diff -Nru roary-3.11.4+dfsg/debian/changelog roary-3.12.0+dfsg/debian/changelog --- roary-3.11.4+dfsg/debian/changelog 2018-01-15 12:40:31.000000000 +0000 +++ roary-3.12.0+dfsg/debian/changelog 2018-01-26 10:17:54.000000000 +0000 @@ -1,3 +1,9 @@ +roary (3.12.0+dfsg-1) unstable; urgency=medium + + * New upstream release. + + -- Sascha Steinbiss Fri, 26 Jan 2018 11:17:54 +0100 + roary (3.11.4+dfsg-1) unstable; urgency=medium * New upstream release. diff -Nru roary-3.11.4+dfsg/dist.ini roary-3.12.0+dfsg/dist.ini --- roary-3.11.4+dfsg/dist.ini 2018-01-16 13:34:28.000000000 +0000 +++ roary-3.12.0+dfsg/dist.ini 2018-01-23 13:46:41.000000000 +0000 @@ -3,7 +3,7 @@ license = GPL_3 copyright_holder = Wellcome Trust Sanger Institute copyright_year = 2013 -version = 3.11.4 +version = 3.12.0 main_module = lib/Bio/Roary.pm [MetaResources] diff -Nru roary-3.11.4+dfsg/lib/Bio/Roary/BedFromGFFRole.pm roary-3.12.0+dfsg/lib/Bio/Roary/BedFromGFFRole.pm --- roary-3.11.4+dfsg/lib/Bio/Roary/BedFromGFFRole.pm 2018-01-16 13:34:28.000000000 +0000 +++ roary-3.12.0+dfsg/lib/Bio/Roary/BedFromGFFRole.pm 2018-01-23 13:46:41.000000000 +0000 @@ -13,7 +13,7 @@ use Bio::Tools::GFF; has '_tags_to_filter' => ( is => 'ro', isa => 'Str', default => '(CDS|ncRNA|tRNA|tmRNA|rRNA)' ); -has 'min_gene_size_in_nucleotides' => ( is => 'ro', isa => 'Int', default => 120 ); +has 'min_gene_size_in_nucleotides' => ( is => 'ro', isa => 'Int', default => 18 ); has 'output_directory' => ( is => 'ro', isa => 'Str', default => '.' ); sub _bed_output_filename { diff -Nru roary-3.11.4+dfsg/t/data/example_annotation_2.gff roary-3.12.0+dfsg/t/data/example_annotation_2.gff --- roary-3.11.4+dfsg/t/data/example_annotation_2.gff 2018-01-16 13:34:28.000000000 +0000 +++ roary-3.12.0+dfsg/t/data/example_annotation_2.gff 2018-01-23 13:46:41.000000000 +0000 @@ -12,7 +12,7 @@ abc|SC|contig000001 Prodigal:2.60 CDS 9419 9646 . + 0 ID=abc_00010;inference=ab initio prediction:Prodigal:2.60;locus_tag=abc_00010;product=hypothetical protein;protein_id=gnl|SC|abc_00010 abc|SC|contig000001 Prodigal:2.60 CDS 9952 10899 . - 0 ID=abc_00011;inference=ab initio prediction:Prodigal:2.60,protein motif:Pfam:PF03595.11;locus_tag=abc_00011;product=C4-dicarboxylate transporter/malic acid transport protein;protein_id=gnl|SC|abc_00011 abc|SC|contig000001 Prodigal:2.60 CDS 11148 11336 . + 0 ID=abc_00012;inference=ab initio prediction:Prodigal:2.60;locus_tag=abc_00012;product=hypothetical protein;protein_id=gnl|SC|abc_00012 -abc|SC|contig000001 Aragorn:1.2.34 tRNA 11803 11878 . - 0 ID=abc_00013;inference=COORDINATES:profile:Aragorn:1.2.34;locus_tag=abc_00013;product=tRNA-Arg(tct) +abc|SC|contig000001 Aragorn:1.2.34 tRNA 11803 11820 . - 0 ID=abc_00013;inference=COORDINATES:profile:Aragorn:1.2.34;locus_tag=abc_00013;product=tRNA-Arg(tct) abc|SC|contig000001 Prodigal:2.60 CDS 12241 12375 . + 0 ID=abc_00014;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:UniProtKB:P11699,protein motif:Pfam:PF05480.5;locus_tag=abc_00014;product=Gonococcal growth inhibitor III,Staphylococcus haemolytic protein;protein_id=gnl|SC|abc_00014 abc|SC|contig000001 Prodigal:2.60 CDS 12432 12566 . + 0 ID=abc_00015;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:UniProtKB:P11699,protein motif:Pfam:PF05480.5;locus_tag=abc_00015;product=Gonococcal growth inhibitor III,Staphylococcus haemolytic protein;protein_id=gnl|SC|abc_00015 abc|SC|contig000001 Prodigal:2.60 CDS 12699 13385 . + 0 ID=abc_00016;eC_number=3.-.-.-;gene=yfnB;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:UniProtKB:O06480,protein motif:CLUSTERS:PRK09449,protein motif:TIGRFAMs:TIGR02254,protein motif:Pfam:PF00702.1;locus_tag=abc_00016;product=Putative HAD-hydrolase yfnB,dUMP phosphatase,HAD hydrolase,haloacid dehalogenase-like hydrolase;protein_id=gnl|SC|abc_00016 diff -Nru roary-3.11.4+dfsg/t/data/example_annotation.gff roary-3.12.0+dfsg/t/data/example_annotation.gff --- roary-3.11.4+dfsg/t/data/example_annotation.gff 2018-01-16 13:34:28.000000000 +0000 +++ roary-3.12.0+dfsg/t/data/example_annotation.gff 2018-01-23 13:46:41.000000000 +0000 @@ -12,7 +12,7 @@ abc|SC|contig000001 Prodigal:2.60 CDS 9419 9646 . + 0 ID=abc_00010;inference=ab initio prediction:Prodigal:2.60;locus_tag=abc_00010;product=hypothetical protein;protein_id=gnl|SC|abc_00010 abc|SC|contig000001 Prodigal:2.60 CDS 9952 10899 . - 0 ID=abc_00011;inference=ab initio prediction:Prodigal:2.60,protein motif:Pfam:PF03595.11;locus_tag=abc_00011;product=C4-dicarboxylate transporter/malic acid transport protein;protein_id=gnl|SC|abc_00011 abc|SC|contig000001 Prodigal:2.60 CDS 11148 11336 . + 0 ID=abc_00012;inference=ab initio prediction:Prodigal:2.60;locus_tag=abc_00012;product=hypothetical protein;protein_id=gnl|SC|abc_00012 -abc|SC|contig000001 Aragorn:1.2.34 tRNA 11803 11878 . - 0 ID=abc_00013;inference=COORDINATES:profile:Aragorn:1.2.34;locus_tag=abc_00013;product=tRNA-Arg(tct) +abc|SC|contig000001 Aragorn:1.2.34 tRNA 11803 11820 . - 0 ID=abc_00013;inference=COORDINATES:profile:Aragorn:1.2.34;locus_tag=abc_00013;product=tRNA-Arg(tct) abc|SC|contig000001 Prodigal:2.60 CDS 12241 12375 . + 0 ID=abc_00014;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:UniProtKB:P11699,protein motif:Pfam:PF05480.5;locus_tag=abc_00014;product=Gonococcal growth inhibitor III,Staphylococcus haemolytic protein;protein_id=gnl|SC|abc_00014 abc|SC|contig000001 Prodigal:2.60 CDS 12432 12566 . + 0 ID=abc_00015;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:UniProtKB:P11699,protein motif:Pfam:PF05480.5;locus_tag=abc_00015;product=Gonococcal growth inhibitor III,Staphylococcus haemolytic protein;protein_id=gnl|SC|abc_00015 abc|SC|contig000001 Prodigal:2.60 CDS 12699 13385 . + 0 ID=abc_00016;eC_number=3.