Submission Results

Sequence Name: Enterococcus faecium DO, whole genome shotgun sequencing project.

GenBank Accession Number: AAAK00000000.3

GenInfo (GI) Number: 48374856

Download Results: AAAK00000000.3.PHASTER.zip

gi|48374856|ref|AAAK00000000.3| Enterococcus faecium DO whole genome shotgun sequence. .2848380, gc%: 37.90%

Download summary as .txt file: summary.txt file_download

Total: 5 prophage regions have been identified, of which 3 regions are intact, 2 regions are incomplete, and 0 regions are questionable.

RegionRegion LengthCompletenessScore# Total ProteinsRegion PositionMost Common PhageGC %Details
142Kbintact1202167953-109968 info_outlinePROPHAGE_Staphy_N31536.42%Show info_outline
223.4Kbincomplete5025303628-327121 info_outlinePHAGE_Lactoc_lato35.97%Show info_outline
346.7Kbintact15055449961-496744 info_outlinePHAGE_Lister_238936.04%Show info_outline
442.7Kbintact11023801843-844613 info_outlinePHAGE_Entero_EFRM3136.74%Show info_outline
512.1Kbincomplete20111594772-1606882 info_outlinePHAGE_Prochl_P_SSM235.91%Show info_outline
Intact (score > 90)
Questionable (score 70-90)
Incomplete (score < 70)
Region: The number assigned to the region.
Region Length: The length of the sequence of that region (in bp).
Completeness: A prediction of whether the region contains a intact or incomplete prophage based on the above criteria.
Score: The score of the region based on the above criteria.
# Total Proteins: The number of ORFs present in the region.
Region Position: The start and end positions of the region on the bacterial chromosome.
Most Common Phage: The phage(s) with the highest number of proteins most similar to those in the region.
GC %: The percentage of GC nucleotides of the region.

Criteria for scoring prophage regions (as intact, questionable, or incomplete):
Method 1:

  1. If the number of certain phage organism in this table is more than or equal to 100% of the total number of CDS of the region, the region is marked with total score 150. If less than 100%, method 2 and 3 will be used.
Method 2:
  1. If the number of certain phage organism in this table is more than 50% of the total number of CDS of the region, that phage organism is considered as the major potential phage for that region; the percentage of the total number of that phage organism in this table in the total number of proteins of the region is calculated and then multipled by 100; the percentage of the length of that phage organism in this table in the length of the region is calculated and then multipled by 50 (phage head's encapsulation capability is considered).
Method 3:
  1. If any of the specific phage-related keywords (such as 'capsid', 'head', 'integrase', 'plate', 'tail', 'fiber', 'coat', 'transposase', 'portal', 'terminase', 'protease' or 'lysin') are present, the score will be increased by 10 for each keyword found.
  2. If the size of the region is greater than 30 Kb, the score will be increased by 10.
  3. If there are at least 40 proteins in the region, the score will be increased by 10.
  4. If all of the phage-related proteins and hypothetical proteins constitute more than 70% of the total number of proteins in the region, the score will be increased by 10.
Compared the total score of method 2 with the total score of method 3, the bigger one is chosen as the total score of the region.
If the region's total score is less than 70, it is marked as incomplete; if between 70 to 90, it is marked as questionable; if greater than 90, it is marked as intact.

gi|48374856|ref|AAAK00000000.3| Enterococcus faecium DO whole genome shotgun sequence. [asmbl_id: NC_000000].2848380, gc%: 37.90%

Download details as .txt file: detail.txt file_download

Hits against Virus and Prophage Database
Hits against Bacterial Database or GenBank File

