LOCUS       NZ_CP063471             7390 bp    DNA     circular CON 17-JUN-2023
DEFINITION  Escherichia coli strain EM20-18-50 plasmid pEM20-18-50_4, complete
            sequence.
ACCESSION   NZ_CP063471
VERSION     NZ_CP063471.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16387510
            Assembly: GCF_016942595.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 7390)
  AUTHORS   Moser,A.I., Campos-Madueno,E.I. and Endimiani,A.
  TITLE     Complete genome and plasmid sequences of MDR Escherichia coli from
            local people and environmental sources in Laos
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 7390)
  AUTHORS   Moser,A.I., Campos-Madueno,E.I. and Endimiani,A.
  TITLE     Direct Submission
  JOURNAL   Submitted (20-OCT-2020) Institute for Infectious Diseases,
            University of Bern, Friedbuehlstrasse 51, Bern 3001, Switzerland
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Flye v. 2.7.1
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 375x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/17/2023 06:49:07
            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)                     :: 4,592
            CDSs (total)                      :: 4,474
            Genes (coding)                    :: 4,235
            CDSs (with protein)               :: 4,235
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 239
            CDSs (without protein)            :: 239
            Pseudo Genes (ambiguous residues) :: 0 of 239
            Pseudo Genes (frameshifted)       :: 66 of 239
            Pseudo Genes (incomplete)         :: 169 of 239
            Pseudo Genes (internal stop)      :: 47 of 239
            Pseudo Genes (multiple problems)  :: 43 of 239
            Pseudo Genes (short protein)      :: 4 of 239
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP063471.1.
            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..7390
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="EM20-18-50"
                     /isolation_source="chicken meat"
                     /db_xref="taxon:562"
                     /plasmid="pEM20-18-50_4"
                     /geo_loc_name="Laos"
                     /collection_date="2018"
                     /collected_by="Institute for Infectious Diseases Bern"
     gene            393..584
                     /locus_tag="IQS25_RS22495"
                     /old_locus_tag="IQS25_22515"
     CDS             393..584
                     /locus_tag="IQS25_RS22495"
                     /old_locus_tag="IQS25_22515"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041614.1"
                     /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_001041614.1"
                     /translation="MNKQQKTAVNMAKFIQDQSLLLLDRLNELDLDHEADFCEKLHEDA
                     ERLYRSLSARLNEQQDGA"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1495..2378
                     /locus_tag="IQS25_RS22500"
                     /old_locus_tag="IQS25_22520"
                     /pseudo=""
     CDS             1495..2378
                     /locus_tag="IQS25_RS22500"
                     /old_locus_tag="IQS25_22520"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016946055.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /name="replication initiation protein"
     gene            2564..3148
                     /locus_tag="IQS25_RS22995"
     CDS             2564..3148
