LOCUS       NZ_CP055606             3840 bp    DNA     circular CON 01-APR-2024
DEFINITION  Escherichia fergusonii strain RHB41-C23 plasmid pRHB41-C23_8,
            complete sequence.
ACCESSION   NZ_CP055606
VERSION     NZ_CP055606.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15148431
            Assembly: GCF_013591455.1
KEYWORDS    RefSeq.
SOURCE      Escherichia fergusonii
  ORGANISM  Escherichia fergusonii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3840)
  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 3840)
  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                     :: RH01 T3-C23
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 145.857560681824x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_013591455.1-RS_2024_04_01
            Annotation Date                   :: 04/01/2024 04:10:29
            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)                     :: 4,801
            CDSs (total)                      :: 4,683
            Genes (coding)                    :: 4,563
            CDSs (with protein)               :: 4,563
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 120
            CDSs (without protein)            :: 120
            Pseudo Genes (ambiguous residues) :: 0 of 120
            Pseudo Genes (frameshifted)       :: 26 of 120
            Pseudo Genes (incomplete)         :: 84 of 120
            Pseudo Genes (internal stop)      :: 18 of 120
            Pseudo Genes (multiple problems)  :: 10 of 120
            Pseudo Genes (short protein)      :: 2 of 120
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP055606.1.
            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..3840
                     /organism="Escherichia fergusonii"
                     /mol_type="genomic DNA"
                     /strain="RHB41-C23"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:564"
                     /plasmid="pRHB41-C23_8"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            join(3771..3840,1..197)
                     /locus_tag="HV014_RS23815"
                     /old_locus_tag="HV014_23825"
     CDS             join(3771..3840,1..197)
                     /locus_tag="HV014_RS23815"
                     /old_locus_tag="HV014_23825"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_213069224.1"
                     /translation="MKRSQLTLIDGCFMFGFSPGELMNLCPDERLLFVRMISAMLRRSG
                     GDAGAVMFEAYRHIVSDTNQARRSCMLDLLESVRHDYVHGGYT"
                     /name="hypothetical protein"
     gene            complement(245..433)
                     /locus_tag="HV014_RS23820"
                     /old_locus_tag="HV014_23830"
     CDS             complement(245..433)
                     /locus_tag="HV014_RS23820"
                     /old_locus_tag="HV014_23830"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165998.1"
                     /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="WP_000165998.1"
                     /translation="MTKQESAALNMAKFIRAQSLLLLEKLDVLDLDDEAADCERMHEQA
                     EALYQKLSARFGIQDGE"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(723..2627)
                     /locus_tag="HV014_RS23825"
                     /old_locus_tag="HV014_23835"
     CDS             complement(723..2627)
                     /locus_tag="HV014_RS23825"
