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_003815795.1_ASM381579v1	CP033910	Mycobacterium avium subsp. paratuberculosis strain MAPK_CN4/13 chromosome, complete genome	1	186872-186952	1	CRISPRCasFinder	no		csa3,cas3,DEDDh,DinG,cas4,WYL	Orphan	CCGCCCTACCCCGCTTCGCGGCG	23	0	0	NA	NA	NA	1	1	Orphan	csa3,cas3,DEDDh,DinG,cas4,WYL	NA,NA	NA|489aa|up_9|CP033910.1_177792_179259_+	pfam00823, PPE, PPE family	NA|113aa|up_8|CP033910.1_179362_179701_+	TIGR04529, hypothetical_protein, hemophore-related protein, Rv0203/Rv1174c family	NA|155aa|up_7|CP033910.1_179734_180199_-	pfam10756, bPH_6, Bacterial PH domain	NA|161aa|up_6|CP033910.1_180195_180678_-	PRK00061, ribH, 6,7-dimethyl-8-ribityllumazine synthase; Provisional	NA|426aa|up_5|CP033910.1_180727_182005_-	PRK09311, PRK09311, bifunctional 3,4-dihydroxy-2-butanone-4-phosphate synthase/GTP cyclohydrolase II	NA|200aa|up_4|CP033910.1_182126_182726_-	PRK09289, PRK09289, riboflavin synthase	NA|236aa|up_3|CP033910.1_182844_183552_+	pfam07161, LppX_LprAFG, LppX_LprAFG lipoprotein	NA|519aa|up_2|CP033910.1_183548_185105_+	TIGR00711, Uncharacterized_MFS-type_transporter_YhcA, drug resistance transporter, EmrB/QacA subfamily	NA|342aa|up_1|CP033910.1_185101_186127_-	TIGR00326, eubact_ribD, riboflavin biosynthesis protein RibD	NA|236aa|up_0|CP033910.1_186123_186831_-	PRK05581, PRK05581, ribulose-phosphate 3-epimerase; Validated	NA|316aa|down_0|CP033910.1_188325_189273_-	PRK00005, fmt, methionyl-tRNA formyltransferase; Reviewed	NA|275aa|down_1|CP033910.1_189430_190255_+	COG2226, UbiE, Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]	NA|162aa|down_2|CP033910.1_190260_190746_-	smart00347, HTH_MARR, helix_turn_helix multiple antibiotic resistance protein	NA|656aa|down_3|CP033910.1_190873_192841_-	PRK14873, PRK14873, primosomal protein N'	NA|264aa|down_4|CP033910.1_192925_193717_-	COG3714, COG3714, Predicted membrane protein [Function unknown]	NA|321aa|down_5|CP033910.1_193715_194678_+	pfam07859, Abhydrolase_3, alpha/beta hydrolase fold	NA|497aa|down_6|CP033910.1_194723_196214_+	COG2072, TrkA, Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]	NA|404aa|down_7|CP033910.1_196363_197575_-	PRK05250, PRK05250, S-adenosylmethionine synthetase; Validated	NA|421aa|down_8|CP033910.1_197671_198934_-	PRK05579, PRK05579, bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated	NA|109aa|down_9|CP033910.1_198955_199282_-	TIGR00690, DNA-directed_RNA_polymerase_subunit_omega, DNA-directed RNA polymerase, omega subunit
GCA_003815795.1_ASM381579v1	CP033910	Mycobacterium avium subsp. paratuberculosis strain MAPK_CN4/13 chromosome, complete genome	2	2403223-2403313	2	CRISPRCasFinder	no		csa3,cas3,DEDDh,DinG,cas4,WYL	Orphan	CCGCCGCGCTGCGGCGGGCATCGTCGCCGGGCT	33	0	0	NA	NA	NA	1	1	Orphan	csa3,cas3,DEDDh,DinG,cas4,WYL	NA,NA|153aa|down_3|CP033910.1_2407460_2407919_+,NA|96aa|down_4|CP033910.1_2408124_2408412_+,NA|71aa|down_7|CP033910.1_2411101_2411314_-	