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_900474725.1_40677_A01	LS483319	Staphylococcus aureus strain NCTC13140 genome assembly, chromosome: 1	1	396724-396824	1	CRISPRCasFinder	no		cas3,csa3,WYL,DinG,DEDDh	Orphan	TTATGAATTGAGTATTAAATTTG	23	0	0	NA	NA	NA	1	1	Orphan	cas3,csa3,WYL,DinG,DEDDh	NA|129aa|up_6|LS483319.1_389330_389717_-,NA|86aa|up_4|LS483319.1_390667_390925_-,NA|221aa|down_1|LS483319.1_397914_398577_-,NA|179aa|down_7|LS483319.1_404668_405205_-	NA|88aa|up_9|LS483319.1_387443_387707_-	cd00093, HTH_XRE, Helix-turn-helix XRE-family like proteins	NA|84aa|up_8|LS483319.1_388006_388258_+	COG2261, COG2261, Predicted membrane protein [Function unknown]	NA|194aa|up_7|LS483319.1_388683_389265_+	COG0406, phoE, Broad specificity phosphatase PhoE and related phosphatases [General function prediction only]	NA|129aa|up_6|LS483319.1_389330_389717_-	NA	NA|209aa|up_5|LS483319.1_389968_390595_-	NF033193, lipo_NDxxF, NDxxF motif lipoprotein	NA|86aa|up_4|LS483319.1_390667_390925_-	NA	NA|508aa|up_3|LS483319.1_391039_392563_-	PRK15317, PRK15317, alkyl hydroperoxide reductase subunit F; Provisional	NA|190aa|up_2|LS483319.1_392578_393148_-	TIGR03137, AhpC, peroxiredoxin	NA|252aa|up_1|LS483319.1_393639_394395_+	cd02146, NfsA-like, nitroreductase similar to Escherichia coli NfsA	NA|463aa|up_0|LS483319.1_394475_395864_-	COG1823, COG1823, Predicted Na+/dicarboxylate symporter [General function prediction only]	NA|319aa|down_0|LS483319.1_396840_397797_-	PRK05035, PRK05035, electron transport complex protein RnfC; Provisional	NA|221aa|down_1|LS483319.1_397914_398577_-	NA	NA|136aa|down_2|LS483319.1_398719_399127_-	pfam11181, YflT, Heat induced stress protein YflT	NA|193aa|down_3|LS483319.1_399639_400218_+	PRK09219, PRK09219, xanthine phosphoribosyltransferase; Validated	NA|423aa|down_4|LS483319.1_400217_401486_+	TIGR03173, pbuX, xanthine permease	NA|489aa|down_5|LS483319.1_401523_402990_+	PRK05567, PRK05567, inosine 5'-monophosphate dehydrogenase; Reviewed	NA|514aa|down_6|LS483319.1_403014_404556_+	PRK00074, guaA, GMP synthase; Reviewed	NA|179aa|down_7|LS483319.1_404668_405205_-	NA	NA|235aa|down_8|LS483319.1_405597_406302_-	pfam02452, PemK_toxin, PemK-like, MazF-like toxin of type II toxin-antitoxin system	NA|91aa|down_9|LS483319.1_406700_406973_-	COG2963, COG2963, Transposase and inactivated derivatives [DNA replication, recombination, and repair]
GCA_900474725.1_40677_A01	LS483319	Staphylococcus aureus strain NCTC13140 genome assembly, chromosome: 1	2	654936-655028	2	CRISPRCasFinder	no		cas3,csa3,WYL,DinG,DEDDh	Orphan	CTAAAGGTGAAGAGGAACGCAGTTGGATGCTA	32	0	0	NA	NA	NA	1	1	Orphan	cas3,csa3,WYL,DinG,DEDDh	NA|36aa|up_3|LS483319.1_651419_651527_+,NA|169aa|down_4|LS483319.1_658775_659282_+,NA|239aa|down_5|LS483319.1_659443_660160_+	NA|313aa|up_9|LS483319.1_645621_646560_+	cd19083, AKR_AKR11A1_11D1, AKR11A and  AKR11D families of aldo-keto reductase (AKR)	NA|179aa|up_8|LS483319.1_646770_647307_+	COG0655, WrbA, Multimeric flavodoxin WrbA [General function prediction only]	NA|159aa|up_7|LS483319.1_647475_647952_+	pfam00583, Acetyltransf_1, Acetyltransferase (GNAT) family	NA|432aa|up_6|LS483319.1_647991_649287_+	COG1078, COG1078, HD superfamily phosphohydrolases [General function prediction only]	NA|169aa|up_5|LS483319.1_649329_649836_+	pfam08741, YwhD, YwhD family	NA|337aa|up_4|LS483319.1_650334_651345_+	PRK09422, PRK09422, ethanol-active dehydrogenase/acetaldehyde-active reductase; Provisional	NA|36aa|up_3|LS483319.1_651419_651527_+	NA	NA|139aa|up_2|LS483319.1_651619_652036_+	COG4506, COG4506, Uncharacterized protein conserved in bacteria [Function unknown]	NA|554aa|up_1|LS483319.1_652032_653694_+	PRK01611, argS, arginyl-tRNA synthetase; Reviewed	NA|212aa|up_0|LS483319.1_654082_654718_+	COG2231, COG2231, Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]	NA|296aa|down_0|LS483319.1_655096_655984_+	cd01143, YvrC, Periplasmic binding protein YvrC	NA|329aa|down_1|LS483319.1_656095_657082_+	pfam01032, FecCD, FecCD transport family	NA|240aa|down_2|LS483319.1_657136_657856_+	COG1011, COG1011, Predicted hydrolase (HAD superfamily) [General function prediction only]	NA|267aa|down_3|LS483319.1_657839_658640_+	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|169aa|down_4|LS483319.1_658775_659282_+	NA	NA|239aa|down_5|LS483319.1_659443_660160_+	NA	NA|263aa|down_6|LS483319.1_660328_661117_+	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|125aa|down_7|LS483319.1_661367_661742_-	TIGR01889, Pleiotropic_Regulator_Of_Virulence, staphylococcal accessory regulator family	NA|310aa|down_8|LS483319.1_662690_663620_-	COG3238, COG3238, Uncharacterized protein conserved in bacteria [Function unknown]	NA|75aa|down_9|LS483319.1_663814_664039_-	pfam11148, DUF2922, Protein of unknown function (DUF2922)
