LOCUS       NZ_CP070917             4710 bp    DNA     linear   CON 17-JUN-2023
DEFINITION  Escherichia coli strain 65COLEC plasmid p65COLEC-3.
ACCESSION   NZ_CP070917
VERSION     NZ_CP070917.1
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 4710)
  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 4710)
  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
            CP070917.1.
            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..4710
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="65COLEC"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p65COLEC-3"
                     /geo_loc_name="Singapore"
                     /collection_date="2019-02"
     gene            845..1480
                     /locus_tag="JR892_RS24220"
                     /old_locus_tag="JR892_24220"
     CDS             845..1480
                     /locus_tag="JR892_RS24220"
                     /old_locus_tag="JR892_24220"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016236519.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_113403431.1"
                     /translation="MNDIFSLIESSRKIKKESIASTVRMPESLHTFIETLACDLELSKQ
                     EIMLKLLEQGARSAQEALAEIEKKELVELGAVEQLEPQTAVGFHILNTNKAHSDEDSEW
                     MLDKGIAAAFYDPWKWNINRIKPNEVVFLYENGKGIVAYGRGTGEVKIRDYHGDKDECH
                     YQELEGFKILENPLSAAQIKKILERNVVFLRTMSAMPDGQKVLNLIEG"
                     /name="hypothetical protein"
     gene            complement(1584..1892)
                     /locus_tag="JR892_RS24225"
                     /old_locus_tag="JR892_24225"
     CDS             complement(1584..1892)
                     /locus_tag="JR892_RS24225"
                     /old_locus_tag="JR892_24225"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012564913.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_113403432.1"
                     /translation="MTDKLKGTASVLNQTKTYEELVQKHSPEVANGLLANAINNALPNA
                     GITSNDVVGFSKVTTALRTGEVDLAKTAEEANADAEAVSANILAGLTAKQKSTDEIK"
                     /name="hypothetical protein"
     gene            complement(2203..2316)
                     /locus_tag="JR892_RS24230"
                     /old_locus_tag="JR892_24230"
     CDS             complement(2203..2316)
                     /locus_tag="JR892_RS24230"
                     /old_locus_tag="JR892_24230"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /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_072003743.1"
                     /translation="MHEPPVQSDYHARSGNYRLESNPERHDKSPLAVATGN"
                     /name="replication initiation protein"
     gene            2777..>3235
                     /locus_tag="JR892_RS24235"
                     /old_locus_tag="JR892_24235"
                     /pseudo=""
     CDS             2777..>3235
                     /locus_tag="JR892_RS24235"
                     /old_locus_tag="JR892_24235"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_076612230.1"
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /note="frameshifted; 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="IS1 family transposase"
                     /name="IS1 family transposase"
     gene            3585..3971
                     /locus_tag="JR892_RS24240"
                     /old_locus_tag="JR892_24240"
     CDS             3585..3971
                     /locus_tag="JR892_RS24240"
                     /old_locus_tag="JR892_24240"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_205900189.1"
                     /translation="MFFYRFITLIFGAVYIATTLTLGESALSSSLYAIGIAKTPSSASG
                     ILTLLLMLWVLVASVMVPKSWKVFAGIYLCLGLSGFLMPKSMHYGAGVYPLVNSLTLLS
