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_000010465.1_ASM1046v1	NC_009641	Staphylococcus aureus subsp. aureus str. Newman, complete genome	1	423151-423251	1	CRISPRCasFinder	no		cas3,DEDDh,DinG,csa3,WYL	Orphan	TTATGAATTGAGTATTAAATTTG	23	0	0	NA	NA	NA	1	1	Orphan	cas3,DEDDh,DinG,csa3,WYL	NA|70aa|up_8|NC_009641.1_414723_414933_-,NA|128aa|up_6|NC_009641.1_415757_416141_-,NA|34aa|up_0|NC_009641.1_422375_422477_+,NA|221aa|down_1|NC_009641.1_424341_425004_-,NA|179aa|down_7|NC_009641.1_431095_431632_-	NA|84aa|up_9|NC_009641.1_414433_414685_+	COG2261, COG2261, Predicted membrane protein [Function unknown]	NA|70aa|up_8|NC_009641.1_414723_414933_-	NA	NA|194aa|up_7|NC_009641.1_415110_415692_+	COG0406, phoE, Broad specificity phosphatase PhoE and related phosphatases [General function prediction only]	NA|128aa|up_6|NC_009641.1_415757_416141_-	NA	NA|209aa|up_5|NC_009641.1_416395_417022_-	NF033193, lipo_NDxxF, NDxxF motif lipoprotein	NA|508aa|up_4|NC_009641.1_417466_418990_-	PRK15317, PRK15317, alkyl hydroperoxide reductase subunit F; Provisional	NA|190aa|up_3|NC_009641.1_419005_419575_-	TIGR03137, AhpC, peroxiredoxin	NA|252aa|up_2|NC_009641.1_420066_420822_+	cd02146, NfsA-like, nitroreductase similar to Escherichia coli NfsA	NA|463aa|up_1|NC_009641.1_420902_422291_-	COG1823, COG1823, Predicted Na+/dicarboxylate symporter [General function prediction only]	NA|34aa|up_0|NC_009641.1_422375_422477_+	NA	NA|319aa|down_0|NC_009641.1_423267_424224_-	PRK05035, PRK05035, electron transport complex protein RnfC; Provisional	NA|221aa|down_1|NC_009641.1_424341_425004_-	NA	NA|136aa|down_2|NC_009641.1_425146_425554_-	pfam11181, YflT, Heat induced stress protein YflT	NA|193aa|down_3|NC_009641.1_426066_426645_+	PRK09219, PRK09219, xanthine phosphoribosyltransferase; Validated	NA|423aa|down_4|NC_009641.1_426644_427913_+	TIGR03173, pbuX, xanthine permease	NA|489aa|down_5|NC_009641.1_427950_429417_+	PRK05567, PRK05567, inosine 5'-monophosphate dehydrogenase; Reviewed	NA|514aa|down_6|NC_009641.1_429441_430983_+	PRK00074, guaA, GMP synthase; Reviewed	NA|179aa|down_7|NC_009641.1_431095_431632_-	NA	NA|235aa|down_8|NC_009641.1_432024_432729_-	pfam02452, PemK_toxin, PemK-like, MazF-like toxin of type II toxin-antitoxin system	NA|91aa|down_9|NC_009641.1_433127_433400_-	COG2963, COG2963, Transposase and inactivated derivatives [DNA replication, recombination, and repair]
GCF_000010465.1_ASM1046v1	NC_009641	Staphylococcus aureus subsp. aureus str. Newman, complete genome	2	662434-662526	2	CRISPRCasFinder	no		cas3,DEDDh,DinG,csa3,WYL	Orphan	CTAAAGGTGAAGAGGAACGCAGTTGGATGCTA	32	0	0	NA	NA	NA	1	1	Orphan	cas3,DEDDh,DinG,csa3,WYL	NA|36aa|up_3|NC_009641.1_658917_659025_+,NA|169aa|down_4|NC_009641.1_666273_666780_+,NA|239aa|down_5|NC_009641.1_666941_667658_+	NA|313aa|up_9|NC_009641.1_653119_654058_+	cd19083, AKR_AKR11A1_11D1, AKR11A and  AKR11D families of aldo-keto reductase (AKR)	NA|179aa|up_8|NC_009641.1_654268_654805_+	COG0655, WrbA, Multimeric flavodoxin WrbA [General function prediction only]	NA|159aa|up_7|NC_009641.1_654973_655450_+	pfam00583, Acetyltransf_1, Acetyltransferase (GNAT) family	NA|432aa|up_6|NC_009641.1_655489_656785_+	COG1078, COG1078, HD superfamily phosphohydrolases [General function prediction only]	NA|174aa|up_5|NC_009641.1_656812_657334_+	pfam08741, YwhD, YwhD family	NA|337aa|up_4|NC_009641.1_657832_658843_+	PRK09422, PRK09422, ethanol-active dehydrogenase/acetaldehyde-active reductase; Provisional	NA|36aa|up_3|NC_009641.1_658917_659025_+	NA	NA|139aa|up_2|NC_009641.1_659117_659534_+	COG4506, COG4506, Uncharacterized protein conserved in bacteria [Function unknown]	NA|554aa|up_1|NC_009641.1_659530_661192_+	PRK01611, argS, arginyl-tRNA synthetase; Reviewed	NA|212aa|up_0|NC_009641.1_661580_662216_+	COG2231, COG2231, Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]	