LOCUS       NZ_CP075708             5654 bp    DNA     linear   CON 27-JUN-2023
DEFINITION  Escherichia coli strain STEC2018-607 plasmid pSTEC2018_607-k.
ACCESSION   NZ_CP075708
VERSION     NZ_CP075708.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16993387
            Assembly: GCF_016403625.2
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  JOURNAL   Unpublished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
            Assembly Name                     :: STEC2018-607
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 80.0x
            Sequencing Technology :: Illumina MiniSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/27/2023 06:12:10
            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)                     :: 5,666
            CDSs (total)                      :: 5,550
            Genes (coding)                    :: 5,293
            CDSs (with protein)               :: 5,293
            Genes (RNA)                       :: 116
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 257
            CDSs (without protein)            :: 257
            Pseudo Genes (ambiguous residues) :: 0 of 257
            Pseudo Genes (frameshifted)       :: 100 of 257
            Pseudo Genes (incomplete)         :: 139 of 257
            Pseudo Genes (internal stop)      :: 55 of 257
            Pseudo Genes (multiple problems)  :: 37 of 257
            Pseudo Genes (short protein)      :: 4 of 257
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP075708.1.
            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/
FEATURES             Location/Qualifiers
     source          1..5654
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="STEC2018-607"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSTEC2018_607-k"
                     /geo_loc_name="Switzerland: Zurich"
                     /lat_lon="47.40 N 8.55 E"
                     /collection_date="2018"
                     /collected_by="ILS/NENT"
     gene            <1..197
                     /locus_tag="JFX52_RS27960"
                     /old_locus_tag="JFX52_27960"
     CDS             <1..197
                     /locus_tag="JFX52_RS27960"
                     /old_locus_tag="JFX52_27960"
                     /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=3
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_215771239.1"
                     /translation="RSMLQIDKKYKDFKTLNRSLIKPSIAELNQKSDLAVTVEPIKKGR
                     TVVALRFLFKEDKQIKAPI"
                     /name="replication initiation protein"
     gene            568..1683
                     /locus_tag="JFX52_RS27965"
                     /old_locus_tag="JFX52_27965"
     CDS             568..1683
                     /locus_tag="JFX52_RS27965"
                     /old_locus_tag="JFX52_27965"
                     /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(1950..4169)
                     /gene="mobQ"
                     /locus_tag="JFX52_RS27970"
                     /old_locus_tag="JFX52_27970"
     CDS             complement(1950..4169)
                     /gene="mobQ"
                     /locus_tag="JFX52_RS27970"
                     /old_locus_tag="JFX52_27970"
