LOCUS       CP098946                3319 bp    DNA     circular BCT 13-APR-2023
DEFINITION  Escherichia coli strain RHB47-C09 plasmid unnamed6, complete
            sequence.
ACCESSION   CP098946
VERSION     CP098946.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15488721
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  JOURNAL   Unpublished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-C09
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 132x
            Sequencing Technology             :: Illumina/Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/15/2022 18:23:50
            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)                     :: 4,868
            CDSs (total)                      :: 4,753
            Genes (coding)                    :: 4,518
            CDSs (with protein)               :: 4,518
            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)              :: 235
            CDSs (without protein)            :: 235
            Pseudo Genes (ambiguous residues) :: 0 of 235
            Pseudo Genes (frameshifted)       :: 69 of 235
            Pseudo Genes (incomplete)         :: 163 of 235
            Pseudo Genes (internal stop)      :: 50 of 235
            Pseudo Genes (multiple problems)  :: 44 of 235
            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-C09"
                     /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            complement(join(3076..3319,1..137))
                     /gene="lsoB"
                     /locus_tag="NFL57_24320"
     CDS             complement(join(3076..3319,1..137))
                     /gene="lsoB"
                     /locus_tag="NFL57_24320"
                     /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="WGC13477.1"
                     /translation="MKKDKKYQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKK
                     SKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNF
                     DKINVNLLSKATSFALKKGIPI"
                     /name="lsoB"
     gene            complement(134..1174)
                     /gene="lsoA"
                     /locus_tag="NFL57_24325"
     CDS             complement(134..1174)
                     /gene="lsoA"
                     /locus_tag="NFL57_24325"
                     /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="WGC13478.1"
                     /translation="MAQNPFKALNINIDKIESALTQNGVTNYSSNVKNERETHISGTYK
                     GIDFLIKLMPSGGNTTIGRASGQNNTYFDEIALIIKENCLYSDTKNFEYTIPKFSDDDR
                     ANLFEFLSEEGITITEDNNNDPNCKHQYIMTTSNGDRVRAKIYKRGSIQFQGKYLQIAS
                     LINDFMCSILNMKEIVEQKNKEFNVDIKKETIESELHSKLPKSIDKIHEDIKKQLSCSL
                     IMKKIDVEMEDYSTYCFSALRAIEGFIYQILNDVCNPSSSKNLGEYFTENKPKYIIREI
                     HQETINGEIAEVLCECYTYWHENRHGLFHMKPGIADTKTINKLESIAIIDTVCQLIDGG
                     VARLKL"
                     /name="lsoA"
     gene            complement(1439..1552)
                     /locus_tag="NFL57_24330"
     CDS             complement(1439..1552)
                     /locus_tag="NFL57_24330"
                     /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="WGC13479.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLSPLAAAIGN"
                     /name="replication initiation protein"
     gene            complement(2039..2233)
                     /locus_tag="NFL57_24335"
     CDS             complement(2039..2233)
                     /locus_tag="NFL57_24335"
                     /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="WGC13475.1"
                     /translation="MNKQQQAVLNMAGFIKSQSLTLLEKLDALDADEQAAMCEKLHELA
                     EELQNSIQTRFEVENSTER"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2518..2841
                     /locus_tag="NFL57_24340"
     CDS             2518..2841
                     /locus_tag="NFL57_24340"
                     /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="WGC13476.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="nikA protein"
     Typing          2269..2509
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.12e-123"
     Typing          complement(1481..2010)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.972"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          2519..2838
