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_000160335.2_ASM16033v2	NC_022113	Staphylococcus aureus subsp. aureus 55/2053, complete sequence	1	564019-564111	1	CRISPRCasFinder	no		cas3,DEDDh,DinG,csa3,WYL	Orphan	CTAAAGGTGAAGAGGAACGCAGTTGGATGCTA	32	0	0	NA	NA	NA	1	1	Orphan	csa3,cas3,DEDDh,DinG,WYL	NA,NA|169aa|down_4|NC_022113.1_567930_568437_+,NA|239aa|down_5|NC_022113.1_568598_569315_+	NA|210aa|up_9|NC_022113.1_553744_554374_+	pfam04276, DUF443, Protein of unknown function (DUF443)	NA|313aa|up_8|NC_022113.1_554826_555765_+	cd19083, AKR_AKR11A1_11D1, AKR11A and  AKR11D families of aldo-keto reductase (AKR)	NA|179aa|up_7|NC_022113.1_555974_556511_+	COG0655, WrbA, Multimeric flavodoxin WrbA [General function prediction only]	NA|159aa|up_6|NC_022113.1_556679_557156_+	pfam00583, Acetyltransf_1, Acetyltransferase (GNAT) family	NA|432aa|up_5|NC_022113.1_557195_558491_+	COG1078, COG1078, HD superfamily phosphohydrolases [General function prediction only]	NA|174aa|up_4|NC_022113.1_558518_559040_+	pfam08741, YwhD, YwhD family	NA|337aa|up_3|NC_022113.1_559538_560549_+	PRK09422, PRK09422, ethanol-active dehydrogenase/acetaldehyde-active reductase; Provisional	NA|139aa|up_2|NC_022113.1_560824_561241_+	COG4506, COG4506, Uncharacterized protein conserved in bacteria [Function unknown]	NA|554aa|up_1|NC_022113.1_561237_562899_+	PRK01611, argS, arginyl-tRNA synthetase; Reviewed	NA|212aa|up_0|NC_022113.1_563234_563870_+	COG2231, COG2231, Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]	NA|296aa|down_0|NC_022113.1_564249_565137_+	cd01143, YvrC, Periplasmic binding protein YvrC	NA|317aa|down_1|NC_022113.1_565286_566237_+	pfam01032, FecCD, FecCD transport family	NA|240aa|down_2|NC_022113.1_566291_567011_+	COG1011, COG1011, Predicted hydrolase (HAD superfamily) [General function prediction only]	NA|267aa|down_3|NC_022113.1_566994_567795_+	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|169aa|down_4|NC_022113.1_567930_568437_+	NA	NA|239aa|down_5|NC_022113.1_568598_569315_+	NA	NA|263aa|down_6|NC_022113.1_569483_570272_+	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|125aa|down_7|NC_022113.1_570521_570896_-	TIGR01889, Pleiotropic_Regulator_Of_Virulence, staphylococcal accessory regulator family	NA|310aa|down_8|NC_022113.1_571843_572773_-	COG3238, COG3238, Uncharacterized protein conserved in bacteria [Function unknown]	NA|75aa|down_9|NC_022113.1_572965_573190_-	pfam11148, DUF2922, Protein of unknown function (DUF2922)
GCF_000160335.2_ASM16033v2	NC_022113	Staphylococcus aureus subsp. aureus 55/2053, complete sequence	2	628748-628847	2	CRISPRCasFinder	no		cas3,DEDDh,DinG,csa3,WYL	Orphan	AAGAGCCCCTAATTAATAAATTAAAAGGGG	30	0	0	NA	NA	NA	1	1	Orphan	csa3,cas3,DEDDh,DinG,WYL	NA|39aa|up_2|NC_022113.1_626685_626802_+,NA|230aa|down_3|NC_022113.1_632592_633282_-,NA|130aa|down_5|NC_022113.1_633918_634308_+,NA|100aa|down_6|NC_022113.1_634445_634745_+	NA|336aa|up_9|NC_022113.1_618481_619489_+	pfam01384, PHO4, Phosphate transporter family	NA|266aa|up_8|NC_022113.1_620075_620873_-	COG3942, COG3942, Surface antigen [General function prediction only]	NA|215aa|up_7|NC_022113.1_621233_621878_+	COG0670, COG0670, Integral membrane protein, interacts with FtsH [General function prediction only]	NA|717aa|up_6|NC_022113.1_622559_624710_+	smart00342, HTH_ARAC, helix_turn_helix, arabinose operon control protein	NA|120aa|up_5|NC_022113.1_624855_625215_+	TIGR01889, Pleiotropic_Regulator_Of_Virulence, staphylococcal accessory regulator family	NA|239aa|up_4|NC_022113.1_625404_626121_+	PRK12378, PRK12378, YebC/PmpR family DNA-binding transcriptional regulator	NA|158aa|up_3|NC_022113.1_626120_626594_+	COG3542, COG3542, Uncharacterized conserved protein [Function unknown]	NA|39aa|up_2|NC_022113.1_626685_626802_+	NA	NA|215aa|up_1|NC_022113.1_626946_627591_+	COG2306, COG2306, Predicted RNA-binding protein, associated with RNAses E/G family [General function prediction only]	NA|289aa|up_0|NC_022113.1_627708_628575_+	COG0583, LysR, Transcriptional regulator [Transcription]	NA|407aa|down_0|NC_022113.1_628864_630085_+	cd17471, MFS_Set, Sugar efflux transporter (Set) family of the Major Facilitator Superfamily of transporters	NA|156aa|down_1|NC_022113.1_630081_630549_+	