LOCUS       CP099297                5128 bp    DNA     circular BCT 13-APR-2023
DEFINITION  Escherichia coli strain RHB02-E3-C03 plasmid unnamed3, complete
            sequence.
ACCESSION   CP099297
VERSION     CP099297.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15488485
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5128)
  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  JOURNAL   Unpublished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 5128)
  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                     :: RHB02-E3-C03
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 90x
            Sequencing Technology             :: Illumina/Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/15/2022 20:19:04
            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)                     :: 5,157
            CDSs (total)                      :: 5,038
            Genes (coding)                    :: 4,820
            CDSs (with protein)               :: 4,820
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 218
            CDSs (without protein)            :: 218
            Pseudo Genes (ambiguous residues) :: 0 of 218
            Pseudo Genes (frameshifted)       :: 62 of 218
            Pseudo Genes (incomplete)         :: 156 of 218
            Pseudo Genes (internal stop)      :: 44 of 218
            Pseudo Genes (multiple problems)  :: 38 of 218
            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..5128
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB02-E3-C03"
                     /isolation_source="Pooled sediment sample collected from
                     floor of pig farm"
                     /db_xref="taxon:562"
                     /plasmid="unnamed3"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            join(4766..5128,1..39)
                     /locus_tag="NFJ21_25750"
     CDS             join(4766..5128,1..39)
                     /locus_tag="NFJ21_25750"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001505260.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WFV15934.1"
                     /translation="MIDIQKLISWLGVEGAKAGLDKSEMTNAELIESFGNLLPKNPSKL
                     KRSDLVEEIILATRRMTHKSVEELMEMSKEDLYSYFHDQKYSRKELLDLLYTLEIRPGS
                     SAKKNLTEFTISEISDIGMYRRVAKGNHA"
                     /name="hypothetical protein"
     gene            complement(859..1092)
                     /locus_tag="NFJ21_25755"
     CDS             complement(859..1092)
                     /locus_tag="NFJ21_25755"
                     /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="WFV15935.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNEQVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(1099..1617)
                     /locus_tag="NFJ21_25760"
     CDS             complement(1099..1617)
                     /locus_tag="NFJ21_25760"
                     /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="WFV15936.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTETMLNDEFSKLEKSVSKAVTSNE
                     TKIKDAIALFTASTEESLKKHREGVKEAMMQHRKDVLKLAGNTGMMLLGMVLFLFTVSG
                     GTLWYLGGRIQANLEEIRIQEETLQKLNAKTWGVEFVQDGRRKFLVLPYGKSATVIPYQ
                     EKDWVQLTE"
                     /name="MbeB family mobilization protein"
     gene            complement(1655..2086)
                     /locus_tag="NFJ21_25765"
                     /pseudo=""
     CDS             complement(1655..2086)
                     /locus_tag="NFJ21_25765"
                     /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(2295..2618)
                     /locus_tag="NFJ21_25770"
     CDS             complement(2295..2618)
                     /locus_tag="NFJ21_25770"
                     /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="WFV15937.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIERELRSLRQVVREHGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2683..2874
                     /locus_tag="NFJ21_25775"
     CDS             2683..2874
                     /locus_tag="NFJ21_25775"
                     /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="WFV15931.1"