NA|328aa|up_9|CP033910.1_2393129_2394113_-	PRK13685, PRK13685, hypothetical protein; Provisional	NA|438aa|up_8|CP033910.1_2394145_2395459_-	PLN03142, PLN03142, Probable chromatin-remodeling complex ATPase chain; Provisional	NA|277aa|up_7|CP033910.1_2395484_2396315_-	pfam04185, Phosphoesterase, Phosphoesterase family	NA|258aa|up_6|CP033910.1_2396479_2397253_+	PRK00129, upp, uracil phosphoribosyltransferase; Reviewed	NA|522aa|up_5|CP033910.1_2397104_2398670_-	cd05799, PGM2, This CD includes PGM2 (phosphoglucomutase 2) and PGM2L1 (phosphoglucomutase 2-like 1)	NA|272aa|up_4|CP033910.1_2398688_2399504_-	PRK08202, PRK08202, purine nucleoside phosphorylase; Provisional	NA|219aa|up_3|CP033910.1_2399602_2400259_+	pfam01083, Cutinase, Cutinase	NA|401aa|up_2|CP033910.1_2400304_2401507_+	cd05672, M20_ACY1L2-like, M20 Peptidase aminoacylase 1-like protein 2-like, amidohydrolase subfamily	NA|393aa|up_1|CP033910.1_2401503_2402682_+	cd08014, M20_Acy1-like, M20 Peptidase aminoacylase 1 subfamily	NA|156aa|up_0|CP033910.1_2402704_2403172_-	pfam13772, AIG2_2, AIG2-like family	NA|472aa|down_0|CP033910.1_2403325_2404741_+	PRK07845, PRK07845, flavoprotein disulfide reductase; Reviewed	NA|585aa|down_1|CP033910.1_2404797_2406552_+	COG0578, GlpA, Glycerol-3-phosphate dehydrogenase [Energy production and conversion]	NA|291aa|down_2|CP033910.1_2406548_2407421_+	cd02558, PSRA_1, Pseudouridine synthase, a subgroup of the RluA family	NA|153aa|down_3|CP033910.1_2407460_2407919_+	NA	NA|96aa|down_4|CP033910.1_2408124_2408412_+	NA	NA|379aa|down_5|CP033910.1_2408643_2409780_+	pfam00823, PPE, PPE family	NA|379aa|down_6|CP033910.1_2409889_2411026_+	pfam00823, PPE, PPE family	NA|71aa|down_7|CP033910.1_2411101_2411314_-	NA	NA|118aa|down_8|CP033910.1_2411399_2411753_-	pfam05305, DUF732, Protein of unknown function (DUF732)	NA|306aa|down_9|CP033910.1_2411944_2412862_+	COG3509, LpqC, Poly(3-hydroxybutyrate) depolymerase [Secondary metabolites biosynthesis, transport, and catabolism]
GCA_003815795.1_ASM381579v1	CP033910	Mycobacterium avium subsp. paratuberculosis strain MAPK_CN4/13 chromosome, complete genome	3	2929491-2929571	3	CRISPRCasFinder	no		csa3,cas3,DEDDh,DinG,cas4,WYL	Orphan	GCCGCCGAAGGCGGGTAGCTGGA	23	0	0	NA	NA	NA	1	1	Orphan	csa3,cas3,DEDDh,DinG,cas4,WYL	NA|80aa|up_3|CP033910.1_2925469_2925709_-,NA	NA|141aa|up_9|CP033910.1_2920545_2920968_-	smart00347, HTH_MARR, helix_turn_helix multiple antibiotic resistance protein	NA|138aa|up_8|CP033910.1_2921086_2921500_+	pfam06150, ChaB, ChaB	NA|280aa|up_7|CP033910.1_2921590_2922430_-	cd05355, SDR_c1, classical (c) SDR, subgroup 1	NA|191aa|up_6|CP033910.1_2922975_2923548_+	pfam09167, DUF1942, Domain of unknown function (DUF1942)	NA|313aa|up_5|CP033910.1_2923643_2924582_+	cd07987, LPLAT_MGAT-like, Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: MGAT-like	NA|232aa|up_4|CP033910.1_2924605_2925301_-	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|CP033910.1_2925469_2925709_-	NA	