LOCUS       NZ_CP048313             6200 bp    DNA     circular CON 25-JUN-2024
DEFINITION  Escherichia coli strain 32-4 plasmid p32-4_C, complete sequence.
ACCESSION   NZ_CP048313
VERSION     NZ_CP048313.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13951925
            Assembly: GCF_010365345.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6200)
  AUTHORS   Nuesch-Inderbinen,M., Stevens,M.J.A. and Stephan,R.
  TITLE     Environmental dissemination of Carbapenemase-producing
            Enterobacteriaceae in Switzerland
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6200)
  AUTHORS   Nuesch-Inderbinen,M., Stevens,M.J.A. and Stephan,R.
  TITLE     Direct Submission
  JOURNAL   Submitted (31-JAN-2020) Institute for Food Safety and Hygiene,
            University of Zurich, Winterthurerstrasse 272, Zurich, Zurich 8057,
            Switzerland
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 29-NOV-2019
            Assembly Method                   :: unicycler v. 0.4.8
            Assembly Name                     :: 32-4.fa
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 80x
            Sequencing Technology :: Oxford Nanopore/illumina minniseq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_010365345.1-RS_2024_06_25
            Annotation Date                   :: 06/25/2024 03:42:36
            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)                     :: 5,109
            CDSs (total)                      :: 4,987
            Genes (coding)                    :: 4,642
            CDSs (with protein)               :: 4,642
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 345
            CDSs (without protein)            :: 345
            Pseudo Genes (ambiguous residues) :: 0 of 345
            Pseudo Genes (frameshifted)       :: 151 of 345
            Pseudo Genes (incomplete)         :: 215 of 345
            Pseudo Genes (internal stop)      :: 53 of 345
            Pseudo Genes (multiple problems)  :: 66 of 345
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP048313.1.
            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..6200
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="32-4"
                     /isolation_source="environment"
                     /db_xref="taxon:562"
                     /plasmid="p32-4_C"
                     /geo_loc_name="Switzerland"
                     /collection_date="2019"
     gene            218..376
                     /locus_tag="GZS16_RS26095"
     CDS             218..376
                     /locus_tag="GZS16_RS26095"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_032287700.1"
                     /translation="MHEPPVQSDRCALSGNYQLESNPERHDKTPLAAAISNRSAREDRL
                     RGLEVEA"
                     /name="hypothetical protein"
     gene            836..1651
                     /gene="sul2"
                     /locus_tag="GZS16_RS24625"
                     /old_locus_tag="GZS16_24625"
     ARG             837..1648
                     /name="sul2"
                     /gene="sul2"
                     /gene_name="sulfonamide-resistant dihydropteroate synthase
                     Sul2"
                     /tool="amrfinderplus"
                     /drug_class="SULFONAMIDE"
                     /identity="100.0"
                     /coverage="100.0"
     ARG             1758..2515
                     /name="APH(3'')-Ib"
                     /gene="APH(3'')-Ib"
                     /gene_name="APH(3'')"
                     /tool="rgi"
                     /drug_class="aminoglycoside antibiotic"
                     /identity="99.21"
                     /coverage="94.38"
     ARG             1713..2512
                     /name="aph(3'')-Ib"
                     /gene="aph(3'')-Ib"
                     /gene_name="aminoglycoside O-phosphotransferase
                     APH(3'')-Ib"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            2515..3351
