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_001465675.1_ASM146567v1	NZ_CP013619	Staphylococcus aureus strain RIVM1607 chromosome, complete genome	1	307202-307401	1	CRISPRCasFinder	no		WYL,csa3,cas3,DEDDh,DinG,TnsE_C	Orphan	TGCAAGTTGGCGGGGCCCCAACACAGAAGCT	31	2	2	307233-307257|307289-307313	NZ_CP013619.1_307402-307426|NZ_CP013619.1_2119495-2119519	NA	3	3	Orphan	WYL,csa3,cas3,DEDDh,DinG,TnsE_C	NA,NA|131aa|down_5|NZ_CP013619.1_312577_312970_+	NA|574aa|up_9|NZ_CP013619.1_294648_296370_+	pfam18674, TarS_C1, TarS beta-glycosyltransferase C-terminal domain 1	NA|225aa|up_8|NZ_CP013619.1_296513_297188_+	PRK13276, PRK13276, iron-sulfur cluster repair di-iron protein ScdA	NA|585aa|up_7|NZ_CP013619.1_297434_299189_+	COG3275, LytS, Putative regulator of cell autolysis [Signal transduction mechanisms]	NA|247aa|up_6|NZ_CP013619.1_299191_299932_+	PRK14084, PRK14084, DNA-binding response regulator	NA|148aa|up_5|NZ_CP013619.1_300044_300488_+	PRK04125, PRK04125, antiholin-like protein LrgA	NA|234aa|up_4|NZ_CP013619.1_300480_301182_+	PRK04288, PRK04288, antiholin-like protein LrgB; Provisional	NA|764aa|up_3|NZ_CP013619.1_301522_303814_+	COG3256, NorB, Nitric oxide reductase large subunit [Inorganic ion transport and metabolism]	NA|235aa|up_2|NZ_CP013619.1_304039_304744_-	COG2188, PhnF, Transcriptional regulators [Transcription]	NA|264aa|up_1|NZ_CP013619.1_304892_305684_+	COG2190, NagE, Phosphotransferase system IIA components [Carbohydrate transport and metabolism]	NA|479aa|up_0|NZ_CP013619.1_305699_307136_+	PRK09589, celA, 6-phospho-beta-glucosidase; Reviewed	NA|254aa|down_0|NZ_CP013619.1_307711_308473_-	pfam13649, Methyltransf_25, Methyltransferase domain	NA|305aa|down_1|NZ_CP013619.1_308724_309639_-	TIGR02152, Putative_ribokinase, ribokinase	NA|135aa|down_2|NZ_CP013619.1_309666_310071_-	PRK11797, PRK11797, D-ribose pyranase; Provisional	NA|294aa|down_3|NZ_CP013619.1_310085_310967_-	pfam06800, Sugar_transport, Sugar transport protein	NA|333aa|down_4|NZ_CP013619.1_311198_312197_-	COG1609, PurR, Transcriptional regulators [Transcription]	NA|131aa|down_5|NZ_CP013619.1_312577_312970_+	NA	NA|459aa|down_6|NZ_CP013619.1_313098_314475_-	TIGR00711, Uncharacterized_MFS-type_transporter_YhcA, drug resistance transporter, EmrB/QacA subfamily	NA|331aa|down_7|NZ_CP013619.1_314708_315701_+	COG3049, COG3049, Penicillin V acylase and related amidases [Cell envelope biogenesis, outer membrane]	NA|317aa|down_8|NZ_CP013619.1_316026_316977_+	COG3942, COG3942, Surface antigen [General function prediction only]	NA|220aa|down_9|NZ_CP013619.1_317028_317688_-	COG1131, CcmA, ABC-type multidrug transport system, ATPase component [Defense mechanisms]
GCF_001465675.1_ASM146567v1	NZ_CP013619	Staphylococcus aureus strain RIVM1607 chromosome, complete genome	2	689511-689619	2	CRISPRCasFinder	no		WYL,csa3,cas3,DEDDh,DinG,TnsE_C	Orphan	AAAGGAACGCAGTTGGATGCTACCGCACAACTGCATAAA	39	0	0	NA	NA	NA	1	1	Orphan	WYL,csa3,cas3,DEDDh,DinG,TnsE_C	NA,NA|169aa|down_4|NZ_CP013619.1_693352_693859_+,NA|239aa|down_5|NZ_CP013619.1_694020_694737_+	NA|209aa|up_9|NZ_CP013619.1_679015_679642_+	pfam04276, DUF443, Protein of unknown function (DUF443)	NA|313aa|up_8|NZ_CP013619.1_679911_680850_+	cd19083, AKR_AKR11A1_11D1, AKR11A and  AKR11D families of aldo-keto reductase (AKR)	NA|179aa|up_7|NZ_CP013619.1_681295_681832_+	COG0655, WrbA, Multimeric flavodoxin WrbA [General function prediction only]	NA|159aa|up_6|NZ_CP013619.1_682001_682478_+	pfam00583, Acetyltransf_1, Acetyltransferase (GNAT) family	NA|432aa|up_5|NZ_CP013619.1_682517_683813_+	COG1078, COG1078, HD superfamily phosphohydrolases [General function prediction only]	NA|174aa|up_4|NZ_CP013619.1_683840_684362_+	