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_000159535.2_ASM15953v2	NC_017342	Staphylococcus aureus subsp. aureus TCH60, complete sequence	1	105603-105758	1	PILER-CR	no		cas3,WYL,csa3,DEDDh,DinG	Orphan	TTGGTGTTGGTTGTGGCGATTGCGGTTGTACATTTGGTGAAGACGG	46	0	0	NA	NA	NA	2	2	Orphan	csa3,RT,cas3,WYL,DEDDh,DinG	NA|103aa|up_9|NC_017342.1_94655_94964_+,NA|496aa|up_8|NC_017342.1_95069_96557_-,NA|40aa|up_4|NC_017342.1_100497_100617_+,NA|51aa|down_5|NC_017342.1_111514_111667_+,NA|179aa|down_7|NC_017342.1_114492_115029_+	NA|103aa|up_9|NC_017342.1_94655_94964_+	NA	NA|496aa|up_8|NC_017342.1_95069_96557_-	NA	NA|233aa|up_7|NC_017342.1_96575_97274_-	PRK13036, PRK13036, superantigen-like protein; Reviewed	NA|411aa|up_6|NC_017342.1_97656_98889_-	cd17258, RMtype1_S_Sau13435ORF2165P-TRD1-CR1_like, Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S	NA|519aa|up_5|NC_017342.1_98881_100438_-	COG0286, HsdM, Type I restriction-modification system methyltransferase subunit [Defense mechanisms]	NA|40aa|up_4|NC_017342.1_100497_100617_+	NA	NA|228aa|up_3|NC_017342.1_100699_101383_-	PRK13038, PRK13038, superantigen-like protein; Reviewed	NA|233aa|up_2|NC_017342.1_101745_102444_-	PRK13345, PRK13345, superantigen-like protein; Reviewed	NA|232aa|up_1|NC_017342.1_102783_103479_-	PRK13346, PRK13346, superantigen-like protein 7; Reviewed	NA|235aa|up_0|NC_017342.1_103925_104630_-	PRK13035, PRK13035, superantigen-like protein 5; Reviewed	NA|344aa|down_0|NC_017342.1_106314_107346_-	PRK13335, PRK13335, superantigen-like protein; Reviewed	NA|234aa|down_1|NC_017342.1_107633_108335_-	PRK13041, PRK13041, superantigen-like protein; Reviewed	NA|227aa|down_2|NC_017342.1_108617_109298_-	PRK13037, PRK13037, superantigen-like protein; Reviewed	NA|282aa|down_3|NC_017342.1_109769_110615_+	cd05269, TMR_SDR_a, triphenylmethane reductase (TMR)-like proteins, NMRa-like, atypical (a) SDRs	NA|120aa|down_4|NC_017342.1_110633_110993_+	COG3759, COG3759, Predicted membrane protein [Function unknown]	NA|51aa|down_5|NC_017342.1_111514_111667_+	NA	NA|109aa|down_6|NC_017342.1_111924_112251_+	COG2963, COG2963, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|179aa|down_7|NC_017342.1_114492_115029_+	NA	NA|514aa|down_8|NC_017342.1_115559_117101_-	PRK00074, guaA, GMP synthase; Reviewed	NA|489aa|down_9|NC_017342.1_117125_118592_-	PRK05567, PRK05567, inosine 5'-monophosphate dehydrogenase; Reviewed
GCF_000159535.2_ASM15953v2	NC_017342	Staphylococcus aureus subsp. aureus TCH60, complete sequence	2	526576-526663	1	CRISPRCasFinder	no		cas3,WYL,csa3,DEDDh,DinG	Orphan	GAAATTCTACAGGCAATGCGAGTTAGGGTG	30	0	0	NA	NA	NA	1	1	Orphan	csa3,RT,cas3,WYL,DEDDh,DinG	NA,NA|166aa|down_6|NC_017342.1_530904_531402_+,NA|64aa|down_7|NC_017342.1_532488_532680_-	NA|371aa|up_9|NC_017342.1_515411_516524_-	TIGR00611, DNA_replication_and_repair_protein_RecF, recF protein	NA|82aa|up_8|NC_017342.1_516520_516766_-	TIGR02988, YaaA_near_RecF, S4 domain protein YaaA	NA|378aa|up_7|NC_017342.1_517146_518280_-	PRK05643, PRK05643, DNA polymerase III subunit beta; Validated	NA|454aa|up_6|NC_017342.1_518557_519919_-	TIGR00362, DnaA, chromosomal replication initiator protein DnaA	NA|46aa|up_5|NC_017342.1_520649_520787_+	pfam00468, Ribosomal_L34, Ribosomal protein L34	NA|118aa|up_4|NC_017342.1_520908_521262_+	PRK00499, rnpA, ribonuclease P; Reviewed	NA|460aa|up_3|NC_017342.1_521405_522785_+	PRK05291, trmE, tRNA uridine-5-carboxymethylaminomethyl(34) synthesis GTPase MnmE	NA|626aa|up_2|NC_017342.1_522851_524729_+	PRK05192, PRK05192, tRNA uridine-5-carboxymethylaminomethyl(34) synthesis enzyme MnmG	NA|240aa|up_1|NC_017342.1_524728_525448_+	PRK00107, gidB, 16S rRNA (guanine(527)-N(7))-methyltransferase RsmG	NA|280aa|up_0|NC_017342.1_525490_526330_+	TIGR04285, parB-like_partition_protein, nucleoid occlusion protein	NA|118aa|down_0|NC_017342.1_526882_527236_+	pfam11345, DUF3147, Protein of unknown function (DUF3147)	NA|132aa|down_1|NC_017342.1_527303_527699_+	pfam11345, DUF3147, Protein of unknown function (DUF3147)	NA|190aa|down_2|NC_017342.1_527951_528521_+	cd00093, HTH_XRE, Helix-turn-helix XRE-family like proteins	NA|67aa|down_3|NC_017342.1_528647_528848_-	COG1278, CspC, Cold shock proteins [Transcription]	NA|268aa|down_4|NC_017342.1_529331_530135_+	cd07477, Peptidases_S8_Subtilisin_subset, Peptidase S8 family domain in Subtilisin proteins	NA|250aa|down_5|NC_017342.1_530153_530903_+	pfam15526, Ntox21, Novel toxin 21	NA|166aa|down_6|NC_017342.1_530904_531402_+	NA	NA|64aa|down_7|NC_017342.1_532488_532680_-	NA	NA|627aa|down_8|NC_017342.1_532771_534652_-	pfam02687, FtsX, FtsX-like permease family	NA|253aa|down_9|NC_017342.1_534641_535400_-	COG1136, SalX, ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]
