LOCUS       NZ_CP142935             4887 bp    DNA     circular CON 31-JAN-2024
DEFINITION  Escherichia coli strain B20123 plasmid pB20123_5, complete sequence.
ACCESSION   NZ_CP142935
VERSION     NZ_CP142935.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN39500237
            Assembly: GCF_036287665.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4887)
  AUTHORS   Maguire,M.
  TITLE     Spatiotemporal and genomic analysis of carbapenem resistance
            elements in Enterobacterales from hospital inpatients and natural
            water ecosystems of an Irish city
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4887)
  AUTHORS   Maguire,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (19-JAN-2024) Bacteriology, University of Galway,
            University Road, Galway, Galway 000000, Ireland
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.9
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 307.0x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/30/2024 19:50:48
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,409
            CDSs (total)                      :: 5,286
            Genes (coding)                    :: 5,021
            CDSs (with protein)               :: 5,021
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 95
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 265
            CDSs (without protein)            :: 265
            Pseudo Genes (ambiguous residues) :: 0 of 265
            Pseudo Genes (frameshifted)       :: 92 of 265
            Pseudo Genes (incomplete)         :: 184 of 265
            Pseudo Genes (internal stop)      :: 54 of 265
            Pseudo Genes (multiple problems)  :: 60 of 265
            Pseudo Genes (short protein)      :: 4 of 265
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP142935.1.
            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..4887
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="B20123"
                     /isolation_source="seawater"
                     /db_xref="taxon:562"
                     /plasmid="pB20123_5"
                     /geo_loc_name="Ireland"
                     /collection_date="2020"
     gene            complement(join(4792..4887,1..36))
                     /locus_tag="VYI63_RS26975"
                     /old_locus_tag="VYI63_26975"
     CDS             complement(join(4792..4887,1..36))
                     /locus_tag="VYI63_RS26975"
                     /old_locus_tag="VYI63_26975"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001385147.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_306295021.1"
                     /translation="MQRAENDPDAFFWFSLDKASLFAVFAAESRSARFCGARNETLW"
                     /name="hypothetical protein"
     gene            complement(1274..1705)
                     /locus_tag="VYI63_RS26980"
                     /old_locus_tag="VYI63_26980"
     CDS             complement(1274..1705)
                     /locus_tag="VYI63_RS26980"
                     /old_locus_tag="VYI63_26980"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000135004.1"
                     /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_024249395.1"
                     /translation="MARVSISEAARLACVSRPTIYKLIKSGELSYTSVVKHGKAVKVID
                     TTELIRVFGSLSFDNERDHAVVKFDDRSTGVNSDFLQNLQHQVALLQAENAGLKDAVNA
                     RDEHINSLRQAMQLLEHKQGTADPQHVRAKSWWQFWKFR"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(1705..1896)
                     /locus_tag="VYI63_RS26985"
                     /old_locus_tag="VYI63_26985"
     CDS             complement(1705..1896)
                     /locus_tag="VYI63_RS26985"
                     /old_locus_tag="VYI63_26985"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000166327.1"
                     /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_021543809.1"
                     /translation="MTKPQKTALNMAKFIKGQTLLLLEKLNELELDAEADLCEKLHEDA
                     ELLCRTLTIRLDGHQGDL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            3144..3722
