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_009912735.1_ASM991273v1	NZ_CP047839	Staphylococcus aureus strain UP_678 chromosome, complete genome	1	864036-864128	1	CRISPRCasFinder	no	cas3	DEDDh,csa3,cas3,DinG,WYL	Unclear	AGTTATCAATTTATTGATTACTGTTTCTTA	30	0	0	NA	NA	NA	1	1	Unclear	DEDDh,csa3,cas3,DinG,WYL,RT	NA,NA	NA|117aa|up_9|NZ_CP047839.1_853599_853950_-	PRK05338, rplS, 50S ribosomal protein L19; Provisional	NA|246aa|up_8|NZ_CP047839.1_854052_854790_-	PRK00026, trmD, tRNA (guanine-N(1)-)-methyltransferase; Reviewed	NA|168aa|up_7|NZ_CP047839.1_854789_855293_-	PRK00122, rimM, 16S rRNA-processing protein RimM; Provisional	NA|92aa|up_6|NZ_CP047839.1_855480_855756_-	COG0228, RpsP, Ribosomal protein S16 [Translation, ribosomal structure and biogenesis]	NA|456aa|up_5|NZ_CP047839.1_856190_857558_-	PRK10867, PRK10867, signal recognition particle protein; Provisional	NA|111aa|up_4|NZ_CP047839.1_857583_857916_-	PRK00118, PRK00118, putative DNA-binding protein; Validated	NA|417aa|up_3|NZ_CP047839.1_857902_859153_-	PRK10416, PRK10416, signal recognition particle-docking protein FtsY; Provisional	NA|1189aa|up_2|NZ_CP047839.1_859152_862719_-	COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]	NA|244aa|up_1|NZ_CP047839.1_862865_863597_-	PRK00102, rnc, ribonuclease III; Reviewed	NA|78aa|up_0|NZ_CP047839.1_863712_863946_-	PRK00982, acpP, acyl carrier protein; Provisional	NA|245aa|down_0|NZ_CP047839.1_864251_864986_-	PRK05557, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase; Validated	NA|309aa|down_1|NZ_CP047839.1_864978_865905_-	COG0331, FabD, (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]	NA|329aa|down_2|NZ_CP047839.1_865897_866884_-	PRK05331, PRK05331, phosphate acyltransferase PlsX	NA|191aa|down_3|NZ_CP047839.1_866888_867461_-	PRK04424, PRK04424, transcription factor FapR	cas3|687aa|down_4|NZ_CP047839.1_867663_869724_-	PRK10917, PRK10917, ATP-dependent DNA helicase RecG; Provisional	NA|549aa|down_5|NZ_CP047839.1_869913_871560_-	COG1461, COG1461, Predicted kinase related to dihydroxyacetone kinase [General function prediction only]	NA|125aa|down_6|NZ_CP047839.1_871574_871949_-	COG1302, COG1302, Uncharacterized protein conserved in bacteria [Function unknown]	NA|63aa|down_7|NZ_CP047839.1_872391_872580_+	PRK00359, rpmB, 50S ribosomal protein L28; Reviewed	NA|214aa|down_8|NZ_CP047839.1_872960_873602_-	COG1564, THI80, Thiamine pyrophosphokinase [Coenzyme metabolism]	NA|215aa|down_9|NZ_CP047839.1_873608_874253_-	COG0036, Rpe, Pentose-5-phosphate-3-epimerase [Carbohydrate transport and metabolism]
GCF_009912735.1_ASM991273v1	NZ_CP047839	Staphylococcus aureus strain UP_678 chromosome, complete genome	2	1164986-1165071	2	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG,WYL	Orphan	CCAACTTGCACATTATTGTAAGCTGGCTTT	30	1	2	1165016-1165041|1165016-1165041	NZ_CP047839.1_2688747-2688772|NZ_CP047839.1_2748832-2748857	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL,RT	NA,NA	NA|301aa|up_9|NZ_CP047839.1_1149020_1149923_-	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|NZ_CP047839.1_1150088_1153742_-	TIGR02785, ATP-dependent_helicase/nuclease_subunit_A, helicase-exonuclease AddAB, AddA subunit, Firmicutes type	NA|1159aa|up_7|NZ_CP047839.1_1153742_1157219_-	TIGR02773, ATP-dependent_helicase/deoxyribonuclease_subunit_B, helicase-exonuclease AddAB, AddB subunit	NA|192aa|up_6|NZ_CP047839.1_1157378_1157954_-	TIGR02227, Inactive_signal_peptidase_IA	NA|175aa|up_5|NZ_CP047839.1_1157969_1158494_-	TIGR02227, Inactive_signal_peptidase_IA	NA|192aa|up_4|NZ_CP047839.1_1158498_1159074_-	COG0398, COG0398, Uncharacterized conserved protein [Function unknown]	NA|444aa|up_3|NZ_CP047839.1_1159399_1160731_-	PRK14097, pgi, glucose-6-phosphate isomerase; Provisional	NA|402aa|up_2|NZ_CP047839.1_1161081_1162287_+	PRK00509, PRK00509, argininosuccinate synthase; Provisional	NA|460aa|up_1|NZ_CP047839.1_1162276_1163656_+	