LOCUS       NZ_CP075728             4084 bp    DNA     circular CON 16-AUG-2023
DEFINITION  Escherichia coli strain CPE35 plasmid unnamed.2, complete sequence.
ACCESSION   NZ_CP075728
VERSION     NZ_CP075728.1
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 4084)
  AUTHORS   Khine,N.O.
  TITLE     Colistin resistant E. coli isolates in pigs and pig farm environment
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4084)
  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
            CP075728.1.
            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..4084
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="CPE35"
                     /isolation_source="Pig feces"
                     /host="Sus scrofa"
                     /db_xref="taxon:562"
                     /plasmid="unnamed.2"
                     /geo_loc_name="Thailand: Bangkok"
                     /collection_date="2017-06-10"
                     /note="mcr-3"
     gene            join(2955..4084,1..1030)
                     /gene="mobQ"
                     /locus_tag="KKZ10_RS24135"
                     /old_locus_tag="KKZ10_23980"
     CDS             join(2955..4084,1..1030)
                     /gene="mobQ"
                     /locus_tag="KKZ10_RS24135"
                     /old_locus_tag="KKZ10_23980"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016240513.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobQ family relaxase"
                     /protein_id="WP_063090928.1"
                     /translation="MAIYHLSMKIISRKNGYSAVASAAYRSGSLMPDERTGLIHDYTRK
                     SGVAEAVILTPATAPTWCTNRAELWNAVEKAERRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALTNAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIVLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYSSEQDKIQSLSQRMEKLRLHYRKVEKQDIPASQMVFETQWQQWGASGLAALRAQL
                     LKREEELRRREQEDTERRRAERLAEQLRKNDNAVMDSGVLRAVVTGYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRSRIFESVDLMRDRSGYICDRSEIGQRPPLQRVYSSA
                     TFEQLLTQVCQTWPQHTRNLRQPKTWPESFCLGEDRQPAIPSLAARKVDFTQGRLPPTL
                     MPVMSSVDRENRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHATERRHDRGWSQ"
                     /name="mobQ"
     gene            complement(1288..1989)
                     /locus_tag="KKZ10_RS24140"
                     /old_locus_tag="KKZ10_23985"
     CDS             complement(1288..1989)
                     /locus_tag="KKZ10_RS24140"
                     /old_locus_tag="KKZ10_23985"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001281399.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /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_001281397.1"
                     /translation="MSDLIAYKSNALVEASYKLTLQEQRFLLLCIGRLKSGADAESPKL
                     QKTMTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKDDEKREEFRWIQYRAQY
                     AKGEARAQITFSDAVMPYLTQLQGQFTRVVIKNISRLSRSYSIRIYELLQQFRSTGERI
                     IALDDFRSMLDIEHKYQTYKSLNQQLLRPCIDELNKKSDLAVTVETIKKGRTVVALHFR
                     FKEDKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(2522..2776)
                     /gene="mobC"
                     /locus_tag="KKZ10_RS24145"
                     /old_locus_tag="KKZ10_23990"
     CDS             complement(2522..2776)
                     /gene="mobC"
                     /locus_tag="KKZ10_RS24145"
                     /old_locus_tag="KKZ10_23990"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091747.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase accessory protein MobC"
                     /protein_id="WP_000091745.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVIVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPGQ"
                     /name="mobC"
     Typing          complement(2778..2954)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          2955..3313
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="94.444"
                     /coverage="100.0"
                     /evalue="1.88e-155"
     Typing          complement(1289..1989)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          6..1027
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.894"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          2869..4082
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.284"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 gatggtattt gaaacacagt ggcagcagtg gggggcttcc ggccttgcag cgctcagagc
       61 tcagttgctt aaacgtgaag aggaattgcg ccggagggag caggaggata cagaacgtcg
      121 tcgcgcggag cgactggctg agcagctcag gaaaaatgac aatgccgtta tggattcagg
      181 ggtactgaga gcagtcgtta cggggtatgg cgaggctccc atgccaggta acggggaaat
      241 gacctgttac cttctgcttc acaaccggaa cggagaatat acgctctggg ggaacgagct
