LOCUS       NZ_CP104624             5427 bp    DNA     circular CON 20-JUN-2024
DEFINITION  Escherichia coli strain AHM9C68I plasmid pHNAH968-5, complete
            sequence.
ACCESSION   NZ_CP104624
VERSION     NZ_CP104624.1
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 5427)
  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 5427)
  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
            CP104624.1.
            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..5427
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="AHM9C68I"
                     /isolation_source="chicken feces"
                     /db_xref="taxon:562"
                     /plasmid="pHNAH968-5"
                     /geo_loc_name="China"
                     /collection_date="2019-12"
     gene            join(5042..5427,1..418)
                     /locus_tag="N5859_RS25055"
                     /old_locus_tag="N5859_24970"
     CDS             join(5042..5427,1..418)
                     /locus_tag="N5859_RS25055"
                     /old_locus_tag="N5859_24970"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000510993.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_029490467.1"
                     /translation="MGIFSQIGSALLNCISKPVDALCEWAKEPLKDREYRREEASKESE
                     HKRNMDVLTAKKRAEHELRMSELNAEYELREKEKTLEVDLEVRRVREIEKAVAEIQEWR
                     KSQELERMERTTAAIARYKEQLTKLNIEVINSIGNMQLDLKERAQKFVYEKAVQYKRLQ
                     DEATEEAMNDLIRIEEKFGDNERAKDILIRAVDTKMGNVIDTSTRFLEELNRDIVSLNQ
                     SIDRLTNQGQKFIESHLERFHIVDATSSLYITSDEKERLLLKNIN"
                     /name="hypothetical protein"
     gene            complement(733..891)
                     /locus_tag="N5859_RS25240"
     CDS             complement(733..891)
                     /locus_tag="N5859_RS25240"
                     /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="replication initiation protein"
                     /protein_id="WP_071593719.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLTPLAAATGNWTRWIEIL
                     RVLEVVA"
                     /name="replication initiation protein"
     gene            complement(1546..1737)
                     /locus_tag="N5859_RS25060"
                     /old_locus_tag="N5859_24975"
     CDS             complement(1546..1737)
                     /locus_tag="N5859_RS25060"
                     /old_locus_tag="N5859_24975"
                     /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            1801..2124
                     /locus_tag="N5859_RS25065"
                     /old_locus_tag="N5859_24980"
     CDS             1801..2124
                     /locus_tag="N5859_RS25065"
                     /old_locus_tag="N5859_24980"
                     /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_000955999.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2333..>2764
                     /locus_tag="N5859_RS25070"
                     /old_locus_tag="N5859_24985"
                     /pseudo=""
     CDS             2333..>2764
                     /locus_tag="N5859_RS25070"
                     /old_locus_tag="N5859_24985"
                     /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            2802..3320
                     /locus_tag="N5859_RS25075"