-.-.-;gene=yfnB;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:UniProtKB:O06480,protein motif:CLUSTERS:PRK09449,protein motif:TIGRFAMs:TIGR02254,protein motif:Pfam:PF00702.1;locus_tag=abc_00016;product=Putative HAD-hydrolase yfnB,dUMP phosphatase,HAD hydrolase,haloacid dehalogenase-like hydrolase;protein_id=gnl|SC|abc_00016 diff -Nru roary-3.11.4+dfsg/t/data/genbank_gbff/genbank2.gff roary-3.12.0+dfsg/t/data/genbank_gbff/genbank2.gff --- roary-3.11.4+dfsg/t/data/genbank_gbff/genbank2.gff 2018-01-16 13:34:28.000000000 +0000 +++ roary-3.12.0+dfsg/t/data/genbank_gbff/genbank2.gff 2018-01-23 13:46:41.000000000 +0000 @@ -17,9 +17,9 @@ CVBR01000001 GenBank mRNA 4176 6542 . + 1 ID=ERS325340_00004.t01;Parent=ERS325340_00004 CVBR01000001 GenBank CDS 4176 6542 . + 1 ID=ERS325340_00004.p01;Parent=ERS325340_00004.t01;Dbxref=GI:804333229;eC_number=6.3.2.-;Name=sspH2;codon_start=1;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_002244314.1;locus_tag=ERS325340_00004;product=secreted effector protein;protein_id=CQU31395.1;transl_table=11;translation=length.788 CVBR01000001 GenBank exon 4176 6542 . + 1 Parent=ERS325340_00004.t01 -CVBR01000001 GenBank gene 7163 7239 . - 1 ID=ERS325340_00005;Name=ERS325340_00005 -CVBR01000001 GenBank tRNA 7163 7239 . - 1 ID=ERS325340_00005.r01;Parent=ERS325340_00005;Name=ERS325340_00005;inference=COORDINATES: profile:Aragorn:1.2.36;product=tRNA-Pro -CVBR01000001 GenBank exon 7163 7239 . - 1 Parent=ERS325340_00005.r01;Name=ERS325340_00005 +CVBR01000001 GenBank gene 7163 7180 . - 1 ID=ERS325340_00005;Name=ERS325340_00005 +CVBR01000001 GenBank tRNA 7163 7180 . - 1 ID=ERS325340_00005.r01;Parent=ERS325340_00005;Name=ERS325340_00005;inference=COORDINATES: profile:Aragorn:1.2.36;product=tRNA-Pro +CVBR01000001 GenBank exon 7163 7180 . - 1 Parent=ERS325340_00005.r01;Name=ERS325340_00005 ##FASTA >CVBR01000001 TAGAGCGCAGTATCCGGCTGGCGCAGGAGAAATAAGACCCTGACGGCCCGGTGGCGTGGC diff -Nru roary-3.11.4+dfsg/t/data/genbank_gbff/genbank3.gff roary-3.12.0+dfsg/t/data/genbank_gbff/genbank3.gff --- roary-3.11.4+dfsg/t/data/genbank_gbff/genbank3.gff 2018-01-16 13:34:28.000000000 +0000 +++ roary-3.12.0+dfsg/t/data/genbank_gbff/genbank3.gff 2018-01-23 13:46:41.000000000 +0000 @@ -17,9 +17,9 @@ CVBT01000001 GenBank mRNA 4180 6546 . + 1 ID=ERS325326_00004.t01;Parent=ERS325326_00004 CVBT01000001 GenBank CDS 4180 6546 . + 1 ID=ERS325326_00004.p01;Parent=ERS325326_00004.t01;Dbxref=GI:804342842;eC_number=6.3.2.-;Name=sspH2;codon_start=1;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_002244314.1;locus_tag=ERS325326_00004;product=secreted effector protein;protein_id=CQU32561.1;transl_table=11;translation=length.788 CVBT01000001 GenBank exon 4180 6546 . + 1 Parent=ERS325326_00004.t01 -CVBT01000001 GenBank gene 7167 7243 . - 1 ID=ERS325326_00005;Name=ERS325326_00005 -CVBT01000001 GenBank tRNA 7167 7243 . - 1 ID=ERS325326_00005.r01;Parent=ERS325326_00005;Name=ERS325326_00005;inference=COORDINATES: profile:Aragorn:1.2.36;product=tRNA-Pro -CVBT01000001 GenBank exon 7167 7243 . - 1 Parent=ERS325326_00005.r01;Name=ERS325326_00005 +CVBT01000001 GenBank gene 7167 7184 . - 1 ID=ERS325326_00005;Name=ERS325326_00005 +CVBT01000001 GenBank tRNA 7167 7184 . - 1 ID=ERS325326_00005.r01;Parent=ERS325326_00005;Name=ERS325326_00005;inference=COORDINATES: profile:Aragorn:1.2.36;product=tRNA-Pro +CVBT01000001 GenBank exon 7167 7184 . - 1 Parent=ERS325326_00005.r01;Name=ERS325326_00005 ##FASTA >CVBT01000001 GTGATAGAGCGCAGTATCCGGCTGGCGCAGGAGAAATAAGACCCTGACGGCCCGGTGGCG diff -Nru roary-3.11.4+dfsg/t/data/locus_tag_gffs/query_1.gff roary-3.12.0+dfsg/t/data/locus_tag_gffs/query_1.gff --- roary-3.11.4+dfsg/t/data/locus_tag_gffs/query_1.gff 2018-01-16 13:34:28.000000000 +0000 +++ roary-3.12.0+dfsg/t/data/locus_tag_gffs/query_1.gff 2018-01-23 13:46:41.000000000 +0000 @@ -12,7 +12,7 @@ abc|SC|contig000001 Prodigal:2.60 CDS 9419 9646 . + 0 inference=ab initio prediction:Prodigal:2.60;locus_tag=abc_00010;product=hypothetical protein;protein_id=gnl|SC|abc_00010 abc|SC|contig000001 Prodigal:2.60 CDS 9952 10899 . - 0 inference=ab initio prediction:Prodigal:2.60,protein motif:Pfam:PF03595.11;locus_tag=abc_00011;product=C4-dicarboxylate transporter/malic acid transport protein;protein_id=gnl|SC|abc_00011 abc|SC|contig000001 Prodigal:2.60 CDS 11148 11336 . + 0 inference=ab initio prediction:Prodigal:2.60;locus_tag=abc_00012;product=hypothetical