LOCUS       NZ_CP057213             5570 bp    DNA     circular CON 02-APR-2024
DEFINITION  Escherichia fergusonii strain RHB33-C07 plasmid pRHB33-C07_4,
            complete sequence.
ACCESSION   NZ_CP057213
VERSION     NZ_CP057213.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15148326
            Assembly: GCF_013819085.1
KEYWORDS    RefSeq.
SOURCE      Escherichia fergusonii
  ORGANISM  Escherichia fergusonii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5570)
  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 5570)
  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                     :: RH14 T3-C07
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 151.359023831922x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_013819085.1-RS_2024_04_02
            Annotation Date                   :: 04/02/2024 04:25:52
            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)                     :: 4,920
            CDSs (total)                      :: 4,796
            Genes (coding)                    :: 4,657
            CDSs (with protein)               :: 4,657
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 92
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 139
            CDSs (without protein)            :: 139
            Pseudo Genes (ambiguous residues) :: 0 of 139
            Pseudo Genes (frameshifted)       :: 48 of 139
            Pseudo Genes (incomplete)         :: 84 of 139
            Pseudo Genes (internal stop)      :: 23 of 139
            Pseudo Genes (multiple problems)  :: 17 of 139
            Pseudo Genes (short protein)      :: 2 of 139
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP057213.1.
            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..5570
                     /organism="Escherichia fergusonii"
                     /mol_type="genomic DNA"
                     /strain="RHB33-C07"
                     /isolation_source="Pooled sheep faecal samples collected
                     from floor of farm"
                     /db_xref="taxon:564"
                     /plasmid="pRHB33-C07_4"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            join(5262..5570,1..210)
                     /locus_tag="HVZ09_RS24380"
                     /old_locus_tag="HVZ09_24335"
     CDS             join(5262..5570,1..210)
                     /locus_tag="HVZ09_RS24380"
                     /old_locus_tag="HVZ09_24335"
                     /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="MbeB family mobilization protein"
                     /protein_id="WP_181667543.1"
                     /translation="MSNLLQTGVEFEKKLKERAESTEKMLNDEFRKLGESVSEAVTSNE
                     TKIKGAIAQFTASTEESLKKHREGVKEAMMQHRKDMLKLAGNTGMRLLGIVFLLFTASG
                     GTLWYLGGRIQANLEEIRIQEETLQKLNAKTWGVEFVQDGRRKFLVLPYGKSAEVIPFQ
                     GKEWVHLKE"
                     /name="MbeB family mobilization protein"
     gene            217..450
                     /locus_tag="HVZ09_RS24385"
                     /old_locus_tag="HVZ09_24340"
     CDS             217..450
                     /locus_tag="HVZ09_RS24385"
                     /old_locus_tag="HVZ09_24340"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /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_004026237.1"
                     /translation="MTELEIHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSEQTERLSQLYSENWR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(816..1955)
                     /gene="dcm"
                     /locus_tag="HVZ09_RS24390"
                     /old_locus_tag="HVZ09_24345"
     CDS             complement(816..1955)
                     /gene="dcm"
                     /locus_tag="HVZ09_RS24390"
                     /old_locus_tag="HVZ09_24345"
