LOCUS       NZ_CP104520             2246 bp    DNA     circular CON 07-OCT-2023
DEFINITION  Escherichia coli strain E4 plasmid p4, complete sequence.
ACCESSION   NZ_CP104520
VERSION     NZ_CP104520.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN30789307
            Assembly: GCF_025369855.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2246)
  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  JOURNAL   Unpublished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 2246)
  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 07:13:46
            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)                     :: 5,178
            CDSs (total)                      :: 5,065
            Genes (coding)                    :: 4,771
            CDSs (with protein)               :: 4,771
            Genes (RNA)                       :: 113
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 294
            CDSs (without protein)            :: 294
            Pseudo Genes (ambiguous residues) :: 0 of 294
            Pseudo Genes (frameshifted)       :: 84 of 294
            Pseudo Genes (incomplete)         :: 206 of 294
            Pseudo Genes (internal stop)      :: 72 of 294
            Pseudo Genes (multiple problems)  :: 62 of 294
            Pseudo Genes (short protein)      :: 4 of 294
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP104520.1.
            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..2246
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="E4"
                     /isolation_source="Pullet"
                     /host="Poultry"
                     /db_xref="taxon:562"
                     /plasmid="p4"
                     /geo_loc_name="USA"
                     /collection_date="2017-05-30"
                     /collected_by="USDA"
     gene            join(1314..2246,1..57)
                     /locus_tag="N5O79_RS25775"
                     /old_locus_tag="N5O79_25775"
     CDS             join(1314..2246,1..57)
                     /locus_tag="N5O79_RS25775"
                     /old_locus_tag="N5O79_25775"
                     /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_065664479.1"
                     /translation="MKNPELQNLTDYSPSDAPWDAHRSVSDDVGGIYLLAAEYERYGAR
                     MASCGGLLRFGWSTLKETGETRLRLREAHFCRVRHCPVCQWRRSLMWQARFYQSLPRIV
                     ADYPDARWMLLTLTVRNCAIGELGETLNRMNAAFQRLKDRKEFRPVQGWIRTTEVTRGS
                     DGSAHPHFHTLMMVPPGMLNGKSYVRHECWVELWRECLRVDYDPNVDVRAVKPRKPKGG
                     ESLACATAELVRGAVAETLKYSTKPADMVADPEWFLELTRQTHKRRFVATGGALKDVLK
                     LDQETDADMVIGDDVSEGDDDGSRIAFEWKTEVRKYRRSPTKDKTESG"
                     /name="protein rep"
     gene            753..1007
                     /locus_tag="N5O79_RS25780"
                     /old_locus_tag="N5O79_25780"
     CDS             753..1007
                     /locus_tag="N5O79_RS25780"
                     /old_locus_tag="N5O79_25780"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_097743053.1"
                     /translation="MSRSAANHLRGGLKDLRMDMFLAHEIKFAVMRKRKHGCENNKPEI
                     YKNLLEVRVFFEVLERIDAVLSVAIPLLVLLRFLVVKRR"
                     /name="hypothetical protein"
