LOCUS       NZ_CP047008             4505 bp    DNA     circular CON 19-JUN-2023
DEFINITION  Escherichia coli strain J-8 plasmid p1, complete sequence.
ACCESSION   NZ_CP047008
VERSION     NZ_CP047008.1
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 4505)
  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  JOURNAL   Unpublished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 4505)
  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
            CP047008.1.
            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..4505
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="J-8"
                     /isolation_source="intestinal and liver"
                     /host="chicken"
                     /db_xref="taxon:562"
                     /plasmid="p1"
                     /geo_loc_name="China:Yangling"
                     /lat_lon="34.16 N 108.02 E"
                     /collection_date="2017-04-14"
                     /genotype="ST156"
     gene            join(4351..4505,1..37)
                     /locus_tag="GQF94_RS25135"
                     /old_locus_tag="GQF94_25095"
     CDS             join(4351..4505,1..37)
                     /locus_tag="GQF94_RS25135"
                     /old_locus_tag="GQF94_25095"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /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_000165987.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGETL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            697..810
                     /locus_tag="GQF94_RS25550"
     CDS             697..810
                     /locus_tag="GQF94_RS25550"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001427889.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLTPLAAAIGN"
                     /name="hypothetical protein"
     gene            complement(1439..1792)
                     /locus_tag="GQF94_RS25140"
                     /old_locus_tag="GQF94_25100"
     CDS             complement(1439..1792)
                     /locus_tag="GQF94_RS25140"
                     /old_locus_tag="GQF94_25100"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001275822.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000005489.1"
                     /translation="MSETVQIESFNAEFLTKQKLHDLIFYRKSFDITNVNDISETVKIV
                     EYVIEHQQKKLTCRVYTEYRSTAVAGSLWSPTALLGAVSAAAIGVHNLATWNPDYEIGK
                     NYVKRTISVRYKK"
                     /name="hypothetical protein"
     gene            complement(2526..2759)
                     /locus_tag="GQF94_RS25145"
                     /old_locus_tag="GQF94_25105"
     CDS             complement(2526..2759)
                     /locus_tag="GQF94_RS25145"
                     /old_locus_tag="GQF94_25105"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /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_141012358.1"
                     /translation="MTELETHLLNALEQLQQDYMQRLNEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSGQTERLSQLYSENWR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2766..3284)
                     /locus_tag="GQF94_RS25150"
                     /old_locus_tag="GQF94_25110"
     CDS             complement(2766..3284)
                     /locus_tag="GQF94_RS25150"
                     /old_locus_tag="GQF94_25110"
                     /inference="COORDINATES: protein motif:HMM:NF016710.2"
                     /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_012564915.1"
                     /translation="MSNLLRTGAEFEKKLKERAESTEKMLNDEFSRLGESVSEAVTSNE
                     TKIKDAIALFTTSTEESLKKHREGVKEAMMQHRKDMLKLAGSSGMRLLGIVFLLFTASG
                     GTLWYLGGRIQTNLEEIRVQEETLRKLNAKTWGVEFVQGGGRKFLVIPQGMSAEVTHYQ
