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_000470865.1_ASM47086v1	NC_022443	Staphylococcus aureus subsp. aureus SA40, complete sequence	1	634460-634567	1	CRISPRCasFinder	no		cas3,DEDDh,DinG,csa3,WYL	Orphan	CAACTGCATAAGAGCCCCTAATCGCTAAAGCTCAAGGGG	39	0	0	NA	NA	NA	1	1	Orphan	cas3,DEDDh,DinG,csa3,WYL	NA|39aa|up_8|NC_022443.1_625217_625334_+,NA|169aa|down_5|NC_022443.1_639213_639720_+,NA|239aa|down_6|NC_022443.1_639881_640598_+	NA|210aa|up_9|NC_022443.1_624531_625161_+	pfam04276, DUF443, Protein of unknown function (DUF443)	NA|39aa|up_8|NC_022443.1_625217_625334_+	NA	NA|313aa|up_7|NC_022443.1_626248_627187_+	cd19083, AKR_AKR11A1_11D1, AKR11A and  AKR11D families of aldo-keto reductase (AKR)	NA|179aa|up_6|NC_022443.1_627396_627933_+	COG0655, WrbA, Multimeric flavodoxin WrbA [General function prediction only]	NA|159aa|up_5|NC_022443.1_628102_628579_+	pfam00583, Acetyltransf_1, Acetyltransferase (GNAT) family	NA|432aa|up_4|NC_022443.1_628618_629914_+	COG1078, COG1078, HD superfamily phosphohydrolases [General function prediction only]	NA|174aa|up_3|NC_022443.1_629941_630463_+	pfam08741, YwhD, YwhD family	NA|337aa|up_2|NC_022443.1_630961_631972_+	PRK09422, PRK09422, ethanol-active dehydrogenase/acetaldehyde-active reductase; Provisional	NA|139aa|up_1|NC_022443.1_632246_632663_+	COG4506, COG4506, Uncharacterized protein conserved in bacteria [Function unknown]	NA|554aa|up_0|NC_022443.1_632659_634321_+	PRK01611, argS, arginyl-tRNA synthetase; Reviewed	NA|212aa|down_0|NC_022443.1_634586_635222_+	COG2231, COG2231, Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]	NA|296aa|down_1|NC_022443.1_635531_636419_+	cd01143, YvrC, Periplasmic binding protein YvrC	NA|317aa|down_2|NC_022443.1_636569_637520_+	pfam01032, FecCD, FecCD transport family	NA|240aa|down_3|NC_022443.1_637574_638294_+	COG1011, COG1011, Predicted hydrolase (HAD superfamily) [General function prediction only]	NA|267aa|down_4|NC_022443.1_638277_639078_+	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|169aa|down_5|NC_022443.1_639213_639720_+	NA	NA|239aa|down_6|NC_022443.1_639881_640598_+	NA	NA|263aa|down_7|NC_022443.1_640766_641555_+	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|125aa|down_8|NC_022443.1_641807_642182_-	TIGR01889, Pleiotropic_Regulator_Of_Virulence, staphylococcal accessory regulator family	NA|310aa|down_9|NC_022443.1_643129_644059_-	COG3238, COG3238, Uncharacterized protein conserved in bacteria [Function unknown]
GCF_000470865.1_ASM47086v1	NC_022443	Staphylococcus aureus subsp. aureus SA40, complete sequence	2	751200-751285	2	CRISPRCasFinder	no		cas3,DEDDh,DinG,csa3,WYL	Orphan	CAATGCGAGTTGGGGTGGGGCCCCAACA	28	1	1	751228-751257	NC_022443.1_792293-792264	NA	1	1	Orphan	cas3,DEDDh,DinG,csa3,WYL	NA|69aa|up_9|NC_022443.1_738043_738250_+,NA|34aa|down_1|NC_022443.1_752728_752830_+,NA|52aa|down_8|NC_022443.1_760994_761150_+	NA|69aa|up_9|NC_022443.1_738043_738250_+	NA	NA|237aa|up_8|NC_022443.1_738346_739057_+	COG2049, DUR1, Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]	NA|335aa|up_7|NC_022443.1_739040_740045_+	COG1984, DUR1, Allophanate hydrolase subunit 2 [Amino acid transport and metabolism]	NA|647aa|up_6|NC_022443.1_740518_742459_+	COG1368, MdoB, Phosphoglycerol transferase and related proteins, alkaline phosphatase superfamily [Cell envelope biogenesis, outer membrane]	NA|628aa|up_5|NC_022443.1_742729_744613_+	COG0488, Uup, ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]	NA|594aa|up_4|NC_022443.1_744624_746406_+	TIGR01389, recQ, ATP-dependent DNA helicase RecQ	NA|326aa|up_3|NC_022443.1_746627_747605_+	COG1125, OpuBA, ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]	NA|505aa|up_2|NC_022443.1_747597_749112_+	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|NC_022443.1_749351_750410_+	PRK03158, PRK03158, histidinol-phosphate aminotransferase; Provisional	NA|181aa|up_0|NC_022443.1_750568_751111_+	COG4502, COG4502, 5'(3')-deoxyribonucleotidase [Nucleotide transport and metabolism]	NA|306aa|down_0|NC_022443.1_751718_752636_-	