                     /old_locus_tag="N5859_24990"
     CDS             2802..3320
                     /locus_tag="N5859_RS25075"
                     /old_locus_tag="N5859_24990"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001447511.1"
                     /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_001749510.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFRKLGESVSEAVTSNE
                     TKIRDAIALFTASTEKSLEKHREGVKEAMMQHRKDVLKLAGNTGMMLLGIVFLLFTASG
                     GTLWYLGGRIQTNLEEIRKQEETLQKLNAKTWGVEFVQDGNRKFLVLPYGKSAEVIPFQ
                     GKEWVHLKE"
                     /name="MbeB family mobilization protein"
     gene            3327..3560
                     /locus_tag="N5859_RS25080"
                     /old_locus_tag="N5859_24995"
     CDS             3327..3560
                     /locus_tag="N5859_RS25080"
                     /old_locus_tag="N5859_24995"
                     /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_000137445.1"
                     /translation="MTELETHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSEQTERLSQLYSENWR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            3920..4513
                     /locus_tag="N5859_RS25085"
                     /old_locus_tag="N5859_25000"
     CDS             3920..4513
                     /locus_tag="N5859_RS25085"
                     /old_locus_tag="N5859_25000"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000130481.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_196993498.1"
                     /translation="MALENIIRFSDSIERWGDSMSKAWEELDVETKGKRTYSMNNDMSG
                     LYNVISRAVEASGADHSINEKLTNVLKRELVDYVSIAHLKTKLSVLYEFEKNYLQLISE
                     YKEEIKFASSLQEDLRKERAKFFSETLKEVHQTLSESQVDNEVASKWIKELVGSYTKSL
                     DLSGGLVEEHTLDTIACIRAEAKLNKPSIEPGNN"
                     /name="hypothetical protein"
     gene            4558..5055
                     /locus_tag="N5859_RS25090"
                     /old_locus_tag="N5859_25005"
     CDS             4558..5055
                     /locus_tag="N5859_RS25090"
                     /old_locus_tag="N5859_25005"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000897048.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_284632979.1"
                     /translation="MTILERKVNDFKLSSSELPEILAALREARECLVSRSINEEPQLYS
                     ALFLYERNEGLLSLSFEREYSIFINSNLECILRRVADIKGKKQGKLQKIMSGLVGFKYS
                     SGDSCADLLFFNGKLEQIRKIYEVFDRDRDRLEYLNYMMKKERVIFEREFERLLGEKNG
                     DF"
                     /name="hypothetical protein"
     Typing          1374..1455
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.3400000000000002e-35"
     Typing          complement(820..1354)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.841"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2115..3664
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.183"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aaacatagaa gtgattaatt ctattgggaa catgcagctt gatttaaagg agcgcgcaca
       61 gaaatttgtc tatgagaaag ctgtacaata taagcgcctg caagatgaag caacggaaga
      121 ggctatgaat gatcttataa gaattgagga aaagtttggt gataatgaga gagctaaaga
      181 tattttaatt cgtgcagttg atactaagat ggggaatgtt attgatacgt caactcggtt
