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_001465635.1_ASM146563v1	NZ_CP013616	Staphylococcus aureus strain RIVM1295 chromosome, complete genome	1	307169-307368	1	CRISPRCasFinder	no		WYL,csa3,cas3,DEDDh,DinG,TnsE_C	Orphan	TGCAAGTTGGCGGGGCCCCAACACAGAAGCT	31	2	2	307200-307224|307256-307280	NZ_CP013616.1_307369-307393|NZ_CP013616.1_2127829-2127853	NA	3	3	Orphan	WYL,csa3,cas3,DEDDh,DinG,TnsE_C	NA,NA|131aa|down_5|NZ_CP013616.1_312544_312937_+	NA|574aa|up_9|NZ_CP013616.1_294615_296337_+	pfam18674, TarS_C1, TarS beta-glycosyltransferase C-terminal domain 1	NA|225aa|up_8|NZ_CP013616.1_296480_297155_+	PRK13276, PRK13276, iron-sulfur cluster repair di-iron protein ScdA	NA|585aa|up_7|NZ_CP013616.1_297401_299156_+	COG3275, LytS, Putative regulator of cell autolysis [Signal transduction mechanisms]	NA|247aa|up_6|NZ_CP013616.1_299158_299899_+	PRK14084, PRK14084, DNA-binding response regulator	NA|148aa|up_5|NZ_CP013616.1_300011_300455_+	PRK04125, PRK04125, antiholin-like protein LrgA	NA|234aa|up_4|NZ_CP013616.1_300447_301149_+	PRK04288, PRK04288, antiholin-like protein LrgB; Provisional	NA|764aa|up_3|NZ_CP013616.1_301489_303781_+	COG3256, NorB, Nitric oxide reductase large subunit [Inorganic ion transport and metabolism]	NA|235aa|up_2|NZ_CP013616.1_304006_304711_-	COG2188, PhnF, Transcriptional regulators [Transcription]	NA|264aa|up_1|NZ_CP013616.1_304859_305651_+	COG2190, NagE, Phosphotransferase system IIA components [Carbohydrate transport and metabolism]	NA|479aa|up_0|NZ_CP013616.1_305666_307103_+	PRK09589, celA, 6-phospho-beta-glucosidase; Reviewed	NA|254aa|down_0|NZ_CP013616.1_307678_308440_-	pfam13649, Methyltransf_25, Methyltransferase domain	NA|305aa|down_1|NZ_CP013616.1_308691_309606_-	TIGR02152, Putative_ribokinase, ribokinase	NA|135aa|down_2|NZ_CP013616.1_309633_310038_-	PRK11797, PRK11797, D-ribose pyranase; Provisional	NA|294aa|down_3|NZ_CP013616.1_310052_310934_-	pfam06800, Sugar_transport, Sugar transport protein	NA|333aa|down_4|NZ_CP013616.1_311165_312164_-	COG1609, PurR, Transcriptional regulators [Transcription]	NA|131aa|down_5|NZ_CP013616.1_312544_312937_+	NA	NA|459aa|down_6|NZ_CP013616.1_313065_314442_-	TIGR00711, Uncharacterized_MFS-type_transporter_YhcA, drug resistance transporter, EmrB/QacA subfamily	NA|331aa|down_7|NZ_CP013616.1_314675_315668_+	COG3049, COG3049, Penicillin V acylase and related amidases [Cell envelope biogenesis, outer membrane]	NA|317aa|down_8|NZ_CP013616.1_315993_316944_+	COG3942, COG3942, Surface antigen [General function prediction only]	NA|220aa|down_9|NZ_CP013616.1_316995_317655_-	COG1131, CcmA, ABC-type multidrug transport system, ATPase component [Defense mechanisms]
GCF_001465635.1_ASM146563v1	NZ_CP013616	Staphylococcus aureus strain RIVM1295 chromosome, complete genome	2	662130-662238	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_CP013616.1_665971_666478_+,NA|239aa|down_5|NZ_CP013616.1_666639_667356_+	NA|209aa|up_9|NZ_CP013616.1_651706_652333_+	pfam04276, DUF443, Protein of unknown function (DUF443)	NA|313aa|up_8|NZ_CP013616.1_652602_653541_+	cd19083, AKR_AKR11A1_11D1, AKR11A and  AKR11D families of aldo-keto reductase (AKR)	NA|179aa|up_7|NZ_CP013616.1_653986_654523_+	COG0655, WrbA, Multimeric flavodoxin WrbA [General function prediction only]	NA|159aa|up_6|NZ_CP013616.1_654692_655169_+	pfam00583, Acetyltransf_1, Acetyltransferase (GNAT) family	NA|432aa|up_5|NZ_CP013616.1_655208_656504_+	COG1078, COG1078, HD superfamily phosphohydrolases [General function prediction only]	NA|174aa|up_4|NZ_CP013616.1_656531_657053_+	pfam08741, YwhD, YwhD family	NA|337aa|up_3|NZ_CP013616.1_657551_658562_+	PRK09422, PRK09422, ethanol-active dehydrogenase/acetaldehyde-active reductase; Provisional	NA|139aa|up_2|NZ_CP013616.1_658837_659254_+	COG4506, COG4506, Uncharacterized protein conserved in bacteria [Function unknown]	NA|554aa|up_1|NZ_CP013616.1_659250_660912_+	PRK01611, argS, arginyl-tRNA synthetase; Reviewed	NA|212aa|up_0|NZ_CP013616.1_661324_661960_+	COG2231, COG2231, Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]	