LOCUS       NZ_CP075857             5631 bp    DNA     circular CON 21-JUL-2023
DEFINITION  Escherichia coli strain S19-651 plasmid pS19_651-e, complete
            sequence.
ACCESSION   NZ_CP075857
VERSION     NZ_CP075857.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16993361
            Assembly: GCF_016404165.2
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5631)
  AUTHORS   Nusch-Inderbinnen,M., Stevens,M.J.A., Cernela,N., Muller,A.,
            Biggel,M. and Stephan,R.
  TITLE     Distribution of virulence factors, antimicrobial resistance genes
            and phylogenetic relatedness among Shiga toxin-producing Escherichia
            coli serogroup O91 from human infections
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5631)
  AUTHORS   Nusch-Inderbinnen,M., Stevens,M.J.A., Cernela,N., Muller,A.,
            Biggel,M. and Stephan,R.
  TITLE     Direct Submission
  JOURNAL   Submitted (15-MAY-2021) Institute for Food Safety and Hygiene,
            University of Zurich, Winterthurerstrasse 272, Zurich, Zurich 8057,
            Switzerland
REFERENCE   3  (bases 1 to 5631)
  AUTHORS   Stevens,M.J.A., Stephan,R. and Nusch-Inderbinnen,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (04-DEC-2020) Institute for Food Safety and Hygiene,
            University of Zurich, Winterthurerstrasse 272, Zurich, Zurich 8057,
            Switzerland
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: MAY-2021
            Assembly Method                   :: unicycler v. 0.4.9b
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 80.0x
            Sequencing Technology :: Oxford Nanopore MinION; Illumina MiniSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/21/2023 04:43:18
            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)                     :: 5,346
            CDSs (total)                      :: 5,228
            Genes (coding)                    :: 4,987
            CDSs (with protein)               :: 4,987
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 241
            CDSs (without protein)            :: 241
            Pseudo Genes (ambiguous residues) :: 0 of 241
            Pseudo Genes (frameshifted)       :: 99 of 241
            Pseudo Genes (incomplete)         :: 130 of 241
            Pseudo Genes (internal stop)      :: 53 of 241
            Pseudo Genes (multiple problems)  :: 41 of 241
            Pseudo Genes (short protein)      :: 4 of 241
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP075857.1.
            Bacteria and source DNA available from Institute Food Hygiene and
            Safety, University Zurich.
            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..5631
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="S19-651"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pS19_651-e"
                     /geo_loc_name="Switzerland: Zurich"
                     /lat_lon="47.40 N 8.55 E"
                     /collection_date="2019"
                     /collected_by="ILS/NENT"
     gene            255..1307
                     /locus_tag="JFY28_RS26465"
                     /old_locus_tag="JFY28_026465"
     CDS             255..1307
                     /locus_tag="JFY28_RS26465"
                     /old_locus_tag="JFY28_026465"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001557502.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001053268.1"
                     /translation="MNLQQRINKLPQLSSSFSFGKDIDNIHSFIFNETSKDKIEDLLRK
                     WVSGNQPCVFGKLASKKIKGLDFHLSIVNSPQLYNDDGHLFDFLRNERVRFKERARRGE
                     VSAHLIYFIHPQLAFARPSEELVDIQKYICSLHMPECYPIKEDVIYTESVPFQDKDGLK
                     IYKAGVNVFYSSAHRTRNHDRRIPGGILISVNAPGHFMRLAIEKGFYKDQEQALADIRN
                     MTIQSVGKGGYSHPEGISTTWHSESNLDRFGCPVHTGNSSYYSGFYHTDVLIPGELTKD
