LOCUS       NZ_CP070910             2257 bp    DNA     linear   CON 17-JUN-2023
DEFINITION  Escherichia coli strain 88COLEC plasmid p88COLEC-4.
ACCESSION   NZ_CP070910
VERSION     NZ_CP070910.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17807536
            Assembly: GCF_017088425.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2257)
  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 2257)
  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                   :: 367x
            Sequencing Technology :: Illumina NovaSeq Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/17/2023 06:41:50
            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)                     :: 4,960
            CDSs (total)                      :: 4,841
            Genes (coding)                    :: 4,641
            CDSs (with protein)               :: 4,641
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 200
            CDSs (without protein)            :: 200
            Pseudo Genes (ambiguous residues) :: 0 of 200
            Pseudo Genes (frameshifted)       :: 51 of 200
            Pseudo Genes (incomplete)         :: 150 of 200
            Pseudo Genes (internal stop)      :: 27 of 200
            Pseudo Genes (multiple problems)  :: 26 of 200
            Pseudo Genes (short protein)      :: 2 of 200
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP070910.1.
            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..2257
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="88COLEC"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p88COLEC-4"
                     /geo_loc_name="Singapore"
                     /collection_date="2019-02"
     gene            <1..789
                     /locus_tag="JR901_RS24505"
                     /old_locus_tag="JR901_24505"
     CDS             <1..789
                     /locus_tag="JR901_RS24505"
                     /old_locus_tag="JR901_24505"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001529700.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_205899169.1"
                     /translation="LRLRDARFCRVRHCPICQWRRSLMWQARFYQSLPKIVAEYPDARW
                     LFLTLTVRNCPITELGDTLTVMNAAFQRLKDRKEFRGVLGWVRTTEVTRGKDGNAHPHF
                     HILLMVSPSMLSGDGYVKHARWVELWRDCLRVEYDPNVDIRVVKSRKPKDGESLPCSVV
                     DQLRGVVVETLKYSTKPADMLVDPEWFLELTRQVHKRRFVATGGVLKDVLQLERETNED
                     LIMADGMAEGADDGSRLAFSWRAVAKKYRRDRTMDKPKQK"
                     /name="protein rep"
     gene            1419..1655
                     /locus_tag="JR901_RS24510"
                     /old_locus_tag="JR901_24510"
     CDS             1419..1655
                     /locus_tag="JR901_RS24510"
                     /old_locus_tag="JR901_24510"
                     /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_065898629.1"
                     /translation="MCNRITAHARLYDYHLVRASPRHPANASRSAKKFRVPLTVPELVK
                     QKIAGSRASGVGSDFVIDDGTGKILGMVVGVTE"
                     /name="hypothetical protein"
     gene            2057..>2257
                     /locus_tag="JR901_RS24515"
                     /old_locus_tag="JR901_24515"
                     /pseudo=""
     CDS             2057..>2257
                     /locus_tag="JR901_RS24515"
                     /old_locus_tag="JR901_24515"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001362017.1"
