LOCUS       NZ_CP030116             1983 bp    DNA     circular CON 17-JUN-2024
DEFINITION  Escherichia coli strain MCJCHV-1 plasmid pNMEC-O75E, complete
            sequence.
ACCESSION   NZ_CP030116
VERSION     NZ_CP030116.1
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 1983)
  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  JOURNAL   Unpublished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 1983)
  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
            CP030116.1.
            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..1983
                     /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-O75E"
                     /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            84..1070
                     /locus_tag="DPQ29_RS26150"
                     /old_locus_tag="DPQ29_26145"
     CDS             84..1070
                     /locus_tag="DPQ29_RS26150"
                     /old_locus_tag="DPQ29_26145"
                     /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_114523788.1"
                     /translation="MKNPELQNLTDYSPSDAPWDAHRSASDDVGGIYLLAAEYERYGAR
                     MASCGGLLRFGWSTIKETGETRLRLREAHFCRVRHCPVCQWRRSLMWQARFYQSLPCIV
                     ADYPDARWMFLTLTVRNCAIGELGETLSRMNMAFQRLKDRKEFRPVQGWIRTTEVTRGS
                     DGSAHPHFHTLMMVPPSMFTRDYVKHARWVELWRECLRVDYDPNVDVRAVKPRKLKDGE
                     SLACATAELVRGAVAETLKYSTKPADMVADPEWFLELTRQTHKRRFVATGGALKDVLKL
                     DQETDADMLIGDDISEGDDDGSRIAFEWKTEVRKYRRSPTKDKTESD"
                     /name="protein rep"
     gene            1226..1657
                     /locus_tag="DPQ29_RS26375"
     CDS             1226..1657
                     /locus_tag="DPQ29_RS26375"
                     /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_162814737.1"
                     /translation="MSAHFVRFPDCQFVDRAEQLWHENGRMICCPVARTARLRGGRRGA
                     KNCRHCASVPVTQTRRNRDRMWECRTAHAHSDIPHLVRASPRHPANASRHAKKFRVPLT
                     VLELVKQKIAGPRASGVGSDFVIDDGTGKTLGMVVGVTE"
                     /name="hypothetical protein"
     Typing          1074..1154
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.341"
                     /coverage="89.0"
                     /evalue="5.64e-30"
     Typing          1415..1493
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.75"
                     /coverage="80.0"
                     /evalue="3.79e-32"
     Typing          complement(797..988)
                     /name="ColpVC"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.373"
                     /coverage="100.0"
                     /evalue="1.34e-84"
ORIGIN
        1 ttcgaattgg tgacacgaca acacaggtga tatggcaatg ataacacgtc ggatgagcca
       61 tcgcccacaa tcgggtggtg cgcatgaaaa atcctgaact ccagaacctc acggactatt
      121 ccccctcaga tgcgccctgg gacgctcaca gaagcgcttc tgacgacgtg ggagggattt
      181 acctgcttgc ggccgaatat gagcgctacg gggcgcgtat ggcctcctgt ggcggtttac
      241 tgcgttttgg gtggtctacc atcaaggaaa ccggagaaac gcgtctgagg ctgcgtgagg
      301 cgcatttctg ccgtgtccgg cactgtcctg tctgccagtg gaggcgctcc ctgatgtggc
      361 aagcccgttt ttatcagtct ttgccgtgta ttgtggctga ctatccagac gcacgatgga
      421 tgtttctgac tctcaccgtg cgcaactgtg ctatcgggga actgggcgag acgctgagcc
      481 gaatgaacat ggccttccag cgactgaaag atcgcaaaga gtttcgacct gttcagggct
      541 ggatccgcac gacggaggtt actcgcggca gcgacggtag cgcacacccg cacttccata
      601 ccctgatgat ggtgccgccc tcgatgttca cgcgtgacta tgtcaaacat gcgcgctggg
      661 ttgaactgtg gcgggagtgc ctgcgggtgg attacgaccc gaatgttgat gtccgggctg
      721 tgaaaccccg caagctgaag gacggcgaat cgctggcctg cgcgaccgcc gaactggtgc
      781 gcggtgcggt ggccgaaacc ctgaaatatt ccactaagcc ggctgacatg gtggccgatc
      841 ctgaatggtt cctcgaactg acccgccaga cgcacaagcg tcgttttgtg gcgaccggcg
      901 gcgcactcaa agacgtgctg aaactcgatc aggaaaccga tgccgacatg ttgatcggtg
      961 atgatatttc cgagggtgac gatgacggtt cacgcatcgc gttcgagtgg aaaaccgagg
     1021 tcagaaagta ccgtcgctca ccgacgaaag ataaaactga atcagactag cagggtgtcg
     1081 gggtgcagcc ctgaccagat ggcaattgtg atagcgtcgc gtgtgacggt attacaattg
     1141 cacatcctgt cccgaaaatt cccgccgttt ctcggttttt tgagcgtcgc agaccgcacg
     1201 acaaacgaaa cgaagtgtag tttgtatgag tgcgcacttc gtgagattcc ccgactgcca
     1261 gtttgtcgat cgcgcggaac agctgtggca cgaaaacggc agaatgattt gctgtccggt
     1321 tgccagaact gcgcgcttac gtggagggcg gcgcggcgca aaaaactgcc gacattgcgc
     1381 cagtgttccg gtgacacaaa cccgcagaaa tcgggacagg atgtgggaat gtcggaccgc
     1441 gcacgcgcac tcagacattc cccacctggt cagggcttcg ccccgacacc ccgccaacgc
     1501 ctcacggcac gcgaaaaaat tccgcgtacc gctcaccgtt cttgaactcg tcaaacagaa
     1561 aatcgcgggg ccccgcgcct ccggcgtggg ttccgatttt gtgattgacg acggcacggg
     1621 gaaaacgctg ggtatggtgg ttggtgtcac ggagtgaggc caaccacctg caagacggtt
     1681 ttttgttgtt cacaaaattg gggtgaaagt ctgtggatga gatgggtgta agtgggtggg
     1741 gttgggaggt tttgggttac tgaaaatcca gctcaaaatt caagcaaatc tcgcgcgcga
     1801 tccttgtatt tatacttaag ggataactct ggcgataaaa aatagcttca ggccttgtgc
     1861 ggcaaggctt tgcggcttat ttgcgttgta gaaggttttg gaagtattct gtcggaagtg
     1921 gtcgcattaa aagcgacccc cgcaactgcg ctaacagttc gggggtgtga ccacctgtag
     1981 gaa
//
