Submission Results

Sequence Name: Not Available

GenBank Accession Number: NZ_LNVF01000009.1

Download Results: NZ_LNVF01000009.1.PHASTEST.zip

gi|00000000|ref|NC_000000| Streptococcus oralis subsp. tigurinus strain AZ_8 79329, gc%: 39.71%

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
125.2Kbintact1303026-25292 info_outlinePHAGE_Strept_5093_NC_012753(11)42.63%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|NZ_LNVF01000009.1| Streptococcus oralis subsp. tigurinus strain AZ_8 79329, gc%: 39.71%

Download details as .txt file:detail.txt file_download

Hypothetical protein
Phage-like protein
Terminase
Head protein
Tail protein
Holin

intact

Region 1, total 29 CDS

#CDS PositionBLAST HitE-ValueSequence
126..181PP_00001;hypothetical protein;phage;PHAGE_Strept_phiARI0131_1_NC_0319013.08e-27Show info_outline
2178..708PP_00002;hypothetical protein;phage;PHAGE_Strept_MM1_NC_0030502.18e-25Show info_outline
3708..899PP_00003;hypothetical protein;phage;PHAGE_Lactob_LBR48_NC_0279907.12e-08Show info_outline
4896..1156PP_00004;hypothetical protein;phage;PHAGE_Strept_EJ_1_NC_0052941.5e-48Show info_outline
51530..1946PP_00005;phage protein;phage;PHAGE_Strept_DCC1738_NC_0243617.74e-92Show info_outline
62190..2681PP_00006;COG3728 phage terminase small subunit;phage;PHAGE_Staphy_80_NC_0306524.8e-35Show info_outline
72665..3960PP_00007;putative terminase large subunit;phage;PHAGE_Strept_315.4_NC_0045870.0Show info_outline
83978..5486PP_00008;putative minor capsid protein;phage;PHAGE_Strept_PH15_NC_0109450.0Show info_outline
95597..7528PP_00009;putative minor capsid protein;phage;PHAGE_Strept_PH15_NC_0109450.0Show info_outline
107994..8620PP_00011;hypothetical protein;phage;PHAGE_Strept_PH15_NC_0109454.9e-68Show info_outline
118626..9471PP_00012;major head protein;phage;PHAGE_Strept_5093_NC_0127532.76e-167Show info_outline
129471..9692PP_00013;hypothetical protein;phage;PHAGE_Strept_PH15_NC_0109454.19e-13Show info_outline
139679..9879PP_00014;hypothetical protein;phage;PHAGE_Strept_PH15_NC_0109451.14e-09Show info_outline
149892..10293PP_00015;hypothetical protein;phage;PHAGE_Strept_5093_NC_0127531.36e-47Show info_outline
1510283..10615PP_00016;minor capsid protein;phage;PHAGE_Temper_phiNIH1.1_NC_0031577.56e-28Show info_outline
1610615..11007PP_00017;putative minor capsid protein;phage;PHAGE_Strept_PH15_NC_0109451.23e-33Show info_outline
1711004..11408PP_00018;putative minor capsid protein;phage;PHAGE_Strept_5093_NC_0127533.35e-47Show info_outline
1811408..11869PP_00019;tail protein;phage;PHAGE_Strept_5093_NC_0127535.5e-60Show info_outline
1911922..12278PP_00020;hypothetical protein;phage;PHAGE_Strept_5093_NC_0127532.04e-24Show info_outline
2012283..12909PP_00021;hypothetical protein;phage;PHAGE_Strept_5093_NC_0127536.68e-65Show info_outline
2112923..16567PP_00022;putative envelope protein;phage;PHAGE_Strept_phiNJ2_NC_0194180.0Show info_outline
2216567..18063PP_00023;phage tail protein;phage;PHAGE_Strept_phiBHN167_NC_0227910.0Show info_outline
2318066..20678PP_00024;putative antireceptor protein;phage;PHAGE_Strept_phiNJ2_NC_0194180.0Show info_outline
2420690..22741PP_00025;tail protein;phage;PHAGE_Strept_Abc2_NC_0136450.0Show info_outline
2522751..23356PP_00026;phage protein;phage;PHAGE_Strept_20617_NC_0235031.92e-34Show info_outline
2623368..23667PP_00027;phage protein;phage;PHAGE_Strept_K13_NC_0243576.84e-66Show info_outline
2723671..24003PP_00028;holin;phage;PHAGE_Strept_phiARI0462_NC_0319422.25e-65Show info_outline
2824006..24893PP_00029;gp56;phage;PHAGE_Strept_SM1_NC_0049960.0Show info_outline
2925047..25292PP_00030;hypothetical protein;phage;PHAGE_Strept_phiARI0031_NC_0319108.84e-48Show info_outline

gi|00000000|ref|NZ_LNVF01000009.1| Streptococcus oralis subsp. tigurinus strain AZ_8 79329, gc%: 39.71%

