LOCUS       NZ_CP075670             5969 bp    DNA     circular CON 27-JUN-2023
DEFINITION  Escherichia coli strain STEC2018-553 plasmid pSTEC2018_553-e,
            complete sequence.
ACCESSION   NZ_CP075670
VERSION     NZ_CP075670.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16993384
            Assembly: GCF_016403675.2
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5969)
  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  JOURNAL   Unpublished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 5969)
  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 5969)
  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                     :: STEC2018-553
            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 06:09:25
            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)                     :: 5,752
            CDSs (total)                      :: 5,624
            Genes (coding)                    :: 5,342
            CDSs (with protein)               :: 5,342
            Genes (RNA)                       :: 128
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 98
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 282
            CDSs (without protein)            :: 282
            Pseudo Genes (ambiguous residues) :: 0 of 282
            Pseudo Genes (frameshifted)       :: 118 of 282
            Pseudo Genes (incomplete)         :: 157 of 282
            Pseudo Genes (internal stop)      :: 61 of 282
            Pseudo Genes (multiple problems)  :: 52 of 282
            Pseudo Genes (short protein)      :: 4 of 282
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP075670.1.
            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..5969
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="STEC2018-553"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSTEC2018_553-e"
                     /geo_loc_name="Switzerland: Zurich"
                     /lat_lon="47.40 N 8.55 E"
                     /collection_date="2018"
                     /collected_by="ILS/NENT"
     gene            join(5704..5969,1..1954)
                     /gene="mobQ"
                     /locus_tag="JFY30_RS28445"
                     /old_locus_tag="JFY30_28445"
     CDS             join(5704..5969,1..1954)
                     /gene="mobQ"
                     /locus_tag="JFY30_RS28445"
                     /old_locus_tag="JFY30_28445"
                     /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_198789119.1"
                     /translation="MAIYHLSMKIISRKNGYSAVASAAYRSGSVIPDDRTGLTHDYTRK
                     RGVDDAVILTPENAPSWCADRSVLWNAVEKAEQRRDSQLAREIELAIPREISRDVARET
                     VLAFVRENFVSRGMIADVAFHHMDRTNPHAHIMLTTRAVGETGFAGKVRDWNDRALAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKAPGLHLGKAACAMEKRGMETERGEQ
                     NRLINSLNLEIQVSRTRLAVIQVQENVRKRELSDAARRAAEALNLTIPAANASADTLRE
                     FIATLPQECGNAWEMTPEFLAMSGKVNDIEREGNALLKEQAILEKEMTGLKKARPVASL
                     LSEIPLMTWAEPEYRKRQLRFWKLGKQIESLRRTYRAVKERDIPARRQAFETQWNTWIA
                     PGMAELKEKLSAREAERRREEAEAEARRKEQEHEARLKRHDNHRLSRETALVGVITELG
                     RTREPGTGRITRYMMLNNRSGKFTVWGDELAHYPQGEGDPVNVYLSPGGAVMVSDIRNG
                     ISESHETLARPERVRMYSGTTVRHLLEQMRHKWPSYGFPALPHHWPDNFYFSDDRRPVT
                     SPLPSADRVDVTAYSAPEQLMPVVFSVARNNHMLHLLLCKGPEEMFVGFVRLEDGLRPV
                     LALPSPDYSHLMVSTITENGIHLEGYGEAINRDADTPYPPKPHLMQFRLKGCQDRLFAA
                     INKPEEMPDYLFRQLGFNQTWHEWKQDEQHRQQQRRPGHYRGMSM"
                     /name="mobQ"
     gene            complement(2012..2692)
                     /locus_tag="JFY30_RS28450"
                     /old_locus_tag="JFY30_28450"
     CDS             complement(2012..2692)
                     /locus_tag="JFY30_RS28450"
