LOCUS       NZ_CP145675             5631 bp    DNA     circular CON 05-APR-2024
DEFINITION  Escherichia coli strain S1-ZIM-01-A plasmid p4-S1-ZIM-01-A, complete
            sequence.
ACCESSION   NZ_CP145675
VERSION     NZ_CP145675.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN33052302
            Assembly: GCF_036884545.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5631)
  AUTHORS   Campos-Madueno,E.I., Aldeia,C. and Endimiani,A.
  TITLE     Strains isolated from intestinal colonization screening for
            multidrug-resistant Enterobacterales in stool samples from healthy
            people living abroad
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5631)
  AUTHORS   Campos-Madueno,E.I., Aldeia,C. and Endimiani,A.
  TITLE     Direct Submission
  JOURNAL   Submitted (09-FEB-2024) Institute for Infectious Diseases,
            University of Bern, Friedbuehlstrasse 25, Bern 3001, Switzerland
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 363.5853X
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_036884545.1-RS_2024_04_05
            Annotation Date                   :: 04/05/2024 17:24:20
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,478
            CDSs (total)                      :: 5,356
            Genes (coding)                    :: 5,141
            CDSs (with protein)               :: 5,141
            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)              :: 215
            CDSs (without protein)            :: 215
            Pseudo Genes (ambiguous residues) :: 0 of 215
            Pseudo Genes (frameshifted)       :: 71 of 215
            Pseudo Genes (incomplete)         :: 162 of 215
            Pseudo Genes (internal stop)      :: 29 of 215
            Pseudo Genes (multiple problems)  :: 48 of 215
            Pseudo Genes (short protein)      :: 4 of 215
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP145675.1.
            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..5631
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="S1-ZIM-01-A"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p4-S1-ZIM-01-A"
                     /geo_loc_name="Switzerland"
                     /lat_lon="46.947928 N 7.422277 E"
                     /collection_date="2022"
                     /collected_by="Institute for Infectious Diseases (IFIK),
                     University of Bern"
     gene            complement(192..383)
                     /locus_tag="V6S34_RS27315"
                     /old_locus_tag="V6S34_27315"
     CDS             complement(192..383)
                     /locus_tag="V6S34_RS27315"
                     /old_locus_tag="V6S34_27315"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165975.1"
                     /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_000165975.1"
                     /translation="MTKQEKTALNMARFIRGQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENR"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            448..771
                     /locus_tag="V6S34_RS27320"
                     /old_locus_tag="V6S34_27320"
     CDS             448..771
                     /locus_tag="V6S34_RS27320"
                     /old_locus_tag="V6S34_27320"
                     /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_024192446.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     AQPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            980..>1411
                     /locus_tag="V6S34_RS27325"
                     /old_locus_tag="V6S34_27325"
                     /pseudo=""
     CDS             980..>1411
