LOCUS       NZ_CP075735             6759 bp    DNA     circular CON 16-AUG-2023
DEFINITION  Escherichia coli strain CP52E plasmid unnamed, complete sequence.
ACCESSION   NZ_CP075735
VERSION     NZ_CP075735.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN19296499
            Assembly: GCF_024499115.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6759)
  AUTHORS   Khine,N.O.
  TITLE     Colistin resistant E. coli isolates in pigs and pig farm environment
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6759)
  AUTHORS   Khine,N.O.
  TITLE     Direct Submission
  JOURNAL   Submitted (21-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 04:22:23
            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)                     :: 4,843
            CDSs (total)                      :: 4,727
            Genes (coding)                    :: 4,479
            CDSs (with protein)               :: 4,479
            Genes (RNA)                       :: 116
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 248
            CDSs (without protein)            :: 248
            Pseudo Genes (ambiguous residues) :: 0 of 248
            Pseudo Genes (frameshifted)       :: 91 of 248
            Pseudo Genes (incomplete)         :: 149 of 248
            Pseudo Genes (internal stop)      :: 43 of 248
            Pseudo Genes (multiple problems)  :: 35 of 248
            Pseudo Genes (short protein)      :: 4 of 248
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP075735.1.
            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..6759
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="CP52E"
                     /isolation_source="Anal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="unnamed"
                     /geo_loc_name="Thailand: Bangkok"
                     /collection_date="2017-06-10"
                     /note="mcr-1"
     gene            complement(join(6750..6759,1..185))
                     /locus_tag="KKZ11_RS24100"
                     /old_locus_tag="KKZ11_23980"
     CDS             complement(join(6750..6759,1..185))
                     /locus_tag="KKZ11_RS24100"
                     /old_locus_tag="KKZ11_23980"
                     /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_001041631.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQIRFEAESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1065..2930
                     /locus_tag="KKZ11_RS24105"
                     /old_locus_tag="KKZ11_23985"
     CDS             1065..2930
                     /locus_tag="KKZ11_RS24105"
                     /old_locus_tag="KKZ11_23985"
                     /EC_number="2.1.1.-"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006816428.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0008168 - methyltransferase activity [Evidence IEA];
                     GO:1904047 - S-adenosyl-L-methionine binding [Evidence
                     IEA]"
                     /GO_process="GO:0006306 - DNA methylation [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="site-specific DNA-methyltransferase"
