LOCUS       CP098939                3319 bp    DNA     circular BCT 13-APR-2023
DEFINITION  Escherichia coli strain RHB47-C15 plasmid unnamed6, complete
            sequence.
ACCESSION   CP098939
VERSION     CP098939.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15488724
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3319)
  AUTHORS   Matlock,W.
  TITLE     Plasmid overlap and evolution between Enterobacterales isolates from
            bloodstream infections and non-human compartments
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3319)
  AUTHORS   Matlock,W.
  TITLE     Direct Submission
  JOURNAL   Submitted (13-JUN-2022) Nuffield Department of Medicine, University
            of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.4
            Assembly Name                     :: RHB47-C15
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 99x
            Sequencing Technology             :: Illumina/Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/15/2022 18:29:18
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.1
            Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
            Genes (total)                     :: 4,850
            CDSs (total)                      :: 4,735
            Genes (coding)                    :: 4,492
            CDSs (with protein)               :: 4,492
            Genes (RNA)                       :: 115
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 83
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 243
            CDSs (without protein)            :: 243
            Pseudo Genes (ambiguous residues) :: 0 of 243
            Pseudo Genes (frameshifted)       :: 70 of 243
            Pseudo Genes (incomplete)         :: 166 of 243
            Pseudo Genes (internal stop)      :: 56 of 243
            Pseudo Genes (multiple problems)  :: 45 of 243
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            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/
FEATURES             Location/Qualifiers
     source          1..3319
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB47-C15"
                     /isolation_source="Pooled faeces sample collected from
                     floor of poultry farm"
                     /db_xref="taxon:562"
                     /plasmid="unnamed6"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            join(2955..3319,1..16)
                     /gene="lsoB"
                     /locus_tag="NFL60_24230"
     CDS             join(2955..3319,1..16)
                     /gene="lsoB"
                     /locus_tag="NFL60_24230"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052605.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system antitoxin LsoB"
                     /protein_id="WGC17968.1"
                     /translation="MKKDKKYQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKK
                     SKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNF
                     DKINVNLLSKATSFALKKGIPI"
                     /name="lsoB"
     gene            complement(251..574)
                     /locus_tag="NFL60_24235"
     CDS             complement(251..574)
                     /locus_tag="NFL60_24235"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="nikA protein"
                     /protein_id="WGC17969.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="nikA protein"
     gene            859..1053
                     /locus_tag="NFL60_24240"
     CDS             859..1053
                     /locus_tag="NFL60_24240"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041639.1"
                     /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="WGC17970.1"
                     /translation="MNKQQQAVLNMAGFIKSQSLTLLEKLDALDADEQAAMCEKLHELA
                     EELQNSIQTRFEVENSTER"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1540..1653
                     /locus_tag="NFL60_24245"
     CDS             1540..1653
                     /locus_tag="NFL60_24245"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WGC17971.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLSPLAAAIGN"
                     /name="replication initiation protein"
     gene            1918..2958
                     /gene="lsoA"
                     /locus_tag="NFL60_24250"
     CDS             1918..2958
                     /gene="lsoA"
                     /locus_tag="NFL60_24250"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052606.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system mRNA
                     endoribonuclease LsoA"
                     /protein_id="WGC17967.1"
                     /translation="MAQNPFKALNINIDKIESALTQNGVTNYSSNVKNERETHISGTYK
                     GIDFLIKLMPSGGNTTIGRASGQNNTYFDEIALIIKENCLYSDTKNFEYTIPKFSDDDR
                     ANLFEFLSEEGITITEDNNNDPNCKHQYIMTTSNGDRVRAKIYKRGSIQFQGKYLQIAS
