LOCUS       NZ_CP123258             4077 bp    DNA     circular CON 18-JUN-2024
DEFINITION  Escherichia coli strain YZMc17-1 plasmid pYZMc17-1_4k, complete
            sequence.
ACCESSION   NZ_CP123258
VERSION     NZ_CP123258.1
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 4077)
  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  JOURNAL   Unpublished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 4077)
  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 4077)
  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
            CP123258.1.
            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..4077
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="YZMc17-1"
                     /isolation_source="feces"
                     /host="chicken"
                     /db_xref="taxon:562"
                     /plasmid="pYZMc17-1_4k"
                     /geo_loc_name="China:Yangzhou"
                     /collection_date="2019-04-01"
     gene            complement(252..506)
                     /gene="mobC"
                     /locus_tag="N4680_RS24535"
                     /old_locus_tag="N4680_24540"
     CDS             complement(252..506)
                     /gene="mobC"
                     /locus_tag="N4680_RS24535"
                     /old_locus_tag="N4680_24540"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091747.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase accessory protein MobC"
                     /protein_id="WP_000091749.1"
                     /translation="MSRTLEQKIAEAEARLQRLKAKSRSLDTAQKVIVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPEQ"
                     /name="mobC"
     gene            685..2832
                     /gene="mobQ"
                     /locus_tag="N4680_RS24540"
                     /old_locus_tag="N4680_24545"
     CDS             685..2832
                     /gene="mobQ"
                     /locus_tag="N4680_RS24540"
                     /old_locus_tag="N4680_24545"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016240513.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobQ family relaxase"
                     /protein_id="WP_072646424.1"
                     /translation="MAIYHLSMKIISRSNGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANADYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIGLPDNATSYTLRDIIEALPKDSN
                     SAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQMAFEKQWQQWGESGLAALRAQL
                     LKREEELRRKEQEDTERSRAEQLRKNDNAVMDSGVLRAVVTGYGEAPMPGNGEMTCYLL
                     LHNRNGEYTLWGNELEKYRTRIFESVDLMRDRSGYICDRSEIGQRPPLQRVYSSATFEQ
                     LLTQVCQTWPQHTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLPPTLMPVM
                     SSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKGLRYA
                     GYGVAVNHDADSHISPAPELMEFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRTWDEW
                     RREEDARTHTTERRHDRGWSQ"
                     /name="mobQ"
     gene            complement(3091..3798)
                     /locus_tag="N4680_RS24545"
                     /old_locus_tag="N4680_24550"
     CDS             complement(3091..3798)
                     /locus_tag="N4680_RS24545"
                     /old_locus_tag="N4680_24550"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001296720.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_001296720.1"
                     /translation="MTSNPLIAYKSNALVEASYKLTLQEQRFLLLCISRLNSGTDVASP
                     ELQKTMTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKDDEKREEFRWIQYRA
                     QYARGEGKAQITFSDAVMPYLTQLKGQFTRVVIKNISNLSRSYSIRIYEILQQFRSTGE
                     RIIALDDFKSSLMLDGKYKDFKTLNRDLIKPCVDELNKKSDLAVTVETIKKGRTVVALH
                     FRFKEDKQIKMTI"
                     /name="replication initiation protein"
     Typing          complement(511..684)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.286"
                     /coverage="98.0"
                     /evalue="2.6299999999999998e-81"
     Typing          685..1043
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.222"
                     /coverage="100.0"
                     /evalue="3.97e-172"
     Typing          complement(3092..3798)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          599..2829
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.326"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gcctgtggat aacttggggt gctgaaaata aaaatcaaat aaaaacaatg tattgcaaaa
       61 aatcaggatt gaaaattccg aatacacccc ctccaaccct gtggaaatcc agtattcatg
      121 cgggttcagc gcatatcacc tgtcgaaaaa ccgtgcgtat gtgctcaacc tggcgactga
      181 ttcacttccg cttcctcgcc cactcgctcg ctaacgttcg gtcgctgggc tgcggcgagc
      241 ggacgataca atcactgctc tggcagcgcc tccagctcgt taatcagcgg cagtattcgc