NA|296aa|down_0|NZ_CP013616.1_662289_663177_+	cd01143, YvrC, Periplasmic binding protein YvrC	NA|317aa|down_1|NZ_CP013616.1_663327_664278_+	pfam01032, FecCD, FecCD transport family	NA|240aa|down_2|NZ_CP013616.1_664332_665052_+	COG1011, COG1011, Predicted hydrolase (HAD superfamily) [General function prediction only]	NA|267aa|down_3|NZ_CP013616.1_665035_665836_+	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|169aa|down_4|NZ_CP013616.1_665971_666478_+	NA	NA|239aa|down_5|NZ_CP013616.1_666639_667356_+	NA	NA|263aa|down_6|NZ_CP013616.1_667524_668313_+	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|125aa|down_7|NZ_CP013616.1_668564_668939_-	TIGR01889, Pleiotropic_Regulator_Of_Virulence, staphylococcal accessory regulator family	NA|310aa|down_8|NZ_CP013616.1_669886_670816_-	COG3238, COG3238, Uncharacterized protein conserved in bacteria [Function unknown]	NA|75aa|down_9|NZ_CP013616.1_671008_671233_-	pfam11148, DUF2922, Protein of unknown function (DUF2922)
GCF_001465635.1_ASM146563v1	NZ_CP013616	Staphylococcus aureus strain RIVM1295 chromosome, complete genome	3	824278-824360	3	CRISPRCasFinder	no		WYL,csa3,cas3,DEDDh,DinG,TnsE_C	Orphan	CACCCCAACTCGCATTGCTTGTAGAA	26	1	25	824304-824334|824304-824334|824304-824334|824304-824334|824304-824334|824304-824334|824304-824334|824304-824334|824304-824334|824304-824334|824304-824334|824304-824334|824304-824334|824304-824334|824304-824334|824304-824334|824304-824334|824304-824334|824304-824334|824304-824334|824304-824334|824304-824334|824304-824334|824304-824334|824304-824334	NZ_CP013616.1_918518-918488|NZ_CP013616.1_957319-957349|NZ_CP013616.1_1973733-1973763|NZ_CP013616.1_1973843-1973873|NZ_CP013616.1_2042100-2042130|NZ_CP013616.1_289239-289269|NZ_CP013616.1_289297-289327|NZ_CP013616.1_382985-382955|NZ_CP013616.1_653699-653669|NZ_CP013616.1_777991-777961|NZ_CP013616.1_869149-869179|NZ_CP013616.1_1051360-1051390|NZ_CP013616.1_1152764-1152734|NZ_CP013616.1_1152818-1152788|NZ_CP013616.1_1785198-1785168|NZ_CP013616.1_1875974-1875944|NZ_CP013616.1_2291250-2291280|NZ_CP013616.1_2336374-2336344|NZ_CP013616.1_833285-833315|NZ_CP013616.1_873287-873257|NZ_CP013616.1_1361714-1361744|NZ_CP013616.1_1402360-1402390|NZ_CP013616.1_2301998-2302028|NZ_CP013616.1_2302053-2302083|NZ_CP013616.1_2737011-2737041	NA	1	1	Orphan	WYL,csa3,cas3,DEDDh,DinG,TnsE_C	NA,NA	NA|280aa|up_9|NZ_CP013616.1_811527_812367_+	COG3942, COG3942, Surface antigen [General function prediction only]	NA|217aa|up_8|NZ_CP013616.1_812540_813191_+	pfam12917, HD_2, HD containing hydrolase-like enzyme	NA|79aa|up_7|NZ_CP013616.1_813187_813424_+	COG4897, CsbA, Uncharacterized protein conserved in bacteria [Function unknown]	NA|662aa|up_6|NZ_CP013616.1_813692_815678_+	PRK05298, PRK05298, excinuclease ABC subunit UvrB	NA|949aa|up_5|NZ_CP013616.1_815685_818532_+	PRK00349, uvrA, excinuclease ABC subunit UvrA	NA|311aa|up_4|NZ_CP013616.1_819141_820074_+	PRK05428, PRK05428, HPr kinase/phosphorylase; Provisional	NA|280aa|up_3|NZ_CP013616.1_820079_820919_+	PRK12437, PRK12437, prolipoprotein diacylglyceryl transferase; Reviewed	NA|162aa|up_2|NZ_CP013616.1_820926_821412_+	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_CP013616.1_821419_822859_+	sd00006, TPR, Tetratricopeptide repeat	NA|312aa|up_0|NZ_CP013616.1_822925_823861_+	TIGR01292, Thioredoxin_reductase, thioredoxin-disulfide reductase	NA|304aa|down_0|NZ_CP013616.1_824628_825540_+	COG1660, COG1660, Predicted P-loop-containing kinase [General function prediction only]	NA|332aa|down_1|NZ_CP013616.1_825536_826532_+	TIGR01826, Putative_gluconeogenesis_factor, conserved hypothetical protein, cofD-related	NA|315aa|down_2|NZ_CP013616.1_826640_827585_+	TIGR00647, DNA_bind_WhiA, DNA-binding protein WhiA	NA|196aa|down_3|NZ_CP013616.1_828154_828742_+	PRK00277, clpP, ATP-dependent Clp protease proteolytic subunit; Reviewed	NA|545aa|down_4|NZ_CP013616.1_828924_830559_+	PRK13529, PRK13529, oxaloacetate-decarboxylating malate dehydrogenase	NA|301aa|down_5|NZ_CP013616.1_830765_831668_-	COG1090, COG1090, Predicted nucleoside-diphosphate sugar epimerase [General function prediction only]	NA|210aa|down_6|NZ_CP013616.1_832370_833000_+	PRK00409, PRK00409, recombination and DNA strand exchange inhibitor protein; Reviewed	NA|338aa|down_7|NZ_CP013616.1_833774_834788_+	COG2390, DeoR, Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]	NA|337aa|down_8|NZ_CP013616.1_834840_835851_+	TIGR01534, Glyceraldehyde-3-phosphate_dehydrogenase, glyceraldehyde-3-phosphate dehydrogenase, type I	NA|397aa|down_9|NZ_CP013616.1_835989_837180_+	PRK00073, pgk, phosphoglycerate kinase; Provisional
