LOCUS       NZ_CP099362             4664 bp    DNA     circular CON 15-APR-2024
DEFINITION  Escherichia fergusonii strain RHB02-E1-C03 plasmid unnamed4,
            complete sequence.
ACCESSION   NZ_CP099362
VERSION     NZ_CP099362.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15488482
            Assembly: GCF_029718025.1
KEYWORDS    RefSeq.
SOURCE      Escherichia fergusonii
  ORGANISM  Escherichia fergusonii
            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  JOURNAL   Unpublished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                     :: RHB02-E1-C03
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 180x
            Sequencing Technology             :: Illumina/Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_029718025.1-RS_2024_04_14
            Annotation Date                   :: 04/14/2024 22:20:15
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,811
            CDSs (total)                      :: 4,691
            Genes (coding)                    :: 4,592
            CDSs (with protein)               :: 4,592
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 90
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 99
            CDSs (without protein)            :: 99
            Pseudo Genes (ambiguous residues) :: 0 of 99
            Pseudo Genes (frameshifted)       :: 32 of 99
            Pseudo Genes (incomplete)         :: 58 of 99
            Pseudo Genes (internal stop)      :: 21 of 99
            Pseudo Genes (multiple problems)  :: 13 of 99
            Pseudo Genes (short protein)      :: 2 of 99
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP099362.1.
            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/
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..4664
                     /organism="Escherichia fergusonii"
                     /mol_type="genomic DNA"
                     /strain="RHB02-E1-C03"
                     /isolation_source="Pooled sediment sample collected from
                     floor of pig farm"
                     /db_xref="taxon:564"
                     /plasmid="unnamed4"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(join(4124..4664,1..1016))
                     /locus_tag="NFJ18_RS23985"
                     /old_locus_tag="NFJ18_23945"
     CDS             complement(join(4124..4664,1..1016))
                     /locus_tag="NFJ18_RS23985"
                     /old_locus_tag="NFJ18_23945"
                     /EC_number="2.7.7.65"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_013199864.1"
                     /GO_function="GO:0052621 - diguanylate cyclase activity
                     [Evidence IEA]; GO:0046872 - metal ion binding [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="sensor domain-containing diguanylate cyclase"
                     /protein_id="WP_224630669.1"
                     /translation="MRIKKPHLRPIVITLSVGGILLTSIFLIAVIMVFQRENIEKDLLY
                     ANSSYAMKMSDVMSGYIEMAQGELAYGAKKIKSTNDIDSLKDEADRLRLQSGMFNSVLV
                     VSNDAVVLATSPESLDLVGTRLNSSASKLAVEEKKPFISSPLKSVAGNLIILLSHPIYD
                     KGGNYIGYVGGSIYLKKHSLFGDVLSRHFFKNNTEISIVSDDGNVIFNNDKSAVDRPMV
                     MSDDLKSKLTASDRGEGAFFSSGHRYLLGYASMKNTAWNVLVYSRADSVTTILIAYAKS
                     VLVLLIIIIIVFSLISYFIASSISLPLEKLAISTNAKDIGASLVYIKAINAWYAEADRL
                     KKALFTYIKVMMERVDSLNEVALKDPLTGVNNRLGFLSKIQNHKRDSGCSVIVIDVDFF
                     KEINDSFGHGVGDEVLVSLAHIINSCCRSEDVVCRFGGEEFVVFLPNTSVVTAKCVAER
                     IRSVIESTVFPNNLRVTISAGVATQDDPLGRIDFLLKNADDALYQAKREGRNKVIVYSA
                     I"
                     /name="sensor domain-containing diguanylate cyclase"
     gene            complement(1362..1577)
                     /locus_tag="NFJ18_RS23990"
                     /old_locus_tag="NFJ18_23950"
     CDS             complement(1362..1577)
                     /locus_tag="NFJ18_RS23990"
                     /old_locus_tag="NFJ18_23950"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137422.1"
                     /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="WP_015589619.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWESAFAEWRTMSGLMQRENA
                     ALSERVTGLSRQVQSLSEQLRRLSSD"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(1581..2066)
                     /locus_tag="NFJ18_RS23995"
                     /old_locus_tag="NFJ18_23955"
     CDS             complement(1581..2066)
                     /locus_tag="NFJ18_RS23995"
                     /old_locus_tag="NFJ18_23955"
                     /inference="COORDINATES: protein motif:HMM:NF016710.4"
                     /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="WP_012565228.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQNTGEMLKAAFSEHEKSVKAELNESA
                     KRISAAILDHDRKLSSAMSQRTKGMVRMVSQTWLTIVLVSALLIASSAGILWWQGQQIL
                     DNYTTIREQKSTQAMLSERNSGVQLSTCGEQRRRCVKVNPEAGRFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            complement(<2101..2805)
                     /locus_tag="NFJ18_RS24090"
                     /pseudo=""
     CDS             complement(<2101..2805)
                     /locus_tag="NFJ18_RS24090"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /note="incomplete; partial in the middle of a contig;
                     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(2744..3067)
                     /locus_tag="NFJ18_RS24005"
                     /old_locus_tag="NFJ18_23965"
     CDS             complement(2744..3067)
                     /locus_tag="NFJ18_RS24005"
                     /old_locus_tag="NFJ18_23965"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /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="WP_015059937.1"
                     /translation="MLTMWVTEGEHRRLLERCDGRQLAAWMRQTCLDEKPARSGKLPSI
                     SPALLRQLAGMGNNLNQIARRVNAGGGTGHDRVQIVAALMAIDAGLERLRHAVLEKGTD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     Typing          complement(3181..3353)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.276"
                     /coverage="100.0"
                     /evalue="9.21e-81"
     Typing          3278..3829
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.639"
                     /coverage="91.0"
                     /evalue="0.0"
     Typing          complement(1259..2754)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="90.982"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(2751..3067)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.453"
                     /coverage="99.0"
                     /evalue="1.9499999999999998e-60"
ORIGIN
        1 ctatcagctt cggcatacca agcattgata gctttaatat aaactagcga agctccgata
       61 tctttagcat tggtagatat agcaagcttt tctaaaggaa gtgaaatact ggaggcaatg
      121 aaatatgaaa taagtgaaaa cacaataatt attataatta gcagaacaag tacactttta
      181 gcataagcaa taagaatagt agtcacactg tcagcacgac tataaaccaa cacattccaa
      241 gcggtatttt tcatactagc ataaccaaga agatatctat gccccgaaga aaaaaatgcc
      301 ccctcacctc tatcagacgc agttaacttt gatttcaaat catcagacat aaccataggc
      361 cgatcaacag cacttttatc gttattaaag atcacattcc catcatcact aacaatgcta
      421 atttcagtgt tgttcttgaa aaaatgcctg ctcaaaacat cgccaaataa actatgtttt
      481 tttagatata tagacccacc gacataccct atgtaattgc cacccttatc ataaatagga
      541 tgtgacaaca aaataatcaa attcccagca actgatttta acggtgaaga tatgaatggt
      601 ttcttttcct caaccgccaa tttgctggca cttgaattca agcgggtacc aactaaatca
      661 agagattctg gcgaagtcgc cagaacaaca gcatcattac taacaacaag aactgaatta
      721 aacataccag actgcaatct taacctatcc gcctcatctt taagtgagtc aatatcatta
      781 gttgatttta ttttttttgc tccatatgct aattcacctt gagccatttc aatataacca
      841 ctcattacat ctgacatttt catagcgtac gatgaattag cataaagcaa atctttttct
      901 atattttcgc gctgaaaaac cataataacg gcaatcagaa aaatagaagt taacaaaatc
      961 ccaccaacgg acaaggttat gactatcgga cgaaggtgag gctttttaat tctcataaaa
     1021 atacactcca tataataaaa aatgccgcat ttaccataac atcccttatc agcaccgccc
     1081 cggacgggtt cggaacaaat gcggcgtcag cccggtaaaa ccggcagcaa actctccgct
     1141 aaaccgcgca ttctgcgcca gataaatttc acccggctgc atggctatgc agtcgggtga
     1201 atggctccgg ctttcagcgc agatgtccgc cgaaagcccc gttttatcag gttatcacag
     1261 tgaagggctg ttatacgtcc gctgtcgctg agatcgctcc agctccagcg ctttctgatg
     1321 ctgcaccacg cgctcctgct cccggtgcag ctcgacggca ttcagtcgct cgacaaccgg
