LOCUS       NZ_CP075744             5591 bp    DNA     circular CON 16-AUG-2023
DEFINITION  Escherichia coli strain CPF6 plasmid pCPF6-unnamed3, complete
            sequence.
ACCESSION   NZ_CP075744
VERSION     NZ_CP075744.1
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 5591)
  AUTHORS   Khine,N.O.
  TITLE     Colistin resistant E. coli isolates in pigs and pig farm environment
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5591)
  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
            CP075744.1.
            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..5591
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="CPF6"
                     /isolation_source="Pig feces"
                     /host="Sus scrofa"
                     /db_xref="taxon:562"
                     /plasmid="pCPF6-unnamed3"
                     /geo_loc_name="Thailand: Bangkok"
                     /collection_date="2018-09-05"
                     /note="mcr-3"
     gene            complement(363..719)
                     /locus_tag="KKZ13_RS25765"
                     /old_locus_tag="KKZ13_25575"
     CDS             complement(363..719)
                     /locus_tag="KKZ13_RS25765"
                     /old_locus_tag="KKZ13_25575"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000075993.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="HigA family addiction module antitoxin"
                     /protein_id="WP_052895113.1"
                     /translation="MSQATRKPSTVGDIILYEYLEPSGLKINDLAEMLNVHRNSASALV
                     NNNRKLSTDMAFRLAKAFDTTAKFWLNIQQSVDLWEVTSSPRLQEEIDRVIPAHEIIER
                     KHIVDNSEKKHAIA"
                     /name="HigA family addiction module antitoxin"
     gene            complement(922..1239)
                     /locus_tag="KKZ13_RS25770"
                     /old_locus_tag="KKZ13_25580"
     CDS             complement(922..1239)
                     /locus_tag="KKZ13_RS25770"
                     /old_locus_tag="KKZ13_25580"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001183575.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /protein_id="WP_001183575.1"
                     /translation="MQQDHEHDDCRIQFRDDWLYQFYKYGKANRKIPTAISASLGRKLD
                     MLNAADKVGDLRSPPGNRFENLNPPLTGYSSIRVNEKYRLIFKWGENGIEDLYLDPHDY
                     R"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            1426..1668
                     /locus_tag="KKZ13_RS25775"
                     /old_locus_tag="KKZ13_25585"
     CDS             1426..1668
                     /locus_tag="KKZ13_RS25775"
                     /old_locus_tag="KKZ13_25585"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001713065.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_052895112.1"
                     /translation="MALVRSGNKSKIFEADKKFNSVFDTEYQPGETCEYEGIYKCTGCG
                     KEVTIAGGKTIPPQNHHQHTPEQGNIRWQLFVYAQ"
                     /name="hypothetical protein"
     gene            1788..2114
                     /locus_tag="KKZ13_RS25780"
                     /old_locus_tag="KKZ13_25590"
     CDS             1788..2114
                     /locus_tag="KKZ13_RS25780"
                     /old_locus_tag="KKZ13_25590"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001377235.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_052895115.1"
                     /translation="MQESQENNSKPPAWRLFYLYLQLTLIYHSIRCIYSVLIGVFMSNE
                     LDSLSEVVKGLTKIELPGGGGGETDSPVVEAAIAVGIVGAAAYGIYKLFGRAEPQKDED
                     KLGF"
                     /name="hypothetical protein"
     gene            complement(2142..2648)
