LOCUS       NZ_CP041681             4734 bp    DNA     circular CON 20-JUN-2024
DEFINITION  Escherichia coli strain ESBL 15 plasmid unnamed3, complete sequence.
ACCESSION   NZ_CP041681
VERSION     NZ_CP041681.1
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 4734)
  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 4734)
  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
            CP041681.1.
            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..4734
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="ESBL 15"
                     /isolation_source="rectum"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="unnamed3"
                     /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(3752..4734,1..37))
                     /locus_tag="FOA56_RS25395"
                     /old_locus_tag="FOA56_25400"
     CDS             complement(join(3752..4734,1..37))
                     /locus_tag="FOA56_RS25395"
                     /old_locus_tag="FOA56_25400"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221104.1"
                     /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_149617736.1"
                     /translation="MSAALQYFEENLPRRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDQNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAVERSLCEKLCADVNYSGLICKNPFHLEWQVMEWREEAYTLDELADYLDLSASA
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLDAVIQRVEMYNASLPVPLSP
                     PECRAIGKSIAKYTHRNFTPETFAQYVANTHTPEIQAARGRKGGKANSSENQSDKGKKS
                     AAVRWTANDDKRRRALDMYILGASTEDIAVAVGVSSRTIRRWMDNSGEWLTKKQIIKC"
                     /name="replication initiation protein"
     gene            536..871
                     /locus_tag="FOA56_RS25400"
                     /old_locus_tag="FOA56_25405"
     CDS             536..871
                     /locus_tag="FOA56_RS25400"
                     /old_locus_tag="FOA56_25405"
                     /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_012512992.1"
                     /translation="MKRIVFSILLPLSFHANAYYLSCEQVGKIAVAVTTSSNEKATQND
                     TKYGDIQKNNLSKIENHAVLFCQEVRKFKVTPETADSWAEYTSLKAELDSEMKNNIKII
                     TRLSVIQ"
                     /name="hypothetical protein"
     gene            complement(923..1246)
                     /locus_tag="FOA56_RS25405"
                     /old_locus_tag="FOA56_25410"
     CDS             complement(923..1246)
                     /locus_tag="FOA56_RS25405"
                     /old_locus_tag="FOA56_25410"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000152444.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_023351684.1"
                     /translation="MTIIFNSDKQTDSESAFEKWLLHHPDGFVVNLRKAANGLSGKSDK
                     HKTFIHSASCHCLSSTKGGFTNGEYQKICSSSFEKAEALAKHMTGLDEIKRCSFCFGKD
                     KEC"
                     /name="hypothetical protein"
     gene            complement(1338..2873)
                     /locus_tag="FOA56_RS25410"
                     /old_locus_tag="FOA56_25415"
     CDS             complement(1338..2873)
                     /locus_tag="FOA56_RS25410"
                     /old_locus_tag="FOA56_25415"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001624483.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobA/MobL family protein"
                     /protein_id="WP_149617735.1"
                     /translation="MASYHCTVKAGAKGSALKHADYISRSGEYKSYKSREDLEFSSSGN
                     MPSWAKKNPAELWKAADEFERKNGTAYREIEIALPRELTREQRIELVEDFVQKELGDRH
                     AYQYAIHNPPGAIDGKEQPHAHIMFCERINDGIERDPQQFFKRANSKSPERGGAKKASI
                     PQTAGERKAALVALRSRWADVQNEHLARHGHESRVDHRSLKEQGIKRTPEVHLGPVHAA
