LOCUS       NZ_CP075671             5698 bp    DNA     linear   CON 27-JUN-2023
DEFINITION  Escherichia coli strain STEC2018-553 plasmid pSTEC2018_553-f.
ACCESSION   NZ_CP075671
VERSION     NZ_CP075671.1
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 5698)
  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  JOURNAL   Unpublished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 5698)
  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 5698)
  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
            CP075671.1.
            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..5698
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="STEC2018-553"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSTEC2018_553-f"
                     /geo_loc_name="Switzerland: Zurich"
                     /lat_lon="47.40 N 8.55 E"
                     /collection_date="2018"
                     /collected_by="ILS/NENT"
     gene            827..1690
                     /locus_tag="JFY30_RS28470"
                     /old_locus_tag="JFY30_28470"
     CDS             827..1690
                     /locus_tag="JFY30_RS28470"
                     /old_locus_tag="JFY30_28470"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006026881.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="thymidylate synthase"
                     /protein_id="WP_042968311.1"
                     /translation="MKSDSTYSNFNHHFHTIAGNSVDELVRNGIYHILSEGELISSRAG
                     EAQQAYGVNYVLRYPINRLHTTRAGAIKYLAREFIAYFNGSLKAEDGLAKASKFWMSLT
                     DQNGNINSNYGYYVFYESVETYGNQYNWVKHVLMSNKDTRRAIININQSYHKSDTKDFP
                     CTIGIQFYIRNNTLYCETTSRSTDVITGLPYDMGFFSFIHELMWKDLCQSGMTGLELGT
                     TVMKTTFTQIYNKTLQKAHEVIENRLVDESKERMPLIDSARDTLSDILNREQKTAIIKW
                     VHSHAK"
                     /name="thymidylate synthase"
     gene            1680..2237
                     /locus_tag="JFY30_RS28475"
                     /old_locus_tag="JFY30_28475"
     CDS             1680..2237
                     /locus_tag="JFY30_RS28475"
                     /old_locus_tag="JFY30_28475"
                     /inference="COORDINATES: protein motif:HMM:NF014041.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="inosine/xanthosine triphosphatase"
                     /protein_id="WP_052086121.1"
                     /translation="MQNNNIIVALCSENIAKIKATKEVCSLAFRNFSLECYSVPSGVSE
                     TPNSDEEALFGCHRRIENLQSKLNREVDLIIALEGLTETTPFGVFLYGWATIKHVPSGK
                     IFYGCSGKVMLPDDITNDLSCDIKLSDLVLKKFTSVSKEDLEQLGTNGILTNKMYTRED
                     EFSTALRCALGSMIAEHNTILL"
                     /name="inosine/xanthosine triphosphatase"
     gene            2268..3557
                     /locus_tag="JFY30_RS28480"
                     /old_locus_tag="JFY30_28480"
     CDS             2268..3557
                     /locus_tag="JFY30_RS28480"
                     /old_locus_tag="JFY30_28480"
                     /inference="COORDINATES: protein motif:HMM:NF014081.2"
                     /GO_function="GO:0016787 - hydrolase activity [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="amidohydrolase family protein"
                     /protein_id="WP_052086118.1"
                     /translation="MKQKTLFKGIKFLNSSSMLLITGDIYIEDDIIVDVGKNLSVSNDT
                     VIIDSEHLIAFPGLVNAHLHPSKEIYGGILDSSPIDVVLDTVHKNNEMETPDAQYTATL