                     /locus_tag="V6S34_RS27325"
                     /old_locus_tag="V6S34_27325"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /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            1449..1979
                     /locus_tag="V6S34_RS27330"
                     /old_locus_tag="V6S34_27330"
     CDS             1449..1979
                     /locus_tag="V6S34_RS27330"
                     /old_locus_tag="V6S34_27330"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001673158.1"
                     /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_001673158.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFRKLEESVNRELTSNE
                     SLIRNAINDHTTALKELLERYQKTTVDTMDAHWKTVLKMSVKRWLWLIIVSVLMFATTG
                     SLLWYQGMKINANMNILREQKESLEKLNAKTWGVRYHEDSNGRFLVLPKGMKAETNWTK
                     DNGKLNAVRLVQE"
                     /name="MbeB family mobilization protein"
     gene            1986..2219
                     /locus_tag="V6S34_RS27335"
                     /old_locus_tag="V6S34_27335"
     CDS             1986..2219
                     /locus_tag="V6S34_RS27335"
                     /old_locus_tag="V6S34_27335"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /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_000137437.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWENAFVELQKMFSLTQRDNA
                     MLNGRVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            2700..3752
                     /locus_tag="V6S34_RS27340"
                     /old_locus_tag="V6S34_27340"
     CDS             2700..3752
                     /locus_tag="V6S34_RS27340"
                     /old_locus_tag="V6S34_27340"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001557502.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001053268.1"
                     /translation="MNLQQRINKLPQLSSSFSFGKDIDNIHSFIFNETSKDKIEDLLRK
                     WVSGNQPCVFGKLASKKIKGLDFHLSIVNSPQLYNDDGHLFDFLRNERVRFKERARRGE
                     VSAHLIYFIHPQLAFARPSEELVDIQKYICSLHMPECYPIKEDVIYTESVPFQDKDGLK
                     IYKAGVNVFYSSAHRTRNHDRRIPGGILISVNAPGHFMRLAIEKGFYKDQEQALADIRN
                     MTIQSVGKGGYSHPEGISTTWHSESNLDRFGCPVHTGNSSYYSGFYHTDVLIPGELTKD
                     ERLLHEIENSDPMIFNWNVLFYVSLEEFPIDDPYYGEFIGIPVDDASMFFNSFQPRKFE
                     NKPLYEKEDD"
                     /name="hypothetical protein"
     gene            3754..4620
                     /locus_tag="V6S34_RS27345"
                     /old_locus_tag="V6S34_27345"
     CDS             3754..4620
                     /locus_tag="V6S34_RS27345"
                     /old_locus_tag="V6S34_27345"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001335763.1"
                     /GO_function="GO:0005215 - 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="DMT family transporter"
                     /protein_id="WP_001335763.1"
                     /translation="MIKGMLFAFLAAFSWGAAIVMSKKGVEELDAGGVFFWQICSAVIL
                     SWIVLFIKRKKLPLNSKAILAYATGVFEPFLAYTFTLYGLYFISAGSASIIFSLESVFI
                     LVLSVLICSVKINSPQYFILFLIGAIVGSILVALPDISNGSNNIVGYCLVVAGVLSAAF
                     YVVISSRLIKSFEPITLLSGQLTFSLILSSLFIFISKSSIYLPLESVIIVFSSGILQYF
                     LAFCFYLNSLRWLPVHLAGIMLYFIPLVALFLSWLFLDEQFTFLQGVGFIVTVLSVYFL
                     NRKYSEE"
                     /name="DMT family transporter"
     Typing          17..98
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.3400000000000002e-35"
     Typing          5004..5191
                     /name="rep_cluster_2401"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="4.63e-94"