COG2839, COG2839, Uncharacterized protein conserved in bacteria [Function unknown]	NA|549aa|down_2|NC_022113.1_630791_632438_+	COG3666, COG3666, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|230aa|down_3|NC_022113.1_632592_633282_-	NA	NA|148aa|down_4|NC_022113.1_633408_633852_+	pfam00583, Acetyltransf_1, Acetyltransferase (GNAT) family	NA|130aa|down_5|NC_022113.1_633918_634308_+	NA	NA|100aa|down_6|NC_022113.1_634445_634745_+	NA	NA|181aa|down_7|NC_022113.1_634824_635367_+	pfam13302, Acetyltransf_3, Acetyltransferase (GNAT) domain	NA|189aa|down_8|NC_022113.1_635461_636028_-	COG1611, COG1611, Predicted Rossmann fold nucleotide-binding protein [General function prediction only]	NA|153aa|down_9|NC_022113.1_636029_636488_-	PRK00124, PRK00124, YaiI/YqxD family protein
GCF_000160335.2_ASM16033v2	NC_022113	Staphylococcus aureus subsp. aureus 55/2053, complete sequence	3	716482-716566	3	CRISPRCasFinder	no	cas3	cas3,DEDDh,DinG,csa3,WYL	Unclear	CACCCCAACTTGCATTGTCTGTAGAA	26	1	2	716508-716540|716508-716540	NC_022113.1_966296-966328|NC_022113.1_2309212-2309180	NA	1	1	Unclear	csa3,cas3,DEDDh,DinG,WYL	NA|33aa|up_1|NC_022113.1_714922_715021_+,NA	NA|254aa|up_9|NC_022113.1_703973_704735_-	COG2966, COG2966, Uncharacterized conserved protein [Function unknown]	NA|357aa|up_8|NC_022113.1_704930_706001_-	cd01949, GGDEF, Diguanylate-cyclase (DGC) or GGDEF domain	NA|352aa|up_7|NC_022113.1_706318_707374_+	cd06853, GT_WecA_like, This subfamily contains Escherichia coli WecA, Bacillus subtilis TagO and related proteins	NA|214aa|up_6|NC_022113.1_707537_708179_-	COG1739, COG1739, Uncharacterized conserved protein [Function unknown]	NA|289aa|up_5|NC_022113.1_708322_709189_+	TIGR00762, DegV, EDD domain protein, DegV family	cas3|361aa|up_4|NC_022113.1_709552_710635_+	COG4098, comFA, Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [DNA replication, recombination, and repair]	NA|191aa|up_3|NC_022113.1_711363_711936_+	COG1544, COG1544, Ribosome-associated protein Y (PSrp-1) [Translation, ribosomal structure and biogenesis]	NA|844aa|up_2|NC_022113.1_712349_714881_+	PRK12904, PRK12904, preprotein translocase subunit SecA; Reviewed	NA|33aa|up_1|NC_022113.1_714922_715021_+	NA	NA|370aa|up_0|NC_022113.1_715195_716306_+	PRK00578, prfB, peptide chain release factor 2; Validated	NA|280aa|down_0|NC_022113.1_717074_717914_+	COG3942, COG3942, Surface antigen [General function prediction only]	NA|217aa|down_1|NC_022113.1_718087_718738_+	pfam12917, HD_2, HD containing hydrolase-like enzyme	NA|79aa|down_2|NC_022113.1_718734_718971_+	COG4897, CsbA, Uncharacterized protein conserved in bacteria [Function unknown]	NA|662aa|down_3|NC_022113.1_719239_721225_+	PRK05298, PRK05298, excinuclease ABC subunit UvrB	NA|949aa|down_4|NC_022113.1_721232_724079_+	PRK00349, uvrA, excinuclease ABC subunit UvrA	NA|311aa|down_5|NC_022113.1_724689_725622_+	PRK05428, PRK05428, HPr kinase/phosphorylase; Provisional	NA|281aa|down_6|NC_022113.1_725627_726470_+	PRK12437, PRK12437, prolipoprotein diacylglyceryl transferase; Reviewed	NA|162aa|down_7|NC_022113.1_726477_726963_+	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|312aa|down_8|NC_022113.1_728477_729413_+	TIGR01292, Thioredoxin_reductase, thioredoxin-disulfide reductase	NA|304aa|down_9|NC_022113.1_730180_731092_+	COG1660, COG1660, Predicted P-loop-containing kinase [General function prediction only]
GCF_000160335.2_ASM16033v2	NC_022113	Staphylococcus aureus subsp. aureus 55/2053, complete sequence	4	774814-774893	4	CRISPRCasFinder	no		cas3,DEDDh,DinG,csa3,WYL	Orphan	CCGTCAGCTTCTGTGTTGGGGCCC	24	0	0	NA	NA	NA	1	1	Orphan	csa3,cas3,DEDDh,DinG,WYL	NA,NA	NA|194aa|up_9|NC_022113.1_767767_768349_+	COG0406, phoE, Broad specificity phosphatase PhoE and related phosphatases [General function prediction only]	NA|206aa|up_8|NC_022113.1_768421_769039_-	COG1279, COG1279, Lysine efflux permease [General function prediction only]	NA|165aa|up_7|NC_022113.1_769194_769689_-	pfam13420, Acetyltransf_4, Acetyltransferase (GNAT) domain	NA|141aa|up_6|NC_022113.1_770087_770510_-	TIGR03561, organ_hyd_perox, peroxiredoxin, Ohr subfamily	NA|239aa|up_5|NC_022113.1_770657_771374_+	PRK13575, PRK13575, type I 3-dehydroquinate dehydratase	