GCF_001465635.1_ASM146563v1	NZ_CP013616	Staphylococcus aureus strain RIVM1295 chromosome, complete genome	4	869069-869148	4	CRISPRCasFinder	no		WYL,csa3,cas3,DEDDh,DinG,TnsE_C	Orphan	CCCCAACTTGCATTGTCTGTAGAA	24	1	12	869093-869124|869093-869124|869093-869124|869093-869124|869093-869124|869093-869124|869093-869124|869093-869124|869093-869124|869093-869124|869093-869124|869093-869124	NZ_CP013616.1_1665223-1665254|NZ_CP013616.1_653757-653726|NZ_CP013616.1_811008-811039|NZ_CP013616.1_824361-824392|NZ_CP013616.1_1077499-1077530|NZ_CP013616.1_2423382-2423351|NZ_CP013616.1_2620800-2620769|NZ_CP013616.1_2736955-2736986|NZ_CP013616.1_833229-833260|NZ_CP013616.1_1357247-1357216|NZ_CP013616.1_1785314-1785283|NZ_CP013616.1_2736899-2736930	NA	1	1	Orphan	WYL,csa3,cas3,DEDDh,DinG,TnsE_C	NA,NA	NA|194aa|up_9|NZ_CP013616.1_862060_862642_+	COG0406, phoE, Broad specificity phosphatase PhoE and related phosphatases [General function prediction only]	NA|206aa|up_8|NZ_CP013616.1_862714_863332_-	COG1279, COG1279, Lysine efflux permease [General function prediction only]	NA|165aa|up_7|NZ_CP013616.1_863480_863975_-	pfam13420, Acetyltransf_4, Acetyltransferase (GNAT) domain	NA|141aa|up_6|NZ_CP013616.1_864373_864796_-	TIGR03561, organ_hyd_perox, peroxiredoxin, Ohr subfamily	NA|239aa|up_5|NZ_CP013616.1_864943_865660_+	PRK13575, PRK13575, type I 3-dehydroquinate dehydratase	NA|180aa|up_4|NZ_CP013616.1_865742_866282_+	cd02135, YdjA-like, nitroreductase family protein similar to Escherichia coli YdjA	NA|107aa|up_3|NZ_CP013616.1_866431_866752_-	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_2|NZ_CP013616.1_866895_867252_+	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_1|NZ_CP013616.1_867409_867790_+	PRK01202, PRK01202, glycine cleavage system protein GcvH	NA|293aa|up_0|NZ_CP013616.1_867969_868848_+	COG3878, COG3878, Uncharacterized protein conserved in bacteria [Function unknown]	NA|129aa|down_0|NZ_CP013616.1_869493_869880_+	COG1658, COG1658, Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]	NA|99aa|down_1|NZ_CP013616.1_869872_870169_+	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|down_2|NZ_CP013616.1_870418_871444_+	COG1135, AbcC, ABC-type metal ion transport system, ATPase component [Inorganic ion transport and metabolism]	NA|232aa|down_3|NZ_CP013616.1_871436_872132_+	COG2011, AbcD, ABC-type metal ion transport system, permease component [Inorganic ion transport and metabolism]	NA|274aa|down_4|NZ_CP013616.1_872149_872971_+	COG1464, NlpA, ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]	NA|65aa|down_5|NZ_CP013616.1_873778_873973_+	COG3237, COG3237, Uncharacterized protein conserved in bacteria [Function unknown]	NA|284aa|down_6|NZ_CP013616.1_874206_875058_-	COG2035, COG2035, Predicted membrane protein [Function unknown]	NA|254aa|down_7|NZ_CP013616.1_875385_876147_+	COG0396, sufC, Cysteine desulfurase activator ATPase [Posttranslational modification, protein turnover, chaperones]	NA|436aa|down_8|NZ_CP013616.1_876245_877553_+	COG0719, SufB, Cysteine desulfurase activator SufB [Posttranslational modification, protein turnover, chaperones]	NA|417aa|down_9|NZ_CP013616.1_877658_878909_+	TIGR01979, Probable_cysteine_desulfurase, cysteine desulfurases, SufSfamily
