LOCUS       NZ_CP041446             2137 bp    DNA     circular CON 21-JUN-2024
DEFINITION  Escherichia coli strain YPE10 plasmid pYPE10-2k, complete sequence.
ACCESSION   NZ_CP041446
VERSION     NZ_CP041446.1
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 2137)
  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  JOURNAL   Unpublished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 2137)
  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
            CP041446.1.
            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..2137
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="YPE10"
                     /isolation_source="Pork"
                     /db_xref="taxon:562"
                     /plasmid="pYPE10-2k"
                     /geo_loc_name="China: Yangzhou"
                     /lat_lon="32.24 N 119.26 E"
                     /collection_date="2019-06"
                     /collected_by="Xiaoyu Lu"
     gene            579..1574
                     /locus_tag="FNP79_RS00525"
                     /old_locus_tag="FNP79_00525"
     CDS             579..1574
                     /locus_tag="FNP79_RS00525"
                     /old_locus_tag="FNP79_00525"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_020240588.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_038989441.1"
                     /translation="MQNPKLKNLTDYSPDDKPWDVHKSQSDDVGGIYLRAAEFEAYAAR
                     MRDCGGLLRFGWSTLKDTGETRLRLREAHFCRVRHCPVCQWRRSLMWQARFYQSLPKIV
                     ADYPDARWMFLTLTVRNCAIEDLGDTLTAMNAAFQRMKVRKEFKSVQGWIRTTEVTRGR
                     DGSAHPHFHTLMMVPPGMLNGHDYVKHYRWVELWRDCLRVDYDPNVDVRAVKPRKPKDG
                     QTLACATAELVRGAVAETLKYSTKPADMVADPDWFLELTRQTHKRRFVATGGALKDVLK
                     LEQETDQDMVIGDDISDGEDDGSRLAFGWDSTPRKYVRLPERDKFKSDPD"
                     /name="protein rep"
     Typing          complement(1295..1485)
                     /name="ColpVC"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.375"
                     /coverage="98.0"
                     /evalue="1.4200000000000001e-44"
ORIGIN
        1 ctctgcgagg aggcacacgc cgttcggaat cggggtccac tctgtttaat agtggactct
       61 tgttgcgatt tgcaacggaa acagccgcgt gcagtgaatg taatactgca cgtttgtctc
      121 aatctgacat ttctcagggg gggcgattta acgtggtttg cttaattttt gagcttacga
      181 atgcttgagt gtttgagtgc ctgaatgctg cttttggggg ttggtttttc ggccctgaaa
      241 ggggcgaaat ccttgtattt atacttaagg gataactcta ggattcaaat tcgcttccag
      301 cccttgtgcc gcaaggcctg agagccaatt tgctcgaaaa tggttttgtg agtatgattt
      361 ctgacaggtg atcgtgtccg cgaactaatt tttgattact tggggtggtt cccaagacct
      421 tacttactga cacgatgata tgagaaaccc ctgcaagtgc taccaacact tcaggggcgc
      481 gatcacctgg ctaaatacgg cttgaaatcg actcgcaaca ggtgatacgg aaatgataac
      541 acacccttcc agcgcctgcc catattggag caggtgctat gcagaatcct aagctaaaga
      601 accttactga ctacagtccc gacgataagc cgtgggacgt tcacaagtcg caatctgatg
      661 atgttggcgg tatctatctg cgtgcagctg aatttgaggc gtatgcggct cgtatgcgcg
      721 attgtggcgg cttgctgcgt tttggctggt ctacccttaa agacaccgga gaaacgcgtt
      781 tacggcttcg tgaggcgcat ttctgccgcg ttcgtcactg ccctgtctgc cagtggaggc
      841 gttccctgat gtggcaagcc cgtttttatc agtctctgcc gaaaatcgtc gctgattacc
      901 ctgatgcccg ctggatgttc ctcacgctca ccgttcgcaa ctgtgcgatc gaggatctcg
      961 gggacacgct tactgccatg aatgccgcat tccagcgcat gaaggttcgc aaggaattta
     1021 aatccgtaca gggatggatt cgcaccacag aagttacccg cggtcgtgat ggctctgcac
     1081 acccccactt tcacaccctg atgatggttc ctcctgggat gctgaacggt catgactacg
     1141 ttaagcacta ccgctgggtt gaactctggc gtgactgcct gcgcgttgat tacgatccta
     1201 atgttgatgt tcgggcagtg aaaccccgca agcctaaaga tggccagact ctggcatgtg
     1261 ccactgctga actggtgcgc ggtgccgttg ctgaaaccct gaaatattcg acaaagccgg
     1321 ctgatatggt tgccgacccg gactggttct tagagctgac ccggcagacg cataaacgcc
     1381 gttttgttgc gaccggtggc gctctgaaag acgttctgaa actggagcag gaaacggatc
     1441 aggacatggt gatcggggat gatatttccg atggtgaaga cgatggttca cgcctcgcct
     1501 ttggctggga ttcgacgcca agaaaatacg tccgtttgcc tgaacgcgat aagtttaaat
     1561 cagatcctga ttagggtgtc ggggcctgcc ctgaccaggt tgtttttgga tgccgctgcg
     1621 tgtggcggta ctccaaaaac acatcttgtc cggtacacag atttcctttg gcattccttc
     1681 gggtttccct gagatttcca ctctgcatac atacacgcat acacgaataa tcaacggcag
     1741 aattcgggca ggatatgtaa agtgggacca ctttacgcct gccttattcg cactctgctc
     1801 aatggaatat taaatctgac agcgttcgcc gccgtcgaat cgtcaacttc taaatcgggg
     1861 gatcccttta gggttccgat ttagtggttg tacgactgca cccctcatac ccttgtgatg
     1921 ggtgatggtt cacatggtga gccatcgccc tgtaaagccg ctttttaccc ccttcaaggc
     1981 gttgcctgtg gggtaggtgc gtaagccctg ccctacaggt gatgccgtgg gggtattttc
     2041 gttttgctcg gtatgcctta ttcgtttaaa tccgccatca ggagtatgcg gggtaaagtc
     2101 gtgcggccgc gatgaggaac ggggattgcc cccgcag
//
