LOCUS       NZ_CP124409             4087 bp    DNA     circular CON 10-JUN-2024
DEFINITION  Escherichia coli strain AVS0935 plasmid pAVS0935-D, complete
            sequence.
ACCESSION   NZ_CP124409
VERSION     NZ_CP124409.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN34360977
            Assembly: GCF_030039395.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4087)
  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  JOURNAL   Unpublished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 4087)
  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_030039395.1-RS_2024_06_10
            Annotation Date                   :: 06/10/2024 05:13:58
            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)                     :: 4,995
            CDSs (total)                      :: 4,884
            Genes (coding)                    :: 4,681
            CDSs (with protein)               :: 4,681
            Genes (RNA)                       :: 111
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 203
            CDSs (without protein)            :: 203
            Pseudo Genes (ambiguous residues) :: 0 of 203
            Pseudo Genes (frameshifted)       :: 78 of 203
            Pseudo Genes (incomplete)         :: 144 of 203
            Pseudo Genes (internal stop)      :: 37 of 203
            Pseudo Genes (multiple problems)  :: 48 of 203
            Pseudo Genes (short protein)      :: 1 of 203
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP124409.1.
            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..4087
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="AVS0935"
                     /isolation_source="environmental: river near WWTP effluent"
                     /db_xref="taxon:562"
                     /plasmid="pAVS0935-D"
                     /geo_loc_name="Switzerland: Kanton Zug"
                     /collection_date="2022-01-13"
                     /collected_by="Amt fuer Verbraucherschutz, Kanton Zug"
     gene            complement(join(3535..4087,1..155))
                     /locus_tag="QJB05_RS24935"
                     /old_locus_tag="QJB05_24935"
     CDS             complement(join(3535..4087,1..155))
                     /locus_tag="QJB05_RS24935"
                     /old_locus_tag="QJB05_24935"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001296720.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_001296720.1"
                     /translation="MTSNPLIAYKSNALVEASYKLTLQEQRFLLLCISRLNSGTDVASP
                     ELQKTMTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKDDEKREEFRWIQYRA
                     QYARGEGKAQITFSDAVMPYLTQLKGQFTRVVIKNISNLSRSYSIRIYEILQQFRSTGE
                     RIIALDDFKSSLMLDGKYKDFKTLNRDLIKPCVDELNKKSDLAVTVETIKKGRTVVALH
                     FRFKEDKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(687..941)
                     /gene="mobC"
                     /locus_tag="QJB05_RS24940"
                     /old_locus_tag="QJB05_24940"
     CDS             complement(687..941)
                     /gene="mobC"
                     /locus_tag="QJB05_RS24940"
                     /old_locus_tag="QJB05_24940"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091747.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase accessory protein MobC"
