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
GCA_003827735.1_ASM382773v1	CP033505	Staphylococcus aureus strain ATCC BAA-39 chromosome, complete genome	1	170111-170192	1	CRISPRCasFinder	no		csa3,cas3,DEDDh,DinG,WYL	Orphan	TTCTACAGGCAATGCAAGTTGGGG	24	1	1	170135-170168	CP033505.1_1452962-1452929	NA	1	1	Orphan	csa3,cas3,DEDDh,DinG,WYL	NA|402aa|up_9|CP033505.1_159256_160462_+,NA|68aa|down_0|CP033505.1_170255_170459_-	NA|402aa|up_9|CP033505.1_159256_160462_+	NA	NA|402aa|up_8|CP033505.1_160462_161668_+	cd03794, GT4_WbuB-like, Escherichia coli WbuB and similar proteins	NA|186aa|up_7|CP033505.1_161678_162236_+	COG2148, WcaJ, Sugar transferases involved in lipopolysaccharide synthesis [Cell envelope biogenesis, outer membrane]	NA|296aa|up_6|CP033505.1_162235_163123_+	cd05232, UDP_G4E_4_SDR_e, UDP-glucose 4 epimerase, subgroup 4, extended (e) SDRs	NA|421aa|up_5|CP033505.1_163176_164439_+	COG0677, WecC, UDP-N-acetyl-D-mannosaminuronate dehydrogenase [Cell envelope biogenesis, outer membrane]	NA|382aa|up_4|CP033505.1_164515_165661_+	COG0381, WecB, UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]	NA|109aa|up_3|CP033505.1_165725_166052_-	PRK13313, PRK13313, staphylobilin-forming heme oxygenase IsdI	NA|128aa|up_2|CP033505.1_166058_166442_-	pfam04304, DUF454, Protein of unknown function (DUF454)	NA|496aa|up_1|CP033505.1_166868_168356_+	cd07117, ALDH_StaphAldA1, Uncharacterized Staphylococcus aureus AldA1 (SACOL0154) aldehyde dehydrogenase-like	NA|320aa|up_0|CP033505.1_169002_169962_+	COG1230, CzcD, Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]	NA|68aa|down_0|CP033505.1_170255_170459_-	NA	NA|171aa|down_1|CP033505.1_170637_171150_+	pfam14026, DUF4242, Protein of unknown function (DUF4242)	NA|247aa|down_2|CP033505.1_171491_172232_+	COG1116, TauB, ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]	NA|325aa|down_3|CP033505.1_172245_173220_+	cd13553, PBP2_NrtA_CpmA_like, Substrate binding domain of ABC-type nitrate/bicarbonate transporters, a member of the type 2 periplasmic binding fold superfamily	NA|254aa|down_4|CP033505.1_173216_173978_+	COG0600, TauC, ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]	NA|345aa|down_5|CP033505.1_173987_175022_+	COG1960, CaiA, Acyl-CoA dehydrogenases [Lipid metabolism]	NA|120aa|down_6|CP033505.1_175238_175598_+	COG5609, COG5609, Uncharacterized conserved protein [Function unknown]	NA|392aa|down_7|CP033505.1_175621_176797_+	PRK07574, PRK07574, NAD-dependent formate dehydrogenase	NA|417aa|down_8|CP033505.1_177182_178433_+	cd17329, MFS_MdtH_MDR_like, Multidrug resistance protein MdtH and similar multidrug resistance (MDR) transporters of the Major Facilitator Superfamily	NA|2287aa|down_9|CP033505.1_178879_185740_+	PRK12467, PRK12467, peptide synthase; Provisional
GCA_003827735.1_ASM382773v1	CP033505	Staphylococcus aureus strain ATCC BAA-39 chromosome, complete genome	2	293433-293573	2	CRISPRCasFinder	no		csa3,cas3,DEDDh,DinG,WYL	Orphan	GGGCCCCAACACAAAGAATTTCGAAAAGAAATTCTACAGGTAATGCAAGTTGG	53	1	8	293486-293520|293486-293520|293486-293520|293486-293520|293486-293520|293486-293520|293486-293520|293486-293520	CP033505.1_864470-864436|CP033505.1_864526-864492|CP033505.1_2312465-2312431|CP033505.1_2476964-2476930|CP033505.1_2749503-2749469|CP033505.1_783734-783768|CP033505.1_1142454-1142488|CP033505.1_2346693-2346727	NA	1	1	Orphan	csa3,cas3,DEDDh,DinG,WYL	NA,NA	NA|563aa|up_9|CP033505.1_281899_283588_+	pfam04464, Glyphos_transf, CDP-Glycerol:Poly(glycerophosphate) glycerophosphotransferase	NA|574aa|up_8|CP033505.1_283620_285342_+	pfam18674, TarS_C1, TarS beta-glycosyltransferase C-terminal domain 1	NA|225aa|up_7|CP033505.1_285485_286160_+	PRK13276, PRK13276, iron-sulfur cluster repair di-iron protein ScdA	NA|585aa|up_6|CP033505.1_286404_288159_+	COG3275, LytS, Putative regulator of cell autolysis [Signal transduction mechanisms]	NA|247aa|up_5|CP033505.1_288161_288902_+	PRK14084, PRK14084, DNA-binding response regulator	NA|146aa|up_4|CP033505.1_289020_289458_+	PRK04125, PRK04125, antiholin-like protein LrgA	NA|234aa|up_3|CP033505.1_289450_290152_+	PRK04288, PRK04288, antiholin-like protein LrgB; Provisional	