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_001854305.1_ASM185430v1	NZ_CP017748	Cupriavidus sp. USMAA2-4 chromosome 1, complete sequence	1	2265899-2265992	1	CRISPRCasFinder	no		RT,cas3,WYL,csa3,DEDDh,DinG	Orphan	GGCCGGCCGCGATCGGATTGCTTGAGGT	28	0	0	NA	NA	NA	1	1	Orphan	RT,cas3,WYL,csa3,DEDDh,DinG,c2c9_V-U4	NA,NA|30aa|down_5|NZ_CP017748.1_2276229_2276319_-,NA|60aa|down_6|NZ_CP017748.1_2276665_2276845_-	NA|502aa|up_9|NZ_CP017748.1_2252481_2253987_-	PRK00012, gatA, Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA	NA|100aa|up_8|NZ_CP017748.1_2254104_2254404_-	PRK00034, gatC, Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatC	NA|348aa|up_7|NZ_CP017748.1_2254981_2256025_+	PRK13927, PRK13927, rod shape-determining protein MreB; Provisional	NA|171aa|up_6|NZ_CP017748.1_2257215_2257728_+	COG2891, MreD, Cell shape-determining protein [Cell envelope biogenesis, outer membrane]	NA|788aa|up_5|NZ_CP017748.1_2257803_2260167_+	TIGR03423, pbp2_mrdA, penicillin-binding protein 2	NA|381aa|up_4|NZ_CP017748.1_2260178_2261321_+	TIGR02210, Rod_shape-determining_protein_RodA, rod shape-determining protein RodA	NA|272aa|up_3|NZ_CP017748.1_2261333_2262149_-	sd00010, SLR, Sel1-like repeat	NA|204aa|up_2|NZ_CP017748.1_2262306_2262918_-	COG1846, MarR, Transcriptional regulators [Transcription]	NA|349aa|up_1|NZ_CP017748.1_2263149_2264196_+	cd13579, PBP2_Bug_NagM, Uncharacterized NagM-like protein of Bug (Bordetella uptake gene) protein family; contains the type 2 periplasmic binding fold	NA|522aa|up_0|NZ_CP017748.1_2264260_2265826_+	cd16028, PMH, Phosphonate monoester hydrolase/phosphodiesterase	NA|232aa|down_0|NZ_CP017748.1_2267583_2268279_-	PRK10529, PRK10529, DNA-binding transcriptional activator KdpE; Provisional	NA|963aa|down_1|NZ_CP017748.1_2268315_2271204_-	COG2205, KdpD, Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]	NA|215aa|down_2|NZ_CP017748.1_2271308_2271953_-	pfam02669, KdpC, K+-transporting ATPase, c chain	NA|754aa|down_3|NZ_CP017748.1_2272008_2274270_-	PRK01122, PRK01122, potassium-transporting ATPase subunit KdpB	NA|606aa|down_4|NZ_CP017748.1_2274412_2276230_-	PRK05482, PRK05482, potassium-transporting ATPase subunit A; Provisional	NA|30aa|down_5|NZ_CP017748.1_2276229_2276319_-	NA	NA|60aa|down_6|NZ_CP017748.1_2276665_2276845_-	NA	NA|258aa|down_7|NZ_CP017748.1_2276843_2277617_+	PRK01973, PRK01973, septum site-determining protein MinC	NA|272aa|down_8|NZ_CP017748.1_2277673_2278489_+	COG2894, MinD, Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]	NA|85aa|down_9|NZ_CP017748.1_2278508_2278763_+	PRK13989, PRK13989, cell division topological specificity factor MinE; Provisional
GCF_001854305.1_ASM185430v1	NZ_CP017748	Cupriavidus sp. USMAA2-4 chromosome 1, complete sequence	2	2298980-2299088	2	CRISPRCasFinder	no	cas3	RT,cas3,WYL,csa3,DEDDh,DinG	Unclear	TCGGTTTGCGGGGCAACGGCCTGTTTCGGCTCTCGTGACT	40	0	0	NA	NA	NA	1	1	Unclear	RT,cas3,WYL,csa3,DEDDh,DinG,c2c9_V-U4	NA,NA	NA|437aa|up_9|NZ_CP017748.1_2286188_2287499_+	PRK06133, PRK06133, glutamate carboxypeptidase; Reviewed	NA|426aa|up_8|NZ_CP017748.1_2287587_2288865_-	cd17478, MFS_FsR, Fosmidomycin resistance protein of the Major Facilitator Superfamily of transporters	NA|280aa|up_7|NZ_CP017748.1_2288971_2289811_+	cd06124, cupin_NimR-like_N, AraC/XylS