LOCUS       NZ_CP041680             5330 bp    DNA     circular CON 20-JUN-2024
DEFINITION  Escherichia coli strain ESBL 15 plasmid unnamed2, complete sequence.
ACCESSION   NZ_CP041680
VERSION     NZ_CP041680.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN12275742
            Assembly: GCF_008370755.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5330)
  AUTHORS   Bakkeren,E., Huisman,J.S., Fattinger,S.A., Hausmann,A., Furter,M.,
            Egli,A., Slack,E., Sellin,M.E., Bonhoeffer,S., Regoes,R.R., Diard,M.
            and Hardt,W.D.
  TITLE     Salmonella persisters promote the spread of antibiotic resistance
            plasmids in the gut
  JOURNAL   Nature 573 (7773), 276-280 (2019)
   PUBMED   31485077
REFERENCE   2  (bases 1 to 5330)
  AUTHORS   Huisman,J.S., Tschudin-Sutter,S., Egli,A., Neher,R., Bonhoeffer,S.
            and Stadler,T.
  TITLE     Direct Submission
  JOURNAL   Submitted (15-JUL-2019) Environmental Systems Science, ETH Zurich,
            Universitaetstrasse 16, Zurich 8092, Switzerland
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.7
            Assembly Name                     :: ESBL15
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 105.0x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_008370755.1-RS_2024_06_20
            Annotation Date                   :: 06/20/2024 03:31:15
            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)                     :: 5,033
            CDSs (total)                      :: 4,908
            Genes (coding)                    :: 4,688
            CDSs (with protein)               :: 4,688
            Genes (RNA)                       :: 125
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 92
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 220
            CDSs (without protein)            :: 220
            Pseudo Genes (ambiguous residues) :: 0 of 220
            Pseudo Genes (frameshifted)       :: 135 of 220
            Pseudo Genes (incomplete)         :: 94 of 220
            Pseudo Genes (internal stop)      :: 44 of 220
            Pseudo Genes (multiple problems)  :: 48 of 220
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP041680.1.
            Bacteria and source DNA available from University Hospital Basel.
            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..5330
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="ESBL 15"
                     /isolation_source="rectum"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="unnamed2"
                     /geo_loc_name="Switzerland: Basel"
                     /lat_lon="47.5596 N 7.5886 E"
                     /collection_date="2013-08-08"
                     /collected_by="University Hospital Basel"
                     /genotype="ST40"
     gene            complement(join(5184..5330,1..>437))
                     /locus_tag="FOA56_RS25355"
                     /old_locus_tag="FOA56_25360"
                     /pseudo=""
     CDS             complement(join(5184..5330,1..>437))
                     /locus_tag="FOA56_RS25355"
                     /old_locus_tag="FOA56_25360"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001697689.1"
                     /note="frameshifted; internal stop; 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="replication initiation protein"
                     /name="replication initiation protein"
