LOCUS       NZ_CP100550             1865 bp    DNA     circular CON 22-JUL-2023
DEFINITION  Escherichia coli strain LH09-a plasmid pLH09-a-F, complete sequence.
ACCESSION   NZ_CP100550
VERSION     NZ_CP100550.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN29499310
            Assembly: GCF_024226085.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 1865)
  AUTHORS   Biggel,M.
  TITLE     ESBL-producing Enterobacteriaceae from poultry
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 1865)
  AUTHORS   Biggel,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (05-JUL-2022) Institute for Food Safety and Hygiene,
            University of Zurich, Winterthurerstrasse 272, Zurich 8057,
            Switzerland
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.5.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100x, 100x
            Sequencing Technology :: Illumina MiniSeq, Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/22/2023 03:12:24
            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)                     :: 5,038
            CDSs (total)                      :: 4,914
            Genes (coding)                    :: 4,764
            CDSs (with protein)               :: 4,764
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 92
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 150
            CDSs (without protein)            :: 150
            Pseudo Genes (ambiguous residues) :: 0 of 150
            Pseudo Genes (frameshifted)       :: 67 of 150
            Pseudo Genes (incomplete)         :: 91 of 150
            Pseudo Genes (internal stop)      :: 35 of 150
            Pseudo Genes (multiple problems)  :: 40 of 150
            Pseudo Genes (short protein)      :: 2 of 150
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP100550.1.
            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..1865
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="LH09-a"
                     /isolation_source="pooled poultry feces"
                     /host="Gallus gallus domesticus"
                     /db_xref="taxon:562"
                     /plasmid="pLH09-a-F"
                     /geo_loc_name="Switzerland"
                     /collection_date="2022"
                     /collected_by="Institute for Food Safety and Hygiene,
                     University of Zurich"
     gene            complement(926..1144)
                     /locus_tag="NLZ06_RS25120"
                     /old_locus_tag="NLZ06_25120"
     CDS             complement(926..1144)
                     /locus_tag="NLZ06_RS25120"
                     /old_locus_tag="NLZ06_25120"
                     /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_141071555.1"
                     /translation="MNTEDKLMLKVDRLLSHDALNQRNILNNWERQFLTSVLAIYRRIN
                     KYSLVGLSPKQKNATYNILKKYKFHTD"
                     /name="hypothetical protein"
     gene            complement(1163..1687)
                     /locus_tag="NLZ06_RS25125"
                     /old_locus_tag="NLZ06_25125"
     CDS             complement(1163..1687)
                     /locus_tag="NLZ06_RS25125"
                     /old_locus_tag="NLZ06_25125"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000893324.1"
                     /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_045145680.1"
                     /translation="MLEQRFEDFEQQKRRDHKAQDQAQNTKQKRDRLNPPDWSQVTKAG
                     WNMLDAISEKVPRAFRLYSFFAQNIDKSCGAVVCDQKFLADYFGVSLRTIQYWIGDLER
                     IGAIVKIPVGIYYAYALDPYQVWRGYNKSKKYAAFNAKTLTQKDGVIDRKLRLMLSRRE
                     EFESSLKPSKS"
                     /name="replication/maintenance protein RepL"
     Typing          complement(197..295)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.0"
                     /coverage="100.0"
                     /evalue="6.26e-40"
     Typing          395..655
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.985"
                     /coverage="100.0"
                     /evalue="1.85e-99"
ORIGIN
        1 acttttttgt tgcacaaggt ttaacgtgtt tatcgagcat ttggggtgtc ggggcgcagc
       61 cctgacccag tcacgtagcg atagcggagt gtatactggc ttactcctct gcaagcctcg
      121 ccagccgtga tttttgccag atttcgtggt tttcacgttc aacagctcca tcgtgttttt
      181 gccgtccgtt caccgttaaa acgcctcaga aatcgggaca ggatgtgtaa tcgtatgacc
      241 gcgcacgcac gccgatacga ttaccacctg gtcagggctt caccccgaca ccccgcatca
      301 gtgcgtaagt gctcaatgtg gcttccggtt ctcttccgct tcctcgtcga ttcgctcgct
      361 acgctcggtc atcgacttgc ggcgagcggg atcacctctc gcatgttgtc ggtgatcccg
      421 ttgttgttct ttcggggatg agtcgccaga tagcccctca aacgcgctca aaagctctca
      481 gacgcacgaa acgggtttta gatgcccgcc agggcatgga aggcgcgaaa aacgcttaca
      541 gaggctctca ggaggttagg cgcgccgata cccctaacca ggggctttca ggtcgccagg
      601 aaccgcgcca gccccctgca aagcccatta gcacggaaca ggtagctaca cggttggtag
      661 gtggtcgtag accgtcgatg ttacagcgat gggggtctgg ggttctcccc agacggtttc
      721 cggttgcgct caaggcgctg ccggaaccgt ggcggctcgg tggttctaga gatcgggaaa
      781 caaaaacacg ctaggggttt tgaggtcggc aaaagagcaa tgcaggatag acaatcatgg
      841 tcaaaatgtt aacattttat ccatgattgt ccaaaaacga tgtttttgcc tgtgcctgcc
      901 gcaggctctt taaaatattt cacttttaat cagtatgaaa tttatatttt tttaaaatgt
      961 tatacgttgc atttttctgt tttggtgata gcccaactaa agaatattta ttgatcctcc
     1021 tatagatagc taaaacactt gttaaaaatt gtctttccca attatttaaa atattgcgtt
     1081 gatttaacgc atcatgacta agtaatcgat caacttttag cattagctta tcttcagtat
     1141 tcatctagac ctccaagact agtcatgatt tagagggctt gagtgagctt tcaaactctt
     1201 ctcttctaga gagcatgagc cgcaacttac gatcaataac accatctttt tgagttaatg
     1261 tttttgcgtt aaatgctgca tattttttag atttattata tccacgccat acctgataag
     1321 gatctaaagc ataagcataa taaataccta ctggtatttt tactattgca ccaatacgtt
     1381 ctaaatctcc gatccaatat tgaattgtcc ttaaactaac cccgaaataa tcagctagga
     1441 atttttgatc acatacaaca gctccacacg atttatctat attttgagca aaaaaagaat
     1501 atagcctaaa tgccctagga accttctcgg atatagcgtc caacatattc caaccagcct
     1561 tagtgacttg tgaccagtca ggtggattca accgatctcg tttttgctta gtgttttggg
     1621 cttgatcttg tgccttgtga tctcgccgtt tttgctgttc aaagtcttca aatcgctgtt
     1681 ccagcatact tgcatcctta cctgcaacaa tctttcgtac cttacgaaat ttatatcgta
     1741 cagtacgaaa caacacacgc aaacatgttt gcgtatacac atgcaaataa cgtttcgtat
     1801 gatggtgtca taagtcattg atattaatcg aaatgttgat ttttgctcta aagatctatc
     1861 aaagc
//
