LOCUS       CP098961                3319 bp    DNA     circular BCT 13-APR-2023
DEFINITION  Escherichia coli strain RHB47-C04 plasmid unnamed6, complete
            sequence.
ACCESSION   CP098961
VERSION     CP098961.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15488719
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  JOURNAL   Unpublished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-C04
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 135x
            Sequencing Technology             :: Illumina/Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/15/2022 18:05:17
            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)                     :: 4,847
            CDSs (total)                      :: 4,733
            Genes (coding)                    :: 4,500
            CDSs (with protein)               :: 4,500
            Genes (RNA)                       :: 114
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 82
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 233
            CDSs (without protein)            :: 233
            Pseudo Genes (ambiguous residues) :: 0 of 233
            Pseudo Genes (frameshifted)       :: 69 of 233
            Pseudo Genes (incomplete)         :: 158 of 233
            Pseudo Genes (internal stop)      :: 50 of 233
            Pseudo Genes (multiple problems)  :: 39 of 233
            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-C04"
                     /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(3291..3319,1..1012)
                     /gene="lsoA"
                     /locus_tag="NFL55_24215"
     CDS             join(3291..3319,1..1012)
                     /gene="lsoA"
                     /locus_tag="NFL55_24215"
                     /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="WGC04380.1"
                     /translation="MAQNPFKALNINIDKIESALTQNGVTNYSSNVKNERETHISGTYK
                     GIDFLIKLMPSGGNTTIGRASGQNNTYFDEIALIIKENCLYSDTKNFEYTIPKFSDDDR
                     ANLFEFLSEEGITITEDNNNDPNCKHQYIMTTSNGDRVRAKIYKRGSIQFQGKYLQIAS
                     LINDFMCSILNMKEIVEQKNKEFNVDIKKETIESELHSKLPKSIDKIHEDIKKQLSCSL
                     IMKKIDVEMEDYSTYCFSALRAIEGFIYQILNDVCNPSSSKNLGEYFTENKPKYIIREI
                     HQETINGEIAEVLCECYTYWHENRHGLFHMKPGIADTKTINKLESIAIIDTVCQLIDGG
                     VARLKL"
                     /name="lsoA"
     gene            1009..1389
                     /gene="lsoB"
                     /locus_tag="NFL55_24220"
     CDS             1009..1389
                     /gene="lsoB"
                     /locus_tag="NFL55_24220"
                     /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="WGC04381.1"
                     /translation="MKKDKKYQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKK
                     SKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNF
                     DKINVNLLSKATSFALKKGIPI"
                     /name="lsoB"
     gene            complement(1624..1947)
                     /locus_tag="NFL55_24225"
     CDS             complement(1624..1947)
                     /locus_tag="NFL55_24225"
                     /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="WGC04382.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="nikA protein"
     gene            2232..2426
                     /locus_tag="NFL55_24230"
     CDS             2232..2426
                     /locus_tag="NFL55_24230"
                     /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="WGC04378.1"
                     /translation="MNKQQQAVLNMAGFIKSQSLTLLEKLDALDADEQAAMCEKLHELA
                     EELQNSIQTRFEVENSTER"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2913..3026
                     /locus_tag="NFL55_24235"
     CDS             2913..3026
                     /locus_tag="NFL55_24235"
                     /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="WGC04379.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLSPLAAAIGN"
                     /name="replication initiation protein"
     Typing          complement(1957..2197)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.12e-123"
     Typing          2456..2985
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.972"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          complement(1628..1947)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="1.76e-62"
