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_900324345.1_17_LA_343	NZ_LT992471	Staphylococcus aureus isolate 17_LA_343 chromosome I	1	336240-336439	1	CRISPRCasFinder	no		cas3,DEDDh,DinG,csa3,TnsE_C,WYL	Orphan	TGCAAGTTGGCGGGGCCCCAACACAGAAGCT	31	2	2	336271-336295|336327-336351	NZ_LT992471.1_336440-336464|NZ_LT992471.1_2285947-2285971	NA	3	3	Orphan	cas3,DEDDh,DinG,csa3,TnsE_C,WYL	NA,NA|131aa|down_5|NZ_LT992471.1_341615_342008_+	NA|574aa|up_9|NZ_LT992471.1_323686_325408_+	pfam18674, TarS_C1, TarS beta-glycosyltransferase C-terminal domain 1	NA|225aa|up_8|NZ_LT992471.1_325551_326226_+	PRK13276, PRK13276, iron-sulfur cluster repair di-iron protein ScdA	NA|585aa|up_7|NZ_LT992471.1_326472_328227_+	COG3275, LytS, Putative regulator of cell autolysis [Signal transduction mechanisms]	NA|247aa|up_6|NZ_LT992471.1_328229_328970_+	PRK14084, PRK14084, DNA-binding response regulator	NA|148aa|up_5|NZ_LT992471.1_329082_329526_+	PRK04125, PRK04125, antiholin-like protein LrgA	NA|234aa|up_4|NZ_LT992471.1_329518_330220_+	PRK04288, PRK04288, antiholin-like protein LrgB; Provisional	NA|764aa|up_3|NZ_LT992471.1_330560_332852_+	COG3256, NorB, Nitric oxide reductase large subunit [Inorganic ion transport and metabolism]	NA|235aa|up_2|NZ_LT992471.1_333077_333782_-	COG2188, PhnF, Transcriptional regulators [Transcription]	NA|264aa|up_1|NZ_LT992471.1_333930_334722_+	COG2190, NagE, Phosphotransferase system IIA components [Carbohydrate transport and metabolism]	NA|479aa|up_0|NZ_LT992471.1_334737_336174_+	PRK09589, celA, 6-phospho-beta-glucosidase; Reviewed	NA|254aa|down_0|NZ_LT992471.1_336749_337511_-	pfam13649, Methyltransf_25, Methyltransferase domain	NA|305aa|down_1|NZ_LT992471.1_337762_338677_-	TIGR02152, Putative_ribokinase, ribokinase	NA|135aa|down_2|NZ_LT992471.1_338704_339109_-	PRK11797, PRK11797, D-ribose pyranase; Provisional	NA|294aa|down_3|NZ_LT992471.1_339123_340005_-	pfam06800, Sugar_transport, Sugar transport protein	NA|333aa|down_4|NZ_LT992471.1_340236_341235_-	COG1609, PurR, Transcriptional regulators [Transcription]	NA|131aa|down_5|NZ_LT992471.1_341615_342008_+	NA	NA|459aa|down_6|NZ_LT992471.1_342136_343513_-	TIGR00711, Uncharacterized_MFS-type_transporter_YhcA, drug resistance transporter, EmrB/QacA subfamily	NA|331aa|down_7|NZ_LT992471.1_343746_344739_+	COG3049, COG3049, Penicillin V acylase and related amidases [Cell envelope biogenesis, outer membrane]	NA|317aa|down_8|NZ_LT992471.1_345064_346015_+	COG3942, COG3942, Surface antigen [General function prediction only]	NA|220aa|down_9|NZ_LT992471.1_346066_346726_-	COG1131, CcmA, ABC-type multidrug transport system, ATPase component [Defense mechanisms]
GCF_900324345.1_17_LA_343	NZ_LT992471	Staphylococcus aureus isolate 17_LA_343 chromosome I	2	753569-753677	2	CRISPRCasFinder	no		cas3,DEDDh,DinG,csa3,TnsE_C,WYL	Orphan	AAAGGAACGCAGTTGGATGCTACCGCACAACTGCATAAA	39	0	0	NA	NA	NA	1	1	Orphan	cas3,DEDDh,DinG,csa3,TnsE_C,WYL	NA,NA|169aa|down_4|NZ_LT992471.1_757410_757917_+,NA|239aa|down_5|NZ_LT992471.1_758078_758795_+	NA|209aa|up_9|NZ_LT992471.1_743073_743700_+	pfam04276, DUF443, Protein of unknown function (DUF443)	NA|313aa|up_8|NZ_LT992471.1_743969_744908_+	cd19083, AKR_AKR11A1_11D1, AKR11A and  AKR11D families of aldo-keto reductase (AKR)	NA|179aa|up_7|NZ_LT992471.1_745353_745890_+	COG0655, WrbA, Multimeric flavodoxin WrbA [General function prediction only]	NA|159aa|up_6|NZ_LT992471.1_746059_746536_+	pfam00583, Acetyltransf_1, Acetyltransferase (GNAT) family	NA|432aa|up_5|NZ_LT992471.1_746575_747871_+	COG1078, COG1078, HD superfamily phosphohydrolases [General function prediction only]	NA|174aa|up_4|NZ_LT992471.1_747898_748420_+	pfam08741, YwhD, YwhD family	NA|337aa|up_3|NZ_LT992471.1_748918_749929_+	PRK09422, PRK09422, ethanol-active dehydrogenase/acetaldehyde-active reductase; Provisional	NA|139aa|up_2|NZ_LT992471.1_750204_750621_+	COG4506, COG4506, Uncharacterized protein conserved in bacteria [Function unknown]	NA|554aa|up_1|NZ_LT992471.1_750617_752279_+	PRK01611, argS, arginyl-tRNA synthetase; Reviewed	NA|212aa|up_0|NZ_LT992471.1_752763_753399_+	COG2231, COG2231, Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]	