      241 tttggaagaa ttaaatagag atattgttag tttaaaccaa agtattgata gactgactaa
      301 tcaaggacaa aaattcattg agagtcattt ggagcgtttt catattgttg atgcgacatc
      361 ttctttatat attacaagtg atgagaaaga gcgattgttg ctgaaaaata ttaattagta
      421 tttttgtgag taatcgcgat cattattttt aatggtcgca ttgtttgttc ttgcggttgc
      481 taatcattag tttttgcctt gtggttgaaa actgagctct atggctatgg ccgaggagtg
      541 ggagtgaaaa gattcaagga tcctcttgtg atcctttttt tctgcgcgta atctgctgcc
      601 tgtaaacaaa aaaaccaccg ctaccaacgg tggtttgttt gccggaatct agagctacca
      661 actctttctt ccgaaggtaa ctggcttggt ggagcacaga taccaaatac tgtccttcta
      721 gtgtagccgc agttaggcca ccacttcaag aactcttaat atctcaatcc accttgtcca
      781 gttaccagtg gctgctgcca gtggcgttaa gtcgtgtctt accgggttgg actcaagacg
      841 atagttaccg gataaggcgc agcggtcggg ctgaacgggg ggttcgtgca cacagcccag
      901 ctcggagcga acgacctaca ccgagccgag ataccaacag cgtgagctat gagaaagcgc
      961 cacgcttccc gaagggagaa aggcggacag gtatccggta agcggcaggg tcggaacagg
     1021 agagcgcacg agggagcttc cagggggaaa cgcctggtat ctttatagtc ctgtcgggtt
     1081 tcgccacctc tgacttgagc gtcgattttt gtgatgctcg tcaggggggc ggagcctatg
     1141 gaaaaacgcc tgttgcgcgg cctttttttg ctcacatgtt ctttccggcc ttatcccctg
     1201 attctgtgga taaccgcatt atcgtttttg agtgagcaga caccgctcgc cgcagccgaa
     1261 cgaccgagcg cagcgagtca gtgagcgagg aagcggaaga gcgtcggaag ttgcattttc
     1321 tccttacgca tctgtgcggt atttcacacc gcatatggtg cactatcaat acaatccgca
     1381 ctgatgccac atagttaagc cagtatacac tccgctatcg ctacgtgact gggtcatggc
     1441 tgcgccccga cacccgctaa aacccgctga cgcgccctgg cgggcttgtc tgctcccggc
     1501 atccgctcac agacaagctg tgaccgtctc cgggagctgc atgtgtcaga ggttttcacc
     1561 gtcatccccg aaacgtgcga ggcagctgcg gtaaagctca tcggcgtggt cgtgaagcga
     1621 ttcacagatg tctgcctgtt catccgcgtc cagttcgttg agcttttcca gcagcgttaa
     1681 tgtctggctt ctgataaagc gcgccatgtt aagggctgtt ttttcctgtt tagtcactga
     1741 tgcctccgtg taagggggat ttctgttcat ggggtaatga taccgatgaa acgcgagagg
     1801 atgctcacga tacgggttac tgatgatgaa catgccaggt tacttgaacg ctgtgagggt
     1861 aaacaactgg cggtatggat gcggcgggtc tgcctgggtg agccggttgc ccgttccggg
     1921 aaactgccga cactggcacc gccgttactg cgtcagctgg ccgccatcgg aaataacctg
     1981 aatcagacag cccgtaaggt gaacagcggg cagtggtctt ccggtgaccg ggttcaggta
     2041 gtggccgcac tgatggccat cggggatgag ctgcgccggc tgcgtctggc cgtcagggaa
     2101 cagggggcgc gggatgatag ttaaatttca tgccagggga aaaggtggtg gcagtggtcc
     2161 ggttgattac ctgctgggga gggagcgtaa ccgcgaaggc gcaacggtgc ttcagggtaa
     2221 tccggaagaa gtccgggaac tcatcgatgc cacgccattt gcgaagaaat acacgtccgg
     2281 tgttctgtcg ttcgcggaga aggagctgcc gccgggagga cgtgaaaaag tgatggcgag
     2341 ctttgagcgt gtactgatgc ccggtctcga aaaaaatcag tacagcatcc tgtgggtgga
     2401 gcaccaggac aagggacggc ttgagctgaa ttttgtcatt ccgaacatgg agctacagac
     2461 cggaaaacgt ctccagccgt actacgaccg cgcagacagg ccgagaattg atgcctggca
     2521 gacgctggtg aatcaccatt acggactgca tgaccccaac gccccggaga accgccggac
     2581 gctgaccctt cctgataacc tgccggaaac gaaacaggca cttgctgaga gcgttacacg
     2641 cggtatagac gcactttacc atgccggaga gataaaagga cgtcaggatg tgattcaggc
     2701 gctcacagag gcggggcttg aagtggtcag ggtgacgcga agcagtatca gcattgcaga
     2761 cccgaacggc gggaggaata tcagactgaa aggagcgttt tatgagcaat cttttacaga