NA|180aa|up_4|NC_022113.1_771456_771996_+	cd02135, YdjA-like, nitroreductase family protein similar to Escherichia coli YdjA	NA|107aa|up_3|NC_022113.1_772145_772466_-	cd02947, TRX_family, TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a TRX domain; and Group II, which are composed of fusion proteins of TRX and additional domains	NA|119aa|up_2|NC_022113.1_772609_772966_+	cd03036, ArsC_like, Arsenate Reductase (ArsC) family, unknown subfamily; uncharacterized proteins containing a CXXC motif with similarity to thioredoxin (TRX)-fold arsenic reductases, ArsC	NA|127aa|up_1|NC_022113.1_773123_773504_+	PRK01202, PRK01202, glycine cleavage system protein GcvH	NA|293aa|up_0|NC_022113.1_773681_774560_+	COG3878, COG3878, Uncharacterized protein conserved in bacteria [Function unknown]	NA|129aa|down_0|NC_022113.1_775149_775536_+	COG1658, COG1658, Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]	NA|99aa|down_1|NC_022113.1_775528_775825_+	cd02947, TRX_family, TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a TRX domain; and Group II, which are composed of fusion proteins of TRX and additional domains	NA|342aa|down_2|NC_022113.1_776074_777100_+	COG1135, AbcC, ABC-type metal ion transport system, ATPase component [Inorganic ion transport and metabolism]	NA|232aa|down_3|NC_022113.1_777092_777788_+	COG2011, AbcD, ABC-type metal ion transport system, permease component [Inorganic ion transport and metabolism]	NA|274aa|down_4|NC_022113.1_777805_778627_+	COG1464, NlpA, ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]	NA|407aa|down_5|NC_022113.1_778769_779990_-	cd01189, INT_ICEBs1_C_like, C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons	NA|463aa|down_6|NC_022113.1_780003_781392_-	pfam02037, SAP, SAP domain	NA|191aa|down_7|NC_022113.1_781418_781991_-	cd00093, HTH_XRE, Helix-turn-helix XRE-family like proteins	NA|74aa|down_8|NC_022113.1_782162_782384_+	COG1476, COG1476, Predicted transcriptional regulators [Transcription]	NA|91aa|down_9|NC_022113.1_782384_782657_+	pfam13545, HTH_Crp_2, Crp-like helix-turn-helix domain
GCF_000160335.2_ASM16033v2	NC_022113	Staphylococcus aureus subsp. aureus 55/2053, complete sequence	5	840149-840234	5	CRISPRCasFinder	no		cas3,DEDDh,DinG,csa3,WYL	Orphan	AAAGTCAGCTTACAATAATGTGCAAGTTGG	30	1	2	840179-840204|840179-840204	NC_022113.1_2051928-2051953|NC_022113.1_2114181-2114206	NA	1	1	Orphan	csa3,cas3,DEDDh,DinG,WYL	NA,NA	NA|499aa|up_9|NC_022113.1_829038_830535_-	PRK07691, PRK07691, putative monovalent cation/H+ antiporter subunit D; Reviewed	NA|114aa|up_8|NC_022113.1_830527_830869_-	PRK08600, PRK08600, putative monovalent cation/H+ antiporter subunit C; Reviewed	NA|143aa|up_7|NC_022113.1_830868_831297_-	PRK12573, PRK12573, Na(+)/H(+) antiporter subunit B	NA|802aa|up_6|NC_022113.1_831289_833695_-	PRK12645, PRK12645, monovalent cation/H+ antiporter subunit A; Reviewed	NA|128aa|up_5|NC_022113.1_833825_834209_-	pfam08810, KapB, Kinase associated protein B	NA|198aa|up_4|NC_022113.1_834272_834866_+	cd01927, cyclophilin_WD40, cyclophilin_WD40: cyclophilin-type peptidylprolyl cis- trans isomerases (cyclophilins) having a WD40 domain	NA|126aa|up_3|NC_022113.1_835280_835658_+	COG1098, VacB, Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]	NA|376aa|up_2|NC_022113.1_836019_837147_+	cd04735, OYE_like_4_FMN, Old yellow enzyme (OYE)-related FMN binding domain, group 4	NA|397aa|up_1|NC_022113.1_837454_838645_+	PRK04073, rocD, ornithine--oxo-acid transaminase; Provisional	NA|415aa|up_0|NC_022113.1_838753_839998_+	COG0334, GdhA, Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism]	NA|310aa|down_0|NC_022113.1_840392_841322_-	cd08601, GDPD_SaGlpQ_like, Glycerophosphodiester phosphodiesterase domain of Staphylococcus aureus and similar proteins	NA|460aa|down_1|NC_022113.1_841563_842943_-	PRK00855, PRK00855, argininosuccinate lyase; Provisional	NA|402aa|down_2|NC_022113.1_842932_844138_-	PRK00509, PRK00509, argininosuccinate synthase; Provisional	NA|444aa|down_3|NC_022113.1_844488_845820_+	PRK14097, pgi, glucose-6-phosphate isomerase; Provisional	NA|192aa|down_4|NC_022113.1_846145_846721_+	COG0398, COG0398, Uncharacterized conserved protein [Function unknown]	NA|175aa|down_5|NC_022113.1_846725_847250_+	TIGR02227, Inactive_signal_peptidase_IA	NA|192aa|down_6|NC_022113.1_847265_847841_+	TIGR02227, Inactive_signal_peptidase_IA	NA|1159aa|down_7|NC_022113.1_848000_851477_+	TIGR02773, ATP-dependent_helicase/deoxyribonuclease_subunit_B, helicase-exonuclease AddAB, AddB subunit	NA|1218aa|down_8|NC_022113.1_851477_855131_+	TIGR02785, ATP-dependent_helicase/nuclease_subunit_A, helicase-exonuclease AddAB, AddA subunit, Firmicutes type	NA|301aa|down_9|NC_022113.1_855296_856199_+	COG0179, MhpD, 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) [Secondary metabolites biosynthesis, transport, and catabolism]
