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_000009585.1_ASM958v1	NC_017333	Staphylococcus aureus subsp. aureus ST398, complete genome	1	315263-315462	1	CRISPRCasFinder	no		WYL,csa3,cas3,DEDDh,DinG,TnsE_C	Orphan	TGCAAGTTGGCGGGGCCCCAACACAGAAGCT	31	2	2	315294-315318|315350-315374	NC_017333.1_315463-315487|NC_017333.1_2223141-2223165	NA	3	3	Orphan	WYL,csa3,cas3,DEDDh,DinG,TnsE_C	NA,NA|131aa|down_5|NC_017333.1_320638_321031_+	NA|574aa|up_9|NC_017333.1_302709_304431_+	pfam18674, TarS_C1, TarS beta-glycosyltransferase C-terminal domain 1	NA|225aa|up_8|NC_017333.1_304574_305249_+	PRK13276, PRK13276, iron-sulfur cluster repair di-iron protein ScdA	NA|585aa|up_7|NC_017333.1_305495_307250_+	COG3275, LytS, Putative regulator of cell autolysis [Signal transduction mechanisms]	NA|247aa|up_6|NC_017333.1_307252_307993_+	PRK14084, PRK14084, DNA-binding response regulator	NA|148aa|up_5|NC_017333.1_308105_308549_+	PRK04125, PRK04125, antiholin-like protein LrgA	NA|234aa|up_4|NC_017333.1_308541_309243_+	PRK04288, PRK04288, antiholin-like protein LrgB; Provisional	NA|764aa|up_3|NC_017333.1_309583_311875_+	COG3256, NorB, Nitric oxide reductase large subunit [Inorganic ion transport and metabolism]	NA|235aa|up_2|NC_017333.1_312100_312805_-	COG2188, PhnF, Transcriptional regulators [Transcription]	NA|264aa|up_1|NC_017333.1_312953_313745_+	COG2190, NagE, Phosphotransferase system IIA components [Carbohydrate transport and metabolism]	NA|479aa|up_0|NC_017333.1_313760_315197_+	PRK09589, celA, 6-phospho-beta-glucosidase; Reviewed	NA|254aa|down_0|NC_017333.1_315772_316534_-	pfam13649, Methyltransf_25, Methyltransferase domain	NA|305aa|down_1|NC_017333.1_316785_317700_-	TIGR02152, Putative_ribokinase, ribokinase	NA|135aa|down_2|NC_017333.1_317727_318132_-	PRK11797, PRK11797, D-ribose pyranase; Provisional	NA|294aa|down_3|NC_017333.1_318146_319028_-	pfam06800, Sugar_transport, Sugar transport protein	NA|333aa|down_4|NC_017333.1_319259_320258_-	COG1609, PurR, Transcriptional regulators [Transcription]	NA|131aa|down_5|NC_017333.1_320638_321031_+	NA	NA|459aa|down_6|NC_017333.1_321159_322536_-	TIGR00711, Uncharacterized_MFS-type_transporter_YhcA, drug resistance transporter, EmrB/QacA subfamily	NA|331aa|down_7|NC_017333.1_322769_323762_+	COG3049, COG3049, Penicillin V acylase and related amidases [Cell envelope biogenesis, outer membrane]	NA|317aa|down_8|NC_017333.1_324087_325038_+	COG3942, COG3942, Surface antigen [General function prediction only]	NA|220aa|down_9|NC_017333.1_325089_325749_-	COG1131, CcmA, ABC-type multidrug transport system, ATPase component [Defense mechanisms]
GCF_000009585.1_ASM958v1	NC_017333	Staphylococcus aureus subsp. aureus ST398, complete genome	2	724389-724497	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|NC_017333.1_728230_728737_+,NA|239aa|down_5|NC_017333.1_728898_729615_+	NA|209aa|up_9|NC_017333.1_714038_714665_+	pfam04276, DUF443, Protein of unknown function (DUF443)	NA|313aa|up_8|NC_017333.1_714934_715873_+	cd19083, AKR_AKR11A1_11D1, AKR11A and  AKR11D families of aldo-keto reductase (AKR)	NA|179aa|up_7|NC_017333.1_716318_716855_+	COG0655, WrbA, Multimeric flavodoxin WrbA [General function prediction only]	NA|159aa|up_6|NC_017333.1_717024_717501_+	pfam00583, Acetyltransf_1, Acetyltransferase (GNAT) family	NA|432aa|up_5|NC_017333.1_717540_718836_+	COG1078, COG1078, HD superfamily phosphohydrolases [General function prediction only]	NA|174aa|up_4|NC_017333.1_718863_719385_+	pfam08741, YwhD, YwhD family	NA|337aa|up_3|NC_017333.1_719882_720893_+	PRK09422, PRK09422, ethanol-active dehydrogenase/acetaldehyde-active reductase; Provisional	NA|139aa|up_2|NC_017333.1_721168_721585_+	COG4506, COG4506, Uncharacterized protein conserved in bacteria [Function unknown]	NA|554aa|up_1|NC_017333.1_721581_723243_+	PRK01611, argS, arginyl-tRNA synthetase; Reviewed	NA|212aa|up_0|NC_017333.1_723583_724219_+	COG2231, COG2231, Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]	NA|296aa|down_0|NC_017333.1_724548_725436_+	cd01143, YvrC, Periplasmic binding protein