LOCUS       NZ_CP063508             6477 bp    DNA     circular CON 17-JUN-2023
DEFINITION  Escherichia coli strain EH09-18-41 plasmid pEH09-18-41_5, complete
            sequence.
ACCESSION   NZ_CP063508
VERSION     NZ_CP063508.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16387495
            Assembly: GCF_016944715.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6477)
  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  JOURNAL   Unpublished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 6477)
  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                   :: 397x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/17/2023 06:32:02
            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)                     :: 5,054
            CDSs (total)                      :: 4,930
            Genes (coding)                    :: 4,724
            CDSs (with protein)               :: 4,724
            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)              :: 206
            CDSs (without protein)            :: 206
            Pseudo Genes (ambiguous residues) :: 0 of 206
            Pseudo Genes (frameshifted)       :: 57 of 206
            Pseudo Genes (incomplete)         :: 149 of 206
            Pseudo Genes (internal stop)      :: 32 of 206
            Pseudo Genes (multiple problems)  :: 34 of 206
            Pseudo Genes (short protein)      :: 4 of 206
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP063508.1.
            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..6477
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="EH09-18-41"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pEH09-18-41_5"
                     /geo_loc_name="Laos"
                     /collection_date="2018"
                     /collected_by="Institute for Infectious Diseases Bern"
     gene            271..483
                     /locus_tag="IQS19_RS24545"
                     /old_locus_tag="IQS19_24555"
     CDS             271..483
                     /locus_tag="IQS19_RS24545"
                     /old_locus_tag="IQS19_24555"
                     /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_000455501.1"
                     /translation="MEYEKSASGSVYLIKSDKGYWLPGGFGYTSNKAEAGRFSVADMAS
                     LNLDGCTLSLFREDKPFGPGKFLGD"
                     /name="hypothetical protein"
     gene            485..691
                     /gene="urfF"
                     /locus_tag="IQS19_RS24550"
                     /old_locus_tag="IQS19_24560"
     CDS             485..691
                     /gene="urfF"
                     /locus_tag="IQS19_RS24550"
                     /old_locus_tag="IQS19_24560"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007857788.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid repression protein F"
                     /protein_id="WP_007857788.1"
                     /translation="MKDQKDKQTGDLLASPDAVRQARYAERMKAKGMRQRKFWLTDDEY
                     EALRECLEELRAAQGGGSDPASA"
                     /name="urfF"
     gene            721..1560
                     /locus_tag="IQS19_RS24555"
                     /old_locus_tag="IQS19_24565"
     CDS             721..1560
                     /locus_tag="IQS19_RS24555"
