LOCUS       NZ_CP075676             1964 bp    DNA     linear   CON 27-JUN-2023
DEFINITION  Escherichia coli strain STEC2018-553 plasmid pSTEC2018_553-k.
ACCESSION   NZ_CP075676
VERSION     NZ_CP075676.1
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 1964)
  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  JOURNAL   Unpublished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 1964)
  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 1964)
  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
            CP075676.1.
            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..1964
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="STEC2018-553"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSTEC2018_553-k"
                     /geo_loc_name="Switzerland: Zurich"
                     /lat_lon="47.40 N 8.55 E"
                     /collection_date="2018"
                     /collected_by="ILS/NENT"
     gene            complement(76..309)
                     /locus_tag="JFY30_RS28550"
                     /old_locus_tag="JFY30_28550"
     CDS             complement(76..309)
                     /locus_tag="JFY30_RS28550"
                     /old_locus_tag="JFY30_28550"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137429.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_000137429.1"
                     /translation="MTELEMHLLNALEQLQQDYTQRLKDWESAFTDLQHMFELTRQENG
                     QLREQCDDLSQQVQRLAGQVDRLSRLFITNSR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(316..858)
                     /locus_tag="JFY30_RS28555"
                     /old_locus_tag="JFY30_28555"
     CDS             complement(316..858)
                     /locus_tag="JFY30_RS28555"
                     /old_locus_tag="JFY30_28555"
                     /inference="COORDINATES: protein motif:HMM:NF016710.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_231201172.1"
                     /translation="MGTDFEKKLKERAVSTENMLNSEFRKLEASVDRELNLNGQKIRDA
                     ISAHTAAVKEQLETLNSAVNAQFSATENELARRQEELLWKLIKGRILYPSLTALCVTGG
                     IFLASWGLIQWQESRIAANILAIRDQEETLAKLREKTWGVTYHEGRNGKFLVLPSGVKG
                     ENNWTVEKKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            complement(<908..1345)
                     /locus_tag="JFY30_RS28970"
                     /pseudo=""
     CDS             complement(<908..1345)
                     /locus_tag="JFY30_RS28970"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(1554..1877)
                     /locus_tag="JFY30_RS28565"
                     /old_locus_tag="JFY30_28565"
     CDS             complement(1554..1877)
                     /locus_tag="JFY30_RS28565"
                     /old_locus_tag="JFY30_28565"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_001444404.1"
                     /translation="MLTIRVTDEEHARLLARCEGKQLASWMRKVCLGAPPSKTSGLPTL
                     APPLLRQFASVGNNLNQIARKINSGQWSGHDRVHVVAALMAIGRELSELRDEVRKQGER
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     Typing          complement(3..1564)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.808"
                     /coverage="98.0"
                     /evalue="0.0"
ORIGIN
        1 cttcccgttc ctgctcttca tgccaggacc gcgcacgctc ccgttccagg cgtgcctgcc
       61 tttcctgttc atcccttatc tgctgttcgt gataaataac cgactcaagc ggtccacctg
      121 cccggctaat ctctgcacct gctgactcaa gtcgtcgcac tgttccctca gttgcccgtt
      181 ctcctgtcgt gtcagctcga acatatgctg caaatccgtg aaggcgctct cccagtcttt
      241 cagccgctgc gtatagtcct gctgcaattg ctctaaggcg ttcagtaagt gcatttccag
      301 ctctgtcata ctcacttact ccctgaccag tcttactgcg ttcttcttct ccaccgtcca
      361 gttgttttcc cccttcaccc cggacggcaa caccagaaat ttcccgttcc tgccctcgtg
      421 atacgtcaca ccccatgttt tttcccggag tttcgccagc gtctcttcct ggtccctgat
      481 agccaggatg ttcgccgcaa tccggctttc ctgccactga atcagccccc atgacgccag
      541 aaaaatcccg cccgtgacgc aaagcgccgt cagcgacggg tacagtatcc gccctttgat
      601 cagcttccag agcagctctt cctgccgccg ggccagttcg ttctctgtgg cgctgaactg
      661 cgcgttcacg gcactgttca gcgtctccag ttgttctttc accgctgctg tgtgtgcgct
      721 gatagcgtct ctgattttct gcccgtttaa gttcagttcc ctgtctacag acgcttcgag
      781 cttcctgaac tcgctgttca gcatgttctc tgtagagacg gcacgctctt tcagtttctt
      841 ctcgaagtct gtccccattt gtaaaagatt gctcatacag cgcccctttc agcctgagat
      901 tacgcccgcc ctccgggtcg gcgatactga tactgctcct ggttgtcctc accacctcaa
      961 aacctgccgc tgtaagcgcc tcagtgacat cctgacgcgt ttttagcgct ccggcatggt
     1021 aaagagcctc cagtcccctc gtaatcgctt ctgcggcctc ctgtttcgct ttcggcagat
     1081 tattcggggt gacaagtgtc cgcctgttct ccggtgcgtt cgggtcgtgc agcccgtaat
     1141 ggtgattcac cagtgtctgc caggcattga ttcgcggacg gtccgcccgg tcgtaatagg
     1201 gctggagccg ttttccgctc gccagctcca tattcgggat gacaaaattc agctcaagac
     1261 gccccttgtc ctggtgctcc acccacagga tgctgtactg atttttttca agaccgggca
     1321 tcagtacccg ctcaaagctc tccatcaccc tttcacgctc tcccggtggc agggtctgct
     1381 ctgcaaaaga cagaaccccc gaggtgtatt ttttcgcaaa cggcgtggca tcgatgagtt
     1441 cccgcacctc ttcgggagca ccccgcagaa ctctcgcccc ttcccggcta cgctcccggc
     1501 ccagcaggta atcaaccgga ccactgccac cgccttttcc cctggcatga aacttaacta
     1561 tcatcccgtt ctccctgttt acggacctca tccctcagct cactcagttc acgtccgatg
     1621 gccatcagtg cagccaccac atgaacccgg tcatgccccg accactgtcc gctgtttatc
     1681 ttccgggcta tctgattcag gttattgccg accgaagcga actggcgcaa cagcggcggt
     1741 gccagtgtcg gaagacctga cgttttcgat ggcggtgccc ccaggcagac cttacgcatc
     1801 catgacgcaa gttgttttcc ctcacaacgt gccagcagcc gcgcatgttc ctcatccgtg
     1861 acccgtatcg tgagcatcct ttcgcgtttc accggtatca ttaaaaacct ccgacagact
     1921 ccccacacat ggagaaacag aactgtgact aaacaggaaa aaac
//
