LOCUS       NZ_CP100529             4150 bp    DNA     circular CON 22-JUL-2023
DEFINITION  Escherichia coli strain LH13-b plasmid pLH13-b-D, complete sequence.
ACCESSION   NZ_CP100529
VERSION     NZ_CP100529.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN29499313
            Assembly: GCF_024225435.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4150)
  AUTHORS   Biggel,M.
  TITLE     ESBL-producing Enterobacteriaceae from poultry
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4150)
  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 03:01:39
            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)                     :: 4,822
            CDSs (total)                      :: 4,704
            Genes (coding)                    :: 4,460
            CDSs (with protein)               :: 4,460
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 244
            CDSs (without protein)            :: 244
            Pseudo Genes (ambiguous residues) :: 0 of 244
            Pseudo Genes (frameshifted)       :: 64 of 244
            Pseudo Genes (incomplete)         :: 174 of 244
            Pseudo Genes (internal stop)      :: 48 of 244
            Pseudo Genes (multiple problems)  :: 40 of 244
            Pseudo Genes (short protein)      :: 3 of 244
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP100529.1.
            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..4150
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="LH13-b"
                     /isolation_source="pooled poultry feces"
                     /host="Gallus gallus domesticus"
                     /db_xref="taxon:562"
                     /plasmid="pLH13-b-D"
                     /geo_loc_name="Switzerland"
                     /collection_date="2022"
                     /collected_by="Institute for Food Safety and Hygiene,
                     University of Zurich"
     gene            join(3901..4150,1..>491)
                     /locus_tag="NLZ09_RS24015"
                     /old_locus_tag="NLZ09_24015"
                     /pseudo=""
     CDS             join(3901..4150,1..>491)
                     /locus_tag="NLZ09_RS24015"
                     /old_locus_tag="NLZ09_24015"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016230929.1"
                     /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="MobA/MobL family protein"
                     /name="MobA/MobL family protein"
     gene            2154..3089
                     /locus_tag="NLZ09_RS24020"
                     /old_locus_tag="NLZ09_24020"
     CDS             2154..3089
                     /locus_tag="NLZ09_RS24020"
                     /old_locus_tag="NLZ09_24020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009440807.1"
                     /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_254541920.1"
                     /translation="MSAALQYFEENLPHRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAVERSLCEKLCADVNYSGLICKNPFHLEWQVMEWREEAYTLDELADYLDLSASE
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLEAVIQRVEMYNASLPVPLSL
                     AECRAIGKSIAKYTHRNFTPETFAQYVADTHTPEIQAKRGRKGGIAKGEAYDDKRFMAL
                     CMLENGYSQKAIAAMLNVHRNTIRNWAMHK"
