LOCUS       NZ_CP124486             5631 bp    DNA     circular CON 10-JUN-2024
DEFINITION  Escherichia coli strain AVS0575 plasmid pAVS0575-C, complete
            sequence.
ACCESSION   NZ_CP124486
VERSION     NZ_CP124486.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN34360961
            Assembly: GCF_030036925.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5631)
  AUTHORS   Biggel,M.
  TITLE     Genomic characteristics of ESBL-producing Escherichia coli ST131
            isolated from the water ecosystem in a defined region in Switzerland
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5631)
  AUTHORS   Biggel,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (26-APR-2023) Institute for Food Safety and Hygiene,
            University of Zurich, Winterthurerstrasse 272, Zurich 8057,
            Switzerland
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.5.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100x, 100x
            Sequencing Technology :: Illumina MiniSeq, Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_030036925.1-RS_2024_06_10
            Annotation Date                   :: 06/10/2024 05:14:35
            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)                     :: 5,069
            CDSs (total)                      :: 4,956
            Genes (coding)                    :: 4,751
            CDSs (with protein)               :: 4,751
            Genes (RNA)                       :: 113
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 205
            CDSs (without protein)            :: 205
            Pseudo Genes (ambiguous residues) :: 0 of 205
            Pseudo Genes (frameshifted)       :: 80 of 205
            Pseudo Genes (incomplete)         :: 145 of 205
            Pseudo Genes (internal stop)      :: 44 of 205
            Pseudo Genes (multiple problems)  :: 55 of 205
            Pseudo Genes (short protein)      :: 1 of 205
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP124486.1.
            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="AVS0575"
                     /isolation_source="environmental: river near WWTP effluent"
                     /db_xref="taxon:562"
                     /plasmid="pAVS0575-C"
                     /geo_loc_name="Switzerland: Kanton Zug"
                     /collection_date="2021-07-07"
                     /collected_by="Amt fuer Verbraucherschutz, Kanton Zug"
     gene            complement(<65..493)
                     /locus_tag="QJP96_RS25415"
                     /pseudo=""
     CDS             complement(<65..493)
                     /locus_tag="QJP96_RS25415"
                     /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            complement(435..758)
                     /locus_tag="QJP96_RS25245"
                     /old_locus_tag="QJP96_25245"
     CDS             complement(435..758)
                     /locus_tag="QJP96_RS25245"
                     /old_locus_tag="QJP96_25245"
                     /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            823..1014
                     /locus_tag="QJP96_RS25250"
                     /old_locus_tag="QJP96_25250"
     CDS             823..1014
                     /locus_tag="QJP96_RS25250"
                     /old_locus_tag="QJP96_25250"
                     /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            complement(2217..3083)
                     /locus_tag="QJP96_RS25255"
                     /old_locus_tag="QJP96_25255"
     CDS             complement(2217..3083)
                     /locus_tag="QJP96_RS25255"
                     /old_locus_tag="QJP96_25255"
                     /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"
     gene            complement(3085..4137)
                     /locus_tag="QJP96_RS25260"
                     /old_locus_tag="QJP96_25260"
     CDS             complement(3085..4137)
                     /locus_tag="QJP96_RS25260"
                     /old_locus_tag="QJP96_25260"
                     /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            complement(4618..4851)
