@@ -89,10 +89,10 @@ - + - + @@ -118,7 +118,7 @@ - + @@ -160,7 +160,7 @@ 10 CDS): 0 +##################### Main parameters of the ICEscreen analysis ##################### +Maximum distance in CDS between consecutive SPs within a segments: 100 +Maximum distance in CDS between consecutive SPs within an IME element: 14 -# Composite elements -Total nested elements (partial or complete): 0 -Host element: 0 -Guest element: 0 -Element that are both host and guest: 0 + +##################### ICEscreen statistics for genome accession NC_004668.1 ##################### -################### Signature proteins detection statistics #################### -# Total SP detected -Total SP: 4 -Total Integrase: 1 -Total Relaxase: 1 -Total Coupling protein: 1 -Total VirB4: 1 +##### Mobile elements ##### +## Number of complete elements +Complete ICE (4 types of SP): 1 +Complete IME (R+I, R+C+I with distance between consecutive SPs <= 14 CDSs): 0 +## Number of complete modules +Conjugation module (R+C+V): 0 +Mobilizable element (R+C with distance between consecutive SPs <= 14 CDS): 0 +## Number of partial elements +Partial ICE (at least V): 0 +Other partial element (R+C, R+V, V+C with distance between consecutive SPs > 14 CDS): 0 +## Composite elements +Total nested elements (partial or complete): 0 +Host element: 0 +Guest element: 0 +Element that are both host and guest: 0 -# Unassigned SP -Unassigned SP: 0 -Unassigned Integrase: 0 -Unassigned Relaxase: 0 -Unassigned Coupling protein: 0 -Unassigned VirB4: 0 +##### Signature proteins ##### +## Total SPs detected +Total SPs: 4 +Total Integrase: 1 +Total Relaxase: 1 +Total Coupling protein: 1 +Total VirB4: 1 +## Unassigned SPs +Unassigned SPs: 0 +Unassigned Integrase: 0 +Unassigned Relaxase: 0 +Unassigned Coupling protein: 0 +Unassigned VirB4: 0 -############################# Segments statistics ############################## -Number of segments: 1 -Segment with one element: 1 -Segment with several elements: 0 -Segment with nested elements: 0 -Segment with no element: 0 +##### Segments ##### +Number of segments with one element: 1 +Number of segments with several elements: 0 +Number of segments with nested elements: 0 +Number of segments with exclusively isolated SPs to manually verify: 0 -############################### Parameters used ################################ -Maximum CDS numbers in initial segments: 100 -Maximum CDS numbers in an IME element: 10 diff -r f08181349fc4 -r 2bb38197ff75 test-data/NC_004668_137848_164286_detected_ME.tsv --- a/test-data/NC_004668_137848_164286_detected_ME.tsv Sat Apr 02 21:05:10 2022 +0000 +++ b/test-data/NC_004668_137848_164286_detected_ME.tsv Tue Dec 06 10:40:53 2022 +0000 @@ -1,2 +1,2 @@ -ICE IME Number segment number category of element category of integrase host ICE / IME guest ICE / IME other ICE / IME colocalized ICEline format ICE SuperFamily From Blast Of SP Conj Module ICE Family From Blast Of SP Conj Module IME Family From Blast Of SP Conj Module family SP conj module HMM integrase upstream integrase downstream relaxase coupling protein VirB4 list ordered SPs SPs conj module to manually review Integrase to manually review comment -2 1 Complete ICE (4 types of SP) one integrase - Tyr C3.R1:V7.I Tn916 ICESt3 C:TcpA, R:MOBT, V:VirB4 WP_002392915.1-25273 WP_002359299.1-3098 