                     /EC_number="2.1.1.37"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000131511.1"
                     /GO_function="GO:0003886 - DNA
                     (cytosine-5-)-methyltransferase activity [Evidence IEA]"
                     /GO_process="GO:0006304 - DNA modification [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DNA (cytosine-5-)-methyltransferase"
                     /protein_id="WP_095186844.1"
                     /translation="MTDNIAATIKGKRERLHMTQKEFADALGLSKYGDRTIRRWERGET
                     KPTGAELKAVMDFPDTPPYPNNENGRYRMIDLFAGIGGTRLGFHQTNAVNVVFSSEWDK
                     FAQKTYHANYGDFPDGDITKIDEKDIPDHEILVGGFPCVAFSQAGLKKGFNDTRGTLFF
                     DIARIIKKKKPHAFLLENVKNLLGHDKGRTFSIIKNTLEELNYTVYYNIFAAKDFGVPQ
                     NRERIYIVGFNKEKVRNHEHFTFPTPLKTKTRVGDILEKSVDNKYTLSDALWNGHQRRK
                     LVNAAAGKGFGYGLFNENSPYTNTISARYYKDGSEILIEQKGSNPRKITPREASRLQGF
                     PSDFIIPVSDTQAYKQFGNSVAVPVINAIAEKIISTLDS"
                     /name="dcm"
     gene            2026..2982
                     /locus_tag="HVZ09_RS24395"
                     /old_locus_tag="HVZ09_24350"
     CDS             2026..2982
                     /locus_tag="HVZ09_RS24395"
                     /old_locus_tag="HVZ09_24350"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_014640333.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0009036 - type II site-specific deoxyribonuclease
                     activity [Evidence IEA]"
                     /GO_process="GO:0009307 - DNA restriction-modification
                     system [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II restriction endonuclease"
                     /protein_id="WP_223673566.1"
                     /translation="MKKLSSRYKRLFFMQRLSPGEFKTLISKERKSHFITPFALVYKTF
                     CDLGYDQKNSDYFLNNPSEYIIAMRKNCWKEFEPFEKEFTTRMLSYLIDEERIKDMSPY
                     DAIRDFTMEYPTHIYDLALSNTQSRRSRAGKEFESILELLMMGAGIPVDVQGAIGKSFF
                     QKNQIGKLVDLVMPGVVQYTSNKRNTMLISAKTTLRERWQEVPEEVNRTGIREMYLATL
                     DDSFSEETINILYEANVVVVTTIENKNFKYKNNNRVLTFEDMLQSAMELSRKWNNVSYT
                     DSEKEEIQQSILKQIEKYSDFPYVVNYYRNRLSALFD"
                     /name="type II restriction endonuclease"
     gene            complement(3174..3335)
                     /locus_tag="HVZ09_RS24895"
     CDS             complement(3174..3335)
                     /locus_tag="HVZ09_RS24895"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001354639.1"
                     /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_071596883.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHALTPLAAATGNRISRARFI
                     QMLTEFLK"
                     /name="replication initiation protein"
     gene            complement(4005..4196)
                     /locus_tag="HVZ09_RS24400"
                     /old_locus_tag="HVZ09_24355"
     CDS             complement(4005..4196)
                     /locus_tag="HVZ09_RS24400"
                     /old_locus_tag="HVZ09_24355"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /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_000165985.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            4228..4584
                     /locus_tag="HVZ09_RS24405"
                     /old_locus_tag="HVZ09_24360"
     CDS             4228..4584
                     /locus_tag="HVZ09_RS24405"
                     /old_locus_tag="HVZ09_24360"
                     /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="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_000538662.1"
                     /translation="MGVMIPMKRERMLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGE
                     PVARSGKLPTLAPPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRR
                     LRLAVREQGTRDDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     Typing          3833..3920
