LOCUS       CP099235                6668 bp    DNA     circular BCT 13-APR-2023
DEFINITION  Escherichia coli strain RHB13-SO-C02 plasmid unnamed4, complete
            sequence.
ACCESSION   CP099235
VERSION     CP099235.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15488538
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  JOURNAL   Unpublished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-C02
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 109x
            Sequencing Technology             :: Illumina/Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/15/2022 21:11:33
            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)                     :: 5,054
            CDSs (total)                      :: 4,932
            Genes (coding)                    :: 4,770
            CDSs (with protein)               :: 4,770
            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)              :: 162
            CDSs (without protein)            :: 162
            Pseudo Genes (ambiguous residues) :: 0 of 162
            Pseudo Genes (frameshifted)       :: 69 of 162
            Pseudo Genes (incomplete)         :: 96 of 162
            Pseudo Genes (internal stop)      :: 35 of 162
            Pseudo Genes (multiple problems)  :: 34 of 162
            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-C02"
                     /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(242..565)
                     /locus_tag="NFJ74_25200"
     CDS             complement(242..565)
                     /locus_tag="NFJ74_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="WFW53604.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            629..820
                     /locus_tag="NFJ74_25205"
     CDS             629..820
                     /locus_tag="NFJ74_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="WFW53605.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2146..2373
                     /locus_tag="NFJ74_25210"
     CDS             2146..2373
                     /locus_tag="NFJ74_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="WFW53607.1"
                     /translation="MLYAIVISTILCPYSKYAIEHIAFNFIKKDFFERRKNLNNAPVAK
                     LNLFMLYNLLCLVLAIPFGLLGLFISIKNN"
                     /name="colicin E1 immunity protein"
     gene            complement(2370..3938)
                     /gene="cea"
                     /locus_tag="NFJ74_25215"
     CDS             complement(2370..3938)
                     /gene="cea"
                     /locus_tag="NFJ74_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="WFW53606.1"
                     /translation="METAVAYYKDGVPYDDKGQVIITLLNGTPDGSGSGGGGGKGGSKS
                     ESSAAIHATAKWSTAQLKKTQAEQAARAKAAAEAQAKAKANRDALTQRLKDIVNEALRH
                     NASRTPSATELAHANNAAMQAEAERLRLAKAEEKARKEAEAAEKAFQEAEQRRKEIERE
                     KAETERQLKLAEAEEKRLAALSEEAKAVEIAQKKLSAAQSEVVKMDGEIKTLNSRLSSS
                     IHARDAEMKTLAGKRNELAQASAKYKELDELVKKLSPRANDPLQNRPFFEATRRRVGAG
                     KIREEKQKQVTASETRINRINADITQIQKAISQVSNNRNAGIARVHEAEENLKKAQNNL
                     LNSQIKDAVDATVSFYQTLTEKYGEKYSKMAQELADKSKGKKIGNVNEALAAFEKYKDV
                     LNKKFSKADRDAIFNALASVKYDDWAKHLDQFAKYLKITGHVSFGYDVVSDILKIKDTG
                     DWKPLFLTLEKKAADAGVSYVVALLFSLLAGTTLGIWGIAIVTGILCSYIDKNKLNTIN
                     EVLGI"
                     /name="cea"
     gene            4198..4635
                     /locus_tag="NFJ74_25220"
     CDS             4198..4635
                     /locus_tag="NFJ74_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="WFW53600.1"
