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_001465755.1_ASM146575v1	NZ_CP013621	Staphylococcus aureus strain RIVM3897 chromosome, complete genome	1	320337-320536	1	CRISPRCasFinder	no		csa3,cas3,DEDDh,DinG,TnsE_C,WYL	Orphan	TGCAAGTTGGCGGGGCCCCAACACAGAAGCT	31	2	2	320368-320392|320424-320448	NZ_CP013621.1_320537-320561|NZ_CP013621.1_2232359-2232383	NA	3	3	Orphan	csa3,cas3,DEDDh,DinG,TnsE_C,WYL	NA,NA|131aa|down_5|NZ_CP013621.1_325712_326105_+	NA|574aa|up_9|NZ_CP013621.1_307783_309505_+	pfam18674, TarS_C1, TarS beta-glycosyltransferase C-terminal domain 1	NA|225aa|up_8|NZ_CP013621.1_309648_310323_+	PRK13276, PRK13276, iron-sulfur cluster repair di-iron protein ScdA	NA|585aa|up_7|NZ_CP013621.1_310569_312324_+	COG3275, LytS, Putative regulator of cell autolysis [Signal transduction mechanisms]	NA|247aa|up_6|NZ_CP013621.1_312326_313067_+	PRK14084, PRK14084, DNA-binding response regulator	NA|148aa|up_5|NZ_CP013621.1_313179_313623_+	PRK04125, PRK04125, antiholin-like protein LrgA	NA|234aa|up_4|NZ_CP013621.1_313615_314317_+	PRK04288, PRK04288, antiholin-like protein LrgB; Provisional	NA|764aa|up_3|NZ_CP013621.1_314657_316949_+	COG3256, NorB, Nitric oxide reductase large subunit [Inorganic ion transport and metabolism]	NA|235aa|up_2|NZ_CP013621.1_317174_317879_-	COG2188, PhnF, Transcriptional regulators [Transcription]	NA|264aa|up_1|NZ_CP013621.1_318027_318819_+	COG2190, NagE, Phosphotransferase system IIA components [Carbohydrate transport and metabolism]	NA|479aa|up_0|NZ_CP013621.1_318834_320271_+	PRK09589, celA, 6-phospho-beta-glucosidase; Reviewed	NA|254aa|down_0|NZ_CP013621.1_320846_321608_-	pfam13649, Methyltransf_25, Methyltransferase domain	NA|305aa|down_1|NZ_CP013621.1_321859_322774_-	TIGR02152, Putative_ribokinase, ribokinase	NA|135aa|down_2|NZ_CP013621.1_322801_323206_-	PRK11797, PRK11797, D-ribose pyranase; Provisional	NA|294aa|down_3|NZ_CP013621.1_323220_324102_-	pfam06800, Sugar_transport, Sugar transport protein	NA|333aa|down_4|NZ_CP013621.1_324333_325332_-	COG1609, PurR, Transcriptional regulators [Transcription]	NA|131aa|down_5|NZ_CP013621.1_325712_326105_+	NA	NA|459aa|down_6|NZ_CP013621.1_326233_327610_-	TIGR00711, Uncharacterized_MFS-type_transporter_YhcA, drug resistance transporter, EmrB/QacA subfamily	NA|331aa|down_7|NZ_CP013621.1_327843_328836_+	COG3049, COG3049, Penicillin V acylase and related amidases [Cell envelope biogenesis, outer membrane]	NA|317aa|down_8|NZ_CP013621.1_329161_330112_+	COG3942, COG3942, Surface antigen [General function prediction only]	NA|220aa|down_9|NZ_CP013621.1_330163_330823_-	COG1131, CcmA, ABC-type multidrug transport system, ATPase component [Defense mechanisms]
GCF_001465755.1_ASM146575v1	NZ_CP013621	Staphylococcus aureus strain RIVM3897 chromosome, complete genome	2	705658-705766	2	CRISPRCasFinder	no		csa3,cas3,DEDDh,DinG,TnsE_C,WYL	Orphan	AAAGGAACGCAGTTGGATGCTACCGCACAACTGCATAAA	39	0	0	NA	NA	NA	1	1	Orphan	csa3,cas3,DEDDh,DinG,TnsE_C,WYL	NA,NA|169aa|down_4|NZ_CP013621.1_709499_710006_+,NA|239aa|down_5|NZ_CP013621.1_710167_710884_+	NA|209aa|up_9|NZ_CP013621.1_695162_695789_+	pfam04276, DUF443, Protein of unknown function (DUF443)	NA|313aa|up_8|NZ_CP013621.1_696058_696997_+	cd19083, AKR_AKR11A1_11D1, AKR11A and  AKR11D families of aldo-keto reductase (AKR)	NA|179aa|up_7|NZ_CP013621.1_697442_697979_+	COG0655, WrbA, Multimeric flavodoxin WrbA [General function prediction only]	NA|159aa|up_6|NZ_CP013621.1_698148_698625_+	pfam00583, Acetyltransf_1, Acetyltransferase (GNAT) family	NA|432aa|up_5|NZ_CP013621.1_698664_699960_+	COG1078, COG1078, HD superfamily phosphohydrolases [General function prediction only]	NA|174aa|up_4|NZ_CP013621.1_699987_700509_+	