LOCUS       NZ_CP058061             4664 bp    DNA     circular CON 01-APR-2024
DEFINITION  Escherichia fergusonii strain RHB02-C22 plasmid pRHB02-C22_5,
            complete sequence.
ACCESSION   NZ_CP058061
VERSION     NZ_CP058061.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15147971
            Assembly: GCF_013923185.1
KEYWORDS    RefSeq.
SOURCE      Escherichia fergusonii
  ORGANISM  Escherichia fergusonii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4664)
  AUTHORS   AbuOun,M., Jones,H., Stubberfield,E., Gilson,D., Shaw,L.P.,
            Hubbard,A.T.M., Chau,K.K., Sebra,R., Peto,T.E.A., Crook,D.W.,
            Read,D.S., Gweon,H.S., Walker,A.S., Stoesser,N., Smith,R.P.,
            Anjum,M.F. and On Behalf Of The Rehab,Consortium.
  TITLE     A genomic epidemiological study shows that prevalence of
            antimicrobial resistance in Enterobacterales is associated with the
            livestock host, as well as antimicrobial usage
  JOURNAL   Microb Genom 7 (10) (2021)
   PUBMED   34609275
REFERENCE   2  (bases 1 to 4664)
  AUTHORS   Shaw,L.P.
  TITLE     Direct Submission
  JOURNAL   Submitted (12-JUN-2020) Nuffield Department of Medicine, University
            of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.7
            Assembly Name                     :: RH02 T1-C22
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 117.004931831572x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_013923185.1-RS_2024_04_01
            Annotation Date                   :: 04/01/2024 04:20:42
            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)                     :: 4,813
            CDSs (total)                      :: 4,694
            Genes (coding)                    :: 4,592
            CDSs (with protein)               :: 4,592
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 102
            CDSs (without protein)            :: 102
            Pseudo Genes (ambiguous residues) :: 0 of 102
            Pseudo Genes (frameshifted)       :: 37 of 102
            Pseudo Genes (incomplete)         :: 57 of 102
            Pseudo Genes (internal stop)      :: 20 of 102
            Pseudo Genes (multiple problems)  :: 13 of 102
            Pseudo Genes (short protein)      :: 2 of 102
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP058061.1.
            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-C22"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:564"
                     /plasmid="pRHB02-C22_5"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            437..922
                     /locus_tag="HVV54_RS23880"
                     /old_locus_tag="HVV54_23880"
     CDS             437..922
                     /locus_tag="HVV54_RS23880"
                     /old_locus_tag="HVV54_23880"
                     /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            926..1141
                     /locus_tag="HVV54_RS23885"
                     /old_locus_tag="HVV54_23885"
     CDS             926..1141
                     /locus_tag="HVV54_RS23885"
                     /old_locus_tag="HVV54_23885"
                     /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            1487..3043
                     /locus_tag="HVV54_RS23890"
                     /old_locus_tag="HVV54_23890"
     CDS             1487..3043
                     /locus_tag="HVV54_RS23890"
                     /old_locus_tag="HVV54_23890"
                     /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            4100..4423
