LOCUS       NZ_CP124379             5630 bp    DNA     circular CON 07-JUN-2024
DEFINITION  Escherichia coli strain AVS0578 plasmid pAVS0578-E, complete
            sequence.
ACCESSION   NZ_CP124379
VERSION     NZ_CP124379.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN34360983
            Assembly: GCF_029990415.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5630)
  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  JOURNAL   Unpublished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 5630)
  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_029990415.1-RS_2024_06_07
            Annotation Date                   :: 06/07/2024 03:37:34
            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)                     :: 5,439
            CDSs (total)                      :: 5,325
            Genes (coding)                    :: 5,097
            CDSs (with protein)               :: 5,097
            Genes (RNA)                       :: 114
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 228
            CDSs (without protein)            :: 228
            Pseudo Genes (ambiguous residues) :: 0 of 228
            Pseudo Genes (frameshifted)       :: 81 of 228
            Pseudo Genes (incomplete)         :: 162 of 228
            Pseudo Genes (internal stop)      :: 38 of 228
            Pseudo Genes (multiple problems)  :: 47 of 228
            Pseudo Genes (short protein)      :: 1 of 228
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP124379.1.
            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..5630
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="AVS0578"
                     /isolation_source="environmental: river/lake"
                     /db_xref="taxon:562"
                     /plasmid="pAVS0578-E"
                     /geo_loc_name="Switzerland: Kanton Zug"
                     /collection_date="2021-07-07"
                     /collected_by="Amt fuer Verbraucherschutz, Kanton Zug"
     gene            complement(1091..1957)
                     /locus_tag="QJP97_RS27035"
                     /old_locus_tag="QJP97_27030"
     CDS             complement(1091..1957)
                     /locus_tag="QJP97_RS27035"
                     /old_locus_tag="QJP97_27030"
                     /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(1959..3011)
                     /locus_tag="QJP97_RS27040"
                     /old_locus_tag="QJP97_27035"
     CDS             complement(1959..3011)
                     /locus_tag="QJP97_RS27040"
                     /old_locus_tag="QJP97_27035"
                     /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(3491..3724)
                     /locus_tag="QJP97_RS27045"
                     /old_locus_tag="QJP97_27040"
     CDS             complement(3491..3724)
                     /locus_tag="QJP97_RS27045"
                     /old_locus_tag="QJP97_27040"
                     /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(3731..4261)
                     /locus_tag="QJP97_RS27050"
                     /old_locus_tag="QJP97_27045"
     CDS             complement(3731..4261)
                     /locus_tag="QJP97_RS27050"
                     /old_locus_tag="QJP97_27045"
                     /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            complement(<4299..4997)
                     /locus_tag="QJP97_RS27305"
                     /pseudo=""
     CDS             complement(<4299..4997)
                     /locus_tag="QJP97_RS27305"
                     /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(4939..5262)
                     /locus_tag="QJP97_RS27060"
                     /old_locus_tag="QJP97_27055"
     CDS             complement(4939..5262)
                     /locus_tag="QJP97_RS27060"
                     /old_locus_tag="QJP97_27055"