                     /old_locus_tag="JFY30_28450"
                     /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_042969097.1"
                     /translation="MFDVQQHRYNYFYNMATVVENLIPEDICDTLVSRINELISEGAVD
                     HVKHSGLGNNAVSDLGGDYNHHIFKGPDIRKHLPELNAIYHAILPLISIITCTDTITSP
                     YELSDVNIKAYPPNGGTLGLHYDTNGITVLLSLMDNKEAPLRIQIPRSHPSKKESWIEH
                     KEIYAKKGGLLIMQGRKVLHDSAPTQTEQKISVIYNYYERHDTYRHKDFDNFVYFGIKP
                     DDLE"
                     /name="hypothetical protein"
     gene            2832..3713
                     /locus_tag="JFY30_RS28455"
                     /old_locus_tag="JFY30_28455"
     CDS             2832..3713
                     /locus_tag="JFY30_RS28455"
                     /old_locus_tag="JFY30_28455"
                     /inference="COORDINATES: protein motif:HMM:NF013088.2"
                     /GO_component="GO:0016020 - membrane [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="EamA family transporter"
                     /protein_id="WP_042969096.1"
                     /translation="MSKSVDIFIGFLVTVLWGANFVVIDVGLRDLDPFALTFLRFLFCA
                     IPLCFFIKRPREMSLVYVSIYGVIFGVGLWWLVNYAMYNGLAAGVSSVFLQFSAFFTII
                     LSAFIFGEKINKVHAVGMIVSFLGLVMMITSSDDSSTIYGIFLVILAALAWALCNMIVK
                     MKKPSDMVGFIVWSSIFSAPSVLILTVIAKGWGPIISIKDNISFASAFSVLFQAYITTV
                     IGYMIWNNLMKKYPATEIAPLSLFVPVSGLTASFFLLDEKLSVFQLIAVVVVCVGIFIF
                     LNASRIKKWINL"
                     /name="EamA family transporter"
     gene            4108..5043
                     /locus_tag="JFY30_RS28460"
                     /old_locus_tag="JFY30_28460"
     CDS             4108..5043
                     /locus_tag="JFY30_RS28460"
                     /old_locus_tag="JFY30_28460"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011666805.1"
                     /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_032488643.1"
                     /translation="MSAALQYFEENLPHRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAIERALCEKLGADVNYSGLICKNPFHLEWLVMEWREEAYTLDELADYLDLSASA
                     RRSIDKHYGMGRNCYLFEMTRKWAYRAIRQGWPVFSQWLDAVIQRVEMYNASLPVPLSP
                     AECRAIGKSIAKYTHRNFTPETFAQYVATTHTPEIQAARGRKGGIAKGAGYEDKRSTAL
                     EMLVNGCTQKAIAEMLGVSDRTIRNWKSGK"
                     /name="replication initiation protein"
     gene            complement(5250..5525)
                     /locus_tag="JFY30_RS28465"
                     /old_locus_tag="JFY30_28465"
     CDS             complement(5250..5525)
                     /locus_tag="JFY30_RS28465"
                     /old_locus_tag="JFY30_28465"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091757.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_062863177.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVIVGAAMLARVRRP
                     EEAQLRAFLLQFLRKEVTRQADMNRLQPLINELEKLPKPPAKPQNH"
                     /name="hypothetical protein"
     Typing          complement(2..93)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="94.624"
                     /coverage="100.0"
                     /evalue="4.83e-32"
     Typing          complement(5530..5703)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.571"
                     /coverage="98.0"
                     /evalue="2.65e-76"
     Typing          complement(5704..5969)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.127"
                     /coverage="100.0"
                     /evalue="9.08e-129"
     Typing          4109..5043
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.132"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          3..1951
