LOCUS       NZ_CP123265             4405 bp    DNA     circular CON 18-JUN-2024
DEFINITION  Escherichia coli strain YZLc4-1 plasmid pYZLc4-1_4k, complete
            sequence.
ACCESSION   NZ_CP123265
VERSION     NZ_CP123265.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN30724595
            Assembly: GCF_025583565.2
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4405)
  AUTHORS   Yin,Y.
  TITLE     Transmission Patterns of Multiple NDM Variants Producing Strains in
            Animal and Environment Settings from Live Poultry Market
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4405)
  AUTHORS   Yin,Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (29-MAR-2023) College of Veterinary Medicine, Yangzhou
            University, 48 Wenhui East Road, Yangzhou, Jiangsu 225009, China
REFERENCE   3  (bases 1 to 4405)
  AUTHORS   Yin,Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (08-SEP-2022) College of Veterinary Medicine, Yangzhou
            University, 48 Wenhui East Road, Yangzhou, Jiangsu 225009, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology             :: Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_025583565.2-RS_2024_06_18
            Annotation Date                   :: 06/18/2024 07:00:33
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,203
            CDSs (total)                      :: 5,083
            Genes (coding)                    :: 4,870
            CDSs (with protein)               :: 4,870
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 213
            CDSs (without protein)            :: 213
            Pseudo Genes (ambiguous residues) :: 0 of 213
            Pseudo Genes (frameshifted)       :: 85 of 213
            Pseudo Genes (incomplete)         :: 134 of 213
            Pseudo Genes (internal stop)      :: 42 of 213
            Pseudo Genes (multiple problems)  :: 43 of 213
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP123265.1.
            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..4405
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="YZLc4-1"
                     /isolation_source="feces"
                     /host="chicken"
                     /db_xref="taxon:562"
                     /plasmid="pYZLc4-1_4k"
                     /geo_loc_name="China:Yangzhou"
                     /collection_date="2019-04-01"
     gene            complement(669..911)
                     /locus_tag="N4697_RS25945"
                     /old_locus_tag="N4697_025950"
     CDS             complement(669..911)
                     /locus_tag="N4697_RS25945"
                     /old_locus_tag="N4697_025950"
                     /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_157915800.1"
                     /translation="MQSLPLNASLNDLADREEPSMRKSFVTCRAIPIYHNVSLRAPPKR
                     AQRDSGAKTVKRGIFPLAKPEKCVRIVFSALHDYA"
                     /name="hypothetical protein"
     gene            1172..2296
                     /locus_tag="N4697_RS25950"
                     /old_locus_tag="N4697_025955"
     CDS             1172..2296
                     /locus_tag="N4697_RS25950"
                     /old_locus_tag="N4697_025955"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_018292354.1"
                     /GO_function="GO:0005524 - ATP binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="ATP-binding protein"
                     /protein_id="WP_000640319.1"
                     /translation="MIYRFEVEGFKGFSDKLVFDLTHRKNYEFNQDCILDGVVKKSLVY
                     GKNGIGKSNLGLALFDIVAHLTEFNVNDGMYNNYINAVNNSGIARFKYDFKFGDNIVTY
                     LYGKRSVKELVFEELFINGRLVTKFNRVLDSNAYFSLSGTETLNTALAESKISIINYIK
                     NNAILNDGIEKDLFNQFIVFVEKMLYFRSLDSNNYLGLEMGRHLITPDIVERGNVDDFE
                     RFLNKAGVKCKLCVMKIQSNNGVVEDIGFDFGSKQIPFYGVASTGTKSLALFYYWLQRF
                     KDEKCVSFIFVDEFDAFYHHSLSMLIVKEMKKAGAQVIITTHNTNVMTNELLRPDCYFI
