LOCUS       NZ_CP075856             5654 bp    DNA     circular CON 21-JUL-2023
DEFINITION  Escherichia coli strain S19-651 plasmid pS19_651-d, complete
            sequence.
ACCESSION   NZ_CP075856
VERSION     NZ_CP075856.1
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 5654)
  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  JOURNAL   Unpublished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 5654)
  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 5654)
  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
            CP075856.1.
            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..5654
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="S19-651"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pS19_651-d"
                     /geo_loc_name="Switzerland: Zurich"
                     /lat_lon="47.40 N 8.55 E"
                     /collection_date="2019"
                     /collected_by="ILS/NENT"
     gene            join(4223..5654,1..788)
                     /gene="mobQ"
                     /locus_tag="JFY28_RS26445"
                     /old_locus_tag="JFY28_026445"
     CDS             join(4223..5654,1..788)
                     /gene="mobQ"
                     /locus_tag="JFY28_RS26445"
                     /old_locus_tag="JFY28_026445"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001029330.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobQ family relaxase"
                     /protein_id="WP_062892503.1"
                     /translation="MAIYHLSMKIISRKNGYSAVASAAYRSGSVIPDDRTGLTHDYTRK
                     RGVDDAVILTPENAPSWCADRSVLWNAVEKAEQRRDSQLAREIELAIPREISRDAARET
                     VLAFVRENFVSQGMIADVAFHHMDRTNPHAHIMLTTRAVGETGFAGKVRDWNDRALAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKAPGLHLGKSACAMEKRGMETERGEQ
                     NRLINSLNLEIQVSRTQLALRKVQETQRKRELSDAARRAAEALNLTIPAANASADTLRE
                     FIATLPQECGNAWEMTPEFVAMNGKANDIKREGNALVKERDILEKEMTGLRKARPVASI
                     LSELPLMTWAEPEYRKRQLRFWKLGKQIESLSRTYRAVKERDIPARRQAFETQWNTWIA
                     PGMAELKEKLSAREAERRREEAEAEARRKEQEHEARLKRHDNHRLSRETALVGVITELG
                     RAREPGTGRITRYMMLSNRAGEFTVWGDELAHYPQSVHDPVNVYLSPGGAVMVSDIREG
                     MPESHETMARPERVRMYSGATVRHVLEQMRQGWPSYGFPALPHHWPDNFYFSDDRRPVA
                     SPLPSAHRVDITADAVPEQLMPVVFSREGNSRTLNLLLCKGPEEMLVGFVRREGGFCPV
                     LVLPSPDYSHLIVSTITENGVCLAGYGEAINHDEDTPYPPEPHLMQFRLKGHHDRLLAA
                     VHKPEEMPDYLFRQLGFNQTWHEWKRDEQHRQQQRRPGHFRGMSM"
                     /name="mobQ"
     gene            complement(1055..2170)
                     /locus_tag="JFY28_RS26450"
                     /old_locus_tag="JFY28_026450"
     CDS             complement(1055..2170)
                     /locus_tag="JFY28_RS26450"
                     /old_locus_tag="JFY28_026450"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000164328.1"
                     /GO_function="GO:0022857 - transmembrane 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="MFS transporter"
                     /protein_id="WP_062892502.1"
                     /translation="MTKIYIYLVLAASLSALSTDMIVPALPELQKAFNADYSLIQLSIS