                     /protein_id="WP_000091745.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVIVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPGQ"
                     /name="mobC"
     gene            1120..3279
                     /gene="mobQ"
                     /locus_tag="QJB05_RS24945"
                     /old_locus_tag="QJB05_24945"
     CDS             1120..3279
                     /gene="mobQ"
                     /locus_tag="QJB05_RS24945"
                     /old_locus_tag="QJB05_24945"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016240513.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobQ family relaxase"
                     /protein_id="WP_001029344.1"
                     /translation="MAIYHLSMKIISRNSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALVNAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIVLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGASGLAALRVQL
                     LKREEELRRKEQEDTERSRAERRAEQLRKNDNAVMDSGVLSAVVTGYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQYTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLLPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHATERRHDRGWSQ"
                     /name="mobQ"
     Typing          complement(943..1119)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          1120..1478
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(3537..4087)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.819"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          1034..3276
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.733"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gtcattgtct tttgcaattc aggtgaagct acgtcagtac cggagttaag tcggcttatg
       61 cagagcaata agaaacgctg ttcttgtaaa gttagcttgt aactggcctc aaccagcgca
      121 ttggacttat aggctatcag agggtttgat gtcattttaa ccaccaggcc aaaaatgagg
      181 tgaaataaaa acctatcacc tttagcattg gtgagcaatt atattttcac cccccatttt
      241 cctgtgaata ttaccttaaa tctcctcacc tttaccttaa attacctcac ccaagcacct
      301 taaattatat cacctttacc ttaaatcata tcacctatag cgttgtaaca ttttgttttc
      361 tataaggaat tttggcgcta aaacaagtat taaaaacaag atcttaaaaa caagatctaa
      421 aaacttaacg acgagcctgt ggataacttg gagtgctgaa aacaaaaaac caataaaaac
      481 aatgcgttgc aaaaaagcag aattgcaagt tccgaataca ccccctccaa ccctgtggaa
      541 atccagtatt catgcgggtt cagcgcatat cacctcccga aaaaccgtgc gtatgtgctc
      601 aatcaggcga cggattcact tccgcttcct cgcccactcg ctcgctaacg ctcggtcgct
      661 gggactgcgg cgagcggacg atacaatcac tgtcctggca gcgcttccag ctcgttaatc
      721 agcggcagta tgcgcgtcac atcagcctgt cgtgtcacct ctgccttcag gaactggagt
      781 aaccaggcac gcaactgcac ctcctccggc tttctgacct ttgccagcaa tgctgcaccc
      841 acaatgacct tctgcgctgt gtccagactc ctgctcttcg ccttcaggcg ctgtaatctg
      901 gcctcagcat cagcaatctt ctgttcgagt gttctgctca tgatgtaact ccgtgcgcga
      961 tgaaaaatcg cattttagcg cgtcactggt agtttaaaaa ctgagctggc ataatgcacg
     1021 gaaaatcacg aagtgcgcac ttatacaatc tccactccgt ttcgattgtg tgcgccctgc
     1081 ggggctgaaa gaaaaccaca aaaaggcatt acggcagaaa tggcgattta tcatctcagc
     1141 atgaaaatca tctccagaaa cagcggctac agcgccgttg cttctgctgc ctatcgttcc
     1201 ggttcactga tgcttgatga gcgtaccgga ctgactcacg actacacccg caaaagcggt
     1261 gtggctgaag ctgtgattct gactcccgcg acagcccctg cctggtgtac gaaccgtgcc
     1321 gaactctgga atgccgttga gaaggccgaa cgccggaaga actcacaact tgcgcgggaa
     1381 attgaactcg ccatcccccg cgaactaccg caggatgccg cacgggaaac cgttctcgcc
