LOCUS       CP099278                3176 bp    DNA     circular BCT 13-APR-2023
DEFINITION  Escherichia coli strain RHB05-SO-C07 plasmid unnamed3, complete
            sequence.
ACCESSION   CP099278
VERSION     CP099278.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15488508
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3176)
  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  JOURNAL   Unpublished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 3176)
  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                     :: RHB05-SO-C07
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 114x
            Sequencing Technology             :: Illumina/Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/15/2022 19:52:34
            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)                     :: 4,543
            CDSs (total)                      :: 4,427
            Genes (coding)                    :: 4,350
            CDSs (with protein)               :: 4,350
            Genes (RNA)                       :: 116
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 77
            CDSs (without protein)            :: 77
            Pseudo Genes (ambiguous residues) :: 0 of 77
            Pseudo Genes (frameshifted)       :: 24 of 77
            Pseudo Genes (incomplete)         :: 49 of 77
            Pseudo Genes (internal stop)      :: 15 of 77
            Pseudo Genes (multiple problems)  :: 10 of 77
            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..3176
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB05-SO-C07"
                     /isolation_source="Pooled soil sample collected from floor
                     of sheep farm"
                     /db_xref="taxon:562"
                     /plasmid="unnamed3"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(join(2858..3176,1..5))
                     /locus_tag="NFJ44_22695"
     CDS             complement(join(2858..3176,1..5))
                     /locus_tag="NFJ44_22695"
                     /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="WFV70119.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="nikA protein"
     gene            277..471
                     /locus_tag="NFJ44_22700"
     CDS             277..471
                     /locus_tag="NFJ44_22700"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041624.1"
                     /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="WFV70120.1"
                     /translation="MNKQQQTVLNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELA
                     EELQNSIQTRFEVENSTEI"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(521..754)
                     /locus_tag="NFJ44_22705"
     CDS             complement(521..754)
                     /locus_tag="NFJ44_22705"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015675076.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WFV70121.1"
                     /translation="MSVDFCDARQGGGAYGKTPAVLASSGALLFAHMFFPALSPDSVDN
                     RITAFECADTARRSRTTERSESVSEEAEERLM"
                     /name="hypothetical protein"
     gene            958..1071
                     /locus_tag="NFJ44_22710"
     CDS             958..1071
                     /locus_tag="NFJ44_22710"
                     /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="WFV70122.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLSPLAAATGN"
                     /name="replication initiation protein"
     gene            1905..2609
                     /locus_tag="NFJ44_22715"
     CDS             1905..2609
                     /locus_tag="NFJ44_22715"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000805974.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="winged helix-turn-helix domain-containing
                     protein"
                     /protein_id="WFV70118.1"
                     /translation="MKPWVKFPSKFVLDGRLKELLWTDDKVGKPSHKVAALKLYIALSM
                     RAESKEAFCHYIDTYITYYSAQATYEELSELTALSRSSISSGIDILERLGLLSVDKVRR
                     KNIYRFPGFDGSKDWCKMPCRALLSRDGKRIEAFHKLKLRSKIELYALKMFIYLCAVRD
                     NHSHYTSASFERINLQTSIPEADIPRTHAYLSGIGLIALVEKRKDGFGGMKKNPPNSYF
                     VTGHNDFFIGKR"
                     /name="winged helix-turn-helix domain-containing protein"
     Typing          complement(15..240)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="89.167"
