LOCUS       NZ_CP104538             2096 bp    DNA     circular CON 07-OCT-2023
DEFINITION  Escherichia coli strain E3 plasmid p2, complete sequence.
ACCESSION   NZ_CP104538
VERSION     NZ_CP104538.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN30789306
            Assembly: GCF_025369835.1
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  JOURNAL   Unpublished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                   :: 10/07/2023 07:23:06
            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)                     :: 4,690
            CDSs (total)                      :: 4,572
            Genes (coding)                    :: 4,359
            CDSs (with protein)               :: 4,359
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 213
            CDSs (without protein)            :: 213
            Pseudo Genes (ambiguous residues) :: 0 of 213
            Pseudo Genes (frameshifted)       :: 69 of 213
            Pseudo Genes (incomplete)         :: 136 of 213
            Pseudo Genes (internal stop)      :: 39 of 213
            Pseudo Genes (multiple problems)  :: 33 of 213
            Pseudo Genes (short protein)      :: 4 of 213
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP104538.1.
            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="E3"
                     /isolation_source="Broiler"
                     /host="Poultry"
                     /db_xref="taxon:562"
                     /plasmid="p2"
                     /geo_loc_name="USA"
                     /collection_date="2017-05-23"
                     /collected_by="USDA"
     gene            join(1796..2096,1..689)
                     /locus_tag="N5O72_RS23335"
                     /old_locus_tag="N5O72_23335"
     CDS             join(1796..2096,1..689)
                     /locus_tag="N5O72_RS23335"
                     /old_locus_tag="N5O72_23335"
                     /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_001362017.1"
                     /translation="MKNPDLQNLTDYSPSDAPWDAHRSVSDDVGGIYLLAAEYERYGAR
                     MALCGGLLRFGWSTLKETGETRLRLREAHFCRVRHCPVCQWRRSLMWQARFYQSLPRIV
                     ADYPDARWMFLTLTVRNCAIGELGEMLNRMNAAFQRMKVRKEFRPVQGWIRTTEVTRGS
                     DGSAHPHFHTLMMVPPGMLNGKSYVRHERWVELWRECLRVDYDPNVDVRAVKPRKPKDG
                     ESLACATAELVRGAVAETLKYSTKPADMVADPEWFLELTRQTHKRRFVATGGALKDVLK
                     LDQETDADMVIGDDISEGDDDGSRIAFEWKTEVRKYRRSPTKDKTESG"
                     /name="protein rep"
     Typing          692..773
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="93.976"
                     /coverage="90.0"
                     /evalue="3.4000000000000004e-27"
     Typing          complement(416..607)
                     /name="ColpVC"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.964"
                     /coverage="100.0"
                     /evalue="6.14e-93"
ORIGIN
        1 cgcgtatcgt ggcggattat cccgatgccc gctggatgtt cctgactctg accgtgcgca
       61 actgtgcgat cggggagctg ggcgagatgc tgaaccggat gaatgcagct tttcagcgca
      121 tgaaggttcg caaggagttc cggcctgtgc agggctggat acgtaccacg gaagtcaccc
      181 gcgggagcga cggcagcgca cacccgcact tccacaccct gatgatggtg ccgcctggca
      241 tgctaaatgg gaaaagttac gtcaggcatg aacgctgggt tgaactctgg cgggagtgtc
      301 tgcgggtcga ttatgacccg aatgttgatg tccgggcagt gaaacctcgt aagccgaagg
      361 acggcgaatc gctggcctgc gcgaccgccg aactggtgcg cggtgcggtg gccgaaaccc
      421 tgaaatattc cacgaagccg gctgacatgg tggccgatcc tgaatggttc ctcgaactga
      481 ctcgccagac gcacaaacgc cgctttgtgg cgaccggcgg cgcactcaaa gacgtgctga
      541 aactcgatca ggaaaccgac gccgacatgg tgatcgggga tgatatttcc gagggcgacg
      601 atgacggttc acgcatcgcg ttcgagtgga aaaccgaggt cagaaagtac cgtcgctcac
      661 cgacgaaaga taaaactgaa tcaggctagc ggggtgtcgg ggtgcacccc tgaccagatg
      721 gcaattgtga tagcgtcgcg tgtgacggta ttacaattac acatcctgtc ccgaaaattc
      781 ccgccgtttc tcggtttttt gagcgtcgca gaccgcacga caaacgaacc taaggtgagt
      841 ttgtataagt gcgcacttcg tgagattccc tgactgccag tttgtcgatt gcgcggaacg
      901 gctgcggcac gaaaacggca aaatgattta ctcgccgttt gtgtgggttg ttttgtgggg
      961 tgtcaatggg gttgtggtct tttttgtggg ttaaagtgtg ggtgattgtg tgggctgtgt
     1021 gttttgagtt gtgggtgatt atgtgggtca ttgtgtgggc tgtatgcacg gcattttttt
     1081 gttctcctaa aacacaggca cgataagcgg cgtacacaaa acggggcgtt tcgctccgtc
     1141 gcttgtgcca aaggggacac ccctttgcaa ccctgtgcgg ttctacgaac caggtcagga
     1201 ctgcgccccg acaccccgcc aacgcctcac ggaacgcgaa aaaattccgc gtaccgttca
     1261 ccgttccctg attcgtcaaa cagaaaatcg cgggggcccg cgcctccggc gtgggttccg
     1321 attttgtgat tgacgacggc acgggaaaaa cactggggat ggtggttggt gtcacggagt
     1381 gaggccaacc acctgcaaga cggttttttt tgttgttcac aaaatcgggg tgaaagtctg
     1441 tggatgagat gggtgtaagt gggtggggtt gggtgttttg ggttactgaa aatcccgctc
     1501 aaaattcaag cgaatctcgc gcgcgatcct tgtatttata cttaagggat aactctagga
     1561 ttcaaattcg cctccagccc ttgtgccgca aggcctgaag ggggatttgt cggaaaatgg
     1621 ttttggagtt attctgtcgg gagtggtcgc attaaaagcg acccccgcaa cgagggcaat
     1681 cgttcggggg tgtgaccacc tgtaggaatt cgaattggtg atacgactaa cacaacaggt
     1741 gatatggcaa tgataacacg tcagatgagc catcgcccac tatcgggtgg tgcgcatgaa
     1801 aaaccctgat ctccagaacc tcacggacta ttccccctca gatgcgccct gggacgctca
     1861 cagaagcgtt tctgatgacg tgggagggat ttacctgctt gcagccgaat atgagcgcta
     1921 cggggcgcgt atggccctct gtggtggttt actgcgtttc gggtggtcta ccctcaagga
     1981 aaccggagaa acgcgtctga ggctgcgtga ggcgcatttc tgccgtgtcc ggcattgtcc
     2041 tgtctgccag tggaggcgct ccctgatgtg gcaagcccgt ttctaccagt ccctgc
//