pfam08741, YwhD, YwhD family	NA|337aa|up_3|NZ_CP013621.1_701007_702018_+	PRK09422, PRK09422, ethanol-active dehydrogenase/acetaldehyde-active reductase; Provisional	NA|139aa|up_2|NZ_CP013621.1_702293_702710_+	COG4506, COG4506, Uncharacterized protein conserved in bacteria [Function unknown]	NA|554aa|up_1|NZ_CP013621.1_702706_704368_+	PRK01611, argS, arginyl-tRNA synthetase; Reviewed	NA|212aa|up_0|NZ_CP013621.1_704852_705488_+	COG2231, COG2231, Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]	NA|296aa|down_0|NZ_CP013621.1_705817_706705_+	cd01143, YvrC, Periplasmic binding protein YvrC	NA|317aa|down_1|NZ_CP013621.1_706855_707806_+	pfam01032, FecCD, FecCD transport family	NA|240aa|down_2|NZ_CP013621.1_707860_708580_+	COG1011, COG1011, Predicted hydrolase (HAD superfamily) [General function prediction only]	NA|267aa|down_3|NZ_CP013621.1_708563_709364_+	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|169aa|down_4|NZ_CP013621.1_709499_710006_+	NA	NA|239aa|down_5|NZ_CP013621.1_710167_710884_+	NA	NA|263aa|down_6|NZ_CP013621.1_711052_711841_+	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|125aa|down_7|NZ_CP013621.1_712092_712467_-	TIGR01889, Pleiotropic_Regulator_Of_Virulence, staphylococcal accessory regulator family	NA|310aa|down_8|NZ_CP013621.1_713414_714344_-	COG3238, COG3238, Uncharacterized protein conserved in bacteria [Function unknown]	NA|75aa|down_9|NZ_CP013621.1_714536_714761_-	pfam11148, DUF2922, Protein of unknown function (DUF2922)
GCF_001465755.1_ASM146575v1	NZ_CP013621	Staphylococcus aureus strain RIVM3897 chromosome, complete genome	3	867874-867956	3	CRISPRCasFinder	no		csa3,cas3,DEDDh,DinG,TnsE_C,WYL	Orphan	CACCCCAACTCGCATTGCTTGTAGAA	26	1	23	867900-867930|867900-867930|867900-867930|867900-867930|867900-867930|867900-867930|867900-867930|867900-867930|867900-867930|867900-867930|867900-867930|867900-867930|867900-867930|867900-867930|867900-867930|867900-867930|867900-867930|867900-867930|867900-867930|867900-867930|867900-867930|867900-867930|867900-867930	NZ_CP013621.1_962188-962158|NZ_CP013621.1_1000989-1001019|NZ_CP013621.1_2087219-2087249|NZ_CP013621.1_2087329-2087359|NZ_CP013621.1_2146536-2146566|NZ_CP013621.1_302465-302495|NZ_CP013621.1_428390-428360|NZ_CP013621.1_697155-697125|NZ_CP013621.1_821587-821557|NZ_CP013621.1_912819-912849|NZ_CP013621.1_1109251-1109281|NZ_CP013621.1_1209579-1209549|NZ_CP013621.1_1209633-1209603|NZ_CP013621.1_1854804-1854774|NZ_CP013621.1_1945582-1945552|NZ_CP013621.1_2395783-2395813|NZ_CP013621.1_2440852-2440822|NZ_CP013621.1_876881-876911|NZ_CP013621.1_916957-916927|NZ_CP013621.1_1418361-1418391|NZ_CP013621.1_1464451-1464481|NZ_CP013621.1_2406531-2406561|NZ_CP013621.1_2855037-2855067	NA	1	1	Orphan	csa3,cas3,DEDDh,DinG,TnsE_C,WYL	NA,NA	NA|280aa|up_9|NZ_CP013621.1_855123_855963_+	COG3942, COG3942, Surface antigen [General function prediction only]	NA|217aa|up_8|NZ_CP013621.1_856136_856787_+	pfam12917, HD_2, HD containing hydrolase-like enzyme	NA|79aa|up_7|NZ_CP013621.1_856783_857020_+	COG4897, CsbA, Uncharacterized protein conserved in bacteria [Function unknown]	NA|662aa|up_6|NZ_CP013621.1_857288_859274_+	PRK05298, PRK05298, excinuclease ABC subunit UvrB	NA|949aa|up_5|NZ_CP013621.1_859281_862128_+	PRK00349, uvrA, excinuclease ABC subunit UvrA	NA|311aa|up_4|NZ_CP013621.1_862737_863670_+	PRK05428, PRK05428, HPr kinase/phosphorylase; Provisional	NA|280aa|up_3|NZ_CP013621.1_863675_864515_+	PRK12437, PRK12437, prolipoprotein diacylglyceryl transferase; Reviewed	NA|162aa|up_2|NZ_CP013621.1_864522_865008_+	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_CP013621.1_865015_866455_+	sd00006, TPR, Tetratricopeptide