                     KSLTTGIKKGVTTFGLFTSRVDHDIKAAKLAECRCVVNFCQSNAWIGTGHKPQHNSVDT
                     VIDKFNSAYTLYQDTLISITPATASELSADDHLLLTLHSIAKQNNKPFVLHVHEGAIQV
                     NQHTNEYGKSGIQRLADLNILDSNTTLVHCCHLSTEDIRLLKASQSQIIHCPISNSFVG
                     AGILPISKLHGYLNIGLGTDAAMVNPENDLAFDAMFALYHHGYDDFSKKITATKLLHMI
                     TEGGAKTLGLKNVGKIEKNFKADLLFFEREKIDTDYINTPVSLLKLLNNERPSVVLING
                     KKIVVNGNLVKSTTKENNYNFKLLRGKVIV"
                     /name="amidohydrolase family protein"
     gene            3554..4183
                     /gene="purN"
                     /locus_tag="JFY30_RS28485"
                     /old_locus_tag="JFY30_28485"
     CDS             3554..4183
                     /gene="purN"
                     /locus_tag="JFY30_RS28485"
                     /old_locus_tag="JFY30_28485"
                     /EC_number="2.1.2.2"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_013185554.1"
                     /GO_function="GO:0004644 - phosphoribosylglycinamide
                     formyltransferase activity [Evidence IEA]"
                     /GO_process="GO:0009152 - purine ribonucleotide
                     biosynthetic process [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="phosphoribosylglycinamide formyltransferase"
                     /protein_id="WP_042968310.1"
                     /translation="MKRIAFLFSGRGSLICPVINAINKSKTPAELSVIITNNADFIPSS
                     NPIFNDRKVDVVNHKNFNSRSKFDEHIANILRARNIDLIILGGFRRIFTKEFAMEFGSI
                     TMNTHPSLLPALPGDKAQQKALNMGLRITGATLHFINEEVDAGPIIDQEPVRILDGMTE
                     NDLRQAIIKVEQKMIYRAVLSFLGGNLKMLDNKVIYKDYMNVQDSE"
                     /name="purN"
     gene            4164..5372
                     /locus_tag="JFY30_RS28490"
                     /old_locus_tag="JFY30_28490"
     CDS             4164..5372
                     /locus_tag="JFY30_RS28490"
                     /old_locus_tag="JFY30_28490"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_013185553.1"
                     /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_052086115.1"
                     /translation="MYKIQNNLIAASLVAGILFLAIISLGLSLAILPLYVNKVAGYSAF
                     YVGLVIATESIATLFSRAFAGRYSDNHGPRKGMILGLSLTGSAGLMCWLTFVFFDPSHM
                     AYGVILLSRIIMGIGESLIFTCSGTWPIGLVGKAHAGKIMSWVGIAMFLGLAIGNFGGT
                     WSYSHSGLNVSALIMTLLPLIGFIIVMVVKPVSVSPSINHVSLAYAVKCVWKAGAGFSL
                     ANIGYASITGFLVLLFMQNNWGEQAAVAISLFGVGYVLSRLTLGWTADRSGLGMTIFSL
                     CVEATGLLLISLSLTPWIAMLGSFLTGFGLSMVYPLLALPAIKSMPDENIGLALSTYES
                     CFDIGILISGLIGGSIVSLFGYPAIFIFAFCCCLLALYAAVLAYRQLDITSSQTKTDHT
                     HSV"
                     /name="MFS transporter"
     Typing          complement(2..187)
                     /name="rep_cluster_2401"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.465"
                     /coverage="99.0"
                     /evalue="2.79e-91"
ORIGIN
        1 acgggacacg tggcgctttc tcatagctca cgtcttctgg tatctcgggg cgacttaggc
       61 agttcgctcc gggctgggct gtatgcagga accccccgtt cagcccgact gctgcgtctt
      121 ctccggtaac tgttctcttg ggtccaaccc ggaaaagaca ccacaaagcg ccactggcag
      181 cagccattgg taactggaca aggtggattg agatattaag agttcttgaa gtgggggcct
      241 aactgaggct acactagaag gacagtattt ggtatctgtg ctccaccaag ccagttaccc