GCF_000159535.2_ASM15953v2	NC_017342	Staphylococcus aureus subsp. aureus TCH60, complete sequence	3	762572-762705	2	PILER-CR	no		cas3,WYL,csa3,DEDDh,DinG	Orphan	TATTGAAGAAGATACAA	17	0	0	NA	NA	NA	2	2	Orphan	csa3,RT,cas3,WYL,DEDDh,DinG	NA|67aa|up_1|NC_017342.1_759745_759946_+,NA|34aa|up_0|NC_017342.1_759994_760096_+,NA|103aa|down_2|NC_017342.1_767825_768134_-,NA|89aa|down_3|NC_017342.1_768277_768544_-,NA|41aa|down_9|NC_017342.1_776864_776987_-	NA|426aa|up_9|NC_017342.1_749741_751019_+	cd17319, MFS_ExuT_GudP_like, Hexuronate transporter, Glucarate transporter, and similar transporters of the Major Facilitator Superfamily	NA|608aa|up_8|NC_017342.1_751495_753319_+	COG1289, COG1289, Predicted membrane protein [Function unknown]	NA|139aa|up_7|NC_017342.1_753457_753874_+	COG4876, COG4876, Uncharacterized protein conserved in bacteria [Function unknown]	NA|231aa|up_6|NC_017342.1_754104_754797_+	COG2357, COG2357, PpGpp synthetase catalytic domain [General function prediction only]	NA|244aa|up_5|NC_017342.1_754961_755693_+	cd01106, HTH_TipAL-Mta, Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA	NA|227aa|up_4|NC_017342.1_755879_756560_+	COG1802, GntR, Transcriptional regulators [Transcription]	NA|518aa|up_3|NC_017342.1_756584_758138_+	TIGR01314, gntK_FGGY, gluconate kinase, FGGY type	NA|453aa|up_2|NC_017342.1_758254_759613_+	TIGR00791, Gluconate_permease, gluconate transporter	NA|67aa|up_1|NC_017342.1_759745_759946_+	NA	NA|34aa|up_0|NC_017342.1_759994_760096_+	NA	NA|907aa|down_0|NC_017342.1_763932_766653_+	pfam10425, SdrG_C_C, C-terminus of bacterial fibrinogen-binding adhesin	NA|289aa|down_1|NC_017342.1_766832_767699_+	COG1210, GalU, UDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]	NA|103aa|down_2|NC_017342.1_767825_768134_-	NA	NA|89aa|down_3|NC_017342.1_768277_768544_-	NA	NA|546aa|down_4|NC_017342.1_768827_770465_-	cd05799, PGM2, This CD includes PGM2 (phosphoglucomutase 2) and PGM2L1 (phosphoglucomutase 2-like 1)	NA|131aa|down_5|NC_017342.1_770751_771144_+	cd03425, MutT_pyrophosphohydrolase, The MutT pyrophosphohydrolase is a prototypical Nudix hydrolase that catalyzes the hydrolysis of nucleoside and deoxynucleoside triphosphates (NTPs and dNTPs) by substitution at a beta-phosphorus to yield a nucleotide monophosphate (NMP) and inorganic pyrophosphate (PPi)	NA|954aa|down_6|NC_017342.1_771145_774007_+	COG1061, SSL2, DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]	NA|258aa|down_7|NC_017342.1_774313_775087_+	pfam04507, DUF576, Csa1 family	NA|265aa|down_8|NC_017342.1_776066_776861_+	pfam04507, DUF576, Csa1 family	NA|41aa|down_9|NC_017342.1_776864_776987_-	NA
GCF_000159535.2_ASM15953v2	NC_017342	Staphylococcus aureus subsp. aureus TCH60, complete sequence	4	766143-766350	3,2	PILER-CR,CRISPRCasFinder	no		cas3,WYL,csa3,DEDDh,DinG	Orphan	TATTGAAGAAGATACAA,GCCAACACCACCGACACCAGAGGTACCA	17,28	1	1	766300-766322	NC_017342.1_762930-762952	NA:NA	2,1	2	Orphan	csa3,RT,cas3,WYL,DEDDh,DinG	NA|67aa|up_2|NC_017342.1_759745_759946_+,NA|34aa|up_1|NC_017342.1_759994_760096_+,NA|103aa|down_1|NC_017342.1_767825_768134_-,NA|89aa|down_2|NC_017342.1_768277_768544_-,NA|41aa|down_8|NC_017342.1_776864_776987_-,NA|64aa|down_9|NC_017342.1_777421_777613_+	NA|608aa|up_9|NC_017342.1_751495_753319_+	COG1289, COG1289, Predicted membrane protein [Function unknown]	NA|139aa|up_8|NC_017342.1_753457_753874_+	COG4876, COG4876, Uncharacterized protein conserved in bacteria [Function unknown]	NA|231aa|up_7|NC_017342.1_754104_754797_+	COG2357, COG2357, PpGpp synthetase catalytic