                     /locus_tag="QJP96_RS25265"
                     /old_locus_tag="QJP96_25265"
     CDS             complement(4618..4851)
                     /locus_tag="QJP96_RS25265"
                     /old_locus_tag="QJP96_25265"
                     /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            complement(4858..5388)
                     /locus_tag="QJP96_RS25270"
                     /old_locus_tag="QJP96_25270"
     CDS             complement(4858..5388)
                     /locus_tag="QJP96_RS25270"
                     /old_locus_tag="QJP96_25270"
                     /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"
     Typing          complement(1109..1190)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.3400000000000002e-35"
     Typing          complement(1647..1834)
                     /name="rep_cluster_2401"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="4.63e-94"
     Typing          complement(3..445)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="99.0"
                     /evalue="4.92e-92"
     Typing          complement(4515..5629)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 tggggtcatg cagaccgtaa tggtgattca ccagcgtctg ccaggcatca attctcggcc
       61 tgtctgcccg gtcgtagtac ggctggaggc gttttccggt ctgtagctcc atgttcggaa
      121 tgacaaaatt cagctcaagc cgtcccttgt cctggtgctc cacccacagg atgctgtact
      181 gatttttctc gagaccgggc atcagtacac gctcaaagct cgccatcact ttttcacgcc
      241 ctccaggcgg cagctccttc tccgcgaacg acagaacacc tgacgtgtat ttcttcgcaa
      301 atggcgtggc atcgatgagt tcccggacct cttccggatt cccctgaagc accgttgccc
      361 cttcccggtt acgctccctt cccagcaggt aatcaaccgg accactgcca ccaccttttc
      421 ccctggcatg aaacttaact atcatcccgc gccccctgtt ccctgaccgc cagacgcagc
      481 cggcgcagct catccccgat ggccatcagt gcggccacca cctgaacccg gtcaccggaa
      541 gaccactgcc cgctgttcac cttcctcgct gtctggttaa ggttattccc gatggcggcc
      601 agctgacgca gtaacggcgg tgccagtgtc ggcagcttcc cggaacgggc aaccggctca
      661 cccaggcaga cccgccgcat ccataccgcc agttgtttac cctcacagcg ttccagtaac
      721 cgggcatgtt catcatcagt aacccgtatc gtgagcatcc tctcgcgttt catcggtatc
      781 attaccccca tgaacagaac ccccccttac acggaggcat cagtgaccaa acaggaaaaa
      841 accgccctta acatggcccg cttcatcaga ggccagacat taacgctgct ggagaagctc
      901 aacgaactgg acgcggatga acaggcagac atctgtgaat cgcttcacga ccacgccgat
      961 gagctttacc gcagttgcct cgcacgcttc ggggatgacg gtgaaaaccg ctgacacatg
     1021 cagctcccgg agacggtcac agcttgtctg tgagcggatg ccgggagcag acaagcccgc
     1081 cagggcgcgt caggccgttg acctttgggg tgtcggggcg aagccctgac ccagtcacgt
     1141 agcgatagcg gagtgtatac tggcttaacc attcggcatc agtgcggatt gtatgaaaag
     1201 tgcgccatgt ccggtgtgaa atgccgcaca gatgcgtaag gagaaaatgc cagttcaggc
     1261 gctcttccgc ttcctcgctc actgactcgc tacgctcggt cgttcggctg cggcgagcgg
     1321 actctccttt ctcaaaaacg ctaaccctgt tatccacaga acccggggat aaaccaggaa
     1381 agaacatgtg cgcaaaaaac gaaaccccgg gaaaggccgc gccggaggcg ctttttccat
     1441 aggctccgcc cccctgacgg acttcacaaa acagacactt tttcggtgca tctgtgggag
     1501 ccttgcggct caaccatgaa atccgccagc ggtggcgaaa cccgacgtgg cttaaagatc
     1561 atcaccgttt ccggtgaatc gctccctcct gcgcccccac gttcccgcca tatcgattac
     1621 cggatacctt ttccgccttt ctcccttacg ggacacgtgg cgctttctca tagctcacgt
     1681 cttctggtat ctcggggcga cttaggcagt tcgctccggg ctgggctgta tgcaggaacc
     1741 ccccgttcag cccgactgct gcgccttctc cggtaactgt tctcttgggt ccaacccgga
     1801 aaagacacca caaagcgcca ctggcagcag ccattggtaa aagtcatgtg cgagatattt
     1861 agagagtact tgaagtggct gccggagtgc ggctacacta gaagaacaat tttggtgact
     1921 cgtctcgcat aagacagtta cctggttaag cagtctgcaa gctgacttaa ccttcgatca
     1981 aaccgccctg caaggcggtt ttttcgttta caggcagcag attacgcgca gaaaaaaagg
     2041 atctcaagag gatcctttga tctttttgtt acaaacgtct ctatttgact cccctgagag
     2101 cgttttagcg cgcctctgac ccccttggtt acattccgac accagaaacg ctcccgtttt
     2161 ttacgtgcat ttggcacggt atcgatggag gccggggggc aatcctgaac agaatgttac
     2221 tcctctgagt attttctgtt aagaaaatat acacttagca cagttacaat aaatcctacc
     2281 ccctgtaaga atgtgaattg ttcatccaaa aacaaccatg acaaaaataa tgcaactagc
