LOCUS       NZ_CP057103             3555 bp    DNA     circular CON 31-MAR-2024
DEFINITION  Escherichia fergusonii strain RHB38-C04 plasmid pRHB38-C04_3,
            complete sequence.
ACCESSION   NZ_CP057103
VERSION     NZ_CP057103.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15148384
            Assembly: GCF_013813425.1
KEYWORDS    RefSeq.
SOURCE      Escherichia fergusonii
  ORGANISM  Escherichia fergusonii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3555)
  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 3555)
  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                     :: RH04 T3-C04
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 155.03934376227x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_013813425.1-RS_2024_03_31
            Annotation Date                   :: 03/31/2024 04:59:35
            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)                     :: 4,462
            CDSs (total)                      :: 4,345
            Genes (coding)                    :: 4,254
            CDSs (with protein)               :: 4,254
            Genes (RNA)                       :: 117
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 91
            CDSs (without protein)            :: 91
            Pseudo Genes (ambiguous residues) :: 0 of 91
            Pseudo Genes (frameshifted)       :: 33 of 91
            Pseudo Genes (incomplete)         :: 47 of 91
            Pseudo Genes (internal stop)      :: 17 of 91
            Pseudo Genes (multiple problems)  :: 8 of 91
            Pseudo Genes (short protein)      :: 2 of 91
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP057103.1.
            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..3555
                     /organism="Escherichia fergusonii"
                     /mol_type="genomic DNA"
                     /strain="RHB38-C04"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:564"
                     /plasmid="pRHB38-C04_3"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            join(2949..3555,1..8)
                     /locus_tag="HVZ67_RS22140"
                     /old_locus_tag="HVZ67_22150"
     CDS             join(2949..3555,1..8)
                     /locus_tag="HVZ67_RS22140"
                     /old_locus_tag="HVZ67_22150"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_052895292.1"
                     /translation="MSTKNAQKEQKKESLITTHWGDDATIHGWTAIPNSLLMLQGDLGI
                     GSTEMCILLNILMHQWPESGESISFPSIGTIASRIGVSKRTIQRGVSNLEALGILTRYQ
                     STRNDPLTNGANIFDSTPLKEYLNKKAKGITISNSNKKKERKKTGITPNIKLPRICPKC
                     LKTKATSHEEIVKFFGVRKTMAGEIINSYCKECRASEKDLF"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(297..620)
                     /gene="mobA"
                     /locus_tag="HVZ67_RS22145"
                     /old_locus_tag="HVZ67_22155"
     CDS             complement(297..620)
                     /gene="mobA"
                     /locus_tag="HVZ67_RS22145"
                     /old_locus_tag="HVZ67_22155"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization protein MobA"
                     /protein_id="WP_000166966.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="mobA"
     gene            904..1098
                     /locus_tag="HVZ67_RS22150"
                     /old_locus_tag="HVZ67_22160"
     CDS             904..1098
                     /locus_tag="HVZ67_RS22150"
                     /old_locus_tag="HVZ67_22160"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041624.1"
                     /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_001041640.1"
                     /translation="MNKQQQTVLNMAGFIKSQSLTLLEKLDALDADEQAAMCEKLHELA
                     EELQNSIQTRFEAENRTGI"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1586..1699
                     /locus_tag="HVZ67_RS22545"
     CDS             1586..1699
                     /locus_tag="HVZ67_RS22545"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001422066.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001712890.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPERHDLTPLAAAIGN"
                     /name="hypothetical protein"
     gene            complement(1904..2629)
                     /locus_tag="HVZ67_RS22155"
                     /old_locus_tag="HVZ67_22165"
     CDS             complement(1904..2629)
                     /locus_tag="HVZ67_RS22155"
                     /old_locus_tag="HVZ67_22165"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001307201.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="NYN domain-containing protein"
                     /protein_id="WP_001427890.1"
                     /translation="MASMETEQQPQQTTEQIEVKTKRVQCFIDGYNLYHAIEETGNKAL
                     HWVDLKSLCKRYLPKNASIDNVFWFSAKPSHLSRAINENYQNYTNALTECGVDVIGGRF
                     KKKNVTCEADNGCGGVFHKHEEKESDVNLAISLVSGACNDEYDIAIIITADSDLCPPIK
                     YVRERFPNKELWLVAPPGRIRRATDLCSLSSRSMEIKNDALRACCMRDEFYKDGVLVAR
                     RPQEWRAVANTRQRRARSR"
