LOCUS       NZ_CP030115             2113 bp    DNA     circular CON 17-JUN-2024
DEFINITION  Escherichia coli strain MCJCHV-1 plasmid pNMEC-O75D, complete
            sequence.
ACCESSION   NZ_CP030115
VERSION     NZ_CP030115.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN09462202
            Assembly: GCF_003344465.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2113)
  AUTHORS   Nielsen,D.W., Ricker,N., Barbieri,N.L., Wynn,J.L.,
            Gomez-Duarte,O.G., Iqbal,J., Nolan,L.K., Allen,H.K. and Logue,C.M.
  TITLE     Complete Genome Sequence of the Multi-drug Resistant Neonatal
            Meningitis Escherichia coli serotype O75:H5:K1 strain mcjchv-1
            (NMEC-O75)
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2113)
  AUTHORS   Nielsen,D.W., Logue,C.M. and Nolan,L.K.
  TITLE     Direct Submission
  JOURNAL   Submitted (20-JUN-2018) Population Health, University of Georgia,
            501 D.W. Brooks Dr., Athens, GA 30602, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 18-APR-2018
            Assembly Method                   :: Canu v. 1.5
            Assembly Name                     :: NMEC-O75
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 320.0x
            Sequencing Technology             :: PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_003344465.1-RS_2024_06_17
            Annotation Date                   :: 06/17/2024 04:59:23
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,924
            CDSs (total)                      :: 4,806
            Genes (coding)                    :: 4,589
            CDSs (with protein)               :: 4,589
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 90
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 217
            CDSs (without protein)            :: 217
            Pseudo Genes (ambiguous residues) :: 0 of 217
            Pseudo Genes (frameshifted)       :: 89 of 217
            Pseudo Genes (incomplete)         :: 146 of 217
            Pseudo Genes (internal stop)      :: 38 of 217
            Pseudo Genes (multiple problems)  :: 50 of 217
            Pseudo Genes (short protein)      :: 1 of 217
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP030115.1.
            Bacteria and source DNA available from Oscar Gomez-Duarte.
            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..2113
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="MCJCHV-1"
                     /serotype="O75:H5:K1"
                     /isolation_source="CSF"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pNMEC-O75D"
                     /geo_loc_name="USA: Nashville, TN"
                     /lat_lon="36.139416 N 86.802280 W"
                     /collection_date="2015"
                     /collected_by="Monroe Carell Jr. Children's Hospital at
                     Vanderbilt University"
     gene            join(1859..2113,1..711)
                     /locus_tag="DPQ29_RS26135"
                     /old_locus_tag="DPQ29_26130"
     CDS             join(1859..2113,1..711)
                     /locus_tag="DPQ29_RS26135"
                     /old_locus_tag="DPQ29_26130"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012421200.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_001287824.1"
                     /translation="MSEDKFLSDYSPRDAVWDTQRTLTDSVGGIYQTAAEFERYALRMA
                     SCSGLLRFGWSTIMETGETRLRLRSAQFCRVRHCPVCQWRRTLMWQARFYQALPKIVVD
                     YPSSRWLFLTLTVRNCEIGELGTVLTAMNAAFKRMEKRKELSPVQGWIRATEVTRGKDG
                     SAHPHFHCLLMVQPSWFKGKNYVKHERWVELWRDCLRVNYEPNIDIRAVKTKTGEVVAN