Download details as .txt file:detail.txt file_download

tRNA
Non phage-like protein
Hypothetical protein
phage replisome organizer N-terminal domain-containing protein

Bacterial, total 50 CDS

#CDS PositionBLAST HitE-ValueSequence
125417..25487tRNA-Cys0.0Showinfo_outline
225791..27767PP_00031; peptide ABC transporter substrate-binding protein0.0Showinfo_outline
327834..29330PP_00032; ABC transporter permease0.0Showinfo_outline
429330..30256PP_00033; oligopeptide ABC transporter permease OppC0.0Showinfo_outline
530265..31332PP_00034; ABC transporter ATP-binding protein0.0Showinfo_outline
631343..32272PP_00035; ATP-binding cassette domain-containing protein0.0Showinfo_outline
732360..33799PP_00036; TrkH family potassium uptake protein0.0Showinfo_outline
833803..35152PP_00037; Trk system potassium transporter TrkA0.0Showinfo_outline
935554..36057PP_00038; tRNA (cytidine(34)-2'-O)-methyltransferase0.0Showinfo_outline
1036471..37034PP_00039; ECF transporter S component0.0Showinfo_outline
1137024..37674PP_00040; phosphatase PAP2 family protein0.0Showinfo_outline
1237702..38121PP_00041; chromosome partitioning protein ParB0.0Showinfo_outline
1338432..39478PP_00042; phenylalanine--tRNA ligase subunit alpha0.0Showinfo_outline
1439478..39987PP_00043; GNAT family N-acetyltransferase0.0Showinfo_outline
1540063..42468PP_00044; phenylalanine--tRNA ligase subunit beta0.0Showinfo_outline
1642719..43612PP_00045; ABC transporter ATP-binding protein0.0Showinfo_outline
1743609..44808PP_00046; ABC transporter permease0.0Showinfo_outline
1845019..45465PP_00047; 50S ribosomal protein L130.0Showinfo_outline
1945484..45876PP_00048; 30S ribosomal protein S90.0Showinfo_outline
2045986..47203PP_00049; tyrosine-type recombinase/integrase0.0Showinfo_outline
2147272..47532PP_00050; helix-turn-helix domain-containing protein0.0Showinfo_outline
2247581..48972PP_00051; Rep family protein0.0Showinfo_outline
2349359..50081PP_00052; hypothetical protein0.0Showinfo_outline
2450083..50622PP_00053; hypothetical protein0.0Showinfo_outline
2550636..51028PP_00054; hypothetical protein0.0Showinfo_outline
2651331..52227PP_00055; hypothetical protein0.0Showinfo_outline
2752338..52676PP_00056; helix-turn-helix domain-containing protein0.0Showinfo_outline
2852808..55516PP_00057; SEC10/PgrA surface exclusion domain-containing protein0.0Showinfo_outline
2955928..57082PP_00058; site-specific integrase0.0Showinfo_outline
3057134..57652PP_00059; helix-turn-helix transcriptional regulator0.0Showinfo_outline
3157800..58081PP_00060; hypothetical protein0.0Showinfo_outline
3258090..58929PP_00061; phage replisome organizer N-terminal domain-containing protein;phage replisome organizer N-terminal domain-containing protein0.0Showinfo_outline
3358922..59281PP_00062; hypothetical protein0.0Showinfo_outline
3459289..59621PP_00063; hypothetical protein0.0Showinfo_outline
3559602..59796PP_00064; hypothetical protein0.0Showinfo_outline
3660998..61213PP_00065; hypothetical protein0.0Showinfo_outline
3761215..61598PP_00066; LysR family transcriptional regulator0.0Showinfo_outline
3861719..63983PP_00067; bifunctional glutamate--cysteine ligase GshA/glutathione synthetase GshB0.0Showinfo_outline
3964360..65429PP_00068; LysR family transcriptional regulator0.0Showinfo_outline
4065953..66336PP_00069; tyrosine-type recombinase/integrase0.0Showinfo_outline
4166676..67884PP_00070; ATP-binding protein0.0Showinfo_outline
4268378..68563PP_00071; LysR family transcriptional regulator0.0Showinfo_outline
4368829..71603PP_00072; cation-transporting P-type ATPase0.0Showinfo_outline
4471752..72680PP_00073; LysR family transcriptional regulator0.0Showinfo_outline
4572737..73649PP_00074; LysR family transcriptional regulator0.0Showinfo_outline
4673762..74112PP_00075; helix-turn-helix domain-containing protein0.0Showinfo_outline
4774465..76090PP_00076; malolactic enzyme0.0Showinfo_outline
4876174..77121PP_00077; AEC family transporter0.0Showinfo_outline
4977705..78670PP_00078; hypothetical protein0.0Showinfo_outline
5078733..79245PP_00079; GNAT family N-acetyltransferase0.0Showinfo_outline

Phage Genes

Bacterial Genes

Phage Regions

GC Skew

GC Content

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Phage Genes

Bacterial Genes

Phage Regions

GC Skew

GC Content

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