LOCUS       NZ_CP109925             4109 bp    DNA     circular CON 05-JUN-2024
DEFINITION  Escherichia coli O125ac:K+:H10 strain C 236-04A plasmid pP10A_1,
            complete sequence.
ACCESSION   NZ_CP109925
VERSION     NZ_CP109925.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN30931041
            Assembly: GCF_025946545.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli O125ac:K+:H10
  ORGANISM  Escherichia coli O125ac:K+:H10
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4109)
  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 4109)
  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_025946545.1-RS_2024_06_05
            Annotation Date                   :: 06/05/2024 03:53:42
            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)                     :: 4,899
            CDSs (total)                      :: 4,782
            Genes (coding)                    :: 4,578
            CDSs (with protein)               :: 4,578
            Genes (RNA)                       :: 117
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 204
            CDSs (without protein)            :: 204
            Pseudo Genes (ambiguous residues) :: 0 of 204
            Pseudo Genes (frameshifted)       :: 58 of 204
            Pseudo Genes (incomplete)         :: 141 of 204
            Pseudo Genes (internal stop)      :: 38 of 204
            Pseudo Genes (multiple problems)  :: 30 of 204
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP109925.1.
            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..4109
                     /organism="Escherichia coli O125ac:K+:H10"
                     /mol_type="genomic DNA"
                     /strain="C 236-04A"
                     /serotype="O125ac:K+:H10"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /culture_collection="SSI<DNK>:C236-04A"
                     /db_xref="taxon:2990470"
                     /plasmid="pP10A_1"
                     /geo_loc_name="Denmark:Copenhagen"
                     /lat_lon="55.68 N 12.59 E"
                     /collection_date="2007"
                     /collected_by="Statens Serum Institut"
     gene            join(4044..4109,1..234)
                     /locus_tag="N8A72_RS24300"
                     /old_locus_tag="N8A72_24300"
     CDS             join(4044..4109,1..234)
                     /locus_tag="N8A72_RS24300"
                     /old_locus_tag="N8A72_24300"
                     /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_023281092.1"
                     /translation="MATATNFDAWLDDVDGDYEEVMALYDSVQNVSDMGLYQCVEGGRG
                     DAWVVSSNHHPEALFLASAVARDTFLKLIRERLCGGEDVDSWYGFQRNISNDHS"
                     /name="hypothetical protein"
     gene            305..1039
                     /locus_tag="N8A72_RS24305"
                     /old_locus_tag="N8A72_24305"
     CDS             305..1039
                     /locus_tag="N8A72_RS24305"
                     /old_locus_tag="N8A72_24305"
                     /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_160384955.1"
                     /translation="MALMVTRRYLLGGEYPSEEFVQASLEKYFFRQGFDIDTGSYIDLI
                     CRDKESRDVVWHIEVKGKTSQPGLDFRTCLGQLVQRMTKDNINYAIAVPRIKQYERLIE
                     ETSILAVSKLNLHWIFVGPDGSVTIKEPDSSTMKNGNGNGNGNGREVSLVNGGFKRFIT
                     GDFMPTCSYGKAPVVFKSSRREMWDWLDDFVISNGVIPSIADIKEEAESRSGKWTLSNV
                     KIEYQFWKIYHLYKGHFFYQSE"
                     /name="hypothetical protein"
     gene            complement(1248..1391)
                     /locus_tag="N8A72_RS24310"
                     /old_locus_tag="N8A72_24310"
     CDS             complement(1248..1391)
                     /locus_tag="N8A72_RS24310"
