LOCUS       CP099302                4066 bp    DNA     circular BCT 13-APR-2023
DEFINITION  Escherichia coli strain RHB02-E1-C06 plasmid unnamed3, complete
            sequence.
ACCESSION   CP099302
VERSION     CP099302.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15488483
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4066)
  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  JOURNAL   Unpublished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 4066)
  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                     :: RHB02-E1-C06
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 96x
            Sequencing Technology             :: Illumina/Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/15/2022 20:15:33
            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)                     :: 4,798
            CDSs (total)                      :: 4,677
            Genes (coding)                    :: 4,490
            CDSs (with protein)               :: 4,490
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 187
            CDSs (without protein)            :: 187
            Pseudo Genes (ambiguous residues) :: 0 of 187
            Pseudo Genes (frameshifted)       :: 60 of 187
            Pseudo Genes (incomplete)         :: 111 of 187
            Pseudo Genes (internal stop)      :: 44 of 187
            Pseudo Genes (multiple problems)  :: 25 of 187
            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..4066
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB02-E1-C06"
                     /isolation_source="Pooled sediment sample collected from
                     floor of pig farm"
                     /db_xref="taxon:562"
                     /plasmid="unnamed3"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(join(3452..4066,1..495))
                     /gene="wzz(fepE)"
                     /locus_tag="NFJ19_23975"
     CDS             complement(join(3452..4066,1..495))
                     /gene="wzz(fepE)"
                     /locus_tag="NFJ19_23975"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+. GO_component:
                     GO:0016020 - membrane [Evidence IEA]; GO_process:
                     GO:0009103 - lipopolysaccharide biosynthetic process
                     [Evidence IEA]"
                     /codon_start=1
                     /transl_table=11
                     /product="LPS O-antigen length regulator Wzz(fepE)"
                     /protein_id="WFV06446.1"
                     /translation="MKISKISDEHFSNYNMLPNGNEEIDLFDLIRVLWAAKIKIVGVIL
                     FFACIGFLVSFVLPQKWTSSAVVTPAESVQWSELNKELSKLHVLGVDFDINRDSAFALF
                     IKKFQSVNSLNEYMRSSPYVMEIIKKKNISALELHRAIVGLSENMKSVDDNASKKNDKS
                     SLYVSWTLSFTAPTSKEAHDVLSGYINYVSSLVVRDLMEDIRNKLEVKTNVEKEILALD
                     EIKIRNQLNADIRRLNYSLEVANAAGIKKPVYSNGQIMKDDPDFPVALGSDGIATKLNI
                     KKSIKDVSELSGELRNRQYVVNQLGVAKVGDVDFMPFQYQLSPTLPVRKDGPSNAIIVI
                     LSSVIGGMLACGYILLRHAMEARKMSVIE"
                     /name="wzz(fepE)"
     gene            complement(1313..1706)
                     /locus_tag="NFJ19_23980"
                     /pseudo=""
     CDS             complement(1313..1706)