pfam08741, YwhD, YwhD family	NA|337aa|up_3|NZ_CP013619.1_684860_685871_+	PRK09422, PRK09422, ethanol-active dehydrogenase/acetaldehyde-active reductase; Provisional	NA|139aa|up_2|NZ_CP013619.1_686146_686563_+	COG4506, COG4506, Uncharacterized protein conserved in bacteria [Function unknown]	NA|554aa|up_1|NZ_CP013619.1_686559_688221_+	PRK01611, argS, arginyl-tRNA synthetase; Reviewed	NA|212aa|up_0|NZ_CP013619.1_688705_689341_+	COG2231, COG2231, Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]	NA|296aa|down_0|NZ_CP013619.1_689670_690558_+	cd01143, YvrC, Periplasmic binding protein YvrC	NA|317aa|down_1|NZ_CP013619.1_690708_691659_+	pfam01032, FecCD, FecCD transport family	NA|240aa|down_2|NZ_CP013619.1_691713_692433_+	COG1011, COG1011, Predicted hydrolase (HAD superfamily) [General function prediction only]	NA|267aa|down_3|NZ_CP013619.1_692416_693217_+	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|169aa|down_4|NZ_CP013619.1_693352_693859_+	NA	NA|239aa|down_5|NZ_CP013619.1_694020_694737_+	NA	NA|263aa|down_6|NZ_CP013619.1_694905_695694_+	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|125aa|down_7|NZ_CP013619.1_695945_696320_-	TIGR01889, Pleiotropic_Regulator_Of_Virulence, staphylococcal accessory regulator family	NA|310aa|down_8|NZ_CP013619.1_697267_698197_-	COG3238, COG3238, Uncharacterized protein conserved in bacteria [Function unknown]	NA|75aa|down_9|NZ_CP013619.1_698389_698614_-	pfam11148, DUF2922, Protein of unknown function (DUF2922)
GCF_001465675.1_ASM146567v1	NZ_CP013619	Staphylococcus aureus strain RIVM1607 chromosome, complete genome	3	851729-851811	3	CRISPRCasFinder	no		WYL,csa3,cas3,DEDDh,DinG,TnsE_C	Orphan	CACCCCAACTCGCATTGCTTGTAGAA	26	1	22	851755-851785|851755-851785|851755-851785|851755-851785|851755-851785|851755-851785|851755-851785|851755-851785|851755-851785|851755-851785|851755-851785|851755-851785|851755-851785|851755-851785|851755-851785|851755-851785|851755-851785|851755-851785|851755-851785|851755-851785|851755-851785|851755-851785	NZ_CP013619.1_984828-984858|NZ_CP013619.1_1965307-1965337|NZ_CP013619.1_1965417-1965447|NZ_CP013619.1_2033675-2033705|NZ_CP013619.1_289272-289302|NZ_CP013619.1_289330-289360|NZ_CP013619.1_383014-382984|NZ_CP013619.1_681008-680978|NZ_CP013619.1_805442-805412|NZ_CP013619.1_896656-896686|NZ_CP013619.1_1077795-1077825|NZ_CP013619.1_1776762-1776732|NZ_CP013619.1_1867548-1867518|NZ_CP013619.1_2282919-2282949|NZ_CP013619.1_2328043-2328013|NZ_CP013619.1_860736-860766|NZ_CP013619.1_900794-900764|NZ_CP013619.1_1386893-1386923|NZ_CP013619.1_1432982-1433012|NZ_CP013619.1_2293667-2293697|NZ_CP013619.1_2293722-2293752|NZ_CP013619.1_2728945-2728975	NA	1	1	Orphan	WYL,csa3,cas3,DEDDh,DinG,TnsE_C	NA,NA	NA|280aa|up_9|NZ_CP013619.1_838978_839818_+	COG3942, COG3942, Surface antigen [General function prediction only]	NA|217aa|up_8|NZ_CP013619.1_839991_840642_+	pfam12917, HD_2, HD containing hydrolase-like enzyme	NA|79aa|up_7|NZ_CP013619.1_840638_840875_+	COG4897, CsbA, Uncharacterized protein conserved in bacteria [Function unknown]	NA|662aa|up_6|NZ_CP013619.1_841143_843129_+	PRK05298, PRK05298, excinuclease ABC subunit UvrB	NA|949aa|up_5|NZ_CP013619.1_843136_845983_+	PRK00349, uvrA, excinuclease ABC subunit UvrA	NA|311aa|up_4|NZ_CP013619.1_846592_847525_+	PRK05428, PRK05428, HPr kinase/phosphorylase; Provisional	NA|280aa|up_3|NZ_CP013619.1_847530_848370_+	PRK12437, PRK12437, prolipoprotein diacylglyceryl transferase; Reviewed	NA|162aa|up_2|NZ_CP013619.1_848377_848863_+	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_CP013619.1_848870_850310_+	sd00006, TPR, Tetratricopeptide repeat	NA|312aa|up_0|NZ_CP013619.1_850376_851312_+	