The following contents displays predicted prophage regions
first line of each prophage describes the prophage information and the following lines describe the proteins and homology proteins in uniprot database
bacteria_id bac_def genome_size prophage_start  prophage_end    key_proteins    best_hit_species    CDS_number  attl_region attr_region
>prophage 1
CP031838	Staphylococcus aureus strain QD-CD9 chromosome, complete genome	2855865	12786	56019	2855865	protease,transposase,tRNA	Bacillus_phage(20.0%)	38	NA	NA
AXS22982.1|12786_14073_+|tRNA	serine--tRNA ligase	tRNA	A0A1B1IVT2	uncultured_Mediterranean_phage	51.2	2.7e-88
AXS22983.1|14724_15420_+	branched-chain amino acid ABC transporter permease	NA	NA	NA	NA	NA
AXS22984.1|15416_15746_+	AzlD domain-containing protein	NA	NA	NA	NA	NA
AXS22985.1|16107_17076_+	alpha/beta fold hydrolase	NA	NA	NA	NA	NA
AXS22986.1|17368_18307_+	DUF2232 domain-containing protein	NA	NA	NA	NA	NA
AXS22987.1|18321_20289_+	DHH family phosphoesterase	NA	NA	NA	NA	NA
AXS22988.1|20285_20732_+	50S ribosomal protein L9	NA	NA	NA	NA	NA
AXS22989.1|20763_22164_+	replicative DNA helicase	NA	A0A1P8VVQ6	Streptococcus_phage	48.1	5.4e-111
AXS22990.1|22213_22441_-	hypothetical protein	NA	NA	NA	NA	NA
AXS22991.1|22441_23725_+	adenylosuccinate synthetase	NA	L7Y4J5	Megavirus	34.6	1.8e-68
AXS22992.1|24920_25622_+	DNA-binding response regulator	NA	W8CYM9	Bacillus_phage	39.2	3.5e-42
AXS22993.1|25634_27461_+	cell wall metabolism sensor histidine kinase WalK	NA	W8CYF6	Bacillus_phage	31.3	1.6e-30
AXS22994.1|27453_28788_+	hypothetical protein	NA	NA	NA	NA	NA
AXS22995.1|28788_29577_+	hypothetical protein	NA	NA	NA	NA	NA
AXS22996.1|29972_30773_+	MBL fold metallo-hydrolase	NA	A0A0C5AJ83	Bacteriophage	35.9	1.0e-37
AXS22997.1|30999_33318_+	LPXTG cell wall anchor domain-containing protein	NA	NA	NA	NA	NA
AXS22998.1|33492_33687_-	hypothetical protein	NA	NA	NA	NA	NA
AXS22999.1|33685_34165_+	23S rRNA (pseudouridine(1915)-N(3))-methyltransferase RlmH	NA	NA	NA	NA	NA
AXS25650.1|35289_35520_+	DUF2975 domain-containing protein	NA	NA	NA	NA	NA
AXS23000.1|35527_35734_+	transcriptional regulator	NA	NA	NA	NA	NA
AXS23001.1|36082_37186_+	DUF418 domain-containing protein	NA	NA	NA	NA	NA
AXS23002.1|37205_37934_+|protease	CPBP family intramembrane metalloprotease	protease	NA	NA	NA	NA
AXS23003.1|38133_39228_+|transposase	IS30 family transposase	transposase	H7BWC8	unidentified_phage	33.9	6.9e-37
AXS23004.1|41823_42225_+	hypothetical protein	NA	NA	NA	NA	NA
AXS23005.1|42268_42370_-	hypothetical protein	NA	NA	NA	NA	NA
AXS23006.1|42388_42772_-	hypothetical protein	NA	A0A2I6AZV9	Macacine_betaherpesvirus	37.4	6.4e-14
AXS23007.1|42755_42977_-|transposase	transposase	transposase	NA	NA	NA	NA
AXS23008.1|43078_43519_-	hypothetical protein	NA	NA	NA	NA	NA
AXS23009.1|44806_45901_-|transposase	IS30 family transposase	transposase	H7BWC8	unidentified_phage	33.9	6.9e-37
AXS23010.1|46100_46829_-|protease	CPBP family intramembrane metalloprotease	protease	NA	NA	NA	NA
AXS23011.1|46848_47952_-	DUF418 domain-containing protein	NA	NA	NA	NA	NA
AXS23012.1|48300_48507_-	transcriptional regulator	NA	NA	NA	NA	NA
AXS25651.1|48514_48745_-	DUF2975 domain-containing protein	NA	NA	NA	NA	NA
AXS23013.1|50364_50622_-	hypothetical protein	NA	NA	NA	NA	NA
AXS23014.1|50689_52480_-	DUF927 domain-containing protein	NA	NA	NA	NA	NA
AXS23015.1|52605_54033_-	hypothetical protein	NA	NA	NA	NA	NA
AXS23016.1|54149_54914_+	hypothetical protein	NA	NA	NA	NA	NA
AXS23017.1|54903_56019_+|protease	ATP-dependent Clp protease ATP-binding subunit	protease	A0A1C3S747	Escherichia_phage	24.3	3.9e-11
>prophage 2
CP031838	Staphylococcus aureus strain QD-CD9 chromosome, complete genome	2855865	769791	823422	2855865	protease,transposase,terminase	Staphylococcus_phage(50.0%)	53	NA	NA
AXS23698.1|769791_770535_-|protease	CPBP family intramembrane metalloprotease	protease	NA	NA	NA	NA
AXS23699.1|770709_770994_+	co-chaperone GroES	NA	A0A221S386	uncultured_virus	46.2	4.7e-14
AXS23700.1|771069_772686_+	molecular chaperone GroEL	NA	A0A240F779	uncultured_virus	54.7	3.4e-157
AXS23701.1|773387_773600_+	pathogenicity island family protein	NA	Q4ZE86	Staphylococcus_phage	74.3	1.1e-23
AXS23702.1|773596_774187_+|terminase	terminase small subunit	terminase	Q4ZE85	Staphylococcus_phage	94.7	1.2e-96
AXS25675.1|774503_774881_+	hypothetical protein	NA	NA	NA	NA	NA
AXS23703.1|775045_775489_+	GNAT family N-acetyltransferase	NA	NA	NA	NA	NA
AXS23704.1|776342_777650_-	TrkH family potassium uptake protein	NA	NA	NA	NA	NA
AXS23705.1|777810_778722_+	iron-hydroxamate ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AXS23706.1|778783_779575_+	class I SAM-dependent methyltransferase	NA	NA	NA	NA	NA
AXS23707.1|779999_781223_-	ArgE/DapE family deacylase	NA	NA	NA	NA	NA
AXS23708.1|781657_782713_+	bi-component leukocidin LukGH subunit H	NA	A0A2I6PDF3	Staphylococcus_phage	32.1	1.3e-35
AXS23709.1|782734_783790_+	bi-component leukocidin LukGH subunit G	NA	A0A1X9IGW5	Staphylococcus_phage	30.6	9.0e-26
AXS23710.1|783988_784981_-	sphingomyelin phosphodiesterase	NA	A0A1P8L6H7	Staphylococcus_phage	99.6	2.4e-161
AXS23711.1|785369_787418_+	MAP domain-containing protein	NA	NA	NA	NA	NA
AXS23712.1|787741_789028_-	aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme	NA	NA	NA	NA	NA
AXS23713.1|789227_789326_+	hypothetical protein	NA	NA	NA	NA	NA
AXS23714.1|789568_789745_+	hypothetical protein	NA	NA	NA	NA	NA
AXS23715.1|790003_790384_+	GntR family transcriptional regulator	NA	NA	NA	NA	NA
AXS23716.1|790380_791277_+	phenol-soluble modulin export ABC transporter ATP-binding protein PmtA	NA	A0A2H4PQG7	Staphylococcus_phage	30.2	1.1e-16
AXS23717.1|791277_791958_+	phenol-soluble modulin export ABC transporter permease subunit PmtB	NA	NA	NA	NA	NA
AXS23718.1|791954_792827_+	phenol-soluble modulin export ABC transporter ATP-binding protein PmtC	NA	A0A2H4PQG7	Staphylococcus_phage	35.2	6.1e-28