                     /protein_id="WP_021558993.1"
                     /translation="MQTELIKELNKVLKAFPQFWNGEELQRSMVSDAISQKQPDLIKAL
                     VDNEKVRSVYGVDIDGIFIFDFDKLCGLLKYKEYWANSFTKYRNKVGLTSEGKYLDYSS
                     DVVLDFPFKDCILEGGMTKENQGKDEIYYNEIIAMDEVDSLLSPKAFTNAKRYTKEGVK
                     ENITKFNDDENLIIKGNNLIALHSIKKLYAGKVKLIYIDPPYNTGSDSFKYNDRFNRST
                     WLTFMKNRLEVAKEMLSDDGFIFIQCDDNESAYLKVLCDSIFGEENYRNSIYWHRTYAG
                     KTVKSKLPWNTDTILFYSKKESSLLEPYTAELSAADIKSYNKDDFDGRGKYNTVSLQKT
                     SSPGPQTTYDYIDNTGKKWSCPEKGWRMTKEKLKALENDNRLYITDKTIREKYYLKERK
                     EIGKQIDNFWHDIGNLNRVSDVAFIDGQKTEKLMQRIISLASKENDIVLDFHLGSGTSA
                     AAAHKMGRRYIGIEQMDYINEITVPRLQKVIEGEQGGISKDVNWQGSGSFVYVELVELN
                     AYFIHEIQKAQSTEELEKLFAVMKTEAYLNYQVALENVLSAEYEVDGILHKVAFSELEL
                     HEQKQLLIEILDKNQLYVNVSDMEDSDLNISESDKAFTRSFYGME"
                     /name="site-specific DNA-methyltransferase"
     gene            2935..5571
                     /locus_tag="KKZ11_RS24110"
                     /old_locus_tag="KKZ11_23990"
     CDS             2935..5571
                     /locus_tag="KKZ11_RS24110"
                     /old_locus_tag="KKZ11_23990"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012443154.1"
                     /GO_function="GO:0005524 - ATP binding [Evidence IEA];
                     GO:0003677 - DNA binding [Evidence IEA]; GO:0016787 -
                     hydrolase activity [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DEAD/DEAH box helicase family protein"
                     /protein_id="WP_052512605.1"
                     /translation="MAKKPKSAGREKLLFNKLKQFDEPGLFHDNYQTPDYIQANLKDIL
                     RPYQHSALRYLHYTQRKRDDALLHYRHLLFHMATGAGKTMVMAGTILYLFKEFGYQNFI
                     FFVHTDAIIQKTRENLLNPQSPKYLFSHELEIDGEKITIAPVDIFPSVPERNTIYLKLS
                     TIHKMHDELNSYRENSITYEDLKEIPLVLLGDEAHHFNAGTKARGKSKTSPENEEQTWE
                     RTIENILDLRPDNRLFEFTATIDLANKDIGQKYRDKVVYQYDLKQFMSDGYSKKVMLLE
                     ANQNDSDKMLDAVLLSQYRKLTAADHGITGFKPVILFKSNKIAISKAKQEEFSQLIAAM
                     TPESIRRHLANKKLQLSSDTSIWHKVIQRYADSDLVTVTGQIQEDFNDFNLLNVNKSDL
                     LEENPVLLNTLEEVDNPVRAVFAVAKVNEGWDVLNLYDIVRISEQASSSKTSTDSEAQL
                     IGRGARYYPFIYDGQRSFTRRFDNSTKDLSVLEQLHYHTINEPAYIKTLHASLEQADID
                     VHQDGGGTVEHARLKEDFKKSAVYQAGKLYFNEVEEIERSSRNWETYSLETRFEIQYQI
                     ACEESLDNLTGTKGGIIKPEPLVLDERFYRKAMQRISFYALDNLKRFFPKLTGIREFIR
                     SDAYLGKLKITVSVPQSLDFTTVPAKDKLHLLENVLLRISENVRRNDQKVKGTYRFISQ
                     PVKEVIKDYSLHIDPSVAINQKITAAPTIGKKWYVYDNAILNQLEHRLIKMLEAFMPKL
                     KARYDDIYVLRNDEQSTRFKLTEFGGVRGFMPDFIMILTRHSDNTYWQVFLEPKGDDRL
                     LDDAWKERMLETLNDRERIVIDENEHVRLVGIKFFANSQMDVFVSDMQNKLNDGESLET
                     SSLSLPL"
                     /name="DEAD/DEAH box helicase family protein"
     gene            complement(5972..6085)
                     /locus_tag="KKZ11_RS24115"
     CDS             complement(5972..6085)