GCF_001465635.1_ASM146563v1	NZ_CP013616	Staphylococcus aureus strain RIVM1295 chromosome, complete genome	5	873556-873636	5	CRISPRCasFinder	no		WYL,csa3,cas3,DEDDh,DinG,TnsE_C	Orphan	TCTTTATCATTTCTGTCCCACTCCC	25	1	1	873581-873611	NZ_CP013616.1_818731-818701	NA	1	1	Orphan	WYL,csa3,cas3,DEDDh,DinG,TnsE_C	NA,NA|105aa|down_7|NZ_CP013616.1_881242_881557_-	NA|180aa|up_9|NZ_CP013616.1_865742_866282_+	cd02135, YdjA-like, nitroreductase family protein similar to Escherichia coli YdjA	NA|107aa|up_8|NZ_CP013616.1_866431_866752_-	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_CP013616.1_866895_867252_+	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_CP013616.1_867409_867790_+	PRK01202, PRK01202, glycine cleavage system protein GcvH	NA|293aa|up_5|NZ_CP013616.1_867969_868848_+	COG3878, COG3878, Uncharacterized protein conserved in bacteria [Function unknown]	NA|129aa|up_4|NZ_CP013616.1_869493_869880_+	COG1658, COG1658, Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]	NA|99aa|up_3|NZ_CP013616.1_869872_870169_+	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_CP013616.1_870418_871444_+	COG1135, AbcC, ABC-type metal ion transport system, ATPase component [Inorganic ion transport and metabolism]	NA|232aa|up_1|NZ_CP013616.1_871436_872132_+	COG2011, AbcD, ABC-type metal ion transport system, permease component [Inorganic ion transport and metabolism]	NA|274aa|up_0|NZ_CP013616.1_872149_872971_+	COG1464, NlpA, ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]	NA|65aa|down_0|NZ_CP013616.1_873778_873973_+	COG3237, COG3237, Uncharacterized protein conserved in bacteria [Function unknown]	NA|284aa|down_1|NZ_CP013616.1_874206_875058_-	COG2035, COG2035, Predicted membrane protein [Function unknown]	NA|254aa|down_2|NZ_CP013616.1_875385_876147_+	COG0396, sufC, Cysteine desulfurase activator ATPase [Posttranslational modification, protein turnover, chaperones]	NA|436aa|down_3|NZ_CP013616.1_876245_877553_+	COG0719, SufB, Cysteine desulfurase activator SufB [Posttranslational modification, protein turnover, chaperones]	NA|417aa|down_4|NZ_CP013616.1_877658_878909_+	TIGR01979, Probable_cysteine_desulfurase, cysteine desulfurases, SufSfamily	NA|155aa|down_5|NZ_CP013616.1_878898_879363_+	TIGR01994, Iron-sulfur_cluster_assembly_scaffold_protein_IscU, SUF system FeS assembly protein, NifU family	NA|466aa|down_6|NZ_CP013616.1_879513_880911_+	TIGR01980, UPF0051_protein_slr0074, FeS assembly protein SufB	NA|105aa|down_7|NZ_CP013616.1_881242_881557_-	NA	NA|347aa|down_8|NZ_CP013616.1_881925_882966_+	COG4536, CorB, Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]	NA|356aa|down_9|NZ_CP013616.1_882979_884047_+	COG2070, COG2070, Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]
GCF_001465635.1_ASM146563v1	NZ_CP013616	Staphylococcus aureus strain RIVM1295 chromosome, complete genome	6	1787631-1787713	6	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_CP013616.1_1772464_1773826_+	COG1113, AnsP, Gamma-aminobutyrate permease and related permeases [Amino acid transport and metabolism]	NA|586aa|up_8|NZ_CP013616.1_1774169_1775927_-	PRK06354, PRK06354, pyruvate kinase; Provisional	NA|323aa|up_7|NZ_CP013616.1_1775948_1776917_-	PRK03202, PRK03202, ATP-dependent 6-phosphofructokinase	NA|315aa|up_6|NZ_CP013616.1_1777185_1778130_-	PRK05724, PRK05724, acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated	NA|286aa|up_5|NZ_CP013616.1_1778129_1778987_-	PRK05654, PRK05654, acetyl-CoA carboxylase carboxyltransferase subunit beta	NA|410aa|up_4|NZ_CP013616.1_1779181_1780411_-	PRK07232, PRK07232, bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed	NA|1066aa|up_3|NZ_CP013616.1_1780859_1784057_-	COG0587, DnaE, DNA polymerase III, alpha subunit [DNA replication, recombination, and repair]	NA|314aa|up_2|NZ_CP013616.1_1784077_1785019_-	COG0618, COG0618, Exopolyphosphatase-related proteins [General function prediction only]	NA|433aa|up_1|NZ_CP013616.1_1785388_1786687_-	COG4109, COG4109, Predicted transcriptional regulator containing CBS domains [Transcription]	NA|138aa|up_0|NZ_CP013616.1_1786891_1787305_+	pfam00582, Usp, Universal stress protein family	NA|230aa|down_0|NZ_CP013616.1_1787810_1788500_-	PRK00685, PRK00685, metal-dependent hydrolase; Provisional	NA|352aa|down_1|NZ_CP013616.1_1788674_1789730_+	