LOCUS       NZ_CP070918             3373 bp    DNA     linear   CON 17-JUN-2023
DEFINITION  Escherichia coli strain 65COLEC plasmid p65COLEC-4.
ACCESSION   NZ_CP070918
VERSION     NZ_CP070918.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17807535
            Assembly: GCF_017088465.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3373)
  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 3373)
  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                   :: 363x
            Sequencing Technology :: Illumina NovaSeq Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/17/2023 06:41:11
            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)                     :: 4,904
            CDSs (total)                      :: 4,785
            Genes (coding)                    :: 4,568
            CDSs (with protein)               :: 4,568
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 217
            CDSs (without protein)            :: 217
            Pseudo Genes (ambiguous residues) :: 0 of 217
            Pseudo Genes (frameshifted)       :: 69 of 217
            Pseudo Genes (incomplete)         :: 138 of 217
            Pseudo Genes (internal stop)      :: 50 of 217
            Pseudo Genes (multiple problems)  :: 38 of 217
            Pseudo Genes (short protein)      :: 3 of 217
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP070918.1.
            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..3373
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="65COLEC"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p65COLEC-4"
                     /geo_loc_name="Singapore"
                     /collection_date="2019-02"
     gene            complement(331..522)
                     /locus_tag="JR892_RS24250"
                     /old_locus_tag="JR892_24250"
     CDS             complement(331..522)
                     /locus_tag="JR892_RS24250"
                     /old_locus_tag="JR892_24250"
                     /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"
     gene            586..909
                     /locus_tag="JR892_RS24255"
                     /old_locus_tag="JR892_24255"
     CDS             586..909
                     /locus_tag="JR892_RS24255"
                     /old_locus_tag="JR892_24255"
                     /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            1118..>1558
                     /locus_tag="JR892_RS24590"
                     /pseudo=""
     CDS             1118..>1558
                     /locus_tag="JR892_RS24590"
                     /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            1587..2147
                     /locus_tag="JR892_RS24265"
                     /old_locus_tag="JR892_24265"
     CDS             1587..2147
                     /locus_tag="JR892_RS24265"
                     /old_locus_tag="JR892_24265"
                     /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_000067487.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKKQLDTLSTTVSMQFSTTEAELSRQQKKLLWRVIKGRILFPALTA
                     LSVTGGIFLGCWGLMEWQESKIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            2154..2387
                     /locus_tag="JR892_RS24270"
                     /old_locus_tag="JR892_24270"
     CDS             2154..2387
                     /locus_tag="JR892_RS24270"
                     /old_locus_tag="JR892_24270"
                     /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"
     Typing          167..250
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="85.882"
                     /coverage="95.0"
                     /evalue="4.11e-16"
     Typing          900..2470
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.439"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ccgaacgtag tgagcgagtg ggcgaggaag cggaagagtc acagaggcaa gcattgtgca
       61 cttacgcgcc tgtgccagtg tccgcgtgtg tgttgtttat cgggcgcgct gtttttacgc
      121 atctgtgcgg ctttttactc ctgacatggt gcacttccca tccactctgc accgatgcaa