NA|235aa|up_2|CP033505.1_290259_290964_-	COG2188, PhnF, Transcriptional regulators [Transcription]	NA|264aa|up_1|CP033505.1_291112_291904_+	COG2190, NagE, Phosphotransferase system IIA components [Carbohydrate transport and metabolism]	NA|479aa|up_0|CP033505.1_291919_293356_+	PRK09589, celA, 6-phospho-beta-glucosidase; Reviewed	NA|254aa|down_0|CP033505.1_293823_294585_-	pfam13649, Methyltransf_25, Methyltransferase domain	NA|253aa|down_1|CP033505.1_294835_295594_-	TIGR02152, Putative_ribokinase, ribokinase	NA|135aa|down_2|CP033505.1_295724_296129_-	PRK11797, PRK11797, D-ribose pyranase; Provisional	NA|203aa|down_3|CP033505.1_296143_296752_-	pfam06800, Sugar_transport, Sugar transport protein	NA|333aa|down_4|CP033505.1_297239_298238_-	COG1609, PurR, Transcriptional regulators [Transcription]	NA|54aa|down_5|CP033505.1_298498_298660_+	COG3666, COG3666, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|459aa|down_6|CP033505.1_298721_300098_-	TIGR00711, Uncharacterized_MFS-type_transporter_YhcA, drug resistance transporter, EmrB/QacA subfamily	NA|331aa|down_7|CP033505.1_300331_301324_+	COG3049, COG3049, Penicillin V acylase and related amidases [Cell envelope biogenesis, outer membrane]	NA|317aa|down_8|CP033505.1_301649_302600_+	pfam01551, Peptidase_M23, Peptidase family M23	NA|126aa|down_9|CP033505.1_302651_303029_-	COG1131, CcmA, ABC-type multidrug transport system, ATPase component [Defense mechanisms]
GCA_003827735.1_ASM382773v1	CP033505	Staphylococcus aureus strain ATCC BAA-39 chromosome, complete genome	3	721361-721458	3	CRISPRCasFinder	no		csa3,cas3,DEDDh,DinG,WYL	Orphan	AAGAGCCCCTAATTAATAAATTAAAAGGG	29	0	0	NA	NA	NA	1	1	Orphan	csa3,cas3,DEDDh,DinG,WYL	NA,NA|230aa|down_2|CP033505.1_723225_723915_-,NA|66aa|down_5|CP033505.1_724745_724943_+,NA|100aa|down_6|CP033505.1_725076_725376_+	NA|206aa|up_9|CP033505.1_710536_711154_+	COG1392, COG1392, Phosphate transport regulator (distant homolog of PhoU) [Inorganic ion transport and metabolism]	NA|336aa|up_8|CP033505.1_711169_712177_+	pfam01384, PHO4, Phosphate transporter family	NA|266aa|up_7|CP033505.1_712765_713563_-	COG3942, COG3942, Surface antigen [General function prediction only]	NA|215aa|up_6|CP033505.1_713923_714568_+	COG0670, COG0670, Integral membrane protein, interacts with FtsH [General function prediction only]	NA|717aa|up_5|CP033505.1_715264_717415_+	smart00342, HTH_ARAC, helix_turn_helix, arabinose operon control protein	NA|142aa|up_4|CP033505.1_717494_717920_+	TIGR01889, Pleiotropic_Regulator_Of_Virulence, staphylococcal accessory regulator family	NA|239aa|up_3|CP033505.1_718109_718826_+	PRK12378, PRK12378, YebC/PmpR family DNA-binding transcriptional regulator	NA|158aa|up_2|CP033505.1_718825_719299_+	COG3542, COG3542, Uncharacterized conserved protein [Function unknown]	NA|215aa|up_1|CP033505.1_719651_720296_+	COG2306, COG2306, Predicted RNA-binding protein, associated with RNAses E/G family [General function prediction only]	NA|235aa|up_0|CP033505.1_720571_721276_+	pfam03466, LysR_substrate, LysR substrate binding domain	NA|383aa|down_0|CP033505.1_721493_722642_+	cd17471, MFS_Set, Sugar efflux transporter (Set) family of the Major Facilitator Superfamily of transporters	NA|163aa|down_1|CP033505.1_722638_723127_+	COG2839, COG2839, Uncharacterized protein conserved in bacteria [Function unknown]	NA|230aa|down_2|CP033505.1_723225_723915_-	NA	NA|148aa|down_3|CP033505.1_724041_724485_+	pfam00583, Acetyltransf_1, Acetyltransferase (GNAT) family	NA|55aa|down_4|CP033505.1_724551_724716_+	TIGR03752, conj_TIGR03752, integrating conjugative element protein, PFL_4705 family	NA|66aa|down_5|CP033505.1_724745_724943_+	NA	NA|100aa|down_6|CP033505.1_725076_725376_+	NA	NA|181aa|down_7|CP033505.1_725453_725996_+	pfam13302, Acetyltransf_3, Acetyltransferase (GNAT) domain	NA|189aa|down_8|CP033505.1_726091_726658_-	COG1611, COG1611, Predicted Rossmann fold nucleotide-binding protein [General function prediction only]	NA|153aa|down_9|CP033505.1_726659_727118_-	PRK00124, PRK00124, YaiI/YqxD family protein
