LOCUS       NZ_CP070909             2334 bp    DNA     linear   CON 17-JUN-2023
DEFINITION  Escherichia coli strain 88COLEC plasmid p88COLEC-3.
ACCESSION   NZ_CP070909
VERSION     NZ_CP070909.1
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 2334)
  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 2334)
  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
            CP070909.1.
            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..2334
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="88COLEC"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p88COLEC-3"
                     /geo_loc_name="Singapore"
                     /collection_date="2019-02"
     gene            921..1466
                     /locus_tag="JR901_RS24500"
                     /old_locus_tag="JR901_24500"
     CDS             921..1466
                     /locus_tag="JR901_RS24500"
                     /old_locus_tag="JR901_24500"
                     /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="SHOCT domain-containing protein"
                     /protein_id="WP_039004747.1"
                     /translation="MRERYLNKISNFDTARIVLFIAIQIISCIFMFWGAIPALIVFFSY
                     LAMRKECNLKPIEKSKDYISVYMLLTAALVLFLFVYKAGMFRRGGDYFLLVFVFILLYV
                     YHLAFHKLWLRTIDENSSIIIENGIFNFNRKNASVGFSRKDVNNIDTLLKLNEARKEGI
                     ISEDEFNKLKKRLNILND"
                     /name="SHOCT domain-containing protein"
     Typing          complement(1724..2078)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.518"
                     /coverage="87.0"
                     /evalue="7.770000000000001e-160"
ORIGIN
        1 tagggtgtac tcccgcgcta tacggcattt tcagaggttt gaccttaatc ggataaccta
       61 aatgcgatac tgcaagagcg acaacttaaa agcgatagcc actgacgcaa aatcaaccac
      121 ttacgaacca agattggtta aataatgcgc ttaacgtaca aaaatttccg atctccaaac
      181 tgaccccttc ttcgcctctt atgtttctcg aatgaatcga tggggacagg aaatgttttg
      241 tgaccaccgc cgcttcgccg gcaccacaaa actgtcggac aagatgtgtt tttggagtac
      301 cgccggcacc aaaaacattt catcaggcgc agcctgatac cctgaatttc gtacgtacga
      361 aattttgctt ttgttcagat cgagggcagg attcgcaaag tgctggcgtt tgtactcaca
      421 tcctttagac gttgcgatgc aggatagggc agacgccgca aaatgacgtc atttgcggta
      481 tctgccccga aaacagaatg ttttctcctg agcctgcagc tggctctcag aacccctacc
      541 gcctcgcaaa gctcgttgct caacgcctca cgaccgcaca gtaaactgtg cacccgttca
      601 ccgttatcga tggggttcag cgagcctttt gagcagttcg caggatttta gccgctaaaa
      661 ttccggccag gcatgttcgt gcatagccat gcagatgcgc agaaatcatc aggcgcgttt
      721 tttcacgata tggacaggga aaggtgccgg aaacgcagag gacgcggcag aaacgcgctg
      781 agggcctctc agggggtgcg ggcaaggggt gttatggtaa atgccccata ttcagttact
      841 gcttttctat tttttgaaat aacattaata tcaggcgatt gattttaaat taattaacta
      901 tgattgaatg gtggtgattt atgcgcgaac ggtatttaaa taaaatatct aattttgata
      961 cggcaagaat agtgttgttt atagccattc aaattatctc ttgtattttt atgttctggg
     1021 gggctattcc tgccttgatt gtttttttct catatttagc catgaggaag gaatgtaatt
     1081 taaagccgat agagaagtct aaggattaca tatccgttta catgcttctt acagccgctt
     1141 tggtactgtt tcttttcgtg tataaagctg gcatgtttag aaggggcggt gattatttcc
     1201 ttctcgtttt tgtttttatt ttgctttatg tttaccatct cgcttttcat aaattatggt
     1261 tgcgaacgat agatgaaaac tcatcaataa taattgaaaa cgggattttt aattttaatc
     1321 gtaaaaatgc atctgtagga tttagtcgga aagatgtaaa taacattgat actcttctta
     1381 aattaaacga ggctagaaaa gaaggtatta taagtgaaga tgagtttaat aaattaaaaa
     1441 aaagactaaa tattcttaac gactgatttt ttgctaacta aaggtaaagc aagcttatga
     1501 atctttgata agattgaata tcttcttgtc attgattttt tatcgtcgta atcttcttcc
     1561 ctgcaaacga aaaaaccacc cggcaaggtg gtttttcgaa ggttcgcaag agttgacgct
     1621 cttttgaacc gcggtaactg gcttggagga gcacagtcac caaaacttgt cctttcagtt
     1681 tagccttaac cggcgcatga cttcaagact aactcctcta aatcaattac cagtggctgc
     1741 tgccagtggt gcttttgcat gtctttccgg gttggactca agacgatagt taccggataa
     1801 ggcgcagcgg tcggactgaa cggggggttc gtgcttacag tccagcttgg agcgaactgc
     1861 ctacccggaa ctgagtgtca ggcgtggaat gagataaacg cggccataac agcggaatga
     1921 caccggtaaa ccgaaaggca ggaacaggag agcgcacgag ggagccgcca gggggaaacg
     1981 cctggtatct ttatagtcct gtcgggtttc gccaccactg atttgagcgt cagatttcgt
     2041 gatgcttgtc aggggggcgg agcctatgga aaaccggcag cccttaagtc tcttctcaca
     2101 cttcatacct ccacgccctt tgattgatcc cgtaacgctc gccgcagagt catgaccgaa
     2161 cgcagtgagc gaatgaccga ggaagcgtaa tttctccggt ggctgcttag gctcctgtcg
     2221 ctccgtacta tcatctttca ccacttacgt tttctgcacg tattgggggt cagtttggat
     2281 atagagaatt attgtacggt aagcctgttt tttgaacaga cttacctata gcaa
//
