LOCUS       NZ_CP099355             4148 bp    DNA     circular CON 15-APR-2024
DEFINITION  Escherichia marmotae strain RHB02-E4-C07 plasmid unnamed4, complete
            sequence.
ACCESSION   NZ_CP099355
VERSION     NZ_CP099355.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15488490
            Assembly: GCF_029717905.1
KEYWORDS    RefSeq.
SOURCE      Escherichia marmotae
  ORGANISM  Escherichia marmotae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4148)
  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  JOURNAL   Unpublished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 4148)
  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-E4-C07
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 135x
            Sequencing Technology             :: Illumina/Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_029717905.1-RS_2024_04_14
            Annotation Date                   :: 04/14/2024 22:21:28
            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)                     :: 4,620
            CDSs (total)                      :: 4,502
            Genes (coding)                    :: 4,336
            CDSs (with protein)               :: 4,336
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 90
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 166
            CDSs (without protein)            :: 166
            Pseudo Genes (ambiguous residues) :: 0 of 166
            Pseudo Genes (frameshifted)       :: 53 of 166
            Pseudo Genes (incomplete)         :: 120 of 166
            Pseudo Genes (internal stop)      :: 24 of 166
            Pseudo Genes (multiple problems)  :: 30 of 166
            Pseudo Genes (short protein)      :: 3 of 166
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP099355.1.
            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..4148
                     /organism="Escherichia marmotae"
                     /mol_type="genomic DNA"
                     /strain="RHB02-E4-C07"
                     /isolation_source="Pooled sediment sample collected from
                     floor of pig farm"
                     /db_xref="taxon:1499973"
                     /plasmid="unnamed4"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(724..927)
                     /locus_tag="NFJ26_RS23015"
                     /old_locus_tag="NFJ26_22915"
     CDS             complement(724..927)
                     /locus_tag="NFJ26_RS23015"
                     /old_locus_tag="NFJ26_22915"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000427298.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="retron Se72 family effector protein"
                     /protein_id="WP_000427298.1"
                     /translation="MENGFVNFYDHVKGYGFIRRERGRDVFFRYDDFLFLGHDVDICKG
                     ILVRFKLEKTDKGFKAVAIQKV"
                     /name="retron Se72 family effector protein"
     gene            complement(932..2071)
                     /locus_tag="NFJ26_RS23020"
                     /old_locus_tag="NFJ26_22920"
     CDS             complement(932..2071)
                     /locus_tag="NFJ26_RS23020"
                     /old_locus_tag="NFJ26_22920"
                     /EC_number="2.7.7.49"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761319.1"
                     /GO_function="GO:0003964 - RNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="reverse transcriptase family protein"
                     /protein_id="WP_032341919.1"
                     /translation="MNKPRFNGTPVASLDSLSAMLGIERKRLDWIVKSVSMSYKQFKVE
                     TGKNKKERQIFEPKRSLKGIQKKINKEIFEKIDYPHYLHGALSGRDYISNAAVHTRKRT
                     VICLDITNFYPSISKKDVCSIFKNLMRFSPEVSLCLTELVTLNNKVPQGGCCSSYIANL