NA|296aa|down_0|NC_009641.1_662594_663482_+	cd01143, YvrC, Periplasmic binding protein YvrC	NA|317aa|down_1|NC_009641.1_663629_664580_+	pfam01032, FecCD, FecCD transport family	NA|240aa|down_2|NC_009641.1_664634_665354_+	COG1011, COG1011, Predicted hydrolase (HAD superfamily) [General function prediction only]	NA|267aa|down_3|NC_009641.1_665337_666138_+	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|169aa|down_4|NC_009641.1_666273_666780_+	NA	NA|239aa|down_5|NC_009641.1_666941_667658_+	NA	NA|263aa|down_6|NC_009641.1_667826_668615_+	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|125aa|down_7|NC_009641.1_668865_669240_-	TIGR01889, Pleiotropic_Regulator_Of_Virulence, staphylococcal accessory regulator family	NA|310aa|down_8|NC_009641.1_670187_671117_-	COG3238, COG3238, Uncharacterized protein conserved in bacteria [Function unknown]	NA|75aa|down_9|NC_009641.1_671311_671536_-	pfam11148, DUF2922, Protein of unknown function (DUF2922)
GCF_000010465.1_ASM1046v1	NC_009641	Staphylococcus aureus subsp. aureus str. Newman, complete genome	3	778512-778594	3	CRISPRCasFinder	no		cas3,DEDDh,DinG,csa3,WYL	Orphan	CCAATTTCTACAGACAATGCAAGTTGG	27	0	0	NA	NA	NA	1	1	Orphan	cas3,DEDDh,DinG,csa3,WYL	NA|69aa|up_9|NC_009641.1_765112_765319_+,NA|34aa|down_1|NC_009641.1_780050_780152_+,NA|52aa|down_8|NC_009641.1_788331_788487_+	NA|69aa|up_9|NC_009641.1_765112_765319_+	NA	NA|237aa|up_8|NC_009641.1_765406_766117_+	COG2049, DUR1, Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]	NA|335aa|up_7|NC_009641.1_766100_767105_+	COG1984, DUR1, Allophanate hydrolase subunit 2 [Amino acid transport and metabolism]	NA|647aa|up_6|NC_009641.1_767578_769519_+	COG1368, MdoB, Phosphoglycerol transferase and related proteins, alkaline phosphatase superfamily [Cell envelope biogenesis, outer membrane]	NA|628aa|up_5|NC_009641.1_769789_771673_+	COG0488, Uup, ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]	NA|594aa|up_4|NC_009641.1_771684_773466_+	TIGR01389, recQ, ATP-dependent DNA helicase RecQ	NA|326aa|up_3|NC_009641.1_773687_774665_+	COG1125, OpuBA, ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]	NA|505aa|up_2|NC_009641.1_774657_776172_+	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_009641.1_776411_777470_+	PRK03158, PRK03158, histidinol-phosphate aminotransferase; Provisional	NA|181aa|up_0|NC_009641.1_777820_778363_+	COG4502, COG4502, 5'(3')-deoxyribonucleotidase [Nucleotide transport and metabolism]	NA|306aa|down_0|NC_009641.1_779042_779960_-	COG1597, LCB5, Sphingosine kinase and enzymes related to eukaryotic diacylglycerol kinase [Lipid metabolism / General function prediction only]	NA|34aa|down_1|NC_009641.1_780050_780152_+	NA	NA|502aa|down_2|NC_009641.1_780229_781735_-	COG3104, PTR2, Dipeptide/tripeptide permease [Amino acid transport and metabolism]	NA|167aa|down_3|NC_009641.1_782075_782576_-	COG0780, COG0780, Enzyme related to GTP cyclohydrolase I [General function prediction only]	NA|289aa|down_4|NC_009641.1_782595_783462_-	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_009641.1_784262_784661_+	COG1780, NrdI, Protein involved in ribonucleotide reduction [Nucleotide transport and metabolism]	NA|702aa|down_6|NC_009641.1_784623_786729_+	PRK07632, PRK07632, ribonucleotide-diphosphate reductase subunit alpha; Validated	NA|324aa|down_7|NC_009641.1_786846_787818_+	TIGR04171, ribonucleotide-diphosphate_reductase_subunit_beta, ribonucleoside-diphosphate reductase, class 1b, beta subunit	NA|52aa|down_8|NC_009641.1_788331_788487_+	NA	NA|324aa|down_9|NC_009641.1_788525_789497_+	COG4606, CeuB, ABC-type enterochelin transport system, permease component [Inorganic ion transport and metabolism]