TIGR01292, Thioredoxin_reductase, thioredoxin-disulfide reductase	NA|304aa|down_0|NZ_CP013619.1_852079_852991_+	COG1660, COG1660, Predicted P-loop-containing kinase [General function prediction only]	NA|332aa|down_1|NZ_CP013619.1_852987_853983_+	TIGR01826, Putative_gluconeogenesis_factor, conserved hypothetical protein, cofD-related	NA|315aa|down_2|NZ_CP013619.1_854091_855036_+	TIGR00647, DNA_bind_WhiA, DNA-binding protein WhiA	NA|196aa|down_3|NZ_CP013619.1_855605_856193_+	PRK00277, clpP, ATP-dependent Clp protease proteolytic subunit; Reviewed	NA|545aa|down_4|NZ_CP013619.1_856375_858010_+	PRK13529, PRK13529, oxaloacetate-decarboxylating malate dehydrogenase	NA|301aa|down_5|NZ_CP013619.1_858216_859119_-	COG1090, COG1090, Predicted nucleoside-diphosphate sugar epimerase [General function prediction only]	NA|210aa|down_6|NZ_CP013619.1_859821_860451_+	PRK00409, PRK00409, recombination and DNA strand exchange inhibitor protein; Reviewed	NA|338aa|down_7|NZ_CP013619.1_861225_862239_+	COG2390, DeoR, Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]	NA|337aa|down_8|NZ_CP013619.1_862291_863302_+	TIGR01534, Glyceraldehyde-3-phosphate_dehydrogenase, glyceraldehyde-3-phosphate dehydrogenase, type I	NA|397aa|down_9|NZ_CP013619.1_863440_864631_+	PRK00073, pgk, phosphoglycerate kinase; Provisional
GCF_001465675.1_ASM146567v1	NZ_CP013619	Staphylococcus aureus strain RIVM1607 chromosome, complete genome	4	901063-901143	4	CRISPRCasFinder	no		WYL,csa3,cas3,DEDDh,DinG,TnsE_C	Orphan	TCTTTATCATTTCTGTCCCACTCCC	25	1	1	901088-901118	NZ_CP013619.1_846182-846152	NA	1	1	Orphan	WYL,csa3,cas3,DEDDh,DinG,TnsE_C	NA,NA|105aa|down_7|NZ_CP013619.1_908749_909064_-	NA|180aa|up_9|NZ_CP013619.1_893193_893733_+	cd02135, YdjA-like, nitroreductase family protein similar to Escherichia coli YdjA	NA|107aa|up_8|NZ_CP013619.1_893882_894203_-	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_CP013619.1_894346_894703_+	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_CP013619.1_894860_895241_+	PRK01202, PRK01202, glycine cleavage system protein GcvH	NA|293aa|up_5|NZ_CP013619.1_895420_896299_+	COG3878, COG3878, Uncharacterized protein conserved in bacteria [Function unknown]	NA|129aa|up_4|NZ_CP013619.1_897000_897387_+	COG1658, COG1658, Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]	NA|99aa|up_3|NZ_CP013619.1_897379_897676_+	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_CP013619.1_897925_898951_+	COG1135, AbcC, ABC-type metal ion transport system, ATPase component [Inorganic ion transport and metabolism]	NA|232aa|up_1|NZ_CP013619.1_898943_899639_+	COG2011, AbcD, ABC-type metal ion transport system, permease component [Inorganic ion transport and metabolism]	NA|274aa|up_0|NZ_CP013619.1_899656_900478_+	COG1464, NlpA, ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]	NA|65aa|down_0|NZ_CP013619.1_901285_901480_+	COG3237, COG3237, Uncharacterized protein conserved in bacteria [Function unknown]	NA|284aa|down_1|NZ_CP013619.1_901713_902565_-	COG2035, COG2035, Predicted membrane protein [Function unknown]	NA|254aa|down_2|NZ_CP013619.1_902892_903654_+	COG0396, sufC, Cysteine desulfurase activator ATPase [Posttranslational modification, protein turnover, chaperones]	NA|436aa|down_3|NZ_CP013619.1_903752_905060_+	COG0719, SufB, Cysteine desulfurase activator SufB [Posttranslational modification, protein turnover, chaperones]	NA|417aa|down_4|NZ_CP013619.1_905165_906416_+	TIGR01979, Probable_cysteine_desulfurase, cysteine desulfurases, SufSfamily	NA|155aa|down_5|NZ_CP013619.1_906405_906870_+	TIGR01994, Iron-sulfur_cluster_assembly_scaffold_protein_IscU, SUF system FeS assembly protein, NifU family	NA|466aa|down_6|NZ_CP013619.1_907020_908418_+	TIGR01980, UPF0051_protein_slr0074, FeS assembly protein SufB	NA|105aa|down_7|NZ_CP013619.1_908749_909064_-	NA	NA|347aa|down_8|NZ_CP013619.1_909432_910473_+	COG4536, CorB, Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]	NA|356aa|down_9|NZ_CP013619.1_910486_911554_+	COG2070, COG2070, Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]