      301 ggttaagcag tccccaactg acttaacctt cgactaaacc gcctccccag gcggtttttt
      361 cgtttacagg cagcagatta cgcgcagaaa aaaaggatct caagaggatc gtttgatctt
      421 ttttagatcc gcccactctt ggaacctcca acacatgcat aaaacgtcaa tggtggggac
      481 gattatcgga cggcagcaca tgtcgtacag cctttacatt cagtgagtta gcagtcctag
      541 atgtaaccac ttgttcaact caattctctt agcgtgggaa aaattcgttt tccaggccga
      601 cccctacacg tcaaaacctg ccaaacatgc ttcaaaaatc aacaaattcg ctgtatcgga
      661 agtttcggcg cttccgcctc actggttaaa aaatagcctt aacgtggttt attttccgaa
      721 ttcctggcgg acctctgtat acatcaagga acgaataaaa atatcgacaa taatacgttt
      781 ttagatatta ttgatgtgca atatattttc ttgcaaaggt tacattatga aaagtgattc
      841 tacatattca aattttaatc atcacttcca tactattgca ggtaattctg ttgatgaact
      901 tgttagaaat ggtatatacc atatcctttc agaaggtgag ttgatctcct ctcgtgcagg
      961 agaggcccaa caagcctatg gcgttaacta tgtattaagg tatccaataa atagactaca
     1021 tacaacaaga gcaggagcaa taaaatatct agccagagaa tttattgctt actttaatgg
     1081 tagtttaaaa gctgaggatg gccttgcaaa agcatctaaa ttctggatga gtttaacaga
     1141 tcaaaatggc aacataaatt ctaattatgg atattatgta ttctatgaat ctgtagaaac
     1201 atatggaaac cagtataact gggtcaaaca tgttcttatg tccaacaaag atacacgtcg
     1261 agcaattata aatataaatc agagttatca taagtctgat acaaaagatt ttccttgtac
     1321 aataggcatt caattttaca taagaaataa cacactctac tgtgaaacga catctagaag
     1381 cactgatgtc attactggat taccatatga catgggattt ttttctttta tacatgaatt
     1441 aatgtggaaa gatttatgtc agagtgggat gacaggacta gagttaggaa caactgtcat
     1501 gaaaacaaca tttactcaga tatataataa aacgctacaa aaagctcatg aggtaattga
     1561 aaaccgatta gtagatgaaa gtaaagaaag aatgccgtta attgattcag caagagatac
     1621 actttccgat attttaaatc gtgaacaaaa gacagctatt ataaaatggg tacactcaca
     1681 tgcaaaataa caatattatt gttgctctat gttctgagaa catagcaaaa ataaaagcga
     1741 caaaagaggt atgcagtcta gcattccgta atttttcatt ggagtgttat agtgtaccat
     1801 ctggagtgag cgaaactccc aattcagatg aagaagctct atttgggtgt catcgacgca
     1861 tcgaaaatct acaatcaaaa ttaaatagag aggtcgattt aatcattgca cttgaaggac
     1921 taaccgaaac aactcctttt ggtgtatttt tgtatggctg ggccaccatc aaacacgtac
     1981 caagtggtaa aatattttat ggttgcagcg gtaaagtcat gctgccagac gatattacaa
     2041 atgatctttc atgtgacata aagctttctg atttagtgct gaaaaaattt acctcagtat
     2101 caaaagaaga tctcgagcaa cttggaacta atggaatact taccaataaa atgtatactc
     2161 gtgaagatga atttagtact gctctacgat gtgctttagg ttctatgatt gcagaacata
     2221 acacgatact tctataaata cagttccgta ttatcaggag ttaatttatg aaacaaaaaa
     2281 ctctcttcaa aggaattaaa ttcttgaatt cttcctctat gttacttatt actggtgaca
     2341 tatatattga ggatgatatt atcgtcgacg ttgggaaaaa tttatctgta agtaacgata
     2401 ctgttattat agactcagaa catcttatcg cttttccagg actagttaat gcacacctac
     2461 atcctagtaa agaaatttat ggaggtatcc tagactcatc accaattgat gttgttttag
     2521 atactgttca taaaaataat gaaatggaaa caccagacgc tcagtatact gctacgctta
     2581 agtctcttac tacaggaata aaaaaaggtg taactacttt tggtttgttc acaagtaggg
     2641 tcgatcatga tatcaaagca gctaagcttg cagaatgccg ttgcgttgtg aatttttgtc
     2701 agagtaatgc atggattgga actggtcata aacctcaaca taactcagtt gatacagtta
     2761 ttgataaatt caattcagcc tatactcttt accaagatac tttaatttca atcacccctg
     2821 ccacagcctc agaattatcc gctgatgatc atctgctttt aactttgcat tctatagcaa
     2881 aacaaaacaa caaaccattt gtgcttcatg ttcatgaagg agcaatacaa gtcaatcagc
     2941 atactaatga atatggaaaa agtggaatcc aacgattagc tgacttaaat atactagatt