COG1597, LCB5, Sphingosine kinase and enzymes related to eukaryotic diacylglycerol kinase [Lipid metabolism / General function prediction only]	NA|34aa|down_1|NC_022443.1_752728_752830_+	NA	NA|502aa|down_2|NC_022443.1_752907_754413_-	COG3104, PTR2, Dipeptide/tripeptide permease [Amino acid transport and metabolism]	NA|167aa|down_3|NC_022443.1_754752_755253_-	COG0780, COG0780, Enzyme related to GTP cyclohydrolase I [General function prediction only]	NA|289aa|down_4|NC_022443.1_755272_756139_-	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_5|NC_022443.1_756939_757338_+	COG1780, NrdI, Protein involved in ribonucleotide reduction [Nucleotide transport and metabolism]	NA|702aa|down_6|NC_022443.1_757300_759406_+	PRK07632, PRK07632, ribonucleotide-diphosphate reductase subunit alpha; Validated	NA|324aa|down_7|NC_022443.1_759523_760495_+	TIGR04171, ribonucleotide-diphosphate_reductase_subunit_beta, ribonucleoside-diphosphate reductase, class 1b, beta subunit	NA|52aa|down_8|NC_022443.1_760994_761150_+	NA	NA|324aa|down_9|NC_022443.1_761188_762160_+	COG4606, CeuB, ABC-type enterochelin transport system, permease component [Inorganic ion transport and metabolism]
GCF_000470865.1_ASM47086v1	NC_022443	Staphylococcus aureus subsp. aureus SA40, complete sequence	3	928299-928456	1,3	PILER-CR,CRISPRCasFinder	no		cas3,DEDDh,DinG,csa3,WYL	Orphan	CCAACTTGCATTGCTTGTAGAATCTCTTTTCGAAATTCT,TCTTTTCGAAATTCTCTGTGTTGGGGCCC	39,29	1	12	928406-928424|928406-928424|928406-928424|928406-928424|928406-928424|928406-928424|928406-928424|928406-928424|928406-928424|928406-928424|928406-928424|928406-928424	NC_022443.1_797609-797627|NC_022443.1_806778-806796|NC_022443.1_1268396-1268414|NC_022443.1_1268454-1268472|NC_022443.1_1919009-1919027|NC_022443.1_2259230-2259212|NC_022443.1_165282-165300|NC_022443.1_598305-598287|NC_022443.1_908135-908117|NC_022443.1_1127063-1127045|NC_022443.1_1343030-1343048|NC_022443.1_1639645-1639663	NA:NA	2,1	2	Orphan	cas3,DEDDh,DinG,csa3,WYL	NA,NA	NA|192aa|up_9|NC_022443.1_914737_915313_+	COG0398, COG0398, Uncharacterized conserved protein [Function unknown]	NA|175aa|up_8|NC_022443.1_915317_915842_+	TIGR02227, Inactive_signal_peptidase_IA	NA|192aa|up_7|NC_022443.1_915857_916433_+	TIGR02227, Inactive_signal_peptidase_IA	NA|1159aa|up_6|NC_022443.1_916592_920069_+	TIGR02773, ATP-dependent_helicase/deoxyribonuclease_subunit_B, helicase-exonuclease AddAB, AddB subunit	NA|1218aa|up_5|NC_022443.1_920069_923723_+	TIGR02785, ATP-dependent_helicase/nuclease_subunit_A, helicase-exonuclease AddAB, AddA subunit, Firmicutes type	NA|301aa|up_4|NC_022443.1_923888_924791_+	COG0179, MhpD, 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) [Secondary metabolites biosynthesis, transport, and catabolism]	NA|130aa|up_3|NC_022443.1_925118_925508_+	PRK13673, PRK13673, hypothetical protein; Provisional	NA|439aa|up_2|NC_022443.1_925679_926996_-	PRK13512, PRK13512, coenzyme A disulfide reductase; Provisional	NA|275aa|up_1|NC_022443.1_927047_927872_-	cd07516, HAD_Pase, phosphatase, similar to Escherichia coli Cof and Thermotoga maritima TM0651; belongs to the haloacid dehalogenase-like superfamily	NA|103aa|up_0|NC_022443.1_927985_928294_+	COG2151, PaaD, Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]	NA|605aa|down_0|NC_022443.1_928947_930762_+	COG1835, COG1835, Predicted acyltransferases [Lipid metabolism]	NA|870aa|down_1|NC_022443.1_930964_933574_+	TIGR03346, chaperone_ClpB, ATP-dependent chaperone ClpB	NA|290aa|down_2|NC_022443.1_933632_934502_-	COG0583, LysR, Transcriptional regulator [Transcription]	NA|382aa|down_3|NC_022443.1_934611_935757_+	COG0119, LeuA, Isopropylmalate/homocitrate/citramalate synthases [Amino acid transport and metabolism]	NA|214aa|down_4|NC_022443.1_935740_936382_+	COG0009, SUA5, Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis]	NA|172aa|down_5|NC_022443.1_937476_937992_+	COG1881, COG1881, Phospholipid-binding protein [General function prediction only]	NA|145aa|down_6|NC_022443.1_938302_938737_+	pfam03642, MAP, MAP domain	NA|62aa|down_7|NC_022443.1_938993_939179_-	pfam11151, DUF2929, Protein of unknown function (DUF2929)	NA|314aa|down_8|NC_022443.1_939473_940415_+	PRK09352, PRK09352, beta-ketoacyl-ACP synthase 3	NA|415aa|down_9|NC_022443.1_940426_941671_+	TIGR03150, fabF, beta-ketoacyl-acyl-carrier-protein synthase II