                     LINDFMCSILNMKEIVEQKNKEFNVDIKKETIESELHSKLPKSIDKIHEDIKKQLSCSL
                     IMKKIDVEMEDYSTYCFSALRAIEGFIYQILNDVCNPSSSKNLGEYFTENKPKYIIREI
                     HQETINGEIAEVLCECYTYWHENRHGLFHMKPGIADTKTINKLESIAIIDTVCQLIDGG
                     VARLKL"
                     /name="lsoA"
     Typing          complement(584..824)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.12e-123"
     Typing          1083..1612
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.972"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          complement(255..574)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="1.76e-62"
ORIGIN
        1 aggcattcca atataatatc aagccagaag acatttacca taacgtctca ttacgcgcac
       61 cgccaaaacg cgctgaacgc gattctgacg cagacaccgc aaaaagagat gttttccccg
      121 gggtaaaccg gaaaaatgcg tcaggatcgc tttcagctca ctgcatagct atgcatgaaa
      181 gtgaatggcg atcggtttgg gggcttacgg cgttcatacc gtctgttttc gacagtttct
      241 ctccgggaag ttaatctgcc ataagcctgg ataacagggc acggtgatac tccgtaatag
      301 cgatcagcac ctccgcatac tctctgtccc cgacacgctt gccgtcgata aagagttttt
      361 tctgcaacgc ccccagtcgc ataacttctt tcagcacccg gtcatcagtc agtgagttaa
      421 ctttcttacc gagagctgcc gcccgtaaaa aaccagaaac ggtcttgccg cattcagcag
      481 ccctttttct gatttcctgg tcttcttctg ccgtcagacg aacagggcga ctgatagccc
      541 gcctgcgcgt attacttcca cttcgttttg tcataaaaca tggctccgta tctgacatgg
      601 ggtgtcgggg cgaagccctg accagggtaa ttgtaatagc gtgcatgtat gcgcggtata
      661 acaattgcac atcctgtcct gtcagcaagc tcgaattacc gacaaaggca cggcagtttt
      721 ttggcagtga cagtattgtc aggcagaaat acccgtcaaa gcgtcagacg gcagaatacc
      781 ggcggtaaaa cagtcgaaaa gtggtacgcg atataatcac acaacgcaga tgacagacag
      841 aacggagaaa acgaaaagat gaacaagcag cagcaagctg tactcaacat ggcaggattc
      901 ataaaaagcc agagcctgac gctgctcgaa aagctggacg cactcgatgc tgacgaacag
      961 gctgccatgt gtgagaagct gcacgaactc gcagaagaac tccagaacag catccagaca
     1021 cgctttgaag tagaaaatag cacagagaga taactctcag gacaggatgc cgaacggcac
     1081 aacagagcgt aaggagaaaa tgtcacataa ggcgctcttc cgcttcctcg ctcactgact
     1141 cgctacgctc ggtcgttcga ctgcggcgag cggtgtcagc tcactcaaaa gcggtaatac
     1201 ggttatccac agaatcaggg gataaagccg gaaagaacat gtgagcaaaa agcaaagcac
     1261 cggaagaagc caacgccgca ggcgtttttc cataggctcc gcccccctga cgagcatcac
     1321 aaaaatcgac gctcaagcca gaggtggcga aacccgacag gactataaag ataccaggcg
     1381 tttccccctg gaagctccct cgtgcgctct cctgttccga ccctgccgct taccggatac
     1441 ctgtccgcct ttctcccttc gggaagcgtg gcgctttctc atagctcacg ctgttggtat
     1501 ctcagttcgg tgtaggtcgt tcgctccaag ctgggctgtg tgcacgaacc ccccgttcag
     1561 cccgaccgct gcgccttatc cggtaactat cgtcttgagt ccaacccggt aagacacgac
     1621 ttatcgccac tggcagcagc cattggtaac tgatttagag gagtttgtct tgaagttatg
     1681 cacctgttaa ggctaaactg aaagaacaga ttttggtgac tgcgctcctc caggccagtt
     1741 accttggttc aaagagttgg tagctcagcg aaccttgaga aaaccaccgt tggtagcggt
     1801 ggtttttctt tatttatgag atgatgaatc aatcggtcta tcaagtcaac gaacagctat
     1861 tccgttgaca aaaaaacaag atctgtacat attcaaaaaa aacaacggat tgacccaatg
     1921 gcacagaacc cgtttaaagc actaaatatc aatattgaca agattgagtc tgctctgacg
     1981 cagaatggcg tcacaaacta ttcctctaat gtaaaaaacg aaagagaaac tcacatatct
     2041 ggcacatata aaggaataga cttcttaata aaactaatgc catcaggcgg aaataccact
     2101 atcggaagag cgtctgggca aaataacact tactttgatg aaatcgcctt gattataaaa
     2161 gaaaactgtt tgtattcaga cacaaagaac tttgaataca ccattccaaa attcagtgat
     2221 gatgacaggg caaatctatt tgaatttctt tctgaagagg ggataacaat aacagaagat
     2281 aataataacg atcctaattg taaacaccaa tatattatga ccaccagcaa tggtgacagg
     2341 gtcagggcaa aaatttacaa gcgcggctct attcaattcc aaggaaaata ccttcaaatc
     2401 gcgagtttga ttaacgattt catgtgctca atactaaaca tgaaagagat tgtcgaacaa
     2461 aaaaataaag aatttaatgt tgacataaaa aaagaaacta ttgagtccga gttgcatagc
     2521 aaactaccaa aaagcatcga taaaatccat gaagatatca aaaaacagct atcatgctcg
     2581 ctaataatga aaaaaataga tgtcgaaatg gaagattact caacatactg cttctctgca
     2641 ttaagagcca tagaaggctt tatatatcaa atacttaatg atgtttgcaa tccatcatca
     2701 tcaaagaacc ttggcgaata cttcactgaa aacaaaccca aatatataat cagagaaata
     2761 caccaagaaa ctataaatgg tgaaatagcg gaagttttgt gtgaatgcta cacttactgg
     2821 catgagaaca ggcatggttt gtttcatatg aaaccaggaa tagctgacac gaagacaatt
     2881 aacaaattag aatcaatcgc aatcatcgat accgtttgcc aattaataga tggtggcgta
     2941 gctaggttga aattatgaaa aaagataaaa aatatcaaat agaagcaata aaaaataaag
     3001 ataaaacttt atttattgtc tatgctactg atatttatag cccgagcgaa tttttctcaa
     3061 aaatcgaatc cgacttgaag aaaaagaaaa gcaagggtga tgtttttttt gatttaataa
     3121 ttcctaacgg tggaaaaaaa gatcgttacg tctatacgtc atttaatggc gagaagtttt
     3181 caagttacac attaaacaaa gttacgaaaa ctgatgaata taatgattta tctgagctct
     3241 cggcttcgtt ctttaaaaaa aactttgata agatcaacgt aaaccttcta tccaaagcca
     3301 catcatttgc tttgaaaaa
//