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.385"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 acttgccatt ccccgagaga tttcccgcga tgtcgcacgg gagaccgttc tcgcttttgt
       61 ccgggaaaac tttgtcagtc ggggcatgat tgccgatgtg gcgttccatc acatggaccg
      121 gaccaatccc catgcgcaca tcatgctgac cacgagagct gtcggggaaa caggatttgc
      181 aggaaaggtc agggactgga acgaccgggc actcgccgag acgtggcgcg catcatgggc
      241 tgaccatgcg aacagagcgc ttgcgaacgc cggctaccag gaagagatag accatcgttc
      301 atacgagcgt cagggactgg agaaagcgcc gggccttcac ctcggaaagg ctgcctgtgc
      361 gatggaaaaa cggggcatgg aaacagaacg cggtgagcag aaccgcctga ttaacagcct
      421 taacctggaa atacaggttt cccgcacaag gctggcagtc atccaggtac aggagaacgt
      481 gcggaaacgg gaactcagcg atgccgcacg tcgtgcagcg gaagccctta acctgaccat
      541 tcccgctgcg aatgcctcag cggataccct gcgggaattc attgccacgc tgccgcagga
      601 atgcgggaac gcgtgggaga tgaccccgga gttcctggcg atgagcggga aggtgaacga
      661 catcgaacgt gaggggaatg cgctgctgaa agagcaggcc attctcgaaa aggagatgac
      721 cggactcaaa aaagcacgcc ctgtcgcgtc ccttctgtca gagattcccc tgatgacatg
      781 ggctgaaccg gaataccgca aaagacaact ccgtttctgg aaactcggga aacagattga
      841 atctcttcgc cgcacctaca gggccgtgaa agaacgggac attcccgccc gtcgtcaggc
      901 ctttgaaacg cagtggaata cgtggattgc gccgggaatg gcagagctga aagaaaaact
      961 gtcagcacgg gaagcggagc ggcgcaggga ggaagccgaa gcggaagcgc gccggaagga
     1021 acaggagcat gaggcgcggc tgaaacgtca tgataaccac cgtctgagcc gtgaaacggc
     1081 attagtcggg gttattacgg agctggggcg tacccgcgag ccgggaacgg gccggataac
     1141 ccgttacatg atgctgaata accgctcggg aaaattcacg gtatggggtg atgagctggc
     1201 acattacccg cagggagaag gtgaccccgt gaatgtttac ctgtcgccag gcggggccgt
     1261 gatggtctcg gatatacgta atggaatatc agaatctcat gagacgctgg cccggcctga
     1321 gcgtgtgaga atgtattccg gtacgacggt ccgtcatctg ctggaacaga tgcgccataa
     1381 gtggccctct tacggttttc cggcactgcc gcatcactgg ccggataatt tttatttcag
     1441 cgacgaccgc aggcctgtca cctctccgct gccgtcagcg gaccgggtgg acgtcaccgc
     1501 ttattccgca ccggagcaac tcatgcccgt tgtattttcg gtggcgcgaa acaaccatat
     1561 gctgcatctg ttgttgtgca aagggccgga ggaaatgttt gtcgggtttg tgcgcctgga
     1621 ggacgggctg cgtcccgttc ttgcgttacc ctcgccggat tacagtcatc tgatggtcag
     1681 caccatcacg gagaacggga tacacctgga aggctacggt gaggccataa accgtgatgc
     1741 tgatactccg tacccaccga aaccgcacct gatgcagttc cggcttaagg gctgtcagga
     1801 caggcttttt gcagccatca acaaaccgga agagatgccg gattatctct tccgtcaact
     1861 cgggtttaat cagacctggc atgagtggaa gcaggacgaa cagcacaggc aacaacaacg
     1921 acgcccggga cactatcggg gcatgagtat gtaaaagtaa ataagactat tttatctggc
     1981 tatttttgtt aaaacagcca gataatgcat actattctaa atcatctggt tttataccaa
     2041 aatagacaaa attatcaaaa tctttatgtc tataagtgtc gtgcctttca tagtaattgt
     2101 aaataacgga tattttttgc tccgtttggg tcggggcgct atcatgtaat acctttcttc
     2161 cttgcattat aagaaggcct cctttttttg catatatttc tttatgttct atccatgatt
     2221 cctttttgct tggatggctt ctaggaattt gtattcttaa tggagcttct ttgttatcca
     2281 ttagagataa taaaacagtt ataccatttg tgtcgtagtg caaccctaat gttccaccat
     2341 ttggagggta tgcttttatg ttgacatctg acagttcata aggtgaagtg atggtatctg
     2401 tgcatgttat aatgcttatt aaaggtaaga ttgcatgata tatggcgttt aactcaggaa
     2461 gatgcttcct tatatctggc cccttgaata tatgatgatt gtagtcacct ccaagatctg
     2521 aaactgcatt gttacctaat cctgagtgct taacgtgatc tacagctcct tcactgatta
     2581 gttcgtttat tcttgatact agagtatcac aaatatcttc gggtatcagg ttttcaacaa
     2641 ctgttgccat gttataaaag tagttatatc tgtgttgttg cacatcaaac atattctttt
     2701 ccttttatgg ttgttgattt tttgtaacat aatcgtgatg gtgtgttgtg tcaatgtttt
     2761 tgttgtgttt gttttttgtt tgtggtaggt aatccttgat tgttgattac ttattgtttt
     2821 ttaggtgatt tatgagcaag agcgttgata tctttattgg ttttttggtc acggttttgt
     2881 ggggagctaa ttttgttgtc attgatgttg gattaaggga tttagacccc tttgctttaa
     2941 cttttttacg atttttattt tgcgcaatac cattgtgttt ttttattaaa cgccccagag