GCF_000010465.1_ASM1046v1	NC_009641	Staphylococcus aureus subsp. aureus str. Newman, complete genome	4	825017-825102	4	CRISPRCasFinder	no	cas3	cas3,DEDDh,DinG,csa3,WYL	Unclear	CCAACTTGCACATTATTGTAAGCTGACTTT	30	1	5	825047-825072|825047-825072|825047-825072|825047-825072|825047-825072	NC_009641.1_788009-787984|NC_009641.1_1178575-1178550|NC_009641.1_2836391-2836416|NC_009641.1_788065-788040|NC_009641.1_917195-917170	NA	1	1	Unclear	cas3,DEDDh,DinG,csa3,WYL	NA,NA	NA|280aa|up_9|NC_009641.1_812269_813109_+	COG3942, COG3942, Surface antigen [General function prediction only]	NA|217aa|up_8|NC_009641.1_813282_813933_+	pfam12917, HD_2, HD containing hydrolase-like enzyme	NA|79aa|up_7|NC_009641.1_813929_814166_+	COG4897, CsbA, Uncharacterized protein conserved in bacteria [Function unknown]	NA|662aa|up_6|NC_009641.1_814434_816420_+	PRK05298, PRK05298, excinuclease ABC subunit UvrB	NA|949aa|up_5|NC_009641.1_816427_819274_+	PRK00349, uvrA, excinuclease ABC subunit UvrA	NA|311aa|up_4|NC_009641.1_819935_820868_+	PRK05428, PRK05428, HPr kinase/phosphorylase; Provisional	NA|280aa|up_3|NC_009641.1_820873_821713_+	PRK12437, PRK12437, prolipoprotein diacylglyceryl transferase; Reviewed	NA|162aa|up_2|NC_009641.1_821720_822206_+	cd04647, LbH_MAT_like, Maltose O-acyltransferase (MAT)-like: This family is composed of maltose O-acetyltransferase, galactoside O-acetyltransferase (GAT), xenobiotic acyltransferase (XAT) and similar proteins	NA|480aa|up_1|NC_009641.1_822213_823653_+	sd00008, TPR_YbbN, C-terminal Tetratricopeptide repeat (TPR) region of YbbN and similar motifs	NA|312aa|up_0|NC_009641.1_823719_824655_+	TIGR01292, Thioredoxin_reductase, thioredoxin-disulfide reductase	NA|304aa|down_0|NC_009641.1_825534_826446_+	COG1660, COG1660, Predicted P-loop-containing kinase [General function prediction only]	NA|332aa|down_1|NC_009641.1_826442_827438_+	TIGR01826, Putative_gluconeogenesis_factor, conserved hypothetical protein, cofD-related	NA|315aa|down_2|NC_009641.1_827547_828492_+	TIGR00647, DNA_bind_WhiA, DNA-binding protein WhiA	NA|196aa|down_3|NC_009641.1_829064_829652_+	PRK00277, clpP, ATP-dependent Clp protease proteolytic subunit; Reviewed	NA|301aa|down_4|NC_009641.1_829894_830797_-	COG1090, COG1090, Predicted nucleoside-diphosphate sugar epimerase [General function prediction only]	NA|210aa|down_5|NC_009641.1_831500_832130_+	PRK00409, PRK00409, recombination and DNA strand exchange inhibitor protein; Reviewed	NA|338aa|down_6|NC_009641.1_832889_833903_+	COG2390, DeoR, Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]	NA|337aa|down_7|NC_009641.1_833955_834966_+	TIGR01534, Glyceraldehyde-3-phosphate_dehydrogenase, glyceraldehyde-3-phosphate dehydrogenase, type I	NA|397aa|down_8|NC_009641.1_835104_836295_+	PRK00073, pgk, phosphoglycerate kinase; Provisional	NA|254aa|down_9|NC_009641.1_836416_837178_+	PRK00042, tpiA, triosephosphate isomerase; Provisional
GCF_000010465.1_ASM1046v1	NC_009641	Staphylococcus aureus subsp. aureus str. Newman, complete genome	5	868347-868428	5	CRISPRCasFinder	no		cas3,DEDDh,DinG,csa3,WYL	Orphan	CCCCAACTTGCATTGTCTGTAGAA	24	1	2	868371-868404|868371-868404	NC_009641.1_1386741-1386708|NC_009641.1_1475151-1475184	NA	1	1	Orphan	cas3,DEDDh,DinG,csa3,WYL	NA,NA	NA|194aa|up_9|NC_009641.1_861450_862032_+	COG0406, phoE, Broad specificity phosphatase PhoE and related phosphatases [General function prediction only]	NA|206aa|up_8|NC_009641.1_862104_862722_-	COG1279, COG1279, Lysine efflux permease [General function prediction only]	NA|165aa|up_7|NC_009641.1_862876_863371_-	pfam13420, Acetyltransf_4, Acetyltransferase (GNAT) domain	NA|141aa|up_6|NC_009641.1_863769_864192_-	TIGR03561, organ_hyd_perox, peroxiredoxin, Ohr subfamily	NA|239aa|up_5|NC_009641.1_864339_865056_+	PRK13575, PRK13575, type I 3-dehydroquinate dehydratase	NA|180aa|up_4|NC_009641.1_865138_865678_+	cd02135, YdjA-like, nitroreductase family protein similar to Escherichia coli YdjA	NA|107aa|up_3|NC_009641.1_865827_866148_-	