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_005707335.1_ASM570733v1	NZ_CP039992	Staphylococcus aureus strain Lr3 chromosome, complete genome	1	279065-279198	1	CRISPRCasFinder	no		WYL,cas3,DEDDh,DinG,csa3	Orphan	TGCAAGTTGGCGGGGCCCCAACA	23	2	18	279088-279119|279088-279119|279088-279119|279088-279119|279088-279119|279088-279119|279088-279119|279088-279119|279088-279119|279088-279119|279088-279119|279088-279119|279088-279119|279143-279175|279143-279175|279143-279175|279143-279175|279143-279175	NZ_CP039992.1_279199-279230|NZ_CP039992.1_792265-792234|NZ_CP039992.1_792323-792292|NZ_CP039992.1_792381-792350|NZ_CP039992.1_851463-851432|NZ_CP039992.1_1015920-1015889|NZ_CP039992.1_1325355-1325386|NZ_CP039992.1_1431862-1431831|NZ_CP039992.1_1431920-1431889|NZ_CP039992.1_1612531-1612500|NZ_CP039992.1_1627045-1627076|NZ_CP039992.1_1930861-1930830|NZ_CP039992.1_2538177-2538208|NZ_CP039992.1_59069-59037|NZ_CP039992.1_1117247-1117279|NZ_CP039992.1_1201065-1201097|NZ_CP039992.1_1627102-1627134|NZ_CP039992.1_2669606-2669574	NA	2	2	Orphan	WYL,cas3,DEDDh,DinG,csa3	NA,NA|45aa|down_1|NZ_CP039992.1_280295_280430_+,NA|60aa|down_6|NZ_CP039992.1_284150_284330_+,NA|131aa|down_7|NZ_CP039992.1_284379_284772_+	NA|574aa|up_9|NZ_CP039992.1_266516_268238_+	pfam18674, TarS_C1, TarS beta-glycosyltransferase C-terminal domain 1	NA|225aa|up_8|NZ_CP039992.1_268381_269056_+	PRK13276, PRK13276, iron-sulfur cluster repair di-iron protein ScdA	NA|580aa|up_7|NZ_CP039992.1_269315_271055_+	COG3275, LytS, Putative regulator of cell autolysis [Signal transduction mechanisms]	NA|247aa|up_6|NZ_CP039992.1_271057_271798_+	PRK14084, PRK14084, DNA-binding response regulator	NA|148aa|up_5|NZ_CP039992.1_271909_272353_+	PRK04125, PRK04125, antiholin-like protein LrgA	NA|234aa|up_4|NZ_CP039992.1_272345_273047_+	PRK04288, PRK04288, antiholin-like protein LrgB; Provisional	NA|764aa|up_3|NZ_CP039992.1_273386_275678_+	COG3256, NorB, Nitric oxide reductase large subunit [Inorganic ion transport and metabolism]	NA|235aa|up_2|NZ_CP039992.1_275903_276608_-	COG2188, PhnF, Transcriptional regulators [Transcription]	NA|264aa|up_1|NZ_CP039992.1_276756_277548_+	COG2190, NagE, Phosphotransferase system IIA components [Carbohydrate transport and metabolism]	NA|479aa|up_0|NZ_CP039992.1_277563_279000_+	PRK09589, celA, 6-phospho-beta-glucosidase; Reviewed	NA|254aa|down_0|NZ_CP039992.1_279515_280277_-	pfam13649, Methyltransf_25, Methyltransferase domain	NA|45aa|down_1|NZ_CP039992.1_280295_280430_+	NA	NA|305aa|down_2|NZ_CP039992.1_280527_281442_-	TIGR02152, Putative_ribokinase, ribokinase	NA|135aa|down_3|NZ_CP039992.1_281469_281874_-	PRK11797, PRK11797, D-ribose pyranase; Provisional	NA|294aa|down_4|NZ_CP039992.1_281888_282770_-	pfam06800, Sugar_transport, Sugar transport protein	NA|333aa|down_5|NZ_CP039992.1_283001_284000_-	COG1609, PurR, Transcriptional regulators [Transcription]	NA|60aa|down_6|NZ_CP039992.1_284150_284330_+	NA	NA|131aa|down_7|NZ_CP039992.1_284379_284772_+	NA	NA|459aa|down_8|NZ_CP039992.1_284899_286276_-	TIGR00711, Uncharacterized_MFS-type_transporter_YhcA, drug resistance transporter, EmrB/QacA subfamily	NA|331aa|down_9|NZ_CP039992.1_286509_287502_+	COG3049, COG3049, Penicillin V acylase and related amidases [Cell envelope biogenesis, outer membrane]
