LOCUS       NZ_CP109923             1459 bp    DNA     circular CON 05-JUN-2024
DEFINITION  Escherichia coli O2:K2:H1 strain C 237-04 plasmid pP7_2, complete
            sequence.
ACCESSION   NZ_CP109923
VERSION     NZ_CP109923.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN30930595
            Assembly: GCF_025946525.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli O2:K2:H1
  ORGANISM  Escherichia coli O2:K2:H1
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 1459)
  AUTHORS   Meski,S., Struve,C., Mirsepasi-Lauridsen,H.C., Petersen,A.M.,
            Jelsbak,L., Skovgaard,O. and Krogfelt,K.A.
  TITLE     Complete Genome Sequences of Extraintestinal Pathogenic Escherichia
            coli Clinical Isolates from Danish Ulcerative Colitis Patients
  JOURNAL   Microbiol Resour Announc 12 (2), e0118622 (2023)
   PUBMED   36715532
REFERENCE   2  (bases 1 to 1459)
  AUTHORS   Skovgaard,O., Krogfelt,K.A., Jelsbak,L. and Meski,S.
  TITLE     Direct Submission
  JOURNAL   Submitted (11-OCT-2022) Department of Science and Environment,
            Roskilde University, Universitetvej 1, Roskilde 4000, Denmark
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: MAY-2022
            Assembly Method :: Flye v. v2.9; Minimap2 v. v2.24-r1122; Miniasm v.
            v0.3-r179; Racon v. v1.4.3; SPAdes v. v3.15
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 300x
            Sequencing Technology :: Oxford Nanopore MinION; BGISEQ-500
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_025946525.1-RS_2024_06_05
            Annotation Date                   :: 06/05/2024 03:39:20
            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)                     :: 4,769
            CDSs (total)                      :: 4,655
            Genes (coding)                    :: 4,460
            CDSs (with protein)               :: 4,460
            Genes (RNA)                       :: 114
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 195
            CDSs (without protein)            :: 195
            Pseudo Genes (ambiguous residues) :: 0 of 195
            Pseudo Genes (frameshifted)       :: 88 of 195
            Pseudo Genes (incomplete)         :: 118 of 195
            Pseudo Genes (internal stop)      :: 44 of 195
            Pseudo Genes (multiple problems)  :: 49 of 195
            Pseudo Genes (short protein)      :: 3 of 195
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP109923.1.
            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..1459
                     /organism="Escherichia coli O2:K2:H1"
                     /mol_type="genomic DNA"
                     /strain="C 237-04"
                     /serotype="O2:K2:H1"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /culture_collection="SSI<DNK>:C237-04"
                     /db_xref="taxon:2990469"
                     /plasmid="pP7_2"
                     /geo_loc_name="Denmark:Copenhagen"
                     /lat_lon="55.68 N 12.59 E"
                     /collection_date="2007"
                     /collected_by="Statens Serum Institut"
     gene            1..477
                     /locus_tag="N7L43_RS23750"
                     /old_locus_tag="N7L43_23750"
     CDS             1..477
                     /locus_tag="N7L43_RS23750"
                     /old_locus_tag="N7L43_23750"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000469298.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /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_000469298.1"
                     /translation="MFIDSEKRLKQLSDEAKKNTEDLEEAKKNSRFTQVSPKGWERVRE
                     LLKDSQGISALKLYSFLAEHIDPTCGAVVADQQFLAEKLGVSRSTIIRWLNYLESKNAL
                     VRIPVAGKVCAYALDPHEVWKGYNTTKNHAAFVTKTLVNKDGDIQRRIMAMFSN"
                     /name="helix-turn-helix domain-containing protein"
     gene            569..790
                     /locus_tag="N7L43_RS23755"
                     /old_locus_tag="N7L43_23755"
     CDS             569..790
                     /locus_tag="N7L43_RS23755"
                     /old_locus_tag="N7L43_23755"
                     /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_171854772.1"
                     /translation="MRVFAPRSPEKTEPPRFPVALKALPETVWGEPQTPIAATLTVYDH
                     LPTAWLPVPCKWALQGAGAVPGDLKAPG"
                     /name="hypothetical protein"
     Typing          1070..1168
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          complement(1273..1381)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.182"
                     /coverage="100.0"
                     /evalue="4.23e-47"
     Typing          complement(710..968)
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.538"
                     /coverage="99.0"
                     /evalue="1.12e-96"
ORIGIN
        1 atgtttattg attcagaaaa acgactgaaa caactttcag atgaggcaaa gaaaaacacc
       61 gaggatctcg aagaagcaaa gaaaaattca aggtttacac aggtatcccc aaaaggttgg
      121 gaacgtgttc gagagctgct gaaggatagc caaggcatat cagcactgaa gctgtactca
      181 tttttagcgg agcatatcga tcctacgtgt ggcgctgtcg ttgcagatca gcaattccta
      241 gctgaaaaac ttggagttag cagaagcaca attattcggt ggctcaatta cttagaatca
      301 aaaaatgcat tagttagaat ccccgttgct ggtaaggttt gtgcgtatgc cctcgatcca
      361 catgaagtct ggaagggata caacactacg aaaaaccatg cagcgtttgt cactaaaaca
      421 ctggtcaaca aagacggtga tattcagcgc cgaatcatgg ccatgttttc aaattgagct
      481 agcggcaggc ggacaaccag gggctacgtg ttaacgttct gaccatgatt gtctatcctg
      541 cattgctctt ttgccgcctc aaaatccttt gcgtgttttt gctccccgtt ctccagaaaa
      601 aaccgagccg ccacggtttc cggtagcgct caaggcgctg ccggaaaccg tctggggaga
      661 accccagacc cccatcgctg caacactgac ggtctacgac cacctaccaa ccgcatggct
      721 gcctgttccg tgcaaatggg ctttgcaggg ggctggcgcg gttcctggcg acctgaaagc
      781 ccctggttag gggtatcggc gcgcttgacc tcctgagagc ctctgtaagc gtttttcgcg
      841 ccttccatgc cctggcgggc atctaaaacc cgtttcgtgc gtctgagagc ttttgagcgc
      901 gtttgagggg ctatctggcg actcaccccc aaaagaacaa caccgggatc accgacaaca
      961 tgcgagagat gatcccgctc gccgcaagtc gatgaccgag cgtagcgagc gaatcgacga
     1021 ggaagcggaa gagaaccgga agccacattg agcacttacg cactgatgcg gggtgtcggg
     1081 gcgaagccct gaccaagtgg taatcgtatc ggcgtgcatg cgcggttata cgattacaca
     1141 tcctgccccg atttctgagg cgttttaacg gtgaacggac ggcaaaaaca cgatggagct
     1201 gttgaacgtg aaaaccacga aatctggcaa caaagggcgt tgcgttgcac gcaacaccct
     1261 tgcctagaat agatctttta cgccgatttg taagttgttg tttttttagt atgtttttta
     1321 tttacctgtc gcatccaggg tgacacaacg ttgtcgcatc ctggatgcga caacacgcaa
     1381 caaggtgttg cacggatgtg tcatgatggc ttagatttga accaacgtta gtgcatggga
     1441 ttttcagagg gaaaaaatc
//