NA|296aa|down_0|NZ_LT992471.1_753728_754616_+	cd01143, YvrC, Periplasmic binding protein YvrC	NA|317aa|down_1|NZ_LT992471.1_754766_755717_+	pfam01032, FecCD, FecCD transport family	NA|240aa|down_2|NZ_LT992471.1_755771_756491_+	COG1011, COG1011, Predicted hydrolase (HAD superfamily) [General function prediction only]	NA|267aa|down_3|NZ_LT992471.1_756474_757275_+	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|169aa|down_4|NZ_LT992471.1_757410_757917_+	NA	NA|239aa|down_5|NZ_LT992471.1_758078_758795_+	NA	NA|263aa|down_6|NZ_LT992471.1_758963_759752_+	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|125aa|down_7|NZ_LT992471.1_760003_760378_-	TIGR01889, Pleiotropic_Regulator_Of_Virulence, staphylococcal accessory regulator family	NA|310aa|down_8|NZ_LT992471.1_761325_762255_-	COG3238, COG3238, Uncharacterized protein conserved in bacteria [Function unknown]	NA|75aa|down_9|NZ_LT992471.1_762447_762672_-	pfam11148, DUF2922, Protein of unknown function (DUF2922)
GCF_900324345.1_17_LA_343	NZ_LT992471	Staphylococcus aureus isolate 17_LA_343 chromosome I	3	915579-915661	3	CRISPRCasFinder	no		cas3,DEDDh,DinG,csa3,TnsE_C,WYL	Orphan	CACCCCAACTCGCATTGCTTGTAGAA	26	1	25	915605-915635|915605-915635|915605-915635|915605-915635|915605-915635|915605-915635|915605-915635|915605-915635|915605-915635|915605-915635|915605-915635|915605-915635|915605-915635|915605-915635|915605-915635|915605-915635|915605-915635|915605-915635|915605-915635|915605-915635|915605-915635|915605-915635|915605-915635|915605-915635|915605-915635	NZ_LT992471.1_1053541-1053511|NZ_LT992471.1_1092342-1092372|NZ_LT992471.1_2085146-2085176|NZ_LT992471.1_2085256-2085286|NZ_LT992471.1_2200151-2200181|NZ_LT992471.1_318310-318340|NZ_LT992471.1_318368-318398|NZ_LT992471.1_459153-459123|NZ_LT992471.1_745066-745036|NZ_LT992471.1_869292-869262|NZ_LT992471.1_1004172-1004202|NZ_LT992471.1_1186641-1186671|NZ_LT992471.1_1286959-1286929|NZ_LT992471.1_1287013-1286983|NZ_LT992471.1_1894055-1894025|NZ_LT992471.1_1984721-1984691|NZ_LT992471.1_2449370-2449400|NZ_LT992471.1_2494493-2494463|NZ_LT992471.1_924586-924616|NZ_LT992471.1_1008310-1008280|NZ_LT992471.1_1498561-1498591|NZ_LT992471.1_1547315-1547345|NZ_LT992471.1_2460118-2460148|NZ_LT992471.1_2460173-2460203|NZ_LT992471.1_2895545-2895575	NA	1	1	Orphan	cas3,DEDDh,DinG,csa3,TnsE_C,WYL	NA,NA	NA|280aa|up_9|NZ_LT992471.1_902828_903668_+	COG3942, COG3942, Surface antigen [General function prediction only]	NA|217aa|up_8|NZ_LT992471.1_903841_904492_+	pfam12917, HD_2, HD containing hydrolase-like enzyme	NA|79aa|up_7|NZ_LT992471.1_904488_904725_+	COG4897, CsbA, Uncharacterized protein conserved in bacteria [Function unknown]	NA|662aa|up_6|NZ_LT992471.1_904993_906979_+	PRK05298, PRK05298, excinuclease ABC subunit UvrB	NA|949aa|up_5|NZ_LT992471.1_906986_909833_+	PRK00349, uvrA, excinuclease ABC subunit UvrA	NA|311aa|up_4|NZ_LT992471.1_910442_911375_+	PRK05428, PRK05428, HPr kinase/phosphorylase; Provisional	NA|280aa|up_3|NZ_LT992471.1_911380_912220_+	PRK12437, PRK12437, prolipoprotein diacylglyceryl transferase; Reviewed	NA|162aa|up_2|NZ_LT992471.1_912227_912713_+	cd04647, LbH_MAT_like, Maltose O-acyltransferase (MAT)-like: This family is composed of maltose O-acetyltransferase, galactoside O-acetyltransferase (GAT), xenobiotic acyltransferase (XAT) and similar proteins	NA|480aa|up_1|NZ_LT992471.1_912720_914160_+	sd00006, TPR, Tetratricopeptide repeat	NA|312aa|up_0|NZ_LT992471.1_914226_915162_+	TIGR01292, Thioredoxin_reductase, thioredoxin-disulfide reductase	NA|304aa|down_0|NZ_LT992471.1_915929_916841_+	COG1660, COG1660, Predicted P-loop-containing kinase [General function prediction only]	NA|332aa|down_1|NZ_LT992471.1_916837_917833_+	TIGR01826, Putative_gluconeogenesis_factor, conserved hypothetical protein, cofD-related	NA|315aa|down_2|NZ_LT992471.1_917941_918886_+	TIGR00647, DNA_bind_WhiA, DNA-binding protein WhiA	NA|196aa|down_3|NZ_LT992471.1_919455_920043_+	PRK00277, clpP, ATP-dependent Clp protease proteolytic subunit; Reviewed	NA|545aa|down_4|NZ_LT992471.1_920225_921860_+	PRK13529, PRK13529, oxaloacetate-decarboxylating