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|NC_009641.1_866291_866648_+	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|NC_009641.1_866805_867186_+	PRK01202, PRK01202, glycine cleavage system protein GcvH	NA|293aa|up_0|NC_009641.1_867364_868243_+	COG3878, COG3878, Uncharacterized protein conserved in bacteria [Function unknown]	NA|129aa|down_0|NC_009641.1_868984_869371_+	COG1658, COG1658, Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]	NA|99aa|down_1|NC_009641.1_869363_869660_+	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|NC_009641.1_869909_870935_+	COG1135, AbcC, ABC-type metal ion transport system, ATPase component [Inorganic ion transport and metabolism]	NA|232aa|down_3|NC_009641.1_870927_871623_+	COG2011, AbcD, ABC-type metal ion transport system, permease component [Inorganic ion transport and metabolism]	NA|274aa|down_4|NC_009641.1_871640_872462_+	COG1464, NlpA, ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]	NA|65aa|down_5|NC_009641.1_872815_873010_+	COG3237, COG3237, Uncharacterized protein conserved in bacteria [Function unknown]	NA|284aa|down_6|NC_009641.1_873242_874094_-	COG2035, COG2035, Predicted membrane protein [Function unknown]	NA|254aa|down_7|NC_009641.1_874421_875183_+	COG0396, sufC, Cysteine desulfurase activator ATPase [Posttranslational modification, protein turnover, chaperones]	NA|436aa|down_8|NC_009641.1_875280_876588_+	COG0719, SufB, Cysteine desulfurase activator SufB [Posttranslational modification, protein turnover, chaperones]	NA|417aa|down_9|NC_009641.1_876693_877944_+	TIGR01979, Probable_cysteine_desulfurase, cysteine desulfurases, SufSfamily
GCF_000010465.1_ASM1046v1	NC_009641	Staphylococcus aureus subsp. aureus str. Newman, complete genome	6	917196-917478	1	CRT	no		cas3,DEDDh,DinG,csa3,WYL	Orphan	AAAGNCAGCTNNNNANANNNTGCAAGTTGG	30	2	6	917226-917251|917226-917251|917226-917251|917226-917251|917340-917365|917340-917365	NC_009641.1_917170-917195|NC_009641.1_787984-788009|NC_009641.1_1178550-1178575|NC_009641.1_2836416-2836391|NC_009641.1_825128-825103|NC_009641.1_384484-384509	NA	4	4	Orphan	cas3,DEDDh,DinG,csa3,WYL	NA,NA	NA|499aa|up_9|NC_009641.1_906084_907581_-	PRK07691, PRK07691, putative monovalent cation/H+ antiporter subunit D; Reviewed	NA|114aa|up_8|NC_009641.1_907573_907915_-	PRK08600, PRK08600, putative monovalent cation/H+ antiporter subunit C; Reviewed	NA|143aa|up_7|NC_009641.1_907914_908343_-	PRK12573, PRK12573, Na(+)/H(+) antiporter subunit B	NA|802aa|up_6|NC_009641.1_908335_910741_-	PRK12645, PRK12645, monovalent cation/H+ antiporter subunit A; Reviewed	NA|128aa|up_5|NC_009641.1_910871_911255_-	pfam08810, KapB, Kinase associated protein B	NA|198aa|up_4|NC_009641.1_911318_911912_+	cd01927, cyclophilin_WD40, cyclophilin_WD40: cyclophilin-type peptidylprolyl cis- trans isomerases (cyclophilins) having a WD40 domain	NA|126aa|up_3|NC_009641.1_912327_912705_+	COG1098, VacB, Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]	NA|376aa|up_2|NC_009641.1_913066_914194_+	cd04735, OYE_like_4_FMN, Old yellow enzyme (OYE)-related FMN binding domain, group 4	NA|397aa|up_1|NC_009641.1_914501_915692_+	PRK04073, rocD, ornithine--oxo-acid transaminase; Provisional	NA|415aa|up_0|NC_009641.1_915800_917045_+	COG0334, GdhA, Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism]	NA|310aa|down_0|NC_009641.1_917547_918477_-	cd08601, GDPD_SaGlpQ_like, Glycerophosphodiester phosphodiesterase domain of Staphylococcus aureus and similar proteins	NA|460aa|down_1|NC_009641.1_918718_920098_-	PRK00855, PRK00855, argininosuccinate lyase; Provisional	NA|402aa|down_2|NC_009641.1_920087_921293_-	PRK00509, PRK00509, argininosuccinate synthase; Provisional	NA|444aa|down_3|NC_009641.1_921643_922975_+	PRK14097, pgi, glucose-6-phosphate isomerase; Provisional	NA|192aa|down_4|NC_009641.1_923299_923875_+	