      301 gtcacatcag cctgccgtgt cacctctgcc ttcaggaact ggagtaacca agctcgcaac
      361 tgcacttcct ccggctttct gacctttgcc agcaatgctg cacccacaat gaccttctgc
      421 gctgtgtcca ggctccggct cttcgccttc aggcgctgta atctggcctc agcttcggca
      481 atcttctgtt cgagtgttct gctcatttcg tgactccgtg cgcggtgaaa aatcgcattt
      541 tagcgcgtca ctggtagttt aaaaactgag ctggcataat gcacggcaaa tcacgaagtg
      601 cgcacttata caatctccac tccgtttcga ttgtgtgcgc cctgcggggc tgaaagaaaa
      661 ctgcaaaaag gcattacggc agaaatggcg atttatcatc tcagtatgaa aatcatctcc
      721 agaagcaacg gctacagcgc cgttgcttct gctgcctatc gttctggttc actaatgctt
      781 gatgagcgta ccggactgac tcacgactac acccgcaaaa gcggtgtggc tgaggctgtg
      841 attctgaccc ccgcgacagc ccctgcctgg tgtacgaacc gtgccgaact ctggaatgcc
      901 gttgagaagg ccgaacgccg gaagaactca caacttgcgc gggaaattga actcgctatc
      961 ccccgtgaac tgccgcagga tgccgcacgg gaaaccgttc tcgcctttgt cagagaaaac
     1021 tttgtcagtc agggcatgat tgctgatgtg gcgttccatc acatggataa aacaaatccc
     1081 catgcgcaca tcatgctgac cacgagggct gtcggacctg ctgggttcgg cggaaaggtc
     1141 agggactgga acgaccggac acatgccgag acgtggcgtg catcatgggc tgaccatgca
     1201 aacagagcac tggcgaacgc cgattatcag gaagagatag accatcgttc atacgagcga
     1261 caggggcttg agaaaacgcc tggtattcac ctcggaaagt ctgcctgtgc gatggaaaca
     1321 cgcggtatcg aaacagaacg cggcgaacag aatcgtctga ttaacaggct taacctggaa
     1381 atacagattt cccgcactga actcaggaac agcgggctga cagagcctgc ccgccgtgtg
     1441 gctgaccttc tgaatatcgg gcttcctgac aacgcaactt cgtacacact acgtgacatt
     1501 atcgaagcgt tgccgaagga cagtaactcg gcatggaaac tcaccagtaa tgccatgtcg
     1561 atgatggcag atatgcaggc gacgcgcaga cgctgggaag agctgaacac cgaacgaaag
     1621 gaagcgatga gccatgctgc cagcctgaaa aaatcatcgc cgttttcgtc cggtttttcc
     1681 cgtattcccc ttatgcaatg ggcggcaccg gaataccgta gtgagcaggg aaaaatccag
     1741 tctctgagcc agcaaatgga aaaattacga cagcattacc ggaaggtgga gaaacaggac
     1801 attcccgcga gtcagatggc atttgaaaaa cagtggcagc agtgggggga atccggcctt
     1861 gcagctctca gagcccagtt gcttaaacgt gaagaggaat tgcgccggaa ggaacaggaa
     1921 gatactgaac gtagtcgcgc ggagcagctc aggaaaaatg acaatgccgt tatggattca
     1981 ggggtgctga gagcagtcgt tacggggtat ggcgaggctc ccatgcctgg taacggggaa
     2041 atgacctgtt accttctgct tcacaaccgg aacggagaat atacgctctg ggggaacgag
     2101 ctggagaaat accgcaccag aatctttgag agtgttgatt taatgcgtga caggagtggt
     2161 tatatctgtg accgaagcga aatcggccaa cgtccgccac tgcaacgtgt ttattcctct
     2221 gcaacctttg agcaactgct gacgcaggtt tgccagacat ggccgcaaca tacccgcaat
     2281 ctccgccagc cgaagacatg gccggagtct ttctgtcttg gagaagaccg ccagccagcc
     2341 atgccatcac tggcagcaag gaaggtggat tttacgcagg gacgtctgcc accgacgctg
     2401 atgccggtaa tgagttctgt cgaccgggaa acccgccagc ttcagctttt gctggtcatg
     2461 ggcgtggatg actctctggg cggtgttgtc cggcttaatg gtacgctgta tcccgcgttt
     2521 gccgttccct cagccgataa cagccagctg gtcatcagtg cactgaccga taaggggtta
     2581 cggtatgcag ggtatggtgt tgccgtaaat cacgatgcag acagccacat atcacctgcg
     2641 ccggaactta tggagtttca tctgaaaacc cgtgaggcac cgctttttgc tgccgtcaac
     2701 acaccagaaa aacagccgga tcatctgttc cgctcgctgg gtttcaatcg tacctgggac
     2761 gaatggcggc gcgaggaaga tgcaagaaca cacaccaccg agaggagaca tgatcgcggt
     2821 tggtcacagt gaatgtgaac aatattttgt tttgtttaac atcgtgttat gttcgtcgat
     2881 gttcttcgat gttcatcgac agggatgaat gcaagaagca cactcacata atgcaagcat
     2941 agttttgttt ttccgccccc aaaaattggg ggttcttttt tttgctgcat cagagcgttt
     3001 ttgacgcaac ttttcacttc aatagtacct tcgtattcct gacacaagaa aaacgcgaca
     3061 gtgagcgttt taggtgcctt aaaatcgatt ctagatcgtc atcttgatct gtttgtcttc
     3121 cttgaagcga aaatgcaggg ctacaaccgt gcgccccttt ttgatcgtct caaccgttac
     3181 agccaggtcg ctttttttgt tcagttcgtc aacacagggt tttattagat ccctgtttaa
     3241 cgttttgaaa tctttatatt taccatcaag catcagtgat gatttaaaat catcgagggc
     3301 gataatacgt tccccagtac tgcggaattg ctggagaatt tcgtatattc ttatgctgta
     3361 acttcttgat aaattagaaa tatttttaat gacgactctg gtgaattgcc ccttcaactg
     3421 tgtcagataa ggcattaccg cgtcagaaaa agtgatttgt gctttcccct ctcccctcgc
     3481 gtactgtgcc cgatactgaa tccagcggaa ctcctcgcgc ttctcgtcgt ccttgagaat
     3541 gatcgacctg tcccacaaac gatcgatcgc ttcctgtagc tgaacctcgg catttttccg
     3601 ccccatatca gggaatgaat caaaatattc cgcagctgta atggtcattg tcttttgcaa
     3661 ttcaggtgaa gctacgtcag taccggagtt aagtcggctt atgcagagca ataagaaacg
     3721 ctgttcttgt aaagttagct tgtaactggc ctcaaccagc gcattggact tataggctat
     3781 cagagggttt gatgtcattt taaccaccag gccaaaaatg aggtgaaata aaaacctatc
     3841 acctttagca ttggtgagca attatatttt caccccccat tttcctgtga atattacctt
     3901 aaatctcctc acctttacct taaattacct cacccaagca ccttaaatta tatcaccttt
     3961 accttaaatt tccccaccta tgcacgtgta acgcattgtt tttaatcagg aatttcgacc
     4021 ctaaaacaag tattaaaaac aagatcttaa aaacaagatc taaaaactta acggcga
//