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="1.76e-62"
ORIGIN
        1 cttttctttt tcttcaagtc ggattcgatt tttgagaaaa attcgctcgg gctataaata
       61 tcagtagcat agacaataaa taaagtttta tctttatttt ttattgcttc tatttgatat
      121 tttttatctt ttttcataat ttcaacctag ctacgccacc atctattaat tggcaaacgg
      181 tatcgatgat tgcgattgat tctaatttgt taattgtctt cgtgtcagct attcctggtt
      241 tcatatgaaa caaaccatgc ctgttctcat gccagtaagt gtagcattca cacaaaactt
      301 ccgctatttc accatttata gtttcttggt gtatttctct gattatatat ttgggtttgt
      361 tttcagtgaa gtattcgcca aggttctttg atgatgatgg attgcaaaca tcattaagta
      421 tttgatatat aaagccttct atggctctta atgcagagaa gcagtatgtt gagtaatctt
      481 ccatttcgac atctattttt ttcattatta gcgagcatga tagctgtttt ttgatatctt
      541 catggatttt atcgatgctt tttggtagtt tgctatgcaa ctcggactca atagtttctt
      601 tttttatgtc aacattaaat tctttatttt tttgttcgac aatctctttc atgtttagta
      661 ttgagcacat gaaatcgtta atcaaactcg cgatttgaag gtattttcct tggaattgaa
      721 tagagccgcg cttgtaaatt tttgccctga ccctgtcacc attgctggtg gtcataatat
      781 attggtgttt acaattagga tcgttattat tatcttctgt tattgttatc ccctcttcag
      841 aaagaaattc aaatagattt gccctgtcat catcactgaa ttttggaatg gtgtattcaa
      901 agttctttgt gtctgaatac aaacagtttt cttttataat caaggcgatt tcatcaaagt
      961 aagtgttatt ttgcccagac gctcttccga tagtggtatt tccgcctgat ggcattagtt
     1021 ttattaagaa gtctattcct ttatatgtgc cagatatgtg agtttctctt tcgtttttta
     1081 cattagagga atagtttgtg acgccattct gcgtcagagc agactcaatc ttgtcaatat
     1141 tgatatttag tgctttaaac gggttctgtg ccattgggtc aatccgttgt tttttttgaa
     1201 tatgtacaga tcttgttttt ttgtcaacgg aatagctgtt cgttgacttg atagaccgat
     1261 tgattcatca tctcataaat aaagaaaaac caccgctacc aacggtggtt ttctcaaggt
     1321 tcgctgagct accaactctt tgaaccaagg taactggcct ggaggagcgc agtcaccaaa
     1381 atctgttctt tcagtttagc cttaacaggt gcataacttc aagacaaact cctctaaatc
     1441 agttaccaat ggctgctgcc agtggcgata agtcgtgtct taccgggttg gactcaagac
     1501 gatagttacc ggataaggcg cagcggtcgg gctgaacggg gggttcgtgc acacagccca
     1561 gcttggagcg aacgacctac accgaactga gataccaaca gcgtgagcta tgagaaagcg
     1621 ccacgcttcc cgaagggaga aaggcggaca ggtatccggt aagcggcagg gtcggaacag
     1681 gagagcgcac gagggagctt ccagggggaa acgcctggta tctttatagt cctgtcgggt
     1741 ttcgccacct ctggcttgag cgtcgatttt tgtgatgctc gtcagggggg cggagcctat
     1801 ggaaaaacgc ctgcggcgtt ggcttcttcc ggtgctttgc tttttgctca catgttcttt
     1861 ccggctttat cccctgattc tgtggataac cgtattaccg cttttgagtg agctgacacc
     1921 gctcgccgca gtcgaacgac cgagcgtagc gagtcagtga gcgaggaagc ggaagagcgc
     1981 cttatgtgac attttctcct tacgctctgt tgtgccgttc ggcatcctgt cctgagagtt
     2041 atctctctgt gctattttct acttcaaagc gtgtctggat gctgttctgg agttcttctg
     2101 cgagttcgtg cagcttctca cacatggcag cctgttcgtc agcatcgagt gcgtccagct
     2161 tttcgagcag cgtcaggctc tggcttttta tgaatcctgc catgttgagt acagcttgct
     2221 gctgcttgtt catcttttcg ttttctccgt tctgtctgtc atctgcgttg tgtgattata
     2281 tcgcgtacca cttttcgact gttttaccgc cggtattctg ccgtctgacg ctttgacggg
     2341 tatttctgcc tgacaatact gtcactgcca aaaaactgcc gtgcctttgt cggtaattcg
     2401 agcttgctga caggacagga tgtgcaattg ttataccgcg catacatgca cgctattaca
     2461 attaccctgg tcagggcttc gccccgacac cccatgtcag atacggagcc atgttttatg
     2521 acaaaacgaa gtggaagtaa tacgcgcagg cgggctatca gtcgccctgt tcgtctgacg
     2581 gcagaagaag accaggaaat cagaaaaagg gctgctgaat gcggcaagac cgtttctggt
     2641 tttttacggg cggcagctct cggtaagaaa gttaactcac tgactgatga ccgggtgctg
     2701 aaagaagtta tgcgactggg ggcgttgcag aaaaaactct ttatcgacgg caagcgtgtc
     2761 ggggacagag agtatgcgga ggtgctgatc gctattacgg agtatcaccg tgccctgtta
     2821 tccaggctta tggcagatta acttcccgga gagaaactgt cgaaaacaga cggtatgaac
     2881 gccgtaagcc cccaaaccga tcgccattca ctttcatgca tagctatgca gtgagctgaa
     2941 agcgatcctg acgcattttt ccggtttacc ccggggaaaa catctctttt tgcggtgtct
     3001 gcgtcagaat cgcgttcagc gcgttttggc ggtgcgcgta atgagacgtt atggtaaatg
     3061 tcttctggct tgatattata ttggaatgcc ttttttcaaa gcaaatgatg tggctttgga
     3121 tagaaggttt acgttgatct tatcaaagtt ttttttaaag aacgaagccg agagctcaga
     3181 taaatcatta tattcatcag ttttcgtaac tttgtttaat gtgtaacttg aaaacttctc
     3241 gccattaaat gacgtataga cgtaacgatc tttttttcca ccgttaggaa ttattaaatc
     3301 aaaaaaaaca tcacccttg
//