PRK00855, PRK00855, argininosuccinate lyase; Provisional	NA|310aa|up_0|NZ_CP047839.1_1163897_1164827_+	cd08601, GDPD_SaGlpQ_like, Glycerophosphodiester phosphodiesterase domain of Staphylococcus aureus and similar proteins	NA|415aa|down_0|NZ_CP047839.1_1165221_1166466_-	COG0334, GdhA, Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism]	NA|397aa|down_1|NZ_CP047839.1_1166574_1167765_-	PRK04073, rocD, ornithine--oxo-acid transaminase; Provisional	NA|376aa|down_2|NZ_CP047839.1_1168072_1169200_-	cd04735, OYE_like_4_FMN, Old yellow enzyme (OYE)-related FMN binding domain, group 4	NA|126aa|down_3|NZ_CP047839.1_1169561_1169939_-	COG1098, VacB, Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]	NA|198aa|down_4|NZ_CP047839.1_1170353_1170947_-	cd01927, cyclophilin_WD40, cyclophilin_WD40: cyclophilin-type peptidylprolyl cis- trans isomerases (cyclophilins) having a WD40 domain	NA|128aa|down_5|NZ_CP047839.1_1171010_1171394_+	pfam08810, KapB, Kinase associated protein B	NA|802aa|down_6|NZ_CP047839.1_1171524_1173930_+	PRK12645, PRK12645, monovalent cation/H+ antiporter subunit A; Reviewed	NA|143aa|down_7|NZ_CP047839.1_1173922_1174351_+	PRK12573, PRK12573, Na(+)/H(+) antiporter subunit B	NA|110aa|down_8|NZ_CP047839.1_1174362_1174692_+	PRK08600, PRK08600, putative monovalent cation/H+ antiporter subunit C; Reviewed	NA|499aa|down_9|NZ_CP047839.1_1174684_1176181_+	PRK07691, PRK07691, putative monovalent cation/H+ antiporter subunit D; Reviewed
GCF_009912735.1_ASM991273v1	NZ_CP047839	Staphylococcus aureus strain UP_678 chromosome, complete genome	3	1213884-1213963	3	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG,WYL	Orphan	GGGCCCCAACATAGAAGCTGACGG	24	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL,RT	NA,NA	NA|414aa|up_9|NZ_CP047839.1_1204433_1205675_-	TIGR01979, Probable_cysteine_desulfurase, cysteine desulfurases, SufSfamily	NA|436aa|up_8|NZ_CP047839.1_1205789_1207097_-	COG0719, SufB, Cysteine desulfurase activator SufB [Posttranslational modification, protein turnover, chaperones]	NA|254aa|up_7|NZ_CP047839.1_1207194_1207956_-	COG0396, sufC, Cysteine desulfurase activator ATPase [Posttranslational modification, protein turnover, chaperones]	NA|284aa|up_6|NZ_CP047839.1_1208283_1209135_+	COG2035, COG2035, Predicted membrane protein [Function unknown]	NA|65aa|up_5|NZ_CP047839.1_1209368_1209563_-	COG3237, COG3237, Uncharacterized protein conserved in bacteria [Function unknown]	NA|274aa|up_4|NZ_CP047839.1_1210148_1210970_-	COG1464, NlpA, ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]	NA|232aa|up_3|NZ_CP047839.1_1210987_1211683_-	COG2011, AbcD, ABC-type metal ion transport system, permease component [Inorganic ion transport and metabolism]	NA|342aa|up_2|NZ_CP047839.1_1211675_1212701_-	COG1135, AbcC, ABC-type metal ion transport system, ATPase component [Inorganic ion transport and metabolism]	NA|99aa|up_1|NZ_CP047839.1_1212950_1213247_-	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|NZ_CP047839.1_1213239_1213626_-	COG1658, COG1658, Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]	NA|293aa|down_0|NZ_CP047839.1_1214216_1215095_-	COG3878, COG3878, Uncharacterized protein conserved in bacteria [Function unknown]	NA|127aa|down_1|NZ_CP047839.1_1215272_1215653_-	PRK01202, PRK01202, glycine cleavage system protein GcvH	NA|119aa|down_2|NZ_CP047839.1_1215810_1216167_-	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|NZ_CP047839.1_1216310_1216631_+	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|NZ_CP047839.1_1216780_1217320_-	cd02135, YdjA-like, nitroreductase family protein similar to Escherichia coli YdjA	NA|239aa|down_5|NZ_CP047839.1_1217402_1218119_-	PRK13575, PRK13575, type I 3-dehydroquinate dehydratase	NA|141aa|down_6|NZ_CP047839.1_1218266_1218689_+	TIGR03561, organ_hyd_perox, peroxiredoxin, Ohr subfamily	NA|165aa|down_7|NZ_CP047839.1_1219087_1219582_+	pfam13420, Acetyltransf_4, Acetyltransferase (GNAT) domain	NA|206aa|down_8|NZ_CP047839.1_1219737_1220355_+	COG1279, COG1279, Lysine efflux permease [General function prediction only]	NA|187aa|down_9|NZ_CP047839.1_1220427_1220988_-	COG0406, phoE, Broad specificity phosphatase PhoE and related phosphatases [General function prediction only]