                     /locus_tag="GZS16_RS24635"
                     /old_locus_tag="GZS16_24635"
     CDS             2515..3351
                     /locus_tag="GZS16_RS24635"
                     /old_locus_tag="GZS16_24635"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000480972.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="aminoglycoside O-phosphotransferase APH(6)-Id"
                     /protein_id="WP_000480968.1"
                     /translation="MFMPPVFPAHWHVSQPVLIADTFSSLVWKVSLPDGTPAIVKGLKP
                     IEDIADELRGADYLVWRNGRGAVRLLGRENNLMLLEYAGERMLSHIVAEHGDYQATEIA
                     AELMAKLYAASEEPLPSALLPIRDRFAALFQRARDDQNAGCQTDYVHAAIIADQMMSNA
                     SELRGLHGDLHHENIMFSSRGWLVIDPVGLVGEVGFGAANMFYDPADRDDLCLDPRRIA
                     QMADAFSRALDVDPRRLLDQAYAYGCLSAAWNADGEEEQRDLAIAAAIKQVRQTSY"
                     /name="aminoglycoside O-phosphotransferase APH(6)-Id"
     gene            complement(<3458..3862)
                     /locus_tag="GZS16_RS24640"
                     /old_locus_tag="GZS16_24640"
                     /pseudo=""
     CDS             complement(<3458..3862)
                     /locus_tag="GZS16_RS24640"
                     /old_locus_tag="GZS16_24640"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001120888.1"
                     /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="IS91 family transposase"
                     /name="IS91 family transposase"
     gene            complement(3906..4295)
                     /locus_tag="GZS16_RS24645"
                     /old_locus_tag="GZS16_24645"
     CDS             complement(3906..4295)
                     /locus_tag="GZS16_RS24645"
                     /old_locus_tag="GZS16_24645"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000102614.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000102614.1"
                     /translation="MSTELNSGTVGGFGHMGPNDPYNDGHSGSGSSGGSFNGGGNGGHD
                     NSSGSSYTASFGLITGRHPITVPGTKNINSVDLSAVINNIIHHEGARNNMYLDTANNVR
                     VGVTGTGWQCLATAGISAEGKRTFR"
                     /name="hypothetical protein"
     gene            4513..4953
                     /locus_tag="GZS16_RS24650"
                     /old_locus_tag="GZS16_24650"
     CDS             4513..4953
                     /locus_tag="GZS16_RS24650"
                     /old_locus_tag="GZS16_24650"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011161230.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_005119689.1"
                     /translation="MAWHTVQETLKLTGKSRSQLYRDMAKGLVSYRTGKNDRREFETSE
                     LIRAYGELRTSETPKRHKEGHSKSVVSQAENAQLDVIQQKLDALQQTVTLMLEDKMARE
                     AENRLRNEEREQLQAEISRLADALAQEKKRGFWSRLFRSGSE"
                     /name="hypothetical protein"
     gene            complement(5698..5847)
                     /locus_tag="GZS16_RS25350"
     CDS             complement(5698..5847)
                     /locus_tag="GZS16_RS25350"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001138880.1"
                     /translation="MPSEYDEQLDSTDTQLPGEYDLFDLMAQVTEENLHAPVDFGSPVG
                     REAL"
                     /name="hypothetical protein"
     ARG             2516..3348
                     /name="aph(6)-Id"
                     /gene="aph(6)-Id"
                     /gene_name="aminoglycoside O-phosphotransferase APH(6)-Id"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          complement(5883..6056)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.429"
                     /coverage="100.0"
                     /evalue="1.19e-84"
     Typing          38..546
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.47"
                     /coverage="99.0"
                     /evalue="3.7599999999999996e-139"
     Typing          5980..6200
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.607"
                     /coverage="99.0"
