LOCUS       CP099112                5264 bp    DNA     circular BCT 13-APR-2023
DEFINITION  Escherichia coli strain RHB40-SO-C05 plasmid unnamed4, complete
            sequence.
ACCESSION   CP099112
VERSION     CP099112.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15488629
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5264)
  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  JOURNAL   Unpublished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 5264)
  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                     :: RHB40-SO-C05
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 150x
            Sequencing Technology             :: Illumina/Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/15/2022 18:33:40
            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)                     :: 5,174
            CDSs (total)                      :: 5,056
            Genes (coding)                    :: 4,893
            CDSs (with protein)               :: 4,893
            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)              :: 163
            CDSs (without protein)            :: 163
            Pseudo Genes (ambiguous residues) :: 0 of 163
            Pseudo Genes (frameshifted)       :: 71 of 163
            Pseudo Genes (incomplete)         :: 101 of 163
            Pseudo Genes (internal stop)      :: 40 of 163
            Pseudo Genes (multiple problems)  :: 44 of 163
            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..5264
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB40-SO-C05"
                     /isolation_source="Pooled soil sample collected from floor
                     of cattle farm"
                     /db_xref="taxon:562"
                     /plasmid="unnamed4"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            join(5003..5264,1..158)
                     /locus_tag="NFK65_25815"
     CDS             join(5003..5264,1..158)
                     /locus_tag="NFK65_25815"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016247941.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Exc2 family lipoprotein"
                     /protein_id="WFZ41898.1"
                     /translation="MRRTGNKLCLIAMITATVALTACTPKGSVEQHTRHYVYASDDGFD
                     PNFSTQKADTTRMMVPFFRQFWDMGAKDKATGKSRSDVQQRIQQFHSQEFLNSLRGTTQ
                     FAGTDYRSKDLTPKKSRLLADTISAVYLDGYEGRQ"
                     /name="Exc2 family lipoprotein"
     gene            928..1122
                     /locus_tag="NFK65_25820"
     CDS             928..1122
                     /locus_tag="NFK65_25820"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /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="WFZ41899.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EEIQNSIQVRFETESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2433..2660
                     /locus_tag="NFK65_25825"
     CDS             2433..2660
                     /locus_tag="NFK65_25825"
                     /inference="COORDINATES: protein motif:HMM:NF015489.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin E1 immunity protein"
                     /protein_id="WFZ41900.1"
                     /translation="MLYAIVISTILCPYSKYAIEYIAFNFIKKVFFERRKNLNNAPVAK
                     LNLFMLYNLLCLVLAIPFGLLGLFISIKNN"
                     /name="colicin E1 immunity protein"
     gene            complement(2657..4225)
                     /gene="cea"
                     /locus_tag="NFK65_25830"
     CDS             complement(2657..4225)
                     /gene="cea"
                     /locus_tag="NFK65_25830"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000447006.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="pore-forming bacteriocin colicin E1"
                     /protein_id="WFZ41896.1"
                     /translation="METAVAYYKDGVPYDDKGQVIITLLNGTPDGSGSGGGGGKGGSKS
                     ESSAAIHATAKWSTAQLKKTQAEQAARAKAAAEAQAKAKANRDALTQRLKDIVNEALRH
                     NASRTPSATELAHANNAAMQAEAERLRLAKAEEKARKEAEAAEKAFQEAEQRRKEIERE
                     KAETERQLKLAEAEEKRLAALSEEAKAVEIAQKKLSAAQSEVVKMDGEIKTLNSRLSSS
