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
CP029962	Salmonella enterica subsp. enterica serovar Typhi strain 343078_228140 chromosome, complete genome	4783156	930543	937855	4783156	protease,integrase	Dickeya_phage(16.67%)	6	931794:931808	942973:942987
AYU37136.1|930543_931662_+	hypothetical protein	NA	A0A140XAI1	Dickeya_phage	39.8	8.1e-09
AYU37137.1|931658_933605_+	macrolide transporter ATP-binding protein/permease	NA	G9BWD6	Planktothrix_phage	43.1	2.0e-39
931794:931808	attL	GGAAAATCAACGCTG	NA	NA	NA	NA
AYU37138.1|933734_933956_-	cold shock-like protein CspD	NA	A0A2H4N7Y6	Lake_Baikal_phage	64.2	9.3e-18
AYU37139.1|934279_934600_+|protease	ATP-dependent Clp protease adaptor protein	protease	A0A1B1IT64	uncultured_Mediterranean_phage	45.7	4.5e-13
AYU37140.1|934630_936907_+|protease	ATP-dependent Clp protease ATP-binding subunit ClpA	protease	A0A223W0B1	Agrobacterium_phage	42.2	1.8e-164
AYU37141.1|937477_937855_-|integrase	integrase	integrase	A0A077KET4	Ralstonia_phage	41.0	1.2e-20
942973:942987	attR	CAGCGTTGATTTTCC	NA	NA	NA	NA
>prophage 2
CP029962	Salmonella enterica subsp. enterica serovar Typhi strain 343078_228140 chromosome, complete genome	4783156	1008993	1086305	4783156	transposase,tail,integrase,protease,terminase	Salmonella_phage(73.33%)	93	991059:991078	1061666:1061685
991059:991078	attL	AACGGCGCCGGGAAATCCAC	NA	NA	NA	NA
AYU37191.1|1008993_1010334_-|integrase	integrase	integrase	S4TSP2	Salmonella_phage	99.8	7.9e-261
AYU37192.1|1010330_1010579_-	excisionase	NA	S4TND0	Salmonella_phage	100.0	4.7e-42
AYU37193.1|1010619_1010865_-	bacteriophage protein	NA	S4TR31	Salmonella_phage	96.2	1.3e-36
AYU37194.1|1010864_1011746_-	DNA methylase	NA	A0A0M4R347	Salmonella_phage	93.0	1.2e-153
AYU37195.1|1011742_1012807_-	bacteriophage protein	NA	T1SBJ4	Salmonella_phage	74.6	6.3e-152
AYU37196.1|1012884_1013565_-	exonuclease	NA	A0A0M3ULE0	Salmonella_phage	98.7	1.9e-130
AYU37197.1|1013561_1014347_-	bacteriophage recombination protein	NA	A0A0M4RD39	Salmonella_phage	99.6	9.7e-150
AYU37198.1|1014352_1014649_-	host-nuclease inhibitor protein	NA	A0A0M5M5Z9	Salmonella_phage	96.9	4.4e-47
AYU37199.1|1014739_1014940_-	prophage Kil protein	NA	G8C7T2	Escherichia_phage	48.4	2.4e-12
AYU37200.1|1015228_1015633_-	DNA-binding protein	NA	H6WRX4	Salmonella_phage	99.3	7.1e-72
AYU37201.1|1015964_1016339_+	DNA-binding protein	NA	S4TTD7	Salmonella_phage	99.2	3.9e-64
AYU37202.1|1016423_1017407_+	bacteriophage protein	NA	H6WRX7	Salmonella_phage	99.7	2.1e-162
AYU37203.1|1017409_1018159_+	DNA replication protein	NA	S4TNF5	Salmonella_phage	99.6	3.6e-138
AYU37204.1|1018169_1018517_+	DNA-binding protein	NA	H6WRX9	Salmonella_phage	90.4	4.8e-53
AYU37205.1|1018513_1019038_+	bacteriophage protein	NA	A0A220NQV2	Salmonella_phage	99.4	1.8e-91
AYU37206.1|1019037_1019511_+	methyltransferase	NA	H9C170	Pectobacterium_phage	80.1	1.6e-67
AYU37207.1|1019514_1020087_+	bacteriophage protein	NA	S4TSR6	Salmonella_phage	68.0	1.3e-66
AYU37208.1|1020180_1020447_+	bacteriophage protein	NA	S4TNF2	Salmonella_phage	100.0	1.5e-46
AYU37209.1|1020528_1020690_+	bacteriophage protein	NA	NA	NA	NA	NA
AYU37210.1|1021122_1021620_+	bacteriophage protein	NA	NA	NA	NA	NA
AYU37211.1|1021804_1022044_+	damage-inducible protein	NA	H6WRY5	Salmonella_phage	100.0	3.9e-38
AYU37212.1|1022033_1022339_+	bacteriophage protein	NA	H6WRY6	Salmonella_phage	100.0	9.8e-42
AYU37213.1|1022378_1022981_+	bacteriophage protein	NA	S4TTI0	Salmonella_phage	99.5	7.5e-110
AYU37214.1|1023189_1023801_+	bacteriophage lambda protein NinG	NA	A0A0M4RU10	Salmonella_phage	99.5	2.5e-92
AYU37215.1|1023933_1024731_+	prophage antitermination protein	NA	A0A0M4S661	Salmonella_phage	99.2	3.4e-150
AYU37216.1|1025129_1025255_+	bacteriophage protein	NA	NA	NA	NA	NA
AYU37217.1|1025390_1025840_-	lipoprotein	NA	NA	NA	NA	NA
AYU37218.1|1026056_1026446_+	prophage membrane protein	NA	K7PHB9	Enterobacterial_phage	70.2	3.1e-40
AYU37219.1|1026432_1026714_+	prophage membrane protein	NA	K7PKN9	Enterobacterial_phage	80.6	2.6e-36
AYU37220.1|1026713_1027328_+	bacteriophage protein	NA	Q8HA86	Salmonella_phage	93.1	3.2e-108
AYU37221.1|1027546_1027801_+	hypothetical protein	NA	NA	NA	NA	NA
AYU37222.1|1027905_1028283_+	hypothetical protein	NA	Q6UAR9	Klebsiella_phage	68.5	4.9e-43
AYU37223.1|1028346_1028607_+	hypothetical protein	NA	NA	NA	NA	NA
AYU37224.1|1028696_1029449_+|terminase	prophage terminase small subunit	terminase	A0A0M3ULJ9	Salmonella_phage	56.5	3.4e-11
AYU37225.1|1029414_1030818_+	bacteriophage protein	NA	A0A077KAW0	Edwardsiella_phage	70.1	6.5e-189
AYU37226.1|1030817_1032287_+	hypothetical protein	NA	A0A0M4S6U1	Salmonella_phage	99.2	1.7e-280
AYU37227.1|1032378_1032909_+	hypothetical protein	NA	A0A0M4REK0	Salmonella_phage	87.4	8.7e-86
AYU37228.1|1032923_1034156_+	hypothetical protein	NA	A0A0M4R5A6	Salmonella_phage	99.0	1.4e-227
AYU37229.1|1034160_1034658_+	bacteriophage protein	NA	A0A0M4QWZ6	Salmonella_phage	99.4	8.7e-88
AYU37230.1|1034669_1035611_+	bacteriophage protein	NA	A0A0M3ULD3	Salmonella_phage	100.0	3.1e-179
AYU37231.1|1035652_1036021_+	bacteriophage protein	NA	A0A0M4RTX5	Salmonella_phage	100.0	8.7e-61
AYU37232.1|1035986_1036394_+	bacteriophage protein	NA	A0A0M5M3S2	Salmonella_phage	97.8	7.1e-72
AYU37233.1|1036390_1036945_+	bacteriophage protein	NA	A0A0M4S631	Salmonella_phage	100.0	4.8e-95
AYU37234.1|1036931_1037321_+	bacteriophage protein	NA	A0A0M3ULK0	Salmonella_phage	98.4	6.0e-68
AYU37235.1|1037295_1037859_+	bacteriophage protein	NA	A0A0M4R331	Salmonella_phage	75.3	8.9e-81