                     /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            5327..5518
                     /locus_tag="QJP97_RS27065"
                     /old_locus_tag="QJP97_27060"
     CDS             5327..5518
                     /locus_tag="QJP97_RS27065"
                     /old_locus_tag="QJP97_27060"
                     /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"
     Typing          complement(521..708)
                     /name="rep_cluster_2401"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="4.63e-94"
     Typing          complement(3388..4949)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tgacccagtc acgtagcgat agcggagtgt atactggctt aaccattcgg catcagtgcg
       61 gattgtatga aaagtgcgcc atgtccggtg tgaaatgccg cacagatgcg taaggagaaa
      121 atgccagttc aggcgctctt ccgcttcctc gctcactgac tcgctacgct cggtcgttcg
      181 gctgcggcga gcggactctc ctttctcaaa aacgctaacc ctgttatcca cagaacccgg
      241 ggataaacca ggaaagaaca tgtgcgcaaa aaacgaaacc ccgggaaagg ccgcgccgga
      301 ggcgcttttt ccataggctc cgcccccctg acggacttca caaaacagac actttttcgg
      361 tgcatctgtg ggagccttgc ggctcaacca tgaaatccgc cagcggtggc gaaacccgac
      421 gtggcttaaa gatcatcacc gtttccggtg aatcgctccc tcctgcgccc ccacgttccc
      481 gccatatcga ttaccggata ccttttccgc ctttctccct tacgggacac gtggcgcttt
      541 ctcatagctc acgtcttctg gtatctcggg gcgacttagg cagttcgctc cgggctgggc
      601 tgtatgcagg aaccccccgt tcagcccgac tgctgcgcct tctccggtaa ctgttctctt
      661 gggtccaacc cggaaaagac accacaaagc gccactggca gcagccattg gtaaaagtca
      721 tgtgcgagat atttagagag tacttgaagt ggctgccgga gtgcggctac actagaagaa
      781 caattttggt gactcgtctc gcataagaca gttacctggt taagcagtct gcaagctgac
      841 ttaaccttcg atcaaaccgc cctgcaaggc ggttttttcg tttacaggca gcagattacg
      901 cgcagaaaaa aaggatctca agaggatcct ttgatctttt tgttacaaac gtctctattt
      961 gactcccctg agagcgtttt agcgcgcctc tgaccccctt ggttacattc cgacaccaga
     1021 aacgctcccg ttttttacgt gcatttggca cggtatcgat ggaggccggg gggcaatcct
     1081 gaacagaatg ttactcctct gagtattttc tgttaagaaa atatacactt agcacagtta
     1141 caataaatcc taccccctgt aagaatgtga attgttcatc caaaaacaac catgacaaaa
     1201 ataatgcaac tagcggaata aagtacaaca ttatccctgc caaatgaact gggagccaac
     1261 gcaaggagtt caagtaaaaa caaaaagcta aaaaatattg taatattcca gatgaaaaaa
     1321 caataatcac ggattccaac ggaagataaa ttgatgattt agatataaaa ataaagagcg
     1381 atgacagtat aagggagaat gtcaactgtc cgctcaataa tgtgataggc tcaaacgatt
     1441 taataaggcg agacgatata acaacataaa atgctgccga taacacaccg gcaacaacaa
     1501 gacaatatcc aacaatatta ttcgatccat tactgatgtc tggcaaggct accaaaatac
     1561 tgccaacaat tgcacctata aggaacaata taaaatattg cggggaatta attttaactg
     1621 agcaaataag aacagacaac accaatataa acactgattc aagtgaaaaa ataattgatg
     1681 cgcttcctgc tgaaataaaa taaagtccgt agagtgtaaa agtatacgct aagaatggtt
     1741 caaaaacgcc tgtcgcataa gcaagtatcg cttttgagtt taatgggagt ttttttcttt
     1801 ttataaaaag aactatccaa gatagtatta ctgcactaca aatctgccag aaaaacaccc
     1861 ctccggcatc tagttcttca actccttttt tgctcattac gatagctgcc ccccatgaga
     1921 acgctgctaa aaaagcaaaa agcattcctt taatcatatt aatcatcctc tttctcataa
     1981 aggggtttgt tttcaaattt ccttggttga aaggagttaa aaaacataga tgcatcatct
     2041 acaggaatac caataaactc tccataataa ggatcatcta taggaaactc ttctaatgaa
     2101 acataaaaca atacattcca gttgaagatc attggatcac tattttctat ttcatggagc
     2161 aatctttcat ccttagttaa ttctcctgga attaatacat cagtatgata aaaaccgctg
     2221 taataagaac tattaccggt gtgcactggg catccaaaac gatccaaatt agattctgaa
     2281 tgccatgttg tagaaatccc ttccggatgt gaatacccac ccttaccaac agactgaata
     2341 gtcatgttac gaatatccgc taacgcttgt tcttgatctt tatagaaacc tttttctatc
     2401 gccagcctca taaaatgccc cggggcattt acagaaataa gtattccccc tggtattctt
     2461 ctatcatgat ttcttgttct atgagcagaa gagtaaaaaa cattaacacc agccttatat
     2521 atttttagcc catctttatc ctgaaatggt acgctttcag tataaataac atcctctttt