GCA_900474725.1_40677_A01	LS483319	Staphylococcus aureus strain NCTC13140 genome assembly, chromosome: 1	3	774401-774483	3	CRISPRCasFinder	no		cas3,csa3,WYL,DinG,DEDDh	Orphan	CCAATTTCTACAGACAATGCAAGTTGG	27	0	0	NA	NA	NA	1	1	Orphan	cas3,csa3,WYL,DinG,DEDDh	NA,NA	NA|237aa|up_9|LS483319.1_759445_760156_+	COG2049, DUR1, Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]	NA|335aa|up_8|LS483319.1_760139_761144_+	COG1984, DUR1, Allophanate hydrolase subunit 2 [Amino acid transport and metabolism]	NA|647aa|up_7|LS483319.1_761617_763558_+	COG1368, MdoB, Phosphoglycerol transferase and related proteins, alkaline phosphatase superfamily [Cell envelope biogenesis, outer membrane]	NA|626aa|up_6|LS483319.1_763834_765712_+	COG0488, Uup, ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]	NA|594aa|up_5|LS483319.1_765723_767505_+	TIGR01389, recQ, ATP-dependent DNA helicase RecQ	NA|326aa|up_4|LS483319.1_767726_768704_+	COG1125, OpuBA, ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]	NA|505aa|up_3|LS483319.1_768696_770211_+	cd13610, PBP2_ChoS, Substrate-binding domain ChoS of an osmoregulated ABC-type transporter and related proteins; type 2 periplasmic-binding protein fold	NA|346aa|up_2|LS483319.1_770450_771488_+	PRK03158, PRK03158, histidinol-phosphate aminotransferase; Provisional	NA|535aa|up_1|LS483319.1_771638_773243_+	pfam13751, DDE_Tnp_1_6, Transposase DDE domain	NA|181aa|up_0|LS483319.1_773709_774252_+	COG4502, COG4502, 5'(3')-deoxyribonucleotidase [Nucleotide transport and metabolism]	NA|306aa|down_0|LS483319.1_774931_775849_-	COG1597, LCB5, Sphingosine kinase and enzymes related to eukaryotic diacylglycerol kinase [Lipid metabolism / General function prediction only]	NA|502aa|down_1|LS483319.1_776118_777624_-	COG3104, PTR2, Dipeptide/tripeptide permease [Amino acid transport and metabolism]	NA|167aa|down_2|LS483319.1_777964_778465_-	COG0780, COG0780, Enzyme related to GTP cyclohydrolase I [General function prediction only]	NA|289aa|down_3|LS483319.1_778484_779351_-	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|LS483319.1_780152_780551_+	COG1780, NrdI, Protein involved in ribonucleotide reduction [Nucleotide transport and metabolism]	NA|702aa|down_5|LS483319.1_780513_782619_+	PRK07632, PRK07632, ribonucleotide-diphosphate reductase subunit alpha; Validated	NA|324aa|down_6|LS483319.1_782736_783708_+	TIGR04171, ribonucleotide-diphosphate_reductase_subunit_beta, ribonucleoside-diphosphate reductase, class 1b, beta subunit	NA|338aa|down_7|LS483319.1_784317_785331_+	COG4606, CeuB, ABC-type enterochelin transport system, permease component [Inorganic ion transport and metabolism]	NA|319aa|down_8|LS483319.1_785317_786274_+	COG4605, CeuC, ABC-type enterochelin transport system, permease component [Inorganic ion transport and metabolism]	NA|254aa|down_9|LS483319.1_786270_787032_+	COG4604, CeuD, ABC-type enterochelin transport system, ATPase component [Inorganic ion transport and metabolism]
GCA_900474725.1_40677_A01	LS483319	Staphylococcus aureus strain NCTC13140 genome assembly, chromosome: 1	4	815398-815478	4	CRISPRCasFinder	no	cas3	cas3,csa3,WYL,DinG,DEDDh	Unclear	TTCTTTATGTTGGGGCCCCGCCAACT	26	1	9	815424-815452|815424-815452|815424-815452|815424-815452|815424-815452|815424-815452|815424-815452|815424-815452|815424-815452	LS483319.1_2906093-2906121|LS483319.1_358219-358191|LS483319.1_358274-358246|LS483319.1_1287562-1287590|LS483319.1_864117-864145|LS483319.1_932619-932647|LS483319.1_1493465-1493437|LS483319.1_2092169-2092197|LS483319.1_2653792-2653764	NA	1	1	Unclear	cas3,csa3,WYL,DinG,DEDDh	NA,NA	cas3|361aa|up_9|LS483319.1_800942_802025_+	COG4098, comFA, Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [DNA