                     VAEQLQSAVAETLKYSVKPEDMANDPEWFLELTRQLHKRRFISTGGALKNVLQLDRETN
                     EDLVIADDVGDGTDDGKRTAFVWDSGKRRYKRAPEKDKSD"
                     /name="protein rep"
     gene            715..981
                     /locus_tag="DPQ29_RS26140"
                     /old_locus_tag="DPQ29_26135"
     CDS             715..981
                     /locus_tag="DPQ29_RS26140"
                     /old_locus_tag="DPQ29_26135"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001024536.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001024536.1"
                     /translation="MNINIEYLNGNKTIGLFFLRSEAVIPDRFKNLILLIDGLSFGTFG
                     FHPHEGFEDELILYIQKTNERVKTLFVKIDLNGIKFGFLRTHS"
                     /name="hypothetical protein"
     Typing          140..371
                     /name="Col(BS512)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.05e-118"
ORIGIN
        1 agaaccctca tgtggcaagc ccgtttttat caggctctac cgaaaatcgt tgtggattac
       61 ccgtcttccc gatggttgtt tctgacgtta actgtcagga actgcgagat aggtgaactt
      121 ggaacagtcc ttacagcaat gaatgcggcg tttaagcgaa tggaaaagcg aaaggagcta
      181 tcacctgttc aggggtggat cagggctacg gaggtgacgc gaggtaagga tggcagcgca
      241 catccgcatt ttcactgtct gctgatggtg caaccttctt ggtttaaagg gaagaactac
      301 gttaagcacg aacgttgggt agaactctgg cgcgattgct tgcgggtgaa ctatgagccg
      361 aatatcgata ttcgggcagt aaaaactaag acaggtgagg ttgtggccaa cgttgccgag
      421 caactgcaaa gcgcggttgc tgaaacgctg aaatactccg ttaaaccgga agatatggca
      481 aacgatcctg agtggtttct tgagctgacg cggcagcttc acaagcgccg ttttatctcg
      541 accggtgggg cgctaaaaaa cgtcctccag ttggatcgag aaaccaatga ggatcttgtc
      601 attgccgacg atgtagggga tggcactgat gacgggaagc ggacggcgtt tgtctgggat
      661 tcaggtaaac ggcgttacaa acgcgcccct gagaaggata aatcggatta acgtatgaat
      721 attaatattg aatacctgaa tggaaataag actattggtt tatttttttt aagaagtgaa
      781 gcggtgattc ctgacaggtt taaaaacctt attttgctta ttgatggatt aagttttggc
      841 acatttggtt ttcatccgca cgaaggtttt gaggatgaat taattttata tattcagaaa
      901 acaaacgaga gggtaaaaac tctttttgtg aaaatagatt taaacggtat caagtttgga
      961 tttttaagaa cgcattctta gttctggaaa agagccagcg gcaggctgag gtgataggta
     1021 cgagattgca tgcaatctct agtgctctgt ctatcctgca ttatcctcag cattatcctc
     1081 agcattatcc tcagcattat cctcagcctt gccaactcga caccaatgca ggatagacaa
     1141 tccgatgtca aatgttaaca ctctgcgagt ggtacatttt ccccggatta tcgtcctgag
     1201 cctgccgctg gctctctttc taccgcctcg ctttgctcgt tgctcaacgc ctcacagaca
     1261 cggattaaaa tccgcatccg ttcaccgttt tttaaagtcc gttaaaagca tgatgccatc
     1321 tccgagagtt aatctcgtca aatgctaaat cgtgggggtc ccctttgggg ttccgattta
     1381 gtgattgacg acaccaccga ttaaaaaact tatgcggggt ggatggtttc acgaagtgag
     1441 gccatccacc tgtaagacag ggttttgttt ttattccctg ttttggtgat cgggtgtgtg
     1501 gaaaaggttg gggtaagccg ttcgggggtg cttgttttgg ggggttaaaa ttgtggttat
     1561 tttttgcgca attctcgcgc gtgatccttg tatttatact taagggataa atggcggata
     1621 tgaaatagtg gtttagccca gtaatgacga ggctttgagt gggttttgac aggtcaaaga
     1681 aaatggagca gaattgaggc gtttttaatc ggcgttgggg agtgcgtcaa cactccccaa
     1741 catttcgaat gtgtcacctc agcggcaaac tctggtgaca tgtactggct cgcaatgcac
     1801 aggtacgtga tgaatatacc acatcaaatc acagcctgcc cagatcggag caggcttaat
     1861 gtcagaagat aaattccttt cggactacag cccccgtgat gcagtttggg atacccagcg
     1921 cacgcttacc gattctgtcg ggggtatcta ccagactgct gctgaattcg agcgctatgc
     1981 actccgtatg gcctcctgta gcggtttgtt acgttttggt tggtctacca tcatggaaac
     2041 cggagaaacg cgcctacggc ttcgtagtgc gcaattttgc cgtgtccgtc attgccctgt
     2101 ctgccagtgg aga
//