GCF_000160335.2_ASM16033v2	NC_022113	Staphylococcus aureus subsp. aureus 55/2053, complete sequence	6	1141663-1141755	6	CRISPRCasFinder	no	cas3	cas3,DEDDh,DinG,csa3,WYL	Unclear	TAAGAAACAGTAATCAATAAATTGATAACT	30	0	0	NA	NA	NA	1	1	Unclear	csa3,cas3,DEDDh,DinG,WYL	NA,NA	NA|215aa|up_9|NC_022113.1_1131538_1132183_+	COG0036, Rpe, Pentose-5-phosphate-3-epimerase [Carbohydrate transport and metabolism]	NA|214aa|up_8|NC_022113.1_1132189_1132831_+	COG1564, THI80, Thiamine pyrophosphokinase [Coenzyme metabolism]	NA|63aa|up_7|NC_022113.1_1133211_1133400_-	PRK00359, rpmB, 50S ribosomal protein L28; Reviewed	NA|125aa|up_6|NC_022113.1_1133842_1134217_+	COG1302, COG1302, Uncharacterized protein conserved in bacteria [Function unknown]	NA|549aa|up_5|NC_022113.1_1134231_1135878_+	COG1461, COG1461, Predicted kinase related to dihydroxyacetone kinase [General function prediction only]	cas3|687aa|up_4|NC_022113.1_1136067_1138128_+	PRK10917, PRK10917, ATP-dependent DNA helicase RecG; Provisional	NA|191aa|up_3|NC_022113.1_1138329_1138902_+	PRK04424, PRK04424, transcription factor FapR	NA|329aa|up_2|NC_022113.1_1138906_1139893_+	PRK05331, PRK05331, phosphate acyltransferase PlsX	NA|309aa|up_1|NC_022113.1_1139885_1140812_+	COG0331, FabD, (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]	NA|245aa|up_0|NC_022113.1_1140804_1141539_+	PRK05557, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase; Validated	NA|78aa|down_0|NC_022113.1_1141844_1142078_+	PRK00982, acpP, acyl carrier protein; Provisional	NA|244aa|down_1|NC_022113.1_1142193_1142925_+	PRK00102, rnc, ribonuclease III; Reviewed	NA|1189aa|down_2|NC_022113.1_1143071_1146638_+	COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]	NA|417aa|down_3|NC_022113.1_1146637_1147888_+	PRK10416, PRK10416, signal recognition particle-docking protein FtsY; Provisional	NA|111aa|down_4|NC_022113.1_1147874_1148207_+	PRK00118, PRK00118, putative DNA-binding protein; Validated	NA|456aa|down_5|NC_022113.1_1148232_1149600_+	PRK10867, PRK10867, signal recognition particle protein; Provisional	NA|92aa|down_6|NC_022113.1_1150034_1150310_+	COG0228, RpsP, Ribosomal protein S16 [Translation, ribosomal structure and biogenesis]	NA|168aa|down_7|NC_022113.1_1150497_1151001_+	PRK00122, rimM, 16S rRNA-processing protein RimM; Provisional	NA|246aa|down_8|NC_022113.1_1151000_1151738_+	PRK00026, trmD, tRNA (guanine-N(1)-)-methyltransferase; Reviewed	NA|117aa|down_9|NC_022113.1_1151840_1152191_+	PRK05338, rplS, 50S ribosomal protein L19; Provisional
GCF_000160335.2_ASM16033v2	NC_022113	Staphylococcus aureus subsp. aureus 55/2053, complete sequence	7	1881813-1881903	7	CRISPRCasFinder	no		cas3,DEDDh,DinG,csa3,WYL	Orphan	GACATTGCAAGTTGGGGAACGGGTCCAACATAG	33	0	0	NA	NA	NA	1	1	Orphan	csa3,cas3,DEDDh,DinG,WYL	NA|132aa|up_0|NC_022113.1_1881066_1881462_-,NA|51aa|down_0|NC_022113.1_1882062_1882215_-	NA|314aa|up_9|NC_022113.1_1867801_1868743_-	PRK13480, PRK13480, 3'-5' exoribonuclease YhaM; Provisional	NA|979aa|up_8|NC_022113.1_1868739_1871676_-	COG4717, COG4717, Uncharacterized conserved protein [Function unknown]	NA|399aa|up_7|NC_022113.1_1871665_1872862_-	COG0420, SbcD, DNA repair exonuclease [DNA replication, recombination, and repair]	NA|375aa|up_6|NC_022113.1_1874163_1875288_-	COG4399, COG4399, Uncharacterized protein conserved in bacteria [Function unknown]	NA|155aa|up_5|NC_022113.1_1875466_1875931_-	COG1476, COG1476, Predicted transcriptional regulators [Transcription]	NA|208aa|up_4|NC_022113.1_1876288_1876912_-	COG2197, CitB, Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]	NA|371aa|up_3|NC_022113.1_1876933_1878046_-	COG4585, COG4585, Signal