                     /locus_tag="IQS25_RS22995"
                     /inference="COORDINATES: protein motif:HMM:NF013884.2"
                     /GO_function="GO:0016747 - acyltransferase activity,
                     transferring groups other than amino-acyl groups [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="acyltransferase family protein"
                     /protein_id="WP_251301896.1"
                     /translation="MFFFGVSGYLVAQSGIRSGDFLIFMTKRIKRIFPALIFCGFVIYF
                     FLGLALQPSMVFTKSTLHSFIDLVFLRGANAMSMANGFVYPHAIDGSLWTLPLEFLCYI
                     ILGVIFCFSKTIRPVLLVFSFMLVLSIYLLSNPTGIGFYSISIQAFVPLATSFFMGVLM
                     SLTKPRWDFWKIKSFLFFSLFFITNLHGWDL"
                     /name="acyltransferase family protein"
     gene            complement(4130..4827)
                     /locus_tag="IQS25_RS22510"
                     /old_locus_tag="IQS25_22530"
     CDS             complement(join(4130..4578,4578..4827))
                     /locus_tag="IQS25_RS22510"
                     /old_locus_tag="IQS25_22530"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_086558267.1"
                     /ribosomal_slippage=""
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /note="programmed frameshift; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS1 family transposase"
                     /protein_id="WP_244569998.1"
                     /translation="MASVSISCPSCSATDGVVRNGKSTAGHQRYLCSHCRKTWQLQFTY
                     TASQPGTHQKIIDMAMNGVGCRATARIMGVGLNTILRHFKKLRLQPVNSRIQPGSDVIV
                     CAEMDEQWGYVGAKSRQRWLFYAYDRIRRTVVAHVSGERTLATLERLPGPLSAFEVVVW
                     MTDGWPLYESRLKGELHVISKRYTQRIERHNLNLRQHLARLGRKPLSFSKSVELHDKVI
                     GHYLNIKHYQ"
                     /name="IS1 family transposase"
     gene            complement(4899..6008)
                     /locus_tag="IQS25_RS22515"
                     /old_locus_tag="IQS25_22535"
     CDS             complement(4899..6008)
                     /locus_tag="IQS25_RS22515"
                     /old_locus_tag="IQS25_22535"
                     /EC_number="2.3.-.-"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_013036402.1"
                     /GO_function="GO:0016747 - acyltransferase activity,
                     transferring groups other than amino-acyl groups [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="acyltransferase"
                     /protein_id="WP_203139995.1"
                     /translation="MNTQTFRGVQALRGIAALSVMLFHFRWNINAQIPGHGDALFGWGA
                     TGVDLFFLISGFVITLSAAKAPQGISGALNFLKKRALRILPAYYIILVISFFLTGAMST
                     FHYADKTENFISALTFMPILPDHAPFYVDDSGMFGVRWTLNYEVMFYLFISVALLFAKR
                     WVWAGVLFAATLVVLPLTLGYQLTLQPAGYKVDSALLGLITNPMTWLFLTGMLIGLALP
                     YLRWLSSSVMAVAAVCSLIAAAYFFSHGMYAGHGLLSSGWVYGLILLTFALSEDVIGKY
                     VPNFLIRLGDISFSLYLIHTLMNNGLGKRFESFGIEDGYVRFVVSIALSCLLAWLSWRY
                     IERPFIRAGKIKTVSKEKNAAASSPASHK"
                     /name="acyltransferase"
     gene            6191..6888
                     /locus_tag="IQS25_RS22520"
                     /old_locus_tag="IQS25_22540"
     CDS             join(6191..6440,6440..6888)
                     /locus_tag="IQS25_RS22520"
                     /old_locus_tag="IQS25_22540"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001743396.1"
                     /ribosomal_slippage=""
