LOCUS       CP099054                5874 bp    DNA     circular BCT 13-APR-2023
DEFINITION  Escherichia coli strain RHB44-C13 plasmid unnamed3, complete
            sequence.
ACCESSION   CP099054
VERSION     CP099054.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15488663
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5874)
  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  JOURNAL   Unpublished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 5874)
  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                     :: RHB44-C13
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 122x
            Sequencing Technology             :: Illumina/Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/15/2022 18:13:49
            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)                     :: 4,904
            CDSs (total)                      :: 4,781
            Genes (coding)                    :: 4,608
            CDSs (with protein)               :: 4,608
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 173
            CDSs (without protein)            :: 173
            Pseudo Genes (ambiguous residues) :: 0 of 173
            Pseudo Genes (frameshifted)       :: 73 of 173
            Pseudo Genes (incomplete)         :: 111 of 173
            Pseudo Genes (internal stop)      :: 39 of 173
            Pseudo Genes (multiple problems)  :: 42 of 173
            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..5874
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB44-C13"
                     /isolation_source="Pooled faeces sample collected from
                     floor of poultry farm"
                     /db_xref="taxon:562"
                     /plasmid="unnamed3"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(join(5297..5874,1..475))
                     /locus_tag="NFK99_24475"
     CDS             complement(join(5297..5874,1..475))
                     /locus_tag="NFK99_24475"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001557502.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WGA54125.1"
                     /translation="MNLQQRINKLPQLSSSFSFGKDIDNIHSFIFNETSKDKIEDLLRK
                     WVSGNQPCVFGKLASKKIKGLDFHLSIVNSPQLYNDDGHLFDFLRNERVRFKERARRGE
                     VSAHLIYFIYPQLAFARPSEELVDIQKYICSLHMPECYPIKEDVIYTESVPFQDKDGLK
                     IYKAGVNVFYSSAHRTRNHDRRIPGGILISVNAPGHFMRLAIEKGFYKDQEQALADIRN
                     MTIQSVGNGGYSHPEGISTTWHSESKLDRFGCPVHTGNSSYYSGFYHTDVLIPGELTKD
                     ERLLHEIDNSDPMIFNWNVLFYVSLEEFPIDDPYYGEFIGVPVDDASMFFNSFQPRKFE
                     NNPLYEKEDD"
                     /name="hypothetical protein"
     gene            complement(1195..1428)
                     /locus_tag="NFK99_24480"
     CDS             complement(1195..1428)
                     /locus_tag="NFK99_24480"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /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="WGA54126.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWENAFVELQKMFSLTQRDNA
                     MLNGRVMQLSQQVQHLSERTERLSQLYSENWR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(1435..1965)
                     /locus_tag="NFK99_24485"
     CDS             complement(1435..1965)
                     /locus_tag="NFK99_24485"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001673158.1"