AYU37236.1|1037862_1039008_+	bacteriophage protein	NA	A0A2H4J8G4	uncultured_Caudovirales_phage	74.5	2.2e-163
AYU37237.1|1039019_1039460_+	bacteriophage protein	NA	A0A2H4J619	uncultured_Caudovirales_phage	74.7	3.5e-56
AYU37238.1|1039463_1039916_+	bacteriophage protein	NA	A0A0M4S6U8	Salmonella_phage	76.6	1.9e-57
AYU37239.1|1040093_1042046_+	bacteriophage protein	NA	A0A0M4REK7	Salmonella_phage	56.0	1.8e-181
AYU37240.1|1042045_1042696_+	bacteriophage protein	NA	A0A0M3ULD5	Salmonella_phage	60.6	3.0e-56
AYU37241.1|1042699_1043002_+	bacteriophage protein	NA	A0A2H4J495	uncultured_Caudovirales_phage	57.0	2.0e-26
AYU37242.1|1043004_1044036_+	bacteriophage protein	NA	A0A2H4J1B2	uncultured_Caudovirales_phage	51.4	1.2e-96
AYU37243.1|1044032_1044368_+	hypothetical protein	NA	A0A2H4J1A5	uncultured_Caudovirales_phage	52.2	1.1e-20
AYU37244.1|1044562_1045294_+	bacteriophage protein	NA	NA	NA	NA	NA
AYU37245.1|1045293_1045722_+	bacteriophage protein	NA	NA	NA	NA	NA
AYU37246.1|1045780_1046536_+	bacteriophage protein	NA	A0A0M5M1K7	Salmonella_phage	85.3	4.1e-105
AYU37247.1|1046623_1046761_+	bacteriophage protein	NA	A0A0M4S639	Salmonella_phage	100.0	2.0e-18
AYU37248.1|1046776_1047130_+	bacteriophage protein	NA	A0A0M4R339	Salmonella_phage	98.3	3.2e-60
AYU37249.1|1047130_1048330_+	bacteriophage protein	NA	A0A0M4RD32	Salmonella_phage	97.5	8.5e-214
AYU37250.1|1048326_1049007_+	bacteriophage protein	NA	A0A0M5M1K4	Salmonella_phage	98.7	6.9e-128
AYU37251.1|1049006_1050518_+|tail	bacteriophage tail protein	tail	S4TP62	Salmonella_phage	59.4	1.5e-111
AYU37252.1|1050532_1051051_+|tail	tail fiber protein	tail	A0A1B0VCD0	Salmonella_phage	62.8	1.7e-46
AYU37253.1|1051972_1052674_-	hypothetical protein	NA	NA	NA	NA	NA
AYU37254.1|1052986_1053265_-	hypothetical protein	NA	S4TNM0	Salmonella_phage	92.3	2.4e-26
AYU37255.1|1053690_1056303_+	aminopeptidase N	NA	A0A0P0IY26	Acinetobacter_phage	22.6	1.1e-19
AYU37256.1|1056510_1057521_+	dihydroorotate dehydrogenase	NA	NA	NA	NA	NA
AYU37257.1|1057683_1058229_+	hypothetical protein	NA	NA	NA	NA	NA
AYU37258.1|1058225_1059335_-	MOSC domain-containing protein	NA	NA	NA	NA	NA
AYU37259.1|1059433_1061542_+	23S rRNA m(2)G2445 methyltransferase	NA	W6LLI2	Streptococcus_phage	29.6	5.1e-20
AYU37260.1|1061554_1063462_+	ABC transporter ATP-binding protein	NA	A0A2K9L3Z8	Tupanvirus	29.8	2.4e-53
1061666:1061685	attR	AACGGCGCCGGGAAATCCAC	NA	NA	NA	NA
AYU37261.1|1063476_1064730_+	inner membrane protein	NA	NA	NA	NA	NA
AYU37262.1|1064734_1066375_+	paraquat-inducible protein B	NA	NA	NA	NA	NA
AYU37263.1|1066371_1066935_+	lipoprotein	NA	NA	NA	NA	NA
AYU37264.1|1067188_1067356_+	ribosome modulation factor	NA	NA	NA	NA	NA
AYU37265.1|1067455_1067974_-	D-3-hydroxydecanoyl-(acyl carrier-protein) dehydratase	NA	NA	NA	NA	NA
AYU37266.1|1068042_1069803_-|protease	ATP-dependent protease	protease	NA	NA	NA	NA
AYU37267.1|1069988_1070441_+	Ter macrodomain organizer matS-binding protein	NA	NA	NA	NA	NA
AYU37268.1|1070512_1071565_-	outer membrane protein A	NA	NA	NA	NA	NA
AYU37269.1|1071919_1072429_-	cell division inhibitor	NA	NA	NA	NA	NA
AYU37270.1|1072645_1073251_+	competence-specific transcriptional regulator TfoX	NA	NA	NA	NA	NA
AYU37271.1|1073237_1075391_-	inner membrane protein	NA	NA	NA	NA	NA
AYU37272.1|1075409_1075856_-	hypothetical protein	NA	NA	NA	NA	NA
AYU37273.1|1075979_1078034_+	helicase IV	NA	A7KV33	Bacillus_phage	27.6	6.5e-20
AYU37274.1|1078069_1078528_-	methylglyoxal synthase	NA	NA	NA	NA	NA
AYU37275.1|1078622_1079285_-	hypothetical protein	NA	NA	NA	NA	NA
AYU37276.1|1079455_1079872_+	hypothetical protein	NA	NA	NA	NA	NA
AYU37277.1|1079916_1080234_-	heat shock protein HspQ	NA	NA	NA	NA	NA
AYU37278.1|1080291_1081503_-	23S rRNA m(5)C1962 methyltransferase	NA	NA	NA	NA	NA
AYU37279.1|1082634_1083093_+|transposase	insertion sequence element IS200 transposase	transposase	NA	NA	NA	NA
AYU37280.1|1083829_1084111_+	acylphosphatase	NA	NA	NA	NA	NA
AYU37281.1|1084107_1084437_-	sulfite reductase	NA	NA	NA	NA	NA
AYU37282.1|1084523_1085183_-	hypothetical protein	NA	A0A2H4JFM9	uncultured_Caudovirales_phage	52.4	2.7e-44
AYU37283.1|1085846_1086305_+|transposase	insertion sequence element IS200 transposase	transposase	NA	NA	NA	NA
>prophage 3
CP029962	Salmonella enterica subsp. enterica serovar Typhi strain 343078_228140 chromosome, complete genome	4783156	1528761	1602359	4783156	plate,protease,transposase,tail,tRNA,head	Burkholderia_virus(44.12%)	72	NA	NA
AYU37682.1|1528761_1529220_-|transposase	insertion sequence element IS200 transposase	transposase	NA	NA	NA	NA
AYU37683.1|1529722_1530004_+	stress response protein	NA	NA	NA	NA	NA
AYU37684.1|1530272_1531094_+|protease	serine protease	protease	NA	NA	NA	NA
AYU37685.1|1531128_1531458_-	multidrug efflux system protein MdtI	NA	NA	NA	NA	NA
AYU37686.1|1531444_1531807_-	multidrug efflux system protein MdtJ	NA	NA	NA	NA	NA
AYU37687.1|1531918_1532089_-	hypothetical protein	NA	NA	NA	NA	NA
AYU37688.1|1532223_1533258_+	hypothetical protein	NA	NA	NA	NA	NA
AYU37689.1|1533432_1534821_-	pyridine nucleotide transhydrogenase subunit beta	NA	NA	NA	NA	NA
AYU37690.1|1534831_1536361_-	pyridine nucleotide transhydrogenase subunit alpha	NA	NA	NA	NA	NA
AYU37691.1|1536887_1537832_+	hypothetical protein	NA	NA	NA	NA	NA
AYU37692.1|1538013_1538403_-	bacteriophage transcriptional regulator	NA	Q6QIE8	Burkholderia_phage	54.2	4.5e-31
AYU37693.1|1538374_1538827_-	hypothetical protein	NA	A4JWM5	Burkholderia_virus	46.6	1.2e-24