      181 aatgaggaaa gccagtatac acatcgctat cgctctgtga actgggtcag ggctgcgccc
      241 cgacacccgc actgacgcgc cctggctggc ttgtctgctc ccggcatccg ctcacaggca
      301 agctgtgaac gtctccggga gctgcatgtt tcagttgctt tcaccgtcat cgccgaagcg
      361 tgcgaggcaa ctgcggtaga gttcgtcggc gtggtcgtga agtgattcgc agatgtctgc
      421 ctgttcgtcc gcgtccagat cgttgagttt ttccagcagg gttagcgtct ggcttctgat
      481 aaagcgagcc atgttaaggg ctgttttttc ctgtttggtc atggtcttaa ggctccttgt
      541 atgggggatt tgttaggggg aatgataccg atgaaacgcg agaagatgct cacgatacgg
      601 gttaccgatg aggagcacgc ccggttactg gaacgctgcg agggtaaacg actggcggaa
      661 tggatgcggc gggtctgtct gggggagccg gttgcacgca caggaaaact gccgacactg
      721 gcaccgccat tgctgcggca tctggctgcc atcgggaaca acctgaacca gacagcccgg
      781 aaggtgaaca gcggccagtg gtcttcgatt gaccgggttc atgtggtggc cgcactgatg
      841 gccatcgagg gtgaattgcg ccagttgcgg caggctgtca gggaacaggg ggtacgggat
      901 gatagttaaa tttcatgcca gggggaaagg cggtggaagt ggcccggtcg attacctgct
      961 ggggcgggag cgtaaccgcg aaggcgcaac ggtgctccgg ggtaacccgg aagaagtgcg
     1021 ggaactcatt gattccacgc cattttcgag gaaatacacg tcaggcgttc tgtcgttcgc
     1081 ggagaaggag ctaccaccgg gtgaacgcga aagagtgatg acgagctttg agcgtgttct
     1141 tatgcccggt ctcgaaaaag accagtacag cattctctgg gtggaacacc aggataaggg
     1201 gcggctcgaa ctgaattttg tcatcccgaa catggagcta cagagcggta agcgcctcca
     1261 gccgtactac gaccgtgcgg acaggccgag gataaatgcc tggcagacgc tggttaatca
     1321 tcattacggg ctgcgtgacc cgaacgcacc ggagaacaga cggacgcttg tcacgccaaa
     1381 taatctgcca aaagcgaaac aggaggccgc agaagcgatt acacggggtc ttgaggctct
     1441 ttaccatgcc ggagcaataa aaacgcgtca ggatgtcaca gaggcgctta cagcggcagg
     1501 ttttgaggtg gtgaggacaa ccaaaagcag catcagtatt gccgacccgg agggggggcg
     1561 gaatctcagg ctaaaggggg cgctgtatga gcaatctttt acaaatggga acagacttcg
     1621 agaagaaact gaaagagcga gccgcttcta ccgagaacat gctgaacagc gagttcagga
     1681 agctcgaaga gtctgtagac aaggcattga gcttaaacag gcagaaaatc agagacgcta
     1741 tcagcgaaca tacaacatcc gtgaaaaagc aactggatac gctgagcacc accgtgagca
     1801 tgcagttcag caccacagag gccgaactgt cccggcagca gaaaaaactg ctctggcggg
     1861 tgatcaaagg gcggatactg tttccggcgc tgaccgcgct cagcgtcacg ggcgggattt
     1921 tcctggggtg ctgggggctg atggagtggc aggaaagcaa gattgcgaaa aatatcctga
     1981 ctatcagaga gcaggaaaac acgctggcga aactcgaggc aaaaacctgg ggggtgacgt
     2041 tcgtcaatgg cgagaacggg aaatttctgg tgttgccgga cggggtgaaa ggggaaaaca
     2101 cctggacggt gggcgacaag aacgccgtga ggctggtcag ggagtaaacg agtatgacgg
     2161 aactggaagg gcatttgctg aacgccttag agcatttgca acaggactat atgcggcggc
     2221 tgaacgagtg ggagagcgcc ttcgcggaat tgcagaagat gcacgaggtt acgcaacgga
     2281 acaacgcgat actgaacgag cgcgtcgtga tattgagtca gcaggtgcag agattagccg
     2341 ggcaagtgga tcgcttgagt cggttattta tcgcgaacaa cagctaaggg atgaacagga
     2401 gcgtgcccgg tacagacatg aggtacagga acgcgcggca cgggttcgga gtgggccatc
     2461 aatggagatg tgaccgggga agtgacgaaa tcttgccatt ttgacccgtt cgacggctgg
     2521 ggcgagcgaa acaaatcgtg tgccgtattt gtgcatagct atgcaacatc ctgaaaacgc
     2581 atttcacgcg tttttgggga ttcagccagg ggaaaacatg gtttttttac tttttgagcg
     2641 taaagacgtg aaaaatctcg ttattgcact tgcgatcttt cgtcggcggg cgtagaacga
     2701 aaacagctcg ccaggaaggc gagctgtttc gggttcattg aggtctctga cctcctcaat
     2761 gttcctgtgg aaactgttga gatccacaac agaaaccagt tcattcagtt tgcatgagcc
     2821 ttctgtattc ttcaagaatt tttcaacagc acagtctccc aggaaccccg aaaaaaacct
     2881 gtttttgcag atacttgcgt atttgcgaga atcgtttgcg gttgggggag ctgtgacgac
     2941 ggcgaccgca cgcgtgagag ttccgctacc ggcgcagaga gtttcatcga cagcggacac
     3001 ctgatgagtt gccacaaaaa ccgtatgtag cgcggctaga ttggttgagt tagaccttgg
     3061 cggcagttcc cggtatgtgg tggcgtgacg ggtgagatgg tgcggcgaag acgcatacgt
     3121 cacgcaggcg cgggttcttc cactgacgcg ccccgtgatc gatggccttg gctccgtccg
     3181 gcatatcgag agcggcaaac tacccgtccc ttcactggga ggggtgagtt gttgccgttc
     3241 cctccgacct tccaccatcc agcatatcgc acgatcccat gtgcaccgct actcctgata
     3301 actccagtgc aaaaaaaaaa acggatctgc atcacaacga gagtgatccc accgctcgcc
     3361 gcagccccag cga
//