                     /old_locus_tag="IQS19_24565"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001517559.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helicase RepA family protein"
                     /protein_id="WP_000190708.1"
                     /translation="MATHKPINILEAFAAAPPPLDYVLPNMVAGTVGALVSPGGAGKSM
                     LALQLAAQIAGGPDLLEVGELPTGPVIYLPAEDPPTAIHHRLHALGAHLSAEERQAVAD
                     GLLIQPLIGSLPNIMAPEWFDGLKRAAEGRRLMVLDTLRRFHIEEENASGPMAQVIGRM
                     EAIAADTGCSIVFLHHASKGAAMMGAGDQQQASRGSSVLVDNIRWQSYLSSMTSAEAEE
                     WGVDDDQRRFFVRFGVSKANYGAPFADRWFRRHDGGVLKPAVLERQRKSKGVPRGEA"
                     /name="helicase RepA family protein"
     gene            1547..2398
                     /gene="repC"
                     /locus_tag="IQS19_RS24560"
                     /old_locus_tag="IQS19_24570"
     CDS             1547..2398
                     /gene="repC"
                     /locus_tag="IQS19_RS24560"
                     /old_locus_tag="IQS19_24570"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000240539.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication protein C, IncQ-type"
                     /protein_id="WP_000240536.1"
                     /translation="MVKPKNKHSLSHVRHDPAHCLAPGLFRALKRGERKRSKLDVTYDY
                     GDGKRIEFSGPEPLGADDLRILQGLVAMAGPNGLVLGPEPKTEGGRQLRLFLEPKWEAV
                     TADAMVVKGSYRALAKEIGAEVDSGGALKHIQDCIERLWKVSIIAQNGRKRQGFRLLSE
                     YASDEADGRLYVALNPLIAQAVMGGGQHVRISMDEVRALDSETARLLHQRLCGWIDPGK
                     TGKASIDTLCGYVWPSEASGSTMRKRRQRVREALPELVALGWTVTEFAAGKYDITRPKA
                     AG"
                     /name="repC"
     gene            2508..3404
                     /gene="estX"
                     /locus_tag="IQS19_RS24565"
                     /old_locus_tag="IQS19_24575"
     CDS             2508..3404
                     /gene="estX"
                     /locus_tag="IQS19_RS24565"
                     /old_locus_tag="IQS19_24575"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016242844.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="alpha/beta fold putative hydrolase EstX"
                     /protein_id="WP_223542816.1"
                     /translation="MNKMLYVKLEGNFSMKEKVVVDKAISLHTESFGDPAHEPIILIMG
                     AMASAVWWPDEFCSQLAKMGRYVIRYDHRDTGKSTSYEPGQAPYSVEELADDVVRVIDG
                     YGLEAAHLVGMSLGGFLSQLVALKYPKRVKSLTLIASERLADADPDMPAFDPAIIEYHQ
                     RAESLDWSDRDAVVAYQVGAWRIISGTAHAFDAEKIQNIAELDFDRTPNILTTFNHTTS
                     GGGERSLERWLGRLNEIAVPTLIIHGTEDPVLPYVHGLALKDAIRGSKMLTLEGTGHEL
                     HHEDWPRIIQAIKGQTS"
                     /name="estX"
     gene            complement(4074..4358)
                     /locus_tag="IQS19_RS24570"
                     /old_locus_tag="IQS19_24580"
     CDS             complement(4074..4358)
                     /locus_tag="IQS19_RS24570"
                     /old_locus_tag="IQS19_24580"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000238497.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="mobilization protein C"
                     /protein_id="WP_000238497.1"
                     /translation="MVKGSNKAADRLAKLEEQRARINAEIQRVRAREQQQERKNETRRK
