LOCUS       NZ_CP046419             4305 bp    DNA     circular CON 18-JUN-2023
DEFINITION  Escherichia coli strain LZYWN_4 plasmid pS4-unknown1, complete
            sequence.
ACCESSION   NZ_CP046419
VERSION     NZ_CP046419.1
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 4305)
  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  JOURNAL   Unpublished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 4305)
  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
            CP046419.1.
            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..4305
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="LZYWN_4"
                     /isolation_source="liver"
                     /host="swine"
                     /db_xref="taxon:562"
                     /plasmid="pS4-unknown1"
                     /geo_loc_name="China:Yangling"
                     /lat_lon="34.16 N 108.02 E"
                     /collection_date="2017-05-21"
                     /collected_by="zengyuan liu"
     gene            complement(join(3998..4305,1..577))
                     /locus_tag="GJV83_RS23775"
                     /old_locus_tag="GJV83_23795"
     CDS             complement(join(3998..4305,1..577))
                     /locus_tag="GJV83_RS23775"
                     /old_locus_tag="GJV83_23795"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001517860.1"
                     /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_001517860.1"
                     /translation="MSNAALHLFNERLPHKPYFSDDLHFGVRIAGKERAILAKYIQFNQ
                     PHAMFWLGFDVDRAGAAIDWSDRNAPAPTLTITNPENGHAHLLYALKTSIRTAPDGKMK
                     PLRYAAAVENALRKKLEADTGYSGLICKNPNHSHWKIAVWQPELYTLDWLADYLDLTTA
                     NDKEIVADYGLGRNCTLFDKTRRWAYRAIRQGWPEYDQWLQACYERASAYNLQFALPLD
                     ENEVMGIAKSIAKWTECNFSKDLFLEYVKNTHSSEIQSKRGKMSKGGGRKSLGEPWVEL
                     GVSRATYFRNRKK"
                     /name="replication initiation protein"
     gene            2166..2642
                     /locus_tag="GJV83_RS23780"
                     /old_locus_tag="GJV83_23805"
     CDS             2166..2642
                     /locus_tag="GJV83_RS23780"
                     /old_locus_tag="GJV83_23805"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_048257201.1"
                     /translation="MISRKSSLTGYIQSKKVSLNMTFSITEVREGRIGSLVITKELYDK
                     LEKYSCSNGLITSTYNHGHGVVRYYTVKYCLQMNYHGQNHPQKYLIKRGGRYPSKYAMV
                     KKTVEELEYSTPTFDAICRNIAIKYPHMVKFANYISETPLKGFAATFNNSVGND"
                     /name="hypothetical protein"
     gene            complement(<2682..>3143)
                     /locus_tag="GJV83_RS23785"
                     /old_locus_tag="GJV83_23810"
                     /pseudo=""
     CDS             complement(<2682..>3143)
                     /locus_tag="GJV83_RS23785"
                     /old_locus_tag="GJV83_23810"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000635827.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus and 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            complement(3360..4001)
                     /locus_tag="GJV83_RS23790"
