LOCUS       NZ_CP041447             1459 bp    DNA     circular CON 21-JUN-2024
DEFINITION  Escherichia coli strain YPE10 plasmid pYPE10-1k, complete sequence.
ACCESSION   NZ_CP041447
VERSION     NZ_CP041447.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN12233488
            Assembly: GCF_008807135.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 1459)
  AUTHORS   Li,R., Lu,X., Liu,Z., Liu,Y., Xiao,X. and Wang,Z.
  TITLE     Application of Nanopore Sequencing for Rapid Characterization of
            tet(X4)-positive E. coli strains
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 1459)
  AUTHORS   Li,R., Lu,X., Liu,Z., Liu,Y., Xiao,X. and Wang,Z.
  TITLE     Direct Submission
  JOURNAL   Submitted (09-JUL-2019) College of Veterinary Medicine (Institute of
            Comparative Medicine), Yangzhou University, Wenhui Road, Yangzhou,
            Jiangsu 225009, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.4
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 80X
            Sequencing Technology :: Oxford Nanopore MinION, Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_008807135.1-RS_2024_06_21
            Annotation Date                   :: 06/21/2024 03:32:59
            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)                      :: 4,946
            Genes (coding)                    :: 4,692
            CDSs (with protein)               :: 4,692
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 254
            CDSs (without protein)            :: 254
            Pseudo Genes (ambiguous residues) :: 0 of 254
            Pseudo Genes (frameshifted)       :: 53 of 254
            Pseudo Genes (incomplete)         :: 192 of 254
            Pseudo Genes (internal stop)      :: 42 of 254
            Pseudo Genes (multiple problems)  :: 30 of 254
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP041447.1.
            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"
                     /mol_type="genomic DNA"
                     /strain="YPE10"
                     /isolation_source="Pork"
                     /db_xref="taxon:562"
                     /plasmid="pYPE10-1k"
                     /geo_loc_name="China: Yangzhou"
                     /lat_lon="32.24 N 119.26 E"
                     /collection_date="2019-06"
                     /collected_by="Xiaoyu Lu"
     gene            1..441
                     /locus_tag="FNP79_RS00530"
                     /old_locus_tag="FNP79_00530"
     CDS             1..441
                     /locus_tag="FNP79_RS00530"
                     /old_locus_tag="FNP79_00530"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000031238.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000031238.1"
                     /translation="MSKDVERITQINDQGEIIGGFVAVIRPKQKSAFQRHFTMNQDALR
                     ILAKELTGEQFKVLMLMLADLDYENFIQIAQADIAETLGMQKTNVSRAVRALLDVGVIF
                     EGPKVGRSKTYRLNEQFGWKGTVTNHKKALKNGFSVIQGGRI"
                     /name="hypothetical protein"
     Typing          1051..1131
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="95.122"
                     /coverage="87.0"
                     /evalue="9.59e-28"
     Typing          complement(676..934)
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.462"
                     /coverage="99.0"
                     /evalue="5.11e-105"
ORIGIN
        1 atgagtaagg atgtcgagag aatcactcag ataaatgacc agggtgagat tatcggcggc
       61 ttcgttgccg ttatccgccc taaacaaaaa tcagcatttc agaggcattt caccatgaat
      121 caagacgcat tacggatctt ggctaaggaa ttaaccgggg agcaattcaa ggtcttaatg
      181 ctgatgcttg cagatctgga ttacgaaaac ttcattcaga tcgcccaagc agatattgct
      241 gaaactttag ggatgcagaa aacgaatgtt agtcgcgccg ttcgcgcgct actggatgtt
      301 ggggtgatct ttgagggacc taaagtcggc agatcaaaaa cataccggct gaatgaacaa
      361 tttggttgga aaggcaccgt aaccaaccac aaaaaggcac tcaaaaacgg ctttagtgtc
      421 attcagggcg gccggattta aagagccagc ggcaggcgga caatccacag aacattgcat
      481 gcaatttcta gtggattgtc tatcctgcat tgctcttttg ccgcctcaaa atcccttgcg
      541 tgtttttgct ccccgatctc cagaacgacc gagccgccac ggttccggca gcgccttgag
      601 cgcaaccgga aaccgtctgg ggagaccccc agccccccca tcgctgtaac accgacggtc
      661 tacgaccacc taccaaccga gtggctgcct gtaccgtgca aatgggcttt gcagggggct
      721 ggcgcggttc ctggcgacct gaaagcccct ggctaggggt atcggcgcgc ctgacctcct
      781 gaaacgctct gtaagcgttt ttcgcgcctt ccatgccctg acgggcattt aaaccccgcc
      841 tcgtgcgtct gagagcttct gagcgcgttt gaagggctat ctgacgactc atccccgaaa
      901 gaacaacagc ggaatcaccg acagcatgcg agagatggca ccgctcgccg cagccccagc
      961 gaccgaacgt tagtgagcga gtgggcgagg aagcggaaga gaaccggaaa ccacattgag
     1021 cacgtacgca ctgatacggg gtgtcggggc gaagccctga ccagatggca aacggaatat
     1081 cgtcgcgggt gacggtatta catttgcaca tcctgtcctg atttctgagg cgttttaacg
     1141 gtgaacggac ggcaaaaaca tgatggagct gttgaacgtg gagagcgcga aatcggacaa
     1201 aaatcacggc tgacgaggct tgcagaggag taagccagta tacactccgc tatcgctacg
     1261 tgactgggtc agggcttcgc cccgacaccc caaagagcag ctaggataaa tatctaatgg
     1321 aatcaatgcg ttagacgcct aatataaaga tacagaaagg agaataaaaa cattaataaa
     1381 atctaagggt tacagttgac atagttatca ataatgataa cactgttatc attattgata
     1441 actcaaatag ggttcaaag
//
