LOCUS       NZ_CP075635             5598 bp    DNA     circular CON 27-JUN-2023
DEFINITION  Escherichia coli strain 2018-166 plasmid pSTEC2018_166-d, complete
            sequence.
ACCESSION   NZ_CP075635
VERSION     NZ_CP075635.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16993346
            Assembly: GCF_016404485.2
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5598)
  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  JOURNAL   Unpublished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 5598)
  AUTHORS   Nusch-Inderbinnen,M., Stevens,M.J.A., Cernela,N., Muller,A.,
            Biggel,M. and Stephan,R.
  TITLE     Direct Submission
  JOURNAL   Submitted (14-MAY-2021) Institute for Food Safety and Hygiene,
            University of Zurich, Winterthurerstrasse 272, Zurich, Zurich 8057,
            Switzerland
REFERENCE   3  (bases 1 to 5598)
  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; SPAdes v. 3.15.2
            Assembly Name                     :: 2018-166_NP
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 80.0x
            Sequencing Technology :: Oxford Nanopore; Illumina MiniSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/27/2023 06:22:39
            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)                     :: 5,465
            CDSs (total)                      :: 5,343
            Genes (coding)                    :: 5,049
            CDSs (with protein)               :: 5,049
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 294
            CDSs (without protein)            :: 294
            Pseudo Genes (ambiguous residues) :: 0 of 294
            Pseudo Genes (frameshifted)       :: 133 of 294
            Pseudo Genes (incomplete)         :: 162 of 294
            Pseudo Genes (internal stop)      :: 52 of 294
            Pseudo Genes (multiple problems)  :: 50 of 294
            Pseudo Genes (short protein)      :: 4 of 294
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP075635.1.
            Bacteria and source DNA available from ILS.
            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..5598
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="2018-166"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSTEC2018_166-d"
                     /geo_loc_name="Switzerland: Zurich"
                     /lat_lon="47.40 N 8.55 E"
                     /collection_date="2018"
                     /collected_by="ILS/NENT"
     gene            1336..1734
                     /locus_tag="JFX80_RS27015"
                     /old_locus_tag="JFX80_27035"
     CDS             1336..1734
                     /locus_tag="JFX80_RS27015"
                     /old_locus_tag="JFX80_27035"
                     /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="helix-turn-helix transcriptional regulator"
                     /protein_id="WP_062863593.1"
                     /translation="MKALRRLLGFSLIDMAKHFNVSPSTYHAYETGKYKAPDNVIQYFW
                     LLHNDVKVLYDDLRYLANNNRASISEQYGRYSEEATHCRIIATSYRSFEAFQKQFKDKK
                     PTYLEYRIREAAILLAAFSGDCEIENVG"
                     /name="helix-turn-helix transcriptional regulator"
     gene            1737..3665
                     /locus_tag="JFX80_RS27020"
                     /old_locus_tag="JFX80_27040"
     CDS             1737..3665
                     /locus_tag="JFX80_RS27020"
                     /old_locus_tag="JFX80_27040"