                     GKDWIQLTE"
                     /name="MbeB family mobilization protein"
     gene            complement(<3322..3753)
                     /locus_tag="GQF94_RS25555"
                     /pseudo=""
     CDS             complement(<3322..3753)
                     /locus_tag="GQF94_RS25555"
                     /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(3962..4285)
                     /locus_tag="GQF94_RS25160"
                     /old_locus_tag="GQF94_25120"
     CDS             complement(3962..4285)
                     /locus_tag="GQF94_RS25160"
                     /old_locus_tag="GQF94_25120"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000955993.1"
                     /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_212040663.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRICLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIERELRSLRQVVREQGAR
                     DDC"
                     /name="MobC family plasmid mobilization relaxosome protein"
     Typing          complement(116..195)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.765"
                     /coverage="94.0"
                     /evalue="8.500000000000001e-33"
     Typing          224..769
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.247"
                     /coverage="98.0"
                     /evalue="0.0"
     Typing          complement(2429..3972)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.058"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(3969..4318)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.308"
                     /coverage="99.0"
                     /evalue="2.69e-64"
ORIGIN
        1 cctcgcacgc ttcggggatg acggtgaaac cctctgacac aagcagctcc cggagacgct
       61 cacagcttgc ctgtgagagg atgccgggag cagacaagcc cgtcagggcg cgtcaggggg
      121 tttcggggcg aagccctgaa ccagtcacgt agcgatagcg gagtgtatac tggcttaact
      181 atgcagcatc agtgcgaatt gtatggaaag cgcaccatgt ccggtgtgaa atgccgcaca
      241 gatgcgtaag gagaaaatgc acgttccggc gctcttccgc ttcctcgctc actgactcgc
      301 tacgctcggt cgttcgactg cggcgagcgg tgtctgctca ctcaaaagcg gagatgcggt
      361 tatccacaga atcaggggat aaagccggaa agaacatgtg agcaaaagac caggagccga
      421 aagaaggccg cgccactggc gtttttccat aggctccgcc cccctgacga gcatcacaga
      481 aatcgacgct caagtcagag gtggcgaaac ccgacaggac tataaagata ccaggcgttt
      541 ccccctggtg gctccctcgt gcgctctcct gttccgaccc tgccgcttac cggatacctg
      601 tccgcctttc tcccttcggg aagcgtggcg ctttctcata gctcacgctg ttggtatctc
      661 agttcggtgt aggtcgttcg ctccaagctg ggctgtgtgc acgaaccccc cgttcagccc
      721 gaccgctgcg ccttatccgg taactatcgt cttgagtcca acccggtaag acacgactta
      781 acgccactgg cagcagccat tggtaactga tttagaggag ttggtcttga agttatgaac
      841 cagttaaggc taaactgaaa agacagcttt tggtgactgc gctcctccaa gccagttacc
      901 ttcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgttgg tagcggtggt
      961 ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga ggatcctttg
     1021 aactttttgt gatccgcgtc caaaatggaa ttcctcacgc taagagaatt gagttgaacg
     1081 agtagataca tccagggcag ttaattcact gaatgtaaag gctgtacgaa atgatctgac
     1141 tgggctgcgt ttgggaaacg tacaatattg tacggttgcg ttatcgcgct cgggtgtact
     1201 cccgtgctat acggcgtttt cagaggattt gacctcaatc ggataatcta aatgcaatac
     1261 tgcaatagct ataacttaaa agggatagcc gttgacgcaa aatcaatctg ttatgcatat
     1321 ctattggtta aataatgcgc ttaacgttca aaattttccg atctccagac tgcccccgtt
     1381 cagctcgcat aggaattatg ggagaggatt ttggctgaac cggacagata taaacccgtt
     1441 actttttata ccttacagat atggttcttt tgacgtaatt cttaccaatt tcatagtccg
     1501 ggttccatgt cgccagatta tggacaccga ttgcggcagc gctcacagct cccagaagtg