                     /name="replication initiation protein"
     gene            complement(3283..3729)
                     /locus_tag="NLZ09_RS24025"
                     /old_locus_tag="NLZ09_24025"
     CDS             complement(3283..3729)
                     /locus_tag="NLZ09_RS24025"
                     /old_locus_tag="NLZ09_24025"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000184721.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="conjugal transfer protein TraD"
                     /protein_id="WP_000184723.1"
                     /translation="MTNREEWLSAKIAYINGLKSPSEQQRLLVLLAEKKNRTTTDEKTL
                     SALIRAEKTAEKAAAAKARVTAIIAAERKAAARAERKARDHELYKAAGLMIVAGLVDSK
                     TGKPKFSAAELVGALAGIAELPRNHPKWQEWERRGKELLTKDSA"
                     /name="conjugal transfer protein TraD"
     Typing          2155..3041
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="97.297"
                     /coverage="95.0"
                     /evalue="0.0"
     Typing          4..1607
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          3902..4149
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="95.0"
                     /evalue="4.12e-47"
ORIGIN
        1 cacgcgaaca acggatagaa cttgttgaag attttgtgca aaaggaactt ggcgatcgcc
       61 atgcctacca gtacgcgatc cacaatccgc caggtgcaat tgacggaaag gaacaaccac
      121 acgcgcatat catgttttgc gagcggatta atgatggtat tgaacgcgat ccgcagcagt
      181 tttttaaacg tgctaacagc aaattaccgg agagaggagg cgcaaaaaag gcacgctttg
      241 gtgaaacaca acaagagcga aaatctgccc ttgttgaatt acgttcccgc tgggcggatg
      301 tgcagaatga gcaccttgcg cgtcacggtc acgagtcgcg cgtagatcat cgttcgctga
      361 aagaacaggg tatcaatcgc acgccggaag ttcatcttgg ccccgttcag gccgccagtc
      421 tgaatggtga gcagattgtt gcaatccagg aacggaggaa tgccgagcgg gaactcaaga
      481 ccgccagaga tgccgcaaat gccattcagc cggaacagga gcaaaagcaa aaaatcaagg
      541 cagttgagcc tgttcgttct gcccgattaa tggatgagta tcgggatgtt gcccggaaag
      601 tgatcacact ggagacaaga cagaatgaga gtcaggaact ggcgctaaaa caccacttgt
      661 ttatgaaggc agaagcgaaa gagcaagaac tggcgaaact gaaagaacaa ctaaaaaaaa
      721 tggacgagca gcgttctgtt tataagaaca agattgatga gaaaaaacag aatattacag
      781 cgttagttga acagaaaaaa tcgctcgaaa gaagttttat tggcctgttt aaaggcggga
      841 tgaaacgtga gcttgaggaa caaatcaaga cacaggtcag ccaactggaa aagaccgagc
      901 acgaggtgaa gcagttggac gagaattatc agcagcttca gatgcaggct gataatgaac
      961 agaagaattt ctcacactca ccggaatatc agtattcgga agcggttttg agcggaatac
     1021 ctcgttcgat tttaaaactg caattcgctc tgttgcccag tgagagcact atcgccttca
     1081 acaagaatgt actggacgta gaacaacgaa aagaagctgc tatagctgcc gaactttgcc
     1141 ttagtgaaga tgagcggcgg caaatcaggc gagagattca ggatgttcta aacggggacg
     1201 cctgcgaagg gcagcagaca gaaactctcc agcagaaacg tcccgagaaa gatgcgcaca
     1261 tcgagtggga acgggaagaa tctccgcaag tcgtcatccc aaaaacttat gtttttttct
     1321 ctgcgtgcag gggcgttaag acagaaatca ggccgtttga gtcgtgcgat gatgctatcg
     1381 agtgggggtt ggttgagtgt gaacttcatg atcgttttaa gcgtgatctc attgtttatc
     1441 gagttgatgc tgaattgata ggaaaaggtg acgatacagt gatgaaaaat gccgaacgca
     1501 ttgatcttac tgatgaactt gaaggatgga atcagcaaac acacatcgaa aaagagagcc
     1561 tttttgaacg agtacagcag cggtcacaag atgatgagct ggagatgtag ttactgacgc
