LOCUS       NZ_CP039302             4664 bp    DNA     circular CON 19-JUN-2024
DEFINITION  Escherichia coli strain PigCaeca_1 plasmid unnamed4, complete
            sequence.
ACCESSION   NZ_CP039302
VERSION     NZ_CP039302.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN11268909
            Assembly: GCF_004801575.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4664)
  AUTHORS   REHAB consortium,T.
  TITLE     The impact of sequencing depth on the inferred taxonomic composition
            and AMR gene content of metagenomic samples
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4664)
  AUTHORS   Shaw,L.P.
  TITLE     Direct Submission
  JOURNAL   Submitted (04-APR-2019) Modernising Medical Microbiology Consortium,
            University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU,
            United Kingdom
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 30x
            Sequencing Technology :: Hybrid assembly: Illumina HiSeq 4000 and
            PacBio RSII
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_004801575.1-RS_2024_06_19
            Annotation Date                   :: 06/19/2024 07:24:00
            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)                     :: 4,850
            CDSs (total)                      :: 4,728
            Genes (coding)                    :: 4,527
            CDSs (with protein)               :: 4,527
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 201
            CDSs (without protein)            :: 201
            Pseudo Genes (ambiguous residues) :: 0 of 201
            Pseudo Genes (frameshifted)       :: 56 of 201
            Pseudo Genes (incomplete)         :: 140 of 201
            Pseudo Genes (internal stop)      :: 40 of 201
            Pseudo Genes (multiple problems)  :: 28 of 201
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP039302.1.
            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..4664
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="PigCaeca_1"
                     /isolation_source="feces"
                     /host="pig"
                     /db_xref="taxon:562"
                     /plasmid="unnamed4"
                     /geo_loc_name="United Kingdom: Yorkshire and the Humber"
                     /lat_lon="53.91 N 1.03 W"
                     /collection_date="2015"
     gene            complement(join(4497..4664,1..156))
                     /locus_tag="E7Z58_RS24310"
                     /old_locus_tag="E7Z58_24320"
     CDS             complement(join(4497..4664,1..156))
                     /locus_tag="E7Z58_RS24310"
                     /old_locus_tag="E7Z58_24320"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /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_015059937.1"
                     /translation="MLTMWVTEGEHRRLLERCDGRQLAAWMRQTCLDEKPARSGKLPSI
                     SPALLRQLAGMGNNLNQIARRVNAGGGTGHDRVQIVAALMAIDAGLERLRHAVLEKGTD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            complement(1213..2769)
                     /locus_tag="E7Z58_RS24320"
                     /old_locus_tag="E7Z58_24330"
     CDS             complement(1213..2769)
                     /locus_tag="E7Z58_RS24320"
                     /old_locus_tag="E7Z58_24330"
                     /EC_number="2.7.7.65"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_013199864.1"
                     /GO_function="GO:0052621 - diguanylate cyclase activity
                     [Evidence IEA]; GO:0046872 - metal ion binding [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="sensor domain-containing diguanylate cyclase"
                     /protein_id="WP_244591359.1"
                     /translation="MRIKKPHLRPIVITLSVGGILLTSIFLIAVIMVFQRENIEKDLLY
                     ANSSYAMKMSDVMSGYIEMAQGELAYGAKKIKSTNDIDSLKDEADRLRLQSGMFNSVLV
                     VSNDAVVLATSPESLDLVGTRLNSSASKLAVEEKKPFISSPLKSVAGNLIILLSHPIYD
                     KGGNYIGYVGGSIYLKKHSLFGDVLSRHFFKNNTEISIVSDDGNVIFNNDKSAVDRPMV
                     MSDDLKSKLTASDRGEGAFFSSGHRYLLGYASMKNTAWNVLVYSRADSVTTILIAYAKS
                     VLVLLIIIIVVFSLISYFIASSISLPLEKLAISTNAKDIGASLVYIKAINAWYAEADRL
