LOCUS       NZ_CP034742             5093 bp    DNA     circular CON 18-JUN-2024
DEFINITION  Escherichia coli strain L65 plasmid pL65-6, complete sequence.
ACCESSION   NZ_CP034742
VERSION     NZ_CP034742.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN10623993
            Assembly: GCF_003999795.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5093)
  AUTHORS   Liu,Z., Li,Y., Li,R., Xiao,X. and Wang,Z.
  TITLE     Emergence of NDM-5 prouducing Escherichia coli from a goose farm in
            Jiangsu, China
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5093)
  AUTHORS   Liu,Z., Li,Y., Li,R., Xiao,X. and Wang,Z.
  TITLE     Direct Submission
  JOURNAL   Submitted (27-DEC-2018) Veterinary, Yangzhou University, 88
            University South Road, Yangzhou, Jiangsu 225009, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: unicycler v. 4.4
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology             :: Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_003999795.1-RS_2024_06_18
            Annotation Date                   :: 06/18/2024 04:15:22
            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)                     :: 4,857
            CDSs (total)                      :: 4,739
            Genes (coding)                    :: 4,575
            CDSs (with protein)               :: 4,575
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 164
            CDSs (without protein)            :: 164
            Pseudo Genes (ambiguous residues) :: 0 of 164
            Pseudo Genes (frameshifted)       :: 73 of 164
            Pseudo Genes (incomplete)         :: 88 of 164
            Pseudo Genes (internal stop)      :: 39 of 164
            Pseudo Genes (multiple problems)  :: 30 of 164
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP034742.1.
            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..5093
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="L65"
                     /db_xref="taxon:562"
                     /plasmid="pL65-6"
                     /geo_loc_name="China"
                     /lat_lon="32.40 N 119.40 E"
                     /collection_date="2018-05-28"
                     /collected_by="Ziyi Liu"
     gene            join(4494..5093,1..3)
                     /locus_tag="EM854_RS24135"
                     /old_locus_tag="EM854_24135"
     CDS             join(4494..5093,1..3)
                     /locus_tag="EM854_RS24135"
                     /old_locus_tag="EM854_24135"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001259273.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="NYN domain-containing protein"
                     /protein_id="WP_250187448.1"
                     /translation="MRTIVYVDGFNFYHGLVKRSGYKWLDLYKLFEEQLLPIRSRESQL
                     IQVKFFTAEIKAKFASRGELAHQAQQAYHRALVQIYGDNLQIIKGYYSERQECAMTFNE
                     GHPPSKTDRTTVWKLEEKQTDVRMALEMYRDAIRGEAEQLVLCTNDSDMIPPIEMIKAD
                     RPELKIGIVVPREQDTSRVISSLASLGDWSLPYVSYE"
                     /name="NYN domain-containing protein"
     gene            complement(1027..1222)
                     /locus_tag="EM854_RS24110"