                     VLVGAMILAKVNSSEWPEDRLMAAMDAYLERDHDRALFGLPPRQKDEPG"
                     /name="mobilization protein C"
     gene            4663..>5196
                     /locus_tag="IQS19_RS25300"
                     /pseudo=""
     CDS             4663..>5196
                     /locus_tag="IQS19_RS25300"
                     /inference="COORDINATES: protein motif:HMM:NF015354.2"
                     /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="MobA/MobL family protein"
                     /name="MobA/MobL family protein"
     gene            5306..5719
                     /locus_tag="IQS19_RS25305"
     CDS             5306..5719
                     /locus_tag="IQS19_RS25305"
                     /inference="COORDINATES: protein motif:HMM:NF036929.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IncQ-type mobilization protein MobB"
                     /protein_id="WP_010890157.1"
                     /translation="MNAIDRVKKSRGINELAEQIEPLAQSMATLADEARQVMSQTQQAS
                     EAQAAEWLKAQRQTGAAWVELAKELREVAAEVSSAAQSARSASRGWHWKLWLTVMLASM
                     MPTVVLLIASLLLLDLTPLTTEDGSIWLRLVAR"
                     /name="IncQ-type mobilization protein MobB"
     Typing          4313..4469
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="6.38e-77"
     Typing          739..1560
                     /name="IncQ1"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="96.0"
                     /evalue="0.0"
     Typing          4559..6477
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cgcagtgccg aggaaatcgg caaggccatg gccgaggcca gcccagcgct ggcagagcgc
       61 aagcccggcc acgaagcgga ttacatcgag cgcaccgtca gcaaggtcat gggtctgccc
      121 agcgtccagc ttgcgcgggc cgagctggca cgggcaccgg caccccgcca gcgaggcatg
      181 gacaggggcg ggccagattt cagcatgtag tgcttgcgtt ggtactcacg cctgttatac
      241 tatgagtact cacgcacaga agggggtttt atggaatacg aaaaaagcgc ttcagggtcg
      301 gtctacctga tcaaaagtga caagggctat tggttgcccg gtggctttgg ttatacgtca
      361 aacaaggccg aggctggccg cttttcagtc gctgatatgg ccagccttaa ccttgacggc
      421 tgcaccttgt ccttgttccg cgaagacaag cctttcggcc ccggcaagtt tctcggtgac
      481 tgatatgaaa gaccaaaagg acaagcagac cggcgacctg ctggccagcc ctgacgctgt
      541 acgccaagcg cgatatgccg agcgcatgaa ggccaaaggg atgcgtcagc gcaagttctg
      601 gctgaccgac gacgaatacg aggcgctgcg cgagtgcctg gaagaactca gagcggcgca
      661 gggcgggggt agtgaccccg ccagcgccta accaccaact gcctgcaaag gaggcaatca
      721 atggctaccc ataagcctat caatattctg gaggcgttcg cagcagcgcc gccaccgctg
      781 gactacgttt tgcccaacat ggtggccggt acggtcgggg cgctggtgtc gcccggtggt
      841 gccggtaaat ccatgctggc cctgcaactg gccgcacaga ttgcaggcgg gccggatctg
      901 ctggaggtgg gcgaactgcc caccggcccg gtgatctacc tgcccgccga agacccgccc
      961 accgccattc atcaccgcct gcacgccctt ggggcgcacc tcagcgccga ggaacggcaa
     1021 gccgtggctg acggcctgct gatccagccg ctgatcggca gcctgcccaa catcatggcc
     1081 ccggagtggt tcgacggcct caagcgcgcc gccgagggcc gccgcctgat ggtgctggac
     1141 acgctgcgcc ggttccacat cgaggaagaa aacgccagcg gccccatggc ccaggtcatc
     1201 ggtcgcatgg aggccatcgc cgccgatacc gggtgctcta tcgtgttcct gcaccatgcc
     1261 agcaagggcg cggccatgat gggcgcaggc gaccagcagc aggccagccg gggcagctcg
