LOCUS       NZ_CP050038             3525 bp    DNA     circular CON 14-JUN-2023
DEFINITION  Escherichia coli strain 58-3 plasmid pCD58-3-2, complete sequence.
ACCESSION   NZ_CP050038
VERSION     NZ_CP050038.1
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 3525)
  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  JOURNAL   Unpublished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 3525)
  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
            CP050038.1.
            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..3525
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="58-3"
                     /host="broiler chicken"
                     /db_xref="taxon:562"
                     /plasmid="pCD58-3-2"
                     /geo_loc_name="China:Sichuan"
                     /collection_date="2019-05-12"
     gene            1104..1229
                     /locus_tag="G9P49_RS22745"
                     /old_locus_tag="G9P49_22780"
     CDS             1104..1229
                     /locus_tag="G9P49_RS22745"
                     /old_locus_tag="G9P49_22780"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_072006160.1"
                     /translation="MHEPPVQSDRCACSGNYRLESNPERHDKAPLAAAIGNLVRR"
                     /name="replication initiation protein"
     gene            1749..2348
                     /locus_tag="G9P49_RS22750"
                     /old_locus_tag="G9P49_22785"
     CDS             1749..2348
                     /locus_tag="G9P49_RS22750"
                     /old_locus_tag="G9P49_22785"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000430080.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="GNVR domain-containing protein"
                     /protein_id="WP_240743510.1"
                     /translation="MSIILFVVFSLILSSIFLLANKNKINIKYELNMIANSPGMIINCG
                     DDFYCKANIIQSIINNKSKSITSNIDERGKKINLSWAGDDRYKPSVTAEVNAIHKAIND
                     WYIQDYKTYKSIINNQDSNYINGTETYAKVSLLTKTNTSGERNFISINNEIVNKKYKPA
                     LIMTLTLIMAIIFSSSYHIIKRSVLEYKNKLNRSFY"
                     /name="GNVR domain-containing protein"
     gene            complement(2522..2722)
                     /locus_tag="G9P49_RS22755"
     CDS             complement(2522..2722)
                     /locus_tag="G9P49_RS22755"
                     /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_094322402.1"
                     /translation="MNINAGYEITSKASIIHQIQLIRGITQNLHAKGELWHQLAVDGLM
                     KLCVYLKNGDGEVANRIPHGE"
                     /name="hypothetical protein"
     gene            2702..3396
                     /locus_tag="G9P49_RS22760"
                     /old_locus_tag="G9P49_22795"
     CDS             join(2702..2948,2948..3396)
                     /locus_tag="G9P49_RS22760"
                     /old_locus_tag="G9P49_22795"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012477181.1"
                     /ribosomal_slippage=""
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /note="programmed frameshift; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS1 family transposase"
                     /protein_id="WP_094322401.1"
                     /translation="MASVNIHCPRCQSARVYRHGQNPKGRDRFRFRDCHRVFQLTYTYQ
                     ARKPGMKELITEMAFNGAGFRDTARTLKIGISTVIRTFKKLAPTRITSSPVAHADVALI
                     CELDEQWSYVGSKARQHWLWYAYNTKTGGVLAYTFGPRTDQTCRELLALLTPFNIGMLT
                     SDDWGSYGRVVPKNKHLTGKIFPQRIERNNLTLRTRIKRLARKTICFSRSVEIHEKVIG
                     AFIEKHMLY"
                     /name="IS1 family transposase"
     Typing          724..1213
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.723"
                     /coverage="81.0"
                     /evalue="0.0"
ORIGIN
        1 ggaatgagtt atcatgcgcc taatttacca taacatctgt tgcccgcacc ctctcagaca
       61 gcctcagcgc gtttctgggt cttcctgcct gtttccggca cttccctgtg cctatatcgt
      121 gaaaaaacgc gcctgatgat tctggcgcgt ctgcatggct atgcacacac atgcatggct
      181 gggattttag ccgctaaaat ccggcaggac gcccaaaagc accactgaac ctcacgaata
      241 acgcctcacg ggtgcgcagt ttactgtgcg gccgtgaggc gttggccagg ccgtcaggca