                     /old_locus_tag="EM854_24110"
                     /pseudo=""
     CDS             complement(1027..1222)
                     /locus_tag="EM854_RS24110"
                     /old_locus_tag="EM854_24110"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2449..3054
                     /locus_tag="EM854_RS24120"
                     /old_locus_tag="EM854_24120"
     CDS             2449..3054
                     /locus_tag="EM854_RS24120"
                     /old_locus_tag="EM854_24120"
                     /inference="COORDINATES: protein motif:HMM:NF024098.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF3800 domain-containing protein"
                     /protein_id="WP_250187449.1"
                     /translation="MHLLYVDESGTPSDPTLNHFVLSGISVFEKQTHWIEQEMNAIAAR
                     FNADDPYERELHGSPMRGGRDGWKNFSFNDRKQAIKDCLALLTQKHRDIRIFACVVPKG
                     ALDGKDVITESFYQISSRFDMYLSRLHHQGATSRGVAIFDKSSTEKSIQSLARTFKDTG
                     YEYGKLRNFSEVPLFLDSKASRLIQLADLVSYSIFQEV"
                     /name="DUF3800 domain-containing protein"
     gene            complement(3302..3565)
                     /locus_tag="EM854_RS24125"
                     /old_locus_tag="EM854_24125"
     CDS             complement(3302..3565)
                     /locus_tag="EM854_RS24125"
                     /old_locus_tag="EM854_24125"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010891192.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein L"
                     /protein_id="WP_072644307.1"
                     /translation="MAVYTSETKKFLDSVSHDKTWWTSRYNPADDVPVSGIYRCTVCGK
                     EITSNKDDPFPPQNHHQHSQSQAIKWQLIVRTDTQGNGCGSK"
                     /name="protein L"
     gene            complement(3730..4146)
                     /locus_tag="EM854_RS24130"
                     /old_locus_tag="EM854_24130"
     CDS             complement(3730..4146)
                     /locus_tag="EM854_RS24130"
                     /old_locus_tag="EM854_24130"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001283459.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /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_057103209.1"
                     /translation="MSDQKNNLDLQKQTLESKWGKEALSMGWSAIPTSLFFLQGALNMT
                     PTTFNVLLHLIIHWWKPYDWPHPSQESIAVRMGVSSRTVQRSLQELENYGLLTKIRTSK
                     DNPKYKGRNIYDMSLLVKSLNILTPDLNAKLNEK"
                     /name="helix-turn-helix domain-containing protein"
     Typing          870..951
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.857"
                     /coverage="98.0"
                     /evalue="1.43e-25"
     Typing          complement(1244..1328)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="85.393"
                     /coverage="87.0"
                     /evalue="5.15e-16"
     Typing          complement(46..569)
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.604"
                     /coverage="99.0"
                     /evalue="7.85e-161"
ORIGIN
        1 taggcgaaag ccaatactga agccaaatca ctggtaaaca gccggatctt cttgtgatcc
       61 ttttactctc gtcgtaatct catgtcctgc aaacaaaaaa accaccgcta ccaacggtgg
