LOCUS       NZ_CP104625             3372 bp    DNA     circular CON 20-JUN-2024
DEFINITION  Escherichia coli strain AHM9C68I plasmid pHNAH968-6, complete
            sequence.
ACCESSION   NZ_CP104625
VERSION     NZ_CP104625.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN30667243
            Assembly: GCF_030169475.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3372)
  AUTHORS   He,W., Gao,M., Lv,L., Wang,J., Cai,Z., Bai,Y., Gao,X., Gao,G.,
            Pu,W., Jiao,Y., Wan,M., Song,Q., Chen,S. and Liu,J.H.
  TITLE     Persistence and molecular epidemiology of blaNDM-positive
            Gram-negative bacteria in three broiler farms: A longitudinal study
            (2015-2021)
  JOURNAL   J Hazard Mater 446, 130725 (2023)
   PUBMED   36630875
REFERENCE   2  (bases 1 to 3372)
  AUTHORS   He,W., Gao,M., Lv,L. and Liu,J.-H.
  TITLE     Direct Submission
  JOURNAL   Submitted (06-SEP-2022) College of Veterinary Medicine, South China
            Agricultural University, Wushan, Tianhe District, Guangzhou,
            Guangdong 510642, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.7
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 200x
            Sequencing Technology             :: Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_030169475.1-RS_2024_06_20
            Annotation Date                   :: 06/20/2024 05:22:39
            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)                     :: 5,036
            CDSs (total)                      :: 4,917
            Genes (coding)                    :: 4,647
            CDSs (with protein)               :: 4,647
            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)              :: 270
            CDSs (without protein)            :: 270
            Pseudo Genes (ambiguous residues) :: 0 of 270
            Pseudo Genes (frameshifted)       :: 82 of 270
            Pseudo Genes (incomplete)         :: 192 of 270
            Pseudo Genes (internal stop)      :: 45 of 270
            Pseudo Genes (multiple problems)  :: 44 of 270
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP104625.1.
            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..3372
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="AHM9C68I"
                     /isolation_source="chicken feces"
                     /db_xref="taxon:562"
                     /plasmid="pHNAH968-6"
                     /geo_loc_name="China"
                     /collection_date="2019-12"
     gene            complement(55..288)
                     /locus_tag="N5859_RS25095"
                     /old_locus_tag="N5859_25010"
     CDS             complement(55..288)
                     /locus_tag="N5859_RS25095"
                     /old_locus_tag="N5859_25010"
                     /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(295..855)
                     /locus_tag="N5859_RS25100"
                     /old_locus_tag="N5859_25015"
     CDS             complement(295..855)
                     /locus_tag="N5859_RS25100"
                     /old_locus_tag="N5859_25015"
                     /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_000067486.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKKQLDTLSTTVSMQFSTTEAELSRQQKKLLWRVIKGRILFPALTA
                     LSVTGGIFLGCWGLMEWQESKIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGMKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            complement(<887..1543)
                     /locus_tag="N5859_RS25105"
                     /old_locus_tag="N5859_25020"
                     /pseudo=""
     CDS             complement(<887..1543)
                     /locus_tag="N5859_RS25105"
                     /old_locus_tag="N5859_25020"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /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(1533..1856)
                     /locus_tag="N5859_RS25110"
                     /old_locus_tag="N5859_25025"
     CDS             complement(1533..1856)
                     /locus_tag="N5859_RS25110"
                     /old_locus_tag="N5859_25025"
                     /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            1920..2111
                     /locus_tag="N5859_RS25115"
                     /old_locus_tag="N5859_25030"
     CDS             1920..2111
                     /locus_tag="N5859_RS25115"
                     /old_locus_tag="N5859_25030"
                     /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_000165979.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNDLDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(2193..2275)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.857"