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /note="programmed frameshift; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS1 family transposase"
                     /protein_id="WP_232209905.1"
                     /translation="MASVSISCPSCSATDGVVRNGKSTAGHQRYLCSHCRKTWQLQFTY
                     TASQPGMHQKIIDMAMNGVGCRATARIMGVGLNTILRHFKKLRPQSVTSRIQPGSDVIV
                     CAEMDEQWGYVGAKSRQRWLFYAYDRLRKTVVAHVSGERTLATLERLPGPLSAFEVVVW
                     MTDGWPLYESRLKGELHVISKRYTQRIERHNLNLRQHLARLGRKPLSFSKSVELHDKVI
                     GHYLNIKHYQ"
                     /name="IS1 family transposase"
     Typing          complement(2..106)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.113"
                     /coverage="93.0"
                     /evalue="2.05e-44"
     Typing          complement(7021..7390)
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="82.228"
                     /coverage="99.0"
                     /evalue="6.8e-82"
ORIGIN
        1 tcccggaact gagtgtcagg cgtggaatga gacaaacgcg gccataacag cggagtgaca
       61 ccggtaaacc gaaaggcagg aacaggagag cgcacgaggg agccatcagg gggaaacgcc
      121 tggtatcttt atagtcctgt cgggtttcgc caccactgat ttgagcgtca gatttcgtga
      181 tgcttgtcag gggggcggag cctatggaaa aacgccccgg cggggcgtgg ccttttcgcc
      241 cttgtcctta gctttcgtta tgcttaccgt tacgttatct gcttatcttc cctccgctcg
      301 ccgcagactc atgaccgaac ggagtgagcg aatgagcgag gaagcggaaa accatcagaa
      361 cgtacagtaa gcactttcgc gccggggcct tcatgaacaa acaacaaaag actgccgtta
      421 acatggctaa attcatccag gatcagtccc tgcttcttct ggacaggctt aatgagctgg
      481 atctggatca tgaggctgat ttctgcgaga aactccatga ggatgcggaa cgcctttacc
      541 gaagcctgtc agcgcgcctg aatgagcagc aggacggtgc gtaatggctc cgttctgggt
      601 attaccggag taataccggc atcgccttaa ttttcattgt gttagcgctt aacattatta
      661 ccccggtaat acccagaatc cctgtatttt ttctttttta tttatttttc atgaagttgc
      721 gatgaaaatc gcagctgcgt taggtgtatg accattttga ggttgaaaaa taatcaacca
      781 tggagggtga tttacgcagg ttaaggggag atcgtgacaa aaaaagcgtt cctcactgta
      841 tcgttcatgc ctgcatgaac gggttattct tcctgactac agaattacat tgctccttca
      901 gttcatacat cacttttaca acacttttgc atcactttta catcattcct tcagctcata
      961 cgtcactttt acgtcagttc catcctctgt gccatttgta catccgaccc ccttcctgaa
     1021 cgtgctgaaa acggtttttc cggctgtgcc ggcaacgcct cacggccacg caataaattg
     1081 cgtccccgtt caccgttttc ggataagaag aacatcggaa acaggactta ccccggctga
     1141 atggcgtgaa tttccgcgct atgcacttgt gcgcatactc atgcatgccg taaaaacaga
     1201 gcctgcgcgt ttctggcggg ttttcgggtg gtttgttgcc tgttttgccg gtttcccgtc
     1261 agaaacgccc tgagggcctc tgaggcggtg cacgcaacgg atgttatggt aaatcgtggt
     1321 gagatcgaca gatagcgtaa gacggtgtaa cgttaaggcc agaaaaaaca aagccccgga
     1381 aatcatgctc attcttggcg gagcgacatg ataaccaggg cctggtcgaa acctgagaag
     1441 gatattagca catgaaccgt gccagacaac agcccgccat aagcgcaggg cacattgcat
     1501 aacgccgcac tcgaactttt taacgaccgc ttaccgcaca agccgtactt ctcggatgat
     1561 cttcacttcg gtgtacgcat cgcaggaaaa gagcgcgcta tcctggcgaa atacatccag
     1621 ttcaatcagc cccatgccat gttctggctg ggatttgacg tcgatcgcgc cggcgctgct
     1681 atcgactgga gcgaccgcaa cgcacccgcg cccacgctga ccatcaccaa tcccgaaaac
     1741 ggacacgcgc acccgcttta cgcgctggaa acctcgatac gcaccgcacc ggacggaaaa
     1801 ataaagccgc ttaagtacgc cgccgcagtt gagaacgcgc tgcgtaaaaa attagaggct
     1861 gataccggat attcgggact catctgcaaa aatccgaatc atagtcactg gaaaatcgcc
     1921 gtatggcagc cggagcctta cacgctggac tggctggccg actctctcga tctgagtgca