WP_002359295.1-1 WP_002359320.1-17920 WP_002359295.1-1, WP_002359299.1-3098, WP_002359320.1-17920, WP_002392915.1-25273 Integrase WP_002392915.1-25273 has been associated to the structure 2 because they are adjacent, this integrase has already be seen rattached to this conjugaison module family, and there is no upstream/downstream ambiguity. +ICE_IME_id Segment_number Genome_accession Category_of_element Category_of_integrase Host_ICE_IME_ids Guest_ICE_IME_ids Colocalized_ICE_IME_ids ICEline_format ICE_consensus_superfamily_SP_conj_module ICE_consensus_family_SP_conj_module IME_relaxase_family_domains_blast HMM_family_SP_conj_module Integrase_upstream Integrase_downstream Relaxase Coupling_protein VirB4 List_SP_ordered_genomic_position Other_potential_SP_conj_module_need_manual_curation_and_review Other_potential_integrase_need_manual_curation_and_review Comments_regarding_structure +ID_1 1 NC_004668.1 Complete ICE (C+R+V+I) one integrase Tyr - - - C3.R1:V7.I Tn916 ICESt3 - C:TcpA, R:MOBT, V:VirB4 - EF_RS00760 EF_RS00650 EF_RS00630 EF_RS00720 EF_RS00630, EF_RS00650, EF_RS00720, EF_RS00760 - - Downstream integrase EF_RS00760 has been associated to the structure ID_1 pre-merging because it is adjacent to the conj module and there is no upstream/downstream ambiguity. diff -r f08181349fc4 -r 2bb38197ff75 test-data/NC_004668_137848_164286_icescreen.embl --- a/test-data/NC_004668_137848_164286_icescreen.embl Sat Apr 02 21:05:10 2022 +0000 +++ b/test-data/NC_004668_137848_164286_icescreen.embl Tue Dec 06 10:40:53 2022 +0000 @@ -11,8 +11,8 @@ XX FH Key Location/Qualifiers FH -FT CDS 1..1511 -FT /origid="WP_002359295.1" +FT CDS 1..1512 +FT /origid="EF_RS00630" FT /function="Coupling Protein" FT /protein_id="WP_002359295.1" FT /locus_tag="EF_RS00630" @@ -20,11 +20,11 @@ FT /color=6 FT /note="ICEscreen prediction: Coupling protein; BlastP FT result (Annotation confidence: HIGH): Coupling protein TcpA -FT [Hit with AAO80014; Identity:100.00%; E-value:0; Query -FT coverage:100.00%]; Hmmscan result: TcpA [Hit with tcpA HMM -FT profile; E-value:0; i-Evalue:0]" -FT CDS 3098..4380 -FT /origid="WP_002359299.1" +FT [Hit with AAO80014; Identity:100.00%; E-value:0.00e+00; +FT Query coverage:100.00%]; Hmmscan result: TcpA [Hit with +FT tcpA HMM profile; E-value:7.00e-94; i-Evalue:8.80e-94]" +FT CDS 3098..4381 +FT /origid="EF_RS00650" FT /function="Relaxase" FT /protein_id="WP_002359299.1" FT /locus_tag="EF_RS00650" @@ -32,11 +32,11 @@ FT /color=7 FT /note="ICEscreen prediction: Relaxase; BlastP result FT (Annotation confidence: HIGH): Relaxase MOBT (PF02486) [Hit -FT with AAO80018; Identity:99.77%; E-value:0; Query +FT with AAO80018; Identity:99.77%; E-value:0.00e+00; Query FT coverage:95.53%]; Hmmscan result: MOBT [Hit with T4SS_MOBT -FT HMM profile; E-value:0; i-Evalue:0]" -FT CDS 17920..20426 -FT /origid="WP_002359320.1" +FT HMM profile; E-value:3.00e-128; i-Evalue:3.40e-128]" +FT CDS 17920..20427 +FT /origid="EF_RS00720" FT /function="VirB4" FT /protein_id="WP_002359320.1" FT /locus_tag="EF_RS00720" @@ -44,11 +44,11 @@ FT /color="184 134 11" FT /note="ICEscreen prediction: VirB4; BlastP result FT (Annotation confidence: HIGH): VirB4 [Hit with CAE52368; -FT Identity:41.15%; E-value:0; Query coverage:99.76%]; Hmmscan -FT result: VirB4 [Hit with T4SS_virb4 