LOCUS       CP099229                6668 bp    DNA     circular BCT 13-APR-2023
DEFINITION  Escherichia coli strain RHB13-SO-C03 plasmid unnamed4, complete
            sequence.
ACCESSION   CP099229
VERSION     CP099229.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15488539
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6668)
  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  JOURNAL   Unpublished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 6668)
  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                     :: RHB13-SO-C03
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100x
            Sequencing Technology             :: Illumina/Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/15/2022 20:29:35
            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)                     :: 5,053
            CDSs (total)                      :: 4,931
            Genes (coding)                    :: 4,768
            CDSs (with protein)               :: 4,768
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 90
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 163
            CDSs (without protein)            :: 163
            Pseudo Genes (ambiguous residues) :: 0 of 163
            Pseudo Genes (frameshifted)       :: 69 of 163
            Pseudo Genes (incomplete)         :: 97 of 163
            Pseudo Genes (internal stop)      :: 35 of 163
            Pseudo Genes (multiple problems)  :: 34 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..6668
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB13-SO-C03"
                     /isolation_source="Pooled soil sample collected from floor
                     of pig farm"
                     /db_xref="taxon:562"
                     /plasmid="unnamed4"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(421..852)
                     /locus_tag="NFJ75_25195"
                     /pseudo=""
     CDS             complement(421..852)
                     /locus_tag="NFJ75_25195"
                     /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(1061..1384)
                     /locus_tag="NFJ75_25200"
     CDS             complement(1061..1384)
                     /locus_tag="NFJ75_25200"
                     /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="WFW58371.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1448..1639
                     /locus_tag="NFJ75_25205"
     CDS             1448..1639
                     /locus_tag="NFJ75_25205"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /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="WFW58372.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2965..3192
                     /locus_tag="NFJ75_25210"
     CDS             2965..3192
                     /locus_tag="NFJ75_25210"
                     /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="WFW58374.1"
                     /translation="MLYAIVISTILCPYSKYAIEHIAFNFIKKDFFERRKNLNNAPVAK
                     LNLFMLYNLLCLVLAIPFGLLGLFISIKNN"
                     /name="colicin E1 immunity protein"
     gene            complement(3189..4757)
                     /gene="cea"
                     /locus_tag="NFJ75_25215"
     CDS             complement(3189..4757)
                     /gene="cea"
                     /locus_tag="NFJ75_25215"
                     /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="WFW58373.1"
                     /translation="METAVAYYKDGVPYDDKGQVIITLLNGTPDGSGSGGGGGKGGSKS
                     ESSAAIHATAKWSTAQLKKTQAEQAARAKAAAEAQAKAKANRDALTQRLKDIVNEALRH
                     NASRTPSATELAHANNAAMQAEAERLRLAKAEEKARKEAEAAEKAFQEAEQRRKEIERE