AYU37694.1|1539021_1539252_-	hypothetical protein	NA	NA	NA	NA	NA
AYU37695.1|1539248_1539932_-	hypothetical protein	NA	A0A2P9JZH4	Alteromonadaceae_phage	37.3	2.6e-34
AYU37696.1|1540516_1540819_-	hypothetical protein	NA	NA	NA	NA	NA
AYU37697.1|1541389_1541920_-	bacteriophage host-nuclease inhibitor protein	NA	L7P7T1	Pseudomonas_phage	66.1	3.4e-58
AYU37698.1|1542219_1543386_-	ExeA protein	NA	A4JWN1	Burkholderia_virus	59.7	3.3e-122
AYU37699.1|1543396_1545166_-	hypothetical protein	NA	Q6QIE0	Burkholderia_phage	68.5	2.8e-229
AYU37700.1|1546610_1546961_+	hypothetical protein	NA	A4JWP3	Burkholderia_virus	53.0	4.5e-22
AYU37701.1|1547675_1548326_+	lipoprotein	NA	Q5ZQY9	Pseudomonas_phage	32.9	8.1e-09
AYU37702.1|1548648_1548960_+	hypothetical protein	NA	A0A0S4L0A3	Pseudomonas_phage	62.6	9.4e-32
AYU37703.1|1548959_1549505_+	hypothetical protein	NA	A4JWJ3	Burkholderia_virus	67.6	9.3e-59
AYU37704.1|1549501_1551097_+	hypothetical protein	NA	A4JWJ4	Burkholderia_virus	62.6	9.3e-184
AYU37705.1|1551096_1552593_+	hypothetical protein	NA	A4JWJ5	Burkholderia_virus	59.6	8.0e-169
AYU37706.1|1552573_1553395_+|head	phage head morphogenesis protein	head	A4JWJ6	Burkholderia_virus	61.2	5.3e-98
AYU37707.1|1553397_1553856_+	bacteriophage protein	NA	Q6QIB8	Burkholderia_phage	44.8	1.5e-30
AYU37708.1|1554070_1555186_+	hypothetical protein	NA	A4JWJ9	Burkholderia_virus	51.1	7.9e-97
AYU37709.1|1555200_1556154_+	hypothetical protein	NA	A4JWK0	Burkholderia_virus	44.5	5.2e-65
AYU37710.1|1556163_1556502_+	hypothetical protein	NA	NA	NA	NA	NA
AYU37711.1|1556503_1556950_+	hypothetical protein	NA	A4JWK2	Burkholderia_virus	52.3	2.2e-34
AYU37712.1|1556949_1557414_+	hypothetical protein	NA	Q6QIB2	Burkholderia_phage	51.7	9.1e-39
AYU37713.1|1557654_1559082_+|tail	bacteriophage tail sheath protein	tail	A4JWK5	Burkholderia_virus	77.4	3.7e-216
AYU37714.1|1559081_1559603_+|tail	tail core protein	tail	A4JWK6	Burkholderia_virus	68.2	8.0e-68
AYU37715.1|1559605_1559887_+	hypothetical protein	NA	NA	NA	NA	NA
AYU37716.1|1559984_1560320_+	hypothetical protein	NA	NA	NA	NA	NA
AYU37717.1|1560495_1562961_+	bacteriophage protein	NA	A4JWL0	Burkholderia_virus	42.6	2.2e-168
AYU37718.1|1562960_1563845_+	hypothetical protein	NA	A4JWL1	Burkholderia_virus	47.0	7.5e-50
AYU37719.1|1563841_1564057_+|tail	bacteriophage tail fiber protein	tail	Q6QIA3	Burkholderia_phage	60.0	2.4e-18
AYU37720.1|1564044_1565199_+	bacteriophage regulatory protein	NA	Q6QIA2	Burkholderia_phage	47.1	4.7e-84
AYU37721.1|1565195_1565723_+|plate	bacteriophage baseplate protein	plate	Q6QIA1	Burkholderia_phage	46.5	1.5e-21
AYU37722.1|1565779_1566127_+|plate	bacteriophage baseplate protein	plate	Q6QIA0	Burkholderia_phage	60.6	8.6e-34
AYU37723.1|1566117_1567221_+|plate	bacteriophage baseplate assembly protein	plate	Q6QI99	Burkholderia_phage	54.3	5.4e-106
AYU37724.1|1567213_1567792_+|tail	bacteriophage tail fiber protein	tail	A4JWL7	Burkholderia_virus	65.8	6.4e-66
AYU37725.1|1567794_1568820_+|tail	bacteriophage tail fiber protein	tail	M1TAS6	Escherichia_phage	53.3	1.6e-64
AYU37726.1|1569333_1569951_+|tail	bacteriophage tail fiber assembly protein	tail	Q9MCR5	Enterobacteria_phage	59.9	5.8e-65
AYU37727.1|1571461_1572034_+	DNA-invertase	NA	A0A0A7NPV4	Enterobacteria_phage	84.7	8.8e-84
AYU37728.1|1572314_1573697_+	amino acid permease	NA	NA	NA	NA	NA
AYU37729.1|1573758_1574094_-	hypothetical protein	NA	NA	NA	NA	NA
AYU37730.1|1574220_1574952_+	two-component response regulator	NA	NA	NA	NA	NA
AYU37731.1|1575432_1576584_+	outer membrane protein	NA	Q1MVN1	Enterobacteria_phage	59.1	3.2e-117
AYU37732.1|1576736_1578443_+	metal-dependent hydrolase	NA	NA	NA	NA	NA
AYU37733.1|1578550_1579855_+	two component sensor kinase	NA	W8CYF6	Bacillus_phage	22.7	5.7e-14
AYU37734.1|1579930_1580860_+	DNA sequence-specific contrahelicase	NA	NA	NA	NA	NA
AYU37735.1|1580856_1582260_-	fumarate hydratase class II	NA	NA	NA	NA	NA
AYU37736.1|1582427_1584074_-	Fumarate hydratase class I	NA	NA	NA	NA	NA
AYU37737.1|1584273_1585449_+	mannose-6-phosphate isomerase	NA	NA	NA	NA	NA
AYU37738.1|1585551_1587060_+	hypothetical protein	NA	NA	NA	NA	NA
AYU37739.1|1587765_1588767_+	adenosine deaminase	NA	NA	NA	NA	NA
AYU37740.1|1588840_1589956_-	oxidoreductase	NA	NA	NA	NA	NA
AYU37741.1|1590058_1590214_+	hypothetical protein	NA	NA	NA	NA	NA
AYU37742.1|1590512_1590728_+	oriC-binding nucleoid-associated protein	NA	NA	NA	NA	NA
AYU37743.1|1590816_1591257_+	hypothetical protein	NA	NA	NA	NA	NA
AYU37744.1|1591333_1591915_+	Na(+)-translocating NADH-quinone reductase subunit E	NA	NA	NA	NA	NA
AYU37745.1|1591914_1592493_+	ferredoxin-like protein	NA	NA	NA	NA	NA
AYU37746.1|1592485_1594507_+	NADH reducing dehydrogenase	NA	NA	NA	NA	NA
AYU37747.1|1594507_1595566_+	electron transport complex protein RnfD	NA	NA	NA	NA	NA
AYU37748.1|1595569_1596190_+	electron transport complex protein RnfG	NA	NA	NA	NA	NA
AYU37749.1|1596192_1596885_+	electron transport complex protein RsxE	NA	NA	NA	NA	NA
AYU37750.1|1596884_1597520_+	endonuclease III	NA	NA	NA	NA	NA
AYU37751.1|1598120_1599626_+	proton/oligopeptide symporter	NA	NA	NA	NA	NA
AYU37752.1|1599730_1600336_+	glutathione S-transferase	NA	NA	NA	NA	NA
AYU37753.1|1601084_1602359_-|tRNA	tyrosyl-tRNA synthetase	tRNA	K4F5T3	Cronobacter_phage	42.1	1.6e-85
>prophage 4
CP029962	Salmonella enterica subsp. enterica serovar Typhi strain 343078_228140 chromosome, complete genome	4783156	1783396	1787808	4783156		Escherichia_phage(50.0%)	6	NA	NA
AYU37937.1|1783396_1783636_+	virulence protein	NA	K7P6H1	Enterobacteria_phage	87.3	5.5e-32