GCA_003827735.1_ASM382773v1	CP033505	Staphylococcus aureus strain ATCC BAA-39 chromosome, complete genome	4	774185-774267	4	CRISPRCasFinder	no		csa3,cas3,DEDDh,DinG,WYL	Orphan	CCAATTTCTACAGACAATGCAAGTTGG	27	0	0	NA	NA	NA	1	1	Orphan	csa3,cas3,DEDDh,DinG,WYL	NA,NA	NA|203aa|up_9|CP033505.1_760168_760777_+	pfam01063, Aminotran_4, Amino-transferase class IV	NA|237aa|up_8|CP033505.1_761136_761847_+	COG2049, DUR1, Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]	NA|335aa|up_7|CP033505.1_761830_762835_+	COG1984, DUR1, Allophanate hydrolase subunit 2 [Amino acid transport and metabolism]	NA|647aa|up_6|CP033505.1_763308_765249_+	COG1368, MdoB, Phosphoglycerol transferase and related proteins, alkaline phosphatase superfamily [Cell envelope biogenesis, outer membrane]	NA|626aa|up_5|CP033505.1_765524_767402_+	COG0488, Uup, ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]	NA|594aa|up_4|CP033505.1_767413_769195_+	TIGR01389, recQ, ATP-dependent DNA helicase RecQ	NA|326aa|up_3|CP033505.1_769416_770394_+	COG1125, OpuBA, ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]	NA|505aa|up_2|CP033505.1_770386_771901_+	cd13610, PBP2_ChoS, Substrate-binding domain ChoS of an osmoregulated ABC-type transporter and related proteins; type 2 periplasmic-binding protein fold	NA|353aa|up_1|CP033505.1_772140_773199_+	PRK03158, PRK03158, histidinol-phosphate aminotransferase; Provisional	NA|181aa|up_0|CP033505.1_773493_774036_+	COG4502, COG4502, 5'(3')-deoxyribonucleotidase [Nucleotide transport and metabolism]	NA|306aa|down_0|CP033505.1_774715_775633_-	COG1597, LCB5, Sphingosine kinase and enzymes related to eukaryotic diacylglycerol kinase [Lipid metabolism / General function prediction only]	NA|502aa|down_1|CP033505.1_775901_777407_-	COG3104, PTR2, Dipeptide/tripeptide permease [Amino acid transport and metabolism]	NA|167aa|down_2|CP033505.1_777747_778248_-	COG0780, COG0780, Enzyme related to GTP cyclohydrolase I [General function prediction only]	NA|289aa|down_3|CP033505.1_778267_779134_-	COG0697, RhaT, Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]	NA|133aa|down_4|CP033505.1_779934_780333_+	COG1780, NrdI, Protein involved in ribonucleotide reduction [Nucleotide transport and metabolism]	NA|702aa|down_5|CP033505.1_780295_782401_+	PRK07632, PRK07632, ribonucleotide-diphosphate reductase subunit alpha; Validated	NA|324aa|down_6|CP033505.1_782518_783490_+	TIGR04171, ribonucleotide-diphosphate_reductase_subunit_beta, ribonucleoside-diphosphate reductase, class 1b, beta subunit	NA|338aa|down_7|CP033505.1_784154_785168_+	COG4606, CeuB, ABC-type enterochelin transport system, permease component [Inorganic ion transport and metabolism]	NA|319aa|down_8|CP033505.1_785154_786111_+	COG4605, CeuC, ABC-type enterochelin transport system, permease component [Inorganic ion transport and metabolism]	NA|254aa|down_9|CP033505.1_786107_786869_+	COG4604, CeuD, ABC-type enterochelin transport system, ATPase component [Inorganic ion transport and metabolism]
GCA_003827735.1_ASM382773v1	CP033505	Staphylococcus aureus strain ATCC BAA-39 chromosome, complete genome	5	820935-821017	5	CRISPRCasFinder	no	cas3	csa3,cas3,DEDDh,DinG,WYL	Unclear	CCAACTTGCATTGTCTGTAGAAATT	25	1	1	820960-820992	CP033505.1_1960999-1961031	NA	1	1	Unclear	csa3,cas3,DEDDh,DinG,WYL	NA,NA	NA|280aa|up_9|CP033505.1_808174_809014_+	COG3942, COG3942, Surface antigen [General function prediction only]	NA|217aa|up_8|CP033505.1_809187_809838_+	pfam12917, HD_2, HD containing hydrolase-like enzyme	NA|79aa|up_7|CP033505.1_809834_810071_+	COG4897, CsbA, Uncharacterized protein conserved in bacteria [Function unknown]	NA|597aa|up_6|CP033505.1_810339_812130_+	PRK05298, PRK05298, excinuclease ABC subunit UvrB	NA|949aa|up_5|CP033505.1_812331_815178_+	PRK00349, uvrA, excinuclease ABC subunit UvrA	NA|311aa|up_4|CP033505.1_815797_816730_+	PRK05428, PRK05428, HPr kinase/phosphorylase; Provisional	NA|280aa|up_3|CP033505.1_816735_817575_+	PRK12437, PRK12437, prolipoprotein diacylglyceryl transferase; Reviewed	NA|162aa|up_2|CP033505.1_817582_818068_+	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|CP033505.1_818075_819515_+	sd00008, TPR_YbbN, C-terminal Tetratricopeptide repeat (TPR) region of YbbN and