YvrC	NA|317aa|down_1|NC_017333.1_725586_726537_+	pfam01032, FecCD, FecCD transport family	NA|240aa|down_2|NC_017333.1_726591_727311_+	COG1011, COG1011, Predicted hydrolase (HAD superfamily) [General function prediction only]	NA|267aa|down_3|NC_017333.1_727294_728095_+	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|169aa|down_4|NC_017333.1_728230_728737_+	NA	NA|239aa|down_5|NC_017333.1_728898_729615_+	NA	NA|263aa|down_6|NC_017333.1_729783_730572_+	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|125aa|down_7|NC_017333.1_730823_731198_-	TIGR01889, Pleiotropic_Regulator_Of_Virulence, staphylococcal accessory regulator family	NA|310aa|down_8|NC_017333.1_732145_733075_-	COG3238, COG3238, Uncharacterized protein conserved in bacteria [Function unknown]	NA|75aa|down_9|NC_017333.1_733267_733492_-	pfam11148, DUF2922, Protein of unknown function (DUF2922)
GCF_000009585.1_ASM958v1	NC_017333	Staphylococcus aureus subsp. aureus ST398, complete genome	3	886613-886695	3	CRISPRCasFinder	no		WYL,csa3,cas3,DEDDh,DinG,TnsE_C	Orphan	CACCCCAACTCGCATTGCTTGTAGAA	26	1	19	886639-886669|886639-886669|886639-886669|886639-886669|886639-886669|886639-886669|886639-886669|886639-886669|886639-886669|886639-886669|886639-886669|886639-886669|886639-886669|886639-886669|886639-886669|886639-886669|886639-886669|886639-886669|886639-886669	NC_017333.1_980925-980895|NC_017333.1_1019726-1019756|NC_017333.1_2056150-2056180|NC_017333.1_2056260-2056290|NC_017333.1_2137882-2137912|NC_017333.1_297275-297305|NC_017333.1_297333-297363|NC_017333.1_297391-297421|NC_017333.1_438250-438220|NC_017333.1_716031-716001|NC_017333.1_840326-840296|NC_017333.1_931556-931586|NC_017333.1_1112635-1112665|NC_017333.1_1212950-1212920|NC_017333.1_1213004-1212974|NC_017333.1_1852300-1852270|NC_017333.1_1942928-1942898|NC_017333.1_2386544-2386574|NC_017333.1_2431667-2431637	NA	1	1	Orphan	WYL,csa3,cas3,DEDDh,DinG,TnsE_C	NA,NA	NA|280aa|up_9|NC_017333.1_873862_874702_+	COG3942, COG3942, Surface antigen [General function prediction only]	NA|217aa|up_8|NC_017333.1_874875_875526_+	pfam12917, HD_2, HD containing hydrolase-like enzyme	NA|79aa|up_7|NC_017333.1_875522_875759_+	COG4897, CsbA, Uncharacterized protein conserved in bacteria [Function unknown]	NA|662aa|up_6|NC_017333.1_876027_878013_+	PRK05298, PRK05298, excinuclease ABC subunit UvrB	NA|949aa|up_5|NC_017333.1_878020_880867_+	PRK00349, uvrA, excinuclease ABC subunit UvrA	NA|311aa|up_4|NC_017333.1_881476_882409_+	PRK05428, PRK05428, HPr kinase/phosphorylase; Provisional	NA|280aa|up_3|NC_017333.1_882414_883254_+	PRK12437, PRK12437, prolipoprotein diacylglyceryl transferase; Reviewed	NA|162aa|up_2|NC_017333.1_883261_883747_+	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|NC_017333.1_883754_885194_+	sd00006, TPR, Tetratricopeptide repeat	NA|312aa|up_0|NC_017333.1_885260_886196_+	TIGR01292, Thioredoxin_reductase, thioredoxin-disulfide reductase	NA|304aa|down_0|NC_017333.1_886963_887875_+	COG1660, COG1660, Predicted P-loop-containing kinase [General function prediction only]	NA|332aa|down_1|NC_017333.1_887871_888867_+	TIGR01826, Putative_gluconeogenesis_factor, conserved hypothetical protein, cofD-related	NA|315aa|down_2|NC_017333.1_888975_889920_+	TIGR00647, DNA_bind_WhiA, DNA-binding protein WhiA	NA|196aa|down_3|NC_017333.1_890489_891077_+	PRK00277, clpP, ATP-dependent Clp protease proteolytic subunit; Reviewed	NA|545aa|down_4|NC_017333.1_891259_892894_+	PRK13529, PRK13529, oxaloacetate-decarboxylating malate dehydrogenase	NA|301aa|down_5|NC_017333.1_893100_894003_-	COG1090, COG1090, Predicted nucleoside-diphosphate sugar epimerase [General function prediction only]	NA|210aa|down_6|NC_017333.1_894705_895335_+	PRK00409, PRK00409, recombination and DNA strand exchange inhibitor protein; Reviewed	NA|338aa|down_7|NC_017333.1_896109_897123_+	COG2390, DeoR, Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]	NA|337aa|down_8|NC_017333.1_897175_898186_+	TIGR01534, Glyceraldehyde-3-phosphate_dehydrogenase, glyceraldehyde-3-phosphate dehydrogenase, type I	NA|397aa|down_9|NC_017333.1_898324_899515_+	PRK00073, pgk, phosphoglycerate kinase; Provisional