AYU37938.1|1784508_1785318_+	toxin-like protein	NA	A5LH53	Enterobacteria_phage	50.0	2.1e-62
AYU37939.1|1785390_1785768_+	hypothetical protein	NA	I1TQ41	Pseudomonas_phage	38.4	2.2e-14
AYU37940.1|1785915_1786458_-	hypothetical protein	NA	A0A0U2S643	Escherichia_phage	67.0	6.2e-71
AYU37941.1|1786649_1787378_-	pertussis toxin subunit ArtA	NA	A0A0U2KD26	Escherichia_phage	53.3	4.9e-63
AYU37942.1|1787394_1787808_-	pertussis-like toxin subunit	NA	A0A0U2KD34	Escherichia_phage	38.6	1.4e-19
>prophage 5
CP029962	Salmonella enterica subsp. enterica serovar Typhi strain 343078_228140 chromosome, complete genome	4783156	1991661	1998895	4783156		Morganella_phage(33.33%)	7	NA	NA
AYU38132.1|1991661_1993092_-	DNA-cytosine methyltransferase	NA	E5E3X6	Burkholderia_phage	57.4	1.0e-104
AYU38133.1|1993165_1993861_-	hypothetical protein	NA	S4W232	Pandoravirus	27.5	2.1e-07
AYU38134.1|1993940_1994252_-	hypothetical protein	NA	NA	NA	NA	NA
AYU38135.1|1994902_1996087_+	outer membrane protein S1	NA	Q1MVN1	Enterobacteria_phage	56.4	1.4e-107
AYU38136.1|1996546_1996759_-	cold shock protein	NA	A0A1W6JNX5	Morganella_phage	70.0	1.5e-20
AYU38137.1|1997204_1998473_-	DNA polymerase V subunit UmuC	NA	I6RSM4	Salmonella_phage	91.2	3.3e-224
AYU38138.1|1998475_1998895_-	DNA polymerase V subunit UmuD	NA	A0A1W6JNS2	Morganella_phage	60.5	8.5e-36
>prophage 6
CP029962	Salmonella enterica subsp. enterica serovar Typhi strain 343078_228140 chromosome, complete genome	4783156	2105196	2115703	4783156		Enterobacteria_phage(37.5%)	10	NA	NA
AYU38235.1|2105196_2106510_-	dehydratase RfbH	NA	H8ZJ36	Ostreococcus_tauri_virus	35.1	7.0e-52
AYU38236.1|2106536_2107616_-	CDP-glucose 4,6-dehydratase	NA	A0A222YY99	Synechococcus_phage	24.1	1.3e-16
AYU38237.1|2107620_2108394_-	glucose-1-phosphate cytidylyltransferase	NA	NA	NA	NA	NA
AYU38238.1|2108409_2109384_-	reductase RfbI	NA	NA	NA	NA	NA
AYU38239.1|2109389_2109941_-	dTDP-4-dehydrorhamnose 3,5-epimerase	NA	I7HJC4	Enterobacteria_phage	58.6	7.7e-53
AYU38240.1|2109941_2110820_-	TDP-glucose pyrophosphorylase	NA	I7I009	Enterobacteria_phage	64.8	2.3e-107
AYU38241.1|2110867_2111767_-	dTDP-4-dehydrorhamnose reductase	NA	A0A291LA50	Escherichia_phage	36.3	7.9e-31
AYU38242.1|2111766_2112852_-	dTDP-glucose 4,6-dehydratase	NA	I7HTA3	Enterobacteria_phage	53.9	1.6e-102
AYU38243.1|2113228_2114122_-	UTP-glucose-1-phosphate uridylyltransferase	NA	A0A127AW70	Bacillus_phage	42.2	4.8e-44
AYU38244.1|2114299_2115703_-	colanic acid biosynthesis protein WcaM	NA	A0A291LBB9	Klebsiella_phage	26.5	1.1e-21
>prophage 7
CP029962	Salmonella enterica subsp. enterica serovar Typhi strain 343078_228140 chromosome, complete genome	4783156	2192932	2202103	4783156	tRNA	Enterobacteria_phage(66.67%)	10	NA	NA
AYU38304.1|2192932_2194966_+|tRNA	methionyl-tRNA synthetase	tRNA	A0A1V0SDF2	Indivirus	26.9	6.1e-55
AYU38305.1|2195206_2195665_+	lipoprotein	NA	Q9EYF5	Enterobacteria_phage	72.5	8.4e-53
AYU38306.1|2195836_2196367_+	lipoprotein	NA	NA	NA	NA	NA
AYU38307.1|2196423_2196891_-	hypothetical protein	NA	Q9EYF4	Enterobacteria_phage	90.3	3.9e-74
AYU38308.1|2196937_2197657_-	two-component system response regulator	NA	NA	NA	NA	NA
AYU38309.1|2197653_2199339_-	two-component system sensor kinase	NA	Q9EYF3	Enterobacteria_phage	91.1	1.1e-278
AYU38310.1|2199561_2200293_+	transcriptional regulator	NA	Q9EYF2	Enterobacteria_phage	87.9	4.5e-101
AYU38311.1|2200352_2200460_+	hypothetical protein	NA	NA	NA	NA	NA
AYU38312.1|2200440_2201172_-	ABC transporter permease	NA	NA	NA	NA	NA
AYU38313.1|2201155_2202103_-	ABC transporter ATP-binding protein	NA	G3M9Y6	Bacillus_virus	31.2	1.7e-23
>prophage 8
CP029962	Salmonella enterica subsp. enterica serovar Typhi strain 343078_228140 chromosome, complete genome	4783156	2737540	2750932	4783156	tail	Salmonella_phage(70.0%)	11	NA	NA
AYU38742.1|2737540_2737759_-	hypothetical protein	NA	Q53ZE7	Salmonella_virus	71.9	1.9e-18
AYU38743.1|2737849_2738950_-	hypothetical protein	NA	A0A1S6KZZ5	Salmonella_phage	88.3	1.0e-176
AYU38744.1|2738946_2739432_-|tail	bacteriophage tail protein	tail	E5G6Q2	Salmonella_phage	80.0	2.4e-66
AYU38745.1|2739428_2742506_-|tail	bacteriophage tail protein	tail	E5G6Q1	Salmonella_phage	63.0	0.0e+00
AYU38746.1|2742498_2742618_-	bacteriophage protein	NA	E5G6Q0	Salmonella_phage	87.2	2.8e-13
AYU38747.1|2742632_2742935_-|tail	phage tail protein	tail	A0A1S6KZZ9	Salmonella_phage	89.0	7.0e-40
AYU38748.1|2742989_2743505_-|tail	major tail tube protein	tail	A0A1S6L002	Salmonella_phage	95.9	5.6e-90
AYU38749.1|2743514_2744687_-|tail	major tail sheath protein	tail	A0A1S6KZY7	Salmonella_phage	90.3	3.5e-204
AYU38750.1|2744829_2745402_-	DNA-invertase	NA	A0A0F7LA37	Escherichia_phage	86.3	1.4e-86
AYU38751.1|2746079_2747195_+	glycosyltransferase	NA	NA	NA	NA	NA
AYU38752.1|2747275_2750932_+	ABC transporter ATP-binding protein/permease	NA	W8CYL7	Bacillus_phage	28.6	1.0e-44
>prophage 9
CP029962	Salmonella enterica subsp. enterica serovar Typhi strain 343078_228140 chromosome, complete genome	4783156	3067894	3111597	4783156	transposase,bacteriocin,tRNA,protease	Bacillus_virus(33.33%)	44	NA	NA
AYU39040.1|3067894_3068353_-|transposase	insertion sequence element IS200 transposase	transposase	NA	NA	NA	NA
AYU39041.1|3068542_3069622_-	fructose 1,6-bisphosphate aldolase	NA	NA	NA	NA	NA
AYU39042.1|3069723_3070887_-	phosphoglycerate kinase	NA	NA	NA	NA	NA
AYU39043.1|3070908_3071955_-	D-erythrose 4-phosphate dehydrogenase	NA	NA	NA	NA	NA