                     /translation="MGHCHFMAWHTLRDALKMTGRSRSQFYRDMRAGLVSYRTGRDGRR
                     EFETSELIRAYGELKQNETPERHSEGHAENPHDQQTERILRELNELKQCLTLMLEDKQA
                     QDMDRRRQEAEREQLQNEIAQLRQALELEKKRGFWSRLFGR"
                     /name="entry exclusion protein 1"
     gene            4716..5135
                     /locus_tag="NFJ74_25225"
     CDS             4716..5135
                     /locus_tag="NFJ74_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="WFW53601.1"
                     /translation="MRRTGNKLCLIAMITATVALTACTPKGSVEQHTRHYVYASDDGFD
                     PNFSTQKADTTRMMVPFFRQFWDMGAKDKATGKSRSDVQQRIQQFHSQEFLNSLRGTTQ
                     FAGTDYRSKDLTPKKSRLLADTISAVYLDGYEGRQ"
                     /name="Exc2 family lipoprotein"
     gene            complement(5453..5707)
                     /locus_tag="NFJ74_25230"
     CDS             complement(5453..5707)
                     /locus_tag="NFJ74_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="WFW53602.1"
                     /translation="MTELETHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSEQTERLSEQTERLSQLYSENWR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(5714..6232)
                     /locus_tag="NFJ74_25235"
     CDS             complement(5714..6232)
                     /locus_tag="NFJ74_25235"
                     /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="WFW53603.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNNEFRRLGESVSEAVTSNE
                     TKIRDAIALFTASTEESLEKHREGVKEAMMQHRRDVLKLAGNTGMMLLGIVFLLFTASG
                     GTLWYLGGRIQANLEEIRKQEETLQKLNAKTWGVEFVQDGNRKFLVLPYGKSAEVIPFQ
                     GKEWVHLKE"
                     /name="MbeB family mobilization protein"
     Typing          complement(906..993)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="6.86e-39"
     Typing          1004..1562
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.365"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(246..595)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.436"
                     /coverage="99.0"
                     /evalue="1.5699999999999999e-68"
     Typing          complement(5350..6668)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.773"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 accgggcatc agtacacgct caaagctcgc catcactttt tcacgtcctc ccggcggcag
       61 ctccttctcc gcgaacgaca gaacaccgga cgtgtatttc ttcgcaaatg gcgtggcatc
      121 gatgagttcc cggacttctt ccggattacc ctgaagcacc gttgcgcctt cgcggttacg
      181 ctccctcccc agcaggtaat caaccggacc actgccacca ccttttcccc tggcatgaaa
      241 tttaactatc atcccgcgcc ccctgttccc tgacggccag acgcagccgg cgcagctcat
      301 ccccgatggc catcagtgcg gccaccacct gaacccggtc accggaagac cactgcccgc
      361 tgttcacctt acgggctgtc tgattcaggt tatttccgat ggcggccagc tgacgcagta
      421 acggcggtgc cagtgtcggc agttttccgg aacgggcaac cggctccccc aggcagaccc
      481 gccgcatcca taccgccagt tgtttaccct cacagcgttc aagtaaccgg gcatgttcat
      541 catcagtaac ccgtattgtg agcatcctct cgcgtttcat cggtatcatt accccatgaa
      601 cagaaatccc ccttacacgg aggcatcagt gactaaacag gaaaaaaccg cccttaacat
      661 ggcccgcttt atcagaagcc agacattaac gctgctggag aagctcaacg aactggacgc
      721 agatgaacag gccgatattt gtgaatcgct tcacgaccac gccgatgagc tttaccgcag
      781 ctgcctcgca cgtttcgggg atgacggtga aaacctctga cacatgcagc tcccggagac
      841 ggtcacagct tgtctgtgag cggatgccgg gagctgacaa gcccgtcagg gcgcgtcagc
      901 aggttttagc gggtgtcggg gcgcagccct gacccagtca cgtagcgata gcggagtgta