GCF_009912735.1_ASM991273v1	NZ_CP047839	Staphylococcus aureus strain UP_678 chromosome, complete genome	4	1287144-1287228	4	CRISPRCasFinder	no	cas3	DEDDh,csa3,cas3,DinG,WYL	Unclear	TTCTACAGGCAATGCAAGTTGGGGTG	26	1	1	1287170-1287202	NZ_CP047839.1_2493770-2493738	NA	1	1	Unclear	DEDDh,csa3,cas3,DinG,WYL,RT	NA,NA	NA|312aa|up_9|NZ_CP047839.1_1274297_1275233_-	TIGR01292, Thioredoxin_reductase, thioredoxin-disulfide reductase	NA|480aa|up_8|NZ_CP047839.1_1275299_1276739_-	sd00008, TPR_YbbN, C-terminal Tetratricopeptide repeat (TPR) region of YbbN and similar motifs	NA|162aa|up_7|NZ_CP047839.1_1276746_1277232_-	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_6|NZ_CP047839.1_1277239_1278082_-	PRK12437, PRK12437, prolipoprotein diacylglyceryl transferase; Reviewed	NA|311aa|up_5|NZ_CP047839.1_1278087_1279020_-	PRK05428, PRK05428, HPr kinase/phosphorylase; Provisional	NA|949aa|up_4|NZ_CP047839.1_1279630_1282477_-	PRK00349, uvrA, excinuclease ABC subunit UvrA	NA|662aa|up_3|NZ_CP047839.1_1282484_1284470_-	PRK05298, PRK05298, excinuclease ABC subunit UvrB	NA|79aa|up_2|NZ_CP047839.1_1284738_1284975_-	COG4897, CsbA, Uncharacterized protein conserved in bacteria [Function unknown]	NA|217aa|up_1|NZ_CP047839.1_1284971_1285622_-	pfam12917, HD_2, HD containing hydrolase-like enzyme	NA|280aa|up_0|NZ_CP047839.1_1285795_1286635_-	COG3942, COG3942, Surface antigen [General function prediction only]	NA|370aa|down_0|NZ_CP047839.1_1287403_1288514_-	PRK00578, prfB, peptide chain release factor 2; Validated	NA|844aa|down_1|NZ_CP047839.1_1288829_1291361_-	PRK12904, PRK12904, preprotein translocase subunit SecA; Reviewed	NA|191aa|down_2|NZ_CP047839.1_1291774_1292347_-	COG1544, COG1544, Ribosome-associated protein Y (PSrp-1) [Translation, ribosomal structure and biogenesis]	NA|225aa|down_3|NZ_CP047839.1_1292407_1293082_-	COG1040, ComFC, Predicted amidophosphoribosyltransferases [General function prediction only]	cas3|361aa|down_4|NZ_CP047839.1_1293074_1294157_-	COG4098, comFA, Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [DNA replication, recombination, and repair]	NA|289aa|down_5|NZ_CP047839.1_1294520_1295387_-	TIGR00762, DegV, EDD domain protein, DegV family	NA|214aa|down_6|NZ_CP047839.1_1295530_1296172_+	COG1739, COG1739, Uncharacterized conserved protein [Function unknown]	NA|352aa|down_7|NZ_CP047839.1_1296335_1297391_-	cd06853, GT_WecA_like, This subfamily contains Escherichia coli WecA, Bacillus subtilis TagO and related proteins	NA|357aa|down_8|NZ_CP047839.1_1297708_1298779_+	cd01949, GGDEF, Diguanylate-cyclase (DGC) or GGDEF domain	NA|254aa|down_9|NZ_CP047839.1_1298974_1299736_+	COG2966, COG2966, Uncharacterized conserved protein [Function unknown]
GCF_009912735.1_ASM991273v1	NZ_CP047839	Staphylococcus aureus strain UP_678 chromosome, complete genome	5	1374864-1374963	5	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG,WYL	Orphan	CCCCTTTTAATTTATTAATTAGGGGCTCTT	30	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL,RT	NA|100aa|up_6|NZ_CP047839.1_1368965_1369265_-,NA|130aa|up_5|NZ_CP047839.1_1369402_1369792_-,NA|230aa|up_3|NZ_CP047839.1_1370428_1371118_+,NA|39aa|down_2|NZ_CP047839.1_1376902_1377019_-	NA|153aa|up_9|NZ_CP047839.1_1367222_1367681_+	PRK00124, PRK00124, YaiI/YqxD family protein	NA|189aa|up_8|NZ_CP047839.1_1367682_1368249_+	COG1611, COG1611, Predicted Rossmann fold nucleotide-binding protein [General function prediction only]	NA|181aa|up_7|NZ_CP047839.1_1368343_1368886_-	pfam13302, Acetyltransf_3, Acetyltransferase (GNAT) domain	NA|100aa|up_6|NZ_CP047839.1_1368965_1369265_-	NA	