     1621 gcttcgcttg tccaacgcct cacagaccgc gaaaggattt cgcgtcccgt tcaccgtttg
     1681 gctgtgatgt atagtgagaa tgcaaccgca acctaactac ttgtttgcac ggtagaaaaa
     1741 caaaaacgga agcattctca aaaatgttct aacgtgcttt tttcagaacg gcaagtttgt
     1801 cattttgccc cgttcgccct tctgaacggt cgaaactgtt cgcgaatcgc ttttgtgcat
     1861 agttatgcag gcccctgaaa acaattctga cgcatttttc tggtttaccc tggtgtttcc
     1921 ttgtcttttt gcgttttttg cgtcagaaag cgactgaggg cgttttaagg ggtacgtaca
     1981 acaggagtta tggtaaatgg atcggggttg cgggaagact cgacaggttt tgtcgttggg
     2041 ggtagtgtaa gcgactgaaa aacaaacgcc cctgaaattc gtgcccacca accacgattg
     2101 ccacgaaata caggggcgtg taggtaacac atacctggaa ggaatcgtaa cacatgagcg
     2161 ccgcgcttca atacttcgaa gaaaatttac ctcaccgccc ctatcacacg gatgatctcg
     2221 ctttcggcct tcgcatctcc ggcaaagggc gtgcgcttct tgcgcggtac atccagcaga
     2281 accagcctca tgcgcagttc tggctggttt ttgacgttga ccgcgagggg gcagcgattg
     2341 actggagcga ccggaacgcc cccgcgccga acatcaccgt taaaaatcct gtgaacggac
     2401 acgctcacct gctctatgca ctcaatatcg ccgtgagaac cgcgcctgat gcgtcggtta
     2461 aggcgctgaa atatgccgca gcggttgaac gttcgctgtg tgagaaactt tgtgcggatg
     2521 tgaactacag cggcctgatt tgcaaaaatc cgttccacct ggaatggcag gtgatggagt
     2581 ggcgcgagga agcctatacc ctcgatgaac tggctgatta tctcgatttg agcgcctcag
     2641 agcgtcgtag catcgataaa cattacggga tgggacgaaa ctgccacctg ttcgaaatga
     2701 cgcgcaaatg ggcttacagg gcgattcgtc agggctggcc agcgttctca cagtggcttg
     2761 aagcggtgat ccagcgtgtc gaaatgtaca acgcatcgct tcccgttccg ctttcactgg
     2821 ctgaatgtcg ggctattggc aagagcattg cgaaatacac gcacaggaac ttcacgccgg
     2881 aaactttcgc acagtatgtg gctgatacgc acacaccaga aatacaggcc aagagaggcc
     2941 ggaaaggtgg catcgctaaa ggcgaagcct acgatgacaa gcgtttcatg gcgctatgta
     3001 tgctggagaa tggatattct cagaaagcta ttgcggcgat gctgaatgta catcgtaata
     3061 cgatccgtaa ttgggcaatg cacaaatagc ctatatcaga taacagcgcc ttttcggcgt
     3121 ctttttgagc cgcgggcttt ccggcgtttt tctcctgtca gcccagcaat ggtgcggctt
     3181 accgcatgat tgaggtggtt gtgctcgccg cagtctcatg accgagcgta gcgagcgaat
     3241 gagcgaggaa gcaccaggga accggaacgt gaacggaggc tcttacgcac tgtctttggt
     3301 tagtagctcc ttcccgcgtc tttcccattc ctgccatttt ggatggttgc gcggtagctc
     3361 tgcgattcct gcgagtgcgc ctaccagttc ggcagcacta aactttggtt ttccggtttt
     3421 gctgtccacc agtcctgcca caatcatgag gcctgcggcc ttgtagagtt catgatcccg
     3481 cgcctttcgt tccgcccttg cggctgcctt ccgttctgcc gctatgattg ccgttaccct
     3541 agcttttgct gcggctgctt tctctgcggt tttttctgcc cgtatcagtg cggacaacgt
     3601 tttttcatcc gtcgttgttc ggtttttttt ctctgccagt aacacaagta atctctgctg
     3661 ctctgacggt gatttcagtc cgttgatgta ggcaattttt gcacttaacc actcttcacg
     3721 atttgtcatt cttacctctg cacttttgcc gttaatgtga gttgttattg tgcataatat
     3781 caccttgtct gcctgcgtgt gagaccgtaa aatcatccct gattaattca gggatgcgca
     3841 cttagacgtt tctctccttc gtcgagaaac tgtgcgctcc tgcggagggc taaaaggcag
     3901 atggctagtt accattgcac cgttaaaact ggtgcaaaag gcagtgcctt aaaacatgct
     3961 gattacattt ccagaaccgg cgaatacgag aactataaat cgcgggagga tctggagttt
     4021 tcgtcatccg gtaacatgcc atcatgggcg aagaaaaatc cctccgagct atggaaagcc
     4081 gcagatgaat ttgaacgaaa aaacgggacg gcataccgtg aaattgagat cgcgttaccg
     4141 cgtgaactga
//