transduction histidine kinase [Signal transduction mechanisms]	NA|274aa|up_2|NC_022113.1_1878208_1879030_+	COG0564, RluA, Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]	NA|462aa|up_1|NC_022113.1_1879485_1880871_-	PRK00485, fumC, fumarate hydratase; Reviewed	NA|132aa|up_0|NC_022113.1_1881066_1881462_-	NA	NA|51aa|down_0|NC_022113.1_1882062_1882215_-	NA	NA|200aa|down_1|NC_022113.1_1882239_1882839_-	COG0363, NagB, 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase [Carbohydrate transport and metabolism]	NA|157aa|down_2|NC_022113.1_1882997_1883468_-	COG0219, CspR, Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]	NA|376aa|down_3|NC_022113.1_1883472_1884600_-	TIGR00276, iron-sulfur_cluster-binding_protein, epoxyqueuosine reductase	NA|241aa|down_4|NC_022113.1_1884750_1885473_-	COG1126, GlnQ, ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]	NA|486aa|down_5|NC_022113.1_1885465_1886923_-	COG0765, HisM, ABC-type amino acid transport system, permease component [Amino acid transport and metabolism]	NA|354aa|down_6|NC_022113.1_1887181_1888243_-	COG3641, PfoR, Predicted membrane protein, putative toxin regulator [General function prediction only]	NA|149aa|down_7|NC_022113.1_1897127_1897574_-	COG0735, Fur, Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]	NA|317aa|down_8|NC_022113.1_1897670_1898621_-	cd12155, PGDH_1, Phosphoglycerate Dehydrogenase, 2-hydroxyacid dehydrogenase family	NA|152aa|down_9|NC_022113.1_1898626_1899082_-	COG1225, Bcp, Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]
GCF_000160335.2_ASM16033v2	NC_022113	Staphylococcus aureus subsp. aureus 55/2053, complete sequence	8	1923117-1923200	8	CRISPRCasFinder	no	DEDDh	cas3,DEDDh,DinG,csa3,WYL	Unclear	CCCCAACTTGCATTGCCTGTAGAA	24	0	0	NA	NA	NA	1	1	Orphan	csa3,cas3,DEDDh,DinG,WYL	NA|92aa|up_6|NC_022113.1_1917364_1917640_+,NA|129aa|up_1|NC_022113.1_1921622_1922009_-,NA|138aa|down_1|NC_022113.1_1924743_1925157_-,NA|37aa|down_2|NC_022113.1_1925185_1925296_-,NA|31aa|down_6|NC_022113.1_1928301_1928394_-	NA|419aa|up_9|NC_022113.1_1915287_1916544_-	pfam02073, Peptidase_M29, Thermophilic metalloprotease (M29)	NA|67aa|up_8|NC_022113.1_1916546_1916747_-	COG4840, COG4840, Uncharacterized protein conserved in bacteria [Function unknown]	NA|155aa|up_7|NC_022113.1_1916893_1917358_+	cd16343, LMWPTP, Low molecular weight protein tyrosine phosphatase	NA|92aa|up_6|NC_022113.1_1917364_1917640_+	NA	NA|406aa|up_5|NC_022113.1_1917917_1919135_+	COG1295, Rbn, Ribonuclease BN family enzyme [Replication, recombination, and repair]	NA|210aa|up_4|NC_022113.1_1919247_1919877_-	COG2197, CitB, Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]	NA|348aa|up_3|NC_022113.1_1919866_1920910_-	COG4585, COG4585, Signal transduction histidine kinase [Signal transduction mechanisms]	NA|234aa|up_2|NC_022113.1_1920906_1921608_-	COG4758, COG4758, Predicted membrane protein [Function unknown]	NA|129aa|up_1|NC_022113.1_1921622_1922009_-	NA	NA|253aa|up_0|NC_022113.1_1922225_1922984_-	PRK05716, PRK05716, methionine aminopeptidase; Validated	NA|329aa|down_0|NC_022113.1_1923568_1924555_+	COG4129, COG4129, Predicted membrane protein [Function unknown]	NA|138aa|down_1|NC_022113.1_1924743_1925157_-	NA	NA|37aa|down_2|NC_022113.1_1925185_1925296_-	NA	NA|244aa|down_3|NC_022113.1_1925381_1926113_-	COG3442, COG3442, Predicted glutamine amidotransferase [General function prediction only]	NA|438aa|down_4|NC_022113.1_1926114_1927428_-	COG0769, MurE, UDP-N-acetylmuramyl tripeptide synthase [Cell envelope biogenesis, outer membrane]	NA|167aa|down_5|NC_022113.1_1927719_1928220_+	COG1528, Ftn, Ferritin-like protein [Inorganic ion transport and metabolism]	NA|31aa|down_6|NC_022113.1_1928301_1928394_-	NA	DEDDh|185aa|down_7|NC_022113.1_1928610_1929165_+	cd06130, DNA_pol_III_epsilon_like, an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III	NA|357aa|down_8|NC_022113.1_1929231_1930302_-	PRK02406, PRK02406, DNA polymerase IV; Validated	NA|177aa|down_9|NC_022113.1_1930548_1931079_-	pfam11667, DUF3267, Putative zincin peptidase