AXS23719.1|792826_793567_+	phenol-soluble modulin export ABC transporter permease subunit PmtD	NA	NA	NA	NA	NA
AXS23720.1|793632_794196_-	thioredoxin family protein	NA	NA	NA	NA	NA
AXS23721.1|794316_794841_+	hypothetical protein	NA	NA	NA	NA	NA
AXS23722.1|794900_795458_+	DUF1700 domain-containing protein	NA	NA	NA	NA	NA
AXS23723.1|795454_796297_+	hypothetical protein	NA	NA	NA	NA	NA
AXS23724.1|796353_797394_-	linear amide C-N hydrolase	NA	NA	NA	NA	NA
AXS23725.1|797844_798018_+	hypothetical protein	NA	NA	NA	NA	NA
AXS23726.1|799040_800192_+|transposase	transposase	transposase	P97010	Streptococcus_pyogenes_phage	31.6	1.8e-11
AXS25676.1|800230_802258_+|transposase	transposase	transposase	NA	NA	NA	NA
AXS23727.1|802266_802632_+|transposase	transposase	transposase	NA	NA	NA	NA
AXS23728.1|802618_804007_+	hypothetical protein	NA	NA	NA	NA	NA
AXS23729.1|804049_804469_-	YolD-like family protein	NA	U3PG23	Staphylococcus_phage	53.5	3.1e-30
AXS23730.1|804773_805619_-	penicillin-hydrolyzing class A beta-lactamase BlaZ	NA	A0A1B0VBP7	Salmonella_phage	33.9	4.4e-31
AXS23731.1|805725_807483_+	beta-lactam sensor/signal transducer BlaR1	NA	NA	NA	NA	NA
AXS23732.1|807472_807853_+	penicillinase repressor BlaI	NA	NA	NA	NA	NA
AXS23733.1|808311_809340_+	hypothetical protein	NA	NA	NA	NA	NA
AXS23734.1|809459_810839_-	aldehyde dehydrogenase	NA	NA	NA	NA	NA
AXS23735.1|810890_811064_+	hypothetical protein	NA	NA	NA	NA	NA
AXS23736.1|811256_812186_-	manganese-dependent inorganic pyrophosphatase	NA	NA	NA	NA	NA
AXS23737.1|812238_812799_-	cysteine hydrolase	NA	G3MA16	Bacillus_virus	41.2	2.0e-32
AXS23738.1|813170_814268_+	pectate lyase	NA	U5PWM6	Bacillus_phage	34.9	2.5e-47
AXS23739.1|814471_816034_+	SLC13 family permease	NA	NA	NA	NA	NA
AXS23740.1|816044_816152_-	hypothetical protein	NA	NA	NA	NA	NA
AXS23741.1|816223_817018_-	prephenate dehydratase	NA	NA	NA	NA	NA
AXS23742.1|817037_818114_-	nitric oxide synthase oxygenase	NA	NA	NA	NA	NA
AXS23743.1|818297_819767_+	nicotinate phosphoribosyltransferase	NA	G3MA18	Bacillus_virus	45.1	3.5e-108
AXS23744.1|819759_820581_+	NAD(+) synthetase	NA	G3MA24	Bacillus_virus	52.7	2.3e-69
AXS23745.1|820851_821454_+	DUF2179 domain-containing protein	NA	NA	NA	NA	NA
AXS23746.1|821434_821608_+	NETI motif-containing protein	NA	NA	NA	NA	NA
AXS23747.1|821898_822225_-	staphostatin A	NA	NA	NA	NA	NA
AXS23748.1|822255_823422_-|protease	cysteine protease staphopain A	protease	NA	NA	NA	NA
>prophage 3
CP031838	Staphylococcus aureus strain QD-CD9 chromosome, complete genome	2855865	916310	921846	2855865	transposase	Staphylococcus_phage(83.33%)	6	NA	NA
AXS23832.1|916310_917075_+	exotoxin	NA	A0A1X9H080	Staphylococcus_phage	37.1	2.3e-31
AXS23833.1|917355_918075_+	exotoxin	NA	A0A1X9H080	Staphylococcus_phage	35.8	2.3e-25
AXS23834.1|918109_918838_+	exotoxin	NA	A0A1X9H080	Staphylococcus_phage	39.2	1.1e-27
AXS23835.1|918991_919762_+	exotoxin	NA	A0A097PAT7	Streptococcus_pyogenes_phage	43.2	1.4e-44
AXS23836.1|919800_920556_+	exotoxin	NA	A0A075M4C7	Staphylococcus_phage	41.0	1.0e-39
AXS23837.1|920673_921846_-|transposase	IS256 family transposase IS256	transposase	A0A0N9STL0	Staphylococcus_phage	100.0	3.5e-135
>prophage 4
CP031838	Staphylococcus aureus strain QD-CD9 chromosome, complete genome	2855865	940285	974789	2855865	protease	Staphylococcus_phage(90.62%)	41	NA	NA
AXS23853.1|940285_941038_-	hypothetical protein	NA	A0A097PAT7	Streptococcus_pyogenes_phage	47.2	4.4e-51
AXS23854.1|941064_941835_-	exotoxin	NA	A0EX09	Staphylococcus_phage	33.5	4.3e-25
AXS23855.1|941834_942461_-	hypothetical protein	NA	A0A2H4PQM7	Staphylococcus_phage	93.8	3.9e-93
AXS23856.1|942534_943530_-	DUF4352 domain-containing protein	NA	A0A2H4PQN2	Staphylococcus_phage	97.2	4.2e-73
AXS23857.1|943610_944261_-	calcium-binding protein	NA	A0A2H4PQM8	Staphylococcus_phage	99.1	3.0e-56
AXS25681.1|944564_945020_+	DUF4909 domain-containing protein	NA	A0A2H4PQN7	Staphylococcus_phage	98.6	1.2e-78
AXS23858.1|945178_946657_+	o-succinylbenzoate--CoA ligase	NA	A0A2H4PQM9	Staphylococcus_phage	100.0	1.5e-289
AXS23859.1|946661_947663_+	o-succinylbenzoate synthase	NA	A0A2H4PQM0	Staphylococcus_phage	98.2	9.7e-187
AXS23860.1|947659_947917_-	membrane protein insertion efficiency factor YidD	NA	A0A2H4PQM5	Staphylococcus_phage	98.8	3.6e-45
AXS23861.1|947982_948456_+	nucleoside triphosphatase YtkD	NA	A0A2H4PQM4	Staphylococcus_phage	96.8	3.0e-82
AXS25682.1|948460_949207_+	S9 family peptidase	NA	A0A2H4PQM6	Staphylococcus_phage	98.8	2.9e-143
AXS23862.1|949584_951177_-	phosphoenolpyruvate carboxykinase (ATP)	NA	A0A2H4PQN1	Staphylococcus_phage	100.0	0.0e+00
AXS23863.1|951548_952742_+	S-adenosylmethionine synthase	NA	A0A2H4PQS6	Staphylococcus_phage	99.7	1.9e-218
AXS23864.1|952866_953775_+	NERD domain-containing protein	NA	A0A2H4PQQ8	Staphylococcus_phage	100.0	3.4e-138
AXS23865.1|953986_954820_+	aldo/keto reductase	NA	A0A2H4PQR8	Staphylococcus_phage	99.3	7.8e-158
AXS23866.1|954831_955011_-	hypothetical protein	NA	NA	NA	NA	NA
AXS23867.1|955202_955556_-	CrcB family protein	NA	A0A2H4PQQ7	Staphylococcus_phage	100.0	2.6e-22
AXS23868.1|955552_955918_-	fluoride efflux transporter CrcB	NA	A0A2H4PQR0	Staphylococcus_phage	100.0	3.6e-59
AXS23869.1|956173_956476_-	hypothetical protein	NA	NA	NA	NA	NA
AXS23870.1|956735_957449_+	transaldolase	NA	M1PR54	Cyanophage	35.3	5.5e-19
AXS23871.1|957888_958524_-|protease	CPBP family intramembrane metalloprotease SdpA	protease	NA	NA	NA	NA
AXS23872.1|958819_959263_+	hypothetical protein	NA	A0A2H4PQT8	Staphylococcus_phage	98.0	3.5e-56
AXS23873.1|959249_959693_-	competence protein ComK	NA	NA	NA	NA	NA
AXS23874.1|959805_960276_-	RNA polymerase sigma factor SigS	NA	A0A2H4PQT5	Staphylococcus_phage	99.4	1.0e-82
AXS23875.1|960474_960699_+	hypothetical protein	NA	NA	NA	NA	NA
AXS23876.1|960974_961829_+	autolysin	NA	Q4ZCC7	Staphylococcus_virus	38.6	9.8e-39
AXS23877.1|962123_962519_-	protein ArsC	NA	A0A2H4PQT9	Staphylococcus_phage	100.0	6.3e-73