domain [General function prediction only]	NA|244aa|up_6|NC_017342.1_754961_755693_+	cd01106, HTH_TipAL-Mta, Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA	NA|227aa|up_5|NC_017342.1_755879_756560_+	COG1802, GntR, Transcriptional regulators [Transcription]	NA|518aa|up_4|NC_017342.1_756584_758138_+	TIGR01314, gntK_FGGY, gluconate kinase, FGGY type	NA|453aa|up_3|NC_017342.1_758254_759613_+	TIGR00791, Gluconate_permease, gluconate transporter	NA|67aa|up_2|NC_017342.1_759745_759946_+	NA	NA|34aa|up_1|NC_017342.1_759994_760096_+	NA	NA|1057aa|up_0|NC_017342.1_760079_763250_+	pfam10425, SdrG_C_C, C-terminus of bacterial fibrinogen-binding adhesin	NA|289aa|down_0|NC_017342.1_766832_767699_+	COG1210, GalU, UDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]	NA|103aa|down_1|NC_017342.1_767825_768134_-	NA	NA|89aa|down_2|NC_017342.1_768277_768544_-	NA	NA|546aa|down_3|NC_017342.1_768827_770465_-	cd05799, PGM2, This CD includes PGM2 (phosphoglucomutase 2) and PGM2L1 (phosphoglucomutase 2-like 1)	NA|131aa|down_4|NC_017342.1_770751_771144_+	cd03425, MutT_pyrophosphohydrolase, The MutT pyrophosphohydrolase is a prototypical Nudix hydrolase that catalyzes the hydrolysis of nucleoside and deoxynucleoside triphosphates (NTPs and dNTPs) by substitution at a beta-phosphorus to yield a nucleotide monophosphate (NMP) and inorganic pyrophosphate (PPi)	NA|954aa|down_5|NC_017342.1_771145_774007_+	COG1061, SSL2, DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]	NA|258aa|down_6|NC_017342.1_774313_775087_+	pfam04507, DUF576, Csa1 family	NA|265aa|down_7|NC_017342.1_776066_776861_+	pfam04507, DUF576, Csa1 family	NA|41aa|down_8|NC_017342.1_776864_776987_-	NA	NA|64aa|down_9|NC_017342.1_777421_777613_+	NA
GCF_000159535.2_ASM15953v2	NC_017342	Staphylococcus aureus subsp. aureus TCH60, complete sequence	5	847646-847750	3	CRISPRCasFinder	no		cas3,WYL,csa3,DEDDh,DinG	Orphan	TGCATAAGCCTTTCTAGCTCATAAAATCCGCAGAAA	36	0	0	NA	NA	NA	1	1	Orphan	csa3,RT,cas3,WYL,DEDDh,DinG	NA|35aa|up_0|NC_017342.1_847286_847391_+,NA|35aa|down_2|NC_017342.1_849921_850026_-	NA|453aa|up_9|NC_017342.1_837244_838603_+	TIGR00508, hypothetical_protein_DESPIG_00326, adenosylmethionine-8-amino-7-oxononanoate transaminase	NA|336aa|up_8|NC_017342.1_838604_839612_+	PRK06256, PRK06256, biotin synthase; Validated	NA|372aa|up_7|NC_017342.1_839589_840705_+	COG0156, BioF, 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]	NA|231aa|up_6|NC_017342.1_840715_841408_+	COG1424, BioW, Pimeloyl-CoA synthetase [Coenzyme metabolism]	NA|156aa|up_5|NC_017342.1_841418_841886_+	pfam06177, QueT, QueT transporter	NA|326aa|up_4|NC_017342.1_841937_842915_-	TIGR01002, synergohymenotropic_toxin, beta-channel forming cytolysin	NA|316aa|up_3|NC_017342.1_842916_843864_-	pfam07968, Leukocidin, Leukocidin/Hemolysin toxin family	NA|310aa|up_2|NC_017342.1_844413_845343_-	pfam07968, Leukocidin, Leukocidin/Hemolysin toxin family	NA|438aa|up_1|NC_017342.1_845878_847192_-	pfam11621, Sbi-IV, C3 binding domain 4 of IgG-bind protein SBI	NA|35aa|up_0|NC_017342.1_847286_847391_+	NA	NA|289aa|down_0|NC_017342.1_847889_848756_+	COG0053, MMT1, Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]	NA|229aa|down_1|NC_017342.1_849082_849769_+	PRK14119, gpmA, phosphoglyceromutase; Provisional	NA|35aa|down_2|NC_017342.1_849921_850026_-	NA	NA|480aa|down_3|NC_017342.1_850199_851639_+	TIGR00711, Uncharacterized_MFS-type_transporter_YhcA, drug resistance transporter, EmrB/QacA subfamily	NA|260aa|down_4|NC_017342.1_851759_852539_+	cd13711, PBP2_Ngo0372_TcyA, Substrate binding domain of ABC transporters involved in cystine import; the type 2 periplasmic binding protein fold	NA|240aa|down_5|NC_017342.1_852519_853239_+	COG0765, HisM, ABC-type amino acid transport system, permease component [Amino acid transport and metabolism]	NA|244aa|down_6|NC_017342.1_853235_853967_+	COG1126, GlnQ, ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]	NA|417aa|down_7|NC_017342.1_854063_855314_-	pfam02388, FemAB, FemAB family	NA|121aa|down_8|NC_017342.1_855568_855931_+	pfam14729, DUF4467, Domain of unknown function with cystatin-like fold (DUF4467)	NA|200aa|down_9|NC_017342.1_855949_856549_+	COG1651, DsbG, Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]
