LOCUS       NZ_CP090454             2994 bp    DNA     circular CON 08-DEC-2023
DEFINITION  Escherichia coli strain PT62 plasmid pPT62-3kb, complete sequence.
ACCESSION   NZ_CP090454
VERSION     NZ_CP090454.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN24648241
            Assembly: GCF_021441965.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2994)
  AUTHORS   Lu,X. and Li,R.
  TITLE     Coexistence of tet(X4), mcr-1 and blaNDM-5 in ST6775 Escherichia
            coli isolates of animal origin in China
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2994)
  AUTHORS   Lu,X. and Li,R.
  TITLE     Direct Submission
  JOURNAL   Submitted (05-JAN-2022) Colloege of Veterinary Medicine, Yangzhou
            University, Shuangqiao Street, YangZhou, JiangSu 225000, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.4
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology :: Illumina HiSeq; QitanTech nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 12/08/2023 10:05:10
            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)                     :: 4,839
            CDSs (total)                      :: 4,723
            Genes (coding)                    :: 4,444
            CDSs (with protein)               :: 4,444
            Genes (RNA)                       :: 116
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 279
            CDSs (without protein)            :: 279
            Pseudo Genes (ambiguous residues) :: 0 of 279
            Pseudo Genes (frameshifted)       :: 78 of 279
            Pseudo Genes (incomplete)         :: 186 of 279
            Pseudo Genes (internal stop)      :: 44 of 279
            Pseudo Genes (multiple problems)  :: 29 of 279
            Pseudo Genes (short protein)      :: 4 of 279
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP090454.1.
            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..2994
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="PT62"
                     /isolation_source="pigeon"
                     /db_xref="taxon:562"
                     /plasmid="pPT62-3kb"
                     /geo_loc_name="China: Jiangsu"
                     /lat_lon="31.91 N 120.26 E"
                     /collection_date="2021-06-17"
                     /collected_by="Xiaoyu Lu"
     gene            502..801
                     /locus_tag="LZ175_RS24075"
                     /old_locus_tag="LZ175_24065"
     CDS             502..801
                     /locus_tag="LZ175_RS24075"
                     /old_locus_tag="LZ175_24065"
                     /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_023281092.1"
                     /translation="MATATNFDAWLDDVDGDYEEVMALYDSVQNVSDMGLYQCVEGGRG
                     DAWVVSSNHHPEALFLASAVARDTFLKLIRERLCGGEDVDSWYGFQRNISNDHS"
                     /name="hypothetical protein"
     gene            872..1600
                     /locus_tag="LZ175_RS24080"
                     /old_locus_tag="LZ175_24070"
     CDS             872..1600
                     /locus_tag="LZ175_RS24080"
                     /old_locus_tag="LZ175_24070"
                     /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_123906176.1"
                     /translation="MALMVTRRYLLGGEYPSEEFVQASLEKYFFRQGFDIDTGSYIDLI
                     CRDKESRDVVWHIEVKGKTSQPGLDFRTCLGQLVQRMTKDNINYAIAVPRIKQYERLIE
                     ETSILAVSKLNLHWIFVGPDGSVTIKEPDSSTMKNGNANGNGREVSLVNGGFKRFIPGD
                     FMPTCSYGKAPVVFKSSRREMWDWLDDFVISNGVIPSIADIKEEAESRSGKWTLSNVKI
                     EYQFWKIYHLYKGHFFYQSE"
                     /name="hypothetical protein"
     gene            complement(<1874..1954)
                     /locus_tag="LZ175_RS24085"
                     /old_locus_tag="LZ175_24075"
                     /pseudo=""
     CDS             complement(<1874..1954)
                     /locus_tag="LZ175_RS24085"
                     /old_locus_tag="LZ175_24075"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001333247.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /name="replication initiation protein"
     gene            2390..2581
                     /locus_tag="LZ175_RS24090"
                     /old_locus_tag="LZ175_24080"
     CDS             2390..2581
                     /locus_tag="LZ175_RS24090"
