LOCUS       NZ_CP089140             3397 bp    DNA     circular CON 21-FEB-2024
DEFINITION  Escherichia coli strain XD35 plasmid pXD35007, complete sequence.
ACCESSION   NZ_CP089140
VERSION     NZ_CP089140.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17183821
            Assembly: GCF_019375055.2
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3397)
  AUTHORS   Peng,Z.
  TITLE     Antimicrobial resistance and population genomics of multidrug drug
            resistant Escherichia coli in pig farms in mainland China: a
            national wide epidemiological and microbiological study
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3397)
  AUTHORS   Peng,Z.
  TITLE     Direct Submission
  JOURNAL   Submitted (06-DEC-2021) College of Veterinary Medicine, Huazhong
            Agricultural University, NO.1 Shizishan Street, Wuhan, Hubei 430070,
            China
REFERENCE   3  (bases 1 to 3397)
  AUTHORS   Peng,Z., Chen,H. and Wang,X.
  TITLE     Direct Submission
  JOURNAL   Submitted (01-JAN-2021) College of Veterinary Medicine, Huazhong
            Agricultural University, No. 1 Shizishan Street, Wuhan, Hubei
            430070, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Canu v. v1.5
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 1052.02x
            Sequencing Technology             :: Oxford Nanopore PromethION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/21/2024 03:28:59
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,403
            CDSs (total)                      :: 5,284
            Genes (coding)                    :: 4,970
            CDSs (with protein)               :: 4,970
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 314
            CDSs (without protein)            :: 314
            Pseudo Genes (ambiguous residues) :: 0 of 314
            Pseudo Genes (frameshifted)       :: 91 of 314
            Pseudo Genes (incomplete)         :: 226 of 314
            Pseudo Genes (internal stop)      :: 46 of 314
            Pseudo Genes (multiple problems)  :: 50 of 314
            Pseudo Genes (short protein)      :: 5 of 314
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP089140.1.
            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..3397
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="XD35"
                     /db_xref="taxon:562"
                     /plasmid="pXD35007"
                     /geo_loc_name="China: Henan"
                     /collection_date="2019-10"
     gene            565..765
                     /locus_tag="K0768_RS03330"
                     /old_locus_tag="LS330_03330"
                     /old_locus_tag="LS330_RS03330"
     CDS             565..765
                     /locus_tag="K0768_RS03330"
                     /old_locus_tag="LS330_03330"
                     /old_locus_tag="LS330_RS03330"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001558245.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="antitoxin VbhA family protein"
                     /protein_id="WP_061585996.1"
                     /translation="MTDDRTLQLRLTGFRKAEASLRLEGMDPSGTPLYESVKTRILSGD
                     ITFDEGRTEIRAHYQKRANSN"
                     /name="antitoxin VbhA family protein"
     gene            complement(1515..1979)
                     /locus_tag="K0768_RS03335"
