LOCUS       NZ_CP103653             2022 bp    DNA     circular CON 21-SEP-2023
DEFINITION  Escherichia coli strain 961 plasmid pMB5823_8, complete sequence.
ACCESSION   NZ_CP103653
VERSION     NZ_CP103653.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN28173990
            Assembly: GCF_024918295.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2022)
  AUTHORS   Shropshire,W.C., Konovalova,A., McDaneld,P.M., Gohel,M., Strope,B.,
            Sahasrabhojane,P., Tran,C.N., Greenberg,D.E., Kim,J., Zhan,X.,
            Aitken,S.L., Bhatti,M., Tor,S., Treangen,T., Hanson,B.M., Arias,C.A.
            and Shelburne,S.A.
  TITLE     Systematic Analysis of Mobile Genetic Elements Mediating
            Beta-lactamase Gene Amplification in Non-Carbapenemase-Producing
            Carbapenem Resistant Enterobacterales Bloodstream Infections
  JOURNAL   mSystems (2022) In press
REFERENCE   2  (bases 1 to 2022)
  AUTHORS   Shropshire,W.C.
  TITLE     Direct Submission
  JOURNAL   Submitted (19-AUG-2022) Infectious Diseases and Infection Control,
            University of Texas MD Anderson Cancer Center, South Campus Research
            Building 4, Houston, TX 77054, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Flye v. 2.8.3-b1695
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 61x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/21/2023 03:24:23
            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)                     :: 5,145
            CDSs (total)                      :: 5,020
            Genes (coding)                    :: 4,743
            CDSs (with protein)               :: 4,743
            Genes (RNA)                       :: 125
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 277
            CDSs (without protein)            :: 277
            Pseudo Genes (ambiguous residues) :: 0 of 277
            Pseudo Genes (frameshifted)       :: 93 of 277
            Pseudo Genes (incomplete)         :: 197 of 277
            Pseudo Genes (internal stop)      :: 55 of 277
            Pseudo Genes (multiple problems)  :: 63 of 277
            Pseudo Genes (short protein)      :: 4 of 277
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP103653.1.
            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..2022
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="961"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pMB5823_8"
                     /geo_loc_name="USA: Houston"
                     /lat_lon="29.7068 N 95.3971 W"
                     /collection_date="2018-06-18"
                     /collected_by="MDACC"
                     /genotype="ST617"
     gene            1..192
                     /locus_tag="M5R18_RS25580"
                     /old_locus_tag="M5R18_25580"
     CDS             1..192
                     /locus_tag="M5R18_RS25580"
                     /old_locus_tag="M5R18_25580"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041614.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_001041614.1"
                     /translation="MNKQQKTAVNMAKFIQDQSLLLLDRLNELDLDHEADFCEKLHEDA
                     ERLYRSLSARLNEQQDGA"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(876..992)
                     /locus_tag="M5R18_RS25585"
                     /old_locus_tag="M5R18_25585"
     CDS             complement(876..992)
                     /locus_tag="M5R18_RS25585"
                     /old_locus_tag="M5R18_25585"
                     /inference="COORDINATES: protein motif:HMM:NF033853.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="small membrane protein"
                     /protein_id="WP_240726601.1"
                     /translation="MDWISLAIAIALLVVAVYSGISYFREKKVISRVFRSKR"
                     /name="small membrane protein"
     Typing          complement(1495..1844)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.307"
                     /coverage="85.0"
                     /evalue="4.64e-162"
ORIGIN
        1 atgaacaaac aacaaaagac tgccgttaac atggctaaat tcatccagga tcagtccctg
       61 cttcttctgg acaggcttaa tgagctggat ctggatcatg aggctgattt ctgcgagaaa
      121 ctccatgagg atgcggaacg cctttaccga agcctgtcag cgcgcctgaa tgagcagcag
      181 gacggtgcgt aatgtctccg ttctgggtat taccggagta ataccagcat cgccttaatt
      241 ttcattgtct tagcgcttaa cattattacc ctggtaatac ccacaatccc tgtatttttt
      301 cttttttatt tatttttcat gaagttgcga tgaaaatcgc ggctgcgtta ggtgtatgac
      361 cattttgagg ttgaaaaata atcaaccatg gcgggtgatt tacgcaggtt aaggggagaa
      421 cgtgacaaaa aaagcgttcc tcactgtatc gttcatgcct gcatgaacgg gttattcttc
      481 ctgactacag aattacattg ctccttcagc tcatacgtca cttttacgtc agttccatcc
      541 tctgtgccat ttgtacatcc gacccccttc ctgaacgtgc tgaaaacggt ttttccggct
      601 gtgccggcaa cgcctcacgg ccacgcaata aattgcgttc ccgttcaccg ttttcgggtg
      661 ggaagaatgc cggaaacagg acttaccccg gctgagttgc gtgaatttcc gcgctatgca
      721 cttgcgcgca tactcatgca tgccgtaaaa acagagcctg cgcgtttctg gcgggttttc
      781 gggtggtttg ttgcctgttt taccggtttc ccgtcagaaa cgccctgagg ccgttttcgc
      841 ggtgcgcgta agaagggatt atggtaaata gggcgctatc gcttactcct aaatacacga
      901 ctgattactt ttttttctct gaagtatgag attcctgagt agacagctac aacaagtaga
      961 gcaatggcga tagcaagtga aatccagtcc ataaatgcct gattaattta ataaaaacag
     1021 ccttttatga tttcataaag ataatatcat ctttttttag catgatactg tcgttactta
     1081 ttgtggagag atgaaacata accgctgttt ttgtatgtgt ttgttaaggc cgttaagatt
     1141 attcttaatc actgattttg tacatatcat caaaataaaa ataaaaaaaa ctaatgcccc
     1201 cgtggtgggt atataacaaa tcacggggtg caggtcagaa ctaccccaaa actttgaatg
     1261 atcgggtggc agactaaatg aaatcttgag attcattcag cctcgtcgta atctctttct
     1321 ctgtaaacga aaaaaccgcc ctgcaaggcg gtttttcgaa ggttcagtaa gttggggaac
     1381 ttctgaaccg tggtaacagt cttatgcgag acgtgtcacc caagctgtcc ttctagtgta
     1441 gccgtagtaa gggcaccact tcaagaactc tcacaatatc tctcgcacat cctgttacca
     1501 gtggctgctg ccagtggcgc atttgcatgt ctttccgggt tggactcaag acgatagtta
     1561 ccggataagg cgcagcggtc ggactgaacg gggggttcgt gcatacagtc cagcttggag
     1621 cgaactgcct acccggaact gagtgtcagg cgtggaatga gacaaacgcg gccataacag
     1681 cggaatgaca ccggtaaacc gaaaggcagg aacaggagag cgcacgaggg agccaccagg
     1741 gggaaacgcc tggtatcttt atagtcctgt cgggtttcgc caccactgat ttgagcgtca
     1801 gatttcgtga tgcttgtcag gggggcggag cctatggaaa aacgccccgc cggggcctgg
     1861 ccttttcgcc ctcgtcctta gctttcgtta tgcttaccgt tacgttatct gcttatcctc
     1921 cctccgctcg ccgcagactc atgaccgaac ggagtgagcg aatgagcgag gaagcggaaa
     1981 accatcagaa cgtacagtaa gcactttcgc gccggggcct tc
//