AYU39044.1|3072328_3072754_+	hypothetical protein	NA	NA	NA	NA	NA
AYU39045.1|3072779_3073358_+	hypothetical protein	NA	NA	NA	NA	NA
AYU39046.1|3073391_3074066_+	hypothetical protein	NA	NA	NA	NA	NA
AYU39047.1|3074047_3074731_+	ABC transporter ATP-binding protein	NA	NA	NA	NA	NA
AYU39048.1|3074724_3075381_+	ABC transporter ATP-binding protein	NA	G3M9Y6	Bacillus_virus	28.6	1.6e-09
AYU39049.1|3075485_3075944_-|transposase	insertion sequence element IS200 transposase	transposase	NA	NA	NA	NA
AYU39050.1|3076132_3078124_-	transketolase	NA	NA	NA	NA	NA
AYU39051.1|3078399_3079158_+|protease	metalloprotease	protease	NA	NA	NA	NA
AYU39052.1|3079258_3080179_-	agmatine ureohydrolase	NA	NA	NA	NA	NA
AYU39053.1|3080406_3082383_-	biosynthetic arginine decarboxylase	NA	NA	NA	NA	NA
AYU39054.1|3082391_3082523_-	hypothetical protein	NA	NA	NA	NA	NA
AYU39055.1|3082817_3083117_-	membrane protein	NA	NA	NA	NA	NA
AYU39056.1|3083172_3084327_+	S-adenosylmethionine synthetase	NA	A0A2H4PQS6	Staphylococcus_phage	63.9	1.5e-130
AYU39057.1|3084819_3086214_+	galactose-proton symport	NA	NA	NA	NA	NA
AYU39058.1|3086292_3086790_+	hypothetical protein	NA	NA	NA	NA	NA
AYU39059.1|3086885_3087593_+	endonuclease I	NA	NA	NA	NA	NA
AYU39060.1|3087669_3088401_+	16S rRNA (uracil(1498)-N(3))-methyltransferase	NA	NA	NA	NA	NA
AYU39061.1|3088420_3089368_+	glutathione synthetase	NA	NA	NA	NA	NA
AYU39062.1|3089583_3090147_+	hypothetical protein	NA	NA	NA	NA	NA
AYU39063.1|3090146_3090563_+	Holliday junction resolvase	NA	NA	NA	NA	NA
AYU39064.1|3090609_3091296_-	global regulatory protein	NA	NA	NA	NA	NA
AYU39065.1|3091425_3092406_-	type II secretion system ATP-binding protein	NA	NA	NA	NA	NA
AYU39066.1|3092423_3093128_+	hypothetical protein	NA	NA	NA	NA	NA
AYU39067.1|3093146_3093713_+	hypothetical protein	NA	NA	NA	NA	NA
AYU39068.1|3093709_3094000_+	hypothetical protein	NA	NA	NA	NA	NA
AYU39069.1|3094007_3094601_+	dITP/XTP pyrophosphatase	NA	NA	NA	NA	NA
AYU39070.1|3094593_3095730_+	oxygen-independent coproporphyrinogen III oxidase	NA	NA	NA	NA	NA
AYU39071.1|3095820_3096828_-	hypothetical protein	NA	NA	NA	NA	NA
AYU39072.1|3096960_3098007_-	L-asparaginase	NA	NA	NA	NA	NA
AYU39073.1|3098325_3098784_+|transposase	insertion sequence element IS200 transposase	transposase	NA	NA	NA	NA
AYU39074.1|3098906_3099626_-	hypothetical protein	NA	NA	NA	NA	NA
AYU39075.1|3099675_3100002_-	hypothetical protein	NA	NA	NA	NA	NA
AYU39076.1|3100001_3100721_-|tRNA	tRNA m(7)G46 methyltransferase	tRNA	NA	NA	NA	NA
AYU39077.1|3100875_3101928_+	A/G-specific adenine glycosylase	NA	NA	NA	NA	NA
AYU39078.1|3101955_3102231_+	oxidative damage protection protein	NA	NA	NA	NA	NA
AYU39079.1|3102343_3103429_+	membrane-bound lytic murein transglycosylase C	NA	A0A0H3V0Q1	Geobacillus_virus	39.0	5.8e-12
AYU39080.1|3103645_3104902_+	nucleoside permease	NA	NA	NA	NA	NA
AYU39081.1|3107512_3108220_+	hypothetical protein	NA	NA	NA	NA	NA
AYU39082.1|3110809_3111076_+|bacteriocin	bacteriocin immunity protein	bacteriocin	NA	NA	NA	NA
AYU39083.1|3111318_3111597_+|bacteriocin	bacteriocin immunity protein	bacteriocin	NA	NA	NA	NA
>prophage 10
CP029962	Salmonella enterica subsp. enterica serovar Typhi strain 343078_228140 chromosome, complete genome	4783156	3489000	3527058	4783156	plate,transposase,portal,tail,integrase,capsid,terminase	Salmonella_phage(82.05%)	46	3483964:3483978	3496130:3496144
3483964:3483978	attL	CGAATTTCTTTTTCA	NA	NA	NA	NA
AYU39411.1|3489000_3490647_-	acetolactate synthase large subunit	NA	A0A0P0CDR3	Ostreococcus_lucimarinus_virus	31.5	9.0e-65
AYU39412.1|3490786_3490885_-	ilvGMEDA operon attenuator peptide	NA	NA	NA	NA	NA
AYU39413.1|3491140_3491470_+	hypothetical protein	NA	NA	NA	NA	NA
AYU39414.1|3491510_3492563_-|integrase	bacteriophage integrase	integrase	A0A218M4I3	Erwinia_phage	57.3	3.6e-107
AYU39415.1|3492958_3493528_-	repressor protein	NA	A0A1S6KZZ7	Salmonella_phage	43.4	2.5e-38
AYU39416.1|3493653_3493875_+	hypothetical protein	NA	NA	NA	NA	NA
AYU39417.1|3493907_3494417_+	regulatory protein cII	NA	E5G6L3	Salmonella_phage	98.8	5.8e-87
AYU39418.1|3494591_3494816_+	hypothetical protein	NA	NA	NA	NA	NA
AYU39419.1|3494838_3495180_+	hypothetical protein	NA	E5G6L5	Salmonella_phage	98.2	1.7e-55
AYU39420.1|3495247_3495481_+	hypothetical protein	NA	E5G6L6	Salmonella_phage	94.8	2.0e-31
AYU39421.1|3495480_3495708_+	hypothetical protein	NA	E5G6L7	Salmonella_phage	100.0	2.7e-36
AYU39422.1|3495704_3496562_+	DNA adenine methylase	NA	E5G6L8	Salmonella_phage	97.2	3.5e-161
3496130:3496144	attR	TGAAAAAGAAATTCG	NA	NA	NA	NA
AYU39423.1|3496558_3498973_+	endonuclease	NA	E5G6L9	Salmonella_phage	97.5	0.0e+00
AYU39424.1|3499126_3499315_+	hypothetical protein	NA	E5G6M0	Salmonella_phage	95.2	7.9e-26
AYU39425.1|3501282_3502197_+	hypothetical protein	NA	NA	NA	NA	NA
AYU39426.1|3502193_3502934_+	hypothetical protein	NA	NA	NA	NA	NA
AYU39427.1|3502968_3504006_-|capsid,portal	capsid portal protein	capsid,portal	A0A1S6KZW5	Salmonella_phage	89.5	1.3e-173
AYU39428.1|3504005_3505772_-|terminase	terminase subunit	terminase	A0A1S6KZW3	Salmonella_phage	99.5	0.0e+00
AYU39429.1|3505914_3506748_+|capsid	capsid scaffolding protein	capsid	A0A1S6KZW9	Salmonella_phage	90.6	1.5e-121
AYU39430.1|3506764_3507823_+|capsid	major capsid protein	capsid	E5G6M6	Salmonella_phage	93.1	1.4e-180
AYU39431.1|3507826_3508477_+|terminase	terminase endonuclease subunit	terminase	E5G6M7	Salmonella_phage	96.3	8.7e-112
AYU39432.1|3508509_3509037_+|capsid	capsid completion protein	capsid	A0A1S6KZW8	Salmonella_phage	89.0	2.1e-76
