LOCUS       NZ_CP075729             3887 bp    DNA     circular CON 16-AUG-2023
DEFINITION  Escherichia coli strain CPE35 plasmid unnamed.3, complete sequence.
ACCESSION   NZ_CP075729
VERSION     NZ_CP075729.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN19296500
            Assembly: GCF_024499175.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3887)
  AUTHORS   Khine,N.O.
  TITLE     Colistin resistant E. coli isolates in pigs and pig farm environment
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3887)
  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 04:23:40
            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)                     :: 4,854
            CDSs (total)                      :: 4,730
            Genes (coding)                    :: 4,508
            CDSs (with protein)               :: 4,508
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 222
            CDSs (without protein)            :: 222
            Pseudo Genes (ambiguous residues) :: 0 of 222
            Pseudo Genes (frameshifted)       :: 59 of 222
            Pseudo Genes (incomplete)         :: 157 of 222
            Pseudo Genes (internal stop)      :: 40 of 222
            Pseudo Genes (multiple problems)  :: 35 of 222
            Pseudo Genes (short protein)      :: 4 of 222
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP075729.1.
            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..3887
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="CPE35"
                     /isolation_source="Pig feces"
                     /host="Sus scrofa"
                     /db_xref="taxon:562"
                     /plasmid="unnamed.3"
                     /geo_loc_name="Thailand: Bangkok"
                     /collection_date="2017-06-10"
                     /note="mcr-3"
     gene            complement(join(3674..3887,1..431))
                     /locus_tag="KKZ10_RS24150"
                     /old_locus_tag="KKZ10_23995"
     CDS             complement(join(3674..3887,1..431))
                     /locus_tag="KKZ10_RS24150"
                     /old_locus_tag="KKZ10_23995"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /GO_function="GO:0004518 - nuclease activity [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="Eco29kI family restriction endonuclease"
                     /protein_id="WP_001529705.1"
                     /translation="MHNKKFDRSEHVYRNDSFLELIKDAVRFFSGTPVHSLPPPERFQG
                     AGVYALYYTGHYSLYDEYSRINRLAYNLPIYVGKAVPAGWRQSRISDHETRAGSELSNR
                     IREHGRNIAKTSNLDLCDFSCRFVIFEATGSDMISTVEAALIKIYKPLWNTVVDGFGNH
                     TPGAGRFAQAKSDWDVIHPGREWAEKCTGVHSEPYFIEERIKQYFSKSNFT"
                     /name="Eco29kI family restriction endonuclease"
     gene            1283..1477
                     /locus_tag="KKZ10_RS24155"
                     /old_locus_tag="KKZ10_24000"
     CDS             1283..1477
                     /locus_tag="KKZ10_RS24155"
                     /old_locus_tag="KKZ10_24000"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /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_001041633.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQVRFETESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(2526..3674)
                     /locus_tag="KKZ10_RS24160"
                     /old_locus_tag="KKZ10_24005"
     CDS             complement(2526..3674)
