LOCUS       CP099156                4664 bp    DNA     circular BCT 13-APR-2023
DEFINITION  Escherichia coli strain RHB28-E3-C06 plasmid unnamed4, complete
            sequence.
ACCESSION   CP099156
VERSION     CP099156.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15488599
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4664)
  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  JOURNAL   Unpublished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 4664)
  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                     :: RHB28-E3-C06
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 112x
            Sequencing Technology             :: Illumina/Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/15/2022 18:26:04
            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)                     :: 4,813
            CDSs (total)                      :: 4,694
            Genes (coding)                    :: 4,500
            CDSs (with protein)               :: 4,500
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 194
            CDSs (without protein)            :: 194
            Pseudo Genes (ambiguous residues) :: 0 of 194
            Pseudo Genes (frameshifted)       :: 74 of 194
            Pseudo Genes (incomplete)         :: 120 of 194
            Pseudo Genes (internal stop)      :: 41 of 194
            Pseudo Genes (multiple problems)  :: 33 of 194
            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..4664
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB28-E3-C06"
                     /isolation_source="Pooled sediment sample collected from
                     floor of pig farm"
                     /db_xref="taxon:562"
                     /plasmid="unnamed4"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(join(3924..4664,1..816))
                     /locus_tag="NFK35_24010"
     CDS             complement(join(3924..4664,1..816))
                     /locus_tag="NFK35_24010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_013199864.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="sensor domain-containing diguanylate cyclase"
                     /protein_id="WFY51588.1"
                     /translation="MRIKKPHLRPIVITLSVGGILLTSIFLIAVIMVFQRENIEKDLLY
                     ANSSYAMKMSDVMSGYIEMAQGELAYGAKKIKSTNDIDSLKDEADRLRLQSGMFNSVLV
                     VSNDAVVLATSPESLDLVGTRLNSSASKLAVEEKKPFISSPLKSVAGNLIILLSHPIYD
                     KGGNYIGYVGGSIYLKKHSLFGDVLSRHFFKNNTEISIVSDDGNVIFNNDKSAVDRPMV
                     MSDDLKSKLTASDRGEGAFFSSGHRYLLGYASMKNTAWNVLVYSRADSVTTILIAYAKS
                     VLVLLIIIIIVFSLISYFIASSISLPLEKLAISTNAKDIGASLVYIKAINAWYAEADRL
                     KKALFTYIKVMMERVDSLNEVALKDPLTGVNNRLGFLSKIQNHKLDSGCSVIVIDVDFF
                     KEINDSFGHGVGDEVLVSLAHIINSCCRSEDVVCRFGGEEFVVFLPNTSVVTAKCVAER
                     IRSVIESTVFPNNLRVTISAGVATQDDPLGRIDFLLKNADDALYQAKREGRNKVIVYSA
                     I"
                     /name="sensor domain-containing diguanylate cyclase"
     gene            complement(1162..1377)
                     /locus_tag="NFK35_24015"
     CDS             complement(1162..1377)
                     /locus_tag="NFK35_24015"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137422.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WFY51589.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWESAFAEWRTMSGLMQRENA
                     ALSERVTGLSRQVQSLSEQLRRLSSD"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(1381..1866)
                     /locus_tag="NFK35_24020"
     CDS             complement(1381..1866)
                     /locus_tag="NFK35_24020"
                     /inference="COORDINATES: protein motif:HMM:NF016710.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WFY51590.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQNTGEMLKAAFSEHEKSVKAELNESA