AYU39433.1|3509036_3509240_+|tail	phage tail protein	tail	E5G6M9	Salmonella_phage	92.5	1.4e-31
AYU39434.1|3509243_3509459_+	hypothetical protein	NA	E5G6N0	Salmonella_phage	80.3	1.8e-26
AYU39435.1|3509478_3509952_+	lysozyme	NA	E5G6N1	Salmonella_phage	91.0	3.7e-80
AYU39436.1|3509953_3510331_+	hypothetical protein	NA	A0A1S6KZZ2	Salmonella_phage	40.0	2.3e-16
AYU39437.1|3510327_3510756_+	regulatory protein	NA	E5G6N2	Salmonella_phage	77.3	2.2e-47
AYU39438.1|3510851_3511283_+|tail	phage tail protein	tail	E5G6N3	Salmonella_phage	95.1	1.5e-72
AYU39439.1|3511275_3511722_+|tail	phage tail completion protein	tail	A0A1S6L001	Salmonella_phage	85.6	6.6e-63
AYU39440.1|3511790_3512369_+|plate	phage baseplate assembly protein	plate	A0A1S6KZX7	Salmonella_phage	86.5	5.5e-94
AYU39441.1|3512365_3512725_+|plate	phage baseplate assembly protein	plate	A0A1S6KZZ4	Salmonella_phage	84.9	6.1e-51
AYU39442.1|3512711_3513620_+|plate	phage baseplate assembly protein	plate	A0A1S6KZY6	Salmonella_phage	89.7	1.3e-142
AYU39443.1|3513612_3514218_+|tail	phage tail protein	tail	A0A1S6L000	Salmonella_phage	92.0	2.0e-110
AYU39444.1|3514214_3515729_+|tail	variable tail fiber protein	tail	M1TAS6	Escherichia_phage	73.0	4.4e-199
AYU39445.1|3515728_3516322_+|tail	tail fiber assembly protein	tail	M1SV83	Escherichia_phage	64.3	9.2e-60
AYU39446.1|3516293_3516734_-|tail	tail fiber assembly protein	tail	A0A0F7LDZ0	Escherichia_phage	68.0	3.1e-52
AYU39447.1|3517156_3517729_+	DNA-invertase	NA	A0A0F7LA37	Escherichia_phage	86.3	1.4e-86
AYU39448.1|3517871_3519044_+|tail	major tail sheath protein	tail	A0A1S6KZY7	Salmonella_phage	90.3	3.5e-204
AYU39449.1|3519053_3519569_+|tail	major tail tube protein	tail	A0A1S6L002	Salmonella_phage	95.9	5.6e-90
AYU39450.1|3519623_3519926_+|tail	phage tail protein	tail	A0A1S6KZZ9	Salmonella_phage	89.0	7.0e-40
AYU39451.1|3519940_3520060_+	bacteriophage protein	NA	E5G6Q0	Salmonella_phage	87.2	2.8e-13
AYU39452.1|3520052_3523130_+|tail	bacteriophage tail protein	tail	E5G6Q1	Salmonella_phage	63.0	0.0e+00
AYU39453.1|3523126_3523612_+|tail	bacteriophage tail protein	tail	E5G6Q2	Salmonella_phage	80.0	2.4e-66
AYU39454.1|3523608_3524709_+	hypothetical protein	NA	A0A1S6KZZ5	Salmonella_phage	88.3	1.0e-176
AYU39455.1|3524799_3525018_+	hypothetical protein	NA	Q53ZE7	Salmonella_virus	69.0	7.5e-20
AYU39456.1|3526599_3527058_+|transposase	insertion sequence element IS200 transposase	transposase	NA	NA	NA	NA
>prophage 11
CP029962	Salmonella enterica subsp. enterica serovar Typhi strain 343078_228140 chromosome, complete genome	4783156	4442914	4517078	4783156	plate,portal,tail,integrase,capsid,terminase	Salmonella_phage(82.98%)	76	4504415:4504431	4517237:4517253
AYU40227.1|4442914_4444864_+	hypothetical protein	NA	A0A2K9V411	Faecalibacterium_phage	38.3	5.9e-31
AYU40228.1|4444935_4445844_+	hypothetical protein	NA	NA	NA	NA	NA
AYU40229.1|4445917_4446817_+	hypothetical protein	NA	NA	NA	NA	NA
AYU40230.1|4446858_4447218_+	hypothetical protein	NA	NA	NA	NA	NA
AYU40231.1|4447317_4447587_-	hypothetical protein	NA	NA	NA	NA	NA
AYU40232.1|4447718_4448993_-	UV protection protein	NA	F1C5A5	Cronobacter_phage	62.0	7.5e-152
AYU40233.1|4449212_4449590_+	hypothetical protein	NA	NA	NA	NA	NA
AYU40234.1|4449676_4449895_-	hypothetical protein	NA	E5G6Q4	Salmonella_phage	75.0	4.9e-27
AYU40235.1|4449962_4451063_-	hypothetical protein	NA	E5G6Q3	Salmonella_phage	92.1	7.9e-190
AYU40236.1|4451059_4451545_-|tail	phage tail protein	tail	E5G6Q2	Salmonella_phage	93.2	9.4e-71
AYU40237.1|4451544_4454325_-	hypothetical protein	NA	A0A2H4JGB2	uncultured_Caudovirales_phage	41.1	3.5e-125
AYU40238.1|4454317_4454437_-	bacteriophage protein	NA	E5G6Q0	Salmonella_phage	94.9	1.2e-14
AYU40239.1|4454451_4454754_-|tail	phage tail protein	tail	E5G6P9	Salmonella_phage	93.9	3.3e-42
AYU40240.1|4454808_4455324_-|tail	major tail tube protein	tail	E5G6P8	Salmonella_phage	99.4	2.7e-92
AYU40241.1|4455333_4456506_-|tail	major tail sheath protein	tail	A0A1S6KZY7	Salmonella_phage	99.5	9.8e-223
AYU40242.1|4457040_4457763_+	invasion-associated secreted protein	NA	NA	NA	NA	NA
AYU40243.1|4457960_4458368_-|tail	phage tail fiber protein	tail	A0A1B0V844	Salmonella_phage	84.2	4.1e-59
AYU40244.1|4458374_4459994_-|tail	phage tail fiber protein	tail	E5G6P0	Salmonella_phage	90.9	2.7e-154
AYU40245.1|4459990_4460596_-|tail	phage tail protein	tail	A0A1S6L000	Salmonella_phage	92.0	2.0e-110
AYU40246.1|4460588_4461497_-|plate	phage baseplate assembly protein	plate	E5G6N8	Salmonella_phage	97.0	5.2e-155
AYU40247.1|4461483_4461843_-|plate	phage baseplate assembly protein	plate	A0A1S6KZZ4	Salmonella_phage	96.6	6.8e-58
AYU40248.1|4461839_4462418_-|plate	phage baseplate assembly protein	plate	E5G6N6	Salmonella_phage	99.5	3.9e-108
AYU40249.1|4462486_4462933_-|tail	phage tail completion protein	tail	A0A1S6L001	Salmonella_phage	90.4	2.2e-66
AYU40250.1|4462925_4463357_-|tail	phage tail protein	tail	A0A1S6KZY0	Salmonella_phage	98.6	2.5e-75
AYU40251.1|4463452_4463878_-	regulatory protein	NA	A0A1S6KZX8	Salmonella_phage	97.9	2.5e-67
AYU40252.1|4463877_4464255_-	hypothetical protein	NA	A0A1S6KZZ2	Salmonella_phage	99.2	1.5e-60
AYU40253.1|4464259_4464730_-	lysozyme	NA	A0A1S6KZY9	Salmonella_phage	97.4	1.0e-85
AYU40254.1|4464749_4464965_-	hypothetical protein	NA	E5G6N0	Salmonella_phage	98.6	3.8e-32
AYU40255.1|4464968_4465172_-|tail	phage tail protein	tail	E5G6M9	Salmonella_phage	100.0	3.8e-34
AYU40256.1|4465171_4465636_-|capsid	capsid completion protein	capsid	A0A1S6KZW8	Salmonella_phage	98.1	2.4e-84