NA|266aa|up_2|CP033910.1_2926040_2926838_+	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|CP033910.1_2926853_2927411_+	PRK00083, frr, ribosome recycling factor; Reviewed	NA|312aa|up_0|CP033910.1_2927443_2928379_+	pfam01148, CTP_transf_1, Cytidylyltransferase family	NA|168aa|down_0|CP033910.1_2929638_2930142_+	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|CP033910.1_2931001_2931256_-	pfam10939, DUF2631, Protein of unknown function (DUF2631)	NA|420aa|down_2|CP033910.1_2931341_2932601_+	PRK05447, PRK05447, 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional	NA|408aa|down_3|CP033910.1_2932620_2933844_+	pfam02163, Peptidase_M50, Peptidase family M50	NA|389aa|down_4|CP033910.1_2933876_2935043_+	PRK00366, ispG, flavodoxin-dependent (E)-4-hydroxy-3-methylbut-2-enyl-diphosphate synthase	NA|285aa|down_5|CP033910.1_2935091_2935946_+	COG3393, COG3393, Predicted acetyltransferase [General function prediction only]	NA|606aa|down_6|CP033910.1_2936074_2937892_+	COG0768, FtsI, Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]	NA|196aa|down_7|CP033910.1_2937937_2938525_+	pfam08044, DUF1707, Domain of unknown function (DUF1707)	NA|286aa|down_8|CP033910.1_2938556_2939414_+	PRK12896, PRK12896, methionine aminopeptidase; Reviewed	NA|498aa|down_9|CP033910.1_2939418_2940912_+	PRK00784, PRK00784, cobyric acid synthase
GCA_003815795.1_ASM381579v1	CP033910	Mycobacterium avium subsp. paratuberculosis strain MAPK_CN4/13 chromosome, complete genome	4	3082911-3082991	4	CRISPRCasFinder	no		csa3,cas3,DEDDh,DinG,cas4,WYL	Orphan	CGCTAATGGCGGTGACCCGCTGCGCC	26	1	1	3082937-3082965	CP033910.1_2348125-2348097	NA	1	1	Orphan	csa3,cas3,DEDDh,DinG,cas4,WYL	NA,NA|176aa|down_4|CP033910.1_3088280_3088808_-,NA|71aa|down_9|CP033910.1_3092682_3092895_-	NA|642aa|up_9|CP033910.1_3072644_3074570_+	PRK05444, PRK05444, 1-deoxy-D-xylulose-5-phosphate synthase; Provisional	NA|429aa|up_8|CP033910.1_3074614_3075901_-	COG0349, Rnd, Ribonuclease D [Translation, ribosomal structure and biogenesis]	NA|206aa|up_7|CP033910.1_3075902_3076520_-	pfam11452, DUF3000, Protein of unknown function (DUF3000)	NA|274aa|up_6|CP033910.1_3076647_3077469_-	PRK07327, PRK07327, enoyl-CoA hydratase/isomerase family protein	NA|358aa|up_5|CP033910.1_3077516_3078590_+	PRK00115, hemE, uroporphyrinogen decarboxylase; Validated	NA|452aa|up_4|CP033910.1_3078586_3079942_+	PRK11883, PRK11883, protoporphyrinogen oxidase; Reviewed	NA|232aa|up_3|CP033910.1_3079947_3080643_+	COG3253, ywfI, Predicted heme peroxidase involved in anaerobic stress response [General function prediction only]	NA|251aa|up_2|CP033910.1_3080639_3081392_+	pfam13649, Methyltransf_25, Methyltransferase domain	NA|283aa|up_1|CP033910.1_3081458_3082307_-	pfam18741, MTES_1575, REase_MTES_1575	NA|135aa|up_0|CP033910.1_3082440_3082845_-	pfam01641, SelR, SelR domain	NA|429aa|down_0|CP033910.1_3083012_3084299_-	pfam09594, GT87, Glycosyltransferase family 87	NA|520aa|down_1|CP033910.1_3084327_3085887_-	