                     /old_locus_tag="HV014_23835"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_003839290.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="methyl-accepting chemotaxis protein"
                     /protein_id="WP_061202242.1"
                     /translation="MSWVYRISMQMKLFIALFPLLLALVWFAGSGIVSRINTEQQMNTI
                     GQLTTLARSAGDVVHQLQSERGMSAGFIGARGQKFRDDLAAQRQLTDKVLATFKRLLTD
                     TNKDLLQGNIAAPLKTFNESIQFLDSTRTAISELTIDSPKASQFYTQTISDVLKFVGGM
                     GHLSTSGSMVNELAAYYSLLNLKEQAGVERALLSNIFSMDRFDDGQFSMFSDVVGQQDA
                     WLTAARSFSTPVQAAELDKSLQSAEATRALELRETAFNKAAEGGFGVNPTDWFNLQTQR
                     IETLQKVENRAVDALQEHAALLAHNARVDWQSFLVISLVALLIAIAFAVMVARSIQQQL
                     NGTLKTIAEMDGDLTRRLDVPGSDELSALNRAYNQAIENIQHIVQEIKSGAVVLRSASS
                     DIAAGNQDLAQRTDEQAASIVETAASMEQISTAITQTADNASEAERLIHSMERDVLEAN
                     RVSNEASQSMAEIRSSSEQISQIVASIDEISFQTNLLALNAAVEAARAGELGKGFAVVA
                     TEVRNLSQRCAREASQIRELINQNMDKIGEGVARVTASGTALKAAAENTGRMKQYVSDI
                     ARAANEQSLGVSQVHQALNQLEQVTQQNAALVSQAASASQMLDGQSEAMSTLVDRFIV"
                     /name="methyl-accepting chemotaxis protein"
     gene            complement(2933..3082)
                     /locus_tag="HV014_RS24310"
     CDS             complement(2933..3082)
                     /locus_tag="HV014_RS24310"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001333247.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_077464408.1"
                     /translation="MHEPPVQSDCCAFSGNYRLESNPERHEKSPLAAATGKQDVREMYR
                     EFLK"
                     /name="replication initiation protein"
     Typing          3445..3617
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="91.379"
                     /coverage="100.0"
                     /evalue="9.47e-61"
     Typing          complement(2924..3520)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.211"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 acctttgccc cgatgaacgt ctgctctttg tgcggatgat ttccgctatg cttcgccgtt
       61 cgggcggtga tgcgggtgct gttatgtttg aggcgtatcg ccatattgtg tccgatacca
      121 atcaagctcg tcgttcctgc atgctcgacc tgctcgaaag cgtcaggcat gactatgtac
      181 acggtggata tacatagttg ccctggatac gcttttcgtc taagtgagcg ttcttttcgt
      241 ctctttattc gccgtcctgt ataccgaagc gtgcgctcag cttctgataa agcgcttctg
      301 cctgttcgtg cattcgctca cagtcggctg cctcgtcatc aagatcgagc acgtcgagtt
      361 tttcgagcag cagcagcgac tgcgcccgga taaattttgc catgttcagt gcggctgatt
      421 cctgttttgt catacggctt tttcccggtt ttatggtgat cgcagactga aatcttactt
      481 cattcacttg agtgcatagc catgcaggta cgcagaaatc atcaggggcg ttttttctcg
      541 atatgggcac agaaaggtgt atgtttcagg tcggagtcct cagaaacgct ctcagagcct
      601 ctcaggcggt gcacgcaaca gatgttatgg taaatcctag ttatttgcag gcataaaaaa
      661 gccgcctttt aggcggtttt ttctgattgt aagttatcaa gaccggatgc tgaacggcag
      721 tatcagacaa taaagcgatc gaccagcgtg gacatcgctt cagactggcc gtccagcatc
      781 tggctggcgc tcgccgcctg agagaccagc gctgcgtttt gctgagtgac ctgctccagc
      841 tgattcagtg cctgatgcac ctgcgacacg ccaagcgact gctcattcgc cgcacgggca
      901 atatcgctca cgtactgttt catccgcccg gtattttccg ccgctgcttt cagcgcggtg
      961 ccggacgcgg tgactcgtgc taccccttcg ccaatcttat ccatattctg gttaatcagc
     1021 tcacggatct gactggcctc tcgtgcacag cgctgggaaa ggttacgcac ctccgtcgcc
     1081 actaccgcaa agcctttgcc aagctcaccg gcacgtgccg cttcaacggc ggcgttaagc
