LOCUS       NZ_CP046420             4237 bp    DNA     circular CON 18-JUN-2023
DEFINITION  Escherichia coli strain LZYWN_4 plasmid pS4-unknown2, complete
            sequence.
ACCESSION   NZ_CP046420
VERSION     NZ_CP046420.1
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 4237)
  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  JOURNAL   Unpublished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 4237)
  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
            CP046420.1.
            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..4237
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="LZYWN_4"
                     /isolation_source="liver"
                     /host="swine"
                     /db_xref="taxon:562"
                     /plasmid="pS4-unknown2"
                     /geo_loc_name="China:Yangling"
                     /lat_lon="34.16 N 108.02 E"
                     /collection_date="2017-05-21"
                     /collected_by="zengyuan liu"
     gene            join(3878..4237,1..156)
                     /locus_tag="GJV83_RS23795"
                     /old_locus_tag="GJV83_23820"
     CDS             join(3878..4237,1..156)
                     /locus_tag="GJV83_RS23795"
                     /old_locus_tag="GJV83_23820"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000097059.1"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA];
                     GO:0006276 - plasmid maintenance [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication/maintenance protein RepL"
                     /protein_id="WP_000097059.1"
                     /translation="MSSLSLQRYETNPFLELMTIPMKGKRIQVSRLGRDDNVLVNQNTG
                     EKFGTHVTTFKRVDSEQFVKLFTANIGLTFDLSSAGIKAFNVLLWAVQKQAFAKDQVLL
                     DSRALDDFLKSYDSLKLSYATLKRGINELEKAQIIAKTMRKGFYFINPNFVFNGDRIAF
                     TTLIERDC"
                     /name="replication/maintenance protein RepL"
     gene            337..627
                     /locus_tag="GJV83_RS23800"
                     /old_locus_tag="GJV83_23825"
     CDS             337..627
                     /locus_tag="GJV83_RS23800"
                     /old_locus_tag="GJV83_23825"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000160396.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="transcriptional regulator"
                     /protein_id="WP_024241218.1"
                     /translation="MTKHDAIRISQLHQIFYDDDGLIDSEKNVTILYSIGFTVDEIAHF
                     RNSTPNTVASQLLNARVKLGCASVSSLKPMILLRLLLNIKEIRFGFETDCK"
                     /name="transcriptional regulator"
     gene            715..978
                     /locus_tag="GJV83_RS23805"
                     /old_locus_tag="GJV83_23830"
     CDS             715..978
                     /locus_tag="GJV83_RS23805"
                     /old_locus_tag="GJV83_23830"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001677227.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="EexN family lipoprotein"
                     /protein_id="WP_000717655.1"
                     /translation="MKKICTLLMSIFILSACGEDTKSSDWWLNHPKEATEKYKECKKSG
                     EDSVNCQNVKKVAGIIGRTYGPMLEILKAESAEYDKQHGLNR"
                     /name="EexN family lipoprotein"
     gene            983..1981
                     /locus_tag="GJV83_RS23810"
                     /old_locus_tag="GJV83_23835"
     CDS             983..1981
                     /locus_tag="GJV83_RS23810"
                     /old_locus_tag="GJV83_23835"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000012467.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type IV secretion system protein"