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.629"
                     /coverage="100.0"
                     /evalue="6.91e-34"
     Typing          complement(3264..3810)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.545"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          4..554
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.194"
                     /coverage="99.0"
                     /evalue="5.459999999999998e-82"
     Typing          4575..5569
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="94.88"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 ggcgggacgc tctggtatct tggcgggcgg atacaggcga acctggaaga aatcaggata
       61 caggaagaga cattgcagaa actgaacgcg aagacatggg gcgtggagtt tgtgcaggac
      121 gggagaagga aattccttgt ccttccgtac gggaaatcag cggaggtgat tccctttcag
      181 gggaaagagt gggtacatct gaaggagtga ctcagagtga cagagctgga aatacatttg
      241 ctgaacgcct tagagcagct gcaacaggac tatatgcagc ggctgagcga atgggagagc
      301 gccttcgtgg aattgcagaa gatgttttcg cttacgcaac gggacaacgc gatgctgaac
      361 gagcgggtca tgcagttgag tcagcaggtg cagcacttga gcgagcagac agaacgcttg
      421 agccagttat acagcgagaa ctggagataa gagaggcacg gctgatacag gagcgcgaac
      481 atgcgttatc cctggaacgg gagcgtcagc cggaaataca ggaacgcacg ctggatggtc
      541 cttcgctggg atggtgaaac catgaaaaat ggcagcctca gtggattaag aggggttaat
      601 gtggcctgta ccatctggtt gcataggtat tcatgcggtt aaaatttatc aggcgcgatc
      661 gcggcagttt ttcgggtggt ttgttgccat ttttacctgt ctgctgccgt gatcgcgctg
      721 aacgcgtttt agcggtgcgt gtaatgcgac gttatggtaa atccatatgg agggggaatt
      781 ggattctggg ccgcattgtg tccttatgac ttagtttatg aatctaaggt cgatatgatt
      841 ttttctgcta ttgcattgat aacagggact gcgactgaat tcccaaattg cttataagcc
      901 tgtgtatccg atacagggat aataaaatca ctaggaaacc cttgaagtct tgacgcttcc
      961 cgcggagtta tttttcttgg gttacttcct ttttgctcta ttaatatttc gctaccatct
     1021 ttatagtacc tcgcacttat ggtattagta tatgggctat tttcattaaa taaaccatac
     1081 ccaaagcctt taccggctgc tgcatttaca agtttcctgc gttggtgtcc attccagagc
     1141 gcatctgata gcgtatattt attgtctacg ctcttttcaa gaatatctcc aactcttgtt
     1201 tttgttttta atggggttgg aaaagtaaaa tgttcatgat ttcttacttt ttctttatta
     1261 aagcctacaa tgtatatgcg ttctctattt tgtggaacac caaagtcttt tgcagcgaag
     1321 atattgtaat acacagtgta attcaattct tcaagtgtgt tttttattat tgaaaaagtt
     1381 ctacctttat catgtcctag caagtttttt acattttcaa gtaaaaaagc atgaggtttt
     1441 tttttcttta ttatccttgc tatatcaaaa aacaaagttc ctcttgtatc attaaatcct
     1501 tttttgagcc ctgcttgaga gaatgctacg caaggaaacc caccgacaag aatttcatga
     1561 tcaggaatat ctttttcatc gatttttgtt atgtccccat cagggaaatc accataattt
     1621 gcatgatatg tcttttgagc aaacttatcc cattcgctgg aaaaaacaac atttacagcg
     1681 ttagtttgat gaaatccaag tctggttcca ccgattccag caaataaatc gatcatgcga
     1741 tatctgccat tctcgttgtt tgggtaaggt ggtgtgtctg gaaagtccat aactgctttt
     1801 agttccgccc cagtaggttt tgtttccccg cgctcccatc ttcttatggt tctgtctcca
     1861 tattttgaaa gaccaagggc gtctgcaaac tctttttgag tcatatgaag tctttctctt
     1921 tttcctttga ttgttgctgc gatattatca gtcatgcatg tctaccagaa ttaagtgttg
     1981 gttttaggac aatttgtcct gttttgattc caattatgaa cgtgcatgaa aaaactttca
     2041 agtagatata aaaggttatt ttttatgcaa agattgagtc ctggtgaatt taaaactcta
     2101 atttctaaag agagaaagtc gcattttatt acgccatttg ctttggttta taaaacattt
     2161 tgtgatttag ggtatgatca aaaaaatagt gattattttt tgaataatcc aagtgaatat
     2221 ataattgcaa tgagaaaaaa ctgttggaaa gaatttgaac catttgaaaa agaattcaca
     2281 acaagaatgt tatcatatct tattgatgaa gaaagaataa aagatatgag tccttatgat
     2341 gccattcgtg attttacgat ggaataccct acacacatat atgatttggc actgtctaac
     2401 actcaatcca gacgtagcag ggcaggaaaa gagtttgagt ctattcttga gctattaatg
     2461 atgggggcag gaattcctgt tgatgtgcag ggggctattg ggaagtcatt ttttcaaaaa