ORIGIN
        1 tatcaatatt gacaagattg agtctgctct gacgcagaat ggcgtcacaa actattcctc
       61 taatgtaaaa aacgaaagag aaactcacat atctggcaca tataaaggaa tagacttctt
      121 aataaaacta atgccatcag gcggaaatac cactatcgga agagcgtctg ggcaaaataa
      181 cacttacttt gatgaaatcg ccttgattat aaaagaaaac tgtttgtatt cagacacaaa
      241 gaactttgaa tacaccattc caaaattcag tgatgatgac agggcaaatc tatttgaatt
      301 tctttctgaa gaggggataa caataacaga agataataat aacgatccta attgtaaaca
      361 ccaatatatt atgaccacca gcaatggtga cagggtcagg gcaaaaattt acaagcgcgg
      421 ctctattcaa ttccaaggaa aataccttca aatcgcgagt ttgattaacg atttcatgtg
      481 ctcaatacta aacatgaaag agattgtcga acaaaaaaat aaagaattta atgttgacat
      541 aaaaaaagaa actattgagt ccgagttgca tagcaaacta ccaaaaagca tcgataaaat
      601 ccatgaagat atcaaaaaac agctatcatg ctcgctaata atgaaaaaaa tagatgtcga
      661 aatggaagat tactcaacat actgcttctc tgcattaaga gccatagaag gctttatata
      721 tcaaatactt aatgatgttt gcaatccatc atcatcaaag aaccttggcg aatacttcac
      781 tgaaaacaaa cccaaatata taatcagaga aatacaccaa gaaactataa atggtgaaat
      841 agcggaagtt ttgtgtgaat gctacactta ctggcatgag aacaggcatg gtttgtttca
      901 tatgaaacca ggaatagctg acacgaagac aattaacaaa ttagaatcaa tcgcaatcat
      961 cgataccgtt tgccaattaa tagatggtgg cgtagctagg ttgaaattat gaaaaaagat
     1021 aaaaaatatc aaatagaagc aataaaaaat aaagataaaa ctttatttat tgtctatgct
     1081 actgatattt atagcccgag cgaatttttc tcaaaaatcg aatccgactt gaagaaaaag
     1141 aaaagcaagg gtgatgtttt ttttgattta ataattccta acggtggaaa aaaagatcgt
     1201 tacgtctata cgtcatttaa tggcgagaag ttttcaagtt acacattaaa caaagttacg
     1261 aaaactgatg aatataatga tttatctgag ctctcggctt cgttctttaa aaaaaacttt
     1321 gataagatca acgtaaacct tctatccaaa gccacatcat ttgctttgaa aaaaggcatt
     1381 ccaatataat atcaagccag aagacattta ccataacgtc tcattacgcg caccgccaaa
     1441 acgcgctgaa cgcgattctg acgcagacac cgcaaaaaga gatgttttcc ccggggtaaa
     1501 ccggaaaaat gcgtcaggat cgctttcagc tcactgcata gctatgcatg aaagtgaatg
     1561 gcgatcggtt tgggggctta cggcgttcat accgtctgtt ttcgacagtt tctctccggg
     1621 aagttaatct gccataagcc tggataacag ggcacggtga tactccgtaa tagcgatcag
     1681 cacctccgca tactctctgt ccccgacacg cttgccgtcg ataaagagtt ttttctgcaa
     1741 cgcccccagt cgcataactt ctttcagcac ccggtcatca gtcagtgagt taactttctt
     1801 accgagagct gccgcccgta aaaaaccaga aacggtcttg ccgcattcag cagccctttt
     1861 tctgatttcc tggtcttctt ctgccgtcag acgaacaggg cgactgatag cccgcctgcg
     1921 cgtattactt ccacttcgtt ttgtcataaa acatggctcc gtatctgaca tggggtgtcg
     1981 gggcgaagcc ctgaccaggg taattgtaat agcgtgcatg tatgcgcggt ataacaattg
     2041 cacatcctgt cctgtcagca agctcgaatt accgacaaag gcacggcagt tttttggcag
     2101 tgacagtatt gtcaggcaga aatacccgtc aaagcgtcag acggcagaat accggcggta
     2161 aaacagtcga aaagtggtac gcgatataat cacacaacgc agatgacaga cagaacggag
     2221 aaaacgaaaa gatgaacaag cagcagcaag ctgtactcaa catggcagga ttcataaaaa
     2281 gccagagcct gacgctgctc gaaaagctgg acgcactcga tgctgacgaa caggctgcca
     2341 tgtgtgagaa gctgcacgaa ctcgcagaag aactccagaa cagcatccag acacgctttg
     2401 aagtagaaaa tagcacagag agataactct caggacagga tgccgaacgg cacaacagag
     2461 cgtaaggaga aaatgtcaca taaggcgctc ttccgcttcc tcgctcactg actcgctacg
     2521 ctcggtcgtt cgactgcggc gagcggtgtc agctcactca aaagcggtaa tacggttatc
     2581 cacagaatca ggggataaag ccggaaagaa catgtgagca aaaagcaaag caccggaaga
     2641 agccaacgcc gcaggcgttt ttccataggc tccgcccccc tgacgagcat cacaaaaatc
     2701 gacgctcaag ccagaggtgg cgaaacccga caggactata aagataccag gcgtttcccc
     2761 ctggaagctc cctcgtgcgc tctcctgttc cgaccctgcc gcttaccgga tacctgtccg
     2821 cctttctccc ttcgggaagc gtggcgcttt ctcatagctc acgctgttgg tatctcagtt
     2881 cggtgtaggt cgttcgctcc aagctgggct gtgtgcacga accccccgtt cagcccgacc
     2941 gctgcgcctt atccggtaac tatcgtcttg agtccaaccc ggtaagacac gacttatcgc
     3001 cactggcagc agccattggt aactgattta gaggagtttg tcttgaagtt atgcacctgt
     3061 taaggctaaa ctgaaagaac agattttggt gactgcgctc ctccaggcca gttaccttgg
     3121 ttcaaagagt tggtagctca gcgaaccttg agaaaaccac cgttggtagc ggtggttttt
     3181 ctttatttat gagatgatga atcaatcggt ctatcaagtc aacgaacagc tattccgttg
     3241 acaaaaaaac aagatctgta catattcaaa aaaaacaacg gattgaccca atggcacaga
     3301 acccgtttaa agcactaaa
//