      961 tactggctta accatgcggc atcagtgcgg attgtatgaa aagtacgcca tgccgggtgt
     1021 gaaatgccgc acagatgcgt aaggagaaaa tgcacgtcca ggcgcttttc cgcttcctcg
     1081 ctcactgact cgctacgctc ggtcgttcga ctgcggcgag cggtactgac tcacacaaaa
     1141 acggtaacac agttatccac agaatcaggg gataaggccg gaaagaacat gtgagcaaaa
     1201 gaccagaaac aggaagaagg ccgcgtagca ggcgtttttc cataggctcc gcccccctga
     1261 cgagcatcac aaaaatagac gctcaagtca gaggtggcga aacccgacag gactataaag
     1321 acaccaggcg tttccccctg gaagctccct cgtgcgctct cctgttccga ccctgccgct
     1381 taccggatac ctgtccgcct ttctcccttc gggaagcgtg gcgctttctc atagctcacg
     1441 ctgttggtat ctcagttcgg tgtaggtcgt tcgctccaag ctgggctgtg tgcacgaacc
     1501 ccccgttcag cccgaccgct gcgccttatc cggtaactat cgtcttgagt ccaacccggt
     1561 aaggcacgcc ttaacgccac tggcagcagc cactggtaac cggattagca gagcgatgat
     1621 ggcacaaacg gtgctacaga gttcttgaag tagtggcccg actacggcta cactagaagg
     1681 acagtatttg gtatctgcgc tctgctgaag ccagttacct tcggaaaaag agttggtagc
     1741 tcttgatccg gcaaacaaac caccgttggt agcggtggtt tttttgtttg caagcagcag
     1801 attacgcgca gaaaaaaagg atctcaagaa gatcctttga tcttttctac tgaaccgcga
     1861 tccccgtcag tttagaagag gaggatggtg cgatggtccc tccctgaaca tcacgtatat
     1921 agttagcctg acatccaaca aggaggttta tcgcgaatat tcccacaaaa aatcttttcc
     1981 tcataactcg atccttataa aatgaaaaga atatatggcg aggtttaatt tatgagctta
     2041 agatactaca taaaaaatat tttatttggc ctgtactgca cacttatata tatatacctt
     2101 ataacaaaaa acagcgaggg gtattatttc cttgtgtcag ataagatgct atatgcaata
     2161 gtgataagca ctattctatg tccatattca aaatatgcta ttgaacacat agcttttaac
     2221 ttcataaaga aagatttttt cgaaagaaga aaaaacctaa ataacgcccc cgtagcaaaa
     2281 ttaaacctat ttatgctata taatctactt tgtttggtcc tagcaatccc atttggattg
     2341 ctaggacttt ttatatcaat aaagaataat taaatcccta acacctcatt tatagtatta
     2401 agtttattct tatcaatata ggagcataga attcctgtaa caatagcaat accccaaata
     2461 cctaatgtag ttccagcaag caagctaaaa agtaaagcaa caacataact cacccctgca
     2521 tctgcagctt tcttctctaa tgtaagaaat agtggcttcc agtcacctgt atccttaatt
     2581 tttaggatat cagataccac atcatatcca aaagaaacat gccccgtaat cttcaagtac
     2641 ttggcaaact gatctaaatg tttagcccag tcatcatact tcaccgatgc caacgcatta
     2701 aaaatagcat cacgatcggc tttgctgaat ttcttattta aaacatcctt gtatttttca
     2761 aaagcagcga gagcttcatt cacattgccg attttcttac ctttagactt atcagcaagt
     2821 tcctgtgcca ttttcgaata tttttcacca tatttttcag tcagcgtttg ataaaagcta
     2881 actgttgcat caacagcatc cttaatctgt gaattaagga gattattctg tgcttttttc
     2941 aaattttctt cagcttcatg aacacgagcg ataccggcat tacgattatt actgacctga
     3001 gaaatagcct tctggatctg agttatatca gcatttatcc ggttaatacg tgtttctgat
     3061 gctgttacct gtttttgttt ttcttctcta atcttaccgg ccccaacccg tcgtctggtt
     3121 gcttcaaaaa aaggacggtt ctgaagcgga tcattggctc ttggtgatag ttttttgacc
     3181 agctcatcca gttctttata tttagcggat gcctgagcca gttcatttcg ttttccagcg
     3241 agcgttttca tttctgcatc acgggcatgg atactggagc ttaaacgaga attgagagtc
     3301 ttaatctctc catccatttt caccacttca gattgtgcag cagaaagttt tttttgggcg
     3361 atctcaacag ctttagcttc ttcactcaat gcagccagtc gtttctcttc agcttcagcc
     3421 agtttcaact ggcgttctgt ttcagccttc tcccgttcaa tctctttacg tcgttgttct
     3481 gcttcctgaa aagccttttc tgctgcttcc gcttctttac gggctttttc ttctgctttc
     3541 gcaaggcgca aacgctctgc ttccgcctgc atagctgcat tattagcatg agcaagctct
     3601 gttgctgaag gcgtacgtga ggcattgtga cgaagagcct cattcacgat atccttcagg
     3661 cgctgagtca gcgcatccct gtttgccttt gctttcgcct gtgcttccgc tgcagctttt
     3721 gcccgggcag cctgctctgc ctgtgttttc tttaattgag cagtagacca tttagcagtt
     3781 gcatgaatag ctgcagaact ttcactttta ctgcctcctt ttccacctcc gccgccagag