COG0006, PepP, Xaa-Pro aminopeptidase [Amino acid transport and metabolism]	NA|373aa|down_2|NZ_CP013616.1_1790045_1791164_-	cd05305, L-AlaDH, Alanine dehydrogenase NAD-binding and catalytic domains	NA|167aa|down_3|NZ_CP013616.1_1791304_1791805_+	pfam00582, Usp, Universal stress protein family	NA|401aa|down_4|NZ_CP013616.1_1792051_1793254_-	PRK00180, PRK00180, acetate kinase A/propionate kinase 2; Reviewed	NA|316aa|down_5|NZ_CP013616.1_1793341_1794289_-	COG0827, COG0827, Adenine-specific DNA methylase [DNA replication, recombination, and repair]	NA|165aa|down_6|NZ_CP013616.1_1794411_1794906_-	PRK00522, tpx, thiol peroxidase	NA|257aa|down_7|NZ_CP013616.1_1795003_1795774_-	PRK10621, PRK10621, hypothetical protein; Provisional	NA|408aa|down_8|NZ_CP013616.1_1795817_1797041_-	PRK01565, PRK01565, thiamine biosynthesis protein ThiI; Provisional	NA|383aa|down_9|NZ_CP013616.1_1797040_1798189_-	COG1104, NifS, Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]
GCF_001465635.1_ASM146563v1	NZ_CP013616	Staphylococcus aureus strain RIVM1295 chromosome, complete genome	7	1875983-1876076	7	CRISPRCasFinder	no	csa3	WYL,csa3,cas3,DEDDh,DinG,TnsE_C	Type I-A	GCAATGCGCGTTGGGGTGTGGGGCCCCAACATAG	34	1	1	1876017-1876042	NZ_CP013616.1_1973805-1973780	NA	1	1	Orphan	WYL,csa3,cas3,DEDDh,DinG,TnsE_C	NA|75aa|up_5|NZ_CP013616.1_1872076_1872301_-,NA|148aa|up_2|NZ_CP013616.1_1873512_1873956_-,NA|101aa|down_1|NZ_CP013616.1_1877210_1877513_+	NA|348aa|up_9|NZ_CP013616.1_1865586_1866630_-	TIGR00326, eubact_ribD, riboflavin biosynthesis protein RibD	csa3|105aa|up_8|NZ_CP013616.1_1869253_1869568_+	cd00090, HTH_ARSR, Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors	NA|431aa|up_7|NZ_CP013616.1_1869567_1870860_+	PRK15445, PRK15445, arsenical efflux pump membrane protein ArsB	NA|285aa|up_6|NZ_CP013616.1_1870946_1871801_-	COG4193, LytD, Beta- N-acetylglucosaminidase [Carbohydrate transport and metabolism]	NA|75aa|up_5|NZ_CP013616.1_1872076_1872301_-	NA	NA|157aa|up_4|NZ_CP013616.1_1872499_1872970_+	COG1595, RpoE, DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]	NA|148aa|up_3|NZ_CP013616.1_1873082_1873526_+	pfam06338, ComK, ComK protein	NA|148aa|up_2|NZ_CP013616.1_1873512_1873956_-	NA	NA|212aa|up_1|NZ_CP013616.1_1874253_1874889_+	pfam02517, Abi, CAAX protease self-immunity	NA|207aa|up_0|NZ_CP013616.1_1875055_1875676_+	pfam02517, Abi, CAAX protease self-immunity	NA|238aa|down_0|NZ_CP013616.1_1876238_1876952_-	PRK12376, PRK12376, putative translaldolase; Provisional	NA|101aa|down_1|NZ_CP013616.1_1877210_1877513_+	NA	NA|122aa|down_2|NZ_CP013616.1_1877767_1878133_+	PRK14201, PRK14201, fluoride efflux transporter CrcB	NA|118aa|down_3|NZ_CP013616.1_1878129_1878483_+	COG0239, CrcB, Integral membrane protein possibly involved in chromosome condensation [Cell division and chromosome partitioning]	NA|278aa|down_4|NZ_CP013616.1_1878732_1879566_-	COG0656, ARA1, Aldo/keto reductases, related to diketogulonate reductase [General function prediction only]	NA|303aa|down_5|NZ_CP013616.1_1879777_1880686_-	pfam08378, NERD, Nuclease-related domain	NA|398aa|down_6|NZ_CP013616.1_1880810_1882004_-	PRK05250, PRK05250, S-adenosylmethionine synthetase; Validated	NA|531aa|down_7|NZ_CP013616.1_1882375_1883968_+	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_CP013616.1_1884264_1885011_-	COG1506, DAP2, Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]	NA|158aa|down_9|NZ_CP013616.1_1885015_1885489_-	TIGR02705, conserved_hypothetical_protein, nucleoside triphosphatase YtkD
