LOCUS       NZ_CP070929             1618 bp    DNA     linear   CON 17-JUN-2023
DEFINITION  Escherichia coli strain 40EC plasmid p40EC-9.
ACCESSION   NZ_CP070929
VERSION     NZ_CP070929.1
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 1618)
  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 1618)
  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
            CP070929.1.
            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..1618
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="40EC"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p40EC-9"
                     /geo_loc_name="Singapore"
                     /collection_date="2019-02"
     gene            complement(<1..252)
                     /locus_tag="JR909_RS25570"
                     /old_locus_tag="JR909_25570"
                     /pseudo=""
     CDS             complement(<1..252)
                     /locus_tag="JR909_RS25570"
                     /old_locus_tag="JR909_25570"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001557684.1"
                     /note="incomplete; too short partial abutting assembly gap;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="repA"
                     /name="repA"
     gene            complement(1433..>1618)
                     /locus_tag="JR909_RS25575"
                     /old_locus_tag="JR909_25575"
                     /pseudo=""
     CDS             complement(1433..>1618)
                     /locus_tag="JR909_RS25575"
                     /old_locus_tag="JR909_25575"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000469298.1"
                     /note="incomplete; too short partial abutting assembly gap;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="repA"
                     /name="repA"
     Typing          complement(673..751)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="93.75"
                     /coverage="87.0"
                     /evalue="1.58e-25"
     Typing          854..1105
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.466"
                     /coverage="97.0"
                     /evalue="3.95e-106"
ORIGIN
        1 gtatgagatc caattacgca cagttcgagt agtcacatca aactgagcag ccagaaaagc
       61 ttggtccgct acaaccgcac cacaagcacc atcgatatgt tgtgccaaaa aagtatacaa
      121 cccaaatgcg ccctgatttc ctttggcaag agccatcagt cgcttccagc ctagtggata
      181 cacttgagtg aatccgaggt tctctctgtc atgtttttct cgatgatctg cgattagatt
      241 ctgggtattc atagcgattc ctatcaaccg gaaacagttg ttcctataat aggaaattta
      301 ttttccatat caatgcttat ttcgttccta ctttcagaag taataggaaa cacatgtatt
      361 tcctatcatg cggaaataca tgtgtttcct attagctaat atttccacaa ataaaaacaa
      421 tgagttacat catccgctaa ttgttatctt aagagcacga tgtttcctaa tgcacgatcg
      481 cttggttttt gtttttttgg ggtttcgggg cgcagccctg aaccagtcac gtagcgatag
      541 cggagtgtat actggcttac tcctctgcaa gcctcgacag cagtgatttt tgccagatct
      601 cgcgctcttc acgttcaacc gcgccatcat ggttttgccg tccgttcacc gctaaaacgc
      661 ctcaggaatc aggacaggat gtgcaattgt aataccgtca cacgcgacgc tatcgcaatt
      721 gccacttggt cagggcttca ccccgacacc cagcatctgt gcgtaagtgc tcaatgtggc
      781 ttccggttct cttccgcttc ctcgcccact cgctcactac gttcggtcgc tggggctgcg
      841 gcgagcggaa ccacctcccg catgttgttg gtgattccgt tgttgttctt tcggggatga
      901 gtcgccagat agcccctcaa acgcgctcag aagctctcag acgcacgaaa cgggttttaa
      961 atgcccgtca gggcatggaa ggcgcgaaaa acgcttacag agggtttcag gaagtcaggc
     1021 gcgccgatac ccctaaccag gggctttcag gtcgccagga accgcgtcag ccccctgcaa
     1081 agcccatttg cacggaacag gcagccacgc ggttggtagg tggtcgtaga ccgtcggtgt
     1141 tgcagcgatg ggggtctggg gttctcccca gacggtttcc ggttgcgctc aaggcgctgc
     1201 cggaaccgtg acagcaagga taaaaattct ccctgcggaa attgagcagg gagggtgaaa
     1261 ataactacct atcacttacg tttgagtttt gaactcagga tgaatatgca tttggtcgtg
     1321 ttgaatttgc aaggatcgac agcgacttta tggttggcaa tggagcaatg caggatagac
     1381 aatcatggtc agaacgttaa cacgttgccc tgattgtctg cctgcggctg gctcaatttg
     1441 aaaacatggc catgattcgg cgcttaattt ccccgtcttt gctgactaag gtctttgtca
     1501 ggaatgctgc tgtaggcttg ttgttgtcat agcctttcca gacctcatgt gggttaagtg
     1561 cataggcgca aactcttccc gcaacaggaa ttttgactat ggctttttgc tcttctag
//
