LOCUS       CP098964                4664 bp    DNA     circular BCT 13-APR-2023
DEFINITION  Escherichia coli strain RHB46-C24 plasmid unnamed2, complete
            sequence.
ACCESSION   CP098964
VERSION     CP098964.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15488718
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  JOURNAL   Unpublished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                     :: RHB46-C24
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 129x
            Sequencing Technology             :: Illumina/Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/15/2022 18:18:28
            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)                     :: 4,739
            CDSs (total)                      :: 4,627
            Genes (coding)                    :: 4,379
            CDSs (with protein)               :: 4,379
            Genes (RNA)                       :: 112
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 83
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 248
            CDSs (without protein)            :: 248
            Pseudo Genes (ambiguous residues) :: 0 of 248
            Pseudo Genes (frameshifted)       :: 51 of 248
            Pseudo Genes (incomplete)         :: 186 of 248
            Pseudo Genes (internal stop)      :: 43 of 248
            Pseudo Genes (multiple problems)  :: 29 of 248
            CRISPR Arrays                     :: 3
            ##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="RHB46-C24"
                     /isolation_source="Pooled faeces sample collected from
                     floor of poultry farm"
                     /db_xref="taxon:562"
                     /plasmid="unnamed2"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(754..936)
                     /locus_tag="NFL54_23670"
                     /pseudo=""
     CDS             complement(754..936)
                     /locus_tag="NFL54_23670"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007798797.1"
                     /note="incomplete; partial on complete genome; missing
                     N-terminus; Derived by automated computational analysis
                     using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="NINE protein"
                     /name="NINE protein"
     gene            933..1175
                     /locus_tag="NFL54_23675"
                     /pseudo=""
     CDS             933..1175
                     /locus_tag="NFL54_23675"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_003862821.1"
                     /note="incomplete; partial on complete genome; missing
                     N-terminus; Derived by automated computational analysis
                     using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="cupin domain-containing protein"
                     /name="cupin domain-containing protein"
     gene            complement(1213..2355)
                     /gene="wzz(fepE)"
                     /locus_tag="NFL54_23680"
     CDS             complement(1213..2355)
                     /gene="wzz(fepE)"
                     /locus_tag="NFL54_23680"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010435173.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology. GO_component:
                     GO:0016020 - membrane [Evidence IEA]; GO_process:
                     GO:0009103 - lipopolysaccharide biosynthetic process
                     [Evidence IEA]"
                     /codon_start=1
                     /transl_table=11
                     /product="LPS O-antigen length regulator Wzz(fepE)"
                     /protein_id="WGB99881.1"
                     /translation="MSAMDFKKNTDLDFPRYATPAVSTKEIDLLGLLDVLLAAKKRIVT
                     IVLAFAVVGLAIAFLIPQKWTSKAVITPAEQTQWNTLRQMMVTLQVLDVDAKVSRGDVF
                     NLFIKKFQSQSLLEEYMKTSPYVMSQLEGTEVDPLELHRAVVNIAEKMKATDNTQVKDA
                     DKAPYTSWTLSFTAPTAGDAQTVLEGYINYISRIVEQETMENIRNQITLKTKVVQQQLE
                     LDRVRLTNIHNTNLQRLNYSLEVANAAGIKKPVYSNGQAVKDDPDYSVALGADGIAQKL
                     QIEKNLKDVAELNADFQNREYYLTQLQKLSVEDVKLEPFRYQLSPSLPVKKDGPGKALI
