LOCUS       NZ_CP047007             5772 bp    DNA     circular CON 19-JUN-2023
DEFINITION  Escherichia coli strain J-8 plasmid p0, complete sequence.
ACCESSION   NZ_CP047007
VERSION     NZ_CP047007.1
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 5772)
  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  JOURNAL   Unpublished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 5772)
  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
            CP047007.1.
            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..5772
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="J-8"
                     /isolation_source="intestinal and liver"
                     /host="chicken"
                     /db_xref="taxon:562"
                     /plasmid="p0"
                     /geo_loc_name="China:Yangling"
                     /lat_lon="34.16 N 108.02 E"
                     /collection_date="2017-04-14"
                     /genotype="ST156"
     gene            complement(join(5118..5772,1..236))
                     /locus_tag="GQF94_RS25095"
                     /old_locus_tag="GQF94_25055"
     CDS             complement(join(5118..5772,1..236))
                     /locus_tag="GQF94_RS25095"
                     /old_locus_tag="GQF94_25055"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015376142.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_021512263.1"
                     /translation="MPDLEIMPLQSPDFYKKNKRAIYEGYKCNCTKDWKKEDRFVVYKA
                     DCTGIDEIINTEISDDNIDTVIKLAEKYTSDKIIISGGHTVVNLNDRFSVSNEVEKSAK
                     FCIDYIIKSTHELNIKPDFLMEINDFYMEKSNGEDIDGGNIYRKLATSPYIIPEVINNY
                     IIEKQNQHNIKINCFYVSEKNMADRFKRHIKRKEKEKPFFKENNSVFMNVDGSSFEVIK
                     NNKPTCAAGNAATFRSIRYKISSNKTFDNYTSHIGVFPLCSMANVINGYKAAASFYSNF
                     NLPCLLIFFGTSCFK"
                     /name="hypothetical protein"
     gene            413..501
                     /locus_tag="GQF94_RS25100"
                     /old_locus_tag="GQF94_25060"
     tRNA            413..501
                     /locus_tag="GQF94_RS25100"
                     /old_locus_tag="GQF94_25060"
                     /product="tRNA-Lys"
                     /inference="COORDINATES: profile:tRNAscan-SE:2.0.12"
                     /note="Derived by automated computational analysis using
                     gene prediction method: tRNAscan-SE."
                     /anticodon=(pos:447..449,aa:Lys,seq:ctt)
                     /name="tRNA-Lys"
     gene            complement(1565..1756)
                     /locus_tag="GQF94_RS25105"
                     /old_locus_tag="GQF94_25065"
     CDS             complement(1565..1756)
                     /locus_tag="GQF94_RS25105"
                     /old_locus_tag="GQF94_25065"
                     /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_000165985.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1820..2143
                     /locus_tag="GQF94_RS25110"
                     /old_locus_tag="GQF94_25070"
     CDS             1820..2143
                     /locus_tag="GQF94_RS25110"
                     /old_locus_tag="GQF94_25070"
                     /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_001430281.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGRLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2352..>2783