GCF_005707335.1_ASM570733v1	NZ_CP039992	Staphylococcus aureus strain Lr3 chromosome, complete genome	2	393039-393139	2	CRISPRCasFinder	no		WYL,cas3,DEDDh,DinG,csa3	Orphan	TTATGAATTGAGTATTAAATTTG	23	0	0	NA	NA	NA	1	1	Orphan	WYL,cas3,DEDDh,DinG,csa3	NA|128aa|up_8|NZ_CP039992.1_385653_386037_-,NA|98aa|up_6|NZ_CP039992.1_386991_387285_-,NA|34aa|up_1|NZ_CP039992.1_392263_392365_+,NA|86aa|up_0|NZ_CP039992.1_392572_392830_-,NA|221aa|down_1|NZ_CP039992.1_394229_394892_-,NA|131aa|down_8|NZ_CP039992.1_403113_403506_-,NA|74aa|down_9|NZ_CP039992.1_403527_403749_-	NA|194aa|up_9|NZ_CP039992.1_385006_385588_+	COG0406, phoE, Broad specificity phosphatase PhoE and related phosphatases [General function prediction only]	NA|128aa|up_8|NZ_CP039992.1_385653_386037_-	NA	NA|209aa|up_7|NZ_CP039992.1_386292_386919_-	NF033193, lipo_NDxxF, NDxxF motif lipoprotein	NA|98aa|up_6|NZ_CP039992.1_386991_387285_-	NA	NA|508aa|up_5|NZ_CP039992.1_387363_388887_-	PRK15317, PRK15317, alkyl hydroperoxide reductase subunit F; Provisional	NA|190aa|up_4|NZ_CP039992.1_388902_389472_-	TIGR03137, AhpC, peroxiredoxin	NA|252aa|up_3|NZ_CP039992.1_389954_390710_+	cd02146, NfsA-like, nitroreductase similar to Escherichia coli NfsA	NA|463aa|up_2|NZ_CP039992.1_390790_392179_-	COG1823, COG1823, Predicted Na+/dicarboxylate symporter [General function prediction only]	NA|34aa|up_1|NZ_CP039992.1_392263_392365_+	NA	NA|86aa|up_0|NZ_CP039992.1_392572_392830_-	NA	NA|319aa|down_0|NZ_CP039992.1_393155_394112_-	PRK05035, PRK05035, electron transport complex protein RnfC; Provisional	NA|221aa|down_1|NZ_CP039992.1_394229_394892_-	NA	NA|136aa|down_2|NZ_CP039992.1_395034_395442_-	pfam11181, YflT, Heat induced stress protein YflT	NA|193aa|down_3|NZ_CP039992.1_395954_396533_+	PRK09219, PRK09219, xanthine phosphoribosyltransferase; Validated	NA|423aa|down_4|NZ_CP039992.1_396532_397801_+	TIGR03173, pbuX, xanthine permease	NA|489aa|down_5|NZ_CP039992.1_397838_399305_+	PRK05567, PRK05567, inosine 5'-monophosphate dehydrogenase; Reviewed	NA|514aa|down_6|NZ_CP039992.1_399329_400871_+	PRK00074, guaA, GMP synthase; Reviewed	NA|369aa|down_7|NZ_CP039992.1_401382_402489_+	pfam07751, Abi_2, Abi-like protein	NA|131aa|down_8|NZ_CP039992.1_403113_403506_-	NA	NA|74aa|down_9|NZ_CP039992.1_403527_403749_-	NA
GCF_005707335.1_ASM570733v1	NZ_CP039992	Staphylococcus aureus strain Lr3 chromosome, complete genome	3	629589-629681	3	CRISPRCasFinder	no		WYL,cas3,DEDDh,DinG,csa3	Orphan	CTAAAGGTGAAGAGGAACGCAGTTGGATGCTA	32	0	0	NA	NA	NA	1	1	Orphan	WYL,cas3,DEDDh,DinG,csa3	NA|97aa|up_1|NZ_CP039992.1_628417_628708_-,NA|169aa|down_4|NZ_CP039992.1_633428_633935_+,NA|239aa|down_5|NZ_CP039992.1_634096_634813_+	NA|313aa|up_9|NZ_CP039992.1_620336_621275_+	cd19083, AKR_AKR11A1_11D1, AKR11A and  AKR11D families of aldo-keto reductase (AKR)	NA|179aa|up_8|NZ_CP039992.1_621485_622022_+	COG0655, WrbA, Multimeric flavodoxin WrbA [General function prediction only]	NA|159aa|up_7|NZ_CP039992.1_622190_622667_+	pfam00583, Acetyltransf_1, Acetyltransferase (GNAT) family	NA|432aa|up_6|NZ_CP039992.1_622706_624002_+	COG1078, COG1078, HD superfamily phosphohydrolases [General function prediction only]	NA|174aa|up_5|NZ_CP039992.1_624029_624551_+	pfam08741, YwhD, YwhD family	NA|337aa|up_4|NZ_CP039992.1_625050_626061_+	PRK09422, PRK09422, ethanol-active dehydrogenase/acetaldehyde-active reductase; Provisional	NA|128aa|up_3|NZ_CP039992.1_626369_626753_+	COG4506, COG4506, Uncharacterized protein conserved in bacteria [Function unknown]	NA|554aa|up_2|NZ_CP039992.1_626749_628411_+	PRK01611, argS, arginyl-tRNA synthetase; Reviewed	NA|97aa|up_1|NZ_CP039992.1_628417_628708_-	NA	NA|212aa|up_0|NZ_CP039992.1_628801_629437_+	COG2231, COG2231, Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]	NA|276aa|down_0|NZ_CP039992.1_629809_630637_+	cd01143, YvrC, Periplasmic binding protein YvrC	NA|317aa|down_1|NZ_CP039992.1_630784_631735_+	pfam01032, FecCD, FecCD transport family	NA|240aa|down_2|NZ_CP039992.1_631789_632509_+	COG1011, COG1011, Predicted hydrolase (HAD superfamily) [General function prediction only]	NA|267aa|down_3|NZ_CP039992.1_632492_633293_+	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|169aa|down_4|NZ_CP039992.1_633428_633935_+	NA	NA|239aa|down_5|NZ_CP039992.1_634096_634813_+	NA	NA|263aa|down_6|NZ_CP039992.1_634981_635770_+	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|125aa|down_7|NZ_CP039992.1_636020_636395_-	TIGR01889, Pleiotropic_Regulator_Of_Virulence, staphylococcal accessory regulator family	NA|310aa|down_8|NZ_CP039992.1_637342_638272_-	COG3238, COG3238, Uncharacterized protein conserved in bacteria [Function unknown]	NA|75aa|down_9|NZ_CP039992.1_638466_638691_-	pfam11148, DUF2922, Protein of unknown function (DUF2922)
