LOCUS       NZ_CP041445             4664 bp    DNA     circular CON 21-JUN-2024
DEFINITION  Escherichia coli strain YPE10 plasmid pYPE10-4k, complete sequence.
ACCESSION   NZ_CP041445
VERSION     NZ_CP041445.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN12233488
            Assembly: GCF_008807135.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4664)
  AUTHORS   Li,R., Lu,X., Liu,Z., Liu,Y., Xiao,X. and Wang,Z.
  TITLE     Application of Nanopore Sequencing for Rapid Characterization of
            tet(X4)-positive E. coli strains
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4664)
  AUTHORS   Li,R., Lu,X., Liu,Z., Liu,Y., Xiao,X. and Wang,Z.
  TITLE     Direct Submission
  JOURNAL   Submitted (09-JUL-2019) College of Veterinary Medicine (Institute of
            Comparative Medicine), Yangzhou University, Wenhui Road, Yangzhou,
            Jiangsu 225009, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.4
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 80X
            Sequencing Technology :: Oxford Nanopore MinION, Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_008807135.1-RS_2024_06_21
            Annotation Date                   :: 06/21/2024 03:32:59
            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)                     :: 5,067
            CDSs (total)                      :: 4,946
            Genes (coding)                    :: 4,692
            CDSs (with protein)               :: 4,692
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 254
            CDSs (without protein)            :: 254
            Pseudo Genes (ambiguous residues) :: 0 of 254
            Pseudo Genes (frameshifted)       :: 53 of 254
            Pseudo Genes (incomplete)         :: 192 of 254
            Pseudo Genes (internal stop)      :: 42 of 254
            Pseudo Genes (multiple problems)  :: 30 of 254
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP041445.1.
            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..4664
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="YPE10"
                     /isolation_source="Pork"
                     /db_xref="taxon:562"
                     /plasmid="pYPE10-4k"
                     /geo_loc_name="China: Yangzhou"
                     /lat_lon="32.24 N 119.26 E"
                     /collection_date="2019-06"
                     /collected_by="Xiaoyu Lu"
     gene            complement(join(3723..4664,1..201))
                     /gene="wzz(fepE)"
                     /locus_tag="FNP79_RS00485"
                     /old_locus_tag="FNP79_00485"
     CDS             complement(join(3723..4664,1..201))
                     /gene="wzz(fepE)"
                     /locus_tag="FNP79_RS00485"
                     /old_locus_tag="FNP79_00485"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /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: GeneMarkS-2+."
                     /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            396..1377
                     /locus_tag="FNP79_RS00490"
                     /old_locus_tag="FNP79_00490"
     CDS             join(396..1187,1189..1377)
                     /locus_tag="FNP79_RS00490"
                     /old_locus_tag="FNP79_00490"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_048909999.1"
                     /ribosomal_slippage=""
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /GO_process="GO:0006313 - DNA transposition [Evidence IEA]"
                     /note="programmed frameshift; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS5-like element IS5 family transposase"
                     /protein_id="WP_225899375.1"
                     /translation="MSHQLTFADSEFSSKRRQTRKEIFLSRMEQILPWQNMVEVIEPFY
                     PKAGNGRRPYPLETMLRIHCMQHWYNLSDGAIEDALYEIASMRLFARLSLDSALPDRTT
                     IMNFRHLLEQHQLARQLFKTINRWLAEAGVMMTQGTLVDATIIEAPSSTKNKEQQRDPE
