LOCUS       NZ_CP100506             5319 bp    DNA     circular CON 22-JUL-2023
DEFINITION  Escherichia coli strain LH50-c plasmid pLH50-c-F, complete sequence.
ACCESSION   NZ_CP100506
VERSION     NZ_CP100506.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN29499317
            Assembly: GCF_024223415.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5319)
  AUTHORS   Biggel,M.
  TITLE     ESBL-producing Enterobacteriaceae from poultry
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5319)
  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 02:51:37
            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)                     :: 5,935
            CDSs (total)                      :: 5,818
            Genes (coding)                    :: 5,517
            CDSs (with protein)               :: 5,517
            Genes (RNA)                       :: 117
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 301
            CDSs (without protein)            :: 301
            Pseudo Genes (ambiguous residues) :: 1 of 301
            Pseudo Genes (frameshifted)       :: 131 of 301
            Pseudo Genes (incomplete)         :: 169 of 301
            Pseudo Genes (internal stop)      :: 69 of 301
            Pseudo Genes (multiple problems)  :: 59 of 301
            Pseudo Genes (short protein)      :: 4 of 301
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP100506.1.
            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..5319
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="LH50-c"
                     /isolation_source="pooled poultry feces"
                     /host="Gallus gallus domesticus"
                     /db_xref="taxon:562"
                     /plasmid="pLH50-c-F"
                     /geo_loc_name="Switzerland"
                     /collection_date="2022"
                     /collected_by="Institute for Food Safety and Hygiene,
                     University of Zurich"
     gene            complement(join(5037..5319,1..419))
                     /locus_tag="NLZ13_RS29520"
                     /old_locus_tag="NLZ13_29525"
     CDS             complement(join(5037..5319,1..419))
                     /locus_tag="NLZ13_RS29520"
                     /old_locus_tag="NLZ13_29525"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001281399.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /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_011666799.1"
                     /translation="MSDLIAYKSNALVEASYKLTLQEQRFLLLCIGRLKSGSDAESTEL
                     QKTMTVTAEEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKDDEKREEFRWIQYRAQY
                     AKGEGKAQITFSDAVMPYLTQLKGQFTRVVIKNISNLSRSYSIRIYELLQQFRSTGERI
                     IALDDFRSMLDIEHKYQTYKSLNQQLLRPCVDELNQKSDLAVTLETIKKGRTVVALHFR
                     FKEDKQIKMTI"
                     /name="replication initiation protein"
     gene            1363..1935
                     /locus_tag="NLZ13_RS29525"
                     /old_locus_tag="NLZ13_29530"
     CDS             1363..1935
                     /locus_tag="NLZ13_RS29525"
                     /old_locus_tag="NLZ13_29530"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001681717.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="LysE family translocator"
                     /protein_id="WP_045145571.1"
                     /translation="MEYSTLFSFAIVTLSQTISIGPGVALVINNAFSQGLKSSIKTSVY
                     IRSGEAIVMVISLFTLSSTSSIEQHFYIIKILGGSYLIYIGVMGLINKKNKKSKVQKPL
                     LIPLLNPKAYLFFAALIPAFIDDNTNIALNFFILGVLFIFISFLTDIIYIAISLTIRDK
                     LTPSFSRYISICSSIFILGTGIYFILT"
                     /name="LysE family translocator"
     gene            complement(<1995..>2108)
                     /locus_tag="NLZ13_RS29530"