GCF_005707335.1_ASM570733v1	NZ_CP039992	Staphylococcus aureus strain Lr3 chromosome, complete genome	4	851362-851443	4	CRISPRCasFinder	no		WYL,cas3,DEDDh,DinG,csa3	Orphan	CCCCAACTTGCATTGTCTGTAGAA	24	0	0	NA	NA	NA	1	1	Orphan	WYL,cas3,DEDDh,DinG,csa3	NA|38aa|up_1|NZ_CP039992.1_850264_850378_+,NA	NA|206aa|up_9|NZ_CP039992.1_845119_845737_-	COG1279, COG1279, Lysine efflux permease [General function prediction only]	NA|165aa|up_8|NZ_CP039992.1_845891_846386_-	pfam13420, Acetyltransf_4, Acetyltransferase (GNAT) domain	NA|141aa|up_7|NZ_CP039992.1_846784_847207_-	TIGR03561, organ_hyd_perox, peroxiredoxin, Ohr subfamily	NA|239aa|up_6|NZ_CP039992.1_847354_848071_+	PRK13575, PRK13575, type I 3-dehydroquinate dehydratase	NA|180aa|up_5|NZ_CP039992.1_848153_848693_+	cd02135, YdjA-like, nitroreductase family protein similar to Escherichia coli YdjA	NA|107aa|up_4|NZ_CP039992.1_848842_849163_-	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_3|NZ_CP039992.1_849306_849663_+	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_2|NZ_CP039992.1_849820_850201_+	PRK01202, PRK01202, glycine cleavage system protein GcvH	NA|38aa|up_1|NZ_CP039992.1_850264_850378_+	NA	NA|293aa|up_0|NZ_CP039992.1_850379_851258_+	COG3878, COG3878, Uncharacterized protein conserved in bacteria [Function unknown]	NA|129aa|down_0|NZ_CP039992.1_851999_852386_+	COG1658, COG1658, Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]	NA|99aa|down_1|NZ_CP039992.1_852378_852675_+	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_CP039992.1_852924_853950_+	COG1135, AbcC, ABC-type metal ion transport system, ATPase component [Inorganic ion transport and metabolism]	NA|232aa|down_3|NZ_CP039992.1_853942_854638_+	COG2011, AbcD, ABC-type metal ion transport system, permease component [Inorganic ion transport and metabolism]	NA|274aa|down_4|NZ_CP039992.1_854654_855476_+	COG1464, NlpA, ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]	NA|65aa|down_5|NZ_CP039992.1_855829_856024_+	COG3237, COG3237, Uncharacterized protein conserved in bacteria [Function unknown]	NA|284aa|down_6|NZ_CP039992.1_856257_857109_-	COG2035, COG2035, Predicted membrane protein [Function unknown]	NA|254aa|down_7|NZ_CP039992.1_857436_858198_+	COG0396, sufC, Cysteine desulfurase activator ATPase [Posttranslational modification, protein turnover, chaperones]	NA|436aa|down_8|NZ_CP039992.1_858296_859604_+	COG0719, SufB, Cysteine desulfurase activator SufB [Posttranslational modification, protein turnover, chaperones]	NA|414aa|down_9|NZ_CP039992.1_859718_860960_+	TIGR01979, Probable_cysteine_desulfurase, cysteine desulfurases, SufSfamily
GCF_005707335.1_ASM570733v1	NZ_CP039992	Staphylococcus aureus strain Lr3 chromosome, complete genome	5	1190127-1190219	5	CRISPRCasFinder	no	cas3	WYL,cas3,DEDDh,DinG,csa3	Unclear	TAAGAAACACTAATCAATAAATTGATAAG	29	0	0	NA	NA	NA	1	1	Unclear	WYL,cas3,DEDDh,DinG,csa3	NA,NA	NA|215aa|up_9|NZ_CP039992.1_1179938_1180583_+	COG0036, Rpe, Pentose-5-phosphate-3-epimerase [Carbohydrate transport and metabolism]	NA|214aa|up_8|NZ_CP039992.1_1180589_1181231_+	COG1564, THI80, Thiamine pyrophosphokinase [Coenzyme metabolism]	NA|63aa|up_7|NZ_CP039992.1_1181611_1181800_-	PRK00359, rpmB, 50S ribosomal protein L28; Reviewed	NA|125aa|up_6|NZ_CP039992.1_1182242_1182617_+	