                     /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_062850873.1"
                     /translation="MAIYHLSMKIISRKNGYSAVASAAYRSGSVIPDDRTGLTHDYTRK
                     RGVDDAVILTPENAPSWCADRSVLWNAVEKAEQRRDSQLAREIELAIPREISRDAARET
                     VLAFVRENFVSQGMIADVAFHHMDRTNPHAHIMLTTRAVGETGFAGKVRDWNDRALAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKAPGLHLGKSACAMEKRGMETERGEQ
                     NRLINSLNLEIQVSRTQLALRKVQETQRKRELSDAARRAAEALNLTIPAANASADTLRE
                     FIATLPQECGNAWEMTPEFVAMNGKANDIKREENALVKERDILEKEMTGLRKARPVASI
                     LSELPLMTWAEPEYRKRQLRFWKLGKQIESLSRTYRAVKERDIPARRQAFETQWNTWIA
                     PGMAELKEKLSAREAERRREEAEAEARRKEQEHEARLKRHDNHRLSRETALVGVITELG
                     RAREPGTGRITRYMMLSNRAGEFTVWGDELAHYPQSVHDPVNVYLSPGGAVMVSDIREG
                     MPESHETMARPERVRMYSGATVRHVLEQMRQGWPSYGFPALPHHWPDNFYFSDDRRPVA
                     SPLPSAHRVDITADAVPEQLMPVVFSREGNSRTLNLLLCKGPEEMLVGFVRREGGFCPV
                     LVLPSPDYSHLIVSTITENGVCLAGYGEAINHDEDTPYPPEPHLMQFRLKGHHDRLLAA
                     VHKPEEMPDYLFRQLGFNQTWHEWKRDEQHRQQQRRPGHFRGMSM"
                     /name="mobQ"
     gene            4348..4626
                     /locus_tag="JFX52_RS27975"
                     /old_locus_tag="JFX52_27975"
     CDS             4348..4626
                     /locus_tag="JFX52_RS27975"
                     /old_locus_tag="JFX52_27975"
                     /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"
     gene            5156..>5654
                     /locus_tag="JFX52_RS27980"
                     /old_locus_tag="JFX52_27980"
     CDS             5156..>5654
                     /locus_tag="JFX52_RS27980"
                     /old_locus_tag="JFX52_27980"
                     /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_215771240.1"
                     /translation="MTDLIAYKSNALVEASYKLTLQEQRLLLLCISRLNSSNATPESQK
                     TMMITAEDFFNSFPDMGRNHAEEKLQEAIDRLWDRSIILKDDEKREEMRWLQYRAHYLK
                     GEAKVQITFADAVMPYLTQLKGQFTKVVIKNISRLSRSYSIRIYEILQQFRSTGERVIA
                     LDD"
                     /name="replication initiation protein"
     Typing          3812..4170
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.389"
                     /coverage="100.0"
                     /evalue="3.99e-167"
     Typing          4171..4341
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="95.93"
                     /coverage="98.0"
                     /evalue="5.6200000000000006e-73"
     Typing          complement(1954..4169)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.158"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttcgcagcat gctacaaatt gataaaaagt ataaggattt caaaacatta aatagatctt
       61 tgataaaacc atcgatagcg gaattgaatc aaaaaagcga tctggctgtg acggtagagc
      121 caatcaagaa ggggcgaacg gtggtcgctc tgcgttttct gttcaaggag gacaaacaga
      181 tcaaagctcc tatctaaatg cacttaaaac gctctcagac gcgttctgac gcaaaaaacg
      241 caaaaagaca aggaaacacc aggccaaacc gaaaaaacgc gtcagaatcg tttttaggta
      301 gatgcataac tatgcacgaa agctatgcgc gatcaatttc gaccgctccg aagggcgaac
      361 aggtcaaaat gacaagtttt ctccctccag atggaaggtt cagcacgggg attttttacc
      421 tccttccatc aacctgaata tgcatctgga agtacccatt agtttctgct caaacactat
