LOCUS       NZ_CP057361             5055 bp    DNA     circular CON 04-APR-2024
DEFINITION  Escherichia fergusonii strain RHB28-C21 plasmid pRHB28-C21_5,
            complete sequence.
ACCESSION   NZ_CP057361
VERSION     NZ_CP057361.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15148274
            Assembly: GCF_013829265.1
KEYWORDS    RefSeq.
SOURCE      Escherichia fergusonii
  ORGANISM  Escherichia fergusonii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5055)
  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 5055)
  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 T2-C21
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 152.972283596324x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_013829265.1-RS_2024_04_04
            Annotation Date                   :: 04/04/2024 05:13:08
            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)                     :: 4,953
            CDSs (total)                      :: 4,834
            Genes (coding)                    :: 4,677
            CDSs (with protein)               :: 4,677
            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)              :: 157
            CDSs (without protein)            :: 157
            Pseudo Genes (ambiguous residues) :: 0 of 157
            Pseudo Genes (frameshifted)       :: 36 of 157
            Pseudo Genes (incomplete)         :: 109 of 157
            Pseudo Genes (internal stop)      :: 22 of 157
            Pseudo Genes (multiple problems)  :: 12 of 157
            Pseudo Genes (short protein)      :: 2 of 157
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP057361.1.
            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..5055
                     /organism="Escherichia fergusonii"
                     /mol_type="genomic DNA"
                     /strain="RHB28-C21"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:564"
                     /plasmid="pRHB28-C21_5"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(join(4063..5055,1..66))
                     /locus_tag="HVY57_RS24485"
                     /old_locus_tag="HVY57_24435"
     CDS             complement(join(4063..5055,1..66))
                     /locus_tag="HVY57_RS24485"
                     /old_locus_tag="HVY57_24435"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012508929.1"
                     /GO_function="GO:0005524 - ATP binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="ParA family protein"
                     /protein_id="WP_023259654.1"
                     /translation="MAIYAVWNNKGGVGKSYLTFQLASEYARQNPTKKVLVIDLCPQAN
                     SSSMLLGGMVNGENTLNQIHSATQRKTISGYIEDRIRSPYIPTNTGSNYVINVSTYNSR
                     IPDNLYLVTGDEQLELQASRVVGASFPGPHDAWRTVHLWINDLISDICNSWDNGDSCVF
                     IDCNPSFSIYTELALTAAERLLIPFSADGSSKRAVKAVLSLVYGERRHLNEPQSDFYLN
                     SNRYSMSLPQIYMYIGNRLTQMNNSSASAFKTVVTEIGDEIWKVWQTKPSLFCIHPNGS
                     STPNNKKSFRNMFQYEVNDANTASVVSGALGIPIATLTAGNKNVAGRTIKVNQTQLDKQ
                     VPNIVALAGMIE"
                     /name="ParA family protein"
     gene            complement(431..562)
                     /locus_tag="HVY57_RS24980"
     CDS             complement(431..562)
                     /locus_tag="HVY57_RS24980"
                     /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="replication initiation protein"