GCF_000470865.1_ASM47086v1	NC_022443	Staphylococcus aureus subsp. aureus SA40, complete sequence	4	1046823-1046915	4	CRISPRCasFinder	no		cas3,DEDDh,DinG,csa3,WYL	Orphan	AAAAGCCCCTAACAACTAAAGGTTGTAAGG	30	0	0	NA	NA	NA	1	1	Orphan	cas3,DEDDh,DinG,csa3,WYL	NA,NA|45aa|down_0|NC_022443.1_1046924_1047059_-,NA|432aa|down_1|NC_022443.1_1047210_1048506_+	NA|224aa|up_9|NC_022443.1_1034617_1035289_+	PRK03619, PRK03619, phosphoribosylformylglycinamidine synthase subunit PurQ	NA|730aa|up_8|NC_022443.1_1035281_1037471_+	PRK01213, PRK01213, phosphoribosylformylglycinamidine synthase subunit PurL	NA|495aa|up_7|NC_022443.1_1037449_1038934_+	PRK07272, PRK07272, amidophosphoribosyltransferase; Provisional	NA|343aa|up_6|NC_022443.1_1038926_1039955_+	PRK05385, PRK05385, phosphoribosylaminoimidazole synthetase; Provisional	NA|189aa|up_5|NC_022443.1_1039957_1040524_+	COG0299, PurN, Folate-dependent phosphoribosylglycinamide formyltransferase PurN [Nucleotide transport and metabolism]	NA|493aa|up_4|NC_022443.1_1040538_1042017_+	PRK00881, purH, bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional	NA|416aa|up_3|NC_022443.1_1042038_1043286_+	PRK13790, PRK13790, phosphoribosylamine--glycine ligase; Provisional	NA|269aa|up_2|NC_022443.1_1043551_1044358_-	COG0619, CbiQ, ABC-type cobalt transport system, permease component CbiQ and related transporters [Inorganic ion transport and metabolism]	NA|467aa|up_1|NC_022443.1_1044350_1045751_-	cd03225, ABC_cobalt_CbiO_domain1, First domain of the ATP-binding cassette component of cobalt transport system	NA|192aa|up_0|NC_022443.1_1045765_1046341_-	COG4721, COG4721, ABC-type cobalt transport system, predicted permease component [Inorganic ion transport and metabolism]	NA|45aa|down_0|NC_022443.1_1046924_1047059_-	NA	NA|432aa|down_1|NC_022443.1_1047210_1048506_+	NA	NA|391aa|down_2|NC_022443.1_1048930_1050103_+	COG1092, COG1092, Predicted SAM-dependent methyltransferases [General function prediction only]	NA|181aa|down_3|NC_022443.1_1050156_1050699_+	pfam05128, DUF697, Domain of unknown function (DUF697)	NA|89aa|down_4|NC_022443.1_1050852_1051119_+	PRK13780, PRK13780, phosphocarrier protein HPr; Provisional	NA|573aa|down_5|NC_022443.1_1051121_1052840_+	COG1080, PtsA, Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]	NA|78aa|down_6|NC_022443.1_1053076_1053310_-	cd02976, NrdH, NrdH-redoxin (NrdH) family; NrdH is a small monomeric protein with a conserved redox active CXXC motif within a TRX fold, characterized by a glutaredoxin (GRX)-like sequence and TRX-like activity profile	NA|454aa|down_7|NC_022443.1_1053507_1054869_+	pfam01654, Cyt_bd_oxida_I, Cytochrome bd terminal oxidase subunit I	NA|340aa|down_8|NC_022443.1_1054865_1055885_+	COG1294, AppB, Cytochrome bd-type quinol oxidase, subunit 2 [Energy production and conversion]	NA|221aa|down_9|NC_022443.1_1056017_1056680_+	COG0569, TrkA, K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]
GCF_000470865.1_ASM47086v1	NC_022443	Staphylococcus aureus subsp. aureus SA40, complete sequence	5	1131059-1131310	2	PILER-CR	no		cas3,DEDDh,DinG,csa3,WYL	Orphan	TGCAAGTTGGCGGGGCCCCAACATAG	26	4	21	1131085-1131114|1131085-1131114|1131085-1131114|1131085-1131114|1131085-1131114|1131085-1131114|1131085-1131114|1131085-1131114|1131085-1131114|1131085-1131114|1131141-1131170|1131197-1131236|1131197-1131236|1131197-1131236|1131197-1131236|1131197-1131236|1131197-1131236|1131197-1131236|1131197-1131236|1131197-1131236|1131263-1131292	NC_022443.1_806777-806748|NC_022443.1_1030658-1030629|NC_022443.1_1604587-1604558|NC_022443.1_1919008-1918979|NC_022443.1_2722124-2722095|NC_022443.1_797552-797523|NC_022443.1_863248-863277|NC_022443.1_1127178-1127207|NC_022443.1_1619889-1619918|NC_022443.1_1917552-1917523|NC_022443.1_760677-760706|NC_022443.1_760677-760716|NC_022443.1_165281-165242|NC_022443.1_598306-598345|NC_022443.1_598362-598401|NC_022443.1_760733-760772|NC_022443.1_806663-806624|NC_022443.1_1131311-1131350|NC_022443.1_2225003-2224964|NC_022443.1_2259286-2259325|NC_022443.1_806719-806690	