                     VLLAGILGGLFACGSVLLREAMLSRNPLPEPITAVTPATE"
                     /name="wzz(fepE)"
     gene            2550..3531
                     /locus_tag="NFL54_23685"
     CDS             join(2550..3341,3343..3531)
                     /locus_tag="NFL54_23685"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_048909999.1"
                     /ribosomal_slippage=""
                     /note="programmed frameshift; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology. GO_function: GO:0004803 - transposase
                     activity [Evidence IEA]"
                     /codon_start=1
                     /transl_table=11
                     /product="IS5 family transposase"
                     /protein_id="WGB99879.1"
                     /translation="MSHQLTFADSEFSSKRRQTRKEIFLSRMEQILPWQNMVEVIEPFY
                     PKAGNGRRPYPLETMLRIHCMQHWYNLSDGAIEDALYEIASMRLFARLSLDSALPDRTT
                     IMNFRHLLEQHQLARQLFKTINRWLAEAGVMMTQGTLVDATIIEAPSSTKNKEQQRDPE
                     MHQTKKGNQWHFGMKAHIGVDAKSGLTHSLVTTAANEHDLNQLGNLLHGEEQFVSADAG
                     YQGAPQREELAEVDVDWLIAERPGKVRTLKQHPRKNKTAHQHEYMKASIRAKVEHPFRI
                     IKRQFGFVKARYKGLLKNDNQLAMLFTLANLFRADQMIRQWERSH"
                     /name="IS5 family transposase"
     gene            complement(3680..3811)
                     /locus_tag="NFL54_23690"
                     /pseudo=""
     CDS             complement(3680..3811)
                     /locus_tag="NFL54_23690"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_013578013.1"
                     /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="zinc-ribbon domain-containing protein"
                     /name="zinc-ribbon domain-containing protein"
     gene            complement(4119..4232)
                     /locus_tag="NFL54_23695"
     CDS             complement(4119..4232)
                     /locus_tag="NFL54_23695"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WGB99880.1"
                     /translation="MHDPPVQSDRCVFSGNYRLESKPERHDKAPLAAATGN"
                     /name="replication initiation protein"
     Typing          complement(4116..4501)
                     /name="rep_cluster_2373"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.116"
                     /coverage="90.0"
                     /evalue="4.83e-172"
ORIGIN
        1 ggctaacgcc gcaaagtgac gtcacctgac gttcctggat tacaaaggtt aaagcagcgg
       61 acaggaaatg ttttgtgccc acagctatgc tggcttattc acaaaacagc gggacaagat
      121 gtgtttttgg agtaccgccg gcccgctaaa gactcctggt tagctcccgc atgtttgcta
      181 tctttttgct accattttgc tacttttttg ctatctccag agtcttctgg tctttcggtt
      241 gctatccttt tgctactttt ttgctatcaa aatgctacct ctcccttctt gcaataaatg
      301 accaaggcac gttagcgatg tatacatcgc cgcgccgcaa gggtgcccct tccgaatccc
      361 gttcatcact gcgtgctgat tcatccacgt taaatccgac ccccttagca ataaatccag
      421 ccatgcctga cggcctggcc aacgcctcac ggccgcacag taaactgcac acccgtgagg
      481 cgttattcgt gaggttcagt ggtgcttttg ggcgtccagc cggattttag cggctaaaat
      541 cccggccatg catgtgtgtg catagccatg cagacgcgcc agaatcatca ggcgcgtttt
      601 ttcacgatat aggcacaggg aagtgtcgga aacaggcagg aagacccaga aacgccctga
      661 gagcctctca ggcggtgcac gcaacggatg ttatggtaaa tctgcctcac agactggtac
      721 aaaaaaagcc ccgcagggct tttttgctat gagttagcca tattttcttg cgaatttttc
      781 atcggaatcg catagataaa taataaactc aataaacgcg atgatcgcgg gtatgaatgt
      841 ccagcaaaaa attagataca ggaatccctg tcctatttta cctaagtaaa atttatgtac
      901 gccaaatcca ccaaggaaga atgctaagaa agatgatggc ggtggaggtc aattttgagc
      961 agggtgcgat tggcccgatg cacaatcacc cgcatgaaca gcttacctat gtgctctccg
     1021 gggagttcga gtttacgata ggtgaagaaa agcagatcgt gacggcgggc gatacgctct
     1081 ataaagcgcc gcacgtgatg cacggctgca tttgcctgaa gcccggcacc cttctggata
     1141 cctttacgcc ggtgcgcgac gatttcctga aataaaaaaa ggcgctgaat cagcgccttt
     1201 ttaatatcgt cgttactctg ttgctggcgt tacggccgtt atcggctctg gcaacggatt
     1261 acgcgagagc attgcctcac gcagcagcac gctgccgcag gcaaacaggc cgcccagaat
     1321 ccctgccagc agcacaatca gggctttgcc cggaccgtct tttttcaccg gcagtgacgg