                     /locus_tag="GQF94_RS25545"
                     /pseudo=""
     CDS             2352..>2783
                     /locus_tag="GQF94_RS25545"
                     /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            2821..3339
                     /locus_tag="GQF94_RS25120"
                     /old_locus_tag="GQF94_25080"
     CDS             2821..3339
                     /locus_tag="GQF94_RS25120"
                     /old_locus_tag="GQF94_25080"
                     /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_001749510.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFRKLGESVSEAVTSNE
                     TKIRDAIALFTASTEKSLEKHREGVKEAMMQHRKDVLKLAGNTGMMLLGIVFLLFTASG
                     GTLWYLGGRIQTNLEEIRKQEETLQKLNAKTWGVEFVQDGNRKFLVLPYGKSAEVIPFQ
                     GKEWVHLKE"
                     /name="MbeB family mobilization protein"
     gene            3346..3579
                     /locus_tag="GQF94_RS25125"
                     /old_locus_tag="GQF94_25085"
     CDS             3346..3579
                     /locus_tag="GQF94_RS25125"
                     /old_locus_tag="GQF94_25085"
                     /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_004026237.1"
                     /translation="MTELEIHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSEQTERLSQLYSENWR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(3973..5106)
                     /locus_tag="GQF94_RS25130"
                     /old_locus_tag="GQF94_25090"
     CDS             complement(3973..5106)
                     /locus_tag="GQF94_RS25130"
                     /old_locus_tag="GQF94_25090"
                     /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_072647583.1"
                     /translation="MKINSIQWPVTFFATSFGAGIFFLPQTVGPKVIGTHGTITILILS
                     SLVSLLGQFTFYRFILITDKKEYVSSAILFIGKKAANAISIAFLLSMLLIAIINITTMI
                     NIICFSLSLNGSERIFVSLIISATLGSSFIFFNSKIEHLASGIAFPSLLIVLFLSIYFY
                     SHPAHPHSTEIQNISTSNLLTLFPVVLFSFNFSPCIQRFAQNKKDTAGDLRFFMFGILL
                     ILIFISFIVFSLSNIFSPSDIKNMREINSDALSYSANVTKNSFVAYISILTMILITSGA
                     YTGTLTGVVDTIVSLGFKNKTLIVFVVSVITFIAGEANFEIIKVIAALSTPIIAITVFI
                     IPSAFFLKTNCNSIFRKIMMTLNLLIGIGICFLAIIL"
                     /name="hypothetical protein"
     Typing          1395..1480
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.701"
                     /coverage="100.0"
                     /evalue="1.86e-34"
     Typing          complement(825..1373)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.937"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2134..3683
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.183"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ataatcttgt ctgatgtgta tttttcggct agttttatta cagtatctat gttgtcatct
       61 gatatttctg tgtttattat ctcatcgatt cctgtgcaat ctgctttgta tacaacaaat
      121 ctgtcttctt ttttccagtc ttttgtacaa ttacatttat agccctcgta tattgctctt
      181 ttgttttttt tataaaaatc tggactttgt aagggcatta tttctaggtc tggcatagtt
      241 atgcttcctt tgtcacaaag aaaatatttt gctaattatg acttatacat atcaatgata
      301 gagatcatgt tagtgtttga tcattgatgt ctcctttatt tatgtgatgc gtctctattt
      361 tttctcttat agtgtcttgg atgttatttg ttaaatatgt attgtttttt gtggagaggt
      421 gggcgagtgg tctaagtcag ggctctcttg aggccatatg cgacaagcgt atcgtaggtt