repeat	NA|312aa|up_0|NZ_CP013621.1_866521_867457_+	TIGR01292, Thioredoxin_reductase, thioredoxin-disulfide reductase	NA|304aa|down_0|NZ_CP013621.1_868224_869136_+	COG1660, COG1660, Predicted P-loop-containing kinase [General function prediction only]	NA|332aa|down_1|NZ_CP013621.1_869132_870128_+	TIGR01826, Putative_gluconeogenesis_factor, conserved hypothetical protein, cofD-related	NA|315aa|down_2|NZ_CP013621.1_870236_871181_+	TIGR00647, DNA_bind_WhiA, DNA-binding protein WhiA	NA|196aa|down_3|NZ_CP013621.1_871750_872338_+	PRK00277, clpP, ATP-dependent Clp protease proteolytic subunit; Reviewed	NA|545aa|down_4|NZ_CP013621.1_872520_874155_+	PRK13529, PRK13529, oxaloacetate-decarboxylating malate dehydrogenase	NA|301aa|down_5|NZ_CP013621.1_874361_875264_-	COG1090, COG1090, Predicted nucleoside-diphosphate sugar epimerase [General function prediction only]	NA|210aa|down_6|NZ_CP013621.1_875966_876596_+	PRK00409, PRK00409, recombination and DNA strand exchange inhibitor protein; Reviewed	NA|338aa|down_7|NZ_CP013621.1_877370_878384_+	COG2390, DeoR, Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]	NA|337aa|down_8|NZ_CP013621.1_878436_879447_+	TIGR01534, Glyceraldehyde-3-phosphate_dehydrogenase, glyceraldehyde-3-phosphate dehydrogenase, type I	NA|397aa|down_9|NZ_CP013621.1_879585_880776_+	PRK00073, pgk, phosphoglycerate kinase; Provisional
GCF_001465755.1_ASM146575v1	NZ_CP013621	Staphylococcus aureus strain RIVM3897 chromosome, complete genome	4	917226-917306	4	CRISPRCasFinder	no		csa3,cas3,DEDDh,DinG,TnsE_C,WYL	Orphan	TCTTTATCATTTCTGTCCCACTCCC	25	1	1	917251-917281	NZ_CP013621.1_862327-862297	NA	1	1	Orphan	csa3,cas3,DEDDh,DinG,TnsE_C,WYL	NA,NA|105aa|down_7|NZ_CP013621.1_924912_925227_-	NA|180aa|up_9|NZ_CP013621.1_909356_909896_+	cd02135, YdjA-like, nitroreductase family protein similar to Escherichia coli YdjA	NA|107aa|up_8|NZ_CP013621.1_910045_910366_-	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_CP013621.1_910509_910866_+	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_CP013621.1_911023_911404_+	PRK01202, PRK01202, glycine cleavage system protein GcvH	NA|293aa|up_5|NZ_CP013621.1_911583_912462_+	COG3878, COG3878, Uncharacterized protein conserved in bacteria [Function unknown]	NA|129aa|up_4|NZ_CP013621.1_913163_913550_+	COG1658, COG1658, Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]	NA|99aa|up_3|NZ_CP013621.1_913542_913839_+	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_CP013621.1_914088_915114_+	COG1135, AbcC, ABC-type metal ion transport system, ATPase component [Inorganic ion transport and metabolism]	NA|232aa|up_1|NZ_CP013621.1_915106_915802_+	COG2011, AbcD, ABC-type metal ion transport system, permease component [Inorganic ion transport and metabolism]	NA|274aa|up_0|NZ_CP013621.1_915819_916641_+	COG1464, NlpA, ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]	NA|65aa|down_0|NZ_CP013621.1_917448_917643_+	COG3237, COG3237, Uncharacterized protein conserved in bacteria [Function unknown]	NA|284aa|down_1|NZ_CP013621.1_917876_918728_-	COG2035, COG2035, Predicted membrane protein [Function unknown]	NA|254aa|down_2|NZ_CP013621.1_919055_919817_+	COG0396, sufC, Cysteine desulfurase activator ATPase [Posttranslational modification, protein turnover, chaperones]	NA|436aa|down_3|NZ_CP013621.1_919915_921223_+	COG0719, SufB, Cysteine desulfurase activator SufB [Posttranslational modification, protein turnover, chaperones]	NA|417aa|down_4|NZ_CP013621.1_921328_922579_+	TIGR01979, Probable_cysteine_desulfurase, cysteine desulfurases, SufSfamily	NA|155aa|down_5|NZ_CP013621.1_922568_923033_+	TIGR01994, Iron-sulfur_cluster_assembly_scaffold_protein_IscU, SUF system FeS assembly protein, NifU family	NA|466aa|down_6|NZ_CP013621.1_923183_924581_+	TIGR01980, UPF0051_protein_slr0074, FeS assembly protein SufB	NA|105aa|down_7|NZ_CP013621.1_924912_925227_-	NA	NA|347aa|down_8|NZ_CP013621.1_925595_926636_+	COG4536, CorB, Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]	NA|356aa|down_9|NZ_CP013621.1_926649_927717_+	COG2070, COG2070, Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]