similar motifs	NA|312aa|up_0|CP033505.1_819581_820517_+	TIGR01292, Thioredoxin_reductase, thioredoxin-disulfide reductase	NA|304aa|down_0|CP033505.1_821282_822194_+	COG1660, COG1660, Predicted P-loop-containing kinase [General function prediction only]	NA|332aa|down_1|CP033505.1_822190_823186_+	TIGR01826, Putative_gluconeogenesis_factor, conserved hypothetical protein, cofD-related	NA|315aa|down_2|CP033505.1_823296_824241_+	TIGR00647, DNA_bind_WhiA, DNA-binding protein WhiA	NA|196aa|down_3|CP033505.1_824813_825401_+	PRK00277, clpP, ATP-dependent Clp protease proteolytic subunit; Reviewed	NA|301aa|down_4|CP033505.1_825643_826546_-	COG1090, COG1090, Predicted nucleoside-diphosphate sugar epimerase [General function prediction only]	NA|210aa|down_5|CP033505.1_827248_827878_+	PRK00409, PRK00409, recombination and DNA strand exchange inhibitor protein; Reviewed	NA|338aa|down_6|CP033505.1_828581_829595_+	COG2390, DeoR, Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]	NA|337aa|down_7|CP033505.1_829647_830658_+	TIGR01534, Glyceraldehyde-3-phosphate_dehydrogenase, glyceraldehyde-3-phosphate dehydrogenase, type I	NA|397aa|down_8|CP033505.1_830796_831987_+	PRK00073, pgk, phosphoglycerate kinase; Provisional	NA|254aa|down_9|CP033505.1_832108_832870_+	PRK00042, tpiA, triosephosphate isomerase; Provisional
GCA_003827735.1_ASM382773v1	CP033505	Staphylococcus aureus strain ATCC BAA-39 chromosome, complete genome	6	864053-864134	6	CRISPRCasFinder	no		csa3,cas3,DEDDh,DinG,WYL	Orphan	CCCCAACTTGCATTGTCTGTAGAA	24	1	1	864077-864110	CP033505.1_1452929-1452962	NA	1	1	Orphan	csa3,cas3,DEDDh,DinG,WYL	NA,NA	NA|194aa|up_9|CP033505.1_857156_857738_+	COG0406, phoE, Broad specificity phosphatase PhoE and related phosphatases [General function prediction only]	NA|206aa|up_8|CP033505.1_857810_858428_-	COG1279, COG1279, Lysine efflux permease [General function prediction only]	NA|165aa|up_7|CP033505.1_858582_859077_-	pfam13420, Acetyltransf_4, Acetyltransferase (GNAT) domain	NA|141aa|up_6|CP033505.1_859475_859898_-	TIGR03561, organ_hyd_perox, peroxiredoxin, Ohr subfamily	NA|239aa|up_5|CP033505.1_860045_860762_+	PRK13575, PRK13575, type I 3-dehydroquinate dehydratase	NA|180aa|up_4|CP033505.1_860844_861384_+	cd02135, YdjA-like, nitroreductase family protein similar to Escherichia coli YdjA	NA|107aa|up_3|CP033505.1_861533_861854_-	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|CP033505.1_861997_862354_+	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|CP033505.1_862511_862892_+	PRK01202, PRK01202, glycine cleavage system protein GcvH	NA|293aa|up_0|CP033505.1_863070_863949_+	COG3878, COG3878, Uncharacterized protein conserved in bacteria [Function unknown]	NA|130aa|down_0|CP033505.1_864855_865245_+	COG1658, COG1658, Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]	NA|99aa|down_1|CP033505.1_865237_865534_+	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|CP033505.1_865783_866809_+	COG1135, AbcC, ABC-type metal ion transport system, ATPase component [Inorganic ion transport and metabolism]	NA|232aa|down_3|CP033505.1_866801_867497_+	COG2011, AbcD, ABC-type metal ion transport system, permease component [Inorganic ion transport and metabolism]	NA|274aa|down_4|CP033505.1_867514_868336_+	COG1464, NlpA, ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]	NA|407aa|down_5|CP033505.1_868478_869699_-	cd01189, INT_ICEBs1_C_like, C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons	NA|243aa|down_6|CP033505.1_870537_871266_-	pfam02876, Stap_Strp_tox_C, Staphylococcal/Streptococcal toxin, beta-grasp domain	NA|245aa|down_7|CP033505.1_871440_872175_-	cd00093, HTH_XRE, Helix-turn-helix XRE-family like proteins	NA|290aa|down_8|CP033505.1_873559_874429_+	smart00942, PriCT_1, Primase C terminal 1 (PriCT-1)	NA|486aa|down_9|CP033505.1_874445_875903_+	pfam05272, VirE, Virulence-associated protein E
