LOCUS       NZ_CP104514             2096 bp    DNA     circular CON 06-OCT-2023
DEFINITION  Escherichia coli strain E2 plasmid p5, complete sequence.
ACCESSION   NZ_CP104514
VERSION     NZ_CP104514.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN30789305
            Assembly: GCF_025369675.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2096)
  AUTHORS   Feng,A., Leigh,S.A., Akter,S., Wang,H., Pharr,T.G., Evans,J.,
            Branton,S.L., Landinez,M.P., Pace,L. and Wan,X.-F.
  TITLE     Genomic Diversity, Pathogenicity and Antimicrobial Resistance of
            Escherichia coli Isolated from Poultry in the Southern United States
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2096)
  AUTHORS   Leigh,S.A.
  TITLE     Direct Submission
  JOURNAL   Submitted (10-SEP-2022) Bond Life Science Center, University of
            Missouri, University of Missouri, Columbia, MO 65201-8522, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.9b
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100%x
            Sequencing Technology             :: Oxford Nanopore; Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 10/06/2023 04:07:46
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,557
            CDSs (total)                      :: 5,428
            Genes (coding)                    :: 5,107
            CDSs (with protein)               :: 5,107
            Genes (RNA)                       :: 129
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 96
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 321
            CDSs (without protein)            :: 321
            Pseudo Genes (ambiguous residues) :: 0 of 321
            Pseudo Genes (frameshifted)       :: 87 of 321
            Pseudo Genes (incomplete)         :: 239 of 321
            Pseudo Genes (internal stop)      :: 48 of 321
            Pseudo Genes (multiple problems)  :: 47 of 321
            Pseudo Genes (short protein)      :: 4 of 321
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP104514.1.
            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..2096
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="E2"
                     /isolation_source="Backyard chicken"
                     /host="Poultry"
                     /db_xref="taxon:562"
                     /plasmid="p5"
                     /geo_loc_name="USA"
                     /collection_date="2017-05-25"
                     /collected_by="USDA"
     gene            complement(417..1406)
                     /locus_tag="N5O74_RS27620"
                     /old_locus_tag="N5O74_27620"
     CDS             complement(417..1406)
                     /locus_tag="N5O74_RS27620"
                     /old_locus_tag="N5O74_27620"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001362017.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_064079801.1"
                     /translation="MKNPDLQNLTDYSPSDAPWDAHRSVSDDVGGIYLLAAEYERYGAR
                     MALCGGLLRFGWSTLKETGETRLRLREAHFCRVRHCPVCQWRRSLMWQARFYQSLPRIV
                     ADYPDARWMFLTLTVRNCAIGELGEMLNRMNAAFQRMKVRKEFRPVQGWIRTTEVTRGS
                     DGSAHPHFHTLMMVPPGMLNGKSYVRHERWVELWRECLRVDYDPNVDVRAVKPRKPKGG
                     ESLACATAELVRGAVTETLKYSTKPADMVADPEWFLELTRQTHKRRFVATGGALKDVLK
                     LDQETDADMVIGDDISEGDDDGSRIAFEWKTEVRKYRRSPTKDKTESG"
                     /name="protein rep"
     Typing          complement(334..415)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="93.976"
                     /coverage="90.0"
                     /evalue="3.4000000000000004e-27"
     Typing          500..691
                     /name="ColpVC"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.964"
                     /coverage="100.0"
                     /evalue="6.14e-93"
ORIGIN
        1 tatcgtgcct gtgttttagg agaacaaaaa aatgccgtgc atacagccca cacaatgacc
       61 cacataatca cccacaactc aaaacacaca gcccacacaa tcacccacac tttaacccac
      121 aaaaaagacc acaaccccat tgacacccca caaaacaacc cacacaaacg gcgagtaaat
      181 cattttgccg ttttcgtgcc gcagccgttc cgcgcaatcg acaaactggc agtcagggaa
      241 tctcacgaag tgcgcactta tacaaactca ccttaggttc gtttgtcgtg cggtctgcga
      301 cgctcaaaaa accgagaaac ggcgggaatt ttcgggacag gatgtgtaat tgtaataccg
      361 tcacacgcga cgctatcaca attgccatct ggtcaggggt gcaccccgac accccgctag
      421 cctgattcag ttttatcttt cgtcggtgag cgacggtact ttctgacctc ggttttccac
      481 tcgaacgcga ttcgtgaacc gtcatcgtcg ccctcggaaa tatcatcacc gatcaccatg
      541 tcggcgtcag tttcctgatc gagtttcagc acgtctttga gtgcgccgcc ggtcgccaca
      601 aagcggcgct tgtgcgtctg gcgggtcagt tcgaggaacc attcaggatc ggccaccatg
      661 tcagccggct tcgtggaata tttcagggtt tcggtcaccg caccgcgcac cagttcggcg
      721 gtcgcgcagg ccagcgattc gccgcccttc ggcttacgag gtttcactgc ccggacatca
      781 acattcgggt cataatcgac ccgcagacac tcccgccaga gttcaaccca gcgttcatgc
      841 ctgacgtaac ttttcccatt tagcatgcca ggcggcacca tcatcagggt gtggaagtgc
      901 gggtgtgcgc tgccgtcgct cccgcgggtg acttccgtgg tacgtatcca gccctgcaca
      961 ggccggaact ccttgcgaac cttcatgcgc tgaaaagctg cattcatccg gttcagcatc
     1021 tcgcccagct ccccgatcgc acagttgcgc acggtcagag tcaggaacat ccagcgggca
     1081 tcgggataat ccgccacgat acgcggcagg gactggtaga aacgggcttg ccacatcagg
     1141 gagcgcctcc actggcagac aggacaatgc cggacacggc agaaatgcgc ctcacgcagc
     1201 ctcagacgcg tttctccggt ttccttgagg gtagaccacc cgaaacgcag taaaccacca
     1261 cagagggcca tacgcgcccc gtagcgctca tattcggctg caagcaggta aatccctccc
     1321 acgtcatcag aaacgcttct gtgagcgtcc cagggcgcat ctgaggggga atagtccgtg
     1381 aggttctgga gatcagggtt tttcatgcgc accacccgat agtgggcgat ggctcatctg
     1441 acgtgttatc attgccatat cacctgttgt gttagtcgta tcaccaattc gaattcctac
     1501 aggtggtcac acccccgaac gattgccctc gttgcggggg tcgcttttaa tgcgaccact
     1561 cccgacagaa taactccaaa accattttcc gacaaatccc ccttcaggcc ttgcggcaca
     1621 agggctggag gcgaatttga atcctagagt tatcccttaa gtataaatac aaggatcgcg
     1681 cgcgagattc gcttgaattt tgagcgggat tttcagtcac ccaaaacacc caaccccacc
     1741 cacttacacc cgtctcatcc acagactttc accccgattt tgtgaacaac aaaaaaaacc
     1801 gtcttgcagg tggttggcct cactgcgtga caccaaccac catccccagt gtttttcccg
     1861 tgccgtcgtc aatcacaaaa tcggaaccca cgccggaggc gcgggccccc gcgattttct
     1921 gtttgacgaa tcagggaacg gtgaacggta cgcggaattt tttcgcgttc cgtgaggcgt
     1981 tggcggggtg tcggggcgca gtcctgacca ggttcgtaga accgcacagg gttgcaaagg
     2041 ggtgtcccct ttggcacaag cgacggagcg aaacgccccg ttttgtgtac gccgct
//