malate dehydrogenase	NA|301aa|down_5|NZ_LT992471.1_922066_922969_-	COG1090, COG1090, Predicted nucleoside-diphosphate sugar epimerase [General function prediction only]	NA|210aa|down_6|NZ_LT992471.1_923671_924301_+	PRK00409, PRK00409, recombination and DNA strand exchange inhibitor protein; Reviewed	NA|338aa|down_7|NZ_LT992471.1_925075_926089_+	COG2390, DeoR, Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]	NA|337aa|down_8|NZ_LT992471.1_926141_927152_+	TIGR01534, Glyceraldehyde-3-phosphate_dehydrogenase, glyceraldehyde-3-phosphate dehydrogenase, type I	NA|397aa|down_9|NZ_LT992471.1_927290_928481_+	PRK00073, pgk, phosphoglycerate kinase; Provisional
GCF_900324345.1_17_LA_343	NZ_LT992471	Staphylococcus aureus isolate 17_LA_343 chromosome I	4	1008579-1008659	4	CRISPRCasFinder	no		cas3,DEDDh,DinG,csa3,TnsE_C,WYL	Orphan	TCTTTATCATTTCTGTCCCACTCCC	25	1	1	1008604-1008634	NZ_LT992471.1_910032-910002	NA	1	1	Orphan	cas3,DEDDh,DinG,csa3,TnsE_C,WYL	NA,NA|105aa|down_7|NZ_LT992471.1_1016265_1016580_-	NA|180aa|up_9|NZ_LT992471.1_1000709_1001249_+	cd02135, YdjA-like, nitroreductase family protein similar to Escherichia coli YdjA	NA|107aa|up_8|NZ_LT992471.1_1001398_1001719_-	cd02947, TRX_family, TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a TRX domain; and Group II, which are composed of fusion proteins of TRX and additional domains	NA|119aa|up_7|NZ_LT992471.1_1001862_1002219_+	cd03036, ArsC_like, Arsenate Reductase (ArsC) family, unknown subfamily; uncharacterized proteins containing a CXXC motif with similarity to thioredoxin (TRX)-fold arsenic reductases, ArsC	NA|127aa|up_6|NZ_LT992471.1_1002376_1002757_+	PRK01202, PRK01202, glycine cleavage system protein GcvH	NA|293aa|up_5|NZ_LT992471.1_1002936_1003815_+	COG3878, COG3878, Uncharacterized protein conserved in bacteria [Function unknown]	NA|129aa|up_4|NZ_LT992471.1_1004516_1004903_+	COG1658, COG1658, Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]	NA|99aa|up_3|NZ_LT992471.1_1004895_1005192_+	cd02947, TRX_family, TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a TRX domain; and Group II, which are composed of fusion proteins of TRX and additional domains	NA|342aa|up_2|NZ_LT992471.1_1005441_1006467_+	COG1135, AbcC, ABC-type metal ion transport system, ATPase component [Inorganic ion transport and metabolism]	NA|232aa|up_1|NZ_LT992471.1_1006459_1007155_+	COG2011, AbcD, ABC-type metal ion transport system, permease component [Inorganic ion transport and metabolism]	NA|274aa|up_0|NZ_LT992471.1_1007172_1007994_+	COG1464, NlpA, ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]	NA|65aa|down_0|NZ_LT992471.1_1008801_1008996_+	COG3237, COG3237, Uncharacterized protein conserved in bacteria [Function unknown]	NA|284aa|down_1|NZ_LT992471.1_1009229_1010081_-	COG2035, COG2035, Predicted membrane protein [Function unknown]	NA|254aa|down_2|NZ_LT992471.1_1010408_1011170_+	COG0396, sufC, Cysteine desulfurase activator ATPase [Posttranslational modification, protein turnover, chaperones]	NA|436aa|down_3|NZ_LT992471.1_1011268_1012576_+	COG0719, SufB, Cysteine desulfurase activator SufB [Posttranslational modification, protein turnover, chaperones]	NA|417aa|down_4|NZ_LT992471.1_1012681_1013932_+	TIGR01979, Probable_cysteine_desulfurase, cysteine desulfurases, SufSfamily	NA|155aa|down_5|NZ_LT992471.1_1013921_1014386_+	TIGR01994, Iron-sulfur_cluster_assembly_scaffold_protein_IscU, SUF system FeS assembly protein, NifU family	NA|466aa|down_6|NZ_LT992471.1_1014536_1015934_+	TIGR01980, UPF0051_protein_slr0074, FeS assembly protein SufB	NA|105aa|down_7|NZ_LT992471.1_1016265_1016580_-	NA	NA|347aa|down_8|NZ_LT992471.1_1016948_1017989_+	COG4536, CorB, Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]	NA|356aa|down_9|NZ_LT992471.1_1018002_1019070_+	COG2070, COG2070, Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]
