LOCUS       NZ_CP123259             3374 bp    DNA     circular CON 18-JUN-2024
DEFINITION  Escherichia coli strain YZMc17-1 plasmid pYZMc17-1_3k, complete
            sequence.
ACCESSION   NZ_CP123259
VERSION     NZ_CP123259.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN30724613
            Assembly: GCF_025583295.2
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3374)
  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  JOURNAL   Unpublished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 3374)
  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 3374)
  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_025583295.2-RS_2024_06_18
            Annotation Date                   :: 06/18/2024 06:54:14
            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)                     :: 4,919
            CDSs (total)                      :: 4,795
            Genes (coding)                    :: 4,560
            CDSs (with protein)               :: 4,560
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 235
            CDSs (without protein)            :: 235
            Pseudo Genes (ambiguous residues) :: 0 of 235
            Pseudo Genes (frameshifted)       :: 90 of 235
            Pseudo Genes (incomplete)         :: 154 of 235
            Pseudo Genes (internal stop)      :: 51 of 235
            Pseudo Genes (multiple problems)  :: 56 of 235
            Pseudo Genes (short protein)      :: 1 of 235
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP123259.1.
            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..3374
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="YZMc17-1"
                     /isolation_source="feces"
                     /host="chicken"
                     /db_xref="taxon:562"
                     /plasmid="pYZMc17-1_3k"
                     /geo_loc_name="China:Yangzhou"
                     /collection_date="2019-04-01"
     gene            complement(876..1067)
                     /locus_tag="N4680_RS24550"
                     /old_locus_tag="N4680_24555"
     CDS             complement(876..1067)
                     /locus_tag="N4680_RS24550"
                     /old_locus_tag="N4680_24555"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165979.1"
                     /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_000165979.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNDLDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1131..1454
                     /locus_tag="N4680_RS24555"
                     /old_locus_tag="N4680_24560"
     CDS             1131..1454
                     /locus_tag="N4680_RS24555"
                     /old_locus_tag="N4680_24560"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_024132211.1"
                     /translation="MLTIRVTDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     SPPLLRHLAAIGNNLNQTARKVNSGQWSSIDRVHVVAALMAIEGELRQLRQAVREQGVR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1663..>2100
                     /locus_tag="N4680_RS24560"
                     /old_locus_tag="N4680_24565"
                     /pseudo=""
     CDS             1663..>2100
                     /locus_tag="N4680_RS24560"
                     /old_locus_tag="N4680_24565"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /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="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            2132..2692
                     /locus_tag="N4680_RS24565"
                     /old_locus_tag="N4680_24570"
     CDS             2132..2692
                     /locus_tag="N4680_RS24565"
                     /old_locus_tag="N4680_24570"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000067488.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_140436684.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISGHTTSVKQQLDTLSATVSTQFSTTEAELSRQQKKLLWQVIKGRILFPALTA
                     LSVTGGIFLGCWGLMEWQESKIAKNILTIREQENTLVKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            2699..2932
                     /locus_tag="N4680_RS24570"
                     /old_locus_tag="N4680_24575"
     CDS             2699..2932
                     /locus_tag="N4680_RS24570"
                     /old_locus_tag="N4680_24575"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137389.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_000137389.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHEVTQRNNA
                     ILNERVVILSQQVQRLAGQVDRLSRLFIANNS"
                     /name="MbeD family mobilization/exclusion protein"
