Submission Results

Sequence Name: Magnetospirillum magnetotacticum MS-1, whole genome shotgun

GenBank Accession Number: AAAP00000000.1

GenInfo (GI) Number: 21614494

Download Results: AAAP00000000.1.PHASTER.zip

gi|21614494|ref|AAAP00000000| Magnetospirillum magnetotacticum MS-1 Magn_1, whole genome shotgun .9211536, gc%: 66.37%

Download summary as .txt file: summary.txt file_download

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

RegionRegion LengthCompletenessScore# Total ProteinsRegion PositionMost Common PhageGC %Details
117.2Kbincomplete40173973608-3990811 info_outlinePHAGE_Tricho_2c65.44%Show info_outline
211.1Kbincomplete40125999451-6010622 info_outlinePHAGE_Strept_261.48%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|21614494|ref|AAAP00000000| Magnetospirillum magnetotacticum MS-1 Magn_1, whole genome shotgun [asmbl_id: NC_000000].9211536, gc%: 66.37%

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 19 CDS

#CDS PositionBLAST HitE-ValueSequence
13973608..3973620attL0.0Showinfo_outline
23974008..3975138PHAGE_Mannhe_phiMHaA1: integrase; PP_05598; phage(gi109289985)4e-42Showinfo_outline
3complement(3975143..3975355)hypothetical protein amb0912 [Magnetospirillum magneticum AMB-1] gi|83310011|ref|YP_420275.1|; PP_055994e-29Showinfo_outline
43976034..3976210hypothetical protein Mchl_1147 [Methylobacterium extorquens CM4] gi|218529147|ref|YP_002419963.1|; PP_056001e-24Showinfo_outline
5complement(3976333..3977013)hypothetical; PP_056010.0Showinfo_outline
63977071..3977283hypothetical; PP_056020.0Showinfo_outline
7complement(3977551..3977670)hypothetical; PP_056030.0Showinfo_outline
8complement(3977774..3977926)hypothetical; PP_056040.0Showinfo_outline
93978375..3978701N-acetyltransferase GCN5 [Methylobacterium extorquens PA1] gi|163850437|ref|YP_001638480.1|; PP_056059e-45Showinfo_outline
103978884..3979018DNA topoisomerase IV subunit A [Magnetospirillum magneticum AMB-1] gi|83311684|ref|YP_421948.1|; PP_056063e-05Showinfo_outline
113978994..3980865PHAGE_Clostr_st: putative DNA gyrase A subunit; PP_05607; phage(gi80159786)2e-44Showinfo_outline
123981147..3981380TRAP-type mannitol/chloroaromatic compound transport system, periplasmic component [Magnetospirillum magneticum AMB-1] gi|83311683|ref|YP_421947.1|; PP_056081e-28Showinfo_outline
13complement(3981454..3982677)PHAGE_Aeromo_vB_AsaM_56: putative portal protein; PP_05609; phage(gi422937534)6e-79Showinfo_outline
14complement(3982767..3982994)PHAGE_Roseob_1: phage terminase large subunit; PP_05610; phage(gi331028117)2e-13Showinfo_outline
15complement(3983009..3983947)PHAGE_Tricho_2c: hypothetical protein TNAV2c_gp141; PP_05611; phage(gi116326827)1e-05Showinfo_outline
16complement(3984049..3984285)PHAGE_Ralsto_RSL1: unnamed protein product; PP_05613; phage(gi189426860)7e-11Showinfo_outline
173984291..3984449hypothetical; PP_056120.0Showinfo_outline
18complement(3984548..3985288)PHAGE_Tricho_2c: hypothetical protein TNAV2c_gp071; PP_05614; phage(gi116326757)5e-15Showinfo_outline
193990811..3990823attR0.0Showinfo_outline

Region 2, total 12 CDS

#CDS PositionBLAST HitE-ValueSequence
15999451..6000803PHAGE_Escher_TL_2011b: putative integrase; PP_07830; phage(gi418487628)1e-22Showinfo_outline
26000141..6000803PROPHAGE_Escher_CFT073: P4 family integrase; PP_07831; phage(gi26248244)1e-13Showinfo_outline
36000793..6001179hypothetical; PP_078320.0Showinfo_outline
46001258..6001452hypothetical; PP_078330.0Showinfo_outline
56001407..6001556hypothetical; PP_078340.0Showinfo_outline
66001617..6002006hypothetical; PP_078350.0Showinfo_outline
76002003..6002803PHAGE_Clostr_st: hypothetical protein CST004; PP_07836; phage(gi80159690)3e-09Showinfo_outline
86002844..6003200hypothetical; PP_078370.0Showinfo_outline
96003260..6006850PHAGE_Bordet_1: primase; PP_07838; phage(gi45569522)2e-16Showinfo_outline
106007027..6007374hypothetical protein amb0571 [Magnetospirillum magneticum AMB-1] gi|83309670|ref|YP_419934.1|; PP_078392e-19Showinfo_outline
116007722..6008198PHAGE_Strept_2: hypothetical protein SpyM3_0947; PP_07840; phage(gi28876231)2e-08Showinfo_outline
12complement(6008439..6010622)PHAGE_Salmon_1: putative bacteriophage tail fiber protein; Lambda gpN homolog; PP_07841; phage(gi169257204)1e-11Showinfo_outline
Magnetospirillum magnetotacticum MS-1 Magn_1, whole genome shotgun
Click on a region to see details.
Intact (score > 90)
Questionable (score 70-90)
Incomplete (score < 70)

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Length: 9211536 bps
Phages: 2
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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.
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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