     2341 ggaataaagt acaacattat ccctgccaaa tgaactggga gccaacgcaa ggagttcaag
     2401 taaaaacaaa aagctaaaaa atattgtaat attccagatg aaaaaacaat aatcacggat
     2461 tccaacggaa gataaattga tgatttagat ataaaaataa agagcgatga cagtataagg
     2521 gagaatgtca actgtccgct caataatgtg ataggctcaa acgatttaat aaggcgagac
     2581 gatataacaa cataaaatgc tgccgataac acaccggcaa caacaagaca atatccaaca
     2641 atattattcg atccattact gatgtctggc aaggctacca aaatactgcc aacaattgca
     2701 cctataagga acaatataaa atattgcggg gaattaattt taactgagca aataagaaca
     2761 gacaacacca atataaacac tgattcaagt gaaaaaataa ttgatgcgct tcctgctgaa
     2821 ataaaataaa gtccgtagag tgtaaaagta tacgctaaga atggttcaaa aacgcctgtc
     2881 gcataagcaa gtatcgcttt tgagtttaat gggagttttt ttctttttat aaaaagaact
     2941 atccaagata gtattactgc actacaaatc tgccagaaaa acacccctcc ggcatctagt
     3001 tcttcaactc cttttttgct cattacgata gctgcccccc atgagaacgc tgctaaaaaa
     3061 gcaaaaagca ttcctttaat catattaatc atcctctttc tcataaaggg gtttgttttc
     3121 aaatttcctt ggttgaaagg agttaaaaaa catagatgca tcatctacag gaataccaat
     3181 aaactctcca taataaggat catctatagg aaactcttct aatgaaacat aaaacaatac
     3241 attccagttg aagatcattg gatcactatt ttctatttca tggagcaatc tttcatcctt
     3301 agttaattct cctggaatta atacatcagt atgataaaaa ccgctgtaat aagaactatt
     3361 accggtgtgc actgggcatc caaaacgatc caaattagat tctgaatgcc atgttgtaga
     3421 aatcccttcc ggatgtgaat acccaccctt accaacagac tgaatagtca tgttacgaat
     3481 atccgctaac gcttgttctt gatctttata gaaacctttt tctatcgcca gcctcataaa
     3541 atgccccggg gcatttacag aaataagtat tccccctggt attcttctat catgatttct
     3601 tgttctatga gcagaagagt aaaaaacatt aacaccagcc ttatatattt ttagcccatc
     3661 tttatcctga aatggtacgc tttcagtata aataacatcc tcttttattg gatagcactc
     3721 tggcatatgc agcgaacaaa tatatttttg tatgtccact aactcttctg atggacgagc
     3781 aaaggcaagt tgtggatgaa taaaataaat gagatgcgca ctgacctctc ctcttcttgc
     3841 gcgttcttta aaacgaactc tttcattacg caaaaaatca aacaaatgac catcatcatt
     3901 atatagttgg gggctattta caatagataa atggaaatca agccctttaa ttttcttgct
     3961 tgccaattta ccaaatacac agggctgatt gcctgacacc cattttctta gtaaatcttc
     4021 aattttatct ttagaagttt cgttaaagat aaatgaatga atattatcaa tatcttttcc
     4081 aaatgaaaaa ctggatgata attgtggtag tttatttata cgttgttgaa gattcatgaa
     4141 agctcccaca agacacctca tatatttttt tatatactga aactacatta tatttattac
     4201 cggcgtaaaa cgaaataatt tattatcgtt accgatattt taaaaaaatc attatttgca
     4261 cagtgttcga gttgttagta tcactccttc ctgaaaatcc gctccattta ccataacgtc
     4321 gcattgtacg caccgccaaa acgcgttcgg tgcgatcacg gcagcagaca ggtaaaaatg
     4381 gcaacaaacc acccgaaaaa ctgccgcgat cgcacctgat aaattttaac cgcatgaata
     4441 cctatgcaac cagatgctac aggccacatt agcccgcctt aatccactga acacgtcatt
     4501 tttcatggtt tcaccatccc agcgaagggc catccagtgt ccgctcctgg atttccggct
     4561 gacgctcccg ctccagagat aactcatgtt cgcgttcctg catcagccgt tcatccctta
     4621 tctcctgttc tcgctgtata actggctcaa gcgttctgtc cgctcgctca agtgctgcac
     4681 ctgctgactc aactgcatga ctcgcccgtt cagcatcgcg ttgtcccgtt gcgtaagcga
     4741 aaacattttc tgcaattcca cgaaggcgtt ctcccattcg ttcagccgct gcatatagtc
     4801 ctgttgcagt tgctctaatg cgttcagcaa atgtctttcc agctccgtca tgctctgtca
     4861 ctcctgcacc agtctcactg cgttcagttt gccgttgtcc ttcgtccagt tcgtttcggc
     4921 tttcatcccc ttcggcaaca ccagaaaacg tccgttgctg tcctcgtgat aacgcacgcc
     4981 ccatgtcttc gcgttcagct tctccagact ctctttctgc tcgcggagaa tattcatatt
     5041 cgcgtttatc ttcatgccct ggtaccacag cagactcccg gtcgtggcaa acatcagtac
     5101 tgagacgata atcagccaca gccagcgttt cacgctcatt ttcagtacgg ttttccagtg
     5161 cgcgtccatc gtatcgacgg tcgttttctg atacctctcc agcagttctt tcagggctgt
     5221 tgtatggtcg ttgatagcgt tcctgattaa agattcgttt gaggtcagtt ccctgtttac
     5281 agattcttcg agcttcctga actcgtcgtt cagcattttc tctgtagatt cggctctctc
     5341 tttcagcttt ttctcgaact ccgcgcccgt ctgtaaaaga ttgctcataa aacgctcctt
     5401 tcagtctgat attcctcccg ccgttcgggt ctgcaatgct gatactgctt cgcgtcaccc
     5461 tgaccacttc aagccccgcc tctgtgagcg cctgaatcac atcctgacgg ccttttatct
     5521 ctccggcatg gtaaagcgcg tctatcccgc gtgtgacgcc ctcagcaagc gcctgtttcg
     5581 tttccggcag gttatcagga agggtcagcg tccggcggtt ctccggggcg t
//
