LOCUS       NZ_CP104635             4234 bp    DNA     circular CON 20-JUN-2024
DEFINITION  Escherichia coli strain AHM21C2872I plasmid pHNAH212872-5, complete
            sequence.
ACCESSION   NZ_CP104635
VERSION     NZ_CP104635.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN30667245
            Assembly: GCF_030169635.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4234)
  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 4234)
  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_030169635.1-RS_2024_06_20
            Annotation Date                   :: 06/20/2024 05:22:57
            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)                     :: 5,322
            CDSs (total)                      :: 5,207
            Genes (coding)                    :: 5,001
            CDSs (with protein)               :: 5,001
            Genes (RNA)                       :: 115
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 206
            CDSs (without protein)            :: 206
            Pseudo Genes (ambiguous residues) :: 0 of 206
            Pseudo Genes (frameshifted)       :: 72 of 206
            Pseudo Genes (incomplete)         :: 145 of 206
            Pseudo Genes (internal stop)      :: 34 of 206
            Pseudo Genes (multiple problems)  :: 37 of 206
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP104635.1.
            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..4234
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="AHM21C2872I"
                     /isolation_source="In-house environment"
                     /db_xref="taxon:562"
                     /plasmid="pHNAH212872-5"
                     /geo_loc_name="China"
                     /collection_date="2021-05"
     gene            126..2345
                     /gene="mobQ"
                     /locus_tag="N5855_RS26550"
                     /old_locus_tag="N5855_26495"
     CDS             126..2345
                     /gene="mobQ"
                     /locus_tag="N5855_RS26550"
                     /old_locus_tag="N5855_26495"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001029330.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobQ family relaxase"
                     /protein_id="WP_063106751.1"
                     /translation="MAIYHLSMKIISRKNGYSAVASAAYRSGSVIPDDRTGLIHDYTRK
                     RGVDDAVILTPANAPSWCGDRSVLWNAVEKAEQRRNSQLAREIELAIPREISREAAREA
                     VLAFVRENFVSRGMIADVAFHHMDRTNPHAHIMLTTRAVGETGFAGKVRDWNDRALAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKAPGLHLGKAACAMEKRGMETERGEQ
                     NRLINSLNLEIQVSRTRLAVIQVQENVRKRELSDAARRAAEALNLTIPAANASADTLRE
                     FIATLPQECGNAWEMTPEFVAMNGKANDIKREGNALVKERDILEKEMTGLRKARPVASI
                     LSELPLMTWAEPEYRKRQLRFWKLEKQIESLLRTYRAVKERDIPVRRQAFETQWNTWIS
                     PGMAELKEKLSAREAERRREEAEAEARRKEQEYDARLKHHDNHRLSRETALAGVITELG
                     RAREPGTGRITRYMMLSNRAGEFTVWGDELAHYPQSVHDPVNVYLSPGGAVMVSDIREG
                     MPESHETMARPERVRMYSGATVRHVLEQMRQGWPSYGFPALPHHWPDNFYFSDDRRPAA
                     SPLPSAHRVDVTAYAAPEQLMPVVFSTERNSRTLNLLLCKGPEEMLVGFVRLEDELRPV
                     LALPSPDYSHLMVSIITENGIHLAGYGEAINRDADTPYPPEPKLMQFRLKGCQDTLFAA
                     INKPEEMPDYLFRQLGFNQTWHEWKRDEQHRQQQRRPGHYRGMSM"
                     /name="mobQ"
     gene            2792..3700
                     /locus_tag="N5855_RS26555"
                     /old_locus_tag="N5855_26500"
     CDS             2792..3700
                     /locus_tag="N5855_RS26555"
