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_000016725.1_ASM1672v1	NC_009468	Acidiphilium cryptum JF-5 plasmid pACRY02, complete sequence	1	35116-37523	1,1,1	PILER-CR,CRISPRCasFinder,CRT	no	cas3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,c2c9_V-U4	c2c9_V-U4,cas14j,cas3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3	Type I-E	GTGTTCCCCGCAGGCGCGGGGATGAACC,GTGTTCCCCGCAGGCGCGGGGATGAACCG,GTGTTCCCCGCAGGCGCGGGGATGAACCG	28,29,29	0	0	NA	NA	I-E:I-E:I-E	35,39,39	39	TypeI-E	DinG,csa3,cas3,cas2,cas1,cas6e,cas5,cas7,cse2gr11,cas8e,DEDDh,c2c9_V-U4,cas14j	NA|90aa|up_9|NC_009468.1_25325_25595_-,NA|275aa|down_1|NC_009468.1_40186_41011_-,NA|138aa|down_2|NC_009468.1_41007_41421_-,NA|61aa|down_5|NC_009468.1_43496_43679_+,NA|184aa|down_8|NC_009468.1_45444_45996_+	NA|90aa|up_9|NC_009468.1_25325_25595_-	NA	NA|108aa|up_8|NC_009468.1_25766_26090_+	PRK12270, kgd, multifunctional oxoglutarate decarboxylase/oxoglutarate dehydrogenase thiamine pyrophosphate-binding subunit/dihydrolipoyllysine-residue succinyltransferase subunit	cas3|893aa|up_7|NC_009468.1_26163_28842_+	PRK09694, PRK09694, CRISPR-associated helicase/endonuclease Cas3	cas8e|530aa|up_6|NC_009468.1_29132_30722_+	cd09729, Cse1_I-E, CRISPR/Cas system-associated protein Cse1	cse2gr11|180aa|up_5|NC_009468.1_30718_31258_+	cd09731, Cse2_I-E, CRISPR/Cas system-associated protein Cse2	cas7|371aa|up_4|NC_009468.1_31257_32370_+	pfam09344, Cas_CT1975, CT1975-like protein	cas5|250aa|up_3|NC_009468.1_32371_33121_+	TIGR01868, hypothetical_protein, CRISPR-associated protein Cas5/CasD, subtype I-E/ECOLI	cas6e|226aa|up_2|NC_009468.1_33126_33804_+	smart01101, CRISPR_assoc, This domain forms an anti-parallel beta strand structure with flanking alpha helical regions	cas1|321aa|up_1|NC_009468.1_33796_34759_+	TIGR03638, cas1_ECOLI, CRISPR-associated endonuclease Cas1, subtype I-E/ECOLI	cas2|109aa|up_0|NC_009468.1_34739_35066_+	PRK11558, PRK11558, putative ssRNA endonuclease; Provisional	NA|691aa|down_0|NC_009468.1_38111_40184_-	pfam03090, Replicase, Replicase family	NA|275aa|down_1|NC_009468.1_40186_41011_-	NA	NA|138aa|down_2|NC_009468.1_41007_41421_-	NA	NA|210aa|down_3|NC_009468.1_41620_42250_+	cd03769, SR_IS607_transposase_like, Serine Recombinase (SR) family, IS607-like transposase subfamily, catalytic domain; members contain a DNA binding domain with homology to MerR/SoxR located N-terminal to the catalytic domain	c2c9_V-U4|400aa|down_4|NC_009468.1_42243_43443_+	COG0675, COG0675, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|61aa|down_5|NC_009468.1_43496_43679_+	NA	NA|207aa|down_6|NC_009468.1_43829_44450_+	PRK00116, ruvA, Holliday junction branch migration protein RuvA	NA|333aa|down_7|NC_009468.1_44446_45445_+	PRK00080, ruvB, Holliday junction branch migration DNA helicase RuvB	NA|184aa|down_8|NC_009468.1_45444_45996_+	NA	NA|52aa|down_9|NC_009468.1_46164_46320_+	pfam09722, DUF2384, Protein of unknown function (DUF2384)
