LOCUS       NZ_CP050039             2389 bp    DNA     circular CON 14-JUN-2023
DEFINITION  Escherichia coli strain 58-3 plasmid pCD58-3-3, complete sequence.
ACCESSION   NZ_CP050039
VERSION     NZ_CP050039.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14278029
            Assembly: GCF_014075795.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2389)
  AUTHORS   Lv,H. and Cui,Q.
  TITLE     Identification of novel plasmids containing the tigecycline
            resistance gene tet(X4) in Escherichia coli isolated from retail
            chicken meat
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2389)
  AUTHORS   Lv,H. and Cui,Q.
  TITLE     Direct Submission
  JOURNAL   Submitted (10-MAR-2020) College of Veterinary Medicine, China
            Agricutural University, Yuanmingyuan West Road, Beijing 100000,
            China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.3.4
            Genome Representation             :: Full
            Expected Final Version            :: No
            Genome Coverage                   :: 100x
            Sequencing Technology             :: Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/14/2023 04:52:48
            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)                     :: 4,613
            CDSs (total)                      :: 4,495
            Genes (coding)                    :: 4,275
            CDSs (with protein)               :: 4,275
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 220
            CDSs (without protein)            :: 220
            Pseudo Genes (ambiguous residues) :: 0 of 220
            Pseudo Genes (frameshifted)       :: 49 of 220
            Pseudo Genes (incomplete)         :: 159 of 220
            Pseudo Genes (internal stop)      :: 39 of 220
            Pseudo Genes (multiple problems)  :: 28 of 220
            Pseudo Genes (short protein)      :: 4 of 220
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP050039.1.
            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..2389
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="58-3"
                     /host="broiler chicken"
                     /db_xref="taxon:562"
                     /plasmid="pCD58-3-3"
                     /geo_loc_name="China:Sichuan"
                     /collection_date="2019-05-12"
     gene            118..531
                     /locus_tag="G9P49_RS22765"
                     /old_locus_tag="G9P49_22800"
     CDS             118..531
                     /locus_tag="G9P49_RS22765"
                     /old_locus_tag="G9P49_22800"
                     /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_182176663.1"
                     /translation="MKIIKWASLSGVLLISACGVSQSEVNSANYGSKPIDNDAKVIGML
                     KESLKDPDSLKVISITTPARGFSKYGFGSTEHGWFTTITYNAKNSYGGYVGAKSITFVY
                     LNGDYKVAVPMSNGERVMLDKVSFSCKDNCQTK"
                     /name="hypothetical protein"
     gene            complement(559..714)
                     /locus_tag="G9P49_RS22770"
                     /old_locus_tag="G9P49_22805"
     CDS             complement(559..714)
                     /locus_tag="G9P49_RS22770"
                     /old_locus_tag="G9P49_22805"
                     /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_152913171.1"
                     /translation="MNSKQKCSHSNLEKEYYLGSATGDYKCLDCGEVGFGKDWPEKERS
                     KNDNEE"
                     /name="hypothetical protein"
     gene            1690..1890
                     /locus_tag="G9P49_RS22775"
                     /old_locus_tag="G9P49_22820"
     CDS             1690..1890
                     /locus_tag="G9P49_RS22775"
