Submission Results

Sequence Name: Listeria monocytogenes serotype 1/2a str. F6854 strain 1/2a F6854

GenBank Accession Number: AADQ01000014.1

GenInfo (GI) Number: 47015571

Download Results: AADQ01000014.1.PHASTER.zip

gi|00000000|ref|NC_000000| Listeria monocytogenes serotype 1/2a str. F6854 strain 1/2a F6854 .62669, gc%: 37.23%

Download summary as .txt file: summary.txt file_download

Total: 1 prophage regions have been identified, of which 1 regions are intact, 0 regions are incomplete, and 0 regions are questionable.

RegionRegion LengthCompletenessScore# Total ProteinsRegion PositionMost Common PhageGC %Details
141.4Kbintact1005826-41477 info_outlinePHAGE_Lister_A118_NC_003216(37)36.19%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|00000000|ref|NC_000000| Listeria monocytogenes serotype 1/2a str. F6854 strain 1/2a F6854 [asmbl_id: NC_000000].62669, gc%: 37.23%

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 60 CDS

#CDS PositionBLAST HitE-ValueSequence
126..301PHAGE_Lister_A006_NC_009815: gp25; LMOf6854_2335; phage(gi157325440)1.53e-24Showinfo_outline
2330..701PHAGE_Lister_A118_NC_003216: gp29; LMOf6854_2336; phage(gi16798812)1.08e-23Showinfo_outline
3622..633attL0.0Showinfo_outline
4707..1156PHAGE_Lister_A118_NC_003216: gp28; LMOf6854_2337; phage(gi16798811)7.12e-85Showinfo_outline
51181..1678PHAGE_Lister_A006_NC_009815: gp22; LMOf6854_2338; phage(gi157325437)2.82e-115Showinfo_outline
61953..2726PHAGE_Lister_A006_NC_009815: gp21; LMOf6854_2339; phage(gi157325436)0.0Showinfo_outline
7complement(2767..3612)PHAGE_Lister_A118_NC_003216: L-alanoyl-D-glutamate peptidase; LMOf6854_2340; phage(gi16798808)0.0Showinfo_outline
8complement(3612..3893)PHAGE_Lister_A118_NC_003216: holin; LMOf6854_2341; phage(gi16798807)8.22e-61Showinfo_outline
9complement(3906..4271)PHAGE_Lister_A118_NC_003216: gp23; LMOf6854_2342; phage(gi16798806)3.15e-82Showinfo_outline
10complement(4299..4457)PHAGE_Lister_A118_NC_003216: gp22; LMOf6854_2343; phage(gi16798805)4.52e-30Showinfo_outline
11complement(4462..4779)PHAGE_Lister_A118_NC_003216: gp21; LMOf6854_2344; phage(gi16798804)6.93e-71Showinfo_outline
12complement(4791..5864)PHAGE_Lister_A118_NC_003216: gp20; LMOf6854_2345; phage(gi16798803)0.0Showinfo_outline
13complement(5864..6892)PHAGE_Lister_A118_NC_003216: gp19; LMOf6854_2346; phage(gi16798802)0.0Showinfo_outline
14complement(6893..7918)PHAGE_Lister_A118_NC_003216: gp18; LMOf6854_2347; phage(gi16798801)0.0Showinfo_outline
15complement(7927..8745)PHAGE_Lister_A118_NC_003216: gp17; LMOf6854_2348; phage(gi16798800)0.0Showinfo_outline
16complement(8747..14110)PHAGE_Lister_A118_NC_003216: putative tape-measure protein; LMOf6854_2349; phage(gi16798799)0.0Showinfo_outline
17complement(14121..14726)PHAGE_Lister_A118_NC_003216: gp15; LMOf6854_2350; phage(gi16798798)4.95e-143Showinfo_outline
18complement(14731..15153)PHAGE_Lister_A118_NC_003216: gp14; LMOf6854_2351; phage(gi16798797)4.44e-70Showinfo_outline
19complement(15205..15498)PHAGE_Lister_A118_NC_003216: gp13; LMOf6854_2352; phage(gi16798796)1.36e-50Showinfo_outline
20complement(15467..15904)PHAGE_Lister_A118_NC_003216: major tail shaft protein; LMOf6854_2353; phage(gi16798795)1.44e-94Showinfo_outline
21complement(15907..16314)PHAGE_Lister_A118_NC_003216: gp11; LMOf6854_2354; phage(gi16798794)3.47e-82Showinfo_outline
22complement(16314..16652)PHAGE_Lister_A118_NC_003216: gp10; LMOf6854_2355; phage(gi16798793)2.36e-67Showinfo_outline
23complement(16652..17014)PHAGE_Lister_A118_NC_003216: gp9; LMOf6854_2356; phage(gi16798792)4.89e-82Showinfo_outline
24complement(17014..17409)PHAGE_Lister_A118_NC_003216: gp8; LMOf6854_2357; phage(gi16798791)1.65e-88Showinfo_outline
25complement(17411..17569)PHAGE_Lister_A118_NC_003216: gp7; LMOf6854_2358; phage(gi16798790)3.47e-26Showinfo_outline
26complement(17569..18405)PHAGE_Strept_315.4_NC_004587: putative major capsid/head protein; LMOf6854_2359; phage(gi28876339)1.98e-74Showinfo_outline
27complement(18428..19027)PHAGE_Lister_A118_NC_003216: putative scaffolding protein; LMOf6854_2360; phage(gi16798788)7.64e-65Showinfo_outline
28complement(19106..20245)PHAGE_Lister_A118_NC_003216: gp4; LMOf6854_2361; phage(gi16798787)0.0Showinfo_outline
29complement(20251..21696)PHAGE_Lister_A118_NC_003216: putative portal protein; LMOf6854_2362; phage(gi16798786)0.0Showinfo_outline