GCF_000009585.1_ASM958v1	NC_017333	Staphylococcus aureus subsp. aureus ST398, complete genome	4	935963-936043	4	CRISPRCasFinder	no		WYL,csa3,cas3,DEDDh,DinG,TnsE_C	Orphan	TCTTTATCATTTCTGTCCCACTCCC	25	1	1	935988-936018	NC_017333.1_881066-881036	NA	1	1	Orphan	WYL,csa3,cas3,DEDDh,DinG,TnsE_C	NA,NA|105aa|down_7|NC_017333.1_943649_943964_-	NA|180aa|up_9|NC_017333.1_928093_928633_+	cd02135, YdjA-like, nitroreductase family protein similar to Escherichia coli YdjA	NA|107aa|up_8|NC_017333.1_928782_929103_-	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|NC_017333.1_929246_929603_+	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|NC_017333.1_929760_930141_+	PRK01202, PRK01202, glycine cleavage system protein GcvH	NA|293aa|up_5|NC_017333.1_930320_931199_+	COG3878, COG3878, Uncharacterized protein conserved in bacteria [Function unknown]	NA|129aa|up_4|NC_017333.1_931900_932287_+	COG1658, COG1658, Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]	NA|99aa|up_3|NC_017333.1_932279_932576_+	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|NC_017333.1_932825_933851_+	COG1135, AbcC, ABC-type metal ion transport system, ATPase component [Inorganic ion transport and metabolism]	NA|232aa|up_1|NC_017333.1_933843_934539_+	COG2011, AbcD, ABC-type metal ion transport system, permease component [Inorganic ion transport and metabolism]	NA|274aa|up_0|NC_017333.1_934556_935378_+	COG1464, NlpA, ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]	NA|65aa|down_0|NC_017333.1_936185_936380_+	COG3237, COG3237, Uncharacterized protein conserved in bacteria [Function unknown]	NA|284aa|down_1|NC_017333.1_936613_937465_-	COG2035, COG2035, Predicted membrane protein [Function unknown]	NA|254aa|down_2|NC_017333.1_937792_938554_+	COG0396, sufC, Cysteine desulfurase activator ATPase [Posttranslational modification, protein turnover, chaperones]	NA|436aa|down_3|NC_017333.1_938652_939960_+	COG0719, SufB, Cysteine desulfurase activator SufB [Posttranslational modification, protein turnover, chaperones]	NA|417aa|down_4|NC_017333.1_940065_941316_+	TIGR01979, Probable_cysteine_desulfurase, cysteine desulfurases, SufSfamily	NA|155aa|down_5|NC_017333.1_941305_941770_+	TIGR01994, Iron-sulfur_cluster_assembly_scaffold_protein_IscU, SUF system FeS assembly protein, NifU family	NA|466aa|down_6|NC_017333.1_941920_943318_+	TIGR01980, UPF0051_protein_slr0074, FeS assembly protein SufB	NA|105aa|down_7|NC_017333.1_943649_943964_-	NA	NA|347aa|down_8|NC_017333.1_944332_945373_+	COG4536, CorB, Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]	NA|356aa|down_9|NC_017333.1_945386_946454_+	COG2070, COG2070, Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]
GCF_000009585.1_ASM958v1	NC_017333	Staphylococcus aureus subsp. aureus ST398, complete genome	5	1602708-1602803	5	CRISPRCasFinder	no		WYL,csa3,cas3,DEDDh,DinG,TnsE_C	Orphan	CGTTTGTTAACTAATATTTGCATT	24	0	0	NA	NA	NA	1	1	Orphan	WYL,csa3,cas3,DEDDh,DinG,TnsE_C	NA|72aa|up_9|NC_017333.1_1596573_1596789_-,NA|139aa|up_8|NC_017333.1_1597004_1597421_-,NA|60aa|up_7|NC_017333.1_1597940_1598120_-,NA|637aa|down_0|NC_017333.1_1604267_1606178_-,NA|53aa|down_4|NC_017333.1_1615112_1615271_-,NA|117aa|down_5|NC_017333.1_1615312_1615663_-,NA|132aa|down_8|NC_017333.1_1616943_1617339_-,NA|134aa|down_9|NC_017333.1_1617339_1617741_-	NA|72aa|up_9|NC_017333.1_1596573_1596789_-	NA	NA|139aa|up_8|NC_017333.1_1597004_1597421_-	NA	NA|60aa|up_7|NC_017333.1_1597940_1598120_-	NA	NA|482aa|up_6|NC_017333.1_1599020_1600466_-	smart00644, Ami_2, Ami_2 domain	NA|146aa|up_5|NC_017333.1_1600446_1600884_-	TIGR01598, holin_phiLC3, holin, phage phi LC3 family	NA|100aa|up_4|NC_017333.1_1601019_1601319_-	pfam11166, DUF2951, Protein of unknown function (DUF2951)	NA|55aa|up_3|NC_017333.1_1601364_1601529_-	pfam09693, Phage_XkdX, Phage uncharacterized protein (Phage_XkdX)	NA|131aa|up_2|NC_017333.1_1601521_1601914_-	pfam11192, DUF2977, Protein of unknown function (DUF2977)	NA|102aa|up_1|NC_017333.1_1601832_1602138_-	