LOCUS       NZ_CP057218             5570 bp    DNA     circular CON 02-APR-2024
DEFINITION  Escherichia fergusonii strain RHB33-C04 plasmid pRHB33-C04_4,
            complete sequence.
ACCESSION   NZ_CP057218
VERSION     NZ_CP057218.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15148325
            Assembly: GCF_013819325.1
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-C04
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 138.730801885388x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_013819325.1-RS_2024_04_02
            Annotation Date                   :: 04/02/2024 04:35:31
            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)                     :: 4,913
            CDSs (total)                      :: 4,789
            Genes (coding)                    :: 4,649
            CDSs (with protein)               :: 4,649
            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)              :: 140
            CDSs (without protein)            :: 140
            Pseudo Genes (ambiguous residues) :: 0 of 140
            Pseudo Genes (frameshifted)       :: 48 of 140
            Pseudo Genes (incomplete)         :: 85 of 140
            Pseudo Genes (internal stop)      :: 23 of 140
            Pseudo Genes (multiple problems)  :: 17 of 140
            Pseudo Genes (short protein)      :: 2 of 140
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP057218.1.
            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-C04"
                     /isolation_source="Pooled sheep faecal samples collected
                     from floor of farm"
                     /db_xref="taxon:564"
                     /plasmid="pRHB33-C04_4"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(join(5480..5570,1..71))
                     /locus_tag="HVZ08_RS24680"
     CDS             complement(join(5480..5570,1..71))
                     /locus_tag="HVZ08_RS24680"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001326446.1"
                     /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(741..932)
                     /locus_tag="HVZ08_RS24335"
                     /old_locus_tag="HVZ08_24340"
     CDS             complement(741..932)
                     /locus_tag="HVZ08_RS24335"
                     /old_locus_tag="HVZ08_24340"
                     /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            997..1320
                     /locus_tag="HVZ08_RS24340"
                     /old_locus_tag="HVZ08_24345"
     CDS             997..1320
                     /locus_tag="HVZ08_RS24340"
                     /old_locus_tag="HVZ08_24345"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /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_000956000.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGTR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1529..>1960
                     /locus_tag="HVZ08_RS24685"
                     /old_locus_tag="HVZ08_24350"
                     /pseudo=""
     CDS             1529..>1960
                     /locus_tag="HVZ08_RS24685"
                     /old_locus_tag="HVZ08_24350"
                     /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            1998..2516
                     /locus_tag="HVZ08_RS24350"
                     /old_locus_tag="HVZ08_24355"
     CDS             1998..2516
                     /locus_tag="HVZ08_RS24350"
                     /old_locus_tag="HVZ08_24355"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001447511.1"
                     /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_181667543.1"
                     /translation="MSNLLQTGVEFEKKLKERAESTEKMLNDEFRKLGESVSEAVTSNE
                     TKIKGAIAQFTASTEESLKKHREGVKEAMMQHRKDMLKLAGNTGMRLLGIVFLLFTASG
                     GTLWYLGGRIQANLEEIRIQEETLQKLNAKTWGVEFVQDGRRKFLVLPYGKSAEVIPFQ
                     GKEWVHLKE"
                     /name="MbeB family mobilization protein"
     gene            2523..2756
                     /locus_tag="HVZ08_RS24355"
                     /old_locus_tag="HVZ08_24360"
     CDS             2523..2756
                     /locus_tag="HVZ08_RS24355"