                     KAETERQLKLAEAEEKRLAALSEEAKAVEIAQKKLSAAQSEVVKMDGEIKTLNSRLSSS
                     IHARDAEMKTLAGKRNELAQASAKYKELDELVKKLSPRANDPLQNRPFFEATRRRVGAG
                     KIREEKQKQVTASETRINRINADITQIQKAISQVSNNRNAGIARVHEAEENLKKAQNNL
                     LNSQIKDAVDATVSFYQTLTEKYGEKYSKMAQELADKSKGKKIGNVNEALAAFEKYKDV
                     LNKKFSKADRDAIFNALASVKYDDWAKHLDQFAKYLKITGHVSFGYDVVSDILKIKDTG
                     DWKPLFLTLEKKAADAGVSYVVALLFSLLAGTTLGIWGIAIVTGILCSYIDKNKLNTIN
                     EVLGI"
                     /name="cea"
     gene            5017..5454
                     /locus_tag="NFJ75_25220"
     CDS             5017..5454
                     /locus_tag="NFJ75_25220"
                     /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="WFW58369.1"
                     /translation="MGHCHFMAWHTLRDALKMTGRSRSQFYRDMRAGLVSYRTGRDGRR
                     EFETSELIRAYGELKQNETPERHSEGHAENPHDQQTERILRELNELKQCLTLMLEDKQA
                     QDMDRRRQEAEREQLQNEIAQLRQALELEKKRGFWSRLFGR"
                     /name="entry exclusion protein 1"
     gene            5535..5954
                     /locus_tag="NFJ75_25225"
     CDS             5535..5954
                     /locus_tag="NFJ75_25225"
                     /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="WFW58370.1"
                     /translation="MRRTGNKLCLIAMITATVALTACTPKGSVEQHTRHYVYASDDGFD
                     PNFSTQKADTTRMMVPFFRQFWDMGAKDKATGKSRSDVQQRIQQFHSQEFLNSLRGTTQ
                     FAGTDYRSKDLTPKKSRLLADTISAVYLDGYEGRQ"
                     /name="Exc2 family lipoprotein"
     gene            complement(6272..6526)
                     /locus_tag="NFJ75_25230"
     CDS             complement(6272..6526)
                     /locus_tag="NFJ75_25230"
                     /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="WFW58375.1"
                     /translation="MTELETHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSEQTERLSEQTERLSQLYSENWR"
                     /name="MbeD family mobilization/exclusion protein"
     Typing          complement(1725..1812)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="6.86e-39"
     Typing          1823..2381
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.365"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(20..1071)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.157"
                     /coverage="90.0"
                     /evalue="0.0"
     Typing          complement(6169..6668)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="4.24e-75"
ORIGIN
        1 aatgtctctt cctgcttcct gatttcttcc aggttcgcct gtatcctccc tccaagatac
       61 cagagcgtcc cgccactcgc ggtaaacagg agaaagacta tccccagtaa catcatgccc
      121 gtattccctg ccagctttaa cacgtccctc ctgtgctgca tcatcgcctc tttcacccct
      181 tcccggtgtt tttccagcga ttcctctgtc gaggctgtga acagggctat agcgtctctg
      241 attttcgtct cgtttgatgt cacagcctcg cttacagatt cgccgagcct cctgaactcg
      301 ttgttcagca ttttctctgt agattcggct ctctctttca gctttttctc gaactccgcg
      361 cccgtctgca aaagattgct cataaaatgc tcctttcagc ctgatattct tcccgccgtt
      421 cggatctgca atgctgatac tgcttcgcgt caccctgacc acttccagcc ccgcctcagt
      481 gagcgcctga atcacatcct gacggccttt tatctctccg gcatggtaaa gtgcatctat
      541 acctcgcgtg acgccctcag caagcgcctg tttcgtttca ggcaggttat cagggagtgt
      601 cagcgtcctg cggttctccg gggcgttcgg gtcatgcagc ccgtaatggt gattcaccag
      661 cgtctgccag gcatcaattc taggcctgtc tgcgcggtcg tagtacggct ggaggcgttt
      721 tccggtctgt agctccatgt tcggaatgac aaaattcagc tcaagccgtc ccttgtcctg
      781 gtgctccacc cacaggatgc tgtactgatt tttttcgaga ccgggcatca gtacacgctc
      841 aaagctcgcc atcacttttt cacgtcctcc cggcggcagc tccttctccg cgaacgacag