     gene            1007..1090
                     /locus_tag="FOA56_RS26590"
                     /old_locus_tag="FOA56_25375"
     CDS             1007..1090
                     /locus_tag="FOA56_RS26590"
                     /old_locus_tag="FOA56_25375"
                     /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="hypothetical protein"
                     /protein_id="WP_058652899.1"
                     /translation="MHEPPVQSDRCALSGNYRLESNPDRHD"
                     /name="hypothetical protein"
     gene            complement(1684..2151)
                     /locus_tag="FOA56_RS25485"
     CDS             complement(1684..2151)
                     /locus_tag="FOA56_RS25485"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011899450.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_154496434.1"
                     /translation="MPAPNNYGVAGSPNSAIAHPDGLDCYGRVPEINSKGDVIPAGDIF
                     LRVGRHIGPNRGFGVRHIWAEHEQELVKLGYATVNDVARFVRDIIRRGVPIYCEFNSTS
                     GKHRPAVLKSSIGIVILEPREAPETESGWIYVVVTAYTRRTAHGTLVGHIE"
                     /name="hypothetical protein"
     gene            3077..3271
                     /locus_tag="FOA56_RS25385"
                     /old_locus_tag="FOA56_25390"
     CDS             3077..3271
                     /locus_tag="FOA56_RS25385"
                     /old_locus_tag="FOA56_25390"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /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_053888061.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQVHFEAENETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(3508..5187)
                     /locus_tag="FOA56_RS25390"
                     /old_locus_tag="FOA56_25395"
     CDS             complement(3508..5187)
                     /locus_tag="FOA56_RS25390"
                     /old_locus_tag="FOA56_25395"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000598747.1"
                     /GO_function="GO:0005524 - ATP binding [Evidence IEA];
                     GO:0016887 - ATP hydrolysis activity [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="AAA family ATPase"
                     /protein_id="WP_053888063.1"
                     /translation="MIKVQLPTREHHHHELNLNYGDVVFFIGQNGSGKSSLLNNLFQKI
                     GSQSSVYVLAHRKNTFSSDIIDFSNSEYKNAQGWIFNEIKGSQCRYRVNYDSQMVAIPI
                     VKLKNKEIARALSFVDSFKSNNNQPAELIKSEVDVLNMVFADAKLSIEFFLDDEANVMA
                     RNIKGEHPDVYPISMLSDGEKSALIIASEIICADENTTIFLDEPERHMHRSIVSPLLSS
                     LMKYRRDCVFFVATHELSLPAFFDNVKVVNVKNCYFSEQREPMCWDFNVVEDYDELFNG
                     VDEQTKIDILGARDKVLFVEGVTSSLDRDLYSAIFPMVSVVSKQKCDLVELAVKGLRLN
                     DEIHRVSAFGIIDNDNKVQAKVDNLKKDFIFSLDVHSIESIYYHPRMIKFVIDFVKEAN
                     GIDNVDTLFMEIHDFAIDAINEKRDHLCCRAVEKTIRADLMSSIPKQQDIKNRIKFNKE
                     IDIECYVNKEIAAFDAMIAERNLEALVSRYPIRETNLLAHVAKKCGFADRSRYELNVIR
                     TIKSNADARAFVLSLLGGLDEAILGCSDTENSPADTNTVFAM"
                     /name="AAA family ATPase"
     Typing          complement(2582..2838)
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="94.208"
                     /coverage="89.0"
                     /evalue="3.43e-107"
     Typing          603..1166
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="85.965"
                     /coverage="89.0"
                     /evalue="7.01e-162"