COG1302, COG1302, Uncharacterized protein conserved in bacteria [Function unknown]	NA|549aa|up_5|NZ_CP039992.1_1182631_1184278_+	COG1461, COG1461, Predicted kinase related to dihydroxyacetone kinase [General function prediction only]	cas3|687aa|up_4|NZ_CP039992.1_1184467_1186528_+	PRK10917, PRK10917, ATP-dependent DNA helicase RecG; Provisional	NA|191aa|up_3|NZ_CP039992.1_1186730_1187303_+	PRK04424, PRK04424, transcription factor FapR	NA|329aa|up_2|NZ_CP039992.1_1187307_1188294_+	PRK05331, PRK05331, phosphate acyltransferase PlsX	NA|309aa|up_1|NZ_CP039992.1_1188286_1189213_+	COG0331, FabD, (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]	NA|245aa|up_0|NZ_CP039992.1_1189205_1189940_+	PRK05557, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase; Validated	NA|78aa|down_0|NZ_CP039992.1_1190309_1190543_+	PRK00982, acpP, acyl carrier protein; Provisional	NA|244aa|down_1|NZ_CP039992.1_1190658_1191390_+	PRK00102, rnc, ribonuclease III; Reviewed	NA|1189aa|down_2|NZ_CP039992.1_1191536_1195103_+	COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]	NA|417aa|down_3|NZ_CP039992.1_1195102_1196353_+	PRK10416, PRK10416, signal recognition particle-docking protein FtsY; Provisional	NA|111aa|down_4|NZ_CP039992.1_1196339_1196672_+	PRK00118, PRK00118, putative DNA-binding protein; Validated	NA|456aa|down_5|NZ_CP039992.1_1196697_1198065_+	PRK10867, PRK10867, signal recognition particle protein; Provisional	NA|92aa|down_6|NZ_CP039992.1_1198499_1198775_+	COG0228, RpsP, Ribosomal protein S16 [Translation, ribosomal structure and biogenesis]	NA|168aa|down_7|NZ_CP039992.1_1198962_1199466_+	PRK00122, rimM, 16S rRNA-processing protein RimM; Provisional	NA|246aa|down_8|NZ_CP039992.1_1199465_1200203_+	PRK00026, trmD, tRNA (guanine-N(1)-)-methyltransferase; Reviewed	NA|117aa|down_9|NZ_CP039992.1_1200305_1200656_+	PRK05338, rplS, 50S ribosomal protein L19; Provisional
GCF_005707335.1_ASM570733v1	NZ_CP039992	Staphylococcus aureus strain Lr3 chromosome, complete genome	6	1646808-1646891	6	CRISPRCasFinder	no		WYL,cas3,DEDDh,DinG,csa3	Orphan	TGTTGGGGGCCCCATCCCCAACTT	24	1	1	1646832-1646867	NZ_CP039992.1_1612438-1612473	NA	1	1	Orphan	WYL,cas3,DEDDh,DinG,csa3	NA,NA|49aa|down_3|NZ_CP039992.1_1650895_1651042_-,NA|43aa|down_8|NZ_CP039992.1_1654078_1654207_-	NA|208aa|up_9|NZ_CP039992.1_1635541_1636165_-	PRK05480, PRK05480, uridine/cytidine kinase; Provisional	NA|423aa|up_8|NZ_CP039992.1_1636164_1637433_-	COG0826, COG0826, Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]	NA|308aa|up_7|NZ_CP039992.1_1637444_1638368_-	COG0826, COG0826, Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]	NA|213aa|up_6|NZ_CP039992.1_1638370_1639009_-	COG4122, COG4122, Predicted O-methyltransferase [General function prediction only]	NA|103aa|up_5|NZ_CP039992.1_1639293_1639602_-	PRK13678, PRK13678, hypothetical protein; Provisional	NA|143aa|up_4|NZ_CP039992.1_1639616_1640045_-	COG0816, COG0816, Predicted endonuclease involved in recombination (possible Holliday junction resolvase in Mycoplasmas and B	NA|87aa|up_3|NZ_CP039992.1_1640048_1640309_-	PRK05473, IreB-like, IreB family regulatory phosphoprotein	NA|877aa|up_2|NZ_CP039992.1_1640371_1643002_-	PRK00252, alaS, alanyl-tRNA synthetase; Reviewed	NA|826aa|up_1|NZ_CP039992.1_1643344_1645822_-	TIGR01448, recD_rel, helicase, putative, RecD/TraA family	NA|223aa|up_0|NZ_CP039992.1_1645823_1646492_-	sd00006, TPR, Tetratricopeptide repeat	NA|373aa|down_0|NZ_CP039992.1_1647072_1648191_-	PRK00143, mnmA, tRNA-specific 2-thiouridylase MnmA; Reviewed	NA|381aa|down_1|NZ_CP039992.1_1648191_1649334_-	COG1104, NifS, Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]	NA|338aa|down_2|NZ_CP039992.1_1649645_1650659_+	TIGR03558, oxido_grp_1, luciferase