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_900324235.1_5_3949	NZ_LT992462	Staphylococcus aureus isolate 5_3949 chromosome I	1	331074-331166	1	CRISPRCasFinder	no	cas3	DinG,DEDDh,cas3,csa3,TnsE_C,WYL	Unclear	AGTTATCAATTTATTGATTACTGTTTCTTA	30	0	0	NA	NA	NA	1	1	Unclear	DinG,DEDDh,cas3,csa3,TnsE_C,WYL	NA,NA	NA|117aa|up_9|NZ_LT992462.1_320637_320988_-	PRK05338, rplS, 50S ribosomal protein L19; Provisional	NA|246aa|up_8|NZ_LT992462.1_321090_321828_-	PRK00026, trmD, tRNA (guanine-N(1)-)-methyltransferase; Reviewed	NA|168aa|up_7|NZ_LT992462.1_321827_322331_-	PRK00122, rimM, 16S rRNA-processing protein RimM; Provisional	NA|92aa|up_6|NZ_LT992462.1_322518_322794_-	COG0228, RpsP, Ribosomal protein S16 [Translation, ribosomal structure and biogenesis]	NA|456aa|up_5|NZ_LT992462.1_323228_324596_-	PRK10867, PRK10867, signal recognition particle protein; Provisional	NA|111aa|up_4|NZ_LT992462.1_324621_324954_-	PRK00118, PRK00118, putative DNA-binding protein; Validated	NA|417aa|up_3|NZ_LT992462.1_324940_326191_-	PRK10416, PRK10416, signal recognition particle-docking protein FtsY; Provisional	NA|1189aa|up_2|NZ_LT992462.1_326190_329757_-	COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]	NA|244aa|up_1|NZ_LT992462.1_329903_330635_-	PRK00102, rnc, ribonuclease III; Reviewed	NA|78aa|up_0|NZ_LT992462.1_330750_330984_-	PRK00982, acpP, acyl carrier protein; Provisional	NA|245aa|down_0|NZ_LT992462.1_331451_332186_-	PRK05557, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase; Validated	NA|309aa|down_1|NZ_LT992462.1_332178_333105_-	COG0331, FabD, (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]	NA|329aa|down_2|NZ_LT992462.1_333097_334084_-	PRK05331, PRK05331, phosphate acyltransferase PlsX	NA|191aa|down_3|NZ_LT992462.1_334088_334661_-	PRK04424, PRK04424, transcription factor FapR	cas3|687aa|down_4|NZ_LT992462.1_334863_336924_-	PRK10917, PRK10917, ATP-dependent DNA helicase RecG; Provisional	NA|549aa|down_5|NZ_LT992462.1_337113_338760_-	COG1461, COG1461, Predicted kinase related to dihydroxyacetone kinase [General function prediction only]	NA|125aa|down_6|NZ_LT992462.1_338774_339149_-	COG1302, COG1302, Uncharacterized protein conserved in bacteria [Function unknown]	NA|63aa|down_7|NZ_LT992462.1_339591_339780_+	PRK00359, rpmB, 50S ribosomal protein L28; Reviewed	NA|214aa|down_8|NZ_LT992462.1_340160_340802_-	COG1564, THI80, Thiamine pyrophosphokinase [Coenzyme metabolism]	NA|215aa|down_9|NZ_LT992462.1_340808_341453_-	COG0036, Rpe, Pentose-5-phosphate-3-epimerase [Carbohydrate transport and metabolism]
GCF_900324235.1_5_3949	NZ_LT992462	Staphylococcus aureus isolate 5_3949 chromosome I	2	680593-680673	2	CRISPRCasFinder	no		DinG,DEDDh,cas3,csa3,TnsE_C,WYL	Orphan	GGGAGTGGGAGAGAAATGATAAAGA	25	1	1	680618-680648	NZ_LT992462.1_823189-823159	NA	1	1	Orphan	DinG,DEDDh,cas3,csa3,TnsE_C,WYL	NA|105aa|up_7|NZ_LT992462.1_672671_672986_+,NA|53aa|down_5|NZ_LT992462.1_685091_685250_+	NA|356aa|up_9|NZ_LT992462.1_670181_671249_-	COG2070, COG2070, Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]	NA|347aa|up_8|NZ_LT992462.1_671262_672303_-	COG4536, CorB, Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]	NA|105aa|up_7|NZ_LT992462.1_672671_672986_+	NA	NA|466aa|up_6|NZ_LT992462.1_673317_674715_-	TIGR01980, UPF0051_protein_slr0074, FeS assembly protein SufB	NA|155aa|up_5|NZ_LT992462.1_674865_675330_-	TIGR01994, Iron-sulfur_cluster_assembly_scaffold_protein_IscU, SUF system FeS assembly protein, NifU family	NA|417aa|up_4|NZ_LT992462.1_675319_676570_-	