pfam11166, DUF2951, Protein of unknown function (DUF2951)	NA|55aa|up_0|NC_017333.1_1602183_1602348_-	pfam09693, Phage_XkdX, Phage uncharacterized protein (Phage_XkdX)	NA|637aa|down_0|NC_017333.1_1604267_1606178_-	NA	NA|97aa|down_1|NC_017333.1_1606193_1606484_-	PRK05926, PRK05926, hypothetical protein; Provisional	NA|528aa|down_2|NC_017333.1_1606483_1608067_-	pfam06605, Prophage_tail, Prophage endopeptidase tail	NA|275aa|down_3|NC_017333.1_1608075_1608900_-	pfam05709, Sipho_tail, Phage tail protein	NA|53aa|down_4|NC_017333.1_1615112_1615271_-	NA	NA|117aa|down_5|NC_017333.1_1615312_1615663_-	NA	NA|152aa|down_6|NC_017333.1_1615720_1616176_-	COG5492, COG5492, Bacterial surface proteins containing Ig-like domains [Cell motility and secretion]	NA|214aa|down_7|NC_017333.1_1616267_1616909_-	TIGR01603, Uncharacterized_phage_related_protein, phage major tail protein, phi13 family	NA|132aa|down_8|NC_017333.1_1616943_1617339_-	NA	NA|134aa|down_9|NC_017333.1_1617339_1617741_-	NA
GCF_000009585.1_ASM958v1	NC_017333	Staphylococcus aureus subsp. aureus ST398, complete genome	6	1854733-1854815	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|NC_017333.1_1839566_1840928_+	COG1113, AnsP, Gamma-aminobutyrate permease and related permeases [Amino acid transport and metabolism]	NA|586aa|up_8|NC_017333.1_1841271_1843029_-	PRK06354, PRK06354, pyruvate kinase; Provisional	NA|323aa|up_7|NC_017333.1_1843050_1844019_-	PRK03202, PRK03202, ATP-dependent 6-phosphofructokinase	NA|315aa|up_6|NC_017333.1_1844287_1845232_-	PRK05724, PRK05724, acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated	NA|286aa|up_5|NC_017333.1_1845231_1846089_-	PRK05654, PRK05654, acetyl-CoA carboxylase carboxyltransferase subunit beta	NA|410aa|up_4|NC_017333.1_1846283_1847513_-	PRK07232, PRK07232, bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed	NA|1066aa|up_3|NC_017333.1_1847961_1851159_-	COG0587, DnaE, DNA polymerase III, alpha subunit [DNA replication, recombination, and repair]	NA|314aa|up_2|NC_017333.1_1851179_1852121_-	COG0618, COG0618, Exopolyphosphatase-related proteins [General function prediction only]	NA|433aa|up_1|NC_017333.1_1852490_1853789_-	COG4109, COG4109, Predicted transcriptional regulator containing CBS domains [Transcription]	NA|138aa|up_0|NC_017333.1_1853993_1854407_+	pfam00582, Usp, Universal stress protein family	NA|230aa|down_0|NC_017333.1_1854912_1855602_-	PRK00685, PRK00685, metal-dependent hydrolase; Provisional	NA|352aa|down_1|NC_017333.1_1855776_1856832_+	COG0006, PepP, Xaa-Pro aminopeptidase [Amino acid transport and metabolism]	NA|373aa|down_2|NC_017333.1_1857147_1858266_-	cd05305, L-AlaDH, Alanine dehydrogenase NAD-binding and catalytic domains	NA|173aa|down_3|NC_017333.1_1858406_1858925_+	pfam00582, Usp, Universal stress protein family	NA|401aa|down_4|NC_017333.1_1859154_1860357_-	PRK00180, PRK00180, acetate kinase A/propionate kinase 2; Reviewed	NA|316aa|down_5|NC_017333.1_1860444_1861392_-	COG0827, COG0827, Adenine-specific DNA methylase [DNA replication, recombination, and repair]	NA|165aa|down_6|NC_017333.1_1861514_1862009_-	PRK00522, tpx, thiol peroxidase	NA|257aa|down_7|NC_017333.1_1862106_1862877_-	PRK10621, PRK10621, hypothetical protein; Provisional	NA|408aa|down_8|NC_017333.1_1862920_1864144_-	PRK01565, PRK01565, thiamine biosynthesis protein ThiI; Provisional	NA|383aa|down_9|NC_017333.1_1864143_1865292_-	COG1104, NifS, Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]