                     /locus_tag="KKZ11_RS24115"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /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_071588254.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLSPLAAATGN"
                     /name="replication initiation protein"
     Typing          222..320
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          445..700
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.248"
                     /coverage="89.0"
                     /evalue="2.69e-98"
     Typing          6585..6670
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="8.58e-38"
     Typing          complement(6014..6567)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.075"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 gtttcacttt cggcctcaaa gcgaatctgg atgctgttct ggagttcttc tgcgagttcg
       61 tgcagtcgtt cgcacatggc cgcctgttcg tcggcatcca gagcatccag tttttcaagc
      121 agtgtcaggc tctggctttt gataaatcgc gccatattca gcgcagtttg ttgttgtttg
      181 ttcaccttcc gttgttctcc gtcagttccg ggtgtcgggg ggaccctgag caggtggtaa
      241 ttgtaagacg ttgcgggcga cggtattaca attgcacatc ctgtcctgtt tctttaggac
      301 gtatcatggc acagcatatc aactgataaa taatccctgt gcagtgcagc cgctgttgca
      361 taaaatttcg ctctgcgtcg agagtttctt aatcaataat tccgctgata ctccggaaaa
      421 acgcgagtct gttctcatgc ctgaaatgcc cacaccccac gcaaaaacaa gtttttgctg
      481 atttttcttt ataaatagag agttatgaca aattagttct tcttgctctc tttgtgatat
      541 ttaaaaaagc ggtgttggcg cagctacaac accgcgccga caccgctttt taggggtggt
      601 actgactatt ttcataaaaa acatcatctt atattagggg tgctgctagc ggcgcggtgt
      661 gtttttttac aggacgcccc tgggggcgct gctaggggtg tctgttcaga tatgtagcaa
      721 tgagtcaggg attcacgaac tgaaaatgtc ctaaaatgtg tctcatgggt actgtatgcg
      781 cccaaaccga tcgtcattca ttttcatgca tagctatgca gtgagctgaa agtgatcctg
      841 acgcattttt ccggtttacc ccggggaaaa catctctttt tgcggtgttt tcggcagaat
      901 cgcgttcagc gcgttttagc ggtgcgcgca agagcgttta tgttaaatac tactcgttct
      961 ggtgcatttt cccgcaactg aatccaactc atcgctgttg ggttccagcg ccgaacgcta
     1021 taccttacaa tcattccaat atttaacagt cataaggcca tgacatgcag accgaattaa
     1081 taaaagaact taacaaggtt ttaaaagcgt tcccgcaatt ctggaatgga gaggaattac
     1141 aacgttcaat ggtgagtgac gctatcagtc aaaagcagcc agatcttatc aaggcattag
     1201 tcgataatga aaaagtccgc tctgtttatg gtgtggatat tgatggcatt tttatctttg
     1261 attttgacaa attatgtggt cttctaaaat acaaagaata ttgggctaat agctttacta
     1321 aataccggaa caaagtggga ttaactagcg aaggtaaata ccttgattac agttctgatg
     1381 tggtgctgga ttttcctttc aaggattgta ttcttgaagg tggaatgacc aaagaaaatc
     1441 agggaaaaga tgagatttat tataatgaaa tcatagcaat ggatgaagtt gactctttgc
     1501 tttctcccaa ggcgttcact aatgctaagc gatataccaa agagggggta aaagaaaata
     1561 tcactaaatt taacgatgat gaaaatttaa taattaaggg aaacaatctc attgcactac
     1621 attcaataaa aaaactttac gcaggaaaag taaagttaat ttatatagac ccgccttaca
     1681 atacagggag tgatagcttt aagtataatg atcgattcaa tcgctcaaca tggttgacat
     1741 tcatgaaaaa taggcttgag gtggctaaag aaatgctttc cgatgatggc tttattttta
     1801 ttcaatgcga tgataatgaa tcagcatatc ttaaagtttt atgtgattca atttttggag