GCF_000159535.2_ASM15953v2	NC_017342	Staphylococcus aureus subsp. aureus TCH60, complete sequence	6	1039835-1039960	4	CRISPRCasFinder	no		cas3,WYL,csa3,DEDDh,DinG	Orphan	TGATATCAAGGGTTTTGTGAGCTTTCGAGTAAAGAGG	37	0	0	NA	NA	NA	1	1	Orphan	csa3,RT,cas3,WYL,DEDDh,DinG	NA,NA|61aa|down_1|NC_017342.1_1040854_1041037_+,NA|56aa|down_8|NC_017342.1_1049385_1049553_-	NA|130aa|up_9|NC_017342.1_1031306_1031696_+	PRK05309, PRK05309, 30S ribosomal protein S11; Validated	NA|315aa|up_8|NC_017342.1_1031770_1032715_+	PRK05182, PRK05182, DNA-directed RNA polymerase subunit alpha; Provisional	NA|123aa|up_7|NC_017342.1_1032731_1033100_+	PRK05591, rplQ, 50S ribosomal protein L17; Validated	NA|270aa|up_6|NC_017342.1_1033632_1034442_+	PRK13648, cbiO, cobalt transporter ATP-binding subunit; Provisional	NA|287aa|up_5|NC_017342.1_1034438_1035299_+	PRK13646, cbiO, energy-coupling factor transporter ATPase	NA|269aa|up_4|NC_017342.1_1035288_1036095_+	COG0619, CbiQ, ABC-type cobalt transport system, permease component CbiQ and related transporters [Inorganic ion transport and metabolism]	NA|265aa|up_3|NC_017342.1_1036099_1036894_+	PRK00021, truA, tRNA pseudouridine(38-40) synthase TruA	NA|146aa|up_2|NC_017342.1_1037142_1037580_+	PRK09216, rplM, 50S ribosomal protein L13; Reviewed	NA|133aa|up_1|NC_017342.1_1037593_1037992_+	PRK00132, rpsI, 30S ribosomal protein S9; Reviewed	NA|479aa|up_0|NC_017342.1_1038340_1039777_+	COG2865, COG2865, Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]	NA|60aa|down_0|NC_017342.1_1040025_1040205_+	PRK09775, PRK09775, type II toxin-antitoxin system HipA family toxin YjjJ	NA|61aa|down_1|NC_017342.1_1040854_1041037_+	NA	NA|555aa|down_2|NC_017342.1_1041506_1043171_+	PRK08617, PRK08617, acetolactate synthase AlsS	NA|235aa|down_3|NC_017342.1_1043207_1043912_+	COG3527, AlsD, Alpha-acetolactate decarboxylase [Secondary metabolites biosynthesis, transport, and catabolism]	NA|142aa|down_4|NC_017342.1_1044302_1044728_-	pfam03642, MAP, MAP domain	NA|272aa|down_5|NC_017342.1_1045022_1045838_+	cd02605, HAD_SPP, sucrose-phosphatase, similar to Synechocystis sp PCC 6803 SPP	NA|285aa|down_6|NC_017342.1_1046048_1046903_+	pfam01551, Peptidase_M23, Peptidase family M23	NA|809aa|down_7|NC_017342.1_1046962_1049389_-	cd01083, GAG_Lyase, Glycosaminoglycan (GAG) polysaccharide lyase family	NA|56aa|down_8|NC_017342.1_1049385_1049553_-	NA	NA|139aa|down_9|NC_017342.1_1049795_1050212_+	cd01109, HTH_YyaN, Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB
GCF_000159535.2_ASM15953v2	NC_017342	Staphylococcus aureus subsp. aureus TCH60, complete sequence	7	1117411-1117501	5	CRISPRCasFinder	no	csa3	cas3,WYL,csa3,DEDDh,DinG	Type I-A	AAGAAGCCCCTAACAACTAAAGTTG	25	0	0	NA	NA	NA	1	1	Orphan	csa3,RT,cas3,WYL,DEDDh,DinG	NA|53aa|up_1|NC_017342.1_1116133_1116292_-,NA|35aa|up_0|NC_017342.1_1116971_1117076_+,NA|364aa|down_0|NC_017342.1_1117517_1118609_-,NA|77aa|down_5|NC_017342.1_1122398_1122629_+	NA|452aa|up_9|NC_017342.1_1096441_1097797_+	PRK14316, glmM, phosphoglucosamine mutase; Provisional	NA|369aa|up_8|NC_017342.1_1105792_1106899_-	PRK02318, PRK02318, mannitol-1-phosphate 5-dehydrogenase; Provisional	NA|145aa|up_7|NC_017342.1_1106898_1107333_-	COG4668, MtlA, Mannitol/fructose-specific phosphotransferase system, IIA domain [Carbohydrate transport and metabolism]	NA|711aa|up_6|NC_017342.1_1107344_1109477_-	COG3711, BglG, Transcriptional antiterminator [Transcription]	NA|513aa|up_5|NC_017342.1_1109511_1111050_-	COG2213, MtlA, Phosphotransferase system, mannitol-specific IIBC component [Carbohydrate transport and metabolism]	NA|602aa|up_4|NC_017342.1_1111730_1113536_+	PRK00331, PRK00331, isomerizing glutamine--fructose-6-phosphate transaminase	NA|261aa|up_3|NC_017342.1_1113767_1114550_+	COG1119, ModF, ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA [Inorganic ion transport and metabolism]	NA|286aa|up_2|NC_017342.1_1114617_1115475_+	COG0561, Cof, Predicted hydrolases of the HAD superfamily [General function prediction only]	