LOCUS       NZ_CP050042             3646 bp    DNA     circular CON 14-JUN-2023
DEFINITION  Escherichia coli strain 63-2 plasmid pCD63-2-2, complete sequence.
ACCESSION   NZ_CP050042
VERSION     NZ_CP050042.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14278030
            Assembly: GCF_014075595.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3646)
  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  JOURNAL   Unpublished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 3646)
  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 05:07:32
            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)                     :: 4,451
            CDSs (total)                      :: 4,332
            Genes (coding)                    :: 4,115
            CDSs (with protein)               :: 4,115
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 217
            CDSs (without protein)            :: 217
            Pseudo Genes (ambiguous residues) :: 0 of 217
            Pseudo Genes (frameshifted)       :: 71 of 217
            Pseudo Genes (incomplete)         :: 143 of 217
            Pseudo Genes (internal stop)      :: 45 of 217
            Pseudo Genes (multiple problems)  :: 38 of 217
            Pseudo Genes (short protein)      :: 4 of 217
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP050042.1.
            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..3646
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="63-2"
                     /host="broiler chicken"
                     /db_xref="taxon:562"
                     /plasmid="pCD63-2-2"
                     /geo_loc_name="China:Sichuan"
                     /collection_date="2019-05-13"
     gene            join(3484..3646,1..206)
                     /locus_tag="G9P50_RS21940"
                     /old_locus_tag="G9P50_21975"
     CDS             join(3484..3646,1..206)
                     /locus_tag="G9P50_RS21940"
                     /old_locus_tag="G9P50_21975"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880027.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001273382.1"
                     /translation="MANFNPGPRTAIAAVRDSKNDIETWKKNGIRREEIVTVLNERYGL
                     NISLVAFDKALYRLRKSTDEPSLADVDSVSAAETNFSEASGPENGFFLSENDFMRAEEE
                     SQRMVESFRDSLGRKKGF"
                     /name="hypothetical protein"
     gene            684..1517
                     /locus_tag="G9P50_RS21945"
                     /old_locus_tag="G9P50_21980"
     CDS             684..1517
                     /locus_tag="G9P50_RS21945"
                     /old_locus_tag="G9P50_21980"
                     /inference="COORDINATES: protein motif:HMM:NF027299.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_046597187.1"
                     /translation="MILLAGKKMKTNYFTHRLFPSDGAVICEPLKTSFDNMIATNRNTA
                     TLANEYHVIQHVSGDVYTFIKTNSRDVFRKLDTSSNICVDLSNILNQHEKIAFASFFIL
                     KGDVIGFSNTLYSPRIGKLAEIYDAAMYSRNGNHNINFEPITNIVTEQDVMNYAHVGKI
                     TMKIEKSQGIIGGLGTLFSGNVKYDDVDSFEIKIIPKRAKDIKDTFAGLMQARPQEVSS
                     VAVSAKEHIGDVATDLNVIMSNTVYDFVNPNDTTTIEVQMEKNYNNNTTLRSLGY"
                     /name="hypothetical protein"
     gene            1528..1965
                     /locus_tag="G9P50_RS21950"
                     /old_locus_tag="G9P50_21985"
     CDS             1528..1965
                     /locus_tag="G9P50_RS21950"
                     /old_locus_tag="G9P50_21985"
                     /inference="COORDINATES: protein motif:HMM:NF027298.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_046597188.1"
                     /translation="MKLKGFWLSAIVIAACNGMGFLFLYLSKTYFFPMVTFKDNLGNLG
                     SSLVTYSTAMMALLIAMVVIIFGLDGPRLHNFKKSGYLHVTYFIYMITFFELGLTMALS
                     LLCLSNISSIKVASYSLTFAFITFLLIGCLGIQLLNIKKNL"
                     /name="hypothetical protein"
     gene            2952..3101
                     /locus_tag="G9P50_RS21955"
                     /old_locus_tag="G9P50_21990"
     CDS             2952..3101
                     /locus_tag="G9P50_RS21955"
                     /old_locus_tag="G9P50_21990"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_164715499.1"
                     /translation="MPSEYDEQPGSTDTQLPGEYDLFDLMAQVTEENLHAPVDFGPPVG
                     REAL"
                     /name="hypothetical protein"
     Typing          2745..2959
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="87.615"
                     /coverage="100.0"
                     /evalue="1.5900000000000002e-64"
     Typing          complement(2283..2769)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="90.101"