AYU40257.1|4465729_4466380_-|terminase	phage terminase	terminase	E5G6M7	Salmonella_phage	99.5	2.4e-114
AYU40258.1|4466383_4467448_-|capsid	major capsid protein	capsid	A0A1S6KZZ3	Salmonella_phage	98.3	1.3e-194
AYU40259.1|4467464_4468298_-|capsid	capsid scaffolding protein	capsid	E5G6M5	Salmonella_phage	87.4	6.1e-126
AYU40260.1|4468440_4470207_+|terminase	terminase subunit	terminase	A0A1S6KZW3	Salmonella_phage	96.4	0.0e+00
AYU40261.1|4470203_4471250_+|capsid,portal	capsid portal protein	capsid,portal	A0A1S6KZW5	Salmonella_phage	86.6	2.1e-176
AYU40262.1|4471298_4471994_-	hypothetical protein	NA	NA	NA	NA	NA
AYU40263.1|4472013_4473078_-	hypothetical protein	NA	NA	NA	NA	NA
AYU40264.1|4473074_4474139_-	hypothetical protein	NA	NA	NA	NA	NA
AYU40265.1|4475063_4475393_-	hypothetical protein	NA	A0A1S6L028	Salmonella_phage	90.8	6.2e-50
AYU40266.1|4475389_4477459_-	bacteriophage replication protein A	NA	A0A1S6L028	Salmonella_phage	95.9	0.0e+00
AYU40267.1|4477449_4478310_-	DNA adenine methylase	NA	E5G6L8	Salmonella_phage	81.8	3.4e-132
AYU40268.1|4478306_4478891_-	exonuclease	NA	A0A1S6L012	Salmonella_phage	73.7	1.1e-76
AYU40269.1|4478887_4479115_-	hypothetical protein	NA	A0A1S6L007	Salmonella_phage	94.7	1.0e-35
AYU40270.1|4479114_4479348_-	hypothetical protein	NA	A0A1S6L021	Salmonella_phage	84.4	9.8e-26
AYU40271.1|4479415_4479757_-	hypothetical protein	NA	A0A1S6L019	Salmonella_phage	99.1	4.6e-56
AYU40272.1|4479720_4479921_-	hypothetical protein	NA	A0A1S6L005	Salmonella_phage	97.0	4.6e-32
AYU40273.1|4479928_4480438_-	phage regulatory protein	NA	A0A1S6L008	Salmonella_phage	94.1	1.3e-83
AYU40274.1|4480470_4480713_-	phage regulatory protein	NA	A0A1S6KZZ6	Salmonella_phage	98.8	2.3e-38
AYU40275.1|4480829_4481462_+	phage repressor protein cI	NA	A0A1S6KZZ7	Salmonella_phage	58.6	1.4e-66
AYU40276.1|4481465_4482491_+|integrase	phage integrase	integrase	A0A1S6L016	Salmonella_phage	98.2	2.7e-200
AYU40277.1|4482597_4482951_-	protein samA'	NA	I6S1S3	Salmonella_phage	59.3	6.7e-10
AYU40278.1|4483567_4483855_+	hypothetical protein	NA	NA	NA	NA	NA
AYU40279.1|4483865_4484756_+	methyltransferase	NA	NA	NA	NA	NA
AYU40280.1|4484755_4485502_+	hypothetical protein	NA	NA	NA	NA	NA
AYU40281.1|4485803_4487774_-	Vi polysaccharide exporter protein	NA	NA	NA	NA	NA
AYU40282.1|4487793_4489098_-	Vi polysaccharide exporter inner-membrane protein	NA	NA	NA	NA	NA
AYU40283.1|4489120_4489816_-	Vi polysaccharide exporter ATP-binding protein	NA	NA	NA	NA	NA
AYU40284.1|4489841_4490636_-	Vi polysaccharide exporter inner-membrane protein	NA	NA	NA	NA	NA
AYU40285.1|4490645_4491713_-	Vi polysaccharide exporter protein	NA	NA	NA	NA	NA
AYU40286.1|4491757_4493494_-	Vi polysaccharide biosynthesis protein TviE	NA	NA	NA	NA	NA
AYU40287.1|4493493_4495989_-	Vi polysaccharide biosynthesis protein	NA	NA	NA	NA	NA
AYU40288.1|4496012_4497059_-	Vi polysaccharide biosynthesis epimerase	NA	A0A2K9L0I7	Tupanvirus	45.0	1.4e-74
AYU40289.1|4497061_4498339_-	Vi polysaccharide biosynthesis UDP-glucose/GDP-mannose dehydrogenase	NA	M1HYW7	Paramecium_bursaria_Chlorella_virus	26.7	1.3e-21
AYU40290.1|4498583_4499123_-	Vi polysaccharide biosynthesis protein	NA	NA	NA	NA	NA
AYU40291.1|4499976_4501488_+	DNA helicase	NA	A0A126DN25	Acinetobacter_phage	29.0	2.0e-42
AYU40292.1|4501471_4503061_+	hypothetical protein	NA	NA	NA	NA	NA
AYU40293.1|4503224_4504238_+|integrase	phage integrase	integrase	NA	NA	NA	NA
4504415:4504431	attL	GTGGTGCCCGGACTCGG	NA	NA	NA	NA
AYU40294.1|4504664_4504958_+	hypothetical protein	NA	NA	NA	NA	NA
AYU40295.1|4504954_4505443_+	hypothetical protein	NA	NA	NA	NA	NA
AYU40296.1|4505622_4506075_-	hypothetical protein	NA	NA	NA	NA	NA
AYU40297.1|4511297_4511759_+	hypothetical protein	NA	NA	NA	NA	NA
AYU40298.1|4511755_4511977_+	transcriptional regulator	NA	A0A2I7S995	Vibrio_phage	58.3	4.6e-17
AYU40299.1|4512833_4513616_+	hypothetical protein	NA	NA	NA	NA	NA
AYU40300.1|4514242_4514467_-	hypothetical protein	NA	NA	NA	NA	NA
AYU40301.1|4514596_4515508_-	hypothetical protein	NA	NA	NA	NA	NA
AYU40302.1|4515818_4517078_-|integrase	bacteriophage integrase	integrase	B7SYF8	Stenotrophomonas_phage	41.7	3.2e-78
4517237:4517253	attR	GTGGTGCCCGGACTCGG	NA	NA	NA	NA
>prophage 12
CP029962	Salmonella enterica subsp. enterica serovar Typhi strain 343078_228140 chromosome, complete genome	4783156	4659330	4669589	4783156	capsid	Enterobacteria_phage(77.78%)	13	NA	NA
AYU40439.1|4659330_4660407_-	protein kinase	NA	A0A2H4UU60	Bodo_saltans_virus	28.2	7.8e-17
AYU40440.1|4660403_4661477_-	protein kinase	NA	G9BWE0	Planktothrix_phage	44.7	6.5e-56
AYU40441.1|4661451_4662615_-	hypothetical protein	NA	NA	NA	NA	NA
AYU40442.1|4662890_4663457_-	phage polarity suppression protein	NA	Q7M2A1	Enterobacteria_phage	64.9	1.8e-60
AYU40443.1|4663472_4663712_-	hypothetical protein	NA	Q7M294	Enterobacteria_phage	60.5	3.7e-20
AYU40444.1|4663715_4664576_-|capsid	phage capsid protein	capsid	NA	NA	NA	NA
AYU40445.1|4664998_4665322_+	phage DNA binding protein	NA	Q7M299	Enterobacteria_phage	70.0	3.6e-26
AYU40446.1|4665305_4665806_+	hypothetical protein	NA	Q7M2A7	Enterobacteria_phage	70.4	9.8e-31
AYU40447.1|4665802_4666030_+	hypothetical protein	NA	NA	NA	NA	NA
AYU40448.1|4666026_4666347_+	P4 phage protein	NA	NA	NA	NA	NA
AYU40449.1|4666361_4667036_+	bacteriophage P4 DNA primase	NA	Q7M2A8	Enterobacteria_phage	75.1	1.4e-85
AYU40450.1|4667032_4668694_+	hypothetical protein	NA	Q7M2A8	Enterobacteria_phage	90.2	1.9e-296