                     /old_locus_tag="LZ175_24080"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041614.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_001041614.1"
                     /translation="MNKQQKTAVNMAKFIQDQSLLLLDRLNELDLDHEADFCEKLHEDA
                     ERLYRSLSARLNEQQDGA"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(1828..2223)
                     /name="rep_cluster_2370"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.462"
                     /coverage="92.0"
                     /evalue="2.95e-159"
ORIGIN
        1 tacatcaaaa gtacatcact tttacatcat ttttacgtca gatctgacct ctgagctatt
       61 cgtacatccg ccccctcttc ctgggcctcc tgcacgtgct gaaaatggtt tttccggctg
      121 tgccggcaac gcctcacggc cacgcaataa attgcgtccc cgttcaccgt tttcgggtaa
      181 gaagaacatc ggaaacagga cttaccccgg ctgaatggcg tgaatttccg cgctatgcac
      241 ttgtgcgcat actcatgcat gccgtaaaaa cagagcctgc gcgtttctgg cgggttttcg
      301 ggtggtttgt tgcctgtttt accggtttcc cgtcagaaac gcgctcaggc cgtctgagcg
      361 gtgcgcgtaa tgcgacgtta tggtaaatgc ctgtcttgct cacttttaga gcatgaggca
      421 aaaaaggtaa aaacttattt gcttaacagc ccctatcact atgtaaatta actcctgaaa
      481 actaaaaaat ggaggattgg catggcgact gctactaatt ttgatgcgtg gttagatgat
      541 gttgatggcg attatgagga ggttatggct ctttatgatt ccgttcagaa tgtaagtgat
      601 atggggttgt atcagtgtgt tgagggtggt cggggtgatg cttgggtcgt gagctctaat
      661 catcatccag aagctctttt tctagcatca gctgtggcta gggatacttt cctcaaattg
      721 attagagaaa ggctatgtgg cggcgaagat gttgattcat ggtatggatt tcaacgaaat
      781 atatcgaatg atcactcgta atcgtacaga gagttcccct tgtaggaact cttaaaatat
      841 gacgttatag taaataggat gcgtaggggt tgtggctctt atggtgacga gaaggtactt
      901 actaggtggt gaatatccct ccgaggaatt tgttcaagct tctttagaaa aatatttttt
      961 tcgacaaggg ttcgatatag atacgggatc ttatattgac cttatttgtc gtgataaaga
     1021 atctagggat gttgtgtggc atattgaagt aaaagggaaa acatcacagc cagggttgga
     1081 ttttcgaact tgtcttggac aattagtgca gagaatgaca aaagataata ttaattatgc
     1141 tattgctgtt ccaagaataa aacagtatga aagattaata gaagaaacga gcattcttgc
     1201 tgttagtaaa ttgaatttac actggatatt tgttgggcct gatggcagtg tgacaattaa
     1261 ggaacctgat agctctacga tgaaaaatgg taatgctaat ggtaatggaa gagaagtttc
     1321 tcttgtgaat ggagggttta aaagatttat tccgggggat tttatgccaa cttgctcata
     1381 tgggaaagct cctgttgtat ttaaatcatc tcggcgagaa atgtgggatt ggttggacga
     1441 ttttgttatt tcaaatgggg tgatcccaag tattgctgat attaaagaag aggctgaatc
     1501 gcggagtggg aaatggacgc tttctaatgt taaaatagag tatcagtttt ggaaaatata
     1561 tcacttgtat aaggggcatt ttttctatca atctgagtag ctgactcatt tgttcatcaa
     1621 atgccatgat cttcttgaga ttcattcgct caaagcgtaa tctctttctc ggaaaacgaa
     1681 aaaaccacct ggggaggtgg tttttcgaag gttcagtaag ttggggaact tctgaaccgt
     1741 ggtaacagtc ttgtgcgaga catgtcacca aatctgtcct ttcagtgtag ccgcagtcag
     1801 gccaccactt caagaactct cgatacatct ctcgcacatc ctgtctacca gtggccgttg
     1861 tcaatggcga ttagtcgtgt cttaccgggt tggactcaag acgatagtta ccggataagg
     1921 cgcagcggtc gggctgaacg gggggttcgt gcacacagcc cagcttggag cgaacgacct
     1981 acaccgaact gagataccaa cagcgtgagc tatgagaaag cgccacgctt cccgaaggga
     2041 gaaaggcgga caggtatctg gtaagcggca gggtcggaac aggagagcgc acgagggagc
     2101 gaccaggggg aaacgcctgg tatctttata gtcctgtcgg gtttcgccac cactgatttg
     2161 agcgtcagat tctgtgatgc ttgtcagggg ggcggagcct atggaaaaac gccccggcgg
     2221 ggcgtggcct tttcgccctt gtccttagct ttcgttatgc ttaccgttac gttatctgct
     2281 tatcctccct ccgctcgccg cagactcatg accgaacgga gggagcgaat gagcgaggaa
     2341 gcggaaaacc atcagaacgt acaataagca ctttcgcgcc ggggctttca tgaacaaaca
     2401 acaaaagact gccgttaaca tggctaaatt catccaggat cagtccctgc ttcttctgga
     2461 caggcttaat gagctggatc tggatcatga ggctgatttc tgcgagaaac tccatgagga
     2521 tgcggaacgc ctttaccgaa gcctgtcagc gcgcctgaat gagcagcagg acggtgcgta
     2581 atggctccgt tctgggtatt accggagtaa taccggcatc gccttaattt tcattgtgtt
     2641 agcgcttaac attattaccc cggtaatacc cagaatccct gtgtttttta ttttttattt
     2701 acttttcatg aagttgcgat gaaaaacgca gctgcgttag gtgtatgtca ttttttagta
     2761 tataaaacga ccactcccga gtgctggcgc cgcaggttaa gtatgattct ggctaaaaag
     2821 cgtccttttc cgggaaaggg tcatgctcgt atgaccctat gggttcagcg actacacata
     2881 aactacaaaa ttgcatctgc ttttacccca gaacgcgggt gtacaacaga attacatcaa
     2941 aagtacatca aaattacatc acttttacgt cagatcgcgg gtgtacaaca gaat
//