                     /old_locus_tag="N8A72_24310"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001505258.1"
                     /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_104459923.1"
                     /translation="MHEPPVQSDCCACSGNYQLESNPERYDKAPLAAATGKQDVREMYL
                     SS"
                     /name="replication initiation protein"
     gene            1952..2101
                     /locus_tag="N8A72_RS24315"
                     /old_locus_tag="N8A72_24315"
     CDS             1952..2101
                     /locus_tag="N8A72_RS24315"
                     /old_locus_tag="N8A72_24315"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_166479530.1"
                     /translation="MPSEYDEQRDATDAPLPGEYDVFDLMAQVTEENLHAPVDSGPPVG
                     REAL"
                     /name="hypothetical protein"
     gene            2581..2772
                     /locus_tag="N8A72_RS24320"
                     /old_locus_tag="N8A72_24320"
     CDS             2581..2772
                     /locus_tag="N8A72_RS24320"
                     /old_locus_tag="N8A72_24320"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000166328.1"
                     /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_000166328.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDAEADLCEKLHDDA
                     EHLFRTLSSRLDALQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2772..3194
                     /locus_tag="N8A72_RS24325"
                     /old_locus_tag="N8A72_24325"
     CDS             2772..3194
                     /locus_tag="N8A72_RS24325"
                     /old_locus_tag="N8A72_24325"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005229777.1"
                     /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_172696149.1"
                     /translation="MARVSISEAARLVKVSRPTIYKMINSGKLSYTSVVKHGKGIKVID
                     TSELIRVFGSLDGVIDAVKHDVKSDAESTGINSVGLHDLQHRIALLEAENDGLKGAVKA
                     RDEHIDSLRQAMQLLEHKHEPSSPPHSPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     Typing          1743..1959
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="86.758"
                     /coverage="100.0"
                     /evalue="9.55e-62"
     Typing          complement(1283..1793)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.762"
                     /coverage="98.0"
                     /evalue="0.0"
ORIGIN
        1 gctctttatg attccgttca gaatgtaagt gatatggggt tgtatcagtg tgttgagggt
       61 ggtcggggtg atgcttgggt cgtgagctct aatcatcatc cagaagctct ttttctagca
      121 tcagctgtgg ctagggatac tttcctcaaa ttgattagag aaaggctatg tggcggcgaa
      181 gatgttgatt catggtatgg atttcaacga aatatatcga atgatcactc gtaatcgtac
      241 agagagttcc ccttgtggga actcttaaaa tatgacgtta tagtaaatag gatgcgtagg
      301 ggttgtggct cttatggtga cgagaaggta cttactaggt ggtgaatatc cctccgagga
      361 atttgttcaa gcttctttag aaaaatattt ttttcgacaa gggttcgata tagatacggg
      421 ttcttatatt gaccttattt gtcgtgataa agaatctagg gatgttgtgt ggcatattga
      481 agtaaaagga aaaacatcac agccagggtt ggattttcga acttgtcttg gacaattagt
      541 gcagagaatg acaaaagata atattaatta cgctattgct gttccaagaa taaaacagta
      601 tgaaagatta atagaagaaa cgagcattct tgctgttagt aaattgaatt tacactggat
      661 atttgttggg cctgatggca gtgtgacaat taaggaacct gatagctcta cgatgaaaaa
      721 tggtaatggt aatggtaatg gtaatggaag agaagtttct cttgtgaatg gggggtttaa
      781 aagatttatt acgggggatt ttatgccaac ttgctcatat gggaaagctc ctgttgtatt
      841 taaatcatct cggcgagaaa tgtgggattg gttggacgat tttgttattt caaatggggt
      901 gatcccaagt attgctgata ttaaagaaga ggctgaatcg cggagtggga aatggacgct
      961 ttctaatgtt aaaatagagt atcagttttg gaaaatatat cacttgtata aggggcattt
     1021 tttctatcaa tctgagtagc tgactcattt gttcatcaaa tgccatgatc ttcttgagat
     1081 tcattcgctc aaagcgtaat ctctttctcg gaaaacgaaa aaaccacccg gcaaggtggt