protein;protein_id=gnl|SC|abc_00012 -abc|SC|contig000001 Aragorn:1.2.34 tRNA 11803 11878 . - 0 inference=COORDINATES:profile:Aragorn:1.2.34;locus_tag=abc_00013;product=tRNA-Arg(tct) +abc|SC|contig000001 Aragorn:1.2.34 tRNA 11803 11820 . - 0 inference=COORDINATES:profile:Aragorn:1.2.34;locus_tag=abc_00013;product=tRNA-Arg(tct) abc|SC|contig000001 Prodigal:2.60 CDS 12241 12375 . + 0 inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:UniProtKB:P11699,protein motif:Pfam:PF05480.5;locus_tag=abc_00014;product=Gonococcal growth inhibitor III,Staphylococcus haemolytic protein;protein_id=gnl|SC|abc_00014 abc|SC|contig000001 Prodigal:2.60 CDS 12432 12566 . + 0 inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:UniProtKB:P11699,protein motif:Pfam:PF05480.5;locus_tag=abc_00015;product=Gonococcal growth inhibitor III,Staphylococcus haemolytic protein;protein_id=gnl|SC|abc_00015 abc|SC|contig000001 Prodigal:2.60 CDS 12699 13385 . + 0 eC_number=3.-.-.-;gene=yfnB;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:UniProtKB:O06480,protein motif:CLUSTERS:PRK09449,protein motif:TIGRFAMs:TIGR02254,protein motif:Pfam:PF00702.1;locus_tag=abc_00016;product=Putative HAD-hydrolase yfnB,dUMP phosphatase,HAD hydrolase,haloacid dehalogenase-like hydrolase;protein_id=gnl|SC|abc_00016 diff -Nru roary-3.11.4+dfsg/t/data/locus_tag_gffs/query_2.gff roary-3.12.0+dfsg/t/data/locus_tag_gffs/query_2.gff --- roary-3.11.4+dfsg/t/data/locus_tag_gffs/query_2.gff 2018-01-16 13:34:28.000000000 +0000 +++ roary-3.12.0+dfsg/t/data/locus_tag_gffs/query_2.gff 2018-01-23 13:46:41.000000000 +0000 @@ -12,7 +12,7 @@ abc|SC|contig000001 Prodigal:2.60 CDS 9419 9646 . + 0 inference=ab initio prediction:Prodigal:2.60;locus_tag="zzz_00010";product=hypothetical protein;protein_id=gnl|SC|abc_00010 abc|SC|contig000001 Prodigal:2.60 CDS 9952 10899 . - 0 inference=ab initio prediction:Prodigal:2.60,protein motif:Pfam:PF03595.11;locus_tag="zzz_00011";product=C4-dicarboxylate transporter/malic acid transport protein;protein_id=gnl|SC|abc_00011 abc|SC|contig000001 Prodigal:2.60 CDS 11148 11336 . + 0 inference=ab initio prediction:Prodigal:2.60;locus_tag="zzz_00012";product=hypothetical protein;protein_id=gnl|SC|abc_00012 -abc|SC|contig000001 Aragorn:1.2.34 tRNA 11803 11878 . - 0 inference=COORDINATES:profile:Aragorn:1.2.34;locus_tag="zzz_00013";product=tRNA-Arg(tct) +abc|SC|contig000001 Aragorn:1.2.34 tRNA 11803 11820 . - 0 inference=COORDINATES:profile:Aragorn:1.2.34;locus_tag="zzz_00013";product=tRNA-Arg(tct) abc|SC|contig000001 Prodigal:2.60 CDS 12241 12375 . + 0 inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:UniProtKB:P11699,protein motif:Pfam:PF05480.5;locus_tag="zzz_00014";product=Gonococcal growth inhibitor III,Staphylococcus haemolytic protein;protein_id=gnl|SC|abc_00014 abc|SC|contig000001 Prodigal:2.60 CDS 12432 12566 . + 0 inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:UniProtKB:P11699,protein motif:Pfam:PF05480.5;locus_tag="zzz_00015";product=Gonococcal growth inhibitor III,Staphylococcus haemolytic protein;protein_id=gnl|SC|abc_00015 abc|SC|contig000001 Prodigal:2.60 CDS 12699 13385 . + 0 eC_number=3.-.-.-;gene=yfnB;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:UniProtKB:O06480,protein motif:CLUSTERS:PRK09449,protein motif:TIGRFAMs:TIGR02254,protein motif:Pfam:PF00702.1;locus_tag="zzz_00016";product=Putative HAD-hydrolase yfnB,dUMP phosphatase,HAD hydrolase,haloacid dehalogenase-like hydrolase;protein_id=gnl|SC|abc_00016 diff -Nru roary-3.11.4+dfsg/t/data/locus_tag_gffs/query_3.gff roary-3.12.0+dfsg/t/data/locus_tag_gffs/query_3.gff --- roary-3.11.4+dfsg/t/data/locus_tag_gffs/query_3.gff 2018-01-16 13:34:28.000000000 +0000 +++ roary-3.12.0+dfsg/t/data/locus_tag_gffs/query_3.gff 2018-01-23 13:46:41.000000000 +0000 @@ -12,7 +12,7 @@ abc|SC|contig000001 Prodigal:2.60 CDS 9419 9646 . + 0 inference=ab initio prediction:Prodigal:2.60;locus_tag=xxx_00010;product=hypothetical protein;protein_id=gnl|SC|abc_00010 abc|SC|contig000001 Prodigal:2.60 CDS 9952 10899 . - 0 inference=ab initio prediction:Prodigal:2.60,protein motif:Pfam:PF03595.11;locus_tag=xxx_00011;product=C4-dicarboxylate transporter/malic acid transport protein;protein_id=gnl|SC|abc_00011 abc|SC|contig000001 Prodigal:2.60 CDS 11148 11336 . + 0 inference=ab initio prediction:Prodigal:2.60;locus_tag=xxx_00012;product=hypothetical protein;protein_id=gnl|SC|abc_00012 -abc|SC|contig000001 Aragorn:1.2.34 tRNA 11803 11878 . - 0 inference=COORDINATES:profile:Aragorn:1.2.34;locus_tag=xxx_00013;product=tRNA-Arg(tct) +abc|SC|contig000001 Aragorn:1.2.34 tRNA 11803 11820 . - 0 inference=COORDINATES:profile:Aragorn:1.2.34;locus_tag=xxx_00013;product=tRNA-Arg(tct) abc|SC|contig000001 Prodigal:2.60 CDS 12241 12375 . + 0 inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:UniProtKB:P11699,protein motif:Pfam:PF05480.5;locus_tag=xxx_00014;product=Gonococcal growth inhibitor III,Staphylococcus haemolytic protein;protein_id=gnl|SC|abc_00014 abc|SC|contig000001 Prodigal:2.60 CDS 12432 12566 . + 0 inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:UniProtKB:P11699,protein motif:Pfam:PF05480.5;locus_tag=xxx_00015;product=Gonococcal growth inhibitor III,Staphylococcus haemolytic protein;protein_id=gnl|SC|abc_00015 abc|SC|contig000001 Prodigal:2.60 CDS 12699 13385 . + 0 eC_number=3.