GCF_001465755.1_ASM146575v1	NZ_CP013621	Staphylococcus aureus strain RIVM3897 chromosome, complete genome	5	1857237-1857319	5	CRISPRCasFinder	no		csa3,cas3,DEDDh,DinG,TnsE_C,WYL	Orphan	GAAGCTGACGAAAAAGTCAGCTTAC	25	0	0	NA	NA	NA	1	1	Orphan	csa3,cas3,DEDDh,DinG,TnsE_C,WYL	NA,NA	NA|454aa|up_9|NZ_CP013621.1_1842070_1843432_+	COG1113, AnsP, Gamma-aminobutyrate permease and related permeases [Amino acid transport and metabolism]	NA|586aa|up_8|NZ_CP013621.1_1843775_1845533_-	PRK06354, PRK06354, pyruvate kinase; Provisional	NA|323aa|up_7|NZ_CP013621.1_1845554_1846523_-	PRK03202, PRK03202, ATP-dependent 6-phosphofructokinase	NA|315aa|up_6|NZ_CP013621.1_1846791_1847736_-	PRK05724, PRK05724, acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated	NA|286aa|up_5|NZ_CP013621.1_1847735_1848593_-	PRK05654, PRK05654, acetyl-CoA carboxylase carboxyltransferase subunit beta	NA|410aa|up_4|NZ_CP013621.1_1848787_1850017_-	PRK07232, PRK07232, bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed	NA|1066aa|up_3|NZ_CP013621.1_1850465_1853663_-	COG0587, DnaE, DNA polymerase III, alpha subunit [DNA replication, recombination, and repair]	NA|314aa|up_2|NZ_CP013621.1_1853683_1854625_-	COG0618, COG0618, Exopolyphosphatase-related proteins [General function prediction only]	NA|433aa|up_1|NZ_CP013621.1_1854994_1856293_-	COG4109, COG4109, Predicted transcriptional regulator containing CBS domains [Transcription]	NA|138aa|up_0|NZ_CP013621.1_1856497_1856911_+	pfam00582, Usp, Universal stress protein family	NA|230aa|down_0|NZ_CP013621.1_1857416_1858106_-	PRK00685, PRK00685, metal-dependent hydrolase; Provisional	NA|352aa|down_1|NZ_CP013621.1_1858280_1859336_+	COG0006, PepP, Xaa-Pro aminopeptidase [Amino acid transport and metabolism]	NA|373aa|down_2|NZ_CP013621.1_1859651_1860770_-	cd05305, L-AlaDH, Alanine dehydrogenase NAD-binding and catalytic domains	NA|167aa|down_3|NZ_CP013621.1_1860910_1861411_+	pfam00582, Usp, Universal stress protein family	NA|401aa|down_4|NZ_CP013621.1_1861657_1862860_-	PRK00180, PRK00180, acetate kinase A/propionate kinase 2; Reviewed	NA|316aa|down_5|NZ_CP013621.1_1862947_1863895_-	COG0827, COG0827, Adenine-specific DNA methylase [DNA replication, recombination, and repair]	NA|165aa|down_6|NZ_CP013621.1_1864017_1864512_-	PRK00522, tpx, thiol peroxidase	NA|257aa|down_7|NZ_CP013621.1_1864609_1865380_-	PRK10621, PRK10621, hypothetical protein; Provisional	NA|408aa|down_8|NZ_CP013621.1_1865423_1866647_-	PRK01565, PRK01565, thiamine biosynthesis protein ThiI; Provisional	NA|383aa|down_9|NZ_CP013621.1_1866646_1867795_-	COG1104, NifS, Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]
GCF_001465755.1_ASM146575v1	NZ_CP013621	Staphylococcus aureus strain RIVM3897 chromosome, complete genome	6	1945591-1945684	6	CRISPRCasFinder	no	csa3	csa3,cas3,DEDDh,DinG,TnsE_C,WYL	Type I-A	GCAATGCGCGTTGGGGTGTGGGGCCCCAACATAG	34	1	1	1945625-1945650	NZ_CP013621.1_2087291-2087266	NA	1	1	Orphan	csa3,cas3,DEDDh,DinG,TnsE_C,WYL	NA|75aa|up_5|NZ_CP013621.1_1941684_1941909_-,NA|148aa|up_2|NZ_CP013621.1_1943120_1943564_-,NA|101aa|down_1|NZ_CP013621.1_1946818_1947121_+	NA|501aa|up_9|NZ_CP013621.1_1936716_1938219_-	COG4529, COG4529, Uncharacterized protein conserved in bacteria [Function unknown]	