LOCUS       NZ_CP075646             6683 bp    DNA     circular CON 27-JUN-2023
DEFINITION  Escherichia coli strain S19-141 plasmid pS19_141-f, complete
            sequence.
ACCESSION   NZ_CP075646
VERSION     NZ_CP075646.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16993351
            Assembly: GCF_016404325.2
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6683)
  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  JOURNAL   Unpublished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 6683)
  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 6683)
  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                     :: S19-141_NP
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 80.0x
            Sequencing Technology :: Oxford Nanopore MinION; Illumina MiniSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/27/2023 06:11:28
            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)                     :: 5,151
            CDSs (total)                      :: 5,035
            Genes (coding)                    :: 4,825
            CDSs (with protein)               :: 4,825
            Genes (RNA)                       :: 116
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 210
            CDSs (without protein)            :: 210
            Pseudo Genes (ambiguous residues) :: 0 of 210
            Pseudo Genes (frameshifted)       :: 90 of 210
            Pseudo Genes (incomplete)         :: 109 of 210
            Pseudo Genes (internal stop)      :: 63 of 210
            Pseudo Genes (multiple problems)  :: 49 of 210
            Pseudo Genes (short protein)      :: 5 of 210
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP075646.1.
            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..6683
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="S19-141"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pS19_141-f"
                     /geo_loc_name="Switzerland: Zurich"
                     /lat_lon="47.40 N 8.55 E"
                     /collection_date="2019"
                     /collected_by="ILS/NENT"
     gene            complement(522..716)
                     /locus_tag="JFX59_RS25585"
                     /old_locus_tag="JFX59_025585"
     CDS             complement(522..716)
                     /locus_tag="JFX59_RS25585"
                     /old_locus_tag="JFX59_025585"
                     /inference="COORDINATES: protein motif:HMM:NF033650.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="ANR family transcriptional regulator"
                     /protein_id="WP_001367294.1"
                     /translation="MNQDKAIYLENKYFSPANEAVRLEREGDYIGAWKKWNDALHYAKG
                     ENIGWCIARAEYCKKTGRF"
                     /name="ANR family transcriptional regulator"
     gene            1335..1520
                     /locus_tag="JFX59_RS25590"
                     /old_locus_tag="JFX59_025590"
     CDS             1335..1520
                     /locus_tag="JFX59_RS25590"
                     /old_locus_tag="JFX59_025590"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041629.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_032314062.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDADEQAAMCERLHELAEEL
                     GNSIQTHFEAQYGTEP"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2187..2300
                     /locus_tag="JFX59_RS25595"
                     /old_locus_tag="JFX59_025595"
     CDS             2187..2300
                     /locus_tag="JFX59_RS25595"
                     /old_locus_tag="JFX59_025595"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001427889.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLTPLAAAIGN"
