LOCUS       NZ_CP030113             6465 bp    DNA     circular CON 17-JUN-2024
DEFINITION  Escherichia coli strain MCJCHV-1 plasmid pNMEC-O75B, complete
            sequence.
ACCESSION   NZ_CP030113
VERSION     NZ_CP030113.1
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 6465)
  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  JOURNAL   Unpublished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 6465)
  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
            CP030113.1.
            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..6465
                     /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-O75B"
                     /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            231..425
                     /locus_tag="DPQ29_RS26075"
                     /old_locus_tag="DPQ29_26070"
     CDS             231..425
                     /locus_tag="DPQ29_RS26075"
                     /old_locus_tag="DPQ29_26070"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /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_001041636.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADVQAAMCERLHELA
                     EELQNSIQVHFEAENETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(662..2341)
                     /locus_tag="DPQ29_RS26080"
                     /old_locus_tag="DPQ29_26075"
     CDS             complement(662..2341)
                     /locus_tag="DPQ29_RS26080"
                     /old_locus_tag="DPQ29_26075"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000598747.1"
                     /GO_function="GO:0005524 - ATP binding [Evidence IEA];
                     GO:0016887 - ATP hydrolysis activity [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="AAA family ATPase"
                     /protein_id="WP_001774712.1"
                     /translation="MIKVQLPTREHRLHELNLNYGDVVFFIGQNGSGKSSLLNNLFQKI
                     GSQSSVYVLAHRKNTFSSDIIDFSNSEYKNAQGWIFNEIKGSQCRYRVNYDSQMVAIPI
                     VKLKNKVIARALSFVDSFKSNNNQPAELIKSEVDVLNMVFADAKLSIEFFLDDEANVMA
                     RNIKGENPDVYPISMLSDGEKSALIIASEIICADENTTIFLDEPERHMHRSIVSPLLSS
                     LMKYRRDCVFFVATHELSLPAFFDNVKVVNVKNCYFSEQREPIYWDFNVVEDYDELFNG
                     VDEQTKIDILGARDKVLFVEGVTSSLDRDLYSAIFPMVSVVSKQKCDLVELAVKGLRLN
                     DEIHRVSAFGIIDNDNKVQAKVDNLKKDFIFSLDVHSIESIYYHPRMIKFVIDFVKEAN
                     GIDNVDALFMEIHDFAIDAINEKRDHLCCRAVEKTIRADLMSAIPKQQDIKNRIKFNKE
                     IDIECYVNKEIAAFDAMIAERNLDALVSRYPIRETNLLAHVAKKCGFADRSRYELNVIR
                     TIKSNADARAFVLSLLGGLDEAILGCSDTENSPADTHTVFAM"
                     /name="AAA family ATPase"
     gene            complement(2338..>2928)
                     /locus_tag="DPQ29_RS26085"
                     /old_locus_tag="DPQ29_26080"
                     /pseudo=""
     CDS             complement(2338..>2928)
                     /locus_tag="DPQ29_RS26085"
                     /old_locus_tag="DPQ29_26080"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001697689.1"
                     /note="internal stop; incomplete; partial in the middle of
                     a contig; missing N-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /name="replication initiation protein"
     gene            3492..3623
                     /locus_tag="DPQ29_RS27045"
                     /old_locus_tag="DPQ29_26090"
     CDS             3492..3623
                     /locus_tag="DPQ29_RS27045"