AXS23878.1|962536_963829_-	arsenical efflux pump membrane protein ArsB	NA	A0A2H4PQU3	Staphylococcus_phage	99.5	5.0e-228
AXS23879.1|963828_964143_-	ArsR family transcriptional regulator	NA	A0A2H4PQT4	Staphylococcus_phage	98.1	9.8e-53
AXS23880.1|964665_966168_+	pyridine nucleotide-disulfide oxidoreductase	NA	A0A2H4PQX2	Staphylococcus_phage	100.0	2.3e-30
AXS23881.1|966660_967692_+	bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase RibD	NA	A0A2H4PQS8	Staphylococcus_phage	98.8	2.0e-195
AXS23882.1|967698_968331_+	riboflavin synthase	NA	A0A2H4PQS5	Staphylococcus_phage	100.0	3.4e-113
AXS23883.1|968341_969523_+	riboflavin biosynthesis protein RibBA	NA	A0A2H4PQS2	Staphylococcus_phage	100.0	1.7e-227
AXS23884.1|969535_970000_+	6,7-dimethyl-8-ribityllumazine synthase	NA	A0A2H4PQS3	Staphylococcus_phage	100.0	4.5e-70
AXS23885.1|970121_971123_-	proline dehydrogenase	NA	A0A2H4PQT6	Staphylococcus_phage	100.0	3.1e-185
AXS25683.1|971031_971223_+	hypothetical protein	NA	NA	NA	NA	NA
AXS23886.1|971234_971354_+	hypothetical protein	NA	NA	NA	NA	NA
AXS23887.1|971356_972184_+	alpha/beta hydrolase	NA	NA	NA	NA	NA
AXS23888.1|972754_973156_+	MarR family transcriptional regulator	NA	NA	NA	NA	NA
AXS23889.1|973275_973839_-	methyltransferase domain-containing protein	NA	A0A2H4PQV0	Staphylococcus_phage	99.5	8.3e-103
AXS23890.1|973835_974789_-	TIGR01212 family radical SAM protein	NA	A0A2H4PQV5	Staphylococcus_phage	100.0	2.2e-79
>prophage 5
CP031838	Staphylococcus aureus strain QD-CD9 chromosome, complete genome	2855865	1104894	1163811	2855865	protease,transposase,tRNA	uncultured_Mediterranean_phage(16.67%)	57	NA	NA
AXS23997.1|1104894_1105980_+|transposase	transposase	transposase	A0A0A8WIF9	Clostridium_phage	25.7	2.9e-11
AXS25689.1|1105982_1107896_+|transposase	transposase	transposase	NA	NA	NA	NA
AXS23998.1|1107897_1108263_+|transposase	transposase	transposase	NA	NA	NA	NA
AXS23999.1|1108545_1108962_-	flavodoxin family protein	NA	NA	NA	NA	NA
AXS24000.1|1109139_1110567_-	chloramphenicol/florfenicol efflux MFS transporter FexA	NA	NA	NA	NA	NA
AXS24001.1|1111622_1111907_+	hypothetical protein	NA	NA	NA	NA	NA
AXS24002.1|1112023_1112221_-	hypothetical protein	NA	NA	NA	NA	NA
AXS24003.1|1112380_1112854_+	DUF4930 family protein	NA	NA	NA	NA	NA
AXS24004.1|1112927_1113047_+	hypothetical protein	NA	NA	NA	NA	NA
AXS24005.1|1113245_1114088_+	rod shape-determining protein MreC	NA	NA	NA	NA	NA
AXS24006.1|1114087_1114618_+	rod shape-determining protein MreD	NA	NA	NA	NA	NA
AXS24007.1|1114853_1115162_+	50S ribosomal protein L21	NA	NA	NA	NA	NA
AXS24008.1|1115167_1115488_+|protease	ribosomal-processing cysteine protease Prp	protease	NA	NA	NA	NA
AXS24009.1|1115499_1115784_+	50S ribosomal protein L27	NA	NA	NA	NA	NA
AXS24010.1|1116267_1117560_+	GTPase ObgE	NA	NA	NA	NA	NA
AXS24011.1|1117572_1118028_+	ACT domain-containing protein	NA	NA	NA	NA	NA
AXS24012.1|1118041_1118644_+	Holliday junction branch migration protein RuvA	NA	NA	NA	NA	NA
AXS24013.1|1118675_1119680_+	Holliday junction branch migration DNA helicase RuvB	NA	B3GAM6	uncultured_virus	29.1	1.7e-05
AXS24014.1|1119681_1120707_+|tRNA	tRNA preQ1(34) S-adenosylmethionine ribosyltransferase-isomerase QueA	tRNA	NA	NA	NA	NA
AXS24015.1|1120729_1121869_+|tRNA	tRNA guanosine(34) transglycosylase Tgt	tRNA	A0A1B1IVQ4	uncultured_Mediterranean_phage	44.7	5.4e-85
AXS24016.1|1121887_1122148_+	preprotein translocase subunit YajC	NA	A0A1B1IVR5	uncultured_Mediterranean_phage	35.3	8.2e-05
AXS24017.1|1122422_1124702_+	protein translocase subunit SecDF	NA	A0A1B1IVP7	uncultured_Mediterranean_phage	35.8	1.8e-31
AXS24018.1|1124904_1127178_+	single-stranded-DNA-specific exonuclease RecJ	NA	A7KV88	Bacillus_phage	29.1	1.1e-63
AXS24019.1|1127199_1127718_+	adenine phosphoribosyltransferase	NA	A0A1V0SKE5	Klosneuvirus	46.5	5.6e-29
AXS24020.1|1128145_1130335_+	bifunctional (p)ppGpp synthetase/guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase	NA	A0A2I2L310	Orpheovirus	37.7	6.9e-12
AXS24021.1|1130346_1130799_+|tRNA	D-tyrosyl-tRNA(Tyr) deacylase	tRNA	NA	NA	NA	NA
AXS24022.1|1130795_1131671_+	cell wall amidase	NA	A0A0N9SGH1	Paenibacillus_phage	33.7	4.7e-12
AXS24023.1|1132131_1133394_+|tRNA	histidine--tRNA ligase	tRNA	NA	NA	NA	NA
AXS24024.1|1133409_1135176_+|tRNA	aspartate--tRNA ligase	tRNA	A0A2K9L0E9	Tupanvirus	27.3	1.3e-16
AXS24025.1|1135508_1135637_+	hypothetical protein	NA	NA	NA	NA	NA
AXS24026.1|1135636_1136410_+|tRNA	tRNA threonylcarbamoyladenosine dehydratase	tRNA	NA	NA	NA	NA
AXS24027.1|1136570_1137845_-	replication-associated recombination protein A	NA	A0A127AWE7	Bacillus_phage	50.7	1.4e-105
AXS24028.1|1137929_1138352_+	Rrf2 family transcriptional regulator	NA	NA	NA	NA	NA
AXS24029.1|1138451_1138634_+	CsbD family protein	NA	NA	NA	NA	NA
AXS24030.1|1138673_1138820_+	hypothetical protein	NA	NA	NA	NA	NA
AXS24031.1|1139056_1140070_-	LLM class flavin-dependent oxidoreductase	NA	NA	NA	NA	NA
AXS24032.1|1140381_1141524_+	cysteine desulfurase	NA	A0A1X7QGF3	Faustovirus	29.3	8.3e-33
AXS24033.1|1141524_1142643_+|tRNA	tRNA 2-thiouridine(34) synthase MnmA	tRNA	NA	NA	NA	NA
AXS24034.1|1143277_1143946_+	tetratricopeptide repeat protein	NA	NA	NA	NA	NA
AXS24035.1|1143947_1146425_+	ATP-dependent RecD-like DNA helicase	NA	A0A0K2FLP8	Brevibacillus_phage	29.0	1.1e-66
AXS24036.1|1146767_1149398_+|tRNA	alanine--tRNA ligase	tRNA	A0A1V0SK38	Klosneuvirus	34.4	3.2e-64
AXS24037.1|1149460_1149721_+	IreB family regulatory phosphoprotein	NA	NA	NA	NA	NA
AXS24038.1|1149724_1150153_+	Holliday junction resolvase RuvX	NA	NA	NA	NA	NA
AXS24039.1|1150167_1150476_+	DUF1292 domain-containing protein	NA	NA	NA	NA	NA
AXS24040.1|1150760_1151399_+	O-methyltransferase	NA	A0A2P1JQT7	Mycobacterium_phage	28.8	1.6e-09
AXS24041.1|1151401_1152325_+	U32 family peptidase	NA	NA	NA	NA	NA
AXS24042.1|1152336_1153605_+|protease	collagenase-like protease	protease	Q6DW11	Phage_TP	31.7	4.0e-36