HMM profile; E-value:0; -FT i-Evalue:0]" -FT CDS 25273..26438 -FT /origid="WP_002392915.1" +FT Identity:41.15%; E-value:0.00e+00; Query coverage:99.76%]; +FT Hmmscan result: VirB4 [Hit with T4SS_virb4 HMM profile; +FT E-value:1.80e-28; i-Evalue:2.40e-28]" +FT CDS 25273..26439 +FT /origid="EF_RS00760" FT /function="Tyrosine Integrase" FT /protein_id="WP_002392915.1" FT /locus_tag="EF_RS00760" @@ -56,16 +56,17 @@ FT /color=8 FT /note="ICEscreen prediction: Tyrosine integrase; BlastP FT result (Annotation confidence: HIGH): Tyrosine integrase -FT [Hit with AAO80040; Identity:100.00%; E-value:0; Query -FT coverage:100.00%]; Hmmscan result: Tyrosine integrase [Hit -FT with Phage_integrase HMM profile; E-value:0; i-Evalue:0]" +FT [Hit with AAO80040; Identity:100.00%; E-value:0.00e+00; +FT Query coverage:100.00%]; Hmmscan result: Tyrosine integrase +FT [Hit with Phage_integrase HMM profile; E-value:4.40e-29; +FT i-Evalue:9.70e-29]" FT mobile_element 1..26439 FT /mobile_element_type="other: integrative and conjugative FT element" -FT /note="ICEscreen prediction: Putative ICE (one integrase - +FT /note="ICEscreen prediction: Putative ICE (one integrase FT Tyr) [Element structure: Single; ICE superfamily: Tn916; -FT ICE family: ICESt3; Relaxase family: MOBT; Coupling protein -FT family: TcpA] (ICEscreen ID: 2)" +FT ICE family: ICESt3; Relaxase family: - (MOBT); Coupling +FT protein family: TcpA] (ICEscreen ID: ID_1)" FT /color=15 XX SQ Sequence 0 BP; 0 A; 0 C; 0 G; 0 T; 0 other; diff -r f08181349fc4 -r 2bb38197ff75 test-data/NC_004668_137848_164286_icescreen.gb --- a/test-data/NC_004668_137848_164286_icescreen.gb Sat Apr 02 21:05:10 2022 +0000 +++ b/test-data/NC_004668_137848_164286_icescreen.gb Tue Dec 06 10:40:53 2022 +0000 @@ -607,8 +607,8 @@ YLTVKKSLYYKNAQTYELVSPKTRASIRTIYLDEDTVHYLRDWKKRQDDVGGIEFILSY NSVPTQKHTVRHIIKRHAKLAEVHDIRIHALRHSHASLLISMGTNALLIKERLGHEDVQ TTLGTYGHLYPSSSTEIANELKGIVNVEFTNQNMASEVTNQFTKGVKK" - CDS 1..1511 - /origid="WP_002359295.1" + CDS 1..1512 + /origid="EF_RS00630" /function="Coupling Protein" /protein_id="WP_002359295.1" /locus_tag="EF_RS00630" @@ -616,11 +616,11 @@ /color=6 /note="ICEscreen prediction: Coupling protein; BlastP result (Annotation confidence: HIGH): Coupling protein TcpA - [Hit with AAO80014; Identity:100.00%; E-value:0; Query - coverage:100.00%]; Hmmscan result: TcpA [Hit with tcpA HMM - profile; E-value:0; i-Evalue:0]" - CDS 3098..4380 - /origid="WP_002359299.1" + [Hit with AAO80014; Identity:100.00%; E-value:0.00e+00; + Query coverage:100.00%]; Hmmscan result: TcpA [Hit with + tcpA HMM profile; E-value:7.00e-94; i-Evalue:8.80e-94]" + CDS 3098..4381 + /origid="EF_RS00650" /function="Relaxase" /protein_id="WP_002359299.1" /locus_tag="EF_RS00650" @@ -628,11 +628,11 @@ /color=7 /note="ICEscreen prediction: Relaxase; BlastP result (Annotation confidence: HIGH): Relaxase MOBT (PF02486) [Hit - with AAO80018; Identity:99.77%; E-value:0; Query + with AAO80018; Identity:99.77%; E-value:0.00e+00; Query coverage:95.53%]; Hmmscan result: MOBT [Hit with T4SS_MOBT - HMM profile; E-value:0; i-Evalue:0]" - CDS 17920..20426 - /origid="WP_002359320.1" + HMM profile; E-value:3.00e-128; i-Evalue:3.40e-128]" + CDS 17920..20427 + /origid="EF_RS00720" /function="VirB4" /protein_id="WP_002359320.1" /locus_tag="EF_RS00720" @@ -640,11 +640,11 @@ /color="184 134 11" /note="ICEscreen prediction: VirB4; BlastP result (Annotation confidence: HIGH): VirB4 [Hit with CAE52368; - Identity:41.15%; E-value:0; Query coverage:99.76%]; Hmmscan - result: VirB4 [Hit with T4SS_virb4 HMM profile; E-value:0; - i-Evalue:0]" - CDS 25273..26438 - /origid="WP_002392915.1" + Identity:41.15%; E-value:0.00e+00; Query coverage:99.76%]; + Hmmscan result: VirB4 [Hit with T4SS_virb4 HMM profile; + E-value:1.80e-28; i-Evalue:2.40e-28]" + CDS 25273..26439 + /origid="EF_RS00760" /function="Tyrosine Integrase" /protein_id="WP_002392915.1" /locus_tag="EF_RS00760" @@ -652,16 +652,17 @@ /color=8 /note="ICEscreen prediction: Tyrosine integrase; BlastP result (Annotation confidence: HIGH): Tyrosine integrase - [Hit with AAO80040; Identity:100.00%; E-value:0; Query - coverage:100.00%]; Hmmscan result: Tyrosine integrase [Hit - with Phage_integrase HMM profile; E-value:0; i-Evalue:0]" + [Hit with AAO80040; Identity:100.00%; E-value:0.00e+00; + Query coverage:100.00%]; Hmmscan result: Tyrosine integrase + [Hit with Phage_integrase HMM profile; E-value:4.40e-29; + i-Evalue:9.70e-29]" mobile_element 1..26439 /mobile_element_type="other: integrative and conjugative element" - /note="ICEscreen prediction: Putative ICE (one integrase - + /note="ICEscreen prediction: Putative ICE (one integrase Tyr) [Element structure: Single; ICE superfamily: Tn916; - ICE family: ICESt3; Relaxase family: MOBT; Coupling protein - family: TcpA] (ICEscreen ID: 2)" + ICE family: ICESt3; Relaxase family: - (MOBT); Coupling + protein family: TcpA] (ICEscreen ID: ID_1)" /color=15 ORIGIN 1 atgttaaaaa aattatttag atatagagga aggcgtattc gttattcttc aagaaacctg diff -r f08181349fc4 -r 2bb38197ff75 test-data/NC_004668_137848_164286_icescreen.gff --- a/test-data/NC_004668_137848_164286_icescreen.gff Sat Apr 02 21:05:10 2022 +0000 +++ b/test-data/NC_004668_137848_164286_icescreen.gff Tue Dec 06 10:40:53 2022 +0000 @@ -1,3 +1,7 @@ ##gff-version 3 -##sequence-region NC_004668.1 1 26439 -NC_004668.1 ICEscreen CDS 1 1511 .+ 1 origid=WP_002359295.1;function=Coupling Protein;protein_id=WP_002359295.1;locus_tag=EF_RS00630;codon_start=1;color=6;Note=ICEscreen prediction%3A Coupling protein%3B BlastP result %28Annotation confidence%3A HIGH%29%3A Coupling protein TcpA %5BHit with AAO80014%3B Identity%3A100.00%25%3B E-value%3A0%3B Query coverage%3A100.00%25%5D%3B Hmmscan result%3A TcpA %5BHit with tcpA HMM profile%3B E-value%3A0%3B i-Evalue%3A0%5DNC_004668.1 ICEscreen CDS 3098 4380 .+ 1 origid=WP_002359299.1;function=Relaxase;protein_id=WP_002359299.1;locus_tag=EF_RS00650;codon_start=1;color=7;Note=ICEscreen prediction%3A Relaxase%3B BlastP result %28Annotation confidence%3A HIGH%29%3A Relaxase MOBT %28PF02486%29 %5BHit with AAO80018%3B Identity%3A99.77%25%3B E-value%3A0%3B Query coverage%3A95.53%25%5D%3B Hmmscan result%3A MOBT %5BHit with T4SS_MOBT HMM profile%3B E-value%3A0%3B i-Evalue%3A0%5DNC_004668.1 ICEscreen CDS 17920 20426 .+ 1 origid=WP_002359320.1;function=VirB4;protein_id=WP_002359320.1;locus_tag=EF_RS00720;codon_start=1;color=184 134 11;Note=ICEscreen prediction%3A VirB4%3B BlastP result %28Annotation confidence%3A HIGH%29%3A VirB4 %5BHit with CAE52368%3B Identity%3A41.15%25%3B E-value%3A0%3B Query coverage%3A99.76%25%5D%3B Hmmscan result%3A VirB4 %5BHit with T4SS_virb4 HMM profile%3B E-value%3A0%3B i-Evalue%3A0%5DNC_004668.1 ICEscreen CDS 25273 26438 .