                     /locus_tag="KKZ13_RS25785"
                     /old_locus_tag="KKZ13_25595"
     CDS             complement(2142..2648)
                     /locus_tag="KKZ13_RS25785"
                     /old_locus_tag="KKZ13_25595"
                     /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="hypothetical protein"
                     /protein_id="WP_161395071.1"
                     /translation="MRLKFIRRDRGSFSGDLLLVLADCRPVRGEAVRGGAGNRCYGKYD
                     FFLQGLPRKLSDLILRKTVPTVYMTHCPVDFISPDFVLRKTIPTIYMAHCPVDFISPDF
                     VLRKTIPTTYMAHCPVDFVSPDFVLRKAIPTIYMAHCSIDLIAHIVSNIHFFYDKAAVN
                     GCYGK"
                     /name="hypothetical protein"
     gene            complement(2837..3070)
                     /locus_tag="KKZ13_RS25790"
                     /old_locus_tag="KKZ13_25600"
     CDS             complement(2837..3070)
                     /locus_tag="KKZ13_RS25790"
                     /old_locus_tag="KKZ13_25600"
                     /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_010976343.1"
                     /translation="MTELETHLLNALEQLQQDYMQRLNEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSERTEHLSQLYSENWR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(3077..3595)
                     /locus_tag="KKZ13_RS25795"
                     /old_locus_tag="KKZ13_25605"
     CDS             complement(3077..3595)
                     /locus_tag="KKZ13_RS25795"
                     /old_locus_tag="KKZ13_25605"
                     /inference="COORDINATES: protein motif:HMM:NF016710.2"
                     /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_012564915.1"
                     /translation="MSNLLRTGAEFEKKLKERAESTEKMLNDEFSRLGESVSEAVTSNE
                     TKIKDAIALFTTSTEESLKKHREGVKEAMMQHRKDMLKLAGSSGMRLLGIVFLLFTASG
                     GTLWYLGGRIQTNLEEIRVQEETLRKLNAKTWGVEFVQGGGRKFLVIPQGMSAEVTHYQ
                     GKDWIQLTE"
                     /name="MbeB family mobilization protein"
     gene            complement(<3633..4064)
                     /locus_tag="KKZ13_RS25800"
                     /pseudo=""
     CDS             complement(<3633..4064)
                     /locus_tag="KKZ13_RS25800"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /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            complement(4273..4596)
                     /locus_tag="KKZ13_RS25805"
                     /old_locus_tag="KKZ13_25615"
     CDS             complement(4273..4596)
                     /locus_tag="KKZ13_RS25805"
                     /old_locus_tag="KKZ13_25615"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000955993.1"
                     /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_000955994.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIEGELRSLRQVVREQGAR
                     DDC"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            4662..4853
                     /locus_tag="KKZ13_RS25810"
                     /old_locus_tag="KKZ13_25620"
     CDS             4662..4853
                     /locus_tag="KKZ13_RS25810"
                     /old_locus_tag="KKZ13_25620"
                     /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"
     Typing          complement(4932..5016)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.03e-37"
     Typing          5040..5585
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.438"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(2740..4283)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.058"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(4280..4629)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.162"