NA|53aa|up_1|NC_017342.1_1116133_1116292_-	NA	NA|35aa|up_0|NC_017342.1_1116971_1117076_+	NA	NA|364aa|down_0|NC_017342.1_1117517_1118609_-	NA	NA|327aa|down_1|NC_017342.1_1118874_1119855_-	COG1230, CzcD, Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]	csa3|107aa|down_2|NC_017342.1_1119856_1120177_-	cd00090, HTH_ARSR, Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors	NA|222aa|down_3|NC_017342.1_1120328_1120994_+	cd05243, SDR_a5, atypical (a) SDRs, subgroup 5	NA|313aa|down_4|NC_017342.1_1121429_1122368_+	COG1482, ManA, Phosphomannose isomerase [Carbohydrate transport and metabolism]	NA|77aa|down_5|NC_017342.1_1122398_1122629_+	NA	NA|458aa|down_6|NC_017342.1_1123301_1124675_+	pfam01878, EVE, EVE domain	NA|138aa|down_7|NC_017342.1_1125123_1125537_+	COG3011, COG3011, Predicted thiol-disulfide oxidoreductase [General function    prediction only]	NA|148aa|down_8|NC_017342.1_1125736_1126180_+	COG0783, Dps, DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]	NA|237aa|down_9|NC_017342.1_1126300_1127011_-	PRK05819, deoD, DeoD-type purine-nucleoside phosphorylase
GCF_000159535.2_ASM15953v2	NC_017342	Staphylococcus aureus subsp. aureus TCH60, complete sequence	8	1621732-1621811	6	CRISPRCasFinder	no		cas3,WYL,csa3,DEDDh,DinG	Orphan	CCCAACATAGAGAATTTCGTAAAGAA	26	0	0	NA	NA	NA	1	1	Orphan	csa3,RT,cas3,WYL,DEDDh,DinG	NA|43aa|up_8|NC_017342.1_1614290_1614419_+,NA|49aa|up_3|NC_017342.1_1617455_1617602_+,NA	NA|589aa|up_9|NC_017342.1_1612191_1613958_+	PRK00476, aspS, aspartyl-tRNA synthetase; Validated	NA|43aa|up_8|NC_017342.1_1614290_1614419_+	NA	NA|258aa|up_7|NC_017342.1_1614418_1615192_+	COG1179, COG1179, Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]	NA|425aa|up_6|NC_017342.1_1615352_1616627_-	PRK13342, PRK13342, recombination factor protein RarA; Reviewed	NA|141aa|up_5|NC_017342.1_1616711_1617134_+	COG1959, COG1959, Predicted transcriptional regulator [Transcription]	NA|61aa|up_4|NC_017342.1_1617233_1617416_+	COG3237, COG3237, Uncharacterized protein conserved in bacteria [Function unknown]	NA|49aa|up_3|NC_017342.1_1617455_1617602_+	NA	NA|338aa|up_2|NC_017342.1_1617838_1618852_-	TIGR03558, oxido_grp_1, luciferase family oxidoreductase, group 1	NA|381aa|up_1|NC_017342.1_1619161_1620304_+	COG1104, NifS, Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]	NA|373aa|up_0|NC_017342.1_1620304_1621423_+	PRK00143, mnmA, tRNA-specific 2-thiouridylase MnmA; Reviewed	NA|223aa|down_0|NC_017342.1_1622104_1622773_+	sd00006, TPR, Tetratricopeptide repeat	NA|826aa|down_1|NC_017342.1_1622774_1625252_+	TIGR01448, recD_rel, helicase, putative, RecD/TraA family	NA|877aa|down_2|NC_017342.1_1625594_1628225_+	PRK00252, alaS, alanyl-tRNA synthetase; Reviewed	NA|87aa|down_3|NC_017342.1_1628287_1628548_+	PRK05473, IreB-like, IreB family regulatory phosphoprotein	NA|143aa|down_4|NC_017342.1_1628551_1628980_+	COG0816, COG0816, Predicted endonuclease involved in recombination (possible Holliday junction resolvase in Mycoplasmas and B	NA|103aa|down_5|NC_017342.1_1628994_1629303_+	PRK13678, PRK13678, hypothetical protein; Provisional	NA|213aa|down_6|NC_017342.1_1629587_1630226_+	COG4122, COG4122, Predicted O-methyltransferase [General function prediction only]	NA|308aa|down_7|NC_017342.1_1630228_1631152_+	COG0826, COG0826, Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]	NA|423aa|down_8|NC_017342.1_1631163_1632432_+	COG0826, COG0826, Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]	NA|208aa|down_9|NC_017342.1_1632431_1633055_+	PRK05480, PRK05480, uridine/cytidine kinase; Provisional