TIGR01979, Probable_cysteine_desulfurase, cysteine desulfurases, SufSfamily	NA|436aa|up_3|NZ_LT992462.1_676675_677983_-	COG0719, SufB, Cysteine desulfurase activator SufB [Posttranslational modification, protein turnover, chaperones]	NA|254aa|up_2|NZ_LT992462.1_678081_678843_-	COG0396, sufC, Cysteine desulfurase activator ATPase [Posttranslational modification, protein turnover, chaperones]	NA|284aa|up_1|NZ_LT992462.1_679170_680022_+	COG2035, COG2035, Predicted membrane protein [Function unknown]	NA|65aa|up_0|NZ_LT992462.1_680255_680450_-	COG3237, COG3237, Uncharacterized protein conserved in bacteria [Function unknown]	NA|274aa|down_0|NZ_LT992462.1_681257_682079_-	COG1464, NlpA, ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]	NA|232aa|down_1|NZ_LT992462.1_682096_682792_-	COG2011, AbcD, ABC-type metal ion transport system, permease component [Inorganic ion transport and metabolism]	NA|342aa|down_2|NZ_LT992462.1_682784_683810_-	COG1135, AbcC, ABC-type metal ion transport system, ATPase component [Inorganic ion transport and metabolism]	NA|99aa|down_3|NZ_LT992462.1_684059_684356_-	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|129aa|down_4|NZ_LT992462.1_684348_684735_-	COG1658, COG1658, Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]	NA|53aa|down_5|NZ_LT992462.1_685091_685250_+	NA	NA|293aa|down_6|NZ_LT992462.1_685436_686315_-	COG3878, COG3878, Uncharacterized protein conserved in bacteria [Function unknown]	NA|127aa|down_7|NZ_LT992462.1_686494_686875_-	PRK01202, PRK01202, glycine cleavage system protein GcvH	NA|119aa|down_8|NZ_LT992462.1_687032_687389_-	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|107aa|down_9|NZ_LT992462.1_687532_687853_+	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
GCF_900324235.1_5_3949	NZ_LT992462	Staphylococcus aureus isolate 5_3949 chromosome I	3	982939-983047	3	CRISPRCasFinder	no		DinG,DEDDh,cas3,csa3,TnsE_C,WYL	Orphan	TTTATGCAGTTGTGCGGTAGCATCCAACTGCGTTCCTTT	39	0	0	NA	NA	NA	1	1	Orphan	DinG,DEDDh,cas3,csa3,TnsE_C,WYL	NA|239aa|up_5|NZ_LT992462.1_977820_978537_-,NA|169aa|up_4|NZ_LT992462.1_978698_979205_-,NA	NA|75aa|up_9|NZ_LT992462.1_973943_974168_+	pfam11148, DUF2922, Protein of unknown function (DUF2922)	NA|310aa|up_8|NZ_LT992462.1_974360_975290_+	COG3238, COG3238, Uncharacterized protein conserved in bacteria [Function unknown]	NA|125aa|up_7|NZ_LT992462.1_976237_976612_+	TIGR01889, Pleiotropic_Regulator_Of_Virulence, staphylococcal accessory regulator family	NA|263aa|up_6|NZ_LT992462.1_976863_977652_-	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|239aa|up_5|NZ_LT992462.1_977820_978537_-	NA	NA|169aa|up_4|NZ_LT992462.1_978698_979205_-	NA	NA|267aa|up_3|NZ_LT992462.1_979340_980141_-	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|240aa|up_2|NZ_LT992462.1_980124_980844_-	COG1011, COG1011, Predicted hydrolase (HAD superfamily) [General function prediction only]	NA|317aa|up_1|NZ_LT992462.1_980898_981849_-	pfam01032, FecCD, FecCD transport family	NA|296aa|up_0|NZ_LT992462.1_981999_982887_-	cd01143, YvrC, Periplasmic binding protein YvrC	NA|212aa|down_0|NZ_LT992462.1_983216_983852_-	COG2231, COG2231, Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]	NA|554aa|down_1|NZ_LT992462.1_984192_985854_-	PRK01611, argS, arginyl-tRNA synthetase; Reviewed	NA|139aa|down_2|NZ_LT992462.1_985850_986267_-	COG4506, COG4506, Uncharacterized protein conserved in bacteria [Function unknown]	NA|337aa|down_3|NZ_LT992462.1_986542_987553_-	PRK09422, PRK09422, ethanol-active dehydrogenase/acetaldehyde-active