LOCUS       NZ_CP145640             5631 bp    DNA     circular CON 05-APR-2024
DEFINITION  Escherichia coli strain S1-ISR-02-A plasmid p4-S1-ISR-02-A, complete
            sequence.
ACCESSION   NZ_CP145640
VERSION     NZ_CP145640.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN33052311
            Assembly: GCF_036884415.1
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  JOURNAL   Unpublished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                   :: 388.9585X
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_036884415.1-RS_2024_04_05
            Annotation Date                   :: 04/05/2024 17:19:59
            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)                     :: 5,339
            CDSs (total)                      :: 5,217
            Genes (coding)                    :: 5,010
            CDSs (with protein)               :: 5,010
            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)              :: 207
            CDSs (without protein)            :: 207
            Pseudo Genes (ambiguous residues) :: 0 of 207
            Pseudo Genes (frameshifted)       :: 57 of 207
            Pseudo Genes (incomplete)         :: 155 of 207
            Pseudo Genes (internal stop)      :: 34 of 207
            Pseudo Genes (multiple problems)  :: 37 of 207
            Pseudo Genes (short protein)      :: 4 of 207
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP145640.1.
            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-ISR-02-A"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p4-S1-ISR-02-A"
                     /geo_loc_name="Switzerland"
                     /lat_lon="46.947928 N 7.422277 E"
                     /collection_date="2021"
                     /collected_by="Institute for Infectious Diseases (IFIK),
                     University of Bern"
     gene            complement(1008..1199)
                     /locus_tag="V6S43_RS26555"
                     /old_locus_tag="V6S43_26560"
     CDS             complement(1008..1199)
                     /locus_tag="V6S43_RS26555"
                     /old_locus_tag="V6S43_26560"
                     /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            1264..1587
                     /locus_tag="V6S43_RS26560"
                     /old_locus_tag="V6S43_26565"
     CDS             1264..1587
                     /locus_tag="V6S43_RS26560"
                     /old_locus_tag="V6S43_26565"
                     /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_000955999.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1796..>2227
                     /locus_tag="V6S43_RS26565"
                     /old_locus_tag="V6S43_26570"
                     /pseudo=""
     CDS             1796..>2227
                     /locus_tag="V6S43_RS26565"
                     /old_locus_tag="V6S43_26570"
                     /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            2265..2795
                     /locus_tag="V6S43_RS26570"
                     /old_locus_tag="V6S43_26575"
     CDS             2265..2795
                     /locus_tag="V6S43_RS26570"
                     /old_locus_tag="V6S43_26575"
                     /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            2802..3035
                     /locus_tag="V6S43_RS26575"
                     /old_locus_tag="V6S43_26580"
     CDS             2802..3035
                     /locus_tag="V6S43_RS26575"
                     /old_locus_tag="V6S43_26580"
                     /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            3516..4568
                     /locus_tag="V6S43_RS26580"
                     /old_locus_tag="V6S43_26585"
     CDS             3516..4568
                     /locus_tag="V6S43_RS26580"
                     /old_locus_tag="V6S43_26585"
                     /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            4570..5436