AXS24043.1|1153604_1154228_+	uridine kinase	NA	A0A1V0SAA3	Catovirus	41.1	2.8e-35
AXS24044.1|1154255_1154732_+	transcription elongation factor GreA	NA	NA	NA	NA	NA
AXS24045.1|1155057_1155792_+	5-oxoprolinase subunit PxpB	NA	NA	NA	NA	NA
AXS24046.1|1155781_1156792_+	biotin-dependent carboxyltransferase family protein	NA	NA	NA	NA	NA
AXS24047.1|1156793_1157243_+	acetyl-CoA carboxylase biotin carboxyl carrier protein subunit	NA	NA	NA	NA	NA
AXS24048.1|1157256_1158618_+	acetyl-CoA carboxylase biotin carboxylase subunit	NA	NA	NA	NA	NA
AXS24049.1|1158617_1159370_+	LamB/YcsF family protein	NA	NA	NA	NA	NA
AXS24050.1|1159381_1160611_+	divalent metal cation transporter	NA	NA	NA	NA	NA
AXS24051.1|1161871_1162264_-	NimC/NimA family protein	NA	NA	NA	NA	NA
AXS24052.1|1162548_1163811_-|transposase	IS1380-like element ISEnca1 family transposase	transposase	A0A1B0VDR3	Salmonella_phage	92.9	1.2e-35
>prophage 6
CP031838	Staphylococcus aureus strain QD-CD9 chromosome, complete genome	2855865	1198996	1207326	2855865	tRNA	Caulobacter_phage(16.67%)	7	NA	NA
AXS24090.1|1198996_1200814_+	DNA primase	NA	A0A0K1LMQ9	Caulobacter_phage	36.0	3.6e-54
AXS24091.1|1201037_1202144_+	RNA polymerase sigma factor SigA	NA	A0A2I7SAT0	Vibrio_phage	38.1	1.1e-37
AXS24092.1|1202274_1202952_+|tRNA	tRNA (adenine-N(1))-methyltransferase	tRNA	NA	NA	NA	NA
AXS24093.1|1202954_1204055_+	Nif3-like dinuclear metal center hexameric protein	NA	A0A1S5V250	Saudi_moumouvirus	29.6	5.2e-08
AXS24094.1|1204168_1205515_+	DEAD/DEAH box helicase	NA	A0A1V0SIR5	Klosneuvirus	34.0	3.1e-55
AXS24095.1|1205524_1206415_+	endonuclease	NA	A0A2H4UU70	Bodo_saltans_virus	36.0	3.4e-26
AXS24096.1|1206540_1207326_+	metal ABC transporter ATP-binding protein	NA	A0A2H4PQG7	Staphylococcus_phage	28.3	4.7e-19
>prophage 7
CP031838	Staphylococcus aureus strain QD-CD9 chromosome, complete genome	2855865	1481415	1497421	2855865	portal,integrase,terminase,head	Staphylococcus_phage(60.87%)	27	1479412:1479429	1503681:1503698
1479412:1479429	attL	ATTCAATCATTAATATAT	NA	NA	NA	NA
AXS24342.1|1481415_1482759_-|head	phage head morphogenesis protein	head	A0A1J0MFV1	Staphylococcus_phage	56.8	1.3e-138
AXS24343.1|1482768_1484196_-|portal	phage portal protein	portal	Q4ZE36	Staphylococcus_virus	71.7	6.8e-194
AXS24344.1|1484208_1485483_-|terminase	PBSX family phage terminase large subunit	terminase	Q4ZE37	Staphylococcus_virus	76.2	3.2e-195
AXS24345.1|1485469_1485898_-	helix-turn-helix domain-containing protein	NA	A1EAE0	Streptococcus_phage	45.1	1.1e-25
AXS24346.1|1486050_1486539_-	RNA polymerase subunit sigma-70	NA	R9TMH4	Paenibacillus_phage	28.3	8.7e-08
AXS24347.1|1486581_1486815_-	hypothetical protein	NA	NA	NA	NA	NA
AXS24348.1|1486815_1487280_-	hypothetical protein	NA	C9E2P0	Enterococcus_phage	43.0	3.2e-20
AXS24349.1|1487276_1487384_-	DUF1381 domain-containing protein	NA	C8CH06	Staphylococcus_phage	87.5	1.2e-07
AXS24350.1|1487514_1488045_-	nucleotide pyrophosphohydrolase	NA	A0A1P8VVP1	Streptococcus_phage	39.1	2.3e-22
AXS24351.1|1488037_1488349_-	hypothetical protein	NA	NA	NA	NA	NA
AXS24352.1|1488354_1488513_-	hypothetical protein	NA	A0A0E3T9L7	Staphylococcus_phage	90.4	6.7e-18
AXS24353.1|1488527_1488818_-	hypothetical protein	NA	A0A223LIA9	Staphylococcus_phage	58.1	7.2e-18
AXS24354.1|1488818_1489721_-	DnaD domain protein	NA	A0A1P8L6F0	Staphylococcus_phage	51.7	2.9e-49
AXS25697.1|1489733_1490228_-	single-stranded DNA-binding protein	NA	A7TWM8	Staphylococcus_phage	94.0	6.4e-83
AXS24355.1|1490308_1491088_-	ATP-binding protein	NA	A0A1W6JPW0	Staphylococcus_phage	88.0	2.3e-127
AXS24356.1|1491088_1491625_-	hypothetical protein	NA	A0A0H3U480	Staphylococcus_phage	81.9	4.8e-76
AXS24357.1|1491629_1491896_-	hypothetical protein	NA	A0A2I6PDG2	Staphylococcus_phage	53.6	3.0e-18
AXS24358.1|1491885_1492203_-	DUF2482 family protein	NA	W5RAK4	Staphylococcus_phage	80.6	1.6e-39
AXS24359.1|1492289_1492451_-	DUF1270 family protein	NA	R4IH12	Staphylococcus_phage	69.8	1.1e-12
AXS24360.1|1492549_1493233_-	phage repressor protein	NA	A9CR56	Staphylococcus_phage	85.6	5.2e-107
AXS24361.1|1493293_1493500_+	hypothetical protein	NA	A1BTY8	Staphylococcus_virus	75.0	3.3e-25
AXS24362.1|1493923_1494199_-	hypothetical protein	NA	NA	NA	NA	NA
AXS24363.1|1494225_1494444_-	DUF739 family protein	NA	A0A2I6PE94	Staphylococcus_phage	62.5	4.9e-19
AXS24364.1|1494611_1495004_+	helix-turn-helix domain-containing protein	NA	A0A2I6PE55	Staphylococcus_phage	53.6	1.6e-28
AXS24365.1|1495150_1495534_+	hypothetical protein	NA	NA	NA	NA	NA
AXS24366.1|1495545_1496241_+	hypothetical protein	NA	A0A2H4J5B8	uncultured_Caudovirales_phage	50.3	1.4e-06
AXS24367.1|1496293_1497421_+|integrase	site-specific integrase	integrase	A0A0C5AN64	Paenibacillus_phage	31.4	6.2e-33
1503681:1503698	attR	ATATATTAATGATTGAAT	NA	NA	NA	NA
>prophage 8
CP031838	Staphylococcus aureus strain QD-CD9 chromosome, complete genome	2855865	1753000	1761473	2855865		Synechococcus_phage(33.33%)	9	NA	NA
AXS24606.1|1753000_1753567_-	phosphoribosylglycinamide formyltransferase	NA	M4QRX9	Synechococcus_phage	40.1	6.1e-29
AXS24607.1|1753569_1754598_-	phosphoribosylformylglycinamidine cyclo-ligase	NA	Q58MH8	Prochlorococcus_phage	41.7	2.0e-62
AXS24608.1|1754590_1756075_-	amidophosphoribosyltransferase	NA	A0A0M3SGR2	Mollivirus	31.7	3.2e-45
AXS24609.1|1756053_1758243_-	phosphoribosylformylglycinamidine synthase subunit PurL	NA	A6N228	Microbacterium_phage	39.8	3.5e-141
AXS24610.1|1758235_1758907_-	phosphoribosylformylglycinamidine synthase subunit PurQ	NA	NA	NA	NA	NA
AXS24611.1|1758908_1759172_-	phosphoribosylformylglycinamidine synthase subunit PurS	NA	NA	NA	NA	NA
AXS24612.1|1759171_1759876_-	phosphoribosylaminoimidazolesuccinocarboxamide synthase	NA	M4R1E8	Synechococcus_phage	42.1	7.3e-48
AXS24613.1|1759879_1761004_-	5-(carboxyamino)imidazole ribonucleotide synthase	NA	NA	NA	NA	NA
AXS24614.1|1760990_1761473_-	5-(carboxyamino)imidazole ribonucleotide mutase	NA	A0A2P0VNU7	Tetraselmis_virus	44.7	6.2e-22