     3841 ccactcccgt caggagtacc attcaaaaga gtaataatta cctgtccctt atcatcataa
     3901 ggaacaccat ctttatagta cgctaccgcg gtttccatta taaaatcctc tttgactttt
     3961 aaaacaataa gttaaaaata aatactgtac atataaccac tggttttata tacagcataa
     4021 aagctacgcc gctgcatttt ccctgtcaag actgtggact tccatttttg tgaaaacgat
     4081 caaaaaaaca gtctttcaca ccacgcgcta ttctcgcccg atgccacaaa aaccagcaca
     4141 aacattaccg ttctcagacc tcattatgtt ttactgaaac tatgagatga gacatctatg
     4201 ggacactgtc actttatggc atggcacaca ctccgggacg cactaaaaat gacaggcaga
     4261 tcgcgttcac agttttaccg tgatatgcgc gcaggccttg tcagttaccg taccggcagg
     4321 gacggacgac gggagtttga aaccagtgaa ctgatccggg catacggcga attaaagcag
     4381 aatgagacac cagaaaggca cagtgaggga catgcagaaa atccacatga tcagcagaca
     4441 gaacgcattc tccgggagct gaatgagctg aaacaatgcc tgacgctgat gcttgaggat
     4501 aaacaggcac aggatatgga tcgcagacgc caggaagcag aacgggaaca gctacaaaat
     4561 gagatagccc agctcaggca ggcactggaa ctggaaaaga aacggggatt ctggtccagg
     4621 ttgttcggtc gctgaacgct gtcagagact gatgataaaa tagtcttcgg ataataactc
     4681 accgagaata aatactttaa ggtagggaga cactcatgag acgtaccgga aacaaacttt
     4741 gtcttatcgc catgataaca gcaacagtag ctctcacagc ctgtacccca aagggcagcg
     4801 tggaacaaca tacccggcat tacgtatatg cttctgatga cggttttgat cccaactttt
     4861 ccacccaaaa agccgacaca acacgaatga tggtgccttt ttttcggcag ttctgggata
     4921 tgggagctaa agataaagcg acaggaaaat cacggagtga tgtgcaacaa cgcattcagc
     4981 agtttcacag ccaggaattt ttaaactcac tccggggcac aactcaattt gcgggtactg
     5041 attaccgcag caaagacctt accccgaaaa aatccaggct gctggctgac acgatttctg
     5101 cggtttatct cgatggctac gagggcagac agtaagtgga tttaccataa tcccttaatt
     5161 gtacgcaccg ctaaaacgcg ttcagcgcga tcacggcagc agacaggtaa aaatggcaac
     5221 aaaccacccg aaaaactgcc gcgatcgcgc ctgataaatt ttaaccgtat gaatacctat
     5281 gcaaccagag ggtacaggcc acattacccc cacttaatcc actgaagctg ccatttttca
     5341 tggtttcacc atcccagcga agggccatcc agcgtgcgtt cctgtatttc cggctgacgc
     5401 tcccgttcca gggataacac atgttcgcgc tcctgtatca gccgttcctc tcttatctcc
     5461 agttctcgct gtataactgg ctcaagcgtt ctgtctgctc gctcaagcgt tctgtctgct
     5521 cgctcaagtg ctgcacctgc tgactcaact gcatgacccg ctcgttcagc atcgcgttgt
     5581 cccgttgcgt aagcgaaaac atcttctgca attccacgaa ggcgctctcc cattcgctca
     5641 gccgctgcat atagtcctgt tgcagctgct ctaaggcgtt cagcaaatgt gtttccagct
     5701 ctgtcactct gtgtcactcc ttcagatgta cccactcttt cccctgaaag ggaatcacct
     5761 ccgctgattt cccgtacgga aggacaagga atttcctgtt cccgtcctgc acaaactcca
     5821 cgccccatgt cttcgcgttc agtttctgca atgtctcttc ctgcttcctg atttcttcca
     5881 ggttcgcctg tatcctccct ccaagatacc agagcgtccc gccactcgcg gtaaacagga
     5941 gaaagactat ccccagtaac atcatgcccg tattccctgc cagctttaac acgtccctcc
     6001 tgtgctgcat catcgcctct ttcacccctt cccggtgttt ttccagcgat tcctctgtcg
     6061 aggctgtgaa cagggctata gcgtctctga ttttcgtctc gtttgatgtc acagcctcgc
     6121 ttacagattc gccgagcctc ctgaactcgt tgttcagcat tttctctgta gattcggctc
     6181 tctctttcag ctttttctcg aactccgcgc ccgtctgcaa aagattgctc ataaaatgct
     6241 cctttcagcc tgatattctt cccgccgttc ggatctgcaa tgctgatact gcttcgcgtc
     6301 accctgacca cttccagccc cgcctcagtg agcgcctgaa tcacatcctg acggcctttt
     6361 atctctccgg catggtaaag tgcatctata cctcgcgtga cgccctcagc aagcgcctgt
     6421 ttcgtttcag gcaggttatc agggagtgtc agcgtcctgc ggttctccgg ggcgttcggg
     6481 tcatgcagcc cgtaatggtg attcaccagc gtctgccagg catcaattct aggcctgtct
     6541 gcgcggtcgt agtacggctg gaggcgtttt ccggtctgta gctccatgtt cggaatgaca
     6601 aaattcagct caagccgtcc cttgtcctgg tgctccaccc acaggatgct gtactgattt
     6661 ttttcgag
//