                     ERLLHEIENSDPMIFNWNVLFYVSLEEFPIDDPYYGEFIGIPVDDASMFFNSFQPRKFE
                     NKPLYEKEDD"
                     /name="hypothetical protein"
     gene            1309..2175
                     /locus_tag="JFY28_RS26470"
                     /old_locus_tag="JFY28_026470"
     CDS             1309..2175
                     /locus_tag="JFY28_RS26470"
                     /old_locus_tag="JFY28_026470"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001335763.1"
                     /GO_function="GO:0005215 - transporter activity [Evidence
                     IEA]"
                     /GO_process="GO:0055085 - transmembrane transport [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DMT family transporter"
                     /protein_id="WP_001335763.1"
                     /translation="MIKGMLFAFLAAFSWGAAIVMSKKGVEELDAGGVFFWQICSAVIL
                     SWIVLFIKRKKLPLNSKAILAYATGVFEPFLAYTFTLYGLYFISAGSASIIFSLESVFI
                     LVLSVLICSVKINSPQYFILFLIGAIVGSILVALPDISNGSNNIVGYCLVVAGVLSAAF
                     YVVISSRLIKSFEPITLLSGQLTFSLILSSLFIFISKSSIYLPLESVIIVFSSGILQYF
                     LAFCFYLNSLRWLPVHLAGIMLYFIPLVALFLSWLFLDEQFTFLQGVGFIVTVLSVYFL
                     NRKYSEE"
                     /name="DMT family transporter"
     gene            complement(3378..3569)
                     /locus_tag="JFY28_RS26475"
                     /old_locus_tag="JFY28_026475"
     CDS             complement(3378..3569)
                     /locus_tag="JFY28_RS26475"
                     /old_locus_tag="JFY28_026475"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165975.1"
                     /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_000165975.1"
                     /translation="MTKQEKTALNMARFIRGQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENR"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            3634..3957
                     /locus_tag="JFY28_RS26480"
                     /old_locus_tag="JFY28_026480"
     CDS             3634..3957
                     /locus_tag="JFY28_RS26480"
                     /old_locus_tag="JFY28_026480"
                     /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_000955999.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            4166..>4597
                     /locus_tag="JFY28_RS26850"
                     /pseudo=""
     CDS             4166..>4597
                     /locus_tag="JFY28_RS26850"
                     /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            4635..5165
                     /locus_tag="JFY28_RS26490"
                     /old_locus_tag="JFY28_026490"
     CDS             4635..5165
                     /locus_tag="JFY28_RS26490"
                     /old_locus_tag="JFY28_026490"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001673158.1"
                     /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_001673158.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFRKLEESVNRELTSNE
                     SLIRNAINDHTTALKELLERYQKTTVDTMDAHWKTVLKMSVKRWLWLIIVSVLMFATTG
                     SLLWYQGMKINANMNILREQKESLEKLNAKTWGVRYHEDSNGRFLVLPKGMKAETNWTK
                     DNGKLNAVRLVQE"
                     /name="MbeB family mobilization protein"
     gene            5172..5405
                     /locus_tag="JFY28_RS26495"
                     /old_locus_tag="JFY28_026495"
     CDS             5172..5405
                     /locus_tag="JFY28_RS26495"
                     /old_locus_tag="JFY28_026495"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /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_000137437.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWENAFVELQKMFSLTQRDNA
                     MLNGRVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     Typing          3203..3284
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.3400000000000002e-35"
     Typing          2559..2746
                     /name="rep_cluster_2401"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="4.63e-94"
     Typing          3948..5509
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.808"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tggtttgttg ccatttttac ctgtctgctg ccgtgatcgc accgaacgcg ttttggcggt
       61 gcgtacaatg cgacgttatg gtaaatggag cggattttca ggaaggagtg atactaacaa
      121 ctcgaacact gtgcaaataa tgattttttt aaaatatcgg taacgataat aaattatttc
      181 gttttacgcc ggtaataaat ataatgtagt ttcagtatat aaaaaaatat atgaggtgtc
      241 ttgtgggagc tttcatgaat cttcaacaac gtataaataa actaccacaa ttatcatcca
      301 gtttttcatt tggaaaagat attgataata ttcattcatt tatctttaac gaaacttcta
      361 aagataaaat tgaagattta ctaagaaaat gggtgtcagg caatcagccc tgtgtatttg
      421 gtaaattggc aagcaagaaa attaaagggc ttgatttcca tttatctatt gtaaatagcc
      481 cccaactata taatgatgat ggtcatttgt ttgatttttt gcgtaatgaa agagttcgtt
      541 ttaaagaacg cgcaagaaga ggagaggtca gtgcgcatct catttatttt attcatccac
      601 aacttgcctt tgctcgtcca tcagaagagt tagtggacat acaaaaatat atttgttcgc
      661 tgcatatgcc agagtgctat ccaataaaag aggatgttat ttatactgaa agcgtaccat
      721 ttcaggataa agatgggcta aaaatatata aggctggtgt taatgttttt tactcttctg
      781 ctcatagaac aagaaatcat gatagaagaa taccaggggg aatacttatt tctgtaaatg
      841 ccccggggca ttttatgagg ctggcgatag aaaaaggttt ctataaagat caagaacaag
      901 cgttagcgga tattcgtaac atgactattc agtctgttgg taagggtggg tattcacatc
      961 cggaagggat ttctacaaca tggcattcag aatctaattt ggatcgtttt ggatgcccag
     1021 tgcacaccgg taatagttct tattacagcg gtttttatca tactgatgta ttaattccag
     1081 gagaattaac taaggatgaa agattgctcc atgaaataga aaatagtgat ccaatgatct
     1141 tcaactggaa tgtattgttt tatgtttcat tagaagagtt tcctatagat gatccttatt
     1201 atggagagtt tattggtatt cctgtagatg atgcatctat gttttttaac tcctttcaac
     1261 caaggaaatt tgaaaacaaa cccctttatg agaaagagga tgattaatat gattaaagga
     1321 atgctttttg cttttttagc agcgttctca tggggggcag ctatcgtaat gagcaaaaaa
     1381 ggagttgaag aactagatgc cggaggggtg tttttctggc agatttgtag tgcagtaata
     1441 ctatcttgga tagttctttt tataaaaaga aaaaaactcc cattaaactc aaaagcgata
     1501 cttgcttatg cgacaggcgt ttttgaacca ttcttagcgt atacttttac actctacgga
     1561 ctttatttta tttcagcagg aagcgcatca attatttttt cacttgaatc agtgtttata
     1621 ttggtgttgt ctgttcttat ttgctcagtt aaaattaatt ccccgcaata ttttatattg
     1681 ttccttatag gtgcaattgt tggcagtatt ttggtagcct tgccagacat cagtaatgga
     1741 tcgaataata ttgttggata ttgtcttgtt gttgccggtg tgttatcggc agcattttat
     1801 gttgttatat cgtctcgcct tattaaatcg tttgagccta tcacattatt gagcggacag
     1861 ttgacattct cccttatact gtcatcgctc tttattttta tatctaaatc atcaatttat
     1921 cttccgttgg aatccgtgat tattgttttt tcatctggaa tattacaata ttttttagct
     1981 ttttgttttt acttgaactc cttgcgttgg ctcccagttc atttggcagg gataatgttg
     2041 tactttattc cgctagttgc attatttttg tcatggttgt ttttggatga acaattcaca
     2101 ttcttacagg gggtaggatt tattgtaact gtgctaagtg tatattttct taacagaaaa
     2161 tactcagagg agtaacattc tgttcaggat tgccccccgg cctccatcga taccgtgcca
     2221 aatgcacgta aaaaacggga gcgtttctgg tgtcggaatg taaccaaggg ggtcagaggc
     2281 gcgctaaaac gctctcaggg gagtcaaata gagacgtttg taacaaaaag atcaaaggat
     2341 cctcttgaga tccttttttt ctgcgcgtaa tctgctgcct gtaaacgaaa aaaccgcctt
     2401 gcagggcggt ttgatcgaag gttaagtcag cttgcagact gcttaaccag gtaactgtct
     2461 tatgcgagac gagtcaccaa aattgttctt ctagtgtagc cgcactccgg cagccacttc
     2521 aagtactctc taaatatctc gcacatgact tttaccaatg gctgctgcca gtggcgcttt
     2581 gtggtgtctt ttccgggttg gacccaagag aacagttacc ggagaaggcg cagcagtcgg