     3001 aaatgtcttt agtatatgtg tctatttatg gtgtgatttt tggagtcggg ttgtggtggc
     3061 ttgtaaatta tgccatgtac aatgggttag ctgctggggt ttcttctgtg tttttacaat
     3121 ttagtgcatt ttttacaatt attttaagtg cttttatatt cggcgagaaa ataaataagg
     3181 ttcatgcggt tggtatgatt gtgtcttttt tagggttggt tatgatgatc acctcatcag
     3241 atgatagttc tactatttat ggtatttttc tagttatatt ggctgcgttg gcatgggcgt
     3301 tgtgcaatat gatcgttaag atgaaaaaac catctgatat ggttggcttc atagtttggt
     3361 caagtatttt ttctgctcct tctgttttga ttttaactgt tattgctaaa ggctgggggc
     3421 cgattatatc tataaaagat aatatatcat ttgcttctgc tttttctgtt ctttttcagg
     3481 catatattac aacagtaata gggtatatga tctggaacaa cttaatgaag aagtatccag
     3541 caacagaaat tgcccctctg tctttgttcg ttccagtatc tggtttgaca gcatcattct
     3601 ttttgctaga tgaaaaacta tccgtatttc aattaatcgc tgtggttgtt gtctgtgtcg
     3661 gtatatttat ctttttaaac gcatccagaa taaaaaaatg gataaattta taactaaacc
     3721 ccgtgcggaa ccttctatgg agagagaaac ttgtcatttt gacccgttcg cccttcggaa
     3781 cggtcgaaat cgatcgcgca tcgctttcgt gaatagttat gcaggctcat gaaaacaatt
     3841 ctgacgcgtt tttctggctt tgcctggtgt ttccttgtct ttttgagttt tttgcgtcag
     3901 aaagcgtctg agggcgtttt aaggggtacg tacaacggga gttatggtaa atggatcggg
     3961 ttttcgggaa ggttcgacag gatttgccgt tgggtgtagt gtaagcgact gaaaaacaaa
     4021 cgcccctgaa attcgtgtct ctccgccaag attgtcacga gaatacaggg gcgaggtcgg
     4081 tcgataacct ggaaggaatc gtaacacatg agcgccgcgc ttcaatactt cgaagaaaat
     4141 ttaccccacc gtccctatca cacggatgat ctcgcttttg gtcttcgcat ctccggcaaa
     4201 gggcgtgcgc ttcttgcgcg gtacatccag cagaaccagc ctcatgcgca gttctggctg
     4261 gtttttgacg ttgaccgcga gggggctgcg attgactgga gcgaccggaa cgcccccgcg
     4321 ccgaacatca ccgtaaaaaa tcccgtgaac ggtcatgctc acctgctcta tgcactcaac
     4381 atcgccgtga gaaccgcgcc tgatgcgtcg gttaaggcac tgaagtacgc tgccgcgata
     4441 gagcgtgcgc tgtgtgagaa acttggtgca gatgtgaact acagcggact gatttgcaaa
     4501 aatccgttcc acctggaatg gctggtgatg gagtggcgcg aggaagccta taccctcgat
     4561 gaactggctg attatctcga tttgagcgcc tcagcgcgcc gtagcatcga taaacattac
     4621 gggatggggc gaaactgcta cctgttcgaa atgacgcgca aatgggctta cagggcgatt
     4681 cgtcagggct ggcctgtatt ctcacaatgg cttgatgccg tgatccagcg tgtcgaaatg
     4741 tacaacgcat cacttcccgt tccgctttct ccggctgaat gtcgggctat tggcaagagc
     4801 atagcgaaat acacgcacag gaacttcacg ccggaaactt tcgcacagta tgtggcgaca
     4861 acgcacacgc cggaaattca agctgcccga ggccgtaaag gtggtatagc caaaggggct
     4921 ggctatgagg ataagcgcag caccgcgctg gaaatgttgg tgaatgggtg tactcaaaag
     4981 gctatagctg aaatgttagg tgtttccgat cgcactattc gaaactggaa aagcggaaaa
     5041 tagcctatat cagataacag cgccttttcg gcgctttttt gagcttttgg tgttcctgtg
     5101 gtttttccgg ttccgtccag caatggcgct ggtttcctcg tgattgcggt ggcagcgctc
     5161 gccgcagtct catgaccgag cgtagcgagc gaatgagcga ggaagcgcaa aggcgtccgg
     5221 tggtgcatgt ggcacttacg cgccggggct tagtggttct gcggtttcgc aggtggtttg
     5281 ggtagcttct ccagctcgtt aatcagcggt tgtagccggt tcatatcggc ctgtcttgtg
     5341 acttcctttc gcaggaactg gagcaggaac gctcgcagtt gcgcttcttc cggcctccgt
     5401 acccttgcca gcatggctgc ccccacaatg actttttgcg ctgtgtccag gctccggctc
     5461 ttcgccttca ggcgctgtaa tcgggcctca gcgtcggcaa tcttctgttc gagtgttctg
     5521 ctcatttcgt gactccgtgc gcggtgaaaa atcgcatttt agcgcgtcac tggtagttta
     5581 aaaactgaac tggcataatg cacggaacat cacgaagtgc gcacttatac aatctccact
     5641 ccgtttcgat tgtgtgcgcc ctgcggggct gaaagaaaac ggcaaaaagg cattacggca
     5701 gaaatggcga tttatcatct cagcatgaaa atcatttcgc gaaaaaacgg ctacagtgcc
     5761 gttgcttctg ctgcctaccg ttccggctct gtcatacccg atgaccgtac cggattaacc
     5821 cacgattaca cccgtaaacg cggcgttgat gatgcggtca ttctcacccc tgagaatgca
     5881 ccgtcatggt gtgctgaccg ttccgttctc tggaatgcgg tcgagaaagc cgaacagcgc
     5941 cgggactccc agctggcaag ggagattga
//
