LOCUS       NZ_CP117234             1919 bp    DNA     circular CON 23-MAR-2024
DEFINITION  Escherichia coli strain ATCC 25922 plasmid pATCC25922_1, complete
            sequence.
ACCESSION   NZ_CP117234
VERSION     NZ_CP117234.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN32977649
            Assembly: GCF_028596225.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 1919)
  AUTHORS   Johnson,J.D., Blankenship,H. and Soehnlen,M.
  TITLE     Long read genome assemblers struggle with small plasmids
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 1919)
  AUTHORS   Johnson,J.D.
  TITLE     Direct Submission
  JOURNAL   Submitted (31-JAN-2023) Bureau of Laboratories, Michigan Department
            of Health and Human Services, 3350 N Martin Luther King Blvd.,
            Lansing, MI 48906, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 2022
            Assembly Method                   :: Trycycler v. v0.5.3
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 140x
            Sequencing Technology             :: Oxford Nanopore, Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_028596225.1-RS_2024_03_23
            Annotation Date                   :: 03/23/2024 03:31:35
            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)                     :: 5,067
            CDSs (total)                      :: 4,951
            Genes (coding)                    :: 4,722
            CDSs (with protein)               :: 4,722
            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)              :: 229
            CDSs (without protein)            :: 229
            Pseudo Genes (ambiguous residues) :: 0 of 229
            Pseudo Genes (frameshifted)       :: 99 of 229
            Pseudo Genes (incomplete)         :: 139 of 229
            Pseudo Genes (internal stop)      :: 51 of 229
            Pseudo Genes (multiple problems)  :: 52 of 229
            Pseudo Genes (short protein)      :: 4 of 229
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP117234.1.
            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..1919
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="ATCC 25922"
                     /db_xref="taxon:562"
                     /plasmid="pATCC25922_1"
                     /geo_loc_name="USA"
                     /collection_date="2022"
     gene            join(1864..1919,1..127)
                     /locus_tag="PQQ28_RS00375"
                     /old_locus_tag="PQQ28_00375"
     CDS             join(1864..1919,1..127)
                     /locus_tag="PQQ28_RS00375"
                     /old_locus_tag="PQQ28_00375"
                     /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_016265984.1"
                     /translation="MLTFIGVVVVAVIAFKLFMLFFSSSESAVERATRKYMENPTSANY
                     KIMVATRMRNEKKRG"
                     /name="hypothetical protein"
     gene            1402..1638
                     /locus_tag="PQQ28_RS00380"
                     /old_locus_tag="PQQ28_00380"
     CDS             1402..1638
                     /locus_tag="PQQ28_RS00380"
                     /old_locus_tag="PQQ28_00380"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001676031.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001676031.1"
                     /translation="MNRLTNLTPAEKKFLDDAIAAAERASGKKLNQPNRHIVLNRARAQ
                     IESQRYADRQRALREDERQQSEFAWSRPRAPRR"
                     /name="hypothetical protein"
     Typing          1065..1238
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.857"
                     /coverage="100.0"
                     /evalue="5.54e-83"
     Typing          complement(577..1098)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.308"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 gctttttttt agttcatccg aatctgccgt cgaacgtgct acccgtaaat atatggagaa
       61 ccctacgagt gctaactata aaataatggt ggctacacgc atgagaaatg agaagaaaag
      121 agggtgatat atgtttgagt ttattggttt tttatttttg cttttggtgt gttatgtctt
      181 tatacaaatg gttgctgtca gggtgtttcc tgaatatgga gtacggaaag cggaggaacg
      241 ataccgtcga aatccatcag cagaaaatga ggatctgtta tggagagcta gaagtcgtat
      301 aactaaacgc aagtaatgtt tcctaagtgt gttgataggc aaacatggtg ggggttacta
      361 ctctcggagt taatgatctt cttgtgatcc tgtcgtttca gtcgtaatct cttgctctga
      421 aaacgaaaaa accacctggg gaggtggttt gatcgaaggt taagtcagtt ggggaactgc
      481 ttaaccaggt aactgggtat acgagaccgc agataccgaa actgttcttt cagtgtagcc
      541 gcagtcaggc ccatacttca agacctctga atctctctct cgtatatccc agttaccagt
      601 ggctgctgcc agtggcgctt tgtcgtgctt tctcgggttg gactcaagat gatagttacc
      661 gggtaaggcg cagcagtcgg actgaacggg gggtttgtgc atacagtcca gcttggagcg
      721 aactgcctac ccggaactga gtgtcaggcg tggaatgaga taaacgcggc cataacagcg
      781 gaatgacacc ggtaaaccga aaggcaggaa caggagagcg cacgagggag ccgccagggg
      841 gaaacgcctg gtatctttat agtcctgtcg ggtttcgcca ccactgattt gagcgtcagg
      901 tttcgtgatg cttgtcaggg gggcggagcc tatggaaaaa cggcttcgcc gcggccctat
      961 cgcttccctg ttaagtctct tcctggcatc ctccaggaaa tctccgcccc gttcgtaagc
     1021 catttccgct cgccgcagtc gaacgaccga gcgtagcgag tcagtgagcg aggaagcgga
     1081 atatatcctg tatcacatat tctgctgacg cgccggtgcc gccttttttc tcctgccaca
     1141 tgaagcactt cactgacacc ctcatccgtg ccaacatagt aagccagtat acactccgct
     1201 agcgctgcgt gactggttca gggctgcgcc ccgaaacccg ctaaaaccac tgccgcgcct
     1261 gcggcttgcc caacgtctca cgtcaccgga ttaaaatccg ctcccgttca ccgtttctgg
     1321 ctgtctttca gcaccgccag cgcttcatcg gttctgctgt gtctggcaga ctgtgcggag
     1381 ttattctgac gggagaatgc tatgaacaga ctgacaaacc tgacacctgc agagaaaaaa
     1441 tttcttgatg atgctattgc cgcagctgag agagcgtcag gcaaaaagct aaatcagccg
     1501 aaccggcata tcgtcctgaa cagagcgcgt gcgcagattg agtcgcagcg ttacgccgac
     1561 cgccagcgtg cattacgtga ggatgagcgg cagcagtccg agtttgcctg gtcacgtccg
     1621 cgcgcgccgc gccgctgatt gcgccttttg gcggtttagt ggtgctgaca ctccgaaatc
     1681 gtctgccatt cacccgcgtg catagccatg caggtacgca gaaatcatca ggggcgtttt
     1741 ttctcgatat gggcacagaa aggtgtatgt ttcaggccgg aggcctcaga aacgcgctga
     1801 gggcgtttga ggcggtgcgg ccaacggatg ttatgtttaa tgttgataac aggagtaaga
     1861 gtgatgctta catttattgg tgtagtggta gtcgccgtta ttgcatttaa attatttat
//