GCA_003827735.1_ASM382773v1	CP033505	Staphylococcus aureus strain ATCC BAA-39 chromosome, complete genome	7	1146385-1146571	1	CRT	no		csa3,cas3,DEDDh,DinG,WYL	Orphan	GGCGGGGCCCCAACATAGA	19	3	35	1146404-1146440|1146404-1146440|1146404-1146440|1146404-1146440|1146404-1146440|1146404-1146440|1146404-1146440|1146404-1146440|1146404-1146440|1146404-1146440|1146460-1146496|1146460-1146496|1146460-1146496|1146460-1146496|1146460-1146496|1146460-1146496|1146460-1146496|1146460-1146496|1146460-1146496|1146460-1146496|1146460-1146496|1146460-1146496|1146460-1146496|1146460-1146496|1146516-1146552|1146516-1146552|1146516-1146552|1146516-1146552|1146516-1146552|1146516-1146552|1146516-1146552|1146516-1146552|1146516-1146552|1146516-1146552|1146516-1146552	CP033505.1_2312415-2312379|CP033505.1_1364511-1364547|CP033505.1_2502257-2502293|CP033505.1_170095-170131|CP033505.1_815538-815502|CP033505.1_864150-864114|CP033505.1_928486-928522|CP033505.1_1636104-1636068|CP033505.1_1970418-1970382|CP033505.1_2635110-2635146|CP033505.1_372627-372663|CP033505.1_828184-828148|CP033505.1_1044405-1044369|CP033505.1_1636162-1636126|CP033505.1_1959669-1959633|CP033505.1_2346687-2346723|CP033505.1_1453003-1452967|CP033505.1_2312471-2312435|CP033505.1_2584558-2584522|CP033505.1_864420-864384|CP033505.1_864476-864440|CP033505.1_864532-864496|CP033505.1_1146572-1146608|CP033505.1_2476970-2476934|CP033505.1_774173-774209|CP033505.1_1452945-1452909|CP033505.1_1497908-1497944|CP033505.1_1497964-1498000|CP033505.1_1961070-1961034|CP033505.1_1961129-1961093|CP033505.1_2346743-2346779|CP033505.1_2749621-2749585|CP033505.1_821031-820995|CP033505.1_2584502-2584466|CP033505.1_2749565-2749529	NA	3	3	Orphan	csa3,cas3,DEDDh,DinG,WYL	NA|169aa|up_6|CP033505.1_1140349_1140856_+,NA|62aa|up_3|CP033505.1_1142708_1142894_-,NA|78aa|up_2|CP033505.1_1143515_1143749_-,NA|66aa|up_0|CP033505.1_1146031_1146229_+,NA|76aa|down_4|CP033505.1_1153603_1153831_+	NA|168aa|up_9|CP033505.1_1137587_1138091_+	COG0622, COG0622, Predicted phosphoesterase [General function prediction only]	NA|117aa|up_8|CP033505.1_1138557_1138908_+	pfam12199, efb-c, Extracellular fibrinogen binding protein C terminal	NA|134aa|up_7|CP033505.1_1139277_1139679_-	PRK13033, PRK13033, formyl peptide receptor-like 1 inhibitory protein; Reviewed	NA|169aa|up_6|CP033505.1_1140349_1140856_+	NA	NA|166aa|up_5|CP033505.1_1141114_1141612_+	pfam12199, efb-c, Extracellular fibrinogen binding protein C terminal	NA|117aa|up_4|CP033505.1_1141762_1142113_+	pfam11546, CompInhib_SCIN, Staphylococcal complement inhibitor SCIN	NA|62aa|up_3|CP033505.1_1142708_1142894_-	NA	NA|78aa|up_2|CP033505.1_1143515_1143749_-	NA	NA|207aa|up_1|CP033505.1_1144225_1144846_-	TIGR01002, synergohymenotropic_toxin, beta-channel forming cytolysin	NA|66aa|up_0|CP033505.1_1146031_1146229_+	NA	NA|242aa|down_0|CP033505.1_1148448_1149174_-	PRK13043, PRK13043, superantigen-like protein; Reviewed	NA|334aa|down_1|CP033505.1_1149611_1150613_+	PRK04284, PRK04284, ornithine carbamoyltransferase; Provisional	NA|312aa|down_2|CP033505.1_1150632_1151568_+	PRK12353, PRK12353, putative amino acid kinase; Reviewed	NA|519aa|down_3|CP033505.1_1151739_1153296_+	COG1288, COG1288, Predicted membrane protein [Function unknown]	NA|76aa|down_4|CP033505.1_1153603_1153831_+	NA	NA|316aa|down_5|CP033505.1_1154135_1155083_-	cd09325, TDT_C4-dicarb_trans, C4-dicarboxylate transporters of the Tellurite-resistance/Dicarboxylate Transporter (TDT) family	NA|63aa|down_6|CP033505.1_1155331_1155520_+	COG2826, Tra8, Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]	NA|45aa|down_7|CP033505.1_1156431_1156566_+	pfam05480, Staph_haemo, Staphylococcus haemolytic protein	NA|45aa|down_8|CP033505.1_1156622_1156757_+	pfam05480, Staph_haemo, Staphylococcus haemolytic protein	NA|229aa|down_9|CP033505.1_1156889_1157576_+	TIGR02254, hydrolase_haloacid_dehalogenase-like_family, noncanonical pyrimidine nucleotidase, YjjG family