NA|130aa|up_5|NZ_CP047839.1_1369402_1369792_-	NA	NA|148aa|up_4|NZ_CP047839.1_1369858_1370302_-	pfam00583, Acetyltransf_1, Acetyltransferase (GNAT) family	NA|230aa|up_3|NZ_CP047839.1_1370428_1371118_+	NA	NA|549aa|up_2|NZ_CP047839.1_1371272_1372919_-	COG3666, COG3666, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|156aa|up_1|NZ_CP047839.1_1373161_1373629_-	COG2839, COG2839, Uncharacterized protein conserved in bacteria [Function unknown]	NA|407aa|up_0|NZ_CP047839.1_1373625_1374846_-	cd17471, MFS_Set, Sugar efflux transporter (Set) family of the Major Facilitator Superfamily of transporters	NA|289aa|down_0|NZ_CP047839.1_1375135_1376002_-	COG0583, LysR, Transcriptional regulator [Transcription]	NA|215aa|down_1|NZ_CP047839.1_1376118_1376763_-	COG2306, COG2306, Predicted RNA-binding protein, associated with RNAses E/G family [General function prediction only]	NA|39aa|down_2|NZ_CP047839.1_1376902_1377019_-	NA	NA|158aa|down_3|NZ_CP047839.1_1377110_1377584_-	COG3542, COG3542, Uncharacterized conserved protein [Function unknown]	NA|239aa|down_4|NZ_CP047839.1_1377583_1378300_-	PRK12378, PRK12378, YebC/PmpR family DNA-binding transcriptional regulator	NA|120aa|down_5|NZ_CP047839.1_1378489_1378849_-	TIGR01889, Pleiotropic_Regulator_Of_Virulence, staphylococcal accessory regulator family	NA|717aa|down_6|NZ_CP047839.1_1378994_1381145_-	smart00342, HTH_ARAC, helix_turn_helix, arabinose operon control protein	NA|215aa|down_7|NZ_CP047839.1_1381826_1382471_-	COG0670, COG0670, Integral membrane protein, interacts with FtsH [General function prediction only]	NA|266aa|down_8|NZ_CP047839.1_1382831_1383629_+	COG3942, COG3942, Surface antigen [General function prediction only]	NA|336aa|down_9|NZ_CP047839.1_1384215_1385223_-	pfam01384, PHO4, Phosphate transporter family
GCF_009912735.1_ASM991273v1	NZ_CP047839	Staphylococcus aureus strain UP_678 chromosome, complete genome	6	1439595-1439687	6	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG,WYL	Orphan	TAGCATCCAACTGCGTTCCTCTTCACCTTTAG	32	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL,RT	NA|239aa|up_5|NZ_CP047839.1_1434390_1435107_-,NA|169aa|up_4|NZ_CP047839.1_1435268_1435775_-,NA|90aa|down_9|NZ_CP047839.1_1450655_1450925_-	NA|75aa|up_9|NZ_CP047839.1_1430515_1430740_+	pfam11148, DUF2922, Protein of unknown function (DUF2922)	NA|310aa|up_8|NZ_CP047839.1_1430932_1431862_+	COG3238, COG3238, Uncharacterized protein conserved in bacteria [Function unknown]	NA|125aa|up_7|NZ_CP047839.1_1432809_1433184_+	TIGR01889, Pleiotropic_Regulator_Of_Virulence, staphylococcal accessory regulator family	NA|263aa|up_6|NZ_CP047839.1_1433433_1434222_-	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|239aa|up_5|NZ_CP047839.1_1434390_1435107_-	NA	NA|169aa|up_4|NZ_CP047839.1_1435268_1435775_-	NA	NA|267aa|up_3|NZ_CP047839.1_1435910_1436711_-	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|240aa|up_2|NZ_CP047839.1_1436694_1437414_-	COG1011, COG1011, Predicted hydrolase (HAD superfamily) [General function prediction only]	NA|317aa|up_1|NZ_CP047839.1_1437468_1438419_-	pfam01032, FecCD, FecCD transport family	NA|276aa|up_0|NZ_CP047839.1_1438568_1439396_-	cd01143, YvrC, Periplasmic binding protein YvrC	NA|212aa|down_0|NZ_CP047839.1_1439835_1440471_-	COG2231, COG2231, Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]	NA|554aa|down_1|NZ_CP047839.1_1440739_1442401_-	PRK01611, argS, arginyl-tRNA synthetase; Reviewed	NA|128aa|down_2|NZ_CP047839.1_1442397_1442781_-	COG4506, COG4506, Uncharacterized protein conserved in bacteria [Function unknown]	NA|337aa|down_3|NZ_CP047839.1_1443089_1444100_-	PRK09422, PRK09422, ethanol-active dehydrogenase/acetaldehyde-active reductase; Provisional	NA|174aa|down_4|NZ_CP047839.1_1444598_1445120_-	pfam08741, YwhD, YwhD family	NA|432aa|down_5|NZ_CP047839.1_1445147_1446443_-	COG1078, COG1078, HD superfamily phosphohydrolases [General function prediction only]	NA|159aa|down_6|NZ_CP047839.1_1446482_1446959_-	pfam00583, Acetyltransf_1, Acetyltransferase (GNAT) family	NA|313aa|down_7|NZ_CP047839.1_1447873_1448812_-	cd19083, AKR_AKR11A1_11D1, AKR11A and  AKR11D families of aldo-keto reductase (AKR)	NA|210aa|down_8|NZ_CP047839.1_1449264_1449894_-	pfam04276, DUF443, Protein of unknown function (DUF443)	NA|90aa|down_9|NZ_CP047839.1_1450655_1450925_-	NA