GCF_000009585.1_ASM958v1	NC_017333	Staphylococcus aureus subsp. aureus ST398, complete genome	7	1942937-1943030	7	CRISPRCasFinder	no	csa3	WYL,csa3,cas3,DEDDh,DinG,TnsE_C	Type I-A	GCAATGCGCGTTGGGGTGTGGGGCCCCAACATAG	34	1	1	1942971-1942996	NC_017333.1_2056222-2056197	NA	1	1	Orphan	WYL,csa3,cas3,DEDDh,DinG,TnsE_C	NA|75aa|up_5|NC_017333.1_1939030_1939255_-,NA|148aa|up_2|NC_017333.1_1940466_1940910_-,NA|101aa|down_1|NC_017333.1_1944164_1944467_+	NA|501aa|up_9|NC_017333.1_1934054_1935557_-	COG4529, COG4529, Uncharacterized protein conserved in bacteria [Function unknown]	csa3|105aa|up_8|NC_017333.1_1936207_1936522_+	cd00090, HTH_ARSR, Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors	NA|431aa|up_7|NC_017333.1_1936521_1937814_+	PRK15445, PRK15445, arsenical efflux pump membrane protein ArsB	NA|285aa|up_6|NC_017333.1_1937900_1938755_-	COG4193, LytD, Beta- N-acetylglucosaminidase [Carbohydrate transport and metabolism]	NA|75aa|up_5|NC_017333.1_1939030_1939255_-	NA	NA|157aa|up_4|NC_017333.1_1939453_1939924_+	COG1595, RpoE, DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]	NA|148aa|up_3|NC_017333.1_1940036_1940480_+	pfam06338, ComK, ComK protein	NA|148aa|up_2|NC_017333.1_1940466_1940910_-	NA	NA|212aa|up_1|NC_017333.1_1941207_1941843_+	pfam02517, Abi, CAAX protease self-immunity	NA|207aa|up_0|NC_017333.1_1942009_1942630_+	pfam02517, Abi, CAAX protease self-immunity	NA|238aa|down_0|NC_017333.1_1943192_1943906_-	PRK12376, PRK12376, putative translaldolase; Provisional	NA|101aa|down_1|NC_017333.1_1944164_1944467_+	NA	NA|122aa|down_2|NC_017333.1_1944721_1945087_+	PRK14201, PRK14201, fluoride efflux transporter CrcB	NA|118aa|down_3|NC_017333.1_1945083_1945437_+	COG0239, CrcB, Integral membrane protein possibly involved in chromosome condensation [Cell division and chromosome partitioning]	NA|278aa|down_4|NC_017333.1_1945686_1946520_-	COG0656, ARA1, Aldo/keto reductases, related to diketogulonate reductase [General function prediction only]	NA|303aa|down_5|NC_017333.1_1946731_1947640_-	pfam08378, NERD, Nuclease-related domain	NA|398aa|down_6|NC_017333.1_1947764_1948958_-	PRK05250, PRK05250, S-adenosylmethionine synthetase; Validated	NA|531aa|down_7|NC_017333.1_1949329_1950922_+	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|NC_017333.1_1951218_1951965_-	COG1506, DAP2, Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]	NA|158aa|down_9|NC_017333.1_1951969_1952443_-	TIGR02705, conserved_hypothetical_protein, nucleoside triphosphatase YtkD
GCF_000009585.1_ASM958v1	NC_017333	Staphylococcus aureus subsp. aureus ST398, complete genome	8	2212067-2212279	8	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|NC_017333.1_2208928_2209066_-,NA|107aa|down_0|NC_017333.1_2212312_2212633_+	NA|232aa|up_9|NC_017333.1_2201620_2202316_+	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|NC_017333.1_2202668_2204189_-	COG0513, SrmB, Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]	NA|452aa|up_7|NC_017333.1_2204704_2206060_-	COG0770, MurF, UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]	NA|357aa|up_6|NC_017333.1_2206074_2207145_-	PRK01966, ddl, D-alanine--D-alanine ligase	NA|401aa|up_5|NC_017333.1_2207462_2208665_+	TIGR02210, Rod_shape-determining_protein_RodA, rod shape-determining protein RodA	NA|46aa|up_4|NC_017333.1_2208928_2209066_-	NA	NA|70aa|up_3|NC_017333.1_2209193_2209403_-	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|NC_017333.1_2209414_2209708_-	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|NC_017333.1_2209873_2211358_+	TIGR04265, bac_cardiolipin, cardiolipin synthase	NA|216aa|up_0|NC_017333.1_2211385_2212033_+	COG1418, COG1418, Predicted HD superfamily hydrolase [General function prediction only]	NA|107aa|down_0|NC_017333.1_2212312_2212633_+	NA	NA|291aa|down_1|NC_017333.1_2214274_2215147_-	PRK02463, PRK02463, OxaA-like protein precursor; Provisional	NA|214aa|down_2|NC_017333.1_2215232_2215874_-	PRK00043, thiE, thiamine phosphate synthase	NA|264aa|down_3|NC_017333.1_2215875_2216667_-	PRK09355, PRK09355, hydroxyethylthiazole kinase; Validated	NA|277aa|down_4|NC_017333.1_2216650_2217481_-	PRK06427, PRK06427, bifunctional hydroxy-methylpyrimidine kinase/ hydroxy-phosphomethylpyrimidine kinase; Reviewed	NA|230aa|down_5|NC_017333.1_2217473_2218163_-	TIGR04306, salvage_TenA, thiaminase II	NA|232aa|down_6|NC_017333.1_2218549_2219245_-	pfam06737, Transglycosylas, Transglycosylase-like domain	NA|132aa|down_7|NC_017333.1_2219633_2220029_-	pfam00436, SSB, Single-strand binding protein family	NA|147aa|down_8|NC_017333.1_2220222_2220663_+	pfam14183, YwpF, YwpF-like protein	NA|147aa|down_9|NC_017333.1_2220719_2221160_-	PRK00006, fabZ, 3-hydroxyacyl-ACP dehydratase FabZ