                     /translation="MTKQEKTAINMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            3505..3636
                     /locus_tag="NFJ21_25780"
     CDS             3505..3636
                     /locus_tag="NFJ21_25780"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001505258.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WFV15932.1"
                     /translation="MHEPPVQSDCCACSGNYRLESNPERHDKAPLAAAMSKGVYKIY"
                     /name="replication initiation protein"
     gene            3885..4769
                     /locus_tag="NFJ21_25785"
     CDS             3885..4769
                     /locus_tag="NFJ21_25785"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001505259.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="ParA family protein"
                     /protein_id="WFV15933.1"
                     /translation="MAVTVGFISEKGGVGKTTSCYHIAEGLSRFHEKRVLVIDADYQRG
                     GITGRFFPKLIENFGNQAPQGTTLFNKYQQLYSAAQQTTDIDIIKFNSGIDVIPADPRL
                     STVSTDKLPSTNNIRSNNAILLQHLKTISAVLSPIADNYDYILIDSHPEVSDVMRSIIY
                     ASDYCVSPVKLDRQSSIGVATVIGEINNVNEDIEMLRKALQVGDSYKDTVFAGAMGMMA
                     REYAEELKQTEQYEYNRLRQAGDIFKHYITEGDGLRVAAAERVSVYDVQISNAYKQASQ
                     FKNLTIEFMRTCR"
                     /name="ParA family protein"
     Typing          complement(2970..3143)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.571"
                     /coverage="100.0"
                     /evalue="1.23e-64"
     Typing          3067..3653
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.723"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          complement(756..2305)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.412"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ggcatgtatc gtcgcgtagc gaaagggaat catgcataaa taaaagccac ctgtgaggtg
       61 gctttttata ggataaaaaa atgccattta atataggcga tatagtttac ttaaagtcag
      121 aatcaaaagc gatgacggtc atcggatatg gatcgtctca aaataacggt tacatagatc
      181 tagctaattg tgcttggcta gataaagaca accgctattg ccaaatacta ttcttgtttc
      241 aaacgatcga aaaaagaatc agttaaaaac tggcttatct tcattgagca taccggacga
      301 acctatttac cataacatcc gttgcccgca ccgcagaaac gcgttcggtg cgatcacggc
      361 agcagacagg taaaaatggc aacaaaccac ccgaaaaact gccgcgatcg cacccggtaa
      421 attttaacca catgcatagc tatgcagcca tgtgaatcac gcaggaattg ccagccagag
      481 acagctgaaa cggatttttt tcatgctttc ggaagcgaag aagacgggga ccggagcggg
      541 aaaacagaag ttcaggggaa tgagcgcgat ctggcaatag aggcaaaaca cagcaacaaa
      601 agacacacca gaatcgcgcc cgtatgcgtt ttaacgcgtt cctgtgtttt cagcaaggtc
      661 tgactgaagc gcgttcccgg tgcccccgaa ccaaccatta tcccaaaaaa tgcaccggaa
      721 acgcgctgac aacattttag cctgtctctg attaccatcc aagcgaaggg ccatcctgtg
      781 tccattcctg tatttccggc tggcgctcac gctccaggga taactcatgt tcgcgctcct
      841 gtatcagccg ttcgtccctt atctcctgtt ctcgctgtat aactggctca agcgttctgt
      901 ccgctcgctc aagtgctgca cctgctgact caactgcatg acctgctcgt tcagcatcgc
      961 gttgtcccgt tgcgtaagcg aaaacatttt ctgcaattcc acgaaggcgc tctcccattc
     1021 gctcagccgc tgcatatagt cctgttgcag ttgctctaag gcgttcagca aatgtctttc
     1081 cagctccgtc actctgtgtc actccgtcag ttgtacccag tccttctcct gatagggaat
     1141 caccgttgcc gatttcccgt acggaaggac cagaaatttc cttctcccgt cctgcacaaa
     1201 ctccacgccc catgtcttcg cgttcagttt ctgcaatgtt tcttcctgta tcctgatttc
     1261 ttccaggttc gcctgtatcc gcccgccaag ataccagagc gtcccgccac tcacggtaaa
     1321 caggaaaagg accatcccca gtaacatcat gcccgtattc cctgccagct ttaacacgtc
     1381 cttcctgtgc tgcatcatcg cctctttcac cccttcccgg tgttttttca gtgattcctc
     1441 tgtcgaagct gtgaacaggg ctatagcgtc tttgattttc gtctcgtttg atgtcacagc
     1501 cttgcttaca gatttttcga gcttgctgaa ctcgtcgttc agcattgtct ctgtagattc
     1561 ggctctctct ttcagctttt tctcgaactc cgcgcccgtc tgtaaaagat tgctcataga
     1621 atgctccttt cagtctgata ttcttcccgc cgttcgggtc tgcaatgctg atactgcttc
     1681 gcgtcaccct gaccacttca agccctgcct ctgtgagcgc ctgaatcaca tcctgacggc
     1741 cttttatctc cccgacatga taaagagcgt ctatcccgcg tgtgacgctc tctgcaagcg
     1801 cctgtttcgt ttccggcagg ttatcaggga gagtcagtat ccggcggttc tccggggcgt