GCF_000159535.2_ASM15953v2	NC_017342	Staphylococcus aureus subsp. aureus TCH60, complete sequence	9	2112872-2112964	7	CRISPRCasFinder	no	cas3	cas3,WYL,csa3,DEDDh,DinG	Unclear	AGTTATCAATTTATTGATTACTGTTTCTTA	30	0	0	NA	NA	NA	1	1	Unclear	csa3,RT,cas3,WYL,DEDDh,DinG	NA,NA	NA|117aa|up_9|NC_017342.1_2102435_2102786_-	PRK05338, rplS, 50S ribosomal protein L19; Provisional	NA|246aa|up_8|NC_017342.1_2102888_2103626_-	PRK00026, trmD, tRNA (guanine-N(1)-)-methyltransferase; Reviewed	NA|168aa|up_7|NC_017342.1_2103625_2104129_-	PRK00122, rimM, 16S rRNA-processing protein RimM; Provisional	NA|92aa|up_6|NC_017342.1_2104316_2104592_-	COG0228, RpsP, Ribosomal protein S16 [Translation, ribosomal structure and biogenesis]	NA|456aa|up_5|NC_017342.1_2105026_2106394_-	PRK10867, PRK10867, signal recognition particle protein; Provisional	NA|111aa|up_4|NC_017342.1_2106419_2106752_-	PRK00118, PRK00118, putative DNA-binding protein; Validated	NA|417aa|up_3|NC_017342.1_2106738_2107989_-	PRK10416, PRK10416, signal recognition particle-docking protein FtsY; Provisional	NA|1189aa|up_2|NC_017342.1_2107988_2111555_-	COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]	NA|244aa|up_1|NC_017342.1_2111701_2112433_-	PRK00102, rnc, ribonuclease III; Reviewed	NA|78aa|up_0|NC_017342.1_2112548_2112782_-	PRK00982, acpP, acyl carrier protein; Provisional	NA|245aa|down_0|NC_017342.1_2113087_2113822_-	PRK05557, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase; Validated	NA|309aa|down_1|NC_017342.1_2113814_2114741_-	COG0331, FabD, (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]	NA|329aa|down_2|NC_017342.1_2114733_2115720_-	PRK05331, PRK05331, phosphate acyltransferase PlsX	NA|191aa|down_3|NC_017342.1_2115724_2116297_-	PRK04424, PRK04424, transcription factor FapR	cas3|687aa|down_4|NC_017342.1_2116499_2118560_-	PRK10917, PRK10917, ATP-dependent DNA helicase RecG; Provisional	NA|549aa|down_5|NC_017342.1_2118749_2120396_-	COG1461, COG1461, Predicted kinase related to dihydroxyacetone kinase [General function prediction only]	NA|125aa|down_6|NC_017342.1_2120410_2120785_-	COG1302, COG1302, Uncharacterized protein conserved in bacteria [Function unknown]	NA|63aa|down_7|NC_017342.1_2121227_2121416_+	PRK00359, rpmB, 50S ribosomal protein L28; Reviewed	NA|214aa|down_8|NC_017342.1_2121796_2122438_-	COG1564, THI80, Thiamine pyrophosphokinase [Coenzyme metabolism]	NA|215aa|down_9|NC_017342.1_2122444_2123089_-	COG0036, Rpe, Pentose-5-phosphate-3-epimerase [Carbohydrate transport and metabolism]
GCF_000159535.2_ASM15953v2	NC_017342	Staphylococcus aureus subsp. aureus TCH60, complete sequence	10	2414443-2414528	8	CRISPRCasFinder	no		cas3,WYL,csa3,DEDDh,DinG	Orphan	CCAACTTGCACATTATTGTAAGCTGGCTTT	30	1	2	2414473-2414498|2414473-2414498	NC_017342.1_1162210-1162235|NC_017342.1_1224412-1224437	NA	1	1	Orphan	csa3,RT,cas3,WYL,DEDDh,DinG	NA,NA	NA|301aa|up_9|NC_017342.1_2398477_2399380_-	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|1218aa|up_8|NC_017342.1_2399545_2403199_-	TIGR02785, ATP-dependent_helicase/nuclease_subunit_A, helicase-exonuclease AddAB, AddA subunit, Firmicutes type	NA|1159aa|up_7|NC_017342.1_2403199_2406676_-	TIGR02773, ATP-dependent_helicase/deoxyribonuclease_subunit_B, helicase-exonuclease AddAB, AddB subunit	NA|192aa|up_6|NC_017342.1_2406835_2407411_-	TIGR02227, Inactive_signal_peptidase_IA	NA|175aa|up_5|NC_017342.1_2407426_2407951_-	TIGR02227, Inactive_signal_peptidase_IA	NA|192aa|up_4|NC_017342.1_2407955_2408531_-	COG0398, COG0398, Uncharacterized conserved protein [Function unknown]	NA|444aa|up_3|NC_017342.1_2408856_2410188_-	PRK14097, pgi, glucose-6-phosphate isomerase; Provisional	NA|402aa|up_2|NC_017342.1_2410538_2411744_+	PRK00509, PRK00509, argininosuccinate synthase; Provisional	NA|460aa|up_1|NC_017342.1_2411733_2413113_+	PRK00855, PRK00855, argininosuccinate lyase; Provisional	NA|310aa|up_0|NC_017342.1_2413354_2414284_+	cd08601, GDPD_SaGlpQ_like, Glycerophosphodiester phosphodiesterase domain of Staphylococcus aureus and similar proteins	NA|415aa|down_0|NC_017342.1_2414678_2415923_-	COG0334, GdhA, Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism]	NA|397aa|down_1|NC_017342.1_2416031_2417222_-	PRK04073, rocD, ornithine--oxo-acid transaminase; Provisional	NA|376aa|down_2|NC_017342.1_2417529_2418657_-	cd04735, OYE_like_4_FMN, Old yellow enzyme (OYE)-related FMN binding domain, group 4	NA|126aa|down_3|NC_017342.1_2419018_2419396_-	COG1098, VacB, Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]	NA|316aa|down_4|NC_017342.1_2419613_2420561_+	COG2826, Tra8, Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]	NA|198aa|down_5|NC_017342.1_2420885_2421479_-	cd01927, cyclophilin_WD40, cyclophilin_WD40: cyclophilin-type peptidylprolyl cis- trans isomerases (cyclophilins) having a WD40 domain	NA|128aa|down_6|NC_017342.1_2421542_2421926_+	pfam08810, KapB, Kinase associated protein B	NA|802aa|down_7|NC_017342.1_2422056_2424462_+	PRK12645, PRK12645, monovalent cation/H+ antiporter subunit A; Reviewed	NA|143aa|down_8|NC_017342.1_2424454_2424883_+	PRK12573, PRK12573, Na(+)/H(+) antiporter subunit B	NA|110aa|down_9|NC_017342.1_2424894_2425224_+	PRK08600, PRK08600, putative monovalent cation/H+ antiporter subunit C; Reviewed