                     /old_locus_tag="G9P49_22820"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000166333.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="antitoxin VbhA family protein"
                     /protein_id="WP_023139298.1"
                     /translation="MARSPDPRQRTEGFRKAEASLRLEGMDPAGTPLYENIKERVISGD
                     ITYEQGRAEILAHYQKRANGH"
                     /name="antitoxin VbhA family protein"
     Typing          complement(786..1296)
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="88.39"
                     /coverage="99.0"
                     /evalue="1.29e-173"
ORIGIN
        1 agaaatgccc tgagggcgtc tgagatggtg cacgcaacgg atgttatggt aaatctatct
       61 ataaatgtct attatagtgg atttcctata gttgtttgga aaatgacaag gatatatatg
      121 aaaataatta agtgggcttc actgtctggt gttcttttaa tatctgcttg tggtgtttct
      181 cagagcgaag taaatagtgc taattatggt tcaaaaccaa tagataatga tgcgaaagtg
      241 attggtatgc ttaaagagag tctaaaagat cctgattctc taaaagttat atcaataacc
      301 acccccgcca gaggtttttc taagtatggc tttggctcta cagagcatgg ctggttcact
      361 actatcacat ataatgcaaa aaactcttat ggcggttatg ttggtgctaa gtccattact
      421 ttcgtttact taaacggaga ttataaagtg gcagtgccaa tgtctaatgg tgagagggtt
      481 atgttagata aagtgtcatt ttcatgtaaa gacaattgcc aaactaaatg ataaaaaagg
      541 tcgcaatagc ggcctttttt attcttcgtt atcattttta cttctttctt tttctggcca
      601 gtccttccca aaaccaacct ccccgcaatc caaacattta taatcgcctg tggcgctacc
      661 caagtagtat tctttttcta gatttgaatg agaacatttt tgtttgctgt tcactacagt
      721 cacctttgga tattcattta ttcgtgaatg atttttatct ataccgacat tgttaaatga
      781 tggaaagatc ttcttgagat cctttttttc tacgcgtaat cttcatgact gtaaacgaaa
      841 aaaccaccct ggcaggtggt ttttcgaagg ttagttaatc ctggcagatt ctctaaccgt
      901 ggtaacagtc ttgtgcgaga catgtcacca aatctgtcct tccagtgtag cctcagtcag
      961 gccgccactt caagaactct gaacacatct ctcgcacaaa cctgttacca gtggctgctg
     1021 ccagtggcgt tttgtcgtgt ctttccgggt tggactcaag acgatagtta ccggataagg
     1081 cgcagcagtc ggactgaacg gggggttcgt gcatacagtc cagcttggag cgaactgcct
     1141 acccggaact gagtgtcagg cgtggaatga gacaaacgcg gccataacag cggaatgaca
     1201 ccggtaaacc gaaaggcagg aacaggagag cgcacgaggg agctaccagg gggaaacgcc
     1261 tgggatcttt atagtcctgt cgggtttcgc caccactgat ttgagcgtca gattctgtga
     1321 tgcttgtcag gggggcgaag cctatggaaa aacggcttcg ccgcggcctt ttctgttccc
     1381 ctctttctcc ttccgctacc cccgaatctg tgggtaactc caggtggact gccggtaccg
     1441 ctcgccgcag ccgaacggcc gagcgtagcg agtcagtgag cgaggaagcg gaagatctgc
     1501 gatgcctgat tgggctcgtg tcgcgccgta ccctctcttt accgccggat tacacagttt
     1561 cctgcaatac tttccttccg gtttacacat tcgtctgcac ggataaacaa cggcagagta
     1621 cgggcaggat atgtaaagta ggcctacttt accgcctgcc ttattcgctt acagctcaaa
     1681 ggaacatcga tggccaggtc ccccgatcca cgacaacgta ctgagggttt ccgcaaagcg
     1741 gaagcgtcgc tgaggcttga aggcatggac cccgccggaa cgccgctgta cgaaaatatc
     1801 aaggagcggg ttatttccgg ggatatcact tacgaacagg gacgggcaga aattctggct
     1861 cattaccaga agcgtgcgaa cggccactga cacggacagg aaactaggta ccatcgcttc
     1921 ctcaaaaaaa caggcgtggc ctctctccgg ccagggtttt cctgtatttg ctatctgttt
     1981 gctacttgtt tgctatctgt ttgctacttg tttgctaccg ctaccctctg ctgtgaaaag
     2041 agtaaggcac gttagcgatg tatacatcgc cgcgccgcaa gggttcccct tccgaatccc
     2101 gttcatcact gcgtgctgat tatccacgtt aaatccgacc tcctgcttgg tagtaaattc
     2161 tgccatgcct gacggcctgg ccaacgcctc acggtcgcac agtaaactgt gcacccgttc
     2221 accgttatcg ggggagttat gcgccggaaa gcaggctttc atgccagcat ccaccccaaa
     2281 tcgaccgcca ttcacctgcg tgcatagcca tgcagccgcg cagaaatcat caggcgcgtt
     2341 ttttcacgat atggacaggg aaagatgccg gaaataagca ggagggcgc
//