                     /name="hypothetical protein"
     gene            complement(2544..3248)
                     /locus_tag="JFX59_RS25600"
                     /old_locus_tag="JFX59_025600"
     CDS             complement(2544..3248)
                     /locus_tag="JFX59_RS25600"
                     /old_locus_tag="JFX59_025600"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001253652.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF2931 family protein"
                     /protein_id="WP_001253651.1"
                     /translation="MRRLPLMVGVIVGVMLAVGCHDRRAGVKTLLGDGMDQWGQKLPYD
                     HWQFNFFYPKNLPALVTMVYLEDGDVRESIFRQLDAARPSQSSVDTWSQRVGSFSASFN
                     IGKALPVRMTVCWDSVIDKKAYETEIWFSRDTWQQMLTAYPDTYKPGKTYYRDNMIIGL
                     APGGAVRIWLEDNGEPVVLQHPARQFTLTGDDMLICKNVPNQIDFSYIKANGYDPFIRD
                     FIKEKPYPYGHW"
                     /name="DUF2931 family protein"
     gene            complement(3259..4950)
                     /locus_tag="JFX59_RS25605"
                     /old_locus_tag="JFX59_025605"
     CDS             complement(3259..4950)
                     /locus_tag="JFX59_RS25605"
                     /old_locus_tag="JFX59_025605"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000229015.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF2235 domain-containing protein"
                     /protein_id="WP_137446151.1"
                     /translation="MVEEDEKNVPGDTCYYRYEIIGDSTHRTSIHNSFKTIQCRRVPVR
                     GITLTVGVFFDGTGNNRANADDLRLAYAHCANLVDEEWARACEKYEKRARAGLGNASWQ
                     GGHTNISRLFDLYQQSDELNDSETEAQVKAYISGIGTADGESDSILGKALGSSLIRQFE
                     GVVTKTDEALEKISAELTRFIKLNRDKVAIAKVQFDVFGFSRGAAAARHFANRVMNQDA
                     AIAAAIDKGTDLTGHHGKLAGEVRFLGLFDTVAAIGSLLNFYDVNGRSNPGVNLELRPS
                     VAQKVFQISAMHECRYNFSLNSIAGMWPELALPGAHSDIGGGYNAGEDEISLLTMPDFE
                     VTRDSADEMQTEVYRKAEKMRQVLYSLPALKYLMPHGEVETKMISWPLVNQNKARASIF
                     EKKVGAAVFMTRRDVPNDWEKVSLRVMLDAAQDAGAVFTPILSSNKELALPSELLPLCD
                     KAIAQGRAVRRGAEPEGFTAEDMRTIGRYLHCSANWNIDSDLSLWVSPSSGEVFLRNNY
                     APTDERSFVWPMAPGKGWVRTVWRMDDQQQWEERARVNADALDGLF"
                     /name="DUF2235 domain-containing protein"
     Typing          complement(1602..1689)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="94.382"
                     /coverage="100.0"
                     /evalue="5.29e-30"
     Typing          6403..6481
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.75"
                     /coverage="87.0"
                     /evalue="3.37e-32"
     Typing          1700..2259
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.907"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aacacacaaa actcacaatt gccatgtcct cattgacacc cccttgccat atagggggat
       61 tttttcgcct gtcctgattg tcttttgccg atggttacgg cagattggaa aagagcgcat
      121 ttgtggtgct ctctccagaa taatatttct cattactcaa actctgatgg cttccccctg
      181 taatccaggg ggatttttta atttatcgct atgcttcgta attcattcag aatacagaca
      241 gtatggttaa tcagtttttc atcatttttg cggtgtttgc cctgtcctgc atcagaacgc
      301 taaaaaacag gattggaatc tctttatgac gaatcctcca tttcaggatt ttttatgtaa
      361 cgtctactac atgcgatccg ttggtgaacc gttagttata tattggttat atgttaatta
      421 tatcttagtt atacttttga tgcgcgtcag ttacagaggc gttttgaggg taaattctgg
      481 cggggaatca aagggggcgc ccctttgatt ccccgccaga attaaaaccg gcctgtcttt
      541 ttacaatatt cagctctggc tatacaccaa cctatatttt ctcctttggc ataatgaagc
      601 gcatcattcc attttttcca tgctccaatg taatcgcctt cacgctccag tctgacagct
      661 tcgtttgcgg gtgaaaaata tttattttct aaataaattg ctttgtcctg attcatactc
      721 gtaatttata tttttatttg aattaaaaaa gagcggcctg tcgggttaat acatattggc
