LOCUS       NZ_CP046421             3282 bp    DNA     circular CON 18-JUN-2023
DEFINITION  Escherichia coli strain LZYWN_4 plasmid pS4-unknown3, complete
            sequence.
ACCESSION   NZ_CP046421
VERSION     NZ_CP046421.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13282710
            Assembly: GCF_017310055.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3282)
  AUTHORS   Liu,Z.
  TITLE     Emergency of IncX4 plasmids ecoding mcr-1 in a clinical isolate of
            Escherichia coli from intestinal
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3282)
  AUTHORS   Liu,Z.
  TITLE     Direct Submission
  JOURNAL   Submitted (15-NOV-2019) College of Veterinary Medicine, Northwest
            A&F University, No. 3 Taicheng Road, Yangling, Shanxi 712100, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.48
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 1.0x
            Sequencing Technology             :: Illumina HiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/18/2023 02:59:59
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,835
            CDSs (total)                      :: 4,717
            Genes (coding)                    :: 4,511
            CDSs (with protein)               :: 4,511
            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)              :: 206
            CDSs (without protein)            :: 206
            Pseudo Genes (ambiguous residues) :: 0 of 206
            Pseudo Genes (frameshifted)       :: 61 of 206
            Pseudo Genes (incomplete)         :: 148 of 206
            Pseudo Genes (internal stop)      :: 34 of 206
            Pseudo Genes (multiple problems)  :: 36 of 206
            Pseudo Genes (short protein)      :: 4 of 206
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP046421.1.
            Bacteria and source DNA available from Xiaoping Song, Traditional
            Chinese Veterinary Medicine Lab,College of vetrinary Medicine,
            Northwest A&F University.
            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..3282
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="LZYWN_4"
                     /isolation_source="liver"
                     /host="swine"
                     /db_xref="taxon:562"
                     /plasmid="pS4-unknown3"
                     /geo_loc_name="China:Yangling"
                     /lat_lon="34.16 N 108.02 E"
                     /collection_date="2017-05-21"
                     /collected_by="zengyuan liu"
     gene            join(3218..3282,1..775)
                     /locus_tag="GJV83_RS23820"
                     /old_locus_tag="GJV83_23845"
     CDS             join(3218..3282,1..775)
                     /locus_tag="GJV83_RS23820"
                     /old_locus_tag="GJV83_23845"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000546749.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="EcsC family protein"
                     /protein_id="WP_001677176.1"
                     /translation="MHLEEEDLRALERAVELLEQDTITETLTQLVGTPIDYLMSKLPKG
                     AEKKIYSLVEKSLNKAANAALWSLDNEPNRIASTKTNKFFAALSGAIGGAFGFSALAIE
                     LPVSTTIMLRSIADIARSEGFDLDRIDTKLECLAVFSFGGPSEDDDAVNTAYYATRNLT
                     AEIVQDLSKEISNIAVKNAASTQTGKWLASLIEKVATRFGIVITEKMAAQAAPVIGALA
                     GATLNTMFTDYYQDMARGHFIVKRLERKYGDELIKAEYIKISDKLTNQNQRKHLNSN"
                     /name="EcsC family protein"
     gene            1886..2080
                     /locus_tag="GJV83_RS23825"
                     /old_locus_tag="GJV83_23850"
     CDS             1886..2080
                     /locus_tag="GJV83_RS23825"
                     /old_locus_tag="GJV83_23850"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /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_001041631.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQIRFEAESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(1372..1627)
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="91.085"
                     /coverage="89.0"
                     /evalue="2.7e-93"
     Typing          complement(1752..1850)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          complement(2161..2246)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.552"
                     /coverage="100.0"