      301 tggctggatt tattgctaag ggggtcggat ttaacgtgga ttaatcagca cgcagtgatg
      361 aacgggattc ggaaggggca cccttgcggc gcggcgatgt atacatcgct aacgtgcctt
      421 ggtcatttat tgcaagaagg gagaggtagc attttgatag caaaaaagta gcaaaaagat
      481 agcaaacatg cgggagctaa ccaggagtct ttagcgggcc ggcggtactc caaaaacaca
      541 tcttgtcccg ctgttttgtg aataagccag catagctgtg ggcacaaaac atttcctgtc
      601 cgctgcttta acctttgtaa tccaggaacg tcaggtgacg tcactttgcg gcgttagccc
      661 tatcctgcat cgtattaaaa aatgcagcta tggcgcgtac ggtgccaaag ataagcccgg
      721 agatattccg cttcctcgct cactgactcg ctccgctcgg tcgttcggct gcggcgagcg
      781 gtaccggctt actggcgggg cggaaatttc caggcatctt ccaggaagaa gcttaacagg
      841 gaagcaagaa ggccacggcg aagccgtttt tccataggct ccgcccccct gacaagcatc
      901 acgaaatctg acgctcaaat cagtggtggc gaaacccgac aggacttaaa gataccaggc
      961 gtttccccct ggtggctccc tcgtgcgctc tcctgttcct gcctttcggt ttaccggtgt
     1021 cattccgctg ttatggccgc gtttatctca ttccacgcct gacactcagt tccgggtagg
     1081 cagttcgctc caagctggac tgtatgcacg aaccccccgt tcagtccgac cgctgcgcct
     1141 gttccggtaa ctatcgactt gagtccaacc cggaaagaca cgacaaagcg ccactggcag
     1201 cagccattgg taacttggtt cgcagatgat ttgttagcta aacacgaggt tgctcttgaa
     1261 gtgtgcgcat cagtacggct acactggaag gacagatttg gttgctgtgc tctgcgaaag
     1321 ccagttacca cggttcagaa acttgccggt ttactgaacc ttcgaaaaaa ccaccttgcc
     1381 gggtggtttt ttcgttttca gaccaagaga ttacggctgt aacacaaaga tctcaagaag
     1441 atcttaaaat atgtggaaag gatacaggct gataacaacc ccctccatag acatgatcga
     1501 acaaaaaaca aacaaaaaaa ttgattttaa gagtttcctc acccctaaat aataggtaaa
     1561 atgtttttta tttgattggc atttaaaatg aaatatacta aatcagcgaa aatattcatc
     1621 acggctattt taattttatt tatttattta tcctatactt taataactat tgttggtata
     1681 taaaaatgga aagcaattca cctgatattg atttcatcga gttatttctc tttcttaaga
     1741 aaaaaatcgt gagtattatt ttgtttgttg ttttctcatt aattttgtca tctattttct
     1801 tgttagcaaa caaaaacaaa ataaatataa agtacgaatt aaacatgatc gctaattcac
     1861 caggcatgat tattaactgt ggggatgatt tttattgcaa agcgaatatt atacaatcaa
     1921 ttataaacaa taaaagcaag tctataacat caaatataga tgaaagaggg aaaaaaataa
     1981 acctgtcatg ggctggtgat gaccgttaca aaccctcggt taccgctgaa gtaaacgcta
     2041 tccataaagc tattaatgac tggtacatcc aagattataa aacttataaa agcataatta
     2101 acaaccagga tagcaactat ataaatggca ctgaaacata tgcaaaagtt tcattattaa
     2161 ctaaaacaaa cacttccgga gaaagaaact ttatttcaat caataatgaa atagtaaata
     2221 aaaagtataa accagctttg attatgactc taacgttaat tatggctatt atcttttcct
     2281 cctcgtacca tataataaaa agatctgtgc ttgaatataa aaataagtta aataggtctt
     2341 tttattagcc tgtaacgatt aataaccgta ttctagcaac atccgttaca cgcctgatgc
     2401 agaaaagccc gctaatagcg ggcctcccga taaatctcac gtgaataagg gtagtcagat
     2461 ctatttctta cccttcttgc ctaactgatt cctcatggca ctgggccaac tacagcagtt
     2521 tttattcccc atgaggaatc cgattggcca cctcgccatc tccattttta agatacacgc
     2581 ataatttcat tagaccatct acagctaact gatgccataa ctcaccttta gcatgaagat
     2641 tctgggtgat acctctaatt agttgaatct gatgtataat actggctttt gaggttatct
     2701 catagccagc gttaatattc attgtccccg ttgtcagtca gctcgggttt accgccatgg
     2761 tcagaaccct aaaggccgtg acagatttcg cttccgtgac tgccaccgtg tgtttcagct
     2821 cacttatact tatcaagcac gtaagccggg tatgaaagag ctgatcactg aaatggcctt
     2881 taatggtgcc gggtttcgcg ataccgccag gacactgaaa attggtatta gcaccgtcat
     2941 ccgaacttta aaaaactcgc gccaacgcga ataacttctt ctcctgttgc ccatgctgat
     3001 gtggcgctta tctgcgagct tgatgagcaa tggagctacg ttggcagtaa agcccggcaa
     3061 cactggctct ggtacgcgta caacaccaaa acaggcggtg tactggccta cacttttggt
     3121 ccccgaaccg atcaaacgtg ccgggagcta ctggcactgc ttaccccctt caacatcggc
     3181 atgctcacca gcgatgactg gggcagctat ggccgggtgg tgccgaagaa taagcatctg
     3241 accggcaaaa tattccccca acgcattgag cgtaataatc tgacgctacg cacccgcatt
     3301 aagcggttgg ctcgtaaaac aatctgcttc tcacgctcag ttgagatcca cgaaaaagtg
     3361 atcggagcgt ttatcgaaaa acacatgctc tactaattgg atgcactacc agattctgaa
     3421 ccgtagatat ataagtctgc atttcagctt catcaatccc gtttttttta ctgaatccat
     3481 ttaccaatat cctgtccata cgttactaaa gaaaataata tatac
//