GCF_000160335.2_ASM16033v2	NC_022113	Staphylococcus aureus subsp. aureus 55/2053, complete sequence	9	1933780-1933971	1	CRT	no	DEDDh	cas3,DEDDh,DinG,csa3,WYL	Unclear	NNTCTNTGTTGGGGCCCNCACC	22	2	10	1933801-1933837|1933801-1933837|1933859-1933892|1933859-1933892|1933859-1933892|1933859-1933892|1933859-1933892|1933859-1933892|1933859-1933892|1933859-1933892	NC_022113.1_729775-729811|NC_022113.1_729833-729869|NC_022113.1_263014-262981|NC_022113.1_342821-342788|NC_022113.1_683374-683341|NC_022113.1_716547-716580|NC_022113.1_992453-992486|NC_022113.1_1718032-1717999|NC_022113.1_2274768-2274801|NC_022113.1_2415108-2415075	NA	3	3	Orphan	csa3,cas3,DEDDh,DinG,WYL	NA|37aa|up_9|NC_022113.1_1925185_1925296_-,NA|31aa|up_5|NC_022113.1_1928301_1928394_-,NA|49aa|down_0|NC_022113.1_1934275_1934422_-	NA|37aa|up_9|NC_022113.1_1925185_1925296_-	NA	NA|244aa|up_8|NC_022113.1_1925381_1926113_-	COG3442, COG3442, Predicted glutamine amidotransferase [General function prediction only]	NA|438aa|up_7|NC_022113.1_1926114_1927428_-	COG0769, MurE, UDP-N-acetylmuramyl tripeptide synthase [Cell envelope biogenesis, outer membrane]	NA|167aa|up_6|NC_022113.1_1927719_1928220_+	COG1528, Ftn, Ferritin-like protein [Inorganic ion transport and metabolism]	NA|31aa|up_5|NC_022113.1_1928301_1928394_-	NA	DEDDh|185aa|up_4|NC_022113.1_1928610_1929165_+	cd06130, DNA_pol_III_epsilon_like, an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III	NA|357aa|up_3|NC_022113.1_1929231_1930302_-	PRK02406, PRK02406, DNA polymerase IV; Validated	NA|177aa|up_2|NC_022113.1_1930548_1931079_-	pfam11667, DUF3267, Putative zincin peptidase	NA|454aa|up_1|NC_022113.1_1931248_1932610_-	COG2265, TrmA, SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]	NA|316aa|up_0|NC_022113.1_1932690_1933638_-	PRK13337, PRK13337, putative lipid kinase; Reviewed	NA|49aa|down_0|NC_022113.1_1934275_1934422_-	NA	NA|476aa|down_1|NC_022113.1_1934460_1935888_-	PRK05477, gatB, Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB	NA|486aa|down_2|NC_022113.1_1935900_1937358_-	PRK00012, gatA, Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA	NA|101aa|down_3|NC_022113.1_1937359_1937662_-	PRK00034, gatC, Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatC	NA|513aa|down_4|NC_022113.1_1938028_1939567_+	TIGR02121, Osmoregulated_proline_transporter, sodium/proline symporter	NA|400aa|down_5|NC_022113.1_1939655_1940855_-	COG4851, CamS, Protein involved in sex pheromone biosynthesis [General function prediction only]	NA|668aa|down_6|NC_022113.1_1940867_1942871_-	PRK07956, ligA, NAD-dependent DNA ligase LigA; Validated	NA|731aa|down_7|NC_022113.1_1942874_1945067_-	TIGR01073, ATP-dependent_DNA_helicase_PcrA, ATP-dependent DNA helicase PcrA	NA|231aa|down_8|NC_022113.1_1945063_1945756_-	COG1646, COG1646, Predicted phosphate-binding enzymes, TIM-barrel fold [General function prediction only]	NA|101aa|down_9|NC_022113.1_1945938_1946241_-	COG4496, COG4496, Uncharacterized protein conserved in bacteria [Function unknown]
GCF_000160335.2_ASM16033v2	NC_022113	Staphylococcus aureus subsp. aureus 55/2053, complete sequence	10	2158915-2159004	9	CRISPRCasFinder	no	csa3	cas3,DEDDh,DinG,csa3,WYL	Type I-A	CAACTTTAGTTGTTAGGGGCTCTT	24	0	0	NA	NA	NA	1	1	Orphan	csa3,cas3,DEDDh,DinG,WYL	NA|77aa|up_5|NC_022113.1_2153786_2154017_-,NA|364aa|up_0|NC_022113.1_2157806_2158898_+,NA|35aa|down_0|NC_022113.1_2159339_2159444_-,NA|53aa|down_1|NC_022113.1_2160123_2160282_+	NA|237aa|up_9|NC_022113.1_2149404_2150115_+	PRK05819, deoD, DeoD-type purine-nucleoside phosphorylase	NA|148aa|up_8|NC_022113.1_2150235_2150679_-	COG0783, Dps, DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]	NA|138aa|up_7|NC_022113.1_2150878_2151292_-	COG3011, COG3011, Predicted thiol-disulfide oxidoreductase [General function    prediction only]	NA|458aa|up_6|NC_022113.1_2151740_2153114_-	pfam01878, EVE, EVE domain	NA|77aa|up_5|NC_022113.1_2153786_2154017_-	NA	NA|313aa|up_4|NC_022113.1_2154047_2154986_-	COG1482, ManA, Phosphomannose isomerase [Carbohydrate transport and metabolism]	NA|222aa|up_3|NC_022113.1_2155421_2156087_-	cd05243, SDR_a5, atypical (a) SDRs, subgroup 5	csa3|107aa|up_2|NC_022113.1_2156238_2156559_+	cd00090, HTH_ARSR, Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors	NA|327aa|up_1|NC_022113.1_2156560_2157541_+	COG1230, CzcD, Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]	NA|364aa|up_0|NC_022113.1_2157806_2158898_+	