                     /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="WGA54127.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFRKLEESVNRELTSNE
                     SLIRNAINDHTTALKELLERYQKTTVDTMDAHWKTVLKMSVKRWLWLIIVSVLMFATTG
                     SLLWYQGMKINANMNILREQKESLEKLNAKTWGVRYHEDSNGRFLVLPKGMKAETNWTK
                     DNGKLNAVRLVQE"
                     /name="MbeB family mobilization protein"
     gene            complement(2003..2434)
                     /locus_tag="NFK99_24490"
                     /pseudo=""
     CDS             complement(2003..2434)
                     /locus_tag="NFK99_24490"
                     /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(2643..2966)
                     /locus_tag="NFK99_24495"
     CDS             complement(2643..2966)
                     /locus_tag="NFK99_24495"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /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="WGA54128.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAAWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALIAIGDELRRLRLAVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3032..3223
                     /locus_tag="NFK99_24500"
     CDS             3032..3223
                     /locus_tag="NFK99_24500"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165975.1"
                     /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="WGA54123.1"
                     /translation="MTKQEKTALNMVRFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENR"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(4429..5295)
                     /locus_tag="NFK99_24505"
     CDS             complement(4429..5295)
                     /locus_tag="NFK99_24505"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001335763.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DMT family transporter"
                     /protein_id="WGA54124.1"
                     /translation="MIKGMLFAFLAAFSWGAAIVMSKKGVEELDAGGVFFWQICSAVIL
                     SWIVLFIKRKKLPLNSKAILAYATGVFEPFLAYTFTLYGLYFISAGSASIIFSLESVFI
                     LVLSVLICSVKINSPQYFILFLIGAIVGSILVALPDISNGSNNIVGYCLVVAGVLSAAF
                     YVVISSRLIKSFEPITLLSGQLTFSLILSSLFIFISKSSIYLPLESVIIVFSSGILQYF
                     LAFCFYLNSLRWLPVHLAGIMLYFIPLVALFLSWLFLDEQFTFLQGVGFIVTVLSVYFL
                     NRKYSEE"
                     /name="DMT family transporter"
     Typing          complement(3318..3399)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.795"
                     /coverage="100.0"
                     /evalue="6.23e-34"
     Typing          complement(3856..4043)
                     /name="rep_cluster_2401"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="4.63e-94"
     Typing          complement(1092..2653)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.232"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tatcctgaaa tggtacgctt tcagtataaa taacatcctc ttttattgga tagcactctg
       61 gcatatgcag cgaacaaata tatttttgta tgtccactaa ctcttctgat ggacgagcaa
      121 atgcaagttg tggataaata aaataaatga gatgcgcact gacctctcct cttcttgcgc
      181 gttctttaaa acgaactctt tcattacgca aaaaatcaaa caaatgacca tcatcattat
      241 atagttgggg gctatttaca atagataaat ggaaatcaag ccctttaatt ttcttgcttg
      301 ccaatttacc aaatacacag ggctgattgc ctgacaccca ttttcttagt aaatcttcaa
      361 ttttatcttt agaagtttcg ttaaagataa atgaatgaat attatcaata tcttttccaa
      421 atgaaaaact ggatgataat tgtggtagtt tatttatacg ttgttgaaga ttcatgaaag