     Typing          712..795
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="87.059"
                     /coverage="95.0"
                     /evalue="8.83e-18"
     Typing          1445..3015
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.006"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cttcaagaat ttttcaacag cacagtctcc caggaacccc gaaaaaaacc tgtttttgca
       61 gatacttgcg tatttgcgag aatcgtttgc ggttggggga gctgtgacga cggcgaccgc
      121 acgcgtgaga gttccgctac cggcgcagag agtttcatcg acagcggaca cctgatgagt
      181 tgccacaaaa accgtatgta gcgcggctag attggttgag ttagaccttg gcggcagttc
      241 ccggtatgtg gtggcgtgac gggtgagatg gtgcggcgaa gacgcatacg tcacgcaggc
      301 gcgggttctt ccactgacgc gccccgtgat cgatggcctt ggctccgtcc ggcatatcga
      361 gagcggcaaa ctacccgtcc cttcactggg aggggtgagt tgttgccgtt ccctccaacc
      421 tttcaccatc cggcatatcg cacgatccca tgtgcaccgc aactcctgat aactccagtg
      481 caaaaaaaaa aaaacggatc tgcatcacaa cgagagtgat cccaccgctc gccgcagccc
      541 cagcgaccga acgtagtgag cgagtgggcg aggaagcgga agagtcacag atgcaagcat
      601 tgtgcactta cgcgcctgtg ccagtgtccg cgtgtgtgct gtttatcggg tgcgctgttt
      661 ttacatctgt gcggcttttt actcctgaca tggtgcactt cccatccatg tctgcaccga
      721 tgcaaaatga gataagccag tatacacatc gctatcgctc tgtgaactgg gtcagggctg
      781 cgccccgaca cccgcactga cgcgccctgg cgggcttgtc tgctcccggc atccgctcac
      841 aggcaagctg tgaacgtctc cgggagctgc atgtttcagt tgctttcacc gtcatcgccg
      901 aagcgtgcga ggcaactgcg gtagagttcg tcggcgtggt cgtgaagtga ttcgcagatg
      961 tctgcctgtt cgtccgcgtc cagatcgttg agtttttcca gcagggttag cgtctggctt
     1021 ctgataaagc gagccatgtt aagggctgtt ttttcctgtt tggtcatggt cttaaggctc
     1081 cttgtatggg ggatttgtta gggggaatga taccgatgaa acgcgagaag atgctcacga
     1141 tacgggttac cgatgaggag cacgcccggt tactggaacg ctgcgagggt aaacgactgg
     1201 cggaatggat gcggcgggtc tgtctggggg agccggttgc acgcacagga aaactgccga
     1261 cactatcgcc gccattgctg cggcatctgg ctgccatcgg gaacaacctg aaccagacag
     1321 cccggaaggt gaacagcggc cagtggtctt cgattgaccg ggttcatgtg gtggccgcac
     1381 tgatggccat cgagggtgaa ttgcgccagt tgcggcaggc tgtcagggaa cagggggtac
     1441 gggatgatag ttaaatttca tgccaggggg aaaggcggtg gaagtggccc ggtcgattac
     1501 ctgctggggc gggagcgtaa ccgcgaaggc gcaacggtgc tccggggtaa cccggaagaa
     1561 gtgcgggaac tcattgattc cacgccattc tcgaagaaat acacttcagg cgttctgtcg
     1621 ttcgcggaga aggagttacc gccgggtgaa cgcgaaagag tgatgacgag ctttgagcgt
     1681 gttcttatgc ccggtctcga aaaagaccag tacagcattc tctgggtgga acaccaggat
     1741 aaggggcggc tcgaactgaa ttttgtcatc ccgaacatgg agctacagag cggtaagcgc
     1801 ctccagccgt actacgaccg cgcggacagg ccgaggataa atgcctggca gacgctggtt
     1861 aatcatcatt acgggctgcg tgacccgaac gcaccggaga acagacggac gcttgtcacg
     1921 ccaaataatc tgccaaaagc gaaacaggag gccgcagaag cgattacacg gggtcttgag
     1981 gcgctttacc atgccggagc aataaaaacg cgtcaggatg tcactgaggc gctcacagcg
     2041 gcaggttttg aggtggtgag gacaaccaga agcagtatca gtattgccga cccggagggt
     2101 gggcggaatc tcaggctaaa gggggcgctg tatgagcaat cttttacaaa tgggaacaga
     2161 cttcgagaag aaactgaaag agcgagccgc ttctaccgag aacatgctga acagcgagtt
     2221 caggaagctc gaagagtctg tagacaaggc actgagctta aacaggcaga aaatcagaga
     2281 cgctatcagc ggacatacaa catccgtgaa acagcaactg gatacactga gcgccaccgt
     2341 gagcacgcag ttcagcacca cagaggccga actgtcccgg cagcagaaaa aactgctctg
     2401 gcaggtgatc aaagggcgga tactgtttcc ggcgctgacc gcgctcagcg tcacgggcgg
     2461 cattttcctg gggtgctggg ggctgatgga gtggcaggaa agcaagattg cgaaaaatat
     2521 cctgactatc agagagcagg aaaacacgct ggtgaaactc gaggcaaaaa cctggggggt
     2581 gacgttcgtc aatggcgaga acgggaaatt tctggtgttg ccggacgggg tgaaagggga
     2641 aaacacctgg acggtgggcg acaagaacgc cgtgaggctg gtcagggagt aaacgagtat
     2701 gacggaactg gaagggcatt tgctgaacgc cttagagcat ttgcaacagg actatatgcg
     2761 gcggctgaac gagtgggaga gcgccttcgc ggaattgcag aagatgcacg aggttacgca
     2821 acggaacaac gcgatactga acgagcgcgt cgtgatattg agtcagcagg tgcagagatt
     2881 agccgggcaa gtggatcgct tgagtcggtt atttatcgcg aacaacagct aagggatgaa
     2941 caggagcgtg cccggtacag acatgaggta caggaacgcg cggcacgggt tcggagtggg
     3001 ccatcaatgg agatgtgacc ggggaagtga cgaaatcttg ccattttgac cagttcgacg
     3061 gctggggcga gcgaaacaaa tcgtgtgccg tatttgtgca tagctatgca acatcctgaa
     3121 aacgcatttc acgcgttttt ggggattcag ccaggggaaa acatggtttt tttacttttt
     3181 gagcgtaaag acgtgaaaaa tctcgttatt gcacttgcga tctttcgtcg gcgggcgtag
     3241 aacgaaaaca gctcgccagg aaggcgagct gtttcgggtt cattgaggtc tctgacctcc
     3301 tcaatgttcc tgtggaaact gttgagatcc acaacagaaa ccagttcatt cagtttgcat
     3361 gagccttctg tatt
//