                     /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="Replication protein"
                     /name="Replication protein"
     Typing          complement(1405..1491)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.591"
                     /coverage="95.0"
                     /evalue="9.38e-33"
     Typing          complement(516..707)
                     /name="Col(MP18)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="88.083"
                     /coverage="100.0"
                     /evalue="6.45e-58"
ORIGIN
        1 ctgcggttac gtgatgcgcg gttctgtcgg gtccggcact gtccgatctg tcagtggagg
       61 cgttccctga tgtggcaagc ccgtttctat cagtccctgc caaagatcgt tgcggaatat
      121 cctgatgcac gctggctgtt cctgaccctg accgtccgta actgtccgat tacggagctt
      181 ggcgacaccc tgaccgtgat gaatgcggcc ttccagcgcc tgaaagatcg caaagagttt
      241 cgcggcgtgc tgggctgggt gcgcacgacg gaagtcaccc gtggcaagga cggcaatgcc
      301 catccccatt ttcatatcct gctgatggtt tccccttcga tgttgtctgg tgatggttat
      361 gtgaaacatg cccgatgggt ggagttgtgg cgcgactgtc tgcgggtgga gtatgacccg
      421 aacgtcgaca tcagggttgt gaagtccagg aaaccgaaag acggtgaatc gttgccctgt
      481 tctgtggtgg atcaactgcg cggggtggtg gttgaaacac tgaaatattc tacaaagccc
      541 gccgacatgc tggtcgatcc tgaatggttc ctagagttaa cacgccaggt acacaagcgc
      601 cgttttgtgg cgacgggtgg tgtgcttaag gacgttttgc aactggagcg ggaaacgaac
      661 gaggatttga ttatggcaga tggcatggca gagggtgcgg atgacggatc gcgtctggcg
      721 ttttcatggc gggcggtggc taaaaagtat cgccgcgatc gcacaatgga taagccaaaa
      781 cagaaataac atctaaaaat cgattttaag gcctctaaaa cgcgctcagg cgcgtttttt
      841 tattgcggta atgcaatttc atcgattcga cgcttcattg cgtcagaggc gtttttagcg
      901 cgcctctgac acgttggtta tcacggcaac agacttcgaa ggtttgccag aagcgcgcaa
      961 tgatttttta acgtgcattt ggcacggtgt cgagggtgtc ggggcgcagc cctgaccagg
     1021 tggggaatgt ctgagtgcgc gtgcgcggtc cgacattccc acatcctgtc ccgaaaattc
     1081 ccgccgtttc tcggtttttt gagcgtcgca gaccgcacga caaacgaaac gaagtgaagt
     1141 ttgtataagt gcacacttcg tgaatttctc tgactgtcag tttgtcgatc gcgcggaacg
     1201 gctgcgtcat gaaaacggca aaatgatttg ctgtccggtc gccgaaattt ttgcgtggct
     1261 gtggtggctg cggtgccaaa aatcatccgc gcgttaagtg cggatgcgta cttagtagtt
     1321 tctctccttc gtcgggaaac tgtgcgctcc tgcggagggg ttaacggcgc agaactgccg
     1381 atgctctgcc agcgttctgg cgaaaaaatc gggacaggat gtgtaatcgt ataaccgcgc
     1441 acgcacggtt atacgattac cacctggtca gggcttcgcc ccgacacccc gccaacgcct
     1501 cacggtccgc gaaaaaattc cgcgtaccgc tcaccgttcc cgaactcgtc aaacagaaaa
     1561 tcgcggggtc ccgcgcctcc ggcgtgggtt ccgattttgt gattgacgac ggcacgggga
     1621 agatactggg gatggtggtt ggtgtcacgg agtgaggcca accacctgtg aggcggtttt
     1681 tgttgttcac aaattcgggg tgaaagtctg tggatgagat gggtgtaagt gggtggggtg
     1741 tgtggctttg gggggctaaa aaatagctcg aaatttgagc aaatctcgcg cgcgatcctt
     1801 gtatttatac ttaagggata actctgggat tcaaatttgc ctctaaacct tgtcaggact
     1861 gggctgaacg gcaatttgct ccgaaatggt tttgagtgta ttttggtttt agcggtcaaa
     1921 aaataaaccc ccgcaacgat gggcgtcgtt cggggggatg accacctgca taaatccgat
     1981 tttttgtgac aaccaacagg tgatatggca atgataacac gtcaatcgtg ccatcgccca
     2041 gaatggggcg gtgggcatga aaaattctga acttcagtac ctgacggatt attcccctgc
     2101 ggacaaaccg tgggatgagc accggagtat ttccgacgat gtgggcggta tttatctgcg
     2161 ggctgccgga tttgaacgct acggcgaacg ggtggagggt tgtagcggca ttctgcgttt
     2221 cgggtggtcc accaacgagg aaaccggaga aacgcgc
//