                     /old_locus_tag="N5855_26500"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009440807.1"
                     /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_058657849.1"
                     /translation="MSAALQYFEENLPHRPYHTDDPAFGLRISGKGRALLARYIQQNQP
                     HAQHWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNLAVRTAPDASVKV
                     LKYAAAIERALCEKLDADVNYSGLICKNPFHLEWQVMEWREEAYTLDELADYLDLSASE
                     RRSVDKHYGLGRNCHLFEITRKWAYRAIRQGWPAFSQWLDAVIQRVEMYNASLPVPLSL
                     AECRAIGKSIAKYTHRKFSPEGFSAVQAARGRKGGLAKGEAYEDKRFMALCMLENGYSQ
                     KAIAAMLDVHRNTIRNWAMHK"
                     /name="replication initiation protein"
     gene            complement(3906..4181)
                     /locus_tag="N5855_RS26560"
                     /old_locus_tag="N5855_26505"
     CDS             complement(3906..4181)
                     /locus_tag="N5855_RS26560"
                     /old_locus_tag="N5855_26505"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091757.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_052995416.1"
                     /translation="MSRTLEQKIAEAEARLQRLKAKSRSLDTAQKVIVGAAMLARVRRP
                     EEAQLRAFLLQFLRKEVTRQADVNRLQPLINELEKLPRPPAKPQNG"
                     /name="hypothetical protein"
     Typing          complement(126..484)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2793..3520
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.376"
                     /coverage="96.0"
                     /evalue="0.0"
     Typing          127..2342
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.099"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 taaaaactga gctggcataa tgcacggcat atcacgaagt gcgcacttat acaatcttca
       61 cttcgtttcg attgtgtgcg ccctgcgggg ctgaaagaaa acggcaaaaa ggcattacgg
      121 cagaaatggc gatttatcat ctcagcatga aaatcatttc gcgaaaaaac ggctacagtg
      181 ccgttgcttc tgctgcctac cgttccggct ctgtcatacc cgatgaccgt accggattaa
      241 tccacgatta cacccgtaaa cgcggcgttg atgatgcggt cattctcacc cctgcgaatg
      301 caccgtcctg gtgtggtgac cgttccgttc tctggaatgc ggtcgagaaa gccgaacagc
      361 gccggaactc ccagctggca agggagattg aactcgccat tccccgtgag atttcccgcg
      421 aggccgcacg ggaggccgtt ctcgcttttg tccgggaaaa ctttgtcagt cggggcatga
      481 ttgccgatgt ggcgttccat catatggacc ggaccaaccc ccatgcacac atcatgctga
      541 ccacgagagc tgtcggggaa acgggattcg caggaaaggt cagggactgg aacgaccggg
      601 cactcgccga gacgtggcgc gcatcatggg ctgaccatgc gaacagagcg cttgcgaacg
      661 ccggctacca ggaagagata gaccatcgtt catacgagcg tcagggactg gagaaagcgc
      721 cgggccttca cctcggaaag gctgcctgtg cgatggaaaa acggggcatg gaaacagaac
      781 gcggtgagca gaaccgcctg attaacagcc ttaacctgga aatacaggtt tcccgcacaa
      841 ggctggcagt catccaggta caggagaacg tgcggaaacg ggaactcagc gatgccgcac
      901 gtcgtgcagc ggaagccctt aatctgacca ttcccgccgc gaatgcctca gcggataccc
      961 tgcgggaatt cattgccaca ctgccgcagg aatgcgggaa cgcatgggag atgacaccgg
     1021 agttcgtggc gatgaacggg aaggcaaacg acatcaaacg tgaggggaat gcgctggtga
     1081 aagagcggga tattctcgaa aaagagatga ccggactcag aaaagcccgt ccggtagcgt
     1141 ccatcctgtc agagcttccc ctgatgacat gggctgaacc ggaataccgc aaaagacaac
     1201 tccgcttctg gaaactcgag aaacagattg aatctcttct ccgcacctac agggccgtga
     1261 aagaacggga cattcccgtc cgtcgtcagg cctttgaaac gcagtggaat acgtggattt
     1321 cgccgggaat ggcagagctg aaagaaaaac tgtcagcacg ggaagcggag cggcgcaggg
     1381 aggaagccga agcggaagcg cgccggaagg aacaggaata tgacgcacgg ctgaaacacc