                     KRISAAILDHDRKLSSAMSQRTKGMVRMVSQTWLTIVLVSALLIASSAGILWWQGQQIL
                     DNYTTIREQKSTQAMLSERNSGVQLSTCGEQRRRCVKVNPEAGRFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            complement(1901..2335)
                     /locus_tag="NFK35_24025"
                     /pseudo=""
     CDS             complement(1901..2335)
                     /locus_tag="NFK35_24025"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /note="incomplete; partial on complete genome; missing
                     C-terminus; Derived by automated computational analysis
                     using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(2544..2867)
                     /locus_tag="NFK35_24030"
     CDS             complement(2544..2867)
                     /locus_tag="NFK35_24030"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WFY51591.1"
                     /translation="MLTMWVTEGEHRRLLERCDGRQLAAWMRQTCLDEKPARSGKLPSI
                     SPALLRQLAGMGNNLNQIARRVNAGGGTGHDRVQIVAALMAIDAGLERLRHAVLEKGTD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     Typing          complement(2981..3153)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.276"
                     /coverage="100.0"
                     /evalue="9.21e-81"
     Typing          3078..3629
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.639"
                     /coverage="91.0"
                     /evalue="0.0"
     Typing          complement(1059..2554)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.182"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(2551..2867)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.453"
                     /coverage="99.0"
                     /evalue="1.9499999999999998e-60"
ORIGIN
        1 agtcacactg tcagcacgac tataaaccaa cacattccaa gcggtatttt tcatactagc
       61 ataaccaaga agatatctat gccccgaaga aaaaaatgcc ccctcacctc tatcagacgc
      121 agttaacttt gatttcaaat catcagacat aaccataggc cgatcaacag cacttttatc
      181 gttattaaag atcacattcc catcatcact aacaatgcta atttcagtgt tgttcttgaa
      241 aaaatgcctg ctcaaaacat cgccaaataa actatgtttt tttagatata tagacccacc
      301 gacataccct atgtaattgc cacccttatc ataaatagga tgtgacaaca aaatgatcaa
      361 attcccagca actgatttta acggtgaaga tatgaatggt ttcttttcct caaccgccaa
      421 tttgctggca cttgaattca agcgggtacc aactaaatca agagattctg gcgaagtcgc
      481 cagaacaaca gcatcattac taacaacaag aactgaatta aacataccag actgcaatct
      541 taacctatcc gcctcatctt taagtgagtc aatatcatta gttgatttta ttttttttgc
      601 tccatatgct aattcacctt gagccatttc aatataacca ctcattacat ctgacatttt
      661 catagcgtac gatgaattag cataaagcaa atctttttct atattttcgc gctgaaaaac
      721 cataataacg gcaatcagaa aaatagaagt taacaaaatc ccaccaacgg acaaggttat
      781 gactatcgga cgaaggtgag gctttttaat tctcataaaa atacactcca tataataaaa
      841 aatgccgcat ttaccataac atcccttatc agcaccgccc cggacgggtt cggaacaaat
      901 gcggcgtcag cccggtaaaa ccggcagcaa actctccgct aaaccgcgca ttctgcgcca
      961 gataaatttc acccggctgc atggctatgc agtcgggtga atggctccgg ctttcagcgc
     1021 agatgtccgc cgaaagcccc attttatcag gttatcacag tgaagggctg ttatacgtcc
     1081 gctgtcgctg agatcgctcc agctccagcg ctttctgatg ctgcaccacg cgctcctgct
     1141 cccggtgcag ctcgacggca ttcagtcgct cgacaaccgg cgcagctgct cgctcaaact
     1201 ctgcacctgc ctgctcaagc ccgtgacgcg ctcgctcagc gctgcgttct cccgttgcat
     1261 aagaccagac atcgtccgcc attccgcgaa ggcgctctcc cactcgtcca gccttttcga
     1321 gtagtcctgc tgtagctgct ctaatgcgct cagcaactgt ttttccagct ccgtcatgtg
     1381 ctatttcccc gccagtatca tccagctcga atcctctccg aaccgtcccg cttccgggtt
     1441 caccttcacg cagcggcgtc tctgctcgcc gcaggtcgag agctgcacgc cgctgttcct
     1501 ctctgacagc atggcctgcg tgctcttctg ctcccggatg gtcgtgtagt tgtcgagtat
     1561 ctgctgcccc tgccaccaca gaatgcccgc gctcgaggcg atcagcagcg cggagaccag