                     /old_locus_tag="NLZ13_29535"
                     /pseudo=""
     CDS             complement(<1995..>2108)
                     /locus_tag="NLZ13_RS29530"
                     /old_locus_tag="NLZ13_29535"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221104.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus and C-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /name="hypothetical protein"
     Typing          complement(5..419)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="87.5"
                     /coverage="99.0"
                     /evalue="6.6e-133"
     Typing          complement(5038..5318)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.262"
                     /coverage="99.0"
                     /evalue="1.89e-113"
ORIGIN
        1 ttggagatat tcttaattac aactctagta aattgcccct tcaactgtgt cagataaggc
       61 atgaccgcat ctgaaaaagt gatttgggct ttgccctcac ctttagcgta ctgtgcccga
      121 tactggatcc agcggaactc ctcgcgcttc tcatcgtcct taaggatgat cgacctgtcc
      181 cacaaacgat caattgcttc ctgtagctga acctcggcat ttttccgccc catatcaggg
      241 aatgagtcga aatactcttc ggcggtaaca gtcatggtct tttgcaattc agtggattct
      301 gcatcagaac ccgacttcaa tcgaccaatg caaagtaaca agaatcgctg ttcctgaaga
      361 gtcaatttat agctggcctc aaccagtgca ttggatttgt aggcaatcag atccgacatt
      421 gtaaatccct caacctaagg caatgagtaa aatataaaca ttcctttagg taaaggcaat
      481 atgatttaat tttaatatcc cttttcctgt ggatattacc ttaaatcata ttgcctttac
      541 cttaaatcat attgcctatc caccttaaat catattgcct ttaccttaaa ttatattacc
      601 tatagtcttc taaactcttg aattccataa gaaaattcga ccctaaaaca agtattaaaa
      661 acaagatctt aaaaacaaga tctaaaaact taacagcaag cctgtggaaa acttggggtg
      721 cgcaaaagga aaaacaagaa aaaacaagat gttacaaaaa tccacttcgc ggactttagc
      781 aaaaaccccg ctcaaccctg tggaaatcca gtattcatgc gggttcggcg catatcacct
      841 gtcgaaaaac cgtgcgtatg tgctcaacct ggctacggtt cacttccgct tcctcgccca
      901 cttgctcgct aacgctcggt cgctggggct gcggcgagcg gagccgccac tcgcttggtt
      961 tgcagggttt cggtatttgg tttggaggtg tgggagcgga tcggagacgc cgcgcaaaag
     1021 aacaccaaac ccccgttcag aagcgcgaac gggtcaaaac agcaaacttt ctcatccaaa
     1081 aagccagcta aacggaacga acccgtatgc aaacaaattt ccagacatat acagtctgga
     1141 caacgaaata tcgacaatat aaaacatcaa tcataatcgt gtttatggcg tgtaaaaaag
     1201 gttatctgat aattagcatt aaatagtcat aacaacaaat gcaaaaactc agaccagggg
     1261 atagaaaaat gaatgacttt ataaatgaat gtatatccgc tccgagaata aatggagtat
     1321 gtatatgaaa agctcccgcg aaatatatca tggtaagtaa atatggaata ttcaacatta
     1381 ttttcatttg ctatcgtaac tttatctcaa actatatcaa taggacctgg tgttgcattg
     1441 gttataaaca acgccttttc acaaggactt aaatcatcaa taaaaacaag tgtatacata
     1501 agatctggcg aagcaatcgt catggtaata tctcttttca cgttatcttc aacatccagc
     1561 atagaacaac acttttacat tataaagatc ttaggtggaa gctatttaat atacataggg
     1621 gtaatgggtt taattaataa aaaaaacaaa aaaagcaaag tacaaaaacc tttacttata
     1681 ccattattaa acccaaaggc gtatttattc tttgcggcat taataccagc atttatagat
     1741 gataatacaa atatcgcatt aaatttcttt atattgggtg ttttgtttat atttatatca
     1801 ttcctgacag atattattta catagctatt agcttgacga taagggataa attaactccg
     1861 tcattctcaa ggtacataag tatatgtagc tccattttta tattaggtac aggtatttat
     1921 tttatcttga cgtgaaacgc cgtttttata ctcatacagc cttagtcatg gcatatttgc
     1981 ttttcggctt catctcgtgc agcctgaatt tctggcgtgt gcgtatcagc cacatactgt
     2041 gcgaaagttt ccggcgtgaa gttcctgtgc gtgtatttcg caatgctctt gccaatagcc
     2101 cgacattcat ccccctgtta aaaaagatgc agaaaaccat ccgttctgaa agttcaactg
     2161 catgagatgc ccttccgata aacagaccag atcgttgata ttgttagttt ttcgtcatca
     2221 cggacggctc tgtaacgcgg ttgctcgcct tcctggctcg tttgatgtcg atgtagcaga
     2281 gcttgcacat gttgagtttt tacaggagtt cgctacctgt gcaccagggc gattttttac