                     /locus_tag="KKZ10_RS24160"
                     /old_locus_tag="KKZ10_24005"
                     /EC_number="2.1.1.37"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_003801590.1"
                     /GO_function="GO:0003886 - DNA
                     (cytosine-5-)-methyltransferase activity [Evidence IEA];
                     GO:0008168 - methyltransferase activity [Evidence IEA];
                     GO:1904047 - S-adenosyl-L-methionine binding [Evidence
                     IEA]"
                     /GO_process="GO:0006304 - DNA modification [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DNA cytosine methyltransferase"
                     /protein_id="WP_001529706.1"
                     /translation="MRSLEIFSGAGGLAKGLELAGFQHVGFVELNKHACDSLRLNFDEE
                     KVFQGDIKNYDLSSLDKIDIVAGGPPCQPFSLGGKHKAHDDSRDMFPFAIKAIEVLQPK
                     AFIFENVKGLLRKSFADYFEYIILRLTYPCLSLSNVSDWRIHLDVLRKARKDKHCGCTY
                     DVSFKLINAADYGVPQIRERVIIVGVRSDLNKKWSFPSVTHTQEKLLWEQHVTGDYWRK
                     HNIDAVIDKGISERLMKRFGIFPPSGKSWVTVRDALKNVPQPYESHGIGDHIFKDGARV
                     YPGHTGSYIDLPSKTLKAGAHGVPGGENMIRYEDGTVRYFTVYEGKLLQTFPREFLIAG
                     AWGEAMRQIGNAVPVLLAQKIGQQLYNLLNEEVEPLLCSNFN"
                     /name="DNA cytosine methyltransferase"
     Typing          complement(769..1024)
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.512"
                     /coverage="89.0"
                     /evalue="1.21e-116"
     Typing          complement(1149..1247)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="6.22e-45"
     Typing          complement(1551..1635)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.837"
                     /coverage="100.0"
                     /evalue="1.41e-35"
     Typing          1655..2204
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.224"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gcggcctcaa ctgtactaat catatcagac cccgtagcct caaagataac aaagcgacat
       61 gaaaaatcac acaaatctag attcgatgtt tttgctatat ttcggccatg ttctctaatt
      121 ctattagata gttcagaacc agccctagtt tcatgatcac taattctaga ctgacgccaa
      181 ccagcaggaa cagccttgcc aacataaata ggaaggttat atgccaacct atttatacga
      241 gaatattcat catataatga ataatgtcct gtatagtaaa gagcatacac cccagcacct
      301 tgaaaccgtt ccggtggtgg taatgaatga acaggcgtac cactaaaaaa acgaacggca
      361 tcttttatta actctaggaa agagtcattt ctataaacat gctcagatct atcaaatttc
      421 ttattgtgca ttatgttttc cgaaaggtct ttatattaac actcctactc aacatcacct
      481 atgatacgat cataaagcta ataccccaac ccatacgcat ttaccataac gtctcattac
      541 gcgcaccgct aaaacgcgct gaacgcgatt ctgccgcgaa caccgcaaaa agagatgttt
      601 taccaagcga aaaccggaaa aatgcgtcag gatcgctttc agctcactgc atagctatgc
      661 atgaaagtga atggcgatcg gtttgggcgc atacggtgcc catgagacac attttcggac
      721 attttcagtt cgtgaatccc tgactcattg ctacatatct gaacagacac ccctagcagc
      781 gcccccaggg gcgtcctgta aaaaaacaca ccgcgccgct agcagcaccc ctaatataaa
      841 atgatgtttt ttatgaaaat agtcagtacc acccctaaaa agcggtgttg gcgcagctac
      901 aacaccgcgc cgacaccgct tttttaaata tcacaaagag agcaagaaga actaatttgt
      961 cataactctc tatttataaa gaaaaatcag caaaaaattg tttttgcgtg gggtgtgggc
     1021 atttcaggca tgagaacaga ctcgcgtttt tccggagtat cagcggaatt attgattaag
     1081 aaacactcga cgcagagcga aattttatgc aacagcggct gcactgcaca gggattattt
     1141 atcagttgat atgctgtgcc atgatacgtc ctaaaaaaac aggacaggat gtgcaattgt