GCF_001465675.1_ASM146567v1	NZ_CP013619	Staphylococcus aureus strain RIVM1607 chromosome, complete genome	5	1779195-1779277	5	CRISPRCasFinder	no		WYL,csa3,cas3,DEDDh,DinG,TnsE_C	Orphan	GAAGCTGACGAAAAAGTCAGCTTAC	25	0	0	NA	NA	NA	1	1	Orphan	WYL,csa3,cas3,DEDDh,DinG,TnsE_C	NA,NA	NA|454aa|up_9|NZ_CP013619.1_1764028_1765390_+	COG1113, AnsP, Gamma-aminobutyrate permease and related permeases [Amino acid transport and metabolism]	NA|586aa|up_8|NZ_CP013619.1_1765733_1767491_-	PRK06354, PRK06354, pyruvate kinase; Provisional	NA|323aa|up_7|NZ_CP013619.1_1767512_1768481_-	PRK03202, PRK03202, ATP-dependent 6-phosphofructokinase	NA|315aa|up_6|NZ_CP013619.1_1768749_1769694_-	PRK05724, PRK05724, acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated	NA|286aa|up_5|NZ_CP013619.1_1769693_1770551_-	PRK05654, PRK05654, acetyl-CoA carboxylase carboxyltransferase subunit beta	NA|410aa|up_4|NZ_CP013619.1_1770745_1771975_-	PRK07232, PRK07232, bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed	NA|1066aa|up_3|NZ_CP013619.1_1772423_1775621_-	COG0587, DnaE, DNA polymerase III, alpha subunit [DNA replication, recombination, and repair]	NA|314aa|up_2|NZ_CP013619.1_1775641_1776583_-	COG0618, COG0618, Exopolyphosphatase-related proteins [General function prediction only]	NA|433aa|up_1|NZ_CP013619.1_1776952_1778251_-	COG4109, COG4109, Predicted transcriptional regulator containing CBS domains [Transcription]	NA|138aa|up_0|NZ_CP013619.1_1778455_1778869_+	pfam00582, Usp, Universal stress protein family	NA|230aa|down_0|NZ_CP013619.1_1779374_1780064_-	PRK00685, PRK00685, metal-dependent hydrolase; Provisional	NA|352aa|down_1|NZ_CP013619.1_1780238_1781294_+	COG0006, PepP, Xaa-Pro aminopeptidase [Amino acid transport and metabolism]	NA|373aa|down_2|NZ_CP013619.1_1781609_1782728_-	cd05305, L-AlaDH, Alanine dehydrogenase NAD-binding and catalytic domains	NA|167aa|down_3|NZ_CP013619.1_1782868_1783369_+	pfam00582, Usp, Universal stress protein family	NA|401aa|down_4|NZ_CP013619.1_1783615_1784818_-	PRK00180, PRK00180, acetate kinase A/propionate kinase 2; Reviewed	NA|316aa|down_5|NZ_CP013619.1_1784905_1785853_-	COG0827, COG0827, Adenine-specific DNA methylase [DNA replication, recombination, and repair]	NA|165aa|down_6|NZ_CP013619.1_1785975_1786470_-	PRK00522, tpx, thiol peroxidase	NA|257aa|down_7|NZ_CP013619.1_1786567_1787338_-	PRK10621, PRK10621, hypothetical protein; Provisional	NA|408aa|down_8|NZ_CP013619.1_1787381_1788605_-	PRK01565, PRK01565, thiamine biosynthesis protein ThiI; Provisional	NA|383aa|down_9|NZ_CP013619.1_1788604_1789753_-	COG1104, NifS, Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]
GCF_001465675.1_ASM146567v1	NZ_CP013619	Staphylococcus aureus strain RIVM1607 chromosome, complete genome	6	1867557-1867650	6	CRISPRCasFinder	no	csa3	WYL,csa3,cas3,DEDDh,DinG,TnsE_C	Type I-A	GCAATGCGCGTTGGGGTGTGGGGCCCCAACATAG	34	1	1	1867591-1867616	NZ_CP013619.1_1965379-1965354	NA	1	1	Orphan	WYL,csa3,cas3,DEDDh,DinG,TnsE_C	NA|75aa|up_5|NZ_CP013619.1_1863650_1863875_-,NA|148aa|up_2|NZ_CP013619.1_1865086_1865530_-,NA|101aa|down_1|NZ_CP013619.1_1868784_1869087_+	NA|501aa|up_9|NZ_CP013619.1_1858674_1860177_-	COG4529, COG4529, Uncharacterized protein conserved in bacteria [Function unknown]	csa3|105aa|up_8|NZ_CP013619.1_1860827_1861142_+	