GCF_000009585.1_ASM958v1	NC_017333	Staphylococcus aureus subsp. aureus ST398, complete genome	9	2267698-2267848	9	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|NC_017333.1_2262570_2262801_-,NA|364aa|up_0|NC_017333.1_2266588_2267680_+,NA|35aa|down_0|NC_017333.1_2268177_2268282_-,NA|53aa|down_1|NC_017333.1_2268961_2269120_+,NA|31aa|down_2|NC_017333.1_2269555_2269648_+	NA|237aa|up_9|NC_017333.1_2258180_2258891_+	PRK05819, deoD, DeoD-type purine-nucleoside phosphorylase	NA|148aa|up_8|NC_017333.1_2259011_2259455_-	COG0783, Dps, DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]	NA|138aa|up_7|NC_017333.1_2259654_2260068_-	COG3011, COG3011, Predicted thiol-disulfide oxidoreductase [General function    prediction only]	NA|458aa|up_6|NC_017333.1_2260525_2261899_-	pfam01878, EVE, EVE domain	NA|77aa|up_5|NC_017333.1_2262570_2262801_-	NA	NA|313aa|up_4|NC_017333.1_2262831_2263770_-	COG1482, ManA, Phosphomannose isomerase [Carbohydrate transport and metabolism]	NA|222aa|up_3|NC_017333.1_2264203_2264869_-	cd05243, SDR_a5, atypical (a) SDRs, subgroup 5	csa3|107aa|up_2|NC_017333.1_2265020_2265341_+	cd00090, HTH_ARSR, Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors	NA|327aa|up_1|NC_017333.1_2265342_2266323_+	COG1230, CzcD, Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]	NA|364aa|up_0|NC_017333.1_2266588_2267680_+	NA	NA|35aa|down_0|NC_017333.1_2268177_2268282_-	NA	NA|53aa|down_1|NC_017333.1_2268961_2269120_+	NA	NA|31aa|down_2|NC_017333.1_2269555_2269648_+	NA	NA|286aa|down_3|NC_017333.1_2269777_2270635_-	COG0561, Cof, Predicted hydrolases of the HAD superfamily [General function prediction only]	NA|261aa|down_4|NC_017333.1_2270702_2271485_-	COG1119, ModF, ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA [Inorganic ion transport and metabolism]	NA|203aa|down_5|NC_017333.1_2271774_2272383_-	pfam08937, DUF1863, MTH538 TIR-like domain (DUF1863)	NA|345aa|down_6|NC_017333.1_2272410_2273445_-	pfam13676, TIR_2, TIR domain	NA|490aa|down_7|NC_017333.1_2273538_2275008_-	pfam18185, STALD, Sir2- and TIR-associating SLOG family	NA|97aa|down_8|NC_017333.1_2275067_2275358_-	pfam11867, DUF3387, Domain of unknown function (DUF3387)	TnsE_C|135aa|down_9|NC_017333.1_2275482_2275887_-	pfam18623, TnsE_C, TnsE C-terminal domain
GCF_000009585.1_ASM958v1	NC_017333	Staphylococcus aureus subsp. aureus ST398, complete genome	10	2431719-2431804	10	CRISPRCasFinder	no	WYL	WYL,csa3,cas3,DEDDh,DinG,TnsE_C	Unclear	AAAGTCAGCTTACAATAATGTGCAAGTTGG	30	1	7	2431749-2431774|2431749-2431774|2431749-2431774|2431749-2431774|2431749-2431774|2431749-2431774|2431749-2431774	NC_017333.1_1732428-1732403|NC_017333.1_931645-931620|NC_017333.1_935765-935790|NC_017333.1_980700-980725|NC_017333.1_1417405-1417430|NC_017333.1_2223179-2223204|NC_017333.1_2563596-2563571	NA	1	1	Orphan	WYL,csa3,cas3,DEDDh,DinG,TnsE_C	NA|65aa|up_6|NC_017333.1_2424463_2424658_-,NA|78aa|down_1|NC_017333.1_2432754_2432988_-,NA|110aa|down_8|NC_017333.1_2441076_2441406_+	NA|109aa|up_9|NC_017333.1_2419862_2420189_-	pfam14470, bPH_3, Bacterial PH domain	NA|248aa|up_8|NC_017333.1_2420252_2420996_-	TIGR01889, Pleiotropic_Regulator_Of_Virulence, staphylococcal accessory regulator family	NA|270aa|up_7|NC_017333.1_2423585_2424395_+	COG3942, COG3942, Surface antigen [General function prediction only]	NA|65aa|up_6|NC_017333.1_2424463_2424658_-	NA	NA|467aa|up_5|NC_017333.1_2424831_2426232_-	TIGR00931, Uncharacterized_Na+/H+_antiporter_HI_1107, Na+/H+ antiporter NhaC	NA|361aa|up_4|NC_017333.1_2426326_2427409_-	pfam02317, Octopine_DH, NAD/NADP octopine/nopaline dehydrogenase, alpha-helical domain	NA|141aa|up_3|NC_017333.1_2427656_2428079_+	COG3296, COG3296, Uncharacterized protein conserved in bacteria [Function unknown]	NA|167aa|up_2|NC_017333.1_2428315_2428816_+	COG3942, COG3942, Surface antigen [General function prediction only]	NA|318aa|up_1|NC_017333.1_2429178_2430132_+	cd12178, 2-Hacid_dh_13, Putative D-isomer specific 2-hydroxyacid dehydrogenases, NAD-binding and catalytic domains	