>prophage 9
CP031838	Staphylococcus aureus strain QD-CD9 chromosome, complete genome	2855865	1780597	1852956	2855865	portal,tail,terminase,integrase,holin,protease,head,capsid,bacteriocin	Staphylococcus_phage(82.89%)	100	1806169:1806195	1850085:1850111
AXS24630.1|1780597_1781608_+|protease	serine protease	protease	A0A2H4PQP7	Staphylococcus_phage	32.3	6.2e-16
AXS24631.1|1781689_1782871_+|protease	cysteine protease staphopain B	protease	NA	NA	NA	NA
AXS24632.1|1782908_1783238_+	staphostatin B	NA	NA	NA	NA	NA
AXS24633.1|1783475_1784297_-	1,4-dihydroxy-2-naphthoyl-CoA synthase	NA	NA	NA	NA	NA
AXS24634.1|1784289_1785093_-	2-succinyl-6-hydroxy-2, 4-cyclohexadiene-1-carboxylate synthase	NA	NA	NA	NA	NA
AXS24635.1|1785079_1786753_-	2-succinyl-5-enolpyruvyl-6-hydroxy-3- cyclohexene-1-carboxylic-acid synthase	NA	NA	NA	NA	NA
AXS24636.1|1786739_1787951_-	isochorismate synthase	NA	NA	NA	NA	NA
AXS24637.1|1788027_1788132_-	hypothetical protein	NA	NA	NA	NA	NA
AXS24638.1|1788282_1789221_+	1,4-dihydroxy-2-naphthoate polyprenyltransferase	NA	NA	NA	NA	NA
AXS24639.1|1789272_1789824_-	GNAT family N-acetyltransferase	NA	NA	NA	NA	NA
AXS24640.1|1789913_1790204_+	NINE protein	NA	A0A060AN66	Enterococcus_phage	38.0	7.5e-07
AXS24641.1|1790267_1790399_+	hypothetical protein	NA	NA	NA	NA	NA
AXS24642.1|1791892_1792249_+	DoxX family protein	NA	NA	NA	NA	NA
AXS24643.1|1792337_1792475_-	poly(glycerol-phosphate) alpha-glucosyltransferase	NA	NA	NA	NA	NA
AXS24644.1|1792615_1792906_+	hypothetical protein	NA	NA	NA	NA	NA
AXS24645.1|1792993_1793635_-	ATP-binding cassette domain-containing protein	NA	G9BWD6	Planktothrix_phage	33.0	1.7e-19
AXS24646.1|1793631_1793952_-	YxeA family protein	NA	NA	NA	NA	NA
AXS25706.1|1795962_1796235_-|bacteriocin	lactococcin 972 family bacteriocin	bacteriocin	NA	NA	NA	NA
AXS24647.1|1796244_1796346_-	hypothetical protein	NA	NA	NA	NA	NA
AXS24648.1|1797261_1797864_-|protease	CPBP family intramembrane metalloprotease	protease	NA	NA	NA	NA
AXS24649.1|1797878_1798055_-	DUF2187 domain-containing protein	NA	NA	NA	NA	NA
AXS24650.1|1798253_1799240_+	lipoate--protein ligase	NA	NA	NA	NA	NA
AXS24651.1|1799320_1799539_-	IDEAL domain-containing protein	NA	NA	NA	NA	NA
AXS24652.1|1799748_1800318_+	competence protein ComK	NA	NA	NA	NA	NA
AXS24653.1|1800804_1802316_-	bifunctional metallophosphatase/5'-nucleotidase	NA	NA	NA	NA	NA
AXS24654.1|1802454_1803813_-	TrkH family potassium uptake protein	NA	NA	NA	NA	NA
AXS24655.1|1803829_1806154_-	PDZ domain-containing protein	NA	W5SAB9	Pithovirus	27.4	2.8e-11
1806169:1806195	attL	TATCATTATGACACATTAACACCTAAT	NA	NA	NA	NA
AXS24656.1|1806715_1808170_-	CHAP domain-containing protein	NA	A7TWL1	Staphylococcus_phage	99.6	4.4e-289
AXS24657.1|1808181_1808484_-|holin	phage holin	holin	A0A2I6PET6	Staphylococcus_phage	100.0	7.0e-48
AXS24658.1|1808619_1808919_-	DUF2951 family protein	NA	A0A2I6PER2	Staphylococcus_phage	100.0	2.0e-31
AXS24659.1|1808964_1809129_-	XkdX family protein	NA	A0A2I6PES4	Staphylococcus_phage	100.0	4.9e-24
AXS24660.1|1809121_1809511_-	DUF2977 domain-containing protein	NA	A0A2I6PER1	Staphylococcus_phage	100.0	2.2e-62
AXS24661.1|1809510_1810977_-	DUF2479 domain-containing protein	NA	A0A2I6PEI6	Staphylococcus_phage	99.0	2.9e-272
AXS24662.1|1810976_1812887_-	hypothetical protein	NA	A0A2I6PF35	Staphylococcus_phage	100.0	0.0e+00
AXS24663.1|1812902_1813193_-	hypothetical protein	NA	A0A2I6PF46	Staphylococcus_phage	100.0	2.1e-49
AXS24664.1|1813192_1814776_-	peptidase	NA	A0A2I6PEQ5	Staphylococcus_phage	100.0	9.3e-309
AXS24665.1|1814784_1815609_-|tail	phage tail family protein	tail	A0A2I6PER3	Staphylococcus_phage	100.0	4.1e-159
AXS24666.1|1815608_1821809_-|tail	phage tail tape measure protein	tail	A0A2K9VBQ5	Staphylococcus_phage	100.0	0.0e+00
AXS24667.1|1821822_1821981_-	hypothetical protein	NA	A0A2I6PES8	Staphylococcus_phage	100.0	1.2e-19
AXS24668.1|1822022_1822373_-	hypothetical protein	NA	A0A2I6PEQ2	Staphylococcus_phage	100.0	1.1e-55
AXS24669.1|1822430_1822886_-	Ig domain-containing protein	NA	A0A2I6PER6	Staphylococcus_phage	100.0	5.7e-78
AXS24670.1|1822977_1823619_-|tail	phage tail protein	tail	A0A2I6PEP6	Staphylococcus_phage	99.5	1.7e-120
AXS24671.1|1823653_1824049_-	DUF3168 domain-containing protein	NA	R4WAV1	Staphylococcus_phage	99.2	4.4e-66
AXS24672.1|1824049_1824451_-	hypothetical protein	NA	R4WAN5	Staphylococcus_phage	100.0	8.1e-68
AXS24673.1|1824447_1824780_-	hypothetical protein	NA	A0A2I6PEH8	Staphylococcus_phage	100.0	3.1e-57
AXS24674.1|1824791_1825070_-|head,tail	phage gp6-like head-tail connector protein	head,tail	A0A2I6PEQ1	Staphylococcus_phage	100.0	2.1e-46
AXS25707.1|1825138_1826302_-|capsid	phage major capsid protein	capsid	A0A2I6PDD7	Staphylococcus_phage	99.7	4.7e-217
AXS24675.1|1826313_1827087_-|protease	Clp protease ClpP	protease	A0A2I6PEQ7	Staphylococcus_phage	100.0	2.4e-137
AXS24676.1|1827070_1828309_-|portal	phage portal protein	portal	A0A2I6PER5	Staphylococcus_phage	100.0	6.9e-235
AXS24677.1|1828313_1830005_-|terminase	terminase large subunit	terminase	Q9B0E3	Staphylococcus_virus	99.5	0.0e+00
AXS24678.1|1829994_1830300_-|terminase	phage terminase small subunit P27 family	terminase	A0A2I6PEQ6	Staphylococcus_phage	100.0	2.9e-49
AXS24679.1|1830427_1830742_-	HNH endonuclease	NA	Q4ZCU3	Staphylococcus_virus	96.2	2.7e-55
AXS24680.1|1830898_1831336_-	transcriptional regulator	NA	A0A2I6PDN2	Staphylococcus_phage	97.9	1.1e-75
AXS24681.1|1832045_1832246_-	DUF1514 domain-containing protein	NA	A0A2I6PEP5	Staphylococcus_phage	100.0	4.9e-26
AXS24682.1|1832313_1832466_-	transcriptional regulator	NA	A0A2I6PEM5	Staphylococcus_phage	100.0	2.0e-19
AXS24683.1|1832462_1832669_-	DUF1381 domain-containing protein	NA	U3PD04	Staphylococcus_phage	94.7	1.9e-12
AXS24684.1|1832665_1832908_-	hypothetical protein	NA	A0A1W6JQI1	Staphylococcus_phage	71.8	6.6e-25
AXS24685.1|1832960_1833455_-	dUTPase	NA	I1W653	Staphylococcus_phage	66.9	2.5e-55