     1861 aagagaatta tagaaactca atctattggc atagaaccta cgcagggaaa actgtaaaaa
     1921 gtaagttgcc atggaataca gatacaatat tgttttattc taaaaaagaa agttcattat
     1981 tagagccata tacagcagaa cttagtgctg ctgacattaa atcctataac aaggatgatt
     2041 ttgatggaag gggtaaatac aacactgtta gcttgcaaaa aacaagctct ccagggccgc
     2101 aaacaactta tgattatata gataatacag gtaagaaatg gagttgccct gaaaaagggt
     2161 ggagaatgac aaaggaaaag ttaaaggctt tggaaaacga caataggcta tatatcactg
     2221 acaaaacaat acgagaaaaa tattatctta aagaaagaaa agagatcggg aaacaaatag
     2281 ataatttttg gcatgacatt gggaatttaa atagggtttc cgatgttgct tttattgatg
     2341 gacaaaaaac tgaaaaatta atgcaacgga taattagcct tgcttccaaa gaaaatgata
     2401 tcgtcttgga ctttcatctc ggcagcggaa ctagcgcagc agcagcccat aaaatgggac
     2461 gtcgctatat cggtattgag cagatggatt acatcaatga gatcaccgtg ccacgtttgc
     2521 aaaaagtcat tgagggtgag cagggaggta tctcaaaaga cgttaactgg caggggagcg
     2581 gcagctttgt ctacgttgaa ctagtggaac tgaacgctta cttcatacat gaaatccaga
     2641 aagcgcagtc cacggaagaa ctcgaaaaac tctttgccgt gatgaagaca gaggcatatc
     2701 tcaactatca ggtggctctg gaaaatgtgc tgtccgctga gtacgaagtg gatgggatcc
     2761 tccataaggt agcattcagt gaactggaac tgcatgagca gaagcagctt ttgattgaaa
     2821 tcctagataa gaaccagctc tacgtgaatg tctctgatat ggaggacagc gacctgaaca
     2881 tttcagagag tgataaagcc tttacccgca gcttctacgg aatggagtga cggcatggcg
     2941 aagaaaccga agtcagcagg tagagagaag ctgctgttta acaaactgaa gcagttcgat
     3001 gaaccaggac tgttccacga taactatcag acgccggact atattcaggc aaacctgaaa
     3061 gatatcctgc gtccctatca gcacagcgca ctgcgttacc tgcattacac gcaacgtaaa
     3121 cgtgatgacg cgcttctgca ttaccgtcac ctgctgtttc acatggcaac cggtgcaggg
     3181 aaaacgatgg ttatggcagg aacgatactc tatctattta aagagttcgg gtatcagaac
     3241 ttcatctttt tcgtacatac cgacgcgatt atccagaaaa cgcgagagaa cctacttaac
     3301 ccgcaatcgc cgaagtacct gttcagtcat gagctggaaa tcgacgggga aaaaatcacc
     3361 atcgcaccgg tagatatatt cccgtccgta ccggaacgca acacgattta cctcaagctc
     3421 tcgactatcc ataagatgca cgatgagctg aacagctatc gagagaacag cattacctac
     3481 gaggatttaa aagaaatccc gcttgtgcta ctcggtgacg aggcgcatca cttcaacgcc
     3541 ggcaccaaag ctagaggcaa gtcgaaaacc tcaccggaga acgaggagca gacttgggag
     3601 cgtacgattg agaacatcct cgacctgcga ccggataacc gcctgttcga gttcaccgct
     3661 accattgacc ttgcaaacaa agatatcgga cagaaatacc gtgacaaggt ggtatatcag
     3721 tatgatctga agcagttcat gtcagacggt tactcgaaaa aggtcatgct gttggaagca
     3781 aaccagaacg acagcgacaa gatgctcgat gcggtactgt taagccagta ccgtaaactg
     3841 acggcagcag atcacggcat caccggcttt aaaccggtca ttctgttcaa gtcgaataag
     3901 attgcgatat caaaggcgaa gcaggaggag ttttcgcaac tgattgccgc catgacacct
     3961 gagagcatca gacgtcatct ggctaacaaa aaactccagc tcagctctga caccagtatc
     4021 tggcataaag tgattcagcg ttacgctgac agtgatttag tgacggtgac tggacaaatt
     4081 caggaggact ttaatgactt taacctgctg aacgtcaaca agtcagacct gctggaggaa
     4141 aaccccgtcc tgctgaatac actggaagaa gtcgataatc cagtgagagc cgtctttgct
     4201 gtcgcgaagg tgaatgaagg ctgggacgta cttaacctct acgatattgt tcgcataagc
     4261 gagcaggcga gcagcagcaa aaccagcacg gacagcgaag cgcagcttat tgggcgaggt
