##gff-version 3 ##sequence-region NC_010655 1 7429 # conversion-by bp_genbank2gff3.pl # organism Akkermansia muciniphila ATCC BAA-835 # Note Akkermansia muciniphila ATCC BAA-835, complete sequence. # date 05-MAY-2024 NC_010655 GenBank region 1 7429 . + 1 ID=NC_010655;Dbxref=BioProject:PRJNA224116,taxon:349741;Name=NC_010655;Note=Akkermansia muciniphila ATCC BAA-835%2C complete sequence.,REFSEQ INFORMATION: The reference sequence is identical to CP001071.1. URL -- http://www.jgi.doe.gov JGI Project ID: 4001612 Source DNA available from Hauke Smidt (Hauke.Smidt@wur.nl) Bacteria available from ATCC: ATCC BAA-835 Contacts: Hauke Smidt (Hauke.Smidt@wur.nl) David Bruce (microbes@cuba.jgi-psf.org) Quality assurance done by JGI-Stanford Annotation done by JGI-ORNL and JGI-PGF Finishing done by JGI-LLNL Finished microbial genomes have been curated to close all gaps with greater than 98%25 coverage of at least two independent clones. Each base pair has a minimum q (quality) value of 30 and the total error rate is less than one per 50000. The JGI and collaborators endorse the principles for the distribution and use of large scale sequencing data adopted by the larger genome sequencing community and urge users of this data to follow them. it is our intention to publish the work of this project in a timely fashion and we welcome collaborative interaction on the project and analysis. (http://www.genome.gov/page.cfm?pageID%3D10506376). The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ \n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Name :: GCF_000020225.1-RS_2024_05_05\nAnnotation Date :: 05/05/2024 14:20:20\nAnnotation Pipeline :: NCBI Prokaryotic Genome\nAnnotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\nset,GeneMarkS-2+\nAnnotation Software revision :: 6.7\nFeatures Annotated :: Gene,CDS,rRNA,tRNA,ncRNA\nGenes (total) :: 2,212\nCDSs (total) :: 2,148\nGenes (coding) :: 2,136\nCDSs (with protein) :: 2,136\nGenes (RNA) :: 64\nrRNAs :: 3,3,3 (5S,16S,23S)\ncomplete rRNAs :: 3,3,3 (5S,16S,23S)\ntRNAs :: 52\nncRNAs :: 3\nPseudo Genes (total) :: 12\nCDSs (without protein) :: 12\nPseudo Genes (ambiguous residues) :: 0 of 12\nPseudo Genes (frameshifted) :: 4 of 12\nPseudo Genes (incomplete) :: 9 of 12\nPseudo Genes (internal stop) :: 0 of 12\nPseudo Genes (multiple problems) :: 1 of 12\nCRISPR Arrays :: 2\n##Genome-Annotation-Data-END##;comment1=REFSEQ INFORMATION: The reference sequence is identical to CP001071.1. URL -- http://www.jgi.doe.gov JGI Project ID: 4001612 Source DNA available from Hauke Smidt (Hauke.Smidt@wur.nl) Bacteria available from ATCC: ATCC BAA-835 Contacts: Hauke Smidt (Hauke.Smidt@wur.nl) David Bruce (microbes@cuba.jgi-psf.org) Quality assurance done by JGI-Stanford Annotation done by JGI-ORNL and JGI-PGF Finishing done by JGI-LLNL Finished microbial genomes have been curated to close all gaps with greater than 98%25 coverage of at least two independent clones. Each base pair has a minimum q (quality) value of 30 and the total error rate is less than one per 50000. The JGI and collaborators endorse the principles for the distribution and use of large scale sequencing data adopted by the larger genome sequencing community and urge users of this data to follow them. it is our intention to publish the work of this project in a timely fashion and we welcome collaborative interaction on the project and analysis. (http://www.genome.gov/page.cfm?pageID%3D10506376). The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ \n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Name :: GCF_000020225.1-RS_2024_05_05\nAnnotation Date :: 05/05/2024 14:20:20\nAnnotation Pipeline :: NCBI