Region 1, total 29 CDS

#CDS PositionBLAST HitE-ValueSequence
167953..67964attL0.0Showinfo_outline
278824..79783PHAGE_Spirop_R8A2B: putative transposase; EfaeDRAFT_2678; phage(gi9626114)3e-21Showinfo_outline
380005..80883ROK; EfaeDRAFT_26790.0Showinfo_outline
4complement(81063..82358)PROPHAGE_Staphy_N315: transposase; EfaeDRAFT_2680; phage(gi15927655)4e-42Showinfo_outline
5complement(82520..83815)PROPHAGE_Staphy_N315: transposase; EfaeDRAFT_2681; phage(gi15927655)5e-64Showinfo_outline
6complement(83992..85077)PROPHAGE_Salmon_CT18: phage integrase; EfaeDRAFT_2682; phage(gi16763128)5e-07Showinfo_outline
785748..86656PROPHAGE_Shewan_MR-1: ISSod6, transposase; EfaeDRAFT_2683; phage(gi24374783)5e-05Showinfo_outline
886712..87209PHAGE_Erwini_phiEaH2: N-acetyltransferase GCN5; EfaeDRAFT_2684; phage(gi431810590)6e-07Showinfo_outline
9complement(87246..87929)conserved hypothetical protein; EfaeDRAFT_26850.0Showinfo_outline
1088041..88052attL0.0Showinfo_outline
1188276..88542conserved hypothetical protein; EfaeDRAFT_27190.0Showinfo_outline
1288569..88868hypothetical protein; EfaeDRAFT_26860.0Showinfo_outline
1389042..89593hypothetical protein; EfaeDRAFT_26870.0Showinfo_outline
1489739..90032hypothetical protein; EfaeDRAFT_27200.0Showinfo_outline
1590396..91394PHAGE_Entero_phiEf11: LysM domain protein; EfaeDRAFT_2688; phage(gi282598770)7e-06Showinfo_outline
1691417..91428attL0.0Showinfo_outline
17complement(91486..92439)PHAGE_Spirop_R8A2B: putative transposase; EfaeDRAFT_2689; phage(gi9626114)3e-24Showinfo_outline
1892544..92555attL0.0Showinfo_outline
19complement(93077..93349)hypothetical protein; EfaeDRAFT_26900.0Showinfo_outline
20complement(93398..94234)PHAGE_Lactob_phiAT3: putative transposase B; EfaeDRAFT_2691; phage(gi48697274)4e-30Showinfo_outline
21complement(94270..94428)transposase (05); EfaeDRAFT_26920.0Showinfo_outline
22complement(94429..94560)transposase (05); EfaeDRAFT_26930.0Showinfo_outline
2394787..94798attR0.0Showinfo_outline
2494835..95377hypothetical protein; EfaeDRAFT_26940.0Showinfo_outline
2595544..95555attR0.0Showinfo_outline
2695660..95971thioredoxin family protein; EfaeDRAFT_27240.0Showinfo_outline
27complement(96001..96837)PHAGE_Lactob_phiAT3: putative transposase B; EfaeDRAFT_2695; phage(gi48697274)3e-30Showinfo_outline
28104791..104802attR0.0Showinfo_outline
29109968..109979attR0.0Showinfo_outline