AXS24686.1|1833447_1833642_-	hypothetical protein	NA	M1SVE4	Staphylococcus_phage	95.1	5.9e-24
AXS24687.1|1833604_1833859_-	DUF1024 family protein	NA	A7TWH5	Staphylococcus_phage	91.7	1.8e-36
AXS24688.1|1833851_1834160_-	hypothetical protein	NA	Q6R826	Staphylococcus_virus	96.0	4.2e-48
AXS24689.1|1834156_1834504_-	hypothetical protein	NA	D2JGL4	Staphylococcus_phage	100.0	5.9e-59
AXS24690.1|1834500_1834902_-	hypothetical protein	NA	A0A2I6PDC0	Staphylococcus_phage	94.7	2.1e-68
AXS24691.1|1834904_1835111_-	hypothetical protein	NA	A0A2K9VBT9	Staphylococcus_phage	100.0	3.0e-34
AXS24692.1|1835124_1835373_-	hypothetical protein	NA	A0A2K9VBX5	Staphylococcus_phage	100.0	1.2e-40
AXS24693.1|1835372_1835627_-	DUF3310 domain-containing protein	NA	A7TWG9	Staphylococcus_phage	96.4	1.8e-41
AXS24694.1|1835626_1835989_-	hypothetical protein	NA	B7T0B4	Staphylococcus_virus	75.8	2.1e-46
AXS24695.1|1835989_1836175_-	DUF3113 family protein	NA	M9NSS9	Staphylococcus_phage	96.7	1.6e-26
AXS24696.1|1836174_1836582_-	RusA family crossover junction endodeoxyribonuclease	NA	A9CR74	Staphylococcus_phage	98.5	8.4e-73
AXS24697.1|1836591_1836813_-	DUF3269 family protein	NA	Q9G021	Staphylococcus_phage	100.0	1.3e-35
AXS24698.1|1836815_1837031_-	hypothetical protein	NA	Q4ZBU5	Staphylococcus_virus	95.8	1.2e-33
AXS24699.1|1837027_1838269_-	damage-inducible protein	NA	Q4ZA50	Staphylococcus_virus	99.3	1.1e-227
AXS24700.1|1838265_1838622_-	hypothetical protein	NA	M9NS37	Staphylococcus_phage	100.0	8.2e-64
AXS24701.1|1838621_1839374_-	DnaD domain protein	NA	C8CGZ1	Staphylococcus_phage	87.3	5.5e-118
AXS24702.1|1839366_1840041_-	hypothetical protein	NA	C8CGZ0	Staphylococcus_phage	98.7	3.4e-127
AXS24703.1|1840054_1840483_-	single-stranded DNA-binding protein	NA	A0A0E3XC62	Staphylococcus_phage	90.8	4.4e-64
AXS24704.1|1840482_1841106_-	DUF1071 domain-containing protein	NA	A0A2H4PQQ6	Staphylococcus_phage	100.0	1.4e-114
AXS24705.1|1841098_1841320_-	DUF2483 domain-containing protein	NA	A7TWM6	Staphylococcus_phage	100.0	3.2e-34
AXS24706.1|1841329_1841590_-	DUF1108 family protein	NA	C8CGY6	Staphylococcus_phage	98.8	2.0e-43
AXS24707.1|1841594_1841897_-	DUF2482 family protein	NA	A0A0F6N3N3	Staphylococcus_phage	97.0	7.7e-47
AXS24708.1|1841991_1842153_-	DUF1270 family protein	NA	A9CR58	Staphylococcus_phage	98.1	1.1e-20
AXS24709.1|1842165_1842429_-	helix-turn-helix domain-containing protein	NA	A0A2I6PEL8	Staphylococcus_phage	98.9	7.4e-46
AXS24710.1|1842455_1842671_-	hypothetical protein	NA	A0A2I6PF01	Staphylococcus_phage	100.0	1.9e-31
AXS24711.1|1842725_1843091_+	hypothetical protein	NA	A0A2I6PF07	Staphylococcus_phage	100.0	2.4e-63
AXS24712.1|1843059_1843305_-	DUF2829 domain-containing protein	NA	A0A2I6PF15	Staphylococcus_phage	100.0	5.1e-41
AXS24713.1|1843371_1843752_+	DUF2513 domain-containing protein	NA	Q4ZCQ5	Staphylococcus_virus	100.0	5.8e-68
AXS24714.1|1843738_1843936_-	hypothetical protein	NA	A7TWF5	Staphylococcus_phage	100.0	4.6e-24
AXS24715.1|1843951_1844704_-	oxidoreductase	NA	M9NTH5	Staphylococcus_phage	100.0	1.1e-139
AXS24716.1|1844754_1845084_+	hypothetical protein	NA	M9NS98	Staphylococcus_phage	100.0	2.7e-53
AXS24717.1|1845072_1845288_-	DUF2829 domain-containing protein	NA	A0A0H3U4C7	Staphylococcus_phage	100.0	4.8e-35
AXS24718.1|1845303_1845567_-	XRE family transcriptional regulator	NA	A0A2I6PF09	Staphylococcus_phage	100.0	7.2e-41
AXS24719.1|1845563_1845737_-	transcriptional regulator	NA	NA	NA	NA	NA
AXS24720.1|1845699_1846413_+	XRE family transcriptional regulator	NA	M9NUL0	Staphylococcus_phage	100.0	1.2e-130
AXS24721.1|1846428_1847361_+	ATP-dependent helicase	NA	A0A2I6PEZ7	Staphylococcus_phage	100.0	5.7e-173
AXS24722.1|1847366_1847708_+	hypothetical protein	NA	A0A2I6PF04	Staphylococcus_phage	100.0	4.6e-56
AXS24723.1|1847911_1848058_+	hypothetical protein	NA	A0A2I6PEK8	Staphylococcus_phage	87.5	1.2e-13
AXS24724.1|1848054_1848669_-	ATPase	NA	A7TW88	Staphylococcus_phage	99.0	2.3e-106
AXS24725.1|1848794_1850000_+|integrase	site-specific integrase	integrase	B7T0F2	Staphylococcus_virus	98.5	1.2e-218
AXS24726.1|1850288_1851092_-	hypothetical protein	NA	S5MAL1	Bacillus_phage	40.5	1.6e-30
1850085:1850111	attR	TATCATTATGACACATTAACACCTAAT	NA	NA	NA	NA
AXS24727.1|1851393_1852956_-	peptide chain release factor 3	NA	A0A1S5SF82	Streptococcus_phage	28.2	1.7e-36
>prophage 10
CP031838	Staphylococcus aureus strain QD-CD9 chromosome, complete genome	2855865	2008100	2016684	2855865	protease,transposase	Streptococcus_phage(33.33%)	8	NA	NA
AXS24880.1|2008100_2009273_+|transposase	IS256 family transposase IS256	transposase	A0A0N9STL0	Staphylococcus_phage	100.0	3.5e-135
AXS24881.1|2009777_2010680_+	epimerase	NA	NA	NA	NA	NA
AXS24882.1|2010922_2011510_-|protease	ATP-dependent Clp protease proteolytic subunit	protease	A0A223W000	Agrobacterium_phage	55.3	8.2e-53
AXS24883.1|2012083_2013028_-	DNA-binding protein WhiA	NA	Q7AWZ3	Streptococcus_phage	40.6	3.1e-54
AXS24884.1|2013138_2014134_-	YvcK family protein	NA	A1IMD5	Streptococcus_phage	41.9	4.8e-53
AXS24885.1|2014130_2015042_-	RNase adaptor protein RapZ	NA	A0A0R8VB27	Thermobifida_phage	36.1	1.1e-08
AXS24886.1|2015236_2015422_+	nitrogen fixation protein NifR	NA	NA	NA	NA	NA
AXS24887.1|2015748_2016684_-	thioredoxin-disulfide reductase	NA	G3MA85	Bacillus_virus	49.2	2.9e-84
>prophage 11
CP031838	Staphylococcus aureus strain QD-CD9 chromosome, complete genome	2855865	2049269	2064000	2855865		uncultured_Caudovirales_phage(50.0%)	17	NA	NA
AXS24918.1|2049269_2050031_-	ATP-binding cassette domain-containing protein	NA	Q9EMR9	Amsacta_moorei_entomopoxvirus	31.6	8.5e-18
AXS24919.1|2050027_2050984_-	iron ABC transporter permease	NA	A0A2H4J116	uncultured_Caudovirales_phage	57.8	1.2e-05
AXS25711.1|2050970_2051942_-	ABC transporter permease	NA	A0A2H4IY97	uncultured_Caudovirales_phage	78.9	9.5e-139
AXS24920.1|2052412_2052517_-	hypothetical protein	NA	NA	NA	NA	NA