family oxidoreductase, group 1	NA|49aa|down_3|NZ_CP039992.1_1650895_1651042_-	NA	NA|61aa|down_4|NZ_CP039992.1_1651081_1651264_-	COG3237, COG3237, Uncharacterized protein conserved in bacteria [Function unknown]	NA|141aa|down_5|NZ_CP039992.1_1651363_1651786_-	COG1959, COG1959, Predicted transcriptional regulator [Transcription]	NA|425aa|down_6|NZ_CP039992.1_1651870_1653145_+	PRK13342, PRK13342, recombination factor protein RarA; Reviewed	NA|258aa|down_7|NZ_CP039992.1_1653305_1654079_-	COG1179, COG1179, Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]	NA|43aa|down_8|NZ_CP039992.1_1654078_1654207_-	NA	NA|589aa|down_9|NZ_CP039992.1_1654539_1656306_-	PRK00476, aspS, aspartyl-tRNA synthetase; Validated
GCF_005707335.1_ASM570733v1	NZ_CP039992	Staphylococcus aureus strain Lr3 chromosome, complete genome	7	1892794-1893059	1	CRT	no		WYL,cas3,DEDDh,DinG,csa3	Orphan	TGCAAGTTGGCGGGGCCACAACATAGANAAATTGGATN	38	2	2	1892887-1892909|1892947-1892966	NZ_CP039992.1_900378-900400|NZ_CP039992.1_1893118-1893137	NA	4	4	Orphan	WYL,cas3,DEDDh,DinG,csa3	NA|33aa|up_8|NZ_CP039992.1_1884032_1884131_-,NA|132aa|up_0|NZ_CP039992.1_1892096_1892492_-,NA|51aa|down_0|NZ_CP039992.1_1893383_1893536_-	NA|399aa|up_9|NZ_CP039992.1_1882545_1883742_-	COG0420, SbcD, DNA repair exonuclease [DNA replication, recombination, and repair]	NA|33aa|up_8|NZ_CP039992.1_1884032_1884131_-	NA	NA|115aa|up_7|NZ_CP039992.1_1884779_1885124_-	PRK13676, PRK13676, YlbF/YmcA family competence regulator	NA|375aa|up_6|NZ_CP039992.1_1885192_1886317_-	COG4399, COG4399, Uncharacterized protein conserved in bacteria [Function unknown]	NA|155aa|up_5|NZ_CP039992.1_1886495_1886960_-	COG1476, COG1476, Predicted transcriptional regulators [Transcription]	NA|208aa|up_4|NZ_CP039992.1_1887315_1887939_-	COG2197, CitB, Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]	NA|371aa|up_3|NZ_CP039992.1_1887960_1889073_-	COG4585, COG4585, Signal transduction histidine kinase [Signal transduction mechanisms]	NA|274aa|up_2|NZ_CP039992.1_1889235_1890057_+	COG0564, RluA, Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]	NA|462aa|up_1|NZ_CP039992.1_1890515_1891901_-	PRK00485, fumC, fumarate hydratase; Reviewed	NA|132aa|up_0|NZ_CP039992.1_1892096_1892492_-	NA	NA|51aa|down_0|NZ_CP039992.1_1893383_1893536_-	NA	NA|200aa|down_1|NZ_CP039992.1_1893560_1894160_-	COG0363, NagB, 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase [Carbohydrate transport and metabolism]	NA|157aa|down_2|NZ_CP039992.1_1894317_1894788_-	COG0219, CspR, Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]	NA|381aa|down_3|NZ_CP039992.1_1894792_1895935_-	TIGR00276, iron-sulfur_cluster-binding_protein, epoxyqueuosine reductase	NA|243aa|down_4|NZ_CP039992.1_1896070_1896799_-	COG1126, GlnQ, ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]	NA|486aa|down_5|NZ_CP039992.1_1896785_1898243_-	COG0765, HisM, ABC-type amino acid transport system, permease component [Amino acid transport and metabolism]	NA|354aa|down_6|NZ_CP039992.1_1898501_1899563_-	COG3641, PfoR, Predicted membrane protein, putative toxin regulator [General function prediction only]	NA|149aa|down_7|NZ_CP039992.1_1903423_1903870_-	COG0735, Fur, Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]	NA|317aa|down_8|NZ_CP039992.1_1903966_1904917_-	cd12155, PGDH_1, Phosphoglycerate Dehydrogenase, 2-hydroxyacid dehydrogenase family	NA|152aa|down_9|NZ_CP039992.1_1904922_1905378_-	COG1225, Bcp, Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]