     2641 gctgaacggg gggttcctgc atacagccca gcccggagcg aactgcctaa gtcgccccga
     2701 gataccagaa gacgtgagct atgagaaagc gccacgtgtc ccgtaaggga gaaaggcgga
     2761 aaaggtatcc ggtaatcgat atggcgggaa cgtgggggcg caggagggag cgattcaccg
     2821 gaaacggtga tgatctttaa gccacgtcgg gtttcgccac cgctggcgga tttcatggtt
     2881 gagccgcaag gctcccacag atgcaccgaa aaagtgtctg ttttgtgaag tccgtcaggg
     2941 gggcggagcc tatggaaaaa gcgcctccgg cgcggccttt cccggggttt cgttttttgc
     3001 gcacatgttc tttcctggtt tatccccggg ttctgtggat aacagggtta gcgtttttga
     3061 gaaaggagag tccgctcgcc gcagccgaac gaccgagcgt agcgagtcag tgagcgagga
     3121 agcggaagag cgcctgaact ggcattttct ccttacgcat ctgtgcggca tttcacaccg
     3181 gacatggcgc acttttcata caatccgcac tgatgccgaa tggttaagcc agtatacact
     3241 ccgctatcgc tacgtgactg ggtcagggct tcgccccgac accccaaagg tcaacggcct
     3301 gacgcgccct ggcgggcttg tctgctcccg gcatccgctc acagacaagc tgtgaccgtc
     3361 tccgggagct gcatgtgtca gcggttttca ccgtcatccc cgaagcgtgc gaggcaactg
     3421 cggtaaagct catcggcgtg gtcgtgaagc gattcacaga tgtctgcctg ttcatccgcg
     3481 tccagttcgt tgagcttctc cagcagcgtt aatgtctggc ctctgatgaa gcgggccatg
     3541 ttaagggcgg ttttttcctg tttggtcact gatgcctccg tgtaaggggg ggttctgttc
     3601 atgggggtaa tgataccgat gaaacgcgag aggatgctca cgatacgggt tactgatgat
     3661 gaacatgccc ggttactgga acgctgtgag ggtaaacaac tggcggtatg gatgcggcgg
     3721 gtctgcctgg gtgagccggt tgcccgttcc gggaagctgc cgacactggc accgccgtta
     3781 ctgcgtcagc tggccgccat cgggaataac cttaaccaga cagcgaggaa ggtgaacagc
     3841 gggcagtggt cttccggtga ccgggttcag gtggtggccg cactgatggc catcggggat
     3901 gagctgcgcc ggctgcgtct ggcggtcagg gaacaggggg cgcgggatga tagttaagtt
     3961 tcatgccagg ggaaaaggtg gtggcagtgg tccggttgat tacctgctgg gaagggagcg
     4021 taaccgggaa ggggcaacgg tgcttcaggg gaatccggaa gaggtccggg aactcatcga
     4081 tgccacgcca tttgcgaaga aatacacgtc aggtgttctg tcgttcgcgg agaaggagct
     4141 gccgcctgga gggcgtgaaa aagtgatggc gagctttgag cgtgtactga tgcccggtct
     4201 cgagaaaaat cagtacagca tcctgtgggt ggagcaccag gacaagggac ggcttgagct
     4261 gaattttgtc attccgaaca tggagctaca gaccggaaaa cgcctccagc cgtactacga
     4321 ccgggcagac aggccgagaa ttgatgcctg gcagacgctg gtgaatcacc attacggtct
     4381 gcatgacccc aacgccccgg agaaccgccg gacgctgacc cttcctgata acctgccgga
     4441 aacgaaacag gcgcttgctg agggcgtcac acgcgggata gacgcgcttt accatgccgg
     4501 agagataaaa ggccgtcagg atgtgattca ggcgctcaca gaggcggggc ttgaagtggt
     4561 cagggtgacg cgaagcagta tcagcattgc agacccgaac ggcgggagga atatcagact
     4621 gaaaggagcg ttttatgagc aatcttttac agacgggcgc ggagttcgag aaaaagctga
     4681 aagagagagc cgaatctaca gagaaaatgc tgaacgacga gttcaggaag ctcgaagaat
     4741 ctgtaaacag ggaactgacc tcaaacgaat ctttaatcag gaacgctatc aacgaccata
     4801 caacagccct gaaagaactg ctggagaggt atcagaaaac gaccgtcgat acgatggacg
     4861 cgcactggaa aaccgtactg aaaatgagcg tgaaacgctg gctgtggctg attatcgtct
     4921 cagtactgat gtttgccacg accgggagtc tgctgtggta ccagggcatg aagataaacg
     4981 cgaatatgaa tattctccgc gagcagaaag agagtctgga gaagctgaac gcgaagacat
     5041 ggggcgtgcg ttatcacgag gacagcaacg gacgttttct ggtgttgccg aaggggatga
     5101 aagccgaaac gaactggacg aaggacaacg gcaaactgaa cgcagtgaga ctggtgcagg
     5161 agtgacagag catgacggag ctggaaagac atttgctgaa cgcattagag caactgcaac
     5221 aggactatat gcagcggctg aacgaatggg agaacgcctt cgtggaattg cagaaaatgt
     5281 tttcgcttac gcaacgggac aacgcgatgc tgaacgggcg agtcatgcag ttgagtcagc
     5341 aggtgcagca cttgagcgag cggacagaac gcttgagcca gttatacagc gagaacagga
     5401 gataagggat gaacggctga tgcaggaacg cgaacatgag ttatctctgg agtgggagcg
     5461 tcagccggaa atccaggagc ggacactgga tggcccttcg ctgggatggt gaaaccatga
     5521 aaaatgacgt gttcagtgga ttaaggcggg ctaatgtggc ctgtagcatc tggttgcata
     5581 ggtattcatg cggttaaaat ttatcaggtg cgatcgcggc agtttttcgg g
//