                     NLNEGQIAAIQEHRAARQQERAARNPAPERQQELEQKQKIRTVERSPELLAQYRKVMKT
                     VIQGEERLARLGDANPDALKEHKLLQNAKAKKKSLSEWSRRIYEGARYLDKLGRNVVSA
                     QRELRELQEQRNALNGIRGLFRGADKREIDARILEQKSVLETAEHERNEFRNKLQQAES
                     EWDKENAAFKRTEGYKYVGDLDRYREREILAAASLENTRQKVAEEVSVARSQMLSLEPE
                     LSMSGDEKAQMRHELLAEMAQERQQQEEYARRIQQSLARGMLNSKERDQGIER"
                     /name="MobA/MobL family protein"
     gene            3045..3491
                     /locus_tag="FOA56_RS25415"
                     /old_locus_tag="FOA56_25420"
     CDS             3045..3491
                     /locus_tag="FOA56_RS25415"
                     /old_locus_tag="FOA56_25420"
                     /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_149617737.1"
                     /translation="MTNREDWLSAKIAYINGLKSPSEQQRLLVLLAEKKNRTTADEKTL
                     SALIRAEKTAEKAAAAKARVTAIIAAERKAAARAERKARDHELYKAAGLMIVAGLVDSK
                     TGKPKFSAAELVGALAGIAELPHNHPKWQEWEKRGKELLAKNSA"
                     /name="conjugal transfer protein TraD"
     Typing          complement(3997..4734)
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.594"
                     /coverage="83.0"
                     /evalue="0.0"
     Typing          complement(1342..2873)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.217"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gtaaattttc ttcgaagtat tgaagcgcgg cgctcatgtg ttacgattcc ttccaggtta
       61 tcgaccgaca tcgcccctgt attttcgtga cagtcttggc ggatagacac gaatttcagg
      121 ggcgtttgtt tttcagtcgc ttacactacc cccaacgaca aaacctgtcg agtcttcccg
      181 caaacccgat ccatttacca taactcctgt tgtgtgcacc ccttaaaacg ccctcagacg
      241 ctttctgacg caaaaaactc aaaaagacaa gtaaacacca ggcaaaacca gaaaaacgcg
      301 tcagaattgt ttctaggaag ctgcataact atgcacaaaa gcgattcgcg aacagtttcg
      361 accgtttaga agggcgaacg ggtcaaaacg gcaaactttc cccatcagaa aacgcctcac
      421 agggagcgaa atcttttcgc tccctgtgag gcgttagaaa aatactaaaa ttgcaaaata
      481 cgtatttgta aatgtagtat ctacatgttt ttttattaaa aacgagacac ctataatgaa
      541 aagaatagta ttctcaatat tattgccatt gtcatttcat gccaacgcgt actatttaag
      601 ttgcgagcaa gttggaaaaa tagcagtagc ggtaaccacc tcatcaaatg aaaaggcaac
      661 tcaaaatgac acaaaatatg gagatattca aaaaaacaat ttatcaaaaa tagaaaatca
      721 tgctgtttta ttttgccaag aagttagaaa atttaaagtc actccagaaa ctgccgatag
      781 ctgggcagaa tatacatccc ttaaagctga attagattca gaaatgaaaa acaacataaa
      841 aattataaca cgactatctg taatccaata aataaaaaga tcgcgataaa aatcgcgatc
      901 ttaccaataa taaagtagca tattagcact ctttatcttt accaaagcag aagctgcaac
      961 gttttatctc atctagccca gtcatatgtt tagctaacgc ctctgctttc tcaaaagaag
     1021 atgagcatat tttctgatat tctccattag taaatccacc tttcgtagaa gagagacaat
     1081 gacaactagc actgtgaata aaagttttat gtttatcact tttacccgac aaaccattag
     1141 cagcttttct caaattaaca acaaagccat caggatggtg aagcaaccat ttctcgaaag
     1201 ctgactcgct atcagtttgt ttatcgctgt taaagataat agtcatttaa tttatcttcc
     1261 atcacaatca atttcatcta ctcgttaact atttttagtt aattcagaaa aatttcttta
     1321 ccagagtaaa tacaacatta tcgttcaata ccctgatcac gctccttact atttaacatt
     1381 cctctagcca aagattgctg tatacgccgt gcgtattctt cttgttgctg cctttcctgt
     1441 gccatttctg ccagtaactc atgtcgcatt tgagcttttt catctccaga catactgagt
     1501 tcaggctcca gagataacat ctggctacgg gcaacggata cttcttcagc aaccttttgc
     1561 ctggtattct ctaaagatgc cgcggccaga atctcacgtt ctctgtacct gtccagatcc
     1621 ccaacgtact tatatccctc ggtacgctta aaagcagcgt tttctttgtc ccactcggat
     1681 tcggcttgct gtagcttgtt cctgaattca ttcctttcat gttcagcggt ttccagcaca
     1741 cttttttgct ccagaatacg cgcatcaatc tcccttttgt cagccccccg aaacaggcca
