LOCUS       CP099104                4664 bp    DNA     circular BCT 13-APR-2023
DEFINITION  Escherichia coli strain RHB41-E2-C05 plasmid unnamed2, complete
            sequence.
ACCESSION   CP099104
VERSION     CP099104.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15488632
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  JOURNAL   Unpublished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                     :: RHB41-E2-C05
            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 18:11:39
            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)                     :: 4,652
            CDSs (total)                      :: 4,535
            Genes (coding)                    :: 4,366
            CDSs (with protein)               :: 4,366
            Genes (RNA)                       :: 117
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 169
            CDSs (without protein)            :: 169
            Pseudo Genes (ambiguous residues) :: 0 of 169
            Pseudo Genes (frameshifted)       :: 59 of 169
            Pseudo Genes (incomplete)         :: 98 of 169
            Pseudo Genes (internal stop)      :: 36 of 169
            Pseudo Genes (multiple problems)  :: 23 of 169
            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="RHB41-E2-C05"
                     /isolation_source="Pooled sediment sample collected from
                     floor of pig farm"
                     /db_xref="taxon:562"
                     /plasmid="unnamed2"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            join(4581..4664,1..1473)
                     /locus_tag="NFK68_23205"
     CDS             join(4581..4664,1..1473)
                     /locus_tag="NFK68_23205"
                     /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="WFZ55175.1"
                     /translation="MRIKKPHLRPIVITLSVGGILLTSIFLIAVIMVFQRENIEKDLLY
                     ANSSYAMKMSDVMSGYIEMAQGELAYGAKKIKSTNDIDSLKDEADRLRLQSGMFNSVLV
                     VSNDAVVLATSPESLDLVGTRLNSSASKLAVEEKKPFISSPLKSVAGNLIILLSHPIYD
                     KGGNYIGYVGGSIYLKKHSLFGDVLSRHFFKNNTEISIVSDDGNVIFNNDKSAVDRPMV
                     MSDDLKSKLTASDRGEGAFFSSGHRYLLGYASMKNTAWNVLVYSRADSVTTILIAYAKS
                     VLVLLIIIIVVFSLISYFIASSISLPLEKLAISTNAKDIGASLVYIKAINAWYAEADRL
                     KKALFTYIKVMMERVDSLNEVALKDPLTGVNNRLGFLSKIQNHKRDSGCSVIVIDVDFF
                     KEINDSFGHGVGDEVLVSLAHIINSCCRSEDVVCRFGGEEFVVFLPNTSVVTAKCVAER
                     IRSVIESTVFPNNLRVTISAGVATQDDPLGRIDFLLKNADDALYQAKREGRNKVIVYSA
                     I"
                     /name="sensor domain-containing diguanylate cyclase"
     gene            2530..2853
                     /locus_tag="NFK68_23210"
     CDS             2530..2853
                     /locus_tag="NFK68_23210"
                     /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="WFZ55176.1"
                     /translation="MLTMWVTEGEHRRLLERCDGRQLAAWMRQTCLDEKPARSGKLPSI
                     SPALLRQLAGMGNNLNQIARRVNAGGGTGHDRVQIVAALMAIDAGLERLRHAVLEKGTD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3062..3496
                     /locus_tag="NFK68_23215"
                     /pseudo=""
     CDS             3062..3496
                     /locus_tag="NFK68_23215"
                     /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            3531..4016
                     /locus_tag="NFK68_23220"
     CDS             3531..4016
                     /locus_tag="NFK68_23220"
                     /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="WFZ55173.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQNTGEMLKAAFSEHEKSVKAELNESA