                     /locus_tag="V6S43_RS26585"
                     /old_locus_tag="V6S43_26590"
     CDS             4570..5436
                     /locus_tag="V6S43_RS26585"
                     /old_locus_tag="V6S43_26590"
                     /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          833..914
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.3400000000000002e-35"
     Typing          189..376
                     /name="rep_cluster_2401"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="4.63e-94"
     Typing          1578..3139
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.808"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tctgctgcct gtaaacgaaa aaaccgcctt gcagggcggt ttgatcgaag gttaagtcag
       61 cttgcagact gcttaaccag gtaactgtct tatgcgagac gagtcaccaa aattgttctt
      121 ctagtgtagc cgcactccgg cagccacttc aagtactctc taaatatctc gcacatgact
      181 tttaccaatg gctgctgcca gtggcgcttt gtggtgtctt ttccgggttg gacccaagag
      241 aacagttacc ggagaaggcg cagcagtcgg gctgaacggg gggttcctgc atacagccca
      301 gcccggagcg aactgcctaa gtcgccccga gataccagaa gacgtgagct atgagaaagc
      361 gccacgtgtc ccgtaaggga gaaaggcgga aaaggtatcc ggtaatcgat atggcgggaa
      421 cgtgggggcg caggagggag cgattcaccg gaaacggtga tgatctttaa gccacgtcgg
      481 gtttcgccac cgctggcgga tttcatggtt gagccgcaag gctcccacag atgcaccgaa
      541 aaagtgtctg ttttgtgaag tccgtcaggg gggcggagcc tatggaaaaa gcgcctccgg
      601 cgcggccttt cccggggttt cgttttttgc gcacatgttc tttcctggtt tatccccggg
      661 ttctgtggat aacagggtta gcgtttttga gaaaggagag tccgctcgcc gcagccgaac
      721 gaccgagcgt agcgagtcag tgagcgagga agcggaagag cgcctgaact ggcattttct
      781 ccttacgcat ctgtgcggca tttcacaccg gacatggcgc acttttcata caatccgcac
      841 tgatgccgaa tggttaagcc agtatacact ccgctatcgc tacgtgactg ggtcagggct
      901 tcgccccgac accccaaagg tcaacggcct gacgcgccct ggcgggcttg tctgctcccg
      961 gcatccgctc acagacaagc tgtgaccgtc tccgggagct gcatgtgtca gcggttttca
     1021 ccgtcatccc cgaagcgtgc gaggcaactg cggtaaagct catcggcgtg gtcgtgaagc
     1081 gattcacaga tgtctgcctg ttcatccgcg tccagttcgt tgagcttctc cagcagcgtt
     1141 aatgtctggc ctctgatgaa gcgggccatg ttaagggcgg ttttttcctg tttggtcact
     1201 gatgcctccg tgtaaggggg ggttctgttc atgggggtaa tgataccgat gaaacgcgag
     1261 aggatgctca cgatacgggt tactgatgat gaacatgccc ggttactgga acgctgtgag
     1321 ggtaaacaac tggcggtatg gatgcggcgg gtctgcctgg gtgagccggt tgcccgttcc
     1381 gggaagctgc cgacactggc accgccgtta ctgcgtcagc tggccgccat cgggaataac
     1441 cttaaccaga cagcgaggaa ggtgaacagc gggcagtggt cttccggtga ccgggttcag
     1501 gtggtggccg cactgatggc catcggggat gagctgcgcc ggctgcgtct ggcggtcagg
     1561 gaacaggggg cgcgggatga tagttaagtt tcatgccagg ggaaaaggtg gtggcagtgg
     1621 tccggttgat tacctgctgg gaagggagcg taaccgggaa ggggcaacgg tgcttcaggg
     1681 gaatccggaa gaggtccggg aactcatcga tgccacgcca tttgcgaaga aatacacgtc
     1741 aggtgttctg tcgttcgcgg agaaggagct gccgcctgga gggcgtgaaa aagtgatggc
     1801 gagctttgag cgtgtactga tgcccggtct cgagaaaaat cagtacagca tcctgtgggt
     1861 ggagcaccag gacaagggac ggcttgagct gaattttgtc atcccgaaca tggagctaca
     1921 gaccggaaaa cgcctccagc cgtactacga ccgggcagac aggccgagaa ttgatgcctg
     1981 gcagacgctg gttaatcacc attacgggct gcatgacccc aacgccccgg agaaccgccg
     2041 gatactgact ctccctgata acctgccgga aacgaaacag gcgcttgctg agggcgtcac
     2101 acgcgggata gacgcgcttt accatgccgg agagataaaa ggccgtcagg atgtgattca
     2161 ggcgctcaca gaggcggggc ttgaagtggt cagggtgacg cgaagcagta tcagcattgc
     2221 agacccgaac ggcgggagga atatcagact gaaaggagcg ttttatgagc aatcttttac
     2281 agacgggcgc ggagttcgag aaaaagctga aagagagagc cgaatctaca gagaaaatgc
     2341 tgaacgacga gttcaggaag ctcgaagaat ctgtaaacag ggaactgacc tcaaacgaat
     2401 ctttaatcag gaacgctatc aacgaccata caacagccct gaaagaactg ctggagaggt
     2461 atcagaaaac gaccgtcgat acgatggacg cgcactggaa aaccgtactg aaaatgagcg
