LOCUS       NZ_CP120556             1565 bp    DNA     circular CON 24-MAY-2024
DEFINITION  Escherichia coli strain B1172 plasmid pB1172_1565, complete
            sequence.
ACCESSION   NZ_CP120556
VERSION     NZ_CP120556.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN33748627
            Assembly: GCF_029536615.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 1565)
  AUTHORS   Fedrova,P., Hrala,M., Micenkova,L., Tom,N., Bosak,J. and Smajs,D.
  TITLE     Complete genome sequences of five Escherichia coli strains with
            probiotic features
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 1565)
  AUTHORS   Fedrova,P., Hrala,M., Micenkova,L., Tom,N., Bosak,J. and Smajs,D.
  TITLE     Direct Submission
  JOURNAL   Submitted (16-MAR-2023) Department of Biology, Masaryk University,
            Kamenice 5, Brno 62500, Czech Republic
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 416x
            Sequencing Technology :: Illumina; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_029536615.1-RS_2024_05_24
            Annotation Date                   :: 05/24/2024 04:44:07
            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)                     :: 5,290
            CDSs (total)                      :: 5,174
            Genes (coding)                    :: 4,916
            CDSs (with protein)               :: 4,916
            Genes (RNA)                       :: 116
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 258
            CDSs (without protein)            :: 258
            Pseudo Genes (ambiguous residues) :: 0 of 258
            Pseudo Genes (frameshifted)       :: 110 of 258
            Pseudo Genes (incomplete)         :: 182 of 258
            Pseudo Genes (internal stop)      :: 45 of 258
            Pseudo Genes (multiple problems)  :: 64 of 258
            Pseudo Genes (short protein)      :: 1 of 258
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP120556.1.
            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..1565
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="B1172"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pB1172_1565"
                     /geo_loc_name="Czech Republic"
                     /collection_date="2009"
     gene            1..585
                     /locus_tag="P5710_RS26400"
                     /old_locus_tag="P5710_26400"
     CDS             1..585
                     /locus_tag="P5710_RS26400"
                     /old_locus_tag="P5710_26400"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001490767.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_032495510.1"
                     /translation="MCKCNTVTRDDIPFAIWSGLRPDTPHQCVRAQCGFRFSSASSPTR
                     SLTFGRWGCGERCHLSHVVGDSAVVLSGISRQIALQTRSEALRRTKRGLNARQGMEGAK
                     NAYRAFQEVRRADTPSQGLSGRQEPRQPPAKPICTVQAATRLVGGRRPSVLQRWGSGVL
                     PRRFPVALKALPEPWRLDRSGDRGAKTRKGF"
                     /name="hypothetical protein"
     gene            complement(687..1166)
                     /locus_tag="P5710_RS26405"
                     /old_locus_tag="P5710_26405"
     CDS             complement(687..1166)
                     /locus_tag="P5710_RS26405"
                     /old_locus_tag="P5710_26405"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001620079.1"
                     /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_000275450.1"
                     /translation="MYIGTEEQRKKRLKELEKLNKESESDPKNNGPFTQVYQKGWERIR
                     ELSKDKQGVVAIPLYSFLAEHIDPSCGAVVADQQFLADKLGVSRSTIKRWLNYLESKNA
                     LVRIPVAGKVCAYALDPHEVWKGYNTSKNYAAFVTKTLVNKDGDIQRRIMAMFSN"
                     /name="helix-turn-helix domain-containing protein"
     Typing          177..437
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.275"
                     /coverage="100.0"
                     /evalue="1.83e-109"
ORIGIN
        1 atgtgcaaat gtaataccgt cacccgcgac gatattccgt ttgccatctg gtcagggctt
       61 cgccccgaca ccccgcatca gtgcgtacgt gctcaatgtg gtttccggtt ctcttccgct
      121 tcctcgccca ctcgctcact aacgttcggt cgctggggct gcggcgagcg gtgccacctc
      181 tcgcatgttg tcggtgattc cgctgttgtt ctttcgggga taagtcgtca gatagccctt
      241 caaacgcgct cagaagctct cagacgcacg aaacggggtt taaatgcccg tcagggcatg
      301 gaaggcgcga aaaacgctta cagagcgttt caggaggtca ggcgcgccga tacccctagc
      361 caggggcttt caggtcgcca ggaaccgcgc cagccccctg caaagcccat ttgcacggta
      421 caggcagcca ctcggttggt aggtggtcgt agaccgtcgg tgttacagcg atgggggtct
      481 ggggttctcc ccagacggtt tccggttgcg ctcaaggcgc tgccggaacc gtggcggctc
      541 gatcgttctg gagatcgggg agcaaaaaca cgcaagggat tttgaggcgg caaaagagca
      601 atgcaggata gacaacccga tgtcaaatgt taacatttga atcagattgt ccaaaaacgg
      661 ggtttttgcc tgtgcctgcc gctggctcaa tttgaaaaca tggccatgat tcggcgctga
      721 atatcaccgt ctttgttgac cagtgtttta gtgacaaacg ccgcgtagtt tttagatgtg
      781 ttgtatccct tccagacttc atgtggatcg agtgcatacg cacaaacctt accagcaaca
      841 ggaattctga ctaacgcgtt ttttgattct aagtagttga gccagcgctt aattgtgctt
      901 cggctaacac ccaatttatc tgctaaaaac tgctgatcgg caacaacagc accgcatgag
      961 ggatctatgt gctcagctaa aaacgagtaa agcggtattg ctacaactcc ctgcttgtcc
     1021 ttcgacagtt ctcggatcct ttcccagccc ttctgataaa cctgggtgaa tgggccgtta
     1081 tttttcggat ctgattccga ttctttgttt aatttttcca gttcttttag acgctttttt
     1141 cgctgctctt cagtcccgat atacatggta aatctccacg gtctaatgat ggctcaaata
     1201 taagccatca tagctcaaac gtaaaccatg ataggtcgac ctagctcaca catgcgtgag
     1261 ctaaccttag accacacatg cgtgagctaa cccataatgc aagtagctaa aaaatcaata
     1321 acttacaaaa tcgcccttaa atatcttttc tgctgaaagt gttgcgcaaa gcggaacact
     1381 tttttggggt gtcggggcga agccctgacc cagtcacgta gcgatagcgg agtgtatact
     1441 ggcttactcc tctgcaagcc ttaccagctg tgatttttgc cagatttcac gctctcaacg
     1501 ttcaacagct ccatcatggt tttgccgtcc gttcaccgct aaaacgcctc agaaatcggg
     1561 acagg
//