                     YLAFTLAIKLRDKYISKINQKTAW"
                     /name="hypothetical protein"
     gene            4022..>4710
                     /locus_tag="JR892_RS24245"
                     /old_locus_tag="JR892_24245"
     CDS             join(4022..4271,4271..>4710)
                     /locus_tag="JR892_RS24245"
                     /old_locus_tag="JR892_24245"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001743396.1"
                     /ribosomal_slippage=""
                     /note="programmed frameshift; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS1-like element IS1A family transposase"
                     /protein_id="WP_226487787.1"
                     /translation="MASVSISCPSCSATDGVVRNGKSTAGHQRYLCSHCRKTWQLQFTY
                     TASQPGTHQKIIDMAMNGVGCRATARIMGVGLNTILRHFKKLRPQSVTSRIQPGSDVIV
                     CAEMDEQWGYVGAKSRQRWLFYAYDSLRKTVVAHVFGERTMATLGRLMSLLSPFDVVIW
                     MTDGWPLYESRLKGKLHVISKRYTQRIERHNLNLRQHLARLGRKSLSFSKSVELHDKVI
                     GHYLNIKH"
                     /name="IS1-like element IS1A family transposase"
     Typing          complement(2200..2586)
                     /name="rep_cluster_2373"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.373"
                     /coverage="90.0"
                     /evalue="2.89e-174"
ORIGIN
        1 catcaataag ttggagtcat tacccgttat agctttttcg cttacccgcg tacgtggtaa
       61 tacgccggta ttacatctta tttctttatt ttcatgtaat tacaggtggt tgtaatacgt
      121 tgcgtattac ataaataaac ggggaattca gtttttacct tttaattcat gcaattgcga
      181 tgaaaatcgc ggttgcgtat ggtgtatggc catttaaggg ataaagaatc atctccttac
      241 cgggctgagc tttgcctatt ctgaggagat ctgtgaaaaa aaacgtccat aactagctcg
      301 ttcatacttg tatgaacagc ttattcctcc tgactactaa taaactacag cgtcactact
      361 gatttactac tgatttacta caaaccggag gggggagact acagaaacac tacagaatta
      421 ctacagaacg gacctttgaa tccagcctca gtctgccatg cctaacagtt ggtcaatgaa
      481 ttgcccaccc gttcaccgtt accaatttgt cctgttttcg tagattacac gatgattttt
      541 acctgaaaga ccggggcgtt cattccggtg catagtcatt cacattcgta aaacgtatca
      601 gaacgatttt gaacggtttt gatggggtaa gacgtgttct tttgcgggtg agggcgtaaa
      661 aacgctctca gagcctctca ggcggtgcgg gcaacggatg ttatggtaaa tacacatcgt
      721 aatgactatt cgtgcatacg ccatcatcta tcacttggag ttagaatcta ttttgattca
      781 attattgcat cgttttttga ttcactatat gcttctataa caaaaccaat ttaaggttca
      841 taaaatgaat gatatttttt ctttaatcga aagctccaga aaaattaaaa aagaatcgat
      901 agcttccaca gtgcgaatgc ccgagtcgtt gcatacgttt atcgaaacgc tggcctgcga
      961 tctcgaactt tcaaagcaag agatcatgct taaactcctt gagcaaggag ccaggagtgc
     1021 tcaagaggcg ttagctgaga ttgaaaagaa ggagttggtt gagttaggcg ctgtagaaca
     1081 actcgagccg cagacagccg ttggcttcca tattttgaat acaaacaaag ctcatagcga
     1141 tgaagactct gaatggatgc ttgacaaagg aatcgctgct gctttttatg atccatggaa
     1201 atggaacatc aatcgaatca agcccaatga agtagtgttt ctgtatgaaa acggtaaagg
     1261 catagttgcc tatggtaggg gtactggtga ggttaaaatt cgcgattatc atggcgataa
     1321 agacgaatgc cactaccaag agctggaagg gtttaaaatt cttgaaaatc cgctatcggc
     1381 tgctcaaatt aagaagatat tggagcggaa tgttgtgttt ttgagaacaa tgtcggctat
     1441 gccagatggt caaaaggtgc tgaaccttat cgaaggttaa gccgagcact tgatggggtt
     1501 gagtgcggtt aaaatttttt tataagtaat tacatacgaa accttggccc gtctagttcg
     1561 ggcttttttg tacctgcggg aaattatttt atttcatctg tacttttttg ttttgctgtc
     1621 aggccagcaa gaatatttgc tgaaacggct tccgcatcgg cattggcttc ttcggctgtt
     1681 tttgctagat caacttctcc tgtacgcaag gccgtcgtca ctttgctgaa tccaacgacg
     1741 tcattcgaag ttattcctgc gttaggcaaa gcattattga tagcatttgc cagcaagccg