     2581 attggatagc actctggcat atgcagcgaa caaatatatt tttgtatgtc cactaactct
     2641 tctgatggac gagcaaaggc aagttgtgga tgaataaaat aaatgagatg cgcactgacc
     2701 tctcctcttc ttgcgcgttc tttaaaacga actctttcat tacgcaaaaa atcaaacaaa
     2761 tgaccatcat cattatatag ttgggggcta tttacaatag ataaatggaa atcaagccct
     2821 ttaattttct tgcttgccaa tttaccaaat acacagggct gattgcctga cacccatttt
     2881 cttagtaaat cttcaatttt atctttagaa gtttcgttaa agataaatga atgaatatta
     2941 tcaatatctt ttccaaatga aaaactggat gataattgtg gtagtttatt tatacgttgt
     3001 tgaagattca tgaaagctcc cacaagacac ctcatatatt ttttatatac tgaaactaca
     3061 ttatatttat taccggcgta aaacgaaata atttattatc gttaccgata ttttaaaaaa
     3121 atcattattt gcacagtgtt cgagttgtta gtatcactcc ttcctgaaaa tccgctccat
     3181 ttaccataac gtcgcattgt acgcaccgcc aaaacgcgtt cggtgcgatc acggcagcag
     3241 acaggtaaaa atggcaacaa accacccgaa aaactgccgc gatcgcacct gataaatttt
     3301 aaccgcatga atacctatgc aaccagatgc tacaggccac attagcccgc cttaatccac
     3361 tgaacacgtc atttttcatg gtttcaccat cccagcgaag ggccatccag tgtccgctcc
     3421 tggatttccg gctgacgctc ccgctccaga gataactcat gttcgcgttc ctgcatcagc
     3481 cgttcatccc ttatctcctg ttctcgctgt ataactggct caagcgttct gtccgctcgc
     3541 tcaagtgctg cacctgctga ctcaactgca tgactcgccc gttcagcatc gcgttgtccc
     3601 gttgcgtaag cgaaaacatt ttctgcaatt ccacgaaggc gttctcccat tcgttcagcc
     3661 gctgcatata gtcctgttgc agttgctcta atgcgttcag caaatgtctt tccagctccg
     3721 tcatgctctg tcactcctgc accagtctca ctgcgttcag tttgccgttg tccttcgtcc
     3781 agttcgtttc ggctttcatc cccttcggca acaccagaaa acgtccgttg ctgtcctcgt
     3841 gataacgcac gccccatgtc ttcgcgttca gcttctccag actctctttc tgctcgcgga
     3901 gaatattcat attcgcgttt atcttcatgc cctggtacca cagcagactc ccggtcgtgg
     3961 caaacatcag tactgagacg ataatcagcc acagccagcg tttcacgctc attttcagta
     4021 cggttttcca gtgcgcgtcc atcgtatcga cggtcgtttt ctgatacctc tccagcagtt
     4081 ctttcagggc tgttgtatgg tcgttgatag cgttcctgat taaagattcg tttgaggtca
     4141 gttccctgtt tacagattct tcgagcttcc tgaactcgtc gttcagcatt ttctctgtag
     4201 attcggctct ctctttcagc tttttctcga actccgcgcc cgtctgtaaa agattgctca
     4261 taaaacgctc ctttcagtct gatattcctc ccgccgttcg ggtctgcaat gctgatactg
     4321 cttcgcgtca ccctgaccac ttcaagcccc gcctctgtga gcgcctgaat cacatcctga
     4381 cggcctttta tctctccggc atggtaaagc gcgtctatcc cgcgtgtgac gccctcagca
     4441 agcgcctgtt tcgtttccgg caggttatca ggaagggtca gcgtccggcg gttctccggg
     4501 gcgttggggt catgcagacc gtaatggtga ttcaccagcg tctgccaggc atcaattctc
     4561 ggcctgtctg cccggtcgta gtacggctgg aggcgttttc cggtctgtag ctccatgttc
     4621 ggaatgacaa aattcagctc aagccgtccc ttgtcctggt gctccaccca caggatgctg
     4681 tactgatttt tctcgagacc gggcatcagt acacgctcaa agctcgccat cactttttca
     4741 cgccctccag gcggcagctc cttctccgcg aacgacagaa cacctgacgt gtatttcttc
     4801 gcaaatggcg tggcatcgat gagttcccgg acctcttccg gattcccctg aagcaccgtt
     4861 gccccttccc ggttacgctc ccttcccagc aggtaatcaa ccggaccact gccaccacct
     4921 tttcccctgg catgaaactt aactatcatc ccgcgccccc tgttccctga ccgccagacg
     4981 cagccggcgc agctcatccc cgatggccat cagtgcggcc accacctgaa cccggtcacc
     5041 ggaagaccac tgcccgctgt tcaccttcct cgctgtctgg ttaaggttat tcccgatggc
     5101 ggccagctga cgcagtaacg gcggtgccag tgtcggcagc ttcccggaac gggcaaccgg
     5161 ctcacccagg cagacccgcc gcatccatac cgccagttgt ttaccctcac agcgttccag
     5221 taaccgggca tgttcatcat cagtaacccg tatcgtgagc atcctctcgc gtttcatcgg
     5281 tatcattacc cccatgaaca gaaccccccc ttacacggag gcatcagtga ccaaacagga
     5341 aaaaaccgcc cttaacatgg cccgcttcat cagaggccag acattaacgc tgctggagaa
     5401 gctcaacgaa ctggacgcgg atgaacaggc agacatctgt gaatcgcttc acgaccacgc
     5461 cgatgagctt taccgcagtt gcctcgcacg cttcggggat gacggtgaaa accgctgaca
     5521 catgcagctc ccggagacgg tcacagcttg tctgtgagcg gatgccggga gcagacaagc
     5581 ccgccagggc gcgtcaggcc gttgaccttt ggggtgtcgg ggcgaagccc
//