      121 tttgtttgcc ggaatcaaga gctaccaact cttttttccg aaggtaactg gctttcacgg
      181 agcgcagata ccaaaactgt ccttccagtg tagccgcagt caggccatca cttcaagaac
      241 tctgtagaag cacttctact actctgctcc gtgaatcctg ttaccaatgg ctgctgccag
      301 tggcgataag tcgtgtcttt ccggattgga ctcaagacga tagttaccgg aaaaggcgca
      361 gcagtcggac tgaacggggg gttcgtgcat acagtccagc ttggagcgaa ctgcctaccc
      421 ggaactgagt gtcaggcgtg gaatgagaca aacgcggcca taacagcgga gtgacaccgg
      481 taaaccgaat ggcaggaaca ggagagcgca cgagggagcc accaggggga aacgcctggt
      541 atctttaagt cctgtcgggt ttcgccacct ctgacttgag cgtcgatttt tgtgatgctc
      601 gtcagggggg cgaagcctat ggaaaaacgc caccggcgct gcctttttcc gggtttcgtc
      661 ttgttgctca catgttcttt ccggcgttat cctcggattc tgtggataac tgtattacca
      721 tctttgagtg agcagacacc gctcgccgca gccgaacgac cgagcgtagc gagtcagtga
      781 gcgaggaagc ggaagagcgc ctgaacaggc atattctcct tacgcatctg tgcggcattt
      841 cactccggat atggcaaact tttcatacaa tccgcactga tgctgcatga ttaagcccgt
      901 atacactccg ctatctctac gtgactggtt cagggcttcg ccccgaaccc cactgacgcg
      961 ccctgacggg cttgtctgct gccgaaaacg ctcgcggaca agccgtgagc gcctccgtca
     1021 gcttcgttat gtccctgttt cactttcggt ctcaaagcga acctggatgc tgttctggag
     1081 ctcttccgcg agttcgtgca gtcgttcgca catggtcgcc tgttcgtcgg catccagagc
     1141 atccagtttt tcaagtagtg tcaggctctg gctttttgat aaatcgcgcc atattcagcg
     1201 caatttgttg ctgtttgttc accttccgtt gttctccgtc agtaccgggt gtcgggtgga
     1261 ccctgaccag gtggtaattg taagacgttg cgggcgacgg tattacaatt gcacatcctg
     1321 tcctgtttct ttaggggtca gtttggatat agagaattat tgtacggtaa gcctgttttt
     1381 tgaacagact tacctatagc aatagggtgt actcccgcgc tatacggcat tttcagaggt
     1441 ttgaccttaa tcggataacc taaatgcgat actgcaagag cgacaactta aaagcgatag
     1501 ccactgacgc aaaatcaacc ccttacgaac caagattggt taaataatgc gcttaacgta
     1561 caaaaatttc cgatctccaa actgacccct tcttcgcctc ttatgtttct cgaatgaatc
     1621 gatggggaca ggaaatgttt tgtggccacc gccgcttcgc cggcaccaca aaactgtcgg
     1681 acaagatgtg tttttggagt accgccggca ccaaaaacat ttcatcaggc gcagcctgat
     1741 accctgaatt tcgtacgtac gaaattttgc ttttgttcag atcgagggca ggattcgcaa
     1801 agtgctggcg tttgtactca catcctttag acgttgcgat gcaggatagg gcagacgccg
     1861 caaaatgacg tcatttgcgg tatctgcccc gaaaacagaa tgttttctcc tgagcctgca
     1921 gctggctctc agaaccccta ccgcctcgca aagctcgttg ctcaacgcct cacgaccgca
     1981 cagtaaactg tgcacccgtt caccgttatc gatggggttc agcgagcctt ttgagcagtt
     2041 cgcaggattt tagccgctaa aattccggcc aggcatgttc gtgcatagcc atgcagatgc
     2101 gcagaaatca tcaggcgcgt tttttcacga tatggacagg gaaagatgcc ggaaataggc
     2161 tggagggcgc agaaatgccc tgagggcgtc tgagatggtg cacgcaacag atgttatggt
     2221 aaatcagaat gacggtgaag aaactatctg attgaattta tgttatttga ttgctcatgg
     2281 ctatggtgtg tgtataaatt atttgggtaa atatgcactt gcctgttatc attgatattg
     2341 agtcagttcg ctgcccatag cggtgtatgc gatgtttatc gcactggctt gcctaattca
     2401 taaaaaggcc gcgcatttgc gcggcctttt tcgtttaagg agtcttagat gcatctcttg
     2461 tacgttgatg agtctggtac accatcagac cctactctta atcattttgt cctttctggt
     2521 atatcagtat ttgaaaagca aactcactgg atagagcaag agatgaatgc aattgcggct