                     LFFNSEYNLYNRLKSMGLSYSRLLDDITISSDKDLSSEEKTKVIKLVHGMVNQYRLSIN
                     ESKTTIEHSKDSSSKLSVTGLWVKHGVPKLTKENRRYIRYLVYICKKQGAYERHTKEYH
                     DLWNRCSGKVAQMSRLGHVQAVELRAILSEIMPVYDDYKISKLKLMAKHYLNKFTPPLT
                     DEQIRKIDRMLYDFDIVGRTNKNLAKLYRRKLVALLPDR"
                     /name="reverse transcriptase family protein"
     gene            complement(2645..2983)
                     /locus_tag="NFJ26_RS23025"
                     /old_locus_tag="NFJ26_22925"
     CDS             complement(2645..2983)
                     /locus_tag="NFJ26_RS23025"
                     /old_locus_tag="NFJ26_22925"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001027011.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001027011.1"
                     /translation="MNISIKNNDLKTIARFDGKTLRDAFSRKIATFDGKILRDASLKKI
                     ATFDGKVLRDASLKKVATFDGKVLRDASLKKVATFDGQNLRDASSKIILSADAEVGIVV
                     MAFVAELI"
                     /name="hypothetical protein"
     gene            complement(3233..3556)
                     /gene="mobA"
                     /locus_tag="NFJ26_RS23030"
                     /old_locus_tag="NFJ26_22930"
     CDS             complement(3233..3556)
                     /gene="mobA"
                     /locus_tag="NFJ26_RS23030"
                     /old_locus_tag="NFJ26_22930"
                     /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            3841..4035
                     /locus_tag="NFJ26_RS23035"
                     /old_locus_tag="NFJ26_22935"
     CDS             3841..4035
                     /locus_tag="NFJ26_RS23035"
                     /old_locus_tag="NFJ26_22935"
                     /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"
     Typing          complement(3566..3806)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.174"
                     /coverage="100.0"
                     /evalue="1.65e-119"
     Typing          77..525
                     /name="rep_cluster_2370"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.778"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(3237..3556)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="3.33e-62"
ORIGIN
        1 gcgagcggtg tcagctcact caaaggcggt aatacggtta tccacagaat caggggataa
       61 agccggaaag aacatgtgag caaaagacaa aggcccagaa gaagggcgag caggaggcgt
      121 ttttccatag gctccgcccc cctgacgagc atcacaaaaa ccgacgctca agtcagaggt
      181 ggcgaaaccc gacaggacta taaagatacc aggcgtttcc ccctggaagc tccctcgtgc
      241 gctctcctgt tccgaccctg ccgcttaccg gatacctgtc cgcctttctc ccttcgggaa
      301 acgtggcgct ttctcatagc tcacgctgtt ggtatctcgg cccggtgtag gtcgttcgct
      361 ccaagctgga ctgtatgcac gaaccccccg ttcagtccga ccgctgcgcc ttatccggta
      421 actatcgact tgaatccaaa ccgagaagac acgacttatc gccactggca gcagccactg
      481 gtaaccgaat tagaggagtt agccttgaag tcatgcgcct gttaaggcta aactgaaaga
      541 acaagttttg gtgactgcgc tcctccaagc cagttacctc ggctcaaaga gttggtagct
      601 ctgagaacct tcgaaaaacc gccctgcaag gcggtttttt cgtttacaca gcaagagatt
      661 acgacgagat agaaaggatc tcaagttctc atatcataaa aacaagctga cacatccacg
      721 atgttatacc ttttgaatcg ctacagcttt aaacccttta tctgtttttt ctaatttaaa
      781 cctaactaaa atacctttac atatatcgac atcatgccct aaaaacaaaa aatcatcata
      841 ccgaaagaaa acatcacgtc cacgctcacg ccttataaag ccataccctt taacatggtc
      901 ataaaaatta acaaatccat tttccatata atcacctatc tggaagtaat gccacaagct
      961 tacgtctata tagttttgca agattcttat tagtccgccc tactatatca aaatcataga
     1021 gcatcctatc tattttcctt atctgctcat cagttaaagg cggcgtaaat ttatttagat
     1081 aatgcttagc catcaacttt aatttagata tcttgtaatc atcataaact ggcattatct
     1141 cagaaagaat cgccctcaat tcaaccgcct ggacatgccc aagcctcgac atttgagcaa