30complement(21754..23064)PHAGE_Strept_phiNJ2_NC_019418: putative phage terminase large subunit; LMOf6854_2363; phage(gi414090227)0.0Showinfo_outline
31complement(23057..23812)PHAGE_Oenoco_phiS11_NC_023571: Phage terminase small subunit; LMOf6854_2364; phage(gi589286628)5.84e-58Showinfo_outline
32complement(23896..24606)PHAGE_Lister_A118_NC_003216: gp68; LMOf6854_2365; phage(gi16798855)2.63e-167Showinfo_outline
33complement(24843..25415)PHAGE_Lister_vB_LmoS_188_NC_028871: RNA polymerase sigma70; LMOf6854_2366; phage(gi971750857)4.28e-123Showinfo_outline
34complement(25503..25658)PHAGE_Lister_vB_LmoS_293_NC_028929: hypothetical protein; LMOf6854_2367; phage(gi971756945)1.58e-29Showinfo_outline
35complement(25677..26090)PHAGE_Lister_A500_NC_009810: gp59; LMOf6854_2368; phage(gi157325018)1.63e-23Showinfo_outline
36complement(26094..26498)PHAGE_Lister_A500_NC_009810: gp58; LMOf6854_2369; phage(gi157325017)5.62e-81Showinfo_outline
37complement(26443..26634)PHAGE_Lister_A500_NC_009810: gp57; LMOf6854_2370; phage(gi157325016)1.29e-36Showinfo_outline
38complement(26653..27135)PHAGE_Lister_A118_NC_003216: putative SSB protein; LMOf6854_2371; phage(gi16798847)1.28e-113Showinfo_outline
39complement(27132..27332)conserved hypothetical protein; LMOf6854_23720.0Showinfo_outline
40complement(27415..27582)conserved hypothetical protein; LMOf6854_23730.0Showinfo_outline
41complement(27579..28040)PHAGE_Brocho_A9_NC_015253: gp39; LMOf6854_2374; phage(gi327197682)6.88e-22Showinfo_outline
42complement(28037..28507)PHAGE_Lister_vB_LmoM_AG20_NC_020871: hypothetical protein; LMOf6854_2375; phage(gi472437272)9.21e-91Showinfo_outline
43complement(28504..28947)PHAGE_Lister_A500_NC_009810: gp52; LMOf6854_2376; phage(gi157325010)3.95e-58Showinfo_outline
44complement(28944..29141)PHAGE_Lister_vB_LmoS_293_NC_028929: hypothetical protein; LMOf6854_2377; phage(gi971756932)2.69e-38Showinfo_outline
45complement(29144..29740)PHAGE_Lister_A118_NC_003216: gp51; LMOf6854_2378; phage(gi16798838)7.37e-55Showinfo_outline
46complement(29737..30549)PHAGE_Lister_2389_NC_003291: methylase; LMOf6854_2379; phage(gi17488539)0.0Showinfo_outline
47complement(30546..31490)PHAGE_Lister_A118_NC_003216: gp49; LMOf6854_2380; phage(gi16798836)0.0Showinfo_outline
48complement(31510..32325)PHAGE_Lister_A118_NC_003216: putative recombinase; LMOf6854_2381; phage(gi16798835)0.0Showinfo_outline
49complement(32328..33287)PHAGE_Lister_A118_NC_003216: gp47; LMOf6854_2382; phage(gi16798834)0.0Showinfo_outline
50complement(33522..33710)PHAGE_Lister_A118_NC_003216: gp45; LMOf6854_2383; phage(gi16798832)9.68e-32Showinfo_outline
51complement(34031..34564)PHAGE_Lister_A006_NC_009815: gp37; LMOf6854_2384; phage(gi157325453)5.56e-111Showinfo_outline
52complement(34687..35463)PHAGE_Lister_A118_NC_003216: putative anti-repressor promoter; LMOf6854_2385; phage(gi16798829)5.71e-150Showinfo_outline
53complement(35726..36007)PHAGE_Lister_A118_NC_003216: gp41; LMOf6854_2386; phage(gi16798827)3.75e-41Showinfo_outline
54complement(36520..36762)PHAGE_Lister_B054_NC_009813: gp42; LMOf6854_2387; phage(gi157325326)5.82e-16Showinfo_outline
5536918..37394PHAGE_Lister_A118_NC_003216: putative repressor protein; LMOf6854_2388; phage(gi16798819)1.33e-13Showinfo_outline
5637775..38476PHAGE_Lister_A118_NC_003216: gp33; LMOf6854_2389; phage(gi16798816)3.74e-112Showinfo_outline
5738497..39177PHAGE_Lister_A118_NC_003216: gp32; LMOf6854_2390; phage(gi16798815)1.93e-05Showinfo_outline
5838891..38902attR0.0Showinfo_outline
5939241..40599PHAGE_Lister_A118_NC_003216: putative integrase; LMOf6854_2391; phage(gi16798814)0.0Showinfo_outline
60complement(41121..41477)PHAGE_Clostr_phiCTC2B_NC_030951: hypothetical protein; LMOf6854_2393; phage(gi100002)1.64e-09Showinfo_outline
Listeria monocytogenes serotype 1/2a str. F6854 strain 1/2a F6854
Click on a region to see details.
Intact (score > 90)
Questionable (score 70-90)
Incomplete (score < 70)

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Length: 62669 bps
Phages: 1
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Click on a region in the genome above to show details here.
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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