                     KRISAAILDHDRKLSSAMSQRTKGMVRMVSQTWLTIVLVSALLIASSAGILWWQGQQIL
                     DNYTTIREQKSTQAMLSERNSGVQLSTCGEQRRRCVKVNPEAGRFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            4020..4235
                     /locus_tag="NFK68_23225"
     CDS             4020..4235
                     /locus_tag="NFK68_23225"
                     /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="WFZ55174.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWESAFAEWRTMSGLMQRENA
                     ALSERVTGLSRQVQSLSEQLRRLSSD"
                     /name="MbeD family mobilization/exclusion protein"
     Typing          2245..2417
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.276"
                     /coverage="100.0"
                     /evalue="9.21e-81"
     Typing          complement(1769..2320)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.639"
                     /coverage="91.0"
                     /evalue="0.0"
     Typing          2531..2847
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.453"
                     /coverage="99.0"
                     /evalue="1.9499999999999998e-60"
     Typing          2844..4339
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.182"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gccgttatta tggtttttca gcgcgaaaat atagaaaaag atttgcttta tgctaattca
       61 tcgtacgcta tgaaaatgtc agatgtaatg agtggttata ttgaaatggc tcaaggtgaa
      121 ttagcatatg gagcaaaaaa aataaaatca actaatgata ttgactcact taaagatgag
      181 gcggataggt taagattgca gtctggtatg tttaattcag ttcttgttgt tagtaatgat
      241 gctgttgttc tggcgacttc gccagaatct cttgatttag ttggtacccg cttgaattca
      301 agtgccagca aattggcggt tgaggaaaag aaaccattca tatcttcacc gttaaaatca
      361 gttgctggga atttgattat tttgttgtca catcctattt atgataaggg tggcaattac
      421 atagggtatg tcggtgggtc tatatatcta aaaaaacata gtttatttgg cgatgttttg
      481 agcaggcatt ttttcaagaa caacactgaa attagcattg ttagtgatga tgggaatgtg
      541 atctttaata acgataaaag tgctgttgat cggcctatgg ttatgtctga tgatttgaaa
      601 tcaaagttaa ctgcgtctga tagaggtgag ggggcatttt tttcttcggg gcatagatat
      661 cttcttggtt atgctagtat gaaaaatacc gcttggaatg tgttggttta tagtcgtgct
      721 gacagtgtga ctactattct tattgcttat gctaaaagtg tacttgttct gctaattata
      781 ataattgttg tgttttcact tatttcatat ttcattgcct ccagtatttc acttccttta
      841 gaaaagcttg ctatatctac caatgctaaa gatatcggag cttcgctagt ttatattaaa
      901 gctatcaatg cttggtatgc cgaagctgat aggcttaaaa aggcgctttt tacgtatatt
      961 aaggtaatga tggaaagagt tgattctcta aatgaggtgg cgcttaaaga tccccttacc
     1021 ggcgtgaata atagattggg gtttttaagt aaaatacaga atcataagcg ggattcaggg
     1081 tgttcagtta ttgtaattga tgttgatttt tttaaagaga taaatgacag tttcgggcat
     1141 ggggtcggag atgaggtgct tgtttctttg gctcatatta ttaattcctg ttgccgtagt
     1201 gaagatgttg tttgtcggtt tggtggcgaa gagtttgttg ttttcctgcc gaatacatct
     1261 gtggtaacag ctaagtgtgt tgcggagcgt attaggagtg ttattgaaag tactgtcttc
     1321 cctaataact tgcgggtcac catatctgct ggtgtggcaa cacaagatga tcctcttggt
     1381 aggatcgatt ttttgctgaa aaatgctgac gatgctcttt atcaagccaa aagggagggg
     1441 cgtaataaag tgattgtata tagcgctatt tgagtttttt gatgatgctt tacgcgctag
     1501 tgtgtcgttt tttttgtggc gaagagtggg caagaagcgg atcctcttgt tatcccttcg
     1561 atgtcgtcgt aatctcatac cctgtaaaca aaaaaaccac cgctaccaac ggtggttcgt
     1621 ttgccggaat tcagagctac caactctttc ttccgaaggt aactggcttt cacggagcgc
     1681 aggtaccaaa actgtccttc cagtgtagcc gcagtcaggc caccacttca agaactctgt
     1741 agaacactct actactccgc tccgtgaatc ctcttactaa tggctaccgc cactggcgat
