LOCUS       NZ_CP100539             3375 bp    DNA     circular CON 22-JUL-2023
DEFINITION  Escherichia coli strain LH10-b-1 plasmid pLH10-b-1-i, complete
            sequence.
ACCESSION   NZ_CP100539
VERSION     NZ_CP100539.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN29499312
            Assembly: GCF_024225755.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3375)
  AUTHORS   Biggel,M.
  TITLE     ESBL-producing Enterobacteriaceae from poultry
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3375)
  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 02:38:36
            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)                     :: 5,291
            CDSs (total)                      :: 5,175
            Genes (coding)                    :: 4,870
            CDSs (with protein)               :: 4,870
            Genes (RNA)                       :: 116
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 305
            CDSs (without protein)            :: 305
            Pseudo Genes (ambiguous residues) :: 0 of 305
            Pseudo Genes (frameshifted)       :: 99 of 305
            Pseudo Genes (incomplete)         :: 210 of 305
            Pseudo Genes (internal stop)      :: 61 of 305
            Pseudo Genes (multiple problems)  :: 59 of 305
            Pseudo Genes (short protein)      :: 4 of 305
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP100539.1.
            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..3375
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="LH10-b-1"
                     /isolation_source="pooled poultry feces"
                     /host="Gallus gallus domesticus"
                     /db_xref="taxon:562"
                     /plasmid="pLH10-b-1-i"
                     /geo_loc_name="Switzerland"
                     /collection_date="2022"
                     /collected_by="Institute for Food Safety and Hygiene,
                     University of Zurich"
     gene            complement(352..543)
                     /locus_tag="NLZ08_RS26325"
                     /old_locus_tag="NLZ08_26330"
     CDS             complement(352..543)
                     /locus_tag="NLZ08_RS26325"
                     /old_locus_tag="NLZ08_26330"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165979.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_000165979.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNDLDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            607..930
                     /locus_tag="NLZ08_RS26330"
                     /old_locus_tag="NLZ08_26335"
     CDS             607..930
                     /locus_tag="NLZ08_RS26330"
                     /old_locus_tag="NLZ08_26335"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_001696562.1"
                     /translation="MLTIRVTDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     APPLLRHLAAIGNNLNQTARKVNSGQWSSIDRVHVVAALMAIEGELRQLRQAVREQGVR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1139..>1579
                     /locus_tag="NLZ08_RS26335"
                     /old_locus_tag="NLZ08_26340"
                     /pseudo=""
     CDS             1139..>1579
                     /locus_tag="NLZ08_RS26335"
                     /old_locus_tag="NLZ08_26340"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /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="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            1608..2168
                     /locus_tag="NLZ08_RS26340"
                     /old_locus_tag="NLZ08_26345"
     CDS             1608..2168
                     /locus_tag="NLZ08_RS26340"
                     /old_locus_tag="NLZ08_26345"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000067488.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_000067486.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKKQLDTLSTTVSMQFSTTEAELSRQQKKLLWRVIKGRILFPALTA
                     LSVTGGIFLGCWGLMEWQESKIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGMKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            2175..2408
                     /locus_tag="NLZ08_RS26345"
                     /old_locus_tag="NLZ08_26350"
     CDS             2175..2408
                     /locus_tag="NLZ08_RS26345"
                     /old_locus_tag="NLZ08_26350"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137389.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_000137389.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHEVTQRNNA
                     ILNERVVILSQQVQRLAGQVDRLSRLFIANNS"
                     /name="MbeD family mobilization/exclusion protein"