     1561 ctgttggtga ccatagggag cctgccaccg cagtgcttct gtattcggtg tatacgcggc
     1621 aggttaattt cttctgctga tgttcaatca catactccac tattttgacg gtttcactga
     1681 tgtcgttaac attcgtgata tcaaaacttt tgcggtaaaa aatcaggtcg tgcagtttct
     1741 gtttggtcaa aaattctgcg ttgaacgact caatctgtac tgtttctgac atccgttgtt
     1801 cctctctttc ttggagtctg tgaatttccc taggcacgcg ccttacggtc aaacgttgca
     1861 ctttttcagg ggcagtgtat gtcagaaaag aatatattga cctgtataaa cgatcaataa
     1921 taagaaattg atcgtcttaa ctgtaagcgt aaaccgactg ccgtatgtgg gggcggtttg
     1981 ggaaacggaa attattgtac gttaggggca ttttttaacc gatactgata agtaactgat
     2041 tgattcatcg tgatcagcta tcgcctttaa gttattgctt ttctcttatc gcatttaggt
     2101 tatctcatgt ccctaaaggt ctgccaaaca ccgtatagcg tccgagcgcg ataacgcaac
     2161 cgtacaatat tgtacgtttc ccaaccacag cgccgccgat gagggtgatt taacataacc
     2221 ctgtattgta cgcaccgcta aaacgcgttc agcgcgatca cggcagcaga caggtaaaaa
     2281 tggcaacaaa ccacccgaaa aactgccgcg atcgcgcctg ataaatttta accgcatgaa
     2341 tacctatgca accagatggt gcggactaca ttagtccgtc aaaatctact gaacctgcca
     2401 ttttttatag tttcgccatc acagcgacaa cgaaggacca tccagtgtgc gttcctgtat
     2461 ttccagctgg cgttcccgtt ccagggataa cgcatgttcg cgctcctgta ttaaccgttc
     2521 ctctcttatc tccagttctc gctgtataac tggctcaagc gttctgtctg cccgctcaag
     2581 tgctgcacct gctgactcaa ctgcatgacc cgctcgttca gcatcgcgtt gtcccgttgc
     2641 gtaagcgaaa acatcttctg caattccacg aaggcgctct cccattcgtt cagccgctgc
     2701 atatagtcct gttgcagctg ctctaaggcg ttcagcaaat gtgtttccag ctctgtcatt
     2761 ccgtatcact ccgtcagttg tatccagtcc ttcccctgat agtgcgtcac ctctgctgac
     2821 atcccttgcg gaatgaccag aaattttctt cccccgccct gaacaaactc cacaccccat
     2881 gtcttcgcgt tcagtttccg caatgtctct tcctgtaccc tgatttcttc caggttcgtc
     2941 tgtatcctcc cgccgagata ccagagcgtc ccgccactcg cggtaaacag gagaaagact
     3001 atccccagca acctcatgcc cgaactccct gccagcttta acatgtcctt ccggtgctgc
     3061 atcatcgcct ctttcacccc ttcccggtgt tttttcagcg attcctctgt cgacgttgtg
     3121 aacagggcta tagcgtcttt gattttcgtc tcgtttgagg tcacagcctc gcttacagat
     3181 tcgccgagcc tgctgaattc gtcgttcagc attttctctg tagattcggc tctctctttc
     3241 agctttttct cgaactccgc gcccgtccgt aaaagattgc tcataaaacg ctcctttcag
     3301 tctgatattc ctcccgccgt tcgggtctgc aatgctgata ctgcttcgcg tcaccctgac
     3361 cacttcaagc cccacctctg tgagcgcctg aatcacatcc tgacggcctt ttatctctcc
     3421 ggcatggtaa agcacctcca ggcctcgtgt aacgctctca gcaagcgcct gtttcgtttc
     3481 cggcaggtta tcagggagtg tcagcgtccg gcggttctct ggggcgttgg ggtcatgcag
     3541 cccgtagtgg tgattcacca gtgtctgcca ggcatcaatt ctcggcctgt ctgcccggtc
     3601 gtagtacggc tggaggcgtt ttccggtctg tagctccatg ttcggaatga caaaattcag
     3661 ctcaagccgc cccttatcct ggtgctccac ccacagaatg ctgtactgat ttttttcgag
     3721 accgggcatc agtacgcgct caaagctctc catcactttt tcacgtcctc ccggcggcag
     3781 ttccttctct gcaaacgaca gaacaccgga cgtgtatttc ttcgcaaatg gcgtggcatc
     3841 gatgagttcc cggacttctt ccggattacc ctgaagcacc gttgcgcctt cccggtttcg
     3901 ctcccttccc agcaggtaat caaccggacc actgccaccg ccttttcccc tggcatgaaa
     3961 tttaacaatc atcccgcgct ccctgttccc tgacgacctg ccgtaagctg cgcaactctc
     4021 tctcgatggc catcagtgcg gccaccacct gaacccggtc accggaagac cattgcccgc
     4081 tgttcacctt cctcgccgtc tgattcaggt tattcccgat ggcagccagc tgacgcagta
     4141 acggcggtgc cagtgtcggc agcttcccgg aacgggcaac cggctcaccc aggcagatcc
     4201 gccgcatcca taccgccagc tgtttaccct cacagcgttc cagtaaccgg gcatgttcat
     4261 catcagtaac ccgtatcgtg agcatcctct cgcgtttcat cggtatcatt acccccatga
     4321 acagaaatcc ccccttacac ggaggcatca gtgaccaaac aggaaaaaac cgcccttaac
     4381 atggcccgct ttatcagaag ccagacatta acgctgctgg agaagctcaa cgaactggac
     4441 gcggatgaac aggcagacat ctgtgaatct cttcacgacc acgccgatga gctttaccgc
     4501 agctg
//
