LOCUS       NZ_CP059912             1079 bp    DNA     circular CON 14-JUN-2023
DEFINITION  Escherichia coli strain 181.1 plasmid p5, complete sequence.
ACCESSION   NZ_CP059912
VERSION     NZ_CP059912.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13613900
            Assembly: GCF_014170615.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 1079)
  AUTHORS   Moffat,J., Chalmers,G., Reid-Smith,R., Mulvey,M., Aguno,A.,
            Calvert,J., Cormier,A., Ricker,N. and Boerlin,P.
  TITLE     Direct Submission
  JOURNAL   Submitted (17-DEC-2019) Pathobiology, University of Guelph, 50 Stone
            Road E, Guelph, Ontario N1G 2W1, Canada
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.4
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 17.8x
            Sequencing Technology             :: Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/14/2023 05:45:49
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,554
            CDSs (total)                      :: 5,429
            Genes (coding)                    :: 5,160
            CDSs (with protein)               :: 5,160
            Genes (RNA)                       :: 125
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 92
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 269
            CDSs (without protein)            :: 269
            Pseudo Genes (ambiguous residues) :: 1 of 269
            Pseudo Genes (frameshifted)       :: 114 of 269
            Pseudo Genes (incomplete)         :: 181 of 269
            Pseudo Genes (internal stop)      :: 51 of 269
            Pseudo Genes (multiple problems)  :: 64 of 269
            Pseudo Genes (short protein)      :: 4 of 269
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP059912.1.
            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/
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..1079
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="181.1"
                     /host="Turkey"
                     /db_xref="taxon:562"
                     /plasmid="p5"
                     /geo_loc_name="Canada"
                     /collection_date="2016/2017"
     gene            complement(join(<1073..1079,1..197))
                     /locus_tag="H5C80_RS27410"
                     /old_locus_tag="H5C80_27410"
                     /pseudo=""
     CDS             complement(join(<1073..1079,1..197))
                     /locus_tag="H5C80_RS27410"
                     /old_locus_tag="H5C80_27410"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_416072.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="lysozyme"
                     /name="lysozyme"
     gene            complement(194..505)
                     /locus_tag="H5C80_RS27415"
                     /old_locus_tag="H5C80_27415"
     CDS             complement(194..505)
                     /locus_tag="H5C80_RS27415"
                     /old_locus_tag="H5C80_27415"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_416073.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="YdfR family protein"
                     /protein_id="WP_000189916.1"
                     /translation="MTQDYELVVKGVRNFENKVTVTVALQDKERFDGEIFDLDVAMDRV
                     EGAALEFYEAAARRSVRQVFLEVAEKLSEKVESYLQHQYSFKIENPANKHERPHHKYL"
                     /name="YdfR family protein"
     gene            complement(510..725)
                     /gene="essD"
                     /locus_tag="H5C80_RS27420"
                     /old_locus_tag="H5C80_27420"
     CDS             complement(510..725)
                     /gene="essD"
                     /locus_tag="H5C80_RS27420"
                     /old_locus_tag="H5C80_27420"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_416074.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="phage lysis protein EssD"
                     /protein_id="WP_000839590.1"
                     /translation="MKSMDKLTTGVAYGTSAGNAGFWALQLLDKVTPSQWAAIGVLGSL
                     VFGLLTYLTNLYFKIKEDRRKAARGE"
                     /name="essD"
     gene            945..>1079
                     /gene="ynfU"
                     /locus_tag="H5C80_RS27565"
                     /pseudo=""
     CDS             945..>1079
                     /gene="ynfU"
                     /locus_tag="H5C80_RS27565"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_010051186.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="putative zinc-binding protein YnfU"
                     /name="ynfU"
ORIGIN
        1 ttgggaaaaa cggtttttcc atccaccact gtggcacccc gacagatggt ccatatgcca
       61 gaaccatcgc ggtatgccat tgtgtggtta ccttcttttt cgtccagaaa ctggtcaagt
      121 atctgaggag cagatgcgcc agcaccaatc agcgccagaa cggcagccga caggccgtat
      181 ctgatttttg tgttcataga tatttatgat gaggacgctc gtgcttattg gcaggatttt
      241 caatcttaaa ggagtactga tgctgcagat aagactcaac tttttctgac aatttttctg
      301 ctacttccag gaagacttgc cggacgctcc ttctggctgc tgcctcataa aactccagcg
      361 cagctccttc aacacggtcc atggcgacat ccaggtcaaa aatttcaccg tcaaagcgtt
      421 ctttgtcctg taaggctaca gttaccgtaa ctttattctc aaaattacgg actcctttca
      481 caaccagttc atagtcttga gtcattggat tactctcctc tcgcagcctt acgcctgtct
      541 tctttaatct tgaaataaag atttgtcaga tacgtcagca ggccaaaaac caggctaccc
      601 agcacaccga ttgcagccca ctgtgacgga gttactttat cgagtaactg caatgcccag
      661 aaaccagcat tacccgccga tgtgccatag gcaacacctg ttgttaactt atccattgat
      721 ttcatatcct caccccgatg tacacggatg gtgcaatatg tttgaaaaga tcggagtcta
      781 cggggtagtt ttgacagcac acgttgttct caacggcgct aaagaaacat acacattaaa
      841 aatgtgagta attattttga aagaaagtca tatataaaat aataatacga gaaatgtttt
      901 catatttagt gtactgtata cggccattta tacaggaaaa gcctatgtca gaacgtaaag
      961 actcaaaatc acgccgtaat tatctcgtta aatgttcctg cccaaactgc acccaagagt
     1021 cagaacacag tttttcaaga gtacaaaaag gtgccctttt gatctgccct cattgcaac
//