     Typing          762..2323
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gcgcactttt catacaatcc gcactgatgc cgaatggtta agccagtata cactccgcta
       61 tcgctacgtg actgggtcag ggcttcgccc cgacacccca aaggtcaacg gcctgacgcg
      121 ccctggcggg cttgtctgct cccggcatcc gctcacagac aagctgtgac cgtctccggg
      181 agctgcatgt gtcagcggtt ttcaccgtca tccccgaagc gtgcgaggca actgcggtaa
      241 agctcatcgg cgtggtcgtg aagcgattca cagatgtctg cctgttcatc cgcgtccagt
      301 tcgttgagct tctccagcag cgttaatgtc tggcctctga tgaagcgggc catgttaagg
      361 gcggtttttt cctgtttggt cactgatgcc tccgtgtaag ggggggttct gttcatgggg
      421 gtaatgatac cgatgaaacg cgagaggatg ctcacgatac gggttactga tgatgaacat
      481 gcccggttac tggaacgctg tgagggtaaa caactggcgg tatggatgcg gcgggtctgc
      541 ctgggtgagc cggttgcccg ttccgggaag ctgccgacac tggcacagcc gttactgcgt
      601 cagctggccg ccatcgggaa taaccttaac cagacagcga ggaaggtgaa cagcgggcag
      661 tggtcttccg gtgaccgggt tcaggtggtg gccgcactga tggccatcgg ggatgagctg
      721 cgccggctgc gtctggcggt cagggaacag ggggcgcggg atgatagtta agtttcatgc
      781 caggggaaaa ggtggtggca gtggtccggt tgattacctg ctgggaaggg agcgtaaccg
      841 ggaaggggca acggtgcttc aggggaatcc ggaagaggtc cgggaactca tcgatgccac
      901 gccatttgcg aagaaataca cgtcaggtgt tctgtcgttc gcggagaagg agctgccgcc
      961 tggagggcgt gaaaaagtga tggcgagctt tgagcgtgta ctgatgcccg gtctcgagaa
     1021 aaatcagtac agcatcctgt gggtggagca ccaggacaag ggacggcttg agctgaattt
     1081 tgtcattccg aacatggagc tacagaccgg aaaacgcctc cagccgtact acgaccgggc
     1141 agacaggccg agaattgatg cctggcagac gctggtgaat caccattacg gtctgcatga
     1201 ccccaacgcc ccggagaacc gccggacgct gacccttcct gataacctgc cggaaacgaa
     1261 acaggcgctt gctgagggcg tcacacgcgg gatagacgcg ctttaccatg ccggagagat
     1321 aaaaggccgt caggatgtga ttcaggcgct cacagaggcg gggcttgaag tggtcagggt
     1381 gacgcgaagc agtatcagca ttgcagaccc gaacggcggg aggaatatca gactgaaagg
     1441 agcgttttat gagcaatctt ttacagacgg gcgcggagtt cgagaaaaag ctgaaagaga
     1501 gagccgaatc tacagagaaa atgctgaacg acgagttcag gaagctcgaa gaatctgtaa
     1561 acagggaact gacctcaaac gaatctttaa tcaggaacgc tatcaacgac catacaacag
     1621 ccctgaaaga actgctggag aggtatcaga aaacgaccgt cgatacgatg gacgcgcact
     1681 ggaaaaccgt actgaaaatg agcgtgaaac gctggctgtg gctgattatc gtctcagtac
     1741 tgatgtttgc cacgaccggg agtctgctgt ggtaccaggg catgaagata aacgcgaata
     1801 tgaatattct ccgcgagcag aaagagagtc tggagaagct gaacgcgaag acatggggcg
     1861 tgcgttatca cgaggacagc aacggacgtt ttctggtgtt gccgaagggg atgaaagccg
     1921 aaacgaactg gacgaaggac aacggcaaac tgaacgcagt gagactggtg caggagtgac
     1981 agagcatgac ggagctggaa agacatttgc tgaacgcatt agagcaactg caacaggact
     2041 atatgcagcg gctgaacgaa tgggagaacg ccttcgtgga attgcagaaa atgttttcgc
     2101 ttacgcaacg ggacaacgcg atgctgaacg ggcgagtcat gcagttgagt cagcaggtgc
     2161 agcacttgag cgagcggaca gaacgcttga gccagttata cagcgagaac aggagataag
     2221 ggatgaacgg ctgatgcagg aacgcgaaca tgagttatct ctggagcggg agcgtcagcc
     2281 ggaaatccag gagcggacac tggatggccc ttcgctggga tggtgaaacc atgaaaaatg
     2341 acgtgttcag tggattaagg cgggctaatg tggcctgtag catctggttg cataggtatt
     2401 catgcggtta aaatttatca ggtgcgatcg cggcagtttt tcgggtggtt tgttgccatt
     2461 tttacctgtc tgctgccgtg atcgcaccga acgcgttttg gcggtgcgta caatgcgacg
     2521 ttatggtaaa tggagcggat tttcaggaag gagtgatact aacaactcga acactgtgca
     2581 aataatgatt tttttaaaat atcggtaacg ataataaatt atttcgtttt acgccggtaa
     2641 taaatataat gtagtttcag tatataaaaa aatatatgag gtgtcttgtg ggagctttca
     2701 tgaatcttca acaacgtata aataaactac cacaattatc atccagtttt tcatttggaa