      781 atgactgttg atatatcagc ccaactgcac gctcgtaatc gttttaacgt gattttcgca
      841 acatggcaat ccgggttcgt ctgtccggta atcaataaaa accgagcgaa aaacgggaca
      901 ggatgtgcgt ttgtttaacc gcgcacgcgc catcaaacaa acaccatctg gtcatggctt
      961 cgcccgacac cccgcgaacg tctctggcca gaactggcca tcacgccggg tcactttgtc
     1021 agatgttaaa aaatcacgcg gtaaacgccg ttattcgcgg gtttgcgcaa gcacctcccg
     1081 tgcgtcactt tgtcaaaacg tcaaagtgac gcacatcagg aaccggcgga acgttcatgt
     1141 ttatgacgac aactgcacac aacgcagaca gaaaatcgcg cacatattca gcaaaaaata
     1201 agcgtcacgg ggtgttaatg tcgcgcagcc cacacacgac ggggcttgtg tgataatttt
     1261 cagtgacgtc acctggcgtg atgaccaggt gacgcacagc cggacgtaaa caccagtaac
     1321 ggagaaggga gaacgtgaac aaacagcagc agaccgcgct caacatggcg cgattcatca
     1381 aaagccagag cctgacgttg ctcgaaaaac tggatgcaga cgaacaggcc gccatgtgcg
     1441 aacgactgca cgaactggcg gaagaactcg gtaacagcat acagacacac tttgaagcgc
     1501 agtacggcac ggaaccataa aggggctggc gaaagcggtc gcggcttgtc cgtgagtgtt
     1561 ttcgccagca gacaagctcg tcagggcgcg tcagcgggtt ttagcgggtg tcggggcgca
     1621 gccatgaccc agtcgcgtag cgatagcgga gagtatactg gcttatacca tgcagaatca
     1681 gtgcggattg tatgaaaagt gcgccatgcc gggtgtgaaa tgccgcacag atgcgtaagg
     1741 agaaaatgca cgtccaggcg cttttccgct tcctcgctca ctgactcgct acgctcggtc
     1801 gttcggctgc ggcgagcggt tctgactcac acaaaaacgg tagcactgtt atccacagaa
     1861 tcaggggata aggccggaaa gaacatgtga gcaaaagacc aggaacagga agaaggccgc
     1921 gccgcaggcg tttttccata ggctccgccc cccctgacga gcatcacaaa aacagacgct
     1981 caagtcagag gtggcgaaac ccgacaggac tataaagata ccaggcgttt ccccctggaa
     2041 gctccctcgt gcgctctcct gttccgaccc tgccgcttac cggatacctg tccgcctttc
     2101 tcccttcggg aagcgtggcg ctttctcata gctcacgctg ttggtatctc agttcggtgt
     2161 aggtcgttcg ctccaagctg ggctgtatgc acgaaccccc cgttcagccc gaccgctgcg
     2221 ccttatccgg taactatcgt cttgagtcca acccggtaag acacgactta acgccactgg
     2281 cagcagccat tggtaactaa acaaggtgga ttccgatatt agagtcttga agtgatcacc
     2341 caactacggc tacactgaaa ggacagtatt cggtatctgc gctccaccaa gccagttacc
     2401 acagtcgatt agaagaggtc gaagacttct aatcggacgg aaaaagccgc cgcaaggcgg
     2461 ctttttccgt ttacaagccg aagattacgc gcagcttaaa aggatctcaa gaagatcatt
     2521 ttaattttgc tgatcgttgc tccctaccag tgaccatacg gatagggctt ttccttgata
     2581 aaatcgcgga taaatggatc gtaaccatta gccttgatgt aactgaaatc aatctggttg
     2641 ggaacgtttt tgcatatcag catatcatct cccgtcagag tgaactgccg ggcaggatgt
     2701 tggagtacaa caggctcgcc attatcctcc agccagatcc gcacggcccc tcccggtgcc
     2761 aatccgataa tcatattgtc ccgataatac gtttttcccg gcttataggt atcaggatag
     2821 gcagtcaaca tctgctgcca cgtatcccgg ctgaaccaga tctccgtctc atatgccttt
     2881 ttatcgataa ccgaatccca acacaccgtc atcctgaccg gcagtgcctt gccaatgtta
     2941 aaactggctg aaaaactgcc tacgcgctgg ctccatgtat ccacactact ctgacttggt
     3001 ctggctgcat caagctgccg aaatatgctt tcccgtacat caccgtcctc cagatacacc
     3061 attgtcacca gtgctggcag gtttttcggg taaaaaaaat taaactgcca gtggtcataa
     3121 ggcagcttct gcccccattg atccataccg tcgcccaaca gcgtcttcac gccagcccta
     3181 cggtcatggc agccgacagc cagcattacg cccactatca cgcccaccat cagcggtaat
     3241 cgtctcattc ctgcctcctc agaacagtcc gtccagcgca tccgcgttta cccgcgcccg
     3301 ctcttcccac tgctgctggt cgtccatccg ccacaccgtc cgcacccagc ctttgcccgg
     3361 tgccatcggc cacacgaacg agcgttcgtc agtcggagca tagttatttc gcagaaaaac
     3421 ttctcccgag gacggactca cccacaggct caagtctgag tcgatgttcc agttcgccga
     3481 gcaatgcagg taacgcccga tggtccgcat atcctccgcc gtgaagccct caggctccgc
     3541 gccacgccgg acagcacgcc cctgagctat ggctttgtca cacaggggaa gcagttctga
     3601 cggcaacgcc agctctttgt tactgctgag tatcggagta aacacagccc cggcgtcttg
     3661 tgccgcatcc agcatcaccc gcaaactcac cttctcccag tcgttcggca catccctgcg