      481 ctcccacaag acacctcata tattttttat atactgaaac tacattatat ttattaccga
      541 cgtaaaacga aataatttat tatcgttacc gatattttaa aaaatcatta tttgcacagt
      601 gttcgagttg ttagtatcac tccttcctga aaatccgctc catttaccat aacgtcgcat
      661 tgtacgcacc gccaaaacgc gttcggtgcg atcacggcag cagacaggta aaaatggcaa
      721 caaaccaccc gaaaaactgc cgcgatcgca cccgataaat tttaaccaca tgcatagcta
      781 tgcagccatg tgaatcacgc aggaattgcc agccagagac tgctgaaacg gatttttttc
      841 atactttcgg aaaggcagaa gacggaaccg gagcggaaaa acagaaattc atgggaatga
      901 gcgcgatctg gcaataacgg caaaacacag caacaaagac acaccagaat cgcgcccgca
      961 tgcgttttaa cgcgttcctg tgttttcagc aagctctgac tgaagcgcgt tcccggtgcc
     1021 cccgaaccaa ccattatccc aaaaaatgca ccggaaacgc gctgccaaca ttttagcctg
     1081 tctctggtta ccatcccagc gaagggccat ccagtgtccg ttcctgaatt tccggctggc
     1141 gctcccgctc cagggataac gcatattcgc gctcctgtat cagccgctca tcccttatct
     1201 ccagttctcg ctgtataact ggctcaagcg ttctgtccgc tcgctcaagt gctgcacctg
     1261 ctgactcaac tgcatgactc gcccgttcag catcgcgttg tcccgttgcg taagcgaaaa
     1321 cattttctgc aattccacga aggcgttctc ccattcgttc agccgctgca tatagtcctg
     1381 ttgcagttgc tctaatgcgt tcagcaaatg tctttccagc tccgtcatgc tctgtcactc
     1441 ctgcaccagt ctcactgcgt tcagtttgcc gttgtccttc gtccagttcg tttcggcttt
     1501 catccccttc ggcaacacca gaaaacgtcc gttgctgtcc tcgtgataac gcacgcccca
     1561 tgtcttcgcg ttcagcttct ccagactctc tttctgctcg cggagaatat tcatattcgc
     1621 gtttatcttc atgccctggt accacagcag actcccggtc gtggcaaaca tcagtactga
     1681 gacgataatc agccacagcc agcgtttcac gctcattttc agtacggttt tccagtgcgc
     1741 gtccatcgta tcgacggtcg ttttctgata cctctccagc agttctttca gggctgttgt
     1801 atggtcgttg atagcgttcc tgattaaaga ttcgtttgag gtcagttccc tgtttacaga
     1861 ttcttcgagc ttcctgaact cgtcgttcag cattttctct gtagattcgg ctctctcttt
     1921 cagctttttc tcgaactccg cgcccgtctg taaaagattg ctcataaaac gctcctttca
     1981 gtctgatatt cctcccgccg ttcgggtctg caatgctgat actgcttcgc gtcaccctga
     2041 ccacttcaag ccccgcctct gtgagcgcct gaatcacatc ctgacggcct tttatctctc
     2101 cggcatggta aagcgcgtct atcccgcgtg tgacgccctc agcaagcgcc tgtttcgttt
     2161 ccggcaggtt atcaggaagg gtcagcgtcc ggcggttctc cggggcgttg gggtcatgca
     2221 gaccgtaatg gtgattcacc agcgtctgcc aggcatcaat tctcggcctg tctgcccggt
     2281 cgtagtacgg ctggaggcgt tttccggtct gtagctccat gttcggaatg acaaaattca
     2341 gctcaagccg tcccttgtcc tggtgctcca cccacaggat gctgtactga tttttctcga
     2401 gaccgggcat cagtacacgc tcaaagctcg ccatcacttt ttcacgccct ccaggcggca
     2461 gctccttctc cgcgaacgac agaacacctg acgtgtattt cttcgcaaat ggcgtggcat
     2521 cgatgagttc ccggacctct tccggattcc cctgaagcac cgttgcccct tcccggttac
     2581 gctcccttcc cagcaggtaa tcaaccggac cactgccacc accttttccc ctggcatgaa
     2641 acttaactat catcccgcgc cccctgttcc ctgaccgcca gacgcagccg gcgcagctca
     2701 tccccgatgg ctatcagtgc ggccaccacc tgaacccggt caccggaaga ccactgcccg
     2761 ctgttcacct tcctcgctgt ctggttaagg ttattcccga tagcggccag ctgacgcagt
     2821 aacggcggtg ccagtgtcgg cagcttcccg gaacgggcaa caggctcacc caggcagacc
     2881 cgccgcatcc atgccgccag ttgtttaccc tcacagcgtt ccagtaaacg ggcatgctca
     2941 tcatcagtca cccgtatcgt gagcatcctc tcgcgtttca tcggtatcat tacccccatg
     3001 aacagaaatc ccccttacac ggaggcatcc agtgactaaa caggaaaaaa ccgcccttaa
     3061 catggtccgc tttatcagaa gccagacatt aacgctgctg gagaagctca acgaactgga
     3121 cgcggatgaa caggcagaca tctgtgaatc gcttcacgac cacgccgatg agctttaccg