     1861 tggggtcatg cagcccgtaa tggtgattaa ccagcgtctg ccaggcatca attctcggcc
     1921 tgtctgccca gtcgtagtac ggctggaggc gttttccgct ctgtagctcc atgttcggaa
     1981 tgacaaaatt cagctcaagc cgtcccttgt cctggtgctc cacccacagg atgctgtact
     2041 gatttttttc gagaccgggc atcagtacac gctcaaagct cgccatcacc ttttcacgtc
     2101 ctcccggcgg cagctccttc tccgcgaacg acagaacacc tgacgtgtat ttcttcgcaa
     2161 atggcgtggc atcgatgagt tcccggactt cttccggatt accctgaagc accgttgccc
     2221 cttcccggtt acgctccctt cccagcaggt aatcaaccgg accactgcca ccgccttttc
     2281 ccctggcatg aaacttaact atcatcccgc gctccatgtt ccctgacgac ctgccgtaag
     2341 ctgcgcaact ctctctcgat ggccatcagt gcggccacca cctgaacccg gtcaccggaa
     2401 gaccactgcc cgctgttcac cttcctcgcc gtctgattca gattattccc gatggcagcc
     2461 agctggcgca gtaacggcgg tgccagtgtc ggcagcttcc cggaacgggc aaccggctca
     2521 cccagacaga cccgccgcat ccataccgcc agctgtttac cctcacagcg ttccagtaac
     2581 cgtgcatgtt catcatcagt aacccgtatc gtgagcatcc tctcgcgttt catcggtatc
     2641 attaccccat gaacagaaat ccccccttac acggaggcat cagtgactaa acaggaaaaa
     2701 accgccatta acatggcccg ctttatcaga agccagacat taacgctgct ggaaaagctc
     2761 aacgaactgg acgcggatga acaggcagac atctgtgaat cgcttcacga ccacgccgat
     2821 gagctttacc gcagctgcct cgcacgcttc ggggatgacg gtgaaaacct ctgacacata
     2881 cagctcccgg agacggtcac agcttgtctg tgagcggatg ccgggagcag acaagcccgt
     2941 cagggcgcgt caggccgttg accttgcggg tgtcggggcg cagccatgac ccagtcacgt
     3001 agcgatagcg gagtgtatac tggcttacta tgttggcatg agtgcgggta tcaggaaagt
     3061 gcttcatgtg gcaggagaaa aaaggcggca ccggagcgtc agcagaatat gtgatacagg
     3121 atatattccg cttcctcgct cactgactcg ctacgctcgg tcgttcgact gcggcgagcg
     3181 gaaatggctt acgaacgggg cggagatttc ctggaagatg ccaggaagat acttaacagg
     3241 gaagcgatag ggtcgcggcg aagccgtttt tccataggct ccgcccccct gacaagcatc
     3301 acgaaatctg acgctcaaat cagtggtggc gaaacccgac aggactataa agataccagg
     3361 cgtttccccc tggtggctcc ctcgtgcgct ctcctgttcc tgcctttcgg tttaccggtg
     3421 tcattccgct gttatggccg cgtttatctc attccacgcc tgacactcag ttccgggtag
     3481 gcagttcgct ccaagctgga ctgtatgcac gaaccccccg ttcagtccga ctgctgcgcc
     3541 tgttccggta actatcgact tgagtccaac ccggaaagac acgacaaagc gccactggca
     3601 gcagccatga gtaaaggggt gtacaagatt tactgagtga gagttcttga agtatcagcc
     3661 ttagagaggc taaactggaa taacagaatt tggtttcagc ggtcttgtac accctgttac
     3721 cacggttcag aagttcccca acttactgaa ccctcgaaaa aaccgactcc ccagtcggtt
     3781 tttttcgttt gatggctaag agtacgctga cgttatactg aacgtcaagg aaagcgttga
     3841 cgctgttccc tctaccaaaa aaaagagatt tgtaaggaat aaaaatggct gtgacagttg
     3901 ggtttattag tgagaaaggt ggggttggta aaacaacgtc ctgttatcac attgccgaag
     3961 gacttagtcg ttttcatgaa aaacgtgttt tagttataga tgcagattat caacgcggag
     4021 gtataactgg aagatttttc cctaaactga tcgaaaactt tggaaatcaa gcaccgcaag
     4081 gaacaacgtt atttaacaag tatcagcaat tatatagcgc ggcacaacaa acgactgaca
     4141 tagacataat taaatttaat agtggtatcg atgtcattcc agccgaccct cgcttatcaa
     4201 ccgtttcaac tgataagcta cctagtacaa acaatataag atcgaacaat gccattcttt
     4261 tacagcattt aaaaaccata agcgctgtat tatcacctat tgcagataat tatgactaca
     4321 tattgattga ttcacacccc gaagtttctg atgtcatgcg ctctataatc tacgcatcag
     4381 attattgtgt atcaccggta aaactagaca ggcaatcatc tattggtgtg gccacggtca
     4441 taggtgagat aaataatgta aatgaagata ttgaaatgct aagaaaggca ctgcaagtcg
     4501 gcgattcata taaggacaca gttttcgccg gagcaatggg aatgatggcc agagaatatg
     4561 cagaagaact gaagcaaaca gagcaatatg aatacaacag gcttcggcaa gcaggtgaca
     4621 tcttcaagca ctacataacg gaaggtgatg ggctaagagt agctgcagca gagcgcgttt
     4681 cagtgtatga tgtacagata agtaacgctt acaaacaagc gtcacagttt aagaacttga
     4741 cgattgagtt tatgaggact tgtcgatgat agatatccaa aaactgatat cttggcttgg
     4801 cgttgaggga gctaaagctg gcttggataa aagtgaaatg actaatgccg agctaattga
     4861 atcctttggt aatttacttc caaagaaccc aagcaaatta aaacgctccg atctcgttga
     4921 ggagattatt ttagcaacaa ggagaatgac acataaatca gttgaagaac tgatggaaat
     4981 gtcaaaagaa gatctgtatt catatttcca cgatcagaaa tatagcagaa aagaacttct
     5041 tgatttgtta tatactcttg aaatcagacc tgggagctca gcaaagaaaa atctaaccga
     5101 gttcacaata agtgagataa gtgatatt
//
