LOCUS       CP098952                3319 bp    DNA     circular BCT 13-APR-2023
DEFINITION  Escherichia coli strain RHB47-C06 plasmid unnamed5, complete
            sequence.
ACCESSION   CP098952
VERSION     CP098952.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15488720
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  JOURNAL   Unpublished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-C06
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 77x
            Sequencing Technology             :: Illumina/Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/15/2022 18:11:22
            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)                     :: 4,839
            CDSs (total)                      :: 4,721
            Genes (coding)                    :: 4,579
            CDSs (with protein)               :: 4,579
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 142
            CDSs (without protein)            :: 142
            Pseudo Genes (ambiguous residues) :: 0 of 142
            Pseudo Genes (frameshifted)       :: 57 of 142
            Pseudo Genes (incomplete)         :: 82 of 142
            Pseudo Genes (internal stop)      :: 38 of 142
            Pseudo Genes (multiple problems)  :: 31 of 142
            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-C06"
                     /isolation_source="Pooled faeces sample collected from
                     floor of poultry farm"
                     /db_xref="taxon:562"
                     /plasmid="unnamed5"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(join(3301..3319,1..1022))
                     /gene="lsoA"
                     /locus_tag="NFL56_24165"
     CDS             complement(join(3301..3319,1..1022))
                     /gene="lsoA"
                     /locus_tag="NFL56_24165"
                     /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="WGC08958.1"
                     /translation="MAQNPFKALNINIDKIESALTQNGVTNYSSNVKNERETHISGTYK
                     GIDFLIKLMPSGGNTTIGRASGQNNTYFDEIALIIKENCLYSDTKNFEYTIPKFSDDDR
                     ANLFEFLSEEGITITEDNNNDPNCKHQYIMTTSNGDRVRAKIYKRGSIQFQGKYLQIAS
                     LINDFMCSILNMKEIVEQKNKEFNVDIKKETIESELHSKLPKSIDKIHEDIKKQLSCSL
                     IMKKIDVEMEDYSTYCFSALRAIEGFIYQILNDVCNPSSSKNLGEYFTENKPKYIIREI
                     HQETINGEIAEVLCECYTYWHENRHGLFHMKPGIADTKTINKLESIAIIDTVCQLIDGG
                     VARLKL"
                     /name="lsoA"
     gene            complement(1287..1400)
                     /locus_tag="NFL56_24170"
     CDS             complement(1287..1400)
                     /locus_tag="NFL56_24170"
                     /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="WGC08959.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLSPLAAAIGN"
                     /name="replication initiation protein"
     gene            complement(1887..2081)
                     /locus_tag="NFL56_24175"
     CDS             complement(1887..2081)
                     /locus_tag="NFL56_24175"
                     /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="WGC08955.1"
                     /translation="MNKQQQAVLNMAGFIKSQSLTLLEKLDALDADEQAAMCEKLHELA
                     EELQNSIQTRFEVENSTER"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2366..2689
                     /locus_tag="NFL56_24180"
     CDS             2366..2689
                     /locus_tag="NFL56_24180"
                     /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="WGC08956.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="nikA protein"
     gene            complement(2924..3304)
                     /gene="lsoB"
                     /locus_tag="NFL56_24185"
     CDS             complement(2924..3304)
                     /gene="lsoB"
                     /locus_tag="NFL56_24185"
                     /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="WGC08957.1"
                     /translation="MKKDKKYQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKK
                     SKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNF
                     DKINVNLLSKATSFALKKGIPI"
                     /name="lsoB"
     Typing          2117..2357
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.12e-123"