cd00090, HTH_ARSR, Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors	NA|431aa|up_7|NZ_CP013619.1_1861141_1862434_+	PRK15445, PRK15445, arsenical efflux pump membrane protein ArsB	NA|285aa|up_6|NZ_CP013619.1_1862520_1863375_-	COG4193, LytD, Beta- N-acetylglucosaminidase [Carbohydrate transport and metabolism]	NA|75aa|up_5|NZ_CP013619.1_1863650_1863875_-	NA	NA|157aa|up_4|NZ_CP013619.1_1864073_1864544_+	COG1595, RpoE, DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]	NA|148aa|up_3|NZ_CP013619.1_1864656_1865100_+	pfam06338, ComK, ComK protein	NA|148aa|up_2|NZ_CP013619.1_1865086_1865530_-	NA	NA|212aa|up_1|NZ_CP013619.1_1865827_1866463_+	pfam02517, Abi, CAAX protease self-immunity	NA|207aa|up_0|NZ_CP013619.1_1866629_1867250_+	pfam02517, Abi, CAAX protease self-immunity	NA|238aa|down_0|NZ_CP013619.1_1867812_1868526_-	PRK12376, PRK12376, putative translaldolase; Provisional	NA|101aa|down_1|NZ_CP013619.1_1868784_1869087_+	NA	NA|122aa|down_2|NZ_CP013619.1_1869341_1869707_+	PRK14201, PRK14201, fluoride efflux transporter CrcB	NA|118aa|down_3|NZ_CP013619.1_1869703_1870057_+	COG0239, CrcB, Integral membrane protein possibly involved in chromosome condensation [Cell division and chromosome partitioning]	NA|278aa|down_4|NZ_CP013619.1_1870306_1871140_-	COG0656, ARA1, Aldo/keto reductases, related to diketogulonate reductase [General function prediction only]	NA|303aa|down_5|NZ_CP013619.1_1871351_1872260_-	pfam08378, NERD, Nuclease-related domain	NA|398aa|down_6|NZ_CP013619.1_1872384_1873578_-	PRK05250, PRK05250, S-adenosylmethionine synthetase; Validated	NA|531aa|down_7|NZ_CP013619.1_1873949_1875542_+	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_CP013619.1_1875838_1876585_-	COG1506, DAP2, Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]	NA|158aa|down_9|NZ_CP013619.1_1876589_1877063_-	TIGR02705, conserved_hypothetical_protein, nucleoside triphosphatase YtkD
GCF_001465675.1_ASM146567v1	NZ_CP013619	Staphylococcus aureus strain RIVM1607 chromosome, complete genome	7	2108421-2108633	7	CRISPRCasFinder	no		WYL,csa3,cas3,DEDDh,DinG,TnsE_C	Orphan	TGATGTGCTGTTGTGGAAGCTTGGTGTCGTGCCATGCTACTTTGATG	47	0	0	NA	NA	NA	2	2	Orphan	WYL,csa3,cas3,DEDDh,DinG,TnsE_C	NA|46aa|up_4|NZ_CP013619.1_2105282_2105420_-,NA|107aa|down_0|NZ_CP013619.1_2108666_2108987_+	NA|232aa|up_9|NZ_CP013619.1_2097974_2098670_+	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_CP013619.1_2099022_2100543_-	COG0513, SrmB, Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]	NA|452aa|up_7|NZ_CP013619.1_2101058_2102414_-	COG0770, MurF, UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]	NA|357aa|up_6|NZ_CP013619.1_2102428_2103499_-	PRK01966, ddl, D-alanine--D-alanine ligase	NA|401aa|up_5|NZ_CP013619.1_2103816_2105019_+	TIGR02210, Rod_shape-determining_protein_RodA, rod shape-determining protein RodA	NA|46aa|up_4|NZ_CP013619.1_2105282_2105420_-	NA	NA|70aa|up_3|NZ_CP013619.1_2105547_2105757_-	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_CP013619.1_2105768_2106062_-	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_CP013619.1_2106227_2107712_+	TIGR04265, bac_cardiolipin, cardiolipin synthase	NA|216aa|up_0|NZ_CP013619.1_2107739_2108387_+	COG1418, COG1418, Predicted HD superfamily hydrolase [General function prediction only]	NA|107aa|down_0|NZ_CP013619.1_2108666_2108987_+	NA	NA|291aa|down_1|NZ_CP013619.1_2110628_2111501_-	PRK02463, PRK02463, OxaA-like protein precursor; Provisional	NA|214aa|down_2|NZ_CP013619.1_2111586_2112228_-	PRK00043, thiE, thiamine phosphate synthase	NA|264aa|down_3|NZ_CP013619.1_2112229_2113021_-	PRK09355, PRK09355, hydroxyethylthiazole kinase; Validated	NA|277aa|down_4|NZ_CP013619.1_2113004_2113835_-	