                     /coverage="93.0"
                     /evalue="5.84e-177"
ORIGIN
        1 ctctttacag attgagaaaa agtacagatg aaccgtctct tgctgatgtg gattctgtgt
       61 ctgctgcaga aacgaatttc tctgaagcca gtgggcctga aaatggtttt tttctgtccg
      121 agaatgactt catgcgagca gaagaagaat ctcaaagaat ggttgagtca ttcagagata
      181 gccttggcag gaagaaagga ttctgatttt gaattctaag tagtgaaata gtggatcctc
      241 tactcgaaat tgtcggacac ctgcaattac ctaccgtgcc ttacggcttg ggcaatgcct
      301 tacggccacg caataaattg cgtccccgtt caccgttttc ggataagaag aacatcggaa
      361 acaggactta ccccggctga atggtgtgaa attctgcgct atgcacttgc gcgcatactc
      421 atgcatgccg taaaaacaga gcctgcgcgt ttctggcggg ttttcgggtg gtttgttgcc
      481 tgttttaccg gtttcccgtc agaaacgccc tgagggcctc tcaggcggtg cacgcaacgg
      541 atgttatggt aaatagagtt ggtggcctag ctttacgacc ttcggtgaca gatcatttaa
      601 tatgcaaaac ttggaatttt caaagaagca ttgttcttcc ataagaaata gaatataaaa
      661 agaagaaaat ataatgcgtt tctatgattt tactagctgg gaaaaaaatg aaaacaaatt
      721 acttcacaca cagattgttt ccttcagatg gcgctgttat ttgtgagcca ttaaaaacta
      781 gttttgataa tatgatcgct actaacagaa acactgcaac gctagccaat gagtatcatg
      841 taattcagca tgtgtctggt gatgtatata cgtttataaa aacaaatagc agagacgttt
      901 ttagaaaact agatacgagt agtaatatat gtgtagatct ctcaaacatc ttaaatcaac
      961 atgaaaaaat agcctttgca tcttttttca tattgaaggg tgatgttata gggtttagta
     1021 atacgttgta ctctcctcgt attgggaagt tggcagaaat atatgatgct gcaatgtatt
     1081 cccgaaatgg gaaccacaac ataaattttg agccgataac aaacatagtt accgagcaag
     1141 atgttatgaa ttatgcccat gttggtaaaa taacgatgaa aatagagaag tctcaaggca
     1201 ttattggtgg gcttggtacg cttttctctg ggaacgtaaa gtatgacgat gtggattcgt
     1261 ttgagataaa gataatccct aaacgggcta aagacataaa ggataccttt gcaggtttga
     1321 tgcaggctag gcctcaagag gttagctcgg tcgctgtgtc agctaaagaa cacattggtg
     1381 acgttgcaac agatttgaat gttataatgt ctaataccgt atatgatttt gtaaatccaa
     1441 atgacactac tactatcgag gttcagatgg aaaaaaatta taataacaat acaacattaa
     1501 gaagtttagg ttactgagga ttgcattgtg aagcttaagg gtttttggtt gagcgctata
     1561 gttatagctg catgtaatgg catgggcttt ttatttctat acctttcaaa aacctatttc
     1621 ttcccgatgg taacgtttaa ggataattta ggtaaccttg gttcttcctt ggttacctat
     1681 tcgacagcga tgatggcgtt gcttattgct atggttgtta taatctttgg cttggatgga
     1741 cctcgcttgc ataactttaa aaaaagcggc tatctccatg ttacatattt tatttatatg
     1801 ataacgtttt tcgagctcgg cttaaccatg gctctttcgt tactttgttt gtccaatatc
     1861 tcaagtatta aggtggcttc ttattcattg acttttgcat ttattacttt tttgttgata
     1921 ggatgtttag gtattcaact cttaaatata aaaaagaatc tttaatcaac caaactgtga
     1981 tgttcatcac aggtgaaacg gtttgtgacc atttttggtg agttgataaa atgcagaatg
     2041 tgtaaggatc gtcttgagat ttttgagagt gcagcgtagt ctcttgctct gtaaacaaaa
     2101 aaaccaccgc taccaacggt ggtttgtttg ccggaagtga gagctaccaa ctctttctcc
     2161 cgaaggtaac tggctttcac ggagcgcaga taccaaaact gtccttttag tgtagccgta
     2221 gtcaggccac cacttcaaga actccataga aatactctac tactctgctc cgtgaatcct
     2281 cttaccaatg gctgctgcca atggcgcgtt gtcgtgtctt tccgggttgg actcaagaag
     2341 acagttaccg gaaaggcgca gtagtcggac tgaacggggg gttcgtgcat acagtccagc
     2401 ttggagcgaa ctgcctaccc ggaactgagt gtcaggcgtg gaatgagata aacgcggcca
     2461 taacagcgga atgacaccgg taaaccgaaa ggcaggaaca ggagagcgca cgagggagct
     2521 accaggggga aacgcctggg atctttatag tcctgtcggg tttcgccgcc actgatttga
     2581 gcgtcagatt ttgtgatgct tgtcaggggg gcggagccta tggaaaaacg gcagcgccgt
     2641 atcctttttc cggcctttcc tgacttgagt gccatctttt tatcttgtca ttcgtgagca
     2701 ggtaacgccc gccgcagtct cacggcagga gcgtagcgac cgagtgagcg aggaggcgtc
     2761 atgtcaccgt tacctgcatt ttgcacttac gtcctatagc cgcattttcc cttgcaacat
     2821 gaataacttc cctgaattac cactccgacc taacatattc agcctgtata cactccgcta
     2881 gcgctacgtg actggttcag ggctgcacct tgaaaccctc taacaacctc tcagctattg
     2941 gatatcaccc catgccatct gaatatgatg aacaaccggg ttcgactgat acgcagcttc
     3001 ccggcgaata tgaccttttt gatttaatgg cgcaggttac tgaagagaac ctgcacgccc
     3061 cggtggattt tgggccacct gtcggccgtg aagcgttata gctttttcgc ttacccccgt
     3121 acgtgtaata cgccggtatt acatcttatt tctttatttt catgtgatta caggtggttg
     3181 taatacgttg cgtattacat aaataaacgg gaaattcagt ttttaccttt taattcatgc
     3241 aattgcgatg aaaatcgcgg ttgcgtatgg tgtatggcca tttaagggat aatgtaacct
     3301 gacttttaaa gaatgaatct atctttggca gcgcatgaga tcgataaaaa gcgttccaca
     3361 tcaggcggtt catggataca tgaaccggaa aggacaaaaa taagacaatt gtaagacatt
     3421 ttttgcgttt tactcttatt tttggactat tatgagacaa gtgtaagaca ttatgggcgg
     3481 tatatggcga attttaatcc tggtccaaga acagccattg cagctgtcag ggattccaag
     3541 aacgatatag aaacctggaa gaaaaatggt atccgtaggg aagagattgt gactgtgctg
     3601 aatgaacgtt acggcctgaa tatctcactg gttgcgtttg ataagg
//