NA	4	4	Orphan	cas3,DEDDh,DinG,csa3,WYL	NA|169aa|up_7|NC_022443.1_1124901_1125408_+,NA|62aa|up_4|NC_022443.1_1127383_1127569_-,NA|78aa|up_3|NC_022443.1_1128186_1128420_-,NA|49aa|up_1|NC_022443.1_1130528_1130675_+,NA|75aa|up_0|NC_022443.1_1130631_1130856_+,NA|76aa|down_6|NC_022443.1_1138323_1138551_+	NA|110aa|up_9|NC_022443.1_1123133_1123463_+	pfam12199, efb-c, Extracellular fibrinogen binding protein C terminal	NA|133aa|up_8|NC_022443.1_1123832_1124231_-	PRK13033, PRK13033, formyl peptide receptor-like 1 inhibitory protein; Reviewed	NA|169aa|up_7|NC_022443.1_1124901_1125408_+	NA	NA|166aa|up_6|NC_022443.1_1125666_1126164_+	pfam12199, efb-c, Extracellular fibrinogen binding protein C terminal	NA|117aa|up_5|NC_022443.1_1126317_1126668_+	pfam11546, CompInhib_SCIN, Staphylococcal complement inhibitor SCIN	NA|62aa|up_4|NC_022443.1_1127383_1127569_-	NA	NA|78aa|up_3|NC_022443.1_1128186_1128420_-	NA	NA|320aa|up_2|NC_022443.1_1128896_1129856_-	TIGR01002, synergohymenotropic_toxin, beta-channel forming cytolysin	NA|49aa|up_1|NC_022443.1_1130528_1130675_+	NA	NA|75aa|up_0|NC_022443.1_1130631_1130856_+	NA	NA|239aa|down_0|NC_022443.1_1131525_1132242_-	PRK13350, PRK13350, superantigen-like protein; Reviewed	NA|242aa|down_1|NC_022443.1_1132349_1133075_-	PRK13349, PRK13349, superantigen-like protein; Reviewed	NA|242aa|down_2|NC_022443.1_1133169_1133895_-	PRK13043, PRK13043, superantigen-like protein; Reviewed	NA|334aa|down_3|NC_022443.1_1134332_1135334_+	PRK04284, PRK04284, ornithine carbamoyltransferase; Provisional	NA|311aa|down_4|NC_022443.1_1135356_1136289_+	PRK12353, PRK12353, putative amino acid kinase; Reviewed	NA|519aa|down_5|NC_022443.1_1136459_1138016_+	COG1288, COG1288, Predicted membrane protein [Function unknown]	NA|76aa|down_6|NC_022443.1_1138323_1138551_+	NA	NA|316aa|down_7|NC_022443.1_1138856_1139804_-	cd09325, TDT_C4-dicarb_trans, C4-dicarboxylate transporters of the Tellurite-resistance/Dicarboxylate Transporter (TDT) family	NA|63aa|down_8|NC_022443.1_1140053_1140242_+	COG2826, Tra8, Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]	NA|45aa|down_9|NC_022443.1_1141154_1141289_+	pfam05480, Staph_haemo, Staphylococcus haemolytic protein
GCF_000470865.1_ASM47086v1	NC_022443	Staphylococcus aureus subsp. aureus SA40, complete sequence	6	1205687-1205779	5	CRISPRCasFinder	no	cas3	cas3,DEDDh,DinG,csa3,WYL	Unclear	TAAGAAACAGTAATCAATAAATTGATAACT	30	0	0	NA	NA	NA	1	1	Unclear	cas3,DEDDh,DinG,csa3,WYL	NA,NA	NA|215aa|up_9|NC_022443.1_1195562_1196207_+	COG0036, Rpe, Pentose-5-phosphate-3-epimerase [Carbohydrate transport and metabolism]	NA|214aa|up_8|NC_022443.1_1196213_1196855_+	COG1564, THI80, Thiamine pyrophosphokinase [Coenzyme metabolism]	NA|63aa|up_7|NC_022443.1_1197236_1197425_-	PRK00359, rpmB, 50S ribosomal protein L28; Reviewed	NA|125aa|up_6|NC_022443.1_1197867_1198242_+	COG1302, COG1302, Uncharacterized protein conserved in bacteria [Function unknown]	NA|549aa|up_5|NC_022443.1_1198256_1199903_+	COG1461, COG1461, Predicted kinase related to dihydroxyacetone kinase [General function prediction only]	cas3|687aa|up_4|NC_022443.1_1200091_1202152_+	PRK10917, PRK10917, ATP-dependent DNA helicase RecG; Provisional	NA|191aa|up_3|NC_022443.1_1202353_1202926_+	PRK04424, PRK04424, transcription factor FapR	NA|329aa|up_2|NC_022443.1_1202930_1203917_+	PRK05331, PRK05331, phosphate acyltransferase PlsX	NA|309aa|up_1|NC_022443.1_1203909_1204836_+	COG0331, FabD, (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]	NA|245aa|up_0|NC_022443.1_1204828_1205563_+	PRK05557, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase; Validated	NA|78aa|down_0|NC_022443.1_1205868_1206102_+	PRK00982, acpP, acyl carrier protein; Provisional	NA|244aa|down_1|NC_022443.1_1206217_1206949_+	