LOCUS       NZ_CP104636             1815 bp    DNA     circular CON 20-JUN-2024
DEFINITION  Escherichia coli strain AHM21C2872I plasmid pHNAH212872-6, complete
            sequence.
ACCESSION   NZ_CP104636
VERSION     NZ_CP104636.1
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 1815)
  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 1815)
  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
            CP104636.1.
            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..1815
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="AHM21C2872I"
                     /isolation_source="In-house environment"
                     /db_xref="taxon:562"
                     /plasmid="pHNAH212872-6"
                     /geo_loc_name="China"
                     /collection_date="2021-05"
     gene            complement(join(1457..1815,1..73))
                     /locus_tag="N5855_RS26565"
                     /old_locus_tag="N5855_26510"
     CDS             complement(join(1457..1815,1..73))
                     /locus_tag="N5855_RS26565"
                     /old_locus_tag="N5855_26510"
                     /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="phage tail protein"
                     /protein_id="WP_284657766.1"
                     /translation="MHFSQPVGGVAKGHGTGTPTGNAEPAKRDVGTGENQIPDMASFAS
                     GDGWMKLPNGKILQYGRGAVTPTLSTQTMRITFSIPFPKKVDCAMLTHSGDGGAPLGAG
                     RGFVMTAEGPTLTGFNSAYRTSSTSDTVSMNYSWWAVGE"
                     /name="phage tail protein"
     gene            63..419
                     /locus_tag="N5855_RS26570"
                     /old_locus_tag="N5855_26515"
     CDS             63..419
                     /locus_tag="N5855_RS26570"
                     /old_locus_tag="N5855_26515"
                     /inference="COORDINATES: protein motif:HMM:NF019126.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="phage tail protein"
                     /protein_id="WP_284657769.1"
                     /translation="MKCNGAPFSAEEYPKLAKVYPTNELPDLRGEFIRGWDDGRGVDSG
                     RLLLSAQDASGVGTFSGGYSDGTAYIPVDNPDKAYPGPTDWTHMAYSVALIYGQTFYAV
                     RPRNIAFNYIVRAA"
                     /name="phage tail protein"
     gene            419..1021
                     /locus_tag="N5855_RS26575"
                     /old_locus_tag="N5855_26520"
     CDS             419..1021
                     /locus_tag="N5855_RS26575"
                     /old_locus_tag="N5855_26520"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_415674.1"
                     /GO_process="GO:0098004 - virus tail fiber assembly
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="tail fiber assembly protein"
                     /protein_id="WP_151140401.1"
                     /translation="MDNAVLNSEFIATKAGDITVYNYNGETREYISTSNEYLAVGVGIP
                     ACSCLDAPGIHKAGYAICRSVDLNSWEYLPDHRGEIVYNTETGDAKEITALGDYPENTT
                     TIAPLTPYDKWDGEKWVTDTEAQHGAAVEAAEAQRQSLIDAAMASISLIQLKLQAGRKL
                     TQAETTRLNAVLDYIDAVTAIDTSTAPDVIWPELPEA"
                     /name="tail fiber assembly protein"
     gene            complement(993..1436)
                     /locus_tag="N5855_RS26580"
                     /old_locus_tag="N5855_26525"
     CDS             complement(993..1436)
                     /locus_tag="N5855_RS26580"
                     /old_locus_tag="N5855_26525"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /GO_process="GO:0098004 - virus tail fiber assembly
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="tail fiber assembly protein"
                     /protein_id="WP_001008234.1"
                     /translation="MNEYVYSARHNAFFPVDMIDKYKSEGWDLSDAKEVNQNIISEFMA
                     EPPQGKIRIAGDDGLPAWADIPPPTHEELIEITESERQLLINQANEYMNSKQWPGKAAI
                     GRLKGEELAQYNLWLDYLDALELVDTSSAPDIEWPTPPAVQAR"
                     /name="tail fiber assembly protein"
ORIGIN
        1 gctcagcgtt acccgttggt gtacctgttc cgtggccttt agccactccg ccaacaggct
       61 ggctgaaatg caatggtgcg cctttttctg ccgaagagta tccgaaactg gcaaaagttt
      121 atccgacaaa tgaattgcca gatttacgtg gtgagtttat tcgtggctgg gatgacgggc
      181 gcggggtgga ttcggggcgt ttacttttgt cagcccagga cgcatcagga gtggggactt
      241 tctcaggcgg ttattcagat ggaaccgcat atattcctgt tgataacccc gacaaagcct
      301 atcccggtcc gacggactgg actcatatgg cctacagtgt agccctaata tatgggcaaa
      361 cattttacgc agtacgaccg cgcaacatcg catttaacta catcgtgagg gccgcataat
      421 ggataatgcc gtattaaata gcgagtttat tgccacgaag gcgggggata ttactgtcta
      481 taattataat ggtgaaactc gggaatatat ttccacttca aatgaatatc ttgccgttgg
      541 tgttggtatc ccggcatgtt cctgtctgga tgcaccaggc atacataagg ctggctatgc
      601 aatttgtcgc tctgtggatt taaattcatg ggaatatctg ccagaccatc gcggtgaaat
      661 cgtctataac accgaaacgg gagatgccaa agaaatcaca gcactaggcg actatcccga
      721 aaatacaacc actatcgccc cgttaacgcc atacgataaa tgggatggtg aaaaatgggt
      781 gacagatact gaggcacaac acggtgccgc agtagaagcg gcagaagcac agcgccagtc
      841 actgattgat gcagcaatgg cttccatcag tctgattcaa ctgaaattgc aggccggacg
      901 taaactgacg caggcagaaa caaccagact taacgctgtg ctggattaca ttgacgcggt
      961 gacggcaata gataccagca ccgcgccgga tgtcatctgg cctgaactgc cggaggcgta
     1021 ggccattcaa tatctggtgc actggaggta tcaaccagct ccagtgcatc cagataatcc
     1081 agccacaaat tatattgcgc cagttcctca cctttcagac gaccaatagc ggctttaccg
     1141 ggccattgct tactgttcat gtattcgttg gcctggttaa ttagtagctg tctttctgat
     1201 tcagtaattt caataagctc ttcatgcgtg ggtggaggaa tatctgccca cgcaggcagc
     1261 ccatcatctc cggcgatacg gatttttcct tgtggcggtt cagccataaa ctcactgata
     1321 atattttgat ttacttcctt agcgtctgat aaatcccatc cctctgattt atatttatca
     1381 atcatatcca cagggaaaaa agcattatgc cttgcgctat aaacatattc gttcatataa
     1441 atcaccctga ataaaattac tcaccaacag cccaccaact gtaattcatc gataccgtgt
     1501 cgctggttga tgacgttctg taagcagaat taaaaccggt taatgttggg ccttctgcgg
     1561 tcatcacgaa tccccgccca gcacctaaag gcgcaccacc atcaccagaa tgagtaagca
     1621 tggcgcagtc cactttttta ggaaaaggga tgctgaatgt aattctcatt gtttgcgtcg
     1681 ataatgtcgg cgtaaccgca ccacgaccat attgcaggat tttaccgttg ggtaatttca
     1741 tccatccatc accactggca aaagaagcca tatccggtat ctgattttcc cctgttccca
     1801 catcccgttt tgccg
//