COG0398, COG0398, Uncharacterized conserved protein [Function unknown]	NA|175aa|down_5|NC_009641.1_923879_924404_+	TIGR02227, Inactive_signal_peptidase_IA	NA|192aa|down_6|NC_009641.1_924419_924995_+	TIGR02227, Inactive_signal_peptidase_IA	NA|1159aa|down_7|NC_009641.1_925154_928631_+	TIGR02773, ATP-dependent_helicase/deoxyribonuclease_subunit_B, helicase-exonuclease AddAB, AddB subunit	NA|1218aa|down_8|NC_009641.1_928631_932285_+	TIGR02785, ATP-dependent_helicase/nuclease_subunit_A, helicase-exonuclease AddAB, AddA subunit, Firmicutes type	NA|301aa|down_9|NC_009641.1_932450_933353_+	COG0179, MhpD, 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) [Secondary metabolites biosynthesis, transport, and catabolism]
GCF_000010465.1_ASM1046v1	NC_009641	Staphylococcus aureus subsp. aureus str. Newman, complete genome	7	1178380-1178566	2	CRT	no		cas3,DEDDh,DinG,csa3,WYL	Orphan	GGCGGGGCCCCAACATAGA	19	3	29	1178399-1178435|1178399-1178435|1178399-1178435|1178399-1178435|1178399-1178435|1178399-1178435|1178399-1178435|1178399-1178435|1178455-1178491|1178455-1178491|1178455-1178491|1178455-1178491|1178455-1178491|1178455-1178491|1178455-1178491|1178455-1178491|1178455-1178491|1178511-1178547|1178511-1178547|1178511-1178547|1178511-1178547|1178511-1178547|1178511-1178547|1178511-1178547|1178511-1178547|1178511-1178547|1178511-1178547|1178511-1178547|1178511-1178547	NC_009641.1_1833208-1833244|NC_009641.1_819621-819585|NC_009641.1_819676-819640|NC_009641.1_868444-868408|NC_009641.1_1654523-1654487|NC_009641.1_2043983-2043947|NC_009641.1_2585398-2585434|NC_009641.1_2836454-2836418|NC_009641.1_384501-384537|NC_009641.1_825111-825075|NC_009641.1_1034617-1034581|NC_009641.1_1386667-1386703|NC_009641.1_1475225-1475189|NC_009641.1_1654581-1654545|NC_009641.1_2670954-2670918|NC_009641.1_1174487-1174523|NC_009641.1_1178567-1178603|NC_009641.1_115392-115428|NC_009641.1_661472-661508|NC_009641.1_777566-777530|NC_009641.1_778500-778536|NC_009641.1_825167-825131|NC_009641.1_1386725-1386761|NC_009641.1_1475167-1475131|NC_009641.1_2034633-2034597|NC_009641.1_2034692-2034656|NC_009641.1_1060751-1060715|NC_009641.1_2560151-2560115|NC_009641.1_1174543-1174579	NA	3	3	Orphan	cas3,DEDDh,DinG,csa3,WYL	NA|31aa|up_9|NC_009641.1_1171034_1171127_-,NA|169aa|up_7|NC_009641.1_1172159_1172666_+,NA|62aa|up_4|NC_009641.1_1174747_1174933_-,NA|78aa|up_3|NC_009641.1_1175554_1175788_-,NA|49aa|up_1|NC_009641.1_1177896_1178043_+,NA|75aa|up_0|NC_009641.1_1177999_1178224_+,NA|76aa|down_6|NC_009641.1_1185579_1185807_+	NA|31aa|up_9|NC_009641.1_1171034_1171127_-	NA	NA|134aa|up_8|NC_009641.1_1171086_1171488_-	PRK13033, PRK13033, formyl peptide receptor-like 1 inhibitory protein; Reviewed	NA|169aa|up_7|NC_009641.1_1172159_1172666_+	NA	NA|166aa|up_6|NC_009641.1_1172924_1173422_+	pfam12199, efb-c, Extracellular fibrinogen binding protein C terminal	NA|117aa|up_5|NC_009641.1_1173575_1173926_+	pfam11546, CompInhib_SCIN, Staphylococcal complement inhibitor SCIN	NA|62aa|up_4|NC_009641.1_1174747_1174933_-	NA	NA|78aa|up_3|NC_009641.1_1175554_1175788_-	NA	NA|320aa|up_2|NC_009641.1_1176264_1177224_-	TIGR01002, synergohymenotropic_toxin, beta-channel forming cytolysin	NA|49aa|up_1|NC_009641.1_1177896_1178043_+	NA	NA|75aa|up_0|NC_009641.1_1177999_1178224_+	NA	NA|239aa|down_0|NC_009641.1_1178780_1179497_-	PRK13350, PRK13350, superantigen-like protein; Reviewed	NA|242aa|down_1|NC_009641.1_1179604_1180330_-	PRK13349, PRK13349, superantigen-like protein; Reviewed	NA|242aa|down_2|NC_009641.1_1180424_1181150_-	PRK13043, PRK13043, superantigen-like protein; Reviewed	NA|334aa|down_3|NC_009641.1_1181587_1182589_+	PRK04284, PRK04284, ornithine carbamoyltransferase; Provisional	NA|311aa|down_4|NC_009641.1_1182611_1183544_+	PRK12353, PRK12353, putative amino acid kinase; Reviewed	NA|519aa|down_5|NC_009641.1_1183715_1185272_+	COG1288, COG1288, Predicted membrane protein [Function unknown]	NA|76aa|down_6|NC_009641.1_1185579_1185807_+	NA	NA|316aa|down_7|NC_009641.1_1186111_1187059_-	cd09325, TDT_C4-dicarb_trans, C4-dicarboxylate transporters of the Tellurite-resistance/Dicarboxylate Transporter (TDT) family	NA|63aa|down_8|NC_009641.1_1187307_1187496_+	COG2826, Tra8, Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]	NA|45aa|down_9|NC_009641.1_1188407_1188542_+	pfam05480, Staph_haemo, Staphylococcus haemolytic protein