     2821 cgggcgcgga gttcgagaaa aagctgaaag agagagccga atctacagag aaaatgctga
     2881 acgacgagtt caggaagctc ggcgagtctg tcagcgaggc tgtgacctca aacgagacga
     2941 aaatcagaga cgctatagcc ctgttcacag cctcgacaga gaaatcgctg gaaaaacacc
     3001 gggaaggggt gaaagaggcg atgatgcagc acaggaagga cgtgttaaag ctggcaggga
     3061 atacgggcat gatgttactg gggatagtct ttctcctgtt taccgcgagt ggcgggacgc
     3121 tctggtatct tggcggacgg atacagacga acctggaaga aatcaggaag caggaagaga
     3181 cattgcagaa actgaacgcg aagacatggg gcgtggagtt tgtgcaggac gggaacagga
     3241 aattccttgt ccttccgtac gggaaatcag cggaggtgat tccctttcag gggaaagagt
     3301 gggtacatct gaaggagtga ctcagagtga cagagctgga aacacatttg ctgaacgcct
     3361 tagagcagct gcaacaggac tatatgcagc ggctgagcga atgggagagc gccttcgtgg
     3421 aattgcagaa gatgttttcg cttacgcaac gggacaacgc gatgctgaac gagcgggtca
     3481 tgcagttgag tcagcaggtg cagcacttga gcgagcagac agaacgcttg agccagttat
     3541 acagcgagaa ctggagataa gagaggcacg gctgatacag gagcgcgaac atgcgttatc
     3601 cctggaacgg gagcgtcagc cggaaataca ggaacgcacg ctggatggtc cttcgctggg
     3661 atggtgaaac catgaaaaat ggcagcttca gtggattaag aggggttaat gtggcctgta
     3721 ccatctggtt gcataggtat tcatgcggtt aaaatttatc aggcgcgatc gcggcagttt
     3781 ttcgggtggt ttgttgccat ttttacctgt ctgctgccgt gatcgcgctg aacgcgtttt
     3841 agcggtgcgt gtaatgcgac gttatggtaa atggatgagt taggcctaag tcatgacaga
     3901 taaaacgacc agtattaaaa tggctttaga aaacataatc agatttagtg actctataga
     3961 gagatgggga gactctatgt cgaaagcgtg ggaagagttg gatgttgaga ccaaaggaaa
     4021 gcgtacttat tctatgaata acgatatgag tggtttatat aatgtaatat cacgggctgt
     4081 tgaagcgtct ggtgccgatc attcaattaa tgaaaaattg acaaatgtct tgaaaagaga
     4141 gttagttgat tatgtcagca ttgcgcatct aaagaccaaa ttgtctgtat tgtatgagtt
     4201 tgaaaagaat tatttgcagc ttatctcaga atataaggaa gaaataaagt ttgcttcctc
     4261 tttgcaagag gatttacgta aagaacgtgc taaattcttt tctgagacat taaaagaggt
     4321 tcatcaaact ctaagtgagt ctcaagttga taatgaagtg gcatcaaaat ggattaaaga
     4381 acttgttggt agttatacca aaagcttgga tctaagcgga ggtcttgttg aagagcatac
     4441 attagataca attgcttgta ttcgcgcgga ggctaaatta aataaaccat ctattgagcc
     4501 gggcaataat taattatggc cggggataga catataaata gtttgcttta tgttcttgtg
     4561 actatattag aacgtaaagt gaatgacttt aaattgtctt cgtcggaact tcctgagata
     4621 ttggctgctt tacgagaggc aagggagtgc cttgtatcgc gcagcatcaa tgaagagcct
     4681 cagttatatt cggcattgtt tttatatgaa agaaatgaag ggctgttaag tctttcattt
     4741 gagagagagt actctatttt tattaactct aatttggagt gtatattgag gagagttgcg
     4801 gatataaaag gtaaaaagca gggtaaattg caaaaaataa tgagtgggct tgtggggttt
     4861 aaatattcaa gtggcgattc ttgtgcggat cttttgtttt ttaatggtaa gcttgaacag
     4921 atacgtaaaa tatatgaagt ctttgatagg gatagagata gacttgaata tcttaactat
     4981 atgatgaaga aagaacgtgt tatttttgaa agagaatttg aacggctttt aggtgaaaaa
     5041 aatggggatt tttagtcaga ttggtagcgc tttgcttaat tgtattagta agcctgttga
     5101 tgcactctgt gaatgggcta aagaaccatt gaaagatagg gaatatagaa gggaggaggc
     5161 ttcaaaggag tctgaacata agcgtaacat ggatgtcttg acggccaaga agcgtgctga
     5221 gcatgaactc agaatgagtg aattgaatgc tgaatatgag ctgagagaaa aagagaaaac
     5281 tcttgaagtt gatttagagg ttcgtcgcgt tcgcgaaata gaaaaagcag tagctgagat
     5341 ccaggaatgg agaaagtcac aggaacttga gaggatggag cgaacaacag cagctattgc
     5401 acgttacaag gagcaactaa cgaaatt
//