                     GFLIVFAFSQLISGTIGDHFGKVRVMTICLIIFLIGSIVCFMANNLNMLILGRILQAIG
                     AGAGPVISKAIAKESFPPLKLKRALSDISSTSATIPLIAPLAGALILDYYNWNVIFIVM
                     GSFSILTMLLSPKEANKQEKKTHQDDIKFVTKDFICGTILVSLMLSSLFCYISISPALF
                     MNDYGLNTFNYSVVFSLSVLFFIIGNQLSKIEKISDPWVLFPLNAISVIPFLILNDNFV
                     ICVIGAMIFNLTLGAYYPIANFISLQINGSRTGLAASITGFTQTVSAGVISFLSVKISD
                     NGVSLGTTLSISCLILALLSIFVTIIGNNKK"
                     /name="MFS transporter"
     gene            complement(2541..3236)
                     /locus_tag="JFY28_RS26455"
                     /old_locus_tag="JFY28_026455"
     CDS             complement(2541..3236)
                     /locus_tag="JFY28_RS26455"
                     /old_locus_tag="JFY28_026455"
                     /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_045133511.1"
                     /translation="MTDLIAYKSNALVEASYKLTLQEQRLLLLCISRLNSSNATPESQK
                     TMMITAEDFFNSFPDMGRNHAEEKLQEAIDRLWDRSIILKDDEKREEMRWLQYRAHYLK
                     GEAKVQITFADAVMPYLTQLKGQFTKVVIKNISRLSRSYSIRIYEILQQFRSTGERVIA
                     LDDFRSMLQIDKKYKDFKTLNRSLIKPSIAELNQKSDLAVTVEPIKKGRTVVALRFLFK
                     EDKQIKAPI"
                     /name="replication initiation protein"
     gene            complement(3766..4044)
                     /locus_tag="JFY28_RS26460"
                     /old_locus_tag="JFY28_026460"
     CDS             complement(3766..4044)
                     /locus_tag="JFY28_RS26460"
                     /old_locus_tag="JFY28_026460"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001514113.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_045133509.1"
                     /translation="MSRTLEQKIAEAEARLQRLKAKSRSLDTAQKVIVGAAMLARVRRP
                     EEAQLRAFLLQFLRKEVTRQADVNRIQPLINELEKLPRPPVKPQKND"
                     /name="hypothetical protein"
     Typing          complement(4049..4222)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.0"
                     /coverage="100.0"
                     /evalue="1.21e-74"
     Typing          complement(4223..4581)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.389"
                     /coverage="100.0"
                     /evalue="3.99e-167"
     Typing          4..785
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="99.0"
                     /evalue="9.84e-177"
     Typing          4224..5653
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.807"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 ccggagaatt cacggtatgg ggtgatgagc tggcgcatta cccccagagt gttcatgacc
       61 cggtgaatgt ttacctgtcg ccaggcgggg ctgtgatggt ctcggatata cgtgagggaa
      121 tgccagaatc tcatgagacg atggcgcggc ctgagcgtgt gagaatgtat tccggtgcga
      181 cggtccggca tgtactggaa cagatgcgcc aggggtggcc ctcttacggt tttccggcgc
      241 tgccgcatca ctggccggat aatttttatt tcagcgacga ccgcaggccc gtagcctctc
      301 cgctgccgtc agcgcaccgg gtggatatca ccgctgatgc tgtaccggaa caactcatgc
      361 ctgttgtatt ttcgagagag ggaaacagca ggacgctgaa tctgttgtta tgcaaagggc
      421 cggaggaaat gcttgtcggg tttgttcgcc gggaaggagg gttttgcccc gttcttgtgc
      481 ttccgtcgcc ggattacagt catctgatag tcagcaccat cacggagaac ggggtatgcc
      541 tggcaggtta cggagaagct ataaaccatg atgaggatac tccgtaccca ccggaaccgc