                     IHARDAEMKTLAGKRNELAQASAKYKELDELVKKLSPRANDPLQNRPFFEATRRRVGAG
                     KIREEKQKQVTASETRINRINADITQIQKAISQVSNNRNAGIARVHEAEENLKKAQNNL
                     LNSQIKDAVDATVSFYQTLTEKYGEKYSKMAQELADKSKGKKIGNVNEALAAFEKYKDV
                     LNKKFSKADRDAIFNALASVKYDDWAKHLDQFAKYLKITGHVSFGYDVVSDILKIKDTG
                     DWKPLFLTLEKKAADAGVSYVVALLFSLLAGTTLGIWGIAIVTGILCSYIDKNKLNTIN
                     EVLGI"
                     /name="cea"
     gene            4485..4922
                     /locus_tag="NFK65_25835"
     CDS             4485..4922
                     /locus_tag="NFK65_25835"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001405929.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="entry exclusion protein 1"
                     /protein_id="WFZ41897.1"
                     /translation="MGHCHFMAWHTLRDALKMTGRSRSQFYRDMRAGLVSYRTGRDGRR
                     EFETSELIRAYGELKQNETPERHSEGHAENPHDQQTERILRELNELKQCLTLMLEDKQA
                     QDMDRRRQEAEREQLQNEIAQLRQALELEKKRGFWSRLFGR"
                     /name="entry exclusion protein 1"
     Typing          complement(414..669)
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.899"
                     /coverage="89.0"
                     /evalue="2.61e-118"
     Typing          complement(794..892)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          complement(1196..1280)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="94.186"
                     /coverage="100.0"
                     /evalue="6.62e-29"
     Typing          1291..1849
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.365"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 agcagtttca cagccaggaa tttttaaact cactccgggg cacaactcaa tttgcgggta
       61 ctgattaccg cagcaaagac cttaccccga aaaaatccag gctgctggct gacacgattt
      121 ctgcggttta tctcgatggc tacgagggca gacagtaagt ggatttacca taatccctta
      181 attgtacgca ccgctaaaac gcgctgaacg cgattctgcc gcaaacaccg caaaaagaga
      241 tgttttcccc ggggtaaacc ggaaaaatgc gtcaggatcg ctttcagctc actgcatagc
      301 tatgcatgaa agtgaatgac gatcggtttg ggcgcataca gtgcccatga gacacatttt
      361 cggacatttt cagttcgtga atccctgact cattgctata tatctgaata gacaccccta
      421 gcagcgcccc caggggcatc ctgtaaaaaa acacaccgcg ccgctagcag cacccctaat
      481 ataagatgat gttttttatg aaaatagtca gtaccacccc taaaaagcgg tgttggcgca
      541 gctacaacac cgcgccgaca ccgctttttt aaatatcaca aagagagcaa gaagaactaa
      601 tttgtcataa ctctctattt ataaagaaaa atcagcaaaa acttgttttt gcgtggggtg
      661 tgggcatttc aggcatgaga acagactcgc gtttttccgg agtatcagcg gaattattga
      721 ttaagaaaca ctcgacgcag agcgaaattt tatgcaacag cggctgcact gcacagggat
      781 tatttatcag ttgatatgct gtgccatgat acgtcctaaa gaaacaggac aggatgtgta
      841 attgtaatac cgtcgcccgc aacgtcttac aattaccacc tggtcagggt ccacccgaca
      901 cccggtactg acggagaaca acggaaggtg aacaaacagc aacaaactgc gctgaatatg
      961 gcgcgattta tcaaaagcca gagcctgaca ctacttgaaa aactggatgc tctggatgcc
     1021 gacgaacagg cggccatgtg cgaacgactg cacgaactcg cggaagagat ccagaacagc
     1081 atccaggttc gctttgagac cgaaagtgaa acagggacat aacgaggctg acggaggcgc
     1141 tcacggcttg tccgcgagcg ttttcggcag cagacaagcc cgccagggcg cgtcaggggg
     1201 tttcggggca aagccctgaa ccagtcacag agcgatagcg atgtgtatac tggcttaact
     1261 atgcggcatc agtgcagatt gtatgaaaag tgccccatgc cgggtgtgaa atgccgcaca
     1321 gatgcgtaag gagaaaatgc gcgtccaggc gcttttccgc ttcctcgctc actgactcgc
     1381 tacgctcggt cgttcgactg cggcgagcgg tactgactca cacaaaaacg gtaacacagt
     1441 tatccacaga atcaggggat aaggccggaa agaacatgtg agcaaaagac caggaacagg
     1501 aagaaggcca cgtagcaggc gtttttccat aggctccgcc cccctgacga gcatcacaaa
     1561 aatagacgct caagtcagag gtggcgaaac ccgacaggac tataaagata ccaggcgttt
     1621 ccccctggaa gctccctcgt gcgctctcct gttccgaccc tgccgcttac cggatacctg
     1681 tccgcctttc tcccttcggg aagcgtggcg ctttctcata gctcacgctg ttggtatctc
     1741 agttcggtgt aggtcgttcg ctccaagctg ggctgtgtgc acgaaccccc cgttcagccc
     1801 gaccgctgcg ccttatccgg taactatcgt cttgagtcca acccggtaag gcacgcctta
     1861 acgccactgg cagcagccac tggtaaccgg attagcagag cgatgatggc acaaacggtg
     1921 ctacagagtt cttgaagtag tggcccgact acggctacac tagaaggaca gtatttggta