PRK00102, rnc, ribonuclease III; Reviewed	NA|1189aa|down_2|NC_022443.1_1207095_1210662_+	COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]	NA|417aa|down_3|NC_022443.1_1210661_1211912_+	PRK10416, PRK10416, signal recognition particle-docking protein FtsY; Provisional	NA|111aa|down_4|NC_022443.1_1211898_1212231_+	PRK00118, PRK00118, putative DNA-binding protein; Validated	NA|456aa|down_5|NC_022443.1_1212256_1213624_+	PRK10867, PRK10867, signal recognition particle protein; Provisional	NA|92aa|down_6|NC_022443.1_1213969_1214245_+	COG0228, RpsP, Ribosomal protein S16 [Translation, ribosomal structure and biogenesis]	NA|168aa|down_7|NC_022443.1_1214432_1214936_+	PRK00122, rimM, 16S rRNA-processing protein RimM; Provisional	NA|246aa|down_8|NC_022443.1_1214935_1215673_+	PRK00026, trmD, tRNA (guanine-N(1)-)-methyltransferase; Reviewed	NA|117aa|down_9|NC_022443.1_1215775_1216126_+	PRK05338, rplS, 50S ribosomal protein L19; Provisional
GCF_000470865.1_ASM47086v1	NC_022443	Staphylococcus aureus subsp. aureus SA40, complete sequence	7	1413743-1413822	6	CRISPRCasFinder	no		cas3,DEDDh,DinG,csa3,WYL	Orphan	CCAACTTGCACATTATTGTAAGCTG	25	0	0	NA	NA	NA	1	1	Orphan	cas3,DEDDh,DinG,csa3,WYL	NA|68aa|up_5|NC_022443.1_1405223_1405427_-,NA	NA|379aa|up_9|NC_022443.1_1399573_1400710_+	pfam05816, TelA, Toxic anion resistance protein (TelA)	NA|448aa|up_8|NC_022443.1_1400783_1402127_-	COG1114, BrnQ, Branched-chain amino acid permeases [Amino acid transport and metabolism]	NA|629aa|up_7|NC_022443.1_1402351_1404238_-	COG4548, NorD, Nitric oxide reductase activation protein [Inorganic ion transport and metabolism]	NA|264aa|up_6|NC_022443.1_1404251_1405043_-	COG0714, COG0714, MoxR-like ATPases [General function prediction only]	NA|68aa|up_5|NC_022443.1_1405223_1405427_-	NA	NA|270aa|up_4|NC_022443.1_1405455_1406265_-	cd08346, PcpA_N_like, N-terminal domain of Sphingobium chlorophenolicum 2,6-dichloro-p-hydroquinone 1,2-dioxygenase (PcpA), and similar proteins	NA|423aa|up_3|NC_022443.1_1406844_1408113_-	PRK05704, PRK05704, 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase	NA|933aa|up_2|NC_022443.1_1408126_1410925_-	PRK09404, sucA, 2-oxoglutarate dehydrogenase E1 component; Reviewed	NA|452aa|up_1|NC_022443.1_1411213_1412569_-	COG0642, BaeS, Signal transduction histidine kinase [Signal transduction mechanisms]	NA|220aa|up_0|NC_022443.1_1412565_1413225_-	COG0745, OmpR, Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]	NA|205aa|down_0|NC_022443.1_1414366_1414981_-	cd03392, PAP2_like_2, PAP2_like_2 proteins	NA|357aa|down_1|NC_022443.1_1414997_1416068_-	PRK12446, PRK12446, undecaprenyldiphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase; Reviewed	NA|170aa|down_2|NC_022443.1_1416079_1416589_-	pfam00583, Acetyltransf_1, Acetyltransferase (GNAT) family	NA|497aa|down_3|NC_022443.1_1416988_1418479_-	COG0793, Prc, Periplasmic protease [Cell envelope biogenesis, outer membrane]	NA|74aa|down_4|NC_022443.1_1418670_1418892_-	COG4479, COG4479, Uncharacterized protein conserved in bacteria [Function unknown]	NA|167aa|down_5|NC_022443.1_1418891_1419392_-	COG2190, NagE, Phosphotransferase system IIA components [Carbohydrate transport and metabolism]	NA|143aa|down_6|NC_022443.1_1419403_1419832_-	PRK00222, PRK00222, peptide-methionine (R)-S-oxide reductase MsrB	NA|178aa|down_7|NC_022443.1_1419824_1420358_-	PRK13014, PRK13014, methionine sulfoxide reductase A; Provisional	NA|280aa|down_8|NC_022443.1_1420447_1421287_-	TIGR00762, DegV, EDD domain protein, DegV family	NA|160aa|down_9|NC_022443.1_1421301_1421781_-	pfam00186, DHFR_1, Dihydrofolate reductase