+ 1 origid=WP_002392915.1;function=Tyrosine Integrase;protein_id=WP_002392915.1;locus_tag=EF_RS00760;codon_start=1;color=8;Note=ICEscreen prediction%3A Tyrosine integrase%3B BlastP result %28Annotation confidence%3A HIGH%29%3A Tyrosine integrase %5BHit with AAO80040%3B Identity%3A100.00%25%3B E-value%3A0%3B Query coverage%3A100.00%25%5D%3B Hmmscan result%3A Tyrosine integrase %5BHit with Phage_integrase HMM profile%3B E-value%3A0%3B i-Evalue%3A0%5DNC_004668.1 ICEscreen mobile_element 1 26439 .+ . mobile_element_type=other%3A integrative and conjugative element;Note=ICEscreen prediction%3A Putative ICE %28one integrase - Tyr%29 %5BElement structure%3A Single%3B ICE superfamily%3A Tn916%3B ICE family%3A ICESt3%3B Relaxase family%3A MOBT%3B Coupling protein family%3A TcpA%5D %28ICEscreen ID%3A 2%29;color=15 \ No newline at end of file +##sequence-region NC_004668.1 1 0 +NC_004668.1 ICEscreen CDS 1 1512 .+ 1 origid=EF_RS00630;function=Coupling Protein;protein_id=WP_002359295.1;locus_tag=EF_RS00630;codon_start=1;color=6;Note=ICEscreen prediction%3A Coupling protein%3B BlastP result %28Annotation confidence%3A HIGH%29%3A Coupling protein TcpA %5BHit with AAO80014%3B Identity%3A100.00%25%3B E-value%3A0.00e%2B00%3B Query coverage%3A100.00%25%5D%3B Hmmscan result%3A TcpA %5BHit with tcpA HMM profile%3B E-value%3A7.00e-94%3B i-Evalue%3A8.80e-94%5D +NC_004668.1 ICEscreen CDS 3098 4381 .+ 1 origid=EF_RS00650;function=Relaxase;protein_id=WP_002359299.1;locus_tag=EF_RS00650;codon_start=1;color=7;Note=ICEscreen prediction%3A Relaxase%3B BlastP result %28Annotation confidence%3A HIGH%29%3A Relaxase MOBT %28PF02486%29 %5BHit with AAO80018%3B Identity%3A99.77%25%3B E-value%3A0.00e%2B00%3B Query coverage%3A95.53%25%5D%3B Hmmscan result%3A MOBT %5BHit with T4SS_MOBT HMM profile%3B E-value%3A3.00e-128%3B i-Evalue%3A3.40e-128%5D +NC_004668.1 ICEscreen CDS 17920 20427 .+ 1 origid=EF_RS00720;function=VirB4;protein_id=WP_002359320.1;locus_tag=EF_RS00720;codon_start=1;color=184 134 11;Note=ICEscreen prediction%3A VirB4%3B BlastP result %28Annotation confidence%3A HIGH%29%3A VirB4 %5BHit with CAE52368%3B Identity%3A41.15%25%3B E-value%3A0.00e%2B00%3B Query coverage%3A99.76%25%5D%3B Hmmscan result%3A VirB4 %5BHit with T4SS_virb4 HMM profile%3B E-value%3A1.80e-28%3B i-Evalue%3A2.40e-28%5D +NC_004668.1 ICEscreen CDS 25273 26439 .+ 1 origid=EF_RS00760;function=Tyrosine Integrase;protein_id=WP_002392915.1;locus_tag=EF_RS00760;codon_start=1;color=8;Note=ICEscreen prediction%3A Tyrosine integrase%3B BlastP result %28Annotation confidence%3A HIGH%29%3A Tyrosine integrase %5BHit with AAO80040%3B Identity%3A100.00%25%3B E-value%3A0.00e%2B00%3B Query coverage%3A100.00%25%5D%3B Hmmscan result%3A Tyrosine integrase %5BHit with Phage_integrase HMM profile%3B E-value%3A4.40e-29%3B i-Evalue%3A9.70e-29%5D +NC_004668.1 ICEscreen mobile_element 1 26439 .+ . mobile_element_type=other%3A integrative and conjugative element;Note=ICEscreen prediction%3A Putative ICE %28one integrase Tyr%29 %5BElement structure%3A Single%3B ICE superfamily%3A Tn916%3B ICE family%3A ICESt3%3B Relaxase family%3A - %28MOBT%29%3B Coupling protein family%3A TcpA%5D %28ICEscreen ID%3A ID_1%29;color=15