LOCUS       NZ_CP099361             5264 bp    DNA     circular CON 15-APR-2024
DEFINITION  Escherichia fergusonii strain RHB02-E1-C03 plasmid unnamed3,
            complete sequence.
ACCESSION   NZ_CP099361
VERSION     NZ_CP099361.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15488482
            Assembly: GCF_029718025.1
KEYWORDS    RefSeq.
SOURCE      Escherichia fergusonii
  ORGANISM  Escherichia fergusonii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5264)
  AUTHORS   Matlock,W.
  TITLE     Plasmid overlap and evolution between Enterobacterales isolates from
            bloodstream infections and non-human compartments
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5264)
  AUTHORS   Matlock,W.
  TITLE     Direct Submission
  JOURNAL   Submitted (13-JUN-2022) Nuffield Department of Medicine, University
            of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.4
            Assembly Name                     :: RHB02-E1-C03
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 180x
            Sequencing Technology             :: Illumina/Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_029718025.1-RS_2024_04_14
            Annotation Date                   :: 04/14/2024 22:20:15
            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)                     :: 4,811
            CDSs (total)                      :: 4,691
            Genes (coding)                    :: 4,592
            CDSs (with protein)               :: 4,592
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 90
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 99
            CDSs (without protein)            :: 99
            Pseudo Genes (ambiguous residues) :: 0 of 99
            Pseudo Genes (frameshifted)       :: 32 of 99
            Pseudo Genes (incomplete)         :: 58 of 99
            Pseudo Genes (internal stop)      :: 21 of 99
            Pseudo Genes (multiple problems)  :: 13 of 99
            Pseudo Genes (short protein)      :: 2 of 99
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP099361.1.
            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..5264
                     /organism="Escherichia fergusonii"
                     /mol_type="genomic DNA"
                     /strain="RHB02-E1-C03"
                     /isolation_source="Pooled sediment sample collected from
                     floor of pig farm"
                     /db_xref="taxon:564"
                     /plasmid="unnamed3"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(189..1757)
                     /gene="cea"
                     /locus_tag="NFJ18_RS23960"
                     /old_locus_tag="NFJ18_23920"
     CDS             complement(189..1757)
                     /gene="cea"
                     /locus_tag="NFJ18_RS23960"
                     /old_locus_tag="NFJ18_23920"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000447006.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="pore-forming bacteriocin colicin E1"
                     /protein_id="WP_000447006.1"
                     /translation="METAVAYYKDGVPYDDKGQVIITLLNGTPDGSGSGGGGGKGGSKS
                     ESSAAIHATAKWSTAQLKKTQAEQAARAKAAAEAQAKAKANRDALTQRLKDIVNEALRH
                     NASRTPSATELAHANNAAMQAEAERLRLAKAEEKARKEAEAAEKAFQEAEQRRKEIERE
                     KAETERQLKLAEAEEKRLAALSEEAKAVEIAQKKLSAAQSEVVKMDGEIKTLNSRLSSS
                     IHARDAEMKTLAGKRNELAQASAKYKELDELVKKLSPRANDPLQNRPFFEATRRRVGAG
                     KIREEKQKQVTASETRINRINADITQIQKAISQVSNNRNAGIARVHEAEENLKKAQNNL