GCF_000470865.1_ASM47086v1	NC_022443	Staphylococcus aureus subsp. aureus SA40, complete sequence	8	1917556-1917637	7	CRISPRCasFinder	no	DEDDh	cas3,DEDDh,DinG,csa3,WYL	Unclear	TGTTGGGGCCCCGCCAACCTGCATT	25	0	0	NA	NA	NA	1	1	Orphan	cas3,DEDDh,DinG,csa3,WYL	NA|92aa|up_6|NC_022443.1_1911753_1912029_+,NA|129aa|up_1|NC_022443.1_1916011_1916398_-,NA|138aa|down_1|NC_022443.1_1919320_1919734_-,NA|37aa|down_2|NC_022443.1_1919762_1919873_-,NA|31aa|down_6|NC_022443.1_1922878_1922971_-	NA|419aa|up_9|NC_022443.1_1909676_1910933_-	pfam02073, Peptidase_M29, Thermophilic metalloprotease (M29)	NA|67aa|up_8|NC_022443.1_1910935_1911136_-	COG4840, COG4840, Uncharacterized protein conserved in bacteria [Function unknown]	NA|155aa|up_7|NC_022443.1_1911282_1911747_+	cd16343, LMWPTP, Low molecular weight protein tyrosine phosphatase	NA|92aa|up_6|NC_022443.1_1911753_1912029_+	NA	NA|406aa|up_5|NC_022443.1_1912306_1913524_+	COG1295, Rbn, Ribonuclease BN family enzyme [Replication, recombination, and repair]	NA|210aa|up_4|NC_022443.1_1913636_1914266_-	COG2197, CitB, Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]	NA|348aa|up_3|NC_022443.1_1914255_1915299_-	COG4585, COG4585, Signal transduction histidine kinase [Signal transduction mechanisms]	NA|234aa|up_2|NC_022443.1_1915295_1915997_-	COG4758, COG4758, Predicted membrane protein [Function unknown]	NA|129aa|up_1|NC_022443.1_1916011_1916398_-	NA	NA|253aa|up_0|NC_022443.1_1916614_1917373_-	PRK05716, PRK05716, methionine aminopeptidase; Validated	NA|329aa|down_0|NC_022443.1_1917901_1918888_+	COG4129, COG4129, Predicted membrane protein [Function unknown]	NA|138aa|down_1|NC_022443.1_1919320_1919734_-	NA	NA|37aa|down_2|NC_022443.1_1919762_1919873_-	NA	NA|244aa|down_3|NC_022443.1_1919958_1920690_-	COG3442, COG3442, Predicted glutamine amidotransferase [General function prediction only]	NA|438aa|down_4|NC_022443.1_1920691_1922005_-	COG0769, MurE, UDP-N-acetylmuramyl tripeptide synthase [Cell envelope biogenesis, outer membrane]	NA|167aa|down_5|NC_022443.1_1922296_1922797_+	COG1528, Ftn, Ferritin-like protein [Inorganic ion transport and metabolism]	NA|31aa|down_6|NC_022443.1_1922878_1922971_-	NA	DEDDh|185aa|down_7|NC_022443.1_1923187_1923742_+	cd06130, DNA_pol_III_epsilon_like, an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III	NA|357aa|down_8|NC_022443.1_1923808_1924879_-	PRK02406, PRK02406, DNA polymerase IV; Validated	NA|177aa|down_9|NC_022443.1_1925125_1925656_-	pfam11667, DUF3267, Putative zincin peptidase
GCF_000470865.1_ASM47086v1	NC_022443	Staphylococcus aureus subsp. aureus SA40, complete sequence	9	1977326-1977411	8	CRISPRCasFinder	no		cas3,DEDDh,DinG,csa3,WYL	Orphan	TGTTGAGGCCCCACCCCAACTTACATTGT	29	0	0	NA	NA	NA	1	1	Orphan	cas3,DEDDh,DinG,csa3,WYL	NA|59aa|up_7|NC_022443.1_1967467_1967644_-,NA|33aa|up_6|NC_022443.1_1967885_1967984_-,NA	NA|299aa|up_9|NC_022443.1_1965653_1966550_-	COG1131, CcmA, ABC-type multidrug transport system, ATPase component [Defense mechanisms]	NA|127aa|up_8|NC_022443.1_1966546_1966927_-	COG1725, COG1725, Predicted transcriptional regulators [Transcription]	NA|59aa|up_7|NC_022443.1_1967467_1967644_-	NA	NA|33aa|up_6|NC_022443.1_1967885_1967984_-	NA	NA|429aa|up_5|NC_022443.1_1968183_1969470_+	PRK08637, PRK08637, hypothetical protein; Provisional	NA|579aa|up_4|NC_022443.1_1969748_1971485_-	pfam03642, MAP, MAP domain	NA|331aa|up_3|NC_022443.1_1971873_1972866_+	TIGR03395, Sphingomyelinase_C, sphingomyelin phosphodiesterase	NA|339aa|up_2|NC_022443.1_1973358_1974375_-	pfam07968, Leukocidin, Leukocidin/Hemolysin toxin family	NA|352aa|up_1|NC_022443.1_1974396_1975452_-	pfam07968, Leukocidin, Leukocidin/Hemolysin toxin family	NA|408aa|up_0|NC_022443.1_1975887_1977111_+	PRK08588, PRK08588, succinyl-diaminopimelate desuccinylase; Reviewed	NA|436aa|down_0|NC_022443.1_1977551_1978859_+	COG0168, TrkG, Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]	NA|539aa|down_1|NC_022443.1_1979399_1981016_-	PRK00013, groEL, chaperonin GroEL; Reviewed	NA|95aa|down_2|NC_022443.1_1981091_1981376_-	PRK00364, groES, co-chaperonin GroES; Reviewed	NA|248aa|down_3|NC_022443.1_1981550_1982294_+	pfam02517, Abi, CAAX protease self-immunity	NA|400aa|down_4|NC_022443.1_1982318_1983518_-	PRK10819, PRK10819, transport protein TonB; Provisional	NA|209aa|down_5|NC_022443.1_1983714_1984341_+	COG3560, FMR2, Predicted oxidoreductase related to nitroreductase [General function prediction only]	NA|262aa|down_6|NC_022443.1_1984701_1985487_+	cd07583, nitrilase_5, Uncharacterized subgroup of the nitrilase superfamily (putative class 13 nitrilases)	NA|45aa|down_7|NC_022443.1_1986085_1986220_-	PRK14752, PRK14752, delta-lysin family phenol-soluble modulin	NA|190aa|down_8|NC_022443.1_1986455_1987025_+	smart00793, AgrB, Accessory gene regulator B	NA|47aa|down_9|NC_022443.1_1987021_1987162_+	pfam05931, AgrD, Staphylococcal AgrD protein