GCF_009912735.1_ASM991273v1	NZ_CP047839	Staphylococcus aureus strain UP_678 chromosome, complete genome	7	2055181-2055268	7	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG,WYL	Orphan	GAAATTCTACAGGCAATGCGAGTTAGGGTG	30	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL,RT	NA,NA|166aa|down_6|NZ_CP047839.1_2059509_2060007_+,NA|64aa|down_7|NZ_CP047839.1_2061093_2061285_-	NA|371aa|up_9|NZ_CP047839.1_2044017_2045130_-	TIGR00611, DNA_replication_and_repair_protein_RecF, recF protein	NA|82aa|up_8|NZ_CP047839.1_2045126_2045372_-	TIGR02988, YaaA_near_RecF, S4 domain protein YaaA	NA|378aa|up_7|NZ_CP047839.1_2045752_2046886_-	PRK05643, PRK05643, DNA polymerase III subunit beta; Validated	NA|454aa|up_6|NZ_CP047839.1_2047163_2048525_-	TIGR00362, DnaA, chromosomal replication initiator protein DnaA	NA|46aa|up_5|NZ_CP047839.1_2049255_2049393_+	pfam00468, Ribosomal_L34, Ribosomal protein L34	NA|118aa|up_4|NZ_CP047839.1_2049513_2049867_+	PRK00499, rnpA, ribonuclease P; Reviewed	NA|460aa|up_3|NZ_CP047839.1_2050010_2051390_+	PRK05291, trmE, tRNA uridine-5-carboxymethylaminomethyl(34) synthesis GTPase MnmE	NA|626aa|up_2|NZ_CP047839.1_2051456_2053334_+	PRK05192, PRK05192, tRNA uridine-5-carboxymethylaminomethyl(34) synthesis enzyme MnmG	NA|240aa|up_1|NZ_CP047839.1_2053333_2054053_+	PRK00107, gidB, 16S rRNA (guanine(527)-N(7))-methyltransferase RsmG	NA|280aa|up_0|NZ_CP047839.1_2054095_2054935_+	TIGR04285, parB-like_partition_protein, nucleoid occlusion protein	NA|118aa|down_0|NZ_CP047839.1_2055487_2055841_+	pfam11345, DUF3147, Protein of unknown function (DUF3147)	NA|132aa|down_1|NZ_CP047839.1_2055908_2056304_+	pfam11345, DUF3147, Protein of unknown function (DUF3147)	NA|190aa|down_2|NZ_CP047839.1_2056556_2057126_+	cd00093, HTH_XRE, Helix-turn-helix XRE-family like proteins	NA|67aa|down_3|NZ_CP047839.1_2057252_2057453_-	COG1278, CspC, Cold shock proteins [Transcription]	NA|268aa|down_4|NZ_CP047839.1_2057936_2058740_+	cd07477, Peptidases_S8_Subtilisin_subset, Peptidase S8 family domain in Subtilisin proteins	NA|250aa|down_5|NZ_CP047839.1_2058758_2059508_+	pfam15526, Ntox21, Novel toxin 21	NA|166aa|down_6|NZ_CP047839.1_2059509_2060007_+	NA	NA|64aa|down_7|NZ_CP047839.1_2061093_2061285_-	NA	NA|627aa|down_8|NZ_CP047839.1_2061376_2063257_-	pfam02687, FtsX, FtsX-like permease family	NA|253aa|down_9|NZ_CP047839.1_2063246_2064005_-	COG1136, SalX, ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]
GCF_009912735.1_ASM991273v1	NZ_CP047839	Staphylococcus aureus strain UP_678 chromosome, complete genome	8	2289210-2289343	1	PILER-CR	no		DEDDh,csa3,cas3,DinG,WYL	Orphan	TATTGAAGAAGATACAA	17	0	0	NA	NA	NA	2	2	Orphan	DEDDh,csa3,cas3,DinG,WYL,RT	NA|67aa|up_0|NZ_CP047839.1_2286382_2286583_+,NA|103aa|down_2|NZ_CP047839.1_2294472_2294781_-,NA|89aa|down_3|NZ_CP047839.1_2294924_2295191_-	NA|204aa|up_9|NZ_CP047839.1_2275216_2275828_-	COG0586, DedA, Uncharacterized membrane-associated protein [Function unknown]	NA|426aa|up_8|NZ_CP047839.1_2276378_2277656_+	cd17319, MFS_ExuT_GudP_like, Hexuronate transporter, Glucarate transporter, and similar transporters of the Major Facilitator Superfamily	NA|608aa|up_7|NZ_CP047839.1_2278132_2279956_+	COG1289, COG1289, Predicted membrane protein [Function unknown]	NA|139aa|up_6|NZ_CP047839.1_2280094_2280511_+	COG4876, COG4876, Uncharacterized protein conserved in bacteria [Function unknown]	NA|231aa|up_5|NZ_CP047839.1_2280741_2281434_+	COG2357, COG2357, PpGpp synthetase catalytic domain [General function prediction only]	