     2521 tgaaacgctg gctgtggctg attatcgtct cagtactgat gtttgccacg accgggagtc
     2581 tgctgtggta ccagggcatg aagataaacg cgaatatgaa tattctccgc gagcagaaag
     2641 agagtctgga gaagctgaac gcgaagacat ggggcgtgcg ttatcacgag gacagcaacg
     2701 gacgttttct ggtgttgccg aaggggatga aagccgaaac gaactggacg aaggacaacg
     2761 gcaaactgaa cgcagtgaga ctggtgcagg agtgacagag catgacggag ctggaaagac
     2821 atttgctgaa cgcattagag caactgcaac aggactatat gcagcggctg aacgaatggg
     2881 agaacgcctt cgtggaattg cagaaaatgt tttcgcttac gcaacgggac aacgcgatgc
     2941 tgaacgggcg agtcatgcag ttgagtcagc aggtgcagca cttgagcgag cggacagaac
     3001 gcttgagcca gttatacagc gagaacagga gataagggat gaacggctga tgcaggaacg
     3061 cgaacatgag ttatctctgg agcgggagcg tcagccggaa atccaggagc ggacactgga
     3121 tggcccttcg ctgggatggt gaaaccatga aaaatgacgt gttcagtgga ttaaggcggg
     3181 ctaatgtggc ctgtagcatc tggttgcata ggtattcatg cggttaaaat ttatcaggtg
     3241 cgatcgcggc agtttttcgg gtggtttgtt gccattttta cctgtctgct gccgtgatcg
     3301 caccgaacgc gttttggcgg tgcgtacaat gcgacgttat ggtaaatgga gcggattttc
     3361 aggaaggagt gatactaaca actcgaacac tgtgcaaata atgatttttt taaaatatcg
     3421 gtaacgataa taaattattt cgttttacgc cggtaataaa tataatgtag tttcagtata
     3481 taaaaaaata tatgaggtgt cttgtgggag ctttcatgaa tcttcaacaa cgtataaata
     3541 aactaccaca attatcatcc agtttttcat ttggaaaaga tattgataat attcattcat
     3601 ttatctttaa cgaaacttct aaagataaaa ttgaagattt actaagaaaa tgggtgtcag
     3661 gcaatcagcc ctgtgtattt ggtaaattgg caagcaagaa aattaaaggg cttgatttcc
     3721 atttatctat tgtaaatagc ccccaactat ataatgatga tggtcatttg tttgattttt
     3781 tgcgtaatga aagagttcgt tttaaagaac gcgcaagaag aggagaggtc agtgcgcatc
     3841 tcatttattt tattcatcca caacttgcct ttgctcgtcc atcagaagag ttagtggaca
     3901 tacaaaaata tatttgttcg ctgcatatgc cagagtgcta tccaataaaa gaggatgtta
     3961 tttatactga aagcgtacca tttcaggata aagatgggct aaaaatatat aaggctggtg
     4021 ttaatgtttt ttactcttct gctcatagaa caagaaatca tgatagaaga ataccagggg
     4081 gaatacttat ttctgtaaat gccccggggc attttatgag gctggcgata gaaaaaggtt
     4141 tctataaaga tcaagaacaa gcgttagcgg atattcgtaa catgactatt cagtctgttg
     4201 gtaagggtgg gtattcacat ccggaaggga tttctacaac atggcattca gaatctaatt
     4261 tggatcgttt tggatgccca gtgcacaccg gtaatagttc ttattacagc ggtttttatc
     4321 atactgatgt attaattcca ggagaattaa ctaaggatga aagattgctc catgaaatag
     4381 aaaatagtga tccaatgatc ttcaactgga atgtattgtt ttatgtttca ttagaagagt
     4441 ttcctataga tgatccttat tatggagagt ttattggtat tcctgtagat gatgcatcta
     4501 tgttttttaa ctcctttcaa ccaaggaaat ttgaaaacaa acccctttat gagaaagagg
     4561 atgattaata tgattaaagg aatgcttttt gcttttttag cagcgttctc atggggggca
     4621 gctatcgtaa tgagcaaaaa aggagttgaa gaactagatg ccggaggggt gtttttctgg
     4681 cagatttgta gtgcagtaat actatcttgg atagttcttt ttataaaaag aaaaaaactc
     4741 ccattaaact caaaagcgat acttgcttat gcgacaggcg tttttgaacc attcttagcg
     4801 tatactttta cactctacgg actttatttt atttcagcag gaagcgcatc aattattttt
     4861 tcacttgaat cagtgtttat attggtgttg tctgttctta tttgctcagt taaaattaat
     4921 tccccgcaat attttatatt gttccttata ggtgcaattg ttggcagtat tttggtagcc
     4981 ttgccagaca tcagtaatgg atcgaataat attgttggat attgtcttgt tgttgccggt
     5041 gtgttatcgg cagcatttta tgttgttata tcgtctcgcc ttattaaatc gtttgagcct
     5101 atcacattat tgagcggaca gttgacattc tcccttatac tgtcatcgct ctttattttt
     5161 atatctaaat catcaattta tcttccgttg gaatccgtga ttattgtttt ttcatctgga
     5221 atattacaat attttttagc tttttgtttt tacttgaact ccttgcgttg gctcccagtt
     5281 catttggcag ggataatgtt gtactttatt ccgctagttg cattattttt gtcatggttg
     5341 tttttggatg aacaattcac attcttacag ggggtaggat ttattgtaac tgtgctaagt
     5401 gtatattttc ttaacagaaa atactcagag gagtaacatt ctgttcagga ttgccccccg
     5461 gcctccatcg ataccgtgcc aaatgcacgt aaaaaacggg agcgtttctg gtgtcggaat
     5521 gtaaccaagg gggtcagagg cgcgctaaaa cgctctcagg ggagtcaaat agagacgttt
     5581 gtaacaaaaa gatcaaagga tcctcttgag atcctttttt tctgcgcgta a
//