GCF_900324345.1_17_LA_343	NZ_LT992471	Staphylococcus aureus isolate 17_LA_343 chromosome I	5	1896370-1896454	5	CRISPRCasFinder	no		cas3,DEDDh,DinG,csa3,TnsE_C,WYL	Orphan	AGAAGCTGACGGAAAAGTCAGCTTACA	27	0	0	NA	NA	NA	1	1	Orphan	cas3,DEDDh,DinG,csa3,TnsE_C,WYL	NA,NA	NA|454aa|up_9|NZ_LT992471.1_1881321_1882683_+	COG1113, AnsP, Gamma-aminobutyrate permease and related permeases [Amino acid transport and metabolism]	NA|586aa|up_8|NZ_LT992471.1_1883026_1884784_-	PRK06354, PRK06354, pyruvate kinase; Provisional	NA|323aa|up_7|NZ_LT992471.1_1884805_1885774_-	PRK03202, PRK03202, ATP-dependent 6-phosphofructokinase	NA|315aa|up_6|NZ_LT992471.1_1886042_1886987_-	PRK05724, PRK05724, acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated	NA|286aa|up_5|NZ_LT992471.1_1886986_1887844_-	PRK05654, PRK05654, acetyl-CoA carboxylase carboxyltransferase subunit beta	NA|410aa|up_4|NZ_LT992471.1_1888038_1889268_-	PRK07232, PRK07232, bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed	NA|1066aa|up_3|NZ_LT992471.1_1889716_1892914_-	COG0587, DnaE, DNA polymerase III, alpha subunit [DNA replication, recombination, and repair]	NA|314aa|up_2|NZ_LT992471.1_1892934_1893876_-	COG0618, COG0618, Exopolyphosphatase-related proteins [General function prediction only]	NA|433aa|up_1|NZ_LT992471.1_1894244_1895543_-	COG4109, COG4109, Predicted transcriptional regulator containing CBS domains [Transcription]	NA|138aa|up_0|NZ_LT992471.1_1895747_1896161_+	pfam00582, Usp, Universal stress protein family	NA|230aa|down_0|NZ_LT992471.1_1896550_1897240_-	PRK00685, PRK00685, metal-dependent hydrolase; Provisional	NA|352aa|down_1|NZ_LT992471.1_1897414_1898470_+	COG0006, PepP, Xaa-Pro aminopeptidase [Amino acid transport and metabolism]	NA|373aa|down_2|NZ_LT992471.1_1898785_1899904_-	cd05305, L-AlaDH, Alanine dehydrogenase NAD-binding and catalytic domains	NA|167aa|down_3|NZ_LT992471.1_1900044_1900545_+	pfam00582, Usp, Universal stress protein family	NA|401aa|down_4|NZ_LT992471.1_1900791_1901994_-	PRK00180, PRK00180, acetate kinase A/propionate kinase 2; Reviewed	NA|316aa|down_5|NZ_LT992471.1_1902081_1903029_-	COG0827, COG0827, Adenine-specific DNA methylase [DNA replication, recombination, and repair]	NA|165aa|down_6|NZ_LT992471.1_1903151_1903646_-	PRK00522, tpx, thiol peroxidase	NA|257aa|down_7|NZ_LT992471.1_1903743_1904514_-	PRK10621, PRK10621, hypothetical protein; Provisional	NA|408aa|down_8|NZ_LT992471.1_1904557_1905781_-	PRK01565, PRK01565, thiamine biosynthesis protein ThiI; Provisional	NA|383aa|down_9|NZ_LT992471.1_1905780_1906929_-	COG1104, NifS, Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]
GCF_900324345.1_17_LA_343	NZ_LT992471	Staphylococcus aureus isolate 17_LA_343 chromosome I	6	1984730-1984823	6	CRISPRCasFinder	no	csa3	cas3,DEDDh,DinG,csa3,TnsE_C,WYL	Type I-A	GCAATGCGCGTTGGGGTGTGGGGCCCCAACATAG	34	1	1	1984764-1984789	NZ_LT992471.1_2085218-2085193	NA	1	1	Orphan	cas3,DEDDh,DinG,csa3,TnsE_C,WYL	NA|75aa|up_5|NZ_LT992471.1_1980823_1981048_-,NA|148aa|up_2|NZ_LT992471.1_1982259_1982703_-,NA|101aa|down_1|NZ_LT992471.1_1985957_1986260_+	NA|501aa|up_9|NZ_LT992471.1_1975847_1977350_-	COG4529, COG4529, Uncharacterized protein conserved in bacteria [Function unknown]	csa3|105aa|up_8|NZ_LT992471.1_1978000_1978315_+	cd00090, HTH_ARSR, Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors	NA|431aa|up_7|NZ_LT992471.1_1978314_1979607_+	PRK15445, PRK15445, arsenical efflux pump membrane protein ArsB	NA|285aa|up_6|NZ_LT992471.1_1979693_1980548_-	COG4193, LytD, Beta- N-acetylglucosaminidase [Carbohydrate transport and metabolism]	NA|75aa|up_5|NZ_LT992471.1_1980823_1981048_-	NA	NA|157aa|up_4|NZ_LT992471.1_1981246_1981717_+	COG1595, RpoE, DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]	NA|148aa|up_3|NZ_LT992471.1_1981829_1982273_+	pfam06338, ComK, ComK protein	NA|148aa|up_2|NZ_LT992471.1_1982259_1982703_-	NA	NA|212aa|up_1|NZ_LT992471.1_1983000_1983636_+	pfam02517, Abi, CAAX protease self-immunity	NA|207aa|up_0|NZ_LT992471.1_1983802_1984423_+	pfam02517, Abi, CAAX protease self-immunity	NA|238aa|down_0|NZ_LT992471.1_1984985_1985699_-	PRK12376, PRK12376, putative translaldolase; Provisional	NA|101aa|down_1|NZ_LT992471.1_1985957_1986260_+	NA	NA|122aa|down_2|NZ_LT992471.1_1986514_1986880_+	PRK14201, PRK14201, fluoride efflux transporter CrcB	NA|118aa|down_3|NZ_LT992471.1_1986876_1987230_+	COG0239, CrcB, Integral membrane protein