                     /name="NYN domain-containing protein"
     Typing          complement(630..869)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.585"
                     /coverage="100.0"
                     /evalue="3.54e-121"
     Typing          1134..1655
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.437"
                     /coverage="95.0"
                     /evalue="0.0"
     Typing          complement(301..620)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="2.86e-62"
ORIGIN
        1 tattttaaac agttgaccat tttttatatg gccaactgcc ccccactcaa gtaaatggga
       61 ctgtttctaa cgctcccatt taccataacg tctcattacg cgcaccgcca aaacgcgctg
      121 aacgcgattc tgccgcagac accgcaaaaa gagatgtttt ccccggggta aaccggaaaa
      181 atgcgtcagg attgctttca gctcactgca tagctatgta tgaaagtgaa tggcgatcgg
      241 tttgggggct tacggcgttc ataccgtctg ttttcgacag ttttctcccc gggaagctaa
      301 tctgccataa gcctggataa cagggcacgg tgatactccg taatagcgat cagcacctcc
      361 gcatattccc tatccccgac acgcttgccg tcgataaaga gttttttctg taacgccccc
      421 agtctcataa cttctttcag tacccgatca tcagtcagtg agttaacttt cttaccgaga
      481 gctgccgccc gtaaaaaacc ggaaacggtc ttgccgcatt cagcagccct ttttctgatt
      541 tcctggtctt cttctgccgt cagacgaaca gggcgactga tagcccgcct gcgcgtatta
      601 cttccacttc gttttgtcat aaaacatggc tccgtatctg acatgggtgt cggggcaaag
      661 ccctgaccag ggtaattgta atagcgtgca tgtatgcgcg gtataacaat tgcacatcct
      721 gtcctgtcag caagctcgaa ttaccgacaa aggcacggca gttttttggc agtgacagtg
      781 ttgtctgaca gaaatgcccg tcaaagagtc agacagcaga ataccggcgg taaaacagtc
      841 gaaaagtggt actcgatata atcacacaac gcagatgaca gaaagaacgg agaaaacaga
      901 aagatgaaca agcagcagca aaccgtactc aacatggcgg gattcataaa aagccagagc
      961 ctgacgctgc tcgaaaaact ggacgcactt gatgctgacg aacaggccgc catgtgtgag
     1021 aagctgcacg aactcgcgga agaacttcag aacagcatac agacacgctt tgaagcggaa
     1081 aatcgcaccg ggatataacg cacccggaca ggatgcagaa cggcatagcg gagcgtaagg
     1141 agaaaatgcc acgtcagacg ctcttccgct tcctcgctca ctgactcgct acgctcggtc
     1201 gttcgactgc ggcgagcggt gtcagctcac tcaaaggcgg taatacggtt atccacagaa
     1261 tcaggggata acgccggaaa gaacatgtga gcaaaaagca aagcaccgga acaagccagc
     1321 gccgatgccg tttttccata ggctccgccc ccctgacgag catcacaaaa atcgacgctc
     1381 aagtcagagg tggcgaaacc cgacaggact ataaagatac caggcgtttc cccctggaag
     1441 ctccctcgtg cgctctcctg ttccgaccct gccgcttacc ggatacctgt ccgcctttct
     1501 cccttcggga agcgtggcgc tttctcatag ctcacgctgt tggtatctca gttcggtgta
     1561 ggtcgttcgc tccaagctgg gctgtgtgca cgaacccccc gttcagcccg accgctgcgc
     1621 cttatccggt aactatcgtc ttgagtccaa cccggaaaga cacgacttaa cgccactggc
     1681 agcagccatt ggtaactgat ttagaggagt tgagtcttga agttatgcac ctgataaggc
     1741 taaactgaaa gaacaagttt tggcgactgt gctcctcaaa gccagttacc tcggttcaaa
     1801 gagcgccaac tctatgaacc ttcgaaaaac cgcccgccaa ggcggttttt tcgttttcaa
     1861 cctagttaga ttaatctcct tgcgctagct gcgtcaacaa agcctaacga cttctagccc
     1921 ttctttgcct ggtattggca acagctcgcc attcctgagg ccttctggct acaagtactc
     1981 catctttgta gaactcatca cgcatacagc aggctctcaa agcatcattc ttgatctcca
     2041 tacttctcga tgacagagag cagagatctg tcgctcgcct gattctcccc ggaggagcta
     2101 caagccaaag ctctttatta gggaatcgct ctcttacgta tttaataggg gggcataagt
     2161 cagaatccgc agtgataata atggctatat catactcatc attacacgca ccagacacta
     2221 gacttatagc caaattaaca tcggactctt tttcttcatg cttatggaaa actccaccac
     2281 atccattatc agcttcgcac gttacattct tttttttaaa acgtccaccg ataacatcaa
     2341 caccacattc ggttaaagcg ttggtgtaat tttgataatt ttcatttatg gctcttgata
     2401 aatgtgatgg cttagcggaa aaccaaaaaa cattatcaat agatgcattt ttaggaaggt
     2461 atctcttgca taaagattta agatcaaccc aatgaagagc tttattacca gtctcttcaa
     2521 ttgcatgata taaattatac ccatcaataa agcactgcac tcgctttgtt tttacttcga
     2581 tttgctcagt agtttgttgt ggttgctgct ctgtttccat acttgccatt tttgacctct
     2641 agatagcaaa aaggcctgca tatgcaggcc tttttgcgtc tcttaaccgc agttaacaga
     2701 ccactgtatg gacgcatcca atacaggaag aattttgtac aatgcgcttc caagcctcga
     2761 cttggatagc cactaagagc ataactctta ggtagtggac tcaacttaag ttctatataa
     2821 aaaaagagca aatggatgac atttatgtca tcctaaaaga tacatgttac tacctaacta
     2881 ctcttatatt aagagtagtt aggtagtaac tgttcacatt ttgatttttt ttcgagagaa
     2941 aagcatctat gagcacaaaa aacgcacaga aagaacaaaa aaaagagtca ttaatcacta
     3001 ctcactgggg agatgatgca accatacatg ggtggacggc tataccaaat agcctcctta
     3061 tgctgcaagg tgatcttggt attgggagta ctgagatgtg tattctgctg aatatattga
     3121 tgcatcaatg gcctgagtca ggggagtcaa tatcttttcc gtcaattggt accattgcat
     3181 caagaatagg tgtatctaaa agaacaattc aacgcggggt tagtaaccta gaggcattgg
     3241 ggatattaac tagataccaa tcaacaagga atgaccctct aaccaatggc gctaatatat
     3301 tcgactcaac tcctctaaaa gaatatttaa acaaaaaagc taaaggcata acaattagca
     3361 acagcaacaa aaagaaagaa agaaagaaaa ccggaattac acccaacata aaattaccac
     3421 gcatttgccc aaaatgtttg aaaactaaag caaccagcca cgaagaaatt gttaaatttt
     3481 ttggcgtgcg aaaaacaatg gctggggaaa taataaattc atattgcaaa gaatgccgag
     3541 cttctgaaaa agatc
//