PRK06427, PRK06427, bifunctional hydroxy-methylpyrimidine kinase/ hydroxy-phosphomethylpyrimidine kinase; Reviewed	NA|230aa|down_5|NZ_CP013619.1_2113827_2114517_-	TIGR04306, salvage_TenA, thiaminase II	NA|232aa|down_6|NZ_CP013619.1_2114903_2115599_-	pfam06737, Transglycosylas, Transglycosylase-like domain	NA|132aa|down_7|NZ_CP013619.1_2115987_2116383_-	pfam00436, SSB, Single-strand binding protein family	NA|147aa|down_8|NZ_CP013619.1_2116576_2117017_+	pfam14183, YwpF, YwpF-like protein	NA|147aa|down_9|NZ_CP013619.1_2117073_2117514_-	PRK00006, fabZ, 3-hydroxyacyl-ACP dehydratase FabZ
GCF_001465675.1_ASM146567v1	NZ_CP013619	Staphylococcus aureus strain RIVM1607 chromosome, complete genome	8	2164052-2164202	8	CRISPRCasFinder	no	csa3,TnsE_C	WYL,csa3,cas3,DEDDh,DinG,TnsE_C	Type I-A	AACTTTAGTTGTTAGGGGCTCTTATGCA	28	0	0	NA	NA	NA	2	2	Orphan	WYL,csa3,cas3,DEDDh,DinG,TnsE_C	NA|77aa|up_5|NZ_CP013619.1_2158924_2159155_-,NA|364aa|up_0|NZ_CP013619.1_2162942_2164034_+,NA|35aa|down_0|NZ_CP013619.1_2164531_2164636_-,NA|53aa|down_1|NZ_CP013619.1_2165315_2165474_+,NA|31aa|down_2|NZ_CP013619.1_2165909_2166002_+	NA|237aa|up_9|NZ_CP013619.1_2154534_2155245_+	PRK05819, deoD, DeoD-type purine-nucleoside phosphorylase	NA|148aa|up_8|NZ_CP013619.1_2155365_2155809_-	COG0783, Dps, DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]	NA|138aa|up_7|NZ_CP013619.1_2156008_2156422_-	COG3011, COG3011, Predicted thiol-disulfide oxidoreductase [General function    prediction only]	NA|458aa|up_6|NZ_CP013619.1_2156879_2158253_-	pfam01878, EVE, EVE domain	NA|77aa|up_5|NZ_CP013619.1_2158924_2159155_-	NA	NA|313aa|up_4|NZ_CP013619.1_2159185_2160124_-	COG1482, ManA, Phosphomannose isomerase [Carbohydrate transport and metabolism]	NA|222aa|up_3|NZ_CP013619.1_2160557_2161223_-	cd05243, SDR_a5, atypical (a) SDRs, subgroup 5	csa3|107aa|up_2|NZ_CP013619.1_2161374_2161695_+	cd00090, HTH_ARSR, Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors	NA|327aa|up_1|NZ_CP013619.1_2161696_2162677_+	COG1230, CzcD, Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]	NA|364aa|up_0|NZ_CP013619.1_2162942_2164034_+	NA	NA|35aa|down_0|NZ_CP013619.1_2164531_2164636_-	NA	NA|53aa|down_1|NZ_CP013619.1_2165315_2165474_+	NA	NA|31aa|down_2|NZ_CP013619.1_2165909_2166002_+	NA	NA|286aa|down_3|NZ_CP013619.1_2166131_2166989_-	COG0561, Cof, Predicted hydrolases of the HAD superfamily [General function prediction only]	NA|261aa|down_4|NZ_CP013619.1_2167056_2167839_-	COG1119, ModF, ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA [Inorganic ion transport and metabolism]	NA|203aa|down_5|NZ_CP013619.1_2168128_2168737_-	pfam08937, DUF1863, MTH538 TIR-like domain (DUF1863)	NA|345aa|down_6|NZ_CP013619.1_2168764_2169799_-	pfam13676, TIR_2, TIR domain	NA|490aa|down_7|NZ_CP013619.1_2169892_2171362_-	pfam18185, STALD, Sir2- and TIR-associating SLOG family	NA|97aa|down_8|NZ_CP013619.1_2171421_2171712_-	pfam11867, DUF3387, Domain of unknown function (DUF3387)	TnsE_C|135aa|down_9|NZ_CP013619.1_2171836_2172241_-	pfam18623, TnsE_C, TnsE C-terminal domain
GCF_001465675.1_ASM146567v1	NZ_CP013619	Staphylococcus aureus strain RIVM1607 chromosome, complete genome	9	2328095-2328180	9	CRISPRCasFinder	no	WYL	WYL,csa3,cas3,DEDDh,DinG,TnsE_C	Unclear	AAAGTCAGCTTACAATAATGTGCAAGTTGG	30	1	7	2328125-2328150|2328125-2328150|2328125-2328150|2328125-2328150|2328125-2328150|2328125-2328150|2328125-2328150	NZ_CP013619.1_1651297-1651272|NZ_CP013619.1_896745-896720|NZ_CP013619.1_900865-900890|NZ_CP013619.1_945800-945825|NZ_CP013619.1_1382564-1382589|NZ_CP013619.1_2119533-2119558|NZ_CP013619.1_2460042-2460017	NA	1	1	Orphan	WYL,csa3,cas3,DEDDh,DinG,TnsE_C	