                     /old_locus_tag="HVZ08_24360"
                     /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(3122..4261)
                     /gene="dcm"
                     /locus_tag="HVZ08_RS24360"
                     /old_locus_tag="HVZ08_24365"
     CDS             complement(3122..4261)
                     /gene="dcm"
                     /locus_tag="HVZ08_RS24360"
                     /old_locus_tag="HVZ08_24365"
                     /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            4332..5288
                     /locus_tag="HVZ08_RS24365"
                     /old_locus_tag="HVZ08_24370"
     CDS             4332..5288
                     /locus_tag="HVZ08_RS24365"
                     /old_locus_tag="HVZ08_24370"
                     /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"
     Typing          569..656
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.629"
                     /coverage="100.0"
                     /evalue="6.91e-34"
     Typing          complement(2..546)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.526"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          1311..2860
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="94.275"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 accgggttgg actcaagacg atagttaccg gataaggcgc agcggtcggg ctgaacgggg
       61 ggttcgtgca cacagcccag cttggagcga acgacctaca ccgggccgag ataccaacag
      121 cgtgagctat gagaaagcgc cacgcttccc gaagggagaa aggcggacag gtatccggta
      181 agcggcaggg tcggaacagg agagcgcacg agggagcttc cagggggaaa cgcctggtat
      241 ctttatagtc ctgtcgggtt tcgccacctc tgacttgagc gtcgattttt gtgatgctcg
      301 tcaggggggc ggagcctatg gaaaaacgcc agcggcgcgg ccttttgttg ccctttgcct
      361 ttttactcac atgttctttc cggccttatc ccctgattct gtggataacc gtatttccgc
      421 ctttgagtga gccggcaccg cttgccgcag ccgaacgacc gagcgcagcg agtcagtgag
      481 cgaggaagcg gaagagcgcc tgatgcggta tgttctcctt acgcatctgt gcggcatttc
      541 acaccgtcca tggcgcactt ttcatacaat ccgcatcgat gccgcatagt taagccagta
      601 tacactccgc tatcgctacg tgactgggtc agggctgcgc cccgacaccc gctaaaacct
      661 gctgacgcgc cctgacgggc ttgtctgctc ccggcatccg ctcacaggca agctgtgacc
      721 gtctccggga gctgcatgtg tcagaggttt tcaccgtcat ccccgaaacg tgcgaggcag
      781 ctgcggtaaa gctcatcggc gtggtcgtga agcgattcac agatgtctgc ctgttcatcc
      841 gcgtccagtt cgttgagctt ttccagcagc gttaatgtct ggcttctgat aaagcgggcc
      901 atgttaaggg cggttttttc ctgtttagtc actgatgcct ccgtgtaagg gggatttctg
      961 ttcatggggg taatgatacc gatgaaacgc gagaggatgc tcacgatacg ggttactgat
     1021 gatgaacatg cccggttact ggaacgctgt gagggtaaac aactggcggt atggatgcgg
     1081 cgggtctgtc tgggtgagcc ggttgcccgt tccgggaaac tgccgacact ggcaccgccg
     1141 ttactgcgtc agctggccgc catcggaaat aacctgaatc agacagcccg taaggtgaac
     1201 agcgggcagt ggtcttccgg tgaccgggtt caggtggtgg ccgcactgat ggccatcggg
     1261 gacgagctgc gccggctgcg tctggccgtc agggaacagg ggacgcggga tgatagttaa
     1321 atttcatgcc aggggaaaag gtggtggcag tggtccggtt gattacctgc tggggaggga
     1381 gcgtaaccgc gaaggcgcaa cggtgcttca gggtaatccg gaagaagtcc gggaactcat
     1441 cgatgccacg ccatttgcga agaaatacac gtcaggcgtt ctgtcgttcg cggagaagga
     1501 gctgccgccg ggaggacgtg aaaaagtgat ggcgagcttt gagcgcgtac tgatgcccgg
     1561 tctcgaaaag aatcagtaca gcatcctgtg ggtggagcac caggacaagg gacggcttga
     1621 gctgaatttt gtcattccga acatggagct acagaccgga aaacgcctcc agccgtacta
     1681 cgaccgggca gacaggccga gaattgatgc ctggcagacg ctggtgaatc accattacgg
     1741 gctgcatgac cccaacgccc cggagaaccg ccggatactg acactccctg ataacctgcc
     1801 ggaaacgaaa caggcgcttg cagagagcgt cacacgcggg atagacgctc tttatcatgt
     1861 cggggagata agaggccgtc aggatgtgat tcaggcgctc acagaggcag ggcttgaagt
     1921 ggtcagggtg acgcgaagca gtatcagcat tgcagacccg aacggcggga agaatatcag
     1981 gctgaaagga gcattttatg agcaatcttt tacagacggg cgtggagttc gagaaaaagc
     2041 tgaaagagag agccgaatct acagagaaaa tgctgaacga cgaattcagg aagctcggcg
     2101 aatctgtaag cgaggctgtg acctcaaacg agacgaaaat caaaggcgct atagcccagt
     2161 ttacggcctc gacggaggaa tcgctgaaaa aacaccggga aggggtgaaa gaggcgatga
     2221 tgcagcaccg gaaggacatg ttaaagctgg cagggaatac gggcatgagg ttgctgggga