     1981 gcgaacgaca aagaggtcgt cgctgccgca actgcaccct gttcgacaaa actcgcaagt
     2041 gggcataccg tgctattcgt cagggctggc ctgagtatga gcagtggctg caagcctgct
     2101 acgaacgagc cagcgcttac aacctgcaat tttcatctcc tctggatgaa aatgaggtga
     2161 gagggatagc taaaagcatt gcaaaatgga ctactaatca atttaatagc aattcatttt
     2221 ctaattttat aattaaaaca cacacatcag aaatacaatc aaagagaggt gttctttctg
     2281 gtgtgtctag gagggctggg agcctggagg agcgaaaacc atgggatgag cttggcataa
     2341 gcagaagaaa atttttctat ttaaagaaaa aggcatgaaa tttattctat ttatatgact
     2401 tggtatttat ttatggctgt tagctctatt catcgtgata atttttttga tgtaatcaga
     2461 ttggttgctt catttcttgt tttatattct catcatttcc ctttaagtgg gttggcagag
     2521 ccgtctttcc ttggttttac tagttttgga gggttggcgg ttattgtttt tttttggtgt
     2581 ctctggttat cttgttgctc aatcaggaat aagatctggt gattttttaa tatttatgac
     2641 caagaggatt aagagaatat ttcccgctct tatcttttgt ggttttgtta tttatttttt
     2701 ccttggcctt gctcttcagc caagcatggt ttttactaag agcacactgc attcttttat
     2761 tgatttggtt tttttgcgcg gcgcaaatgc catgtctatg gctaatggat ttgtctatcc
     2821 tcatgctata gatggtagcc tatggactct tccgctggag tttttatgct acataatact
     2881 aggtgttatt ttttgttttt caaaaacaat aagaccagtt cttttggttt tttcttttat
     2941 gctagtgctt agtatatatt tattgtcaaa tccaacagga attgggtttt actctatatc
     3001 tattcaggcg tttgtgcctt tggcaacttc tttttttatg ggagttctaa tgtcgctaac
     3061 taaacctagg tgggactttt ggaaaattaa atcatttttg tttttcagtc ttttttttat
     3121 tactaatctc catggatggg acttatgaaa taaaagctct cggatatgtc attatcccag
     3181 tgttaactat tatcgcaggt gtgtcattta gggataagtt aataaatggg agattcgatt
     3241 attcttatgg tatctacata tatgctttcc ctgtacagca agtaattata aattacggag
     3301 gctgtgggtt ttggctttca atgttattta gtgcgattgt tactttgata ttagcttctc
     3361 tatcatggca tttaatagag aagagaatgc ttataaaata aattgacgca ctcgcctttt
     3421 aattactaac cgtgactaca caatgcaact ttataacttg catcagaatc aagtagacga
     3481 atagaggcag agcgatttta gttaccaact gatgcatgct cggggggggg gggggactgc
     3541 ggctgcgagc caagaaccta tattgactcg cagcctatta atttttctgt atgtgcactg
     3601 ttgatatgtt ttgcactcga acctatatca gataacagct tttttttaga ttcagtttat
     3661 tcggtttacc tgcctactat caactactta ctccgccaca agctttccct ctgccctatg
     3721 cccatgctgc gaatttttcg cacttcatat gcgaatattc tcactccttt tgcacgcaac
     3781 gctcgccgca gtctcatgac cgaacgaagt gagcgaatga gcgaggaagc gtcatttcag
     3841 gggtcagttt ggatatagag aattattgta cggcaagcct gttttttgaa caggcttacc
     3901 tatggcgata gggtgtaccc ccacgctata cgccatttcc cgtggatttt gtctaaccgg
     3961 ataacctaaa tgcgatacgg attacgcgat aatttgaaag cgatagccac tggcactaaa
     4021 tcaatccctt acgggttcac ttggtaaata aatcgctaaa cgtacaataa tttccgatct
     4081 ccaaactgac tcctactata tcattcgaag ttagggtaat gctgccaact tactgatagt
     4141 gttttatgtt cagataatgc ccgatgactt tgtcatgcag ctccaccgat tttgagaacg
     4201 acagtggctt cctgcccagc cttgccagat gctgcctcag attcaggtta tgccgctcaa
     4261 tgcgctgcgt atatcgcttg ctgataacgt gcagttctcc cttcaggcgt gattcataaa
     4321 gcggccagcc atccgtcatc cataccacga cctcaaaggc cgacagcggg cccggaagac
     4381 gctccagcgt ggccagcgtg cgttcaccgg atacgtgcgc cacaaccgtc ctccgtatcc
     4441 tgtcatacgc gtaaaacaac cagcgctggc gtgatttagc gccgacgtaa ccccactgtt
     4501 cgtccatttc cgcgcaaaca atgacgtcac tgcccggttg tatgcgtgag tttaccggct
     4561 gcagcctgag ttttttaagt gtcgtaaaat cgtgttgagg ccaacgccca taatgcgggc
     4621 ggttgcccgg catccaacgc cattcatggc catatcaatg attttctggt gtgtaccggg
