##gff-version 3 ##sequence-region NC_008255 1 8764 # conversion-by bp_genbank2gff3.pl # organism Cytophaga hutchinsonii ATCC 33406 # Note Cytophaga hutchinsonii ATCC 33406, complete sequence. # date 05-OCT-2022 NC_008255 GenBank region 1 8764 . + 1 ID=NC_008255;Dbxref=BioProject:PRJNA224116,taxon:269798;Name=NC_008255;Note=Cytophaga hutchinsonii ATCC 33406%2C complete sequence.,REFSEQ INFORMATION: The reference sequence is identical to CP000383.1. URL -- http://www.jgi.doe.gov JGI Project ID: 2351473 Source DNA and bacteria available from Mark McBride Contacts: Mark McBride (mcbride@uwm.edu) Paul Richardson (microbes@cuba.jgi-psf.org) Plasmid and fosmid libraries were prepared at the Joint Genome Institute (JGI) Production Genomics Facility (JGI-PGF) in Walnut Creek,CA. Shotgun sequencing was performed at the JGI-PGF to a coverage of 15x. Large (40 kb),medium (8 kb) and small (3 kb) insert random libraries were partially sequenced with average success rate of 90%25 and average high-quality read lengths of 634 nucleotides. Finishing was performed at JGI-LANL starting with 29 contigs and 2 scaffolds. Repetitive regions were identified,assembled and finished by manually checking paired reads close to each repeat in the assembly with consed and then making a subassembly for each repetitive region. 27 gaps were closed with primer walks and 2 by PCR. Gene predictions were obtained using Glimmer and tRNAs were identified using tRNAScan-SE. Basic analysis of the gene predictions was performed by comparing coding sequences against the PFam,BLOCKS and Prodom databases. Gene definitions and functional classes were added manually by a team of annotators at JGI-LANL,using BLAST results in addition to information from the basic analysis. A total of 3793 features have been annotated on the sequence record. 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 Date :: 10/05/2022 08:32:38\nAnnotation Pipeline :: NCBI Prokaryotic Genome\nAnnotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\nset,GeneMarkS-2+\nAnnotation Software revision :: 6.3\nFeatures Annotated :: Gene,CDS,rRNA,tRNA,ncRNA,\nrepeat_region\nGenes (total) :: 3,747\nCDSs (total) :: 3,696\nGenes (coding) :: 3,674\nCDSs (with protein) :: 3,674\nGenes (RNA) :: 51\nrRNAs :: 3,3,3 (5S,16S,23S)\ncomplete rRNAs :: 3,3,3 (5S,16S,23S)\ntRNAs :: 39\nncRNAs :: 3\nPseudo Genes (total) :: 22\nCDSs (without protein) :: 22\nPseudo Genes (ambiguous residues) :: 0 of 22\nPseudo Genes (frameshifted) :: 1 of 22\nPseudo Genes (incomplete) :: 18 of 22\nPseudo Genes (internal stop) :: 3 of 22\n##Genome-Annotation-Data-END##;comment1=REFSEQ INFORMATION: The reference sequence is identical to CP000383.1. URL -- http://www.jgi.doe.gov JGI Project ID: 2351473 Source DNA and bacteria available from Mark McBride Contacts: Mark McBride (mcbride@uwm.edu) Paul Richardson (microbes@cuba.jgi-psf.org) Plasmid and fosmid libraries were prepared at the Joint Genome Institute (JGI) Production Genomics Facility (JGI-PGF) in Walnut Creek%2C CA. Shotgun sequencing was performed at the JGI-PGF to a coverage of 15x. Large (40 kb)%2C medium (8 kb) and small (3 kb) insert random libraries were partially sequenced with average success rate of 90%25 and average high-quality read lengths of 634 nucleotides. Finishing was performed at JGI-LANL starting with 29 contigs and 2 scaffolds. Repetitive regions were identified%2C assembled and finished by manually checking paired reads close to each repeat in the assembly with consed and then making a subassembly for each repetitive region. 27 gaps were closed with primer walks and 2 by PCR. Gene predictions were obtained using Glimmer and tRNAs were identified using tRNAScan-SE. Basic analysis of the gene predictions was performed by comparing coding sequences against the PFam%2C BLOCKS and Prodom databases. Gene definitions and functional classes were added manually by a team of annotators at JGI-LANL%2C using BLAST results in addition to information from the basic analysis. A total of 3793 features have been annotated on the sequence record. 