                     /locus_tag="HVV54_RS23895"
                     /old_locus_tag="HVV54_23895"
     CDS             4100..4423
                     /locus_tag="HVV54_RS23895"
                     /old_locus_tag="HVV54_23895"
                     /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          3815..3987
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.276"
                     /coverage="100.0"
                     /evalue="9.21e-81"
     Typing          complement(3339..3890)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.639"
                     /coverage="91.0"
                     /evalue="0.0"
     Typing          2..1245
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="90.843"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          4101..4417
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.453"
                     /coverage="99.0"
                     /evalue="1.9499999999999998e-60"
     Typing          4414..4664
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.81"
                     /coverage="97.0"
                     /evalue="9.38e-46"
ORIGIN
        1 cttggtaaag accagtacag catcctgtgg gtggagcatc gtgacaaggg gcggcttgag
       61 ctgaattttc tgatcccgaa cacggagctg ctgaccggca gacggctcca gccgtattac
      121 gatcgcgccg accgtccacg catcgatgcc tggcagacca tcgtgaacgg cagactgggg
      181 ctgcacgacc cgaacgcacc ggagaaccgg cgggcactgg tcacaccgtc tgcactgcct
      241 aaagcgaagc aggaggctgc agaagcgatt acacgcggtc tgcttgctct tgcctcatcc
      301 ggggagctga aaacccgtca ggatgtcact gaggcgctgg aaagcgcagg ttttgaggtg
      361 gtccgcacca caaaaagcag tatcagcatt gccgacccgg acggggggcg aaacatccga
      421 ctgaagggag ccatttatga acagtctttt aacgctggcg aaggacttag agcagaaatc
      481 gaaagcgcag cagcagaata ccggcgagat gctgaaagcc gcattcagcg agcacgagaa
      541 atctgtaaaa gcggaactga acgaaagcgc gaagagaatc agcgccgcca tcctcgacca
      601 cgaccggaaa ctgtcctcag ccatgagcca gcgcacgaaa ggcatggtgc gcatggtcag
      661 ccagacgtgg ctgaccatcg tcctggtctc cgcgctgctg atcgcctcga gcgcgggcat
      721 tctgtggtgg caggggcagc agatactcga caactacacg accatccggg agcagaagag
      781 cacgcaggcc atgctgtcag agaggaacag cggcgtgcag ctctcgacct gcggcgagca
      841 gagacgccgc tgcgtgaagg tgaacccgga agcgggacgg ttcggagagg attcgagctg
      901 gatgatactg gcggggaaat agcacatgac ggagctggaa aaacagttgc tgagcgcatt
      961 agagcagcta cagcaggact actcgaaaag gctggacgag tgggagagcg ccttcgcgga
     1021 atggcggacg atgtctggtc ttatgcaacg ggagaacgca gcgctgagcg agcgcgtcac
     1081 gggcttgagc aggcaggtgc agagtttgag cgagcagctg cgccggttgt cgagcgactg
     1141 aatgccgtcg agctgcaccg ggagcaggag cgcgtggtgc agcatcagaa agcgctggag
     1201 ctggagcgat ctcagcgaca gcggacgtat aacagccctt cactgtgata acctgataaa
     1261 acggggcttt cggcggacat ctgcgctgaa agccggagcc attcacccga ctgcatagcc
     1321 atgcagccgg gtgaaattta tctggcgcag aatgcgcggt ttagcggaga gtttgctgcc
     1381 ggttttaccg ggctgacgcc gcatttgttc cgaacccgtc cggggcggtg ctgataaggg
     1441 atgttatggt aaatgcggca ttttttatta tatggagtgt atttttatga gaattaaaaa
     1501 gcctcacctt cgtccgatag tcataacctt gtccgttggt gggattttgt taacttctat
     1561 ttttctgatt gccgttatta tggtttttca gcgcgaaaat atagaaaaag atttgcttta
     1621 tgctaattca tcgtacgcta tgaaaatgtc agatgtaatg agtggttata ttgaaatggc
     1681 tcaaggtgaa ttagcatatg gagcaaaaaa aataaaatca actaatgata ttgactcact
     1741 taaagatgag gcggataggt taagattgca gtctggtatg tttaattcag ttcttgttgt
     1801 tagtaatgat gctgttgttc tggcgacttc gccagaatct cttgatttag ttggtacccg
