LOCUS       NZ_CP110121             3684 bp    DNA     circular CON 25-JUN-2023
DEFINITION  Escherichia coli strain 2-331 plasmid p2-331_4, complete sequence.
ACCESSION   NZ_CP110121
VERSION     NZ_CP110121.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN31436521
            Assembly: GCF_030012585.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3684)
  AUTHORS   Grevskott,D.H., Salva-Serra,F., Moore,E.R.B. and Marathe,N.P.
  TITLE     Complete sequence of a new conjugative multidrug-resistance encoding
            IncFII/IncFIA/IncFIB plasmid carrying NDM-6 metallo-beta-lactamase
            from pathogenic Escherichia coli sequence type 167 isolated from
            sewage in Norway
  JOURNAL   J Glob Antimicrob Resist 33, 291-293 (2023)
   PUBMED   37086893
REFERENCE   2  (bases 1 to 3684)
  AUTHORS   Grevskott,D.H., Salva-Serra,F., Moore,E.R.B. and Marathe,N.P.
  TITLE     Direct Submission
  JOURNAL   Submitted (25-OCT-2022) Contaminants and Biohazards, Institute of
            Marine Research, Nordnesboder 3, Bergen 5005, Norway
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology             :: Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/25/2023 10:51:25
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,128
            CDSs (total)                      :: 5,009
            Genes (coding)                    :: 4,738
            CDSs (with protein)               :: 4,738
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 271
            CDSs (without protein)            :: 271
            Pseudo Genes (ambiguous residues) :: 0 of 271
            Pseudo Genes (frameshifted)       :: 88 of 271
            Pseudo Genes (incomplete)         :: 181 of 271
            Pseudo Genes (internal stop)      :: 59 of 271
            Pseudo Genes (multiple problems)  :: 56 of 271
            Pseudo Genes (short protein)      :: 4 of 271
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP110121.1.
            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..3684
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="2-331"
                     /isolation_source="Sewage"
                     /db_xref="taxon:562"
                     /plasmid="p2-331_4"
                     /geo_loc_name="Norway: Bergen"
                     /lat_lon="60.39 N 5.32 E"
                     /collection_date="2020-08-05"
                     /collected_by="Insitute of Marine Research"
     gene            join(3625..3684,1..87)
                     /locus_tag="OMD12_RS25605"
                     /old_locus_tag="OMD12_25420"
     CDS             join(3625..3684,1..87)
                     /locus_tag="OMD12_RS25605"
                     /old_locus_tag="OMD12_25420"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001717510.1"
                     /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_073545459.1"
                     /translation="MHEPPVQSDCCTLSGNYHLESNPVRHAQAPLAAATGKKVYKRLLI
                     QSS"
                     /name="replication initiation protein"
     gene            complement(545..826)
                     /locus_tag="OMD12_RS25610"
                     /old_locus_tag="OMD12_25425"
     CDS             complement(545..826)
                     /locus_tag="OMD12_RS25610"
                     /old_locus_tag="OMD12_25425"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000594459.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /protein_id="WP_032440460.1"
                     /translation="MIKNIKHKGLRSFAEEGSTAGIQPSMAKRLRMILTTLSTATCIQD
                     VVDVRALGCHPLKGERKGEYSVEVNGNWRVVFKVEEPNVLDVDLEDYH"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            1163..1456