possibly involved in chromosome condensation [Cell division and chromosome partitioning]	NA|278aa|down_4|NZ_LT992471.1_1987479_1988313_-	COG0656, ARA1, Aldo/keto reductases, related to diketogulonate reductase [General function prediction only]	NA|303aa|down_5|NZ_LT992471.1_1988524_1989433_-	pfam08378, NERD, Nuclease-related domain	NA|398aa|down_6|NZ_LT992471.1_1989557_1990751_-	PRK05250, PRK05250, S-adenosylmethionine synthetase; Validated	NA|531aa|down_7|NZ_LT992471.1_1991122_1992715_+	cd00484, PEPCK_ATP, Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis	NA|249aa|down_8|NZ_LT992471.1_1993011_1993758_-	COG1506, DAP2, Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]	NA|158aa|down_9|NZ_LT992471.1_1993762_1994236_-	TIGR02705, conserved_hypothetical_protein, nucleoside triphosphatase YtkD
GCF_900324345.1_17_LA_343	NZ_LT992471	Staphylococcus aureus isolate 17_LA_343 chromosome I	7	2274873-2275085	7	CRISPRCasFinder	no		cas3,DEDDh,DinG,csa3,TnsE_C,WYL	Orphan	TGATGTGCTGTTGTGGAAGCTTGGTGTCGTGCCATGCTACTTTGATG	47	0	0	NA	NA	NA	2	2	Orphan	cas3,DEDDh,DinG,csa3,TnsE_C,WYL	NA|46aa|up_4|NZ_LT992471.1_2271734_2271872_-,NA|107aa|down_0|NZ_LT992471.1_2275118_2275439_+	NA|232aa|up_9|NZ_LT992471.1_2264426_2265122_+	COG0745, OmpR, Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]	NA|507aa|up_8|NZ_LT992471.1_2265474_2266995_-	COG0513, SrmB, Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]	NA|452aa|up_7|NZ_LT992471.1_2267510_2268866_-	COG0770, MurF, UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]	NA|357aa|up_6|NZ_LT992471.1_2268880_2269951_-	PRK01966, ddl, D-alanine--D-alanine ligase	NA|401aa|up_5|NZ_LT992471.1_2270268_2271471_+	TIGR02210, Rod_shape-determining_protein_RodA, rod shape-determining protein RodA	NA|46aa|up_4|NZ_LT992471.1_2271734_2271872_-	NA	NA|70aa|up_3|NZ_LT992471.1_2271999_2272209_-	cd00371, HMA, Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones	NA|98aa|up_2|NZ_LT992471.1_2272220_2272514_-	cd10152, SaCsoR-like_DUF156, Staphylococcus aureus copper-sensitive operon repressor (CsoR), and related domains; this family was previously known as part of DUF156	NA|495aa|up_1|NZ_LT992471.1_2272679_2274164_+	TIGR04265, bac_cardiolipin, cardiolipin synthase	NA|216aa|up_0|NZ_LT992471.1_2274191_2274839_+	COG1418, COG1418, Predicted HD superfamily hydrolase [General function prediction only]	NA|107aa|down_0|NZ_LT992471.1_2275118_2275439_+	NA	NA|291aa|down_1|NZ_LT992471.1_2277080_2277953_-	PRK02463, PRK02463, OxaA-like protein precursor; Provisional	NA|214aa|down_2|NZ_LT992471.1_2278038_2278680_-	PRK00043, thiE, thiamine phosphate synthase	NA|264aa|down_3|NZ_LT992471.1_2278681_2279473_-	PRK09355, PRK09355, hydroxyethylthiazole kinase; Validated	NA|277aa|down_4|NZ_LT992471.1_2279456_2280287_-	PRK06427, PRK06427, bifunctional hydroxy-methylpyrimidine kinase/ hydroxy-phosphomethylpyrimidine kinase; Reviewed	NA|230aa|down_5|NZ_LT992471.1_2280279_2280969_-	TIGR04306, salvage_TenA, thiaminase II	NA|232aa|down_6|NZ_LT992471.1_2281355_2282051_-	pfam06737, Transglycosylas, Transglycosylase-like domain	NA|132aa|down_7|NZ_LT992471.1_2282439_2282835_-	pfam00436, SSB, Single-strand binding protein family	NA|147aa|down_8|NZ_LT992471.1_2283028_2283469_+	pfam14183, YwpF, YwpF-like protein	NA|147aa|down_9|NZ_LT992471.1_2283525_2283966_-	PRK00006, fabZ, 3-hydroxyacyl-ACP dehydratase FabZ
GCF_900324345.1_17_LA_343	NZ_LT992471	Staphylococcus aureus isolate 17_LA_343 chromosome I	8	2330504-2330654	8	CRISPRCasFinder	no	csa3,TnsE_C	cas3,DEDDh,DinG,csa3,TnsE_C,WYL	Type I-A	AACTTTAGTTGTTAGGGGCTCTTATGCA	28	0	0	NA	NA	NA	2	2	Orphan	cas3,DEDDh,DinG,csa3,TnsE_C,WYL	NA|77aa|up_5|NZ_LT992471.1_2325376_2325607_-,NA|364aa|up_0|NZ_LT992471.1_2329394_2330486_+,NA|35aa|down_0|NZ_LT992471.1_2330983_2331088_-,NA|53aa|down_1|NZ_LT992471.1_2331767_2331926_+,NA|31aa|down_2|NZ_LT992471.1_2332361_2332454_+	NA|237aa|up_9|NZ_LT992471.1_2320986_2321697_+	PRK05819, deoD, DeoD-type purine-nucleoside phosphorylase	NA|148aa|up_8|NZ_LT992471.1_2321817_2322261_-	COG0783, Dps, DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]	NA|138aa|up_7|NZ_LT992471.1_2322460_2322874_-	