Region 2, total 29 CDS

#CDS PositionBLAST HitE-ValueSequence
1complement(303628..304437)PHAGE_Lactoc_Q54: putative HAD hydrolase; EfaeDRAFT_2377; phage(gi115304277)2e-05Showinfo_outline
2304513..304525attL0.0Showinfo_outline
3304711..305628PHAGE_Archae_virus: hypothetical protein BJ1_gp01; EfaeDRAFT_2378; phage(gi119756986)1e-21Showinfo_outline
4305621..306523PHAGE_Archae_virus: hypothetical protein BJ1_gp01; EfaeDRAFT_2379; phage(gi119756986)1e-17Showinfo_outline
5306556..306906hypothetical protein; EfaeDRAFT_23800.0Showinfo_outline
6306940..307878PHAGE_Lactob_1: Mg2+/Co2+ transport protein CorA; EfaeDRAFT_2381; phage(gi226377699)7e-05Showinfo_outline
7307956..308849PHAGE_Tricho_2c: hypothetical protein TNAV2c_gp071; EfaeDRAFT_2382; phage(gi116326757)4e-59Showinfo_outline
8308887..309450conserved hypothetical protein; EfaeDRAFT_23830.0Showinfo_outline
9309464..309652conserved hypothetical protein; EfaeDRAFT_24230.0Showinfo_outline
10309665..310567PHAGE_Lactoc_lato: putative tail lysin; EfaeDRAFT_2384; phage(gi30089904)6e-06Showinfo_outline
11310599..310841Transglycosylase-associated protein; EfaeDRAFT_23850.0Showinfo_outline
12complement(311097..311468)hypothetical protein; EfaeDRAFT_24240.0Showinfo_outline
13complement(312104..312331)PHAGE_Lactoc_lato: hypothetical protein P335p08; EfaeDRAFT_2386; phage(gi30089869)1e-05Showinfo_outline
14complement(312340..312813)conserved hypothetical protein; EfaeDRAFT_23870.0Showinfo_outline
15complement(313454..313717)hypothetical protein; EfaeDRAFT_24250.0Showinfo_outline
16314044..314610conserved hypothetical protein; EfaeDRAFT_23880.0Showinfo_outline
17314623..314811conserved hypothetical protein; EfaeDRAFT_24260.0Showinfo_outline
18314824..315381Protein of unknown function DUF322; EfaeDRAFT_23890.0Showinfo_outline
19315413..315655Transglycosylase-associated protein; EfaeDRAFT_23900.0Showinfo_outline
20315996..317210Rh-like protein/ammonium transporter; EfaeDRAFT_23910.0Showinfo_outline
21317241..318668Amino acid permease-associated region; EfaeDRAFT_23920.0Showinfo_outline
22318691..319617Glutaminase; EfaeDRAFT_23930.0Showinfo_outline
23complement(320121..321080)PHAGE_Spirop_R8A2B: putative transposase; EfaeDRAFT_2394; phage(gi9626114)2e-24Showinfo_outline
24321182..321203attL0.0Showinfo_outline
25321293..322075Transposase, IS4; EfaeDRAFT_23950.0Showinfo_outline
26322135..323613PHAGE_Staphy_phiPVL108: putative transposase; EfaeDRAFT_2396; phage(gi119443708)1e-17Showinfo_outline
27324118..324672PHAGE_Bacill_BtCS33: integrase; EfaeDRAFT_2397; phage(gi392972759)4e-37Showinfo_outline
28324839..324860attR0.0Showinfo_outline
29327121..327133attR0.0Showinfo_outline