NA|244aa|up_4|NZ_CP047839.1_2281598_2282330_+	cd01106, HTH_TipAL-Mta, Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA	NA|227aa|up_3|NZ_CP047839.1_2282516_2283197_+	COG1802, GntR, Transcriptional regulators [Transcription]	NA|518aa|up_2|NZ_CP047839.1_2283221_2284775_+	TIGR01314, gntK_FGGY, gluconate kinase, FGGY type	NA|453aa|up_1|NZ_CP047839.1_2284891_2286250_+	TIGR00791, Gluconate_permease, gluconate transporter	NA|67aa|up_0|NZ_CP047839.1_2286382_2286583_+	NA	NA|910aa|down_0|NZ_CP047839.1_2290570_2293300_+	pfam10425, SdrG_C_C, C-terminus of bacterial fibrinogen-binding adhesin	NA|289aa|down_1|NZ_CP047839.1_2293479_2294346_+	COG1210, GalU, UDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]	NA|103aa|down_2|NZ_CP047839.1_2294472_2294781_-	NA	NA|89aa|down_3|NZ_CP047839.1_2294924_2295191_-	NA	NA|603aa|down_4|NZ_CP047839.1_2295474_2297283_-	cd05799, PGM2, This CD includes PGM2 (phosphoglucomutase 2) and PGM2L1 (phosphoglucomutase 2-like 1)	NA|131aa|down_5|NZ_CP047839.1_2297399_2297792_+	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|NZ_CP047839.1_2297793_2300655_+	COG1061, SSL2, DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]	NA|258aa|down_7|NZ_CP047839.1_2300961_2301735_+	pfam04507, DUF576, Csa1 family	NA|254aa|down_8|NZ_CP047839.1_2301844_2302606_+	pfam04507, DUF576, Csa1 family	NA|265aa|down_9|NZ_CP047839.1_2302715_2303510_+	pfam04507, DUF576, Csa1 family
GCF_009912735.1_ASM991273v1	NZ_CP047839	Staphylococcus aureus strain UP_678 chromosome, complete genome	9	2292781-2293039	2,8	PILER-CR,CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG,WYL	Orphan	TATTGAAGAAGATACAA,GCCAACACCACCGACACCAGAGGTACCA	17,28	1	1	2292938-2292960	NZ_CP047839.1_2289568-2289590	NA:NA	2,2	2	Orphan	DEDDh,csa3,cas3,DinG,WYL,RT	NA|67aa|up_1|NZ_CP047839.1_2286382_2286583_+,NA|103aa|down_1|NZ_CP047839.1_2294472_2294781_-,NA|89aa|down_2|NZ_CP047839.1_2294924_2295191_-,NA|41aa|down_9|NZ_CP047839.1_2303513_2303636_-	NA|426aa|up_9|NZ_CP047839.1_2276378_2277656_+	cd17319, MFS_ExuT_GudP_like, Hexuronate transporter, Glucarate transporter, and similar transporters of the Major Facilitator Superfamily	NA|608aa|up_8|NZ_CP047839.1_2278132_2279956_+	COG1289, COG1289, Predicted membrane protein [Function unknown]	NA|139aa|up_7|NZ_CP047839.1_2280094_2280511_+	COG4876, COG4876, Uncharacterized protein conserved in bacteria [Function unknown]	NA|231aa|up_6|NZ_CP047839.1_2280741_2281434_+	COG2357, COG2357, PpGpp synthetase catalytic domain [General function prediction only]	NA|244aa|up_5|NZ_CP047839.1_2281598_2282330_+	cd01106, HTH_TipAL-Mta, Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA	NA|227aa|up_4|NZ_CP047839.1_2282516_2283197_+	COG1802, GntR, Transcriptional regulators [Transcription]	NA|518aa|up_3|NZ_CP047839.1_2283221_2284775_+	TIGR01314, gntK_FGGY, gluconate kinase, FGGY type	NA|453aa|up_2|NZ_CP047839.1_2284891_2286250_+	TIGR00791, Gluconate_permease, gluconate transporter	NA|67aa|up_1|NZ_CP047839.1_2286382_2286583_+	NA	NA|1057aa|up_0|NZ_CP047839.1_2286717_2289888_+	pfam10425, SdrG_C_C, C-terminus of bacterial fibrinogen-binding adhesin	NA|289aa|down_0|NZ_CP047839.1_2293479_2294346_+	COG1210, GalU, UDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]	NA|103aa|down_1|NZ_CP047839.1_2294472_2294781_-	NA	NA|89aa|down_2|NZ_CP047839.1_2294924_2295191_-	NA	NA|603aa|down_3|NZ_CP047839.1_2295474_2297283_-	cd05799, PGM2, This CD includes PGM2 (phosphoglucomutase 2) and PGM2L1 (phosphoglucomutase 2-like 1)	NA|131aa|down_4|NZ_CP047839.1_2297399_2297792_+	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|NZ_CP047839.1_2297793_2300655_+	COG1061, SSL2, DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]	NA|258aa|down_6|NZ_CP047839.1_2300961_2301735_+	pfam04507, DUF576, Csa1 family	NA|254aa|down_7|NZ_CP047839.1_2301844_2302606_+	pfam04507, DUF576, Csa1 family	NA|265aa|down_8|NZ_CP047839.1_2302715_2303510_+	pfam04507, DUF576, Csa1 family	NA|41aa|down_9|NZ_CP047839.1_2303513_2303636_-	NA