GCF_000010465.1_ASM1046v1	NC_009641	Staphylococcus aureus subsp. aureus str. Newman, complete genome	8	1833248-1833474	6	CRISPRCasFinder	no		cas3,DEDDh,DinG,csa3,WYL	Orphan	GGGCCCCAACACAGAAGCTGGCCAATAGTCAGCTTTCAATAATGTGCAAGTTGG	54	0	0	NA	NA	NA	1	1	Orphan	cas3,DEDDh,DinG,csa3,WYL	NA,NA	NA|199aa|up_9|NC_009641.1_1823803_1824400_-	PRK00629, pheT, phenylalanyl-tRNA synthetase subunit beta; Reviewed	NA|286aa|up_8|NC_009641.1_1824428_1825286_-	PRK13668, PRK13668, hypothetical protein; Provisional	NA|104aa|up_7|NC_009641.1_1825385_1825697_-	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|359aa|up_6|NC_009641.1_1825761_1826838_-	cd05656, M42_Frv, M42 Peptidase, endoglucanases	NA|104aa|up_5|NC_009641.1_1826924_1827236_+	COG5584, COG5584, Predicted small secreted protein [Function unknown]	NA|281aa|up_4|NC_009641.1_1827360_1828203_-	cd07728, YtnP-like_MBL-fold, Bacillus subtilis YtnP and related proteins; MBL-fold metallo hydrolase domain	NA|215aa|up_3|NC_009641.1_1828672_1829317_-	PRK00121, trmB, tRNA (guanine-N(7)-)-methyltransferase; Reviewed	NA|264aa|up_2|NC_009641.1_1829331_1830123_-	COG0510, ycfN, Thiamine kinase and related kinases [Coenzyme transport and metabolism]	NA|283aa|up_1|NC_009641.1_1830672_1831521_-	TIGR01121, D-alanine_aminotransferase, D-amino acid aminotransferase	NA|470aa|up_0|NC_009641.1_1831524_1832934_-	PRK07318, PRK07318, dipeptidase PepV; Reviewed	NA|141aa|down_0|NC_009641.1_1833853_1834276_-	pfam12732, YtxH, YtxH-like protein	NA|232aa|down_1|NC_009641.1_1834292_1834988_-	COG1187, RsuA, 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]	NA|554aa|down_2|NC_009641.1_1834984_1836646_-	cd13124, MATE_SpoVB_like, Stage V sporulation protein B, also known as Stage III sporulation protein F, and related proteins	NA|423aa|down_3|NC_009641.1_1837052_1838321_+	pfam03486, HI0933_like, HI0933-like protein	NA|2187aa|down_4|NC_009641.1_1838437_1844998_-	TIGR04263, cell_wall_surface_anchor_family_protein, SasC/Mrp/FmtB intercellular aggregation domain	NA|104aa|down_5|NC_009641.1_1845323_1845635_-	cd00158, RHOD, Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein	NA|806aa|down_6|NC_009641.1_1845656_1848074_-	PRK00390, leuS, leucyl-tRNA synthetase; Validated	NA|394aa|down_7|NC_009641.1_1848361_1849543_-	cd17329, MFS_MdtH_MDR_like, Multidrug resistance protein MdtH and similar multidrug resistance (MDR) transporters of the Major Facilitator Superfamily	NA|318aa|down_8|NC_009641.1_1849652_1850606_+	COG1242, COG1242, Predicted Fe-S oxidoreductase [General function prediction only]	NA|188aa|down_9|NC_009641.1_1850602_1851166_+	pfam06962, rRNA_methylase, Putative rRNA methylase
GCF_000010465.1_ASM1046v1	NC_009641	Staphylococcus aureus subsp. aureus str. Newman, complete genome	9	2033125-2033203	7	CRISPRCasFinder	no	DEDDh	cas3,DEDDh,DinG,csa3,WYL	Unclear	TGTTGGGGCCCCGCCAACCTGCA	23	1	5	2033148-2033180|2033148-2033180|2033148-2033180|2033148-2033180|2033148-2033180	NC_009641.1_825083-825115|NC_009641.1_1386695-1386663|NC_009641.1_1654553-1654585|NC_009641.1_2670926-2670958|NC_009641.1_1475197-1475229	NA	1	1	Orphan	cas3,DEDDh,DinG,csa3,WYL	NA|92aa|up_6|NC_009641.1_2027319_2027595_+,NA|129aa|up_1|NC_009641.1_2031580_2031967_-,NA|138aa|down_1|NC_009641.1_2034945_2035359_-,NA|31aa|down_5|NC_009641.1_2038504_2038597_-	NA|419aa|up_9|NC_009641.1_2025242_2026499_-	