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.
Totally 1 intact prophage regions have been identified.
REGION REGION_LENGTH COMPLETENESS(score) SPECIFIC_KEYWORD REGION_POSITION TRNA_NUM TOTAL_PROTEIN_NUM PHAGE_HIT_PROTEIN_NUM HYPOTHETICAL_PROTEIN_NUM PHAGE+HYPO_PROTEIN_PERCENTAGE BACTERIAL_PROTEIN_NUM ATT_SITE_SHOWUP PHAGE_SPECIES_NUM MOST_COMMON_PHAGE_NAME(hit_genes_count) FIRST_MOST_COMMON_PHAGE_NUM FIRST_MOST_COMMON_PHAGE_PERCENTAGE GC_PERCENTAGE
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1 10.8Kb intact(128) integrase,head 651-11460 0 12 12 0 100% 0 no 1 PHAGE_Entero_P4_NC_001609(12),PHAGE_Loktan_pCB2051_A_NC_020853(1),PHAGE_Entero_N15_NC_001901(1),PHAGE_Salmon_SP_004_NC_021774(1),PHAGE_Ralsto_RSY1_NC_025115(1),PHAGE_Serrat_Eta_NC_021563(1),PHAGE_Stenot_S1_NC_011589(1),PHAGE_Shewan_1/41_NC_025458(1),PHAGE_Salmon_118970_sal3_NC_031940(1),PHAGE_Staphy_Twort_NC_007021(1),PHAGE_Entero_186_NC_001317(1),PHAGE_Yersin_PY54_NC_005069(1),PHAGE_Entero_PsP3_NC_005340(1),PHAGE_Salico_CGphi29_NC_020844(1),PHAGE_Xantho_vB_XveM_DIBBI_NC_017981(1),PHAGE_Burkho_KL3_NC_015266(1) 12 100% 50.12%