-.-.-;gene=yfnB;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:UniProtKB:O06480,protein motif:CLUSTERS:PRK09449,protein motif:TIGRFAMs:TIGR02254,protein motif:Pfam:PF00702.1;locus_tag=xxx_00016;product=Putative HAD-hydrolase yfnB,dUMP phosphatase,HAD hydrolase,haloacid dehalogenase-like hydrolase;protein_id=gnl|SC|abc_00016 diff -Nru roary-3.11.4+dfsg/t/data/real_data_1.gff roary-3.12.0+dfsg/t/data/real_data_1.gff --- roary-3.11.4+dfsg/t/data/real_data_1.gff 2018-01-16 13:34:28.000000000 +0000 +++ roary-3.12.0+dfsg/t/data/real_data_1.gff 2018-01-23 13:46:41.000000000 +0000 @@ -2,7 +2,7 @@ ##sequence-region ERS111111|SC|contig000020 1 92255 ERS111111|SC|contig000020 Prodigal:2.60 CDS 241 921 . - 0 ID=11111_1#11_04055;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_002145956.2,protein motif:Pfam:PF07108.5;locus_tag=11111_1#11_04055;product=pathogenicity island-encoded protein A,PipA protein;protein_id=gnl|SC|11111_1#11_04055 ERS111111|SC|contig000020 Prodigal:2.60 CDS 1144 2019 . - 0 ID=11111_1#11_04056;gene=pipB2_2;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_002145957.1,similar to AA sequence:UniProtKB:Q8ZMM8,protein motif:CLUSTERS:PRK15197,protein motif:Cdd:COG5351,protein motif:Pfam:PF00805.16;locus_tag=11111_1#11_04056;product=secreted effector protein,Type III effector pipB2,secreted effector protein PipB,Uncharacterized protein conserved in bacteria,Pentapeptide repeats (8 copies);protein_id=gnl|SC|11111_1#11_04056 -ERS111111|SC|contig000020 Infernal:1.1 ncRNA 2139 2237 . + 0 ID=11111_1#11_04057;inference=COORDINATES:profile:Infernal:1.1;locus_tag=11111_1#11_04057;product=isrI +ERS111111|SC|contig000020 Infernal:1.1 ncRNA 2139 2156 . + 0 ID=11111_1#11_04057;inference=COORDINATES:profile:Infernal:1.1;locus_tag=11111_1#11_04057;product=isrI ERS111111|SC|contig000020 Prodigal:2.60 CDS 2567 2908 . - 0 ID=11111_1#11_04058;gene=sigE;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_002145959.1,similar to AA sequence:UniProtKB:O30917,protein motif:CLUSTERS:PRK15202,protein motif:Pfam:PF07824.6;locus_tag=11111_1#11_04058;product=chaperone protein SigE,Chaperone protein sigE,type III secretion chaperone protein SigE,Type III secretion chaperone domain;protein_id=gnl|SC|11111_1#11_04058 ERS111111|SC|contig000020 Prodigal:2.60 CDS 2925 4610 . - 0 ID=11111_1#11_04059;eC_number=3.1.3.-,3.1.3.-;gene=sopB;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_002145960.1,similar to AA sequence:UniProtKB:O30916,protein motif:CLUSTERS:PRK15378,protein motif:Pfam:PF05925.6;locus_tag=11111_1#11_04059;product=inositol phosphate phosphatase SopB,Inositol phosphate phosphatase sopB,inositol phosphate phosphatase SopB,Enterobacterial virulence protein IpgD;protein_id=gnl|SC|11111_1#11_04059 ERS111111|SC|contig000020 Prodigal:2.60 CDS 5332 6801 . - 0 ID=11111_1#11_04060;eC_number=3.4.-.-;gene=pepD_2;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_002215025.1,similar to AA sequence:UniProtKB:Q8G6Z9,protein motif:Pfam:PF03577.9;locus_tag=11111_1#11_04060;product=peptidase family C69,Dipeptidase,Peptidase family C69;protein_id=gnl|SC|11111_1#11_04060 @@ -47,7 +47,7 @@ ERS111111|SC|contig000020 Prodigal:2.60 CDS 44992 45684 . + 0 ID=11111_1#11_04099;gene=yiiy;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_216068.1,similar to AA sequence:UniProtKB:Q934G3,protein motif:CLUSTERS:PRK09980,protein motif:Cdd:COG3203,protein motif:Pfam:PF06178.7;locus_tag=11111_1#11_04099;product=outer membrane protein,Oligogalacturonate-specific porin kdgM precursor,outer membrane porin L,Outer membrane protein (porin),Oligogalacturonate-specific porin protein (KdgM);protein_id=gnl|SC|11111_1#11_04099 ERS111111|SC|contig000020 Prodigal:2.60 CDS 45967 47247 . + 0 ID=11111_1#11_04100;gene=nanT_3;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_001570893.1,similar to AA sequence:UniProtKB:P41036,protein motif:CLUSTERS:PRK12307,protein motif:Cdd:COG2814,protein motif:TIGRFAMs:TIGR00891,protein motif:Pfam:PF00083.18;locus_tag=11111_1#11_04100;product=putative sialic acid transporter,Sialic acid permease,putative sialic acid transporter,Arabinose efflux permease,MFS transporter%2C sialate:H+ symporter (SHS) family,Sugar (and other) transporter;protein_id=gnl|SC|11111_1#11_04100 ERS111111|SC|contig000020 Prodigal:2.60 CDS 47261 48364 . + 0 ID=11111_1#11_04101;eC_number=1.1.1.292;gene=yjhC;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_216069.1,similar to AA sequence:UniProtKB:Q2I8V6,protein motif:CLUSTERS:PRK11579,protein motif:Pfam:PF01408.16;locus_tag=11111_1#11_04101;product=dehydrogenase-like protein,1%2C5-anhydro-D-fructose reductase,putative oxidoreductase,Oxidoreductase family%2C NAD-binding Rossmann fold;protein_id=gnl|SC|11111_1#11_04101 -ERS111111|SC|contig000020 Aragorn:1.2.36 