pfam02073, Peptidase_M29, Thermophilic metalloprotease (M29)	NA|67aa|up_8|NC_009641.1_2026501_2026702_-	COG4840, COG4840, Uncharacterized protein conserved in bacteria [Function unknown]	NA|155aa|up_7|NC_009641.1_2026848_2027313_+	cd16343, LMWPTP, Low molecular weight protein tyrosine phosphatase	NA|92aa|up_6|NC_009641.1_2027319_2027595_+	NA	NA|406aa|up_5|NC_009641.1_2027872_2029090_+	COG1295, Rbn, Ribonuclease BN family enzyme [Replication, recombination, and repair]	NA|210aa|up_4|NC_009641.1_2029205_2029835_-	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_009641.1_2029824_2030868_-	COG4585, COG4585, Signal transduction histidine kinase [Signal transduction mechanisms]	NA|234aa|up_2|NC_009641.1_2030864_2031566_-	COG4758, COG4758, Predicted membrane protein [Function unknown]	NA|129aa|up_1|NC_009641.1_2031580_2031967_-	NA	NA|253aa|up_0|NC_009641.1_2032183_2032942_-	PRK05716, PRK05716, methionine aminopeptidase; Validated	NA|329aa|down_0|NC_009641.1_2033469_2034456_+	COG4129, COG4129, Predicted membrane protein [Function unknown]	NA|138aa|down_1|NC_009641.1_2034945_2035359_-	NA	NA|244aa|down_2|NC_009641.1_2035584_2036316_-	COG3442, COG3442, Predicted glutamine amidotransferase [General function prediction only]	NA|438aa|down_3|NC_009641.1_2036317_2037631_-	COG0769, MurE, UDP-N-acetylmuramyl tripeptide synthase [Cell envelope biogenesis, outer membrane]	NA|167aa|down_4|NC_009641.1_2037922_2038423_+	COG1528, Ftn, Ferritin-like protein [Inorganic ion transport and metabolism]	NA|31aa|down_5|NC_009641.1_2038504_2038597_-	NA	DEDDh|185aa|down_6|NC_009641.1_2038811_2039366_+	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_7|NC_009641.1_2039433_2040504_-	PRK02406, PRK02406, DNA polymerase IV; Validated	NA|177aa|down_8|NC_009641.1_2040750_2041281_-	pfam11667, DUF3267, Putative zincin peptidase	NA|454aa|down_9|NC_009641.1_2041450_2042812_-	COG2265, TrmA, SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]
GCF_000010465.1_ASM1046v1	NC_009641	Staphylococcus aureus subsp. aureus str. Newman, complete genome	10	2269338-2269418	8	CRISPRCasFinder	no	csa3	cas3,DEDDh,DinG,csa3,WYL	Type I-A	TTACAACTTTAGTTGTTAGGGGCT	24	0	0	NA	NA	NA	1	1	Orphan	cas3,DEDDh,DinG,csa3,WYL	NA|77aa|up_5|NC_009641.1_2264213_2264444_-,NA|364aa|up_0|NC_009641.1_2268232_2269324_+,NA|35aa|down_0|NC_009641.1_2269757_2269862_-,NA|31aa|down_2|NC_009641.1_2271973_2272066_+	NA|237aa|up_9|NC_009641.1_2259823_2260534_+	PRK05819, deoD, DeoD-type purine-nucleoside phosphorylase	NA|148aa|up_8|NC_009641.1_2260654_2261098_-	COG0783, Dps, DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]	NA|138aa|up_7|NC_009641.1_2261297_2261711_-	COG3011, COG3011, Predicted thiol-disulfide oxidoreductase [General function    prediction only]	NA|458aa|up_6|NC_009641.1_2262168_2263542_-	pfam01878, EVE, EVE domain	NA|77aa|up_5|NC_009641.1_2264213_2264444_-	NA	NA|313aa|up_4|NC_009641.1_2264474_2265413_-	COG1482, ManA, Phosphomannose isomerase [Carbohydrate transport and metabolism]	NA|222aa|up_3|NC_009641.1_2265847_2266513_-	cd05243, SDR_a5, atypical (a) SDRs, subgroup 5	csa3|107aa|up_2|NC_009641.1_2266664_2266985_+	cd00090, HTH_ARSR, Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors	NA|327aa|up_1|NC_009641.1_2266986_2267967_+	COG1230, CzcD, Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]	NA|364aa|up_0|NC_009641.1_2268232_2269324_+	NA	NA|35aa|down_0|NC_009641.1_2269757_2269862_-	NA	NA|379aa|down_1|NC_009641.1_2270548_2271685_-	pfam02037, SAP, SAP domain	NA|31aa|down_2|NC_009641.1_2271973_2272066_+	NA	NA|286aa|down_3|NC_009641.1_2272770_2273628_-	COG0561, Cof, Predicted hydrolases of the HAD superfamily [General function prediction only]	NA|261aa|down_4|NC_009641.1_2273695_2274478_-	COG1119, ModF, ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA [Inorganic ion