GCF_000159535.2_ASM15953v2	NC_017342	Staphylococcus aureus subsp. aureus TCH60, complete sequence	11	2480902-2480981	9	CRISPRCasFinder	no		cas3,WYL,csa3,DEDDh,DinG	Orphan	GGGCCCCAACATAGAAGCTGACGG	24	0	0	NA	NA	NA	1	1	Orphan	csa3,RT,cas3,WYL,DEDDh,DinG	NA|52aa|up_9|NC_017342.1_2472970_2473126_-,NA	NA|52aa|up_9|NC_017342.1_2472970_2473126_-	NA	NA|91aa|up_8|NC_017342.1_2473137_2473410_-	pfam13545, HTH_Crp_2, Crp-like helix-turn-helix domain	NA|74aa|up_7|NC_017342.1_2473410_2473632_-	COG1476, COG1476, Predicted transcriptional regulators [Transcription]	NA|463aa|up_6|NC_017342.1_2474401_2475790_+	pfam02037, SAP, SAP domain	NA|407aa|up_5|NC_017342.1_2475803_2477024_+	cd01189, INT_ICEBs1_C_like, C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons	NA|274aa|up_4|NC_017342.1_2477166_2477988_-	COG1464, NlpA, ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]	NA|232aa|up_3|NC_017342.1_2478005_2478701_-	COG2011, AbcD, ABC-type metal ion transport system, permease component [Inorganic ion transport and metabolism]	NA|342aa|up_2|NC_017342.1_2478693_2479719_-	COG1135, AbcC, ABC-type metal ion transport system, ATPase component [Inorganic ion transport and metabolism]	NA|99aa|up_1|NC_017342.1_2479968_2480265_-	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|129aa|up_0|NC_017342.1_2480257_2480644_-	COG1658, COG1658, Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]	NA|293aa|down_0|NC_017342.1_2481234_2482113_-	COG3878, COG3878, Uncharacterized protein conserved in bacteria [Function unknown]	NA|127aa|down_1|NC_017342.1_2482290_2482671_-	PRK01202, PRK01202, glycine cleavage system protein GcvH	NA|119aa|down_2|NC_017342.1_2482828_2483185_-	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|107aa|down_3|NC_017342.1_2483328_2483649_+	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|180aa|down_4|NC_017342.1_2483798_2484338_-	cd02135, YdjA-like, nitroreductase family protein similar to Escherichia coli YdjA	NA|239aa|down_5|NC_017342.1_2484420_2485137_-	PRK13575, PRK13575, type I 3-dehydroquinate dehydratase	NA|141aa|down_6|NC_017342.1_2485284_2485707_+	TIGR03561, organ_hyd_perox, peroxiredoxin, Ohr subfamily	NA|165aa|down_7|NC_017342.1_2486105_2486600_+	pfam13420, Acetyltransf_4, Acetyltransferase (GNAT) domain	NA|206aa|down_8|NC_017342.1_2486756_2487374_+	COG1279, COG1279, Lysine efflux permease [General function prediction only]	NA|187aa|down_9|NC_017342.1_2487446_2488007_-	COG0406, phoE, Broad specificity phosphatase PhoE and related phosphatases [General function prediction only]
GCF_000159535.2_ASM15953v2	NC_017342	Staphylococcus aureus subsp. aureus TCH60, complete sequence	12	2539199-2539283	10	CRISPRCasFinder	no	cas3	cas3,WYL,csa3,DEDDh,DinG	Unclear	TTCTACAGGCAATGCAAGTTGGGGTG	26	1	2	2539225-2539257|2539225-2539257	NC_017342.1_967250-967218|NC_017342.1_2288351-2288383	NA	1	1	Unclear	csa3,RT,cas3,WYL,DEDDh,DinG	NA,NA|33aa|down_1|NC_017342.1_2540743_2540842_-	NA|304aa|up_9|NC_017342.1_2524674_2525586_-	COG1660, COG1660, Predicted P-loop-containing kinase [General function prediction only]	NA|312aa|up_8|NC_017342.1_2526353_2527289_-	TIGR01292, Thioredoxin_reductase, thioredoxin-disulfide reductase	NA|480aa|up_7|NC_017342.1_2527355_2528795_-	sd00008, TPR_YbbN, C-terminal Tetratricopeptide repeat (TPR) region of YbbN and similar motifs	NA|162aa|up_6|NC_017342.1_2528802_2529288_-	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|281aa|up_5|NC_017342.1_2529295_2530138_-	PRK12437, PRK12437, prolipoprotein diacylglyceryl transferase; Reviewed	NA|949aa|up_4|NC_017342.1_2531685_2534532_-	PRK00349, uvrA, excinuclease