tRNA 48701 48788 . - 0 ID=11111_1#11_04102;inference=COORDINATES:profile:Aragorn:1.2.36;locus_tag=11111_1#11_04102;product=tRNA-Ser(gga) +ERS111111|SC|contig000020 Aragorn:1.2.36 tRNA 48701 48718 . - 0 ID=11111_1#11_04102;inference=COORDINATES:profile:Aragorn:1.2.36;locus_tag=11111_1#11_04102;product=tRNA-Ser(gga) ERS111111|SC|contig000020 Prodigal:2.60 CDS 49024 49962 . + 0 ID=11111_1#11_04103;eC_number=1.1.1.79;gene=ghrA;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_004729856.1,similar to AA sequence:UniProtKB:Q8ZQ30,protein motif:CLUSTERS:PRK15469,protein motif:Cdd:COG1932,protein motif:TIGRFAMs:TIGR01327,protein motif:Pfam:PF02826.13;locus_tag=11111_1#11_04103;product=2-hydroxyacid dehydrogenase,Glyoxylate/hydroxypyruvate reductase A,bifunctional glyoxylate/hydroxypyruvate reductase A,Phosphoserine aminotransferase,phosphoglycerate dehydrogenase,D-isomer specific 2-hydroxyacid dehydrogenase%2C NAD binding domain;protein_id=gnl|SC|11111_1#11_04103 ERS111111|SC|contig000020 Prodigal:2.60 CDS 50047 50784 . + 0 ID=11111_1#11_04104;eC_number=3.1.3.-;gene=ycdX;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_001570887.1,similar to AA sequence:UniProtKB:P75914,protein motif:CLUSTERS:PRK09248,protein motif:Cdd:COG1387,protein motif:TIGRFAMs:TIGR01856,protein motif:Pfam:PF02811.13;locus_tag=11111_1#11_04104;product=putative hydrolase,Probable phosphatase YcdX,putative hydrolase,Histidinol phosphatase and related hydrolases of the PHP family,histidinol phosphate phosphatase%2C HisJ family,PHP domain;protein_id=gnl|SC|11111_1#11_04104 ERS111111|SC|contig000020 Prodigal:2.60 CDS 50808 51362 . + 0 ID=11111_1#11_04105;gene=ycdY;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_002146908.1,similar to AA sequence:UniProtKB:P75915,protein motif:CLUSTERS:PRK11621,protein motif:Cdd:COG3381,protein motif:Pfam:PF02613.9;locus_tag=11111_1#11_04105;product=chaperone%2C TorD family,Chaperone protein YcdY,twin-argninine leader-binding protein DmsD,Uncharacterized component of anaerobic dehydrogenases,Nitrate reductase delta subunit;protein_id=gnl|SC|11111_1#11_04105 @@ -72,7 +72,7 @@ ERS111111|SC|contig000020 Prodigal:2.60 CDS 67715 68767 . + 0 ID=11111_1#11_04124;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_006087420.1,protein motif:CLUSTERS:PRK00142,protein motif:Cdd:COG2210,protein motif:Pfam:PF00581.14;locus_tag=11111_1#11_04124;product=Rhodanese-like sulfurtransferase,putative rhodanese-related sulfurtransferase,Uncharacterized conserved protein,Rhodanese-like domain;protein_id=gnl|SC|11111_1#11_04124 ERS111111|SC|contig000020 Prodigal:2.60 CDS 68819 69394 . - 0 ID=11111_1#11_04125;gene=yceI_2;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_006087865.1,similar to AA sequence:UniProtKB:P0A8X2,protein motif:CLUSTERS:PRK03757,protein motif:Cdd:COG2353,protein motif:Pfam:PF04264.7;locus_tag=11111_1#11_04125;product=YceI protein,hypothetical protein,hypothetical protein,Uncharacterized conserved protein,YceI-like domain;protein_id=gnl|SC|11111_1#11_04125 ERS111111|SC|contig000020 Prodigal:2.60 CDS 69391 69795 . - 0 ID=11111_1#11_04126;gene=yceJ;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_005212184.1,similar to AA sequence:UniProtKB:P75925,protein motif:CLUSTERS:PRK11513,protein motif:Pfam:PF00033.13;locus_tag=11111_1#11_04126;product=cytochrome b561-like protein 2,Cytochrome b561 homolog 2,cytochrome b561,Cytochrome b(N-terminal)/b6/petB;protein_id=gnl|SC|11111_1#11_04126 -ERS111111|SC|contig000020 Prodigal:2.60 CDS 70226 70339 . - 0 ID=11111_1#11_04127;gene=yceO;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_216094.1,similar to AA sequence:UniProtKB:P64442,protein motif:Pfam:PF10968.2;locus_tag=11111_1#11_04127;product=inner membrane protein,hypothetical protein,Protein of unknown function (DUF2770);protein_id=gnl|SC|11111_1#11_04127 +ERS111111|SC|contig000020 Prodigal:2.60 CDS 70226 70243 . - 0 ID=11111_1#11_04127;gene=yceO;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_216094.1,similar to AA sequence:UniProtKB:P64442,protein motif:Pfam:PF10968.2;locus_tag=11111_1#11_04127;product=inner membrane protein,hypothetical protein,Protein of unknown function (DUF2770);protein_id=gnl|SC|11111_1#11_04127 ERS111111|SC|contig000020 Prodigal:2.60 CDS 70380 71498 . - 0 ID=11111_1#11_04128;eC_number=1.5.3.1,1.5.3.-;gene=solA;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_004729880.1,similar to AA sequence:UniProtKB:P40874,protein motif:CLUSTERS:PRK11259,protein motif:Cdd:COG4121,protein motif:TIGRFAMs:TIGR01377,protein motif:Pfam:PF01266.18;locus_tag=11111_1#11_04128;product=sarcosine oxidase,N-methyl-L-tryptophan oxidase,N-methyltryptophan oxidase,Uncharacterized conserved protein,sarcosine oxidase%2C monomeric form,FAD dependent oxidoreductase;protein_id=gnl|SC|11111_1#11_04128 ERS111111|SC|contig000020 Prodigal:2.60 CDS 71611 71865 . - 0 ID=11111_1#11_04129;gene=bssS;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_001570863.1,protein motif:CLUSTERS:PRK12301;locus_tag=11111_1#11_04129;product=biofilm formation regulatory protein BssS,biofilm formation regulatory protein BssS;protein_id=gnl|SC|11111_1#11_04129 ERS111111|SC|contig000020 Prodigal:2.60 CDS 72155 72418 . - 0 ID=11111_1#11_04130;gene=dinI_3;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_004729882.1,similar to AA sequence:UniProtKB:P0ABR1,protein motif:CLUSTERS:PRK10597,protein motif:Pfam:PF06183.7;locus_tag=11111_1#11_04130;product=damage-inducible protein,DNA-damage-inducible protein I,DNA damage-inducible protein I,DinI-like family;protein_id=gnl|SC|11111_1#11_04130 @@ -98,7 +98,7 @@ ERS111111|SC|contig000020 Prodigal:2.60 CDS 88429 89379 . + 0 ID=11111_1#11_04150;eC_number=3.2.1.