     1141 ttttcgaagg ttcattaacc ggcaagttta tgaaccgtgg taacagtctt gtgcgagaca
     1201 tgtcaccaaa tccgtccttc cagtgtagcc tcagttaggt cttcacttca agaactcaaa
     1261 tacatctctc gcacatcctg tttaccagtg gctgctgcca gtggcgcttt gtcgtacctt
     1321 tccgggttgg actcaagttg atagttaccg gaacaggcgc agcagtcgga ctgaacgggg
     1381 ggttcgtgca tacagtccag cttggagcga actgcctacc cggaactgag tgtcaggcgt
     1441 ggaatgagac aaacgcggcc ataacagcgg aatgacaccg gtaaaccgaa tggcaggaac
     1501 aggagagcgc acgagggagc taccaggggg aaacgcctgg gatctttata gtcctgtcgg
     1561 gtttcgccac cactgatttg agcgtcagat tttcgtgatg cttgtcaggg gggcggagcc
     1621 tatggaaaaa cggcagctcc gcagcctttt gctgccccgc ttgtcatgcc gtatgtcttt
     1681 gctcttatcc gtgtgcaggt aacgcccgcc gcagactcac ggcaggagcg tcagcgaccg
     1741 agtgagcgag gaggcgtcat atcaccgtaa cctccatttt ctcctgtacg ccctgccgct
     1801 gcatttttcc cctgccacat gaagcacttt cattacgtgt tactcatccg taacatatta
     1861 agccagtata cactccgcta gcgctacgtg actggttcag ggctgcgccc cgaaacccgc
     1921 taacaatctc tcagctactg gatatcaccc catgccatct gagtatgatg aacaacggga
     1981 tgcgactgat gctccgcttc ccggcgaata tgacgttttt gatttaatgg cgcaggttac
     2041 tgaagagaac ctgcacgccc ctgtggattc cgggccgcct gtcggccggg aagcgttata
     2101 gctttttcgc ttgcccgcgt acgcggtaat acgccggtat tacattttat ttctttattt
     2161 tcatgtaatt acaggtgatt gtaatacgtt gcgtattaca tgaataaacg gagatttcag
     2221 tttttacctt ttaattcatg cagttgcgat gaaaatcgcg gctgcgttag gtgtatgacc
     2281 atttaagggg caaaaaatta tcattctggc cgggtgtact gcgcaggtta aggagcattg
     2341 gtgacgaaaa agcgtcttta actgcttcgt tcatgcttgc atgaacggat tatttttccg
     2401 gactacaggc aaactacagg aagactacaa aagttgatga tttaatcctg atttttagtg
     2461 cgatgactac agataaacta caaaataact acaggattac ctcagatccg ttctctgaac
     2521 catttgtaca tccgaccccc ttaccggttt acactgagca cagatgctct gagggccctt
     2581 atgacgaaac aacagaaaac agcgctgaac atggctaaat tcatccagaa tcagtctctg
     2641 ctcctgctgg agaagcttaa cgagcttgat ctcgatgctg aggccgacct ttgtgagaaa
     2701 ctccacgatg atgcggagca tcttttccgt acactgtcct cgagactgga tgcattacag
     2761 gatggtaact gatggccaga gtgtctatta gtgaagcagc acggcttgtt aaggttagtc
     2821 gccctactat ttacaagatg attaacagtg gtaagttaag ttacacctct gttgtaaagc
     2881 acgggaaggg tattaaagtt attgatacat cagagcttat tagagtgttt ggttctcttg
     2941 atggtgtaat cgatgctgta aaacatgatg taaaaagtga cgcagaatct acaggtatta
     3001 acagcgttgg tttacatgat ttacaacata gaatcgcttt acttgaagct gaaaacgatg
     3061 gtcttaaagg ggctgttaag gctcgagatg agcatattga ttcccttcgt caggctatgc
     3121 agcttctgga gcacaagcac gaaccttctt caccacccca ttccccgtgg tggaaattct
     3181 ggaaaaaatc ctgatcccgc catgcttgag ttttcctctc cggccatgcc ggggcgttcg
     3241 tgaaccttcc caaaaatcgc cagatctctg aacgctcctc acactaaaaa tatccacacc
     3301 ccacgcaaaa ttaaattttt gcagataact cattaatatc agtcagttgg ttgttattaa
     3361 attacgcagt attaccttct gtaaggtcaa tccaagtcgt cggtgattcg tgtacgactt
     3421 gccgacgact cgtcatagag tcatcgacga ctcactccac actatcagta acttatgacg
     3481 acttgactct agagtcgaat cgtcgctttg gcgttttttt gaccgtggtg actctagagt
     3541 caagtcacga gtcgaatcgc cggtgaatcg tgtggtgagt cgtccggcga cttgccataa
     3601 cgtgattgcc ggccgtcgac gaacccgatt cctgaacgtg ctgaaaaccg gttttccggc
     3661 tgcgccggca acgcttcacg gccacgcaat aaattgcgtc cccgttcacc gttttcagtc
     3721 gggtttggtg cgggttttga gttgtctggc gtgaattcag gatgaaatct acctccagcc
     3781 agtctggtgc ataacaattc atgcccgtaa aacccatcag cgcgattttg aggcgttttc
     3841 agggggtaag acgtaggatt taatgggtta cgccccagaa tcgtttctcg agcgtttgag
     3901 cggtgcgtgt aatgcgacgt tatggtaaat gcctgtcttg ctcactttta gagcatgagg
     3961 caaaaagggt aaaaacttat ttgcttaaca gcccctatca ctatgtaaat taactcctga
     4021 aaactaaaaa atggaggatt ggcatggcga ctgctactaa ttttgatgcg tggttagatg
     4081 atgttgatgg cgattatgag gaggttatg
//