NA|65aa|up_6|NZ_CP013619.1_2320839_2321034_-,NA|78aa|down_1|NZ_CP013619.1_2329130_2329364_-,NA|110aa|down_8|NZ_CP013619.1_2337452_2337782_+	NA|248aa|up_9|NZ_CP013619.1_2316627_2317371_-	TIGR01889, Pleiotropic_Regulator_Of_Virulence, staphylococcal accessory regulator family	NA|652aa|up_8|NZ_CP013619.1_2317396_2319352_-	COG2207, AraC, AraC-type DNA-binding domain-containing proteins [Transcription]	NA|270aa|up_7|NZ_CP013619.1_2319961_2320771_+	COG3942, COG3942, Surface antigen [General function prediction only]	NA|65aa|up_6|NZ_CP013619.1_2320839_2321034_-	NA	NA|467aa|up_5|NZ_CP013619.1_2321207_2322608_-	TIGR00931, Uncharacterized_Na+/H+_antiporter_HI_1107, Na+/H+ antiporter NhaC	NA|361aa|up_4|NZ_CP013619.1_2322702_2323785_-	pfam02317, Octopine_DH, NAD/NADP octopine/nopaline dehydrogenase, alpha-helical domain	NA|141aa|up_3|NZ_CP013619.1_2324032_2324455_+	COG3296, COG3296, Uncharacterized protein conserved in bacteria [Function unknown]	NA|167aa|up_2|NZ_CP013619.1_2324691_2325192_+	COG3942, COG3942, Surface antigen [General function prediction only]	NA|318aa|up_1|NZ_CP013619.1_2325554_2326508_+	cd12178, 2-Hacid_dh_13, Putative D-isomer specific 2-hydroxyacid dehydrogenases, NAD-binding and catalytic domains	NA|375aa|up_0|NZ_CP013619.1_2326599_2327724_-	PRK06753, PRK06753, hypothetical protein; Provisional	NA|259aa|down_0|NZ_CP013619.1_2328332_2329109_-	COG4193, LytD, Beta- N-acetylglucosaminidase [Carbohydrate transport and metabolism]	NA|78aa|down_1|NZ_CP013619.1_2329130_2329364_-	NA	NA|158aa|down_2|NZ_CP013619.1_2329658_2330132_-	COG2427, COG2427, Uncharacterized conserved protein [Function unknown]	NA|985aa|down_3|NZ_CP013619.1_2330131_2333086_-	COG3383, COG3383, Uncharacterized anaerobic dehydrogenase [General function prediction only]	NA|316aa|down_4|NZ_CP013619.1_2333687_2334635_-	PRK09379, PRK09379, LytR family transcriptional regulator	NA|266aa|down_5|NZ_CP013619.1_2334767_2335565_-	COG0483, SuhB, Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]	WYL|231aa|down_6|NZ_CP013619.1_2335949_2336642_+	COG2378, COG2378, Predicted transcriptional regulator [Transcription]	NA|246aa|down_7|NZ_CP013619.1_2336666_2337404_-	pfam02517, Abi, CAAX protease self-immunity	NA|110aa|down_8|NZ_CP013619.1_2337452_2337782_+	NA	NA|291aa|down_9|NZ_CP013619.1_2338226_2339099_+	COG1737, RpiR, Transcriptional regulators [Transcription]
GCF_001465675.1_ASM146567v1	NZ_CP013619	Staphylococcus aureus strain RIVM1607 chromosome, complete genome	10	2504306-2504400	10	CRISPRCasFinder	no		WYL,csa3,cas3,DEDDh,DinG,TnsE_C	Orphan	AGGCTCTTATGCAGTTGGTGCGAAGCAA	28	0	0	NA	NA	NA	1	1	Orphan	WYL,csa3,cas3,DEDDh,DinG,TnsE_C	NA|249aa|up_9|NZ_CP013619.1_2493891_2494638_+,NA|121aa|down_0|NZ_CP013619.1_2505068_2505431_-,NA|105aa|down_8|NZ_CP013619.1_2512243_2512558_+	NA|249aa|up_9|NZ_CP013619.1_2493891_2494638_+	NA	NA|398aa|up_8|NZ_CP013619.1_2494861_2496055_-	cd17489, MFS_YfcJ_like, Escherichia coli YfcJ, YhhS, and similar transporters of the Major Facilitator Superfamily	NA|250aa|up_7|NZ_CP013619.1_2496066_2496816_-	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_CP013619.1_2496808_2497624_-	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_CP013619.1_2497620_2498490_-	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_CP013619.1_2498486_2499422_-	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_CP013619.1_2499434_2501033_-	TIGR02294, Nickel-binding_periplasmic_protein, nickel ABC transporter, nickel/metallophore periplasmic binding protein	NA|434aa|up_2|NZ_CP013619.1_2501175_2502477_-	COG4408, COG4408, Uncharacterized protein conserved in bacteria [Function unknown]	NA|273aa|up_1|NZ_CP013619.1_2502469_2503288_-	