family transcriptional regulators similar to NimR, N-terminal cupin domain	NA|382aa|up_6|NZ_CP017748.1_2290661_2291807_+	pfam00665, rve, Integrase core domain	NA|429aa|up_5|NZ_CP017748.1_2292050_2293337_-	cd05666, M20_Acy1-like, M20 Peptidase aminoacylase 1 subfamily	NA|283aa|up_4|NZ_CP017748.1_2293560_2294409_-	COG0179, MhpD, 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) [Secondary metabolites biosynthesis, transport, and catabolism]	NA|243aa|up_3|NZ_CP017748.1_2294405_2295134_-	COG1802, GntR, Transcriptional regulators [Transcription]	NA|433aa|up_2|NZ_CP017748.1_2295333_2296632_+	cd17319, MFS_ExuT_GudP_like, Hexuronate transporter, Glucarate transporter, and similar transporters of the Major Facilitator Superfamily	NA|243aa|up_1|NZ_CP017748.1_2296746_2297475_+	COG3473, COG3473, Maleate cis-trans isomerase [Secondary metabolites biosynthesis, transport, and catabolism]	NA|474aa|up_0|NZ_CP017748.1_2297529_2298951_+	PRK13404, PRK13404, dihydropyrimidinase; Provisional	NA|246aa|down_0|NZ_CP017748.1_2299972_2300710_+	COG4126, COG4126, Hydantoin racemase [Amino acid transport and metabolism]	NA|311aa|down_1|NZ_CP017748.1_2300818_2301751_-	COG0583, LysR, Transcriptional regulator [Transcription]	NA|209aa|down_2|NZ_CP017748.1_2301897_2302524_+	PRK10542, PRK10542, glutathionine S-transferase; Provisional	NA|263aa|down_3|NZ_CP017748.1_2302555_2303344_-	COG0426, FpaA, Uncharacterized flavoproteins [Energy production and conversion]	NA|218aa|down_4|NZ_CP017748.1_2303487_2304141_-	COG0386, BtuE, Glutathione peroxidase [Posttranslational modification, protein turnover, chaperones]	NA|499aa|down_5|NZ_CP017748.1_2304299_2305796_-	cd17502, MFS_Azr1_MDR_like, Saccharomyces cerevisiae Azole resistance protein 1 (Azr1p), and similar multidrug resistance (MDR) transporters of the Major Facilitator Superfamily	NA|388aa|down_6|NZ_CP017748.1_2306172_2307336_+	cd19963, PBP1_BMP-like, periplasmic binding component of a basic membrane lipoprotein (BMP) from Brucella abortus and its close homologs in other bacteria	NA|362aa|down_7|NZ_CP017748.1_2307332_2308418_+	COG4638, HcaE, Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]	NA|147aa|down_8|NZ_CP017748.1_2308631_2309072_-	cd04623, CBS_pair_bac_euk, Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains present in bacteria and eukaryotes	NA|246aa|down_9|NZ_CP017748.1_2309331_2310069_-	COG1309, AcrR, Transcriptional regulator [Transcription]
GCF_001854305.1_ASM185430v1	NZ_CP017748	Cupriavidus sp. USMAA2-4 chromosome 1, complete sequence	3	2627308-2627442	1	PILER-CR	no		RT,cas3,WYL,csa3,DEDDh,DinG	Orphan	CGATGTTTCACGTGAAACACAGGCCGG	27	0	0	NA	NA	NA	2	2	Orphan	RT,cas3,WYL,csa3,DEDDh,DinG,c2c9_V-U4	NA|125aa|up_7|NZ_CP017748.1_2618157_2618532_+,NA	NA|295aa|up_9|NZ_CP017748.1_2615673_2616558_+	COG0559, LivH, Branched-chain amino acid ABC-type transport system, permease components [Amino acid transport and metabolism]	NA|340aa|up_8|NZ_CP017748.1_2616584_2617604_+	cd06581, TM_PBP1_LivM_like, Transmembrane subunit (TM) of Escherichia coli LivM and related proteins	NA|125aa|up_7|NZ_CP017748.1_2618157_2618532_+	NA	NA|385aa|up_6|NZ_CP017748.1_2618826_2619981_+	cd06333, PBP1_ABC_RPA1789-like, type 1 periplasmic binding-protein component (CouP) of an