NA	NA|35aa|down_0|NC_022113.1_2159339_2159444_-	NA	NA|53aa|down_1|NC_022113.1_2160123_2160282_+	NA	NA|286aa|down_2|NC_022113.1_2160940_2161798_-	COG0561, Cof, Predicted hydrolases of the HAD superfamily [General function prediction only]	NA|261aa|down_3|NC_022113.1_2161865_2162648_-	COG1119, ModF, ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA [Inorganic ion transport and metabolism]	NA|602aa|down_4|NC_022113.1_2162879_2164685_-	PRK00331, PRK00331, isomerizing glutamine--fructose-6-phosphate transaminase	NA|513aa|down_5|NC_022113.1_2165365_2166904_+	COG2213, MtlA, Phosphotransferase system, mannitol-specific IIBC component [Carbohydrate transport and metabolism]	NA|711aa|down_6|NC_022113.1_2166938_2169071_+	COG3711, BglG, Transcriptional antiterminator [Transcription]	NA|145aa|down_7|NC_022113.1_2169082_2169517_+	COG4668, MtlA, Mannitol/fructose-specific phosphotransferase system, IIA domain [Carbohydrate transport and metabolism]	NA|369aa|down_8|NC_022113.1_2169516_2170623_+	PRK02318, PRK02318, mannitol-1-phosphate 5-dehydrogenase; Provisional	NA|452aa|down_9|NC_022113.1_2178618_2179974_-	PRK14316, glmM, phosphoglucosamine mutase; Provisional
GCF_000160335.2_ASM16033v2	NC_022113	Staphylococcus aureus subsp. aureus 55/2053, complete sequence	11	2177929-2178130	1	PILER-CR	no		cas3,DEDDh,DinG,csa3,WYL	Orphan	TCCTTGGTTGGCAGGTGCAGCTGGATGTGCTGTA	34	0	0	NA	NA	NA	2	2	Orphan	csa3,cas3,DEDDh,DinG,WYL	NA|364aa|up_9|NC_022113.1_2157806_2158898_+,NA|35aa|up_8|NC_022113.1_2159339_2159444_-,NA|53aa|up_7|NC_022113.1_2160123_2160282_+,NA	NA|364aa|up_9|NC_022113.1_2157806_2158898_+	NA	NA|35aa|up_8|NC_022113.1_2159339_2159444_-	NA	NA|53aa|up_7|NC_022113.1_2160123_2160282_+	NA	NA|286aa|up_6|NC_022113.1_2160940_2161798_-	COG0561, Cof, Predicted hydrolases of the HAD superfamily [General function prediction only]	NA|261aa|up_5|NC_022113.1_2161865_2162648_-	COG1119, ModF, ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA [Inorganic ion transport and metabolism]	NA|602aa|up_4|NC_022113.1_2162879_2164685_-	PRK00331, PRK00331, isomerizing glutamine--fructose-6-phosphate transaminase	NA|513aa|up_3|NC_022113.1_2165365_2166904_+	COG2213, MtlA, Phosphotransferase system, mannitol-specific IIBC component [Carbohydrate transport and metabolism]	NA|711aa|up_2|NC_022113.1_2166938_2169071_+	COG3711, BglG, Transcriptional antiterminator [Transcription]	NA|145aa|up_1|NC_022113.1_2169082_2169517_+	COG4668, MtlA, Mannitol/fructose-specific phosphotransferase system, IIA domain [Carbohydrate transport and metabolism]	NA|369aa|up_0|NC_022113.1_2169516_2170623_+	PRK02318, PRK02318, mannitol-1-phosphate 5-dehydrogenase; Provisional	NA|452aa|down_0|NC_022113.1_2178618_2179974_-	PRK14316, glmM, phosphoglucosamine mutase; Provisional	NA|311aa|down_1|NC_022113.1_2180000_2180933_-	COG4856, COG4856, Uncharacterized protein conserved in bacteria [Function unknown]	NA|270aa|down_2|NC_022113.1_2180934_2181744_-	COG1624, COG1624, Uncharacterized conserved protein [Function unknown]	NA|303aa|down_3|NC_022113.1_2181933_2182842_-	cd09989, Arginase, Arginase family	NA|355aa|down_4|NC_022113.1_2189058_2190123_-	pfam10609, ParA, NUBPL iron-transfer P-loop NTPase	NA|481aa|down_5|NC_022113.1_2190270_2191713_-	TIGR00711, Uncharacterized_MFS-type_transporter_YhcA, drug resistance transporter, EmrB/QacA subfamily	NA|158aa|down_6|NC_022113.1_2191901_2192375_-	pfam17080, SepA, Multidrug Resistance efflux pump	NA|448aa|down_7|NC_022113.1_2192496_2193840_-	TIGR00711, Uncharacterized_MFS-type_transporter_YhcA, drug resistance transporter, EmrB/QacA subfamily	NA|228aa|down_8|NC_022113.1_2194017_2194701_-	COG1272, COG1272, Predicted membrane protein, hemolysin III homolog [General function prediction only]	NA|396aa|down_9|NC_022113.1_2194719_2195907_-	cd04193, UDPGlcNAc_PPase, UDPGlcNAc pyrophosphorylase catalayzes the synthesis of UDPGlcNAc