Region 3, total 60 CDS

#CDS PositionBLAST HitE-ValueSequence
1449961..449972attL0.0Showinfo_outline
2451648..451848PHAGE_Lactoc_bIL309: integrase; EfaeDRAFT_2157; phage(gi13095806)3e-10Showinfo_outline
3451883..451895attL0.0Showinfo_outline
4452097..452399hypothetical protein; EfaeDRAFT_22480.0Showinfo_outline
5complement(452435..452806)hypothetical protein; EfaeDRAFT_21580.0Showinfo_outline
6complement(452808..453260)hypothetical protein; EfaeDRAFT_22490.0Showinfo_outline
7complement(453223..453630)hypothetical protein; EfaeDRAFT_21590.0Showinfo_outline
8453974..454468PROPHAGE_Ralsto_GMI1000: ISRSO11-transposase ORFA protein; EfaeDRAFT_2160; phage(gi17546156)3e-20Showinfo_outline
9complement(454553..455389)PHAGE_Lactob_phiAT3: putative transposase B; EfaeDRAFT_2161; phage(gi48697274)9e-30Showinfo_outline
10complement(455425..455715)PHAGE_Lactob_phiAT3: putative transposase A; EfaeDRAFT_2162; phage(gi48697273)2e-08Showinfo_outline
11complement(456392..456465)tRNA0.0Showinfo_outline
12complement(456655..457680)PHAGE_Entero_1: amidase; EfaeDRAFT_2163; phage(gi225626379)1e-63Showinfo_outline
13complement(457677..457901)PHAGE_Lactoc_ul36: putative holin; EfaeDRAFT_2250; phage(gi21716128)5e-12Showinfo_outline
14complement(457898..458191)PHAGE_Lister_P70: hypothetical protein; EfaeDRAFT_2251; phage(gi410490647)7e-05Showinfo_outline
15complement(458229..458375)Phage uncharacterised protein XkdX; EfaeDRAFT_22520.0Showinfo_outline
16complement(458368..458814)conserved hypothetical protein; EfaeDRAFT_21640.0Showinfo_outline
17complement(458977..461103)PHAGE_Lactob_1: minor tail protein; EfaeDRAFT_2165; phage(gi62327113)5e-09Showinfo_outline
18complement(461127..463418)PHAGE_Lister_2389: Gp14 protein; EfaeDRAFT_2166; phage(gi17488517)1e-67Showinfo_outline
19complement(463428..464165)PHAGE_Lister_2389: Gp13 protein; EfaeDRAFT_2167; phage(gi17488516)3e-18Showinfo_outline
20complement(464216..467647)PHAGE_Lister_2389: tail tape measure protein; EfaeDRAFT_2168; phage(gi17488515)2e-88Showinfo_outline
21complement(467849..468211)PHAGE_Lister_2389: Gp11 protein; EfaeDRAFT_2169; phage(gi17488514)2e-06Showinfo_outline
22complement(468231..468839)PHAGE_Lister_2389: major tail protein a; EfaeDRAFT_2170; phage(gi17488513)5e-37Showinfo_outline
23complement(468851..469255)PHAGE_Lister_2389: Gp9 protein; EfaeDRAFT_2171; phage(gi17488512)1e-08Showinfo_outline
24complement(469248..469703)PHAGE_Lister_2389: Gp8 protein; EfaeDRAFT_2172; phage(gi17488511)5e-10Showinfo_outline
25complement(469639..469992)PHAGE_Lister_2389: Gp7 protein; EfaeDRAFT_2173; phage(gi17488510)1e-09Showinfo_outline
26complement(469982..470293)PHAGE_Lister_2389: Gp6 protein; EfaeDRAFT_2174; phage(gi17488509)3e-08Showinfo_outline
27complement(470290..471165)PHAGE_Entero_phiFL1A: hypothetical protein; EfaeDRAFT_2175; phage(gi281416374)2e-131Showinfo_outline
28complement(471175..472335)PHAGE_Lister_2389: major capsid protein a; EfaeDRAFT_2176; phage(gi17488508)1e-95Showinfo_outline
29complement(472335..473021)PHAGE_Staphy_SMSAP5: protease; EfaeDRAFT_2177; phage(gi422935811)2e-34Showinfo_outline
30complement(472984..474162)PHAGE_Lister_2389: hypothetical protein 2389gp03; EfaeDRAFT_2178; phage(gi17488506)8e-60Showinfo_outline
31complement(474182..475876)PHAGE_Lister_2389: terminase large subunit; EfaeDRAFT_2179; phage(gi17488505)7e-106Showinfo_outline
32complement(475854..476168)PHAGE_Clostr_phiCD6356: putative terminase small subunit; EfaeDRAFT_2180; phage(gi326536848)2e-09Showinfo_outline
33complement(476271..476588)PHAGE_Lister_2389: Gp55 protein; EfaeDRAFT_2253; phage(gi17488560)7e-11Showinfo_outline
34complement(476557..476901)PHAGE_Lister_2389: Gp54 protein; EfaeDRAFT_2181; phage(gi17488559)3e-20Showinfo_outline
35477938..478225PHAGE_Staphy_CN125: hypothetical protein CURR004; EfaeDRAFT_2254; phage(gi239507426)1e-17Showinfo_outline
36complement(478683..479096)PHAGE_Entero_phiEf11: phage autolysin transcriptional regulator ArpU family; EfaeDRAFT_2182; phage(gi282598742)5e-60Showinfo_outline
37complement(479173..479469)hypothetical protein; EfaeDRAFT_22550.0Showinfo_outline
38complement(479466..480023)PHAGE_Entero_phiEF24C: hypothetical protein EFP_gp160; EfaeDRAFT_2183; phage(gi158079456)2e-14Showinfo_outline
39complement(480020..480439)PHAGE_Entero_phiFL2A: YopX superfamily protein; EfaeDRAFT_2184; phage(gi281416516)1e-32Showinfo_outline
40complement(480641..480997)PHAGE_Lactoc_T: hypothetical protein BK5-Tp56; EfaeDRAFT_2185; phage(gi14251179)9e-18Showinfo_outline
41complement(480997..481302)hypothetical protein; EfaeDRAFT_22560.0Showinfo_outline
42complement(481457..481759)hypothetical protein; EfaeDRAFT_22570.0Showinfo_outline
43complement(481921..482190)hypothetical protein; EfaeDRAFT_22580.0Showinfo_outline
44complement(482202..482951)PHAGE_Lactob_c5: putative DNA replication protein; EfaeDRAFT_2186; phage(gi418488187)8e-38Showinfo_outline
45complement(482954..483640)PHAGE_Entero_phiEf11: conserved hypothetical protein; EfaeDRAFT_2187; phage(gi282598737)1e-89Showinfo_outline
46complement(483646..484317)PHAGE_Bacill_L: gp28; EfaeDRAFT_2188; phage(gi216905993)1e-32Showinfo_outline
47complement(484310..484651)hypothetical protein; EfaeDRAFT_21890.0Showinfo_outline
48complement(484829..485527)PHAGE_Entero_phiFL3A: anti-repressor protein; EfaeDRAFT_2190; phage(gi281416221)5e-29Showinfo_outline
49485614..486084hypothetical protein; EfaeDRAFT_21910.0Showinfo_outline
50complement(486293..486631)PHAGE_Staphy_EW: ORF040; EfaeDRAFT_2192; phage(gi66395845)1e-10Showinfo_outline
51complement(486865..487611)PHAGE_Staphy_phiMR25: putative anti-repressor protein; EfaeDRAFT_2193; phage(gi189427129)1e-52Showinfo_outline
52487689..487997hypothetical protein; EfaeDRAFT_22440.0Showinfo_outline
53complement(487968..488225)hypothetical protein; EfaeDRAFT_22470.0Showinfo_outline
54complement(488523..488663)hypothetical protein; EfaeDRAFT_21940.0Showinfo_outline
55488957..489277PHAGE_Strept_6: putative repressor; EfaeDRAFT_2195; phage(gi28876485)3e-23Showinfo_outline
56489295..489726PHAGE_Lactoc_bIL285: Orf3; EfaeDRAFT_2196; phage(gi13095683)4e-08Showinfo_outline
57489853..490437PHAGE_Lister_A500: gp32; EfaeDRAFT_2197; phage(gi157324991)1e-19Showinfo_outline
58490554..491693PHAGE_Lactoc_bIL309: integrase; EfaeDRAFT_2198; phage(gi13095806)6e-100Showinfo_outline
59491760..491772attR0.0Showinfo_outline
60496744..496755attR0.0Showinfo_outline