reductase; Provisional	NA|174aa|down_4|NZ_LT992462.1_988051_988573_-	pfam08741, YwhD, YwhD family	NA|432aa|down_5|NZ_LT992462.1_988600_989896_-	COG1078, COG1078, HD superfamily phosphohydrolases [General function prediction only]	NA|159aa|down_6|NZ_LT992462.1_989935_990412_-	pfam00583, Acetyltransf_1, Acetyltransferase (GNAT) family	NA|179aa|down_7|NZ_LT992462.1_990581_991118_-	COG0655, WrbA, Multimeric flavodoxin WrbA [General function prediction only]	NA|313aa|down_8|NZ_LT992462.1_991563_992502_-	cd19083, AKR_AKR11A1_11D1, AKR11A and  AKR11D families of aldo-keto reductase (AKR)	NA|209aa|down_9|NZ_LT992462.1_992771_993398_-	pfam04276, DUF443, Protein of unknown function (DUF443)
GCF_900324235.1_5_3949	NZ_LT992462	Staphylococcus aureus isolate 5_3949 chromosome I	4	1551972-1552054	4	CRISPRCasFinder	no		DinG,DEDDh,cas3,csa3,TnsE_C,WYL	Orphan	GAAGCTGACGAAAAAGTCAGCTTAC	25	0	0	NA	NA	NA	1	1	Orphan	DinG,DEDDh,cas3,csa3,TnsE_C,WYL	NA,NA	NA|454aa|up_9|NZ_LT992462.1_1536805_1538167_+	COG1113, AnsP, Gamma-aminobutyrate permease and related permeases [Amino acid transport and metabolism]	NA|586aa|up_8|NZ_LT992462.1_1538510_1540268_-	PRK06354, PRK06354, pyruvate kinase; Provisional	NA|323aa|up_7|NZ_LT992462.1_1540289_1541258_-	PRK03202, PRK03202, ATP-dependent 6-phosphofructokinase	NA|315aa|up_6|NZ_LT992462.1_1541526_1542471_-	PRK05724, PRK05724, acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated	NA|286aa|up_5|NZ_LT992462.1_1542470_1543328_-	PRK05654, PRK05654, acetyl-CoA carboxylase carboxyltransferase subunit beta	NA|410aa|up_4|NZ_LT992462.1_1543522_1544752_-	PRK07232, PRK07232, bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed	NA|1066aa|up_3|NZ_LT992462.1_1545200_1548398_-	COG0587, DnaE, DNA polymerase III, alpha subunit [DNA replication, recombination, and repair]	NA|314aa|up_2|NZ_LT992462.1_1548418_1549360_-	COG0618, COG0618, Exopolyphosphatase-related proteins [General function prediction only]	NA|433aa|up_1|NZ_LT992462.1_1549729_1551028_-	COG4109, COG4109, Predicted transcriptional regulator containing CBS domains [Transcription]	NA|138aa|up_0|NZ_LT992462.1_1551232_1551646_+	pfam00582, Usp, Universal stress protein family	NA|230aa|down_0|NZ_LT992462.1_1552151_1552841_-	PRK00685, PRK00685, metal-dependent hydrolase; Provisional	NA|352aa|down_1|NZ_LT992462.1_1553015_1554071_+	COG0006, PepP, Xaa-Pro aminopeptidase [Amino acid transport and metabolism]	NA|373aa|down_2|NZ_LT992462.1_1554386_1555505_-	cd05305, L-AlaDH, Alanine dehydrogenase NAD-binding and catalytic domains	NA|167aa|down_3|NZ_LT992462.1_1555645_1556146_+	pfam00582, Usp, Universal stress protein family	NA|401aa|down_4|NZ_LT992462.1_1556392_1557595_-	PRK00180, PRK00180, acetate kinase A/propionate kinase 2; Reviewed	NA|316aa|down_5|NZ_LT992462.1_1557682_1558630_-	COG0827, COG0827, Adenine-specific DNA methylase [DNA replication, recombination, and repair]	NA|165aa|down_6|NZ_LT992462.1_1558752_1559247_-	PRK00522, tpx, thiol peroxidase	NA|257aa|down_7|NZ_LT992462.1_1559344_1560115_-	PRK10621, PRK10621, hypothetical protein; Provisional	NA|408aa|down_8|NZ_LT992462.1_1560158_1561382_-	PRK01565, PRK01565, thiamine biosynthesis protein ThiI; Provisional	NA|383aa|down_9|NZ_LT992462.1_1561381_1562530_-	COG1104, NifS, Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]