GCF_000160335.2_ASM16033v2	NC_022113	Staphylococcus aureus subsp. aureus 55/2053, complete sequence	12	2236461-2236586	10	CRISPRCasFinder	no		cas3,DEDDh,DinG,csa3,WYL	Orphan	CCTCTTTACTCGAAAGCTCACAAAACTCTTGATATCA	37	0	0	NA	NA	NA	1	1	Orphan	csa3,cas3,DEDDh,DinG,WYL	NA|56aa|up_8|NC_022113.1_2226867_2227035_+,NA|61aa|up_1|NC_022113.1_2235383_2235566_-,NA	NA|283aa|up_9|NC_022113.1_2225290_2226139_-	cd19133, AKR_AKR5F1, the AKR5F family of aldo-keto reductase (AKR)	NA|56aa|up_8|NC_022113.1_2226867_2227035_+	NA	NA|809aa|up_7|NC_022113.1_2227031_2229458_+	cd01083, GAG_Lyase, Glycosaminoglycan (GAG) polysaccharide lyase family	NA|285aa|up_6|NC_022113.1_2229517_2230372_-	pfam01551, Peptidase_M23, Peptidase family M23	NA|272aa|up_5|NC_022113.1_2230582_2231398_-	cd02605, HAD_SPP, sucrose-phosphatase, similar to Synechocystis sp PCC 6803 SPP	NA|142aa|up_4|NC_022113.1_2231692_2232118_+	pfam03642, MAP, MAP domain	NA|235aa|up_3|NC_022113.1_2232508_2233213_-	COG3527, AlsD, Alpha-acetolactate decarboxylase [Secondary metabolites biosynthesis, transport, and catabolism]	NA|555aa|up_2|NC_022113.1_2233249_2234914_-	PRK08617, PRK08617, acetolactate synthase AlsS	NA|61aa|up_1|NC_022113.1_2235383_2235566_-	NA	NA|60aa|up_0|NC_022113.1_2236215_2236395_-	PRK09775, PRK09775, type II toxin-antitoxin system HipA family toxin YjjJ	NA|479aa|down_0|NC_022113.1_2236643_2238080_-	COG2865, COG2865, Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]	NA|133aa|down_1|NC_022113.1_2238428_2238827_-	PRK00132, rpsI, 30S ribosomal protein S9; Reviewed	NA|146aa|down_2|NC_022113.1_2238840_2239278_-	PRK09216, rplM, 50S ribosomal protein L13; Reviewed	NA|265aa|down_3|NC_022113.1_2239525_2240320_-	PRK00021, truA, tRNA pseudouridine(38-40) synthase TruA	NA|269aa|down_4|NC_022113.1_2240324_2241131_-	COG0619, CbiQ, ABC-type cobalt transport system, permease component CbiQ and related transporters [Inorganic ion transport and metabolism]	NA|287aa|down_5|NC_022113.1_2241120_2241981_-	PRK13646, cbiO, energy-coupling factor transporter ATPase	NA|270aa|down_6|NC_022113.1_2241977_2242787_-	PRK13648, cbiO, cobalt transporter ATP-binding subunit; Provisional	NA|123aa|down_7|NC_022113.1_2243319_2243688_-	PRK05591, rplQ, 50S ribosomal protein L17; Validated	NA|315aa|down_8|NC_022113.1_2243704_2244649_-	PRK05182, PRK05182, DNA-directed RNA polymerase subunit alpha; Provisional	NA|130aa|down_9|NC_022113.1_2244723_2245113_-	PRK05309, PRK05309, 30S ribosomal protein S11; Validated
GCF_000160335.2_ASM16033v2	NC_022113	Staphylococcus aureus subsp. aureus 55/2053, complete sequence	13	2750751-2750834	11	CRISPRCasFinder	no		cas3,DEDDh,DinG,csa3,WYL	Orphan	TTTCGAAATTCTCTGTGTTGGGACCC	26	1	3	2750777-2750808|2750777-2750808|2750777-2750808	NC_022113.1_2309180-2309149|NC_022113.1_716540-716571|NC_022113.1_966386-966417	NA	1	1	Orphan	csa3,cas3,DEDDh,DinG,WYL	NA|64aa|up_7|NC_022113.1_2744702_2744894_+,NA|166aa|up_6|NC_022113.1_2745980_2746478_-,NA	NA|253aa|up_9|NC_022113.1_2741982_2742741_+	COG1136, SalX, ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]	NA|627aa|up_8|NC_022113.1_2742730_2744611_+	pfam02687, FtsX, FtsX-like permease family	NA|64aa|up_7|NC_022113.1_2744702_2744894_+	NA	NA|166aa|up_6|NC_022113.1_2745980_2746478_-	NA	NA|250aa|up_5|NC_022113.1_2746479_2747229_-	pfam15526, Ntox21, Novel toxin 21	NA|268aa|up_4|NC_022113.1_2747247_2748051_-	cd07477, Peptidases_S8_Subtilisin_subset, Peptidase S8 family domain in Subtilisin proteins	NA|67aa|up_3|NC_022113.1_2748534_2748735_+	COG1278, CspC, Cold shock proteins [Transcription]	NA|190aa|up_2|NC_022113.1_2748861_2749431_-	cd00093, HTH_XRE, Helix-turn-helix XRE-family like proteins	NA|132aa|up_1|NC_022113.1_2749683_2750079_-	pfam11345, DUF3147, Protein of unknown function (DUF3147)	NA|118aa|up_0|NC_022113.1_2750146_2750500_-	pfam11345, DUF3147, Protein of unknown function (DUF3147)	NA|280aa|down_0|NC_022113.1_2751052_2751892_-	TIGR04285, parB-like_partition_protein, nucleoid occlusion protein	NA|240aa|down_1|NC_022113.1_2751934_2752654_-	PRK00107, gidB, 16S rRNA (guanine(527)-N(7))-methyltransferase RsmG	NA|626aa|down_2|NC_022113.1_2752653_2754531_-	PRK05192, PRK05192, tRNA uridine-5-carboxymethylaminomethyl(34) synthesis enzyme MnmG	NA|460aa|down_3|NC_022113.1_2754597_2755977_-	PRK05291, trmE, tRNA uridine-5-carboxymethylaminomethyl(34) synthesis GTPase MnmE	NA|118aa|down_4|NC_022113.1_2756120_2756474_-	PRK00499, rnpA, ribonuclease P; Reviewed	NA|46aa|down_5|NC_022113.1_2756594_2756732_-	pfam00468, Ribosomal_L34, Ribosomal protein L34	NA|NA	NA	NA|NA	NA	NA|NA	NA	NA|NA	NA