csa3|105aa|up_8|NZ_CP013621.1_1938861_1939176_+	cd00090, HTH_ARSR, Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors	NA|431aa|up_7|NZ_CP013621.1_1939175_1940468_+	PRK15445, PRK15445, arsenical efflux pump membrane protein ArsB	NA|285aa|up_6|NZ_CP013621.1_1940554_1941409_-	COG4193, LytD, Beta- N-acetylglucosaminidase [Carbohydrate transport and metabolism]	NA|75aa|up_5|NZ_CP013621.1_1941684_1941909_-	NA	NA|157aa|up_4|NZ_CP013621.1_1942107_1942578_+	COG1595, RpoE, DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]	NA|148aa|up_3|NZ_CP013621.1_1942690_1943134_+	pfam06338, ComK, ComK protein	NA|148aa|up_2|NZ_CP013621.1_1943120_1943564_-	NA	NA|212aa|up_1|NZ_CP013621.1_1943861_1944497_+	pfam02517, Abi, CAAX protease self-immunity	NA|207aa|up_0|NZ_CP013621.1_1944663_1945284_+	pfam02517, Abi, CAAX protease self-immunity	NA|238aa|down_0|NZ_CP013621.1_1945846_1946560_-	PRK12376, PRK12376, putative translaldolase; Provisional	NA|101aa|down_1|NZ_CP013621.1_1946818_1947121_+	NA	NA|122aa|down_2|NZ_CP013621.1_1947375_1947741_+	PRK14201, PRK14201, fluoride efflux transporter CrcB	NA|118aa|down_3|NZ_CP013621.1_1947737_1948091_+	COG0239, CrcB, Integral membrane protein possibly involved in chromosome condensation [Cell division and chromosome partitioning]	NA|278aa|down_4|NZ_CP013621.1_1948340_1949174_-	COG0656, ARA1, Aldo/keto reductases, related to diketogulonate reductase [General function prediction only]	NA|303aa|down_5|NZ_CP013621.1_1949385_1950294_-	pfam08378, NERD, Nuclease-related domain	NA|398aa|down_6|NZ_CP013621.1_1950418_1951612_-	PRK05250, PRK05250, S-adenosylmethionine synthetase; Validated	NA|531aa|down_7|NZ_CP013621.1_1951983_1953576_+	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_CP013621.1_1953872_1954619_-	COG1506, DAP2, Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]	NA|158aa|down_9|NZ_CP013621.1_1954623_1955097_-	TIGR02705, conserved_hypothetical_protein, nucleoside triphosphatase YtkD
GCF_001465755.1_ASM146575v1	NZ_CP013621	Staphylococcus aureus strain RIVM3897 chromosome, complete genome	7	2221285-2221497	7	CRISPRCasFinder	no		csa3,cas3,DEDDh,DinG,TnsE_C,WYL	Orphan	TGATGTGCTGTTGTGGAAGCTTGGTGTCGTGCCATGCTACTTTGATG	47	0	0	NA	NA	NA	2	2	Orphan	csa3,cas3,DEDDh,DinG,TnsE_C,WYL	NA|46aa|up_4|NZ_CP013621.1_2218146_2218284_-,NA|107aa|down_0|NZ_CP013621.1_2221530_2221851_+	NA|232aa|up_9|NZ_CP013621.1_2210838_2211534_+	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_CP013621.1_2211886_2213407_-	COG0513, SrmB, Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]	NA|452aa|up_7|NZ_CP013621.1_2213922_2215278_-	COG0770, MurF, UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]	NA|357aa|up_6|NZ_CP013621.1_2215292_2216363_-	PRK01966, ddl, D-alanine--D-alanine ligase	NA|401aa|up_5|NZ_CP013621.1_2216680_2217883_+	TIGR02210, Rod_shape-determining_protein_RodA, rod shape-determining protein RodA	NA|46aa|up_4|NZ_CP013621.1_2218146_2218284_-	NA	NA|70aa|up_3|NZ_CP013621.1_2218411_2218621_-	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_CP013621.1_2218632_2218926_-	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_CP013621.1_2219091_2220576_+	TIGR04265, bac_cardiolipin, cardiolipin synthase	NA|216aa|up_0|NZ_CP013621.1_2220603_2221251_+	COG1418, COG1418, Predicted HD superfamily hydrolase [General function prediction only]	NA|107aa|down_0|NZ_CP013621.1_2221530_2221851_+	NA	NA|291aa|down_1|NZ_CP013621.1_2223492_2224365_-	PRK02463, PRK02463, OxaA-like protein precursor; Provisional	NA|214aa|down_2|NZ_CP013621.1_2224450_2225092_-	PRK00043, thiE, thiamine phosphate synthase	NA|264aa|down_3|NZ_CP013621.1_2225093_2225885_-	PRK09355, PRK09355, hydroxyethylthiazole kinase; Validated	