Region 4, total 25 CDS

#CDS PositionBLAST HitE-ValueSequence
1801843..801855attL0.0Showinfo_outline
2complement(810740..811075)PHAGE_Entero_EFRM31: head-tail adaptor protein; EfaeDRAFT_1962; phage(gi327198118)2e-14Showinfo_outline
3complement(811062..811346)PHAGE_Entero_EFRM31: head-tail joining protein; EfaeDRAFT_1963; phage(gi327198117)8e-09Showinfo_outline
4complement(811402..812925)PHAGE_Entero_EFRM31: major capsid protein; EfaeDRAFT_1964; phage(gi327198115)8e-50Showinfo_outline
5complement(812918..814093)PHAGE_Entero_EFRM31: portal protein; EfaeDRAFT_1965; phage(gi327198113)9e-56Showinfo_outline
6complement(814248..815942)PHAGE_Lactob_LF1: bacteriophage terminase large subunit; EfaeDRAFT_1966; phage(gi418489385)9e-124Showinfo_outline
7complement(815939..816412)PHAGE_Burkho_phiE125: putative terminase (small subunit); EfaeDRAFT_1967; phage(gi17975162)4e-13Showinfo_outline
8complement(817372..817779)conserved hypothetical protein; EfaeDRAFT_19680.0Showinfo_outline
9complement(818045..819520)PHAGE_Staphy_2638A: ORF003; EfaeDRAFT_1969; phage(gi66395453)5e-68Showinfo_outline
10complement(819510..820358)PHAGE_Lactoc_bIL310: hypothetical protein bIL310p24; EfaeDRAFT_1970; phage(gi13095885)1e-22Showinfo_outline
11complement(820395..820757)hypothetical protein; EfaeDRAFT_19710.0Showinfo_outline
12complement(821057..821461)conserved hypothetical protein - phage associated; EfaeDRAFT_19720.0Showinfo_outline
13complement(821442..821681)PHAGE_Haemop_Aaphi23: putative antirepressor protein Ant; EfaeDRAFT_1973; phage(gi31544021)2e-06Showinfo_outline
14complement(821678..821989)hypothetical protein; EfaeDRAFT_19740.0Showinfo_outline
15complement(822033..822326)hypothetical protein; EfaeDRAFT_19810.0Showinfo_outline
16822616..823167PHAGE_Lactoc_bIL311: repressor; EfaeDRAFT_1975; phage(gi13095660)5e-07Showinfo_outline
17823228..824373PROPHAGE_Oceano_HTE831: integrase; EfaeDRAFT_1976; phage(gi23097608)7e-64Showinfo_outline
18complement(824454..824759)Protein of unknown function DUF1292; EfaeDRAFT_19770.0Showinfo_outline
19complement(824784..825215)Conserved hypothetical protein 250; EfaeDRAFT_19780.0Showinfo_outline
20complement(825212..825478)protein of unknown function DUF965; EfaeDRAFT_19790.0Showinfo_outline
21complement(825733..826461)PHAGE_Strept_P9: streptodornase; EfaeDRAFT_1980; phage(gi157311188)2e-07Showinfo_outline
22826463..826963PROPHAGE_Staphy_N315: transposase; EfaeDRAFT_2259; phage(gi15927655)1e-09Showinfo_outline
23complement(827119..828093)PHAGE_Parame_AR158: hypothetical protein AR158_C327L; EfaeDRAFT_2260; phage(gi157953517)3e-26Showinfo_outline
24828503..829753PROPHAGE_Escher_CFT073: transposase; EfaeDRAFT_2261; phage(gi26248352)7e-12Showinfo_outline
25844613..844625attR0.0Showinfo_outline