-;gene=flgJ;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_004729902.1,similar to AA sequence:UniProtKB:P15931,protein motif:CLUSTERS:PRK05684,protein motif:Cdd:COG3951,protein motif:TIGRFAMs:TIGR02541,protein motif:Pfam:PF01832.14;locus_tag=11111_1#11_04150;product=flagellar protein FlgJ,Peptidoglycan hydrolase flgJ,flagellar rod assembly protein/muramidase FlgJ,Rod binding protein,flagellar rod assembly protein/muramidase FlgJ,Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase;protein_id=gnl|SC|11111_1#11_04150 ERS111111|SC|contig000020 Prodigal:2.60 CDS 89444 91105 . + 0 ID=11111_1#11_04151;gene=flgK;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_004729903.1,similar to AA sequence:UniProtKB:P0A1J5,protein motif:CLUSTERS:PRK08147,protein motif:Cdd:COG1749,protein motif:TIGRFAMs:TIGR02492,protein motif:Pfam:PF06429.7;locus_tag=11111_1#11_04151;product=flagellar hook-associated protein 1,Flagellar hook-associated protein 1,flagellar hook-associated protein FlgK,Flagellar hook protein FlgE,flagellar hook-associated protein FlgK,Domain of unknown function (DUF1078);protein_id=gnl|SC|11111_1#11_04151 ERS111111|SC|contig000020 Prodigal:2.60 CDS 91120 92073 . + 0 ID=11111_1#11_04152;gene=flgL;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_004729904.1,similar to AA sequence:UniProtKB:P16326,protein motif:CLUSTERS:PRK08027,protein motif:Cdd:COG3951,protein motif:TIGRFAMs:TIGR02550,protein motif:Pfam:PF00669.14;locus_tag=11111_1#11_04152;product=flagellar hook-associated protein 3,Hook-filament junction protein,flagellar hook-associated protein FlgL,Rod binding protein,flagellar hook-associated protein 3,Bacterial flagellin N-terminal helical region;protein_id=gnl|SC|11111_1#11_04152 -ERS111111|SC|contig000020 Infernal:1.1 ncRNA 92162 92255 . + 0 ID=11111_1#11_04153;inference=COORDINATES:profile:Infernal:1.1;locus_tag=11111_1#11_04153;product=STnc490k +ERS111111|SC|contig000020 Infernal:1.1 ncRNA 92162 92179 . + 0 ID=11111_1#11_04153;inference=COORDINATES:profile:Infernal:1.1;locus_tag=11111_1#11_04153;product=STnc490k ##FASTA >ERS111111|SC|contig000020 TATCCGGGCAGCCCGTTTACGGGCCGTAAGTAACGAAGTTTGATGCAAATGTCAGATCGT diff -Nru roary-3.11.4+dfsg/t/data/real_data_2.gff roary-3.12.0+dfsg/t/data/real_data_2.gff --- roary-3.11.4+dfsg/t/data/real_data_2.gff 2018-01-16 13:34:28.000000000 +0000 +++ roary-3.12.0+dfsg/t/data/real_data_2.gff 2018-01-23 13:46:41.000000000 +0000 @@ -2,7 +2,7 @@ ##sequence-region ERS222222|SC|contig000020 1 92255 ERS222222|SC|contig000020 Prodigal:2.60 CDS 241 921 . - 0 ID=22222_2#22_04055;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_002145956.2,protein motif:Pfam:PF07108.5;locus_tag=22222_2#22_04055;product=pathogenicity island-encoded protein A,PipA protein;protein_id=gnl|SC|22222_2#22_04055 ERS222222|SC|contig000020 Prodigal:2.60 CDS 1144 2019 . - 0 ID=22222_2#22_04056;gene=pipB2_2;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_002145957.1,similar to AA sequence:UniProtKB:Q8ZMM8,protein motif:CLUSTERS:PRK15197,protein motif:Cdd:COG5351,protein motif:Pfam:PF00805.16;locus_tag=22222_2#22_04056;product=secreted effector protein,Type III effector pipB2,secreted effector protein PipB,Uncharacterized protein conserved in bacteria,Pentapeptide repeats (8 copies);protein_id=gnl|SC|22222_2#22_04056 -ERS222222|SC|contig000020 Infernal:1.1 ncRNA 2139 2237 . + 0 ID=22222_2#22_04057;inference=COORDINATES:profile:Infernal:1.1;locus_tag=22222_2#22_04057;product=isrI +ERS222222|SC|contig000020 Infernal:1.1 ncRNA 2139 2156 . + 0 ID=22222_2#22_04057;inference=COORDINATES:profile:Infernal:1.1;locus_tag=22222_2#22_04057;product=isrI ERS222222|SC|contig000020 Prodigal:2.60 CDS 2567 2908 . - 0 ID=22222_2#22_04058;gene=sigE;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_002145959.1,similar to AA sequence:UniProtKB:O30917,protein motif:CLUSTERS:PRK15202,protein motif:Pfam:PF07824.6;locus_tag=22222_2#22_04058;product=chaperone protein SigE,Chaperone protein sigE,type III secretion chaperone protein SigE,Type III secretion chaperone domain;protein_id=gnl|SC|22222_2#22_04058 ERS222222|SC|contig000020 Prodigal:2.60 CDS 2925 4610 . - 0 ID=22222_2#22_04059;eC_number=3.1.3.-,3.1.3.