     1321 gtactggtcg ataacatccg ctggcagtcc tacctgtcga gcatgaccag cgccgaggcc
     1381 gaggaatggg gtgtggacga cgaccagcgc cggttcttcg tccgcttcgg tgtgagcaag
     1441 gccaactatg gcgcaccgtt cgctgatcgg tggttcaggc ggcatgacgg cggggtgctc
     1501 aagcccgccg tgctggagag gcagcgcaag agcaaggggg tgccccgtgg tgaagcctaa
     1561 gaacaagcac agcctcagcc acgtccggca cgacccggcg cactgtctgg cccccggcct
     1621 gttccgtgcc ctcaagcggg gcgagcgcaa gcgcagcaag ctggacgtga cgtatgacta
     1681 cggcgacggc aagcggatcg agttcagcgg cccggagccg ctgggcgctg atgatctgcg
     1741 catcctgcaa gggctggtgg ccatggctgg gcctaatggc ctagtgcttg gcccggaacc
     1801 caagaccgaa ggcggacggc agctccggct gttcctggaa cccaagtggg aggccgtcac
     1861 cgctgatgcc atggtggtca aaggtagcta tcgggcgctg gcaaaggaaa tcggggcaga
     1921 ggtcgatagt ggtggggcgc tcaagcacat acaggactgc atcgagcgcc tttggaaggt
     1981 atccatcatc gcccagaatg gccgcaagcg gcaggggttt cggctgctgt cggagtacgc
     2041 cagcgacgag gcggacgggc gcctgtacgt ggccctgaac cccttgatcg cgcaggccgt
     2101 catgggtggc ggccagcatg tgcgcatcag catggacgag gtgcgggcgc tggacagcga
     2161 aaccgcccgc ctgctgcacc agcggctgtg tggctggatc gaccccggca aaaccggcaa
     2221 ggcttccata gataccttgt gcggctatgt ctggccgtca gaggccagtg gttcgaccat
     2281 gcgcaagcgc cgccagcggg tgcgcgaggc gttgccggag ctggtcgcgc tgggctggac
     2341 ggtaaccgag ttcgcggcgg gcaagtacga catcacccgg cccaaggcgg caggctgacc
     2401 ccccccactc tattgtaaac aagacatttt tatctttata aaacaattgg ttggggatgt
     2461 ttgagcgcaa ttaacaggca gccaaaactg gcaaaatgag catgcctatg aataaaatgt
     2521 tgtacgtaaa actcgaaggc aattttagta tgaaagaaaa ggtagttgtt gataaagcga
     2581 tttcactcca taccgaatca ttcggcgacc cggcccatga acccattatc ctgatcatgg
     2641 gggcaatggc gtctgcggtg tggtggcctg atgagttttg ctcccaacta gccaaaatgg
     2701 gtcgctatgt gatccggtac gaccaccgtg ataccgggaa atcaacaagc tatgagccag
     2761 gtcaagctcc atattccgtt gaagaattag cagatgatgt ggttcgcgtc attgatggtt
     2821 atggtctgga agctgctcat ttagtcggca tgtctttggg gggatttctt tcccagcttg
     2881 tagctctcaa gtatccgaaa cgtgtgaaga gcttgacgct gattgcttca gaacggcttg
     2941 cagatgcaga tcctgatatg cccgcttttg atcctgccat cattgagtat caccaacggg
     3001 cggaatcgct ggattggtct gatagagatg ctgtcgtcgc gtatcaggtc ggagcgtggc
     3061 gaatcatctc aggtactgcg catgcttttg acgctgagaa gatacaaaat atcgctgagt
     3121 tagattttga tcgcactccg aatatcctga caacattcaa ccacactact tcaggtggtg
     3181 gcgagagatc gctcgagaga tggctcggga gattaaatga gatagctgta ccaactttga
     3241 tcattcacgg cacggaggat cctgtacttc cttatgtgca tgggttggca ctgaaagatg
     3301 cgattcgtgg ttcaaaaatg ctgacactcg aaggcacggg acatgagttg catcatgaag
     3361 actggccgag gattatccag gcgattaagg ggcaaacgtc atagctatcg gttgcaccgt
     3421 acaacaagtt gctgcaccgt aaaaattact cgctgcgctc gcaattttcc ggtgagcaag
     3481 gcgttaaaca tcatgaggga agcggtgatc gctgaggcat gttccgcgtc cttgcaatac
     3541 tgtgtttaca tacagtctat cgcttagcgg aaagttcttt taccctcagc cgaaatgcct
     3601 gccgttgcta gacattgcca gccagtgccc gtcactcccg tactaactgt cacgaacccc
     3661 tgcaataact gtcacgcccc cctgcaataa ctgtcacgaa cccctgcaat aactgtcacg
     3721 cccccaaacc tgcaaaccca gcaggggcgg gggctggcgg ggtgttggaa aaatccatcc
     3781 atgattatct aagaataatc cactaggcgc ggttatcagc gcccttgtgg ggcgctgctg
     3841 cccttgccca atatgcccgg ccagaggccg gatagctggt ctattcgctg cgctaggcta