                     /protein_id="WP_000012467.1"
                     /translation="MSGFFEKFNSEVVSKIEEMTKPLQSQLGQDMLSLLSAGISVYILW
                     VGYQILAGKRQTPLQDLVWDLSKFAIILTFVSNADGYLTAAMDAIKSMKDGFLGKPVWA
                     TLDTMWSTTQLLADKVYAMDQSKYVSVEGGIGSMLVWGGSILIMSVAAVIYMLADVTMQ
                     LAILVAPIFIGCYMFGFTRVMFNNWLGILFSSVFTVIFAGVLVKIGTEFQTDMLSQISR
                     DANSTNILTMGAMAFVIGVLIAVFVWKSSSFAQQLAGAGVEGTLQGMALLGIGAAGMAV
                     EKTRNQMKRGTRTAAEWAGEKGEQKRASIGALGMEARRRASLEKARARNSA"
                     /name="type IV secretion system protein"
     gene            1978..2691
                     /locus_tag="GJV83_RS23815"
                     /old_locus_tag="GJV83_23840"
     CDS             1978..2691
                     /locus_tag="GJV83_RS23815"
                     /old_locus_tag="GJV83_23840"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001590713.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type IV secretion system protein"
                     /protein_id="WP_001590713.1"
                     /translation="MNKKLIFSVLLCLFSFGSVAGIPVAIDASPEWAVEATRWTERLKQ
                     WSETARHYQSQIQAYKDQLATATGIRNIAAFTNELSNLQSELANIYKQGNSYISDFTSN
                     PEGALSSQAKNLFSKYGAFNMCSTGIESSDNLCKARIVSTAASIEQGNEINKQLSSAMS
                     QIQSLSNRIESSKDMKESQDLANALQAQSLKIQAIKMQYDVWDSKNRADAEMLKEQKYA
                     EYRLRQKNAKIPSFE"
                     /name="type IV secretion system protein"
     Typing          984..1786
                     /name="MPF_T"
                     /typing="mate-pair-formation"
                     /tool="MOB-suite"
                     /identity="89.552"
                     /coverage="91.0"
                     /evalue="1.15e-160"
ORIGIN
        1 cttagttatg ctacgttaaa gagaggaatt aacgagttag aaaaagctca gattatagca
       61 aagacaatgc gtaaaggatt ttattttata aaccccaatt ttgtatttaa tggagatcga
      121 atagcattta caaccctaat tgagagggat tgttaatcga tagaacaata caatgcagga
      181 tagacaatca tggtcaaaat gttaacattt tatccatgat tgtccaaaaa cgatgttttt
      241 gcctgtgcct gccgcaggct actagaagta gtcgcaggcg aacaaaagtg gtgttttgtt
      301 cgcctgctaa tcacaacaac ctggctagag gtttttatga ctaaacatga tgctatacgc
      361 atttctcaac ttcatcaaat tttttacgat gatgatggat taattgattc agaaaagaac
      421 gtgactattt tatacagtat aggatttaca gttgatgaaa tagctcattt tagaaattca
      481 acaccaaaca cagttgcgag tcagctatta aatgcaaggg ttaaattagg ttgcgcctcg
      541 gtttcatctt taaagccaat gatcttatta agattgcttt tgaacataaa agagattcgt
      601 tttggattcg aaactgattg caaataatat agttcaatag gtatttttgc tcttgactag
      661 aattacaatt gctgattgta tcagcaattg taatgtccat acgaggaatc aaagatgaaa
      721 aaaatttgta cgctcttaat gtctattttc attctttccg catgtggtga agatacaaaa
      781 tcatcagatt ggtggcttaa tcatcccaaa gaagcgacgg agaaatataa ggagtgtaaa
      841 aagtcagggg aagattctgt taattgtcaa aatgttaaaa aagttgccgg aattattggt
      901 agaacctatg gccctatgct tgaaatactt aaggctgagt cagctgaata tgataagcaa
      961 catggattga acaggtgata acatgtctgg tttctttgaa aagtttaata gcgaagttgt
     1021 tagtaaaatc gaagagatga ccaaaccact tcaaagtcaa ttaggtcagg atatgttatc
     1081 tcttctaagt gcaggtatta gcgtttatat cctctgggtt ggctatcaaa tattggcagg
     1141 gaaacgccag accccattac aagatctcgt ctgggatcta tcaaaatttg ccattatttt
     1201 aacattcgta agcaatgctg atggctatct gacggcagca atggatgcta ttaaatctat
     1261 gaaggatggg ttccttggta aacctgtatg ggcaacgcta gataccatgt ggagtacaac
     1321 tcagcttttg gctgacaaag tttatgctat ggatcaatcc aaatatgtgt cagttgaagg