                     MDDKGITPLFEKTDKELREAHNIEKMYKAGTFND"
                     /name="ATP-binding protein"
     gene            2289..3071
                     /locus_tag="N4697_RS25955"
                     /old_locus_tag="N4697_025960"
     CDS             2289..3071
                     /locus_tag="N4697_RS25955"
                     /old_locus_tag="N4697_025960"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000140057.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_079948273.1"
                     /translation="MTERILFVFEGEKTEKTITDSLLKKFIENDKRVVLSSFKTDIYSL
                     YKLMSEDEDLDVFAVLKEKNPDLVDFDRDSFSQLFLFFDYDGHAPAASDEKIDKLLSFF
                     NEETENGKLFISYPMVESIKCISHIDAIEDFCRHTVKICDCSKFKGYVAEYAHKSLIHF
                     NLYSDEIWNDVVRMHCVKSNFIMKGNMIFPSNYFSQKDIFGMQKSKYIDPNGSVSTLSS
                     FPMLLLDFFGHQRLFVLVSGEQIEDGDVLSSEEAQRTI"
                     /name="hypothetical protein"
     gene            complement(3235..3348)
                     /locus_tag="N4697_RS26070"
     CDS             complement(3235..3348)
                     /locus_tag="N4697_RS26070"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001422066.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001712890.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPERHDLTPLAAAIGN"
                     /name="hypothetical protein"
     gene            complement(3900..4103)
                     /locus_tag="N4697_RS25960"
                     /old_locus_tag="N4697_025965"
     CDS             complement(3900..4103)
                     /locus_tag="N4697_RS25960"
                     /old_locus_tag="N4697_025965"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041634.1"
                     /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_079948274.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAIMCERLHELA
                     EELQNSIQTHFEAQYGIGVEQP"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          4226..4306
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.683"
                     /coverage="89.0"
                     /evalue="5.6799999999999995e-25"
     Typing          complement(3277..3768)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.348"
                     /coverage="88.0"
                     /evalue="0.0"
ORIGIN
        1 ttgccaccag gacgaccgta tccggctgcc tgacacagga caggatgtgt aattgtaata
       61 ccgtcacccg tgacgctatt acaattacct cctgctcagg gtttcacccc gataccccgg
      121 cgtaatgctc tgacggccag cgcaaattta ttcgcttttt ctgagagtcc tgtagcccga
      181 accaggaccg gctccgcgcc tgaaattccc ctctcctctg acctgcattt accacacctg
      241 tcgcaaaact gcgttttgcg tgattttact ttaaattcag ttggttatag tggcgtttat
      301 ctggcaaaaa attctatttt gtcggatgtg gtgggctgat gatgggcttc tacgcccaca
      361 gttagcccac catcagccca cttttgtggg ttttatattg ataatcatag tgatagcaaa
      421 aatgtgggcg ttttgtgggc taatagagtg ggctgatggt ggcctcttat ttgtatgaaa
      481 tataacggat aaatttttat gatacatcgg tgtgcccatc ggtattttgt gtgtgggcta
      541 atggtgggct gttgaatgtc gttgctgacg gatgtgttct ggcatggaat gtgacgcaga
      601 cagaaagaaa actgccaaaa ataagcctca gggacagcgg acgcgcccag accgattgcc
      661 attcagtttc atgcatagtc atgcaacgcg ctgaaaacaa tcctgacgca tttttccggt
      721 ttagccaggg ggaaaatacc tctttttacg gtttttgcgc cagaatcgcg ctgagcgcgt
      781 tttggcggtg cgcgtaatga gacgttatgg taaatcggta tggcacggca agttacaaaa
      841 cttttacgca ttgaaggctc ttcgcggtca gccaggtcgt ttagcgaggc attgagcggt
      901 aatgactgca tacgtcttcc cactcgccgt agcgaaagcg acggtaggca cgaacgaata
      961 cgcttttacg tttcattttg tactctcctg tcttcgtcag ttgtaggaac tgacacctat
     1021 aaaaaacagc aagcatgctg agtttcatag gactgcgaga gccttcgctt gcaactttaa
     1081 ttgcagcgat aagaaaaatc aatatctata tttggtgtaa tttttttacg gtgccatgat
     1141 atagttacgg catctttgat gtgaggcttt tatgatatac agatttgaag ttgaggggtt
     1201 taaggggttt tcagacaaat tagtgtttga tcttactcat aggaagaatt atgaatttaa
     1261 tcaagattgt atacttgatg gtgttgtcaa aaaatcattg gtatacggta aaaatggtat