      901 aacaccggac gtgtatttct tcgcaaatgg cgtggcatcg atgagttccc ggacttcttc
      961 cggattaccc tgaagcaccg ttgcgccttc gcggttacgc tccctcccca gcaggtaatc
     1021 aaccggacca ctgccaccac cttttcccct ggcatgaaat ttaactatca tcccgcgccc
     1081 cctgttccct gacggccaga cgcagccggc gcagctcatc cccgatggcc atcagtgcgg
     1141 ccaccacctg aacccggtca ccggaagacc actgcccgct gttcacctta cgggctgtct
     1201 gattcaggtt atttccgatg gcggccagct gacgcagtaa cggcggtgcc agtgtcggca
     1261 gttttccgga acgggcaacc ggctccccca ggcagacccg ccgcatccat accgccagtt
     1321 gtttaccctc acagcgttca agtaaccggg catgttcatc atcagtaacc cgtattgtga
     1381 gcatcctctc gcgtttcatc ggtatcatta ccccatgaac agaaatcccc cttacacgga
     1441 ggcatcagtg actaaacagg aaaaaaccgc ccttaacatg gcccgcttta tcagaagcca
     1501 gacattaacg ctgctggaga agctcaacga actggacgca gatgaacagg ccgatatttg
     1561 tgaatcgctt cacgaccacg ccgatgagct ttaccgcagc tgcctcgcac gtttcgggga
     1621 tgacggtgaa aacctctgac acatgcagct cccggagacg gtcacagctt gtctgtgagc
     1681 ggatgccggg agctgacaag cccgtcaggg cgcgtcagca ggttttagcg ggtgtcgggg
     1741 cgcagccctg acccagtcac gtagcgatag cggagtgtat actggcttaa ccatgcggca
     1801 tcagtgcgga ttgtatgaaa agtacgccat gccgggtgtg aaatgccgca cagatgcgta
     1861 aggagaaaat gcacgtccag gcgcttttcc gcttcctcgc tcactgactc gctacgctcg
     1921 gtcgttcgac tgcggcgagc ggtactgact cacacaaaaa cggtaacaca gttatccaca
     1981 gaatcagggg ataaggccgg aaagaacatg tgagcaaaag accagaaaca ggaagaaggc
     2041 cgcgtagcag gcgtttttcc ataggctccg cccccctgac gagcatcaca aaaatagacg
     2101 ctcaagtcag aggtggcgaa acccgacagg actataaaga caccaggcgt ttccccctgg
     2161 aagctccctc gtgcgctctc ctgttccgac cctgccgctt accggatacc tgtccgcctt
     2221 tctcccttcg ggaagcgtgg cgctttctca tagctcacgc tgttggtatc tcagttcggt
     2281 gtaggtcgtt cgctccaagc tgggctgtgt gcacgaaccc cccgttcagc ccgaccgctg
     2341 cgccttatcc ggtaactatc gtcttgagtc caacccggta aggcacgcct taacgccact
     2401 ggcagcagcc actggtaacc ggattagcag agcgatgatg gcacaaacgg tgctacagag
     2461 ttcttgaagt agtggcccga ctacggctac actagaagga cagtatttgg tatctgcgct
     2521 ctgctgaagc cagttacctt cggaaaaaga gttggtagct cttgatccgg caaacaaacc
     2581 accgttggta gcggtggttt ttttgtttgc aagcagcaga ttacgcgcag aaaaaaagga
     2641 tctcaagaag atcctttgat cttttctact gaaccgcgat ccccgtcagt ttagaagagg
     2701 aggatggtgc gatggtccct ccctgaacat cacgtatata gttagcctga catccaacaa
     2761 ggaggtttat cgcgaatatt cccacaaaaa atcttttcct cataactcga tccttataaa
     2821 atgaaaagaa tatatggcga ggtttaattt atgagcttaa gatactacat aaaaaatatt
     2881 ttatttggcc tgtactgcac acttatatat atatacctta taacaaaaaa cagcgagggg
     2941 tattatttcc ttgtgtcaga taagatgcta tatgcaatag tgataagcac tattctatgt
     3001 ccatattcaa aatatgctat tgaacacata gcttttaact tcataaagaa agattttttc
     3061 gaaagaagaa aaaacctaaa taacgccccc gtagcaaaat taaacctatt tatgctatat
     3121 aatctacttt gtttggtcct agcaatccca tttggattgc taggactttt tatatcaata
     3181 aagaataatt aaatccctaa cacctcattt atagtattaa gtttattctt atcaatatag
     3241 gagcatagaa ttcctgtaac aatagcaata ccccaaatac ctaatgtagt tccagcaagc
     3301 aagctaaaaa gtaaagcaac aacataactc acccctgcat ctgcagcttt cttctctaat
     3361 gtaagaaata gtggcttcca gtcacctgta tccttaattt ttaggatatc agataccaca
     3421 tcatatccaa aagaaacatg ccccgtaatc ttcaagtact tggcaaactg atctaaatgt
     3481 ttagcccagt catcatactt caccgatgcc aacgcattaa aaatagcatc acgatcggct
     3541 ttgctgaatt tcttatttaa aacatccttg tatttttcaa aagcagcgag agcttcattc
     3601 acattgccga ttttcttacc tttagactta tcagcaagtt cctgtgccat tttcgaatat
     3661 ttttcaccat atttttcagt cagcgtttga taaaagctaa ctgttgcatc aacagcatcc
     3721 ttaatctgtg aattaaggag attattctgt gcttttttca aattttcttc agcttcatga