ORIGIN
        1 ataaaatcat caaatgatga ctctgtaaaa tttttattag tccacttagc tacacttttg
       61 gcaataccca tgacttcgtt ttcgtctaaa ggtgcggaga actgcaggtt gtaggcttta
      121 gcgcgttcaa agcaggcttg tagccattgg tcatactgcg gccagccttg gcggatagca
      181 cggtaagccc acttgcgggt tttatcgaag agggtgcagt tacggcctaa accgtagtcc
      241 ggtaggattt cgcggtcatt agctgcgcca aggtcgaggt agtcggctaa ccagtcgagg
      301 gcctagagct caggctgcca aacggtgatc tgccagtgca ggtggttcgg attcttgcaa
      361 attagccctg aataccccgc atcggcgccc aattttttac gcagcgcatt ctcaatggcg
      421 gcagcatatt tgaggggggc ggcgagcccc ctgaaccagt cacagaaggc acctcgcaga
      481 ggggacgctg tgagtactga cttaacgatg cggtagcagt gcggattgta tgaaaagtgc
      541 gccatggacg gtgtgaaatg ccgcacagat gcgtaaggag aaaatgcaaa tgcctacgct
      601 cttccgcttc ctcgctcact aactcgctgc gctcggtcgt tcggctgcgg cgagcggtat
      661 cagctcactc agagacggta atacggttat ccacagaatc aggggataag gccggaaaga
      721 acatgtgagc aaaaaggcaa agccagggca aaaggccgcg ccgctggcgt ttttccatag
      781 gctccgcccc cctgacaagc atcacagaat ctgacgctca aatcagtggt ggcgaaaccc
      841 gacaggactt aaagatacca ggcgtttccc cctggtggct ccctcgtgcg ctctcctgtt
      901 cctgcctttc ggtttaccgg tgtcattccg ctgttatggc cgcgtttatc tcattccacg
      961 cctgacactc agttccgggt aggcagttcg ctccaagctg gactgtatgc acgaaccccc
     1021 cgttcagtcc gaccgctgcg ccttgtccgg taactatcgt cttgagtcca acccggatag
     1081 acacgactaa tcgccattgg caacggccat tggtaagcag gatgtgcgag agatgtaacg
     1141 agagttcttg aagtggcggc ctaactgagg ctacactgaa aggacagtat ttggtgacat
     1201 gtctcgcaca agactgttac cacggttaga gaatctgcca ggattaacta accttcgaaa
     1261 aaaccacctg ccagggtggt tttttcgttt ctgagcaaga gactacgacg agccactgat
     1321 gatctcaagt gttcatttct gatatccaca gcagaataac tgttaggata tagggtatct
     1381 atagtcagga gcttcaagaa agccagacac agcaatggat tccggcgtta tcgagaaaaa
     1441 ttagtatata ggttgcaacc aaaatgttgg ttgcaaatct acatcacgat gtttatgatt
     1501 attgtactgc aagagcattc gcagggggca tcaaccagta ataggccttc tgtgccgggc
     1561 agtcagatgg ctggtcatct gccgggtagt tacgacaagc gtcggtttct gaaccctatg
     1621 tgctaaggaa atgctgcgac taccaacgaa ttcataaagg gcgcttttta gcgccctatt
     1681 tttttattca atatgaccaa ccaaagtacc gtgcgccgtc cttcgtgtgt acgcagtcac
     1741 aacgacatag atccaaccag actcagtttc aggcgcttct ctgggctcaa gaattacgat
     1801 gcctatcgac gactttagca ctgctggccg atgtttaccg cttgtactgt tgaactcgca
     1861 atatattggt acgccacgac gaataatatc ccgaacgaaa cgagccacat cattaacggt
     1921 cgcatatccc agcttaacca gttcctgctc gtgctcagcc cagatatggc gaacaccaaa
     1981 tccccggtta gggccaatat gcctaccaac acgcaagaag atgtcgccag caggaataac
     2041 atcaccttta gaattaattt cagggacacg gccatagcaa tcaagcccat caggatgagc
     2101 tatagcgctg ttaggtgaac cagccacacc gtaattgttt ggagcaggca caaaacgatc
     2161 cttattgagt agagtccgca tatggtacca gagaggaaac aagcggaagg agcccaagaa
     2221 aaaagcagag acgataaaaa gaatccttat ggattatttt ttgtcctttc atccttggtg
     2281 cataaggata tcacacctga aaatatggcg tgtgaatcgc cctagcagct agatttacca
     2341 taacatccgt tgcccgcacc gcagaaacgc gctgaacgcg attctgacgc aaataccgca
     2401 aaaagagatg ttttccccaa ggcaaaccga aaaaatgcgt caggatcgtt ttcagctcgc
     2461 tgcatagcta ttcatgaaag tgaatagtga acggtttggg cgcatacggt gcccatgaga
     2521 cacattttcg gacattttca gttcgtgaat ccctgactca ttgctacata tctgaacaga
     2581 cacccctagc agcgccacca ggggcatcct gtaaaaaaac acaccgcgcc gctagcagca