                     /old_locus_tag="DPQ29_26090"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001422066.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_071525238.1"
                     /translation="MHDPPVQSDRCALSGNYHLESNPERHDLSPLAAAIGKGCTRDY"
                     /name="replication initiation protein"
     gene            4263..4778
                     /locus_tag="DPQ29_RS26105"
                     /old_locus_tag="DPQ29_26100"
     CDS             4263..4778
                     /locus_tag="DPQ29_RS26105"
                     /old_locus_tag="DPQ29_26100"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000675351.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type III toxin-antitoxin system ToxN/AbiQ family
                     toxin"
                     /protein_id="WP_000675351.1"
                     /translation="MKFYTISSRYIEYLKGFEDKVPNSEDPNYQNPKAFIGIVLEIQGH
                     KYLAPLTSPKPWHSTIKESSPSFFKLHENGVPENQLGLINLKFMIPIIEAEVSLLDLNG
                     MPNTAYKRMLYKQLQFIRVNSDKIAEKSELLRKLVLQGKMQGTCNFSLLEEKYRDFGKE
                     ANDTEEGE"
                     /name="type III toxin-antitoxin system ToxN/AbiQ family
                     toxin"
     gene            5192..5902
                     /locus_tag="DPQ29_RS26110"
                     /old_locus_tag="DPQ29_26105"
     CDS             5192..5902
                     /locus_tag="DPQ29_RS26110"
                     /old_locus_tag="DPQ29_26105"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000967646.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000967645.1"
                     /translation="MLYWKKMPSLWIGNRIAEFSDLDTAKAIAALKIYLTFCLFCKESD
                     SGHRTVELTFSNLCEIASLSRSLVNEGLKILYAKELIKNISPTARKKIYTVDVLENHND
                     GWCKLPFKGVVDEDKKISAFQSMHNRYPFELLALQTYMYLLYARDNNSDYTLARKKTIC
                     KKLKCKLPELNKAITYLIHIGLLDRVVKKSIENIPLEMFHDSYYFYIKTGSKSALTYRR
                     KSEPPVIPEADLPF"
                     /name="hypothetical protein"
     Typing          complement(96..195)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.02"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          complement(6181..6436)
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="94.574"
                     /coverage="89.0"
                     /evalue="2.65e-108"
     Typing          3088..3660
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.828"
                     /coverage="90.0"
                     /evalue="5.34e-173"
ORIGIN
        1 ggagtatcag cggaattatt gattaagaaa cactcgacgc agagcgaaat tttatgcaac
       61 agcggctgca ctgcacaggg attatttatc agttgatatg ctgtgccatg atacgtccta
      121 aaaaaaacag gacaggatgt gcaattgtaa taccgtcgcc cgcaacgtct tacaattacc
      181 acctagtcag ggtccacccg acacccggta ctgacggaga acaacggaag gtgaacaaac
      241 agcaacaaac tgcgctgaat atggcgcgat ttatcaaaag ccagagcctg acactgcttg
      301 aaaaactgga tgctctggat gccgacgtac aggcggccat gtgtgaacga ctgcacgaac
      361 tcgcagaaga actccagaac agcatccagg ttcactttga ggccgaaaat gaaacaggaa
      421 cataacgaag ctgacgaagg cggtcacggc ttgcccgtga gcattttcgt cagcagacaa
      481 gcccgtcagg gcgcgtcagc gggttttaac gggtgtcggg gcgcagccct gacccagtca
      541 cgtagcgata gcggagtgta tactgactta atacagcaac tatcgtacat cgcggtcaag
      601 tcacgcacaa acaaaaagcc ccgcaaaagc agggctgtta tctgatatag gttgtttagt
      661 ctcacatagc aaaaactgta tgggtatcag ctgggctatt ttccgtatct gaacatccca
      721 aaatagcttc atctaaccct ccgaggaggg ataaaacaaa tgctctagcg tcagcattac
      781 tcttgatcgt acgaatcacg tttaactcat atctagagcg atcggcaaaa ccacattttt
      841 tagctacatg tgccaacaaa tttgtttctc ggatagggta gcgtgagact aacgcatcca
