LOCUS       NZ_CP075745             3461 bp    DNA     circular CON 16-AUG-2023
DEFINITION  Escherichia coli strain CPF6 plasmid pCPF6.4, complete sequence.
ACCESSION   NZ_CP075745
VERSION     NZ_CP075745.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN19296497
            Assembly: GCF_024499155.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3461)
  AUTHORS   Khine,N.O.
  TITLE     Colistin resistant E. coli isolates in pigs and pig farm environment
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3461)
  AUTHORS   Khine,N.O.
  TITLE     Direct Submission
  JOURNAL   Submitted (24-MAY-2021) Veterinary Microbiology, Chulalongkorn
            University, 39, Henry Dunant Road, Faculty of Veterinary Science,
            Bangkok, Bangkok 10400, Thailand
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: SPAdes v. galaxy verion 3.12.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 10x
            Sequencing Technology :: Oxford Nanopore MinION; Illumina NovaSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 08/16/2023 05:13:02
            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)                     :: 5,189
            CDSs (total)                      :: 5,067
            Genes (coding)                    :: 4,851
            CDSs (with protein)               :: 4,851
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 216
            CDSs (without protein)            :: 216
            Pseudo Genes (ambiguous residues) :: 0 of 216
            Pseudo Genes (frameshifted)       :: 66 of 216
            Pseudo Genes (incomplete)         :: 158 of 216
            Pseudo Genes (internal stop)      :: 32 of 216
            Pseudo Genes (multiple problems)  :: 42 of 216
            Pseudo Genes (short protein)      :: 4 of 216
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP075745.1.
            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..3461
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="CPF6"
                     /isolation_source="Pig feces"
                     /host="Sus scrofa"
                     /db_xref="taxon:562"
                     /plasmid="pCPF6.4"
                     /geo_loc_name="Thailand: Bangkok"
                     /collection_date="2018-09-05"
                     /note="mcr-3"
     gene            complement(373..573)
                     /locus_tag="KKZ13_RS25815"
                     /old_locus_tag="KKZ13_25625"
     CDS             complement(373..573)
                     /locus_tag="KKZ13_RS25815"
                     /old_locus_tag="KKZ13_25625"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001558245.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="antitoxin VbhA family protein"
                     /protein_id="WP_256626271.1"
                     /translation="MIDDRTRQLRVDGFRKAEASLRLEGMAPSGTPLYESVKARILSGE
                     ITYGEGRDEILAHYQKRGDRN"
                     /name="antitoxin VbhA family protein"
     gene            complement(1473..2126)
                     /locus_tag="KKZ13_RS25820"
                     /old_locus_tag="KKZ13_25630"
     CDS             complement(1473..2126)
                     /locus_tag="KKZ13_RS25820"
                     /old_locus_tag="KKZ13_25630"
                     /inference="COORDINATES: protein motif:HMM:NF014045.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="NYN domain-containing protein"
                     /protein_id="WP_074581898.1"
                     /translation="MKKQRTIVYVDGFNLYYGALKDKAGCRWLNIEEMVKSILPSKPTP
                     INDIVAVKYFTAKISSRANHPNQVNHQNIYLKALKTIPNLEVVLGRYDTHIVRSKLAAP
                     IVGVGSYVDVYKTEEKGSDVNLATHLLHDAHTSAFDVAIVITNDSDLALPIEFVVSKLN
                     KKVGVISPYPKASMHLCKVSSFTRVIRRSNITSSQFADQITDSDGTVLVKPTGW"
                     /name="NYN domain-containing protein"
     gene            2795..3400
                     /locus_tag="KKZ13_RS25825"
                     /old_locus_tag="KKZ13_25635"
     CDS             2795..3400
                     /locus_tag="KKZ13_RS25825"
                     /old_locus_tag="KKZ13_25635"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012537770.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_224706372.1"
                     /translation="MSGRRFGRLPNWWSRSANGDDFLLMSLKSNDTGTGIAAMKCLLAL
                     SVLIDFHSRIAEVSLSGMEELTGLSRPMVIRGLARLEELGVVVSDKDYRTNRYELTIKS
                     NDSYWAKVPVDTVRKRLKTISNRGIAPFTALKLYITILNLRYKDKTTVQVMHDTLRNYT
                     GIQTNQVRHGLDVLYSSALLHLMPREDRATNEYQILGL"
                     /name="helix-turn-helix domain-containing protein"