                     /locus_tag="NFJ19_23980"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009310048.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(1706..1897)
                     /locus_tag="NFJ19_23985"
     CDS             complement(1706..1897)
                     /locus_tag="NFJ19_23985"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000166328.1"
                     /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="WFV06447.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDVEADLCEKLHDDA
                     EHLFRTLSSRLDALQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(2366..2515)
                     /locus_tag="NFJ19_23990"
     CDS             complement(2366..2515)
                     /locus_tag="NFJ19_23990"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WFV06445.1"
                     /translation="MPSEYDEQPDATDALFPGEYDLFDLMAHVTEENLHAPVDSGPPVG
                     REAL"
                     /name="hypothetical protein"
     Typing          complement(2509..2723)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="84.091"
                     /coverage="100.0"
                     /evalue="3.48e-51"
     Typing          2704..3232
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.545"
                     /coverage="89.0"
                     /evalue="1.2e-144"
ORIGIN
        1 caatgatgac ttgtcgtttt tcttactggc attatcatca accgacttca tattttcact
       61 caacccaaca attgcacgat gcagttcgag agcgctaatg ttcttctttt taattatctc
      121 cataacataa ggagatgatc tcatatactc attcaacgaa ttaacggact gaaatttctt
      181 aataaacaga gcaaatgcgc tatcacgatt gatatcaaaa tccactccca gaacatgaag
      241 cttggaaagc tccttattta attcactcca ttgaacagac tcagcaggag taaccacagc
      301 agagctagtc catttttgtg gcaaaacaaa agaaacaaga aagccaatac aagcaaaaaa
      361 tagaatcacc ccaacaattt ttatttttgc tgcccataaa actctaatca agtcaaaaag
      421 gtcaatttct tcattaccat tcggcaacat gttgtaatta gaaaaatgtt cgtcagatat
      481 ctttgagatt ttcattgaaa aaatacaata tattaacata tggttttttt attctatcat
      541 atgttaggaa aaatcctaaa aaccattcag cagacattta acataacatt ttattgtacg
      601 caccactaaa acggcctcag ggcgtttctg acgggaaacc ggtaaaacag gcaacaaacc
      661 acccgaaaac ccgccagaaa cgcgcaggct ctgtttttac ggcatgcatg agtatgcacg
      721 caagtgcata gcgcgaaaat tcacgccatt cagccagggt aagtcctgtt tccggcgttc
      781 ttcctatccg aaaacggtga acggggacgc aatttattgc gtggccgtga agcgttgccg
      841 gcgcagccgg aaaaccggtt ttcagcacga tcaggaatcg ggttcatcga cggccggcaa
      901 tcacgttatg gcaagtcgcc ggacgactca ccagacaatt caccggcgat tcgactcgtg
      961 acttgactct agagtcgtaa aggtcaaaaa aacaccaaaa tgacgattca actctagagt
     1021 caagtcatca taagttactg atagtcttaa gtgagtcgtc gatgactcta tgacgagtcg
     1081 tcagcaagtc gtacacgaat cgccgacgac tttgattcac cttacagaaa gtaatactgc
     1141 gtaatttaat aacccacaac taactgatat taatgagtta tcttcaaaat tttaattttg
     1201 cgtagggtgt gggtattttt agtggtgagg agcgttcaga gatctgacga tttttgggaa
     1261 ggttcaggaa ctccccggga tggccggaga ggaaaactga agcatgacgg ggtcaggatt
     1321 ttttccagaa tttccaccat ggcgccgggg attcagttaa ttttgcctgg tgattttcaa
     1381 gaaggagcat agcctgtttc aggctgtcaa tgtgcgaatc cttggacaaa agtaaggtgt
     1441 tcaatctcct gtttcagatg acgagtcacc tgttcactct ggtcagcaga ggctgtatca
