LOCUS       NZ_CP124440             4064 bp    DNA     circular CON 10-JUN-2024
DEFINITION  Escherichia coli strain AVS0790 plasmid pAVS0790-D, complete
            sequence.
ACCESSION   NZ_CP124440
VERSION     NZ_CP124440.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN34360970
            Assembly: GCF_030038665.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4064)
  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  JOURNAL   Unpublished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 4064)
  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_030038665.1-RS_2024_06_10
            Annotation Date                   :: 06/10/2024 05:11:55
            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)                     :: 5,212
            CDSs (total)                      :: 5,103
            Genes (coding)                    :: 4,894
            CDSs (with protein)               :: 4,894
            Genes (RNA)                       :: 109
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 82
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 209
            CDSs (without protein)            :: 209
            Pseudo Genes (ambiguous residues) :: 0 of 209
            Pseudo Genes (frameshifted)       :: 72 of 209
            Pseudo Genes (incomplete)         :: 152 of 209
            Pseudo Genes (internal stop)      :: 40 of 209
            Pseudo Genes (multiple problems)  :: 46 of 209
            Pseudo Genes (short protein)      :: 1 of 209
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP124440.1.
            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..4064
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="AVS0790"
                     /isolation_source="wastewater efflux"
                     /db_xref="taxon:562"
                     /plasmid="pAVS0790-D"
                     /geo_loc_name="Switzerland: Kanton Zug"
                     /collection_date="2021-08-18"
                     /collected_by="Amt fuer Verbraucherschutz, Kanton Zug"
     gene            join(4056..4064,1..693)
                     /locus_tag="QJP66_RS25990"
                     /old_locus_tag="QJP66_25990"
     CDS             join(4056..4064,1..693)
                     /locus_tag="QJP66_RS25990"
                     /old_locus_tag="QJP66_25990"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001281399.1"
                     /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_001281395.1"
                     /translation="MSDLIAYKSNALIEASYKLTLQEQRFLLVCISRLKSGEDSPSPDE
                     QKTMTITAAEFHDAFPDMGRQHAEARLKEAIDRLWDRSVIIKNEEKREEFRWVQYRAQY
                     FKGEAKVDITFSDAIMPYLTQLKGQFTRVVVKNVSSLSSTYSIRIYELLQQFRSTGDRT
                     IAIDDFRTMLAVEDKYQQFKDLNKMIIKPAIAELNEKSDLVVTVETIKKGRTVVALHFR
                     FKEDKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(942..3089)
                     /gene="mobQ"
                     /locus_tag="QJP66_RS25995"
                     /old_locus_tag="QJP66_25995"
     CDS             complement(942..3089)
                     /gene="mobQ"
                     /locus_tag="QJP66_RS25995"
                     /old_locus_tag="QJP66_25995"
                     /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_053920598.1"
                     /translation="MAIYHLSMKIISRSSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPHELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAIGPAGFSGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNGGLTEPARRVADLLNIGLPDNATSYTLRDIIEALPKDSN
                     SAWKLTSNAMSMMADMQATRRRWEELKTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQMAFEKQWQQWGESGLAALRAQL
                     LKREEELRRKEQEDTERSRAEQLRKNDNAVMDSGVLRAVVTGYGEAPMPGNGEMTCYLL
                     LHNRNGEYTLWGNELEKYRTRIFESVDLMRDRSGYICDRSEIGQRPPLQRVYSSATFEQ
                     LLTQVCQTWPQHTRNLRQPKTWPESFCLGEDRQPAMPSPAARKVDFMQGRLPPTLMPVM
                     SSVDRETRQLQLLLVMGVDDSLGGVIRLNGTLYPAFAVPSADNRHLVISALTDKGLRYA
                     GYGVAVNHDADSHISPAPELMQFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRTWEEW
                     QREEDARTHTTERRHDRGWSQ"
                     /name="mobQ"
     gene            3268..3522
                     /gene="mobC"
                     /locus_tag="QJP66_RS26000"
                     /old_locus_tag="QJP66_26000"
     CDS             3268..3522
                     /gene="mobC"
                     /locus_tag="QJP66_RS26000"
                     /old_locus_tag="QJP66_26000"
                     /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_000091746.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVVVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPEQ"
                     /name="mobC"
     Typing          complement(2732..3090)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          3091..3267
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          2..693
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(946..3176)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.856"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ctgatagctt acaaatcaaa cgcccttatc gaggcaagct acaagctcac tttgcaggaa
       61 cagcgcttcc tgctggtctg tatcagccgc ctaaaatccg gagaagattc cccttcgccg
      121 gatgaacaaa aaaccatgac catcacggct gcagagtttc atgatgcctt tcctgacatg
      181 ggacggcagc acgctgaagc taggctcaag gaagcgatag atcgcctctg ggacaggtca
      241 gtaatcatca agaacgagga aaaacgagaa gagttccgct gggtgcagta ccgggcgcag
      301 tatttcaaag gtgaggcgaa agtagatatc accttctccg atgccatcat gccgtatctg
      361 acacagctca aggggcagtt tacgcgggta gtcgtgaaga acgtctccag cctttccagc
      421 acctacagca tccgcattta cgagctgctc cagcagttcc gcagcaccgg tgacagaacg
      481 atagctatcg atgatttccg aaccatgctt gccgttgaag ataaatatca acaattcaaa
      541 gacttgaata agatgataat caagccagcc atcgccgaac tgaacgaaaa aagcgatctg
      601 gttgtaactg ttgagacgat caaaaagggg cgcacggttg tagccctgca ttttcgcttc
      661 aaggaagaca aacagatcaa gatgacgatc taaaatcgat tttaaggcac ctaaaacgct
      721 ccctgctgcg ttttttttgt gttagtagtg cgaaggtact attgaagtga aaaattgcgt
      781 caaaaacgct ctgatgcagc gaaaaaagac cccccaattt ttggggggcg gaaaaacaaa
      841 actatgcttg cgttatgtga gtgtgcttct tgcattcatc cctgtcgatg aacatcgacg
      901 aacataacac gatgttaaac aaaacaaaat attgttcaca ttcactgtga ccaaccgcga
      961 tcatgtctcc tctcggtggt gtgtgttcgt gcatcttcct cgcgctgcca ttcctcccag
     1021 gtacgattaa aacccagcga gcggaacaga tgatccggct gtttttctgg tgtgttgacg
     1081 gcagcaaaaa gcggtgcctc acgggttttc agatgaaact gcatcagttc tggtgcaggt
     1141 gatatgtggc tgtctgcatc gtgatttacg gcaacaccat accctgcata ccgtaacccc
     1201 ttatcggtca gcgcactgat gaccagatgc ctgttatcgg ctgagggaac ggcaaacgcg
     1261 ggatacagcg taccattaag ccggataaca ccgcccagag agtcatccac gcccatgacc
     1321 agcaaaagct gaagctggcg ggtttcccgg tcgacagaac tcatgaccgg catcagcgtc