GCF_005707335.1_ASM570733v1	NZ_CP039992	Staphylococcus aureus strain Lr3 chromosome, complete genome	8	2121664-2121744	7	CRISPRCasFinder	no	csa3	WYL,cas3,DEDDh,DinG,csa3	Type I-A	CAACTTTAGTTGTTAGGGGCTCTT	24	0	0	NA	NA	NA	1	1	Orphan	WYL,cas3,DEDDh,DinG,csa3	NA|77aa|up_5|NZ_CP039992.1_2116538_2116769_-,NA|364aa|up_0|NZ_CP039992.1_2120555_2121647_+,NA|35aa|down_0|NZ_CP039992.1_2122079_2122184_-,NA|61aa|down_1|NZ_CP039992.1_2122616_2122799_-,NA|53aa|down_2|NZ_CP039992.1_2122863_2123022_+,NA|31aa|down_3|NZ_CP039992.1_2123458_2123551_+	NA|237aa|up_9|NZ_CP039992.1_2112149_2112860_+	PRK05819, deoD, DeoD-type purine-nucleoside phosphorylase	NA|148aa|up_8|NZ_CP039992.1_2112980_2113424_-	COG0783, Dps, DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]	NA|138aa|up_7|NZ_CP039992.1_2113623_2114037_-	COG3011, COG3011, Predicted thiol-disulfide oxidoreductase [General function    prediction only]	NA|458aa|up_6|NZ_CP039992.1_2114493_2115867_-	pfam01878, EVE, EVE domain	NA|77aa|up_5|NZ_CP039992.1_2116538_2116769_-	NA	NA|313aa|up_4|NZ_CP039992.1_2116799_2117738_-	COG1482, ManA, Phosphomannose isomerase [Carbohydrate transport and metabolism]	NA|222aa|up_3|NZ_CP039992.1_2118173_2118839_-	cd05243, SDR_a5, atypical (a) SDRs, subgroup 5	csa3|107aa|up_2|NZ_CP039992.1_2118990_2119311_+	cd00090, HTH_ARSR, Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors	NA|326aa|up_1|NZ_CP039992.1_2119312_2120290_+	COG1230, CzcD, Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]	NA|364aa|up_0|NZ_CP039992.1_2120555_2121647_+	NA	NA|35aa|down_0|NZ_CP039992.1_2122079_2122184_-	NA	NA|61aa|down_1|NZ_CP039992.1_2122616_2122799_-	NA	NA|53aa|down_2|NZ_CP039992.1_2122863_2123022_+	NA	NA|31aa|down_3|NZ_CP039992.1_2123458_2123551_+	NA	NA|286aa|down_4|NZ_CP039992.1_2123679_2124537_-	COG0561, Cof, Predicted hydrolases of the HAD superfamily [General function prediction only]	NA|261aa|down_5|NZ_CP039992.1_2124604_2125387_-	COG1119, ModF, ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA [Inorganic ion transport and metabolism]	NA|602aa|down_6|NZ_CP039992.1_2125618_2127424_-	PRK00331, PRK00331, isomerizing glutamine--fructose-6-phosphate transaminase	NA|513aa|down_7|NZ_CP039992.1_2128104_2129643_+	COG2213, MtlA, Phosphotransferase system, mannitol-specific IIBC component [Carbohydrate transport and metabolism]	NA|711aa|down_8|NZ_CP039992.1_2129677_2131810_+	COG3711, BglG, Transcriptional antiterminator [Transcription]	NA|145aa|down_9|NZ_CP039992.1_2131821_2132256_+	COG4668, MtlA, Mannitol/fructose-specific phosphotransferase system, IIA domain [Carbohydrate transport and metabolism]
GCF_005707335.1_ASM570733v1	NZ_CP039992	Staphylococcus aureus strain Lr3 chromosome, complete genome	9	2133985-2134070	8	CRISPRCasFinder	no	csa3	WYL,cas3,DEDDh,DinG,csa3	Type I-A	CCAACTGATTTTTGCGTATCATTAGT	26	0	0	NA	NA	NA	1	1	Orphan	WYL,cas3,DEDDh,DinG,csa3	NA|61aa|up_9|NZ_CP039992.1_2122616_2122799_-,NA|53aa|up_8|NZ_CP039992.1_2122863_2123022_+,NA|31aa|up_7|NZ_CP039992.1_2123458_2123551_+,NA	NA|61aa|up_9|NZ_CP039992.1_2122616_2122799_-	NA	NA|53aa|up_8|NZ_CP039992.1_2122863_2123022_+	NA	NA|31aa|up_7|NZ_CP039992.1_2123458_2123551_+	NA	NA|286aa|up_6|NZ_CP039992.1_2123679_2124537_-	COG0561, Cof, Predicted hydrolases of the HAD superfamily [General function prediction only]	NA|261aa|up_5|NZ_CP039992.1_2124604_2125387_-	COG1119, ModF, ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA [Inorganic ion transport and metabolism]	NA|602aa|up_4|NZ_CP039992.1_2125618_2127424_-	PRK00331, PRK00331, isomerizing glutamine--fructose-6-phosphate transaminase	NA|513aa|up_3|NZ_CP039992.1_2128104_2129643_+	COG2213, MtlA, Phosphotransferase system, mannitol-specific IIBC component [Carbohydrate transport and metabolism]	NA|711aa|up_2|NZ_CP039992.1_2129677_2131810_+	COG3711, BglG, Transcriptional antiterminator [Transcription]	NA|145aa|up_1|NZ_CP039992.1_2131821_2132256_+	COG4668, MtlA, Mannitol/fructose-specific phosphotransferase system, IIA domain [Carbohydrate transport and metabolism]	NA|369aa|up_0|NZ_CP039992.1_2132255_2133362_+	