     3901 cacaccgccc caccgctgcg cggcaggggg aaaggcgggc aaagcccgct aaaccccaca
     3961 ccaaaccccg cagaaatacg ctggagcgct tttagccgct ttagcggcct ttccccctac
     4021 ccgaagggtg ggggcgcgtg tgcagccccg cagggcctgt ctcggtcgat cattcagccc
     4081 ggctcatcct tctggcgtgg cggcagaccg aacaaggcgc ggtcgtggtc gcgttcaagg
     4141 tacgcatcca ttgccgccat gagccgatcc tccggccact cgctgctgtt caccttggcc
     4201 aaaatcatgg cccccaccag caccttgcgc cttgtttcgt tcttgcgctc ttgctgctgt
     4261 tcccttgccc gcacccgctg aatttcggca ttgattcgcg ctcgttgttc ttcgagcttg
     4321 gccagccgat ccgccgcctt gttgctcccc ttaaccatct tgacacccca ttgttaatgt
     4381 gctgtctcgt aggctatcat ggaggcacag cggcggcaat cccgacccta ctttgtaggg
     4441 ggagggcgca cttaccggtt tctcttcgag aaactggcct aacggccacc cttcgggcgg
     4501 tgcgctctcc gagggccatt gcatggagcc gaaaagcaaa agcaacagcg aggcagcatg
     4561 gcgatttatc accttacggc gaaaaccggc agcaggtcgg gcggccaatc ggccagggcc
     4621 aaggccgact acatccagcg cgaaggcaag tatgcccgcg acatggatga agtcttgcac
     4681 gccgaatccg ggcacatgcc ggagttcgtc gagcggcccg ccgactactg ggatgctgcc
     4741 gacctgtatg aacgcgccaa tgggcggctg ttcaaggagg tcgaatttgc cctgccggtc
     4801 gagctgaccc tcgaccagca gaaggcgctg gcgtccgagt tcgcccagca cctgactggt
     4861 gccgagcgcc tgccgtatac gctggccatc catgccggtg gcggcgagaa cccgcactgc
     4921 cacctgatga tctccgagcg gatcaatgac ggcatcgagc ggcccgccgc tcagtggttc
     4981 aagcggtaca acggcaagac cccggagaag ggcggggcac agaagaccga agcgctcaag
     5041 cccaaggcat ggcttgagca gacccgcgag gcatgggccg accatgccaa ccgggcatta
     5101 gagcgggctg gccacgacgc ccgcattgac cacagaacac ttgaggcgca gggcatcgag
     5161 cgcctgcccg gtgttcacct ggggccgaac gtggtggaga tggaaggccg gggcatccgc
     5221 accgaccggg cagacgtggc cctgaacatc gacaccgcca acgcccagat catcgactta
     5281 caggaatacc gggaggcaat agaccatgaa cgcaatcgac agagtgaaga aatccagagg
     5341 catcaacgag ttagcggagc agatcgaacc gctggcccag agcatggcga cactggccga
     5401 cgaagcccgg caggtcatga gccagaccca gcaggccagc gaggcgcagg cggcggagtg
     5461 gctgaaagcc cagcgccaga caggggcggc atgggtggag ctggccaaag agttgcggga
     5521 ggtagccgcc gaggtgagca gcgccgcgca gagcgcccgg agcgcgtcgc gggggtggca
     5581 ctggaagcta tggctaaccg tgatgctggc ttccatgatg cctacggtgg tgctgctgat
     5641 cgcatcgttg ctcttgctcg acctgacgcc actgacaacc gaggacggct cgatctggct
     5701 gcgcttggtg gcccgatgaa gaacgacagg actttgcagg ccataggccg acagctcaag
     5761 gccatgggct gtgagcgctt cgatatcggc gtcagggacg ccaccaccgg ccagatgatg
     5821 aaccgggaat ggtcagccgc cgaagtgctc cagaacacgc catggctcaa gcggatgaat
     5881 gcccagggca atgacgtgta tatcaggccc gccgagcagg agcggcatgg tctggtgctg
     5941 gtggacgacc tcagcgagtt tgacctggat gacatgaaag ccgagggccg ggagcctgcc
     6001 ctggtagtgg aaaccagccc gaagaactat caggcatggg tcaaggtggc cgacgccgca
     6061 ggcggtgaac ttcgggggca gattgcccgg acgctggcca gcgagtacga cgccgacccg
     6121 gccagcgccg acagccgcca ctatggccgc ttggcgggct tcaccaaccg caaggacaag
     6181 cacaccaccc gcgccggtta tcagccgtgg gtgctgctgc gtgaatccaa gggcaagacc
     6241 gccaccgctg gcccggcgct ggtgcagcag gctggccagc agatcgagca ggcccagcgg
     6301 cagcaggaga aggcccgcag gctggccagc ctcgaactgc ccgagcggca gcttagccgc
     6361 caccggcgca cggcgctgga cgagtaccgc agcgagatgg ccgggctggt caagcgcttc
     6421 ggtgatgacc tcagcaagtg cgactttatc gccgcgcaga agctggccag ccggggc
//