                     /inference="COORDINATES: protein motif:HMM:NF014581.2"
                     /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="type IV secretory system conjugative DNA transfer
                     family protein"
                     /protein_id="WP_062863592.1"
                     /translation="MDYIYFAYFSLKNDSTVAYIIASVIAFILGWISSSGFWCKQFVLL
                     GIPKSMIAARKKEWTGQNSTPGLAFFIDCDSPADEVLKIRNGYYNRYRLAWCSLAVFLV
                     ILAGFLVLEIYTFGLFQTLDKISALNFDRFYLQTVIFFILGGIIGFVHIQSKKPNNKSR
                     ELARINDIQDKARRKAAQRGNSLTDIRDVSFAAPAKFSPLEQMDKFSPGDRVFLGFNGS
                     AYKENSPISVTRRFWNTANIQIIGAPGSGKTKMATNCILQCVRDFGDSCLFFDPKNDEH
                     APQVLHNNLPAGKFVKLDLRAGTPPQINPFGGLSYTDLKNLIINCFGMQESGKESDFYK
                     LMQQDAANAVSKEFHGNANIFSLIDAFHRLDEKTKEPAKAFISRLESLAELSCIHTESG
                     FSLENAIEEGMCVYIVGSTSDLNVRFLQQILFARCIQNVMKREANREYRQLLIMVDEIR
                     YCLSPYVVDSLGTVRSKKCHLLLAHQSEGDFAAVQGKDFQSVRTAIMDNISLRWIYRAT
                     NAESAERASKETGLIRATTADRKALAVENNEEVMSGDVNIRETQRYAFDANTMLSLPEG
                     MAVVVGLPKEKNNARSELIYTHHIEYSPSTIALPEAPALVRQTLDTLLQPAPKAEPHSP
                     LSAEDFR"
                     /name="type IV secretory system conjugative DNA transfer
                     family protein"
     gene            3665..4402
                     /locus_tag="JFX80_RS27025"
                     /old_locus_tag="JFX80_27045"
     CDS             3665..4402
                     /locus_tag="JFX80_RS27025"
                     /old_locus_tag="JFX80_27045"
                     /inference="COORDINATES: protein motif:HMM:NF025186.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication-relaxation family protein"
                     /protein_id="WP_062863591.1"
                     /translation="MLYSTRDAIVERNAKKRRDTLTFLAEETCSTSSVIALLLNIKSVP
                     RANDFLRSLEKQEIVCCSDTFIAGRKVRLWGLTEHGAALSGREKVQPFHPSRVSPTQLQ
                     HRLDIQRIRLMLQSHPAVSDWRYPSQRRKGERSHDAEFRLNERIIGLEVERTVKSRSRY
                     EQIVSDFFVRIMRTKEDERANVPQYCWYVCPTEEIALRVGDALKRCTRINNNGKWESLP
                     EAIIAEQRFKAFTYDAVEKWAKK"
                     /name="replication-relaxation family protein"
     gene            complement(4443..5405)
                     /locus_tag="JFX80_RS27030"
                     /old_locus_tag="JFX80_27050"
     CDS             complement(4443..5405)
                     /locus_tag="JFX80_RS27030"
                     /old_locus_tag="JFX80_27050"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016946646.1"
                     /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_198788103.1"
                     /translation="MSELVVYKANELAVSRYDLTEHETKLILCCVALLNPTLDKPTRED
                     RTITFTYQQYAEMMGLSPDNAYHRLHKATSELMTRTVEIIYPTGDISKRIFQWVNYAEF
                     NRKTQSLTLVFSEDIIPYLFQLKKFIKYNLDYVKAFENKYSMRIYEWLLKELTQRKTHR
                     ANIEISIAEFKFMLLLEKHYPEFKELNRWVLKPITKDLNTHSNMKLAIGKRGRPADTLI
                     FQVVLNQPVEPGDNGKNAPKNTTRTPIPALNMTEDELLYRALVNVLHRALIAKIQLTKF
                     DAKFLCDMQSKYHLNASFSWLTDKQREKLEKTLSKYRAF"
                     /name="replication initiation protein"
ORIGIN
        1 ttttgaaaac gcgaagccct agaataaaaa gagaataaaa gatctaaaag agaatagatc
       61 cgccgcctgt ggataacctg gcaaaatcga cgattcgaaa ctgtgccgcc tcggttccgg
      121 tagcgccttg agcgccaccg gaaaccgtca gggggatacc ccctgacccc ctccgcaata