     Typing          60..141
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.386"
                     /coverage="90.0"
                     /evalue="1.57e-30"
     Typing          complement(2030..2221)
                     /name="ColpVC"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.891"
                     /coverage="100.0"
                     /evalue="2.88e-86"
ORIGIN
        1 accgaggtca gaaagtaccg tcgctcaccg acgaaagata aaactgaatc aggctagcgg
       61 ggtgtcgggg cgaagccctg acctgatggt aattgtaata gcgtcgcgtg tgacggtatt
      121 acaattacac atcctgtccc gaaaattccc gccgtttctc ggttttttga gcatcgcaga
      181 tcgcacgaca aacgaaacga agtgaagttt gtataagtgc gcacttcgtg ggtgttctgt
      241 gccgccagtt tgtcgaatgc gtggcggagc tgcgcgacaa aaatggcaaa ataattcgct
      301 gtccgttcgc cagaattttg cacgaccgtg gtggctgcag gagcgcagaa cggcagaaaa
      361 atgccagcgt tccggcaaaa aaaatcggaa caagaaatcc ctgtgtttta ctccgatgca
      421 ggatagggca aacgccgcaa agtgacgtct ctgacgccat tccgcaacgt ttgcccggtg
      481 acctacagtc ggttcaacaa acaaaaaaac cgctgcggag tcgggacaag atacatcttt
      541 gtattaccgc cacacggtcg gtactccaaa catcctggtc agggctgcgc cccgacaccc
      601 ccgccaacgc ctcacggtac gcgaaaaatt ccgcgcaccc ctcaccgttc ccgaactcgt
      661 caaacagaaa atcgtggggt cccgcgcctc tggcgtgggt tccgattttg tgattgacga
      721 cggcacggga aaaacactgg ggatggtggt tggtgtcacg gagtgccgcc aaccacctgc
      781 gaggcggttt gaaagatctg cggatggata tgtttttagc gcatgaaatt aaattcgcag
      841 taatgcgaaa acgaaaacat gggtgcgaaa ataacaaacc agagatttat aaaaacttgt
      901 tggaggtgag ggtgtttttt gaggttcttg aacgcattga tgcggtgctt agcgttgcga
      961 tcccgcttct ggtgttattg cgtttcttgg ttgtgaaaag gcgctgattt ttgcgtttat
     1021 tttttgctca aatctcgcgc gcgatccttg tatttatact taagggataa ctctgggatt
     1081 caaattcgcc tccagccctt gtgccgcaag gcctgagtgg ggatttgtcg gaaaatggtt
     1141 ttggagttat tctgtcggga gtggtcgcat taaaagcgac ccccgcaacg agtggcatcg
     1201 ttcgggggtg tgaccacctg taggaattcg aattggtgat acgactaaca caacaggtga
     1261 tatggcaatg ataacacgtc aaatgagcca tcgcccacag ttgggtggtg tgcatgaaaa
     1321 atcctgaact ccagaacctc acggactatt ccccctcaga tgcgccctgg gacgctcaca
     1381 gaagcgtttc tgacgatgtg ggagggattt acctgcttgc ggccgaatat gagcgctacg
     1441 gggcgcgtat ggcctcctgt ggcggtttac tgcggttcgg gtggtctacc ctcaaggaaa
     1501 ccggagaaac gcgtctgagg ctgcgtgagg cgcatttctg ccgtgttcgg cactgtcctg
     1561 tctgccagtg gaggcgctcc ctgatgtggc aagcccgttt ctaccagtcc ctgccgcgta
     1621 tcgtggcgga ttatcctgat gcccgctgga tgctcctgac cctgaccgtg cgcaactgtg
     1681 cgatcgggga gttgggcgag acgctgaacc ggatgaacgc agctttccag cgactgaagg
     1741 atcgcaaaga gttccgacct gtgcagggct ggatacgtac cactgaagtc acccgcggca
     1801 gtgatggtag cgcacacccg cacttccaca ccctgatgat ggtgccgcct ggcatgctaa
     1861 atgggaaaag ttacgtcagg catgaatgct gggttgagtt gtggcgggag tgtctgcggg
     1921 tcgattatga cccgaatgtt gatgttcggg cagtgaaacc tcgtaagccg aagggcggcg
     1981 aatcgctggc ctgcgcgacc gccgaactgg tgcgcggcgc ggtggccgaa accctgaaat
     2041 attccacgaa gccggctgac atggtggccg atcctgaatg gttcctcgaa ctgacccgcc
     2101 agacacacaa gcgccgcttt gtggcgaccg gcggcgcact caaagacgta ctgaagctcg
     2161 atcaggaaac cgacgccgat atggtgatcg gggatgatgt ttccgagggc gatgatgacg
     2221 gttcacgcat cgcgttcgag tggaaa
//