GCF_001465635.1_ASM146563v1	NZ_CP013616	Staphylococcus aureus strain RIVM1295 chromosome, complete genome	8	2172386-2172536	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_CP013616.1_2167258_2167489_-,NA|364aa|up_0|NZ_CP013616.1_2171276_2172368_+,NA|35aa|down_0|NZ_CP013616.1_2172865_2172970_-,NA|53aa|down_1|NZ_CP013616.1_2173649_2173808_+,NA|31aa|down_2|NZ_CP013616.1_2174243_2174336_+	NA|237aa|up_9|NZ_CP013616.1_2162868_2163579_+	PRK05819, deoD, DeoD-type purine-nucleoside phosphorylase	NA|148aa|up_8|NZ_CP013616.1_2163699_2164143_-	COG0783, Dps, DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]	NA|138aa|up_7|NZ_CP013616.1_2164342_2164756_-	COG3011, COG3011, Predicted thiol-disulfide oxidoreductase [General function    prediction only]	NA|458aa|up_6|NZ_CP013616.1_2165213_2166587_-	pfam01878, EVE, EVE domain	NA|77aa|up_5|NZ_CP013616.1_2167258_2167489_-	NA	NA|313aa|up_4|NZ_CP013616.1_2167519_2168458_-	COG1482, ManA, Phosphomannose isomerase [Carbohydrate transport and metabolism]	NA|222aa|up_3|NZ_CP013616.1_2168891_2169557_-	cd05243, SDR_a5, atypical (a) SDRs, subgroup 5	csa3|107aa|up_2|NZ_CP013616.1_2169708_2170029_+	cd00090, HTH_ARSR, Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors	NA|327aa|up_1|NZ_CP013616.1_2170030_2171011_+	COG1230, CzcD, Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]	NA|364aa|up_0|NZ_CP013616.1_2171276_2172368_+	NA	NA|35aa|down_0|NZ_CP013616.1_2172865_2172970_-	NA	NA|53aa|down_1|NZ_CP013616.1_2173649_2173808_+	NA	NA|31aa|down_2|NZ_CP013616.1_2174243_2174336_+	NA	NA|286aa|down_3|NZ_CP013616.1_2174465_2175323_-	COG0561, Cof, Predicted hydrolases of the HAD superfamily [General function prediction only]	NA|261aa|down_4|NZ_CP013616.1_2175390_2176173_-	COG1119, ModF, ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA [Inorganic ion transport and metabolism]	NA|203aa|down_5|NZ_CP013616.1_2176462_2177071_-	pfam08937, DUF1863, MTH538 TIR-like domain (DUF1863)	NA|345aa|down_6|NZ_CP013616.1_2177098_2178133_-	pfam13676, TIR_2, TIR domain	NA|500aa|down_7|NZ_CP013616.1_2178195_2179695_-	pfam18185, STALD, Sir2- and TIR-associating SLOG family	NA|97aa|down_8|NZ_CP013616.1_2179754_2180045_-	pfam11867, DUF3387, Domain of unknown function (DUF3387)	TnsE_C|135aa|down_9|NZ_CP013616.1_2180169_2180574_-	pfam18623, TnsE_C, TnsE C-terminal domain
GCF_001465635.1_ASM146563v1	NZ_CP013616	Staphylococcus aureus strain RIVM1295 chromosome, complete genome	9	2336426-2336511	9	CRISPRCasFinder	no	WYL	WYL,csa3,cas3,DEDDh,DinG,TnsE_C	Unclear	AAAGTCAGCTTACAATAATGTGCAAGTTGG	30	1	7	2336456-2336481|2336456-2336481|2336456-2336481|2336456-2336481|2336456-2336481|2336456-2336481|2336456-2336481	NZ_CP013616.1_1665200-1665175|NZ_CP013616.1_869238-869213|NZ_CP013616.1_873358-873383|NZ_CP013616.1_918293-918318|NZ_CP013616.1_1357385-1357410|NZ_CP013616.1_2127867-2127892|NZ_CP013616.1_2468304-2468279	NA	1	1	Orphan	WYL,csa3,cas3,DEDDh,DinG,TnsE_C	NA|65aa|up_6|NZ_CP013616.1_2329170_2329365_-,NA|78aa|down_1|NZ_CP013616.1_2337461_2337695_-,NA|110aa|down_8|NZ_CP013616.1_2345783_2346113_+	NA|109aa|up_9|NZ_CP013616.1_2324568_2324895_-	pfam14470, bPH_3, Bacterial PH domain	NA|248aa|up_8|NZ_CP013616.1_2324958_2325702_-	TIGR01889, Pleiotropic_Regulator_Of_Virulence, staphylococcal accessory regulator family	NA|270aa|up_7|NZ_CP013616.1_2328292_2329102_+	COG3942, COG3942, Surface antigen [General function prediction only]	NA|65aa|up_6|NZ_CP013616.1_2329170_2329365_-	NA	NA|467aa|up_5|NZ_CP013616.1_2329538_2330939_-	TIGR00931, Uncharacterized_Na+/H+_antiporter_HI_1107, Na+/H+ antiporter NhaC	NA|361aa|up_4|NZ_CP013616.1_2331033_2332116_-	pfam02317, Octopine_DH, NAD/NADP octopine/nopaline dehydrogenase, alpha-helical domain	NA|141aa|up_3|NZ_CP013616.1_2332363_2332786_+	COG3296, COG3296, Uncharacterized protein conserved in bacteria [Function unknown]	NA|167aa|up_2|NZ_CP013616.1_2333022_2333523_+	COG3942, COG3942, Surface antigen [General function prediction only]	NA|318aa|up_1|NZ_CP013616.1_2333885_2334839_+	cd12178, 2-Hacid_dh_13, Putative D-isomer specific 2-hydroxyacid dehydrogenases, NAD-binding and catalytic domains	NA|375aa|up_0|NZ_CP013616.1_2334930_2336055_-	PRK06753, PRK06753, hypothetical protein; Provisional	NA|259aa|down_0|NZ_CP013616.1_2336663_2337440_-	COG4193, LytD, Beta- N-acetylglucosaminidase [Carbohydrate transport and metabolism]	NA|78aa|down_1|NZ_CP013616.1_2337461_2337695_-	NA	NA|158aa|down_2|NZ_CP013616.1_2337989_2338463_-	COG2427, COG2427, Uncharacterized conserved protein [Function unknown]	NA|985aa|down_3|NZ_CP013616.1_2338462_2341417_-	