     1621 gacgatggtc agccacgtct ggctgaccat gcgcaccatg cctttcgtgc gctggctcat
     1681 ggctgaggac agtttccggt cgtggtcgag gatggcggcg ctgattctct tcgcgctttc
     1741 gttcagttcc gcttttacag atttctcgtg ctcgctgaat gcggctttca gcatctcgcc
     1801 ggtattctgc tgctgcgctt tcgatttctg ctctaagtcc ttcgccagcg ttaaaagact
     1861 gttcataaat ggctcccttc agtcggatgt ttcgcccccc gtccgggtcg gcaatgctga
     1921 tactgctttt tgtggtgcgg accacctcaa aacctgcgct ttccagcgcc tcagtgacat
     1981 cctgacgggt tttcagctcc ccggatgagg caagagcaag cagaccgcgt gtaatcgctt
     2041 ctgcagcctc ctgcttcgct ttaggcagtg cagacggtgt gaccagtgcc cgccggttct
     2101 ccggtgcgtt cgggtcgtgc agccccagtc tgccgttcac gatggtctgc caggcatcga
     2161 tgcgtggacg gtcggcgcga tcgtaatacg gctggagccg tctgccggtc agcagctccg
     2221 tgttcgggat cagaaaattc agctcaagcc gccccttgtc acgatgctcc acccacagga
     2281 tgctgtactg gtctttatca agtccgggca tcagaacccg ctcaaagctt gccatcagct
     2341 tttcccgctg gccggaaggt aaatccgctt ccgcaaacga cagtaccccg gaggtgtatt
     2401 tcttaacgta aggcgacgcg tcaatcagct cccggacttc ttccggcttc ccctgcagga
     2461 cggtggcgcc ttcacgctgc cggtctttac ccagcagata gtccaccggc ccggcgccac
     2521 cgccgcgacc gcgtggatga aatttaacga tcatcgtccg ttcctttctc aagaacggcg
     2581 tgccgcagcc gctcaagtcc ggcatcgatg gccatcagcg ccgcaacaat ctgcaccctg
     2641 tcatggccgg taccgccgcc ggcgttaaca cggcgggcta tctggttcag gttattgccc
     2701 atgccggcaa gctggcgcag cagcgccggc gagattgagg gaagctttcc ggaacgtgcc
     2761 ggcttttcgt ccaggcaggt ctgccgcatc cacgccgcca gctgcctgcc gtcacagcgc
     2821 tcaagcagcc gccggtgctc gccctccgtc acccacatgg tgagcatctt gttccgtttc
     2881 tctgacaaac cggcctcctg ataacgccgg gacgggcggg aaaggctttc ccggtcggcg
     2941 cggggttgga caagccgcag gcgcgtcagg cttttggcgg gtttcggggc gcagccctga
     3001 accagtcacg tagcgctagc ggagtgtata ctggcttact atgttggcac ggatgcgagt
     3061 gtcagtgaag tgcttcatgt ggcaggagaa aaatgcagca gcggagcgtc agcagaatat
     3121 gtgatacagg atatattccg cttcctcgct cactgactcg ctgcgctcgg tcgttcggct
     3181 gcggcgagcg gtaccgactt acaggcgggg cggaaatttc ctgggagatg ccaggaagaa
     3241 gcttaacagg gaagcgataa ggccacggcg aagccgtttt tccataggct ccgcccccct
     3301 gacaagcatc acgaaatctg acgctcaaat cagtggtggc gaaacccgac aggacttaaa
     3361 gataccaggc gtttccccct ggtggctccc tcgtgcgctc tcctgttcct gcctttcggt
     3421 ttaccgatgt caatccgctg ttatggccgc gtttatctca ttccacgcct gacactcggt
     3481 tccgggaagg cagttcgctc caagctggac tgtatgcacg aaccccccgt tcagcccgac
     3541 taccacgttg tcccggtaac tatcatcttg agtccaaccc ggaacagaca cgaaaaatcg
     3601 ccagtggcgg tagccattag taagaggatt cacggagcgg agtagtagag tgttctacag
     3661 agttcttgaa gtggtggcct gactgcggct acactggaag gacagttttg gtacctgcgc
     3721 tccgtgaaag ccagttacct tcggaagaaa gagttggtag ctctgaattc cggcaaacga
     3781 accaccgttg gtagcggtgg tttttttgtt tacagggtat gagattacga cgacatcgaa
     3841 gggataacaa gaggatccgc ttcttgccca ctcttcgcca caaaaaaaac gacacactag
     3901 cgcgtaaagc atcatcaaaa aactcaaata gcgctatata caatcacttt attacgcccc
     3961 tcccttttgg cttgataaag agcatcgtca gcatttttca gcaaaaaatc gatcctacca
     4021 agaggatcat cttgtgttgc cacaccagca gatatggtga cccgcaagtt attagggaag
     4081 acagtacttt caataacact cctaatacgc tccgcaacac acttagctgt taccacagat
     4141 gtattcggca ggaaaacaac aaactcttcg ccaccaaacc gacaaacaac atcttcacta
     4201 cggcaacagg aattaataat atgagccaaa gaaacaagca cctcatctcc gaccccatgc
     4261 ccgaaactgt catttatctc tttaaaaaaa tcaacatcaa ttacaataac tgaacaccct
     4321 gaatccagct tatgattctg tattttactt aaaaacccca atctattatt cacgccggta
     4381 aggggatctt taagcgccac ctcatttaga gaatcaactc tttccatcat taccttaata
     4441 tacgtaaaaa gcgccttttt aagcctatca gcttcggcat accaagcatt gatagcttta
     4501 atataaacta gcgaagctcc gatatcttta gcattggtag atatagcaag cttttctaaa
     4561 ggaagtgaaa tactggaggc aatgaaatat gaaataagtg aaaacacaat aattattata
     4621 attagcagaa caagtacact tttagcataa gcaataagaa tagt
//