replication, recombination, and repair]	NA|225aa|up_8|LS483319.1_802017_802692_+	COG1040, ComFC, Predicted amidophosphoribosyltransferases [General function prediction only]	NA|191aa|up_7|LS483319.1_802752_803325_+	COG1544, COG1544, Ribosome-associated protein Y (PSrp-1) [Translation, ribosomal structure and biogenesis]	NA|844aa|up_6|LS483319.1_803738_806270_+	PRK12904, PRK12904, preprotein translocase subunit SecA; Reviewed	NA|331aa|up_5|LS483319.1_806702_807695_+	PRK00578, prfB, peptide chain release factor 2; Validated	NA|280aa|up_4|LS483319.1_808103_808943_+	COG3942, COG3942, Surface antigen [General function prediction only]	NA|217aa|up_3|LS483319.1_809116_809767_+	pfam12917, HD_2, HD containing hydrolase-like enzyme	NA|79aa|up_2|LS483319.1_809763_810000_+	COG4897, CsbA, Uncharacterized protein conserved in bacteria [Function unknown]	NA|662aa|up_1|LS483319.1_810268_812254_+	PRK05298, PRK05298, excinuclease ABC subunit UvrB	NA|949aa|up_0|LS483319.1_812261_815108_+	PRK00349, uvrA, excinuclease ABC subunit UvrA	NA|311aa|down_0|LS483319.1_815714_816647_+	PRK05428, PRK05428, HPr kinase/phosphorylase; Provisional	NA|280aa|down_1|LS483319.1_816652_817492_+	PRK12437, PRK12437, prolipoprotein diacylglyceryl transferase; Reviewed	NA|162aa|down_2|LS483319.1_817499_817985_+	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|down_3|LS483319.1_817992_819432_+	sd00008, TPR_YbbN, C-terminal Tetratricopeptide repeat (TPR) region of YbbN and similar motifs	NA|312aa|down_4|LS483319.1_819498_820434_+	TIGR01292, Thioredoxin_reductase, thioredoxin-disulfide reductase	NA|304aa|down_5|LS483319.1_821313_822225_+	COG1660, COG1660, Predicted P-loop-containing kinase [General function prediction only]	NA|332aa|down_6|LS483319.1_822221_823217_+	TIGR01826, Putative_gluconeogenesis_factor, conserved hypothetical protein, cofD-related	NA|315aa|down_7|LS483319.1_823326_824271_+	TIGR00647, DNA_bind_WhiA, DNA-binding protein WhiA	NA|196aa|down_8|LS483319.1_824843_825431_+	PRK00277, clpP, ATP-dependent Clp protease proteolytic subunit; Reviewed	NA|290aa|down_9|LS483319.1_825673_826543_-	COG1090, COG1090, Predicted nucleoside-diphosphate sugar epimerase [General function prediction only]
GCA_900474725.1_40677_A01	LS483319	Staphylococcus aureus strain NCTC13140 genome assembly, chromosome: 1	5	820796-820881	5	CRISPRCasFinder	no	cas3	cas3,csa3,WYL,DinG,DEDDh	Unclear	CCAACTTGCACATTATTGTAAGCTGACTTT	30	1	6	820826-820851|820826-820851|820826-820851|820826-820851|820826-820851|820826-820851	LS483319.1_783899-783874|LS483319.1_1990677-1990702|LS483319.1_2906005-2906030|LS483319.1_2906061-2906086|LS483319.1_783955-783930|LS483319.1_912893-912868	NA	1	1	Unclear	cas3,csa3,WYL,DinG,DEDDh	NA,NA	NA|280aa|up_9|LS483319.1_808103_808943_+	COG3942, COG3942, Surface antigen [General function prediction only]	NA|217aa|up_8|LS483319.1_809116_809767_+	pfam12917, HD_2, HD containing hydrolase-like enzyme	NA|79aa|up_7|LS483319.1_809763_810000_+	COG4897, CsbA, Uncharacterized protein conserved in bacteria [Function unknown]	NA|662aa|up_6|LS483319.1_810268_812254_+	PRK05298, PRK05298, excinuclease ABC subunit UvrB	NA|949aa|up_5|LS483319.1_812261_815108_+	PRK00349, uvrA, excinuclease ABC subunit UvrA	NA|311aa|up_4|LS483319.1_815714_816647_+	PRK05428, PRK05428, HPr kinase/phosphorylase; Provisional	NA|280aa|up_3|LS483319.1_816652_817492_+	PRK12437, PRK12437, prolipoprotein diacylglyceryl transferase; Reviewed	NA|162aa|up_2|LS483319.1_817499_817985_+	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|LS483319.1_817992_819432_+	sd00008, TPR_YbbN, C-terminal Tetratricopeptide repeat (TPR) region of YbbN and similar motifs	NA|312aa|up_0|LS483319.1_819498_820434_+	TIGR01292, Thioredoxin_reductase, thioredoxin-disulfide reductase	NA|304aa|down_0|LS483319.1_821313_822225_+	COG1660, COG1660, Predicted P-loop-containing kinase [General function prediction only]	NA|332aa|down_1|LS483319.1_822221_823217_+	TIGR01826, Putative_gluconeogenesis_factor, conserved hypothetical protein, cofD-related	NA|315aa|down_2|LS483319.1_823326_824271_+	TIGR00647, DNA_bind_WhiA, DNA-binding protein WhiA	NA|196aa|down_3|LS483319.1_824843_825431_+	PRK00277, clpP, ATP-dependent Clp protease proteolytic subunit; Reviewed	