ABC system (CouPSTU; RPA1789, RPA1791-1793), involved in active transport of lignin-derived aromatic substrates, and its close homologs	NA|351aa|up_5|NZ_CP017748.1_2620437_2621490_+	COG0559, LivH, Branched-chain amino acid ABC-type transport system, permease components [Amino acid transport and metabolism]	NA|610aa|up_4|NZ_CP017748.1_2621493_2623323_+	COG0411, LivG, ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]	NA|248aa|up_3|NZ_CP017748.1_2623336_2624080_+	COG0410, LivF, ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]	NA|315aa|up_2|NZ_CP017748.1_2624344_2625289_-	PRK11139, PRK11139, DNA-binding transcriptional activator GcvA; Provisional	NA|335aa|up_1|NZ_CP017748.1_2625413_2626418_+	cd13577, PBP2_BugE_Glu, Glutamate transporter of Bug (Bordetella uptake gene) protein family; contains the type 2 periplasmic binding fold	NA|292aa|up_0|NZ_CP017748.1_2626420_2627296_+	pfam05013, FGase, N-formylglutamate amidohydrolase	NA|655aa|down_0|NZ_CP017748.1_2627521_2629486_+	PRK05192, PRK05192, tRNA uridine-5-carboxymethylaminomethyl(34) synthesis enzyme MnmG	NA|237aa|down_1|NZ_CP017748.1_2629486_2630197_+	PRK00107, gidB, 16S rRNA (guanine(527)-N(7))-methyltransferase RsmG	NA|258aa|down_2|NZ_CP017748.1_2630276_2631050_+	pfam13614, AAA_31, AAA domain	NA|301aa|down_3|NZ_CP017748.1_2631115_2632018_+	TIGR04285, parB-like_partition_protein, nucleoid occlusion protein	NA|158aa|down_4|NZ_CP017748.1_2632342_2632816_+	COG3312, AtpI, F0F1-type ATP synthase, subunit I [Energy production and conversion]	NA|289aa|down_5|NZ_CP017748.1_2633054_2633921_+	PRK05815, PRK05815, F0F1 ATP synthase subunit A; Validated	NA|89aa|down_6|NZ_CP017748.1_2633982_2634249_+	PRK06876, PRK06876, F0F1 ATP synthase subunit C; Validated	NA|157aa|down_7|NZ_CP017748.1_2634348_2634819_+	PRK05759, PRK05759, F0F1 ATP synthase subunit B; Validated	NA|181aa|down_8|NZ_CP017748.1_2634821_2635364_+	PRK05758, PRK05758, F0F1 ATP synthase subunit delta; Validated	NA|514aa|down_9|NZ_CP017748.1_2635414_2636956_+	PRK09281, PRK09281, F0F1 ATP synthase subunit alpha; Validated
GCF_001854305.1_ASM185430v1	NZ_CP017749	Cupriavidus sp. USMAA2-4 chromosome 2, complete sequence	1	2242540-2242636	1	CRISPRCasFinder	no		csa3,DEDDh	Orphan	GCCGCAGTGCAGGGCGCCGCGCGCG	25	0	0	NA	NA	NA	1	1	Orphan	RT,cas3,WYL,csa3,DEDDh,DinG,c2c9_V-U4	NA|57aa|up_5|NZ_CP017749.1_2236881_2237052_+,NA|198aa|up_0|NZ_CP017749.1_2241502_2242096_-,NA|48aa|down_0|NZ_CP017749.1_2243353_2243497_-,NA|68aa|down_5|NZ_CP017749.1_2248761_2248965_-,NA|252aa|down_9|NZ_CP017749.1_2254334_2255090_+	NA|323aa|up_9|NZ_CP017749.1_2231596_2232565_-	cd08422, PBP2_CrgA_like, The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain	NA|506aa|up_8|NZ_CP017749.1_2232672_2234190_+	cd07085, ALDH_F6_MMSDH, Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2	NA|194aa|up_7|NZ_CP017749.1_2234317_2234899_-	pfam13649, Methyltransf_25, Methyltransferase domain	NA|461aa|up_6|NZ_CP017749.1_2235066_2236449_-	COG2252, COG2252, Xanthine/uracil/vitamin C permease [Nucleotide transport and    metabolism]	NA|57aa|up_5|NZ_CP017749.1_2236881_2237052_+	NA	NA|288aa|up_4|NZ_CP017749.1_2237156_2238020_-	cd08422, PBP2_CrgA_like, The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain	NA|511aa|up_3|NZ_CP017749.1_2238193_2239726_+	