                     /evalue="2.9e-61"
ORIGIN
        1 ccctgacaag catcgcaaaa tctgacgctc aaatcagtgg tggcgaaacc cgacaggact
       61 ataaagatcc caggcgtttc cccctggtag ctccctcgtg cgctctcctg ttcctgcctt
      121 tcggtttacc ggtgtcattc cgctgttatg gccgcggttt ctcattccac gcctgacact
      181 cagttccgtg aaggcagttc gctccaagct ggactgtatg cacgaacccc ccgttcagtc
      241 cgaccgctgc gccttgtccg gtaactatca acttgagtcc aacccggaaa gacacgacaa
      301 aacgccactg gcagcagcca ttagtaacag gagtgcacga gaagatagat taagaggtct
      361 tgaagtagag gcctgactgc ggctacactg aaagaacagt tttggtaatg gcggtctcgt
      421 gaaccctgtt accgggttaa gcagttcccc aactgactta accttcgaac aaaccgcctc
      481 cccaggcggt tttttcgttt acagagcaag agattacgat tcattgaaaa ggatctcaag
      541 aagatccttt gtagattact atcaattaat cttccgaaca tgacaccagt cactgttgat
      601 tacggttaaa ccgctccgta acaggtttcc ctcgtattgg tgacttgcag caccaaagaa
      661 gcaaaaaaga taaatatatc tacttattga gagatgatat atttatttcc aaaatgctac
      721 agatacatca tcatgaaacg gatcaccgca aacaggttac tcgcctgggg attccctttc
      781 gacccgagca tccgtatgag actcatgctc gattattatt attatagaag cccccatgaa
      841 taaatcgctc atcattttcg gcatcgtcaa cataacctcg gacagtttct ccgatggagg
      901 ccggtatctg gcgccagacg cagccattgc gcaggcgcgt aagctgatgg ccgagggggc
      961 agatgtgatc gacctcggtc cggcatccag caatcccgac gccgcgcctg tttcgtccga
     1021 cacagaaatc gcgcgtatcg cgccggtgct ggacgcgctc aaggcagatg gcattcccgt
     1081 ctcgctcgac agttatcaac ccgcgacgca agcctatgcc ttgtcgcgtg gtgtggccta
     1141 tctcaatgat attcgcggtt ttccagacgc tgcgttctat ccgcaattgg cgaaatcatc
     1201 tgccaaactc gtcgttatgc attcggtgca agacgggcag gcagatcggc gcgaggcacc
     1261 cgctggcgac atcatggatc acattgcggc gttctttgac gcgcgcatcg cggcgctgac
     1321 gggtgccggt atcaaacgca accgccttgt ccttgatccc ggcatggggt tttttctggg
     1381 ggctgctccc gaaacctcgc tctcggtgct ggcgcggttc gatgaattgc ggctgcgctt
     1441 cgatttgccg gtgcttctgt ctgtttcgcg caaatccttt ctgcgcgcgc tcacaggccg
     1501 tggtccgggg gatgtcgggg ccgcgacact cgctgcagag cttgccgccg ccgcaggtgg
     1561 agctgacttc atccgcacac acgagccgcg ccccttgcgc gacgggctgg cggtattggc
     1621 ggcgctgaaa gaaaccgcaa gaattcgtta actgcacatt cgggatattt ctctatattc
     1681 gcgcttcatc agaaaactga aggaacctcc attaaatcga actaatattt tttttggtga
     1741 atcgcattct gactggttgc ctgtcagagg cggagaatct ggtgattttg tttttcgacg
     1801 tggtgacggg catgccttcg cgaaaatcgc acctgcttcc cgccgcggtg agctcgctgg
     1861 agagcgtgac cgcctcattt ggctcaaagg tcgaggtgtg gcttgccccg aggtcatcaa
     1921 ctggcaggag gaacaggagg gtgcatgctt ggtgataacg gcaattccgg gagtaccggc
     1981 ggctgatctg tctggagcgg atttgctcaa agcgtggccg tcaatggggc agcaacttgg
     2041 cgctgttcac agcctatcgg ttgatcaatg tccgtttgag cgcaggctgt cgcgaatgtt
     2101 cggacgcgcc gttgatgtgg tgtcccgcaa tgccgtcaat cccgacttct taccggacga
     2161 ggacaagagt acgccgcagc tcgatctttt ggctcgtgtc gaacgagagc taccggtgcg
     2221 gctcgaccaa gagcgcaccg atatggttgt ttgccatggt gatccctgca tgccgaactt
     2281 catggtggac cctaaaactc ttcaatgcac gggtctgatc gaccttgggc ggctcggaac
     2341 agcagatcgc tatgccgatt tggcactcat gattgctaac gccgaagaga actgggcagc
     2401 gccagatgaa gcagagcgcg ccttcgctgt cctattcaat gtattgggga tcgaagcccc
     2461 cgaccgcgaa cgccttgcct tctatctgcg attggaccct ctgacttggg gttgatgttc
     2521 atgccgcctg tttttcctgc tcattggcac gtttcgcaac ctgttctcat tgcggacacc
     2581 ttttccagcc tcgtttggaa agtttcattg ccagacggga ctcctgcaat cgtcaaggga
     2641 ttgaaaccta tagaagacat tgctgatgaa ctgcgcgggg ccgactatct ggtatggcgc
     2701 aatgggaggg gagcagtccg gttgctcggt cgtgagaaca atctgatgtt gctcgaatat
     2761 gccggggagc gaatgctctc tcacatcgtt gccgagcacg gcgactacca ggcgaccgaa
     2821 attgcagcgg aactaatggc gaagctgtat gccgcatctg aggaacccct gccttctgcc
     2881 cttctcccga tccgggatcg ctttgcagct ttgtttcagc gggcgcgcga tgatcaaaac
     2941 gcaggttgtc aaactgacta cgtccacgcg gcgattatag ccgatcaaat gatgagcaat
     3001 gcctcggaac tgcgtgggct acatggcgat ctgcatcatg aaaacatcat gttctccagt