PRK02318, PRK02318, mannitol-1-phosphate 5-dehydrogenase; Provisional	NA|452aa|down_0|NZ_CP039992.1_2141403_2142759_-	PRK14316, glmM, phosphoglucosamine mutase; Provisional	NA|311aa|down_1|NZ_CP039992.1_2142785_2143718_-	COG4856, COG4856, Uncharacterized protein conserved in bacteria [Function unknown]	NA|270aa|down_2|NZ_CP039992.1_2143719_2144529_-	COG1624, COG1624, Uncharacterized conserved protein [Function unknown]	NA|303aa|down_3|NZ_CP039992.1_2144717_2145626_-	cd09989, Arginase, Arginase family	NA|355aa|down_4|NZ_CP039992.1_2146852_2147917_-	pfam10609, ParA, NUBPL iron-transfer P-loop NTPase	NA|481aa|down_5|NZ_CP039992.1_2148064_2149507_-	TIGR00711, Uncharacterized_MFS-type_transporter_YhcA, drug resistance transporter, EmrB/QacA subfamily	NA|158aa|down_6|NZ_CP039992.1_2149829_2150303_-	pfam17080, SepA, Multidrug Resistance efflux pump	NA|448aa|down_7|NZ_CP039992.1_2150401_2151745_-	TIGR00711, Uncharacterized_MFS-type_transporter_YhcA, drug resistance transporter, EmrB/QacA subfamily	NA|228aa|down_8|NZ_CP039992.1_2151921_2152605_-	COG1272, COG1272, Predicted membrane protein, hemolysin III homolog [General function prediction only]	NA|396aa|down_9|NZ_CP039992.1_2152623_2153811_-	cd04193, UDPGlcNAc_PPase, UDPGlcNAc pyrophosphorylase catalayzes the synthesis of UDPGlcNAc
GCF_005707335.1_ASM570733v1	NZ_CP039992	Staphylococcus aureus strain Lr3 chromosome, complete genome	10	2230397-2230589	2,9	CRT,CRISPRCasFinder	no		WYL,cas3,DEDDh,DinG,csa3	Orphan	TGTTGGGGCCCCGCCAACTTGCA,TCTATGTTGGGGCCCCGCCAACTTG	23,25	3	21	2230475-2230510|2230475-2230510|2230475-2230510|2230534-2230566|2230534-2230566|2230534-2230566|2230534-2230566|2230534-2230566|2230534-2230566|2230534-2230566|2230532-2230562|2230532-2230562|2230532-2230562|2230532-2230562|2230532-2230562|2230532-2230562|2230532-2230562|2230532-2230562|2230532-2230562|2230532-2230562|2230532-2230562	NZ_CP039992.1_1117227-1117192|NZ_CP039992.1_1792905-1792870|NZ_CP039992.1_1612380-1612415|NZ_CP039992.1_2219617-2219649|NZ_CP039992.1_2505101-2505133|NZ_CP039992.1_1325445-1325413|NZ_CP039992.1_213647-213679|NZ_CP039992.1_799500-799532|NZ_CP039992.1_851701-851733|NZ_CP039992.1_1929487-1929519|NZ_CP039992.1_1015944-1015974|NZ_CP039992.1_1016002-1016032|NZ_CP039992.1_1612439-1612469|NZ_CP039992.1_2219615-2219645|NZ_CP039992.1_2505099-2505129|NZ_CP039992.1_354430-354400|NZ_CP039992.1_1325447-1325417|NZ_CP039992.1_213645-213675|NZ_CP039992.1_799498-799528|NZ_CP039992.1_851699-851729|NZ_CP039992.1_1929485-1929515	NA:NA	3,1	3	Orphan	WYL,cas3,DEDDh,DinG,csa3	NA|55aa|up_9|NZ_CP039992.1_2220924_2221089_+,NA|106aa|up_8|NZ_CP039992.1_2221333_2221651_+,NA|84aa|up_5|NZ_CP039992.1_2226775_2227027_+,NA|62aa|up_0|NZ_CP039992.1_2230166_2230352_+,NA	NA|55aa|up_9|NZ_CP039992.1_2220924_2221089_+	NA	NA|106aa|up_8|NZ_CP039992.1_2221333_2221651_+	NA	NA|1056aa|up_7|NZ_CP039992.1_2221837_2225005_-	COG0841, AcrB, Cation/multidrug efflux pump [Defense mechanisms]	NA|422aa|up_6|NZ_CP039992.1_2225121_2226387_-	COG2348, COG2348, Peptidoglycan interpeptide bridge formation enzyme [Cell wall/membrane/envelope biogenesis]	NA|84aa|up_5|NZ_CP039992.1_2226775_2227027_+	NA	NA|255aa|up_4|NZ_CP039992.1_2227018_2227783_-	pfam13468, Glyoxalase_3, Glyoxalase-like domain	NA|147aa|up_3|NZ_CP039992.1_2227944_2228385_+	smart00347, HTH_MARR, helix_turn_helix multiple antibiotic resistance protein	NA|404aa|up_2|NZ_CP039992.1_2228377_2229589_+	cd17489, MFS_YfcJ_like, Escherichia coli YfcJ, YhhS, and similar transporters of the Major Facilitator Superfamily	NA|117aa|up_1|NZ_CP039992.1_2229690_2230041_-	TIGR01889, Pleiotropic_Regulator_Of_Virulence, staphylococcal accessory regulator family	NA|62aa|up_0|NZ_CP039992.1_2230166_2230352_+	NA	