      481 cgaatcctac cctctccgcc attttgttga tcgtttcccc caccatttgt tgaattgaga
      541 ggggttttga aaaaagatca aaggatcctc ttgagatcct ttttttctgc gcgtaatctg
      601 ctgcctgtaa acaaaaaaac caccgctacc aacggtggtt cgtttgccgg aatcaagagc
      661 taccaactct ttttcccgaa ggtaactggc ttggtggagc gcagatacca aatactgtcc
      721 ttctagtgta gcctcagtta ggccaccact tcaagaactc ttaatatctc aatccacctt
      781 gtccagttac caatggctgc tgccagtggc gttaaggcgt gtcttaccgg gttggactca
      841 agacgatagt taccggataa ggcgcagcgg tcgggctgaa cggggggttc gtgcacacag
      901 cccagcttgg agcgaacgac ctacaccgaa ctgagatacc aacagcgtga gctatgagaa
      961 agcgccacgc ttcccgaagg gagaaaggcg gagaggtatc cggtaagcgg cagggtcgga
     1021 acaggagagc gcacgaggga gcttccaggg ggaaacgcct ggtatcttta tagtcctgtc
     1081 gggtttcgcc acctctgact tgagcgtcga tttttgtgat gctcgtcagg ggggcggagc
     1141 ctatggaaaa acgccaccgg cgcggccttt tttcggggcc tcttttttgc tcacatgttt
     1201 tttccggcgt tatcccctga ttctgtggat aaccgtatat ccgtctttga gtgagctgat
     1261 accgctcgcc gcagccgaac gaccgagcgc agcgagtcag tgagcgagga agcggaagag
     1321 cgcctgatgc ggtattttct ccttacgcat ctgtgcggta tttcacaccg catatggtgc
     1381 actctcagta caatctgctc tgatgccgca tagttaagcc agtatacact ccgctatcgc
     1441 tacgtgactg ggtcagggct gcgccccgac acccgctaaa acctgctgac gcgccctgac
     1501 gggcttgtca gctcccggca tccgctcaca gacaagctgt gaccgtctcc gggagctgca
     1561 tgtgtcagag gttttcaccg tcatccccga agcgtgcgag gcagctgcgg taaagctcat
     1621 cggcgtggtc gtgaagcgat tcacagatgt ctgcctgttc atccgcgtcc agttcgttga
     1681 gcttctccag cagcgttaat gtctggcttc tgataaagcg cgccatgtta agggctgttt
     1741 tttcctgttt agtcactgat gcctccgtgt aagggggatt tctgttcatg gggtaatgat
     1801 accgatgaaa cgcgagagga tgctcacgat acgggttact gatgatgaac atgcccggtt
     1861 acttgaacgc tgtgagggta aacaactggc ggtatggatg cggcgggtct gcctggggga
     1921 gccggttgcc cgttccggga ggctgccgac actggcaccg ccgttactgc gtcagctggc
     1981 cgccatcgga aataacctga atcagacagc gaggaaggtg aacagcgggc agtggtcttc
     2041 cggtgaccgg gttcaggtgg tggccgcact gatggccatc ggggatgagc tgcgccggct
     2101 gcgtctggcc gtcagggaac agggggcgcg ggatgatagt taaatttcat gccaggggaa
     2161 aaggtggtgg cagtggtccg gttgattacc tgctggggag ggagcgtaac cgcgaaggcg
     2221 caacggtgct tcagggtaat ccggaagaag tccgggaact catcgatgcc acgccatttg
     2281 cgaagaaata cacgtccggt gttctgtcgt tcgcggagaa ggaactgccg ccgggaggac
     2341 gtgaaaaagt gatggcgagc tttgagcgtg tactgatgcc cggtctcgaa aaaaatcagt
     2401 acagcatcct gtgggtggag caccaggaca agggacggct tgagctgaat tttgtcattc
     2461 cgaacatgga gctacagacc ggaaaacgcc tccagccgta ctacgaccgc gcagacaggc
     2521 cgagaattga tgcctggcag acgctggtga atcaccatta cggactgcat gaccccaacg
     2581 ccccggagaa ccgccggacg ctgacccttc ctgataacct gccggaaacg aaacaggcac
     2641 ttgctgagag cgttacacgc ggtatagacg cactttacca tgccggtgag ataaaaggcc
     2701 gtcaggatgt gattcaggcg ctcacagagg cggggcttga agtggtcagg gtgacgcgaa
     2761 gcagtatcag cattgcagac ccgaacggcg ggaggaatat caggctgaaa ggagcatttt
     2821 atgagcaatc ttttacagac gggcgcggag ttcgagaaaa agctgaaaga gagagccgaa
     2881 tctacagaga aaatgctgaa cgacgagttc aggaagctcg gcgagtctgt cagcgaggct
     2941 gtgacctcaa acgagacgaa aatcagagac gctatagccc tgttcacagc ctcgacagag
     3001 aaatcgctgg aaaaacaccg ggaaggggtg aaagaggcga tgatgcagca caggaaggac
     3061 gtgttaaagc tggcagggaa tacgggcatg atgttactgg ggatagtctt tctcctgttt