-;gene=sopB;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_002145960.1,similar to AA sequence:UniProtKB:O30916,protein motif:CLUSTERS:PRK15378,protein motif:Pfam:PF05925.6;locus_tag=22222_2#22_04059;product=inositol phosphate phosphatase SopB,Inositol phosphate phosphatase sopB,inositol phosphate phosphatase SopB,Enterobacterial virulence protein IpgD;protein_id=gnl|SC|22222_2#22_04059 ERS222222|SC|contig000020 Prodigal:2.60 CDS 5332 6801 . - 0 ID=22222_2#22_04060;eC_number=3.4.-.-;gene=pepD_2;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_002215025.1,similar to AA sequence:UniProtKB:Q8G6Z9,protein motif:Pfam:PF03577.9;locus_tag=22222_2#22_04060;product=peptidase family C69,Dipeptidase,Peptidase family C69;protein_id=gnl|SC|22222_2#22_04060 @@ -47,7 +47,7 @@ ERS222222|SC|contig000020 Prodigal:2.60 CDS 44992 45684 . + 0 ID=22222_2#22_04099;gene=yiiy;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_216068.1,similar to AA sequence:UniProtKB:Q934G3,protein motif:CLUSTERS:PRK09980,protein motif:Cdd:COG3203,protein motif:Pfam:PF06178.7;locus_tag=22222_2#22_04099;product=outer membrane protein,Oligogalacturonate-specific porin kdgM precursor,outer membrane porin L,Outer membrane protein (porin),Oligogalacturonate-specific porin protein (KdgM);protein_id=gnl|SC|22222_2#22_04099 ERS222222|SC|contig000020 Prodigal:2.60 CDS 45967 47247 . + 0 ID=22222_2#22_04100;gene=nanT_3;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_001570893.1,similar to AA sequence:UniProtKB:P41036,protein motif:CLUSTERS:PRK12307,protein motif:Cdd:COG2814,protein motif:TIGRFAMs:TIGR00891,protein motif:Pfam:PF00083.18;locus_tag=22222_2#22_04100;product=putative sialic acid transporter,Sialic acid permease,putative sialic acid transporter,Arabinose efflux permease,MFS transporter%2C sialate:H+ symporter (SHS) family,Sugar (and other) transporter;protein_id=gnl|SC|22222_2#22_04100 ERS222222|SC|contig000020 Prodigal:2.60 CDS 47261 48364 . + 0 ID=22222_2#22_04101;eC_number=1.1.1.292;gene=yjhC;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_216069.1,similar to AA sequence:UniProtKB:Q2I8V6,protein motif:CLUSTERS:PRK11579,protein motif:Pfam:PF01408.16;locus_tag=22222_2#22_04101;product=dehydrogenase-like protein,1%2C5-anhydro-D-fructose reductase,putative oxidoreductase,Oxidoreductase family%2C NAD-binding Rossmann fold;protein_id=gnl|SC|22222_2#22_04101 -ERS222222|SC|contig000020 Aragorn:1.2.36 tRNA 48701 48788 . - 0 ID=22222_2#22_04102;inference=COORDINATES:profile:Aragorn:1.2.36;locus_tag=22222_2#22_04102;product=tRNA-Ser(gga) +ERS222222|SC|contig000020 Aragorn:1.2.36 tRNA 48701 48718 . - 0 ID=22222_2#22_04102;inference=COORDINATES:profile:Aragorn:1.2.36;locus_tag=22222_2#22_04102;product=tRNA-Ser(gga) ERS222222|SC|contig000020 Prodigal:2.60 CDS 49024 49962 . + 0 ID=22222_2#22_04103;eC_number=1.1.1.79;gene=ghrA;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_004729856.1,similar to AA sequence:UniProtKB:Q8ZQ30,protein motif:CLUSTERS:PRK15469,protein motif:Cdd:COG1932,protein motif:TIGRFAMs:TIGR01327,protein motif:Pfam:PF02826.13;locus_tag=22222_2#22_04103;product=2-hydroxyacid dehydrogenase,Glyoxylate/hydroxypyruvate reductase A,bifunctional glyoxylate/hydroxypyruvate reductase A,Phosphoserine aminotransferase,phosphoglycerate dehydrogenase,D-isomer specific 2-hydroxyacid dehydrogenase%2C NAD binding domain;protein_id=gnl|SC|22222_2#22_04103 ERS222222|SC|contig000020 Prodigal:2.60 CDS 50047 50784 . + 0 ID=22222_2#22_04104;eC_number=3.1.3.-;gene=ycdX;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_001570887.1,similar to AA sequence:UniProtKB:P75914,protein motif:CLUSTERS:PRK09248,protein motif:Cdd:COG1387,protein motif:TIGRFAMs:TIGR01856,protein motif:Pfam:PF02811.13;locus_tag=22222_2#22_04104;product=putative hydrolase,Probable phosphatase YcdX,putative hydrolase,Histidinol phosphatase and related hydrolases of the PHP family,histidinol phosphate phosphatase%2C HisJ family,PHP domain;protein_id=gnl|SC|22222_2#22_04104 ERS222222|SC|contig000020 Prodigal:2.60 CDS 50808 51362 . + 0 ID=22222_2#22_04105;gene=ycdY;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_002146908.1,similar to AA sequence:UniProtKB:P75915,protein motif:CLUSTERS:PRK11621,protein motif:Cdd:COG3381,protein motif:Pfam:PF02613.9;locus_tag=22222_2#22_04105;product=chaperone%2C TorD family,Chaperone protein YcdY,twin-argninine leader-binding protein DmsD,Uncharacterized component of anaerobic dehydrogenases,Nitrate reductase delta subunit;protein_id=gnl|SC|22222_2#22_04105 @@ -72,7 +72,7 @@ ERS222222|SC|contig000020 Prodigal:2.60 CDS 67715 68767 . + 0 ID=22222_2#22_04124;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_006087420.1,protein motif:CLUSTERS:PRK00142,protein motif:Cdd:COG2210,protein motif:Pfam:PF00581.14;locus_tag=22222_2#22_04124;product=Rhodanese-like sulfurtransferase,putative rhodanese-related sulfurtransferase,Uncharacterized conserved protein,Rhodanese-like domain;protein_id=gnl|SC|22222_2#22_04124 ERS222222|SC|contig000020 Prodigal:2.60 CDS 68819 69394 . - 0 ID=22222_2#22_04125;gene=yceI_2;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_006087865.1,similar to AA sequence:UniProtKB:P0A8X2,protein motif:CLUSTERS:PRK03757,protein motif:Cdd:COG2353,protein