ABC subunit UvrA	NA|662aa|up_3|NC_017342.1_2534539_2536525_-	PRK05298, PRK05298, excinuclease ABC subunit UvrB	NA|79aa|up_2|NC_017342.1_2536793_2537030_-	COG4897, CsbA, Uncharacterized protein conserved in bacteria [Function unknown]	NA|217aa|up_1|NC_017342.1_2537026_2537677_-	pfam12917, HD_2, HD containing hydrolase-like enzyme	NA|280aa|up_0|NC_017342.1_2537850_2538690_-	COG3942, COG3942, Surface antigen [General function prediction only]	NA|370aa|down_0|NC_017342.1_2539458_2540569_-	PRK00578, prfB, peptide chain release factor 2; Validated	NA|33aa|down_1|NC_017342.1_2540743_2540842_-	NA	NA|844aa|down_2|NC_017342.1_2540883_2543415_-	PRK12904, PRK12904, preprotein translocase subunit SecA; Reviewed	NA|191aa|down_3|NC_017342.1_2543828_2544401_-	COG1544, COG1544, Ribosome-associated protein Y (PSrp-1) [Translation, ribosomal structure and biogenesis]	NA|225aa|down_4|NC_017342.1_2544461_2545136_-	COG1040, ComFC, Predicted amidophosphoribosyltransferases [General function prediction only]	cas3|361aa|down_5|NC_017342.1_2545128_2546211_-	COG4098, comFA, Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [DNA replication, recombination, and repair]	NA|289aa|down_6|NC_017342.1_2546574_2547441_-	TIGR00762, DegV, EDD domain protein, DegV family	NA|352aa|down_7|NC_017342.1_2548388_2549444_-	cd06853, GT_WecA_like, This subfamily contains Escherichia coli WecA, Bacillus subtilis TagO and related proteins	NA|357aa|down_8|NC_017342.1_2549761_2550832_+	cd01949, GGDEF, Diguanylate-cyclase (DGC) or GGDEF domain	NA|254aa|down_9|NC_017342.1_2551027_2551789_+	COG2966, COG2966, Uncharacterized conserved protein [Function unknown]
GCF_000159535.2_ASM15953v2	NC_017342	Staphylococcus aureus subsp. aureus TCH60, complete sequence	13	2691580-2691672	11	CRISPRCasFinder	no		cas3,WYL,csa3,DEDDh,DinG	Orphan	TAGCATCCAACTGCGTTCCTCTTCACCTTTAG	32	0	0	NA	NA	NA	1	1	Orphan	csa3,RT,cas3,WYL,DEDDh,DinG	NA|239aa|up_5|NC_017342.1_2686375_2687092_-,NA|169aa|up_4|NC_017342.1_2687253_2687760_-,NA	NA|75aa|up_9|NC_017342.1_2682502_2682727_+	pfam11148, DUF2922, Protein of unknown function (DUF2922)	NA|310aa|up_8|NC_017342.1_2682919_2683849_+	COG3238, COG3238, Uncharacterized protein conserved in bacteria [Function unknown]	NA|125aa|up_7|NC_017342.1_2684795_2685170_+	TIGR01889, Pleiotropic_Regulator_Of_Virulence, staphylococcal accessory regulator family	NA|263aa|up_6|NC_017342.1_2685420_2686209_-	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|239aa|up_5|NC_017342.1_2686375_2687092_-	NA	NA|169aa|up_4|NC_017342.1_2687253_2687760_-	NA	NA|267aa|up_3|NC_017342.1_2687895_2688696_-	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|240aa|up_2|NC_017342.1_2688679_2689399_-	COG1011, COG1011, Predicted hydrolase (HAD superfamily) [General function prediction only]	NA|317aa|up_1|NC_017342.1_2689453_2690404_-	pfam01032, FecCD, FecCD transport family	NA|276aa|up_0|NC_017342.1_2690553_2691381_-	cd01143, YvrC, Periplasmic binding protein YvrC	NA|212aa|down_0|NC_017342.1_2691820_2692456_-	COG2231, COG2231, Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]	NA|554aa|down_1|NC_017342.1_2692863_2694525_-	PRK01611, argS, arginyl-tRNA synthetase; Reviewed	NA|128aa|down_2|NC_017342.1_2694521_2694905_-	COG4506, COG4506, Uncharacterized protein conserved in bacteria [Function unknown]	NA|337aa|down_3|NC_017342.1_2695213_2696224_-	PRK09422, PRK09422, ethanol-active dehydrogenase/acetaldehyde-active reductase; Provisional	NA|174aa|down_4|NC_017342.1_2696721_2697243_-	pfam08741, YwhD, YwhD family	NA|432aa|down_5|NC_017342.1_2697270_2698566_-	COG1078, COG1078, HD superfamily phosphohydrolases [General function prediction only]	NA|159aa|down_6|NC_017342.1_2698605_2699082_-	pfam00583, Acetyltransf_1, Acetyltransferase (GNAT) family	NA|179aa|down_7|NC_017342.1_2699250_2699787_-	COG0655, WrbA, Multimeric flavodoxin WrbA [General function prediction only]	NA|313aa|down_8|NC_017342.1_2699996_2700935_-	cd19083, AKR_AKR11A1_11D1, AKR11A and  AKR11D families of aldo-keto reductase (AKR)	NA|210aa|down_9|NC_017342.1_2701387_2702017_-	pfam04276, DUF443, Protein of unknown function (DUF443)