TIGR00711, Uncharacterized_MFS-type_transporter_YhcA, drug resistance transporter, EmrB/QacA subfamily	NA|295aa|up_2|NZ_CP017749.1_2239760_2240645_-	COG0583, LysR, Transcriptional regulator [Transcription]	NA|173aa|up_1|NZ_CP017749.1_2240847_2241366_+	COG4125, COG4125, Predicted membrane protein [Function unknown]	NA|198aa|up_0|NZ_CP017749.1_2241502_2242096_-	NA	NA|48aa|down_0|NZ_CP017749.1_2243353_2243497_-	NA	NA|388aa|down_1|NZ_CP017749.1_2243863_2245027_+	pfam15902, Sortilin-Vps10, Sortilin, neurotensin receptor 3,	NA|87aa|down_2|NZ_CP017749.1_2245068_2245329_+	cd17074, Ubl_CysO_like, ubiquitin-like (Ubl) domain found in Mycobacterium tuberculosis CysO and similar proteins	NA|323aa|down_3|NZ_CP017749.1_2245518_2246487_+	COG0835, CheW, Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]	NA|550aa|down_4|NZ_CP017749.1_2247057_2248707_+	PRK11660, PRK11660, putative transporter; Provisional	NA|68aa|down_5|NZ_CP017749.1_2248761_2248965_-	NA	NA|368aa|down_6|NZ_CP017749.1_2249823_2250927_-	PRK11856, PRK11856, branched-chain alpha-keto acid dehydrogenase subunit E2; Reviewed	NA|326aa|down_7|NZ_CP017749.1_2251006_2251984_-	COG0022, AcoB, Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit [Energy production and conversion]	NA|361aa|down_8|NZ_CP017749.1_2252093_2253176_-	TIGR03181, PDH_E1_alph_x, pyruvate dehydrogenase E1 component, alpha subunit	NA|252aa|down_9|NZ_CP017749.1_2254334_2255090_+	NA
GCF_001854305.1_ASM185430v1	NZ_CP017749	Cupriavidus sp. USMAA2-4 chromosome 2, complete sequence	2	3082763-3082865	2	CRISPRCasFinder	no		csa3,DEDDh	Orphan	AGTTCGACCCCTACAGCCAGGGTGC	25	0	0	NA	NA	NA	1	1	Orphan	RT,cas3,WYL,csa3,DEDDh,DinG,c2c9_V-U4	NA,NA|302aa|down_1|NZ_CP017749.1_3084979_3085885_-	NA|662aa|up_9|NZ_CP017749.1_3066573_3068559_-	pfam04632, FUSC, Fusaric acid resistance protein family	NA|159aa|up_8|NZ_CP017749.1_3068563_3069040_-	COG1846, MarR, Transcriptional regulators [Transcription]	NA|416aa|up_7|NZ_CP017749.1_3069265_3070513_-	COG3174, COG3174, Predicted membrane protein [Function unknown]	NA|518aa|up_6|NZ_CP017749.1_3070699_3072253_+	COG2187, COG2187, Uncharacterized protein conserved in bacteria [Function unknown]	NA|327aa|up_5|NZ_CP017749.1_3072493_3073474_+	PRK03598, PRK03598, putative efflux pump membrane fusion protein; Provisional	NA|929aa|up_4|NZ_CP017749.1_3073477_3076264_+	COG1131, CcmA, ABC-type multidrug transport system, ATPase component [Defense mechanisms]	NA|376aa|up_3|NZ_CP017749.1_3076266_3077394_+	pfam12698, ABC2_membrane_3, ABC-2 family transporter protein	NA|458aa|up_2|NZ_CP017749.1_3077558_3078932_+	COG1538, TolC, Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]	NA|690aa|up_1|NZ_CP017749.1_3079110_3081180_+	PRK10060, PRK10060, cyclic di-GMP phosphodiesterase	NA|308aa|up_0|NZ_CP017749.1_3081532_3082456_+	cd13688, PBP2_GltI_DEBP, Substrate-binding domain of ABC aspartate-glutamate transporter; the type 2 periplasmic binding protein fold	NA|569aa|down_0|NZ_CP017749.1_3083073_3084780_-	PRK15041, PRK15041, methyl-accepting chemotaxis protein	NA|302aa|down_1|NZ_CP017749.1_3084979_3085885_-	NA	NA|190aa|down_2|NZ_CP017749.1_3086101_3086671_+	COG3247, HdeD, Uncharacterized conserved protein [Function unknown]	NA|582aa|down_3|NZ_CP017749.1_3086981_3088727_+	