LOCUS       NZ_CP047457             4145 bp    DNA     circular CON 25-JUN-2024
DEFINITION  Escherichia coli strain ZF31 plasmid pZF31-4kb, complete sequence.
ACCESSION   NZ_CP047457
VERSION     NZ_CP047457.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13742197
            Assembly: GCF_011045875.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4145)
  AUTHORS   Peng,K. and Li,R.
  TITLE     The genomic epidemiology of tigecycline resistance gene tet(X)
            variants in a swine farm in China
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4145)
  AUTHORS   Peng,K. and Li,R.
  TITLE     Direct Submission
  JOURNAL   Submitted (07-JAN-2020) College of Veterinary Medicine, Yangzhou
            University, No. 567, Wenchang Middle Road, Hanjiang District, Yangz,
            Yangzhou, Jiangsu 225000, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.4
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 50.0x
            Sequencing Technology :: Oxford Nanopore MiniION; Illumina HiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_011045875.1-RS_2024_06_25
            Annotation Date                   :: 06/25/2024 03:50:15
            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)                     :: 4,686
            CDSs (total)                      :: 4,565
            Genes (coding)                    :: 4,318
            CDSs (with protein)               :: 4,318
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 83
            ncRNAs                            :: 16
            Pseudo Genes (total)              :: 247
            CDSs (without protein)            :: 247
            Pseudo Genes (ambiguous residues) :: 0 of 247
            Pseudo Genes (frameshifted)       :: 68 of 247
            Pseudo Genes (incomplete)         :: 182 of 247
            Pseudo Genes (internal stop)      :: 33 of 247
            Pseudo Genes (multiple problems)  :: 34 of 247
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP047457.1.
            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..4145
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="ZF31"
                     /isolation_source="a feces sample of swine origin"
                     /db_xref="taxon:562"
                     /plasmid="pZF31-4kb"
                     /geo_loc_name="China: Nantong, jiangsu province"
                     /lat_lon="31.41 N 120.11 E"
                     /collection_date="2018-05"
                     /collected_by="College of Veterinary Medicine, Yangzhou
                     University"
     gene            complement(join(3069..4145,1..66))
                     /gene="wzz(fepE)"
                     /locus_tag="GTK48_RS22470"
                     /old_locus_tag="GTK48_22410"
     CDS             complement(join(3069..4145,1..66))
                     /gene="wzz(fepE)"
                     /locus_tag="GTK48_RS22470"
                     /old_locus_tag="GTK48_22410"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010435173.1"
                     /GO_component="GO:0016020 - membrane [Evidence IEA]"
                     /GO_process="GO:0009103 - lipopolysaccharide biosynthetic
                     process [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="LPS O-antigen length regulator Wzz(fepE)"
                     /protein_id="WP_021544858.1"
                     /translation="MSAMDFKKNTDLDFPRYATPAVSTKEIDLLGLLDVLLAAKKRIVT
                     IVLAFAVVGLAIAFLIPQKWTSKAVITPAEQTQWNTLRQMMVTLQVLDVDAKVSRGDVF
                     NLFIKKFQSQSLLEEYMKTSPYVMSQLEGTEVDPLELHRAVVNIAEKMKATDNTQVKDA
                     DKAPYTSWTLSFTAPTAGDAQTVLEGYINYISRIVEQETMENIRNQITLKTKVVQQQLE
                     LDRVRLTNIHNTNLQRLNYSLEVANAAGIKKPVYSNGQAVKDDPDYSVALGADGIAQKL
                     QIEKNLKDVAELNADFQNREYYLTQLQKLSVEDVKLEPFRYQLSPSLPVKKDGPGKALI
                     VLLAGILGGLFACGSVLLREAMLSRNPLPEPITAVTPATE"
                     /name="wzz(fepE)"