NA|290aa|down_4|LS483319.1_825673_826543_-	COG1090, COG1090, Predicted nucleoside-diphosphate sugar epimerase [General function prediction only]	NA|210aa|down_5|LS483319.1_827278_827908_+	PRK00409, PRK00409, recombination and DNA strand exchange inhibitor protein; Reviewed	NA|338aa|down_6|LS483319.1_828667_829681_+	COG2390, DeoR, Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]	NA|337aa|down_7|LS483319.1_829733_830744_+	TIGR01534, Glyceraldehyde-3-phosphate_dehydrogenase, glyceraldehyde-3-phosphate dehydrogenase, type I	NA|397aa|down_8|LS483319.1_830882_832073_+	PRK00073, pgk, phosphoglycerate kinase; Provisional	NA|254aa|down_9|LS483319.1_832194_832956_+	PRK00042, tpiA, triosephosphate isomerase; Provisional
GCA_900474725.1_40677_A01	LS483319	Staphylococcus aureus strain NCTC13140 genome assembly, chromosome: 1	6	864051-864132	6	CRISPRCasFinder	no		cas3,csa3,WYL,DinG,DEDDh	Orphan	CCCCAACTTGCATTGTCTGTAGAA	24	1	2	864075-864108|864075-864108	LS483319.1_1686148-1686115|LS483319.1_1775300-1775333	NA	1	1	Orphan	cas3,csa3,WYL,DinG,DEDDh	NA|38aa|up_1|LS483319.1_862953_863067_+,NA	NA|206aa|up_9|LS483319.1_857808_858426_-	COG1279, COG1279, Lysine efflux permease [General function prediction only]	NA|165aa|up_8|LS483319.1_858580_859075_-	pfam13420, Acetyltransf_4, Acetyltransferase (GNAT) domain	NA|141aa|up_7|LS483319.1_859473_859896_-	TIGR03561, organ_hyd_perox, peroxiredoxin, Ohr subfamily	NA|239aa|up_6|LS483319.1_860043_860760_+	PRK13575, PRK13575, type I 3-dehydroquinate dehydratase	NA|180aa|up_5|LS483319.1_860842_861382_+	cd02135, YdjA-like, nitroreductase family protein similar to Escherichia coli YdjA	NA|107aa|up_4|LS483319.1_861531_861852_-	cd02947, TRX_family, TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a TRX domain; and Group II, which are composed of fusion proteins of TRX and additional domains	NA|119aa|up_3|LS483319.1_861995_862352_+	cd03036, ArsC_like, Arsenate Reductase (ArsC) family, unknown subfamily; uncharacterized proteins containing a CXXC motif with similarity to thioredoxin (TRX)-fold arsenic reductases, ArsC	NA|127aa|up_2|LS483319.1_862509_862890_+	PRK01202, PRK01202, glycine cleavage system protein GcvH	NA|38aa|up_1|LS483319.1_862953_863067_+	NA	NA|293aa|up_0|LS483319.1_863068_863947_+	COG3878, COG3878, Uncharacterized protein conserved in bacteria [Function unknown]	NA|130aa|down_0|LS483319.1_864685_865075_+	COG1658, COG1658, Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]	NA|99aa|down_1|LS483319.1_865067_865364_+	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|LS483319.1_865613_866639_+	COG1135, AbcC, ABC-type metal ion transport system, ATPase component [Inorganic ion transport and metabolism]	NA|232aa|down_3|LS483319.1_866631_867327_+	COG2011, AbcD, ABC-type metal ion transport system, permease component [Inorganic ion transport and metabolism]	NA|274aa|down_4|LS483319.1_867344_868166_+	COG1464, NlpA, ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]	NA|65aa|down_5|LS483319.1_868519_868714_+	COG3237, COG3237, Uncharacterized protein conserved in bacteria [Function unknown]	NA|284aa|down_6|LS483319.1_868946_869798_-	COG2035, COG2035, Predicted membrane protein [Function unknown]	NA|254aa|down_7|LS483319.1_870125_870887_+	COG0396, sufC, Cysteine desulfurase activator ATPase [Posttranslational modification, protein turnover, chaperones]	NA|436aa|down_8|LS483319.1_870984_872292_+	COG0719, SufB, Cysteine desulfurase activator SufB [Posttranslational modification, protein turnover, chaperones]	NA|414aa|down_9|LS483319.1_872406_873648_+	TIGR01979, Probable_cysteine_desulfurase, cysteine desulfurases, SufSfamily