     4681 ctgagaggcg gtgtaagtga actgtagctg ccatgtttta cggcagtgag agcagagata
     4741 gcgctgatgt ccggcagtac ttttaccgtt acgcaccacc ccgtcagtag ctgaacagga
     4801 gggacagctg atagaaacag aagccactgg agcacctcaa aaacaccatc atacactaaa
     4861 tcagtaaatt ggcagcatta tccaggtgct gctatttatt atttatggct tgctggagaa
     4921 gatgctgcag catttttttc cttactgaca gttttaattt tacctgcccg aataaacggc
     4981 ctttcaatat agcgccatga gagccaggca agtaaacatg aaagagcaat ggaaactaca
     5041 aacctcacat atccgtcttc aatcccaaaa ctttcgaatc gctttcctaa tccattattc
     5101 atcaaggtat ggattaaata aagagagaaa gaaatatcgc ctaaccgaat taaaaagttt
     5161 ggcacatatt tcccgatgac atcttcagaa agagcaaagg ttaatagaat aagtccatat
     5221 acccagcccg aactgaggag cccatgcccg gcatacatgc catgactaaa gaagtaggct
     5281 gctgcaatca ggctacatac tgcagcaact gccataacac tggatgatag ccatctcaga
     5341 taaggaagcg ccagtccaat caacatcccg gtaaggaaca accaagtcat tgggttagtg
     5401 attaatccca gcagggctga atcaacctta taaccggcag gctgaagagt tagctgataa
     5461 cctaaagtta aaggcagcac aacaagcgtt gccgcaaaca gaacgccagc ccatacccag
     5521 cgcttagcaa acagaagagc gacggatata aacaggtaaa acataacctc ataattcagc
     5581 gtccatctga cgccaaacat tccgctatca tcaacataaa aaggcgcatg atcggggagt
     5641 atcggcataa aggtcaatgc gctgataaaa ttttccgttt tatctgcata atgaaacgtg
     5701 ctcatcgcac cggtcaggaa gaaagaaatg accagaatga tgtagtaagc cggcaatatt
     5761 ctcagcgccc ttttctttaa aaaattaagg gcgccgctaa tgccctgagg tgcttttgcg
     5821 gcgctcagcg ttataacgaa tccgctgata agaaagaaga gatcgacacc cgttgctccc
     5881 catccaaaaa gcgcatctcc atgtcccggg atttgagcat ttatgttcca tcggaagtgg
     5941 aaaagcataa cgcttagcgc agcaattcct ctcagcgcct gtacgcctct aaaagtctga
     6001 gtgttcatat tgtttaagct taatcgcagc attgtgtaaa cagaaaggca ggaatcttac
     6061 aggctaattt actgtcttgc acagactgca acagcaacaa aacataatgt gtgattttgg
     6121 ttattcggcg tatcgggtga tgctgccaac ttactgattt agtgtatgat ggtgtttttg
     6181 aggtgctcca gtggcttctg tttctatcag ctgtccctcc tgttcagcta ctgacggggt
     6241 ggtgcgtaac ggcaaaagta ccgccggaca tcagcgctat ctctgctctc actgccgtaa
     6301 aacatggcaa ctgcagttca cttacaccgc ttctcaaccc ggtatgcacc agaaaatcat
     6361 tgatatggcc atgaatggcg ttggatgccg ggcaacagcc cgcattatgg gcgttggcct
     6421 caacacgatt ttacgtcact taaaaaactc aggccgcagt cggtaacctc gcgcatacag
     6481 ccgggcagtg acgtcatcgt ctgcgcggaa atggacgaac agtggggcta tgtcggggct
     6541 aaatcgcgcc agcgctggct gttttacgcg tatgacaggc tccggaagac ggttgttgcg
     6601 cacgtatccg gtgaacgcac gctggccacg ctggagcgtc ttccgggccc gctgtcggcc
     6661 tttgaggttg tggtatggat gacggatggc tggccgcttt atgaatcacg cctgaaggga
     6721 gaactgcacg ttatcagcaa gcgatatacg cagcgcattg agcggcataa cctgaatctg
     6781 aggcagcatc tggcaaggct gggcaggaag ccactgtcgt tctcaaaatc ggtggagctg
     6841 catgacaaag tcatcggaca ctatctgaac ataaaacact atcagtaagt tggcagcatt
     6901 acccatatgt cgctgggcca actcttctgg tttctgggtt ttttatcgtg gattacaagg
     6961 ccgtcatctg ataatgcccc taatggggca gatctctagg atagtagcaa tacagcaagg
     7021 aacttcttga gatcctttct gttgcgtcgt aatctcatgt cctgcaaaca aaaaaaccac
     7081 cgctaccaac ggtggttcgt ttgccggaat caagagctac caactctttt ttccgaaggt
     7141 aactggcttt cacggagcgc agataccaaa actgtccttc cagtgtagcc gcagtcaggc
     7201 caccacttca agaactctgt agaagcactc tactactctg ctccgtgaat cctgttacca
     7261 gtggctgctg ccagtggcga taagtcgtgt ctttccggat tggactcaag acgatagtta
     7321 ccggataagg cgcagcggtc ggactgaacg gggggttcgt gcatacagtc cagcttggag
     7381 cgaactgcct
//