                     LNSQIKDAVDATVSFYQTLTEKYGEKYSKMAQELADKSKGKKIGNVNEALAAFEKYKDV
                     LNKKFSKADRDAIFNALASVKYDDWAKHLDQFAKYLKITGHVSFGYDVVSDILKIKDTG
                     DWKPLFLTLEKKAADAGVSYVVALLFSLLAGTTLGIWGIAIVTGILCSYIDKNKLNTIN
                     EVLGI"
                     /name="cea"
     gene            2017..2454
                     /locus_tag="NFJ18_RS23965"
                     /old_locus_tag="NFJ18_23925"
     CDS             2017..2454
                     /locus_tag="NFJ18_RS23965"
                     /old_locus_tag="NFJ18_23925"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001405929.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001405929.1"
                     /translation="MGHCHFMAWHTLRDALKMTGRSRSQFYRDMRAGLVSYRTGRDGRR
                     EFETSELIRAYGELKQNETPERHSEGHAENPHDQQTERILRELNELKQCLTLMLEDKQA
                     QDMDRRRQEAEREQLQNEIAQLRQALELEKKRGFWSRLFGR"
                     /name="hypothetical protein"
     gene            2535..2954
                     /locus_tag="NFJ18_RS23970"
                     /old_locus_tag="NFJ18_23930"
     CDS             2535..2954
                     /locus_tag="NFJ18_RS23970"
                     /old_locus_tag="NFJ18_23930"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016247941.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Exc2 family lipoprotein"
                     /protein_id="WP_001254967.1"
                     /translation="MRRTGNKLCLIAMITATVALTACTPKGSVEQHTRHYVYASDDGFD
                     PNFSTQKADTTRMMVPFFRQFWDMGAKDKATGKSRSDVQQRIQQFHSQEFLNSLRGTTQ
                     FAGTDYRSKDLTPKKSRLLADTISAVYLDGYEGRQ"
                     /name="Exc2 family lipoprotein"
     gene            3724..3918
                     /locus_tag="NFJ18_RS23975"
                     /old_locus_tag="NFJ18_23935"
     CDS             3724..3918
                     /locus_tag="NFJ18_RS23975"
                     /old_locus_tag="NFJ18_23935"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /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_052962668.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EEIQNSIQVRFETESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            4573..4731
                     /locus_tag="NFJ18_RS24085"
     CDS             4573..4731
                     /locus_tag="NFJ18_RS24085"
                     /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_071531517.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHALTPLAAATGNRISRAMMA
                     QTVLQSS"
                     /name="replication initiation protein"
     gene            complement(4930..5067)
                     /locus_tag="NFJ18_RS23980"
                     /old_locus_tag="NFJ18_23940"
     CDS             complement(4930..5067)
                     /locus_tag="NFJ18_RS23980"
                     /old_locus_tag="NFJ18_23940"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001405930.1"
                     /GO_component="GO:0019867 - outer membrane [Evidence IEA]"
                     /GO_process="GO:0019835 - cytolysis [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin release lysis protein"
                     /protein_id="WP_001405930.1"
                     /translation="MRKRFFVGIFAINLLVGCQANYIRDVQGGTIAPSSSSKLTGIAVQ
                     "
                     /name="colicin release lysis protein"
     Typing          complement(3210..3465)
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.899"
                     /coverage="89.0"
                     /evalue="2.61e-118"