GCF_000470865.1_ASM47086v1	NC_022443	Staphylococcus aureus subsp. aureus SA40, complete sequence	10	2224909-2224993	9	CRISPRCasFinder	no		cas3,DEDDh,DinG,csa3,WYL	Orphan	CCAACTTGCACATTATTGTATGCTGACTTT	30	1	2	2224939-2224963|2224939-2224963	NC_022443.1_1813908-1813932|NC_022443.1_2224995-2225019	NA	1	1	Orphan	cas3,DEDDh,DinG,csa3,WYL	NA|55aa|up_9|NC_022443.1_2215416_2215581_+,NA|106aa|up_8|NC_022443.1_2215825_2216143_+,NA|84aa|up_5|NC_022443.1_2221267_2221519_+,NA|57aa|up_0|NC_022443.1_2224659_2224830_+,NA	NA|55aa|up_9|NC_022443.1_2215416_2215581_+	NA	NA|106aa|up_8|NC_022443.1_2215825_2216143_+	NA	NA|1056aa|up_7|NC_022443.1_2216329_2219497_-	COG0841, AcrB, Cation/multidrug efflux pump [Defense mechanisms]	NA|422aa|up_6|NC_022443.1_2219613_2220879_-	COG2348, COG2348, Peptidoglycan interpeptide bridge formation enzyme [Cell wall/membrane/envelope biogenesis]	NA|84aa|up_5|NC_022443.1_2221267_2221519_+	NA	NA|255aa|up_4|NC_022443.1_2221510_2222275_-	pfam13468, Glyoxalase_3, Glyoxalase-like domain	NA|147aa|up_3|NC_022443.1_2222437_2222878_+	smart00347, HTH_MARR, helix_turn_helix multiple antibiotic resistance protein	NA|404aa|up_2|NC_022443.1_2222870_2224082_+	cd17489, MFS_YfcJ_like, Escherichia coli YfcJ, YhhS, and similar transporters of the Major Facilitator Superfamily	NA|117aa|up_1|NC_022443.1_2224183_2224534_-	TIGR01889, Pleiotropic_Regulator_Of_Virulence, staphylococcal accessory regulator family	NA|57aa|up_0|NC_022443.1_2224659_2224830_+	NA	NA|341aa|down_0|NC_022443.1_2225170_2226193_-	TIGR02666, Cyclic_pyranopterin_monophosphate_synthase, molybdenum cofactor biosynthesis protein A, bacterial	NA|200aa|down_1|NC_022443.1_2226212_2226812_-	PRK00317, mobA, molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed	NA|78aa|down_2|NC_022443.1_2226818_2227052_-	cd00754, Ubl_MoaD, ubiquitin-like (Ubl) domain found in molybdenum cofactor biosynthesis protein D (MoaD) and similar proteins	NA|149aa|down_3|NC_022443.1_2227057_2227504_-	COG0314, MoaE, Molybdopterin converting factor, large subunit [Coenzyme metabolism]	NA|162aa|down_4|NC_022443.1_2227517_2228003_-	COG1763, MobB, Molybdopterin-guanine dinucleotide biosynthesis protein [Coenzyme metabolism]	NA|420aa|down_5|NC_022443.1_2227999_2229259_-	cd00887, MoeA, MoeA family	NA|165aa|down_6|NC_022443.1_2229321_2229816_+	PRK09364, moaC, cyclic pyranopterin monophosphate synthase MoaC	NA|169aa|down_7|NC_022443.1_2229817_2230324_-	COG0521, MoaB, Molybdopterin biosynthesis enzymes [Coenzyme metabolism]	NA|335aa|down_8|NC_022443.1_2230354_2231359_-	PRK07688, PRK07688, thiamine/molybdopterin biosynthesis ThiF/MoeB-like protein; Validated	NA|202aa|down_9|NC_022443.1_2231527_2232133_-	COG4148, ModC, ABC-type molybdate transport system, ATPase component [Inorganic ion transport and metabolism]
GCF_000470865.1_ASM47086v1	NC_022443	Staphylococcus aureus subsp. aureus SA40, complete sequence	11	2379535-2379627	10	CRISPRCasFinder	no		cas3,DEDDh,DinG,csa3,WYL	Orphan	TTCTTCAAATTTATTTGTTAGAAAG	25	0	0	NA	NA	NA	1	1	Orphan	cas3,DEDDh,DinG,csa3,WYL	NA|35aa|up_2|NC_022443.1_2377188_2377293_+,NA|32aa|down_0|NC_022443.1_2379831_2379927_-	NA|200aa|up_9|NC_022443.1_2370665_2371265_-	COG1651, DsbG, Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]	NA|121aa|up_8|NC_022443.1_2371283_2371646_-	pfam14729, DUF4467, Domain of unknown function with cystatin-like fold (DUF4467)	NA|417aa|up_7|NC_022443.1_2371900_2373151_+	pfam02388, FemAB, FemAB family	NA|244aa|up_6|NC_022443.1_2373247_2373979_-	COG1126, GlnQ, ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]	NA|240aa|up_5|NC_022443.1_2373975_2374695_-	COG0765, HisM, ABC-type amino acid transport system, permease