GCF_900324235.1_5_3949	NZ_LT992462	Staphylococcus aureus isolate 5_3949 chromosome I	5	1640326-1640419	5	CRISPRCasFinder	no	csa3	DinG,DEDDh,cas3,csa3,TnsE_C,WYL	Type I-A	GCAATGCGCGTTGGGGTGTGGGGCCCCAACATAG	34	1	1	1640360-1640385	NZ_LT992462.1_1738151-1738126	NA	1	1	Orphan	DinG,DEDDh,cas3,csa3,TnsE_C,WYL	NA|75aa|up_5|NZ_LT992462.1_1636419_1636644_-,NA|148aa|up_2|NZ_LT992462.1_1637855_1638299_-,NA|101aa|down_1|NZ_LT992462.1_1641553_1641856_+	NA|501aa|up_9|NZ_LT992462.1_1631451_1632954_-	COG4529, COG4529, Uncharacterized protein conserved in bacteria [Function unknown]	csa3|105aa|up_8|NZ_LT992462.1_1633596_1633911_+	cd00090, HTH_ARSR, Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors	NA|431aa|up_7|NZ_LT992462.1_1633910_1635203_+	PRK15445, PRK15445, arsenical efflux pump membrane protein ArsB	NA|285aa|up_6|NZ_LT992462.1_1635289_1636144_-	COG4193, LytD, Beta- N-acetylglucosaminidase [Carbohydrate transport and metabolism]	NA|75aa|up_5|NZ_LT992462.1_1636419_1636644_-	NA	NA|157aa|up_4|NZ_LT992462.1_1636842_1637313_+	COG1595, RpoE, DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]	NA|148aa|up_3|NZ_LT992462.1_1637425_1637869_+	pfam06338, ComK, ComK protein	NA|148aa|up_2|NZ_LT992462.1_1637855_1638299_-	NA	NA|212aa|up_1|NZ_LT992462.1_1638596_1639232_+	pfam02517, Abi, CAAX protease self-immunity	NA|207aa|up_0|NZ_LT992462.1_1639398_1640019_+	pfam02517, Abi, CAAX protease self-immunity	NA|238aa|down_0|NZ_LT992462.1_1640581_1641295_-	PRK12376, PRK12376, putative translaldolase; Provisional	NA|101aa|down_1|NZ_LT992462.1_1641553_1641856_+	NA	NA|122aa|down_2|NZ_LT992462.1_1642110_1642476_+	PRK14201, PRK14201, fluoride efflux transporter CrcB	NA|118aa|down_3|NZ_LT992462.1_1642472_1642826_+	COG0239, CrcB, Integral membrane protein possibly involved in chromosome condensation [Cell division and chromosome partitioning]	NA|278aa|down_4|NZ_LT992462.1_1643075_1643909_-	COG0656, ARA1, Aldo/keto reductases, related to diketogulonate reductase [General function prediction only]	NA|303aa|down_5|NZ_LT992462.1_1644120_1645029_-	pfam08378, NERD, Nuclease-related domain	NA|398aa|down_6|NZ_LT992462.1_1645153_1646347_-	PRK05250, PRK05250, S-adenosylmethionine synthetase; Validated	NA|531aa|down_7|NZ_LT992462.1_1646718_1648311_+	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_LT992462.1_1648607_1649354_-	COG1506, DAP2, Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]	NA|158aa|down_9|NZ_LT992462.1_1649358_1649832_-	TIGR02705, conserved_hypothetical_protein, nucleoside triphosphatase YtkD
GCF_900324235.1_5_3949	NZ_LT992462	Staphylococcus aureus isolate 5_3949 chromosome I	6	1904597-1904809	6	CRISPRCasFinder	no		DinG,DEDDh,cas3,csa3,TnsE_C,WYL	Orphan	TGATGTGCTGTTGTGGAAGCTTGGTGTCGTGCCATGCTACTTTGATG	47	0	0	NA	NA	NA	2	2	Orphan	DinG,DEDDh,cas3,csa3,TnsE_C,WYL	NA|46aa|up_4|NZ_LT992462.1_1901458_1901596_-,NA|107aa|down_0|NZ_LT992462.1_1904842_1905163_+	NA|232aa|up_9|NZ_LT992462.1_1894150_1894846_+	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_LT992462.1_1895198_1896719_-	COG0513, SrmB, Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]	NA|452aa|up_7|NZ_LT992462.1_1897234_1898590_-	COG0770, MurF, UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]	NA|357aa|up_6|NZ_LT992462.1_1898604_1899675_-	PRK01966, ddl, D-alanine--D-alanine ligase	NA|401aa|up_5|NZ_LT992462.1_1899992_1901195_+	TIGR02210, Rod_shape-determining_protein_RodA, rod shape-determining protein RodA	NA|46aa|up_4|NZ_LT992462.1_1901458_1901596_-	NA	NA|70aa|up_3|NZ_LT992462.1_1901723_1901933_-	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_LT992462.1_1901944_1902238_-	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_LT992462.1_1902403_1903888_+	TIGR04265, bac_cardiolipin, cardiolipin synthase	