GCF_000016725.1_ASM1672v1	NC_009470	Acidiphilium cryptum JF-5 plasmid pACRY04, complete sequence	1	25677-25888	1,1,1	PILER-CR,CRISPRCasFinder,CRT	no			Orphan	CCGTTCCCCGCGCACGCGGGGATGAACCGC,CCGTTCCCCGCGCACGCGGGGATG,CCGTTCCCCGCGCACGCGGGGATGAACCG	30,24,29	0	0	NA	NA	I-E:I-E:I-E	2,3,3	3	Orphan	DinG,csa3,cas3,cas2,cas1,cas6e,cas5,cas7,cse2gr11,cas8e,DEDDh,c2c9_V-U4,cas14j	NA|99aa|up_9|NC_009470.1_12940_13237_+,NA|236aa|up_1|NC_009470.1_23392_24100_+,NA|142aa|up_0|NC_009470.1_24703_25129_-,NA|89aa|down_0|NC_009470.1_25912_26179_-,NA|189aa|down_1|NC_009470.1_26564_27131_-,NA|120aa|down_5|NC_009470.1_29990_30350_+,NA|218aa|down_6|NC_009470.1_30433_31087_+	NA|99aa|up_9|NC_009470.1_12940_13237_+	NA	NA|239aa|up_8|NC_009470.1_13257_13974_+	COG1285, SapB, Uncharacterized membrane protein [Function unknown]	NA|878aa|up_7|NC_009470.1_14026_16660_+	pfam01526, DDE_Tnp_Tn3, Tn3 transposase DDE domain	NA|1007aa|up_6|NC_009470.1_16678_19699_-	pfam01526, DDE_Tnp_Tn3, Tn3 transposase DDE domain	NA|403aa|up_5|NC_009470.1_19768_20977_-	pfam00872, Transposase_mut, Transposase, Mutator family	NA|198aa|up_4|NC_009470.1_21119_21713_-	cd03768, SR_ResInv, Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain	NA|187aa|up_3|NC_009470.1_22381_22942_+	TIGR02881, Stage_V_sporulation_protein_K, stage V sporulation protein K	NA|109aa|up_2|NC_009470.1_22935_23262_+	PRK12270, kgd, multifunctional oxoglutarate decarboxylase/oxoglutarate dehydrogenase thiamine pyrophosphate-binding subunit/dihydrolipoyllysine-residue succinyltransferase subunit	NA|236aa|up_1|NC_009470.1_23392_24100_+	NA	NA|142aa|up_0|NC_009470.1_24703_25129_-	NA	NA|89aa|down_0|NC_009470.1_25912_26179_-	NA	NA|189aa|down_1|NC_009470.1_26564_27131_-	NA	NA|452aa|down_2|NC_009470.1_27153_28509_-	pfam03428, RP-C, Replication protein C N-terminal domain	NA|70aa|down_3|NC_009470.1_28696_28906_-	COG0864, NikR, Predicted transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain and a metal-binding domain [Transcription]	NA|228aa|down_4|NC_009470.1_29310_29994_+	cd02042, ParAB_family, partition proteins ParAB family	NA|120aa|down_5|NC_009470.1_29990_30350_+	NA	NA|218aa|down_6|NC_009470.1_30433_31087_+	NA	NA|413aa|down_7|NC_009470.1_31097_32336_-	pfam09019, EcoRII-C, EcoRII C terminal	NA|155aa|down_8|NC_009470.1_32322_32787_-	COG3727, Vsr, DNA G:T-mismatch repair endonuclease [DNA replication, recombination, and repair]	NA|421aa|down_9|NC_009470.1_32779_34042_-	PRK10458, PRK10458, DNA cytosine methylase; Provisional
GCF_000016725.1_ASM1672v1	NC_009467	Acidiphilium cryptum JF-5 plasmid pACRY01, complete sequence	1	157782-157905	1	CRISPRCasFinder	no	csa3	csa3	Type I-A	GCGGGGTGGCGGGCAAGCGGCGGTG	25	2	2	157807-157829|157855-157880	NC_009467.1_157775-157797|NC_009468.1_106065-106040	NA	2	2	Orphan	DinG,csa3,cas3,cas2,cas1,cas6e,cas5,cas7,cse2gr11,cas8e,DEDDh,c2c9_V-U4,cas14j	NA,NA|58aa|down_2|NC_009467.1_162131_162305_+	NA|410aa|up_9|NC_009467.1_147822_149052_-	PRK11033, zntA, zinc/cadmium/mercury/lead-transporting ATPase; Provisional	NA|269aa|up_8|NC_009467.1_149079_149886_-	pfam01695, IstB_IS21, IstB-like ATP binding protein	NA|509aa|up_7|NC_009467.1_149875_151402_-	COG4584, COG4584, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|345aa|up_6|NC_009467.1_151499_152534_-	PRK11033, zntA, zinc/cadmium/mercury/lead-transporting ATPase; Provisional	NA|143aa|up_5|NC_009467.1_152599_153028_+	cd04785, HTH_CadR-PbrR-like, Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators	NA|416aa|up_4|NC_009467.1_153037_154285_-	cd17325, MFS_MdtG_SLC18_like, bacterial MdtG-like and eukaryotic solute carrier 18 (SLC18) family of the Major Facilitator Superfamily of transporters	NA|244aa|up_3|NC_009467.1_154281_155013_-	cd07724, POD-like_MBL-fold, ETHE1 (PDO type I), persulfide dioxygenase A (PDOA, PDO type II) and related