     2761 aagatattga taatattcat tcatttatct ttaacgaaac ttctaaagat aaaattgaag
     2821 atttactaag aaaatgggtg tcaggcaatc agccctgtgt atttggtaaa ttggcaagca
     2881 agaaaattaa agggcttgat ttccatttat ctattgtaaa tagcccccaa ctatataatg
     2941 atgatggtca tttgtttgat tttttgcgta atgaaagagt tcgttttaaa gaacgcgcaa
     3001 gaagaggaga ggtcagtgcg catctcattt attttattca tccacaactt gcctttgctc
     3061 gtccatcaga agagttagtg gacatacaaa aatatatttg ttcgctgcat atgccagagt
     3121 gctatccaat aaaagaggat gttatttata ctgaaagcgt accatttcag gataaagatg
     3181 ggctaaaaat atataaggct ggtgttaatg ttttttactc ttctgctcat agaacaagaa
     3241 atcatgatag aagaatacca gggggaatac ttatttctgt aaatgccccg gggcatttta
     3301 tgaggctggc gatagaaaaa ggtttctata aagatcaaga acaagcgtta gcggatattc
     3361 gtaacatgac tattcagtct gttggtaagg gtgggtattc acatccggaa gggatttcta
     3421 caacatggca ttcagaatct aatttggatc gttttggatg cccagtgcac accggtaata
     3481 gttcttatta cagcggtttt tatcatactg atgtattaat tccaggggaa ttaactaagg
     3541 atgaaagatt gctccatgaa atagaaaata gtgatccaat gatcttcaac tggaatgtat
     3601 tgttttatgt ttcattagaa gagtttccta tagatgatcc ttattatgga gagtttattg
     3661 gtattcctgt agatgatgca tctatgtttt ttaactcctt tcaaccaagg aaatttgaaa
     3721 acaaacccct ttatgagaaa gaggatgatt aatatgatta aaggaatgct ttttgctttt
     3781 ttagcagcgt tctcatgggg ggcagctatc gtaatgagca aaaaaggagt tgaagaacta
     3841 gatgccggag gggtgttttt ctggcagatt tgtagtgcag taatactatc ttggatagtt
     3901 ctttttataa aaagaaaaaa actcccatta aactcaaaag cgatacttgc ttatgcgaca
     3961 ggcgtttttg aaccattctt agcgtatact tttacactct acggacttta ttttatttca
     4021 gcaggaagcg catcaattat tttttcactt gaatcagtgt ttatattggt gttgtctgtt
     4081 cttatttgct cagttaaaat taattccccg caatatttta tattgttcct tataggtgca
     4141 attgttggca gtattttggt agccttgcca gacatcagta atggatcgaa taatattgtt
     4201 ggatattgtc ttgttgttgc cggtgtgtta tcggcagcat tttatgttgt tatatcgtct
     4261 cgccttatta aatcgtttga gcctatcaca ttattgagcg gacagttgac attctccctt
     4321 atactgtcat cgctctttat ttttatatct aaatcatcaa tttatcttcc gttggaatcc
     4381 gtgattattg ttttttcatc tggaatatta caatattttt tagctttttg tttttacttg
     4441 aactccttgc gttggctccc agttcatttg gcagggataa tgttgtactt tattccgcta
     4501 gttgcattat ttttgtcatg gttgtttttg gatgaacaat tcacattctt acagggggta
     4561 ggatttattg taactgtgct aagtgtatat tttcttaaca gaaaatactc agaggagtaa
     4621 cattctgttc aggattgccc cccggcctcc atcgataccg tgccaaatgc acgtaaaaaa
     4681 cgggagcgtt tctggtgtcg gaatgtaacc aagggggtca gaggcgcgct aaaacgctct
     4741 caggggagtc aaatagagac gtttgtaaca aaaagatcaa aggatcctct tgagatcctt
     4801 tttttctgcg cgtaatctgc tgcctgtaaa cgaaaaaacc gccttgcagg gcggtttgat
     4861 cgaaggttaa gtcagcttgc agactgctta accaggtaac tgtcttatgc gagacgagtc
     4921 accaaaattg ttcttctagt gtagccgcac tccggcagcc acttcaagta ctctctaaat
     4981 atctcgcaca tgacttttac caatggctgc tgccagtggc gctttgtggt gtcttttccg
     5041 ggttggaccc aagagaacag ttaccggaga aggcgcagca gtcgggctga acggggggtt
     5101 cctgcataca gcccagcccg gagcgaactg cctaagtcgc cccgagatac cagaagacgt
     5161 gagctatgag aaagcgccac gtgtcccgta agggagaaag gcggaaaagg tatccggtaa
     5221 tcgatatggc gggaacgtgg gggcgcagga gggagcgatt caccggaaac ggtgatgatc
     5281 tttaagccac gtcgggtttc gccaccgctg gcggatttca tggttgagcc gcaaggctcc
     5341 cacagatgca ccgaaaaagt gtctgttttg tgaagtccgt caggggggcg gagcctatgg
     5401 aaaaagcgcc tccggcgcgg cctttcccgg ggtttcgttt tttgcgcaca tgttctttcc
     5461 tggtttatcc ccgggttctg tggataacag ggttagcgtt tttgagaaag gagagtccgc
     5521 tcgccgcagc cgaacgaccg agcgtagcga gtcagtgagc gaggaagcgg aagagcgcct
     5581 gaactggcat tttctcctta cgcatctgtg cggcatttca caccggacat g
//