     4321 gcgcgttact acccgttcat ttatgacggt caacgtagct tcacccgccg ttttgataac
     4381 agtacgaagg atttgagcgt actggagcaa ctgcactatc acaccatcaa tgaaccggcg
     4441 tacatcaaaa cactgcacgc ctctctggag caggcggaca ttgacgtgca tcaggatggc
     4501 ggaggtacgg ttgaacacgc cagattgaaa gaagacttta aaaagtccgc cgtgtatcag
     4561 gcgggtaagc tgtactttaa cgaagtggaa gagattgaga gaagcagccg aaactgggaa
     4621 acctactcgc tggaaacacg ctttgaaata cagtatcaga tcgcttgcga ggagtcgctg
     4681 gacaacctga caggcacaaa ggggggtatc ataaaaccgg aaccactggt actggacgag
     4741 cgtttttacc gcaaggcgat gcaaagaatc agcttttacg cgctagataa cctgaaacgc
     4801 ttcttcccga aactgacagg tattcgggag ttcatacgca gtgacgccta tcttggtaag
     4861 ctgaaaatca ccgtcagcgt accgcagtca ctggatttca ccaccgtacc ggcaaaagat
     4921 aagctgcacc tactggaaaa cgttttgctg cgtatctcag agaatgtgcg tcgcaatgac
     4981 cagaaggtaa aaggcacgta ccgatttatc agccagccgg tgaaagaggt gattaaagat
     5041 tacagtttgc atattgaccc gtcggtagcc attaaccaga aaatcaccgc cgctcccacc
     5101 attggtaaaa aatggtacgt gtacgataat gcgatactaa atcagcttga gcatcgtctg
     5161 ataaaaatgc tggaagcatt catgccgaag ctaaaagcgc gttatgacga tatttacgta
     5221 ctgcgtaacg acgagcagtc aacgcgcttt aagctcacgg agttcggcgg cgtgcgtggg
     5281 tttatgccag atttcatcat gatactgacg cgccattcag acaacactta ctggcaggtg
     5341 ttccttgaac cgaaggggga tgaccgtctg ctggatgacg catggaaaga acggatgctc
     5401 gaaacactga atgacaggga gcgcattgta attgatgaaa atgagcacgt cagactggtt
     5461 gggattaaat tctttgccaa tagccagatg gacgtttttg tcagcgacat gcagaacaag
     5521 ctgaatgatg gagaatcgct cgaaacctcc tcgctctccc taccactgta agtcacgaca
     5581 ataaaataac ggagcattac gctccgttat tttattgtta tctcgaacta cctcccaggg
     5641 aggtgatgat tgctcctgta atggttgcat tgtttgttct tgctgttgcg aatcattagt
     5701 tttgaatggt ggttaaaaac cgttcgctat gtttatgcct ggggggggat gagggggaaa
     5761 agattcaagg atcctcttgt gatccttttt ttctgcgcgt aatctgcagc ctgtaaacga
     5821 aaaaaccacc ctggcaggtg gtttttcgaa ggttagctaa tcctggcaga ttatctaacc
     5881 gggtaactgg cttggaggag cgcagtcacc aaaatctgtt ctttcagttt agccttaaca
     5941 ggtgcataac ttcaagacaa actcctctaa atcagttacc agtggctgct gccagtggcg
     6001 ataagtcgtg tcttaccggg ttggactcaa gacgatagtt accggataag gcgcagcggt
     6061 cgggctgaac ggggggttcg tgcacacagc ccagcttgga gcgaacgacc tacaccgaac
     6121 cgagatacca acagcgtgag ctatgagaaa gcgccacgct tcccgaaggg agaaaggcgg
     6181 acaggtatcc ggtaagcggc agggtcggaa caggagagcg cacgagggag cttccagggg
     6241 gaaacgcctg gtatctttat agtcctgtcg ggtttcgccg actctgactt gagcgtcgat
     6301 ttttgtgatg ctcgtcaggg gggcggagcc tatggaaaaa cgccagcggc gcggcctttt
     6361 tccggttcct gctcttttgc tcacatgttc tttccggcct tatcccctga ttcggtggat
     6421 aatctaatta ctgtctttgc gtgagttgat accgctcgcc gcagccgaac gaccgagcgt
     6481 agcgagtcag tgagcgagga agcggaagag cgtcggaagt tgcattttct ccttacgcat
     6541 ctgtgcggca tttcacatcg gttatggtgt acttttcata caatctgcac tgatgccgca
     6601 tagttaagcc agtatacact ccgctatcgc tacgtgactg ggtcatggct gcgccccgac
     6661 acccgctaaa accccctgac gcgccctgac gggcttgtct gctgacgaaa acgcccacgg
     6721 gaaagccgtg accgcctccg tcagcttcgt tatgttcct
//
