LOCUS       NZ_CP047463             4145 bp    DNA     circular CON 25-JUN-2024
DEFINITION  Escherichia coli strain ZF34 plasmid pZF34-4kb, complete sequence.
ACCESSION   NZ_CP047463
VERSION     NZ_CP047463.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13743100
            Assembly: GCF_011045895.1
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  JOURNAL   Unpublished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_011045895.1-RS_2024_06_25
            Annotation Date                   :: 06/25/2024 03:39:02
            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)                     :: 4,684
            CDSs (total)                      :: 4,562
            Genes (coding)                    :: 4,315
            CDSs (with protein)               :: 4,315
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 16
            Pseudo Genes (total)              :: 247
            CDSs (without protein)            :: 247
            Pseudo Genes (ambiguous residues) :: 0 of 247
            Pseudo Genes (frameshifted)       :: 70 of 247
            Pseudo Genes (incomplete)         :: 181 of 247
            Pseudo Genes (internal stop)      :: 33 of 247
            Pseudo Genes (multiple problems)  :: 35 of 247
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP047463.1.
            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="ZF34"
                     /isolation_source="a feces sample of swine origin"
                     /db_xref="taxon:562"
                     /plasmid="pZF34-4kb"
                     /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            join(3900..4145,1..217)
                     /locus_tag="GTK64_RS22485"
                     /old_locus_tag="GTK64_22420"
                     /pseudo=""
     CDS             join(3900..4145,1..217)
                     /locus_tag="GTK64_RS22485"
                     /old_locus_tag="GTK64_22420"
                     /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(<366..497)
                     /locus_tag="GTK64_RS23565"
                     /pseudo=""
     CDS             complement(<366..497)
                     /locus_tag="GTK64_RS23565"
                     /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(805..918)
                     /locus_tag="GTK64_RS23760"
     CDS             complement(805..918)
                     /locus_tag="GTK64_RS23760"
                     /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(2104..>2286)
                     /locus_tag="GTK64_RS22505"
                     /old_locus_tag="GTK64_22425"
                     /pseudo=""
     CDS             complement(2104..>2286)
                     /locus_tag="GTK64_RS22505"
                     /old_locus_tag="GTK64_22425"
                     /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            <2283..2525
                     /locus_tag="GTK64_RS22510"
                     /old_locus_tag="GTK64_22430"
                     /pseudo=""
     CDS             <2283..2525
                     /locus_tag="GTK64_RS22510"
                     /old_locus_tag="GTK64_22430"
                     /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"
     gene            complement(2563..3705)
                     /gene="wzz(fepE)"
                     /locus_tag="GTK64_RS22515"
                     /old_locus_tag="GTK64_22435"
     CDS             complement(2563..3705)
                     /gene="wzz(fepE)"
                     /locus_tag="GTK64_RS22515"
                     /old_locus_tag="GTK64_22435"
                     /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)"
     Typing          complement(802..1187)
                     /name="rep_cluster_2373"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.373"
                     /coverage="90.0"
                     /evalue="1.04e-173"
ORIGIN
        1 gaaatcgcct ccatgcgtct gtttgcccgg ttacatgaaa gccagcatcc gggccaaggt
       61 ggagcaccca tttcgcatca tcaagcgaca gttcggcttc gtgaaagcca gatacaaggg
      121 gttgctgaaa aacgataacc aactggcgat gttattcacg ctggccaacc tgtttcgggc
      181 ggaccaaatg atacgtcagt gggagagatc tcactaaaaa ctgggaataa cgccttaaat
      241 ggcgaagaaa cggtctaaat aggctgattc aaggcattta cgggagaaaa aaatcggctc
      301 aaacatgaag aaatgaaatg actgagtcaa ccgagaagaa tttccccgct tattcgcacc
      361 ttccctaata gcgcggctgc gattctactt ttttcacctg aacctgaaga ggcgtttgtg
      421 gctccgcagt gtgggcatga ctttgctgtt tcgtgtattt ccttgccgca tcctcggcag
      481 taaaccattg aactcatttt ttatcctcga gcttattttt agttgggatg cataatatcc