                     /protein_id="WP_071787289.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLTPLSAATGKGCTRYY"
                     /name="replication initiation protein"
     gene            complement(1231..1422)
                     /locus_tag="HVY57_RS24490"
                     /old_locus_tag="HVY57_24440"
     CDS             complement(1231..1422)
                     /locus_tag="HVY57_RS24490"
                     /old_locus_tag="HVY57_24440"
                     /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            1487..1810
                     /locus_tag="HVY57_RS24495"
                     /old_locus_tag="HVY57_24445"
     CDS             1487..1810
                     /locus_tag="HVY57_RS24495"
                     /old_locus_tag="HVY57_24445"
                     /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_000955999.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2019..>2450
                     /locus_tag="HVY57_RS24865"
                     /pseudo=""
     CDS             2019..>2450
                     /locus_tag="HVY57_RS24865"
                     /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            2488..3006
                     /locus_tag="HVY57_RS24505"
                     /old_locus_tag="HVY57_24455"
     CDS             2488..3006
                     /locus_tag="HVY57_RS24505"
                     /old_locus_tag="HVY57_24455"
                     /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_061672795.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNNEFRKLGESVSEAVTSNE
                     TKIRDAIALFTASTEKSLEKHREGVKEAMMQHRKDVLKLAGNTGMMLLGIVFLLFTASG
                     GTLWYLGGRIQANLEEIRIQEETLQKLNAKTWGVEFVQDGRRKFLVLPYGKSATVIPYQ
                     GKDWVQLTE"
                     /name="MbeB family mobilization protein"
     gene            3013..3246
                     /locus_tag="HVY57_RS24510"
                     /old_locus_tag="HVY57_24460"
     CDS             3013..3246
                     /locus_tag="HVY57_RS24510"
                     /old_locus_tag="HVY57_24460"
                     /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_061672798.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSEQTERLSQLYSENWR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            3604..3789
                     /locus_tag="HVY57_RS24515"
                     /old_locus_tag="HVY57_24465"
     CDS             3604..3789
                     /locus_tag="HVY57_RS24515"
                     /old_locus_tag="HVY57_24465"
                     /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_074518866.1"
                     /translation="MTEDNVKNISDYRKNNDAVDANSSAISGKSAPAKLSEKLRNTVPS
                     GLRAQMRQQMRNKHGF"
                     /name="hypothetical protein"
     gene            3779..4033
                     /locus_tag="HVY57_RS24520"
                     /old_locus_tag="HVY57_24470"
     CDS             3779..4033
                     /locus_tag="HVY57_RS24520"
                     /old_locus_tag="HVY57_24470"
                     /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_023259653.1"
                     /translation="MDSNNSQKNLQDKHADLLDKTYTLGWLDGYSEGYDDAIEDCQNAL
                     NKLENENELLNEIIENKDNVISEMASSVGRALQTVKKNK"
                     /name="hypothetical protein"