                     /old_locus_tag="GJV83_23815"
     CDS             complement(3360..4001)
                     /locus_tag="GJV83_RS23790"
                     /old_locus_tag="GJV83_23815"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_152935331.1"
                     /translation="MRLKNWLIPLVAWIVIFMGLKLILGGGCNDGWGSSSIGRMGACSH
                     HGGVNHTPGFIAFFISTAIAAYLFFKIDEMDTRKIKNAHSIQASYFEMESTSAPFNPCY
                     SLRLSSKEINFTHSSSWDGDKTVINIPSSPEELKYILSLSEKIKKDIENFREENTTFGC
                     DGEFVSIKTFNGSQEMSFVTPMLFISFESISPATLEMMTYLRNRLGFDLH"
                     /name="hypothetical protein"
     Typing          1612..1962
                     /name="rep_cluster_2373"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.591"
                     /coverage="81.0"
                     /evalue="2.93e-164"
ORIGIN
        1 gaatagctcg gtatgcccat ctgcgggttt tatcgaacaa agtgcagtta cggcctaagc
       61 cgtaatcagc aacgatttct ttatcgttcg cggtggtcaa gtcgagatag tcagctagcc
      121 agtccagtgt gtacagttct ggctgccaca cggcaatttt ccaatggcta tggttcgggt
      181 ttttgcagat tagtcctgaa taacccgtat cggcctctaa ttttttacgt agcgcgttct
      241 ctacagcggc ggcgtagcgc agcggcttca tttttccgtc tggcgcagta cggatcgaag
      301 ttttcagcgc atagagcagg tgcgcgtgtc cgttttcggg attggtgatg gtcagcgtgg
      361 gcgcgggcgc gttgcggtcg ctccagtcta tggcggcacc ggcgcgatcg acatcgaatc
      421 ccagccagaa catggcgtga ggctgattga actggatata tttcgccaga atggcgcgtt
      481 ctttaccggc aattcgtaca ccaaagtgca gatcgtccga aaagtacggc ttatgcggca
      541 aacgctcatt gaaaagatgg agtgcagcgt tactcaatcc ggcctgcgct tatggcgggc
      601 tgttgtctgg cacggttcat gtgctaagat tcctttaagg tttcgtacct ggccctggtt
      661 atcatgtgca tccgccaaga ttgagcatga tttccggggc ttcgtttttt cttgtcttaa
      721 cgttacaccg tctggcaact tctgtcgaac ccacaacaat ttaccataac atctcttgcg
      781 tgcaccgccg cagaggccct cagcgcgttt ctgccgcgtg cgggccgttt ccggcacctt
      841 tccctgtcca tatcgtgaaa aaacgcgcct gatgatttct gcgcgcctgc atggctatgc
      901 acggaagtga atggcggccg gtttcggacg aatgctggca ctaaaggcga attttgaaca
      961 aaaaaaacgg acatcgaggg tcaggatgtc cgacaaaatt tgcacaaaca gtcagccggt
     1021 accgatcaga gagccggcaa ataagtatga cagtaaaaag tggttatcaa ctgcccccgc
     1081 gctgctgatt gcgcagtttt agggctttgg ccagtgcagg caggcccggc cggaatcagg
     1141 ggatctggta acggtgaacg ggtgcacagt tgactgtgcg gccgtgaggc gttggccaag
     1201 ccgccaggtg cggcagcttc cggtgggtac aaacgccagc actttgcgaa tcctgcccta
     1261 gatctcaaca gcagagaaat ttcgtacgca cgaaactcag cgtatcgggc ggcgcctgat
     1321 gaaacattct ggagtgtcgg cggtactcca aaaacacatc ttgtcccgct gatgttgtca
     1381 ctggcgcaaa gcggcggtaa tgacaagaca tttcctgtcc gcatcaatac gtgcagaaaa
     1441 cgtaagtggt gaaagatgat agtacggagc gacaggagcc taagcagcca ccggagaaat
     1501 tacgcttcct cggtcattcg ctcactgcgt tcggtcatga ctctgcggcg agcgttacgg
     1561 gatcaatcaa agggcgtgga ggtatgaagt gtgagaagag acttaagggc tgccggtttt
     1621 ccataggctc cgcccccctg acaagcatca cgaaatctga cgctcaaatc agcggtggcg
     1681 aaacccgaca ggactataaa gatcccaggc gtttccccct ggtagctccc tcgtgcgctc
     1741 tcctgttcct gcctttcggt ttaccggtgt cattccgctg ttatggccgc gtttatctca