     3181 cagttgcctc gcacgcttcg gggatgacgg tgaaaaccgc tgacacatgc agctcccgga
     3241 gacggtcaca gcttgtctgt gagcggatgc cgggagcaga caagcccgcc agggcgcgtc
     3301 aggccgttga cctttggggt gtcggggcga agccctgacc cagtcacgta gcgatagcgg
     3361 agtgtatact ggcttaatca ttcggcatca gtgcggattg tatgaaaagt gcgccatgtc
     3421 gggtgtgaaa tgccgcacag atgcgtaagg agaaaatgcc agttcaggcg ctcttccgct
     3481 tcctcgctca ctgactcgct acgctcggtc gttcggctgc ggcgagcgga ctctcctttc
     3541 tcaaaaacgc taaccctgtt atccacagaa cccggggata aaccaggaaa gaacatgtgc
     3601 gcaaaaaacg aaaccccgga aaaggccgcg ccggaggcgc tttttccata ggctccgccc
     3661 ccctgacgga cttcacaaaa cagacacttt ttcggtgcat ctgtgggagc cttgcggctc
     3721 aaccatgaaa tccgccagcg gtggcgaaac ccgacgtggc ttaaagatca tcaccgtttc
     3781 cggtgaatcg ctccctcctg cgcccccacg ttcccgccat atcgattacc ggataccttt
     3841 tccgcctttc tcccttacgg gacacgtggc gctttctcat agctcacgtc ttctggtatc
     3901 tcggggcgac ttaggcagtt cgctccgggc tgggctgtat gcaggaaccc cccgttcagc
     3961 ccgactgctg cgccttctcc ggtaactgtt ctcttgggtc caacccggaa aagacaccac
     4021 aaagcgccac tggcagcagc cattggtaaa agtcatgtgc gagatattta gagagtactt
     4081 gaagtggctg ccggagtgcg gctacactag aagaacaatt ttggtgactc gtctcgcata
     4141 agacagttac ctggttaagc agtctgcaag ctgacttaac cttcgatcaa accgccctgc
     4201 aaggcggttt tttcgtttac aggcagcaga ttacgcgcag aaaaaaagga tctcaagagg
     4261 atcctttgat ctttttgtta caaacgtctc tatttgactc ccctgagagc gttttagcgc
     4321 gcctctgccc ccccttggtt acattccgac accagaaacg ctcccgtttt ttacgtgcat
     4381 ttggcacggt atcgatggag gccggggggg gcaatcctga acagaatgtt actcctctga
     4441 gtattttctg ttaagaaaat atacacttag cacagttaca ataaatccta ccccctgtaa
     4501 gaatgtgaat tgttcatcca aaaacaacca tgacaaaaat aatgcaacta gcggaataaa
     4561 gtacaacatt atccctgcca aatgaactgg gagccaacgc aaggagttca agtaaaaaca
     4621 aaaagctaaa aaatattgta atattccaga tgaaaaaaca ataatcacgg attccaacgg
     4681 aagataaatt gaggatttag atataaaaat aaagagcgat gacagtataa gggagaatgt
     4741 caactgtccg ctcaataatg tgataggctc aaacgattta ataaggcgag acgatataac
     4801 aacataaaat gctgccgata acacaccggc aacaacaaga caatatccaa caatattatt
     4861 cgatccatta ctgatgtctg gcaaggctac caaaatactg ccaacaattg cacctataag
     4921 gaacaatata aaatattgcg gggaattaat tttaactgag caaataagaa cagacaacac
     4981 caatataaac actgattcaa gtgaaaaaat aattgatgcg cttcctgctg aaataaaata
     5041 aagtccgtag agtgtaaaag tatacgctaa gaatggttca aaaacgcctg tcgcataagc
     5101 aagtatcgct tttgagttta atgggagttt ttttcttttt ataaaaagaa ctatccaaga
     5161 tagtattact gcactacaaa tctgccagaa aaacacccct ccggcatcta gttcttcaac
     5221 tccttttttg ctcattacga tagctgcccc ccatgagaac gctgctaaaa aagcaaaaag
     5281 cattccttta atcatattaa tcatcctctt tctcataaag ggggttgttt tcaaatttcc
     5341 ttggttgaaa ggagttaaaa aacatagatg catcatctac aggaacacca ataaactctc
     5401 cataataagg atcatctata ggaaactctt ctaatgaaac ataaaacaat acattccagt
     5461 tgaagatcat tggatcacta ttatctattt catggagcaa tctttcatcc ttagttaatt
     5521 ctcctggaat taatacatca gtatgataaa aaccgctgta ataagaacta ttaccggtgt
     5581 gcactgggca tccaaaacga tccaatttag attctgaatg ccatgttgta gaaatccctt
     5641 ccggatgtga atacccaccg ttaccaacag actgaatagt catgttacga atatccgcta
     5701 acgcttgttc ttgatcttta tagaaacctt tttctatcgc cagcctcata aaatgccccg
     5761 gggcatttac agaaataagt attccccccg gtattcttct atcatgattt cttgttctat
     5821 gagcagaaga gtaaaaaaca ttaacaccag ccttatatat ttttagccca tctt
//