     2641 cccctaatat aaaatgatgt tttttatgaa aatagtcagt accaccccta caaagcggtg
     2701 tcggcgcggt gttgtagccg cgccgacacc gcttttttaa atatcacaaa gagagtaaga
     2761 gcaactaatt tgtcataact ctctatttat aaaagaaaaa tcagcaaaaa cttgtttttg
     2821 cgtggggtgt gggcatttca ggcatgagaa cagactcgtg tttttccgga gtatcaacgg
     2881 aatgtttgat taaaaaacac ttgccgcaga gcgagatttt atgcaaccgc ggctgttgtg
     2941 cacaggtatt atttatccgg ccataatact gcctgaagaa acaggacagg atatgcaatt
     3001 gtaataccgt cgcatgcaac ctcttacaat taccacctag tcagggacca accgacaccg
     3061 acagagaacg cgtaaggtga acaaacagca acaaactgcg ctgaatatgg cgcgatttat
     3121 caaaagccag agcctaacac tgcttgaaaa actggatgct ctggatgccg acgaacaggc
     3181 ggccatgtgt gaacgactgc acgaactcgc agaagaactc cagaacagca tccaggttca
     3241 ctttgaggcc gaaaatgaaa caggaacata acgaagctga cgaagtcggt cacggcttgc
     3301 ccgtgagcat tttcgtcagc agacaagccc gtcagggcgc gtcagcgggt tttaacgggt
     3361 gtcggggcgc agccctgacc cagtcacgta gcgatagcgg agtgtatact gacttaatac
     3421 agcaactatc gtacatcgcg gtcaagtcac gcacaaacaa aaagccccgc aaaagcaggg
     3481 ctgttatctg atataggttg tttagtctca catagcaaaa actgtattgg tatcagctgg
     3541 gctattttcc gtatctgaac atcccaaaat agcttcatct aaccctccga ggagggataa
     3601 aacaaatgct ctagcgtcag cattactctt gatcgtacga atcacgttta actcatatct
     3661 agagcgatcg gcaaaaccac attttttagc tacatgtgcc aacaaatttg tttctcggat
     3721 agggtagcgt gagactaacg cctccaaatt tcgttccgcg atcattgcat caaatgcagc
     3781 aatttcttta ttaacataac attcaatatc aatttcttta ttaaacttaa tgcggttttt
     3841 aatatcttgc tgttttggta tggacgacat taagtctgcc cttattgttt tttcaactgc
     3901 acggcagcat aagtgatcgc gcttttcatt tatggcatca atagcgaagt catgaatttc
     3961 cataaataag gtatcaacat tatctatccc attagcctct tttacaaagt caatgacaaa
     4021 cttaatcatt ctaggatgat aataaatcga ctcaatagaa tgaacgtcga ggctaaaaat
     4081 gaagtctttc tttaagttat cgaccttcgc ctgcaccttg ttatcattat caatgatacc
     4141 aaacgccgat actcgatgaa tttcgtcatt tagtctcaag ccttttaccg ccaattcaac
     4201 caaatcacat ttttgtttag atacaactga aaccatagga aatatggccg aatataaatc
     4261 acggtcaagg ctagacgtaa caccttcaac aaatagaacc ttatccctag cgccaagtat
     4321 atctatttta gtttgttcat caacaccatt gaataattca tcataatcct caacaacatt
     4381 gaaatcccag cacatcggtt ctctttgttc ggaaaaatag cagtttttaa cgttaaccac
     4441 tttcacgtta tcaaaaaacg caggcaagct taactcgtgg gtggcaacaa aaaaaacaca
     4501 atctctacga tatttcatta aagatgaaag cagcggagac acaatgcttc tgtgcatatg
     4561 tcgctcaggc tcatctaaga aaatagttgt gttttcatca gcgcaaataa tctcactggc
     4621 aataattagt gcactttttt caccgtcaga aagcattgat ataggataaa catcaggatg
     4681 ttcaccttta atattccgtg ccataacgtt ggcttcatca tctagaaaga actcaataga
     4741 taatttagca tcagcaaaaa ccatgtttag aacatcaacc tctgacttta ttaactctgc
     4801 cggctgattg ttatttgatt taaatgaatc tacgaaactt aaagccctgg ctatctcttt
     4861 gttttttaat tttactatag gtatggcaac catctgtgag tcataattaa ctctgtatct
     4921 acattgactg cctttaattt cattaaaaat ccatccctgc gcatttttat actcactatt
     4981 actgaaatca ataatgtcgc tgctgaatgt attttttcta tgcgctaaaa catatactga
     5041 tgattgagat cctatttttt gaaaaagatt atttaatagg ctggatttac cactaccatt
     5101 ctgaccaata aaaaaaacga catcgccata attaagatta agctcatgat gatgatgttc
     5161 tctagtaggc aactgaactt ttatcatttt cctttctctt tagcttttaa tctaaaatac
     5221 gttgaacgac taattcctaa attaatccat ggagagttta atgaagtcct acctcctcct
     5281 ttactttttt cccacgtaga gattggatgt ctgccgaatg gggctttttt
//