                     /locus_tag="OMD12_RS25615"
                     /old_locus_tag="OMD12_25430"
     CDS             1163..1456
                     /locus_tag="OMD12_RS25615"
                     /old_locus_tag="OMD12_25430"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000609279.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="HigA family addiction module antitoxin"
                     /protein_id="WP_023317864.1"
                     /translation="MINLYDPVHPGEFIREMFMEPFEIPAAELADKLDVSQSTLSRLLN
                     GKTDLSYEMALRLSKVVGRSAESWVNMQTQFSLSKSRKSLAAELEHLHPMFP"
                     /name="HigA family addiction module antitoxin"
     gene            1520..1822
                     /locus_tag="OMD12_RS25620"
                     /old_locus_tag="OMD12_25435"
     CDS             1520..1822
                     /locus_tag="OMD12_RS25620"
                     /old_locus_tag="OMD12_25435"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006326557.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF3892 domain-containing protein"
                     /protein_id="WP_039023182.1"
                     /translation="MVDFYISAIKMDSAGQHIEFVKVHKINRDGSWNTAGSISSRKFIS
                     ELISMGKASFMTVVKNSSTGKWNLGAKVEAMDDGYITTDPNKTKLDNLGNLPKFV"
                     /name="DUF3892 domain-containing protein"
     gene            complement(2607..3029)
                     /locus_tag="OMD12_RS25625"
                     /old_locus_tag="OMD12_25440"
     CDS             complement(2607..3029)
                     /locus_tag="OMD12_RS25625"
                     /old_locus_tag="OMD12_25440"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005229777.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_039023181.1"
                     /translation="MARVSISEAARLVKVSRPTIYKMINSGKLSYTSVLKHGKTIKVID
                     TSELIRVFGSLDGVIDTVKYDVKSDAGSTGVNSVGLHDLQHRIALLEAENDGLKGAVKA
                     RDEHIDSLRQAMQLLEHKHEPSSPPDSPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(3029..3220)
                     /locus_tag="OMD12_RS25630"
                     /old_locus_tag="OMD12_25445"
     CDS             complement(3029..3220)
                     /locus_tag="OMD12_RS25630"
                     /old_locus_tag="OMD12_25445"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000166328.1"
                     /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_039023180.1"
                     /translation="MSKQQKTALNMAKFIQNQSLLLLEKLNELDLDAEADLCEKLHDDA
                     EHLFRTLSSRLDELQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          3269..3684
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.019"
                     /coverage="82.0"
                     /evalue="1.32e-143"
ORIGIN
        1 tccaacccgg taagacacgc acaagcgcca ctggcagcag ccactggtaa gaaggtgtac
       61 aagagattac tgatacagag ttcttgaagt ctcagcccaa ctacggctaa actgaaagga
      121 cagaatttgg tttcagcggt cttgtacacc ctgttaccac ggttcagaag ttcccaaact
      181 tactgaaccc tcgaaaaaac cgcctcccca ggcggttttt tcgtctcggc gagtaagata
      241 cgctttatca ttcaaagcag tcaaggaaga accaagacag ctcactcacc agcaggctcc
      301 tttttattgg tagacacatg cttctggaca gtatcagccc ctgcacaaag tacagcagct
      361 aacaagaacc atccccagcc atcaatacca cgaaaagcta ggactccagc aatagttacg
      421 ctaatcaacg ggaacaataa aaccataaag gatctcatac tttctccaga ggttactttt
      481 ttaataaagt ccctaatcca tccgtacttt cacttggatg gattagcaac ttacttattg
      541 ataactaatg ataatcttca agatcaacgt ctaagacgtt tggttcctca accttgaaaa
      601 ctacccgcca gttcccatta acttcaacgg aatactcgcc tttacgctcc ccctttaggg
      661 ggtggcaccc taacgcccta acgtcaacaa cgtcttgaat gcaagttgct gtgcttagcg
      721 tagtcaaaat catgcgaagt cttttcgcca tactgggctg aataccggcg gtgctacctt