     1501 cgctgttcag agacctgtcc agaatggtgt tcacccttcg gttgttcaaa gggaccaaag
     1561 acacgtaaaa gctctgaagt atctaccatt tttgcattgc gttcaccgct acaggtggac
     1621 aggtcacctg ctttaattaa cctgtgcagt gttgttctac tcttacccgt cagtcgggca
     1681 gcctcactaa tagatactct ggccatcagt taccatcctg taatgcatcc agtctcgagg
     1741 acagtgtacg gaaaagatgc tccgcatcat cgtggagttt ctcacaaagg tccgcctcaa
     1801 catcgagatc aagctcgtta agcttctcca gcaggagcag agactgattc tggatgaatt
     1861 tagccatgtt cagcgctgtt ttctgttgtt tcgtcataag ggccctcaga gcatcagtgc
     1921 tcagtataaa ccggtaaggg ggtcggatgt acgaatggtt cagagaacgg atctgaggtt
     1981 atcctgtagt tattttgtag tttatctgta gtcatcgcac taaaacgcag gattaaatca
     2041 tcaacttttg tagtcttcct gtagtctgga aaaataatcc gttcatgcaa gcatgaacga
     2101 agcagttaaa gacgcttttt cgtcgccgat gatccttaac ctgcgcagat cacccagcca
     2161 gaatgataat tttttgcccc ttaaatggtc atacacctaa cgcagccgcg atttttatcg
     2221 caactgcatg aattaaatga aaaaaatgga gttatttcgt gtattagcgt aatacgcaac
     2281 gtattacaat catctgtaac aacatgaaaa taaacaaata acatgtaata ccagcgtatt
     2341 acatgtacgc tggccagcga aaaagctata acgcttcccg gccgacaggc gggccagaat
     2401 ccaccggggc gtgcaggttc tcttcagtaa catgagccat taagtcaaaa aggtcatatt
     2461 cgccgggaaa cagagcatca gtcgcatccg gttgttcatc atactcagat ggcatggtgt
     2521 gatatccagt agctgagggg tgttagcggg tttcggggcg cagccctgaa ccagtcacgt
     2581 agcgctagcg gagtgcatac tggctaaata ttttaaaccg aagtggtgat ttgccaaagt
     2641 gcttcatgtg gcaggagtga aatgaggctt accggcgtca ggagaagatg ctggttcagg
     2701 tgatattccg cttcctcgct cactgactcg ctgcgctcgg tcgttcggct gcggcgagcg
     2761 gtgcaggctt acgaatgggg cggaaattta tttcctggtg gatgccagga agaaacttaa
     2821 cagggatacg ataaggccgc ggcaaagccg tttttccata ggctccgccc ccctgacaag
     2881 catcacgaaa tctgacgctc aaatcagtgg tggcgaaacc cgacaggact ataaagatac
     2941 caggcgtttc cccctggtgg ctccctcttg cgctctcctg ttcccgtcct gcggcatccg
     3001 tgtagtggtg gaagctttac ctaaatcacc acgccccgtt ccgtttagac agttcgctcc
     3061 aagctgggct gtatgcaaga accccccgtt cagcccgacc gctgcgcctt atccggtaac
     3121 tatcgtcttg agtccaaccc ggtaagacac gacttaacgc cattggcagc ggccactggt
     3181 aaacaggatg tgcgagagat gtattgagag ttcttgaagt ggcagcctta ctgaggctac
     3241 actagaagga cagatttggt gacatgtctc gcacaagact gttaccacgg ttcagaagtt
     3301 ccccaactta ctgaaccttc gaaaaaccac ctccccaggt ggttttttcg ttttctagag
     3361 tagaagacta cggctgtaag agaatgatct caagaagatc ctttgaactt tttataaaag
     3421 ttgcttataa aatgatgcat cagcacaact tttactcaat cacactcatc tttctggcct
     3481 ccatggcatg acgtaaaagt atatagccac atgcaagcat ccctccaatg acagaagaaa
     3541 gaattacaat tatggcatta cttggcccat cctttctgac cggtaacgtt gggctcaatt
     3601 gatactgaaa cggcataaaa tcaacatccc ccactttcgc cacacccaat tgattcacaa
     3661 catattgacg atttcgcaac tccccactca attccgaaac atccttgatt gattttttga
     3721 tgttcaattt agttgctata ccatcagaac cgagagccac aggaaaatct ggatcatcct
     3781 tcataatctg accattgctg tatacaggtt tttttattcc agccgcatta gcaacctcca
     3841 gtgaataatt gaggcgtcga atatctgcat tcagctggtt tctaattttt atctcatcca
     3901 gtgcaagaat ttctttttca acattagttt taacttctag tttatttctt atatcttcca
     3961 tcaaatccct tacaacaagg gaagaaacat aattaatata cccagacaac acatcgtgag
     4021 cttctttact tgttggagca gtaaaactca gagtccatga tacata
//