     1321 agggaaaagc aacttagggc ttgctctttt tgatattgtc gctcacttaa ctgagtttaa
     1381 tgttaatgat ggcatgtata ataactatat aaatgcagtt aacaactctg gtattgcgag
     1441 atttaagtat gattttaaat ttggtgataa tattgtaact tatttatatg gaaaaaggag
     1501 tgtgaaagaa cttgtttttg aagagttgtt tatcaatggc aggcttgtaa ctaaatttaa
     1561 tagagtgctt gattcaaatg cctatttctc attatcagga acagaaactt taaacactgc
     1621 tcttgcggag tctaaaatat cgatcattaa ttatataaaa aataacgcca tccttaatga
     1681 tggtatcgaa aaagatctat ttaatcagtt tattgttttt gttgagaaaa tgttgtactt
     1741 cagatctctt gattcaaata attatcttgg actagagatg gggcgacacc taatcactcc
     1801 ggatatcgtg gagagaggta atgttgatga ttttgaaagg tttttgaata aagcaggggt
     1861 taaatgtaaa ctttgcgtaa tgaaaattca aagtaataat ggagttgttg aagatattgg
     1921 ctttgacttt gggagtaagc aaattccatt ctatggagtt gcgtccacag gtacaaaatc
     1981 attagctctt ttttattact ggttgcaacg atttaaagat gaaaaatgtg tttcatttat
     2041 ctttgtagat gagtttgatg ctttttatca tcactcgctt tccatgctta ttgttaagga
     2101 gatgaaaaaa gccggcgccc aggtgataat tacaacgcat aatacaaatg tcatgacgaa
     2161 tgagttgctt aggcctgatt gttacttcat tatggatgat aaagggatta ctccactttt
     2221 cgagaaaaca gacaaagagt tgcgagaagc tcataatata gagaaaatgt ataaagcggg
     2281 tacatttaat gactgagcgg attttatttg tttttgaggg ggagaaaacg gagaagacta
     2341 tcactgatag tcttttaaaa aaattcattg agaatgataa gagggttgtt ctttcttcat
     2401 ttaagacaga tatatattca ctttataagt tgatgagtga ggatgaagat cttgatgtat
     2461 ttgccgtgtt gaaggaaaaa aatcctgact tagtagattt tgatagagat tctttctctc
     2521 agctttttct gttctttgat tatgatgggc atgctccagc tgcttctgac gaaaagatag
     2581 ataagctact aagttttttt aatgaggaaa ctgaaaacgg taaattattt atcagttatc
     2641 ctatggttga gtctataaaa tgtatctcgc atattgatgc gattgaggat ttttgtaggc
     2701 atacagtaaa aatatgtgat tgttctaagt ttaaggggta tgttgcagaa tatgctcata
     2761 agtcattgat tcactttaat ttgtattctg atgagatttg gaatgatgtg gttaggatgc
     2821 attgtgtgaa atctaatttc ataatgaagg ggaatatgat ttttccttct aattattttt
     2881 cacagaaaga tatattcggt atgcagaaat caaaatatat agatccaaat ggctctgtat
     2941 ctacattaag ttcattcccg atgttacttt tagacttttt tgggcaccaa agattgtttg
     3001 tgctggtcag cggtgaacaa attgaggatg gagacgtatt gagttcggag gaagcccagc
     3061 gtactatttg aaaagaaaaa accacccggc aaggtggttt tttcgaaggt tcagtaaccg
     3121 gcaagtttct gaaccgaggt aactggctaa tagaatagag gagctcagtc accaaaactt
     3181 gttctttcag tttagcctta accggcgcat aacatcaaga ctaactcctc taaatcagtt
     3241 accaatggct gctgccagtg gcgttaagtc gtgtctttcc gggttggact caagacgata
     3301 gttaccggat aaggcgcagc ggtcgggctg aacggggggt tcgtgcacac agcccagctt
     3361 ggagcgaacg acctacaccg aactgagata ccaacagcgt gagctatgag aaagcgccac
     3421 gcttcccgaa gggagaaagg cggacaggta tccggtaaac ggcagggtcg gaacaggaga
     3481 gcgcacgagg gagcttccag ggggaaacgc ctggtatctt tatagtcctg tcgggtttcg
     3541 ccacctctga cttgagcgtc gatttttgtg atgctcgtca gggggggcgg agcctatgga
     3601 aaaacggcat cgtcgcagcc ttttacggtc gtgctctttt gcacacatgt tctgtcctgg
     3661 ttatcccccg attctgtgga taaactgcct gccgttatta gagagccgcc accgctcgcc
     3721 gcagccccag cgaccgaacg tagtgagcga gtgggcgagg aagcggaatt tctccgcccg
     3781 tttgctttga gcacttacgc gccagtgtct ttctcaggtc actgtcctga cgcgccctgc
     3841 gggcttgtct gctggcgaaa acgctcacgg acaagccgcg accgctttcg ccagcgtctt
     3901 tatggttgtt ccactccaat gccgtactgc gcttcaaaat gcgtctgtat gctgttctgc
     3961 agttcttccg ccagttcgtg cagccgttca cacatgattg cctgttcgtc ggcatcgagg
     4021 gcatccagct tttcaagcag tgtcagactc tggcttttga tgaatcgcgc catgttaagt
     4081 gcggtttgct gctgtttgtt caccttctgt cgttctccgt tctgtctctg tattcagcat
     4141 catgtgatta tgccgtgttc cgttctttgc ctggacagtg agcgtttttc cggttgtttg
     4201 atgttcatcc gttcatcaca tcgtgggtgt cggggtaaag ccctgaccag gttgtaatcg
     4261 tatgaacgtg cgtgcgcggt tatacgatta cacatcctgt cccgttcatg gggtcgtgtt
     4321 accggcagtt gttgcgtcgc tcctgtttcg tgccgtaaat cttttgcgga tgtgacgggg
     4381 tacagttgta ccccctgccg gactg
//