GCA_900474725.1_40677_A01	LS483319	Staphylococcus aureus strain NCTC13140 genome assembly, chromosome: 1	7	912894-913232	1	CRT	no		cas3,csa3,WYL,DinG,DEDDh	Orphan	AAAGNCAGCTNNNNANANNNTGCAAGTTGG	30	3	10	912924-912949|912924-912949|912980-913005|912980-913005|912980-913005|912980-913005|912980-913005|913094-913119|913094-913119|913094-913119	LS483319.1_912868-912893|LS483319.1_864435-864410|LS483319.1_912868-912893|LS483319.1_783874-783899|LS483319.1_1990702-1990677|LS483319.1_2906030-2906005|LS483319.1_2906086-2906061|LS483319.1_820907-820882|LS483319.1_2081470-2081445|LS483319.1_358057-358082	NA	5	5	Orphan	cas3,csa3,WYL,DinG,DEDDh	NA,NA	NA|499aa|up_9|LS483319.1_901782_903279_-	PRK07691, PRK07691, putative monovalent cation/H+ antiporter subunit D; Reviewed	NA|114aa|up_8|LS483319.1_903271_903613_-	PRK08600, PRK08600, putative monovalent cation/H+ antiporter subunit C; Reviewed	NA|143aa|up_7|LS483319.1_903612_904041_-	PRK12573, PRK12573, Na(+)/H(+) antiporter subunit B	NA|802aa|up_6|LS483319.1_904033_906439_-	PRK12645, PRK12645, monovalent cation/H+ antiporter subunit A; Reviewed	NA|128aa|up_5|LS483319.1_906569_906953_-	pfam08810, KapB, Kinase associated protein B	NA|198aa|up_4|LS483319.1_907016_907610_+	cd01927, cyclophilin_WD40, cyclophilin_WD40: cyclophilin-type peptidylprolyl cis- trans isomerases (cyclophilins) having a WD40 domain	NA|126aa|up_3|LS483319.1_908025_908403_+	COG1098, VacB, Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]	NA|376aa|up_2|LS483319.1_908764_909892_+	cd04735, OYE_like_4_FMN, Old yellow enzyme (OYE)-related FMN binding domain, group 4	NA|397aa|up_1|LS483319.1_910199_911390_+	PRK04073, rocD, ornithine--oxo-acid transaminase; Provisional	NA|415aa|up_0|LS483319.1_911498_912743_+	COG0334, GdhA, Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism]	NA|310aa|down_0|LS483319.1_913301_914231_-	cd08601, GDPD_SaGlpQ_like, Glycerophosphodiester phosphodiesterase domain of Staphylococcus aureus and similar proteins	NA|460aa|down_1|LS483319.1_914472_915852_-	PRK00855, PRK00855, argininosuccinate lyase; Provisional	NA|402aa|down_2|LS483319.1_915841_917047_-	PRK00509, PRK00509, argininosuccinate synthase; Provisional	NA|444aa|down_3|LS483319.1_917397_918729_+	PRK14097, pgi, glucose-6-phosphate isomerase; Provisional	NA|192aa|down_4|LS483319.1_919053_919629_+	COG0398, COG0398, Uncharacterized conserved protein [Function unknown]	NA|175aa|down_5|LS483319.1_919633_920158_+	TIGR02227, Inactive_signal_peptidase_IA	NA|192aa|down_6|LS483319.1_920173_920749_+	TIGR02227, Inactive_signal_peptidase_IA	NA|1159aa|down_7|LS483319.1_920908_924385_+	TIGR02773, ATP-dependent_helicase/deoxyribonuclease_subunit_B, helicase-exonuclease AddAB, AddB subunit	NA|1218aa|down_8|LS483319.1_924385_928039_+	TIGR02785, ATP-dependent_helicase/nuclease_subunit_A, helicase-exonuclease AddAB, AddA subunit, Firmicutes type	NA|301aa|down_9|LS483319.1_928204_929107_+	COG0179, MhpD, 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) [Secondary metabolites biosynthesis, transport, and catabolism]
GCA_900474725.1_40677_A01	LS483319	Staphylococcus aureus strain NCTC13140 genome assembly, chromosome: 1	8	1046622-1046709	7	CRISPRCasFinder	no		cas3,csa3,WYL,DinG,DEDDh	Orphan	CCCCTAACAACTAAAAGTTGTAAGG	25	0	0	NA	NA	NA	1	1	Orphan	cas3,csa3,WYL,DinG,DEDDh	NA|40aa|up_0|LS483319.1_1046498_1046618_+,NA|45aa|down_0|LS483319.1_1046718_1046853_-,NA|432aa|down_1|LS483319.1_1047004_1048300_+	NA|730aa|up_9|LS483319.1_1035076_1037266_+	PRK01213, PRK01213, phosphoribosylformylglycinamidine synthase subunit PurL	NA|495aa|up_8|LS483319.1_1037244_1038729_+	PRK07272, PRK07272, amidophosphoribosyltransferase; Provisional	NA|343aa|up_7|LS483319.1_1038721_1039750_+	PRK05385, PRK05385, phosphoribosylaminoimidazole synthetase; Provisional	NA|189aa|up_6|LS483319.1_1039752_1040319_+	COG0299, PurN, Folate-dependent phosphoribosylglycinamide formyltransferase PurN [Nucleotide transport and metabolism]	NA|493aa|up_5|LS483319.1_1040333_1041812_+	PRK00881, purH, bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional	NA|416aa|up_4|LS483319.1_1041833_1043081_+	PRK13790, PRK13790, phosphoribosylamine--glycine ligase; Provisional	NA|269aa|up_3|LS483319.1_1043345_1044152_-	COG0619, CbiQ, ABC-type cobalt transport system, permease component CbiQ and related transporters [Inorganic ion transport and metabolism]	NA|467aa|up_2|LS483319.1_1044144_1045545_-	cd03225, ABC_cobalt_CbiO_domain1, First domain of the ATP-binding cassette component of cobalt transport system	NA|192aa|up_1|LS483319.1_1045559_1046135_-	COG4721, COG4721, ABC-type cobalt transport system, predicted permease component [Inorganic ion transport and metabolism]	NA|40aa|up_0|LS483319.1_1046498_1046618_+	NA	NA|45aa|down_0|LS483319.1_1046718_1046853_-	NA	NA|432aa|down_1|LS483319.1_1047004_1048300_+	NA	NA|391aa|down_2|LS483319.1_1048724_1049897_+	