LOCUS       NZ_CP047009             3373 bp    DNA     circular CON 19-JUN-2023
DEFINITION  Escherichia coli strain J-8 plasmid p2, complete sequence.
ACCESSION   NZ_CP047009
VERSION     NZ_CP047009.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13563033
            Assembly: GCF_018279085.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3373)
  AUTHORS   Liu,Z. and Chen,P.
  TITLE     Emergency of NDM-5-harbouring plasmid and mcr-1-harboring chromosome
            in a clinical isolate of Cronobacter sakazakii
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3373)
  AUTHORS   Liu,Z. and Chen,P.
  TITLE     Direct Submission
  JOURNAL   Submitted (17-DEC-2019) College of Veterinary Medicine, Northwest
            A&F University, No. 3 Taicheng Road, Yangling, Shanxi 712100, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler Version v. v0.48
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 80.0x
            Sequencing Technology             :: Illumina HiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/19/2023 03:21:11
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,090
            CDSs (total)                      :: 4,967
            Genes (coding)                    :: 4,755
            CDSs (with protein)               :: 4,755
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 92
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 212
            CDSs (without protein)            :: 212
            Pseudo Genes (ambiguous residues) :: 0 of 212
            Pseudo Genes (frameshifted)       :: 81 of 212
            Pseudo Genes (incomplete)         :: 141 of 212
            Pseudo Genes (internal stop)      :: 41 of 212
            Pseudo Genes (multiple problems)  :: 47 of 212
            Pseudo Genes (short protein)      :: 2 of 212
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP047009.1.
            Bacteria and source DNA available from xiaoping song , Traditional
            Chinese Veterinary Medicine Lab,College of vetrinary Medicine,
            Northwest A&F University.
            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..3373
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="J-8"
                     /isolation_source="intestinal and liver"
                     /host="chicken"
                     /db_xref="taxon:562"
                     /plasmid="p2"
                     /geo_loc_name="China:Yangling"
                     /lat_lon="34.16 N 108.02 E"
                     /collection_date="2017-04-14"
                     /genotype="ST156"
     gene            complement(185..418)
                     /locus_tag="GQF94_RS25165"
                     /old_locus_tag="GQF94_25125"
     CDS             complement(185..418)
                     /locus_tag="GQF94_RS25165"
                     /old_locus_tag="GQF94_25125"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137389.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_000137389.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHEVTQRNNA
                     ILNERVVILSQQVQRLAGQVDRLSRLFIANNS"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(425..985)
                     /locus_tag="GQF94_RS25170"
                     /old_locus_tag="GQF94_25130"
     CDS             complement(425..985)
                     /locus_tag="GQF94_RS25170"
                     /old_locus_tag="GQF94_25130"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000067488.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_000067487.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKKQLDTLSTTVSMQFSTTEAELSRQQKKLLWRVIKGRILFPALTA
                     LSVTGGIFLGCWGLMEWQESKIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            complement(<1014..1454)
                     /locus_tag="GQF94_RS25560"
                     /pseudo=""
     CDS             complement(<1014..1454)
                     /locus_tag="GQF94_RS25560"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(1663..1986)
                     /locus_tag="GQF94_RS25180"
                     /old_locus_tag="GQF94_25140"
     CDS             complement(1663..1986)
                     /locus_tag="GQF94_RS25180"
                     /old_locus_tag="GQF94_25140"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_001696562.1"
                     /translation="MLTIRVTDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     APPLLRHLAAIGNNLNQTARKVNSGQWSSIDRVHVVAALMAIEGELRQLRQAVREQGVR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2050..2241
                     /locus_tag="GQF94_RS25185"
                     /old_locus_tag="GQF94_25145"
     CDS             2050..2241
                     /locus_tag="GQF94_RS25185"
                     /old_locus_tag="GQF94_25145"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165979.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_062914769.1"