     Typing          1061..1146
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="8.58e-38"
     Typing          complement(491..1039)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.595"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          1801..3350
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.511"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tagttgaaag gtaagataac ttttccccac tccgcctttg ttattccata cggcatagat
       61 cgccatctat cactcctaat atagttttgt tgttagcttt aagtcagagt actagagatt
      121 attgttctac tgttagtttc tttcagctaa ctgactgtgt ttcgagcggt atggttagat
      181 gagggtgtcc gtattggcat gacctcttca gcatagtagg aacgtgattg aaaggatttc
      241 ttgagatcct tattcgtggg atgtaatctt ctgcactgta aacgaaaaaa ccacctgggg
      301 aggtggtttt tcgaaggatc agtaagttgg ggaacttctg aaccgtggta acagggtgta
      361 caagaccact gccaccaaat ctgtcctttc agtttagctg tagttaggct tcaacttcaa
      421 gaactctgcg ttagtaatat cttgtacatc ccttaccagt ggctgctgac agtggcgtta
      481 agtcgtgtct taccgggttg gactcaagac gatagttacc ggataaggcg cagcggtcgg
      541 gctgaacggg gggttcgtgc acacagccca gcttggagcg aacgacctac accgaactga
      601 gataccaaca gcgtgagcta tgagaaagcg ccacgcttcc cgaagggaga aaggcggaca
      661 ggtatccggt aagcggcagg gtcggaacag gagagcgcac gagggagctt ccagggggaa
      721 acgcctggta tctttatagt cctgtcgggt ttcgccacct ctgacttgag cgtcgatttt
      781 tgtgatgctc gtcagggggg cggagcctat ggaaaaacgc caacagcgca gccttttccg
      841 ggttctcgtt ttttgctcac atgtttcttt tggcgttatc ccctgattct gtggataacc
      901 gcatctccgc ttttgagtga gccgacaccg ctcgccgcag ccgaacgacc gagcgtagcg
      961 agtcagtgag cgaggaagcg gaagagcgcc ggaacgtgca ttttctcctt acgcatctgt
     1021 gcggcatttc acaccgcata tggcgctctt ttcttacaat ctgcactgat gccgcatggt
     1081 taagccagta tacactccgc tatcgctacg tgactgggtc atggctgcgc cccgacaccc
     1141 gctaaaacct gctgacgcgc cctgacgggc ttgtctgctc ccggcatccg ctcacagaca
     1201 agctgtgacc gtctccggga gctgcatgtg tcagaggttt tcaccgtcat ccccgaaacg
     1261 tgcgaggcag ctgcggtaaa gctcatcggc gtggtcgtga agcgattcac agatgtctgc
     1321 ctgttcatct gcgtccagtt cgttgagctt ctccagcagc gttaatgtct ggcttctgat
     1381 aaagcgggcc atgttaaggg cggttttttc ctgtttagtc actgatgcct ccgtgtaagg
     1441 gggtatttct gttcatgggg taatgatacc gatgaaacgc gagaggatgc tcacgatacg
     1501 ggttactgat gatgaacatg ccaggttact tgaacgctgt gagggtaaac aactggcagt
     1561 atggatgcgg cgggtctgcc tgggtgagcc ggttgcccgt tccgggaagc tgccgacact
     1621 ggcaccgccg ttactgcgtc agctggccgc catcgggaat aacctgaatc agacagcgag
     1681 gaaggtgaac agcgggcagt ggtcttccgg tgaccgggtt caggtggtgg ccgcactgat
     1741 ggccatcggg gatgagctgc gccggctgcg tctggccgtc agggaacagg gggcgcggga
     1801 tgatagttaa atttcatgcc aggggaaaag gtggtggcag tggtccggtt gattacctgc
     1861 tggggaggga gcgtaaccgc gaaggcgcaa cggtgcttca gggtaatccg gaagaagtcc
     1921 gggaactcat cgatgccacg ccatttgcga agaaatacac gtccggtgtt ctgtcgttcg
     1981 cggagaagga gctgccgccg ggaggacgtg aaaaagtgat ggcgagcttt gagcgtgtac
     2041 tgatgcccgg tctcgaaaaa aatcagtaca gcatcctgtg ggtggagcac caggacaagg
     2101 gacggcttga gctgaatttt gtcattccga acatggagct acagaccgga aaacgcctcc
     2161 agccgtacta cgaccgcgca gacaggccta gaattgatgc ctggcagacg ctggttaatc
     2221 accattacgg gctgcatgac ccgaacgccc cggagaaccg caggacgctg acactctctg
     2281 ataatctgcc ggaaacgaaa caggcgattg ctgagggcgt tacacgcggg atagacgcgc
     2341 tttaccatgc cggagagata aaaggccgtc aggatgtgat tcaggcgctc acagaggcgg