NA|216aa|up_0|NZ_LT992462.1_1903915_1904563_+	COG1418, COG1418, Predicted HD superfamily hydrolase [General function prediction only]	NA|107aa|down_0|NZ_LT992462.1_1904842_1905163_+	NA	NA|291aa|down_1|NZ_LT992462.1_1906804_1907677_-	PRK02463, PRK02463, OxaA-like protein precursor; Provisional	NA|214aa|down_2|NZ_LT992462.1_1907762_1908404_-	PRK00043, thiE, thiamine phosphate synthase	NA|264aa|down_3|NZ_LT992462.1_1908405_1909197_-	PRK09355, PRK09355, hydroxyethylthiazole kinase; Validated	NA|277aa|down_4|NZ_LT992462.1_1909180_1910011_-	PRK06427, PRK06427, bifunctional hydroxy-methylpyrimidine kinase/ hydroxy-phosphomethylpyrimidine kinase; Reviewed	NA|230aa|down_5|NZ_LT992462.1_1910003_1910693_-	TIGR04306, salvage_TenA, thiaminase II	NA|232aa|down_6|NZ_LT992462.1_1911079_1911775_-	pfam06737, Transglycosylas, Transglycosylase-like domain	NA|132aa|down_7|NZ_LT992462.1_1912163_1912559_-	pfam00436, SSB, Single-strand binding protein family	NA|147aa|down_8|NZ_LT992462.1_1912752_1913193_+	pfam14183, YwpF, YwpF-like protein	NA|147aa|down_9|NZ_LT992462.1_1913249_1913690_-	PRK00006, fabZ, 3-hydroxyacyl-ACP dehydratase FabZ
GCF_900324235.1_5_3949	NZ_LT992462	Staphylococcus aureus isolate 5_3949 chromosome I	7	1960228-1960378	7	CRISPRCasFinder	no	csa3,TnsE_C	DinG,DEDDh,cas3,csa3,TnsE_C,WYL	Type I-A	AACTTTAGTTGTTAGGGGCTCTTATGCA	28	0	0	NA	NA	NA	2	2	Orphan	DinG,DEDDh,cas3,csa3,TnsE_C,WYL	NA|77aa|up_5|NZ_LT992462.1_1955100_1955331_-,NA|364aa|up_0|NZ_LT992462.1_1959118_1960210_+,NA|35aa|down_0|NZ_LT992462.1_1960707_1960812_-,NA|53aa|down_2|NZ_LT992462.1_1961491_1961650_+,NA|31aa|down_3|NZ_LT992462.1_1962085_1962178_+	NA|237aa|up_9|NZ_LT992462.1_1950710_1951421_+	PRK05819, deoD, DeoD-type purine-nucleoside phosphorylase	NA|148aa|up_8|NZ_LT992462.1_1951541_1951985_-	COG0783, Dps, DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]	NA|138aa|up_7|NZ_LT992462.1_1952184_1952598_-	COG3011, COG3011, Predicted thiol-disulfide oxidoreductase [General function    prediction only]	NA|458aa|up_6|NZ_LT992462.1_1953055_1954429_-	pfam01878, EVE, EVE domain	NA|77aa|up_5|NZ_LT992462.1_1955100_1955331_-	NA	NA|313aa|up_4|NZ_LT992462.1_1955361_1956300_-	COG1482, ManA, Phosphomannose isomerase [Carbohydrate transport and metabolism]	NA|222aa|up_3|NZ_LT992462.1_1956733_1957399_-	cd05243, SDR_a5, atypical (a) SDRs, subgroup 5	csa3|107aa|up_2|NZ_LT992462.1_1957550_1957871_+	cd00090, HTH_ARSR, Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors	NA|327aa|up_1|NZ_LT992462.1_1957872_1958853_+	COG1230, CzcD, Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]	NA|364aa|up_0|NZ_LT992462.1_1959118_1960210_+	NA	NA|35aa|down_0|NZ_LT992462.1_1960707_1960812_-	NA	NA|57aa|down_1|NZ_LT992462.1_1961328_1961499_+	COG4584, COG4584, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|53aa|down_2|NZ_LT992462.1_1961491_1961650_+	NA	NA|31aa|down_3|NZ_LT992462.1_1962085_1962178_+	NA	NA|286aa|down_4|NZ_LT992462.1_1962307_1963165_-	COG0561, Cof, Predicted hydrolases of the HAD superfamily [General function prediction only]	NA|261aa|down_5|NZ_LT992462.1_1963232_1964015_-	COG1119, ModF, ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA [Inorganic ion transport and metabolism]	NA|203aa|down_6|NZ_LT992462.1_1964304_1964913_-	pfam08937, DUF1863, MTH538 TIR-like domain (DUF1863)	NA|345aa|down_7|NZ_LT992462.1_1964940_1965975_-	pfam13676, TIR_2, TIR domain	NA|490aa|down_8|NZ_LT992462.1_1966068_1967538_-	pfam18185, STALD, Sir2- and TIR-associating SLOG family	NA|97aa|down_9|NZ_LT992462.1_1967597_1967888_-	pfam11867, DUF3387, Domain of unknown function (DUF3387)