     Typing          complement(3590..3688)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          complement(3992..4076)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="94.186"
                     /coverage="100.0"
                     /evalue="6.62e-29"
     Typing          4087..4645
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.365"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ccatattcaa aatatgctat tgaatacata gcttttaact tcataaagaa agtttttttc
       61 gaaagaagaa aaaacctaaa taacgccccc gtagcaaaat taaacctatt tatgctatat
      121 aatctacttt gtttggtcct agcaatccca tttggattgc taggactttt tatatcaata
      181 aagaataatt aaatccctaa cacctcattt atagtattaa gtttattctt atcaatatag
      241 gagcatagaa ttcctgtaac aatagcaata ccccaaatac ctaatgtagt tccagcaagc
      301 aagctaaaaa gtaaagcaac aacataactc acccctgcat ctgcagcttt cttctctaat
      361 gtaagaaata gtggcttcca gtcacctgta tccttaattt ttaggatatc agataccaca
      421 tcatatccaa aagaaacatg ccccgtaatc ttcaagtact tggcaaactg atctaaatgt
      481 ttagcccagt catcatactt caccgatgcc aacgcattaa aaatagcatc acgatcggct
      541 ttgctgaatt tcttatttaa aacatccttg tatttttcaa aagcagcgag agcttcattc
      601 acattgccga ttttcttacc tttagactta tcagcaagtt cctgtgccat tttcgaatat
      661 ttttcaccat atttttcagt cagcgtttga taaaagctaa ctgttgcatc aacagcatcc
      721 ttaatctgtg aattaaggag attattctgt gcttttttca aattttcttc agcttcatga
      781 acacgagcga taccggcatt acgattatta ctgacctgag aaatagcctt ctggatctga
      841 gttatatcag catttatccg gttaatacgt gtttctgatg ctgttacctg tttttgtttt
      901 tcttctctaa tcttaccggc cccaacccgt cgtctggttg cttcaaaaaa aggacggttc
      961 tgaagcggat cattggctct tggtgatagt tttttgacca gctcatccag ttctttatat
     1021 ttagcggatg cctgagccag ttcatttcgt tttccagcga gcgttttcat ttctgcatca
     1081 cgggcatgga tactggagct taaacgagaa ttgagagtct taatctctcc atccattttc
     1141 accacttcag attgtgcagc agaaagtttt ttttgggcga tctcaacagc tttagcttct
     1201 tcactcaatg cagccagtcg tttctcttca gcttcagcca gtttcaactg gcgttctgtt
     1261 tcagccttct cccgttcaat ctctttacgt cgttgttctg cttcctgaaa agccttttct
     1321 gctgcttccg cttctttacg ggctttttct tctgctttcg caaggcgcaa acgctctgct
     1381 tccgcctgca tagctgcatt attagcatga gcaagctctg ttgctgaagg cgtacgtgag
     1441 gcattgtgac gaagagcctc attcacgata tccttcaggc gctgagtcag cgcatccctg
     1501 tttgcctttg ctttcgcctg tgcttccgct gcagcttttg cccgggcagc ctgctctgcc
     1561 tgtgttttct ttaattgagc agtagaccat ttagcagttg catgaatagc tgcagaactt
     1621 tcacttttac tgcctccttt tccacctccg ccgccagagc cactcccgtc aggagtacca
     1681 ttcaaaagag taataattac ctgtccctta tcatcataag gaacaccatc tttatagtac
     1741 gctaccgcgg tttccattat aaaatcctct ttgactttta aaacaataag ttaaaaataa
     1801 atactgtaca tataaccact ggttttatat acagcataaa agctacgccg ctgcattttc
     1861 cctgtcaaga ctgtggactt ccatttttgt gaaaacgatc aaaaaaacag tctttcacac
     1921 cacgcgctat tctcgcccga tgccacaaaa accagcacaa acattaccgt tctcagacct
     1981 cattatgttt tactgaaact atgagatgag acatctatgg gacactgtca ctttatggca
     2041 tggcacacac tccgggacgc actaaaaatg acaggcagat cgcgttcaca gttttaccgt
     2101 gatatgcgcg caggccttgt cagttaccgt accggcaggg acggacgacg ggagtttgaa
     2161 accagtgaac tgatccgggc atacggcgaa ttaaagcaga atgagacacc agaaaggcac
     2221 agtgagggac atgcagaaaa tccacatgat cagcagacag aacgcattct ccgggagctg
     2281 aatgagctga aacaatgcct gacgctgatg cttgaggata aacaggcaca ggatatggat
     2341 cgcagacgcc aggaagcaga acgggaacag ctacaaaatg agatagccca gctcaggcag
     2401 gcactggaac tggaaaagaa acggggattc tggtccaggt tgttcggtcg ctgaacgctg