     1381 ggtggcagac gtccctgcat aaaatccacc ttccttgccg ctggtgatgg catggctggc
     1441 tggcggtctt ctccaagaca gaaagactcc ggccatgtct tcggctggcg gagattgcgg
     1501 gtatgttgcg gccatgtctg gcaaacctgc gtcagcagtt gctcaaaggt tgcagaggaa
     1561 taaacacgtt gcagtggcgg acgttggccg atttcgcttc ggtcacagat ataaccactc
     1621 ctgtcacgca ttaaatcaac actctcaaag attctggtgc ggtatttctc cagctcgttc
     1681 ccccagagcg tatattctcc gttccggttg tgaagcagaa ggtaacaggt catttccccg
     1741 ttaccaggca tgggagcctc gccatacccc gtaacgactg ctctcagcac ccctgaatcc
     1801 ataacggcat tgtcattttt cctgagctgc tccgcgcgac tacgttcagt atcttcctgt
     1861 tccttccggc gcaattcctc ttcacgttta agcaactggg ctctgagagc tgcaaggccg
     1921 gattcccccc actgctgcca ctgtttttca aatgccatct gactcgcggg aatgtcctgt
     1981 ttctccacct tccggtaatg ctgtcgtaat ttttccattt gctggctcag agactggatt
     2041 tttccctgct cactacggta ttccggtgcc gcccattgca tcaggggaat acgggaaaaa
     2101 ccggacgaaa acggcgatga ttttttcagg ctggcagcat ggctcatcgc ttcctttcgt
     2161 tcggtcttca gctcttccca gcgtctgcgc gtcgcctgca tatctgccat catcgacatg
     2221 gcattactgg tgagtttcca tgccgagtta ctgtccttcg gcaacgcttc gataatgtca
     2281 cgtagtgtgt acgaagttgc gttgtcagga agcccgatat tcagaaggtc agccacacgg
     2341 cgggcaggct ctgtcagccc tccgttcctg agttcggtgc gggaaatctg tatttccagg
     2401 ttaagcctgt taatcagacg attctgttcg ccgcgttctg tttcgatacc gcgtgtttcc
     2461 atcgcacagg cagactttcc gaggtgaata ccaggcgttt tctcaagccc ctgtcgctcg
     2521 tatgaacgat ggtctatctc ttcctgataa ccggcgttcg ccagtgccct gtttgcatgg
     2581 tcagcccatg atgcccgcca cgtctcggca tgtgtccggt cgttccagtc cctgaccttt
     2641 ccgctgaacc cagcaggtcc gatagccctc gtggtcagca tgatgtgcgc atggggattt
     2701 gttttatcca tgtgatggaa cgccacatca gcaatcatgc cctgactgac aaagttttct
     2761 ctgacaaagg cgagaacggt ttcccgtgcg gcatcctgcg gcagttcgtg ggggatggcg
     2821 agttcaattt cccgcgcaag ttgtgagttc ttccggcgtt cggccttctc aacggcattc
     2881 cagagttcgg cacggttcgt acaccaggca ggggcggtgg cgggggtcag aatcacagcc
     2941 tcagccacac cgcttttgcg ggtgtagtcg tgagtcagtc cggtacgctc atcaagcatc
     3001 agtgaaccgg aacgataggc agcggaagct acggcgctgt agccgctgct tctggagata
     3061 attttcatgc tgagatgata aatcgccatt tctgccgtaa tgcctttttg tagttttctt
     3121 tcagccccgc agggcgcaca caatcgaaac ggagtggaga ttgtataagt gcgcacttcg
     3181 tgatttgccg tgcattatgc cagctcagtt tttaaactac cagtgacgcg ctaaaatgcg
     3241 atttttcatc gcgcacggag ttacatcatg agcagaacgc tcgaacagaa gattgctgat
     3301 gctgaggcga gattacagcg cctgaaggcg aagagccgga gcctggacac agcgcagaag
     3361 gttgttgtgg gtgctgcatt gctggcaaag gtcagaaagc cggaggaggt gcagttgcgt
     3421 gcctggttac tccagttcct gaaggcagag gtgacacgac aggctgatgt gacgcgcata
     3481 ctgccgctga ttaacgagct ggaggcgctg ccagaacagt gattgtatcg tccgctcgcc
     3541 gcagccccag cgaccgagcg ttagcgagcg agtgggcgag gaagcggaag tgaatcagtc
     3601 gccaggttga gcacatacgc acggtttttc ggcaggtgat atgcgctgaa cccgcatgaa
     3661 tactgggttt ccacagggtt ggagggggtg tattcgaaac ttgcaattct gctttattgc
     3721 aacgcattgt ttttattggt tttttgtttt cagcacccca agttatccac aggctcgccg
     3781 ttaagttttt aagatcttat ttttagatct ttttttttaa aaccttttta ggtcttgtaa
     3841 caccatgatt ttaaagatgt tctggcaaga taagtggagc ttttgggggt gaaaggtgga
     3901 gcttttgggg gtgaaaggtg gagcttttgg gggtgaaagg tggagctttt gggggtgtaa
     3961 tccacagaaa aagggggttg caaaaaaaaa acttccaccc atatgataag tggcgtacag
     4021 taaaaaaacg ccaccaatag caacgagcaa gcgaaatgtc agat
//