                     /coverage="99.0"
                     /evalue="1.95e-64"
ORIGIN
        1 acttatcgcc actggcagca gccactggta acaggattag cagagcgagg tatgtaggcg
       61 gtgctacaga gttcttgaag tggtggccta actacggcta cactggaagg acagtatttg
      121 gtatctgcgc tctgctaagc cagttaccag gttaagcagt tccccaactg acttaacctt
      181 cgaaaaaccg cctccccagg cggttttttc gtttacagag caagagatta cgcgtacaga
      241 gcacggatct caagaagatc gtaagaagaa agttaacatg agtgttttta tccctcaaaa
      301 agaaggcttc tatttataga agccttcttt ttgagggata acttatattt ttttaaaaaa
      361 aatcatgcaa tagcatgttt cttctcagaa ttatcaacaa tgtgtttcct ttctatgatt
      421 tcatgagcgg gaatcactct gtctatttct tcttgcaatc gagggctact agtaacctcc
      481 cataaatcaa cagactgctg tatatttagc cagaactttg cagtggtatc gaaggcttta
      541 gccaacctaa aagccatatc ggtagacagc tttctattat tgttaactaa agcactggca
      601 gagtttctat gcacattcaa catttcagcc aagtcattga tttttaaacc acttggttcg
      661 agatattcat aaagaataat atcccctaca gttgatggct ttctagttgc ttgggacatg
      721 ctttactcct aaatttttta cttctctctg ttagatgagg aagataagta tttcgtctat
      781 taccagctgt agcgatgagt aattatctta aatatagtca cgtcatttag tttattaatc
      841 attatttgta atgacatttt aatgtaggtg agggaacgcc tcacctactt gttttataag
      901 ataacagcca cgacctgtta tctatcggta atcatgtgga tcgagataca aatcctcgat
      961 tccgttttca ccccacttaa atattaagcg gtacttctca ttcacccgta tggatgaata
     1021 ccctgtcaat ggagggttga gattctcaaa tcggtttccc gggggagacc gcaaatctcc
     1081 aactttatca gcagcattca gcatatccag cttgcgacct aatgaagcac taatcgcagt
     1141 tggaatcttt cgattggctt taccatattt gtaaaactgg tatagccaat cgtctcgaaa
     1201 ctgaatgcgg caatcatcat gttcatgatc ttgctgcatt tttcttttac ctcaattttt
     1261 gccgcaactt ggcaattttt tagatcacct tcttacctcc gatatagtac agcaaacaca
     1321 acaaatgcac aacagcacag tgcacttgtg caaccaataa ccatactgta gaatgcaccc
     1381 acacacagtg cagatgtgca aaatagaggg taatttggag gttacatggc tcttgttcgt
     1441 tcaggaaaca aaagcaagat ttttgaagca gataagaagt ttaactcggt ttttgacact
     1501 gaatatcagc cgggagaaac atgtgaatat gaagggattt ataaatgtac cggttgcggt
     1561 aaagaagtaa ctatcgcagg tgggaaaaca atcccaccac aaaaccacca ccaacatacc
     1621 cccgagcaag ggaacattcg ttggcaattg tttgtttatg ctcagtgagg aatagaaaat
     1681 ggcagatcgt cgaccactca acccacacgt tgtcgttcct aaaccaggcg gcggaactca
     1741 acctcgtgac cgtaacaatg acggaagggt cagaggaaaa cgctcagatg caggaaagcc
     1801 aagaaaataa cagcaagccg ccagcctggc ggctttttta tttatatcta cagctgacac
     1861 tgatttacca tagcatccgc tgtatctact cagtcttgat aggagttttt atgagtaatg
     1921 aattagacag cctttcagaa gtagttaaag gactcacaaa gatagagctg cctggcggcg
     1981 gtggcggtga aaccgatagc cctgtagttg aggcagctat agctgttggc attgtagggg
     2041 ctgctgcata tgggatttat aagctttttg gtcgcgcaga accccagaaa gatgaggaca
     2101 aactcggttt ctagaaccat aaggcagcat caaaacggca ttcatttacc ataacatccg
     2161 ttaactgcgg ccttgtcata aaagaaatgg atattggaga caatgtgagc aataagatct
     2221 atagaacagt gagccatgta gatggttgga atggccttcc tcagtacgaa atcaggggag
     2281 acaaaatcta caggacagtg agccatgtag gtggttggaa tggtcttcct caatacgaaa
     2341 tcaggggaaa taaaatctac aggacagtga gccatgtaga tggttggaat ggtcttcctc
     2401 aatacgaaat caggggaaat aaaatctaca ggacagtgag tcatgtaaac ggttggaacg
     2461 gtcttccgca atatgagatc agataatttg cggggcaaac cctgcaaaaa gaaatcatat
     2521 ttaccataac atctgttgcc cgcaccgccc cggacagctt cgccgcgaac ggggcggcag
     2581 tcagccaaaa ccaacaacaa atcacccgaa aagctaccgc gatcgcgcct gataaatttt
     2641 aaccgcatga atacctatgc aaccagatgg tgcagactac attagcccgt caaaatccac
     2701 tgaatctgcc attttttatg gtttcgccat cacagcgaca acgaaggacc atccagtgtg