                     /coverage="99.0"
                     /evalue="1.38e-25"
     Typing          complement(12..1543)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.411"
                     /coverage="98.0"
                     /evalue="0.0"
ORIGIN
        1 gtgccgcgcg ttcctgtacc tcatgtctgt accgggcacg ctcctgttca tcccttagct
       61 gttgttcgcg ataaataacc gactcaagcg atccacttgc ccggctaatc tctgcacctg
      121 ctgactcaat atcacgacgc gctcgttcag tatcgcgttg ttccgttgcg taacctcgtg
      181 catcttctgc aattccgcga aggcgctctc ccactcgttc agccgccgca tatagtcctg
      241 ttgcaaatgc tctaaggcgt tcagcaaatg cccttccagt tccgtcatac tcgtttactc
      301 cctgaccagc ctcacggcgt tcttgtcgcc caccgtccag gtgttttccc ctttcatccc
      361 gtccggcaac accagaaatt tcccgttctc gccattgacg aacgtcaccc cccaggtttt
      421 tgcctcgagt ttcgccagcg tgttttcctg ctctctgata gtcaggatat ttttcgcaat
      481 cttgctttcc tgccactcca tcagccccca gcaccccagg aaaatcccgc ccgtgacgct
      541 gagcgcggtc agcgccggaa acagtatccg ccctttgatc acccgccaga gcagtttttt
      601 ctgctgccgg gacagttcgg cctctgtggt gctgaactgc atgctcacgg tggtgctcag
      661 cgtatccagt tgctttttca cggatgttgt atgttcgctg atagcgtctc tgattttctg
      721 cctgtttaag ctcaatgcct tgtctacaga ctcttcgagc ttcctgaact cgctgttcag
      781 catgttctcg gtagaagcgg ctcgctcttt cagtttcttc tcgaagtctg ttcccatttg
      841 taaaagattg ctcatacagc gcccccttta gcctgagatt ccgccccccc tccgggtcgg
      901 caatactgat gctgcttttg gttgtcctca ccacctcaaa acctgccgct gtaagcgcct
      961 ctgtgacatc ctgacgcgtt tttattgctc cggcatggta aagagcctca agaccccgtg
     1021 taatcgcttc tgcggcctcc tgtttcgctt ttggcagatt atttggcgtg acaagcgtcc
     1081 gtctgttctc cggtgcgttc gggtcacgca gcccgtaatg atgattaacc agcgtctgcc
     1141 aggcatttat cctcggcctg tccgcacggt cgtagtacgg ctggaggcgc ttaccgctct
     1201 gtagctccat gttcgggatg acaaaattca gttcgagccg ccccttatcc tggtgttcca
     1261 cccagagaat gctgtactgg tctttttcga gaccgggcat aagaacacgc tcaaagctcg
     1321 tcatcactct ttcgcgttca cccggtggta gctccttctc cgcgaacgac agaacgcctg
     1381 acgtgtattt cttcgaaaat ggcgtggaat caatgagttc ccgcacttct tccgggttac
     1441 cccggagcac cgttgcgcct tcgcggttac gctcccgccc cagcaggtaa tcgaccgggc
     1501 cacttccacc gcctttcccc ctagcatgaa atttaactat catcccgtac cccctgttcc
     1561 ctgacagcct gccgcaactg gcgcaattca ccctcgatgg ccatcagtgc ggccaccaca
     1621 tgaacccggt caatcgaaga ccactggccg ctgttcacct tccgggctgt ctggttcagg
     1681 ttgttcccga tggcagccag atgccgcagc aatggcggtg ccagtgtcgg cagttttcct
     1741 gtgcgtgcaa ccggctcccc cagacagacc cgccgcatcc attccgccag tcgtttaccc
     1801 tcgcagcgtt ccagtaaccg ggcgtgctcc tcatcggtaa cccgtatcgt gagcatcttc
     1861 tcgcgtttca tcggtatcat tccccctaac aaatccccca tacaaggagc cttaagacca
     1921 tgaccaaaca ggaaaaaaca gcccttaaca tggctcgctt tatcagaagc cagacgctaa
     1981 ccctgctgga aaaactcaac gatctggacg cggacgaaca ggcagacatc tgcgaatcac
     2041 ttcacgacca cgccgacgaa ctctaccgca gttgcctcgc acgcttcggc gatgacggtg
     2101 aaagcaactg aaacatgcag ctcccggaga cgttcacagc ttgcctgtga gcggatgccg
     2161 ggagcagaca agcccgccag ggcgcgtcag tgcgggtgtc ggggcgaagc cctgacccag
     2221 tcacgtagcg atagcggagt gtatactggc ttacctcatt ttgcatcggt gcagagtgga
     2281 tgggaagtgc accatgtcag gagtaaaaag ccgcacagat gcgtaaaaac agcgcgcccg
     2341 ataaacaaca cacacgcgga cactggcaca ggcgcgtaag tgcacaatgc ttgcctctgt
     2401 gactcttccg cttcctcgcc cactcgctca ctacgttcgg tcgctggggc tgcggcgagc
     2461 ggtgggatca ctctcgttgt gatgcagatc cgtttttttt tttgcactgg agttatcagg
     2521 agtagcggtg cacatgggat cgtgcgatat gctggatggt ggaaggtcgg agggaacggc
     2581 aacaactcac ccctcccagt gaagggacgg gtagtttgcc gctctcgata tgccggacgg
     2641 agccaaggcc atcgatcacg gggcgcgtca gtggaagaac ccgcgcctgc gtgacgtatg
     2701 cgtcttcgcc gcaccatctc acccgtcacg ccaccacata ccgggaactg ccgccaaggt
     2761 ctaactcaac caatctagcc gcgctacata cggtttttgt ggcaactcat caggtgtccg
     2821 ctgtcgatga aactctctgc gccggtagcg gaactctcac gcgtgcggtc gccgtcgtca
     2881 cagctccccc aaccgcaaac gattctcaca aatacgcaag tatctgcaaa aacaggtttt
     2941 tttcggggtt cctgggagac tgtgctgttg aaaaattctt gaagaataca gaaggctcat
     3001 gcaaactgaa tgaactggtt tctgttgtgg atctcaacag tttccacagg aacattgagg
     3061 aggtcagaga cctcaatgaa cccgaaacag ctcgccttcc tggcgagctg ttttcgttct
     3121 acgcccgccg acgaaagatc gcaagtgcaa taacgagatt tttcacgtct ttacgctcaa
     3181 aaagtaaaaa aaccatgttt tcccctggct gaatccccaa aaacgcgtga aatgcgtttt
     3241 caggatgttg catagctatg cacaaatacg gcacacgatt tgtttcgctc gccccagccg
     3301 tcgaacgggt caaaatggca agatttcgtc acttccccgg tcacatctcc attgatggcc
     3361 cactccgaac cc
//