pfam08386, Abhydrolase_4, TAP-like protein	NA|374aa|down_2|CP033910.1_3086663_3087785_+	pfam03969, AFG1_ATPase, AFG1-like ATPase	NA|177aa|down_3|CP033910.1_3087762_3088293_-	pfam00583, Acetyltransf_1, Acetyltransferase (GNAT) family	NA|176aa|down_4|CP033910.1_3088280_3088808_-	NA	NA|251aa|down_5|CP033910.1_3088847_3089600_-	COG0542, clpA, ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]	NA|123aa|down_6|CP033910.1_3089696_3090065_+	pfam05305, DUF732, Protein of unknown function (DUF732)	NA|115aa|down_7|CP033910.1_3090264_3090609_+	pfam05305, DUF732, Protein of unknown function (DUF732)	NA|310aa|down_8|CP033910.1_3090637_3091567_+	pfam09678, Caa3_CtaG, Cytochrome c oxidase caa3 assembly factor (Caa3_CtaG)	NA|71aa|down_9|CP033910.1_3092682_3092895_-	NA
GCA_003815795.1_ASM381579v1	CP033910	Mycobacterium avium subsp. paratuberculosis strain MAPK_CN4/13 chromosome, complete genome	5	3112101-3112191	5	CRISPRCasFinder	no		csa3,cas3,DEDDh,DinG,cas4,WYL	Orphan	GACTGCGTCCGACTGCGTCCCACC	24	0	0	NA	NA	NA	1	1	Orphan	csa3,cas3,DEDDh,DinG,cas4,WYL	NA|174aa|up_5|CP033910.1_3105307_3105829_-,NA|100aa|up_3|CP033910.1_3106405_3106705_-,NA|184aa|up_2|CP033910.1_3109620_3110172_+,NA|105aa|down_0|CP033910.1_3112291_3112606_+,NA|97aa|down_1|CP033910.1_3112602_3112893_+,NA|75aa|down_2|CP033910.1_3113235_3113460_+,NA|93aa|down_4|CP033910.1_3113968_3114247_-,NA|80aa|down_5|CP033910.1_3114382_3114622_+,NA|145aa|down_6|CP033910.1_3114614_3115049_+,NA|77aa|down_7|CP033910.1_3115117_3115348_+,NA|61aa|down_8|CP033910.1_3115577_3115760_+	NA|296aa|up_9|CP033910.1_3100093_3100981_-	COG1414, IclR, Transcriptional regulator [Transcription]	NA|268aa|up_8|CP033910.1_3101985_3102789_+	pfam06314, ADC, Acetoacetate decarboxylase (ADC)	NA|405aa|up_7|CP033910.1_3102792_3104007_+	pfam04909, Amidohydro_2, Amidohydrolase	NA|423aa|up_6|CP033910.1_3104031_3105300_+	pfam04909, Amidohydro_2, Amidohydrolase	NA|174aa|up_5|CP033910.1_3105307_3105829_-	NA	NA|103aa|up_4|CP033910.1_3105905_3106214_-	COG5178, PRP8, U5 snRNP spliceosome subunit [RNA processing and modification]	NA|100aa|up_3|CP033910.1_3106405_3106705_-	NA	NA|184aa|up_2|CP033910.1_3109620_3110172_+	NA	NA|71aa|up_1|CP033910.1_3110266_3110479_+	TIGR01764, Probable_excisionase, DNA binding domain, excisionase family	NA|159aa|up_0|CP033910.1_3110475_3110952_+	pfam10888, DUF2742, Protein of unknown function (DUF2742)	NA|105aa|down_0|CP033910.1_3112291_3112606_+	NA	NA|97aa|down_1|CP033910.1_3112602_3112893_+	NA	NA|75aa|down_2|CP033910.1_3113235_3113460_+	NA	NA|147aa|down_3|CP033910.1_3113459_3113900_+	pfam12728, HTH_17, Helix-turn-helix domain	NA|93aa|down_4|CP033910.1_3113968_3114247_-	NA	NA|80aa|down_5|CP033910.1_3114382_3114622_+	NA	NA|145aa|down_6|CP033910.1_3114614_3115049_+	NA	NA|77aa|down_7|CP033910.1_3115117_3115348_+	NA	NA|61aa|down_8|CP033910.1_3115577_3115760_+	NA	NA|103aa|down_9|CP033910.1_3115738_3116047_-	smart01040, Bro-N, BRO family, N-terminal domain