                     MHQTKKGNQWHFGMKAHIGVDAKSGLTHSLVTTAANEHDLNQLGNLLHGEEQFVSADAG
                     YQGAPQREELAEVDVDWLIAERPGKVRTLKQHPRKNKTAHQHEYMKASIRAKVEHPFRI
                     IKRQFGFVKARYKGLLKNDNQLAMLFTLANLFRADQMIRQWERSH"
                     /name="IS5-like element IS5 family transposase"
     gene            complement(<1526..1657)
                     /locus_tag="FNP79_RS25870"
                     /old_locus_tag="FNP79_00495"
                     /pseudo=""
     CDS             complement(<1526..1657)
                     /locus_tag="FNP79_RS25870"
                     /old_locus_tag="FNP79_00495"
                     /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(1965..2078)
                     /locus_tag="FNP79_RS00505"
                     /old_locus_tag="FNP79_00505"
     CDS             complement(1965..2078)
                     /locus_tag="FNP79_RS00505"
                     /old_locus_tag="FNP79_00505"
                     /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(3264..>3446)
                     /locus_tag="FNP79_RS00515"
                     /old_locus_tag="FNP79_00515"
                     /pseudo=""
     CDS             complement(3264..>3446)
                     /locus_tag="FNP79_RS00515"
                     /old_locus_tag="FNP79_00515"
                     /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            <3443..3685
                     /locus_tag="FNP79_RS00520"
                     /old_locus_tag="FNP79_00520"
                     /pseudo=""
     CDS             <3443..3685
                     /locus_tag="FNP79_RS00520"
                     /old_locus_tag="FNP79_00520"
                     /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(1962..2347)
                     /name="rep_cluster_2373"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.373"
                     /coverage="90.0"
                     /evalue="1.04e-173"
ORIGIN
        1 actggtccat ttttgcggga ttaaaaacgc aatggccaac cctactacgg cgaacgccag
       61 gacgatcgtc acaatacgtt ttttggctgc cagaagtacg tctaacaacc ccaggagatc
      121 tatctctttg gtgcttaccg ccggagtggc ataacgggga aaatcgaggt ccgtgttttt
      181 cttgaaatcc atcgctgaca taaccgttct tctttttgga gcgcagtaaa tttctgcctg
      241 attggttgca gtggtcggat gatacaagaa agtaagaata atctgaacgc cagattgatc
      301 tatctgtaga ccgactatca gatttaggga aggtgcgaac aagtccctga tatgagatca
      361 tgtttgtcat ctggagccat ggaacagggt tcatcatgag tcatcaactt accttcgccg
      421 acagtgaatt cagcagtaag cgccgtcaga ccagaaaaga gattttcttg tcccgcatgg
      481 agcagattct gccatggcaa aacatggtgg aagtcatcga gccgttttac cccaaggctg
      541 gtaatggccg gcgaccttat ccgctggaaa ccatgctacg cattcactgc atgcagcatt
      601 ggtacaacct gagcgatggc gcgatcgaag atgctctgta cgaaatcgcc tccatgcgtc
      661 tgtttgcccg gttatccctg gatagcgcct tgccggaccg caccaccatc atgaatttcc
      721 gccacctgct ggagcagcat caactggccc gccaattatt caagaccatc aatcgctggc
      781 tggccgaagc aggcgtcatg atgactcaag gcaccttggt cgatgccacc atcattgagg
      841 cacccagctc gaccaagaac aaagagcagc aacgcgatcc ggagatgcat cagactaaga
      901 aaggcaatca gtggcacttt ggcatgaagg cccacattgg tgtcgatgcc aagagtggcc
      961 tgacccacag cctagtcacc accgcggcca acgagcatga cctcaatcag ctgggtaatc
     1021 tgctgcatgg agaggagcaa tttgtctcag ccgatgccgg ctaccaaggg gcgccacagc
     1081 gcgaggagct ggccgaggtg gatgtggact ggctgatcgc cgagcgcccc ggcaaggtaa
     1141 gaaccttgaa acagcatcca cgcaagaaca aaacggccca tcaacatcga atacatgaaa
     1201 gccagcatcc gggccaaggt ggagcaccca tttcgcatca tcaagcgaca gttcggcttc
     1261 gtgaaagcca gatacaaggg gttgctgaaa aacgataacc aactggcgat gttattcacg
     1321 ctggccaacc tgtttcgggc ggaccaaatg atacgtcagt gggagagatc tcactaaaaa
     1381 ctgggaataa cgccttaaat ggcgaagaaa cggtctaaat aggctgattc aaggcattta
     1441 cgggagaaaa aaatcggctc aaacatgaag aaatgaaatg actgagtcaa ccgagaagaa
     1501 tttccccgct tattcgcacc ttccctaata gcgcggctgc gattctactt ttttcacctg