      481 cgcagtgcta tctcaaaata taaaatatac cgatggtgta agtattttaa atatgataaa
      541 taagaatatt tttatcaggg gttaattatg acaaagatat atatttacct tgttcttgct
      601 gcatcattat cggcattatc aactgacatg attgtgcctg cgttaccaga actacagaaa
      661 gcatttaatg ctgactattc attaattcaa ctaagtatta gtggatttct tattgtattt
      721 gcatttagtc aactgatatc aggtactata ggtgatcatt ttggaaaggt acgcgtgatg
      781 actatatgct taattatatt tcttattggc agcattgtat gctttatggc caataattta
      841 aatatgctta ttttgggtag aattctgcag gcaataggtg caggtgctgg acctgtaata
      901 tcaaaagcaa ttgctaaaga gtcttttcca ccactaaagc taaaaagagc actttctgac
      961 atatcatcga caagtgcgac aataccatta atagcacctc tggctggagc attaatactt
     1021 gattattata actggaatgt aatatttatt gtaatggggt catttagcat tctaaccatg
     1081 ctcctgtcac ctaaagaggc taataaacag gagaaaaaaa cacatcaaga cgatataaaa
     1141 tttgtgacta aagatttcat ctgcgggaca atactcgttt cactaatgct aagctcacta
     1201 ttttgctaca tatcaatatc acccgcacta tttatgaatg actatggatt aaatacattt
     1261 aactactctg ttgttttttc cctatcagtt ttatttttca tcattggaaa ccaattatca
     1321 aaaatcgaaa aaatatcaga tccatgggtt ttatttcctc taaatgcaat atcagtcata
     1381 ccctttctca tattaaatga taattttgta atatgtgtta ttggagcaat gattttcaat
     1441 ttaactcttg gcgcatacta tccaatagct aattttatct cattacagat aaacggttca
     1501 cgaactggct tggccgcatc aattacagga tttactcaaa cagtaagcgc aggggtaatc
     1561 agtttccttt cagtaaaaat aagcgataat ggagtttctt tgggaactac tttaagtatc
     1621 agctgtctta ttcttgcatt attgtcaata ttcgtaacta ttatagggaa taataaaaaa
     1681 tgaattggca ataaagaaaa agctatcaca atatgcaaaa aaatgcatga tcgtggtttt
     1741 gctacaaccg ttgctatgta tcctacagtg gaagagggaa aggcgattct acgttgtgca
     1801 atatctgcta ttcataccag agaaaatata gatagcctac ataaaaactt tatggaatgt
     1861 attaacgaac cgggttagta atatcatggc ctctttatat agaggccctc tatttcattt
     1921 tttatggccc gtggcgcagc cctcgaatat cacatactca tgccccggaa gtgcccgggg
     1981 cggcgttgtt gttgcctgtg ctgttcgtcc cgcttccact catgccaggt ctgattaaaa
     2041 ccgagttgac ggaagagata atccggcatc tcttccggtt tgtggacagc agccaaaagc
     2101 ctgtcatgat ggcctttgag ccggaactgc atcaggtgcg gttccggtgg gtacggagta
     2161 tcctcatcat ggtttatagc ttctccgtaa cctgccaggc ataccccgtt ctccgtgatg
     2221 gtgctgacta tcagatgact gtaatccggc gacggaagca caagaacggg gcaaaaccct
     2281 ccttcccggc gaacaaaccc gacaagcatt tcctccggcc ctttgcataa caacagattc
     2341 agcgtcctgc tgtttccctc tctcgaaaat acaacaggca tgagttgttc cggtacagca
     2401 tcagcggtga tatccacccg gtgcgctgac ggcagcggag aggctacggg cctgcggtcg
     2461 tcgctgaaat aaaaattatc cggccagtga tgcggcagcg ccggaaaacc gtaagagggc
     2521 cacccctggc gcatctgttc cagtacatgc cggaccgtcg caccggaata cattctcaca
     2581 cgctcaggcc gcgccatcgt ctcatgagat tctggcattc cctcacgtat atccgagacc
     2641 atcacagccc cgcctggcga caggtaaaca ttcaccgggt catgaacact ctgggggtaa
     2701 tgcgccagct catcacccca taccgtgaat tctccggctc tgttactcaa catcatgtag
     2761 cgggttatcc tgcccgttcc cggctctctg gcacgcccca gctccgtaat aaccccgact
     2821 aatgccgttt cacggctcag acggtggtta tcatgacgtt tcagccgcgc ctcatgctcc
     2881 tgttccttcc ggcgcgcttc cgcttcggct tcctccctgc gccgctccgc ttcccgtgct
     2941 gacagttttt ctttcagctc tgccattccc ggcgcaatcc acgtattcca ctgcgtttca
     3001 aaggcctgac gacgggcggg aatgtcccgt tctttcacgg ccctgtaagt gcggctgaga