motif:Pfam:PF04264.7;locus_tag=22222_2#22_04125;product=YceI protein,hypothetical protein,hypothetical protein,Uncharacterized conserved protein,YceI-like domain;protein_id=gnl|SC|22222_2#22_04125 ERS222222|SC|contig000020 Prodigal:2.60 CDS 69391 69795 . - 0 ID=22222_2#22_04126;gene=yceJ;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_005212184.1,similar to AA sequence:UniProtKB:P75925,protein motif:CLUSTERS:PRK11513,protein motif:Pfam:PF00033.13;locus_tag=22222_2#22_04126;product=cytochrome b561-like protein 2,Cytochrome b561 homolog 2,cytochrome b561,Cytochrome b(N-terminal)/b6/petB;protein_id=gnl|SC|22222_2#22_04126 -ERS222222|SC|contig000020 Prodigal:2.60 CDS 70226 70339 . - 0 ID=22222_2#22_04127;gene=yceO;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_216094.1,similar to AA sequence:UniProtKB:P64442,protein motif:Pfam:PF10968.2;locus_tag=22222_2#22_04127;product=inner membrane protein,hypothetical protein,Protein of unknown function (DUF2770);protein_id=gnl|SC|22222_2#22_04127 +ERS222222|SC|contig000020 Prodigal:2.60 CDS 70226 70243 . - 0 ID=22222_2#22_04127;gene=yceO;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_216094.1,similar to AA sequence:UniProtKB:P64442,protein motif:Pfam:PF10968.2;locus_tag=22222_2#22_04127;product=inner membrane protein,hypothetical protein,Protein of unknown function (DUF2770);protein_id=gnl|SC|22222_2#22_04127 ERS222222|SC|contig000020 Prodigal:2.60 CDS 70380 71498 . - 0 ID=22222_2#22_04128;eC_number=1.5.3.1,1.5.3.-;gene=solA;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_004729880.1,similar to AA sequence:UniProtKB:P40874,protein motif:CLUSTERS:PRK11259,protein motif:Cdd:COG4121,protein motif:TIGRFAMs:TIGR01377,protein motif:Pfam:PF01266.18;locus_tag=22222_2#22_04128;product=sarcosine oxidase,N-methyl-L-tryptophan oxidase,N-methyltryptophan oxidase,Uncharacterized conserved protein,sarcosine oxidase%2C monomeric form,FAD dependent oxidoreductase;protein_id=gnl|SC|22222_2#22_04128 ERS222222|SC|contig000020 Prodigal:2.60 CDS 71611 71865 . - 0 ID=22222_2#22_04129;gene=bssS;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_001570863.1,protein motif:CLUSTERS:PRK12301;locus_tag=22222_2#22_04129;product=biofilm formation regulatory protein BssS,biofilm formation regulatory protein BssS;protein_id=gnl|SC|22222_2#22_04129 ERS222222|SC|contig000020 Prodigal:2.60 CDS 72155 72418 . - 0 ID=22222_2#22_04130;gene=dinI_3;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_004729882.1,similar to AA sequence:UniProtKB:P0ABR1,protein motif:CLUSTERS:PRK10597,protein motif:Pfam:PF06183.7;locus_tag=22222_2#22_04130;product=damage-inducible protein,DNA-damage-inducible protein I,DNA damage-inducible protein I,DinI-like family;protein_id=gnl|SC|22222_2#22_04130 @@ -98,7 +98,7 @@ ERS222222|SC|contig000020 Prodigal:2.60 CDS 88429 89379 . + 0 ID=22222_2#22_04150;eC_number=3.2.1.-;gene=flgJ;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_004729902.1,similar to AA sequence:UniProtKB:P15931,protein motif:CLUSTERS:PRK05684,protein motif:Cdd:COG3951,protein motif:TIGRFAMs:TIGR02541,protein motif:Pfam:PF01832.14;locus_tag=22222_2#22_04150;product=flagellar protein FlgJ,Peptidoglycan hydrolase flgJ,flagellar rod assembly protein/muramidase FlgJ,Rod binding protein,flagellar rod assembly protein/muramidase FlgJ,Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase;protein_id=gnl|SC|22222_2#22_04150 ERS222222|SC|contig000020 Prodigal:2.60 CDS 89444 91105 . + 0 ID=22222_2#22_04151;gene=flgK;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_004729903.1,similar to AA sequence:UniProtKB:P0A1J5,protein motif:CLUSTERS:PRK08147,protein motif:Cdd:COG1749,protein motif:TIGRFAMs:TIGR02492,protein motif:Pfam:PF06429.7;locus_tag=22222_2#22_04151;product=flagellar hook-associated protein 1,Flagellar hook-associated protein 1,flagellar hook-associated protein FlgK,Flagellar hook protein FlgE,flagellar hook-associated protein FlgK,Domain of unknown function (DUF1078);protein_id=gnl|SC|22222_2#22_04151 ERS222222|SC|contig000020 Prodigal:2.60 CDS 91120 92073 . + 0 ID=22222_2#22_04152;gene=flgL;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_004729904.1,similar to AA sequence:UniProtKB:P16326,protein motif:CLUSTERS:PRK08027,protein motif:Cdd:COG3951,protein motif:TIGRFAMs:TIGR02550,protein motif:Pfam:PF00669.14;locus_tag=22222_2#22_04152;product=flagellar hook-associated protein 3,Hook-filament junction protein,flagellar hook-associated protein FlgL,Rod binding protein,flagellar hook-associated protein 3,Bacterial flagellin N-terminal helical region;protein_id=gnl|SC|22222_2#22_04152 -ERS222222|SC|contig000020 Infernal:1.1 ncRNA 92162 92255 . + 0 ID=22222_2#22_04153;inference=COORDINATES:profile:Infernal:1.1;locus_tag=22222_2#22_04153;product=STnc490k +ERS222222|SC|contig000020 Infernal:1.1 ncRNA 92162 92179 . + 0 ID=22222_2#22_04153;inference=COORDINATES:profile:Infernal:1.1;locus_tag=22222_2#22_04153;product=STnc490k ##FASTA >ERS222222|SC|contig000020 TATCCGGGCAGCCCGTTTACGGGCCGTAAGTAACGAAGTTTGATGCAAATGTCAGATCGT