      541 gatgttttat aacgatatgc atcctatatg ctcgggtggg atagatttcc attatggtga
      601 aggatcttct tgagatcctt tctgtagcgt cgtaatctct tgctcagtaa acgaaaaaac
      661 cgcccagcaa ggcggttttt cgaaggttct cagagctgca actctttgaa ccgtggtaac
      721 tggcttatga ggagcgcagt aaccaaatct gttctttcag tttagcctta acaggcgcat
      781 aacttcaaga ctaactcctc taaatcagtt accagtggct gctgccagtg gcgctttgtc
      841 gtgtctttcc ggcttggact caagtcgata gttaccggag aagacgcagc ggtcggactg
      901 aacggggggt tcgtgcatac agtccagctt ggagcgaact gcctacccgg aactgagtgt
      961 caggcgtgga atgagataaa cgcggccata acagcggaat gacaccggta aaccgaaagg
     1021 caggaacagg agagcgcacg agggagccac cagggggaaa cgcctggtat ctttaagtcc
     1081 tgtcgggttt cgccaccact gatttgagcg tcagattctg tgatgcttgt caggggggcg
     1141 gagcctatgg aaaaccggca acgccgcggc cttttctttt gcctctcgat cctctctcat
     1201 tgcctgtgcc ttaatgtctc cgttccctcc gctcgccgca gccgaacgac cgagcgtagc
     1261 gagtcagtga gcgaggaagc ggaatatccc cggacttatc ttcggcaccg tacgcgccag
     1321 tgctgcattt tttaatacga tgcaggatag ggctaacgcc gcaaagtgac gtcacctgac
     1381 gttcctggat tacaaaggtt aaagcagcgg acaggaaatg ttttgtgccc acagctatgc
     1441 tggcttattc acaaaacagc gggacaagat gtgtttttgg agtaccgccg gcccgctaaa
     1501 gactcctggt tagctcccgc atgtttgcta tctttttgct accattttgc tacttttttg
     1561 ctatctccag agtcttctgg tctttcggtt gctatccttt tgctactttt ttgctatcaa
     1621 aatgctacct ctcccttctt gcaataaatg accaaggcac gttagcgatg tatacatcgc
     1681 cgcgccgcaa gggtgcccct tccgaatccc gttcatcact gcgtgctgat tcatccacgt
     1741 taaatccgac ccccttagca ataaatccag ccatgcctga cggcctggcc aacgcctcac
     1801 ggccgcacag taaactgcac acccgtgagg cgttattcgt gaggttcagt ggtgcttttg
     1861 ggcgtccagc cggattttag ccgctaaaat cccggccatg catgtgtgtg catagccatg
     1921 cagacgcgcc agaatcatca ggcgcgtttt ttcacgatat aggcacaggg aagtgtcgga
     1981 aacaggcagg aagacccaga aacgccctga gagcctctca ggcggtgcac gcaacggatg
     2041 ttatggtaaa tctgcctcac agactggtac aaaaaaagcc ccgcagggct tttttgctat
     2101 gagttagcca tattttcttg cgaatttttc atcggaatcg catagataaa taataaactc
     2161 aataaacgcg atgatcgcgg gtatgaatgt ccagcaaaaa attagataca ggaatccctg
     2221 tcctatttta cctaagtaaa atttatgtac gccaaatcca ccaaggaaga atgctaagaa
     2281 agatgatggc ggtggaggtc aattttgagc agggtgcgat tggcccgatg cacaatcacc
     2341 cgcatgaaca gcttacctat gtgctctccg gggagttcga gtttacgata ggtgaagaaa
     2401 agcagatcgt gacggcgggc gatacgctct ataaagcgcc gcacgtgatg cacggctgca
     2461 tttgcctgaa gcccggcacc cttctggata cctttacgcc ggtgcgcgac gatttcctga
     2521 aataaaaaaa ggcgctgaat cagcgccttt ttaatatcgt cgttactctg ttgctggcgt
     2581 tacggccgtt atcggctctg gcaacggatt acgcgagagc attgcctcac gcagcagcac
     2641 gctgccgcag gcaaacaggc cgcccagaat ccctgccagc agcacaatca gggctttgcc
     2701 cggaccgtct tttttcaccg gcagtgacgg tgaaagctga tacctgaagg gttcaagctt
     2761 cacgtcttcc acggacagtt tttgcaactg agtcagatag tattcacggt tctggaaatc
     2821 cgcattcagc tcggccacgt ccttcagatt cttttcaatc tgcagctttt gcgcaatacc
     2881 gtcagcaccc agcgccacgg agtagtcagg atcgtctttt accgcctgtc cgttgctgta
     2941 aaccggcttc ttaatgcctg ccgcgttcgc cacttccagc gaatagttga ggcgctgcag
     3001 gttggtgttg tggatattgg tcagacgcac gcgatccagc tccagctgct gctgaacgac
     3061 tttcgttttc agcgtgatct ggttacggat attttccatc gtctcctgct caacaatgcg
     3121 ggagatatag ttgatgtaac cttccagaac cgtctgcgcg tctcccgccg tcggggcggt
     3181 aaagctcagc gtccatgagg tatacggcgc tttgtctgcg tctttaacct gcgtgttatc
     3241 tgtcgctttc attttctcag caatattcac caccgcgcga tgcagctcca gcgggtctac
     3301 ctcggtgcct tccagctgag acatcacgta cggggaggtt ttcatgtact cttcgagcag
     3361 cgactgcgac tgaaactttt tgatgaacag gttaaacacg tctccacggc tcaccttcgc
     3421 gtcgacgtcc agcacctgca gcgtcaccat catctggcgc agcgtgttcc actgcgtctg
     3481 ctcggccggc gtgatcacgg ctttactggt ccatttttgc gggattaaaa acgcaatggc
     3541 caaccctact acggcgaacg ccaggacgat cgtcacaata cgttttttgg ctgccagaag
     3601 tacgtctaac aaccccagga gatctatctc tttggtgctt accgccggag tggcataacg
     3661 gggaaaatcg aggtccgtgt ttttcttgaa atccatcgct gacataaccg ttcttctttt
     3721 tggagcgcag taaatttctg cctgattggt tgcagtggtc ggatgataca agaaagtaag
     3781 aataatctga acgccagatt gatctatctg tagaccgact atcagattta gggaaggtgc
     3841 gaacaagtcc ctgatatgag atcatgtttg tcatctggag ccatggaaca gggttcatca
     3901 tgagtcatca acttaccttc gccgacagtg aattcagcag taagcgccgt cagaccagaa
     3961 aagagatttt cttgtcccgc atggagcaga ttctgccatg gcaaaacatg gtggaagtca
     4021 tcgagccgtt ttaccccaag gctggtaatg gccggcgacc ttatccgctg gaaaccatgc
     4081 tacgcattca ctgcatgcag cattggtaca acctgagcga tggcgcgatc gaagatgctc
     4141 tgtac
//