COG3011, COG3011, Predicted thiol-disulfide oxidoreductase [General function    prediction only]	NA|458aa|up_6|NZ_LT992471.1_2323331_2324705_-	pfam01878, EVE, EVE domain	NA|77aa|up_5|NZ_LT992471.1_2325376_2325607_-	NA	NA|313aa|up_4|NZ_LT992471.1_2325637_2326576_-	COG1482, ManA, Phosphomannose isomerase [Carbohydrate transport and metabolism]	NA|222aa|up_3|NZ_LT992471.1_2327009_2327675_-	cd05243, SDR_a5, atypical (a) SDRs, subgroup 5	csa3|107aa|up_2|NZ_LT992471.1_2327826_2328147_+	cd00090, HTH_ARSR, Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors	NA|327aa|up_1|NZ_LT992471.1_2328148_2329129_+	COG1230, CzcD, Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]	NA|364aa|up_0|NZ_LT992471.1_2329394_2330486_+	NA	NA|35aa|down_0|NZ_LT992471.1_2330983_2331088_-	NA	NA|53aa|down_1|NZ_LT992471.1_2331767_2331926_+	NA	NA|31aa|down_2|NZ_LT992471.1_2332361_2332454_+	NA	NA|286aa|down_3|NZ_LT992471.1_2332583_2333441_-	COG0561, Cof, Predicted hydrolases of the HAD superfamily [General function prediction only]	NA|261aa|down_4|NZ_LT992471.1_2333508_2334291_-	COG1119, ModF, ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA [Inorganic ion transport and metabolism]	NA|203aa|down_5|NZ_LT992471.1_2334580_2335189_-	pfam08937, DUF1863, MTH538 TIR-like domain (DUF1863)	NA|345aa|down_6|NZ_LT992471.1_2335216_2336251_-	pfam13676, TIR_2, TIR domain	NA|490aa|down_7|NZ_LT992471.1_2336344_2337814_-	pfam18185, STALD, Sir2- and TIR-associating SLOG family	NA|97aa|down_8|NZ_LT992471.1_2337873_2338164_-	pfam11867, DUF3387, Domain of unknown function (DUF3387)	TnsE_C|135aa|down_9|NZ_LT992471.1_2338288_2338693_-	pfam18623, TnsE_C, TnsE C-terminal domain
GCF_900324345.1_17_LA_343	NZ_LT992471	Staphylococcus aureus isolate 17_LA_343 chromosome I	9	2494545-2494630	9	CRISPRCasFinder	no	WYL	cas3,DEDDh,DinG,csa3,TnsE_C,WYL	Unclear	AAAGTCAGCTTACAATAATGTGCAAGTTGG	30	1	7	2494575-2494600|2494575-2494600|2494575-2494600|2494575-2494600|2494575-2494600|2494575-2494600|2494575-2494600	NZ_LT992471.1_1769901-1769876|NZ_LT992471.1_1004261-1004236|NZ_LT992471.1_1008381-1008406|NZ_LT992471.1_1053316-1053341|NZ_LT992471.1_1494232-1494257|NZ_LT992471.1_2285985-2286010|NZ_LT992471.1_2626422-2626397	NA	1	1	Orphan	cas3,DEDDh,DinG,csa3,TnsE_C,WYL	NA|65aa|up_6|NZ_LT992471.1_2487289_2487484_-,NA|78aa|down_1|NZ_LT992471.1_2495580_2495814_-,NA|110aa|down_8|NZ_LT992471.1_2503902_2504232_+	NA|248aa|up_9|NZ_LT992471.1_2483078_2483822_-	TIGR01889, Pleiotropic_Regulator_Of_Virulence, staphylococcal accessory regulator family	NA|652aa|up_8|NZ_LT992471.1_2483847_2485803_-	COG2207, AraC, AraC-type DNA-binding domain-containing proteins [Transcription]	NA|270aa|up_7|NZ_LT992471.1_2486411_2487221_+	COG3942, COG3942, Surface antigen [General function prediction only]	NA|65aa|up_6|NZ_LT992471.1_2487289_2487484_-	NA	NA|467aa|up_5|NZ_LT992471.1_2487657_2489058_-	TIGR00931, Uncharacterized_Na+/H+_antiporter_HI_1107, Na+/H+ antiporter NhaC	NA|361aa|up_4|NZ_LT992471.1_2489152_2490235_-	pfam02317, Octopine_DH, NAD/NADP octopine/nopaline dehydrogenase, alpha-helical domain	NA|141aa|up_3|NZ_LT992471.1_2490482_2490905_+	COG3296, COG3296, Uncharacterized protein conserved in bacteria [Function unknown]	NA|167aa|up_2|NZ_LT992471.1_2491141_2491642_+	COG3942, COG3942, Surface antigen [General function prediction only]	NA|318aa|up_1|NZ_LT992471.1_2492004_2492958_+	cd12178, 2-Hacid_dh_13, Putative D-isomer specific 2-hydroxyacid dehydrogenases, NAD-binding and catalytic domains	NA|375aa|up_0|NZ_LT992471.1_2493049_2494174_-	PRK06753, PRK06753, hypothetical protein; Provisional	NA|259aa|down_0|NZ_LT992471.1_2494782_2495559_-	COG4193, LytD, Beta- N-acetylglucosaminidase [Carbohydrate transport and metabolism]	NA|78aa|down_1|NZ_LT992471.1_2495580_2495814_-	NA	NA|158aa|down_2|NZ_LT992471.1_2496108_2496582_-	COG2427, COG2427, Uncharacterized conserved protein [Function unknown]	NA|985aa|down_3|NZ_LT992471.1_2496581_2499536_-	COG3383, COG3383, Uncharacterized anaerobic dehydrogenase [General function prediction only]	NA|316aa|down_4|NZ_LT992471.1_2500137_2501085_-	PRK09379, PRK09379, LytR family transcriptional regulator	NA|266aa|down_5|NZ_LT992471.1_2501217_2502015_-	COG0483, SuhB, Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]	WYL|231aa|down_6|NZ_LT992471.1_2502399_2503092_+	COG2378, COG2378, Predicted transcriptional regulator [Transcription]	NA|246aa|down_7|NZ_LT992471.1_2503116_2503854_-	pfam02517, Abi, CAAX protease self-immunity	NA|110aa|down_8|NZ_LT992471.1_2503902_2504232_+	NA	NA|291aa|down_9|NZ_LT992471.1_2504676_2505549_+	COG1737, RpiR, Transcriptional regulators [Transcription]