     1441 atgataacca tcgcctgagc cgagaaacgg cattagccgg ggttattacg gagctggggc
     1501 gtgccagaga gccgggaacg ggcaggataa cccgctacat gatgctgagt aacagagccg
     1561 gagaattcac ggtatggggt gatgagctgg cgcattaccc ccagagtgtt catgacccgg
     1621 tgaatgttta cctgtcgcca ggcggggctg tgatggtctc ggatatacgt gagggaatgc
     1681 cagaatctca tgagacgatg gcgcggcctg agcgtgtgag aatgtattcc ggtgcgacgg
     1741 tccggcatgt actggaacag atgcgccagg ggtggccctc ttacggtttt ccggcgctgc
     1801 cgcatcactg gccggataat ttttatttca gcgacgaccg caggcccgca gcctctccgc
     1861 tgccgtcagc gcaccgggtg gacgtcaccg cttatgcggc accggagcaa ctcatgcccg
     1921 ttgtcttttc gacagagcga aacagcagga cgctgaatct gctgttgtgc aaagggccgg
     1981 aggaaatgct tgtcggtttt gtgcgcctgg aggacgagct gcgtcccgtt cttgcgcttc
     2041 cgtcgccgga ttacagtcat ctgatggtaa gcatcatcac agagaacggg atacacctgg
     2101 caggctacgg tgaggccata aaccgtgatg ctgatactcc gtacccaccg gaaccgaagc
     2161 tgatgcagtt caggcttaag ggctgtcagg acacgctttt tgctgccatc aacaaaccgg
     2221 aagagatgcc ggattatctc ttccgtcaac tcggatttaa tcagacctgg catgaatgga
     2281 agcgggacga acagcacagg caacaacaac gacgccccgg acattaccgg ggcatgagta
     2341 tgtgatatcc ggggctgcac cccgaacccc gccaacgtct cacgggacac gaaaaaattc
     2401 cgcgtcccgt gaggcgtttt ctggatgaga aagtttgccg ttttgacccg ttcgcgcttc
     2461 tgaacggtcg aaaccgatcg cgcatcgctt tcgtgaatag ttatgcagac ccctgaaaac
     2521 gattctgacg cgtttttctg gtttggcctg gtgttttctt gtctttttgt gttttttgcg
     2581 tcagaacgcg tctgagagcg ttttaagggg tacgtacaac aggagttatg gtaaatggat
     2641 cggtttttcg ggaaggatcg acaggatttg ccgttgggtg tagtgtaagc gactgaaaaa
     2701 caaacgcccc tgaaattcgt gtagatccgc caagactttc acgaagatac aggggcgatg
     2761 tcggtcgata acctggaagg aatcgtaaca catgagcgcc gcgcttcaat acttcgaaga
     2821 aaatttacct caccgtccct atcacacgga tgatcccgct ttcggccttc gcatctccgg
     2881 caaagggcgt gcgcttcttg cgcggtacat tcagcagaac cagccacatg cgcaacactg
     2941 gctggttttt gacgttgacc gcgagggggc tgcgattgac tggagcgacc ggaacgcccc
     3001 cgcgccgaac atcaccgtaa aaaatcccgt gaatgggcac gctcacctgc tatacgcgct
     3061 caatcttgcc gtgagaaccg cgcctgatgc gtcggttaag gtgctgaaat acgccgctgc
     3121 aattgaacgt gcgctgtgtg agaaacttga cgcagatgtg aactacagcg gactgatttg
     3181 caaaaatccg ttccacctgg aatggcaggt gatggagtgg cgcgaggaag cctataccct
     3241 cgatgaactg gctgattatc tcgatttgag cgcctcagag cgtcgtagcg tcgataaaca
     3301 ttacgggctg gggcgaaact gccacctgtt cgaaataacg cgtaaatggg cttacagagc
     3361 gattcgtcag ggatggccag cattctcaca gtggcttgat gccgtgatcc agcgtgtcga
     3421 aatgtacaac gcatcgcttc ccgttcctct ttcactggct gaatgccggg ctattggcaa
     3481 gagcattgcg aaatacacgc acagaaaatt ctcaccggaa ggcttttccg ctgtacaggc
     3541 cgctcgaggc cggaaaggtg gccttgctaa aggcgaagcc tacgaggaca agcgtttcat
     3601 ggcgctatgt atgctggaga atggatattc tcagaaagct attgcggcga tgctggatgt
     3661 acatcgaaat acgatccgta attgggcaat gcacaaatag ccttatcaga taacagcgcc
     3721 ttttcggcgc ttttttgagc tgttggcgtt cctgcggttt ttccggttcc gcccagcaat
     3781 ggcgctggtt tcctcgtgat tgcggtggta gcgctcgccg cagcctcatg accgagcgta
     3841 gcgagcgaat gtgcgaggaa gcgcaaaggc gtccggtggt gcatgtggca cttacgcgcc
     3901 ggggcttatc cgttctgcgg tttcgcaggt ggtcttggta gcttctccag ctcgttaatc
     3961 agtggttgta gccggttcac atcggcctgt cttgtgactt cctttcgcag gaactggagc
     4021 aggaacgcac gcagttgcgc ctcttccggc ctccgtaccc tcgccagcat ggctgctccc
     4081 acaatgactt tttgcgcagt gtccaggctc cggctcttcg ccttcaggcg ctgcaatctg
     4141 gcctcagctt cagcaatctt ctgttcgagt gttctgctca tttcgtgact ccttgcgcgg
     4201 tgaaaaatcg cattttagct cgtcactggt agtt
//
