LOCUS       NZ_CP070928             3375 bp    DNA     linear   CON 17-JUN-2023
DEFINITION  Escherichia coli strain 40EC plasmid p40EC-8.
ACCESSION   NZ_CP070928
VERSION     NZ_CP070928.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17807534
            Assembly: GCF_017088445.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3375)
  AUTHORS   Ding,Y., Saw,W.-Y., Tan,L.W.L., Moong,D.K.N., Nagarajan,N., Teo,Y.Y.
            and Seedorf,H.
  TITLE     Whole-genome analysis of antimicrobial-resistant Escherichia coli in
            human gut microbiota reveals its origin and flexibility in
            transmitting mcr-1
  JOURNAL   bioRxiv (2021)
REFERENCE   2  (bases 1 to 3375)
  AUTHORS   Ding,Y. and Seedorf,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (05-FEB-2021) Henning Seedorf Group, Temasek Life Sciences
            Laboratory Limited, 1 Research Link National University of Singapore
            Singapore, Singapore 117604, Singapore
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 378x
            Sequencing Technology :: Illumina NovaSeq Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/17/2023 06:58:43
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,165
            CDSs (total)                      :: 5,048
            Genes (coding)                    :: 4,866
            CDSs (with protein)               :: 4,866
            Genes (RNA)                       :: 117
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 182
            CDSs (without protein)            :: 182
            Pseudo Genes (ambiguous residues) :: 0 of 182
            Pseudo Genes (frameshifted)       :: 66 of 182
            Pseudo Genes (incomplete)         :: 118 of 182
            Pseudo Genes (internal stop)      :: 38 of 182
            Pseudo Genes (multiple problems)  :: 39 of 182
            Pseudo Genes (short protein)      :: 3 of 182
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP070928.1.
            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/
FEATURES             Location/Qualifiers
     source          1..3375
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="40EC"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p40EC-8"
                     /geo_loc_name="Singapore"
                     /collection_date="2019-02"
     gene            <1..659
                     /locus_tag="JR909_RS25960"
     CDS             <1..659
                     /locus_tag="JR909_RS25960"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=3
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_227181539.1"
                     /translation="MVEGRRERQQLTPPSEGTGSLPLSICRTEPRPSITGRVSGRTRAC
                     VTYASSPHHLTRHATTYRELPPRSNSTNLAALHTVFVATHQVSAVDETLCAGSGTLTRA
                     VAVVTAPPTANDSHKYASICKNRFFSGFLGDCAVEKFLKNTEGSCKLNELVSVVDLNSF
                     HRNIEEVRDLNEPETARLPGELFSFYARRRKIASAITRFFTSLRSKSKKTMFSPG"
                     /name="hypothetical protein"
     gene            complement(874..1107)
                     /locus_tag="JR909_RS25545"
                     /old_locus_tag="JR909_25545"
     CDS             complement(874..1107)
                     /locus_tag="JR909_RS25545"
                     /old_locus_tag="JR909_25545"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137389.1"
                     /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_000137389.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHEVTQRNNA
                     ILNERVVILSQQVQRLAGQVDRLSRLFIANNS"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(1114..1674)
                     /locus_tag="JR909_RS25550"
                     /old_locus_tag="JR909_25550"
     CDS             complement(1114..1674)
                     /locus_tag="JR909_RS25550"
                     /old_locus_tag="JR909_25550"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000067488.1"
                     /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_000067486.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKKQLDTLSTTVSMQFSTTEAELSRQQKKLLWRVIKGRILFPALTA
                     LSVTGGIFLGCWGLMEWQESKIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGMKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            complement(<1703..2143)
                     /locus_tag="JR909_RS25965"
                     /pseudo=""
     CDS             complement(<1703..2143)
                     /locus_tag="JR909_RS25965"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /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            complement(2352..2675)
                     /locus_tag="JR909_RS25560"
                     /old_locus_tag="JR909_25560"
     CDS             complement(2352..2675)
                     /locus_tag="JR909_RS25560"
                     /old_locus_tag="JR909_25560"
                     /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_001696562.1"
                     /translation="MLTIRVTDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     APPLLRHLAAIGNNLNQTARKVNSGQWSSIDRVHVVAALMAIEGELRQLRQAVREQGVR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2739..2930