                     /old_locus_tag="LS330_03335"
                     /old_locus_tag="LS330_RS03335"
     CDS             complement(1515..1979)
                     /locus_tag="K0768_RS03335"
                     /old_locus_tag="LS330_03335"
                     /old_locus_tag="LS330_RS03335"
                     /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_061583928.1"
                     /translation="MEDKNNLSSEVKNHVSKWGKTNISAGWTIIPNALLENQSRLGLSC
                     IDTMVLINLIMHWWEKDNPPRPSKKRLANMLGVSLKTVQRSFIHLEQCGAIKRIPRYKE
                     GKDNARTTNHYDLNGLVDLLEGFSKELIEEREANRKSEVNRPKKRGNPKS"
                     /name="hypothetical protein"
     gene            2219..2827
                     /locus_tag="K0768_RS03340"
                     /old_locus_tag="LS330_03340"
                     /old_locus_tag="LS330_RS03340"
     CDS             2219..2827
                     /locus_tag="K0768_RS03340"
                     /old_locus_tag="LS330_03340"
                     /old_locus_tag="LS330_RS03340"
                     /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_063859057.1"
                     /translation="MAKCLLVKVRRETSVAVFRQCEIREKYLAIYKESFDEVITYLEKA
                     GALEPGVLRLTTIDDNAIRAWKSQWKGRSRKHAHGAWDWQNLVSKRARSCKRFDVAVWG
                     EDVLCGLSVGKLTRGKKTVRMDYLEACPTAHPLEKRITMIVVAVALSVAKKVGAQHVAI
                     FNPIKDKEEKVLKHYQSYGFTQRMLYGRFLKNVLYKEVV"
                     /name="hypothetical protein"
     gene            complement(2831..3001)
                     /locus_tag="K0768_RS03345"
                     /old_locus_tag="LS330_03345"
                     /old_locus_tag="LS330_RS03345"
     CDS             complement(2831..3001)
                     /locus_tag="K0768_RS03345"
                     /old_locus_tag="LS330_03345"
                     /old_locus_tag="LS330_RS03345"
                     /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_153449163.1"
                     /translation="MSYVSERKSELVKAQQRKMDPSSPNSAPINQGLMDFILLAMKVDD
                     GFVQRGRIHGA"
                     /name="hypothetical protein"
     Typing          complement(3..514)
                     /name="rep_cluster_2324"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.38"
                     /coverage="92.0"
                     /evalue="0.0"
ORIGIN
        1 ctgaacgggg agttcgtgca tacagcccag cttggagcga accacctaca aggaacccag
       61 ttgcacgggt aggaatgaga aaacgccacc ttacggcgga ctgcaacggg taaacctcag
      121 ggtgggaaca ggagagcgca cgagggagcg acccatcgga aacggtgggg atctttaagt
      181 cctgtcaggt ttcgccactt ctgatttgag cgccggaaat cacctgattt ctgtgaagct
      241 tgtcaggagg gcgaagccta tggaaaaccg gcaatcccca gaacctcctt atggccttct
      301 gcctgagcag gtaacgctcg ccgcagtgtc atgaccgaac gaagtgagcg aatgaccgag
      361 gaagcgtaat gtctgtaatg ctgaacaggg atcgtgtcgc tcggtacaca cgtttcctcc
      421 ctgattacac acccggctgc aacagtttcc tgtcgttttc cacttttccc tgcacagcta
      481 tacaacggca acatccgggc aggacatgta aagttagcta actttacgcc tgccttattc
      541 gcatgactgc tcaaaggaaa aaccatgact gatgatcgga cactgcaact gcgcctgaca
      601 gggttccgta aagcggaggc ctctctcagg cttgaaggga tggatccatc aggaaccccg
      661 ctttatgaat cggtaaagac aaggattctt tccggtgaca tcaccttcga tgaaggccgc
      721 actgagatac gggctcatta ccagaagcgg gcgaacagta actgacgcgg acaggaaatg