     3121 accgcgagtg gcgggacgct ctggtatctt ggcggacgga tacagacgaa cctggaagaa
     3181 atcaggaagc aggaagagac attgcagaaa ctgaacgcga agacatgggg cgtggagttt
     3241 gtgcaggacg ggaacaggaa attccttgtc cttccgtacg ggaaatcagc ggaggtgatt
     3301 ccctttcagg ggaaagagtg ggtacatctg aaggagtgac acagagtgac agagctggaa
     3361 attcatttgc tgaacgcctt agagcagctg caacaggact atatgcagcg gctgagcgaa
     3421 tgggagagcg ccttcgtgga attgcagaag atgttttcgc ttacacaacg ggacaacgcg
     3481 atgctgaacg agcgggtcat gcagttgagt cagcaggtgc agcacttgag cgagcagaca
     3541 gaacgcttga gccagttata cagcgagaac tggagataag agaggaacgg ttgatacagg
     3601 agcgcgaaca tgtgttatcc ctggaacggg agcgtcagcc ggaaatacag gaacgcacgc
     3661 tggatggccc ttcgctggga tggtgaaacc atgaaaaatg gcagcttcag tggattaagt
     3721 ggggggaatg tggcctgtac catctggttg cataggtatt catacggtta aaatttatca
     3781 ggcgcgatcg cggcagtttt tcgggtggtt tgttgccatt tttacctgtc tgctgccgtg
     3841 atcgcgctga acgcgtttta gcggtgcgta caatattgtc gttatgttaa atggtttgga
     3901 tgatcccccc attttccaca tttggttgtg acgattaaga taaactcgtc agaatatttg
     3961 ggtgaggaat aatcataata tgatggctag gaagcatatt ccaataccta tgagcaggtt
     4021 caacgtcatc attatttttc taaaaatact gttacaattt gtttttaaaa agaatgctga
     4081 tgggataatg aatactgtta ttgctataat tggggttgat aatgcagcaa taacttttat
     4141 aatttcgaaa ttggcttcgc ctgctataaa tgtgataaca gatacgacaa aaacgattaa
     4201 tgttttgttt ttaaatccaa gggatactat tgtatcaaca acgcctgtta gtgtacctgt
     4261 atatgcaccg ctggtaatta aaatcatggt taatatggaa atgtaagcaa cgaaactatt
     4321 ttttgttacg ttggcgctat atgataatgc atcgctgtta atctcgcgca tgttttttat
     4381 gtctgaaggt gagaatatat tgcttaatga gaacacgatg aatgagataa atattaaaat
     4441 taatagtatc ccaaacatga aaaaacgtaa atcaccggct gtatcttttt tgttttgagc
     4501 aaagcgttgt atacatggtg aaaaattaaa actaaataaa acaactggaa atagagtaag
     4561 taaattactt gtactaatat tttgtatttc tgtagaatgt ggatgtgctg gatgtgaata
     4621 gaaatatata gataagaaca gtacaataag caaagatgga aatgctattc ctgatgcgag
     4681 atgctctatc tttgaattaa aaaagataaa agaagaacca agggttgcag aaataatcag
     4741 tgacacaaat attcgctctg aaccatttag acttaggcta aagcaaataa tatttatcat
     4801 tgttgttatg tttataattg ctattaacag cattgataat aggaatgcaa tactgatagc
     4861 atttgcggct ttttttccga taaataatat ggcagaacta acgtattctt ttttgtctgt
     4921 aattaaaatg aatctataaa atgtaaattg ccctaataaa gataccaaag atgataaaat
     4981 cagtattgtt attgttccgt gagttcctat gactttgggg cctacagtct ggggtaggaa
     5041 aaaaatccct gccccaaatg atgttgcaaa gaatgttact ggccattgga tgctatttat
     5101 cttcattttt gaacctttca tttgaagcat gatgttccaa agaaaataag taaacatgga
     5161 agattaaaat tactataaaa agatgctgct gctttatagc cattaattac attagccatt
     5221 gagcacaatg ggaatacacc tatgtgtgat gtgtaattgt caaatgtctt gttcgatgaa
     5281 attttatatc gaatcgagcg aaatgtagct gcgttacctg ctgcacaagt cggtttgtta
     5341 ttttttatca cttcaaatga tgaaccatcg acattcataa aaacagagtt gttttcttta
     5401 aaaaatggct tttctttttc ttttctttta atgtgtcgtt taaaacgatc tgccatgttt
     5461 ttttcactaa catagaaaca atttattttt atattatgct gattctgttt ctctataata
     5521 tagttattta ttacttctgg tattatatag ggtgatgtgg ctagttttct ataaatatta
     5581 ccaccatcga tatcttcgcc atttgatttt tccatgtaga aatcatttat ttccatgagg
     5641 aaatcaggtt ttatatttag ctcatgtgtt gattttatta tgtagtcaat gcaaaattta
     5701 gccgattttt caacctcatt actaactgaa aaacggtcat tcaaattcac aacagtatgt
     5761 ccaccagata ta
//