     2521 aaccaaatag gtaaacttgt agatcttgtt atgccaggtg tagtccagta cacatctaac
     2581 aaaagaaata caatgttgat ttccgctaaa acaacgctga gggagcgatg gcaagaagta
     2641 cctgaagagg ttaatagaac aggtattaga gaaatgtatc tagctacact agatgattct
     2701 tttagcgagg agacaataaa tatattatac gaggctaatg tggtcgttgt aacgacgata
     2761 gaaaataaaa atttcaaata taaaaataat aatagggtgc taacctttga agatatgcta
     2821 cagtcagcaa tggaattatc aagaaagtgg aataatgtaa gttacacaga ctctgaaaaa
     2881 gaggaaattc aacagtcaat attaaaacaa atagaaaaat atagtgattt cccttatgtt
     2941 gttaattatt atagaaatag gcttagtgct ctttttgact aaaaaactaa aaggatctct
     3001 tgagatcctt tttttctgcg cgtaatcttg gacctgtaaa cgaaaaaacc accctggcag
     3061 gtggtttttt cgaaggttag ctaatcctgg cagattatct aaccgaggta atctggcttc
     3121 agcagagcac agataccaaa tactgtcctt ccagtgtagc cgtagttagg ccatcacttc
     3181 aagaactctg taagcatctg gataaatctc gctctgctaa tccggttacc agtggctgct
     3241 gccagtggcg ttaaggcgtg tcttaccggg ttggactcaa gacgatagtt accggataag
     3301 gcgcagcggt cgggctgaac ggggggttcg tgcacacagc ccagcttgga gcgaacgacc
     3361 tacaccgggc cgagatacca acagcgtgag ctatgagaaa gcgccacgct tcccgaaggg
     3421 agaaaggcgg acaggtatcc ggtaagcggc agggtcggaa caggagagcg cacgagggag
     3481 cttccagggg gaaacgcctg gtatctttat agtcctgtcg ggtttcgcca cctctgactt
     3541 gagcgtcgat ttttgtgatg ctcgtcaggg gggcggagcc tatggaaaaa cgccagcggc
     3601 gcggcctttt gttgcccttt gcctttttac tcacatgttc tttccggcct tatcccctga
     3661 ttctgtggat aaccgtattt ccgcctttga gtgagccggc accgcttgcc gcagccgaac
     3721 gaccgagcgc agcgagtcag tgagcgagga agcggaagag cgcctgatgc ggtatgttct
     3781 ccttacgcat ctgtgcggca tttcacaccg tccatggcgc acttttcata caatccgcat
     3841 cgatgccgca tagttaagcc agtatacact ccgctatcgc tacgtgactg ggtcagggct
     3901 gcgccccgac acccgctaaa acctgctgac gcgccctgac gggcttgtct gctcccggca
     3961 tccgctcaca ggcaagctgt gaccgtctcc gggagctgca tgtgtcagag gttttcaccg
     4021 tcatccccga aacgtgcgag gcagctgcgg taaagctcat cggcgtggtc gtgaagcgat
     4081 tcacagatgt ctgcctgttc atccgcgtcc agttcgttga gcttttccag cagcgttaat
     4141 gtctggcttc tgataaagcg ggccatgtta agggcggttt tttcctgttt agtcactgat
     4201 gcctccgtgt aagggggatt tctgttcatg ggggtaatga taccgatgaa acgcgagagg
     4261 atgctcacga tacgggttac tgatgatgaa catgcccggt tactggaacg ctgtgagggt
     4321 aaacaactgg cggtatggat gcggcgggtc tgtctgggtg agccggttgc ccgttccggg
     4381 aaactgccga cactggcacc gccgttactg cgtcagctgg ccgccatcgg aaataacctg
     4441 aatcagacag cccgtaaggt gaacagcggg cagtggtctt ccggtgaccg ggttcaggtg
     4501 gtggccgcac tgatggccat cggggacgag ctgcgccggc tgcgtctggc cgtcagggaa
     4561 caggggacgc gggatgatag ttaaatttca tgccagggga aaaggtggtg gcagtggtcc
     4621 ggttgattac ctgctgggga gggagcgtaa ccgcgaaggc gcaacggtgc ttcagggtaa
     4681 tccggaagaa gtccgggaac tcatcgatgc cacgccattt gcgaagaaat acacgtcagg
     4741 cgttctgtcg ttcgcggaga aggagctgcc gccgggagga cgtgaaaaag tgatggcgag
     4801 ctttgagcgc gtactgatgc ccggtctcga aaagaatcag tacagcatcc tgtgggtgga
     4861 gcaccaggac aagggacggc ttgagctgaa ttttgtcatt ccgaacatgg agctacagac
     4921 cggaaaacgc ctccagccgt actacgaccg ggcagacagg ccgagaattg atgcctggca
     4981 gacgctggtg aatcaccatt acgggctgca tgaccccaac gccccggaga accgccggat
     5041 actgacactc cctgataacc tgccggaaac gaaacaggcg cttgcagaga gcgtcacacg
     5101 cgggatagac gctctttatc atgtcgggga gataagaggc cgtcaggatg tgattcaggc
     5161 gctcacagag gcagggcttg aagtggtcag ggtgacgcga agcagtatca gcattgcaga
     5221 cccgaacggc gggaagaata tcaggctgaa aggagcattt tatgagcaat cttttacaga
     5281 cgggcgtgga gttcgagaaa aagctgaaag agagagccga atctacagag aaaatgctga
     5341 acgacgaatt caggaagctc ggcgaatctg taagcgaggc tgtgacctca aacgagacga
     5401 aaatcaaagg cgctatagcc cagtttacgg cctcgacgga ggaatcgctg aaaaaacacc
     5461 gggaaggggt gaaagaggcg atgatgcagc accggaagga catgttaaag ctggcaggga
     5521 atacgggcat gaggttgctg gggatagtct ttctcctgtt taccgcgagt
//