GCF_900324345.1_17_LA_343	NZ_LT992471	Staphylococcus aureus isolate 17_LA_343 chromosome I	10	2610961-2611055	10	CRISPRCasFinder	no		cas3,DEDDh,DinG,csa3,TnsE_C,WYL	Orphan	TTCTTCAAATTTATTTGTTAGAAAGGC	27	0	0	NA	NA	NA	1	1	Orphan	cas3,DEDDh,DinG,csa3,TnsE_C,WYL	NA|35aa|up_2|NZ_LT992471.1_2608681_2608786_+,NA|40aa|down_0|NZ_LT992471.1_2611233_2611353_-	NA|200aa|up_9|NZ_LT992471.1_2602158_2602758_-	COG1651, DsbG, Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]	NA|121aa|up_8|NZ_LT992471.1_2602776_2603139_-	pfam14729, DUF4467, Domain of unknown function with cystatin-like fold (DUF4467)	NA|417aa|up_7|NZ_LT992471.1_2603393_2604644_+	pfam02388, FemAB, FemAB family	NA|244aa|up_6|NZ_LT992471.1_2604740_2605472_-	COG1126, GlnQ, ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]	NA|240aa|up_5|NZ_LT992471.1_2605468_2606188_-	COG0765, HisM, ABC-type amino acid transport system, permease component [Amino acid transport and metabolism]	NA|260aa|up_4|NZ_LT992471.1_2606168_2606948_-	cd13711, PBP2_Ngo0372_TcyA, Substrate binding domain of ABC transporters involved in cystine import; the type 2 periplasmic binding protein fold	NA|480aa|up_3|NZ_LT992471.1_2607068_2608508_-	TIGR00711, Uncharacterized_MFS-type_transporter_YhcA, drug resistance transporter, EmrB/QacA subfamily	NA|35aa|up_2|NZ_LT992471.1_2608681_2608786_+	NA	NA|229aa|up_1|NZ_LT992471.1_2608939_2609626_-	PRK14119, gpmA, phosphoglyceromutase; Provisional	NA|289aa|up_0|NZ_LT992471.1_2609952_2610819_-	COG0053, MMT1, Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]	NA|40aa|down_0|NZ_LT992471.1_2611233_2611353_-	NA	NA|437aa|down_1|NZ_LT992471.1_2611447_2612758_+	pfam11621, Sbi-IV, C3 binding domain 4 of IgG-bind protein SBI	NA|310aa|down_2|NZ_LT992471.1_2613293_2614223_+	pfam07968, Leukocidin, Leukocidin/Hemolysin toxin family	NA|316aa|down_3|NZ_LT992471.1_2614790_2615738_+	pfam07968, Leukocidin, Leukocidin/Hemolysin toxin family	NA|326aa|down_4|NZ_LT992471.1_2615739_2616717_+	TIGR01002, synergohymenotropic_toxin, beta-channel forming cytolysin	NA|156aa|down_5|NZ_LT992471.1_2616768_2617236_-	pfam06177, QueT, QueT transporter	NA|231aa|down_6|NZ_LT992471.1_2617246_2617939_-	COG1424, BioW, Pimeloyl-CoA synthetase [Coenzyme metabolism]	NA|372aa|down_7|NZ_LT992471.1_2617949_2619065_-	COG0156, BioF, 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]	NA|336aa|down_8|NZ_LT992471.1_2619042_2620050_-	PRK06256, PRK06256, biotin synthase; Validated	NA|453aa|down_9|NZ_LT992471.1_2620051_2621410_-	TIGR00508, hypothetical_protein_DESPIG_00326, adenosylmethionine-8-amino-7-oxononanoate transaminase
GCF_900324345.1_17_LA_343	NZ_LT992471	Staphylococcus aureus isolate 17_LA_343 chromosome I	11	2670685-2670779	11	CRISPRCasFinder	no		cas3,DEDDh,DinG,csa3,TnsE_C,WYL	Orphan	AGGCTCTTATGCAGTTGGTGCGAAGCAA	28	0	0	NA	NA	NA	1	1	Orphan	cas3,DEDDh,DinG,csa3,TnsE_C,WYL	NA|249aa|up_8|NZ_LT992471.1_2660271_2661018_+,NA|121aa|down_0|NZ_LT992471.1_2671447_2671810_-,NA|105aa|down_8|NZ_LT992471.1_2678622_2678937_+	NA|526aa|up_9|NZ_LT992471.1_2658499_2660077_-	COG0069, GltB, Glutamate synthase domain 2 [Amino acid transport and metabolism]	NA|249aa|up_8|NZ_LT992471.1_2660271_2661018_+	NA	NA|250aa|up_7|NZ_LT992471.1_2662445_2663195_-	COG1124, DppF, ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]	NA|272aa|up_6|NZ_LT992471.1_2663187_2664003_-	COG0444, DppD, ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]	NA|290aa|up_5|NZ_LT992471.1_2663999_2664869_-	COG1173, DppC, ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]	NA|312aa|up_4|NZ_LT992471.1_2664865_2665801_-	COG0601, DppB, ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]	