                     /translation="MTKQEKTALNMARFIRNQTLTLLEKLNDLDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(2323..2403)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="86.585"
                     /coverage="93.0"
                     /evalue="4.04e-16"
     Typing          complement(103..1673)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.628"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ggatgttgca tagctatgca caaatacggc acacgatttg tttcgctcgc cccagccgtc
       61 gaacgggtca aaatggcaag atttcgtcac ttctccggtc acatctccat tgatggccca
      121 ctccgaaccc gtgccgcgcg ttcctgtacc tcatgtctgt accgggcacg ctcctgttca
      181 tcccttagct gttgttcgcg ataaataacc gactcaagcg atccacttgc ccggctaatc
      241 tctgcacctg ctgactcaat atcacgacgc gctcgttcag tatcgcgttg ttccgttgcg
      301 taacctcgtg catcttctgc aattccgcga aggcgctctc ccactcgttc agccgccgca
      361 tatagtcctg ttgcaaatgc tctaaggcgt tcagcaaatg cccttccagt tccgtcatac
      421 tcgtttactc cctgaccagc ctcacggcgt tcttgtcgcc caccgtccag gtgttttccc
      481 ctttcacccc gtccggcaac accagaaatt tcccgttctc gccattgacg aacgtcaccc
      541 cccaggtttt tgcctcgagt ttcgccagcg tgttttcctg ctctctgata gtcaggatat
      601 ttttcgcaat cttgctttcc tgccactcca tcagccccca gcaccccagg aaaatcccgc
      661 ccgtgacgct gagcgcggtc agcgccggaa acagtatccg ccctttgatc acccgccaga
      721 gcagtttttt ctgctgccgg gacagttcgg cctctgtggt gctgaactgc atgctcacgg
      781 tggtgctcag cgtatccagt tgctttttca cggatgttgt atgttcgctg atagcgtctc
      841 tgattttctg cctgtttaag ctcaatgcct tgtctacaga ctcttcgagc ttcctgaact
      901 cgctgttcag catgttctcg gtagaagcgg ctcgctcttt cagtttcttc tcgaagtctg
      961 ttcccatttg taaaagattg ctcatacagc gcccccttta gcctgagatt ccgccccccc
     1021 tccgggtcgg caatactgat gctgcttttg gttgtcctca ccacctcaaa acctgccgct
     1081 gtaagcgcct ctgtgacatc ctgacgcgtt tttattgctc cggcatggta aagagcctca
     1141 agaccccgtg taatcgcttc tgcggcctcc tgtttcgctt ttggcagatt atttggcgtg
     1201 acaagcgtcc gtctgttctc cggtgcgttc gggtcacgca gcccgtaatg atgattaacc
     1261 agcgtctgcc aggcatttat cctcggcctg tccgcacggt cgtagtacgg ctggaggcgc
     1321 ttaccgctct gtagctccat gttcgggatg acaaaattca gttcgagccg ccccttatcc
     1381 tggtgttcca cccagagaat gctgtactgg tctttttcga gaccgggcat aagaacacgc
     1441 tcaaagctcg tcatcactct ttcgcgttca cccggtggta gctccttctc cgcgaacgac
     1501 agaacgcctg acgtgtattt cttcgaaaat ggcgtggaat caatgagttc ccgcacttct
     1561 tccgggttac cccggagcac cgttgcgcct tcgcggttac gctcccgccc cagcaggtaa
     1621 tcgaccgggc cacttccacc gcctttcccc ctggcatgaa atttaactat catcccgtac
     1681 cccctgttcc ctgacagcct gccgcaactg gcgcaattca ccctcgatgg ccatcagtgc
     1741 ggccaccaca tgaacccggt caatcgaaga ccactggccg ctgttcacct tccgggctgt
     1801 ctggttcagg ttgttcccga tggcagccag atgccgcagc aatggcggtg ccagtgtcgg
     1861 cagttttcct gtgcgtgcaa ccggctcccc cagacagacc cgccgcatcc attccgccag
     1921 tcgtttaccc tcgcagcgtt ccagtaaccg ggcgtgctcc tcatcggtaa cccgtatcgt
     1981 gagcatcttc tcgcgtttca tcggtatcat tccccctaac aaatccccca tacaaggagc
     2041 cttaagacca tgaccaaaca ggaaaaaaca gcccttaaca tggctcgctt tatcagaaac
     2101 cagacgctaa ccctgctgga aaaactcaac gatctggacg cggacgaaca ggcagacatc
     2161 tgcgaatcac ttcacgacca cgccgacgaa ctctaccgca gttgcctcgc acgcttcggc
     2221 gatgacggtg aaagcaactg aaacatgcag ctcccggaga cgttcacagc ttgcctgtga
     2281 gcggatgccg ggagcagaca agcccgccag ggcgcgtcag tgcgggtgtc ggggcgcagc
     2341 cctgacccag ttcacagagc gatagcgatg tgtatactgg ctttcctcat tttgcatcgg
     2401 tgcagagtgg atgggaagtg caccatgtca ggagtaaaaa gccgcacaga tgcgtaaaaa
     2461 cagcgcgccc gataaacaac acacacgcgg acactggcac aggcgcgtaa gtgcacaatg
     2521 cttgcctctg tgactcttcc gcttcctcgc ccactcgctc actacgttcg gtcgctgggg
     2581 ctgcggcgag cggtgggatc actctcgttg tgatgcagat ccgttttttt ttttgcactg
     2641 gagttatcag gagtagcggt gcacatggga tcgtgcgata tgctggatgg tggaaggtcg
     2701 gagggaacgg caacaactca cccctcccag tgaagggacg ggtagtttgc cgctctcgat
     2761 atgccggacg gagccaaggc catcgatcac ggggcgcgtc agtggaagaa cccgcgcctg
     2821 cgtgacgtat gcgtcttcgc cgcaccatct cacccgtcac gccaccacat accgggaact
     2881 gccgccaagg tctaactcaa ccaatctagc cgcgctacat acggtttttg tggcaactca
     2941 tcaggtgtcc gctgtcgatg aaactctctg cgccggtagc ggaactctca cgcgtgcggt
     3001 cgccgtcgtc acagctcccc caaccgcaaa cgattctcgc aaatacgcaa gtatctgcaa
     3061 aaacaggttt ttttcggggt tcctgggaga ctgtgctgtt gaaaaactct tgaagaatac
     3121 agaaggctca tgcaaactga atgaactggt ttctgttgtg gatctcaaca gtttccacag
     3181 gaacattgag gaggtcagag acctcaatga acccgaaaca gctcgccttc ctggcgagct
     3241 gttttcgttc tacgcccacc gacgaaagat cgcaagtgca ataacgagat ttttcacgtc
     3301 tttacgctca aaaagtaaaa aaaccatgtt ttcccctggc tgaatcccca aaaacgcgtg
     3361 aaatgcgttt tca
//