     Typing          complement(1329..1858)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.972"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          2367..2686
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="1.76e-62"
ORIGIN
        1 acgccaccat ctattaattg gcaaacggta tcgatgattg cgattgattc taatttgtta
       61 attgtcttcg tgtcagctat tcctggtttc atatgaaaca aaccatgcct gttctcatgc
      121 cagtaagtgt agcattcaca caaaacttcc gctatttcac catttatagt ttcttggtgt
      181 atttctctga ttatatattt gggtttgttt tcagtgaagt attcgccaag gttctttgat
      241 gatgatggat tgcaaacatc attaagtatt tgatatataa agccttctat ggctcttaat
      301 gcagagaagc agtatgttga gtaatcttcc atttcgacat ctattttttt cattattagc
      361 gagcatgata gctgtttttt gatatcttca tggattttat cgatgctttt tggtagtttg
      421 ctatgcaact cggactcaat agtttctttt tttatgtcaa cattaaattc tttatttttt
      481 tgttcgacaa tctctttcat gtttagtatt gagcacatga aatcgttaat caaactcgcg
      541 atttgaaggt attttccttg gaattgaata gagccgcgct tgtaaatttt tgccctgacc
      601 ctgtcaccat tgctggtggt cataatatat tggtgtttac aattaggatc gttattatta
      661 tcttctgtta ttgttatccc ctcttcagaa agaaattcaa atagatttgc cctgtcatca
      721 tcactgaatt ttggaatggt gtattcaaag ttctttgtgt ctgaatacaa acagttttct
      781 tttataatca aggcgatttc atcaaagtaa gtgttatttt gcccagacgc tcttccgata
      841 gtggtatttc cgcctgatgg cattagtttt attaagaagt ctattccttt atatgtgcca
      901 gatatgtgag tttctctttc gttttttaca ttagaggaat agtttgtgac gccattctgc
      961 gtcagagcag actcaatctt gtcaatattg atatttagtg ctttaaacgg gttctgtgcc
     1021 attgggtcaa tccgttgttt tttttgaata tgtacagatc ttgttttttt gtcaacggaa
     1081 tagctgttcg ttgacttgat agaccgattg attcatcatc tcataaataa agaaaaacca
     1141 ccgctaccaa cggtggtttt ctcaaggttc gctgagctac caactctttg aaccaaggta
     1201 actggcctgg aggagcgcag tcaccaaaat ctgttctttc agtttagcct taacaggtgc
     1261 ataacttcaa gacaaactcc tctaaatcag ttaccaatgg ctgctgccag tggcgataag
     1321 tcgtgtctta ccgggttgga ctcaagacga tagttaccgg ataaggcgca gcggtcgggc
     1381 tgaacggggg gttcgtgcac acagcccagc ttggagcgaa cgacctacac cgaactgaga
     1441 taccaacagc gtgagctatg agaaagcgcc acgcttcccg aagggagaaa ggcggacagg
     1501 tatccggtaa gcggcagggt cggaacagga gagcgcacga gggagcttcc agggggaaac
     1561 gcctggtatc tttatagtcc tgtcgggttt cgccacctct ggcttgagcg tcgatttttg
     1621 tgatgctcgt caggggggcg gagcctatgg aaaaacgcct gcggcgttgg cttcttccgg
     1681 tgctttgctt tttgctcaca tgttctttcc ggctttatcc cctgattctg tggataaccg
     1741 tattaccgct tttgagtgag ctgacaccgc tcgccgcagt cgaacgaccg agcgtagcga
     1801 gtcagtgagc gaggaagcgg aagagcgcct tatgtgacat tttctcctta cgctctgttg
     1861 tgccgttcgg catcctgtcc tgagagttat ctctctgtgc tattttctac ttcaaagcgt
     1921 gtctggatgc tgttctggag ttcttctgcg agttcgtgca gcttctcaca catggcagcc
     1981 tgttcgtcag catcgagtgc gtccagcttt tcgagcagcg tcaggctctg gctttttatg
     2041 aatcctgcca tgttgagtac agcttgctgc tgcttgttca tcttttcgtt ttctccgttc
     2101 tgtctgtcat ctgcgttgtg tgattatatc gcgtaccact tttcgactgt tttaccgccg
     2161 gtattctgcc gtctgacgct ttgacgggta tttctgcctg acaatactgt cactgccaaa
     2221 aaactgccgt gcctttgtcg gtaattcgag cttgctgaca ggacaggatg tgcaattgtt
     2281 ataccgcgca tacatgcacg ctattacaat taccctggtc agggcttcgc cccgacaccc
     2341 catgtcagat acggagccat gttttatgac aaaacgaagt ggaagtaata cgcgcaggcg
     2401 ggctatcagt cgccctgttc gtctgacggc agaagaagac caggaaatca gaaaaagggc
     2461 tgctgaatgc ggcaagaccg tttctggttt tttacgggcg gcagctctcg gtaagaaagt
     2521 taactcactg actgatgacc gggtgctgaa agaagttatg cgactggggg cgttgcagaa
     2581 aaaactcttt atcgacggca agcgtgtcgg ggacagagag tatgcggagg tgctgatcgc
     2641 tattacggag tatcaccgtg ccctgttatc caggcttatg gcagattaac ttcccggaga
     2701 gaaactgtcg aaaacagacg gtatgaacgc cgtaagcccc caaaccgatc gccattcact
     2761 ttcatgcata gctatgcagt gagctgaaag cgatcctgac gcatttttcc ggtttacccc
     2821 ggggaaaaca tctctttttg cggtgtctgc gtcagaatcg cgttcagcgc gttttggcgg
     2881 tgcgcgtaat gagacgttat ggtaaatgtc ttctggcttg atattatatt ggaatgcctt
     2941 ttttcaaagc aaatgatgtg gctttggata gaaggtttac gttgatctta tcaaagtttt
     3001 ttttaaagaa cgaagccgag agctcagata aatcattata ttcatcagtt ttcgtaactt
     3061 tgtttaatgt gtaacttgaa aacttctcgc cattaaatga cgtatagacg taacgatctt
     3121 tttttccacc gttaggaatt attaaatcaa aaaaaacatc acccttgctt ttctttttct
     3181 tcaagtcgga ttcgattttt gagaaaaatt cgctcgggct ataaatatca gtagcataga
     3241 caataaataa agttttatct ttatttttta ttgcttctat ttgatatttt ttatcttttt
     3301 tcataatttc aacctagct
//