                     KKALFTYIKVMMERVDSLNEVALKDPLTGVNNRLGFLSKIQNHKRDSGCSVIVIDVDFF
                     KEINDSFGHGVGDEVLVSLAHIINSCCRSEDVVCRFGGEEFVVFLPNTSVVTAKCVAER
                     IRSVIESTVFPNNLRVTISAGVATQDDPLGRIDFLLKNADDALYQAKREGRNKVIVYSA
                     I"
                     /name="sensor domain-containing diguanylate cyclase"
     gene            complement(3115..3330)
                     /locus_tag="E7Z58_RS24325"
     CDS             complement(3115..3330)
                     /locus_tag="E7Z58_RS24325"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137422.1"
                     /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_015589619.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWESAFAEWRTMSGLMQRENA
                     ALSERVTGLSRQVQSLSEQLRRLSSD"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(3334..3819)
                     /locus_tag="E7Z58_RS24330"
     CDS             complement(3334..3819)
                     /locus_tag="E7Z58_RS24330"
                     /inference="COORDINATES: protein motif:HMM:NF016710.4"
                     /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_012565228.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQNTGEMLKAAFSEHEKSVKAELNESA
                     KRISAAILDHDRKLSSAMSQRTKGMVRMVSQTWLTIVLVSALLIASSAGILWWQGQQIL
                     DNYTTIREQKSTQAMLSERNSGVQLSTCGEQRRRCVKVNPEAGRFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            complement(<3854..4558)
                     /locus_tag="E7Z58_RS24995"
                     /pseudo=""
     CDS             complement(<3854..4558)
                     /locus_tag="E7Z58_RS24995"
                     /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"
     Typing          complement(270..442)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.276"
                     /coverage="100.0"
                     /evalue="9.21e-81"
     Typing          367..918
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.639"
                     /coverage="91.0"
                     /evalue="0.0"
     Typing          complement(3012..4507)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.182"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(4504..4664)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.593"
                     /coverage="99.0"
                     /evalue="2.58e-24"
ORIGIN
        1 ctggcgcagc agcgccggcg agattgaggg aagctttccg gaacgtgccg gcttttcgtc
       61 caggcaggtc tgccgcatcc acgccgccag ctgcctgccg tcacagcgct caagcagccg
      121 ccggtgctcg ccctccgtca cccacatggt gagcatcttg ttccgtttct ctgacaaacc
      181 ggcctcctga taacgccggg acgggcggga aaggctttcc cggtcggcgc ggggttggac
      241 aagccgcagg cgcgtcaggc ttttggcggg tttcggggcg cagccctgaa ccagtcacgt
      301 agcgctagcg gagtgtatac tggcttacta tgttggcacg gatgcgagtg tcagtgaagt
      361 gcttcatgtg gcaggagaaa aatgcagcag cggagcgtca gcagaatatg tgatacagga
      421 tatattccgc ttcctcgctc actgactcgc tgcgctcggt cgttcggctg cggcgagcgg
      481 taccgactta caggcggggc ggaaatttcc tgggagatgc caggaagaag cttaacaggg
      541 aagcgataag gccacggcga agccgttttt ccataggctc cgcccccctg acaagcatca
      601 cgaaatctga cgctcaaatc agtggtggcg aaacccgaca ggacttaaag ataccaggcg
      661 tttccccctg gtggctccct cgtgcgctct cctgttcctg cctttcggtt taccgatgtc
      721 aatccgctgt tatggccgcg tttatctcat tccacgcctg acactcggtt ccgggaaggc
      781 agttcgctcc aagctggact gtatgcacga accccccgtt cagcccgact accacgttgt
      841 cccggtaact atcatcttga gtccaacccg gaacagacac gaaaaatcgc cagtggcggt
      901 agccattagt aagaggattc acggagcgga gtagtagagt gttctacaga gttcttgaag
      961 tggtggcctg actgcggcta cactggaagg acagttttgg tacctgcgct ccgtgaaagc
     1021 cagttacctt cggaagaaag agttggtagc tctgaattcc ggcaaacgaa ccaccgttgg
     1081 tagcggtggt ttttttgttt acagggtatg agattacgac gacatcgaag ggataacaag
     1141 aggatccgct tcttgcccac tcttcgccac aaaaaaaacg acacactagc gcgtaaagca
     1201 tcatcaaaaa actcaaatag cgctatatac aatcacttta ttacgcccct cccttttggc
     1261 ttgataaaga gcatcgtcag catttttcag caaaaaatcg atcctaccaa gaggatcatc
     1321 ttgtgttgcc acaccagcag atatggtgac ccgcaagtta ttagggaaga cagtactttc