                     /locus_tag="VYI63_RS26990"
                     /old_locus_tag="VYI63_26990"
     CDS             3144..3722
                     /locus_tag="VYI63_RS26990"
                     /old_locus_tag="VYI63_26990"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009310049.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_021543812.1"
                     /translation="MAKLPLPPLPLPIAPPSTVKNSGSERAKKSGRRTLAAKRKTLLEE
                     LWGDELEQLKVWNRHEHDGYTTVPRTLTYISRILDYLGGTGQPLSQTYLALWCRVFDEG
                     FVEIKDKDGFAYEAGFSGQRAVTTWTGRMRKLRDLGFITTKPGTSGEFQYVILLNPLTV
                     IKELYEGKEKDERYNALVGRMQEVGAKWE"
                     /name="hypothetical protein"
     gene            3726..4271
                     /locus_tag="VYI63_RS26995"
                     /old_locus_tag="VYI63_26995"
     CDS             3726..4271
                     /locus_tag="VYI63_RS26995"
                     /old_locus_tag="VYI63_26995"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009310050.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_021543811.1"
                     /translation="MASYFPTLEISGKEFDFTHLEPFIMHVNSDMAKKVLKVHVRFTNH
                     CFTKGYEPFYHPEGEPIIYDHSENKRTFCPIRYRLSLALPEIIKRLCDPAEKVYQTSAK
                     RNWTYSITIDDPEGPYHLFFEIRRASRDERHLQDLNVVIESAYPEDRGYGPPSLLGRIG
                     FVGLCGRVFCGKPLATKR"
                     /name="hypothetical protein"
     Typing          659..914
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.154"
                     /coverage="99.0"
                     /evalue="3.2100000000000013e-72"
     Typing          complement(2272..2502)
                     /name="rep_cluster_2392"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.966"
                     /coverage="91.0"
                     /evalue="6.509999999999999e-94"
ORIGIN
        1 gaaaaatgcg tcaggatcgt tttcagctcg ctgcatagct atgcatgaga gtgaatggcg
       61 aacggtttgg gtgcatacag tgcccatgag gcacattttc agacattttc agttcgtgaa
      121 ttccaagcat tttttacagg acacccctag gggcgctgct aggggtgtcc tgtaaaaaga
      181 tgcgacgcgc ccctagggac gaccctacat taattaactg ttttttataa agattgtcag
      241 tactgaccct aagtagggtc gtcatagcat cgccataggg tcgtcaacga cgtgcttttg
      301 cataaatctg aaaaagaaaa tacattttta aaacaataac atcatgattt aaaaagaaaa
      361 tcagcaaaaa gttagttttg cgtggggtgt gggcatttca ggcatgagaa cagactcgcg
      421 tttttccggg gtatctgcgg aatttttgat taaaaaaaca tcgacgcaga gcgaaatttt
      481 atgcaacagc ggctgtactg cacagggatt atttatcagt tgatatgctg tgtcatgata
      541 ctacctgaag aaacaggaca ggatgtttaa ttgtaatacc ggcacacaca acgtattgcc
      601 acttggtcag agtttccccc acaacatcag tgcgaacgtg cttaatgctc gctacggctc
      661 tctcatgttg ccggtgattc cgttgttgtt ctttcaggaa tgagtcatca gatagcccca
      721 gaaactcgct caaaagcact cagacgcgtg aaacgggttt tagatgcccg tcagggcatg
      781 gaaggcgcga ataacgctta cagagcgttt caggaggtca ggcgcgccga tacctaacta
      841 ggggatttca tgtcgctggg aaccgagtca tcccctgcaa agccaattcg cacggaacag
      901 taagccactc ggttggtaga tggtcgtaga ccgtcagtgc tacagcaatg ggggtctccc
      961 cagacggttt cctgttgcgc tcaaggctct gccggaaccg tagcggcaag gataaaaaac
     1021 cctgcgcacc ttcccgcagg ggaaggtgaa aataactacc tatctcttac gtttgagttt
     1081 tgaactcaga ctgaatatgc atttgatagt gttgaatttg caagaatcgg cggcgatttt
     1141 acggtcgaca aaagagcaat gcaggaatat cgactccaac tcaatgctct taatgtggga
     1201 aaatttccgt tttccaaatt accccaaact gagtggcaga ccgaacgcta tggctgggat
     1261 gcgtggtaat ggctcaacgg aatttccaaa actgccacca agactttgct cggacatgct
     1321 gcggatcagc agtgccctgc ttatgctcca gtagctgcat ggcctgacga agtgaattga
     1381 tatgttcgtc ccgggcattc actgcatctt tcagcccggc gttttctgcc tgcaaaagtg
     1441 ctacctgatg ctgtaaattc tgtaaaaaat cactgttaac acctgtcgag cggtcgtcaa
     1501 attttacaac agcatggtca cgttcattgt caaaagaaag agaaccaaaa acacgaataa
     1561 gctctgtagt atcaataact tttacagctt tcccatgctt tacaacagag gtgtaactta
     1621 actcaccaga tttaattaac ttgtaaatag tcggacgact gacacaagca aggcgtgccg