      181 ttcaacatcg acgcgtaagt gccaaacttc gccacagctc tattccgccc cctccgccca
      241 ctcgctcgct aacgctcggt cgctagggct acggcgggca gtttctccaa acgcaaaccc
      301 caaccccaac ttattcggcg ctggcgagcc tcagacgcct taaacgccca tcaggcgacc
      361 caacctacca cctacccaaa aaaaacgcgc cagaatcgct ctcagcgcgt tttaagggca
      421 tatgagatat gaatccacag tggcaaaaaa caaaaaacca cattccttga ccgccaaagt
      481 aatgagatta aaaaaacacc atatggggat catacatcgg ggtatctgct agccccgtat
      541 acgatcccca tatgtgatcc ccgtctatga tccctatatg cagggctgtc gccctgtgta
      601 gttcatccgc tagggcggac gaactacaag gggaaccccc agtaatttcg cgggctggac
      661 gcccccaaaa ttactgcgtt tcccctcttt ctggcttttg tctgctggac gccgacaaca
      721 ccagaaattc acctgccgtt cgtcacgcta tgcgtgacca acctacaaaa tgacgtgctg
      781 aacgcccgca ttttctaggt tggtcacgca gcgtttcact gtcgtttcac ttgcggtgac
      841 gaacggcgag aaggatcaaa atcaacgctc tggggagcgt cgatttttct cacccgctgg
      901 ggcgggttcg ccttctctgt gtgctgcgcg ttttcttctg gggaagaaag acgcttgcat
      961 ctttcgaaat gctggacgca attcgaaaga cgggacgcga gcaatccgct ggggcggctg
     1021 gctcgctaac gctgtcttgg gtcagcgttc ccgcacaact gcaccgcctg ccaaattctg
     1081 agcaccgttt ttctacctag tggtttgaac gaggtatgcg aaaaaaattc gcttttctgc
     1141 ttgacgactc cgaccaatag tgaaagatat caacgtcgtc ttcttgttat ttttttggaa
     1201 aatatgaaaa ttcgaaaaga tgtcgtccgt atctcaaacg attgttatat tggggctacc
     1261 agccatagca tgttatcaag gaaatacggg gaaccgtata agtgttcact ttatccctcg
     1321 ggagcacaga acaccatgaa agcattgcgc agattgttgg gcttttcgct aatagacatg
     1381 gcaaagcact tcaatgtttc gccaagtact tatcatgcct atgagacggg aaaatacaaa
     1441 gcgccagata atgttattca gtatttttgg cttctgcaca atgacgttaa agttttatat
     1501 gatgacctac gttatctcgc taataataac cgggcatcaa ttagtgagca gtacggcaga
     1561 tattctgaag aggctacgca ctgtcgcatc attgctacaa gttaccgctc gtttgaagcg
     1621 tttcaaaaac aattcaaaga caaaaaaccc acttatttgg agtatcgaat aagggaggca
     1681 gctatactgt tagctgcatt tagcggtgac tgtgaaatag agaatgtagg gtgattatgg
     1741 attatattta ctttgcgtat ttttctctga aaaatgattc aacggttgca tacattatcg
     1801 cttcagttat tgctttcatt ttgggatgga tttcttcctc tggattctgg tgtaaacagt
     1861 ttgtccttct tggaatacca aaatctatga tagccgccag gaagaaagaa tggacgggac
     1921 aaaacagcac gcccggactg gcatttttca ttgattgcga ctctcctgct gatgaggtgt
     1981 tgaagattcg aaatggttat tacaatcggt atcgtcttgc ctggtgttca ctggctgttt
     2041 ttctcgtgat tcttgcagga tttctggtac ttgaaatata cactttcggt ttattccaga
     2101 cactggacaa aatcagcgca ctgaacttcg accgttttta tctacagacg gtaattttct
     2161 ttattctcgg ggggattatt ggatttgttc acattcaatc aaaaaaaccg aataacaaat
     2221 ctcgtgaact cgcacgaata aacgatatac aggacaaagc aagacgaaaa gcagcccagc
     2281 gcggcaattc tctgacagat atcagggatg tttcgtttgc agcgcctgca aagttttccc
     2341 cgctcgaaca aatggataaa ttttcgcctg gcgaccgggt ttttctcggc tttaacggct
     2401 ctgcgtacaa agaaaactcg cctatatctg tcacccgtcg tttctggaat accgccaaca
     2461 ttcaaatcat cggcgcacct ggtagcggca aaacgaaaat ggcgaccaac tgcatcctgc
     2521 aatgcgtgcg cgatttcggt gattcatgtc tgttttttga ccccaaaaat gatgagcatg
     2581 ccccacaggt gttacacaac aatctgcctg ccggaaaatt cgttaagctc gatctccgtg
     2641 ctggtactcc gccacagatc aacccgttcg gcggactctc atacaccgat ttgaagaacc
     2701 tgatcatcaa ttgtttcggg atgcaggaaa gcggaaaaga atcggatttc tacaagctca
     2761 tgcaacagga tgccgccaat gccgtgtcga aagagtttca cggtaacgcc aacatttttt
     2821 ccctgataga tgctttccat cgcctcgatg aaaagaccaa agaacctgca aaagcattca