GCF_900324235.1_5_3949	NZ_LT992462	Staphylococcus aureus isolate 5_3949 chromosome I	8	2124216-2124301	8	CRISPRCasFinder	no	WYL	DinG,DEDDh,cas3,csa3,TnsE_C,WYL	Unclear	AAAGTCAGCTTACAATAATGTGCAAGTTGG	30	1	7	2124246-2124271|2124246-2124271|2124246-2124271|2124246-2124271|2124246-2124271|2124246-2124271|2124246-2124271	NZ_LT992462.1_1429486-1429461|NZ_LT992462.1_684991-685016|NZ_LT992462.1_199088-199063|NZ_LT992462.1_635936-635911|NZ_LT992462.1_680871-680846|NZ_LT992462.1_1915709-1915734|NZ_LT992462.1_2256102-2256077	NA	1	1	Orphan	DinG,DEDDh,cas3,csa3,TnsE_C,WYL	NA|65aa|up_6|NZ_LT992462.1_2116960_2117155_-,NA|78aa|down_1|NZ_LT992462.1_2125251_2125485_-,NA|110aa|down_8|NZ_LT992462.1_2133573_2133903_+	NA|248aa|up_9|NZ_LT992462.1_2112748_2113492_-	TIGR01889, Pleiotropic_Regulator_Of_Virulence, staphylococcal accessory regulator family	NA|652aa|up_8|NZ_LT992462.1_2113517_2115473_-	COG2207, AraC, AraC-type DNA-binding domain-containing proteins [Transcription]	NA|270aa|up_7|NZ_LT992462.1_2116082_2116892_+	COG3942, COG3942, Surface antigen [General function prediction only]	NA|65aa|up_6|NZ_LT992462.1_2116960_2117155_-	NA	NA|467aa|up_5|NZ_LT992462.1_2117328_2118729_-	TIGR00931, Uncharacterized_Na+/H+_antiporter_HI_1107, Na+/H+ antiporter NhaC	NA|361aa|up_4|NZ_LT992462.1_2118823_2119906_-	pfam02317, Octopine_DH, NAD/NADP octopine/nopaline dehydrogenase, alpha-helical domain	NA|141aa|up_3|NZ_LT992462.1_2120153_2120576_+	COG3296, COG3296, Uncharacterized protein conserved in bacteria [Function unknown]	NA|167aa|up_2|NZ_LT992462.1_2120812_2121313_+	COG3942, COG3942, Surface antigen [General function prediction only]	NA|318aa|up_1|NZ_LT992462.1_2121675_2122629_+	cd12178, 2-Hacid_dh_13, Putative D-isomer specific 2-hydroxyacid dehydrogenases, NAD-binding and catalytic domains	NA|375aa|up_0|NZ_LT992462.1_2122720_2123845_-	PRK06753, PRK06753, hypothetical protein; Provisional	NA|259aa|down_0|NZ_LT992462.1_2124453_2125230_-	COG4193, LytD, Beta- N-acetylglucosaminidase [Carbohydrate transport and metabolism]	NA|78aa|down_1|NZ_LT992462.1_2125251_2125485_-	NA	NA|158aa|down_2|NZ_LT992462.1_2125779_2126253_-	COG2427, COG2427, Uncharacterized conserved protein [Function unknown]	NA|985aa|down_3|NZ_LT992462.1_2126252_2129207_-	COG3383, COG3383, Uncharacterized anaerobic dehydrogenase [General function prediction only]	NA|316aa|down_4|NZ_LT992462.1_2129808_2130756_-	PRK09379, PRK09379, LytR family transcriptional regulator	NA|266aa|down_5|NZ_LT992462.1_2130888_2131686_-	COG0483, SuhB, Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]	WYL|231aa|down_6|NZ_LT992462.1_2132070_2132763_+	COG2378, COG2378, Predicted transcriptional regulator [Transcription]	NA|246aa|down_7|NZ_LT992462.1_2132787_2133525_-	pfam02517, Abi, CAAX protease self-immunity	NA|110aa|down_8|NZ_LT992462.1_2133573_2133903_+	NA	NA|291aa|down_9|NZ_LT992462.1_2134347_2135220_+	COG1737, RpiR, Transcriptional regulators [Transcription]
GCF_900324235.1_5_3949	NZ_LT992462	Staphylococcus aureus isolate 5_3949 chromosome I	9	2300365-2300459	9	CRISPRCasFinder	no		DinG,DEDDh,cas3,csa3,TnsE_C,WYL	Orphan	AGGCTCTTATGCAGTTGGTGCGAAGCAA	28	0	0	NA	NA	NA	1	1	Orphan	DinG,DEDDh,cas3,csa3,TnsE_C,WYL	NA|249aa|up_9|NZ_LT992462.1_2289950_2290697_+,NA|121aa|down_0|NZ_LT992462.1_2301127_2301490_-,NA|105aa|down_8|NZ_LT992462.1_2308302_2308617_+	NA|249aa|up_9|NZ_LT992462.1_2289950_2290697_+	NA	NA|398aa|up_8|NZ_LT992462.1_2290920_2292114_-	cd17489, MFS_YfcJ_like, Escherichia coli