     1201 aataccgtcg cccgcaacgt cttacaatta ccacctggtc agggtccacc cgacacccgg
     1261 tactgacgga gaacaacgga aggtgaacaa acagcaacaa actgcgctga atatggcgcg
     1321 atttatcaaa agccagagcc tgacactgct tgaaaaactg gatgctctgg atgccgacga
     1381 acaggcggcc atgtgcgaac gactgcacga actcgcggaa gaactccaga acagcatcca
     1441 ggttcgcttt gagaccgaaa gtgaaacagg aacataacga agctgacgga ggcgctcacg
     1501 gcttgtccgc gagcgttttc ggcagcagac aagcccgcca gggcgcgtca gcgggtgtcg
     1561 gggcgaagcc ctgacccagt cacgtagcga tagcggagtg tatactggct taactatgcg
     1621 gcatcagtgc ggattgtaag aaaacagcgc catatgcggt gtgaaatgct gcacagatgc
     1681 gtaaggagaa aatgcagctt ccggcgctct tccgcttcct cgctcactga ctcgctacgc
     1741 tcggtcgttc ggctgcggcg agcggtgtct gctcactcaa aagcagtgat actgttatcc
     1801 acagaatcaa ggtataaagc cggaaagaac atgtgagcaa aaagcaaagc accggaagaa
     1861 gccagcgacg caggcgtttt tccataggct ccgcccccct gacgagcatc acaaaaatcg
     1921 acgctcaagt cagaggtggc gaaacccgac aggactataa agataccagg cgtttccccc
     1981 tggaagctcc ctcgtgcgct ctcctgttcc gaccctgccg cttaccggat acctctccgc
     2041 ctttctccct tcgggaagcg tggcgctttc tcatagctca cgctgttggt atctcagttc
     2101 ggtgtaggtc gttcgctcca agctgggctg tgtgcacgaa ccccccgttc agcccgaccg
     2161 ctgcgcctta tccggtaact atcgtcttga gtccaacccg gtaagacacg ccttaacgcc
     2221 actggcagca gccattggta actggacaag gtggattgag atattaagag ttcttgaagt
     2281 ggtggcctaa ctgaggctac actagaagga cagtatttgg tatctgcgct ccaccaagcc
     2341 agttaccttc gggaaaaaga gttggtagct cttgattccg gcaaacgaac caccgttggt
     2401 agcggtggtt tttttgttta caggcagcag attacgcgca gaaaaaaagg atctcaagaa
     2461 gatcctttga tctttttttg caaattgcct ctatggctgt atcaccacca tagagacaca
     2521 aacttttaat tgaagttaga gcacaataac ggctcaacct cttcattcaa taagttatac
     2581 aattgctgcc ctatcttctg agctagcaac acaggaactg cattaccaat ctgcctcata
     2641 gcctcccccc aagctcctgc aatcagaaac tctcgaggaa aagtctgaag aagcttccct
     2701 tcataaaccg taaaataacg aacagtccca tcctcatacc taatcatatt ttcacctcca
     2761 ggtacgccat gagcgccagc cttaagtgtt tttgaaggca aatcgatata acttccagta
     2821 tgaccaggat aaactcgagc gccatcttta aagatatgat ctccaatacc atgtgactca
     2881 tacggttgag gaacattctt taatgcgtcc ctaacagtaa cccagctttt ccccgatggg
     2941 gggaaaatac caaaacgttt cattaaacgc tcagaaatac ctttatctat aaccgcatca
     3001 atattatgct ttcgccaata gtcaccagta acatgctgtt cccacagcaa tttttcttga
     3061 gtatgcgtta cacttggaaa agaccatttt ttattcaaat cacttcgaac accaacaatt
     3121 atgacccgtt ccctaatttg tggaactcca taatcagctg cattgattaa tttaaaactg
     3181 acatcatatg tacacccaca gtgtttatcc ttgcgagctt ttcttaatac atctagatgt
     3241 attctccaat cacttacatt acttaacgat aaacaaggat aagtcaaacg aagaattatg
     3301 tattcaaaat agtccgcaaa tgattttcta agcaaccctt taacattttc aaaaataaaa
     3361 gcttttggtt gcaatacttc aattgctttt attgcaaatg gaaacatatc cctagagtca
     3421 tcatgagctt tatgttttcc gcccaatgaa aatggttggc aaggaggccc gccagcaaca
     3481 atatctattt tatctagaga tgaaaggtca taatttttaa tatctccctg aaataccttc
     3541 tcctcatcaa aattaagtcg caaagaatca catgcatgct tgtttaactc aacaaatcct
     3601 acatgctgaa atcctgccaa ctctagacct ttagccaagc cgccggctcc tgaaaaaatc
     3661 tctaatgatc tcattatgta aaattactct tagaaaaata ctgtttaatt ctctcctcaa
     3721 taaagtatgg ctcagaatga acacctgtac atttctcagc ccactccctg ccaggatgta
     3781 ttacatccca atcagattta gcttgcgcaa atcgcccggc accaggggta tgatttccaa
     3841 agccatcaac aacggtattc cacaaaggct tataaatttt aataaga
//