     1801 ttttcgtgtc tgttccgggt tggactcaag atgatagtta ccgggacaac gtggtagtcg
     1861 ggctgaacgg ggggttcgtg catacagtcc agcttggagc gaactgcctt cccggaaccg
     1921 agtgtcaggc gtggaatgag ataaacgcgg ccataacagc ggattgacat cggtaaaccg
     1981 aaaggcagga acaggagagc gcacgaggga gccaccaggg ggaaacgcct ggtatcttta
     2041 agtcctgtcg ggtttcgcca ccactgattt gagcgtcaga tttcgtgatg cttgtcaggg
     2101 gggcggagcc tatggaaaaa cggcttcgcc gtggccttat cgcttccctg ttaagcttct
     2161 tcctggcatc tcccaggaaa tttccgcccc gcctgtaagt cggtaccgct cgccgcagcc
     2221 gaacgaccga gcgcagcgag tcagtgagcg aggaagcgga atatatcctg tatcacatat
     2281 tctgctgacg ctccgctgct gcatttttct cctgccacat gaagcacttc actgacactc
     2341 gcatccgtgc caacatagta agccagtata cactccgcta gcgctacgtg actggttcag
     2401 ggctgcgccc cgaaacccgc caaaagcctg acgcgcctgc ggcttgtcca accccgcgcc
     2461 gaccgggaaa gcctttcccg cccgtcccgg cgttatcagg aggccggttt gtcagagaaa
     2521 cggaacaaga tgctcaccat gtgggtgacg gagggcgagc accggcggct gcttgagcgc
     2581 tgtgacggca ggcagctggc ggcgtggatg cggcagacct gcctggacga aaagccggca
     2641 cgttccggaa agcttccctc aatctcgccg gcgctgctgc gccagcttgc cggcatgggc
     2701 aataacctga accagatagc ccgccgtgtt aacgccggcg gcggtaccgg ccatgacagg
     2761 gtgcagattg ttgcggcgct gatggccatc gatgccggac ttgagcggct gcggcacgcc
     2821 gttcttgaga aaggaacgga cgatgatcgt taaatttcat ccacgcggtc gcggcggtgg
     2881 cgccgggccg gtggactatc tgctgggtaa agaccggcag cgtgaaggcg ccaccgtcct
     2941 gcaggggaag ccggaagaag tccgggagct gattgacgcg tcgccttacg ttaagaaata
     3001 cacctccggg gtactgtcgt ttgcggaagc ggatttacct tccggccagc gggaaaagct
     3061 gatggcaagc tttgagcggg ttctgatgcc cggacttgat aaagaccagt acagcatcct
     3121 gtgggtggag catcgtgaca aggggcggct tgagctgaat tttctgatcc cgaacacgga
     3181 gctgctgacc ggcagacggc tccagccgta ttacgatcgc gccgaccgtc cacgcatcga
     3241 tgcctggcag accatcgtga acggcagact ggggctgcac gacccgaacg caccggagaa
     3301 ccggcgggca ctggtcacac cgtctgcact gcctaaagcg aagcaggagg ctgcagaagc
     3361 gattacacgc ggtctgcttg ctcttgcctc atccggggag ctgaaaaccc gtcaggatgt
     3421 cactgaggcg ctggaaagcg caggttttga ggtggtccgc accacaaaaa gcagtatcag
     3481 cattgccgac ccggacgggg ggcgaaacat ccgactgaag ggagccattt atgaacagtc
     3541 ttttaacgct ggcgaaggac ttagagcaga aatcgaaagc gcagcagcag aataccggcg
     3601 agatgctgaa agccgcattc agcgagcacg agaaatctgt aaaagcggaa ctgaacgaaa
     3661 gcgcgaagag aatcagcgcc gccatcctcg accacgaccg gaaactgtcc tcagccatga
     3721 gccagcgcac gaaaggcatg gtgcgcatgg tcagccagac gtggctgacc atcgtcctgg
     3781 tctccgcgct gctgatcgcc tcgagcgcgg gcattctgtg gtggcagggg cagcagatac
     3841 tcgacaacta cacgaccatc cgggagcaga agagcacgca ggccatgctg tcagagagga
     3901 acagcggcgt gcagctctcg acctgcggcg agcagagacg ccgctgcgtg aaggtgaacc
     3961 cggaagcggg acggttcgga gaggattcga gctggatgat actggcgggg aaatagcaca
     4021 tgacggagct ggaaaaacag ttgctgagcg cattagagca gctacagcag gactactcga
     4081 aaaggctgga cgagtgggag agcgccttcg cggaatggcg gacgatgtct ggtcttatgc
     4141 aacgggagaa cgcagcgctg agcgagcgcg tcacgggctt gagcaggcag gtgcagagtt
     4201 tgagcgagca gctgcgccgg ttgtcgagcg actgaatgcc gtcgagctgc accgggagca
     4261 ggagcgcgtg gtgcagcatc agaaagcgct ggagctggag cgatctcagc gacagcggac
     4321 gtataacagc ccttcactgt gataacctga taaaatgggg ctttcggcgg acatctgcgc
     4381 tgaaagccgg agccattcac ccgactgcat agccatgcag ccgggtgaaa tttatctggc
     4441 gcagaatgcg cggtttagcg gagagtttgc tgccggtttt accgggctga cgccgcattt
     4501 gttccgaacc cgtccggggc ggtgctgata agggatgtta tggtaaatgc ggcatttttt
     4561 attatatgga gtgtattttt atgagaatta aaaagcctca ccttcgtccg atagtcataa
     4621 ccttgtccgt tggtgggatt ttgttaactt ctatttttct gatt
//