     1801 cgaatcccat tcaaagcatt gcgttgttcc tgtagctccc gcagctccct ttgtgcggaa
     1861 acaacattac gccccagttt gtctaaatac cgtgcccctt catatattcg cctgctccat
     1921 tcggaaagag attttttttt agctttcgca ttctgaagca gcttatgttc tttgagcgca
     1981 tcggggttgg catcccctaa acgagcaagc ctttcctctc cctgaatgac cgttttcata
     2041 accttgcggt actgagccag taactccggt gaacgctcaa ctgtcctgat tttttgcttt
     2101 tgctccagtt cctgttggcg ctctggcgct gggttgcgtg ctgcgcgttc ttgctgacgc
     2161 gccgccctgt gctcctgaat tgccgcgatc tgcccctcgt tcagattggc ggcgtgaaca
     2221 gggccaagat gaacttccgg cgtgcgcttg atgccctgtt ctttcagcga acgatgatct
     2281 acgcgcgact cgtgaccgtg tcgcgcaagg tgctcattct gcacatcagc ccagcgggaa
     2341 cgtagcgcaa caagggcggc ttttcgctct ccggcggtct ggggaatact cgcctttttt
     2401 gcgcctcccc gctccggtga tttgctgttg gcgcgtttaa aaaattgctg cggatcgcgt
     2461 tcaataccat cattaatccg ctcgcaaaac atgatatgcg cgtgtggctg ttcctttccg
     2521 tcgattgcac ctggcggatt gtggatcgcg tactggtagg catggcgatc gccaagttcc
     2581 ttttgcacga aatcttcaac aagttctatc cgttgttcgc gtgtcagttc acgcggtaat
     2641 gcgatctcaa tttcacggta tgccgtcccg ttttttcgtt caaattcatc tgcggctttc
     2701 cacagttctg cgggattttt cttcgcccat gatggcatgt taccggatga cgaaaactcc
     2761 agatcctccc gcgatttgta gctcttatat tcgccggatc tggaaatgta atcagcatgt
     2821 tttaaggcac tgccttttgc tccagctttg acagtgcaat ggtagcttgc catctgcctt
     2881 ttagccctcc gcaggagcgc acagtttctc gacgaaggag agaaactact aagtgcgcat
     2941 ccctgaatta atcagggatg attttacggt ctcacacgca ggcagacaag gtgatattat
     3001 gcacaataac aactcacatt aacggcaaaa gtgcagaggt aaggatgaca aatcgtgaag
     3061 actggttaag tgcaaaaatt gcctacatca acggactgaa atcaccgtca gagcagcaga
     3121 gattacttgt gttactggca gagaaaaaaa accgaacaac ggcggatgaa aaaacgttgt
     3181 ccgcactgat acgggcagaa aaaaccgcag agaaagcagc cgcagcaaaa gccagggtaa
     3241 cggcaatcat agcggcagaa cggaaggcag ccgcaagggc agaacgaaag gcgcgggatc
     3301 atgaacttta caaggccgca ggcctcatga ttgtggcagg actggtggac agcaaaaccg
     3361 gaaaaccaaa gtttagtgct gccgaactgg taggcgcact cgcaggaatc gcagagctac
     3421 cgcacaacca tcccaaatgg caggaatggg aaaaacgcgg gaaagagcta ctcgccaaaa
     3481 acagtgcgta agagcctccg ttcacgttcc ggttccctgg tgcttcctcg ctcattcgct
     3541 cgctacgctc ggtcatgaga ctgcggcgag cacgaccacc tcaatcatgc ggtaagccgc
     3601 accattgctg ggctgagagg agaaaaccgc cggaaagccc gctgctcaaa aggacgccga
     3661 aaggcgctgt tatctgatat aggcttgttc atgtccgcga atttaaccaa ccattaacaa
     3721 aaaacggggg gtagtgttgc ttctttgtta actaacattt aattatttgt ttcttggtta
     3781 gccattctcc agaattatcc atccagcgtc gaatagtccg gctgctaaca ccaaccgcca
     3841 ctgcaatatc ttccgttgac gctcccaaga tatacatatc aagcgcccta cgacgtttgt
     3901 cgtcgttagc agtccaccga acagcggcgc tttttttccc tttgtccgac tgattttctg
     3961 acgaattggc cttcccgccc ttgcgaccgc gtgctgcctg aatttctggc gtgtgcgtat
     4021 tagccacata ctgtgcgaaa gtttccggcg tgaagttcct gtgcgtgtat ttcgcaatgc
     4081 tcttgccaat agcccgacat tcaggcggag aaagcggaac gggaagcgat gcgttgtaca
     4141 tttcgacacg ctgaatcacg gcatcaagcc actgtgagaa tgctggccag ccctgacgaa
     4201 tcgccctgta agcccatttg cgcgtcattt cgaacaggtg gcagtttcgc cccatcccgt
     4261 aatgtttatc gatgctacga cgcgctgagg cgctcaaatc gagataatca gccagttcat
     4321 cgagggtata ggcttcctcg cgccactcca tcacctgcca ttccaggtgg aacggatttt
     4381 tgcaaatcag tccgctgtag ttcacatcag cacaaagttt ctcacacagc gaacgttcaa
     4441 ccgctgcggc atatttcagc gccttaaccg acgcatcagg cgcggttctc acggcgatat
     4501 tgagtgcata gagcaggtga gcgtgtccgt tcacaggatt tttaacggtg atgttcggcg
     4561 cgggggcgtt ctggtcgctc cagtcaatcg ctgccccctc gcggtcaacg tcaaaaacca
     4621 gccagaactg cgcatgaggc tggttctgct ggatgtaccg cgcaagcagc gcacgccctt
     4681 tgccggagat gcgaagacca aaagcgagat catccgtgtg atagggacgg cggg
//