     3001 caaatacaac attagtgcat tgctgtcatc tttccacaga agatatcaga ctacttaaag
     3061 caagccagtc acagataatc cattgcccca ttagtaatag ttttgttggc gcaggtatac
     3121 ttccaatttc taaacttcat ggatatttaa atatcggatt gggtacggat gcggcaatgg
     3181 ttaatccaga aaacgatctt gcgtttgatg ctatgtttgc cttgtatcat catggttatg
     3241 atgatttcag taagaaaata acagctacaa aactgcttca tatgataact gaaggcgggg
     3301 ccaaaacact gggattaaaa aatgttggaa aaatagaaaa aaactttaaa gcggatctac
     3361 ttttcttcga aagagaaaag atagatactg attatatcaa tacgccagtt tccttgttaa
     3421 aattattaaa caatgaacgt ccttcagttg tattaatcaa tggaaaaaaa atagttgtta
     3481 atggtaattt agtgaaaagc acaactaaag aaaataatta taatttcaag ttattaagag
     3541 ggaaggttat cgtatgaaaa gaatcgcctt cctattttca gggcgtggta gtctgatatg
     3601 tcctgttatt aatgccataa acaaaagtaa aactcctgcc gagttgagtg ttataataac
     3661 caataacgct gattttattc cctcttctaa tcctattttt aatgatagga aagtggatgt
     3721 ggtaaatcat aaaaatttta attcacgtag taagtttgac gaacacattg caaatatttt
     3781 acgcgccaga aatatagatt taattattct tggcggtttt agacgtattt ttacgaaaga
     3841 gttcgccatg gagtttggct caataacaat gaatactcat ccatctttac ttccagcatt
     3901 acctggtgat aaagctcaac aaaaagccct taatatggga ctacgtatta caggagccac
     3961 actacatttt ataaatgaag aggttgatgc aggacctatt atcgatcagg agccagttag
     4021 gattctagat ggtatgacag agaacgatct acgccaggcc attattaaag ttgagcaaaa
     4081 aatgatttac agagcagtct tatctttttt aggtggaaac ttaaaaatgt tagacaataa
     4141 ggttatatat aaggactata tgaatgtaca agattcagaa taatttgatt gctgctagct
     4201 tagttgctgg catccttttt cttgccataa ttagtcttgg cctgtctctg gctattcttc
     4261 cattgtatgt aaataaagtc gcaggttatt ctgcattcta tgtcggttta gttattgcaa
     4321 ctgaatcgat agctacgctc ttttcacgcg cgtttgcggg gcgatattct gataaccatg
     4381 gtcctagaaa agggatgatt ctggggcttt cccttactgg atctgcagga ctgatgtgtt
     4441 ggctgacatt tgttttcttt gatccttcac atatggcgta tggcgtaatt ctgctttctc
     4501 gcatcattat gggtattggt gaaagcctta tttttacttg tagtggaact tggcctatag
     4561 ggttggttgg aaaagctcac gcaggaaaga tcatgtcatg ggtaggtatc gccatgtttt
     4621 tgggacttgc cattggtaat tttggcggta cttggtcata cagtcattca ggtttaaacg
     4681 tatccgcctt aataatgact ttattacctc ttattggttt tattattgtc atggtagtta
     4741 aaccagtatc tgtttctcca tccataaatc atgtatcgct agcttatgca gttaaatgtg
     4801 tgtggaaagc tggcgctggt ttctcgttgg ctaacatcgg atacgcttct attactggat
     4861 tcttggtact gctatttatg caaaacaact ggggagaaca agctgcggta gccatttcac
     4921 tttttggtgt gggctacgtt ctgtcaaggc ttacgcttgg atggacggct gacagatccg
     4981 gtcttggaat gacgatattt tctctatgtg ttgaggctac gggactgctt ttaattagcc
     5041 tatcattaac cccatggata gctatgctgg gttctttcct tacaggattc ggattatcca
     5101 tggtatatcc gttattggca ttaccagcca taaaaagtat gcctgatgaa aacattggac
     5161 tagcgctaag tacttacgag tcttgttttg acattggtat ccttatatct gggttaatag
     5221 gaggaagtat tgtttcactc tttggttacc cagcaatatt tatatttgct ttttgttgtt
     5281 gcctgctagc gctatatgca gctgttctgg cttatcgtca gttagacata acttcttccc
     5341 agacaaagac agaccatact cattctgttt aattcaatgg tgcaagagga actttactgt
     5401 gatgagtcaa ccgaagagtc aaaaccgtaa gtttctgttc aaatgttccc gcaacaccta
     5461 atagcaatca attcaagccc ctcatggggc ttttttgtta ttcatggatt taccataatc
     5521 ccttattgta cgcaccgctg aaatgcgttc agcgcaatca cggctgctga caggtaaaaa
     5581 tggcaacaaa ccccccgaaa agctgccgcg atcgcacctg ataaatttta accgcatgca
     5641 tagctattca gccatgtgaa taacgctggt tttgcctgcg taaacctcat gacactgt
//