GCA_003827735.1_ASM382773v1	CP033505	Staphylococcus aureus strain ATCC BAA-39 chromosome, complete genome	8	1387595-1387700	7	CRISPRCasFinder	no		csa3,cas3,DEDDh,DinG,WYL	Orphan	TAATGCCGATTGATTTAGCTTTATC	25	0	0	NA	NA	NA	1	1	Orphan	csa3,cas3,DEDDh,DinG,WYL	NA,NA	NA|487aa|up_9|CP033505.1_1374589_1376050_+	pfam01235, Na_Ala_symp, Sodium:alanine symporter family	NA|246aa|up_8|CP033505.1_1376662_1377400_+	COG3711, BglG, Transcriptional antiterminator [Transcription]	NA|403aa|up_7|CP033505.1_1377534_1378743_+	COG0628, yhhT, Predicted permease, member of the PurR regulon [General function prediction only]	NA|841aa|up_6|CP033505.1_1379223_1381746_+	COG2898, COG2898, Uncharacterized conserved protein [Function unknown]	NA|440aa|up_5|CP033505.1_1381820_1383140_-	COG3464, COG3464, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|170aa|up_4|CP033505.1_1383468_1383978_-	PRK14054, PRK14054, peptide-methionine (S)-S-oxide reductase	NA|258aa|up_3|CP033505.1_1384114_1384888_+	COG1316, LytR, Transcriptional regulator [Transcription]	NA|63aa|up_2|CP033505.1_1385183_1385372_-	PRK02220, PRK02220, 4-oxalocrotonate tautomerase; Provisional	NA|286aa|up_1|CP033505.1_1385668_1386526_+	cd01700, PolY_Pol_V_umuC, umuC subunit of DNA Polymerase V	NA|264aa|up_0|CP033505.1_1386662_1387454_-	PRK06545, PRK06545, prephenate dehydrogenase; Validated	NA|344aa|down_0|CP033505.1_1387970_1389002_+	cd05657, M42_glucanase_like, M42 Peptidase, endoglucanase-like subfamily	NA|469aa|down_1|CP033505.1_1389493_1390900_+	PRK13567, PRK13567, anthranilate synthase component I; Provisional	NA|189aa|down_2|CP033505.1_1390896_1391463_+	COG0512, PabA, Anthranilate/para-aminobenzoate synthases component II [Amino acid transport and metabolism / Coenzyme metabolism]	NA|333aa|down_3|CP033505.1_1391468_1392467_+	PRK00188, trpD, anthranilate phosphoribosyltransferase; Provisional	NA|261aa|down_4|CP033505.1_1392468_1393251_+	PRK00278, trpC, indole-3-glycerol phosphate synthase TrpC	NA|212aa|down_5|CP033505.1_1393247_1393883_+	PRK13958, PRK13958, N-(5'-phosphoribosyl)anthranilate isomerase; Provisional	NA|405aa|down_6|CP033505.1_1393875_1395090_+	PRK04346, PRK04346, tryptophan synthase subunit beta; Validated	NA|243aa|down_7|CP033505.1_1395082_1395811_+	PRK13111, trpA, tryptophan synthase subunit alpha; Provisional	NA|421aa|down_8|CP033505.1_1396132_1397395_+	pfam02388, FemAB, FemAB family	NA|420aa|down_9|CP033505.1_1397413_1398673_+	pfam02388, FemAB, FemAB family
GCA_003827735.1_ASM382773v1	CP033505	Staphylococcus aureus strain ATCC BAA-39 chromosome, complete genome	9	1531729-1531870	8	CRISPRCasFinder	no		csa3,cas3,DEDDh,DinG,WYL	Orphan	TCTTTTTGTTTTTTAACGGCGAATGAACGTACTGGCTCTTTAGATGCA	48	0	0	NA	NA	NA	1	1	Orphan	csa3,cas3,DEDDh,DinG,WYL	NA,NA	NA|388aa|up_9|CP033505.1_1521405_1522569_-	PRK05382, PRK05382, chorismate synthase; Validated	NA|150aa|up_8|CP033505.1_1523359_1523809_-	PRK00668, ndk, mulitfunctional nucleoside diphosphate kinase/apyrimidinic endonuclease/3'-; Validated	NA|320aa|up_7|CP033505.1_1523900_1524860_-	TIGR02748, Heptaprenyl_diphosphate_synthase_component_2, heptaprenyl diphosphate synthase component II	NA|145aa|up_6|CP033505.1_1524861_1525296_-	TIGR02752, Demethylmenaquinone_methyltransferase, demethylmenaquinone methyltransferase	NA|191aa|up_5|CP033505.1_1525535_1526108_-	pfam07307, HEPPP_synt_1, Heptaprenyl diphosphate synthase (HEPPP synthase) subunit 1	NA|91aa|up_4|CP033505.1_1526538_1526811_-	cd13831, HU, histone-like DNA-binding protein HU	NA|333aa|up_3|CP033505.1_1526981_1527980_-	PRK00094, gpsA, NAD(P)H-dependent glycerol-3-phosphate dehydrogenase	NA|437aa|up_2|CP033505.1_1527996_1529307_-	PRK00093, PRK00093, GTP-binding protein Der; Reviewed	NA|300aa|up_1|CP033505.1_1529528_1530428_-	PRK06676, rpsA, 30S ribosomal protein S1; Reviewed	NA|98aa|up_0|CP033505.1_1531409_1531703_-	PRK00023, cmk, (d)CMP kinase	NA|262aa|down_0|CP033505.1_1532202_1532988_+	cd08964, L-asparaginase_II, Type II (periplasmic) bacterial L-asparaginase	NA|329aa|down_1|CP033505.1_1533446_1534433_-	TIGR04018, thioredoxin_reductase, putative bacillithiol system oxidoreductase, YpdA family	NA|363aa|down_2|CP033505.1_1534834_1535923_-	cd00118, LysM, Lysin Motif is a small domain involved in binding peptidoglycan	NA|460aa|down_3|CP033505.1_1536398_1537778_-	COG0514, RecQ, Superfamily II DNA helicase [DNA replication, recombination, and repair]	NA|243aa|down_4|CP033505.1_1537767_1538496_-	COG4955, COG4955, Uncharacterized protein conserved in bacteria [Function unknown]	NA|83aa|down_5|CP033505.1_1538812_1539061_+	COG1141, Fer, Ferredoxin [Energy production and conversion]	NA|182aa|down_6|CP033505.1_1539166_1539712_-	COG3601, COG3601, Predicted membrane protein [Function unknown]	NA|311aa|down_7|CP033505.1_1540100_1541033_-	pfam07901, DUF1672, Protein of unknown function (DUF1672)	NA|283aa|down_8|CP033505.1_1541487_1542336_-	pfam07901, DUF1672, Protein of unknown function (DUF1672)	NA|308aa|down_9|CP033505.1_1542600_1543524_-	pfam07901, DUF1672, Protein of unknown function (DUF1672)