     2341 tccccgtcat cttacgatga cgccttccga catcagaacg atttttcata tttattcctt
     2401 ttttcaacaa tttaatacac ttacctctca tgtattatga agtttaaaaa gacattccgg
     2461 cgtggccgtc cgtgaaaacg gacgcgccgg aaaggcatgg acacgttact gaaagacgct
     2521 gtcagacaga cgaaacggtc atcagaacgc tggtcacgag cgacgatttt ctggctggcc
     2581 ttacgtgatg ctgctttcag ggcagattgt tgtggcgtca cttggtgttc cctccggtcg
     2641 cacgcaagtg acgccgcaca gcttcagact ccacgtacac acgcaagcag ccaaatttca
     2701 aatggcctta tgccgtgcgc acagtcacaa gaagctcatg cagccagaca gaaaatcttt
     2761 aagacgcaga tatataaggc atttcgccac tctgcgagag gaaaactcgt aagtttcatg
     2821 acatacaaaa ccgtacgggt aatccgaagg taaaaataac gtacctcagt caccagctac
     2881 tggtgacatc cgtttccaga ggctaaacgg atgttgccgc catataggca tcctcttcca
     2941 ggctcatggg atattgcagt cacccgaagg cgctcctctc agactgccgg aacattggct
     3001 ggtcatcctg agatgacagt gtggtcgcgt aagcctccct ctcagaccac cgggagattg
     3061 gttggtcgcc ggagcgacag gttttcggac aaatactagc caaaaacaga acacaagatc
     3121 aacaactccg ctggcggaag catacctgcc tggacaccgc taccgggaca cgttaaaaca
     3181 acacccgcgt gtttccggcg agcgaaattt caggggtact gagcgcagtc gttacggggt
     3241 atggcggcgc gatgaacagc acagaaaaca ggaaagatat cctggaaacc acaggggaat
     3301 gagcatgtag gtatctttgg tgttatccgg atcgccgtaa atcctgccat gaaggacaga
     3361 ttttgacggc gatcaggata aaaaatgcca taatgattgt ggccttaaaa ttatcgaaaa
     3421 cacgaattta gttttacatt tgtgcgcgta tgtacgcctc aaaaaaacaa ccaacgaaaa
     3481 acaactcatc aacaaaataa taacaaaacc ttcttgtttt gtgatttatg ttgcacagtt
     3541 tgattgtaag tcacatctgt gaaacgaaat tgttttgcgc tatggcatct gatgagataa
     3601 aagaaagagg ggtgtttctg tatcgtaaag tctctagccg gatagctttt cattagtagt
     3661 acagaaacat ccccactcat caggattcag gatcgatagc cattcgatat aagactgctg
     3721 attgtgtctt cgttaaaatc tatcttttca cgtgagaatt aagaactgtt aattcatcgt
     3781 ttgtatcccc tatcattagg ataggggata tttttatcgc aaaatacaca ccaaaagtag
     3841 tgttatataa gttttcaatg accgtttctt actgaaaaga agatagggga ttcgtgttga
     3901 catcctccat gccctgaagg acggggtttt acggcgcacc gagtaaatat tccccccgaa
     3961 agcccagtat cggggggaag atgcattaac ggttcgtctt cggacactac cgtgattgcg
     4021 gtgatgagca tatcagctca acgggagaaa ttgaacgcgt ttctgacagt gtggctaaca
     4081 cggcgaaata gacctcagat atctgccaga aacgcgtcac gtatttttaa cgtgtatcaa
     4141 tatccatgtc gagatagtta tccggtgtgc tgtaaaaccc cgtccttcag ggcatggagg
     4201 atgtcaactt agatatggat aaaaaaaacc ctcaatgaat gagggtaagt gtaaggaagt
     4261 acctgattta ttttacatat tgaccatcaa taactgagca aaaaaaaata acaaaaccat
     4321 gacatagata caacctattt ttcctgtgca agattacctc gtttgccata aaactccgtt
     4381 cttcagctca aggaaaattt tgaaaaccat agcgtatatc actatatgaa tgaatatatt
     4441 attgccatat tgtagtgtaa tatttattat tttttgattg tttttagttt attattttat
     4501 ttttttttct atatttccaa agataatctt tttatattct gtttctcgat actagacata
     4561 aaatcaaatt cacgataaat attaattgcg cgtttctgcc cccccacacc tactaattac
     4621 tacctgtgtt tagttacaca atcagaaacg cgctttttaa gcgttaaaat agcgtgatga
     4681 actcctacag atattcaaat acctctacgt catcgtgaaa ggacgcgctt tgccagaggc
     4741 gaggttttgt tttcaagtgt gccctggtgc ttgatatcca tcccgtcctg aaggttggag
     4801 attcctacgt tgctcaggct tgctctttag tcacacatga gtcacttcga tgggggactg
     4861 ctgctggcgg cattaacgca tctctcacgt caagtaacac aagtaatgtt cgacatggtt
     4921 tgccataccg ctctctaaaa tcgattttga cgcaatttat ttgcttggta gtaccatcgc
     4981 atacctgaca ccaaaaaaac gaaccagatg gcgttttaga tgccttaaaa tcgattttag
     5041 atcgtcatct tgatctgttt gtcttccttg aagcgaaaat gcagggctac aaccgtgcgc
     5101 cccttcttga tcgtctcaag cgttacagcc aagtcgcttt tttgattcag ttcgtcaacg
     5161 caaggtctta ataattgctg gttcagagac ttatatgttt gatatttatg ctctatatca
     5221 agcattgagc gaaaatcatc gagggcgata atacgttccc ctgtgctgcg gaattgctgg
     5281 agaagttcgt atattcttat gctgtaactt cttgataaa
//