YfcJ, YhhS, and similar transporters of the Major Facilitator Superfamily	NA|250aa|up_7|NZ_LT992462.1_2292125_2292875_-	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_LT992462.1_2292867_2293683_-	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_LT992462.1_2293679_2294549_-	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_LT992462.1_2294545_2295481_-	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_LT992462.1_2295493_2297092_-	TIGR02294, Nickel-binding_periplasmic_protein, nickel ABC transporter, nickel/metallophore periplasmic binding protein	NA|434aa|up_2|NZ_LT992462.1_2297234_2298536_-	COG4408, COG4408, Uncharacterized protein conserved in bacteria [Function unknown]	NA|273aa|up_1|NZ_LT992462.1_2298528_2299347_-	cd08261, Zn_ADH7, Alcohol dehydrogenases of the MDR family	NA|274aa|up_0|NZ_LT992462.1_2299357_2300179_-	COG0253, DapF, Diaminopimelate epimerase [Amino acid transport and metabolism]	NA|121aa|down_0|NZ_LT992462.1_2301127_2301490_-	NA	NA|273aa|down_1|NZ_LT992462.1_2301752_2302571_-	PRK08589, PRK08589, SDR family oxidoreductase	NA|513aa|down_2|NZ_LT992462.1_2302804_2304343_+	pfam03806, ABG_transport, AbgT putative transporter family	NA|141aa|down_3|NZ_LT992462.1_2304454_2304877_-	COG2128, COG2128, Uncharacterized conserved protein [Function unknown]	NA|133aa|down_4|NZ_LT992462.1_2305348_2305747_-	pfam07252, DUF1433, Protein of unknown function (DUF1433)	NA|137aa|down_5|NZ_LT992462.1_2305773_2306184_-	pfam07252, DUF1433, Protein of unknown function (DUF1433)	NA|128aa|down_6|NZ_LT992462.1_2306638_2307022_-	pfam07252, DUF1433, Protein of unknown function (DUF1433)	NA|403aa|down_7|NZ_LT992462.1_2307088_2308297_+	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_LT992462.1_2308302_2308617_+	NA	NA|140aa|down_9|NZ_LT992462.1_2310493_2310913_-	pfam07252, DUF1433, Protein of unknown function (DUF1433)
GCF_900324235.1_5_3949	NZ_LT992462	Staphylococcus aureus isolate 5_3949 chromosome I	10	2328310-2328420	10	CRISPRCasFinder	no		DinG,DEDDh,cas3,csa3,TnsE_C,WYL	Orphan	GGTACTTCTGGTGTCGGTGGCGTTGGT	27	0	0	NA	NA	NA	1	1	Orphan	DinG,DEDDh,cas3,csa3,TnsE_C,WYL	NA|89aa|up_2|NZ_LT992462.1_2322613_2322880_+,NA|103aa|up_1|NZ_LT992462.1_2323023_2323332_+,NA	NA|452aa|up_9|NZ_LT992462.1_2314007_2315363_-	cd00519, Lipase_3, Lipase (class 3)	NA|262aa|up_8|NZ_LT992462.1_2315359_2316145_-	pfam04507, DUF576, Csa1 family	NA|255aa|up_7|NZ_LT992462.1_2316392_2317157_-	pfam04507, DUF576, Csa1 family	NA|258aa|up_6|NZ_LT992462.1_2317268_2318042_-	pfam04507, DUF576, Csa1 family	NA|310aa|up_5|NZ_LT992462.1_2318284_2319214_-	pfam09019, EcoRII-C, EcoRII C terminal	NA|398aa|up_4|NZ_LT992462.1_2319309_2320503_+	TIGR00675, Modification_methylase, DNA-methyltransferase (dcm)	NA|584aa|up_3|NZ_LT992462.1_2320578_2322330_+	cd05799, PGM2, This CD includes PGM2 (phosphoglucomutase 2) and PGM2L1 (phosphoglucomutase 2-like 1)	NA|89aa|up_2|NZ_LT992462.1_2322613_2322880_+	NA	NA|103aa|up_1|NZ_LT992462.1_2323023_2323332_+	NA	NA|289aa|up_0|NZ_LT992462.1_2323457_2324324_-	COG1210, GalU, UDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]	NA|453aa|down_0|NZ_LT992462.1_2331560_2332919_-	TIGR00791, Gluconate_permease, gluconate transporter	NA|518aa|down_1|NZ_LT992462.1_2333035_2334589_-	TIGR01314, gntK_FGGY, gluconate kinase, FGGY type	NA|226aa|down_2|NZ_LT992462.1_2334613_2335291_-	COG1802, GntR, Transcriptional regulators [Transcription]	NA|255aa|down_3|NZ_LT992462.1_2335447_2336212_-	cd01106, HTH_TipAL-Mta, Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA	NA|231aa|down_4|NZ_LT992462.1_2336376_2337069_-	COG2357, COG2357, PpGpp synthetase catalytic domain [General function prediction only]	NA|139aa|down_5|NZ_LT992462.1_2337299_2337716_-	COG4876, COG4876, Uncharacterized protein conserved in bacteria [Function unknown]	NA|608aa|down_6|NZ_LT992462.1_2337854_2339678_-	COG1289, COG1289, Predicted membrane protein [Function unknown]	NA|426aa|down_7|NZ_LT992462.1_2340589_2341867_-	cd17319, MFS_ExuT_GudP_like, Hexuronate transporter, Glucarate transporter, and similar transporters of the Major Facilitator Superfamily	NA|204aa|down_8|NZ_LT992462.1_2342413_2343025_+	COG0586, DedA, Uncharacterized membrane-associated protein [Function unknown]	NA|388aa|down_9|NZ_LT992462.1_2343122_2344286_-	cd17474, MFS_YfmO_like, Bacillus subtilis multidrug efflux protein YfmO and similar transporters of the Major Facilitator Superfamily
GCF_900324235.1_5_3949	NZ_LT992462	Staphylococcus aureus isolate 5_3949 chromosome I	11	2872926-2873125	11	CRISPRCasFinder	no		DinG,DEDDh,cas3,csa3,TnsE_C,WYL	Orphan	TGCAAGTTGGCGGGGCCCCAACACAGAAGCT	31	2	2	2872957-2872981|2873013-2873037	NZ_LT992462.1_2873126-2873150|NZ_LT992462.1_1915671-1915695	NA	3	3	Orphan	DinG,DEDDh,cas3,csa3,TnsE_C,WYL	NA,NA|131aa|down_5|NZ_LT992462.1_2878301_2878694_+	NA|574aa|up_9|NZ_LT992462.1_2860372_2862094_+	pfam18674, TarS_C1, TarS beta-glycosyltransferase C-terminal domain 1	NA|225aa|up_8|NZ_LT992462.1_2862237_2862912_+	PRK13276, PRK13276, iron-sulfur cluster repair di-iron protein ScdA	NA|585aa|up_7|NZ_LT992462.1_2863158_2864913_+	COG3275, LytS, Putative regulator of cell autolysis [Signal transduction mechanisms]	NA|247aa|up_6|NZ_LT992462.1_2864915_2865656_+	PRK14084, PRK14084, DNA-binding response regulator	NA|148aa|up_5|NZ_LT992462.1_2865768_2866212_+	PRK04125, PRK04125, antiholin-like protein LrgA	NA|234aa|up_4|NZ_LT992462.1_2866204_2866906_+	PRK04288, PRK04288, antiholin-like protein LrgB; Provisional	NA|764aa|up_3|NZ_LT992462.1_2867246_2869538_+	COG3256, NorB, Nitric oxide reductase large subunit [Inorganic ion transport and metabolism]	NA|235aa|up_2|NZ_LT992462.1_2869763_2870468_-	COG2188, PhnF, Transcriptional regulators [Transcription]	NA|264aa|up_1|NZ_LT992462.1_2870616_2871408_+	COG2190, NagE, Phosphotransferase system IIA components [Carbohydrate transport and metabolism]	NA|479aa|up_0|NZ_LT992462.1_2871423_2872860_+	PRK09589, celA, 6-phospho-beta-glucosidase; Reviewed	NA|254aa|down_0|NZ_LT992462.1_2873435_2874197_-	pfam13649, Methyltransf_25, Methyltransferase domain	NA|305aa|down_1|NZ_LT992462.1_2874448_2875363_-	TIGR02152, Putative_ribokinase, ribokinase	NA|135aa|down_2|NZ_LT992462.1_2875390_2875795_-	PRK11797, PRK11797, D-ribose pyranase; Provisional	NA|294aa|down_3|NZ_LT992462.1_2875809_2876691_-	pfam06800, Sugar_transport, Sugar transport protein	NA|333aa|down_4|NZ_LT992462.1_2876922_2877921_-	COG1609, PurR, Transcriptional regulators [Transcription]	NA|131aa|down_5|NZ_LT992462.1_2878301_2878694_+	NA	NA|459aa|down_6|NZ_LT992462.1_2878822_2880199_-	TIGR00711, Uncharacterized_MFS-type_transporter_YhcA, drug resistance transporter, EmrB/QacA subfamily	NA|331aa|down_7|NZ_LT992462.1_2880432_2881425_+	COG3049, COG3049, Penicillin V acylase and related amidases [Cell envelope biogenesis, outer membrane]	NA|317aa|down_8|NZ_LT992462.1_2881750_2882701_+	COG3942, COG3942, Surface antigen [General function prediction only]	NA|220aa|down_9|NZ_LT992462.1_2882752_2883412_-	COG1131, CcmA, ABC-type multidrug transport system, ATPase component [Defense mechanisms]