                     /evalue="8.64e-33"
     Typing          2268..2817
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.471"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aattacagaa acactaaccc aattagttgg aaccccaata gattacttaa tgagtaaact
       61 tcccaaagga gcagaaaaga aaatttatag cctagtagaa aaatctctca acaaagctgc
      121 taatgcagcc ttatggagcc tagacaatga acctaaccga atagcatcaa ctaagacaaa
      181 taagttcttt gctgccttat ctggagccat tggtggtgct tttggctttt ctgcattagc
      241 aattgagtta ccagtttcaa cgacaattat gcttcgttca attgcggaca tagcaagaag
      301 tgaaggtttt gatctagata ggattgatac aaaactagag tgtttagcgg tgttttcctt
      361 cggaggacca tctgaggacg atgatgcagt taatactgca tactatgcaa caaggaattt
      421 gactgctgag atcgtacaag atttatccaa agaaatttct aacattgctg tcaagaacgc
      481 tgcttcaaca caaacaggaa aatggttagc ttcgttaata gaaaaagttg cgacaagatt
      541 tggtatagtt attacagaaa aaatggcagc tcaagctgct cctgttattg gagcactggc
      601 tggagccaca ttaaacacga tgtttaccga ctattatcaa gatatggctc gaggtcattt
      661 tattgtcaaa agacttgaga gaaaatatgg tgatgaattg ataaaggctg aatatataaa
      721 aatctcagat aaactcacca atcagaacca acggaagcat ttgaacagca actaacggtt
      781 tcactaagtg catagcaccg ttatggccag gtgctatgga gggtgtcaac tcacgaacaa
      841 tcacacaaac aacaaaatta tttatgattt tattttaaac attatattcg caacaactga
      901 attaatgaaa ttggcttttt ttgaatcaac taaaacagag ccacaatttg ggcactgact
      961 aaaagcattc cccccatcaa ctaaaacatc gctacattta ggcacagttt tacaccaatg
     1021 gcatgataaa catttatagg tcatagccat tctaatcatt accaatttca actccacgca
     1081 caaaataaat agttaaccca gcatctacga atatcaatca tatttaccat aatcccgtat
     1141 tgcgcgcacc gctaaaacgc gctgaacgcg attctgccgc aaacaccgca aaaagagatg
     1201 ttttccccgg ggtaaaccgg aaaaatgcgt caggctcgct ttcagctcac tgcatagcta
     1261 tgcatgaaag tgaatgacga tcggtttggg cgcatacagt gcccatgaga cacattttcg
     1321 gacattttca gttcgtgaat ccctgactca ttgctacata tctgaacaga cacccctggc
     1381 agcgccccca ggggcgtcct gtaaaaaaac acaccgcgca gctagcagca cccctaatat
     1441 aagatgatgt tttttatgaa aatagtcagt accaccccta aaaagcggtg tcggcgcggt
     1501 gttgtagctg cgccaacacc gcttttttaa atatcacaaa gagagcaaga agaactaatt
     1561 tgtcataact ctctatttat aaagaaaaat cagcaaaaaa ttgtttttgc gtggggtgtg
     1621 ggcatttcag gcatgagaac agactcgcgt ttttccggag tatcagcgga attattgatt
     1681 aagaaacact cgacgcagag cgaaatttta tgcaacagcg gctgcactgc acagggatta
     1741 tttatcagtt gatatgctgt gccatgatac gtcctaaaga aacaggacag gatgtgcaat
     1801 tgtaataccg tcgcccgcaa cgtcttacaa ttaccacctg ctcagggtcc ccccgacacc
     1861 cggaactgac ggagaacaac ggaaggtgaa caaacaacaa caaactgcgc tgaatatggc
     1921 gcgatttatc aaaagccaga gcctgacact gcttgaaaaa ctggatgctc tggatgctga
     1981 cgaacaggcg gccatgtgcg aacgactgca cgaactcgca gaagaactcc agaacagcat
     2041 ccagattcgc tttgaggccg aaagtgaaac aggaacataa cgaagctgac ggaggcggtc
     2101 acggctttcc cgtgggcgtt ttcgtcagca gacaagcccg tcagggcgcg tcagggggtt
     2161 ttagcgggtg tcggggcgca gccatgaccc agtcacgtag cgatagcgga gtgtatactg
     2221 gcttaactat gtatcatcag tgcagattat aagaaaagag caccatatgc gatgtgaaat
     2281 accgcacaga tgcgtaagga gaaaatgccg catcaggcgc tcttccgctt cctcgctcac
     2341 tgactcgcta cgctcggtcg ttcggctgcg gcgagcggtg ccggctcact caaaggcggt
     2401 aatacggtta tccacagaat caggggataa ggccggaaag aacatgtgag caaaaaggca
     2461 aagggcaacg aaaggccgcg ccgctggcgt ttttccatag gctccgcccc cctgacgagc
     2521 atcacaaaaa tcgacgctca agtcagaggt ggcgaaaccc gacaggacta taaagatacc
     2581 aggcgtttcc ccctggtggc tccctcgtgc gctctcctgt tccgaccctg ccgcttaccg
     2641 gatacctgtc cgcctttctc ccttcgggaa gcgtggcgct ttctcatagc tcacgctgtt
     2701 ggtatctcag ttcggtgtag gtcgttcgct ccaagctggg ctgtgtgcac gaaccccccg
     2761 ttcagcccga ccgctgcgcc ttatccggta actatcgtct tgagtccaac ccggtaagac
     2821 acgacaaagc gccactggca gcagccactg gtaactggac aaggtggatt gagatattaa
     2881 gagttcttga agtggtggcc taactgcggc tacactagaa ggacagtatt tggtatctgt
     2941 gctccaccaa gccagttacc cggttaagca gtccccaact gacttaacct tcgactaaac
     3001 cgcctcccca ggcggttttt tcgtttactg gcagcagatt acgcgcagaa aaaaaggatc
     3061 tcaagaggat cctttgatct tttcatcact cctacttcac ggacaacaat gatatcggca
     3121 tctcgcccgt tgaatcactg aattctccca aggtaagatc ccaaaacaga ccacttacaa
     3181 aaagtaggct acagattgat tcataaggga tttttacatg catcttgaag aagaagatct
     3241 gcgcgcttta gaaagagccg tagaattatt agaacaagat ac
//