COG1092, COG1092, Predicted SAM-dependent methyltransferases [General function prediction only]	NA|181aa|down_3|LS483319.1_1049950_1050493_+	pfam05128, DUF697, Domain of unknown function (DUF697)	NA|89aa|down_4|LS483319.1_1050646_1050913_+	PRK13780, PRK13780, phosphocarrier protein HPr; Provisional	NA|573aa|down_5|LS483319.1_1050915_1052634_+	COG1080, PtsA, Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]	NA|78aa|down_6|LS483319.1_1052870_1053104_-	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|LS483319.1_1053301_1054663_+	pfam01654, Cyt_bd_oxida_I, Cytochrome bd terminal oxidase subunit I	NA|340aa|down_8|LS483319.1_1054659_1055679_+	COG1294, AppB, Cytochrome bd-type quinol oxidase, subunit 2 [Energy production and conversion]	NA|221aa|down_9|LS483319.1_1055811_1056474_+	COG0569, TrkA, K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]
GCA_900474725.1_40677_A01	LS483319	Staphylococcus aureus strain NCTC13140 genome assembly, chromosome: 1	9	1990686-1990872	2	CRT	no		cas3,csa3,WYL,DinG,DEDDh	Orphan	TCTATGTTGGGGCCCCGCC	19	3	28	1990705-1990741|1990705-1990741|1990705-1990741|1990705-1990741|1990705-1990741|1990705-1990741|1990705-1990741|1990705-1990741|1990705-1990741|1990705-1990741|1990705-1990741|1990761-1990797|1990761-1990797|1990761-1990797|1990761-1990797|1990761-1990797|1990761-1990797|1990761-1990797|1990761-1990797|1990761-1990797|1990761-1990797|1990761-1990797|1990817-1990853|1990817-1990853|1990817-1990853|1990817-1990853|1990817-1990853|1990817-1990853	LS483319.1_137871-137835|LS483319.1_654010-653974|LS483319.1_773419-773455|LS483319.1_774425-774389|LS483319.1_820910-820946|LS483319.1_1686168-1686132|LS483319.1_1775280-1775316|LS483319.1_2082874-2082910|LS483319.1_1056530-1056566|LS483319.1_2628478-2628514|LS483319.1_1994673-1994709|LS483319.1_358110-358074|LS483319.1_820854-820890|LS483319.1_1030334-1030370|LS483319.1_1775338-1775374|LS483319.1_2081417-2081453|LS483319.1_1493412-1493376|LS483319.1_1686110-1686074|LS483319.1_2740668-2740704|LS483319.1_1990649-1990685|LS483319.1_2081358-2081394|LS483319.1_2906033-2906069|LS483319.1_1287557-1287593|LS483319.1_864112-864148|LS483319.1_1493470-1493434|LS483319.1_2092164-2092200|LS483319.1_2653797-2653761|LS483319.1_2906088-2906124	NA	3	3	Orphan	cas3,csa3,WYL,DinG,DEDDh	NA|76aa|up_6|LS483319.1_1983444_1983672_-,NA|66aa|down_0|LS483319.1_1991027_1991225_-,NA|78aa|down_2|LS483319.1_1993463_1993697_+,NA|62aa|down_3|LS483319.1_1994318_1994504_+,NA|169aa|down_6|LS483319.1_1996585_1997092_-	NA|45aa|up_9|LS483319.1_1980709_1980844_-	pfam05480, Staph_haemo, Staphylococcus haemolytic protein	NA|63aa|up_8|LS483319.1_1981755_1981944_-	COG2826, Tra8, Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]	NA|316aa|up_7|LS483319.1_1982192_1983140_+	cd09325, TDT_C4-dicarb_trans, C4-dicarboxylate transporters of the Tellurite-resistance/Dicarboxylate Transporter (TDT) family	NA|76aa|up_6|LS483319.1_1983444_1983672_-	NA	NA|519aa|up_5|LS483319.1_1983979_1985536_-	COG1288, COG1288, Predicted membrane protein [Function unknown]	NA|312aa|up_4|LS483319.1_1985707_1986643_-	PRK12353, PRK12353, putative amino acid kinase; Reviewed	NA|334aa|up_3|LS483319.1_1986662_1987664_-	PRK04284, PRK04284, ornithine carbamoyltransferase; Provisional	NA|242aa|up_2|LS483319.1_1988101_1988827_+	PRK13043, PRK13043, superantigen-like protein; Reviewed	NA|242aa|up_1|LS483319.1_1988921_1989647_+	PRK13349, PRK13349, superantigen-like protein; Reviewed	NA|239aa|up_0|LS483319.1_1989754_1990471_+	PRK13350, PRK13350, superantigen-like protein; Reviewed	NA|66aa|down_0|LS483319.1_1991027_1991225_-	NA	NA|320aa|down_1|LS483319.1_1992027_1992987_+	TIGR01002, synergohymenotropic_toxin, beta-channel forming cytolysin	NA|78aa|down_2|LS483319.1_1993463_1993697_+	NA	NA|62aa|down_3|LS483319.1_1994318_1994504_+	NA	NA|117aa|down_4|LS483319.1_1995325_1995676_-	pfam11546, CompInhib_SCIN, Staphylococcal complement inhibitor SCIN	NA|166aa|down_5|LS483319.1_1995829_1996327_-	pfam12199, efb-c, Extracellular fibrinogen binding protein C terminal	NA|169aa|down_6|LS483319.1_1996585_1997092_-	NA	NA|134aa|down_7|LS483319.1_1997763_1998165_+	PRK13033, PRK13033, formyl peptide receptor-like 1 inhibitory protein; Reviewed	NA|110aa|down_8|LS483319.1_1998533_1998863_-	pfam12199, efb-c, Extracellular fibrinogen binding protein C terminal	NA|168aa|down_9|LS483319.1_1999351_1999855_-	COG0622, COG0622, Predicted phosphoesterase [General function prediction only]