     2461 tcagagactg atgataaaat agtcttcgga taataactca ccgagaataa atactttaag
     2521 gtagggagac actcatgaga cgtaccggaa acaaactttg tcttatcgcc atgataacag
     2581 caacagtagc tctcacagcc tgtaccccaa agggcagcgt ggaacaacat acccggcatt
     2641 acgtatatgc ttctgatgac ggttttgatc ccaacttttc cacccaaaaa gccgacacaa
     2701 cacgaatgat ggtgcctttt tttcggcagt tctgggatat gggagctaaa gataaagcga
     2761 caggaaaatc acggagtgat gtgcaacaac gcattcagca gtttcacagc caggaatttt
     2821 taaactcact ccggggcaca actcaatttg cgggtactga ttaccgcagc aaagacctta
     2881 ccccgaaaaa atccaggctg ctggctgaca cgatttctgc ggtttatctc gatggctacg
     2941 agggcagaca gtaagtggat ttaccataat cccttaattg tacgcaccgc taaaacgcgc
     3001 tgaacgcgat tctgccgcaa acaccgcaaa aagagatgtt ttccccgggg taaaccggaa
     3061 aaatgcgtca ggatcgcttt cagctcactg catagctatg catgaaagtg aatgacgatc
     3121 ggtttgggcg catacagtgc ccatgagaca cattttcgga cattttcagt tcgtgaatcc
     3181 ctgactcatt gctatatatc tgaatagaca cccctagcag cgcccccagg ggcatcctgt
     3241 aaaaaaacac accgcgccgc tagcagcacc cctaatataa gatgatgttt tttatgaaaa
     3301 tagtcagtac cacccctaaa aagcggtgtt ggcgcagcta caacaccgcg ccgacaccgc
     3361 ttttttaaat atcacaaaga gagcaagaag aactaatttg tcataactct ctatttataa
     3421 agaaaaatca gcaaaaactt gtttttgcgt ggggtgtggg catttcaggc atgagaacag
     3481 actcgcgttt ttccggagta tcagcggaat tattgattaa gaaacactcg acgcagagcg
     3541 aaattttatg caacagcggc tgcactgcac agggattatt tatcagttga tatgctgtgc
     3601 catgatacgt cctaaagaaa caggacagga tgtgtaattg taataccgtc gcccgcaacg
     3661 tcttacaatt accacctggt cagggtccac ccgacacccg gtactgacgg agaacaacgg
     3721 aaggtgaaca aacagcaaca aactgcgctg aatatggcgc gatttatcaa aagccagagc
     3781 ctgacactac ttgaaaaact ggatgctctg gatgccgacg aacaggcggc catgtgcgaa
     3841 cgactgcacg aactcgcgga agagatccag aacagcatcc aggttcgctt tgagaccgaa
     3901 agtgaaacag ggacataacg aggctgacgg aggcgctcac ggcttgtccg cgagcgtttt
     3961 cggcagcaga caagcccgcc agggcgcgtc agggggtttc ggggcaaagc cctgaaccag
     4021 tcacagagcg atagcgatgt gtatactggc ttaactatgc ggcatcagtg cagattgtat
     4081 gaaaagtgcc ccatgccggg tgtgaaatgc cgcacagatg cgtaaggaga aaatgcgcgt
     4141 ccaggcgctt ttccgcttcc tcgctcactg actcgctacg ctcggtcgtt cgactgcggc
     4201 gagcggtact gactcacaca aaaacggtaa cacagttatc cacagaatca ggggataagg
     4261 ccggaaagaa catgtgagca aaagaccagg aacaggaaga aggccacgta gcaggcgttt
     4321 ttccataggc tccgcccccc tgacgagcat cacaaaaata gacgctcaag tcagaggtgg
     4381 cgaaacccga caggactata aagataccag gcgtttcccc ctggaagctc cctcgtgcgc
     4441 tctcctgttc cgaccctgcc gcttaccgga tacctgtccg cctttctccc ttcgggaagc
     4501 gtggcgcttt ctcatagctc acgctgttgg tatctcagtt cggtgtaggt cgttcgctcc
     4561 aagctgggct gtgtgcacga accccccgtt cagcccgacc gctgcgcctt atccggtaac
     4621 tatcgtcttg agtccaaccc ggtaaggcac gccttaacgc cactggcagc agccactggt
     4681 aaccggatta gcagagcgat gatggcacaa acggtgctac agagttcttg aagtagtggc
     4741 ccgactacgg ctacactaga aggacagtat ttggtatctg cgctctgctg aagccagtta
     4801 ccttcggaaa aagagttggt agctcttgat ccggcaaaca aaccaccgtt ggtagcggtg
     4861 gtttttttgt ttgcaagcag cagattacgc gcagaaaaaa aggatctcaa gaagatcctt
     4921 tgatcttttc tactgaaccg cgatccccgt cagtttagaa gaggaggatg gtgcgatggt
     4981 ccctccctga acatcacgta tatagttagc ctgacatcca acaaggaggt ttatcgcgaa
     5041 tattcccaca aaaaatcttt tcctcataac tcgatcctta taaaatgaaa agaatatatg
     5101 gcgaggttta atttatgagc ttaagatact acataaaaaa tattttattt ggcctgtact
     5161 gcacacttat atatatatac cttataacaa aaaacagcga agggtattat ttccttgtgt
     5221 cagataagat gctatatgca atagtgataa gcactattct atgt
//