AYU40451.1|4669430_4669589_+	recombinase	NA	Q7M297	Enterobacteria_phage	57.4	3.9e-10
>prophage 1
CP029963	Salmonella enterica subsp. enterica serovar Typhi strain 343078_228140 plasmid pK91, complete sequence	93445	148	43568	93445	protease,transposase	Shigella_phage(31.25%)	33	NA	NA
AYU40542.1|148_1009_-	beta-lactamase	NA	Q1MVP3	Enterobacteria_phage	100.0	4.6e-161
AYU40543.1|1191_1749_-	TnpR	NA	Q1MVP4	Enterobacteria_phage	100.0	7.0e-94
AYU40544.1|1912_4918_+|transposase	transposase	transposase	Q1MVP5	Enterobacteria_phage	100.0	0.0e+00
AYU40545.1|4942_5479_-	IS2 resolvase	NA	Q9ZXG3	Shigella_phage	69.7	1.2e-69
AYU40546.1|5607_5802_-|transposase	transposase	transposase	Q76S41	Shigella_phage	82.8	2.7e-21
AYU40547.1|5811_6003_-|transposase	IS2 transposase	transposase	Q76S41	Shigella_phage	72.2	3.2e-14
AYU40548.1|6370_7027_+	quinolone resistance protein	NA	NA	NA	NA	NA
AYU40549.1|7345_7783_-	resolvase protein	NA	A0A219YB42	Aeromonas_phage	43.8	5.2e-20
AYU40550.1|7806_9201_-	hypothetical protein	NA	NA	NA	NA	NA
AYU40551.1|9234_9807_-	resolvase-like protein	NA	M9Q1K0	Clostridium_phage	39.4	3.4e-19
AYU40552.1|9943_10534_-	hypothetical protein	NA	NA	NA	NA	NA
AYU40553.1|10640_11363_-|transposase	IS6 family transposase	transposase	A0A077SL39	Escherichia_phage	100.0	3.2e-139
AYU40554.1|11345_12224_+|transposase	transposase	transposase	A0A1B0V7H9	Salmonella_phage	100.0	7.7e-156
AYU40555.1|12281_12524_+	hypothetical protein	NA	NA	NA	NA	NA
AYU40556.1|12555_13218_-	RK2 tetracycline repressor protein	NA	NA	NA	NA	NA
AYU40557.1|13296_14496_+	tetracycline resistance protein A	NA	NA	NA	NA	NA
AYU40558.1|14527_15412_-	PecM protein	NA	NA	NA	NA	NA
AYU40559.1|15876_17697_+|transposase	ed transposase	transposase	A0A1B0V7H9	Salmonella_phage	100.0	0.0e+00
AYU40560.1|18348_19251_+|transposase	transposase	transposase	A0A1B0V7H9	Salmonella_phage	100.0	7.9e-156
AYU40561.1|20187_21711_+	Group II intron-encoded protein ltrA	NA	A0A0U4J920	Pseudomonas_phage	31.6	8.1e-44
AYU40562.1|22252_23329_+|transposase	transposase of ISEc21	transposase	NA	NA	NA	NA
AYU40563.1|23731_25822_-|protease	Lon protease	protease	NA	NA	NA	NA
AYU40564.1|25838_28496_-	hypothetical protein	NA	NA	NA	NA	NA
AYU40565.1|28495_32125_-	Type I restriction-modification system methyltransferase subunit	NA	NA	NA	NA	NA
AYU40566.1|32140_33904_-	hypothetical protein	NA	NA	NA	NA	NA
AYU40567.1|33920_37598_-	hypothetical protein	NA	NA	NA	NA	NA
AYU40568.1|37616_38201_-	hypothetical protein	NA	NA	NA	NA	NA
AYU40569.1|38197_38797_-	hypothetical protein	NA	NA	NA	NA	NA
AYU40570.1|38806_39694_-	hypothetical protein	NA	NA	NA	NA	NA
AYU40571.1|39801_40212_-	hypothetical protein	NA	NA	NA	NA	NA
AYU40572.1|40553_41231_-|transposase	transposase	transposase	S5WIU1	Leptospira_phage	43.2	2.2e-41
AYU40573.1|42333_42729_+|transposase	transposase	transposase	Q76S41	Shigella_phage	75.4	1.4e-43
AYU40574.1|42731_43568_+|transposase	transposase InsF for insertion sequence IS3A/B/C/D/E/fA	transposase	Q9ZXG3	Shigella_phage	62.7	4.3e-95
>prophage 2
CP029963	Salmonella enterica subsp. enterica serovar Typhi strain 343078_228140 plasmid pK91, complete sequence	93445	66566	87856	93445	transposase	Escherichia_phage(42.11%)	26	NA	NA
AYU40600.1|66566_67094_+	Endonuclease	NA	A0A1B2LRT6	Wolbachia_phage	39.5	2.8e-20
AYU40601.1|67125_67557_-	hypothetical protein	NA	NA	NA	NA	NA
AYU40602.1|68036_69002_-	DNA primase TraC	NA	A0A1V0EEV1	Caulobacter_phage	42.7	1.3e-58
AYU40603.1|69453_69879_+	Error-prone repair protein UmuD	NA	A0A1W6JNS2	Morganella_phage	50.4	2.9e-31
AYU40604.1|69878_71150_+	protein UmuC	NA	F1C5A5	Cronobacter_phage	63.7	5.6e-155
AYU40605.1|71210_71480_+	Orf44	NA	NA	NA	NA	NA
AYU40606.1|71533_71839_+	hypothetical protein	NA	NA	NA	NA	NA
AYU40607.1|72528_73503_-	plasmid partitioning protein	NA	I3WF22	Macacine_betaherpesvirus	89.7	1.7e-156
AYU40608.1|73499_74675_-	plasmid partition protein SopA	NA	A0A2I6B2X3	Macacine_betaherpesvirus	97.4	2.8e-225
AYU40609.1|75394_76417_+	hypothetical protein	NA	J9Q7H0	Salmonella_phage	53.9	6.8e-87
AYU40610.1|76582_77044_-	hypothetical protein	NA	A0A1B0V7H9	Salmonella_phage	57.1	5.9e-38
AYU40611.1|77174_78374_-|transposase	IS1294 transposase	transposase	NA	NA	NA	NA
AYU40612.1|78586_79300_-|transposase	transposase	transposase	Q1MVF0	Enterobacteria_phage	86.5	2.6e-109
AYU40613.1|79497_79788_+	hypothetical protein	NA	A0A077SK55	Escherichia_phage	87.3	1.8e-32
AYU40614.1|79857_80124_+	hypothetical protein	NA	NA	NA	NA	NA
AYU40615.1|80126_80375_+	DNA polymerase III subunit theta	NA	Q71T70	Escherichia_phage	85.4	2.8e-31
AYU40616.1|80483_80879_+	DNA polymerase V subunit	NA	Q1MVE7	Enterobacteria_phage	76.2	2.1e-52
AYU40617.1|80951_81173_+	antitoxin of P1 addiction system	NA	A0A222YXU1	Escherichia_phage	100.0	6.7e-32
AYU40618.1|81172_81553_+	death on curing protein	NA	Q71T66	Escherichia_phage	90.3	1.8e-56
AYU40619.1|81636_82437_-	hypothetical protein	NA	A0A222YXM9	Escherichia_phage	71.1	9.4e-92
AYU40620.1|82450_82945_-	deoxyuridine 5'-triphosphate nucleotidohydrolase	NA	A0A222YYP1	Escherichia_phage	88.4	1.5e-79
AYU40621.1|82937_83429_-	hypothetical protein	NA	NA	NA	NA	NA
AYU40622.1|83425_83680_-	hypothetical protein	NA	Q5QBE7	Escherichia_phage	75.0	2.1e-29
AYU40623.1|83842_84871_-	site-specific tyrosine recombinase XerC	NA	Q5XLQ5	Enterobacteria_phage	42.1	1.1e-60
AYU40624.1|85268_86306_+	hypothetical protein	NA	NA	NA	NA	NA
AYU40625.1|87133_87856_+|transposase	IS6 family transposase	transposase	A0A077SL39	Escherichia_phage	100.0	3.2e-139