GCA_900474725.1_40677_A01	LS483319	Staphylococcus aureus strain NCTC13140 genome assembly, chromosome: 1	10	1994722-1994966	3	CRT	no		cas3,csa3,WYL,DinG,DEDDh	Orphan	CCCCGCCAACTTGCANNNT	19	1	1	1994911-1994947	LS483319.1_1994967-1995003	NA	4	4	Orphan	cas3,csa3,WYL,DinG,DEDDh	NA|66aa|up_3|LS483319.1_1991027_1991225_-,NA|78aa|up_1|LS483319.1_1993463_1993697_+,NA|62aa|up_0|LS483319.1_1994318_1994504_+,NA|169aa|down_2|LS483319.1_1996585_1997092_-	NA|519aa|up_9|LS483319.1_1983979_1985536_-	COG1288, COG1288, Predicted membrane protein [Function unknown]	NA|312aa|up_8|LS483319.1_1985707_1986643_-	PRK12353, PRK12353, putative amino acid kinase; Reviewed	NA|334aa|up_7|LS483319.1_1986662_1987664_-	PRK04284, PRK04284, ornithine carbamoyltransferase; Provisional	NA|242aa|up_6|LS483319.1_1988101_1988827_+	PRK13043, PRK13043, superantigen-like protein; Reviewed	NA|242aa|up_5|LS483319.1_1988921_1989647_+	PRK13349, PRK13349, superantigen-like protein; Reviewed	NA|239aa|up_4|LS483319.1_1989754_1990471_+	PRK13350, PRK13350, superantigen-like protein; Reviewed	NA|66aa|up_3|LS483319.1_1991027_1991225_-	NA	NA|320aa|up_2|LS483319.1_1992027_1992987_+	TIGR01002, synergohymenotropic_toxin, beta-channel forming cytolysin	NA|78aa|up_1|LS483319.1_1993463_1993697_+	NA	NA|62aa|up_0|LS483319.1_1994318_1994504_+	NA	NA|117aa|down_0|LS483319.1_1995325_1995676_-	pfam11546, CompInhib_SCIN, Staphylococcal complement inhibitor SCIN	NA|166aa|down_1|LS483319.1_1995829_1996327_-	pfam12199, efb-c, Extracellular fibrinogen binding protein C terminal	NA|169aa|down_2|LS483319.1_1996585_1997092_-	NA	NA|134aa|down_3|LS483319.1_1997763_1998165_+	PRK13033, PRK13033, formyl peptide receptor-like 1 inhibitory protein; Reviewed	NA|110aa|down_4|LS483319.1_1998533_1998863_-	pfam12199, efb-c, Extracellular fibrinogen binding protein C terminal	NA|168aa|down_5|LS483319.1_1999351_1999855_-	COG0622, COG0622, Predicted phosphoesterase [General function prediction only]	NA|196aa|down_6|LS483319.1_1999847_2000435_-	PRK14822, PRK14822, XTP/dITP diphosphatase	NA|267aa|down_7|LS483319.1_2000446_2001247_-	PRK00865, PRK00865, glutamate racemase; Provisional	NA|272aa|down_8|LS483319.1_2001482_2002298_-	PRK08640, sdhB, succinate dehydrogenase iron-sulfur subunit; Reviewed	NA|589aa|down_9|LS483319.1_2002297_2004064_-	PRK08641, sdhA, succinate dehydrogenase flavoprotein subunit; Reviewed
GCA_900474725.1_40677_A01	LS483319	Staphylococcus aureus strain NCTC13140 genome assembly, chromosome: 1	11	2336847-2336997	8	CRISPRCasFinder	no	csa3	cas3,csa3,WYL,DinG,DEDDh	Type I-A	AACTTTAGTTGTTAGGGGCTCTTATGCA	28	0	0	NA	NA	NA	2	2	Orphan	cas3,csa3,WYL,DinG,DEDDh	NA|77aa|up_5|LS483319.1_2331718_2331949_-,NA|364aa|up_0|LS483319.1_2335737_2336829_+,NA	NA|237aa|up_9|LS483319.1_2327328_2328039_+	PRK05819, deoD, DeoD-type purine-nucleoside phosphorylase	NA|148aa|up_8|LS483319.1_2328159_2328603_-	COG0783, Dps, DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]	NA|138aa|up_7|LS483319.1_2328802_2329216_-	COG3011, COG3011, Predicted thiol-disulfide oxidoreductase [General function    prediction only]	NA|458aa|up_6|LS483319.1_2329673_2331047_-	pfam01878, EVE, EVE domain	NA|77aa|up_5|LS483319.1_2331718_2331949_-	NA	NA|313aa|up_4|LS483319.1_2331979_2332918_-	COG1482, ManA, Phosphomannose isomerase [Carbohydrate transport and metabolism]	NA|222aa|up_3|LS483319.1_2333352_2334018_-	cd05243, SDR_a5, atypical (a) SDRs, subgroup 5	csa3|107aa|up_2|LS483319.1_2334169_2334490_+	cd00090, HTH_ARSR, Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors	NA|327aa|up_1|LS483319.1_2334491_2335472_+	COG1230, CzcD, Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]	NA|364aa|up_0|LS483319.1_2335737_2336829_+	NA	NA|68aa|down_0|LS483319.1_2337857_2338061_-	cd03768, SR_ResInv, Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain	NA|379aa|down_1|LS483319.1_2338119_2339256_-	pfam02037, SAP, SAP domain	NA|286aa|down_2|LS483319.1_2340341_2341199_-	COG0561, Cof, Predicted hydrolases of the HAD superfamily [General function prediction