     1201 ccttgccaga gcatctattc cataaatcat ggtactcttt cgtatgacgt tcataagcac
     1261 cttgtttttt acatatataa actaagtacc tgatataacg tctattttct tttgttaact
     1321 taggaacgcc atgctttacc cacaacccag tgacactaag tttagaagac gaatcttttg
     1381 agtgctctat cgttgtctta ctttcattta ttgaaagtct gtactgattc accattccgt
     1441 gaacgagttt tattactttt gttttttcct ctgatgaaag atccttatca gaggatatag
     1501 taatatcatc taaaagcctt gaatatgaaa gccccataga cttcaatcta ttatagagat
     1561 tatactcact attaaaaaat aaaagatttg caatataact agaacagcac ccaccctgag
     1621 gaaccttatt attcaacgtc acaagttccg ttaagcacaa agaaacctca ggagaaaaac
     1681 gcattaaatt tttaaaaata gaacaaacat cttttttact aatgctggga taaaaattgg
     1741 tgatatcaag acatataact gttcttttcc tagtatgaac agcggcatta gatatataat
     1801 cgcgaccact taacgcccca tgcaaataat gagggtaatc aattttctca aaaatttctt
     1861 tatttatttt tttttgaatt cctttcaaag atctcttggg ttcaaaaatt tgcctttctt
     1921 ttttattctt ccctgtttca accttaaact gcttgtacga catcgataca gacttgacta
     1981 tccagtccaa tctttttctt tctatgccta acatcgcaga taaagaatcc aaagatgcaa
     2041 caggagttcc attaaacctg ggtttattca tgatgtttga gttaaaagtc gattagttaa
     2101 aaagtttcga tacgtaatct attactttaa acataatcaa gcacatagaa aacaaaaact
     2161 gtgttttttt cagtgcctcc agagagccaa cctctctttt tttcttcatc tgaccgtctc
     2221 cagaacaaga tgaagagctc ttggttacgt taatgttgat gttgataata aacatgatgc
     2281 aactcctatt ggttatgaaa ttttgccaga ccagtaggaa agcaaggaaa aactctattg
     2341 gctctttggg acttttaact cacattgcca gacaatcgtc gctattcttt tagtgctgat
     2401 acacgctcag gggcgttctc accattaatt agcggccagg ccggtcatga tctcatgcga
     2461 gatcgcctta aaaacaaggc atcggtttcc ttgcgcaaca tacacgtaac catttgttaa
     2521 agagcgagag ccaggcgtgg ttcgcccgct tcgctgatta ttataaagtt ttttatcttt
     2581 ctgtcaccaa caagaaagcg ccttatcctg ccagcgatag gctaaaaggt atgcagcatg
     2641 agattcaaat caactcagct acaaaggcca taacaacaat cccaacctca gcatcggcac
     2701 tcaggataat ttttgaacta gcatctctta aattctgacc gtcaaaggtt gctacttttt
     2761 ttaaagaggc atcccttaaa accttgccat caaaagtcgc cacttttttt aaagaggcat
     2821 cccttaaaac cttgccatca aaagtcgcta ttttttttaa gctagcatcc cttaaaatct
     2881 tgccatcaaa agtcgctatt tttctcgaaa aggcatctct taaggtttta ccgtcaaacc
     2941 gagcaatagt ttttaagtca ttgtttttta ttgaaatatt catttatcac caatagtaat
     3001 ttaaccaatt gtatttacca taatccctta attgtacgca ccgctgaaac gcgctgaacg
     3061 caattctgac gcaaataccg caaaaagaga ggtttagccc cgaaaaaaca ggaaggatgc
     3121 gtcaggatcg ttttcagctc actgcatagc tatgcatgaa agcgaatggt gatcactttg
     3181 ggagcttacg gtgttcatac cgtctgtttt cgacagtttt ctccccggga agctaatctg
     3241 ccataagcct ggataacagg gcacggtgat actccgtaat agcgatcagt acctccgcat
     3301 actccctgtc cccgacacgc ttgccgtcga taaagagttt tttctgtaac gcccccagtc
     3361 tcataacttc tttcagtacc cgatcatcag tcagtgagtt aactttctta ccgagagctg
     3421 ccgcccgtaa aaaaccggaa acggtcttgc cgcattcagc agcccttttt ctgatttcct
     3481 ggtcttcttc tgccgtcaga cgaacagggc gactgatagc ccgcctgcgc gtattacttc
     3541 cacttcgttt tgtcataaaa catggctccg tatctgacat ggggtgtcgg ggcaaagccc
     3601 tgaccagggt aattgtaata gcgtgcatgt atgcgcggta taacaattac acatcctgtc
     3661 ctgtcagcaa gctcgaatta ccgacaaagg cacggcagtt ttttggcagt gacagtgttg
     3721 tctgacagaa atgcccgtca aagagtcaga cagcagaata ccgacggtaa aacagtcgaa
     3781 aagtggtacg cgatataatc acacaaagca gatgacagaa agaacggaga aaacagaaag
     3841 atgaacaagc agcagcaaac cgtactcaac atggcaggat tcataaaaag ccagagcctg
     3901 acgctgctcg aaaaactgga cgcacttgat gctgacgaac aggcagccat gtgtgagaag
     3961 ctgcacgaac tcgcggaaga acttcagaac agcatacaga cacgctttga agcggaaaat
     4021 cgcaccggga tataacgcat caggacagga tgcagaacgg catagaggag cgtaaggaga
     4081 aaatgtcaca taaggcgctc ttccgcttcc tcgctcactg actcgctacg ctcggtcgtt
     4141 cgactgcg
//