AXS24921.1|2052649_2053621_-	class 1b ribonucleoside-diphosphate reductase subunit beta	NA	A0A2H4J4P3	uncultured_Caudovirales_phage	91.3	4.2e-171
AXS24922.1|2053738_2055844_-	class 1b ribonucleoside-diphosphate reductase subunit alpha	NA	A0A2H4J2N6	uncultured_Caudovirales_phage	91.7	0.0e+00
AXS24923.1|2055806_2056205_-	protein NrdI	NA	A0A2H4J545	uncultured_Caudovirales_phage	72.0	1.2e-52
AXS24924.1|2056354_2056621_-	ribonucleoside-diphosphate reductase	NA	NA	NA	NA	NA
AXS24925.1|2057005_2057872_+	DMT family transporter	NA	NA	NA	NA	NA
AXS24926.1|2057891_2058392_+	NADPH-dependent 7-cyano-7-deazaguanine reductase QueF	NA	E7DN65	Pneumococcus_phage	71.5	5.9e-52
AXS24927.1|2058421_2058667_+	hypothetical protein	NA	NA	NA	NA	NA
AXS24928.1|2058732_2060238_+	peptide MFS transporter	NA	A0A0P0IY73	Acinetobacter_phage	32.2	2.0e-58
AXS24929.1|2060315_2060417_-	hypothetical protein	NA	NA	NA	NA	NA
AXS24930.1|2060507_2061425_+	diacylglycerol kinase family lipid kinase	NA	A0A1V0SBJ0	Catovirus	22.0	3.7e-07
AXS24931.1|2061837_2061933_-	hypothetical protein	NA	NA	NA	NA	NA
AXS24932.1|2062104_2062647_-	5'(3')-deoxyribonucleotidase	NA	NA	NA	NA	NA
AXS24933.1|2062941_2064000_-	histidinol-phosphate transaminase	NA	A0A1X6WGT4	Pacmanvirus	26.7	7.9e-22
>prophage 12
CP031838	Staphylococcus aureus strain QD-CD9 chromosome, complete genome	2855865	2075972	2083791	2855865		Pandoravirus(16.67%)	10	NA	NA
AXS24943.1|2075972_2077124_-	anthranilate synthase component I family protein	NA	S4VNU7	Pandoravirus	36.1	1.2e-23
AXS24944.1|2077107_2077701_-	aminodeoxychorismate/anthranilate synthase component II	NA	A0A0P0IKJ1	Acinetobacter_phage	42.4	1.4e-36
AXS24945.1|2078051_2078720_+	7-cyano-7-deazaguanine synthase QueC	NA	A0A2H4J8Q7	uncultured_Caudovirales_phage	57.1	1.1e-64
AXS24946.1|2078721_2079141_+	6-carboxytetrahydropterin synthase QueD	NA	S4U060	uncultured_phage	28.7	6.3e-07
AXS24947.1|2079144_2079858_+	7-carboxy-7-deazaguanine synthase QueE	NA	A0A1U9WRB6	Streptococcus_virus	43.5	6.5e-52
AXS24948.1|2079956_2080541_+	hypothetical protein	NA	NA	NA	NA	NA
AXS24949.1|2080820_2081261_+	hypothetical protein	NA	NA	NA	NA	NA
AXS24950.1|2081601_2082075_+	DoxX family protein	NA	NA	NA	NA	NA
AXS24951.1|2082049_2082736_+	DNA-binding response regulator	NA	NA	NA	NA	NA
AXS24952.1|2082735_2083791_+	two-component sensor histidine kinase	NA	A0A1V0SGX0	Hokovirus	29.5	1.6e-14
>prophage 13
CP031838	Staphylococcus aureus strain QD-CD9 chromosome, complete genome	2855865	2420768	2430312	2855865	integrase	Staphylococcus_phage(33.33%)	10	2413513:2413532	2427275:2427294
2413513:2413532	attL	TATAATTATTCCCACTCAAT	NA	NA	NA	NA
AXS25252.1|2420768_2421113_-	pathogenicity island protein	NA	A0A1W6JQD5	Staphylococcus_phage	64.3	1.2e-40
AXS25253.1|2421783_2424156_-	DNA primase	NA	A0A2H4JCU9	uncultured_Caudovirales_phage	39.3	3.7e-136
AXS25254.1|2424246_2424540_-	DUF1474 family protein	NA	A0A1W6JQH0	Staphylococcus_phage	46.1	1.7e-14
AXS25255.1|2424540_2424765_-	hypothetical protein	NA	A0A1W6JPA6	Staphylococcus_phage	58.8	7.5e-15
AXS25256.1|2424950_2425211_-	DNA-binding protein	NA	NA	NA	NA	NA
AXS25257.1|2425207_2425447_-	XRE family transcriptional regulator	NA	Q38329	Lactococcus_phage	40.0	2.5e-08
AXS25258.1|2425579_2425966_+	XRE family transcriptional regulator	NA	U3PIS7	Lactobacillus_phage	41.2	3.8e-06
AXS25259.1|2426049_2427186_+|integrase	site-specific integrase	integrase	A0A1S5S7K9	Streptococcus_phage	42.5	1.0e-75
AXS25260.1|2427279_2428821_-	GMP synthase (glutamine-hydrolyzing)	NA	A0A1V0SH76	Hokovirus	32.6	1.2e-23
2427275:2427294	attR	TATAATTATTCCCACTCAAT	NA	NA	NA	NA
AXS25261.1|2428845_2430312_-	IMP dehydrogenase	NA	A0A1V0SHK8	Klosneuvirus	40.5	5.2e-96
>prophage 14
CP031838	Staphylococcus aureus strain QD-CD9 chromosome, complete genome	2855865	2744245	2828672	2855865	transposase,tRNA	Staphylococcus_phage(50.0%)	90	NA	NA
AXS25541.1|2744245_2744641_-	protein ArsC	NA	A0A2H4PQT9	Staphylococcus_phage	86.3	8.5e-62
AXS25542.1|2744658_2745948_-	arsenical efflux pump membrane protein ArsB	NA	A0A2H4PQU3	Staphylococcus_phage	81.8	1.7e-188
AXS25543.1|2745947_2746262_-	ArsR family transcriptional regulator	NA	A0A2H4PQT4	Staphylococcus_phage	73.1	3.6e-39
AXS25544.1|2746322_2746922_-	recombinase family protein	NA	E5FFF9	Burkholderia_phage	30.8	3.1e-15
AXS25545.1|2747428_2748103_-|transposase	IS6 family transposase	transposase	A0A0N9RU54	Staphylococcus_phage	98.7	1.7e-126
AXS25546.1|2748428_2749199_-	aminoglycoside O-nucleotidyltransferase ANT(4')-Ia	NA	NA	NA	NA	NA
AXS25547.1|2749358_2750342_-	protein rep	NA	A0A286QS97	Streptococcus_phage	62.0	6.1e-08
AXS25548.1|2750585_2751260_-|transposase	IS6 family transposase	transposase	A0A0N9RU54	Staphylococcus_phage	98.7	1.7e-126
AXS25745.1|2751454_2752357_+	hypothetical protein	NA	NA	NA	NA	NA
AXS25549.1|2752372_2752816_+	AP2 domain-containing protein	NA	A0A2H4J5K3	uncultured_Caudovirales_phage	43.6	1.5e-22
AXS25550.1|2752839_2753265_+	hypothetical protein	NA	NA	NA	NA	NA
AXS25551.1|2753397_2754072_+|transposase	IS6 family transposase	transposase	A0A0N9RU54	Staphylococcus_phage	97.3	4.1e-125
AXS25552.1|2754210_2754435_-	XRE family transcriptional regulator	NA	NA	NA	NA	NA
AXS25553.1|2754934_2756014_+|transposase	ISL3 family transposase	transposase	A0A1S5SBP9	Streptococcus_phage	33.5	1.6e-38
AXS25746.1|2756037_2756154_+	hypothetical protein	NA	NA	NA	NA	NA
AXS25554.1|2756462_2757266_-	lincosamide nucleotidyltransferase Lnu(B)	NA	NA	NA	NA	NA
AXS25555.1|2757319_2758804_-	ABC-F type ribosomal protection protein Lsa(E)	NA	A0A2H4UUX5	Bodo_saltans_virus	26.0	2.6e-26
AXS25556.1|2759892_2760351_+	hypothetical protein	NA	NA	NA	NA	NA
AXS25747.1|2760401_2760653_-	hypothetical protein	NA	NA	NA	NA	NA
AXS25557.1|2760870_2761680_-	ANT(9) family aminoglycoside nucleotidyltransferase Spw	NA	NA	NA	NA	NA
AXS25558.1|2761811_2762339_-	adenine phosphoribosyltransferase	NA	A0A1X9I6E2	Streptococcus_phage	100.0	1.9e-93