only]	NA|261aa|down_3|LS483319.1_2341266_2342049_-	COG1119, ModF, ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA [Inorganic ion transport and metabolism]	NA|602aa|down_4|LS483319.1_2342280_2344086_-	PRK00331, PRK00331, isomerizing glutamine--fructose-6-phosphate transaminase	NA|513aa|down_5|LS483319.1_2344766_2346305_+	COG2213, MtlA, Phosphotransferase system, mannitol-specific IIBC component [Carbohydrate transport and metabolism]	NA|711aa|down_6|LS483319.1_2346339_2348472_+	COG3711, BglG, Transcriptional antiterminator [Transcription]	NA|145aa|down_7|LS483319.1_2348483_2348918_+	COG4668, MtlA, Mannitol/fructose-specific phosphotransferase system, IIA domain [Carbohydrate transport and metabolism]	NA|369aa|down_8|LS483319.1_2348917_2350024_+	PRK02318, PRK02318, mannitol-1-phosphate 5-dehydrogenase; Provisional	NA|2479aa|down_9|LS483319.1_2350342_2357779_-	TIGR04263, cell_wall_surface_anchor_family_protein, SasC/Mrp/FmtB intercellular aggregation domain
GCA_900474725.1_40677_A01	LS483319	Staphylococcus aureus strain NCTC13140 genome assembly, chromosome: 1	12	2461011-2461204	4	CRT	no		cas3,csa3,WYL,DinG,DEDDh	Orphan	TGTTGGGGCCCCGCCAACTTGCA	23	3	12	2461034-2461066|2461034-2461066|2461034-2461066|2461034-2461066|2461034-2461066|2461090-2461125|2461090-2461125|2461090-2461125|2461149-2461181|2461149-2461181|2461149-2461181|2461149-2461181	LS483319.1_820862-820894|LS483319.1_1686102-1686070|LS483319.1_1775346-1775378|LS483319.1_2081425-2081457|LS483319.1_2740676-2740708|LS483319.1_1287562-1287597|LS483319.1_1493465-1493430|LS483319.1_2092169-2092204|LS483319.1_820862-820894|LS483319.1_1775346-1775378|LS483319.1_2081425-2081457|LS483319.1_2740676-2740708	NA	3	3	Orphan	cas3,csa3,WYL,DinG,DEDDh	NA|55aa|up_8|LS483319.1_2451538_2451703_+,NA|106aa|up_7|LS483319.1_2451947_2452265_+,NA|84aa|up_4|LS483319.1_2457389_2457641_+,NA	NA|303aa|up_9|LS483319.1_2450497_2451406_-	COG0679, COG0679, Predicted permeases [General function prediction only]	NA|55aa|up_8|LS483319.1_2451538_2451703_+	NA	NA|106aa|up_7|LS483319.1_2451947_2452265_+	NA	NA|1056aa|up_6|LS483319.1_2452451_2455619_-	COG0841, AcrB, Cation/multidrug efflux pump [Defense mechanisms]	NA|422aa|up_5|LS483319.1_2455735_2457001_-	COG2348, COG2348, Peptidoglycan interpeptide bridge formation enzyme [Cell wall/membrane/envelope biogenesis]	NA|84aa|up_4|LS483319.1_2457389_2457641_+	NA	NA|255aa|up_3|LS483319.1_2457632_2458397_-	pfam13468, Glyoxalase_3, Glyoxalase-like domain	NA|147aa|up_2|LS483319.1_2458558_2458999_+	smart00347, HTH_MARR, helix_turn_helix multiple antibiotic resistance protein	NA|404aa|up_1|LS483319.1_2458991_2460203_+	cd17489, MFS_YfcJ_like, Escherichia coli YfcJ, YhhS, and similar transporters of the Major Facilitator Superfamily	NA|117aa|up_0|LS483319.1_2460304_2460655_-	TIGR01889, Pleiotropic_Regulator_Of_Virulence, staphylococcal accessory regulator family	NA|341aa|down_0|LS483319.1_2461345_2462368_-	TIGR02666, Cyclic_pyranopterin_monophosphate_synthase, molybdenum cofactor biosynthesis protein A, bacterial	NA|200aa|down_1|LS483319.1_2462387_2462987_-	PRK00317, mobA, molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed	NA|78aa|down_2|LS483319.1_2462993_2463227_-	cd00754, Ubl_MoaD, ubiquitin-like (Ubl) domain found in molybdenum cofactor biosynthesis protein D (MoaD) and similar proteins	NA|149aa|down_3|LS483319.1_2463232_2463679_-	COG0314, MoaE, Molybdopterin converting factor, large subunit [Coenzyme metabolism]	NA|162aa|down_4|LS483319.1_2463692_2464178_-	COG1763, MobB, Molybdopterin-guanine dinucleotide biosynthesis protein [Coenzyme metabolism]	NA|420aa|down_5|LS483319.1_2464174_2465434_-	cd00887, MoeA, MoeA family	NA|169aa|down_6|LS483319.1_2465992_2466499_-	COG0521, MoaB, Molybdopterin biosynthesis enzymes [Coenzyme metabolism]	NA|335aa|down_7|LS483319.1_2466529_2467534_-	PRK07688, PRK07688, thiamine/molybdopterin biosynthesis ThiF/MoeB-like protein; Validated	NA|202aa|down_8|LS483319.1_2467703_2468309_-	COG4148, ModC, ABC-type molybdate transport system, ATPase component [Inorganic ion transport and metabolism]	NA|224aa|down_9|LS483319.1_2468309_2468981_-	COG4149, ModC, ABC-type molybdate transport system, permease component [Inorganic ion transport and metabolism]