transport and metabolism]	NA|602aa|down_5|NC_009641.1_2274709_2276515_-	PRK00331, PRK00331, isomerizing glutamine--fructose-6-phosphate transaminase	NA|513aa|down_6|NC_009641.1_2277195_2278734_+	COG2213, MtlA, Phosphotransferase system, mannitol-specific IIBC component [Carbohydrate transport and metabolism]	NA|711aa|down_7|NC_009641.1_2278768_2280901_+	COG3711, BglG, Transcriptional antiterminator [Transcription]	NA|145aa|down_8|NC_009641.1_2280912_2281347_+	COG4668, MtlA, Mannitol/fructose-specific phosphotransferase system, IIA domain [Carbohydrate transport and metabolism]	NA|369aa|down_9|NC_009641.1_2281346_2282453_+	PRK02318, PRK02318, mannitol-1-phosphate 5-dehydrogenase; Provisional
GCF_000010465.1_ASM1046v1	NC_009641	Staphylococcus aureus subsp. aureus str. Newman, complete genome	11	2393437-2393630	3	CRT	no		cas3,DEDDh,DinG,csa3,WYL	Orphan	TGTTGGGGCCCCGCCAACTTGCA	23	3	10	2393460-2393492|2393460-2393492|2393460-2393492|2393460-2393492|2393516-2393551|2393516-2393551|2393516-2393551|2393575-2393607|2393575-2393607|2393575-2393607	NC_009641.1_825083-825115|NC_009641.1_1386695-1386663|NC_009641.1_1475197-1475229|NC_009641.1_2670926-2670958|NC_009641.1_1833239-1833204|NC_009641.1_1654492-1654527|NC_009641.1_2043952-2043987|NC_009641.1_825083-825115|NC_009641.1_1386695-1386663|NC_009641.1_2670926-2670958	NA	3	3	Orphan	cas3,DEDDh,DinG,csa3,WYL	NA|55aa|up_9|NC_009641.1_2383964_2384129_+,NA|106aa|up_8|NC_009641.1_2384373_2384691_+,NA|84aa|up_5|NC_009641.1_2389815_2390067_+,NA|57aa|up_0|NC_009641.1_2393206_2393377_+,NA	NA|55aa|up_9|NC_009641.1_2383964_2384129_+	NA	NA|106aa|up_8|NC_009641.1_2384373_2384691_+	NA	NA|1056aa|up_7|NC_009641.1_2384877_2388045_-	COG0841, AcrB, Cation/multidrug efflux pump [Defense mechanisms]	NA|422aa|up_6|NC_009641.1_2388161_2389427_-	COG2348, COG2348, Peptidoglycan interpeptide bridge formation enzyme [Cell wall/membrane/envelope biogenesis]	NA|84aa|up_5|NC_009641.1_2389815_2390067_+	NA	NA|255aa|up_4|NC_009641.1_2390058_2390823_-	pfam13468, Glyoxalase_3, Glyoxalase-like domain	NA|147aa|up_3|NC_009641.1_2390984_2391425_+	smart00347, HTH_MARR, helix_turn_helix multiple antibiotic resistance protein	NA|404aa|up_2|NC_009641.1_2391417_2392629_+	cd17489, MFS_YfcJ_like, Escherichia coli YfcJ, YhhS, and similar transporters of the Major Facilitator Superfamily	NA|117aa|up_1|NC_009641.1_2392730_2393081_-	TIGR01889, Pleiotropic_Regulator_Of_Virulence, staphylococcal accessory regulator family	NA|57aa|up_0|NC_009641.1_2393206_2393377_+	NA	NA|341aa|down_0|NC_009641.1_2393771_2394794_-	TIGR02666, Cyclic_pyranopterin_monophosphate_synthase, molybdenum cofactor biosynthesis protein A, bacterial	NA|200aa|down_1|NC_009641.1_2394813_2395413_-	PRK00317, mobA, molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed	NA|78aa|down_2|NC_009641.1_2395419_2395653_-	cd00754, Ubl_MoaD, ubiquitin-like (Ubl) domain found in molybdenum cofactor biosynthesis protein D (MoaD) and similar proteins	NA|149aa|down_3|NC_009641.1_2395658_2396105_-	COG0314, MoaE, Molybdopterin converting factor, large subunit [Coenzyme metabolism]	NA|162aa|down_4|NC_009641.1_2396118_2396604_-	COG1763, MobB, Molybdopterin-guanine dinucleotide biosynthesis protein [Coenzyme metabolism]	NA|420aa|down_5|NC_009641.1_2396600_2397860_-	cd00887, MoeA, MoeA family	NA|165aa|down_6|NC_009641.1_2397922_2398417_+	PRK09364, moaC, cyclic pyranopterin monophosphate synthase MoaC	NA|169aa|down_7|NC_009641.1_2398418_2398925_-	COG0521, MoaB, Molybdopterin biosynthesis enzymes [Coenzyme metabolism]	NA|335aa|down_8|NC_009641.1_2398955_2399960_-	PRK07688, PRK07688, thiamine/molybdopterin biosynthesis ThiF/MoeB-like protein; Validated	NA|202aa|down_9|NC_009641.1_2400129_2400735_-	COG4148, ModC, ABC-type molybdate transport system, ATPase component [Inorganic ion transport and metabolism]