GCF_009912735.1_ASM991273v1	NZ_CP047839	Staphylococcus aureus strain UP_678 chromosome, complete genome	10	2374295-2374399	9	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG,WYL	Orphan	TGCATAAGCCTTTCTAGCTCATAAAATCCGCAGAAA	36	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL,RT	NA|35aa|up_0|NZ_CP047839.1_2373935_2374040_+,NA|35aa|down_2|NZ_CP047839.1_2376570_2376675_-	NA|453aa|up_9|NZ_CP047839.1_2363893_2365252_+	TIGR00508, hypothetical_protein_DESPIG_00326, adenosylmethionine-8-amino-7-oxononanoate transaminase	NA|336aa|up_8|NZ_CP047839.1_2365253_2366261_+	PRK06256, PRK06256, biotin synthase; Validated	NA|372aa|up_7|NZ_CP047839.1_2366238_2367354_+	COG0156, BioF, 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]	NA|231aa|up_6|NZ_CP047839.1_2367364_2368057_+	COG1424, BioW, Pimeloyl-CoA synthetase [Coenzyme metabolism]	NA|156aa|up_5|NZ_CP047839.1_2368067_2368535_+	pfam06177, QueT, QueT transporter	NA|326aa|up_4|NZ_CP047839.1_2368586_2369564_-	TIGR01002, synergohymenotropic_toxin, beta-channel forming cytolysin	NA|316aa|up_3|NZ_CP047839.1_2369565_2370513_-	pfam07968, Leukocidin, Leukocidin/Hemolysin toxin family	NA|310aa|up_2|NZ_CP047839.1_2371062_2371992_-	pfam07968, Leukocidin, Leukocidin/Hemolysin toxin family	NA|438aa|up_1|NZ_CP047839.1_2372527_2373841_-	pfam11621, Sbi-IV, C3 binding domain 4 of IgG-bind protein SBI	NA|35aa|up_0|NZ_CP047839.1_2373935_2374040_+	NA	NA|289aa|down_0|NZ_CP047839.1_2374538_2375405_+	COG0053, MMT1, Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]	NA|229aa|down_1|NZ_CP047839.1_2375731_2376418_+	PRK14119, gpmA, phosphoglyceromutase; Provisional	NA|35aa|down_2|NZ_CP047839.1_2376570_2376675_-	NA	NA|480aa|down_3|NZ_CP047839.1_2376848_2378288_+	TIGR00711, Uncharacterized_MFS-type_transporter_YhcA, drug resistance transporter, EmrB/QacA subfamily	NA|260aa|down_4|NZ_CP047839.1_2378408_2379188_+	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|NZ_CP047839.1_2379168_2379888_+	COG0765, HisM, ABC-type amino acid transport system, permease component [Amino acid transport and metabolism]	NA|244aa|down_6|NZ_CP047839.1_2379884_2380616_+	COG1126, GlnQ, ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]	NA|417aa|down_7|NZ_CP047839.1_2380712_2381963_-	pfam02388, FemAB, FemAB family	NA|121aa|down_8|NZ_CP047839.1_2382217_2382580_+	pfam14729, DUF4467, Domain of unknown function with cystatin-like fold (DUF4467)	NA|200aa|down_9|NZ_CP047839.1_2382598_2383198_+	COG1651, DsbG, Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]
GCF_009912735.1_ASM991273v1	NZ_CP047839	Staphylococcus aureus strain UP_678 chromosome, complete genome	11	2566365-2566490	10	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG,WYL	Orphan	TGATATCAAGGGTTTTGTGAGCTTTCGAGTAAAGAGG	37	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL,RT	NA,NA|61aa|down_1|NZ_CP047839.1_2567384_2567567_+,NA|56aa|down_8|NZ_CP047839.1_2575915_2576083_-	NA|130aa|up_9|NZ_CP047839.1_2557836_2558226_+	PRK05309, PRK05309, 30S ribosomal protein S11; Validated	NA|315aa|up_8|NZ_CP047839.1_2558300_2559245_+	PRK05182, PRK05182, DNA-directed RNA polymerase subunit alpha; Provisional	NA|123aa|up_7|NZ_CP047839.1_2559261_2559630_+	PRK05591, rplQ, 50S ribosomal protein L17; Validated	NA|270aa|up_6|NZ_CP047839.1_2560162_2560972_+	PRK13648, cbiO, cobalt transporter ATP-binding subunit; Provisional	NA|287aa|up_5|NZ_CP047839.1_2560968_2561829_+	PRK13646, cbiO, energy-coupling factor transporter ATPase	NA|269aa|up_4|NZ_CP047839.1_2561818_2562625_+	COG0619, CbiQ, ABC-type cobalt transport system, permease component CbiQ and related transporters [Inorganic ion transport and metabolism]	NA|265aa|up_3|NZ_CP047839.1_2562629_2563424_+	PRK00021, truA, tRNA pseudouridine(38-40) synthase TruA	NA|146aa|up_2|NZ_CP047839.1_2563672_2564110_+	PRK09216, rplM, 50S ribosomal protein