     3061 gattcaatct gtttcccgag tttccagaaa cggagttgtc ttttgcggta ttccggttca
     3121 gcccatgtca tcaggggaag ctctgacagg atggacgcta ccggacgggc ttttctgagt
     3181 ccggtcatct ctttttcgag aatatcccgc tctttcacca gcgcattctc ctcacgtttg
     3241 atgtcgtttg ccttcccgtt catcgccacg aactcagggg tcatctccca tgcgttcccg
     3301 cattcctgcg gcagtgtggc aatgaattcc cgcagggtat ccgctgaggc attcgcggcg
     3361 ggaatggtca gattaagggc ttccgctgcg cgacgtgcgg catcgctgag ttcccgctta
     3421 cgctgcgttt cctgaacctt cctgagcgcc agctgcgtgc gggaaacctg tatttccagg
     3481 ttaaggctgt taatcaggcg gttctgctca ccgcgttctg tttccatgcc ccgtttttcc
     3541 atcgcacagg cagactttcc gaggtgaagg cccggcgctt tctccagtcc ctgacgctcg
     3601 tatgaacgat ggtctatctc ttcctggtag ccggcgttag caagcgctct gttcgcatgg
     3661 tcagcccatg atgcgcgcca cgtctcggcg agtgcccggt cgttccagtc cctgaccttt
     3721 cctgcgaatc ccgtttcccc gacagctctt gtggtcagca tgatgtgcgc atggggatta
     3781 gtccggtcca tgtgatggaa cgccacatcg gcaatcatgc cctggctgac aaagttttcc
     3841 ctgacaaaag cgagaacggt ttcccgtgcg gcatcgcggg aaatctctcg gggaatggca
     3901 agttcaatct cccttgccag ctgggagtcc cggcgctgtt cggctttctc gaccgcattc
     3961 cagagaacgg aacggtcagc acaccatgac ggtgcattct caggggtgag aatgaccgca
     4021 tcatcaacgc cgcgtttacg ggtgtaatcg tgggttaatc cggtacggtc atcgggtatg
     4081 acagagccgg aacggtaggc agcagaagca acggcactgt agccgttttt tcgcgaaatg
     4141 attttcatgc tgagatgata aatcgccatt tctgccgtaa tgcctttttg ccgttttctg
     4201 tcagccccgc agggcgcaca caatcgaaac ggagtggaga ttgtataagt gcgcacttcg
     4261 tgatgtgccg tgcattatgc cagttcagtt ttgcaactac cagtgacgcg ataaaatgcg
     4321 atttttcacc gcgcacggag tcacaaaatg agcagaacac tcgaacagaa gattgccgaa
     4381 gctgaggcca gattacagcg cctgaaggcg aagagccgga gcctggacac ggcgcaaaaa
     4441 gtcattgtgg gggctgccat gctggcgagg gtacggaggc cggaagaagc gcaactgcgt
     4501 gcgttcctgc tccagtttct gcgaaaggaa gtcacaagac aggcggatgt gaaccggata
     4561 caaccgctga ttaacgagct ggagaagcta cccagaccac ctgtgaaacc gcaaaagaac
     4621 gattgatcgc cttccgctcg ccgcagcccc agcgaccgag cgttagcgag taagtgggcg
     4681 aggaagcggc agaagtgccg ttgctgaatg tggcacgtac gcactgtttt cagaaaggtg
     4741 atcctctctg aacctgcatg aatactggat ttccacaggt ttgcatgttg tttttgcaga
     4801 acgcggcaaa ctgatttttt ataacatgtt gttttttagt gtttttttgt tttcccgctt
     4861 tgagttttca acaggcacgc cgttaagttt ttagatcttg tttttatata cttgttttta
     4921 tacttgtttt agggttgaga tttctttttt aaatcaatat gttgcaatga cataggtgaa
     4981 cattttgggg gtataggtga acattttggg ggtggttagg tgaacatttt gggggtatag
     5041 gtgaacattt tgggggtggt tatccacaga aaaaggtgaa tcaaaaaaaa aatattgcac
     5101 ttatggtaaa ggttaattac tttttttttt gttaacctat caattgggga acgtaatgac
     5161 ggatttgatt gcttacaaat cgaacgcatt ggttgaagct agctacaaac taaccttgca
     5221 ggagcaacgc ttgcttttgc tttgtattag ccgattgaac tccagcaatg cgacgccgga
     5281 atcgcagaaa actatgatga ttacggcaga ggattttttt aattcatttc ctgacatggg
     5341 tcggaatcac gccgaagaaa aattacaaga agcgatagat cgtttatggg ataggtcgat
     5401 tattctcaaa gatgacgaga agcgagaaga aatgcgttgg ctccagtatc gagcacacta
     5461 cctcaagggc gaagctaaag ttcagataac cttcgcagat gctgtaatgc cctatctgac
     5521 acaattaaaa ggtcaattca cgaaagtagt aattaaaaat atatcaagat tatcaaggag
     5581 ctacagtatt cggatctacg aaattctcca gcaattccgt agcacaggag agagggttat
     5641 tgctcttgat gatt
//