NA|277aa|down_4|NZ_CP013621.1_2225868_2226699_-	PRK06427, PRK06427, bifunctional hydroxy-methylpyrimidine kinase/ hydroxy-phosphomethylpyrimidine kinase; Reviewed	NA|230aa|down_5|NZ_CP013621.1_2226691_2227381_-	TIGR04306, salvage_TenA, thiaminase II	NA|232aa|down_6|NZ_CP013621.1_2227767_2228463_-	pfam06737, Transglycosylas, Transglycosylase-like domain	NA|132aa|down_7|NZ_CP013621.1_2228851_2229247_-	pfam00436, SSB, Single-strand binding protein family	NA|147aa|down_8|NZ_CP013621.1_2229440_2229881_+	pfam14183, YwpF, YwpF-like protein	NA|147aa|down_9|NZ_CP013621.1_2229937_2230378_-	PRK00006, fabZ, 3-hydroxyacyl-ACP dehydratase FabZ
GCF_001465755.1_ASM146575v1	NZ_CP013621	Staphylococcus aureus strain RIVM3897 chromosome, complete genome	8	2276916-2277066	8	CRISPRCasFinder	no	csa3,TnsE_C	csa3,cas3,DEDDh,DinG,TnsE_C,WYL	Type I-A	AACTTTAGTTGTTAGGGGCTCTTATGCA	28	0	0	NA	NA	NA	2	2	Orphan	csa3,cas3,DEDDh,DinG,TnsE_C,WYL	NA|77aa|up_5|NZ_CP013621.1_2271788_2272019_-,NA|364aa|up_0|NZ_CP013621.1_2275806_2276898_+,NA|35aa|down_0|NZ_CP013621.1_2277395_2277500_-,NA|53aa|down_2|NZ_CP013621.1_2278179_2278338_+,NA|31aa|down_3|NZ_CP013621.1_2278773_2278866_+	NA|237aa|up_9|NZ_CP013621.1_2267398_2268109_+	PRK05819, deoD, DeoD-type purine-nucleoside phosphorylase	NA|148aa|up_8|NZ_CP013621.1_2268229_2268673_-	COG0783, Dps, DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]	NA|138aa|up_7|NZ_CP013621.1_2268872_2269286_-	COG3011, COG3011, Predicted thiol-disulfide oxidoreductase [General function    prediction only]	NA|458aa|up_6|NZ_CP013621.1_2269743_2271117_-	pfam01878, EVE, EVE domain	NA|77aa|up_5|NZ_CP013621.1_2271788_2272019_-	NA	NA|313aa|up_4|NZ_CP013621.1_2272049_2272988_-	COG1482, ManA, Phosphomannose isomerase [Carbohydrate transport and metabolism]	NA|222aa|up_3|NZ_CP013621.1_2273421_2274087_-	cd05243, SDR_a5, atypical (a) SDRs, subgroup 5	csa3|107aa|up_2|NZ_CP013621.1_2274238_2274559_+	cd00090, HTH_ARSR, Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors	NA|327aa|up_1|NZ_CP013621.1_2274560_2275541_+	COG1230, CzcD, Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]	NA|364aa|up_0|NZ_CP013621.1_2275806_2276898_+	NA	NA|35aa|down_0|NZ_CP013621.1_2277395_2277500_-	NA	NA|57aa|down_1|NZ_CP013621.1_2278016_2278187_+	COG4584, COG4584, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|53aa|down_2|NZ_CP013621.1_2278179_2278338_+	NA	NA|31aa|down_3|NZ_CP013621.1_2278773_2278866_+	NA	NA|286aa|down_4|NZ_CP013621.1_2278995_2279853_-	COG0561, Cof, Predicted hydrolases of the HAD superfamily [General function prediction only]	NA|261aa|down_5|NZ_CP013621.1_2279920_2280703_-	COG1119, ModF, ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA [Inorganic ion transport and metabolism]	NA|203aa|down_6|NZ_CP013621.1_2280992_2281601_-	pfam08937, DUF1863, MTH538 TIR-like domain (DUF1863)	NA|345aa|down_7|NZ_CP013621.1_2281628_2282663_-	pfam13676, TIR_2, TIR domain	NA|490aa|down_8|NZ_CP013621.1_2282756_2284226_-	pfam18185, STALD, Sir2- and TIR-associating SLOG family	TnsE_C|135aa|down_9|NZ_CP013621.1_2284700_2285105_-	pfam18623, TnsE_C, TnsE C-terminal domain
GCF_001465755.1_ASM146575v1	NZ_CP013621	Staphylococcus aureus strain RIVM3897 chromosome, complete genome	9	2440904-2440989	9	CRISPRCasFinder	no	WYL	csa3,cas3,DEDDh,DinG,TnsE_C,WYL	Unclear	AAAGTCAGCTTACAATAATGTGCAAGTTGG	30	1	6	2440934-2440959|2440934-2440959|2440934-2440959|2440934-2440959|2440934-2440959|2440934-2440959	NZ_CP013621.1_1728119-1728094|NZ_CP013621.1_912908-912883|NZ_CP013621.1_961963-961988|NZ_CP013621.1_1414032-1414057|NZ_CP013621.1_2232397-2232422|NZ_CP013621.1_2572850-2572825	NA	1	1	Orphan	csa3,cas3,DEDDh,DinG,TnsE_C,WYL	