cd08261, Zn_ADH7, Alcohol dehydrogenases of the MDR family	NA|274aa|up_0|NZ_CP013619.1_2503298_2504120_-	COG0253, DapF, Diaminopimelate epimerase [Amino acid transport and metabolism]	NA|121aa|down_0|NZ_CP013619.1_2505068_2505431_-	NA	NA|273aa|down_1|NZ_CP013619.1_2505693_2506512_-	PRK08589, PRK08589, SDR family oxidoreductase	NA|513aa|down_2|NZ_CP013619.1_2506745_2508284_+	pfam03806, ABG_transport, AbgT putative transporter family	NA|141aa|down_3|NZ_CP013619.1_2508395_2508818_-	COG2128, COG2128, Uncharacterized conserved protein [Function unknown]	NA|133aa|down_4|NZ_CP013619.1_2509289_2509688_-	pfam07252, DUF1433, Protein of unknown function (DUF1433)	NA|137aa|down_5|NZ_CP013619.1_2509714_2510125_-	pfam07252, DUF1433, Protein of unknown function (DUF1433)	NA|128aa|down_6|NZ_CP013619.1_2510579_2510963_-	pfam07252, DUF1433, Protein of unknown function (DUF1433)	NA|403aa|down_7|NZ_CP013619.1_2511029_2512238_+	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_CP013619.1_2512243_2512558_+	NA	NA|140aa|down_9|NZ_CP013619.1_2514434_2514854_-	pfam07252, DUF1433, Protein of unknown function (DUF1433)
GCF_001465675.1_ASM146567v1	NZ_CP013619	Staphylococcus aureus strain RIVM1607 chromosome, complete genome	11	2532251-2532361	11	CRISPRCasFinder	no		WYL,csa3,cas3,DEDDh,DinG,TnsE_C	Orphan	GGTACTTCTGGTGTCGGTGGCGTTGGT	27	0	0	NA	NA	NA	1	1	Orphan	WYL,csa3,cas3,DEDDh,DinG,TnsE_C	NA|89aa|up_2|NZ_CP013619.1_2526554_2526821_+,NA|103aa|up_1|NZ_CP013619.1_2526964_2527273_+,NA	NA|452aa|up_9|NZ_CP013619.1_2517948_2519304_-	cd00519, Lipase_3, Lipase (class 3)	NA|262aa|up_8|NZ_CP013619.1_2519300_2520086_-	pfam04507, DUF576, Csa1 family	NA|255aa|up_7|NZ_CP013619.1_2520333_2521098_-	pfam04507, DUF576, Csa1 family	NA|258aa|up_6|NZ_CP013619.1_2521209_2521983_-	pfam04507, DUF576, Csa1 family	NA|310aa|up_5|NZ_CP013619.1_2522225_2523155_-	pfam09019, EcoRII-C, EcoRII C terminal	NA|398aa|up_4|NZ_CP013619.1_2523250_2524444_+	TIGR00675, Modification_methylase, DNA-methyltransferase (dcm)	NA|584aa|up_3|NZ_CP013619.1_2524519_2526271_+	cd05799, PGM2, This CD includes PGM2 (phosphoglucomutase 2) and PGM2L1 (phosphoglucomutase 2-like 1)	NA|89aa|up_2|NZ_CP013619.1_2526554_2526821_+	NA	NA|103aa|up_1|NZ_CP013619.1_2526964_2527273_+	NA	NA|289aa|up_0|NZ_CP013619.1_2527398_2528265_-	COG1210, GalU, UDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]	NA|453aa|down_0|NZ_CP013619.1_2535501_2536860_-	TIGR00791, Gluconate_permease, gluconate transporter	NA|518aa|down_1|NZ_CP013619.1_2536976_2538530_-	TIGR01314, gntK_FGGY, gluconate kinase, FGGY type	NA|226aa|down_2|NZ_CP013619.1_2538554_2539232_-	COG1802, GntR, Transcriptional regulators [Transcription]	NA|255aa|down_3|NZ_CP013619.1_2539388_2540153_-	cd01106, HTH_TipAL-Mta, Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA	NA|231aa|down_4|NZ_CP013619.1_2540317_2541010_-	COG2357, COG2357, PpGpp synthetase catalytic domain [General function prediction only]	NA|139aa|down_5|NZ_CP013619.1_2541240_2541657_-	COG4876, COG4876, Uncharacterized protein conserved in bacteria [Function unknown]	NA|608aa|down_6|NZ_CP013619.1_2541795_2543619_-	COG1289, COG1289, Predicted membrane protein [Function unknown]	NA|426aa|down_7|NZ_CP013619.1_2544530_2545808_-	cd17319, MFS_ExuT_GudP_like, Hexuronate transporter, Glucarate transporter, and similar transporters of the Major Facilitator Superfamily	NA|204aa|down_8|NZ_CP013619.1_2546354_2546966_+	COG0586, DedA, Uncharacterized membrane-associated protein [Function unknown]	NA|388aa|down_9|NZ_CP013619.1_2547063_2548227_-	cd17474, MFS_YfmO_like, Bacillus subtilis multidrug efflux protein YfmO and similar transporters of the Major Facilitator Superfamily