     3781 acacgagcga taccggcatt acgattatta ctgacctgag aaatagcctt ctggatctga
     3841 gttatatcag catttatccg gttaatacgt gtttctgatg ctgttacctg tttttgtttt
     3901 tcttctctaa tcttaccggc cccaacccgt cgtctggttg cttcaaaaaa aggacggttc
     3961 tgaagcggat cattggctct tggtgatagt tttttgacca gctcatccag ttctttatat
     4021 ttagcggatg cctgagccag ttcatttcgt tttccagcga gcgttttcat ttctgcatca
     4081 cgggcatgga tactggagct taaacgagaa ttgagagtct taatctctcc atccattttc
     4141 accacttcag attgtgcagc agaaagtttt ttttgggcga tctcaacagc tttagcttct
     4201 tcactcaatg cagccagtcg tttctcttca gcttcagcca gtttcaactg gcgttctgtt
     4261 tcagccttct cccgttcaat ctctttacgt cgttgttctg cttcctgaaa agccttttct
     4321 gctgcttccg cttctttacg ggctttttct tctgctttcg caaggcgcaa acgctctgct
     4381 tccgcctgca tagctgcatt attagcatga gcaagctctg ttgctgaagg cgtacgtgag
     4441 gcattgtgac gaagagcctc attcacgata tccttcaggc gctgagtcag cgcatccctg
     4501 tttgcctttg ctttcgcctg tgcttccgct gcagcttttg cccgggcagc ctgctctgcc
     4561 tgtgttttct ttaattgagc agtagaccat ttagcagttg catgaatagc tgcagaactt
     4621 tcacttttac tgcctccttt tccacctccg ccgccagagc cactcccgtc aggagtacca
     4681 ttcaaaagag taataattac ctgtccctta tcatcataag gaacaccatc tttatagtac
     4741 gctaccgcgg tttccattat aaaatcctct ttgactttta aaacaataag ttaaaaataa
     4801 atactgtaca tataaccact ggttttatat acagcataaa agctacgccg ctgcattttc
     4861 cctgtcaaga ctgtggactt ccatttttgt gaaaacgatc aaaaaaacag tctttcacac
     4921 cacgcgctat tctcgcccga tgccacaaaa accagcacaa acattaccgt tctcagacct
     4981 cattatgttt tactgaaact atgagatgag acatctatgg gacactgtca ctttatggca
     5041 tggcacacac tccgggacgc actaaaaatg acaggcagat cgcgttcaca gttttaccgt
     5101 gatatgcgcg caggccttgt cagttaccgt accggcaggg acggacgacg ggagtttgaa
     5161 accagtgaac tgatccgggc atacggcgaa ttaaagcaga atgagacacc agaaaggcac
     5221 agtgagggac atgcagaaaa tccacatgat cagcagacag aacgcattct ccgggagctg
     5281 aatgagctga aacaatgcct gacgctgatg cttgaggata aacaggcaca ggatatggat
     5341 cgcagacgcc aggaagcaga acgggaacag ctacaaaatg agatagccca gctcaggcag
     5401 gcactggaac tggaaaagaa acggggattc tggtccaggt tgttcggtcg ctgaacgctg
     5461 tcagagactg atgataaaat agtcttcgga taataactca ccgagaataa atactttaag
     5521 gtagggagac actcatgaga cgtaccggaa acaaactttg tcttatcgcc atgataacag
     5581 caacagtagc tctcacagcc tgtaccccaa agggcagcgt ggaacaacat acccggcatt
     5641 acgtatatgc ttctgatgac ggttttgatc ccaacttttc cacccaaaaa gccgacacaa
     5701 cacgaatgat ggtgcctttt tttcggcagt tctgggatat gggagctaaa gataaagcga
     5761 caggaaaatc acggagtgat gtgcaacaac gcattcagca gtttcacagc caggaatttt
     5821 taaactcact ccggggcaca actcaatttg cgggtactga ttaccgcagc aaagacctta
     5881 ccccgaaaaa atccaggctg ctggctgaca cgatttctgc ggtttatctc gatggctacg
     5941 agggcagaca gtaagtggat ttaccataat cccttaattg tacgcaccgc taaaacgcgt
     6001 tcagcgcgat cacggcagca gacaggtaaa aatggcaaca aaccacccga aaaactgccg
     6061 cgatcgcgcc tgataaattt taaccgtatg aatacctatg caaccagagg gtacaggcca
     6121 cattaccccc acttaatcca ctgaagctgc catttttcat ggtttcacca tcccagcgaa
     6181 gggccatcca gcgtgcgttc ctgtatttcc ggctgacgct cccgttccag ggataacaca
     6241 tgttcgcgct cctgtatcag ccgttcctct cttatctcca gttctcgctg tataactggc
     6301 tcaagcgttc tgtctgctcg ctcaagcgtt ctgtctgctc gctcaagtgc tgcacctgct
     6361 gactcaactg catgacccgc tcgttcagca tcgcgttgtc ccgttgcgta agcgaaaaca
     6421 tcttctgcaa ttccacgaag gcgctctccc attcgctcag ccgctgcata tagtcctgtt
     6481 gcagctgctc taaggcgttc agcaaatgtg tttccagctc tgtcactctg tgtcactcct
     6541 tcagatgtac ccactctttc ccctgaaagg gaatcacctc cgctgatttc ccgtacggaa
     6601 ggacaaggaa tttcctgttc ccgtcctgca caaactccac gccccatgtc ttcgcgttca
     6661 gtttctgc
//