L13; Reviewed	NA|133aa|up_1|NZ_CP047839.1_2564123_2564522_+	PRK00132, rpsI, 30S ribosomal protein S9; Reviewed	NA|479aa|up_0|NZ_CP047839.1_2564870_2566307_+	COG2865, COG2865, Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]	NA|60aa|down_0|NZ_CP047839.1_2566555_2566735_+	PRK09775, PRK09775, type II toxin-antitoxin system HipA family toxin YjjJ	NA|61aa|down_1|NZ_CP047839.1_2567384_2567567_+	NA	NA|555aa|down_2|NZ_CP047839.1_2568036_2569701_+	PRK08617, PRK08617, acetolactate synthase AlsS	NA|235aa|down_3|NZ_CP047839.1_2569737_2570442_+	COG3527, AlsD, Alpha-acetolactate decarboxylase [Secondary metabolites biosynthesis, transport, and catabolism]	NA|142aa|down_4|NZ_CP047839.1_2570832_2571258_-	pfam03642, MAP, MAP domain	NA|272aa|down_5|NZ_CP047839.1_2571552_2572368_+	cd02605, HAD_SPP, sucrose-phosphatase, similar to Synechocystis sp PCC 6803 SPP	NA|285aa|down_6|NZ_CP047839.1_2572578_2573433_+	pfam01551, Peptidase_M23, Peptidase family M23	NA|809aa|down_7|NZ_CP047839.1_2573492_2575919_-	cd01083, GAG_Lyase, Glycosaminoglycan (GAG) polysaccharide lyase family	NA|56aa|down_8|NZ_CP047839.1_2575915_2576083_-	NA	NA|139aa|down_9|NZ_CP047839.1_2576325_2576742_+	cd01109, HTH_YyaN, Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB
GCF_009912735.1_ASM991273v1	NZ_CP047839	Staphylococcus aureus strain UP_678 chromosome, complete genome	12	2643948-2644038	11	CRISPRCasFinder	no	csa3	DEDDh,csa3,cas3,DinG,WYL	Type I-A	AAGAAGCCCCTAACAACTAAAGTTG	25	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL,RT	NA|53aa|up_1|NZ_CP047839.1_2642670_2642829_-,NA|35aa|up_0|NZ_CP047839.1_2643508_2643613_+,NA|364aa|down_0|NZ_CP047839.1_2644054_2645146_-,NA|77aa|down_5|NZ_CP047839.1_2648935_2649166_+	NA|452aa|up_9|NZ_CP047839.1_2622978_2624334_+	PRK14316, glmM, phosphoglucosamine mutase; Provisional	NA|369aa|up_8|NZ_CP047839.1_2632329_2633436_-	PRK02318, PRK02318, mannitol-1-phosphate 5-dehydrogenase; Provisional	NA|145aa|up_7|NZ_CP047839.1_2633435_2633870_-	COG4668, MtlA, Mannitol/fructose-specific phosphotransferase system, IIA domain [Carbohydrate transport and metabolism]	NA|711aa|up_6|NZ_CP047839.1_2633881_2636014_-	COG3711, BglG, Transcriptional antiterminator [Transcription]	NA|513aa|up_5|NZ_CP047839.1_2636048_2637587_-	COG2213, MtlA, Phosphotransferase system, mannitol-specific IIBC component [Carbohydrate transport and metabolism]	NA|602aa|up_4|NZ_CP047839.1_2638267_2640073_+	PRK00331, PRK00331, isomerizing glutamine--fructose-6-phosphate transaminase	NA|261aa|up_3|NZ_CP047839.1_2640304_2641087_+	COG1119, ModF, ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA [Inorganic ion transport and metabolism]	NA|286aa|up_2|NZ_CP047839.1_2641154_2642012_+	COG0561, Cof, Predicted hydrolases of the HAD superfamily [General function prediction only]	NA|53aa|up_1|NZ_CP047839.1_2642670_2642829_-	NA	NA|35aa|up_0|NZ_CP047839.1_2643508_2643613_+	NA	NA|364aa|down_0|NZ_CP047839.1_2644054_2645146_-	NA	NA|327aa|down_1|NZ_CP047839.1_2645411_2646392_-	COG1230, CzcD, Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]	csa3|107aa|down_2|NZ_CP047839.1_2646393_2646714_-	cd00090, HTH_ARSR, Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors	NA|222aa|down_3|NZ_CP047839.1_2646865_2647531_+	cd05243, SDR_a5, atypical (a) SDRs, subgroup 5	NA|313aa|down_4|NZ_CP047839.1_2647966_2648905_+	COG1482, ManA, Phosphomannose isomerase [Carbohydrate transport and metabolism]	NA|77aa|down_5|NZ_CP047839.1_2648935_2649166_+	NA	NA|458aa|down_6|NZ_CP047839.1_2649838_2651212_+	pfam01878, EVE, EVE domain	NA|138aa|down_7|NZ_CP047839.1_2651660_2652074_+	COG3011, COG3011, Predicted thiol-disulfide oxidoreductase [General function    prediction only]	NA|148aa|down_8|NZ_CP047839.1_2652273_2652717_+	COG0783, Dps, DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]	NA|237aa|down_9|NZ_CP047839.1_2652837_2653548_-	PRK05819, deoD, DeoD-type purine-nucleoside phosphorylase