NA|65aa|up_6|NZ_CP013621.1_2433648_2433843_-,NA|78aa|down_1|NZ_CP013621.1_2441939_2442173_-,NA|110aa|down_8|NZ_CP013621.1_2450261_2450591_+	NA|248aa|up_9|NZ_CP013621.1_2429436_2430180_-	TIGR01889, Pleiotropic_Regulator_Of_Virulence, staphylococcal accessory regulator family	NA|652aa|up_8|NZ_CP013621.1_2430205_2432161_-	COG2207, AraC, AraC-type DNA-binding domain-containing proteins [Transcription]	NA|270aa|up_7|NZ_CP013621.1_2432770_2433580_+	COG3942, COG3942, Surface antigen [General function prediction only]	NA|65aa|up_6|NZ_CP013621.1_2433648_2433843_-	NA	NA|467aa|up_5|NZ_CP013621.1_2434016_2435417_-	TIGR00931, Uncharacterized_Na+/H+_antiporter_HI_1107, Na+/H+ antiporter NhaC	NA|361aa|up_4|NZ_CP013621.1_2435511_2436594_-	pfam02317, Octopine_DH, NAD/NADP octopine/nopaline dehydrogenase, alpha-helical domain	NA|141aa|up_3|NZ_CP013621.1_2436841_2437264_+	COG3296, COG3296, Uncharacterized protein conserved in bacteria [Function unknown]	NA|167aa|up_2|NZ_CP013621.1_2437500_2438001_+	COG3942, COG3942, Surface antigen [General function prediction only]	NA|318aa|up_1|NZ_CP013621.1_2438363_2439317_+	cd12178, 2-Hacid_dh_13, Putative D-isomer specific 2-hydroxyacid dehydrogenases, NAD-binding and catalytic domains	NA|375aa|up_0|NZ_CP013621.1_2439408_2440533_-	PRK06753, PRK06753, hypothetical protein; Provisional	NA|259aa|down_0|NZ_CP013621.1_2441141_2441918_-	COG4193, LytD, Beta- N-acetylglucosaminidase [Carbohydrate transport and metabolism]	NA|78aa|down_1|NZ_CP013621.1_2441939_2442173_-	NA	NA|158aa|down_2|NZ_CP013621.1_2442467_2442941_-	COG2427, COG2427, Uncharacterized conserved protein [Function unknown]	NA|985aa|down_3|NZ_CP013621.1_2442940_2445895_-	COG3383, COG3383, Uncharacterized anaerobic dehydrogenase [General function prediction only]	NA|316aa|down_4|NZ_CP013621.1_2446496_2447444_-	PRK09379, PRK09379, LytR family transcriptional regulator	NA|266aa|down_5|NZ_CP013621.1_2447576_2448374_-	COG0483, SuhB, Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]	WYL|231aa|down_6|NZ_CP013621.1_2448758_2449451_+	COG2378, COG2378, Predicted transcriptional regulator [Transcription]	NA|246aa|down_7|NZ_CP013621.1_2449475_2450213_-	pfam02517, Abi, CAAX protease self-immunity	NA|110aa|down_8|NZ_CP013621.1_2450261_2450591_+	NA	NA|291aa|down_9|NZ_CP013621.1_2451035_2451908_+	COG1737, RpiR, Transcriptional regulators [Transcription]
GCF_001465755.1_ASM146575v1	NZ_CP013621	Staphylococcus aureus strain RIVM3897 chromosome, complete genome	10	2617116-2617210	10	CRISPRCasFinder	no		csa3,cas3,DEDDh,DinG,TnsE_C,WYL	Orphan	AGGCTCTTATGCAGTTGGTGCGAAGCAA	28	0	0	NA	NA	NA	1	1	Orphan	csa3,cas3,DEDDh,DinG,TnsE_C,WYL	NA|249aa|up_9|NZ_CP013621.1_2606701_2607448_+,NA|121aa|down_0|NZ_CP013621.1_2617878_2618241_-,NA|105aa|down_8|NZ_CP013621.1_2625053_2625368_+	NA|249aa|up_9|NZ_CP013621.1_2606701_2607448_+	NA	NA|398aa|up_8|NZ_CP013621.1_2607671_2608865_-	cd17489, MFS_YfcJ_like, Escherichia coli YfcJ, YhhS, and similar transporters of the Major Facilitator Superfamily	NA|250aa|up_7|NZ_CP013621.1_2608876_2609626_-	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_CP013621.1_2609618_2610434_-	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_CP013621.1_2610430_2611300_-	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_CP013621.1_2611296_2612232_-	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_CP013621.1_2612244_2613843_-	TIGR02294, Nickel-binding_periplasmic_protein, nickel ABC transporter, nickel/metallophore periplasmic binding protein	NA|434aa|up_2|NZ_CP013621.1_2613985_2615287_-	COG4408, COG4408, Uncharacterized protein conserved in bacteria [Function unknown]	NA|273aa|up_1|NZ_CP013621.1_2615279_2616098_-	