     1441 tttgtcagag aaaactttgt cagtcagggc atgattgctg atgtggcgtt ccatcacatg
     1501 gataaaacaa atccccatgc gcacatcatg ctgaccacga gagctgtcgg acctgctgga
     1561 ttcggtggaa aggtcaggga ctggaacgac cggacacatg ccgagacgtg gcgtgcatca
     1621 tgggctgacc atgcgaacag ggcactggtg aacgccggtt atcaggaaga gatagaccat
     1681 cgttcatacg agcgacaggg gcttgagaaa acgcctggta ttcacctcgg aaagtctgcc
     1741 tgtgcgatgg aaacacgcgg tatcgaaaca gaacgcggcg aacagaatcg tctgattaac
     1801 agacttaacc tggaaataca gatttcccgt accgaactca gaaacagcgg gctgacagag
     1861 cctgcccgcc gtgtggctga ccttctgaat atcgtgcttc ctgacaacgc aacttcgtac
     1921 acactacgtg acatcatcga agcgttgccg aaggacagta atgcggcatg gaaactcacc
     1981 agtaatgcca tgtcgatgat ggcagatatg caggcgacgc gcagacgctg ggaagagctg
     2041 aacaccgaac gaaaggaagc gatgagccat gctgccagcc tgaaaaaatc atcgccgttt
     2101 tcgtccggtt tttcccgtat tcccctgatg caatgggcgg caccggaata ccgtagcgaa
     2161 cagggaaaaa tccagtcgct gagccagcaa atggaaaaat tgcgacagca ttaccggaag
     2221 gtggagaaac aggacattcc cgcgagtcag acggcatttg aaaaacagtg gcagcagtgg
     2281 ggggcatccg gccttgcagc tctcagagtc cagttgctta aacgtgaaga ggaattgcgc
     2341 cggaaggagc aggaggatac agaacgtagt cgcgcggagc gacgagcgga acagctcagg
     2401 aaaaatgaca atgccgttat ggattcaggg gtactgagcg cagtcgttac ggggtatggc
     2461 gaggccccca tgcctggtaa cggggaaatg acctgttacc ttctgcttca caaccggaac
     2521 ggagaataca cgctctgggg gaacgagctg gagaaatacc gcaccagaat ctttgagcgt
     2581 gttgatttaa tgcgtgacag gagtggttat atctgtgacc gaagcgaaat cggtcaacat
     2641 ccaccactgc aacgtgttta ttcctctgcg acctttgagc aacttctgac gcaggtttgc
     2701 cagacatggc cgcaatatac ccgcaatctc cgccagccga agacatggcc ggagtctttc
     2761 tgtcttggag aagaccgcca gccagccatg ccatcactgg cagcaaggaa ggtggatttt
     2821 acgcagggac gtctgctacc gacgctgatg ccggtaatga gttctgtcga ccgggaaacc
     2881 cgccagcttc agcttttgct ggtcatgggc gtggatgact ctctgggcgg tgttgtccgg
     2941 cttaatggta cgctgtatcc cgcgtttgcc gttccctcag ccgataacag ccagctggtc
     3001 atcagtgcac tgaccgataa ggggttacgg tatgcagggt atggtgttgc cgtaaatcac
     3061 gatgcagaca gccacatatc acctgcgccg gaacttatgg agtttcatct gaaaacccgt
     3121 gaggcaccgc tttttgctgc cgtcaacaca ccagaaaaac agccggatca tctgttccgc
     3181 tcgctgggtt ttaatcgtac ctgggacgaa tggcggcgcg aggaagatgc acgaacacac
     3241 gccaccgaga ggagacatga tcgcggttgg tcacagtgaa tgtgaacaat attttgtttt
     3301 gtttaacatc gtgttatgtt cgtcgatgtt cttcgatgtt catcgacagg gatgaatgca
     3361 agaagcacac acataatgca agcatagttt tgtttttccg cccccaaaaa atgggggttc
     3421 ttttttcgct gcattagagc gcttttgacg caatttttca cttcaatagt accttcgcac
     3481 tactaacaca aaaaaaacgc agcagggagc gttttaggtg ccttaaaatc gattttagat
     3541 cgtcatcttg atttgtttgt cttccttgaa gcgaaaatgc agggctacaa ccgtgcgccc
     3601 ctttttgatc gtctcaaccg ttacagccag gtcgcttttt ttgttcagtt cgtcaacaca
     3661 gggttttatt agatccctgt ttaacgtttt gaaatcttta tatttaccat caagcatcag
     3721 tgatgattta aaatcatcga gggcgataat acgttcccca gtactgcgga attgctggag
     3781 aatttcgtat attcttatgc tgtaacttct tgataaatta gaaatatttt taatgacgac
     3841 tctggtgaat tgccccttca actgtgtcag ataaggcatt accgcgtcag aaaaagtgat
     3901 ttgtgctttc ccctctcccc tcgcgtactg tgcccgatac tgaatccagc ggaactcctc
     3961 gcgcttctcg tcgtccttga gaatgatcga cctgtcccac aaacgatcga tcgcttcctg
     4021 tagctgaacc tcggcatttt tccgccccat atcagggaat gaatcaaaat attccgcagc
     4081 tgtaatg
//