component [Amino acid transport and metabolism]	NA|260aa|up_4|NC_022443.1_2374675_2375455_-	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_022443.1_2375575_2377015_-	TIGR00711, Uncharacterized_MFS-type_transporter_YhcA, drug resistance transporter, EmrB/QacA subfamily	NA|35aa|up_2|NC_022443.1_2377188_2377293_+	NA	NA|229aa|up_1|NC_022443.1_2377446_2378133_-	PRK14119, gpmA, phosphoglyceromutase; Provisional	NA|289aa|up_0|NC_022443.1_2378458_2379325_-	COG0053, MMT1, Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]	NA|32aa|down_0|NC_022443.1_2379831_2379927_-	NA	NA|437aa|down_1|NC_022443.1_2380021_2381332_+	pfam11621, Sbi-IV, C3 binding domain 4 of IgG-bind protein SBI	NA|310aa|down_2|NC_022443.1_2381823_2382753_+	pfam07968, Leukocidin, Leukocidin/Hemolysin toxin family	NA|316aa|down_3|NC_022443.1_2383320_2384268_+	pfam07968, Leukocidin, Leukocidin/Hemolysin toxin family	NA|326aa|down_4|NC_022443.1_2384269_2385247_+	TIGR01002, synergohymenotropic_toxin, beta-channel forming cytolysin	NA|156aa|down_5|NC_022443.1_2385298_2385766_-	pfam06177, QueT, QueT transporter	NA|231aa|down_6|NC_022443.1_2385776_2386469_-	COG1424, BioW, Pimeloyl-CoA synthetase [Coenzyme metabolism]	NA|372aa|down_7|NC_022443.1_2386479_2387595_-	COG0156, BioF, 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]	NA|336aa|down_8|NC_022443.1_2387572_2388580_-	PRK06256, PRK06256, biotin synthase; Validated	NA|453aa|down_9|NC_022443.1_2388581_2389940_-	TIGR00508, hypothetical_protein_DESPIG_00326, adenosylmethionine-8-amino-7-oxononanoate transaminase
GCF_000470865.1_ASM47086v1	NC_022443	Staphylococcus aureus subsp. aureus SA40, complete sequence	12	2722029-2722114	11	CRISPRCasFinder	no		cas3,DEDDh,DinG,csa3,WYL	Orphan	CCAACTTGCACATTATTGTAAGCTGACTTT	30	1	12	2722059-2722084|2722059-2722084|2722059-2722084|2722059-2722084|2722059-2722084|2722059-2722084|2722059-2722084|2722059-2722084|2722059-2722084|2722059-2722084|2722059-2722084|2722059-2722084	NC_022443.1_598371-598346|NC_022443.1_1131320-1131295|NC_022443.1_1268329-1268354|NC_022443.1_760686-760661|NC_022443.1_760742-760717|NC_022443.1_806654-806679|NC_022443.1_1785087-1785062|NC_022443.1_1967281-1967306|NC_022443.1_2142532-2142557|NC_022443.1_2259295-2259270|NC_022443.1_2063218-2063193|NC_022443.1_2063556-2063531	NA	1	1	Orphan	cas3,DEDDh,DinG,csa3,WYL	NA|64aa|up_6|NC_022443.1_2717506_2717698_+,NA|166aa|up_5|NC_022443.1_2718304_2718802_-,NA|64aa|up_4|NC_022443.1_2719258_2719450_+,NA	NA|171aa|up_9|NC_022443.1_2713983_2714496_-	COG3247, HdeD, Uncharacterized conserved protein [Function unknown]	NA|253aa|up_8|NC_022443.1_2714785_2715544_+	COG1136, SalX, ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]	NA|627aa|up_7|NC_022443.1_2715533_2717414_+	pfam02687, FtsX, FtsX-like permease family	NA|64aa|up_6|NC_022443.1_2717506_2717698_+	NA	NA|166aa|up_5|NC_022443.1_2718304_2718802_-	NA	NA|64aa|up_4|NC_022443.1_2719258_2719450_+	NA	NA|67aa|up_3|NC_022443.1_2719841_2720042_+	COG1278, CspC, Cold shock proteins [Transcription]	NA|190aa|up_2|NC_022443.1_2720168_2720738_-	cd00093, HTH_XRE, Helix-turn-helix XRE-family like proteins	NA|132aa|up_1|NC_022443.1_2720988_2721384_-	pfam11345, DUF3147, Protein of unknown function (DUF3147)	NA|118aa|up_0|NC_022443.1_2721451_2721805_-	pfam11345, DUF3147, Protein of unknown function (DUF3147)	NA|280aa|down_0|NC_022443.1_2722414_2723254_-	TIGR04285, parB-like_partition_protein, nucleoid occlusion protein	NA|240aa|down_1|NC_022443.1_2723296_2724016_-	PRK00107, gidB, 16S rRNA (guanine(527)-N(7))-methyltransferase RsmG	NA|626aa|down_2|NC_022443.1_2724015_2725893_-	PRK05192, PRK05192, tRNA uridine-5-carboxymethylaminomethyl(34) synthesis enzyme MnmG	NA|460aa|down_3|NC_022443.1_2725959_2727339_-	PRK05291, trmE, tRNA uridine-5-carboxymethylaminomethyl(34) synthesis GTPase MnmE	NA|118aa|down_4|NC_022443.1_2727482_2727836_-	PRK00499, rnpA, ribonuclease P; Reviewed	NA|46aa|down_5|NC_022443.1_2727956_2728094_-	pfam00468, Ribosomal_L34, Ribosomal protein L34	NA|NA	NA	NA|NA	NA	NA|NA	NA	NA|NA	NA