COG3383, COG3383, Uncharacterized anaerobic dehydrogenase [General function prediction only]	NA|316aa|down_4|NZ_CP013616.1_2342018_2342966_-	PRK09379, PRK09379, LytR family transcriptional regulator	NA|266aa|down_5|NZ_CP013616.1_2343098_2343896_-	COG0483, SuhB, Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]	WYL|231aa|down_6|NZ_CP013616.1_2344280_2344973_+	COG2378, COG2378, Predicted transcriptional regulator [Transcription]	NA|246aa|down_7|NZ_CP013616.1_2344997_2345735_-	pfam02517, Abi, CAAX protease self-immunity	NA|110aa|down_8|NZ_CP013616.1_2345783_2346113_+	NA	NA|291aa|down_9|NZ_CP013616.1_2346557_2347430_+	COG1737, RpiR, Transcriptional regulators [Transcription]
GCF_001465635.1_ASM146563v1	NZ_CP013616	Staphylococcus aureus strain RIVM1295 chromosome, complete genome	10	2452843-2452937	10	CRISPRCasFinder	no		WYL,csa3,cas3,DEDDh,DinG,TnsE_C	Orphan	TTCTTCAAATTTATTTGTTAGAAAGGC	27	0	0	NA	NA	NA	1	1	Orphan	WYL,csa3,cas3,DEDDh,DinG,TnsE_C	NA|35aa|up_2|NZ_CP013616.1_2450563_2450668_+,NA|40aa|down_0|NZ_CP013616.1_2453115_2453235_-	NA|200aa|up_9|NZ_CP013616.1_2444040_2444640_-	COG1651, DsbG, Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]	NA|121aa|up_8|NZ_CP013616.1_2444658_2445021_-	pfam14729, DUF4467, Domain of unknown function with cystatin-like fold (DUF4467)	NA|417aa|up_7|NZ_CP013616.1_2445275_2446526_+	pfam02388, FemAB, FemAB family	NA|244aa|up_6|NZ_CP013616.1_2446622_2447354_-	COG1126, GlnQ, ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]	NA|240aa|up_5|NZ_CP013616.1_2447350_2448070_-	COG0765, HisM, ABC-type amino acid transport system, permease component [Amino acid transport and metabolism]	NA|260aa|up_4|NZ_CP013616.1_2448050_2448830_-	cd13711, PBP2_Ngo0372_TcyA, Substrate binding domain of ABC transporters involved in cystine import; the type 2 periplasmic binding protein fold	NA|480aa|up_3|NZ_CP013616.1_2448950_2450390_-	TIGR00711, Uncharacterized_MFS-type_transporter_YhcA, drug resistance transporter, EmrB/QacA subfamily	NA|35aa|up_2|NZ_CP013616.1_2450563_2450668_+	NA	NA|229aa|up_1|NZ_CP013616.1_2450821_2451508_-	PRK14119, gpmA, phosphoglyceromutase; Provisional	NA|289aa|up_0|NZ_CP013616.1_2451834_2452701_-	COG0053, MMT1, Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]	NA|40aa|down_0|NZ_CP013616.1_2453115_2453235_-	NA	NA|437aa|down_1|NZ_CP013616.1_2453329_2454640_+	pfam11621, Sbi-IV, C3 binding domain 4 of IgG-bind protein SBI	NA|310aa|down_2|NZ_CP013616.1_2455175_2456105_+	pfam07968, Leukocidin, Leukocidin/Hemolysin toxin family	NA|321aa|down_3|NZ_CP013616.1_2456672_2457635_+	pfam07968, Leukocidin, Leukocidin/Hemolysin toxin family	NA|326aa|down_4|NZ_CP013616.1_2457621_2458599_+	TIGR01002, synergohymenotropic_toxin, beta-channel forming cytolysin	NA|156aa|down_5|NZ_CP013616.1_2458650_2459118_-	pfam06177, QueT, QueT transporter	NA|231aa|down_6|NZ_CP013616.1_2459128_2459821_-	COG1424, BioW, Pimeloyl-CoA synthetase [Coenzyme metabolism]	NA|372aa|down_7|NZ_CP013616.1_2459831_2460947_-	COG0156, BioF, 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]	NA|336aa|down_8|NZ_CP013616.1_2460924_2461932_-	PRK06256, PRK06256, biotin synthase; Validated	NA|453aa|down_9|NZ_CP013616.1_2461933_2463292_-	TIGR00508, hypothetical_protein_DESPIG_00326, adenosylmethionine-8-amino-7-oxononanoate transaminase
GCF_001465635.1_ASM146563v1	NZ_CP013616	Staphylococcus aureus strain RIVM1295 chromosome, complete genome	11	2512567-2512661	11	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_CP013616.1_2502152_2502899_+,NA|121aa|down_0|NZ_CP013616.1_2513329_2513692_-,NA|105aa|down_8|NZ_CP013616.1_2520504_2520819_+	NA|249aa|up_9|NZ_CP013616.1_2502152_2502899_+	NA	NA|398aa|up_8|NZ_CP013616.1_2503122_2504316_-	cd17489, MFS_YfcJ_like, Escherichia coli YfcJ, YhhS, and similar transporters of the Major Facilitator Superfamily	NA|250aa|up_7|NZ_CP013616.1_2504327_2505077_-	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_CP013616.1_2505069_2505885_-	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_CP013616.1_2505881_2506751_-	