GCA_003827735.1_ASM382773v1	CP033505	Staphylococcus aureus strain ATCC BAA-39 chromosome, complete genome	10	1755191-1755277	9	CRISPRCasFinder	no		csa3,cas3,DEDDh,DinG,WYL	Orphan	ATGCAAGTTGGGGTGGGGCCCCAACATAGA	30	0	0	NA	NA	NA	1	1	Orphan	csa3,cas3,DEDDh,DinG,WYL	NA,NA	NA|454aa|up_9|CP033505.1_1740615_1741977_+	COG1113, AnsP, Gamma-aminobutyrate permease and related permeases [Amino acid transport and metabolism]	NA|269aa|up_8|CP033505.1_1742009_1742816_-	COG3666, COG3666, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|276aa|up_7|CP033505.1_1742833_1743661_-	COG3666, COG3666, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|586aa|up_6|CP033505.1_1744301_1746059_-	PRK06354, PRK06354, pyruvate kinase; Provisional	NA|323aa|up_5|CP033505.1_1746080_1747049_-	PRK03202, PRK03202, ATP-dependent 6-phosphofructokinase	NA|236aa|up_4|CP033505.1_1747317_1748025_-	PRK05724, PRK05724, acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated	NA|286aa|up_3|CP033505.1_1748259_1749117_-	PRK05654, PRK05654, acetyl-CoA carboxylase carboxyltransferase subunit beta	NA|323aa|up_2|CP033505.1_1749311_1750280_-	PRK07232, PRK07232, bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed	NA|1066aa|up_1|CP033505.1_1750931_1754129_-	COG0587, DnaE, DNA polymerase III, alpha subunit [DNA replication, recombination, and repair]	NA|262aa|up_0|CP033505.1_1754149_1754935_-	COG0618, COG0618, Exopolyphosphatase-related proteins [General function prediction only]	NA|350aa|down_0|CP033505.1_1755367_1756417_-	COG4109, COG4109, Predicted transcriptional regulator containing CBS domains [Transcription]	NA|138aa|down_1|CP033505.1_1756808_1757222_+	pfam00582, Usp, Universal stress protein family	NA|141aa|down_2|CP033505.1_1757526_1757949_-	PRK00685, PRK00685, metal-dependent hydrolase; Provisional	NA|352aa|down_3|CP033505.1_1758339_1759395_+	COG0006, PepP, Xaa-Pro aminopeptidase [Amino acid transport and metabolism]	NA|373aa|down_4|CP033505.1_1759710_1760829_-	cd05305, L-AlaDH, Alanine dehydrogenase NAD-binding and catalytic domains	NA|167aa|down_5|CP033505.1_1760969_1761470_+	pfam00582, Usp, Universal stress protein family	NA|401aa|down_6|CP033505.1_1761489_1762692_-	PRK00180, PRK00180, acetate kinase A/propionate kinase 2; Reviewed	NA|301aa|down_7|CP033505.1_1762823_1763726_-	COG0827, COG0827, Adenine-specific DNA methylase [DNA replication, recombination, and repair]	NA|165aa|down_8|CP033505.1_1763848_1764343_-	PRK00522, tpx, thiol peroxidase	NA|257aa|down_9|CP033505.1_1764440_1765211_-	PRK10621, PRK10621, hypothetical protein; Provisional
GCA_003827735.1_ASM382773v1	CP033505	Staphylococcus aureus strain ATCC BAA-39 chromosome, complete genome	11	2195661-2195817	1	PILER-CR	no	csa3	csa3,cas3,DEDDh,DinG,WYL	Type I-A	CCCCTACTTTTCAACTTTAGTTGTTAGGGGCTCTTATGCAG	41	0	0	NA	NA	NA	2	2	Orphan	csa3,cas3,DEDDh,DinG,WYL	NA|77aa|up_5|CP033505.1_2190537_2190768_-,NA|364aa|up_0|CP033505.1_2194556_2195648_+,NA	NA|237aa|up_9|CP033505.1_2186146_2186857_+	PRK05819, deoD, DeoD-type purine-nucleoside phosphorylase	NA|148aa|up_8|CP033505.1_2186977_2187421_-	COG0783, Dps, DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]	NA|138aa|up_7|CP033505.1_2187620_2188034_-	COG3011, COG3011, Predicted thiol-disulfide oxidoreductase [General function    prediction only]	NA|458aa|up_6|CP033505.1_2188490_2189864_-	pfam01878, EVE, EVE domain	NA|77aa|up_5|CP033505.1_2190537_2190768_-	NA	NA|313aa|up_4|CP033505.1_2190798_2191737_-	COG1482, ManA, Phosphomannose isomerase [Carbohydrate transport and metabolism]	NA|222aa|up_3|CP033505.1_2192171_2192837_-	cd05243, SDR_a5, atypical (a) SDRs, subgroup 5	csa3|107aa|up_2|CP033505.1_2192988_2193309_+	cd00090, HTH_ARSR, Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors	NA|327aa|up_1|CP033505.1_2193310_2194291_+	COG1230, CzcD, Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]	NA|364aa|up_0|CP033505.1_2194556_2195648_+	NA	NA|303aa|down_0|CP033505.1_2197582_2198491_-	pfam02037, SAP, SAP domain	NA|286aa|down_1|CP033505.1_2199498_2200356_-	COG0561, Cof, Predicted hydrolases of the HAD superfamily [General function prediction only]	NA|261aa|down_2|CP033505.1_2200423_2201206_-	COG1119, ModF, ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA [Inorganic ion transport and metabolism]	NA|602aa|down_3|CP033505.1_2201437_2203243_-	PRK00331, PRK00331, isomerizing glutamine--fructose-6-phosphate transaminase	NA|513aa|down_4|CP033505.1_2203923_2205462_+	COG2213, MtlA, Phosphotransferase system, mannitol-specific IIBC component [Carbohydrate transport and metabolism]	NA|720aa|down_5|CP033505.1_2205496_2207656_+	COG3711, BglG, Transcriptional antiterminator [Transcription]	NA|145aa|down_6|CP033505.1_2207639_2208074_+	COG4668, MtlA, Mannitol/fructose-specific phosphotransferase system, IIA domain [Carbohydrate transport and metabolism]	NA|369aa|down_7|CP033505.1_2208073_2209180_+	PRK02318, PRK02318, mannitol-1-phosphate 5-dehydrogenase; Provisional	NA|606aa|down_8|CP033505.1_2209498_2211316_-	PRK08581, PRK08581, amidase domain-containing protein	NA|1867aa|down_9|CP033505.1_2211318_2216919_-	TIGR04263, cell_wall_surface_anchor_family_protein, SasC/Mrp/FmtB intercellular aggregation domain
GCA_003827735.1_ASM382773v1	CP033505	Staphylococcus aureus strain ATCC BAA-39 chromosome, complete genome	12	2635126-2635207	10	CRISPRCasFinder	no		csa3,cas3,DEDDh,DinG,WYL	Orphan	TTCTACAGGCAATGCAAGTTGGGG	24	1	1	2635150-2635183	CP033505.1_1452962-1452929	NA	1	1	Orphan	csa3,cas3,DEDDh,DinG,WYL	NA|166aa|up_9|CP033505.1_2625539_2626037_-,NA|68aa|up_3|CP033505.1_2632926_2633130_+,NA|107aa|up_1|CP033505.1_2634137_2634458_+,NA	NA|166aa|up_9|CP033505.1_2625539_2626037_-	NA	NA|256aa|up_8|CP033505.1_2626202_2626970_-	COG3942, COG3942, Surface antigen [General function prediction only]	NA|604aa|up_7|CP033505.1_2627330_2629142_-	COG1835, COG1835, Predicted acyltransferases [Lipid metabolism]	NA|163aa|up_6|CP033505.1_2629652_2630141_-	pfam13508, Acetyltransf_7, Acetyltransferase (GNAT) domain	NA|234aa|up_5|CP033505.1_2630416_2631118_-	cd13925, RPF, core lysozyme-like domain of resuscitation-promoting factor proteins	NA|352aa|up_4|CP033505.1_2631725_2632781_-	COG3641, PfoR, Predicted membrane protein, putative toxin regulator [General function prediction only]	NA|68aa|up_3|CP033505.1_2632926_2633130_+	NA	NA|196aa|up_2|CP033505.1_2633172_2633760_+	COG1309, AcrR, Transcriptional regulator [Transcription]	NA|107aa|up_1|CP033505.1_2634137_2634458_+	NA	NA|77aa|up_0|CP033505.1_2634677_2634908_+	COG4224, COG4224, Uncharacterized protein conserved in bacteria [Function unknown]	NA|274aa|down_0|CP033505.1_2635705_2636527_-	cd05251, NmrA_like_SDR_a, NmrA (a transcriptional regulator) and HSCARG (an NADPH sensor) like proteins, atypical (a) SDRs	NA|100aa|down_1|CP033505.1_2636546_2636846_-	COG4367, COG4367, Uncharacterized protein conserved in bacteria [Function unknown]	NA|186aa|down_2|CP033505.1_2636977_2637535_+	COG1309, AcrR, Transcriptional regulator [Transcription]	NA|235aa|down_3|CP033505.1_2637527_2638232_+	cd05324, carb_red_PTCR-like_SDR_c, Porcine testicular carbonyl reductase (PTCR)-like, classical (c) SDRs	NA|337aa|down_4|CP033505.1_2638318_2639329_+	COG2159, COG2159, Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only]	NA|277aa|down_5|CP033505.1_2639348_2640179_+	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|311aa|down_6|CP033505.1_2640282_2641215_-	COG0523, COG0523, Putative GTPases (G3E family) [General function prediction only]	NA|449aa|down_7|CP033505.1_2641311_2642658_-	COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion transport and metabolism]	NA|369aa|down_8|CP033505.1_2642645_2643752_-	pfam13738, Pyr_redox_3, Pyridine nucleotide-disulphide oxidoreductase	NA|99aa|down_9|CP033505.1_2644046_2644343_-	COG4495, COG4495, Uncharacterized protein conserved in bacteria [Function unknown]