     1381 aataacactc ctaatacgct ccgcaacaca cttagctgtt accacagatg tattcggcag
     1441 gaaaacaaca aactcttcgc caccaaaccg acaaacaaca tcttcactac ggcaacagga
     1501 attaataata tgagccaaag aaacaagcac ctcatctccg accccatgcc cgaaactgtc
     1561 atttatctct ttaaaaaaat caacatcaat tacaataact gaacaccctg aatcccgctt
     1621 atgattctgt attttactta aaaaccccaa tctattattc acgccggtaa ggggatcttt
     1681 aagcgccacc tcatttagag aatcaactct ttccatcatt accttaatat acgtaaaaag
     1741 cgccttttta agcctatcag cttcggcata ccaagcattg atagctttaa tataaactag
     1801 cgaagctccg atatctttag cattggtaga tatagcaagc ttttctaaag gaagtgaaat
     1861 actggaggca atgaaatatg aaataagtga aaacacaaca attattataa ttagcagaac
     1921 aagtacactt ttagcataag caataagaat agtagtcaca ctgtcagcac gactataaac
     1981 caacacattc caagcggtat ttttcatact agcataacca agaagatatc tatgccccga
     2041 agaaaaaaat gccccctcac ctctatcaga cgcagttaac tttgatttca aatcatcaga
     2101 cataaccata ggccgatcaa cagcactttt atcgttatta aagatcacat tcccatcatc
     2161 actaacaatg ctaatttcag tgttgttctt gaaaaaatgc ctgctcaaaa catcgccaaa
     2221 taaactatgt ttttttagat atatagaccc accgacatac cctatgtaat tgccaccctt
     2281 atcataaata ggatgtgaca acaaaataat caaattccca gcaactgatt ttaacggtga
     2341 agatatgaat ggtttctttt cctcaaccgc caatttgctg gcacttgaat tcaagcgggt
     2401 accaactaaa tcaagagatt ctggcgaagt cgccagaaca acagcatcat tactaacaac
     2461 aagaactgaa ttaaacatac cagactgcaa tcttaaccta tccgcctcat ctttaagtga
     2521 gtcaatatca ttagttgatt ttattttttt tgctccatat gctaattcac cttgagccat
     2581 ttcaatataa ccactcatta catctgacat tttcatagcg tacgatgaat tagcataaag
     2641 caaatctttt tctatatttt cgcgctgaaa aaccataata acggcaatca gaaaaataga
     2701 agttaacaaa atcccaccaa cggacaaggt tatgactatc ggacgaaggt gaggcttttt
     2761 aattctcata aaaatacact ccatataata aaaaatgccg catttaccat aacatccctt
     2821 atcagcaccg ccccggacgg gttcggaaca aatgcggcgt cagcccggta aaaccggcag
     2881 caaactctcc gctaaaccgc gcattctgcg ccagataaat ttcacccggc tgcatggcta
     2941 tgcagtcggg tgaatggctc cggctttcag cgcagatgtc cgccgaaagc cccgttttat
     3001 caggttatca cagtgaaggg ctgttatacg tccgctgtcg ctgagatcgc tccagctcca
     3061 gcgctttctg atgctgcacc acgcgctcct gctcccggtg cagctcgacg gcattcagtc
     3121 gctcgacaac cggcgcagct gctcgctcaa actctgcacc tgcctgctca agcccgtgac
     3181 gcgctcgctc agcgctgcgt tctcccgttg cataagacca gacatcgtcc gccattccgc
     3241 gaaggcgctc tcccactcgt ccagcctttt cgagtagtcc tgctgtagct gctctaatgc
     3301 gctcagcaac tgtttttcca gctccgtcat gtgctatttc cccgccagta tcatccagct
     3361 cgaatcctct ccgaaccgtc ccgcttccgg gttcaccttc acgcagcggc gtctctgctc
     3421 gccgcaggtc gagagctgca cgccgctgtt cctctctgac agcatggcct gcgtgctctt
     3481 ctgctcccgg atggtcgtgt agttgtcgag tatctgctgc ccctgccacc acagaatgcc
     3541 cgcgctcgag gcgatcagca gcgcggagac caggacgatg gtcagccacg tctggctgac
     3601 catgcgcacc atgcctttcg tgcgctggct catggctgag gacagtttcc ggtcgtggtc
     3661 gaggatggcg gcgctgattc tcttcgcgct ttcgttcagt tccgctttta cagatttctc
     3721 gtgctcgctg aatgcggctt tcagcatctc gccggtattc tgctgctgcg ctttcgattt
     3781 ctgctctaag tccttcgcca gcgttaaaag actgttcata aatggctccc ttcagtcgga
     3841 tgtttcgccc cccgtccggg tcggcaatgc tgatactgct ttttgtggtg cggaccacct
     3901 caaaacctgc gctttccagc gcctcagtga catcctgacg ggttttcagc tccccggatg
     3961 aggcaagagc aagcagaccg cgtgtaatcg cttctgcagc ctcctgcttc gctttaggca
     4021 gtgcagacgg tgtgaccagt gcccgccggt tctccggtgc gttcgggtcg tgcagcccca
     4081 gtctgccgtt cacgatggtc tgccaggcat cgatgcgtgg acggtcggcg cgatcgtaat
     4141 acggctggag ccgtctgccg gtcagcagct ccgtgttcgg gatcagaaaa ttcagctcaa
     4201 gccgcccctt gtcacgatgc tccacccaca ggatgctgta ctggtcttta tcaagtccgg
     4261 gcatcagaac ccgctcaaag cttgccatca gcttttcccg ctggccggaa ggtaaatccg
     4321 cttccgcaaa cgacagtacc ccggaggtgt atttcttaac gtaaggcgac gcgtcaatca
     4381 gctcccggac ttcttccggc ttcccctgca ggacggtggc gccttcacgc tgccggtctt
     4441 tacccagcag atagtccacc ggcccggcgc caccgccgcg accgcgtgga tgaaatttaa
     4501 cgatcatcgt ccgttccttt ctcaagaacg gcgtgccgca gccgctcaag tccggcatcg
     4561 atggccatca gcgccgcaac aatctgcacc ctgtcatggc cggtaccgcc gccggcgtta
     4621 acacggcggg ctatctggtt caggttattg cccatgccgg caag
//