proteins; MBL-fold metallo-hydrolase domain	csa3|222aa|up_2|NC_009467.1_155098_155764_+	cd00158, RHOD, Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein	NA|96aa|up_1|NC_009467.1_155936_156224_-	TIGR02607, Virulence-associated_protein_I, addiction module antidote protein, HigA family	NA|93aa|up_0|NC_009467.1_156235_156514_-	pfam05015, HigB-like_toxin, RelE-like toxin of type II toxin-antitoxin system HigB	NA|408aa|down_0|NC_009467.1_159793_161017_+	pfam00872, Transposase_mut, Transposase, Mutator family	NA|72aa|down_1|NC_009467.1_161919_162135_+	pfam10387, DUF2442, Protein of unknown function (DUF2442)	NA|58aa|down_2|NC_009467.1_162131_162305_+	NA	NA|93aa|down_3|NC_009467.1_162307_162586_+	COG3668, ParE, Plasmid stabilization system protein [General function prediction only]	NA|187aa|down_4|NC_009467.1_162992_163553_+	pfam07700, HNOB, Haem-NO-binding	NA|621aa|down_5|NC_009467.1_163558_165421_+	COG5001, COG5001, Predicted signal transduction protein containing a membrane domain, an EAL and a GGDEF domain [Signal transduction mechanisms]	NA|418aa|down_6|NC_009467.1_165731_166985_-	pfam01610, DDE_Tnp_ISL3, Transposase	NA|269aa|down_7|NC_009467.1_167327_168134_+	COG0745, OmpR, Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]	NA|230aa|down_8|NC_009467.1_168316_169006_-	pfam07589, VPEP, PEP-CTERM motif	csa3|222aa|down_9|NC_009467.1_169880_170546_-	cd00158, RHOD, Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein
GCF_000016725.1_ASM1672v1	NC_009484	Acidiphilium cryptum JF-5, complete genome	1	232843-232968	1	CRT	no		DinG,csa3,cas3,cas2,cas1,cas6e,cas5,cas7,cse2gr11,cas8e,DEDDh	Orphan	GGTGCCGCCGATGCCGCC	18	3	4	232861-232878|232897-232914|232933-232950|232933-232950	NC_009484.1_216010-216027|NC_009484.1_1629885-1629868|NC_009484.1_748713-748730|NC_009484.1_777177-777160	NA	3	3	Orphan	DinG,csa3,cas3,cas2,cas1,cas6e,cas5,cas7,cse2gr11,cas8e,DEDDh,c2c9_V-U4,cas14j	NA,NA|278aa|down_0|NC_009484.1_233059_233893_-,NA|271aa|down_1|NC_009484.1_234070_234883_+,NA|281aa|down_6|NC_009484.1_240828_241671_+	NA|306aa|up_9|NC_009484.1_219238_220156_+	PRK12921, PRK12921, oxidoreductase	NA|212aa|up_8|NC_009484.1_220128_220764_-	TIGR04282, hypothetical_protein, transferase 1, rSAM/selenodomain-associated	NA|706aa|up_7|NC_009484.1_220748_222866_-	PRK06370, PRK06370, FAD-containing oxidoreductase	NA|580aa|up_6|NC_009484.1_222873_224613_-	COG0535, COG0535, Predicted Fe-S oxidoreductases [General function prediction only]	NA|466aa|up_5|NC_009484.1_224623_226021_-	cd17371, MFS_MucK, Cis,cis-muconate transport protein and similar proteins of the Major Facilitator Superfamily	NA|308aa|up_4|NC_009484.1_226340_227264_+	cd00408, DHDPS-like, Dihydrodipicolinate synthase family	NA|523aa|up_3|NC_009484.1_227260_228829_+	cd07129, ALDH_KGSADH, Alpha-Ketoglutaric Semialdehyde Dehydrogenase	NA|238aa|up_2|NC_009484.1_228857_229571_-	PRK08245, PRK08245, hypothetical protein; Validated	NA|288aa|up_1|NC_009484.1_230054_230918_+	cd07336, M48B_HtpX_like, Peptidase M48 subfamily B HtpX-like membrane-bound metallopeptidase	NA|177aa|up_0|NC_009484.1_230999_231530_-	COG0071, IbpA, Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]	NA|278aa|down_0|NC_009484.1_233059_233893_-	NA	NA|271aa|down_1|NC_009484.1_234070_234883_+	NA	NA|475aa|down_2|NC_009484.1_235042_236467_+	COG4671, COG4671, Predicted glycosyl transferase [General function