     gene            261..723
                     /locus_tag="GTK48_RS22475"
                     /old_locus_tag="GTK48_22415"
                     /pseudo=""
     CDS             261..723
                     /locus_tag="GTK48_RS22475"
                     /old_locus_tag="GTK48_22415"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_416498.2"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="transposase"
                     /name="transposase"
     gene            complement(<872..1003)
                     /locus_tag="GTK48_RS23570"
                     /pseudo=""
     CDS             complement(<872..1003)
                     /locus_tag="GTK48_RS23570"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_013578013.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="zinc-ribbon domain-containing protein"
                     /name="zinc-ribbon domain-containing protein"
     gene            complement(1311..1424)
                     /locus_tag="GTK48_RS23750"
     CDS             complement(1311..1424)
                     /locus_tag="GTK48_RS23750"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /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_071778980.1"
                     /translation="MHEPPVQSDRCVFSGNYRLESKPERHDKAPLAAATGN"
                     /name="replication initiation protein"
     gene            complement(2610..>2792)
                     /locus_tag="GTK48_RS22495"
                     /old_locus_tag="GTK48_22420"
                     /pseudo=""
     CDS             complement(2610..>2792)
                     /locus_tag="GTK48_RS22495"
                     /old_locus_tag="GTK48_22420"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007798797.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="NINE protein"
                     /name="NINE protein"
     gene            <2789..3031
                     /locus_tag="GTK48_RS22500"
                     /old_locus_tag="GTK48_22425"
                     /pseudo=""
     CDS             <2789..3031
                     /locus_tag="GTK48_RS22500"
                     /old_locus_tag="GTK48_22425"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_003862821.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="cupin domain-containing protein"
                     /name="cupin domain-containing protein"
     Typing          complement(1308..1693)
                     /name="rep_cluster_2373"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.373"
                     /coverage="90.0"
                     /evalue="1.04e-173"
ORIGIN
        1 taccgccgga gtggcataac ggggaaaatc gaggtccgtg tttttcttga aatccatcgc
       61 tgacataacc gttcttcttt ttggagcgca gtaaatttct gcctgattgg ttgcagtggt
      121 cggatgatac aagaaagtaa gaataatctg aacgccagat tgatctatct gtagaccgac
      181 tatcagattt agggaaggtg cgaacaagtc cctgatatga gatcatgttt gtcatctgga
      241 gccatggaac agggttcatc atgagtcatc aacttacctt cgccgacagt gaattcagca
      301 gtaagcgccg tcagaccaga aaagagattt tcttgtcccg catggagcag attctgccat
      361 ggcaaaacat ggtggaagtc atcgagccgt tttaccccaa ggctggtaat ggccggcgac
      421 cttatccgct ggaaaccatg ctacgcattc actgcatgca gcattggtac aacctgagcg
      481 atggcgcgat cgaagatgct ctgtacgaaa tcgcctccat gcgtctgttt gcccggttac
      541 atgaaagcca gcatccgggc caaggtggag cacccatttc gcatcatcaa gcgacagttc
      601 ggcttcgtga aagccagata caaggggttg ctgaaaaacg ataaccaact ggcgatgtta
      661 ttcacgctgg ccaacctgtt tcgggcggac caaatgatac gtcagtggga gagatctcac
      721 taaaaactgg gaataacgcc ttaaatggcg aagaaacggt ctaaataggc tgattcaagg
      781 catttacggg agaaaaaaat cggctcaaac atgaagaaat gaaatgactg agtcaaccga
      841 gaagaatttc cccgcttatt cgcaccttcc ctaatagcgc ggctgcgatt ctactttttt
      901 cacctgaacc tgaagaggcg tttgtggctc cgcagtgtgg gcatgacttt gctgtttcgt
      961 gtatttcctt gccgcatcct cggcagtaaa ccattgaact cattttttat cctcgagctt
     1021 atttttagtt gggatgcata atatccgatg ttttataacg atatgcatcc tatatgctcg
