LOCUS       NZ_CP116488             1454 bp    DNA     circular CON 27-FEB-2024
DEFINITION  Escherichia coli strain GTEN_24 plasmid unnamed8, complete sequence.
ACCESSION   NZ_CP116488
VERSION     NZ_CP116488.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN11230615
            Assembly: GCF_028215995.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 1454)
  AUTHORS   Yorki,S., Shea,T., Worby,C.J., Cuomo,C., LaRocque,R.C., Manson,A.L.
            and Earl,A.M.
  TITLE     Comparison of long and short read metagenomic assembly for
            low-abundance species and resistance genes
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 1454)
  AUTHORS   Yorki,S., LaRocque,R.C., Worby,C.J., Shea,T., Earl,A.M.,
            Walker,B.J., Manson,A.L., Sridhar,S., Turbett,S., Becker,M.,
            Oliver,E., Bronson,R., Leung,D., Knouse,M., Hagmann,S., Kelly,P.,
            Harris,J. and Ryan,E.
  TITLE     Direct Submission
  JOURNAL   Submitted (05-JAN-2023) Infectious Diseases & Microbiome, Broad
            Institute of MIT and Harvard, 75 Ames St., Cambridge, MA 02142, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.4
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology             :: Illumina; Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/27/2024 02:21:11
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,977
            CDSs (total)                      :: 4,853
            Genes (coding)                    :: 4,676
            CDSs (with protein)               :: 4,676
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 177
            CDSs (without protein)            :: 177
            Pseudo Genes (ambiguous residues) :: 0 of 177
            Pseudo Genes (frameshifted)       :: 69 of 177
            Pseudo Genes (incomplete)         :: 118 of 177
            Pseudo Genes (internal stop)      :: 28 of 177
            Pseudo Genes (multiple problems)  :: 33 of 177
            Pseudo Genes (short protein)      :: 2 of 177
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP116488.1.
            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/
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..1454
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="GTEN_24"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="unnamed8"
                     /geo_loc_name="USA: Massachusetts"
                     /collection_date="2018"
                     /collected_by="Massachusetts General Hospital"
     gene            complement(668..1099)
                     /locus_tag="E5Q65_RS24835"
     CDS             complement(668..1099)
                     /locus_tag="E5Q65_RS24835"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001233485.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_063269671.1"
                     /translation="MRRVTQIDQESGEELGGFVAVIRPKQKSSFQRHFTMNQAALITIA
                     NELNHDQIRVLMALLADLDYENYIQVAQIDIADALKMQKTNVSRAIKNLIDFGIIIEGP
                     RIGRSKTYRLNPQFGWKGTVSNHRKALKNGLSVIQGGRV"
                     /name="helix-turn-helix domain-containing protein"
     Typing          175..433
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.0"
                     /coverage="99.0"
                     /evalue="1.09e-111"
ORIGIN
        1 tgtgcaaatg taataccgtc acccgcgacg atattccgtt tgccgtctgg tcagggcttc
       61 gccccgacac cccgcatcag tgcgtacgtg ctcaatgtgg tttccggttc tcttccgctt
      121 cctcgcccac tcgctcacta cgttcggtcg ctggggctgc ggcgagcggt gtcacctctc
      181 gcatgttgtc ggtgattccg ttgttgttct ttcggggatg agtcgccaga tagcccctca
      241 aacgcgctca gaagctctca gacacacgaa acgggtttta aatgcccgtc agggcatgga
      301 aggcgcgaaa aacgcttaca gaggctctca ggaggtcagg cgcgccgata cccctaacca
      361 ggggctttca ggtcgctagg aaccgcgtca gccccctgca aagcctattt gcacggcaca
      421 ggcagctatt cggctggttg gtggtcgtag accgtcggtg ttacagcgat gggggtctgg
      481 ggttctcccc agacggtttc cggttgcgct caaggcgctg ccggaaccgt ggcggcgcgg
      541 tcgttctggg gatcggggag caaaaacaag caagggattt tgaggcggca aaagagcaat
      601 gcaggataga caatcatggt caaaacgtta acacgtagcc cctgattgtc cgcctgccgc
      661 tggctcttta aaccctgcca ccctgaatga cgctaagacc attcttgagt gctttcctgt
      721 gattgcttac cgtccctttc catccgaact gaggattcaa gcgataggtt ttactacgcc
      781 cgatccttgg tccttcgatg atgatcccaa aatcaatcaa gttttttatt gcgcgactga
      841 cgttcgtttt ttgcattttc aatgcatccg caatatcgat ttgcgcaact tggatgtagt
      901 tttcgtagtc aagatcagct agcaaagcca ttaaaacacg aatttgatca tgattaagtt
      961 cgtttgcaat cgtgattaac gcagcctgat tcatcgtaaa atgcctctga aatgacgatt
     1021 tttgcttggg acgaataact gcaacaaatc cgcccaactc ctctcctgac tcttggtcta
     1081 tctgtgtaac tcttctcacg gcttcctccg ttctagagaa aatagttatc tctcaagata
     1141 actaagttat ctctcaagat aactatttgt caaaagatcc cgcttctggc gcggcttcca
     1201 gaagaccccc ttctgtatct tattactctc gcaaccaaaa caaagttttc atggggtgtc
     1261 ggggcgaagc cctgacccag tcacgtagcg ccagcggagt gtatactggc ttattccgct
     1321 acaagcctcg cttattccgc tacaagcctc gccagccgtg atttttgcca gatttcacgc
     1381 tctcaacgct caacagctcc atcatggttt tgccgtccgt tcaccgctaa aacgcctcag
     1441 aaatcgggac agga
//