     1801 ttccacgcct gacactcagt tccgggtagg cagttcgctc caagctggac tgtaagcacg
     1861 aaccccccgt tcagtccgac cgctgcgcct tacccggtaa ctatcgtctt gagtccaacc
     1921 cggaaagaca cgacaaaacg ccactggcag cagccattgg tagagggtgt acaagagatt
     1981 actgatgcag agttcttgaa gttagagcca aactacggct aaactggaag gacaaatttg
     2041 gtggcagcgg tcttgtacac cctgttacca cggttcagaa gttcccccaa cttactgaac
     2101 cttcgaaaaa ccacctcccc aggtggtttt ttcgtttctg gataagagac tacgacgaca
     2161 gacggatgat ctcaagaaaa tcctctctaa caggttatat tcagagtaaa aaagtgagct
     2221 taaatatgac tttttcaata acagaagtgc gtgaggggcg tatcggttct ttagttatta
     2281 caaaagagct ttacgataaa ttagaaaaat actcttgctc aaatggatta ataacatcca
     2341 catacaacca tggtcatggc gttgttagat actacaccgt gaaatattgc ctccagatga
     2401 actatcacgg acaaaatcat cctcaaaaat atcttattaa aagagggggg agatatccca
     2461 gcaagtatgc aatggtcaaa aaaaccgttg aagagttaga gtattcaaca ccgacatttg
     2521 acgcaatatg taggaacata gcaataaaat acccacacat ggtcaagttt gctaattaca
     2581 tatcagaaac cccattaaaa ggcttcgccg caacctttaa taactccgtt ggtaatgatt
     2641 aagtgttatt taccataaca tcccttgcgc gcaccgcctg aagcgctaaa agactgctca
     2701 taaatggctc ccttcagtcg gatgtttcgc cccccgtccg ggtcggcaat gctgatactg
     2761 ttttttgtgg tgcggaccac ctcaaaacct gccgctgtga gcgcccctgt gacgtcctcg
     2821 cgcgttttta gctccccgga tgaggctaag gccagcaacc cccgtgtaat cgcctgagcg
     2881 gcttccatct tcgtttccgg cagtgcggac ggcgtgacca gtaaccgccg gttctccggg
     2941 gcgtttggat catgcagccc cagtctgccg ttcaccacgg tctgccaggc atcgatgcgc
     3001 ggccggtcgg cgcgatcgta gtacggctgc aggcgtttcc cggtcagcag ttcagtgttg
     3061 gggatcagga aattcagctc cagccgcccc ttgtcggtgt gctccaccca cagaatgctg
     3121 tactggtctt tatcgagccc gggcggcacg gtgttggaca agccgcaggc gcgtcagtcg
     3181 cttttagcgg gtttcggggc gcagccctga accagtcacg tagcgctagc ggagtgtata
     3241 ctggctgaag ataggtgcag tatgtcagat tctatgctgg ctgcaaaaaa acagccctct
     3301 gctagagagg gctgttatct gatataggtt gtttagtctc actaaagcta agatgacctt
     3361 caatgaaggt caaaacctaa cctattcctt aggtaagtca tcatttcaag cgttgcggga
     3421 gatatacttt caaagctaat gaatagcatt ggggtaacaa agctcatctc ttgggagcca
     3481 ttaaaagttt taatggacac aaactccccg tcacatccaa aagtggtgtt ttcttctcta
     3541 aaattttcaa tgtctttttt tattttctct gataaagata gaatgtattt taactcctcg
     3601 ggggaggatg ggatattaat aacagtcttg tcaccatccc aactagaact gtgagtgaaa
     3661 ttgatttcct ttgaacttaa ccttaacgaa tagcaaggat tgaaaggagc gctagtagac
     3721 tccatttcaa aataacttgc ttgaatgcta tgggcgtttt ttattttcct tgtatccatt
     3781 tcatctattt taaaaaaaag ataggcggca atggccgtgg aaatgaaaaa agcaatgaag
     3841 cctggggtat ggttaacacc gccatgatga gagcaggccc ccatccttcc tattgaggac
     3901 gaaccccatc catcattgca cccgccacct aaaattaact tcaaccccat aaaaataaca
     3961 atccatgcaa caagtgggat aagccagttt ttcaatctca ttttttccga ttcctaaagt
     4021 aagtagctct acttacacct aattcaaccc acggttcgcc aagagacttt ctacctccac
     4081 ctttactcat tttgcctctt tttgattgta tttctgaaga atgcgtattt tttacgtatt
     4141 ccaaaaacaa atctttgctg aaattacact cagtccattt agcaatgctt tttgctattc
     4201 ccataacctc attttcatcc agaggtaatg caaactgcag gttgtaagcg ctggcacgtt
     4261 catagcaggc ttgcagccac tggtcatatt caggccagcc ctgac
//