NA|341aa|down_0|NZ_CP039992.1_2230730_2231753_-	TIGR02666, Cyclic_pyranopterin_monophosphate_synthase, molybdenum cofactor biosynthesis protein A, bacterial	NA|200aa|down_1|NZ_CP039992.1_2231772_2232372_-	PRK00317, mobA, molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed	NA|78aa|down_2|NZ_CP039992.1_2232378_2232612_-	cd00754, Ubl_MoaD, ubiquitin-like (Ubl) domain found in molybdenum cofactor biosynthesis protein D (MoaD) and similar proteins	NA|149aa|down_3|NZ_CP039992.1_2232617_2233064_-	COG0314, MoaE, Molybdopterin converting factor, large subunit [Coenzyme metabolism]	NA|162aa|down_4|NZ_CP039992.1_2233077_2233563_-	COG1763, MobB, Molybdopterin-guanine dinucleotide biosynthesis protein [Coenzyme metabolism]	NA|420aa|down_5|NZ_CP039992.1_2233559_2234819_-	cd00887, MoeA, MoeA family	NA|165aa|down_6|NZ_CP039992.1_2234881_2235376_+	PRK09364, moaC, cyclic pyranopterin monophosphate synthase MoaC	NA|169aa|down_7|NZ_CP039992.1_2235377_2235884_-	COG0521, MoaB, Molybdopterin biosynthesis enzymes [Coenzyme metabolism]	NA|335aa|down_8|NZ_CP039992.1_2235914_2236919_-	PRK07688, PRK07688, thiamine/molybdopterin biosynthesis ThiF/MoeB-like protein; Validated	NA|202aa|down_9|NZ_CP039992.1_2237088_2237694_-	COG4148, ModC, ABC-type molybdate transport system, ATPase component [Inorganic ion transport and metabolism]
GCF_005707335.1_ASM570733v1	NZ_CP039992	Staphylococcus aureus strain Lr3 chromosome, complete genome	11	2380684-2380781	10	CRISPRCasFinder	no		WYL,cas3,DEDDh,DinG,csa3	Orphan	TTTCTGCGAATTTTATGAGCTAGAAAGGC	29	0	0	NA	NA	NA	1	1	Orphan	WYL,cas3,DEDDh,DinG,csa3	NA|35aa|up_2|NZ_CP039992.1_2378406_2378511_+,NA|35aa|down_0|NZ_CP039992.1_2380974_2381079_-,NA|61aa|down_2|NZ_CP039992.1_2382675_2382858_-	NA|200aa|up_9|NZ_CP039992.1_2371883_2372483_-	COG1651, DsbG, Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]	NA|121aa|up_8|NZ_CP039992.1_2372501_2372864_-	pfam14729, DUF4467, Domain of unknown function with cystatin-like fold (DUF4467)	NA|417aa|up_7|NZ_CP039992.1_2373118_2374369_+	pfam02388, FemAB, FemAB family	NA|244aa|up_6|NZ_CP039992.1_2374465_2375197_-	COG1126, GlnQ, ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]	NA|240aa|up_5|NZ_CP039992.1_2375193_2375913_-	COG0765, HisM, ABC-type amino acid transport system, permease component [Amino acid transport and metabolism]	NA|260aa|up_4|NZ_CP039992.1_2375893_2376673_-	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_CP039992.1_2376793_2378233_-	TIGR00711, Uncharacterized_MFS-type_transporter_YhcA, drug resistance transporter, EmrB/QacA subfamily	NA|35aa|up_2|NZ_CP039992.1_2378406_2378511_+	NA	NA|229aa|up_1|NZ_CP039992.1_2378664_2379351_-	PRK14119, gpmA, phosphoglyceromutase; Provisional	NA|289aa|up_0|NZ_CP039992.1_2379677_2380544_-	COG0053, MMT1, Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]	NA|35aa|down_0|NZ_CP039992.1_2380974_2381079_-	NA	NA|428aa|down_1|NZ_CP039992.1_2381173_2382457_+	pfam11621, Sbi-IV, C3 binding domain 4 of IgG-bind protein SBI	NA|61aa|down_2|NZ_CP039992.1_2382675_2382858_-	NA	NA|310aa|down_3|NZ_CP039992.1_2382992_2383922_+	pfam07968, Leukocidin, Leukocidin/Hemolysin toxin family	NA|316aa|down_4|NZ_CP039992.1_2384488_2385436_+	pfam07968, Leukocidin, Leukocidin/Hemolysin toxin family	NA|326aa|down_5|NZ_CP039992.1_2385437_2386415_+	TIGR01002, synergohymenotropic_toxin, beta-channel forming cytolysin	NA|156aa|down_6|NZ_CP039992.1_2386466_2386934_-	pfam06177, QueT, QueT transporter	NA|231aa|down_7|NZ_CP039992.1_2386944_2387637_-	COG1424, BioW, Pimeloyl-CoA synthetase [Coenzyme metabolism]	NA|372aa|down_8|NZ_CP039992.1_2387647_2388763_-	COG0156, BioF, 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]	NA|336aa|down_9|NZ_CP039992.1_2388740_2389748_-	PRK06256, PRK06256, biotin synthase; Validated
