LOCUS       NZ_CP123243             2042 bp    DNA     circular CON 18-JUN-2024
DEFINITION  Escherichia coli strain YZLc1-3 plasmid pYZLc1-3_2k, complete
            sequence.
ACCESSION   NZ_CP123243
VERSION     NZ_CP123243.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN30724592
            Assembly: GCF_025583585.2
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2042)
  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  JOURNAL   Unpublished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 2042)
  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 2042)
  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_025583585.2-RS_2024_06_18
            Annotation Date                   :: 06/18/2024 07:18:39
            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)                     :: 5,303
            CDSs (total)                      :: 5,180
            Genes (coding)                    :: 4,952
            CDSs (with protein)               :: 4,952
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 90
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 228
            CDSs (without protein)            :: 228
            Pseudo Genes (ambiguous residues) :: 0 of 228
            Pseudo Genes (frameshifted)       :: 78 of 228
            Pseudo Genes (incomplete)         :: 160 of 228
            Pseudo Genes (internal stop)      :: 47 of 228
            Pseudo Genes (multiple problems)  :: 51 of 228
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP123243.1.
            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..2042
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="YZLc1-3"
                     /isolation_source="feces"
                     /host="chicken"
                     /db_xref="taxon:562"
                     /plasmid="pYZLc1-3_2k"
                     /geo_loc_name="China:Yangzhou"
                     /collection_date="2019-04-01"
     gene            join(1571..2042,1..497)
                     /gene="mobV"
                     /locus_tag="N4725_RS26470"
                     /old_locus_tag="N4725_26470"
     CDS             join(1571..2042,1..497)
                     /gene="mobV"
                     /locus_tag="N4725_RS26470"
                     /old_locus_tag="N4725_26470"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000024818.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0006310 - DNA recombination [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobV family relaxase"
                     /protein_id="WP_262934566.1"
                     /translation="MANYAIMRCKKLTGMGSVASALQHCYRERETPNANAERTPENYCS
                     VSKSTDQAMGRVRELLPEKRRKDAVLAVEYVMTASPEWWKEATPRQQAEFFARSEQWLE
                     KKYGKDRVVAAVVHRDEATPHLSAFVVPLTQDGRLSAKEFIGGRSKMREDQSTYAESVK
                     KLGLERGIEGSRATHQTVQHYYESIKRGTRSQVSISPEALEPRVLRKGIFTKDVEDQAA
                     IAKRLSHAVNDGFAGTIAMASQSAQNAKRARELQKTMDAQQKRLQSVTEPFKGLSREQM
                     TEILMMAQRFKQQNQEKEKQQRVEREKQRQMRSRGMGGMER"
                     /name="mobV"
     gene            complement(561..887)
                     /locus_tag="N4725_RS26475"
                     /old_locus_tag="N4725_26475"
     CDS             complement(561..887)
                     /locus_tag="N4725_RS26475"
                     /old_locus_tag="N4725_26475"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001614210.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_001070513.1"
                     /translation="MNQAALITIANELNHDQMRVLMALLAELDYENYIQVAQIDIAEAL
                     TMQKTNVSRAVKNLIDFGIILEGPKIGRSKTYRLNPQFGWKGTVSNHKKALKNGLSVIQ
                     GGRT"
                     /name="helix-turn-helix domain-containing protein"
     Typing          4..494
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="94.512"
                     /coverage="96.0"
                     /evalue="1.23e-80"
     Typing          1563..2041
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.75"
                     /coverage="96.0"
                     /evalue="8.840000000000004e-103"
ORIGIN
        1 acgctgaatc agtaaaaaaa ctgggtcttg agcgcggcat cgagggaagc cgcgccacgc
       61 atcagacagt tcagcactac tacgaatcga taaagcgtgg cacccgtagc caggtatcga
      121 tctcgccgga ggcgctggag ccgcgtgtat tgcggaaggg cattttcacc aaagacgtgg
      181 aagatcaggc agccatagcc aaacgtctaa gccacgcagt gaacgatggc tttgcaggaa
      241 ccatcgctat ggcctctcag agcgcccaga acgcaaaaag agcgcgtgag ctacagaaga
      301 ctatggatgc gcagcagaaa cgcctacaga gcgtcacaga gccttttaag gggctttcca
      361 gagagcagat gaccgaaatc ctgatgatgg ctcagcggtt taagcagcaa aaccaggaga
      421 aggagaaaca gcagcgtgtt gaacgtgaga aacagcgaca gatgcgatcg cgtggcatgg
      481 gcggtatgga gcgttagttt tgatgcgatg caggataggg ctaacgccgc aaaatgacgc
      541 catttgcggc attccagaga tcaggttctg ccgccctgta taacgctgag gccgtttttc
      601 agtgcttttt tgtggttgct gacagtacct ttccagccga actggggatt taggcggtac
      661 gttttgctcc gcccaatctt cggtccttcc agtatgatcc cgaaatcaat caggtttttt
      721 accgcacgac tgacatttgt tttttgcata gtcagcgctt ctgcaatatc tatctgcgcg
      781 acctggatgt agttctcgta atccagctct gcgagcaagg ccatcagtac acgcatctgg
      841 tcatggttta gctcattggc aatggtaatt agcgcggctt gattcatagt aaagtgcctc
      901 tggaatgatg acttttgttt gggacgaatc actgctacaa aaccacctaa ttcctcccct
      961 gtactttggt ctacctgcgt gattctccgc atctaaaaat ctccaatttc aggaaaaata
     1021 gttatctctc aagataacta agttatctct agagataact attgtcaaaa actttccgct
     1081 tgtggcgcgg cttccgagac atccccttct gtatcttatt actctccgta ctcatacatc
     1141 ggcaaaatca ggcgtttttc tgcccgttcg gtgcgaacga atttctatgt acgggaagtg
     1201 gaaattccgc ttcctcgaac ggacagactc gcggcgatgc cgctccctaa tccgttcttg
     1261 cggcgagcgg ttcctgctct ttcaaaaacg atattcattg cctgatttcg tcaagggcga
     1321 gcgtagcgag tgccatttac ccttgacgac tcaccggata aaacaggctt ggcagtggtg
     1381 ggaggtgacg cggagcgacg ccttccacct gccagaccgc cgttgatttt gacctttgga
     1441 agcgcagctt cccgaacgat tttgcgaagc aaagtctagt gagtacacta tcatcttgat
     1501 agtggcccgc cggaggtatc gcaatgcgct cccccgcctg gctgaatgaa tgccggaatc
     1561 aggggggaac atggcgaact acgcgataat gcgctgcaaa aagctgacgg gaatgggaag
     1621 cgtggccagc gcgttgcagc actgctaccg agagcgtgag acgccgaacg ctaacgctga
     1681 acggacacca gaaaactact gctctgtgtc caaatcaacg gatcaggcaa tggggcgtgt
     1741 gcgggagctg ctgccggaaa aacgccgtaa agatgcggta ctggccgttg aatacgttat
     1801 gacagcaagc cctgagtggt ggaaagaggc cacaccacgg cagcaggcgg agtttttcgc
     1861 ccgctctgag caatggctgg agaagaaata cgggaaggat cgtgttgtgg cggcggtggt
     1921 tcaccgggac gaggccaccc cgcacctgtc tgcgttcgtg gtgccattga cgcaggatgg
     1981 acggctgtcc gcgaaagagt ttattggtgg gcggtcaaag atgcgtgaag atcagagcac
     2041 ct
//