     3061 cgcggctggc tggtgataga tcccgtcggt ctggtcggtg aagtgggctt tggcgccgcc
     3121 aatatgttct acgatccggc tgacagagac gacctttgtc tcgatcctag acgcattgca
     3181 cagatggcgg acgcattctc tcgtgcgctg gacgtcgatc cgcgtcgcct gctcgaccag
     3241 gcgtacgctt atgggtgcct ttccgcagct tggaacgcgg atggagaaga ggagcaacgc
     3301 gatctagcta tcgcggccgc gatcaagcag gtgcgacaga cgtcatacta gatatcaagc
     3361 gacttctcct atcccctggg aacacatcaa tctcaccgga gaatatcgct ggccaaagcc
     3421 ttagcgtagg attccgcccc ttcccgcaaa cgaccccaaa caggaaacgc agctgaaacg
     3481 ggaagctcaa cacccactga cgcatgggtt gttcaggcag tacttcatca accagcaagg
     3541 cggcactttc ggccatccgc cgcgccccac agctcgggca gaaaccgcga cgcttacagc
     3601 tgaaagcgac caggtgctcg gcgtggcaag actcgcagcg aacccgtaga aagccatgct
     3661 ccagccgccc gcattggaga aattcttcaa attcccgttg cacatagccc ggcaattcct
     3721 ttccctgctc tgccataagc gcagcgaatg ccgggtaata ctcgtcaacg atctgataga
     3781 gaagggtttg ctcgggtcgg tggctctggt aacgaccagt atcccgatcc cggctggccg
     3841 tcctggccgc cacatgaggc atgttccgcg tccttgcaat actgtgttta catacagtct
     3901 atcgcttagc ggaaagttct tttaccctca gccgaaatgc ctgccgttgc tagacattgc
     3961 cagccagtgc ccgtcactcc cactcttaca ttgttcgcag tatctaggta catgttattg
     4021 cgtgcacctt catgatgtat aatgttatta atgacagcag aaagatcgac agaattaata
     4081 ttcttcgtac ctgggacagt tatcgggtgt cggccagtga tgagaccaaa ggatgcagta
     4141 taagatgaac cactactatt atcatggcca ccattaccac caccgttaaa actacctccc
     4201 gaacttccag agccgctatg accatcattg taggggtcat ttggtcccat gtgaccaaaa
     4261 ccaccgacag taccgctatt taactctgta ctcataaaat tatcctcttt gacttttaaa
     4321 aacagcaaaa actgtattta taacaatgtg tttatataca gtattcgaaa tactacgccc
     4381 gtcaaaacca caccgtcaac aggttttttg tgtatttttc acgcctcacg ggcagcctca
     4441 gaccttttgt gttaaaacag taatatgttc tgctgttaca atacggtaca cacaggagac
     4501 actgtcactt ttatggcatg gcacacagtt caagagacac tgaaattaac aggaaagtcg
     4561 cgctcgcaat tatatcgtga catggctaaa ggccttgtca gctatcgcac aggaaaaaat
     4621 gatcgccggg agttcgagac cagtgaactg attcgggcct atggcgagct gcgcacttct
     4681 gagacaccaa aaaggcacaa ggagggacac tccaaatctg tcgttagcca ggcggaaaat
     4741 gctcagctag acgtcattca gcagaaactg gacgctctgc agcagactgt taccctaatg
     4801 cttgaagaca agatggcgcg ggaagcagaa aaccgcctgc gaaatgagga gagggaacaa
     4861 ctacaggccg aaattagccg tctggctgac gcgctggcac aggaaaaaaa gcggggattc
     4921 tggtcgcggc tgtttcgctc cggttcagag taacagtgca ggtgactctg atttaccata
     4981 acatctgtta tcagcaccgc ctgagaggcc ctcagggcgt ttctgacggg aaaccggtaa
     5041 aacaggcaac aaaccacccg aaaacccgcc agaaacgcgc aggctctgtt tttacggcat
     5101 gcatgagtat gcgcacaagt gcatagcgcg gaaattcaca ccattcagcc ggggtaagtc
     5161 ctgtttccgg cgttcttccc atccgaaaac ggtgaacggg gacgcaattt attgcgtggc
     5221 cgtgaagcgt tgccggcgca gccggaaaac ccgctgtcag cacgttcagg aagggggtga
     5281 tgtacaaatg gcacagagga tgaaagtgac gtatgagctg aaggaatgat gtaaaagtga
     5341 tgtataagtg atgtaaaagt gatgtatgaa ctgaaggagc gatgtaattc tgtagtcagg
     5401 aagaataacc cgttcatgca ggcatgaacg atacagtgag gaacgctttt tttgtcacga
     5461 tctcccctta acctgcgtaa atcacccgcc atggttgatt atttttcaac ctcaaaatgg
     5521 tcatacacct aacgcagccg cgattttcat cgcaactgca tgaattaaaa gaaaaaaaag
     5581 gaatatttcg ttttcacgag taatacccgg gtattaaaaa tccactgtaa ttacatgaaa
     5641 ataaagaaat aaaaggtaat accggagtat taccacgtac gcgggcaagc gaaaaagcta
     5701 taacgcttcc cggccgacag gcgacccaaa atccacaggg gcatgcaggt tctcttcagt
     5761 aacctgcgcc attaaatcaa aaaggtcata ttcgccggga agctgcgtat cagtcgaatc
     5821 cagttgttca tcatattcag atggcatggg gtgatatcca gtagctgaga ggttgttagc
     5881 gggtttcggg gcgcagccct gaaccagtca tgtagcgcta gcggagtgta tactggctta
     5941 ctatgttgcc acgattgcga aaatcagtga agtgcttcat gtggcaggag aaaaaaggca
     6001 gcaccggcgc gtcagcagaa tatgcgatac aggagatatt ccgcttcctc gctcactgac
     6061 tcgctacgct cggtcgttcg gctgcggcga gcggtaccgg cttacggacg gggacggaaa
     6121 tttcctggaa gataccagga agacacttag caaagaagag ataaggccac ggcgaagccg
     6181 tttttccata ggctccgccc
//