      901 aatttcgttc cgcgatcatt gcatcaaatg cagcaatttc tttattaaca taacattcaa
      961 tatcaatttc tttattaaac ttaatgcggt tcttaatatc ttgctgtttt ggtatggccg
     1021 acattaagtc tgcccttatt gttttttcaa ctgcacggca gcataagtga tcgcgctttt
     1081 catttatggc atcaatagcg aagtcatgaa tttccataaa taaggcatca acattatcta
     1141 tcccattagc ctcttttaca aagtcaatga caaacttaat cattctagga tgataataaa
     1201 tcgactcaat agaatgaacg tcgagactaa aaatgaagtc tttctttaag ttatcgacct
     1261 tcgcctgcac cttgttatca ttatcaatga taccaaacgc cgatactcga tgaatttcgt
     1321 catttagtct caagcctttt accgccaatt caaccaaatc acatttttgt ttagatacaa
     1381 ctgaaaccat aggaaatatg gccgaatata aatcacggtc aaggctagac gtaacacctt
     1441 caacaaatag aaccttatcc ctagcgccaa gtatatctat tttagtttgc tcatcaacac
     1501 cattgaataa ttcgtcataa tcctcaacaa cattgaaatc ccagtatatc ggttctcttt
     1561 gttcggaaaa atagcagttt ttaacgttaa ccactttcac gttatcaaaa aacgcaggca
     1621 agcttaactc gtgggtggca acaaaaaaaa cacaatctct acgatatttc attaaagatg
     1681 aaagcagcgg agacacaatg cttctgtgca tatgtcgctc aggctcatct aagaaaatag
     1741 ttgtgttttc atcagcgcaa ataatctcac tggcaataat tagtgcactt ttttcaccgt
     1801 cagaaagcat tgatatagga taaacatcag gattttcacc tttaatattc cttgccataa
     1861 cgttggcttc atcatctaga aagaactcaa tagataattt ggcatcagca aaaaccatgt
     1921 ttagaacatc aacctctgac tttattaact ctgccggctg attgttattt gatttaaatg
     1981 aatctacgaa acttaaagcc ctggctatca ctttgttttt taattttact ataggtatgg
     2041 caaccatctg tgagtcataa ttaactctgt atctacattg actgccttta atttcattaa
     2101 aaatccatcc ctgcgcattt ttatactcac tattactgaa atcaataatg tcgctgctga
     2161 atgtattttt tctatgcgct aaaacatata ctgatgattg agatcctatt ttttgaaaaa
     2221 gattatttaa taggctggat ttaccactac cattctgacc aataaaaaaa acgacatcgc
     2281 cataattaag attaagctca tgaagacgat gttctctagt aggtaactga acttttatca
     2341 ttttcctttc tctttagctt ttaatctaaa atacgttgaa cgactaattc ctaaattaat
     2401 ccatggagag tttaatgaag gcctacctcc tcctttactt tttttcccac atagagattg
     2461 gatgtctgcc gaatgggtct tttttataaa atcatcaaat gatgactctg taaaattttt
     2521 attagtccac ttagctacac ttttggcaat acccatgact tcgttctcgt ctaaaggtgc
     2581 ggagaactgc aggttgtagg ctttagcgcg ttcaaagcaa gcttgtagcc attggtcata
     2641 ctgcggccag ccttggtgga tagcgcggta agcccacttg cgggttttat cgaagagggt
     2701 gcagttacgg cctaaaccgt agtccggtag gatttcgcgg tcattagctg cgccaaggtc
     2761 gaggtagtcg gctaatcagt cgagggtgta gagctcaggc tgccaaacgg tgatctgcca
     2821 gtgcaggtgg ttcggattct cgcaaattag ccctgaatac cccgcatcgg cgcccaattt
     2881 tttacgcagc gcattctcaa tgacggctgc atatttgagg ggggcggcaa gccccctgaa
     2941 ccagtcacag aaggcacctc gcagagggga cgctgtgagt actgacttaa ctatgcggta
     3001 tcagtgcgga ttgtatgaaa agtgcgctat tgacggtgtg aaatgccgca cagatgcgta
     3061 aggagaaaat gcaaatgcct acgctcttcc gcttcctcgc tcactaactc gctgcgctcg
     3121 gtcgttcggc tgcggcgagc ggtatcagct cactcagaga cggtaatacg gttatccaca
     3181 gaatcagggg ataaggccgg aaagaacatg tgagcaaaaa ggcaaagcca gggcaaaagg
     3241 ccgcgccgct ggcgtttttc cataggctcc gcccccctga caagcatcac agaatctgac
     3301 gctcaaatca gtggtggcga aacccgacag gacttaaaga taccaggcgt ttccccctgg
     3361 tggctccctc gtgcgctctc ctgttcctgc ctttcggttt accggtgtca ttccgctgtt
     3421 atggccgcgt ttatctcatt ccacgcctga cactcggttc cgggtaggca gttcgctcca
     3481 agctggactg tatgcacgac ccccccgttc agtccgaccg ctgcgccttg tccggtaact
     3541 atcatcttga gtccaacccg gaaagacacg acttatcgcc actggctgcg gccattggta
     3601 aggggtgtac aagagattac tgatgcagag ttcttgaagt tagaaccaaa ctacggctaa