     1141 gccagcaagt tggtctggaa agaaatctca tcaattgacg caacaatctg ggaaatctgc
     1201 tcgctggaag aacgaatttc cgccatgctc tgactggcct cgttagagac gcgattagct
     1261 tccagtacgt cccgctccat cgaatgtatc agacgctccg cctcgctggc gttatcggcg
     1321 gtctgggtga tcgcagtaga aatctgctcc atgctggcgg ccgtttccac aatcgatgcc
     1381 gcctgttcat ccgtacgctg ggccagatcc tgattaccgg cagcgatatc actactggcg
     1441 ctacgcaaca ccaccgcacc ggacttaatt tcttgcacga tatgctgaat attctcaatc
     1501 gcttggttat aggcacggtt cagggctgag agctcgtcgc tgccggggac gtcaagacga
     1561 cgtgtcaggt cgccgtccat ctctgcgatg gttttcagcg taccgttcag ttgctgctgg
     1621 atactgcgtg ccaccatcac cgcaaaggcg atagcaatca gtagggcaac caggctgatt
     1681 accaggaagg actgccagtc gacacgggca ttgtgggcaa gcagcgcagc atgttcctgc
     1741 aaggcatcca ccgcgcgatt ttccaccttt tgcagcgttt caatacgctg ggtctgaagg
     1801 ttaaaccagt cagtcgggtt gactccaaat ccgccttcgg cggctttatt aaaagccgtc
     1861 tcccgcagtt caagagcacg agttgcttca gcggactgaa gagatttgtc cagctcagcc
     1921 gcctgcacag gtgtgctaaa gctgcgagct gccgtcagcc aggcatcctg ctggcctacc
     1981 acatcgctaa acatgctgaa ctggccgtcg tcaaagcgat ccatcgagaa gatattggac
     2041 agcagcgcac gttctacacc agcctgctcc ttcaaattca agagactata ataagccgcc
     2101 agttcgttca ccatcgagcc tgaggtgctt aaatgcccca tcccgccgac aaacttcagc
     2161 acgtcagaga tggtttgggt atagaactga ctcgcttttg gtgaatcgat agttaattcg
     2221 ctgatggcgg tacgggttga gtcgagaaac tgaatacttt cattaaacgt tttcaggggg
     2281 gcggcaatat ttccctggag taaatcctta ttcgtatcgg tcagcaaccg cttaaatgtt
     2341 gccagcacct tgtcggttaa ctgccgctgg gcagctaagt catcgcgaaa cttttggccg
     2401 cgcgcgccga taaatccagc gctcattcca cgttcgctct ggagttgatg caccacatca
     2461 cccgcgctgc gggcgagcgt ggtgagctgt ccaatggtgt tcatctgctg ttcggtattg
     2521 atacggctga caatacccga accggcgaac cagaccaagg caagcagtag cgggaataat
     2581 gcaataaaca acttcatttg cattgaaata cgataaaccc atgacatatc gatactttcc
     2641 ttactttctt gagggatcgc aggagtatcg gtagatacat gcataaactt tatagtttat
     2701 tgttggggga acgggcacca cattcggcag tggcgctggt agcaatccat aaaggatctt
     2761 cttgagatcc tttgacgatc gtcgtaatct cttgctctgt aaacgaaaaa accacccttg
     2821 caggtggttt ttcgaaggtt agataatcct ggcagattct ctaaccgtgg taacagtctt
     2881 gtgcgagaca tgtcaccaaa tttgtccttc tagtgtagcc tcagtcaggc cactacttca
     2941 agaactctcg atacatctct cgcacatcct gtttaccagt ggccgctgcc agtggcgatt
     3001 tttcgtgtct ttccgggttg gactcaagac gatagttacc ggaaaaggcg cagcagtcgg
     3061 actgaacggg gggttcgtgc atacagtcca gcttggagcg aactgccttc ccggaactga
     3121 gtgtcaggcg tggaatgaga taaacgcggc cataacagcg gaatgacacc ggtaaaccga
     3181 aaggcaggaa caggagagcg cacgagggag ctaccagggg gaaacgcctg ggatctttat
     3241 agtcctgtcg ggtttcgccg ccactgattt gagcgtcaga tttcgtgatg cttgtcaggg
     3301 gggcggagcc tatggaaaaa cggcttcgcc gcggccttac cgtttccctg ttaagtttct
     3361 tcctggcatc tcccaggaaa tttccgcccc attcgtaatc ccgcaccgct cgccgcagcc
     3421 gaacgaccga gcgcagcgag tcagtgagcg aggaagcgga atatctcctg tctcatatat
     3481 tccgcttacg ctctgctgct gcattttcct cctgccacat gaagcacttc actgattccc
     3541 gcacccgtgc ctacataata agccagtata cactccgcta gcgctacgtg actggttcag
     3601 ggctgcgccc cgacacccgc taaaagcact gacgcgcctg cggcttgccc aaccccgcgc
     3661 cgtccgggaa agaatttccc gatcgacccg acgtttctgt ttacctgtga tgttaacgtt
     3721 tggatctttt tcccgggttt acctatttta atgaagcgta atgaagcgta atgaagcgtt
     3781 cacagctgac gttaatagat gggtgcttca tgtttggttt ttcaccagga gaacttatga
//