      601 acctgatgca gttccggctc aaaggccatc atgacaggct tttggctgct gtccacaaac
      661 cggaagagat gccggattat ctcttccgtc aactcggttt taatcagacc tggcatgagt
      721 ggaagcggga cgaacagcac aggcaacaac aacgccgccc cgggcacttc cggggcatga
      781 gtatgtgata ttcgagggct gcgccacggg ccataaaaaa tgaaatagag ggcctctata
      841 taaagaggcc atgatattac taacccggtt cgttaataca ttccataaag tttttatgta
      901 ggctatctat attttctctg gtatgaatag cagatattgc acaacgtaga atcgcctttc
      961 cctcttccac tgtaggatac atagcaacgg ttgtagcaaa accacgatca tgcatttttt
     1021 tgcatattgt gatagctttt tctttattgc caattcattt tttattattc cctataatag
     1081 ttacgaatat tgacaataat gcaagaataa gacagctgat acttaaagta gttcccaaag
     1141 aaactccatt atcgcttatt tttactgaaa ggaaactgat tacccctgcg cttactgttt
     1201 gagtaaatcc tgtaattgat gcggccaagc cagttcgtga accgtttatc tgtaatgaga
     1261 taaaattagc tattggatag tatgcgccaa gagttaaatt gaaaatcatt gctccaataa
     1321 cacatattac aaaattatca tttaatatga gaaagggtat gactgatatt gcatttagag
     1381 gaaataaaac ccatggatct gatatttttt cgatttttga taattggttt ccaatgatga
     1441 aaaataaaac tgatagggaa aaaacaacag agtagttaaa tgtatttaat ccatagtcat
     1501 tcataaatag tgcgggtgat attgatatgt agcaaaatag tgagcttagc attagtgaaa
     1561 cgagtattgt cccgcagatg aaatctttag tcacaaattt tatatcgtct tgatgtgttt
     1621 ttttctcctg tttattagcc tctttaggtg acaggagcat ggttagaatg ctaaatgacc
     1681 ccattacaat aaatattaca ttccagttat aataatcaag tattaatgct ccagccagag
     1741 gtgctattaa tggtattgtc gcacttgtcg atgatatgtc agaaagtgct ctttttagct
     1801 ttagtggtgg aaaagactct ttagcaattg cttttgatat tacaggtcca gcacctgcac
     1861 ctattgcctg cagaattcta cccaaaataa gcatatttaa attattggcc ataaagcata
     1921 caatgctgcc aataagaaat ataattaagc atatagtcat cacgcgtacc tttccaaaat
     1981 gatcacctat agtacctgat atcagttgac taaatgcaaa tacaataaga aatccactaa
     2041 tacttagttg aattaatgaa tagtcagcat taaatgcttt ctgtagttct ggtaacgcag
     2101 gcacaatcat gtcagttgat aatgccgata atgatgcagc aagaacaagg taaatatata
     2161 tctttgtcat aattaacccc tgataaaaat attcttattt atcatattta aaatacttac
     2221 accatcggta tattttatat tttgagatag cactgcgata gtgtttgagc agaaactaat
     2281 gggtacttcc agatgcatat tcaggttgat ggaaggaggt aaaaaatccc cgtgctgaac
     2341 cttccatctg gagggagaaa acttgtcatt ttgacctgtt cgcccttcgg agcggtcgaa
     2401 attgatcgcg catagctttc gtgcatagtt atgcatctac ctaaaaacga ttctgacgcg
     2461 ttttttcggt ttggcctggt gtttccttgt ctttttgcgt tttttgcgtc agaacgcgtc
     2521 tgagagcgtt ttaagtgcat ttagatagga gctttgatct gtttgtcctc cttgaacaga
     2581 aaacgcagag cgaccaccgt tcgccccttc ttgattggct ctaccgtcac agccagatcg
     2641 cttttttgat tcaattccgc tatcgatggt tttatcaaag atctatttaa tgttttgaaa
     2701 tccttatact ttttatcaat ttgtagcatg ctgcgaaaat catcaagagc aataaccctc
     2761 tctcctgtgc tacggaattg ctggagaatt tcgtagatcc gaatactgta gctccttgat
     2821 aatcttgata tatttttaat tactactttc gtgaattgac cttttaattg tgtcagatag
     2881 ggcattacag catctgcgaa ggttatctga actttagctt cgcccttgag gtagtgtgct
     2941 cgatactgga gccaacgcat ttcttctcgc ttctcgtcat ctttgagaat aatcgaccta
     3001 tcccataaac gatctatcgc ttcttgtaat ttttcttcgg cgtgattccg acccatgtca
     3061 ggaaatgaat taaaaaaatc ctctgccgta atcatcatag ttttctgcga ttccggcgtc