prediction only]	NA|455aa|down_3|NC_009484.1_236466_237831_+	cd03798, GT4_WlbH-like, Bordetella parapertussis WlbH and similar proteins	NA|400aa|down_4|NC_009484.1_237827_239027_+	cd03798, GT4_WlbH-like, Bordetella parapertussis WlbH and similar proteins	NA|603aa|down_5|NC_009484.1_239023_240832_+	COG1132, MdlB, ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]	NA|281aa|down_6|NC_009484.1_240828_241671_+	NA	NA|219aa|down_7|NC_009484.1_241627_242284_+	pfam00300, His_Phos_1, Histidine phosphatase superfamily (branch 1)	NA|454aa|down_8|NC_009484.1_242288_243650_+	COG1004, Ugd, Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]	NA|234aa|down_9|NC_009484.1_243646_244348_-	PRK07577, PRK07577, SDR family oxidoreductase
GCF_000016725.1_ASM1672v1	NC_009484	Acidiphilium cryptum JF-5, complete genome	2	1300540-1302395	2	CRT	no		DinG,csa3,cas3,cas2,cas1,cas6e,cas5,cas7,cse2gr11,cas8e,DEDDh	Orphan	GCACCCGTNGCGCCNGTGGC	20	0	0	NA	NA	NA	32	32	Orphan	DinG,csa3,cas3,cas2,cas1,cas6e,cas5,cas7,cse2gr11,cas8e,DEDDh,c2c9_V-U4,cas14j	NA,NA|200aa|down_3|NC_009484.1_1308726_1309326_+,NA|141aa|down_7|NC_009484.1_1311760_1312183_+	NA|519aa|up_9|NC_009484.1_1286955_1288512_-	TIGR02963, Includes:_Xanthine_dehydrogenase, xanthine dehydrogenase, small subunit	NA|307aa|up_8|NC_009484.1_1288606_1289527_-	cd08449, PBP2_XapR, The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved in xanthosine catabolism, contains the type 2 periplasmic binding fold	NA|595aa|up_7|NC_009484.1_1289681_1291466_+	PRK11269, PRK11269, glyoxylate carboligase; Provisional	NA|269aa|up_6|NC_009484.1_1291485_1292292_+	TIGR03234, OH-pyruv-isom, hydroxypyruvate isomerase	NA|293aa|up_5|NC_009484.1_1292288_1293167_+	PRK15059, PRK15059, 2-hydroxy-3-oxopropionate reductase	NA|440aa|up_4|NC_009484.1_1293166_1294486_+	COG2379, GckA, Putative glycerate kinase [Carbohydrate transport and metabolism]	NA|432aa|up_3|NC_009484.1_1294491_1295787_+	cd03884, M20_bAS, M20 Peptidase beta-alanine synthase, an amidohydrolase	NA|415aa|up_2|NC_009484.1_1295789_1297034_+	cd02697, M20_like, M20 Zn-peptidases include exopeptidases	NA|308aa|up_1|NC_009484.1_1297071_1297995_+	TIGR03212, uraD_N-term-dom, putative urate catabolism protein	NA|308aa|up_0|NC_009484.1_1298014_1298938_+	cd08463, PBP2_DntR_like_4, The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold	NA|413aa|down_0|NC_009484.1_1304663_1305902_+	cd00801, INT_P4_C, Bacteriophage P4 integrase, C-terminal catalytic domain	NA|62aa|down_1|NC_009484.1_1306155_1306341_+	COG3311, AlpA, Predicted transcriptional regulator [Transcription]	NA|718aa|down_2|NC_009484.1_1306310_1308464_+	pfam13481, AAA_25, AAA domain	NA|200aa|down_3|NC_009484.1_1308726_1309326_+	NA	NA|132aa|down_4|NC_009484.1_1309318_1309714_+	PRK09863, PRK09863, putative frv operon regulatory protein; Provisional	NA|297aa|down_5|NC_009484.1_1309851_1310742_+	TIGR02794, Protein_TolA, TolA protein	NA|209aa|down_6|NC_009484.1_1310945_1311572_+	pfam03544, TonB_C, Gram-negative bacterial TonB protein C-terminal	NA|141aa|down_7|NC_009484.1_1311760_1312183_+	NA	NA|185aa|down_8|NC_009484.1_1312751_1313306_-	COG0652, PpiB, Peptidyl-prolyl cis-trans isomerase (rotamase) - cyclophilin family [Posttranslational modification, protein turnover, chaperones]	NA|170aa|down_9|NC_009484.1_1313302_1313812_-	PRK00168, coaD, phosphopantetheine adenylyltransferase; Provisional