NA|533aa|up_3|NZ_LT992471.1_2665813_2667412_-	TIGR02294, Nickel-binding_periplasmic_protein, nickel ABC transporter, nickel/metallophore periplasmic binding protein	NA|434aa|up_2|NZ_LT992471.1_2667554_2668856_-	COG4408, COG4408, Uncharacterized protein conserved in bacteria [Function unknown]	NA|273aa|up_1|NZ_LT992471.1_2668848_2669667_-	cd08261, Zn_ADH7, Alcohol dehydrogenases of the MDR family	NA|274aa|up_0|NZ_LT992471.1_2669677_2670499_-	COG0253, DapF, Diaminopimelate epimerase [Amino acid transport and metabolism]	NA|121aa|down_0|NZ_LT992471.1_2671447_2671810_-	NA	NA|273aa|down_1|NZ_LT992471.1_2672072_2672891_-	PRK08589, PRK08589, SDR family oxidoreductase	NA|513aa|down_2|NZ_LT992471.1_2673124_2674663_+	pfam03806, ABG_transport, AbgT putative transporter family	NA|141aa|down_3|NZ_LT992471.1_2674774_2675197_-	COG2128, COG2128, Uncharacterized conserved protein [Function unknown]	NA|133aa|down_4|NZ_LT992471.1_2675668_2676067_-	pfam07252, DUF1433, Protein of unknown function (DUF1433)	NA|137aa|down_5|NZ_LT992471.1_2676093_2676504_-	pfam07252, DUF1433, Protein of unknown function (DUF1433)	NA|128aa|down_6|NZ_LT992471.1_2676958_2677342_-	pfam07252, DUF1433, Protein of unknown function (DUF1433)	NA|403aa|down_7|NZ_LT992471.1_2677408_2678617_+	cd07657, F-BAR_Fes_Fer, The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Fes (feline sarcoma) and Fer (Fes related) tyrosine kinases	NA|105aa|down_8|NZ_LT992471.1_2678622_2678937_+	NA	NA|140aa|down_9|NZ_LT992471.1_2680812_2681232_-	pfam07252, DUF1433, Protein of unknown function (DUF1433)
GCF_900324345.1_17_LA_343	NZ_LT992471	Staphylococcus aureus isolate 17_LA_343 chromosome I	12	2698629-2698739	12	CRISPRCasFinder	no		cas3,DEDDh,DinG,csa3,TnsE_C,WYL	Orphan	GGTACTTCTGGTGTCGGTGGCGTTGGT	27	0	0	NA	NA	NA	1	1	Orphan	cas3,DEDDh,DinG,csa3,TnsE_C,WYL	NA|89aa|up_2|NZ_LT992471.1_2692932_2693199_+,NA|103aa|up_1|NZ_LT992471.1_2693342_2693651_+,NA	NA|452aa|up_9|NZ_LT992471.1_2684326_2685682_-	cd00519, Lipase_3, Lipase (class 3)	NA|262aa|up_8|NZ_LT992471.1_2685678_2686464_-	pfam04507, DUF576, Csa1 family	NA|255aa|up_7|NZ_LT992471.1_2686711_2687476_-	pfam04507, DUF576, Csa1 family	NA|258aa|up_6|NZ_LT992471.1_2687587_2688361_-	pfam04507, DUF576, Csa1 family	NA|310aa|up_5|NZ_LT992471.1_2688603_2689533_-	pfam09019, EcoRII-C, EcoRII C terminal	NA|398aa|up_4|NZ_LT992471.1_2689628_2690822_+	TIGR00675, Modification_methylase, DNA-methyltransferase (dcm)	NA|584aa|up_3|NZ_LT992471.1_2690897_2692649_+	cd05799, PGM2, This CD includes PGM2 (phosphoglucomutase 2) and PGM2L1 (phosphoglucomutase 2-like 1)	NA|89aa|up_2|NZ_LT992471.1_2692932_2693199_+	NA	NA|103aa|up_1|NZ_LT992471.1_2693342_2693651_+	NA	NA|289aa|up_0|NZ_LT992471.1_2693776_2694643_-	COG1210, GalU, UDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]	NA|453aa|down_0|NZ_LT992471.1_2701879_2703238_-	TIGR00791, Gluconate_permease, gluconate transporter	NA|518aa|down_1|NZ_LT992471.1_2703354_2704908_-	TIGR01314, gntK_FGGY, gluconate kinase, FGGY type	NA|226aa|down_2|NZ_LT992471.1_2704932_2705610_-	COG1802, GntR, Transcriptional regulators [Transcription]	NA|255aa|down_3|NZ_LT992471.1_2705766_2706531_-	cd01106, HTH_TipAL-Mta, Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA	NA|231aa|down_4|NZ_LT992471.1_2706695_2707388_-	COG2357, COG2357, PpGpp synthetase catalytic domain [General function prediction only]	NA|139aa|down_5|NZ_LT992471.1_2707618_2708035_-	COG4876, COG4876, Uncharacterized protein conserved in bacteria [Function unknown]	NA|608aa|down_6|NZ_LT992471.1_2708173_2709997_-	COG1289, COG1289, Predicted membrane protein [Function unknown]	NA|426aa|down_7|NZ_LT992471.1_2710907_2712185_-	cd17319, MFS_ExuT_GudP_like, Hexuronate transporter, Glucarate transporter, and similar transporters of the Major Facilitator Superfamily	NA|204aa|down_8|NZ_LT992471.1_2712731_2713343_+	COG0586, DedA, Uncharacterized membrane-associated protein [Function unknown]	NA|388aa|down_9|NZ_LT992471.1_2713440_2714604_-	cd17474, MFS_YfmO_like, Bacillus subtilis multidrug efflux protein YfmO and similar transporters of the Major Facilitator Superfamily