     3121 gcattgctgg agttcaatcg gctaatacaa agcaaaagca agcgttgctc ctgcaaggtt
     3181 agtttgtagc tagcttcaac caatgcgttc gatttgtaag caatcaaatc cgtcattacg
     3241 ttccccaatt gataggttaa caaaaaaaaa agtaattaac ctttaccata agtgcaatat
     3301 tttttttttg attcaccttt ttctgtggat aaccaccccc aaaatgttca cctatacccc
     3361 caaaatgttc acctaaccac ccccaaaatg ttcacctata cccccaaaat gttcacctat
     3421 gtcattgcaa catattgatt taaaaaagaa atctcaaccc taaaacaagt ataaaaacaa
     3481 gtatataaaa acaagatcta aaaacttaac ggcgtgcctg ttgaaaactc aaagcgggaa
     3541 aacaaaaaaa cactaaaaaa caacatgtta taaaaaatca gtttgccgcg ttctgcaaaa
     3601 acaacatgca aacctgtgga aatccagtat tcatgcaggt tcagagagga tcacctttct
     3661 gaaaacagtg cgtacgtgcc acattcagca acggcacttc tgccgcttcc tcgcccactt
     3721 actcgctaac gctcggtcgc tggggctgcg gcgagcggaa ggcgatcaat cgttcttttg
     3781 cggtttcaca ggtggtctgg gtagcttctc cagctcgtta atcagcggtt gtatccggtt
     3841 cacatccgcc tgtcttgtga cttcctttcg cagaaactgg agcaggaacg cacgcagttg
     3901 cgcttcttcc ggcctccgta ccctcgccag catggcagcc cccacaatga ctttttgcgc
     3961 cgtgtccagg ctccggctct tcgccttcag gcgctgtaat ctggcctcag cttcggcaat
     4021 cttctgttcg agtgttctgc tcattttgtg actccgtgcg cggtgaaaaa tcgcatttta
     4081 gcgcgtcact ggtagttgca aaactgaact ggcataatgc acggcacatc acgaagtgcg
     4141 cacttataca atctccactc cgtttcgatt gtgtgcgccc tgcggggctg acagaaaacg
     4201 gcaaaaaggc attacggcag aaatggcgat ttatcatctc agcatgaaaa tcatttcgcg
     4261 aaaaaacggc tacagtgccg ttgcttctgc tgcctaccgt tccggctctg tcatacccga
     4321 tgaccgtacc ggattaaccc acgattacac ccgtaaacgc ggcgttgatg atgcggtcat
     4381 tctcacccct gagaatgcac cgtcatggtg tgctgaccgt tccgttctct ggaatgcggt
     4441 cgagaaagcc gaacagcgcc gggactccca gctggcaagg gagattgaac ttgccattcc
     4501 ccgagagatt tcccgcgatg ccgcacggga aaccgttctc gcttttgtca gggaaaactt
     4561 tgtcagccag ggcatgattg ccgatgtggc gttccatcac atggaccgga ctaatcccca
     4621 tgcgcacatc atgctgacca caagagctgt cggggaaacg ggattcgcag gaaaggtcag
     4681 ggactggaac gaccgggcac tcgccgagac gtggcgcgca tcatgggctg accatgcgaa
     4741 cagagcgctt gctaacgccg gctaccagga agagatagac catcgttcat acgagcgtca
     4801 gggactggag aaagcgccgg gccttcacct cggaaagtct gcctgtgcga tggaaaaacg
     4861 gggcatggaa acagaacgcg gtgagcagaa ccgcctgatt aacagcctta acctggaaat
     4921 acaggtttcc cgcacgcagc tggcgctcag gaaggttcag gaaacgcagc gtaagcggga
     4981 actcagcgat gccgcacgtc gcgcagcgga agcccttaat ctgaccattc ccgccgcgaa
     5041 tgcctcagcg gataccctgc gggaattcat tgccacactg ccgcaggaat gcgggaacgc
     5101 atgggagatg acccctgagt tcgtggcgat gaacgggaag gcaaacgaca tcaaacgtga
     5161 ggggaatgcg ctggtgaaag agcgggatat tctcgaaaaa gagatgaccg gactcagaaa
     5221 agcccgtccg gtagcgtcca tcctgtcaga gcttcccctg atgacatggg ctgaaccgga
     5281 ataccgcaaa agacaactcc gtttctggaa actcgggaaa cagattgaat ctctcagccg
     5341 cacttacagg gccgtgaaag aacgggacat tcccgcccgt cgtcaggcct ttgaaacgca
     5401 gtggaatacg tggattgcgc cgggaatggc agagctgaaa gaaaaactgt cagcacggga
     5461 agcggagcgg cgcagggagg aagccgaagc ggaagcgcgc cggaaggaac aggagcatga
     5521 ggcgcggctg aaacgtcatg ataaccaccg tctgagccgt gaaacggcat tagtcggggt
     5581 tattacggag ctggggcgtg ccagagagcc gggaacgggc aggataaccc gctacatgat
     5641 gttgagtaac agag
//