NA|375aa|up_0|NC_017333.1_2430223_2431348_-	PRK06753, PRK06753, hypothetical protein; Provisional	NA|259aa|down_0|NC_017333.1_2431956_2432733_-	COG4193, LytD, Beta- N-acetylglucosaminidase [Carbohydrate transport and metabolism]	NA|78aa|down_1|NC_017333.1_2432754_2432988_-	NA	NA|158aa|down_2|NC_017333.1_2433282_2433756_-	COG2427, COG2427, Uncharacterized conserved protein [Function unknown]	NA|985aa|down_3|NC_017333.1_2433755_2436710_-	COG3383, COG3383, Uncharacterized anaerobic dehydrogenase [General function prediction only]	NA|316aa|down_4|NC_017333.1_2437311_2438259_-	PRK09379, PRK09379, LytR family transcriptional regulator	NA|266aa|down_5|NC_017333.1_2438391_2439189_-	COG0483, SuhB, Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]	WYL|231aa|down_6|NC_017333.1_2439573_2440266_+	COG2378, COG2378, Predicted transcriptional regulator [Transcription]	NA|246aa|down_7|NC_017333.1_2440290_2441028_-	pfam02517, Abi, CAAX protease self-immunity	NA|110aa|down_8|NC_017333.1_2441076_2441406_+	NA	NA|291aa|down_9|NC_017333.1_2441850_2442723_+	COG1737, RpiR, Transcriptional regulators [Transcription]
GCF_000009585.1_ASM958v1	NC_017333	Staphylococcus aureus subsp. aureus ST398, complete genome	11	2548135-2548229	11	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|NC_017333.1_2545856_2545961_+,NA|40aa|down_0|NC_017333.1_2548407_2548527_-	NA|200aa|up_9|NC_017333.1_2539333_2539933_-	COG1651, DsbG, Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]	NA|121aa|up_8|NC_017333.1_2539951_2540314_-	pfam14729, DUF4467, Domain of unknown function with cystatin-like fold (DUF4467)	NA|417aa|up_7|NC_017333.1_2540568_2541819_+	pfam02388, FemAB, FemAB family	NA|244aa|up_6|NC_017333.1_2541915_2542647_-	COG1126, GlnQ, ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]	NA|240aa|up_5|NC_017333.1_2542643_2543363_-	COG0765, HisM, ABC-type amino acid transport system, permease component [Amino acid transport and metabolism]	NA|260aa|up_4|NC_017333.1_2543343_2544123_-	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|NC_017333.1_2544243_2545683_-	TIGR00711, Uncharacterized_MFS-type_transporter_YhcA, drug resistance transporter, EmrB/QacA subfamily	NA|35aa|up_2|NC_017333.1_2545856_2545961_+	NA	NA|229aa|up_1|NC_017333.1_2546114_2546801_-	PRK14119, gpmA, phosphoglyceromutase; Provisional	NA|289aa|up_0|NC_017333.1_2547126_2547993_-	COG0053, MMT1, Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]	NA|40aa|down_0|NC_017333.1_2548407_2548527_-	NA	NA|437aa|down_1|NC_017333.1_2548621_2549932_+	pfam11621, Sbi-IV, C3 binding domain 4 of IgG-bind protein SBI	NA|310aa|down_2|NC_017333.1_2550467_2551397_+	pfam07968, Leukocidin, Leukocidin/Hemolysin toxin family	NA|316aa|down_3|NC_017333.1_2551964_2552912_+	pfam07968, Leukocidin, Leukocidin/Hemolysin toxin family	NA|326aa|down_4|NC_017333.1_2552913_2553891_+	TIGR01002, synergohymenotropic_toxin, beta-channel forming cytolysin	NA|156aa|down_5|NC_017333.1_2553942_2554410_-	pfam06177, QueT, QueT transporter	NA|231aa|down_6|NC_017333.1_2554420_2555113_-	COG1424, BioW, Pimeloyl-CoA synthetase [Coenzyme metabolism]	NA|372aa|down_7|NC_017333.1_2555123_2556239_-	COG0156, BioF, 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]	NA|336aa|down_8|NC_017333.1_2556216_2557224_-	PRK06256, PRK06256, biotin synthase; Validated	NA|453aa|down_9|NC_017333.1_2557225_2558584_-	TIGR00508, hypothetical_protein_DESPIG_00326, adenosylmethionine-8-amino-7-oxononanoate transaminase
GCF_000009585.1_ASM958v1	NC_017333	Staphylococcus aureus subsp. aureus ST398, complete genome	12	2607860-2607954	12	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|NC_017333.1_2597445_2598192_+,NA|121aa|down_0|NC_017333.1_2608622_2608985_-,NA|105aa|down_8|NC_017333.1_2615797_2616112_+	NA|249aa|up_9|NC_017333.1_2597445_2598192_+	NA	NA|398aa|up_8|NC_017333.1_2598415_2599609_-	cd17489, MFS_YfcJ_like, Escherichia coli YfcJ, YhhS, and similar transporters of the Major Facilitator Superfamily	NA|250aa|up_7|NC_017333.1_2599620_2600370_-	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|NC_017333.1_2600362_2601178_-	