     1981 tctgcgctct gctgaagcca gttaccttcg gaaaaagagt tggtagctct tgatccggca
     2041 aacaaaccac cgttggtagc ggtggttttt ttgtttgcaa gcagcagatt acgcgcagaa
     2101 aaaaaggatc tcaagaagat cctttgatct tttctactga accgcgatcc ccgtcagttt
     2161 agaagaggag gatggtgcga tggtccctcc ctgaacatca cgtatatagt tagcctgaca
     2221 tccaacaagg aggtttatcg cgaatattcc cacaaaaaat cttttcctca taactcgatc
     2281 cttataaaat gaaaagaata tatggcgagg tttaatttat gagcttaaga tactacataa
     2341 aaaatatttt atttggcctg tactgcacac ttatatatat ataccttata acaaaaaaca
     2401 gcgaagggta ttatttcctt gtgtcagata agatgctata tgcaatagtg ataagcacta
     2461 ttctatgtcc atattcaaaa tatgctattg aatacatagc ttttaacttc ataaagaaag
     2521 tttttttcga aagaagaaaa aacctaaata acgcccccgt agcaaaatta aacctattta
     2581 tgctatataa tctactttgt ttggtcctag caatcccatt tggattgcta ggacttttta
     2641 tatcaataaa gaataattaa atccctaaca cctcatttat agtattaagt ttattcttat
     2701 caatatagga gcatagaatt cctgtaacaa tagcaatacc ccaaatacct aatgtagttc
     2761 cagcaagcaa gctaaaaagt aaagcaacaa cataactcac ccctgcatct gcagctttct
     2821 tctctaatgt aagaaatagt ggcttccagt cacctgtatc cttaattttt aggatatcag
     2881 ataccacatc atatccaaaa gaaacatgcc ccgtaatctt caagtacttg gcaaactgat
     2941 ctaaatgttt agcccagtca tcatacttca ccgatgccaa cgcattaaaa atagcatcac
     3001 gatcggcttt gctgaatttc ttatttaaaa catccttgta tttttcaaaa gcagcgagag
     3061 cttcattcac attgccgatt ttcttacctt tagacttatc agcaagttcc tgtgccattt
     3121 tcgaatattt ttcaccatat ttttcagtca gcgtttgata aaagctaact gttgcatcaa
     3181 cagcatcctt aatctgtgaa ttaaggagat tattctgtgc ttttttcaaa ttttcttcag
     3241 cttcatgaac acgagcgata ccggcattac gattattact gacctgagaa atagccttct
     3301 ggatctgagt tatatcagca tttatccggt taatacgtgt ttctgatgct gttacctgtt
     3361 tttgtttttc ttctctaatc ttaccggccc caacccgtcg tctggttgct tcaaaaaaag
     3421 gacggttctg aagcggatca ttggctcttg gtgatagttt tttgaccagc tcatccagtt
     3481 ctttatattt agcggatgcc tgagccagtt catttcgttt tccagcgagc gttttcattt
     3541 ctgcatcacg ggcatggata ctggagctta aacgagaatt gagagtctta atctctccat
     3601 ccattttcac cacttcagat tgtgcagcag aaagtttttt ttgggcgatc tcaacagctt
     3661 tagcttcttc actcaatgca gccagtcgtt tctcttcagc ttcagccagt ttcaactggc
     3721 gttctgtttc agccttctcc cgttcaatct ctttacgtcg ttgttctgct tcctgaaaag
     3781 ccttttctgc tgcttccgct tctttacggg ctttttcttc tgctttcgca aggcgcaaac
     3841 gctctgcttc cgcctgcata gctgcattat tagcatgagc aagctctgtt gctgaaggcg
     3901 tacgtgaggc attgtgacga agagcctcat tcacgatatc cttcaggcgc tgagtcagcg
     3961 catccctgtt tgcctttgct ttcgcctgtg cttccgctgc agcttttgcc cgggcagcct
     4021 gctctgcctg tgttttcttt aattgagcag tagaccattt agcagttgca tgaatagctg
     4081 cagaactttc acttttactg cctccttttc cacctccgcc gccagagcca ctcccgtcag
     4141 gagtaccatt caaaagagta ataattacct gtcccttatc atcataagga acaccatctt
     4201 tatagtacgc taccgcggtt tccattataa aatcctcttt gacttttaaa acaataagtt
     4261 aaaaataaat actgtacata taaccactgg ttttatatac agcataaaag ctacgccgct
     4321 gcattttccc tgtcaagact gtggacttcc atttttgtga aaacgatcaa aaaaacagtc
     4381 tttcacacca cgcgctattc tcgcccgatg ccacaaaaac cagcacaaac attaccgttc
     4441 tcagacctca ttatgtttta ctgaaactat gagatgagac atctatggga cactgtcact
     4501 ttatggcatg gcacacactc cgggacgcac taaaaatgac aggcagatcg cgttcacagt
     4561 tttaccgtga tatgcgcgca ggccttgtca gttaccgtac cggcagggac ggacgacggg
     4621 agtttgaaac cagtgaactg atccgggcat acggcgaatt aaagcagaat gagacaccag
     4681 aaaggcacag tgagggacat gcagaaaatc cacatgatca gcagacagaa cgcattctcc
     4741 gggagctgaa tgagctgaaa caatgcctga cgctgatgct tgaggataaa caggcacagg
     4801 atatggatcg cagacgccag gaagcagaac gggaacagct acaaaatgag atagcccagc
     4861 tcaggcaggc actggaactg gaaaagaaac ggggattctg gtccaggttg ttcggtcgct
     4921 gaacgctgtc agagactgat gataaaatag tcttcggata ataactcacc gagaataaat
     4981 actttaaggt agggagacac tcatgagacg taccggaaac aaactttgtc ttatcgccat
     5041 gataacagca acagtagctc tcacagcctg taccccaaag ggcagcgtgg aacaacatac
     5101 ccggcattac gtatatgctt ctgatgacgg ttttgatccc aacttttcca cccaaaaagc
     5161 cgacacaaca cgaatgatgg tgcctttttt tcggcagttc tgggatatgg gagctaaaga
     5221 taaagcgaca ggaaaatcac ggagtgatgt gcaacaacgc attc
//