     1381 cgcagctgct cgctcaaact ctgcacctgc ctgctcaagc ccgtgacgcg ctcgctcagc
     1441 gctgcgttct cccgttgcat aagaccagac atcgtccgcc attccgcgaa ggcgctctcc
     1501 cactcgtcca gccttttcga gtagtcctgc tgtagctgct ctaatgcgct cagcaactgt
     1561 ttttccagct ccgtcatgtg ctatttcccc gccagtatca tccagctcga atcctctccg
     1621 aaccgtcccg cttccgggtt caccttcacg cagcggcgtc tctgctcgcc gcaggtcgag
     1681 agctgcacgc cgctgttcct ctctgacagc atggcctgcg tgctcttctg ctcccggatg
     1741 gtcgtgtagt tgtcgagtat ctgctgcccc tgccaccaca gaatgcccgc gctcgaggcg
     1801 atcagcagcg cggagaccag gacgatggtc agccacgtct ggctgaccat gcgcaccatg
     1861 cctttcgtgc gctggctcat ggctgaggac agtttccggt cgtggtcgag gatggcggcg
     1921 ctgattctct tcgcgctttc gttcagttcc gcttttacag atttctcgtg ctcgctgaat
     1981 gcggctttca gcatctcgcc ggtattctgc tgctgcgctt tcgatttctg ctctaagtcc
     2041 ttcgccagcg ttaaaagact gttcataaat ggctcccttc agtcggatgt ttcgcccccc
     2101 gtccgggtcg gcaatgctga tactgctttt tgtggtgcgg accacctcaa aacctgcgct
     2161 ttccagcgcc tcagtgacat cctgacgggt tttcagctcc ccggatgagg caagagcaag
     2221 cagaccgcgt gtaatcgctt ctgcagcctc ctgcttcgct ttaggcagtg cagacggtgt
     2281 gaccagtgcc cgccggttct ccggtgcgtt cgggtcgtgc agccccagtc tgccgttcac
     2341 gatggtctgc caggcatcga tgcgtggacg gtcggcgcga tcgtaatacg gctggagccg
     2401 tctgccggtc agcagctccg tgttcgggat cagaaaattc agctcaagcc gccccttgtc
     2461 acgatgctcc acccacagga tgctgtactg gtctttacca agtccgggca tcagaacccg
     2521 ctcaaagctt gccatcagct tttcccgctg gccggaaggt aaatccgctt ccgcaaacga
     2581 cagtaccccg gaggtgtatt tcttaacgta aggcgacgcg tcaatcagct cccggacttc
     2641 ttccggcttc ccctgcagga cggtggcgcc ttcacgctgc cggtctttac ccagcagata
     2701 gtccaccggc ccggcgccac cgccgcgacc gcgtggatga aatttaacga tcatcgtccg
     2761 ttcctttctc aagaacggcg tgccgcagcc gctcaagtcc ggcatcgatg gccatcagcg
     2821 ccgcaacaat ctgcaccctg tcatggccgg taccgccgcc ggcgttaaca cggcgggcta
     2881 tctggttcag gttattgccc atgccggcaa gctggcgcag cagcgccggc gagattgagg
     2941 gaagctttcc ggaacgtgcc ggcttttcgt ccaggcaggt ctgccgcatc cacgccgcca
     3001 gctgcctgcc gtcacagcgc tcaagcagcc gccggtgctc gccctccgtc acccacatgg
     3061 tgagcatctt gttccgtttc tctgacaaac cggcctcctg ataacgccgg gacgggcggg
     3121 aaaggctttc ccggtcggcg cggggttgga caagccgcag gcgcgtcagg cttttggcgg
     3181 gtttcggggc gcagccctga accagtcacg tagcgctagc ggagtgtata ctggcttact
     3241 atgttggcac ggatgcgagt gtcagtgaag tgcttcatgt ggcaggagaa aaatgcagca
     3301 gcggagcgtc agcagaatat gtgatacagg atatattccg cttcctcgct cactgactcg
     3361 ctgcgctcgg tcgttcggct gcggcgagcg gtaccgactt acaggcgggg cggaaatttc
     3421 ctgggagatg ccaggaagaa gcttaacagg gaagcgataa ggccacggcg aagccgtttt
     3481 tccataggct ccgcccccct gacaagcatc acgaaatctg acgctcaaat cagtggtggc
     3541 gaaacccgac aggacttaaa gataccaggc gtttccccct ggtggctccc tcgtgcgctc
     3601 tcctgttcct gcctttcggt ttaccgatgt caatccgctg ttatggccgc gtttatctca
     3661 ttccacgcct gacactcggt tccgggaagg cagttcgctc caagctggac tgtatgcacg
     3721 aaccccccgt tcagcccgac taccacgttg tcccggtaac tatcatcttg agtccaaccc
     3781 ggaacagaca cgaaaaatcg ccagtggcgg tagccattag taagaggatt cacggagcgg
     3841 agtagtagag tgttctacag agttcttgaa gtggtggcct gactgcggct acactggaag
     3901 gacagttttg gtacctgcgc tccgtgaaag ccagttacct tcggaagaaa gagttggtag
     3961 ctctgaattc cggcaaacga accaccgttg gtagcggtgg tttttttgtt tacagggtat
     4021 gagattacga cgacatcgaa gggataacaa gaggatccgc ttcttgccca ctcttcgcca
     4081 caaaaaaaac gacacactag cgcgtaaagc atcatcaaaa aactcaaata gcgctatata
     4141 caatcacttt attacgcccc tcccttttgg cttgataaag agcatcgtca gcatttttca
     4201 gcaaaaaatc gatcctacca agaggatcat cttgtgttgc cacaccagca gatatggtga
     4261 cccgcaagtt attagggaag acagtacttt caataacact cctaatacgc tccgcaacac
     4321 acttagctgt taccacagat gtattcggca ggaaaacaac aaactcttcg ccaccaaacc
     4381 gacaaacaac atcttcacta cggcaacagg aattaataat atgagccaaa gaaacaagca
     4441 cctcatctcc gaccccatgc ccgaaactgt catttatctc tttaaaaaaa tcaacatcaa
     4501 ttacaataac tgaacaccct gaatcccgct tatgattctg tattttactt aaaaacccca
     4561 atctattatt cacgccggta aggggatctt taagcgccac ctcatttaga gaatcaactc
     4621 tttccatcat taccttaata tacgtaaaaa gcgccttttt aagc
//