     2761 cgttcctgta tttccagctg gcgttcccgt tccagggata acgcatgttc gcgctcctgt
     2821 atcagccgtt cctctcttat ctccagttct cgctgtataa ctggctcaag tgttctgtcc
     2881 gctcgctcaa gtgctgtacc tgctgactca actgcatgac ccgctcgttc agcatcgcgt
     2941 tgtcccgttg cgtaagcgaa aacatcttct gcaattccac gaaggcgctc tcccattcgt
     3001 tcagccgctg catatagtcc tgttgcagct gctctaaggc gttcagcaaa tgtgtttcca
     3061 gctctgtcat tccgtatcac tccgtcagtt gtatccagtc cttcccctga tagtgcgtca
     3121 cctctgctga catcccttgc ggaatgacca gaaattttct tcccccgccc tgaacaaact
     3181 ccacacccca tgtcttcgcg ttcagtttcc gcaatgtctc ttcctgtacc ctgatttctt
     3241 ccaggttcgt ctgtatcctc ccgccgagat accagagcgt cccgccactc gcggtaaaca
     3301 ggagaaagac tatccccagc aacctcatgc ccgaactccc tgccagcttt aacatgtcct
     3361 tccggtgctg catcatcgcc tctttcaccc cttcccggtg ttttttcagc gattcctctg
     3421 tcgacgttgt gaacagggct atagcgtctt tgattttcgt ctcgtttgag gtcacagcct
     3481 cgcttacaga ttcgccgagc ctgctgaatt cgtcgttcag cattttctct gtagattcgg
     3541 ctctctcttt cagctttttc tcgaactccg cgcccgtccg taaaagattg ctcataaaat
     3601 gctcctttca gtctgatatt cctcccgccg ttcgggtctg caatgctgat actgcttcgc
     3661 gtcaccctga ccacttcaag ccccacctct gtgagcgcct gaatcacatc ctgacggcct
     3721 tttatctccc cggcatggta aagcacctcc aggcctcgtg taacgctctc agcaagcgcc
     3781 tgtttcgttt ccggcaggtt atcagggagg gtcagcgttc tgcggttctc cggggcgttg
     3841 gggtcatgta gcccgtaatg gtgattcacc agtgtctgcc aggcatcaat tctcggcctg
     3901 tctgcccggt cgtagtacgg ctggaggcgt tttccgctct gtagctccat gttcggaatg
     3961 acaaaattca gctcaagacg ccccttgtcc tggtgctcca cccacagaat gctgtactga
     4021 tttttttcga gaccgggcat cagtacgcgc tcaaagctct ccatcacttt ttcacgtcct
     4081 cccggcggca gttccttctc tgcgaacgac agaacaccgg acgtgtattt cttcgcaaat
     4141 ggcgtggcat cgatgagttc cctgacttct tccggattac cctgaagcac cgttgcccct
     4201 tcccggttac gctcccttcc cagcaggtaa tcaaccggac cactgccacc gccttttccc
     4261 ctggcatgaa atttaacaat catcccgcgc tccctgctcc ctgacgacct gccgtaagct
     4321 gcgcaactct ccctcgatgg ccatcagtgc ggccaccacc tgaacccggt caccggaaga
     4381 ccactgcccg ctgtttacct tcctcgctgt ctgattcagg ttattcccga tggcagccag
     4441 ctgacgcagt aacggcggtg ccagtgtcgg cagcttcccg gaacgggcaa ccggctcacc
     4501 caggcagacc cgccgcatcc ataccgccag ttgtttaccc tcacagcgtt ccagtaaccg
     4561 ggcatgttca tcatcagtaa cccgtatcgt gagcatcctc tcgcgtttca tcggtatcat
     4621 tacccccatg aacagaaacc cccccttaca cggaggcatc agtgactaaa caggaaaaaa
     4681 ccgcccttaa catggcccgc tttatcagaa gccagacatt aacgctgctg gagaagctca
     4741 acgaactgga cgcggacgaa caggcagata tctgtgaatc gcttcacgac cacgctgatg
     4801 agctttaccg cagctgcctc gcgcgtttcg gtgatgacgg tgaaaacctc tgacacatgc
     4861 agctcccgga gacggtcaca gcttgcctgt gagcggatgc cgggagcaga caagcccgtc
     4921 agggcgcgtc agggggtttc ggggcgaagc cctgaaccag ttacgtagcg atagcggagt
     4981 gtatactggc ttaaccatgc ggcatcagtg cagattgtat gaaaagtgcg ccatgccggg
     5041 tgtgaaatgc cgcacagatg cgtaaggaga aaatgcagca tcagacgctc ttccgcttcc
     5101 tcgctcactg actcgctacg ctcggtcgtt cggctgcggc gagcggtgcc ggctcactca
     5161 aaggcggtaa tacggttatc cacagaatca ggggataagg ccggaaagaa catgtgagca
     5221 aaaaggcaaa gggcaacgaa aggccgcgcc gctggcgttt ttccataggc tccgcccccc
     5281 tgacgagcat cacaaaaatc gacgctcaag tcagaggtgg cgaaacccga caggactata
     5341 aagataccag gcgtttcccc ctggaagctc cctcgtgcgc tctcctgttc cgaccctgcc
     5401 gcttaccgga tacctgtccg cctttctccc ttcgggaagc gtggcgcttt ctcatagctc
     5461 acgctgttgg tatctcagtt cggtgtaggt cgttcgctcc aagctgggct gtgtgcacga
     5521 accccccgtt cagcccgacc gctgcgcctt atccggtaac tatcgtcttg agtccaaccc
     5581 ggtaagacac g
//