                     /locus_tag="JR909_RS25565"
                     /old_locus_tag="JR909_25565"
     CDS             2739..2930
                     /locus_tag="JR909_RS25565"
                     /old_locus_tag="JR909_25565"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165979.1"
                     /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_000165979.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNDLDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(3012..3092)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="87.805"
                     /coverage="93.0"
                     /evalue="8.68e-18"
     Typing          complement(792..2362)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.439"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ggatggtgga aggtcggagg gaacggcaac aactcacccc tcccagtgaa gggacgggta
       61 gtttgccgct ctcgatatgc cggacggagc caaggccatc gatcacgggg cgcgtcagtg
      121 gaagaacccg cgcctgcgtg acgtatgcgt cttcgccgca ccatctcacc cgtcacgcca
      181 ccacataccg ggaactgccg ccaaggtcta actcaaccaa tctagccgcg ctacatacgg
      241 tttttgtggc aactcatcag gtgtccgctg tcgatgaaac tctctgcgcc ggtagcggaa
      301 ctctcacgcg tgcggtcgcc gtcgtcacag ctcccccaac cgcaaacgat tctcacaaat
      361 acgcaagtat ctgcaaaaac aggttttttt cggggttcct gggagactgt gctgttgaaa
      421 aattcttgaa gaatacagaa ggctcatgca aactgaatga actggtttct gttgtggatc
      481 tcaacagttt ccacaggaac attgaggagg tcagagacct caatgaaccc gaaacagctc
      541 gccttcctgg cgagctgttt tcgttctacg cccgccgacg aaagatcgca agtgcaataa
      601 cgagattttt cacgtcttta cgctcaaaaa gtaaaaaaac catgttttcc cctggctgaa
      661 tccccaaaaa cgcgtgaaat gcgttttcag gatgttgcat agctatgcac aaatacggca
      721 cacgatttgt ttcgctcgcc ccagccgtcg aacgggtcaa aatggcaaga tttcgtcact
      781 tccccggtca catctccatt gatggcccac tccgaacccg tgccgcgcgt tcctgtacct
      841 catgtctgta ccgggcacgc tcctgttcat cccttagctg ttgttcgcga taaataaccg
      901 actcaagcga tccacttgcc cggctaatct ctgcacctgc tgactcaata tcacgacgcg
      961 ctcgttcagt atcgcgttgt tccgttgcgt aacctcgtgc atcttctgca attccgcgaa
     1021 ggcgctctcc cactcgttca gccgccgcat atagtcctgt tgcaaatgct ctaaggcgtt
     1081 cagcaaatgc ccttccagtt ccgtcatact cgtttactcc ctgaccagcc tcacggcgtt
     1141 cttgtcgccc accgtccagg tgttttcccc tttcatcccg tccggcaaca ccagaaattt
     1201 cccgttctcg ccattgacga acgtcacccc ccaggttttt gcctcgagtt tcgccagcgt
     1261 gttttcctgc tctctgatag tcaggatatt tttcgcaatc ttgctttcct gccactccat
     1321 cagcccccag caccccagga aaatcccgcc cgtgacgctg agcgcggtca gcgccggaaa
     1381 cagtatccgc cctttgatca cccgccagag cagttttttc tgctgccggg acagttcggc
     1441 ctctgtggtg ctgaactgca tgctcacggt ggtgctcagc gtatccagtt gctttttcac
     1501 ggatgttgta tgttcgctga tagcgtctct gattttctgc ctgtttaagc tcaatgcctt
     1561 gtctacagac tcttcgagct tcctgaactc gctgttcagc atgttctcgg tagaagcggc
     1621 tcgctctttc agtttcttct cgaagtctgt tcccatttgt aaaagattgc tcatacagcg
     1681 ccccctttag cctgagattc cgccccccct ccgggtcggc aatactgatg ctgcttttgg
     1741 ttgtcctcac cacctcaaaa cctgccgctg taagcgcctc tgtgacatcc tgacgcgttt
     1801 ttattgctcc ggcatggtaa agagcctcaa gaccccgtgt aatcgcttct gcggcctcct
     1861 gtttcgcttt tggcagatta tttggcgtga caagcgtccg tctgttctcc ggtgcgttcg
     1921 ggtcacgcag cccgtaatga tgattaacca gcgtctgcca ggcatttatc ctcggcctgt
     1981 ccgcacggtc gtagtacggc tggaggcgct taccgctctg tagctccatg ttcgggatga
     2041 caaaattcag ttcgagccgc cccttatcct ggtgttccac ccagagaatg ctgtactggt
     2101 ctttttcgag accgggcata agaacacgct caaagctcgt catcactctt tcgcgttcac
     2161 ccggtggtag ctccttctcc gcgaacgaca gaacgcctga cgtgtatttc ttcgaaaatg
     2221 gcgtggaatc aatgagttcc cgcacttctt ccgggttacc ccggagcacc gttgcgcctt
     2281 cgcggttacg ctcccgcccc agcaggtaat cgaccgggcc acttccaccg cctttccccc
     2341 tggcatgaaa tttaactatc atcccgtacc ccctgttccc tgacagcctg ccgcaactgg
     2401 cgcaattcac cctcgatggc catcagtgcg gccaccacat gaacccggtc aatcgaagac
     2461 cactggccgc tgttcacctt ccgggctgtc tggttcaggt tgttcccgat ggcagccaga
     2521 tgccgcagca atggcggtgc cagtgtcggc agttttcctg tgcgtgcaac cggctccccc
     2581 agacagaccc gccgcatcca ttccgccagt cgtttaccct cgcagcgttc cagtaaccgg
     2641 gcgtgctcct catcggtaac ccgtatcgtg agcatcttct cgcgtttcat cggtatcatt
     2701 ccccctaaca aatcccccat acaaggagcc ttaagaccat gaccaaacag gaaaaaacag
     2761 cccttaacat ggctcgcttt atcagaagcc agacgctaac cctgctggaa aaactcaacg
     2821 atctggacgc ggacgaacag gcagacatct gcgaatcact tcacgaccac gccgacgaac
     2881 tctaccgcag ttgcctcgca cgcttcggcg atgacggtga aagcaactga aacatgcagc
     2941 tcccggagac gttcacagct tgcctgtgag cggatgccgg gagcagacaa gcccgccagg
     3001 gcgcgtcagt gcgggtgtcg gggcgcagcc ctgacccagt tcacagagcg atagcgatgt
     3061 gtatactggc ttacctcatt ttgcatcggt gcagagtgga tgggaagtgc accatgtcag
     3121 gagtaaaaag ccgcacagat gcgtaaaaac agcgcgcccg ataaacaaca cacacgcgga
     3181 cactggcaca ggcgcgtaag tgcacaatgc ttgcctctgt gactcttccg cttcctcgcc
     3241 cactcgctca ctacgttcgg tcgctggggc tgcggcgagc ggtgggatca ctctcgttgt
     3301 gatgcagatc cgtttttttt tttttgcact ggagttatca ggagtagcgg tgcacatggg
     3361 atcgtgcgat atgct
//