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|NC_017333.1_2601174_2602044_-	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|NC_017333.1_2602040_2602976_-	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|NC_017333.1_2602988_2604587_-	TIGR02294, Nickel-binding_periplasmic_protein, nickel ABC transporter, nickel/metallophore periplasmic binding protein	NA|434aa|up_2|NC_017333.1_2604729_2606031_-	COG4408, COG4408, Uncharacterized protein conserved in bacteria [Function unknown]	NA|273aa|up_1|NC_017333.1_2606023_2606842_-	cd08261, Zn_ADH7, Alcohol dehydrogenases of the MDR family	NA|274aa|up_0|NC_017333.1_2606852_2607674_-	COG0253, DapF, Diaminopimelate epimerase [Amino acid transport and metabolism]	NA|121aa|down_0|NC_017333.1_2608622_2608985_-	NA	NA|273aa|down_1|NC_017333.1_2609247_2610066_-	PRK08589, PRK08589, SDR family oxidoreductase	NA|513aa|down_2|NC_017333.1_2610299_2611838_+	pfam03806, ABG_transport, AbgT putative transporter family	NA|141aa|down_3|NC_017333.1_2611949_2612372_-	COG2128, COG2128, Uncharacterized conserved protein [Function unknown]	NA|133aa|down_4|NC_017333.1_2612843_2613242_-	pfam07252, DUF1433, Protein of unknown function (DUF1433)	NA|137aa|down_5|NC_017333.1_2613268_2613679_-	pfam07252, DUF1433, Protein of unknown function (DUF1433)	NA|128aa|down_6|NC_017333.1_2614133_2614517_-	pfam07252, DUF1433, Protein of unknown function (DUF1433)	NA|403aa|down_7|NC_017333.1_2614583_2615792_+	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|NC_017333.1_2615797_2616112_+	NA	NA|140aa|down_9|NC_017333.1_2617988_2618408_-	pfam07252, DUF1433, Protein of unknown function (DUF1433)
GCF_000009585.1_ASM958v1	NC_017333	Staphylococcus aureus subsp. aureus ST398, complete genome	13	2635805-2635915	13	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|NC_017333.1_2630108_2630375_+,NA|103aa|up_1|NC_017333.1_2630518_2630827_+,NA	NA|452aa|up_9|NC_017333.1_2621502_2622858_-	cd00519, Lipase_3, Lipase (class 3)	NA|262aa|up_8|NC_017333.1_2622854_2623640_-	pfam04507, DUF576, Csa1 family	NA|255aa|up_7|NC_017333.1_2623887_2624652_-	pfam04507, DUF576, Csa1 family	NA|258aa|up_6|NC_017333.1_2624763_2625537_-	pfam04507, DUF576, Csa1 family	NA|310aa|up_5|NC_017333.1_2625779_2626709_-	pfam09019, EcoRII-C, EcoRII C terminal	NA|398aa|up_4|NC_017333.1_2626804_2627998_+	TIGR00675, Modification_methylase, DNA-methyltransferase (dcm)	NA|584aa|up_3|NC_017333.1_2628073_2629825_+	cd05799, PGM2, This CD includes PGM2 (phosphoglucomutase 2) and PGM2L1 (phosphoglucomutase 2-like 1)	NA|89aa|up_2|NC_017333.1_2630108_2630375_+	NA	NA|103aa|up_1|NC_017333.1_2630518_2630827_+	NA	NA|289aa|up_0|NC_017333.1_2630952_2631819_-	COG1210, GalU, UDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]	NA|453aa|down_0|NC_017333.1_2639055_2640414_-	TIGR00791, Gluconate_permease, gluconate transporter	NA|518aa|down_1|NC_017333.1_2640530_2642084_-	TIGR01314, gntK_FGGY, gluconate kinase, FGGY type	NA|226aa|down_2|NC_017333.1_2642108_2642786_-	COG1802, GntR, Transcriptional regulators [Transcription]	NA|255aa|down_3|NC_017333.1_2642942_2643707_-	cd01106, HTH_TipAL-Mta, Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA	NA|231aa|down_4|NC_017333.1_2643871_2644564_-	COG2357, COG2357, PpGpp synthetase catalytic domain [General function prediction only]	NA|139aa|down_5|NC_017333.1_2644794_2645211_-	COG4876, COG4876, Uncharacterized protein conserved in bacteria [Function unknown]	NA|608aa|down_6|NC_017333.1_2645349_2647173_-	COG1289, COG1289, Predicted membrane protein [Function unknown]	NA|426aa|down_7|NC_017333.1_2648084_2649362_-	cd17319, MFS_ExuT_GudP_like, Hexuronate transporter, Glucarate transporter, and similar transporters of the Major Facilitator Superfamily	NA|204aa|down_8|NC_017333.1_2649908_2650520_+	COG0586, DedA, Uncharacterized membrane-associated protein [Function unknown]	NA|388aa|down_9|NC_017333.1_2650617_2651781_-	cd17474, MFS_YfmO_like, Bacillus subtilis multidrug efflux protein YfmO and similar transporters of the Major Facilitator Superfamily