AXS25559.1|2762382_2763246_-	aminoglycoside nucleotidyltransferase ANT(6)-Ia	NA	A0A1X9I6F2	Streptococcus_phage	100.0	8.7e-168
AXS25560.1|2763278_2764013_-	class I SAM-dependent methyltransferase	NA	A0A1X9I6N4	Streptococcus_phage	100.0	1.5e-141
AXS25561.1|2763993_2764827_-	nucleotidyltransferase domain-containing protein	NA	A0A1X9I6C9	Streptococcus_phage	93.3	2.0e-145
AXS25562.1|2764862_2765537_+|transposase	IS6 family transposase	transposase	A0A0N9RU54	Staphylococcus_phage	97.8	5.4e-125
AXS25748.1|2765722_2765785_+	tetracycline resistance leader peptide	NA	NA	NA	NA	NA
AXS25563.1|2765818_2767195_+	tetracycline efflux MFS transporter Tet(L)	NA	NA	NA	NA	NA
AXS25564.1|2767243_2767444_-	hypothetical protein	NA	NA	NA	NA	NA
AXS25565.1|2767758_2769021_+	plasmid recombination protein	NA	NA	NA	NA	NA
AXS25566.1|2769145_2769820_+|transposase	IS6 family transposase	transposase	A0A0N9RU54	Staphylococcus_phage	97.8	1.6e-124
AXS25567.1|2769851_2770115_-	hypothetical protein	NA	NA	NA	NA	NA
AXS25568.1|2770581_2771754_+|transposase	IS256 family transposase IS256	transposase	A0A0N9STL0	Staphylococcus_phage	100.0	3.5e-135
AXS25749.1|2771810_2772203_+	GNAT family N-acetyltransferase	NA	A0A0N7GFH7	Staphylococcus_phage	100.0	6.9e-72
AXS25569.1|2772203_2773643_+	bifunctional aminoglycoside N-acetyltransferase AAC(6')-Ie/aminoglycoside O-phosphotransferase APH(2'')-Ia	NA	A0A1X9I6C2	Streptococcus_phage	100.0	3.8e-285
AXS25570.1|2773772_2774945_-|transposase	IS256 family transposase IS256	transposase	A0A0N9STL0	Staphylococcus_phage	100.0	3.5e-135
AXS25571.1|2775544_2776174_-	recombinase family protein	NA	E5FFF9	Burkholderia_phage	29.1	3.1e-13
AXS25572.1|2776523_2777369_-	BlaZ family penicillin-hydrolyzing class A beta-lactamase PC1	NA	A0A1B0VBP7	Salmonella_phage	34.0	1.5e-31
AXS25573.1|2777475_2779233_+	beta-lactam sensor/signal transducer BlaR1	NA	NA	NA	NA	NA
AXS25574.1|2779222_2779603_+	penicillinase repressor BlaI	NA	NA	NA	NA	NA
AXS25575.1|2779866_2780460_+	recombinase family protein	NA	A0A0A7NPV4	Enterobacteria_phage	51.7	5.0e-42
AXS25576.1|2780431_2781874_+|transposase	transposase	transposase	NA	NA	NA	NA
AXS25577.1|2781866_2782682_+	ATP-binding protein	NA	NA	NA	NA	NA
AXS25578.1|2782920_2783121_+	hypothetical protein	NA	NA	NA	NA	NA
AXS25579.1|2783153_2783474_+	ArsR family transcriptional regulator	NA	NA	NA	NA	NA
AXS25580.1|2783563_2784448_+	permease	NA	NA	NA	NA	NA
AXS25581.1|2784467_2785523_+	methyltransferase domain-containing protein	NA	NA	NA	NA	NA
AXS25582.1|2785547_2785691_+	hypothetical protein	NA	NA	NA	NA	NA
AXS25583.1|2785730_2787200_+|transposase	transposase	transposase	NA	NA	NA	NA
AXS25584.1|2787192_2788029_+	ATP-binding protein	NA	A0A2K9VH00	Faecalibacterium_phage	23.9	1.1e-07
AXS25585.1|2788048_2788609_+	recombinase family protein	NA	E5FFF9	Burkholderia_phage	31.3	1.3e-15
AXS25586.1|2789391_2789865_-	DUF1648 domain-containing protein	NA	NA	NA	NA	NA
AXS25750.1|2790215_2791991_+	oleate hydratase	NA	NA	NA	NA	NA
AXS25751.1|2792314_2793976_+	Na/Pi cotransporter family protein	NA	NA	NA	NA	NA
AXS25587.1|2794462_2795851_-	MFS transporter	NA	NA	NA	NA	NA
AXS25588.1|2795852_2797031_-	amidohydrolase	NA	NA	NA	NA	NA
AXS25752.1|2797180_2799379_-	helix-turn-helix domain-containing protein	NA	NA	NA	NA	NA
AXS25589.1|2799514_2800285_-	tandem-type lipoprotein	NA	NA	NA	NA	NA
AXS25590.1|2800349_2801117_-	DUF576 domain-containing protein	NA	NA	NA	NA	NA
AXS25753.1|2801184_2801955_-	tandem-type lipoprotein	NA	NA	NA	NA	NA
AXS25591.1|2802006_2802777_-	tandem-type lipoprotein	NA	NA	NA	NA	NA
AXS25592.1|2802997_2803984_-	1-phosphatidylinositol phosphodiesterase	NA	NA	NA	NA	NA
AXS25593.1|2804189_2804672_-	hypothetical protein	NA	NA	NA	NA	NA
AXS25594.1|2804728_2807881_-	ATPase	NA	NA	NA	NA	NA
AXS25595.1|2808147_2808750_-	hypothetical protein	NA	NA	NA	NA	NA
AXS25596.1|2808958_2809255_-	TfoX family protein	NA	NA	NA	NA	NA
AXS25597.1|2809303_2809507_-	hypothetical protein	NA	NA	NA	NA	NA
AXS25754.1|2809869_2810802_+|tRNA	tRNA-dihydrouridine synthase	tRNA	NA	NA	NA	NA
AXS25598.1|2810901_2811102_+	hypothetical protein	NA	NA	NA	NA	NA
AXS25599.1|2811098_2811200_+	universal stress protein	NA	NA	NA	NA	NA
AXS25600.1|2811467_2812661_-	NAD(P)/FAD-dependent oxidoreductase	NA	NA	NA	NA	NA
AXS25601.1|2812679_2814014_-	MBL fold metallo-hydrolase	NA	NA	NA	NA	NA
AXS25602.1|2814044_2815112_-	dihydroneopterin aldolase	NA	A0A2H4PQR9	Staphylococcus_phage	41.5	3.5e-09
AXS25603.1|2815248_2815509_+	metal-sensitive transcriptional regulator	NA	NA	NA	NA	NA
AXS25604.1|2815508_2816264_+	sulfite exporter TauE/SafE family protein	NA	NA	NA	NA	NA
AXS25605.1|2816361_2816463_+	hypothetical protein	NA	NA	NA	NA	NA
AXS25606.1|2816478_2816931_+|tRNA	tRNA-dihydrouridine synthase	tRNA	NA	NA	NA	NA
AXS25607.1|2817024_2818770_-	TIGR04141 family sporadically distributed protein	NA	NA	NA	NA	NA
AXS25608.1|2818916_2819009_-	hypothetical protein	NA	NA	NA	NA	NA
AXS25609.1|2818972_2819107_+	hypothetical protein	NA	NA	NA	NA	NA
AXS25610.1|2819205_2819391_+	hypothetical protein	NA	NA	NA	NA	NA
AXS25611.1|2819490_2820663_+|transposase	IS256 family transposase IS256	transposase	A0A0N9STL0	Staphylococcus_phage	100.0	3.5e-135
AXS25612.1|2820796_2820973_-	hypothetical protein	NA	NA	NA	NA	NA
AXS25613.1|2821842_2822160_+	hypothetical protein	NA	NA	NA	NA	NA
AXS25614.1|2822228_2822954_+	hypothetical protein	NA	NA	NA	NA	NA
AXS25615.1|2823058_2823286_+	hypothetical protein	NA	NA	NA	NA	NA
AXS25616.1|2823319_2825509_-	hypothetical protein	NA	NA	NA	NA	NA
AXS25617.1|2825521_2826196_-	hypothetical protein	NA	NA	NA	NA	NA
AXS25618.1|2826231_2826906_+|transposase	IS6 family transposase IS431mec	transposase	A0A0N9RU54	Staphylococcus_phage	99.1	2.6e-127
AXS25619.1|2826937_2827177_-	hypothetical protein	NA	NA	NA	NA	NA
AXS25620.1|2827997_2828672_-|transposase	IS6 family transposase	transposase	A0A0N9RU54	Staphylococcus_phage	98.2	4.4e-127