      301 ggagaaatac cgctccagaa tttttgagag tgttgattta atgcgtgaca ggagtggtta
      361 tatctgtgac cgaagcgaaa tcggtcaacg tccaccactg caacgtgttt attcctctgc
      421 gacctttgag caactgctga cgcaggtttg ccagacatgg ccgcaacata cccgtaatct
      481 ccgccagccg aaaacatggc cggagtcttt ctgtcttgga gaagaccgcc agccagccat
      541 tccatcactg gcggcaagga aggtggattt tacgcaggga cgtctgccac cgacgctgat
      601 gccggtaatg agttctgtcg accgggaaaa ccgccagctt cagcttttgc tggtcatggg
      661 cgtggatgac tctctgggcg gtgttgtccg gcttaatggt acgctgtatc ccgcgtttgc
      721 cgttccctca gccgataaca gccagctggt catcagtgca ctgaccgata aggggttacg
      781 gtatgcaggg tatggtgttg ccgtaaatca cgatgcagac agccacatat cacctgcgcc
      841 ggaacttatg gagtttcatc tgaaaacccg tgaggcaccg ctttttgctg ccgtcaacac
      901 accagaaaaa cagccggatc atctgttccg ctcgctgggt tttaatcgta cctgggacga
      961 atggcggcgc gaggaagatg cacgaacaca cgccaccgag aggagacatg atcgcggttg
     1021 gtcacagtga atgtgaacaa tattttgttt tatttaacat cgtgttatgt tcgtcgatgt
     1081 tcttcgatgt tcatcgacag ggatgaatgc aagaagcaca cacacataat gcaagcatag
     1141 ttttgttttt ccgcccccaa aaaatggggg ttcttttttc gctgcattag agcgcttttg
     1201 acgcaatttt tcacttcaat agtaccttcg cactactaac acaaaaaaaa cgcagcaggg
     1261 agcgttttag gtgccttaaa atcgatttta gatcgtcatc ttgatttgtt tgtcttcctt
     1321 gaagcgaaaa tgcagggcta caaccgtgcg cccctttttg atcgtctcaa ccgttacagc
     1381 caggtcgctt tttttgttca gttcgtcaat gcagggtctt aataattgct ggttaagtga
     1441 tttatatgtt tgatatttat gctctatatc aagcattgag cgaaaatcat cgagagcgat
     1501 aatacgttcg ccagtactgc ggaactgctg gaggagttcg tatatcctta tactgtaact
     1561 tcttgataat ctagatatat tcttgattac aactctagta aattgccctt gtagttgtgt
     1621 caaataaggc attactgcgt cagaaaatgt tatttgtgct ctggcctcgc ctttagcgta
     1681 ctgtgcccga tactggatcc agcggaactc ctcacgtttc tcgtcatcct tgagaatgat
     1741 tgacctgtcc cacaaacgat caattgcttc ctgtaactga acctcggcat ttttccgccc
     1801 catgtcaggg aatgaatcga aatattccgc agctgtaatg gtcattgtct tttgcaattt
     1861 tggagattct gcatcagccc cagacttcaa tcgaccgatg caaagtaaca aaaatcgctg
     1921 ttcctgtagg gtcaatttat aactggcttc aaccagcgca ttggatttat aggcaattag
     1981 atccgacata gagcatccct ccccaaaagg taatgaataa aagataaaca taccctcaac
     2041 gaaaggcaat gcctttttat tttaatatcc ctttttctgt gaatattacc ttaaatcata
     2101 ttgcctttac cttaaattcc ttcacctaaa caccttaaat catattacct ttaccttaaa
     2161 tcatattacc tatagcgttg taacattttg ttttctataa ggaattttgg cgctaaaaca
     2221 agtattaaaa acaagatctt aaaaacaaga tctaaaaact taacgacgag cctgtggata
     2281 acttggagtg ctgaaaacaa aaaaccaata aaaacaatgc gttgcaaaaa agcagaattg
     2341 caagttccga ataccccccc tccaaccctg tggaaatcca gtattcatgc gggttcagcg
     2401 catatcacct cccgaaaaac cgtgcgtatg tgctcaatca ggcgacggat tcacttccgc
     2461 ttcctcgccc actcgctcgc taacgctcgg tcgctgggac tgcggcgagc ggacgataca
     2521 atcactgtcc tggcagcgct tccagctcgt taatcagcgg cagtatgcgc gtcacatcag
     2581 cctgtcgtgt cacctctgcc ttcaggaact ggagtaacca ggcacgcaac tgcacctcct
     2641 ccggctttct gacctttgcc agcaatgctg cacccacaat gaccttctgc gctgtgtcca
     2701 gactcctgct cttcgccttc aggcgctgta atctggcctc agcatcagca atcttctgtt
     2761 cgagtgttct gctcatgatg taactccgtg cgcgatgaaa aatcgcattt tagcgcgtca
     2821 ctggtagttt aaaaactgag ctggcataat gcacggaaaa tcacgaagtg cgcacttata
     2881 caatctccac tccgtttcga ttgtgtgcgc cctgcggggc tgaaagaaaa ccacaaaaag
     2941 gcattacggc agaaatggcg atttatcatc tcagcatgaa aatcatttcg cgaaaaaacg
     3001 gctacagcgc cgttgcttct gctgcctatc gttccggttc actgatgcct gatgagcgta
     3061 ccggactgat tcacgattac acccgcaaaa gcggcgtggc tgaggccgtg attctgactc
     3121 ccgcaaccgc ccccacctgg tgtacgaacc gtgccgaact ctggaatgct gttgagaagg
     3181 ctgagcgccg gaagaactca caacttgcgc gggaaattga actcgccatc ccccgcgaac
     3241 tgccgcagga tgccgcacgg gaaaccgttc tcgcctttgt cagggaaaac tttgtcagtc
     3301 agggcatgat tgctgatgtg gcgttccatc acatggataa aacaaatccc catgcgcaca
     3361 tcatgctgac cacaagagct gtcggacctg cgggatttgg aggaaaggtc agggactgga
     3421 acgaccggac acatgccgag acatggcggg catcatgggc tgaccatgcg aacagggcac
     3481 tgacgaacgc cggttatcag gaagagatag accatcgttc atacgagcga caggggcttg
     3541 agaaaacgcc tggtattcac cttggaaagt ctgcctgtgc gatggaaaca cgcggtatcg
     3601 agacagaacg cggcgaacag aatcgtctga ttaacaggct taacctggaa atacagattt
     3661 cccgtaccga actcaggaac agcgggctga cagagcctgc ccgccgtgtg gctgaccttc
     3721 tgaatatcgt gcttcctgac aacgcaactt cgtacacact acgtgacatc atcgaagcgt
     3781 tgccgaagga cagtaacgcg gcatggaaac tcaccagtaa tgccatgtcg atgatggcag
     3841 atatgcaggc gacgcgcaga cgctgggaag agctgaacac cgaacgaaag gaagcgatga
     3901 gccatgctgc cagcctgaaa aaatcatcgc cgttttcgtc cggtttttcc cgtattcccc
     3961 tgatgcaatg ggctgcaccg gaatacagca gcgaacagga caaaattcag tcgctgagcc
     4021 agcgcatgga aaaattacgg ctgcattacc ggaaggttga gaaacaggac attcccgcga
     4081 gtca
//