     3661 actggaagga cgaatttggt ggcagcggtc ttgtacaccc tgttaccacg gttcagaagt
     3721 tccccaactt actgaaccat cgaaaaacca cctccccagg tggttttttc gttttcagag
     3781 caagagatta cgcgtagaaa aaaaggatct caagcagatc ctttttgatt catgtcataa
     3841 cccaacttac cccccccaca ctgaactgat gaaaaaaaca gtcaactctg gaatcagtac
     3901 tttaaaaaag cctcaaatga cattttgagg ggatacagcg gcaagggcta caactacaca
     3961 gctgcaagtt acctagttgt aagcctaggc gaagatcagg tatactcgaa tcaaggtgat
     4021 ttgctacctt taagtgcagc tagaaattca ggtgatttgc tacctttaag tgcagctaga
     4081 aattcaggtg atttgctacc ttaagtgcag ctagaaattc aggtgatttg ctacctttaa
     4141 gtgcagctag aaattcaggt gatttgctac cttaagtgca gctagaaatt taggtcattt
     4201 actaccttaa agtaatacag taaaagaggc gactacacag tcgccttttt tacgagaaaa
     4261 aaatgaaatt ttacactata tcaagcagat acattgaata cctaaaggga ttcgaagaca
     4321 aagttcccaa tagcgaagat cctaactatc agaatccgaa agctttcatt ggcattgtgt
     4381 tagagattca agggcataag tatctagccc ctttaacatc cccaaagcca tggcatagca
     4441 ctattaaaga atcatcgcct agcttcttta agctccatga aaatggtgtc cccgaaaatc
     4501 agctcggatt gattaatctg aagttcatga ttccaatcat cgaagccgaa gtatccttac
     4561 ttgacttgaa cggtatgccg aataccgcct acaagagaat gctctataag cagctccagt
     4621 ttattcgtgt aaattcagac aaaatagctg agaaatcaga gcttttaagg aagctcgtcc
     4681 tgcaaggaaa aatgcaagga acatgtaatt tttccctgtt agaagaaaaa taccgagatt
     4741 tcggcaaaga agctaatgac acggaagaag gcgagtaacg cttcattgcc atcctgaata
     4801 gtgtccgaaa ccgagtgatc ttggacacta ttcaggtcta atattcaaaa ctcaacggtt
     4861 cgactcacat acatagttca cggtgaacca tattatgatt aatacaaata ccaaaactca
     4921 aataaaaaac cgttaaaaac aacaagataa aaaattaaca tcacttttat ctttctagat
     4981 agatttttgt gaaggcgtta caacgccttc acaccctgag ataataaaaa caacaagaag
     5041 cgattacgag gggtgaaaaa tgtttgagaa aggcgtgtgt ctggttgaga ggcttgcgaa
     5101 agtcgcagcg gtaataacta accttgtgct ctcactttct atattgggat tggtctattt
     5161 catctttcaa aacttggcct tgaggtgatt catgctgtac tggaaaaaaa tgccttcact
     5221 atggatagga aataggatcg ctgaattcag cgatcttgat acagcaaaag ctatagcggc
     5281 attaaaaatt tatttaacat tctgcctgtt ttgcaaagag tcagactctg gccacagaac
     5341 ggttgagtta acctttagca acctttgcga gatagcgtca ttaagccgtt ccttggtgaa
     5401 cgaaggcctt aaaattcttt atgcaaaaga gctgataaaa aacatatcgc cgactgcacg
     5461 aaaaaagatt tataccgtgg atgtgctaga aaatcataat gatggatggt gcaagcttcc
     5521 atttaaagga gttgtcgacg aggacaaaaa aataagtgca tttcaatcca tgcacaacag
     5581 atatcccttt gagttactag ccttacaaac ttacatgtat cttctttacg ctcgtgataa
     5641 taacagcgac tacacactgg ctaggaaaaa gaccatatgc aaaaaattga aatgcaaatt
     5701 acctgaacta aacaaagcaa tcacctacct tatccatata ggtttgcttg atagagttgt
     5761 gaaaaaatcc atagaaaaca tacctctaga gatgtttcat gactcgtact atttctatat
     5821 aaaaacaggc agtaagagcg ctctaaccta cagaaggaaa tcagaaccgc cagttattcc
     5881 agaagccgac ttaccatttt gattgtttat tccacaccaa ttatcacacg gattgaacat
     5941 aacatccgtt gcccgcacct cagaaacgcg ctgaacgcga ttctgacgca aataccgcaa
     6001 aaagagatgt tttccccaag gtaaaccgaa aaaatgcgtc aggatcgttt tcagctcgct
     6061 gcatagctat gcatgaaagt gaatggcgaa cggtttgggc gcatacggtg cccatgagac
     6121 acattttcgg acattttcag ttcgtgaatc cctgactcat tgctacatat ctgaacagac
     6181 acccctagca gcgcccccag gggcatcctg taaaaaaaca caccgcgccg ctagcagcac
     6241 ccctaatata aaatgatgtt ttttatgaaa atagtcagta ccacccctac aaagcggtgt
     6301 cggcgcggtg ttgtagccgc gccgacaccg cttttttaaa tatcacaaag agagcaagag
     6361 aaactaattt gtcataactc tctatttata aagaaaaatc agcaaaaaat tgtttttgcg
     6421 tggggtgtgg gcatttcagg catgagaaca gactcgcgtt tttcc
//