     Typing          188..271
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="87.059"
                     /coverage="95.0"
                     /evalue="8.83e-18"
     Typing          921..2491
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.439"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cgctcgccgc agccccagcg accgaacgta gtgagcgagt gggcgaggaa gcggaagagt
       61 cacagaggca agcattgtgc acttacgcgc ctgtgccagt gtccgcgtgt gtgttgttta
      121 tcgggcgcgc tgtttttacg catctgtgcg gctttttact cctgacatgg tgcacttccc
      181 atccactctg caccgatgca aaatgaggta agccagtata cacatcgcta tcgctctgtg
      241 aactgggtca gggctgcgcc ccgacacccg cactgacgcg ccctggcggg cttgtctgct
      301 cccggcatcc gctcacaggc aagctgtgaa cgtctccggg agctgcatgt ttcagttgct
      361 ttcaccgtca tcgccgaagc gtgcgaggca actgcggtag agttcgtcgg cgtggtcgtg
      421 aagtgattcg cagatgtctg cctgttcgtc cgcgtccaga tcgttgagtt tttccagcag
      481 ggttagcgtc tggcttctga taaagcgagc catgttaagg gctgtttttt cctgtttggt
      541 catggtctta aggctccttg tatgggggat ttgttagggg gaatgatacc gatgaaacgc
      601 gagaagatgc tcacgatacg ggttaccgat gaggagcacg cccggttact ggaacgctgc
      661 gagggtaaac gactggcgga atggatgcgg cgggtctgtc tgggggagcc ggttgcacgc
      721 acaggaaaac tgccgacact ggctccgcca ttgctgcggc atctggctgc catcgggaac
      781 aacctgaacc agacagcccg gaaggtgaac agcggccagt ggtcttcgat tgaccgggtt
      841 catgtggtgg ccgcactgat ggccatcgag ggtgaattgc gccagttgcg gcaggctgtc
      901 agggaacagg gggtacggga tgatagttaa atttcatgcc agggggaaag gcggtggaag
      961 tggcccggtc gattacctgc tggggcggga gcgtaaccgc gaaggcgcaa cggtgctccg
     1021 gggtaacccg gaagaagtgc gggaactcat tgattccacg ccattttcga agaaatacac
     1081 gtcaggcgtt ctgtcgttcg cggagaagga gctaccaccg ggtgaacgcg aaagagtgat
     1141 gacgagcttt gagcgtgttc ttatgcccgg tctcgaaaaa gaccagtaca gcattctctg
     1201 ggtggaacac caggataagg ggcggctcga actgaatttt gtcatcccga acatggagct
     1261 acagagcggt aagcgcctcc agccgtacta cgaccgtgcg gacaggccga ggataaatgc
     1321 ctggcagacg ctggttaatc atcattacgg gctgcgtgac ccgaacgcac cggagaacag
     1381 acggacgctt gtcacgccaa ataatctgcc aaaagcgaaa caggaggccg cagaagcgat
     1441 tacacggggt cttgaggctc tttaccatgc cggagcaata aaaacgcgtc aggatgtcac
     1501 agaggcgctt acagcggcag gttttgaggt ggtgaggaca accaaaagca gcatcagtat
     1561 tgccgacccg gagggggggc ggaatctcag gctaaagggg gcgctgtatg agcaatcttt
     1621 tacaaatggg aacagacttc gagaagaaac tgaaagagcg agccgcttct accgagaaca
     1681 tgctgaacag cgagttcagg aagctcgaag agtctgtaga caaggcattg agcttaaaca
     1741 ggcagaaaat cagagacgct atcagcgaac atacaacatc cgtgaaaaag caactggata
     1801 cgctgagcac caccgtgagc atgcagttca gcaccacaga ggccgaactg tcccggcagc
     1861 agaaaaaact gctctggcgg gtgatcaaag ggcggatact gtttccggcg ctgaccgcgc
     1921 tcagcgtcac gggcgggatt ttcctggggt gctgggggct gatggagtgg caggaaagca
     1981 agattgcgaa aaatatcctg actatcagag agcaggaaaa cacgctggcg aaactcgagg
     2041 caaaaacctg gggggtgacg ttcgtcaatg gcgagaacgg gaaatttctg gtgttgccgg
     2101 acgggatgaa aggggaaaac acctggacgg tgggcgacaa gaacgccgtg aggctggtca
     2161 gggagtaaac gagtatgacg gaactggaag ggcatttgct gaacgcctta gagcatttgc
     2221 aacaggacta tatgcggcgg ctgaacgagt gggagagcgc cttcgcggaa ttgcagaaga
     2281 tgcacgaggt tacgcaacgg aacaacgcga tactgaacga gcgcgtcgtg atattgagtc
     2341 agcaggtgca gagattagcc gggcaagtgg atcgcttgag tcggttattt atcgcgaaca
     2401 acagctaagg gatgaacagg agcgtgcccg gtacagacat gaggtacagg aacgcgcggc
     2461 acgggttcgg agtgggccat caatggagat gtgaccgggg aagtgacgaa atcttgccat
     2521 tttgacccgt tcgacggctg gggcgagcga aacaaatcgt gtgccgtatt tgtgcatagc
     2581 tatgcaacat cctgaaaacg catttcacgc gtttttgggg attcagccag gggaaaacat
     2641 ggttttttta ctttttgagc gtaaagacgt gaaaaatctc gttattgcac ttgcgatctt
     2701 tcgtcggcgg gcgtagaacg aaaacagctc gccaggaagg cgagctgttt cgggttcatt
     2761 gaggtctctg acctcctcaa tgttcctgtg gaaactgttg agatccacaa cagaaaccag
     2821 ttcattcagt ttgcatgagc cttctgtatt cttcaagaat ttttcaacag cacagtctcc
     2881 caggaacccc gaaaaaaacc tgtttttgca gatacttgcg tatttgcgag aatcgtttgc
     2941 ggttggggga gctgtgacga cggcgaccgc acgcgtgaga gttccgctac cggcgcagag
     3001 agtttcatcg acagcggaca cctgatgagt tgccacaaaa accgtatgta gcgcggctag
     3061 attggttgag ttagaccttg gcggcagttc ccggtatgtg gtggcgtgac gggtgagatg
     3121 gtgcggcgaa gacgcatacg tcacgcaggc gcgggttctt ccactgacgc gccccgtgat
     3181 cgatggcctt ggctccgtcc ggcatatcga gagcggcaaa ctacccgtcc cttcactggg
     3241 aggggtgagt tgttgccgtt ccctccgacc ttccaccatc cagcatatcg cacgatccca
     3301 tgtgcaccgc tactcctgat aactccagtg caaaaaaaaa aaaacggatc tgcatcacaa
     3361 cgagagtgat cccac
//