Region 5, total 13 CDS

#CDS PositionBLAST HitE-ValueSequence
1complement(1594772..1595683)PHAGE_Prochl_P_SSM2: glycosyltransferase family 11; EfaeDRAFT_1143; phage(gi61806136)4e-11Showinfo_outline
21595468..1595479attL0.0Showinfo_outline
3complement(1595821..1596687)PHAGE_Parame_1: hypothetical protein; EfaeDRAFT_1144; phage(gi145309288)1e-10Showinfo_outline
4complement(1596684..1597850)hypothetical protein; EfaeDRAFT_11450.0Showinfo_outline
5complement(1597864..1599939)PHAGE_Staphy_phiN315: probable ss-1,3-N-acetylglucosaminyltransferase; EfaeDRAFT_1146; phage(gi30043988)1e-05Showinfo_outline
6complement(1600213..1601025)PHAGE_Acidia_virus: hypothetical protein ATV_gp34; EfaeDRAFT_1155; phage(gi75750403)1e-04Showinfo_outline
7complement(1601039..1602289)PHAGE_Acanth_1: hypothetical protein ATCV1_Z571L; EfaeDRAFT_1147; phage(gi155371518)2e-104Showinfo_outline
8complement(1602309..1603367)PHAGE_Cafete_BV_PW1: putative NAD-dependent epimerase/dehydratase; EfaeDRAFT_1148; phage(gi310831207)5e-32Showinfo_outline
9complement(1603401..1604195)Glycosyl transferase WecB/TagA/CpsF; EfaeDRAFT_11490.0Showinfo_outline
10complement(1604526..1604942)sugar transferase; EfaeDRAFT_11500.0Showinfo_outline
11complement(1605501..1605719)hypothetical protein; EfaeDRAFT_11560.0Showinfo_outline
121605749..1605760attR0.0Showinfo_outline
13complement(1605929..1606882)PHAGE_Spirop_R8A2B: putative transposase; EfaeDRAFT_1151; phage(gi9626114)1e-23Showinfo_outline
Enterococcus faecium DO whole genome shotgun sequence.
Click on a region to see details.
Intact (score > 90)
Questionable (score 70-90)
Incomplete (score < 70)

Viewer Options
Length: 2848380 bps
Phages: 5
arrow_upwardarrow_upwardarrow_upward
Click on a region in the genome above to show details here.
Viewer Options
Click on a sequence to see details.
Viewer Options
Click on a sequence to see details.
Viewer Options
Click on a sequence to see details.
Viewer Options
Click on a sequence to see details.
Viewer Options
Click on a sequence to see details.
Lysis
Terminase
Portal Protein
Protease
Coat Protein
Tail Shaft
Attachment Site
Integrase
Phage-like Protein
Hypotheical Protein
Other
Transposase
Fiber Protein
Plate Protein
tRNA

Download data as .txt file: png_input file_download