     1381 tgaaagctga tacctgaagg gttcaagctt cacgtcttcc acggacagtt tttgcaactg
     1441 agtcagatag tattcacggt tctggaaatc cgcattcagc tcggccacgt ccttcagatt
     1501 cttttcaatc tgcagctttt gcgcaatacc gtcagcaccc agcgccacgg agtagtcagg
     1561 atcgtctttt accgcctgtc cgttgctgta aaccggcttc ttaatgcctg ccgcgttcgc
     1621 cacttccagc gaatagttga ggcgctgcag gttggtgttg tggatattgg tcagacgcac
     1681 gcgatccagc tccagctgct gctgaacgac tttcgttttc agcgtgatct ggttacggat
     1741 attttccatc gtctcctgct caacaatgcg ggagatatag ttgatgtaac cttccagaac
     1801 cgtctgcgcg tctcccgccg tcggggcggt aaagctcagc gtccatgagg tatacggcgc
     1861 tttgtctgcg tctttaacct gcgtgttatc tgtcgctttc attttctcag caatattcac
     1921 caccgcgcga tgcagctcca gcgggtctac ctcggtgcct tccagctgag acatcacgta
     1981 cggggaggtt ttcatgtact cttcgagcag cgactgcgac tgaaactttt tgatgaacag
     2041 gttaaacacg tctccacggc tcaccttcgc gtcgacgtcc agcacctgca gcgtcaccat
     2101 catctggcgc agcgtgttcc actgcgtctg ctcggccggc gtgatcacgg ctttactggt
     2161 ccatttttgc gggattaaaa acgcaatggc caaccctact acggcgaacg ccaggacgat
     2221 cgtcacaata cgttttttgg ctgccagaag tacgtctaac aaccccagga gatctatctc
     2281 tttggtgctt accgccggag tggcataacg gggaaaatcg aggtccgtgt ttttcttgaa
     2341 atccatcgct gacataaccg ttcttctttt tggagcgcag taaatttctg cctgattggt
     2401 tgcagtggtc ggatgataca agaaagtaag aataatctta acgccagatt gatctatctg
     2461 tagaccgact atcagattta gggaaggtgc gaacaagtcc ctgatatgag atcatgtttg
     2521 tcatctggag ccatggaaca gggttcatca tgagtcatca acttaccttc gccgacagtg
     2581 aattcagcag taagcgccgt cagaccagaa aagagatttt cttgtcccgc atggagcaga
     2641 ttctgccatg gcaaaacatg gtggaagtca tcgagccgtt ttaccccaag gctggtaatg
     2701 gccggcgacc ttatccgctg gaaaccatgc tacgcattca ctgcatgcag cattggtaca
     2761 acctgagcga tggcgcgatc gaagatgctc tgtacgaaat cgcctccatg cgtctgtttg
     2821 cccggttatc cctggatagc gccttgccgg accgcaccac catcatgaat ttccgccacc
     2881 tgctggagca gcatcaactg gcccgccaat tgttcaagac catcaatcgc tggctggccg
     2941 aagcaggcgt catgatgact caaggcacct tggtcgatgc caccatcatt gaggcaccca
     3001 gctcgaccaa gaacaaagag cagcaacgcg atccggagat gcatcagact aagaaaggca
     3061 atcagtggca ctttggcatg aaggcccaca ttggtgtcga tgccaagagt ggcctgaccc
     3121 acagcctagt caccaccgcg gccaacgagc atgacctcaa tcagctgggt aatctgctgc
     3181 atggagagga gcaatttgtc tcagccgatg ccggctacca aggggcgcca cagcgcgagg
     3241 agctggccga ggtggatgtg gactggctga tcgccgagcg ccccggcaag gtaagaacct
     3301 tgaaacagca tccacgcaag aacaaaacgg cccatcaaca tcgaatacat gaaagccagc
     3361 atccgggcca aggtggagca cccatttcgc atcatcaagc gacagttcgg cttcgtgaaa
     3421 gccagataca aggggttgct gaaaaacgat aaccaactgg cgatgttatt cacgctggcc
     3481 aacctgtttc gggcggacca aatgatacgt cagtgggaga gatctcacta aaaactggga
     3541 ataacgcctt aaatggcgaa gaaacggtct aaataggctg attcaaggca tttacgggag
     3601 aaaaaaatcg gctcaaacat gaagaaatga aatgactgag tcaaccgaga agaatttccc
     3661 cgcttattcg caccttccct aatagcgcgg ctgcgattct acttttttca cctgaacctg
     3721 aagaggcgtt tgtggctccg cagtgtgggc atgactttgc tgtttcgtgt atttccttgc
     3781 cgcatcctcg gcagtaaacc attgaactca ttttttatcc tcgagcttat ttttagttgg
     3841 gatgcataat atccgatgtt ttataacgat atgcatccta tatgctcggg tgggatagat
     3901 ttccattatg gtgaaggatc ttcttgagat cctttctgta gcgtcgtaat ctcttgctca
     3961 gtaaacgaaa aaaccgccca gcaaggcggt ttttcgaagg ttctcagagc tgcaactctt
     4021 tgaaccgtgg taactggctt atgaggagcg cagtaaccaa atctgttctt tcagtttagc
     4081 cttaacaggc gcataacttc aagactaact cctctaaatc agttaccagt ggctgctgcc
     4141 agtggcgctt tgtcgtgtct ttccggcttg gactcaagtc gatagttacc ggagaagacg
     4201 cagcggtcgg actgaacggg ggggtcgtgc atacagtcca gcttggagcg aactgcctac
     4261 ccggaactga gtgtcaggcg tggaatgaga taaacgcggc cataacagcg gaatgacacc
     4321 ggtaaaccga aaggcaggaa caggagagcg cacgagggag ccaccagggg gaaacgcctg
     4381 gtatctttaa gtcctgtcgg gtttcgccac cactgatttg agcgtcagat tctgtgatgc
     4441 ttgtcagggg ggcggagcct atggaaaacc ggcaacgccg cggccttttc ttttgcctct
     4501 cgatcctctc tcattgcctg tgccttaatg tctccgttcc ctccgctcgc cgcagccgaa
     4561 cgaccgagcg tagcgagtca gtgagcgagg aagcggaata tccccggact tatcttcggc
     4621 accgtacgcg ccagtgctgc attttttaat acgatgcagg atag
//