      781 cttcagcaaa gctcctaagt cctttatgtt ttatgttttt tatcatctac aatccccata
      841 tttttttcgt ctatacctgt atctatattt taaaatcatt ttaattagtt ccattttgcc
      901 cccttgcttt attaaaacaa ttgacgtaag tttgttcttg aggtcaatca cctcatttga
      961 cttcaacgaa tcctaagggt aaaatactgc gccttgaaaa ggccataaaa gcccatacat
     1021 acgcagtagc tttgactcca acgagtatcc taaagctgac tgcttttttt gtcaatatca
     1081 tgaacttgca cattgtgcaa tgcgcatact gaaaggcagt aatttttttg tataatcaaa
     1141 tacaaaacaa acagaggaag gcatgataaa tctttacgat cctgttcatc ctggtgagtt
     1201 tatcagagaa atgttcatgg aaccgttcga aatacctgcc gcagagttag ccgataaact
     1261 tgatgtatcc cagtctacct taagtagact gttaaatggg aaaacagact taagctatga
     1321 aatggcactt agattgtcga aggtcgtagg ccgctctgca gagtcgtggg taaacatgca
     1381 gacccaattc agcctgtcaa aaagtcgcaa atctttagcg gcagagctgg aacacttgca
     1441 tccaatgttt ccatgaaaaa agcccgcaga acgcgggctt ttgttacgta aaacacccag
     1501 cagccatcag gaggcaacca tggtagattt ctatatctca gcaatcaaaa tggacagtgc
     1561 tggtcagcac atcgaattcg taaaagttca taaaataaac cgagatggct catggaacac
     1621 tgccggctca atcagctctc gcaaattcat cagcgagctg atcagcatgg gaaaagccag
     1681 ctttatgaca gttgtaaaga acagctctac tggtaagtgg aacctaggag ccaaagtgga
     1741 agcgatggac gatggctaca taaccacaga tccaaacaaa actaaactcg ataacttggg
     1801 aaatctgccg aaatttgtct gatatgcaat aacatccact aagttccagc agaatcccct
     1861 ccctaatgat ttaacataaa gtcataattg tacgcaccgc cagaacggcc tcagggcgtt
     1921 tctgacagga aaccggtaaa acaggcaaca aaccacccga aaacccgtca gaaacgcgca
     1981 ggctctgttt ttacggcatg catgagtatg cacgcaagtg catagcgcga aaattcacgc
     2041 cattcagcca gggtaagtcc tgtttccggc gttcttccca tccgaaaacg gtgaacgggg
     2101 acgcaattta ttgcgtggcc gtgaagcgtt gccggcgcag ccggaaaacc ggttttcagc
     2161 acgttcagga atcgtgttcg tcgacggccg gcaatcacgt catggcaagt cgccggacga
     2221 ctcaccacac gattcaccgg cgactcttca ctagagtcgt acccagagtc gccgagtcta
     2281 aaaaacaacc aaacggggag tcgggtctag agtcgggtcg ttattaactc attgttttta
     2341 tagctctgag tcgttaccga ctctatgacg actcgccggg gactctatga cgagtcgtca
     2401 tagagtcgga tctatgtaaa taaaatttaa aaaccgaaac ttcaggaaag taagctactg
     2461 atattaaata caaatctgca aaattttaat tttgcgtagt gtgtgggtat ttttagtcgt
     2521 gaggagcgtt cagagatctg gcgatttttg ggaaggttca ggaactcccc gggatggccg
     2581 gagaggaaaa cggaagcatg acggagtcag gattttttcc agaatttcca ccacggggaa
     2641 tcgggtggtg aagaaggttc gtgcttgtgc tccagaagct gcatagcctg acgaagggaa
     2701 tcaatatgct catctcgagc cttaacagcc cctttaagac catcgttttc agcttctagt
     2761 aaagcaattc tatgttgtaa atcatgtaaa ccaacgctgt taacacctgt agatcctgcg
     2821 tcacttttta catcatattt tacagtatcg atgacaccat caagagaacc aaaaactcta
     2881 ataagctctg aagtatcaat aactttaatg gtcttcccgt gctttaaaac agaggtgtaa
     2941 cttaacttcc cactgttaat catcttgtaa attgtggggc gactaacctt aacaagccgt
     3001 gccgcttcac taatagacac tctggccatc agttaccatc ctgtaattca tccagtctcg
     3061 aggacagtgt acggaaaaga tgctccgcat catcgtggag tttctcacaa aggtcggcct
     3121 ctgcatcaag atcaagctcg ttaagcttct ccagcaggag cagagactga ttctggatga
     3181 atttagccat gttcagcgct gttttctgtt gtttcgacat aagaggcctc agagcgtcag
     3241 tgctcagtgt aggtatgttc tcttttccgc ttcctcgctc actcagtcgc tacgctcctg
     3301 ccgttcggct gcggcgagcg gtcgcaatac acacataacg acataggaca gacagcacgg
     3361 agagggagaa ggccgcacac cggccgtttt tccataggct ccgcccccct gacaagcatc
     3421 acgaaatctg acgctcaaat cagtggtggc gaaccccgac aggactataa agataccagg
     3481 cgtttccccc tgatggctcc ctcgtgcgct ctcctgttcc tgcctttcgg tttaccggtg
     3541 tcattccgct gttatggccg cgtttatctc attccacgcc agacactcag ttccgggtag
     3601 gcagttcgct ccaagctgga ctgtatgcac gaaccccccg ttcagtccga ctgctgcacc
     3661 ttatccggta actatcatct tgag
//