                     /coverage="99.0"
                     /evalue="4.9e-75"
     Typing          501..1030
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.6"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          complement(2862..3175)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.048"
                     /coverage="98.0"
                     /evalue="8.55e-61"
ORIGIN
        1 gtcataaaac atggctccgt atctgacatg gggtgtcggg gcgaagccct gaccagggta
       61 attgtaatag cgtgcatgta tgcgcggtat aacaattgca catcctgtcc tgtctgcaag
      121 ttcgaattac caacaaagca ctgctgtttt ttggcagtga cagtgttgtc tgactgaaat
      181 gtccgtcggc agaataccgg cggtaagacg gtccaaaagt ggtgcgcgat ataatcacac
      241 gacgcagatg acagacagaa cggagaaaac agaaagatga acaagcagca gcaaactgta
      301 ctcaacatgg cgggattcat aaaaagccag agcctgacgc tgctcgaaaa actggacgca
      361 ctcgatgctg acgagcaggc caccatgtgt gagaagctgc acgaactcgc agaagaactc
      421 cagaacagca tacagacacg ctttgaagta gaaaatagca cagagatata acgctcaggg
      481 caggatgccg aacggcacaa cagagcgtaa ggagaaaatg tcacataagg cgctcttccg
      541 cttcctcgct cactgactcg ctacgctcgg tcgttcgact gcggcgagcg gtgtcagcgc
      601 actcaaaggc ggtaatacgg ttatccacag aatcagggga taaagccgga aagaacatgt
      661 gagcaaaaag caaagcaccg gaagaagcca gcaccgcagg cgtttttcca taggctccgc
      721 ccccctgacg agcatcacaa aaatcgacgc tcaagtcaga ggtggcgaaa cccgacagga
      781 ctataaagat accaggcgtt tccccctgga agctccctcg tgcgctctcc tgttccgacc
      841 ctgccgttta ccggatacct gtccgccttt ctcccttcgg gaagcgtggc gctttctcat
      901 agctcacgct gtaggtatct cggcccggtg taggtcgttc gctccaagct gggctgtgtg
      961 cacgaacccc ccgttcagcc cgaccgctgc gccttatccg gtaactatcg tcttgagtcc
     1021 aacccggtaa gacacgactt atcgccactg gcagcagcca ctggtaactg atttagagga
     1081 gtttgtcttg aagttatgcg cctgttaagg ctaaactgaa agaacagatt ttggtgactg
     1141 cgctcctcca agccagttac cttggttcaa agagcgccaa ctctaagaac cttcgaaaaa
     1201 ccgcctgcca aggcggtttt ttcgtttcca atggaagata cgctgtcaat gatgcataag
     1261 tcaactaact aacaatcttc ataaacatag caatatgcgc acaactatcg tccatataag
     1321 gcaattacaa tgacgactgt tatgtacgca gacacggctt ttggatatgt actaattagg
     1381 cgaattgaat tgaaatgaac aacaatgaca gacaggcaat caccagactg tctgtcgtta
     1441 ctaagctgtc gccagttaaa aatcggatcc gctaaagccg cgccatctaa gtcagcatct
     1501 caataatcaa tttccttcat acgctataaa aacacccaga cagagcatct tttatgctcc
     1561 acaccctcag cgccataaca tcttctacaa tccctttcat gaactattga ttactttaaa
     1621 aagacgattc aattttgctt caagcaaatg attttaaaag aaaaaattgg aataatttta
     1681 ttttaaagac taacctatat ctagatagat attgccaaga cgtgcttaaa ttttcctatc
     1741 aaaaagactg aaaccatagg aaattatatg gaagccgata aatatataat gataatcaaa
     1801 tacttatcag acaactctca caaactaacc ccgcttgtct tggcggtttc ggttcttgtc
     1861 gcctttctat caatcctgtt tattgcaatg cgcatggggt aacaatgaag ccttgggtaa
     1921 aatttccttc aaagttcgta ctagatggac gcttaaaaga gcttttatgg actgatgaca
     1981 aggtaggaaa accgtcacat aaggtcgcag ccttaaaact gtatatagcg ctgtccatga
     2041 gagctgaaag taaagaggct ttctgtcatt acatagatac ctacataaca tattattcag
     2101 ctcaggcgac ctatgaggaa ctctcggaac tgacagccct gagcagatca tcaatatcat
     2161 caggcattga tattttagag agacttgggc tgttatcagt agataaagtt aggcgaaaaa
     2221 atatctaccg attccctggg tttgatggtt cgaaggactg gtgcaaaatg ccttgtagag
     2281 cgttgttatc tcgtgatggc aaacggattg aagcattcca taaacttaag ttaagaagca
     2341 agattgagct ttatgcgcta aagatgttca tctacttatg tgctgttcga gacaatcaca
     2401 gtcattatac aagcgcttca tttgaaagaa taaacttgca gacttctatt ccagaagcgg
     2461 acatacctag gacgcatgcc tacctgagcg ggataggact catagcttta gtagagaaac
     2521 gaaaagatgg gtttggcggc atgaagaaaa accctccaaa ttcctacttt gttactggtc
     2581 ataatgactt ttttatagga aagcgataat caataaaaac atcaaataac atgatcgcta
     2641 tttaccataa cgtcgcatta cgcgcaccgc taaaacgcgc tgaacgcgat tctgccgcaa
     2701 acaccgcaaa aagagatgtt ttccccgggg taaaccggaa aaatgcgtca ggatcgcttt
     2761 cagctcactg catagctatg catgaaagtg aatggcgatc ggtttggggg cttacggcgt
     2821 tcataccgtc tgttttcgac agtttctctc cgggaagcta atctgccata agcctggata
     2881 acagggcccg gtgatactcc gtaatagcga tcagcacctc cgcatactct ctgtccccga
     2941 cacgcttgcc gtcgataaag agttttttct gtaacgcccc cagtctcata acttctttca
     3001 gtacccgatc atcagtcagt gagttaactt tcttaccgag agctgccgcc cgtaaaaaac
     3061 cggaaacggt cttgccgcat tcagcagccc tttttctgat ttcctggtct tcttctgccg
     3121 tcagacgaac agggcgactg atagcccgcc tgcgcgtatt acttccactt cgtttt
//