      781 ttttgtggcc accgccgctg cgccggcgcc acaaaatggc gggacaagat gtgtttttgg
      841 agtaccgccg gcactccaga atgtttcatc aggccccgcc cgataccctg aatttcgtac
      901 gtacgaaatt tcgctgctgt tcagatcgag agcaggattc gcaaattgct ggcgtttgca
      961 cccactgtaa atctgccgcg cctggcggct tggccaacgc ttcacgaacg cacagtaaac
     1021 tgcgcactcg ttcaccgtta ccagaaaggc cattgcggga ataattcttt cagtcgttct
     1081 acgagatcaa gcagctcatt catgaccttc agcatgacgc ttatcagttt caaaaattta
     1141 ggcatataaa aatttcctgt acggagttgg gtctggatca ggaaattagg gactttgtaa
     1201 ttttcagcgg tagaaaaatc agtttttcta aaaaaatttt ttaggcggcg aaaagtgaag
     1261 taatgagcac tgcttcgtgc tgaaaatgag gctcaggcag gtgttttgca gcgaaggcgc
     1321 gcgtcattca ctctcgtgca tagccatgca gcggcctaaa aatcatcagg ggcgtttttc
     1381 aggagtatgg acagggaaag gtgccggaaa cggcccggac gccccaggat cgcgctgagg
     1441 ggctctcagg gggtgcgggc aagagatgtt atggtaaatt ggactctcta caggagagtg
     1501 tgtttgtcag cctattaact tttcggatta ccgcgcttct taggtctatt aacttcactt
     1561 tttcgattcg cctctctttc ttcgataagc tctttcgaaa aaccttccag caggtctacc
     1621 agtccgttca gatcgtaatg gtttgttgtt ctggcattgt ctttcccttc tttgtatcga
     1681 ggtatccgct tgatggcacc acactgttcc aaatgaataa aacttctttg aacggttttt
     1741 agtgaaacgc ccagcatgtt cgccagtctc tttttcgaag gtcttggggg gttatctttt
     1801 tcccaccaat gcattatgag gtttatgaga accatcgtat caatacagct aagacccaac
     1861 ctggactgat tttccagtaa ggcatttggg ataatcgtcc atcctgcaga aatgtttgtc
     1921 ttcccccact tgcttacgtg gttctttact tcgctcgaca ggttattttt gtcttccata
     1981 aaacatgcat cctgtggtca tctgaggcta gagggcattt tatatattga acgttttacc
     2041 gttcaccttg cgtcattgtc ttaacgtatt gtcccactat atctttttct gtgtggtcaa
     2101 atcagaccgt accctatggt ttttaaagtc cacagggtgg ggtttaaatg taccatagga
     2161 tatggtcttt gttgaccact aaccaaaatg ttagcaaatg atttaaagtg gtttttttat
     2221 ggcaaaatgt ttactggtca aggtcaggag ggagacgagc gtggcggttt ttagacaatg
     2281 cgaaattaga gaaaaatatc tcgcgattta caaagagtca ttcgatgaag ttataactta
     2341 tcttgagaag gcaggtgctt tagagcccgg cgttttaagg ctcactacaa tcgatgacaa
     2401 tgctattcgt gcatggaaga gccaatggaa aggcaggtct cgtaagcacg ctcatggtgc
     2461 ttgggattgg cagaaccttg tatcaaagag agctcgttct tgtaaaagat ttgatgtggc
     2521 tgtttgggga gaggatgtgc tttgtgggct ttcagttgga aagctaaccc gtggtaaaaa
     2581 gacagttaga atggattatc tagaggcttg tccaacagct catccgttgg agaaacgaat
     2641 cacaatgatt gtggttgctg tggctctgtc agtagctaaa aaagtagggg cacagcacgt
     2701 agccatattc aacccgataa aagacaaaga agaaaaagtg ttaaaacact accagtctta
     2761 cgggtttaca caaagaatgt tgtatggacg ctttttgaaa aacgtgctgt acaaagaagt
     2821 tgtttgatag ctatgcgccg tgaatacgac cacgttgaac aaagccgtca tctactttca
     2881 tagcaagcag gatgaagtcc ataagaccct gattgattgg agctgaatta ggagaggatg
     2941 gatccatttt gcgttgctgt gcctttacca gctcactttt gcgctcagat acataactca
     3001 tcttgtgact ctctgtcttg tatggggatg tagacactat aacaagtgga taaaaaaata
     3061 acgagatctc tatattttca aaaagagatg actgttgttg actcgcctct tctgcaaagc
     3121 gtactctttt ctctcaaaag aaaaaaaccg cctttgcggg gcggtttttt tccagttcat
     3181 tgagtttgcg gctctttgaa cctaggtaac agtcttgtgc gagacgtgtc accaaatctg
     3241 tccttccagt gtagctgtag tcaggcttta acttcaagaa ctctcgatac acctctcgca
     3301 ctcactgcta ccaatggcta ccgccagtgg cgctttgtcg tgtctttcag ggttggattc
     3361 aagagtacag ttacctgata aagacgtggt agtcggg
//