     1681 cttcgctaat agataccctg gccattatag atccccctga tgaccatcca gacgaatagt
     1741 cagagtgcga cagagtagtt ccgcatcctc atggagcttt tcgcaaaggt ccgcctcagc
     1801 atcgagctcg agttcattaa gtttttccag caaaagcagg gtctgcccct taataaactt
     1861 cgccatatta agcgcagttt tctgtggttt cgtcatcaca gcgtcagtgc tccatgttaa
     1921 ctctggttct tttccgcttc ctcgaccgtt cgctcgctac gctcggtcac ttgtctgcgg
     1981 cgagcggacg gggcttacgg agaagcaggt aagagagtag atgatggacg taaggaaagg
     2041 gcagccaaaa agcatgagaa ggccacgccc cctgggcgtt ttaccatagg ctccgccccc
     2101 ctgacgagca tcacagaatc tgacgctcaa atcagtggtg gcgaaacccg acaggactat
     2161 aaagatacca ggcgtttccc cctggtggct ccctcttgcg ctctcctgtt cccgccatgc
     2221 ggcttacgtg ttgtggtgga agccttacct aaatcaccac gtcccgttcc gtttagacag
     2281 ttcgctccaa gctgggctgt atgcaagaac cccccgttca gcccgactac cacgttgttt
     2341 cggtaactat catcttgagt ccaacccgga acagacacga aaaatcgcca gtggtggtag
     2401 ccattggtaa acaggatgtg cgagagatgt atcgagagtt cttgaagtga tggccttact
     2461 ccggctacac tgaaaggaca gatttggtga catgtctcgc acaagactgt taccacggtt
     2521 agaaaatctg ccaggattaa ctaaccttcg aaaaaccacc tgccagggtg gttttttcgt
     2581 ttacagagca agagattacg cgcagaaaaa aaggatctca agaagaacct ttttatttca
     2641 tgctcactgg tacgccccct ccccgtaaaa ctcaaaacgc ttaacgcaga ataatgtcaa
     2701 tttccccaat cagcatccac acattactct cacgtcgtct cagacacact caagcaagtg
     2761 ccaaggccat cccccccccc ctctaatgcc ggaaaaaatc gcacacaggg cacagtgagc
     2821 agccatttcg cttcgtatta aatagctgtc gaaaattatt accttgcccc cttgcatccc
     2881 cattcagcac agcgagcaca ttcagcacat atcagcacat tcagtacagc gagcacagaa
     2941 accagtcata actcattgaa taaaggccac catatgctgt atttattaca actcatacat
     3001 cgagatgtaa taaatagata ttcataagat gtctatagat tgataggcaa cagcacaatt
     3061 gcacacaaaa caacatacaa gtcattgttt taaaagaaaa aacaactaaa ataaccgcat
     3121 gttaaatgat tttggagaat ataatggcga agctaccact gccaccactg ccactaccaa
     3181 tagcgccacc gtcaacagta aaaaatagtg gttcagaaag agcgaagaag tcaggaagga
     3241 gaactcttgc tgcaaaaagg aaaactttgt tagaagagct atggggagac gagcttgaac
     3301 aactcaaggt atggaatcgc catgaacatg acgggtatac aacagtgcca agaacgctga
     3361 catatatcag tcggatcctc gattacctcg gaggtacggg ccagccattg tctcaaacat
     3421 atctggctct ttggtgcaga gtatttgatg aaggatttgt ggaaataaag gataaagatg
     3481 gatttgctta tgaggctggt tttagcggac agcgagctgt aaccacatgg acagggagga
     3541 tgaggaaact aagagattta ggtttcataa ctacaaaacc aggcacatca ggtgagtttc
     3601 aatatgtaat tttgcttaac ccgctgactg tcattaaaga gttatacgaa ggtaaagaaa
     3661 aagatgaaag gtataacgca ttggtgggac gtatgcagga ggttggcgct aaatgggagt
     3721 aattcatggc tagctatttc ccaacgttag aaatatcagg aaaagagttc gatttcacgc
     3781 accttgagcc attcattatg cacgtaaata gtgacatggc taaaaaggta ttaaaagtac
     3841 atgtgagatt cacaaatcat tgtttcacaa aaggttatga gcctttttat catccggaag
     3901 gagaaccgat aatttacgac catagcgaga ataagagaac gttttgccca attagatata
     3961 gattatcttt ggcgttacct gagattatca aacgtctatg tgatccagca gaaaaagtgt
     4021 atcaaacatc ggcaaagaga aactggacct actccattac aattgatgat ccggaagggc
     4081 catatcactt attttttgaa ataagacgcg cctcacgtga tgagagacat ctgcaagatt
     4141 tgaatgttgt tatcgagagt gcctatcctg aagatcgggg gtacgggcct ccgtcattac
     4201 taggtcgaat tggttttgta ggcttatgcg gtagggtatt ttgtgggaaa ccacttgcga
     4261 ctaaaagatg aaaaaaaagc acctgaaagg tgcctttttt tcatctttgg taatcgttcc
     4321 ggacaccact agcttttgct taggttcgcc ttgcgcgaac acaggaacaa ggtttgccct
     4381 gctgggtagc gttcaatctc atccggtcag tcgctacgat gtaaacaata taacaaaacc
     4441 aattacgcaa ttcagcacca tcaattcaat gcaacgcctc aaatgatata gagcaccatg
     4501 agtacaaaaa ccatagttaa ccgcatgaat ttacaaggcc atatgtattt tataaaacaa
     4561 ctcagcattc gagttacttt ataaaataca tatggccttg tagcccatca tgattttgct
     4621 acaacagaaa aaacatagtc atttgttttt attgaaaaaa attagacttc tgtatctatc
     4681 gtttttgatg ttttagcaat cgttccgtat ggcttactgt ggctaaacat gctgatgatt
     4741 acacccagct tgttcaggtc taccgtttac agctcatagc gttcggagta tttaccataa
     4801 cgtctcatta cgcgcaccgc agaaacgcgc tgaacgcgat tctgccgcaa acaccgcaaa
     4861 aagagatgct ttatccagtg aaaacca
//