Prokaryotic Genome\nAnnotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\nset%3B GeneMarkS-2+\nAnnotation Software revision :: 6.7\nFeatures Annotated :: Gene%3B CDS%3B rRNA%3B tRNA%3B ncRNA\nGenes (total) :: 2%2C212\nCDSs (total) :: 2%2C148\nGenes (coding) :: 2%2C136\nCDSs (with protein) :: 2%2C136\nGenes (RNA) :: 64\nrRNAs :: 3%2C 3%2C 3 (5S%2C 16S%2C 23S)\ncomplete rRNAs :: 3%2C 3%2C 3 (5S%2C 16S%2C 23S)\ntRNAs :: 52\nncRNAs :: 3\nPseudo Genes (total) :: 12\nCDSs (without protein) :: 12\nPseudo Genes (ambiguous residues) :: 0 of 12\nPseudo Genes (frameshifted) :: 4 of 12\nPseudo Genes (incomplete) :: 9 of 12\nPseudo Genes (internal stop) :: 0 of 12\nPseudo Genes (multiple problems) :: 1 of 12\nCRISPR Arrays :: 2\n##Genome-Annotation-Data-END##;culture_collection=ATCC:BAA-835;date=05-MAY-2024;mol_type=genomic DNA;organism=Akkermansia muciniphila ATCC BAA-835;strain=ATCC BAA-835;type_material=type strain of Akkermansia muciniphila NC_010655 GenBank gene 1 2724 . - 1 ID=AMUC_RS05890;Name=AMUC_RS05890;old_locus_tag=Amuc_1098 NC_010655 GenBank mRNA 1 2724 . - 1 ID=AMUC_RS05890;Parent=AMUC_RS05890 NC_010655 GenBank CDS 1 2724 . - 1 ID=AMUC_RS05890;Parent=AMUC_RS05890;Name=AMUC_RS05890;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: protein motif:HMM:NF042912.1;old_locus_tag=Amuc_1098;product=Amuc_1098 family type IV pilus outer membrane protein;protein_id=WP_012420139.1;transl_table=11;translation=length.907 NC_010655 GenBank exon 1 2724 . - 1 Parent=AMUC_RS05890 NC_010655 GenBank gene 2796 3809 . - 1 ID=AMUC_RS05895;Name=AMUC_RS05895;old_locus_tag=Amuc_1099 NC_010655 GenBank mRNA 2796 3809 . - 1 ID=AMUC_RS05895;Parent=AMUC_RS05895 NC_010655 GenBank CDS 2796 3809 . - 1 ID=AMUC_RS05895;Parent=AMUC_RS05895;Name=AMUC_RS05895;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: protein motif:HMM:NF042425.1;old_locus_tag=Amuc_1099;product=Amuc_1099 family pilus-like system protein;protein_id=WP_012420140.1;transl_table=11;translation=length.337 NC_010655 GenBank exon 2796 3809 . - 1 Parent=AMUC_RS05895 NC_010655 GenBank gene 3845 4798 . - 1 ID=AMUC_RS12805;Name=AMUC_RS12805;old_locus_tag=Amuc_1100 NC_010655 GenBank mRNA 3845 4798 . - 1 ID=AMUC_RS12805;Parent=AMUC_RS12805 NC_010655 GenBank CDS 3845 4798 . - 1 ID=AMUC_RS12805;Parent=AMUC_RS12805;Name=AMUC_RS12805;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: protein motif:HMM:NF038287.2;old_locus_tag=Amuc_1100;product=Amuc_1100 family pilus-like protein;protein_id=WP_012420141.1;transl_table=11;translation=length.317 NC_010655 GenBank exon 3845 4798 . - 1 Parent=AMUC_RS12805 NC_010655 GenBank gene 4828 6666 . - 1 ID=AMUC_RS05905;Name=AMUC_RS05905;old_locus_tag=Amuc_1101 NC_010655 GenBank mRNA 4828 6666 . - 1 ID=AMUC_RS05905;Parent=AMUC_RS05905 NC_010655 GenBank CDS 4828 6666 . - 1 ID=AMUC_RS05905;Parent=AMUC_RS05905;Name=AMUC_RS05905;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: protein motif:HMM:NF045709.1;old_locus_tag=Amuc_1101;product=Amuc_1101 family PilM-like pilus complex protein;protein_id=WP_081429135.1;transl_table=11;translation=length.612 NC_010655 GenBank exon 4828 6666 . - 1 Parent=AMUC_RS05905 NC_010655 GenBank gene 6713 7429 . - 1 ID=AMUC_RS05910;Name=AMUC_RS05910;old_locus_tag=Amuc_1102 NC_010655 GenBank mRNA 6713 7429 . - 1 ID=AMUC_RS05910;Parent=AMUC_RS05910 NC_010655 GenBank CDS 6713 7429 . - 1 ID=AMUC_RS05910;Parent=AMUC_RS05910;Name=AMUC_RS05910;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_012420143.1;old_locus_tag=Amuc_1102;product=Amuc_1102 family pilus-like protein;protein_id=WP_012420143.1;transl_table=11;translation=length.238 NC_010655 GenBank exon 6713 7429 . - 1 Parent=AMUC_RS05910