cd08261, Zn_ADH7, Alcohol dehydrogenases of the MDR family	NA|274aa|up_0|NZ_CP013621.1_2616108_2616930_-	COG0253, DapF, Diaminopimelate epimerase [Amino acid transport and metabolism]	NA|121aa|down_0|NZ_CP013621.1_2617878_2618241_-	NA	NA|273aa|down_1|NZ_CP013621.1_2618503_2619322_-	PRK08589, PRK08589, SDR family oxidoreductase	NA|513aa|down_2|NZ_CP013621.1_2619555_2621094_+	pfam03806, ABG_transport, AbgT putative transporter family	NA|141aa|down_3|NZ_CP013621.1_2621205_2621628_-	COG2128, COG2128, Uncharacterized conserved protein [Function unknown]	NA|133aa|down_4|NZ_CP013621.1_2622099_2622498_-	pfam07252, DUF1433, Protein of unknown function (DUF1433)	NA|137aa|down_5|NZ_CP013621.1_2622524_2622935_-	pfam07252, DUF1433, Protein of unknown function (DUF1433)	NA|128aa|down_6|NZ_CP013621.1_2623389_2623773_-	pfam07252, DUF1433, Protein of unknown function (DUF1433)	NA|403aa|down_7|NZ_CP013621.1_2623839_2625048_+	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_CP013621.1_2625053_2625368_+	NA	NA|140aa|down_9|NZ_CP013621.1_2627244_2627664_-	pfam07252, DUF1433, Protein of unknown function (DUF1433)
GCF_001465755.1_ASM146575v1	NZ_CP013621	Staphylococcus aureus strain RIVM3897 chromosome, complete genome	11	2645061-2645171	11	CRISPRCasFinder	no		csa3,cas3,DEDDh,DinG,TnsE_C,WYL	Orphan	GGTACTTCTGGTGTCGGTGGCGTTGGT	27	0	0	NA	NA	NA	1	1	Orphan	csa3,cas3,DEDDh,DinG,TnsE_C,WYL	NA|89aa|up_2|NZ_CP013621.1_2639364_2639631_+,NA|103aa|up_1|NZ_CP013621.1_2639774_2640083_+,NA	NA|452aa|up_9|NZ_CP013621.1_2630758_2632114_-	cd00519, Lipase_3, Lipase (class 3)	NA|262aa|up_8|NZ_CP013621.1_2632110_2632896_-	pfam04507, DUF576, Csa1 family	NA|255aa|up_7|NZ_CP013621.1_2633143_2633908_-	pfam04507, DUF576, Csa1 family	NA|258aa|up_6|NZ_CP013621.1_2634019_2634793_-	pfam04507, DUF576, Csa1 family	NA|310aa|up_5|NZ_CP013621.1_2635035_2635965_-	pfam09019, EcoRII-C, EcoRII C terminal	NA|398aa|up_4|NZ_CP013621.1_2636060_2637254_+	TIGR00675, Modification_methylase, DNA-methyltransferase (dcm)	NA|584aa|up_3|NZ_CP013621.1_2637329_2639081_+	cd05799, PGM2, This CD includes PGM2 (phosphoglucomutase 2) and PGM2L1 (phosphoglucomutase 2-like 1)	NA|89aa|up_2|NZ_CP013621.1_2639364_2639631_+	NA	NA|103aa|up_1|NZ_CP013621.1_2639774_2640083_+	NA	NA|289aa|up_0|NZ_CP013621.1_2640208_2641075_-	COG1210, GalU, UDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]	NA|453aa|down_0|NZ_CP013621.1_2648311_2649670_-	TIGR00791, Gluconate_permease, gluconate transporter	NA|518aa|down_1|NZ_CP013621.1_2649786_2651340_-	TIGR01314, gntK_FGGY, gluconate kinase, FGGY type	NA|226aa|down_2|NZ_CP013621.1_2651364_2652042_-	COG1802, GntR, Transcriptional regulators [Transcription]	NA|255aa|down_3|NZ_CP013621.1_2652198_2652963_-	cd01106, HTH_TipAL-Mta, Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA	NA|231aa|down_4|NZ_CP013621.1_2653127_2653820_-	COG2357, COG2357, PpGpp synthetase catalytic domain [General function prediction only]	NA|139aa|down_5|NZ_CP013621.1_2654050_2654467_-	COG4876, COG4876, Uncharacterized protein conserved in bacteria [Function unknown]	NA|608aa|down_6|NZ_CP013621.1_2654604_2656428_-	COG1289, COG1289, Predicted membrane protein [Function unknown]	NA|426aa|down_7|NZ_CP013621.1_2657339_2658617_-	cd17319, MFS_ExuT_GudP_like, Hexuronate transporter, Glucarate transporter, and similar transporters of the Major Facilitator Superfamily	NA|204aa|down_8|NZ_CP013621.1_2659163_2659775_+	COG0586, DedA, Uncharacterized membrane-associated protein [Function unknown]	NA|388aa|down_9|NZ_CP013621.1_2659872_2661036_-	cd17474, MFS_YfmO_like, Bacillus subtilis multidrug efflux protein YfmO and similar transporters of the Major Facilitator Superfamily