     1561 aacctgaaga ggcgtttgtg gctccgcagt gtgggcatga ctttgctgtt tcgtgtattt
     1621 ccttgccgca tcctcggcag taaaccattg aactcatttt ttatcctcga gcttattttt
     1681 agttgggatg cataatatcc gatgttttat aacgatatgc atcctatatg ctcgggtggg
     1741 atagatttcc attatggtga aggatcttct tgagatcctt tctgtagcgt cgtaatctct
     1801 tgctcagtaa acgaaaaaac cgcccagcaa ggcggttttt cgaaggttct cagagctgca
     1861 actctttgaa ccgtggtaac tggcttatga ggagcgcagt aaccaaatct gttctttcag
     1921 tttagcctta acaggcgcat aacttcaaga ctaactcctc taaatcagtt accagtggct
     1981 gctgccagtg gcgctttgtc gtgtctttcc ggcttggact caagtcgata gttaccggag
     2041 aagacgcagc ggtcggactg aacggggggt tcgtgcatac agtccagctt ggagcgaact
     2101 gcctacccgg aactgagtgt caggcgtgga atgagataaa cgcggccata acagcggaat
     2161 gacaccggta aaccgaaagg caggaacagg agagcgcacg agggagccac cagggggaaa
     2221 cgcctggtat ctttaagtcc tgtcgggttt cgccaccact gatttgagcg tcagattctg
     2281 tgatgcttgt caggggggcg gagcctatgg aaaaccggca acgccgcggc cttttctttt
     2341 gcctctcgat cctctctcat tgcctgtgcc ttaatgtctc cgttccctcc gctcgccgca
     2401 gccgaacgac cgagcgtagc gagtcagtga gcgaggaagc ggaatatccc cggacttatc
     2461 ttcggcaccg tacgcgccag tgctgcattt tttaatacga tgcaggatag ggctaacgcc
     2521 gcaaagtgac gtcacctgac gttcctggat tacaaaggtt aaagcagcgg acaggaaatg
     2581 ttttgtgccc acagctatgc tggcttattc acaaaacagc gggacaagat gtgtttttgg
     2641 agtaccgccg gcccgctaaa gactcctggt tagctcccgc atgtttgcta tctttttgct
     2701 accattttgc tacttttttg ctatctccag agtcttctgg tctttcggtt gctatccttt
     2761 tgctactttt ttgctatcaa aatgctacct ctcccttctt gcaataaatg accaaggcac
     2821 gttagcgatg tatacatcgc cgcgccgcaa gggtgcccct tccgaatccc gttcatcact
     2881 gcgtgctgat tcatccacgt taaatccgac ccccttagca ataaatccag ccatgcctga
     2941 cggcctggcc aacgcctcac ggccgcacag taaactgcac acccgtgagg cgttattcgt
     3001 gaggttcagt ggtgcttttg ggcgtccagc cggattttag ccgctaaaat cccggccatg
     3061 catgtgtgtg catagccatg cagacgcgcc agaatcatca ggcgcgtttt ttcacgatat
     3121 aggcacaggg aagtgtcgga aacaggcagg aagacccaga aacgccctga gagcctctca
     3181 ggcggtgcac gcaacggatg ttatggtaaa tctgcctcac agactggtac aaaaaaagcc
     3241 ccgcagggct tttttgctat gagttagcca tattttcttg cgaatttttc atcggaatcg
     3301 catagataaa taataaactc aataaacgcg atgatcgcgg gtatgaatgt ccagcaaaaa
     3361 attagataca ggaatccctg tcctatttta cctaagtaaa atttatgtac gccaaatcca
     3421 ccaaggaaga atgctaagaa agatgatggc ggtggaggtc aattttgagc agggtgcgat
     3481 tggcccgatg cacaatcacc cgcatgaaca gcttacctat gtgctctccg gggagttcga
     3541 gtttacgata ggtgaagaaa agcagatcgt gacggcgggc gatacgctct ataaagcgcc
     3601 gcacgtgatg cacggctgca tttgcctgaa gcccggcacc cttctggata cctttacgcc
     3661 ggtgcgcgac gatttcctga aataaaaaaa ggcgctgaat cagcgccttt ttaatatcgt
     3721 cgttactctg ttgctggcgt tacggccgtt atcggctctg gcaacggatt acgcgagagc
     3781 attgcctcac gcagcagcac gctgccgcag gcaaacaggc cgcccagaat ccctgccagc
     3841 agcacaatca gggctttgcc cggaccgtct tttttcaccg gcagtgacgg tgaaagctga
     3901 tacctgaagg gttcaagctt cacgtcttcc acggacagtt tttgcaactg agtcagatag
     3961 tattcacggt tctggaaatc cgcattcagc tcggccacgt ccttcagatt cttttcaatc
     4021 tgcagctttt gcgcaatacc gtcagcaccc agcgccacgg agtagtcagg atcgtctttt
     4081 accgcctgtc cgttgctgta aaccggcttc ttaatgcctg ccgcgttcgc cacttccagc
     4141 gaatagttga ggcgctgcag gttggtgttg tggatattgg tcagacgcac gcgatccagc
     4201 tccagctgct gctgaacgac tttcgttttc agcgtgatct ggttacggat attttccatc
     4261 gtctcctgct caacaatgcg ggagatatag ttgatgtaac cttccagaac cgtctgcgcg
     4321 tctcccgccg tcggggcggt aaagctcagc gtccatgagg tatacggcgc tttgtctgcg
     4381 tctttaacct gcgtgttatc tgtcgctttc attttctcag caatattcac caccgcgcga
     4441 tgcagctcca gcgggtctac ctcggtgcct tccagctgag acatcacgta cggggaggtt
     4501 ttcatgtact cttcgagcag cgactgcgac tgaaactttt tgatgaacag gttaaacacg
     4561 tctccacggc tcaccttcgc gtcgacgtcc agcacctgca gcgtcaccat catctggcgc
     4621 agcgtgttcc actgcgtctg ctcggccggc gtgatcacgg cttt
//