     2581 cgatttaatg ctgatgaccc gtatgaaaga gaattgcatg gttcaccgat gagaggtgga
     2641 cgagatggct ggaaaaattt ttctttcaat gacagaaaac aagcgatcaa agattgctta
     2701 gcactcctta ctcaaaagca tcgggatatt cgcatatttg catgtgttgt acccaaggga
     2761 gccttagatg ggaaggatgt aataacagag tctttttatc aaatatcgtc tcgtttcgac
     2821 atgtatttaa gtcgcttaca tcaccaagga gcaacgtctc gaggggtggc catttttgat
     2881 aaatcgtcga cagaaaaaag tattcaatct cttgcccgta cgtttaaaga tactggatat
     2941 gagtatggaa aacttcgcaa cttctctgaa gtacctttat ttttggattc caaagcgtca
     3001 aggctgattc agcttgctga tcttgtgtcg tactcaattt ttcaggaagt ttgagttcaa
     3061 tgatgatgag ttctacaaaa atcatagaga atcgctttga ctaccataat ggtaaagttc
     3121 acgggcttta cgtagcccac taatggaata gttgtgaata cgcactatct ataagtaaga
     3181 gttccttgtg accatcgacg cgaagcccgc tacgcgggct ttttcatgcg tagcgtacaa
     3241 cggatgttat gtttaatccg tctgaccgct aggtacaaaa aagcccctaa gggcttttga
     3301 gttatttaga accacaacca tttccttgcg tatctgttct gacaattaat tgccacttga
     3361 ttgcctgact ttggctgtgt tgatgatggt tttgcggcgg aaacgggtca tctttattgc
     3421 tagttatctc ttttccgcaa acagtacaac gatagatccc tgataccggt acatcgtcag
     3481 ctgggttata tcgtgatgtc caccaagttt tatcgtgaga aacactgtct aaaaattttt
     3541 tagtctcaga ggtgtataca gccatttgcc tttcctttcc aaaatgtata gggcggaggg
     3601 ggatcctttt tataagtttg gtttttttta gcgtttttca atcatctggc gatgattgaa
     3661 aaacgctaaa atagagatgc tatggtaaat ataagctgta atggtctgat ttttaaaatt
     3721 attttatggt tacttttcgt tcagtttggc attaaggtct ggcgtaagaa tgtttagtga
     3781 cttaactaaa agagacatat cgtaaatgtt tcgccctttg tacttagggt tgtccttgct
     3841 tgtacgaatt tttgtaagca atccgtaatt ttcaagttct tggagtgagc gttgaactgt
     3901 tcttgatgaa actcccattc taaccgcgat gctctcttga gatggatgtg gccaatcata
     3961 gggtttccac cagtggatga ttagatgaag tagcacattg aatgttgtgg gggtcatatt
     4021 gagtgcgccc tgcaggaaga aaagggatgt aggaatggct gaccatccca tgcttaacgc
     4081 ctccttcccc catttagatt caagtgtctg tttttgaagg tctaaattat ttttttgatc
     4141 tgacatatac caacctgcta agctgaagtc ttcatagaag acttcagctt agcaggttgg
     4201 taaattaatt catataatta gtacgacacc atcgcgctta taatatcatt atatttaact
     4261 atacttaatc tacactcacc tcttggtagc gcgattaagt tacgcagctc ccttgaggct
     4321 ctaaacctcc ctttaggtgg gcagcgatta agttacgcgt cttccttcag gagcttgaaa
     4381 ccgccctctc ggttagtttt aaccctgagg aactacaact taaactgttt gctaacgtta
     4441 gtttttgttg ttaaaaccgc ctttagaggc ggttttttta tgcgcgaaat aaaatgagaa
     4501 caatagttta cgtagatggg tttaattttt atcacggatt ggttaagcgt tcgggatata
     4561 agtggttaga tctctataaa ctctttgaag aacaactact tccgataaga tcaagagagt
     4621 cacagttgat tcaggtgaag ttctttactg ctgagatcaa agcaaagttt gcttctcggg
     4681 gtgaattggc gcaccaggct cagcaagcct accatcgagc attagtacag atctatggcg
     4741 ataacctaca gataatcaaa ggttattact cagagcgtca ggaatgtgca atgaccttta
     4801 atgaggggca tccgccatca aaaacggata gaacaacggt ctggaagtta gaagaaaagc
     4861 agaccgacgt tagaatggct ttagaaatgt atcgcgatgc gatccgtggt gaggcagaac
     4921 aattggttct ctgtactaac gactcagata tgataccgcc aatagaaatg ataaaagccg
     4981 atcgacctga gttaaaaata ggaattgtag tgccaaggga acaagatact agtcgagtga
     5041 ttagtagtct ggctagttta ggggattgga gcttgccata tgtatcctat gaa
//