     2401 ggcttgaagt ggtcagggtg acgcgaagca gtatcagcat tgcagacccg aacggcggga
     2461 ggaatatcag actgaaagga gcgttttatg agcaatcttt tacagacggg cgcggagttc
     2521 gagaaaaagc tgaaagagag agccgaatct acagagaaaa tgctgaacaa cgagttcagg
     2581 aagctcggcg agtctgtcag cgaggctgtg acctcaaacg agacgaaaat cagagacgct
     2641 atagccctgt tcacagcctc gacagagaaa tcgctggaaa aacaccggga aggggtgaaa
     2701 gaggcgatga tgcagcacag gaaggacgtg ttaaagctgg cagggaatac gggcatgatg
     2761 ttactgggga tagtctttct cctgtttacc gcgagtggcg ggacgctctg gtatcttggc
     2821 gggcggatac aggcgaacct ggaagaaatc aggatacagg aagaaacatt gcagaaactg
     2881 aacgcgaaga catggggcgt ggagtttgtg caggacggga gaaggaaatt tctggtcctt
     2941 ccgtacggga aatcggcaac ggtgattccc tatcagggga aggactgggt acaactgacg
     3001 gagtgacaca gagtgacgga gctggaaaga catttgctga acgcattaga gcaactgcaa
     3061 caggactata tgcagcggct gagcgaatgg gagagcgcct tcgtggaatt gcagaagatg
     3121 ttttcgctta cgcaacggga caacgcgatg ctgaacgagc gggtcatgca gttgagtcag
     3181 caggtgcagc acttgagcga gcagacagaa cgcttgagcc agttatacag cgagaactgg
     3241 agataagaga ggaacggctg atacaggagc gcgaacatgc gttatccctg gaacgggagc
     3301 gtcagccgga aatacaggaa cgcacgctgg atggtccttc gctgggatgg tgaaaccatg
     3361 aaaaatggca gcttcagtgg attaagaggg gttaatgtgg cctgtaccat ctggttgcat
     3421 aggtattcat gcggttaaaa tttatcaggc gcgatcgcgg cagtttttcg ggtggtttgt
     3481 tgccattttt acctgtctgc tgccgtgatc gcgctgaacg cgttttagcg gtgcgcgtaa
     3541 ggggtgttat gttcaattct ccagcgtata ttgggctgtt tacagcaata ggtgtaatgt
     3601 tctatgactg aagataacgt taagaatatt agcgactaca gaaagaataa tgatgctgtt
     3661 gatgctaata gtagtgctat ttcaggtaaa agcgctccag ctaagctgag tgagaaactt
     3721 agaaatacag ttccttctgg actgagggcc caaatgcgcc aacaaatgag gaataaacat
     3781 ggattctaat aacagtcaga aaaaccttca agataagcat gctgatcttc tggataaaac
     3841 ttatactctc ggctggttgg atgggtattc agaagggtat gatgatgcca ttgaagattg
     3901 tcaaaatgcc ttgaataaac tggaaaatga aaacgaattg ctcaatgaaa ttattgaaaa
     3961 caaagataat gtaatcagtg aaatggcatc tagtgtgggc agggcgttgc aaacggtaaa
     4021 gaaaaataaa taaaaacagg cccttgaaaa agggcctgtt ttttactcaa tcataccggc
     4081 aagagcgaca atgttgggca cttgcttatc aagctgtgtc tgatttacct ttattgttct
     4141 tcccgcaaca ttcttatttc ctgcggttag tgtggcaatt ggaataccaa gtgctcctga
     4201 tacgacagat gctgtattgg catcatttac ttcatactgg aacatgttcc taaaggattt
     4261 tttattattc ggcgttgagc ttccatttgg atgaatgcag aataaacttg gttttgtttg
     4321 ccacactttc caaatctcat cgccgatctc tgttaccaca gttttgaatg cgctagctga
     4381 tgagttgttc atttgagtta atctgtttcc aatatacatg tatatttgtg gtaatgacat
     4441 agaataacga ttgctgttta aatagaaatc tgactgtggt tcgttcagat gacgtcgctc
     4501 gccataaact aaagaaagaa ctgctttaac agctcttttt gatgaaccat cagcagagaa
     4561 tggaattaat aggcgttcag ctgcggttaa tgctaactcg gtataaatag agaagctggg
     4621 attgcagtcg atgaaaacgc agctgtcgcc attatcccat gagttacaaa tgtcactaat
     4681 tagatcgtta atccaaagat gaacagttct ccatgcgtca tgaggtccag ggaatgatgc
     4741 tccaacaact cttgatgctt gaagttctaa ttgctcatcg ccagtaacaa gatatagatt
     4801 atctgggatt ctgctattgt atgtagatac gttgattacg tagttagaac ctgtatttgt
     4861 cggaatatat ggacttctaa tcctatcctc aatatatcca gaaatagtct ttctttgtgt
     4921 tgcagaatga atctgattta gcgtattttc gccattaacc atcccgccaa gtaacattga
     4981 ggatgagtta gcttgtgggc atagatcaat caccagaacc ttttttgtcg ggttctgtct
     5041 ggcgtactca gaggc
//