     1381 tggaatcggg tcaatgttgg tttggggagg aagtatcctg attatgtctg tagcggctgt
     1441 tatttacatg cttgccgatg taacaatgca gttagctatt cttgtagctc cgatatttat
     1501 cggttgttat atgtttggat tcactagagt aatgtttaat aactggcttg gtatattatt
     1561 ttctagtgta tttactgtta tttttgctgg agttctcgtc aaaattggta ccgagtttca
     1621 aactgatatg cttagtcaga tatcgagaga tgctaactca acaaatattt taacaatggg
     1681 cgcaatggca tttgtaattg gagttctgat tgctgtcttt gtctggaaat catcgagttt
     1741 cgcgcagcag cttgccggtg caggtgttga aggtactctt cagggaatgg ctcttttagg
     1801 gattggggct gctggaatgg ccgtagagaa aacgagaaac cagatgaaac gtggaacgcg
     1861 aacagccgcc gaatgggcag gtgaaaaagg ggagcagaaa cgggcttcaa taggcgcatt
     1921 gggaatggaa gcaagaagac gagcatccct ggaaaaagca cgtgcgagga attcagcatg
     1981 aacaaaaaac taattttttc agtacttttg tgcttatttt catttggttc tgtcgcaggt
     2041 attccggttg ctattgatgc cagtccggaa tgggctgttg aagccacaag atggacagaa
     2101 cgactcaaac aatggtctga aacagcgcgg cattatcaaa gtcagattca ggcatataaa
     2161 gaccagttag ccacggcaac aggtataagg aatattgcgg cattcacaaa tgaactaagt
     2221 aacctacaat cagagctggc aaacatttat aagcagggga acagttatat ttctgatttt
     2281 accagtaatc ctgaaggtgc attaagtagt caggcgaaaa atctgttcag caagtatggt
     2341 gcttttaata tgtgttctac aggcattgaa agttctgata acctttgtaa ggccagaata
     2401 gtttcaacgg ccgctagcat tgaacaggga aatgagataa ataagcagct atcaagtgca
     2461 atgtctcaga ttcagagttt aagtaaccga attgagtctt caaaggatat gaaagaatcc
     2521 caggatttgg ctaacgcatt gcaggcgcag tcgttaaaaa tacaggcaat taaaatgcag
     2581 tatgatgtat gggatagtaa aaacagggct gatgcggaaa tgttgaaaga gcaaaagtat
     2641 gctgagtatc gcctgcgtca gaaaaatgca aagataccga gtttcgaatg atatgataaa
     2701 gctaaataag ctaaaagaat gggtagataa tcattggtct agattgaata gtaccggttc
     2761 tacaccgccg ccactgttaa tctcgctacc aatcatagtt attgttttaa gtgtggagct
     2821 tacgttaaag ctgattaatg ctttaatgta ttatggtaca ttgcaattta tcactgataa
     2881 aattgaaaag aggtttgttc ccagcggtgg tataaaagaa agactccttt ttacgttaaa
     2941 gctgttttgt attttacttc tgttattaat agtaatgcga ttttcaatga agtaaaaaat
     3001 aaaggtcatc gaatagatgg ccttttctat tctaaattct aaatatagag cctgcggcag
     3061 gcacaggcaa aaacatcgtt tttggacaat ctgattcaaa tgttaacatt tgacatcgga
     3121 ttgtctatcc tgcattgctc ttttgccgac ctcaaaaccc ctagcgtgtt tttgtttccc
     3181 gatctctaga accaccgagc cgccacggtt ccggcagcgc cttgagcgca accggaaacc
     3241 gtctggggag aaccccagac ccccatcgct gtaacatcga cggtctacga ccacctacca
     3301 accgtgtggc tacctgttcc atgctaatgg gctttgcagg gggctggcgc ggttcctggc
     3361 gacctgaaag cccctggtta ggggtatcgg cgcgtctgac ctcctgaaac cctctgtaag
     3421 catttttcgc gccttccatg ccctgacggg catctaaagc ccgtttcgtg cgtctgagcg
     3481 cgttttaaga gctaagacga ctaaaacatt accaacacct gaaaatcgcg ttctggtgct
     3541 ctggatggcc cacagaacgc attttcgaac agaacagcaa cggcatttct gacaacatgc
     3601 gagaggtgat cccgctcgcc gcagccccag cgaccgaacg tagtgagcga gtgggcgagg
     3661 aagcggaaga gaattgatag ccataattga gcacctacgc tccttagtta agaactaaga
     3721 agggaaattc tcggaacccg catgaatcct agaaagtggt gatcaggatc tgtaccttgt
     3781 aagctcagat ccggtacctt gcaggctcaa aaattgcttg attttgagct tatgaggatt
     3841 tattgtgaat ctccaaagcc caaaaaagga tgcaataatg agctcgctaa gcttacagag
     3901 atacgaaaca aacccgtttt tagagcttat gacgatcccg atgaaaggga aacggataca
     3961 agtatctcgt cttgggcggg atgacaatgt tttggttaat caaaacacgg gagaaaagtt
     4021 tggaacacat gtaaccactt ttaagcgtgt agatagtgag caatttgtta agttgtttac
     4081 tgcgaatatt gggttaacgt ttgatttatc atcggcagga attaaagctt ttaatgttct
     4141 tttatgggct gttcaaaaac aagcctttgc aaaggatcag gttcttttgg attcaagggc
     4201 tcttgatgac tttttaaaaa gctatgatag cttaaaa
//