     2881 tctccaggct ggaatccctt gcggaattat cctgcattca cacggagtct ggattctccc
     2941 tggagaatgc gatcgaagaa ggcatgtgcg tttatatcgt cggctccacg agcgacctca
     3001 acgttcgttt tctgcaacaa atacttttcg cgcgctgtat acaaaacgtc atgaagcgcg
     3061 aagcgaatcg ggaataccgt cagctactta tcatggttga tgaaatccgt tattgcctgt
     3121 cgccctacgt cgttgattca ctgggaaccg tccgcagcaa aaaatgtcat ctgctccttg
     3181 ctcaccagtc cgaaggcgat tttgcagccg tccagggaaa agatttccag tccgtcagaa
     3241 ccgctatcat ggacaacatt tctctgcgct ggatctacag ggctacaaat gccgaatctg
     3301 ccgaacgcgc ctcaaaggaa accggcctga ttcgtgcgac aacagcagat cgcaaagccc
     3361 ttgcagttga aaacaacgaa gaagtgatgt ccggagatgt taatatccgc gaaacacagc
     3421 gttacgcatt tgatgccaat accatgctct cgttaccgga aggcatggcg gtagttgttg
     3481 gtctcccaaa agaaaaaaac aatgcccgct cggagttgat ctacacgcat cacattgaat
     3541 actcgccatc aaccattgcc cttccggaag ctccggctct ggtccgacag actctggata
     3601 ctctgctaca gccagcacca aaagcagagc cgcactcacc cctaagcgca gaggacttcc
     3661 gctaatgctg tattctaccc gtgatgcaat tgtcgagcgg aacgccaaaa aacggcgcga
     3721 tactctgact tttctggcag aagaaacgtg cagcacgtcg tcagtgattg ctctcctgct
     3781 taatatcaaa tcagtgcccc gcgccaacga ttttctgcgc tctctggaga aacaggaaat
     3841 tgtctgctgt tccgatacct tcattgctgg ccgcaaagta cgcctttggg ggttaacgga
     3901 acatggtgcg gcactttctg ggcgggagaa agtccaacca ttccaccctt ccagagtgtc
     3961 cccgacgcaa ctgcaacacc gccttgatat tcagcgtatc cggctgatgc tccagtcgca
     4021 tcctgccgtg tctgactggc gttatccctc gcaaagacga aaaggtgagc ggtcacacga
     4081 tgccgagttt cgattaaacg agcgaatcat cgggctggaa gttgaacgaa ccgtgaaaag
     4141 ccgcagccgg tacgagcaaa tcgtttcaga tttttttgtc cgaatcatgc ggacaaagga
     4201 agacgaacgc gcgaacgtac cgcagtactg ctggtatgtc tgccctacgg aagaaatcgc
     4261 attacgcgtg ggggacgcat tgaaaaggtg caccagaatt aacaacaacg ggaagtggga
     4321 atcactgccg gaagcaatta ttgcagagca acgttttaag gcattcacct atgatgccgt
     4381 ggaaaagtgg gcaaaaaaat aaataaaggc ggcgtgagcc gcctttgttt ccagggtagg
     4441 tgttaaaagg cgcgatattt gctcaacgtt ttttcgagtt tttctctttg tttatcggtc
     4501 agccatgaaa aagaagcatt aagatgatat ttgctttgca tatcacataa aaatttcgca
     4561 tcaaatttcg tcaactggat tttagcgatt agcgccctgt gcaagacgtt taccagtgcc
     4621 ctatataaca gttcatcctc tgtcatattg agagcaggga tcggtgttct tgttgtattt
     4681 ttcggagcat ttttaccgtt atcgcccggt tcgactggct gattcagcac cacctgaaat
     4741 atcagtgtat ccgcagggcg accacgttta ccaatagcca acttcatgtt actgtgcgtg
     4801 ttaaggtctt ttgttattgg ttttaacacc caacggttta gttctttaaa ttcagggtaa
     4861 tgtttttcca gtaacaacat gaatttaaat tcagcgatac tgatttcaat attggctctg
     4921 tgagttttgc gctgtgttaa ttcttttaaa agccattcgt atatgcgcat cgagtatttg
     4981 ttttcgaacg cttttacata atccagatta tatttaatga atttctttaa ctggaacagg
     5041 taagggataa tgtcttcact aaaaaccaaa gttaatgatt gggtttttct attaaattca
     5101 gcgtaattaa cccattgaaa tatacgttta gaaatatctc ctgtagggta gattatttct
     5161 accgttctgg tcattaactc actggttgct ttgtgtaatc tgtgatacgc gttatcagga
     5221 gataacccca tcatctcggc atattgctga tacgtgaatg taattgtcct gtcttcgcgg
     5281 gtgggtttat ccagtgttgg attgagtagc gccacacagc acagaattaa cttggtttca
     5341 tgctccgtca ggtcataacg actgacggcc agttcgttcg ctttgtatac aaccagttcg
     5401 gacataaatc accttggtgt tgatataata tttagctaca ccaacataca taagcgtagg
     5461 atggcgatca agcaccactt tttagtgatg gcctgtgaat actgtgattt ttactacacc
     5521 gttcgatgac ttatttgtga tttttactac accctttatg atttttacta caccttttgc
     5581 ctcgtaaccc tttgtttt
//