     Typing          617..1283
                     /name="rep_cluster_2324"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="90.76"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gacgcgtccg ggccgtttcc ggcatctttc cctctccaga tccctaaaaa gtgcccctga
       61 tgatttctgc gcgcctgcat ggctatgcat acgagtgaat agcagccgat ttcgggcgga
      121 tgctggcact aaaggcggat tttcggtgat taacttcccc gataacggtg aacgggtgcg
      181 cagtttactg tgcgaccgtg aggcgttggc caggccgtca ggcatggctg agcaacatga
      241 ggagagcaga tttaacgtgg gtgatcagca cgcagaaatt tcgacgcgtc gaaatttttc
      301 agggtgtcgg gcggagcctg accaagaggc tttggcgtgc cggcggtact ccaaagacac
      361 atcttgtccg cgtcagttgc ggtcaccgcg cttctggtaa tgagccagta tttcatcacg
      421 gccttctcca taggtgatct caccggaaag aatacgcgcc ttaaccgatt catagagcgg
      481 agttccggag ggggccatgc cttcaagccg gagagaagcc tcggccttac ggaatccgtc
      541 tacacgaagt tgtcgtgtac gatcatcaat catgggtttt ccgttgagca gtcatgcgaa
      601 taaggcaggc gtaaagtggg cccactttac atatcctgcc cgaatcttgc cgttgtatag
      661 ctgtgcagac aaaagtggaa aacgacagga aaccgttgca accggatatg taattggaga
      721 ggaaacagga gtaccgagcg atacgagccc tgttcagcat tacagacatt acgcttcctc
      781 ggtcattcgc tcacttcgtt cggtcatgac gctgcggcga gcgttacttg tacttgctca
      841 ggcagaaggc catggcggag agtaaaagag aactgggacg ttgccggttt tccataggct
      901 tcgccctcct gacgagactc acagaaatca ggcaatttcc ggagctcaaa tcagaagtgg
      961 cgaaacccga caggacttaa agatccccac cgtttccgat gggtcgctcc ctcgtgcgct
     1021 ctcctgttcc caccctgagg tttacccgtt gcagaccgcc gtaaggtggc gttttctcat
     1081 tcctacccgt gcaactgagt tccttgtagg tggttcgctc caagctgggc tgtatgcacg
     1141 aactccccgt tcaacccgac taccgcgcct attcaggtaa ctgtactctt gaatccaacc
     1201 ctgaaagaca cgacaaagcg ccactggcgg tagccattgg tagctggttc acggagcggg
     1261 aaagtacatg caagtacaca tagagttctt gaagtgtcag cctaactaca gctacactga
     1321 aaggacagtt ttggtgactg cgctccgtta aagccagtta ccttggttaa gaatctgcca
     1381 ggatttttaa ccttcgaaaa aaccacctgc cagggtggtt ttttcgtttc catagaaaga
     1441 tacgcgtttc atcctctaaa cgtcaagcga cgtcaccatc cagtaggttt cactaaaacg
     1501 gtaccatcac tatccgtaat ttgatcagca aactgcgagc tagttatatt cgaacgtctt
     1561 ataaccctag taaaagaaga tactttgcat aaatgcatgc tagctttcgg gtatggggaa
     1621 atcaccccaa ccttcttgtt taatttgcta acaacaaatt caataggcaa tgctaaatca
     1681 gagtcgttgg taataactat ggcgacatca aaagcagaag tatgagcatc atgtaataaa
     1741 tgcgttgcaa ggtttacatc tgaacctttt tcttctgttt tataaacatc aacatatgac
     1801 cctacgccta ctatcggcgc agcaagctta gaacgcacta tgtgggtgtc atagcggccc
     1861 aatacgactt caagattagg aattgttttt aaagctttaa ggtatatatt ttgatgatta
     1921 acctgattag gatggtttgc tcttgatgat attttcgcag tgaagtattt aactgcaact
     1981 atatcattaa taggtgtagg ctttgatgga agtattgatt taaccatctc ttcgatattc
     2041 aaccagcggc acccagcttt atcttttaga gcaccataat ataagttgaa tccgtcgaca
     2101 taaacaatcg ttctttgttt tttcattttt gttatgtcca tatatgctga aacctccact
     2161 agggaggttt cgcggtcgca ccgtagtgcg aggttgtata ttttttgctg aggttgccct
     2221 cgcgccagcg cagaacgctg ggtagtgatg caaattctat acggaagtat aaaacttgca
     2281 accaaaaaaa ttcaccatgc tacaattaga cttggcgagc ttactttagt aagctcgcca
     2341 agtctaattg tagcatggtg atagaaaaaa tcaacaactt acttgtagcc atgggatcta
     2401 ggacctctat cggccttgct tgtcatttac catgtgatta attattaagc taaaaaacac
     2461 catctcaacc cgcattattt tgcatttata gctctcccat ttactagtaa aaaacatgga
     2521 aaacaatgat taagtatttg aattttatga ataagttcac aaaaataaaa tatcgcttaa
     2581 tctagattag tattgtagtg tggtgttaaa actttcagtc tcgacgatca ccttaggagg
     2641 ctgaggttta tggaaactct aaacaacata atttctactt tagcttcggc accacctgaa
     2701 gctttggttg caatagtatc gctaggtgcc atgtttttta tattcatgat aataaaggta
     2761 tttttctcgt ttttagaaaa gaaatggaat taaaatgagt ggcagacgtt ttggcaggct
     2821 tccaaattgg tggtcgcgct ccgcgaatgg agatgatttt ctattaatga gcctaaaatc
     2881 taatgacaca ggaacaggaa ttgcggcaat gaagtgtctg ctagccttgt ctgtgctcat
     2941 tgattttcat tctcgaatag cagaagtctc tttaagcggt atggaagagc taaccgggct
     3001 tagtagacca atggttatcc gcgggttagc taggcttgaa gaactaggag ttgttgtctc
     3061 tgacaaggat tacagaacaa accggtatga acttacgata aaaagtaatg acagttactg
     3121 ggcaaaagtt cctgtcgata cagtccgaaa aagacttaaa accatatcca atagagggat
     3181 tgcaccattc actgctttaa aattgtacat aacaatattg aatctaaggt acaaagataa
     3241 aacaactgtt caagtcatgc acgatacact cagaaactac accggaattc agacaaacca
     3301 ggtaagacat ggtcttgatg tgctatacag cagtgctctg cttcacctca tgccgcgtga
     3361 agaccgtgcg acaaatgagt atcaaatatt aggcctatag catccatatt taccataaca
     3421 tcccttgccc gcaccccctg agaggccctc agcgcgatcc t
//