     1081 ggtgggatag atttccatta tggtgaagga tcttcttgag atcctttctg tagcgtcgta
     1141 atctcttgct cagtaaacga aaaaaccgcc cagcaaggcg gtttttcgaa ggttctcaga
     1201 gctgcaactc tttgaaccgt ggtaactggc ttatgaggag cgcagtaacc aaatctgttc
     1261 tttcagttta gccttaacag gcgcataact tcaagactaa ctcctctaaa tcagttacca
     1321 gtggctgctg ccagtggcgc tttgtcgtgt ctttccggct tggactcaag tcgatagtta
     1381 ccggagaaga cgcagcggtc ggactgaacg gggggttcgt gcatacagtc cagcttggag
     1441 cgaactgcct acccggaact gagtgtcagg cgtggaatga gataaacgcg gccataacag
     1501 cggaatgaca ccggtaaacc gaaaggcagg aacaggagag cgcacgaggg agccaccagg
     1561 gggaaacgcc tggtatcttt aagtcctgtc gggtttcgcc accactgatt tgagcgtcag
     1621 attctgtgat gcttgtcagg ggggcggagc ctatggaaaa ccggcaacgc cgcggccttt
     1681 tcttttgcct ctcgatcctc tctcattgcc tgtgccttaa tgtctccgtt ccctccgctc
     1741 gccgcagccg aacgaccgag cgtagcgagt cagtgagcga ggaagcggaa tatccccgga
     1801 cttatcttcg gcaccgtacg cgccagtgct gcatttttta atacgatgca ggatagggct
     1861 aacgccgcaa agtgacgtca cctgacgttc ctggattaca aaggttaaag cagcggacag
     1921 gaaatgtttt gtgcccacag ctatgctggc ttattcacaa aacagcggga caagatgtgt
     1981 ttttggagta ccgccggccc gctaaagact cctggttagc tcccgcatgt ttgctatctt
     2041 tttgctacca ttttgctact tttttgctat ctccagagtc ttctggtctt tcggttgcta
     2101 tccttttgct acttttttgc tatcaaaatg ctacctctcc cttcttgcaa taaatgacca
     2161 aggcacgtta gcgatgtata catcgccgcg ccgcaagggt gccccttccg aatcccgttc
     2221 atcactgcgt gctgattcat ccacgttaaa tccgaccccc ttagcaataa atccagccat
     2281 gcctgacggc ctggccaacg cctcacggcc gcacagtaaa ctgcacaccc gtgaggcgtt
     2341 attcgtgagg ttcagtggtg cttttgggcg tccagccgga ttttagccgc taaaatcccg
     2401 gccatgcatg tgtgtgcata gccatgcaga cgcgccagaa tcatcaggcg cgttttttca
     2461 cgatataggc acagggaagt gtcggaaaca ggcaggaaga cccagaaacg ccctgagagc
     2521 ctctcaggcg gtgcacgcaa cggatgttat ggtaaatctg cctcacagac tggtacaaaa
     2581 aaagccccgc agggcttttt tgctatgagt tagccatatt ttcttgcgaa tttttcatcg
     2641 gaatcgcata gataaataat aaactcaata aacgcgatga tcgcgggtat gaatgtccag
     2701 caaaaaatta gatacaggaa tccctgtcct attttaccta agtaaaattt atgtacgcca
     2761 aatccaccaa ggaagaatgc taagaaagat gatggcggtg gaggtcaatt ttgagcaggg
     2821 tgcgattggc ccgatgcaca atcacccgca tgaacagctt acctatgtgc tctccgggga
     2881 gttcgagttt acgataggtg aagaaaagca gatcgtgacg gcgggcgata cgctctataa
     2941 agcgccgcac gtgatgcacg gctgcatttg cctgaagccc ggcacccttc tggatacctt
     3001 tacgccggtg cgcgacgatt tcctgaaata aaaaaaggcg ctgaatcagc gcctttttaa
     3061 tatcgtcgtt actctgttgc tggcgttacg gccgttatcg gctctggcaa cggattacgc
     3121 gagagcattg cctcacgcag cagcacgctg ccgcaggcaa acaggccgcc cagaatccct
     3181 gccagcagca caatcagggc tttgcccgga ccgtcttttt tcaccggcag tgacggtgaa
     3241 agctgatacc tgaagggttc aagcttcacg tcttccacgg acagtttttg caactgagtc
     3301 agatagtatt cacggttctg gaaatccgca ttcagctcgg ccacgtcctt cagattcttt
     3361 tcaatctgca gcttttgcgc aataccgtca gcacccagcg ccacggagta gtcaggatcg
     3421 tcttttaccg cctgtccgtt gctgtaaacc ggcttcttaa tgcctgccgc gttcgccact
     3481 tccagcgaat agttgaggcg ctgcaggttg gtgttgtgga tattggtcag acgcacgcga
     3541 tccagctcca gctgctgctg aacgactttc gttttcagcg tgatctggtt acggatattt
     3601 tccatcgtct cctgctcaac aatgcgggag atatagttga tgtaaccttc cagaaccgtc
     3661 tgcgcgtctc ccgccgtcgg ggcggtaaag ctcagcgtcc atgaggtata cggcgctttg
     3721 tctgcgtctt taacctgcgt gttatctgtc gctttcattt tctcagcaat attcaccacc
     3781 gcgcgatgca gctccagcgg gtctacctcg gtgccttcca gctgagacat cacgtacggg
     3841 gaggttttca tgtactcttc gagcagcgac tgcgactgaa actttttgat gaacaggtta
     3901 aacacgtctc cacggctcac cttcgcgtcg acgtccagca cctgcagcgt caccatcatc
     3961 tggcgcagcg tgttccactg cgtctgctcg gccggcgtga tcacggcttt actggtccat
     4021 ttttgcggga ttaaaaacgc aatggccaac cctactacgg cgaacgccag gacgatcgtc
     4081 acaatacgtt ttttggctgc cagaagtacg tctaacaacc ccaggagatc tatctctttg
     4141 gtgct
//