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_CP013616.1_2506747_2507683_-	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_CP013616.1_2507695_2509294_-	TIGR02294, Nickel-binding_periplasmic_protein, nickel ABC transporter, nickel/metallophore periplasmic binding protein	NA|434aa|up_2|NZ_CP013616.1_2509436_2510738_-	COG4408, COG4408, Uncharacterized protein conserved in bacteria [Function unknown]	NA|273aa|up_1|NZ_CP013616.1_2510730_2511549_-	cd08261, Zn_ADH7, Alcohol dehydrogenases of the MDR family	NA|274aa|up_0|NZ_CP013616.1_2511559_2512381_-	COG0253, DapF, Diaminopimelate epimerase [Amino acid transport and metabolism]	NA|121aa|down_0|NZ_CP013616.1_2513329_2513692_-	NA	NA|273aa|down_1|NZ_CP013616.1_2513954_2514773_-	PRK08589, PRK08589, SDR family oxidoreductase	NA|513aa|down_2|NZ_CP013616.1_2515006_2516545_+	pfam03806, ABG_transport, AbgT putative transporter family	NA|141aa|down_3|NZ_CP013616.1_2516656_2517079_-	COG2128, COG2128, Uncharacterized conserved protein [Function unknown]	NA|133aa|down_4|NZ_CP013616.1_2517550_2517949_-	pfam07252, DUF1433, Protein of unknown function (DUF1433)	NA|137aa|down_5|NZ_CP013616.1_2517975_2518386_-	pfam07252, DUF1433, Protein of unknown function (DUF1433)	NA|128aa|down_6|NZ_CP013616.1_2518840_2519224_-	pfam07252, DUF1433, Protein of unknown function (DUF1433)	NA|403aa|down_7|NZ_CP013616.1_2519290_2520499_+	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_CP013616.1_2520504_2520819_+	NA	NA|140aa|down_9|NZ_CP013616.1_2522695_2523115_-	pfam07252, DUF1433, Protein of unknown function (DUF1433)
GCF_001465635.1_ASM146563v1	NZ_CP013616	Staphylococcus aureus strain RIVM1295 chromosome, complete genome	12	2540512-2540622	12	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_3|NZ_CP013616.1_2534815_2535082_+,NA|103aa|up_2|NZ_CP013616.1_2535225_2535534_+,NA	NA|262aa|up_9|NZ_CP013616.1_2527561_2528347_-	pfam04507, DUF576, Csa1 family	NA|255aa|up_8|NZ_CP013616.1_2528594_2529359_-	pfam04507, DUF576, Csa1 family	NA|258aa|up_7|NZ_CP013616.1_2529470_2530244_-	pfam04507, DUF576, Csa1 family	NA|310aa|up_6|NZ_CP013616.1_2530486_2531416_-	pfam09019, EcoRII-C, EcoRII C terminal	NA|398aa|up_5|NZ_CP013616.1_2531511_2532705_+	TIGR00675, Modification_methylase, DNA-methyltransferase (dcm)	NA|584aa|up_4|NZ_CP013616.1_2532780_2534532_+	cd05799, PGM2, This CD includes PGM2 (phosphoglucomutase 2) and PGM2L1 (phosphoglucomutase 2-like 1)	NA|89aa|up_3|NZ_CP013616.1_2534815_2535082_+	NA	NA|103aa|up_2|NZ_CP013616.1_2535225_2535534_+	NA	NA|289aa|up_1|NZ_CP013616.1_2535659_2536526_-	COG1210, GalU, UDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]	NA|952aa|up_0|NZ_CP013616.1_2536705_2539561_-	pfam10425, SdrG_C_C, C-terminus of bacterial fibrinogen-binding adhesin	NA|453aa|down_0|NZ_CP013616.1_2543762_2545121_-	TIGR00791, Gluconate_permease, gluconate transporter	NA|518aa|down_1|NZ_CP013616.1_2545237_2546791_-	TIGR01314, gntK_FGGY, gluconate kinase, FGGY type	NA|226aa|down_2|NZ_CP013616.1_2546815_2547493_-	COG1802, GntR, Transcriptional regulators [Transcription]	NA|255aa|down_3|NZ_CP013616.1_2547649_2548414_-	cd01106, HTH_TipAL-Mta, Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA	NA|231aa|down_4|NZ_CP013616.1_2548578_2549271_-	COG2357, COG2357, PpGpp synthetase catalytic domain [General function prediction only]	NA|139aa|down_5|NZ_CP013616.1_2549500_2549917_-	COG4876, COG4876, Uncharacterized protein conserved in bacteria [Function unknown]	NA|608aa|down_6|NZ_CP013616.1_2550055_2551879_-	COG1289, COG1289, Predicted membrane protein [Function unknown]	NA|426aa|down_7|NZ_CP013616.1_2552790_2554068_-	cd17319, MFS_ExuT_GudP_like, Hexuronate transporter, Glucarate transporter, and similar transporters of the Major Facilitator Superfamily	NA|204aa|down_8|NZ_CP013616.1_2554614_2555226_+	COG0586, DedA, Uncharacterized membrane-associated protein [Function unknown]	NA|388aa|down_9|NZ_CP013616.1_2555323_2556487_-	cd17474, MFS_YfmO_like, Bacillus subtilis multidrug efflux protein YfmO and similar transporters of the Major Facilitator Superfamily