COG1807, ArnT, 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]	NA|124aa|down_4|NZ_CP017749.1_3088734_3089106_+	PRK02971, PRK02971, 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol flippase subunit ArnF; Provisional	NA|395aa|down_5|NZ_CP017749.1_3089118_3090303_+	COG0399, WecE, Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]	NA|334aa|down_6|NZ_CP017749.1_3090281_3091283_+	PRK10714, PRK10714, undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional	NA|315aa|down_7|NZ_CP017749.1_3091270_3092215_+	PRK06988, PRK06988, formyltransferase	NA|351aa|down_8|NZ_CP017749.1_3092211_3093264_+	PRK11908, PRK11908, bifunctional UDP-4-keto-pentose/UDP-xylose synthase	NA|297aa|down_9|NZ_CP017749.1_3093275_3094166_+	cd10939, CE4_ArnD, Catalytic domain of Escherichia coli 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD and other bacterial homologs
GCF_001854305.1_ASM185430v1	NZ_CP017750	Cupriavidus sp. USMAA2-4 plasmid unnamed1, complete sequence	1	282407-282714	1	CRISPRCasFinder	no	c2c9_V-U4	c2c9_V-U4	Type V-U4	AGGCCGGTATGCACCGGTGCATAT	24	0	0	NA	NA	NA	5	5	TypeV-U4	RT,cas3,WYL,csa3,DEDDh,DinG,c2c9_V-U4	NA|80aa|up_9|NZ_CP017750.1_271001_271241_+,NA|175aa|up_7|NZ_CP017750.1_274196_274721_+,NA|369aa|up_6|NZ_CP017750.1_274720_275827_+,NA|260aa|up_3|NZ_CP017750.1_277891_278671_+,NA|405aa|down_3|NZ_CP017750.1_285554_286769_-,NA|78aa|down_5|NZ_CP017750.1_288649_288883_+,NA|201aa|down_7|NZ_CP017750.1_291073_291676_-,NA|216aa|down_9|NZ_CP017750.1_292261_292909_-	NA|80aa|up_9|NZ_CP017750.1_271001_271241_+	NA	NA|810aa|up_8|NZ_CP017750.1_271617_274047_+	COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]	NA|175aa|up_7|NZ_CP017750.1_274196_274721_+	NA	NA|369aa|up_6|NZ_CP017750.1_274720_275827_+	NA	NA|208aa|up_5|NZ_CP017750.1_275854_276478_+	PRK06958, PRK06958, single-stranded DNA-binding protein; Provisional	NA|343aa|up_4|NZ_CP017750.1_276634_277663_+	COG4643, COG4643, Uncharacterized protein conserved in bacteria [Function unknown]	NA|260aa|up_3|NZ_CP017750.1_277891_278671_+	NA	NA|305aa|up_2|NZ_CP017750.1_278761_279676_+	cd00397, DNA_BRE_C, DNA breaking-rejoining enzymes, C-terminal catalytic domain	NA|365aa|up_1|NZ_CP017750.1_280029_281124_+	COG1192, Soj, ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]	NA|374aa|up_0|NZ_CP017750.1_281116_282238_+	TIGR00180, Probable_chromosome-partitioning_protein_ParB, ParB/RepB/Spo0J family partition protein	NA|425aa|down_0|NZ_CP017750.1_283120_284395_+	COG3355, COG3355, Predicted transcriptional regulator [Transcription]	NA|94aa|down_1|NZ_CP017750.1_284591_284873_+	pfam08681, DUF1778, Protein of unknown function (DUF1778)	NA|169aa|down_2|NZ_CP017750.1_284869_285376_+	pfam00583, Acetyltransf_1, Acetyltransferase (GNAT) family	NA|405aa|down_3|NZ_CP017750.1_285554_286769_-	NA	NA|502aa|down_4|NZ_CP017750.1_286949_288455_+	pfam07693, KAP_NTPase, KAP family P-loop domain	NA|78aa|down_5|NZ_CP017750.1_288649_288883_+	NA	NA|704aa|down_6|NZ_CP017750.1_288908_291020_+	PRK00236, xerC, site-specific tyrosine recombinase XerC; Reviewed	NA|201aa|down_7|NZ_CP017750.1_291073_291676_-	NA	NA|84aa|down_8|NZ_CP017750.1_291955_292207_+	COG2916, Hns, DNA-binding protein H-NS [General function prediction only]	NA|216aa|down_9|NZ_CP017750.1_292261_292909_-	NA