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 Date :: 10/05/2022 08:32:38\nAnnotation Pipeline :: NCBI Prokaryotic Genome\nAnnotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\nset%3B GeneMarkS-2+\nAnnotation Software revision :: 6.3\nFeatures Annotated :: Gene%3B CDS%3B rRNA%3B tRNA%3B ncRNA%3B\nrepeat_region\nGenes (total) :: 3%2C747\nCDSs (total) :: 3%2C696\nGenes (coding) :: 3%2C674\nCDSs (with protein) :: 3%2C674\nGenes (RNA) :: 51\nrRNAs :: 3%2C 3%2C 3 (5S%2C 16S%2C 23S)\ncomplete rRNAs :: 3%2C 3%2C 3 (5S%2C 16S%2C 23S)\ntRNAs :: 39\nncRNAs :: 3\nPseudo Genes (total) :: 22\nCDSs (without protein) :: 22\nPseudo Genes (ambiguous residues) :: 0 of 22\nPseudo Genes (frameshifted) :: 1 of 22\nPseudo Genes (incomplete) :: 18 of 22\nPseudo Genes (internal stop) :: 3 of 22\n##Genome-Annotation-Data-END##;culture_collection=ATCC:33406;date=05-OCT-2022;mol_type=genomic DNA;organism=Cytophaga hutchinsonii ATCC 33406;strain=ATCC 33406;type_material=type strain of Cytophaga hutchinsonii NC_008255 GenBank gene 1 1617 . - 1 ID=CHU_RS04470;Name=CHU_RS04470;old_locus_tag=CHU_0919 NC_008255 GenBank mRNA 1 1617 . - 1 ID=CHU_RS04470.t01;Parent=CHU_RS04470 NC_008255 GenBank CDS 1 1617 . - 1 ID=CHU_RS04470;Parent=CHU_RS04470.t01;Name=CHU_RS04470;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_018343001.1;old_locus_tag=CHU_0919;product=hypothetical protein;protein_id=WP_011584315.1;transl_table=11;translation=length.538 NC_008255 GenBank exon 1 1617 . - 1 Parent=CHU_RS04470.t01 NC_008255 GenBank gene 1607 2143 . - 1 ID=CHU_RS18795;Name=CHU_RS18795 NC_008255 GenBank mRNA 1607 2143 . - 1 ID=CHU_RS18795.t01;Parent=CHU_RS18795 NC_008255 GenBank CDS 1607 2143 . - 1 ID=CHU_RS18795;Parent=CHU_RS18795.t01;Name=CHU_RS18795;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: protein motif:HMM:NF014453.2;product=sugar transferase;protein_id=WP_177254166.1;transl_table=11;translation=length.178 NC_008255 GenBank exon 1607 2143 . - 1 Parent=CHU_RS18795.t01 NC_008255 GenBank gene 2046 2852 . - 1 ID=CHU_RS04475;Name=CHU_RS04475 NC_008255 GenBank mRNA 2046 2852 . - 1 ID=CHU_RS04475.t01;Parent=CHU_RS04475 NC_008255 GenBank CDS 2046 2852 . - 1 ID=CHU_RS04475;Parent=CHU_RS04475.t01;Name=CHU_RS04475;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: protein motif:HMM:NF025104.2;product=hypothetical protein;protein_id=WP_177254165.1;transl_table=11;translation=length.268 NC_008255 GenBank exon 2046 2852 . - 1 Parent=CHU_RS04475.t01 NC_008255 GenBank gene 3084 5276 . - 1 ID=CHU_RS04480;Name=CHU_RS04480;old_locus_tag=CHU_0922 NC_008255 GenBank mRNA 3084 5276 . - 1 ID=CHU_RS04480.t01;Parent=CHU_RS04480 NC_008255 GenBank CDS 3084 5276 . - 1 ID=CHU_RS04480;Parent=CHU_RS04480.t01;Name=CHU_RS04480;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: protein motif:HMM:TIGR04183.1;old_locus_tag=CHU_0922;product=T9SS type A sorting domain-containing protein;protein_id=WP_011584316.1;transl_table=11;translation=length.730 NC_008255 GenBank exon 3084 5276 . - 1 Parent=CHU_RS04480.t01 NC_008255 GenBank gene 5293 6069 . - 1 ID=CHU_RS04485;Name=CHU_RS04485;old_locus_tag=CHU_0923 NC_008255 GenBank mRNA 5293 6069 . - 1 ID=CHU_RS04485.t01;Parent=CHU_RS04485 NC_008255 GenBank CDS 5293 6069 . - 1 ID=CHU_RS04485;Parent=CHU_RS04485.t01;Name=CHU_RS04485;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_018342998.1;old_locus_tag=CHU_0923;product=PASTA domain-containing protein;protein_id=WP_011584317.1;transl_table=11;translation=length.258 NC_008255 GenBank exon 5293 6069 . - 1 Parent=CHU_RS04485.t01 NC_008255 GenBank gene 6071 8764 . - 1 ID=CHU_RS04490;Name=CHU_RS04490;old_locus_tag=CHU_0924 NC_008255 GenBank mRNA 6071 8764 . - 1 ID=CHU_RS04490.t01;Parent=CHU_RS04490 NC_008255 GenBank CDS 6071 8764 . - 1 ID=CHU_RS04490;Parent=CHU_RS04490.t01;eC_number=6.3.2.4;Name=CHU_RS04490;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_018342997.1;old_locus_tag=CHU_0924;product=D-alanine--D-alanine ligase;protein_id=WP_011584318.1;transl_table=11;translation=length.897 NC_008255 GenBank exon 6071 8764 . - 1 Parent=CHU_RS04490.t01