     2281 tagtctttct cctgtttacc gcgagtggcg ggacgctctg gtatcttggc gggcggatac
     2341 aggcgaacct ggaagaaatc aggatacagg aagagacatt gcagaaactg aacgcgaaga
     2401 catggggcgt ggagtttgtg caggacggga gaaggaaatt ccttgtcctt ccgtacggga
     2461 aatcagcgga ggtgattccc tttcagggga aagagtgggt acatctgaag gagtgactca
     2521 gagtgacaga gctggaaata catttgctga acgccttaga gcagctgcaa caggactata
     2581 tgcagcggct gagcgaatgg gagagcgcct tcgtggaatt gcagaagatg ttttcgctta
     2641 cgcaacggga caacgcgatg ctgaacgagc gggtcatgca gttgagtcag caggtgcagc
     2701 acttgagcga gcagacagaa cgcttgagcc agttatacag cgagaactgg agataagaga
     2761 ggcacggctg atacaggagc gcgaacatgc gttatccctg gaacgggagc gtcagccgga
     2821 aatacaggaa cgcacgctgg atggtccttc gctgggatgg tgaaaccatg aaaaatggca
     2881 gcctcagtgg attaagaggg gttaatgtgg cctgtaccat ctggttgcat aggtattcat
     2941 gcggttaaaa tttatcaggc gcgatcgcgg cagtttttcg ggtggtttgt tgccattttt
     3001 acctgtctgc tgccgtgatc gcgctgaacg cgttttagcg gtgcgtgtaa tgcgacgtta
     3061 tggtaaatcc atatggaggg ggaattggat tctgggccgc attgtgtcct tatgacttag
     3121 tttatgaatc taaggtcgat atgatttttt ctgctattgc attgataaca gggactgcga
     3181 ctgaattccc aaattgctta taagcctgtg tatccgatac agggataata aaatcactag
     3241 gaaacccttg aagtcttgac gcttcccgcg gagttatttt tcttgggtta cttccttttt
     3301 gctctattaa tatttcgcta ccatctttat agtacctcgc acttatggta ttagtatatg
     3361 ggctattttc attaaataaa ccatacccaa agcctttacc ggctgctgca tttacaagtt
     3421 tcctgcgttg gtgtccattc cagagcgcat ctgatagcgt atatttattg tctacgctct
     3481 tttcaagaat atctccaact cttgtttttg tttttaatgg ggttggaaaa gtaaaatgtt
     3541 catgatttct tactttttct ttattaaagc ctacaatgta tatgcgttct ctattttgtg
     3601 gaacaccaaa gtcttttgca gcgaagatat tgtaatacac agtgtaattc aattcttcaa
     3661 gtgtgttttt tattattgaa aaagttctac ctttatcatg tcctagcaag ttttttacat
     3721 tttcaagtaa aaaagcatga ggtttttttt tctttattat ccttgctata tcaaaaaaca
     3781 aagttcctct tgtatcatta aatccttttt tgagccctgc ttgagagaat gctacgcaag
     3841 gaaacccacc gacaagaatt tcatgatcag gaatatcttt ttcatcgatt tttgttatgt
     3901 ccccatcagg gaaatcacca taatttgcat gatatgtctt ttgagcaaac ttatcccatt
     3961 cgctggaaaa aacaacattt acagcgttag tttgatgaaa tccaagtctg gttccaccga
     4021 ttccagcaaa taaatcgatc atgcgatatc tgccattctc gttgtttggg taaggtggtg
     4081 tgtctggaaa gtccataact gcttttagtt ccgccccagt aggttttgtt tccccgcgct
     4141 cccatcttct tatggttctg tctccatatt ttgaaagacc aagggcgtct gcaaactctt
     4201 tttgagtcat atgaagtctt tctctttttc ctttgattgt tgctgcgata ttatcagtca
     4261 tgcatgtcta ccagaattaa gtgttggttt taggacaatt tgtcctgttt tgattccaat
     4321 tatgaacgtg catgaaaaaa ctttcaagta gatataaaag gttatttttt atgcaaagat
     4381 tgagtcctgg tgaatttaaa actctaattt ctaaagagag aaagtcgcat tttattacgc
     4441 catttgcttt ggtttataaa acattttgtg atttagggta tgatcaaaaa aatagtgatt
     4501 attttttgaa taatccaagt gaatatataa ttgcaatgag aaaaaactgt tggaaagaat
     4561 ttgaaccatt tgaaaaagaa ttcacaacaa gaatgttatc atatcttatt gatgaagaaa
     4621 gaataaaaga tatgagtcct tatgatgcca ttcgtgattt tacgatggaa taccctacac
     4681 acatatatga tttggcactg tctaacactc aatccagacg tagcagggca ggaaaagagt
     4741 ttgagtctat tcttgagcta ttaatgatgg gggcaggaat tcctgttgat gtgcaggggg
     4801 ctattgggaa gtcatttttt caaaaaaacc aaataggtaa acttgtagat cttgttatgc
     4861 caggtgtagt ccagtacaca tctaacaaaa gaaatacaat gttgatttcc gctaaaacaa
     4921 cgctgaggga gcgatggcaa gaagtacctg aagaggttaa tagaacaggt attagagaaa
     4981 tgtatctagc tacactagat gattctttta gcgaggagac aataaatata ttatacgagg
     5041 ctaatgtggt cgttgtaacg acgatagaaa ataaaaattt caaatataaa aataataata
     5101 gggtgctaac ctttgaagat atgctacagt cagcaatgga attatcaaga aagtggaata
     5161 atgtaagtta cacagactct gaaaaagagg aaattcaaca gtcaatatta aaacaaatag
     5221 aaaaatatag tgatttccct tatgttgtta attattatag aaataggctt agtgctcttt
     5281 ttgactaaaa aactaaaagg atctcttgag atcctttttt tctgcgcgta atcttggacc
     5341 tgtaaacgaa aaaaccaccc tggcaggtgg ttttttcgaa ggttagctaa tcctggcaga
     5401 ttatctaacc gaggtaatct ggcttcagca gagcacagat accaaatact gtccttccag
     5461 tgtagccgta gttaggccat cacttcaaga actctgtaag catctggata aatctcgctc
     5521 tgctaatccg gttaccagtg gctgctgcca gtggcgttaa ggcgtgtctt
//
