REase_MTES_1575	NA|135aa|up_0|CP033428.1_4180698_4181103_-	pfam01641, SelR, SelR domain	NA|429aa|down_0|CP033428.1_4181270_4182557_-	pfam09594, GT87, Glycosyltransferase family 87	NA|520aa|down_1|CP033428.1_4182585_4184145_-	pfam08386, Abhydrolase_4, TAP-like protein	NA|255aa|down_2|CP033428.1_4184159_4184924_-	PRK14059, PRK14059, pyrimidine reductase family protein	NA|374aa|down_3|CP033428.1_4184922_4186044_+	pfam03969, AFG1_ATPase, AFG1-like ATPase	NA|177aa|down_4|CP033428.1_4186021_4186552_-	pfam00583, Acetyltransf_1, Acetyltransferase (GNAT) family	NA|176aa|down_5|CP033428.1_4186539_4187067_-	NA	NA|251aa|down_6|CP033428.1_4187106_4187859_-	COG0542, clpA, ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]	NA|123aa|down_7|CP033428.1_4187955_4188324_+	pfam05305, DUF732, Protein of unknown function (DUF732)	NA|115aa|down_8|CP033428.1_4188523_4188868_+	pfam05305, DUF732, Protein of unknown function (DUF732)	NA|310aa|down_9|CP033428.1_4188896_4189826_+	pfam09678, Caa3_CtaG, Cytochrome c oxidase caa3 assembly factor (Caa3_CtaG)
GCA_003713025.1_ASM371302v1	CP033428	Mycobacterium avium subsp. paratuberculosis strain MAPK_CN7/15 chromosome, complete genome	7	4210358-4210448	7	CRISPRCasFinder	no		csa3,DEDDh,cas4,WYL,cas3,DinG	Orphan	GACTGCGTCCGACTGCGTCCCACC	24	0	0	NA	NA	NA	1	1	Orphan	csa3,DEDDh,cas4,WYL,cas3,DinG	NA|174aa|up_5|CP033428.1_4203564_4204086_-,NA|100aa|up_3|CP033428.1_4204662_4204962_-,NA|184aa|up_2|CP033428.1_4207877_4208429_+,NA|105aa|down_0|CP033428.1_4210548_4210863_+,NA|97aa|down_1|CP033428.1_4210859_4211150_+,NA|75aa|down_2|CP033428.1_4211492_4211717_+,NA|93aa|down_4|CP033428.1_4212225_4212504_-,NA|80aa|down_5|CP033428.1_4212639_4212879_+,NA|145aa|down_6|CP033428.1_4212871_4213306_+,NA|77aa|down_7|CP033428.1_4213374_4213605_+,NA|61aa|down_8|CP033428.1_4213834_4214017_+	NA|313aa|up_9|CP033428.1_4199307_4200246_+	PRK06194, PRK06194, hypothetical protein; Provisional	NA|268aa|up_8|CP033428.1_4200242_4201046_+	pfam06314, ADC, Acetoacetate decarboxylase (ADC)	NA|405aa|up_7|CP033428.1_4201049_4202264_+	pfam04909, Amidohydro_2, Amidohydrolase	NA|423aa|up_6|CP033428.1_4202288_4203557_+	pfam04909, Amidohydro_2, Amidohydrolase	NA|174aa|up_5|CP033428.1_4203564_4204086_-	NA	NA|103aa|up_4|CP033428.1_4204162_4204471_-	COG5178, PRP8, U5 snRNP spliceosome subunit [RNA processing and modification]	NA|100aa|up_3|CP033428.1_4204662_4204962_-	NA	NA|184aa|up_2|CP033428.1_4207877_4208429_+	NA	NA|71aa|up_1|CP033428.1_4208523_4208736_+	TIGR01764, Probable_excisionase, DNA binding domain, excisionase family	NA|159aa|up_0|CP033428.1_4208732_4209209_+	pfam10888, DUF2742, Protein of unknown function (DUF2742)	NA|105aa|down_0|CP033428.1_4210548_4210863_+	NA	NA|97aa|down_1|CP033428.1_4210859_4211150_+	NA	NA|75aa|down_2|CP033428.1_4211492_4211717_+	NA	NA|147aa|down_3|CP033428.1_4211716_4212157_+	pfam12728, HTH_17, Helix-turn-helix domain	NA|93aa|down_4|CP033428.1_4212225_4212504_-	NA	NA|80aa|down_5|CP033428.1_4212639_4212879_+	NA	NA|145aa|down_6|CP033428.1_4212871_4213306_+	NA	NA|77aa|down_7|CP033428.1_4213374_4213605_+	NA	NA|61aa|down_8|CP033428.1_4213834_4214017_+	NA	NA|103aa|down_9|CP033428.1_4213995_4214304_-	smart01040, Bro-N, BRO family, N-terminal domain