     1861 cttgaattca agtgccagca aattggcggt tgaggaaaag aaaccattca tatcttcacc
     1921 gttaaaatca gttgctggga atttgattat tttgttgtca catcctattt atgataaggg
     1981 tggcaattac atagggtatg tcggtgggtc tatatatcta aaaaaacata gtttatttgg
     2041 cgatgttttg agcaggcatt ttttcaagaa caacactgaa attagcattg ttagtgatga
     2101 tgggaatgtg atctttaata acgataaaag tgctgttgat cggcctatgg ttatgtctga
     2161 tgatttgaaa tcaaagttaa ctgcgtctga tagaggtgag ggggcatttt tttcttcggg
     2221 gcatagatat cttcttggtt atgctagtat gaaaaatacc gcttggaatg tgttggttta
     2281 tagtcgtgct gacagtgtga ctactattct tattgcttat gctaaaagtg tacttgttct
     2341 gctaattata ataattattg tgttttcact tatttcatat ttcattgcct ccagtatttc
     2401 acttccttta gaaaagcttg ctatatctac caatgctaaa gatatcggag cttcgctagt
     2461 ttatattaaa gctatcaatg cttggtatgc cgaagctgat aggcttaaaa aggcgctttt
     2521 tacgtatatt aaggtaatga tggaaagagt tgattctcta aatgaggtgg cgcttaaaga
     2581 tccccttacc ggcgtgaata atagattggg gtttttaagt aaaatacaga atcataagcg
     2641 ggattcaggg tgttcagtta ttgtaattga tgttgatttt tttaaagaga taaatgacag
     2701 tttcgggcat ggggtcggag atgaggtgct tgtttctttg gctcatatta ttaattcctg
     2761 ttgccgtagt gaagatgttg tttgtcggtt tggtggcgaa gagtttgttg ttttcctgcc
     2821 gaatacatct gtggtaacag ctaagtgtgt tgcggagcgt attaggagtg ttattgaaag
     2881 tactgtcttc cctaataact tgcgggtcac catatctgct ggtgtggcaa cacaagatga
     2941 tcctcttggt aggatcgatt ttttgctgaa aaatgctgac gatgctcttt atcaagccaa
     3001 aagggagggg cgtaataaag tgattgtata tagcgctatt tgagtttttt gatgatgctt
     3061 tacgcgctag tgtgtcgttt tttttgtggc gaagagtggg caagaagcgg atcctcttgt
     3121 tatcccttcg atgtcgtcgt aatctcatac cctgtaaaca aaaaaaccac cgctaccaac
     3181 ggtggttcgt ttgccggaat tcagagctac caactctttc ttccgaaggt aactggcttt
     3241 cacggagcgc aggtaccaaa actgtccttc cagtgtagcc gcagtcaggc caccacttca
     3301 agaactctgt agaacactct actactccgc tccgtgaatc ctcttactaa tggctaccgc
     3361 cactggcgat ttttcgtgtc tgttccgggt tggactcaag atgatagtta ccgggacaac
     3421 gtggtagtcg ggctgaacgg ggggttcgtg catacagtcc agcttggagc gaactgcctt
     3481 cccggaaccg agtgtcaggc gtggaatgag ataaacgcgg ccataacagc ggattgacat
     3541 cggtaaaccg aaaggcagga acaggagagc gcacgaggga gccaccaggg ggaaacgcct
     3601 ggtatcttta agtcctgtcg ggtttcgcca ccactgattt gagcgtcaga tttcgtgatg
     3661 cttgtcaggg gggcggagcc tatggaaaaa cggcttcgcc gtggccttat cgcttccctg
     3721 ttaagcttct tcctggcatc tcccaggaaa tttccgcccc gcctgtaagt cggtaccgct
     3781 cgccgcagcc gaacgaccga gcgcagcgag tcagtgagcg aggaagcgga atatatcctg
     3841 tatcacatat tctgctgacg ctccgctgct gcatttttct cctgccacat gaagcacttc
     3901 actgacactc gcatccgtgc caacatagta agccagtata cactccgcta gcgctacgtg
     3961 actggttcag ggctgcgccc cgaaacccgc caaaagcctg acgcgcctgc ggcttgtcca
     4021 accccgcgcc gaccgggaaa gcctttcccg cccgtcccgg cgttatcagg aggccggttt
     4081 gtcagagaaa cggaacaaga tgctcaccat gtgggtgacg gagggcgagc accggcggct
     4141 gcttgagcgc tgtgacggca ggcagctggc ggcgtggatg cggcagacct gcctggacga
     4201 aaagccggca cgttccggaa agcttccctc aatctcgccg gcgctgctgc gccagcttgc
     4261 cggcatgggc aataacctga accagatagc ccgccgtgtt aacgccggcg gcggtaccgg
     4321 ccatgacagg gtgcagattg ttgcggcgct gatggccatc gatgccggac ttgagcggct
     4381 gcggcacgcc gttcttgaga aaggaacgga cgatgatcgt taaatttcat ccacgcggtc
     4441 gcggcggtgg cgccgggccg gtggactatc tgctgggtaa agaccggcag cgtgaaggcg
     4501 ccaccgtcct gcaggggaag ccggaagaag tccgggagct gattgacgcg tcgccttacg
     4561 ttaagaaata cacctccggg gtactgtcgt ttgcggaagc ggatttacct tccggccagc
     4621 gggaaaagct gatggcaagc tttgagcggg ttctgatgcc cgga
//