     3721 cgtcataaac actgccgcgc ccactttctt ctcaaaaata gacgcacgcg ccttgttctg
     3781 attgaccagt ggccacgaaa tcattttcgt ctccacctca ccgtgcggca tcaggtactt
     3841 cagcgccggc agtgagtaca gcacctgacg catcttctcc gccttacggt acacctccgt
     3901 ctgcatttca tccgcgctgt cgcgcgtcac ctcaaaatcc ggcatcgtca gcagggagat
     3961 ttcatcctct cctgcgttat agcccccgcc aatgtccgag tgcgcccccg gcagcgccag
     4021 ctccggccac atccccgcga tgctgttcag gctgaagtta taccgacact catgcatcgc
     4081 gctaatctga aacaccttct gcgccactga aggacgcagt tcgagattca ccccgggatt
     4141 gctgcgtccg ttaacgtcgt agaagttcaa caggctcccg atagccgcca ctgtgtcaaa
     4201 cagccctaaa aagcgcacct ctcccgccag tttcccgtgg tgcccggtca ggtctgtccc
     4261 tttgtctatt gccgccgcta tcgccgcatc ctggttcatc acccggttgg caaaatgccg
     4321 tgcagccgcc gcgccgcggc tgaatccgaa cacgtcaaac tgcaccttcg caatcgccac
     4381 tttgtcacga ttaagtttga taaagcgggt cagttctgcg ctgatcttct ccagtgcttc
     4441 atcggtcttt gtcaccaccc cttcaaactg tcggataagg ctgctgccca gcgctttacc
     4501 cagtatcgaa tcactttctc cgtctgccgt cccgatgccg ctgatatagg ctttgacctg
     4561 cgcctcagtc tcgctgtcgt taagttcatc gctttgctga taaagatcga acagccggga
     4621 aatattagtg tggccgccct gccagcttgc attacccagc ccagctctgg cgcgcttttc
     4681 atacttctca catgccctag cccactcctc gtcaaccaga ttggcacagt gggcatatgc
     4741 cagccgtaga tcgtctgcgt tcgcccggtt attccccgtc ccgtcaaaga acacccccac
     4801 cgtcagcgtt atccccctga ccggcacccg ccgacactgg atggttttaa aactgttgtg
     4861 tatgctggtt cgatgggtac tgtccccaat aatttcatac cggtaataac aggtatcgcc
     4921 cggcacattt ttttcatctt cttcgaccat aaaaatcctt atttatctga aagataaaat
     4981 cagtagcaaa atccttcggg acttttttac atctgcctgt tagacgtatt taccataatc
     5041 ccttaattgt acgcaccgca gaaacgcgct cagcgcgatt ctggcgcaaa aaccgcaaaa
     5101 atagatgttt tcccccgggt aaaccggaaa aatgcgtcag gattgttttc atggcactgc
     5161 atgactatgc atgaaactga atggagatcg gtttgggcgc gcctgatgcc cataaggcgc
     5221 attttcggac gttttcagcc ctgatgagaa gaaatcagac agtagttaca gacgagtcgt
     5281 gagcgattca ccccgggagt catcaacgag tcatccagta ttttcctcgc gactctctgg
     5341 cgactcgcct tctctgaaca ccagagagac agtgtgttga gtcatcgata aatcaccgac
     5401 gactcgttgc cgaatcatcc agtagtcgcc gacgactcgc ttttgtatac acctgaataa
     5461 gaaaatatat ttttagaacc ataacgacat gatttaaaaa gcaaatcagc aaaaagttgg
     5521 ttttgcgtag tgtgtgggca tttcaggcat gagaacagac tcgcgttttt ccggaagaac
     5581 tgcggggatt tttgattaaa caatactcac cgcagaacgg aattttatgc aacgccggca
     5641 gtgctgcacg gggattttta atccccagca tgtcagaggg tgcggatgac ggttcccgtc
     5701 tggcgttttc atgggaaccg gttgtcaaaa aataccagcg tgatcagtcg agggataagc
     5761 gcagattaat cagtgatgat tgagcgcgaa tctgacaacg agtatagcga cacagcaaca
     5821 aaaaagacgc cagaaacgcg ctcagaggct ttgtaacgcg attttttaca tgaggcaatg
     5881 gcttcggttg ttttttcgct ttgaggcgtt caggcgtgtt cagggcgcga ttctggtaca
     5941 tacctgactg taatcatccc tacgaactac tctttgcacc agaaacgcgc aggtgtgttt
     6001 tagcgtgtct ccggcatgat gtcgagttgt gcggtaatga gtgagcaaaa aaaatcccct
     6061 ggattacagg gggaacccat tatcagactt tgaagtttat ttgttatttg atggagtgag
     6121 cacgaatccc ggagatgacg ttcaggtggc aggaaacgcg ctcagacgct ttctaacgca
     6181 cttttttgca tcgggcaatg gttttgccgc cagaggcgtt ttgagcgcgt ttctggcgct
     6241 tgctgctact gccaaaccat ccccatggcc agttgatgcc agaaacgcgc aggagttttg
     6301 tagcgcgtct ccggtcccta atcaatgaat tcccggtcat taacatgcgt ttacccggaa
     6361 acgcgccctg atgttctatc gtatcgcggg aacggtgtcg agggtgtcgg ggcaaagccc
     6421 tgaccaggtg gtaatcgtat agccgtgcgt gcgcggttat acgattacac atcctgtccc
     6481 ggaatcagga ttgtttttcg cgcacaactg cggcaaattc atcccgttgc ggttgcaacg
     6541 atgggtatat caaaactacg aaaattattc aggcatttgc tacccccctt gccctggcct
     6601 ccaccagtca cgggggattt ttttgttgtc tctcatgacg aactacggca aatttctgac
     6661 gttgcaaact gcaacacata aaa
//