     1801 ttagctactt caggtgaatg cttctgaacc aattcctcat aagttttggt ttgattaaga
     1861 acgctagctg ttcctttgag tttgtctgtc atgtaaacct ctagtctgtg atgagtcagg
     1921 agtagaaaat tttatgtaca agactcgcgt taggcgggca ctcatactga agcaaaatca
     1981 ctgctaaaca gccggatctt cttgtgatcc ttttactctc gtcgtaatct cattccctgt
     2041 aaacaaaaaa accaccgcta ccaacggtgg ttcgtttgcc ggaatcaaga gctaccaact
     2101 ctttcttccg aaggtaactg gcttggagga gcgcagtcac caaaactgtc ctttcagtgt
     2161 agctgcatcg caccaggaac ttcaagactc tcctcctcta aatcagttac cagtggctac
     2221 cgccaatggc gatttatcgt gtctttccgg gttggactca agtcgatagt taccggaacg
     2281 ggcgtggtag tcggactgaa cggggggttc gtgcatacag tccagcttgg agcgaactgc
     2341 cttcccggaa ctgagtgtca ggcgtggaat gagataaacg cggccataac agcggaatga
     2401 caccggtaaa ccgaaaggca ggaacaggag agcgcacgag ggagccacca gggggaaacg
     2461 cctgggatct ttatagtcct gtcgggtttc gccaccactg atttgagcgt cagattctgt
     2521 gatgcttgtc aggggggcgg agcctatgga aaaccggcaa cgccgcggcc ttttcttttg
     2581 cctctcgatc ctctctcatt gcctgtgcct taatgtctcc gttccctccg ctcgccgcag
     2641 ccgaacgacc gagcgtagcg agtcagtgag cgaggaagcg gaatatctcc tgtattgcat
     2701 cttctgctga cgcgccggtg cggtgatgct gccaacttac tgatttagtg tatgatggtg
     2761 tttttgaggt gctccagtgg cttctgtttc tatcagctgt ccctcctgtt cagctactga
     2821 cgggggtggt gcgtaacggc aaaagcaccg ccggacatca gcgttatctc tgctctcact
     2881 gccgtaaaac atggcaactg cagttcactt acaccgcttc tcaacccggt acgcaccaga
     2941 aaatcattga tatggccatg aatggcgttg gatgccgggc aactgcacgc attatgggcg
     3001 ttggcctcaa cacgatttta cgtcacttaa aaaactcagg ccgcagtcgg taacctcgcg
     3061 catacagccg ggcagtgacg tcatcgtctg cgcggaaatg gacgaacagt ggggctatgt
     3121 cggggctaaa tcgcgccagc gctggctgtt ttacgcgtat gacagtctcc ggaagacggt
     3181 tgtggcgcac gtcttcggtg aacgcactat ggcgacgctg gggcgtgtca tttcgtttcg
     3241 gctccccctg tttttccctt tcttcgctgg acgctcatca ggataaaaac aaaaagacta
     3301 ccgccctcgt tttactcggt tggtcaaatc gcttcttgcc acaaacttgt tttgtggcaa
     3361 gaagcgattt cgcatcgttt tacttgtcag tttgaatgat gttaaaaacg cactcagaag
     3421 ctcgcaaaac cgttctaaac tttcagcgta gatttggttt tgaggggctt taatggggat
     3481 gaacgggcgg ttttcgctaa ctaactcgcc cgtttaacat aaaagggatt agaagaacct
     3541 atgtttatgt aaaatctaca attatttaat ataggcgggc tattatgttt ttctatcgat
     3601 ttatcacttt aatttttggg gctgtgtata ttgctacaac tctaacattg ggagagtcgg
     3661 cgttatcctc ttcgctttat gcaataggga ttgctaaaac ccctagctcc gcttctggta
     3721 ttttgactct tttgttgatg ttgtgggttt tagttgcttc ggtcatggtg cctaaatctt
     3781 ggaaagtttt tgctggcatt tatctatgct tgggtttgtc agggttcctt atgccgaaaa
     3841 gcatgcatta tggtgccggt gtttacccat tggtaaactc tttaacactt cttagttatc
     3901 tggcctttac ccttgcaata aagctaagag acaaatacat ctccaaaata aatcaaaaaa
     3961 ctgcctggtg atgctgccaa cttactgatt tagtgtatga tggtgttttt gaggtgctcc
     4021 agtggcttct gtttctatca gctgtccctc ctgttcagct actgacgggg tggtgcgtaa
     4081 cggcaaaagc accgccggac atcagcgcta tctctgctct cactgccgta aaacatggca
     4141 actgcagttc acttacaccg cttctcaacc cggtacgcac cagaaaatca ttgatatggc
     4201 catgaatggc gttggatgcc gggcaacagc ccgcattatg ggcgttggcc tcaacacgat
     4261 tttacgtcac ttaaaaaact caggccgcag tcggtaacct cgcgcataca gccgggcagt
     4321 gacgtcatcg tctgcgcgga aatggacgaa cagtggggct atgtcggggc taaatcgcgc
     4381 cagcgctggc tgttttacgc gtatgacagt ctccggaaga cggttgtggc gcacgtcttc
     4441 ggtgaacgca ctatggcgac gctggggcgt cttatgagcc tgctgtcacc ctttgacgtg
     4501 gtgatatgga tgacggatgg ctggccgctg tatgaatccc gcctgaaggg aaagctgcac
     4561 gtaatcagca agcgatatac gcagcgaatt gagcggcata acctgaatct gaggcagcac
     4621 ctggcacggc tgggacggaa gtcgctgtcg ttctcaaaat cggtggagct gcatgacaaa
     4681 gtcatcgggc attatctgaa cataaaacac
//
