LOCUS       NZ_CP063461             5759 bp    DNA     circular CON 17-JUN-2023
DEFINITION  Escherichia coli strain EM22-18-53 plasmid pEM22-18-53_2, complete
            sequence.
ACCESSION   NZ_CP063461
VERSION     NZ_CP063461.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16387511
            Assembly: GCF_016942575.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5759)
  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  JOURNAL   Unpublished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 5759)
  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                   :: 740x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/17/2023 06:38:10
            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)                     :: 4,984
            CDSs (total)                      :: 4,864
            Genes (coding)                    :: 4,564
            CDSs (with protein)               :: 4,564
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 300
            CDSs (without protein)            :: 300
            Pseudo Genes (ambiguous residues) :: 1 of 300
            Pseudo Genes (frameshifted)       :: 126 of 300
            Pseudo Genes (incomplete)         :: 171 of 300
            Pseudo Genes (internal stop)      :: 50 of 300
            Pseudo Genes (multiple problems)  :: 45 of 300
            Pseudo Genes (short protein)      :: 4 of 300
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP063461.1.
            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..5759
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="EM22-18-53"
                     /isolation_source="chicken meat"
                     /db_xref="taxon:562"
                     /plasmid="pEM22-18-53_2"
                     /geo_loc_name="Laos"
                     /collection_date="2018"
                     /collected_by="Institute for Infectious Diseases Bern"
     gene            complement(695..886)
                     /locus_tag="IQS26_RS23150"
                     /old_locus_tag="IQS26_23160"
     CDS             complement(695..886)
                     /locus_tag="IQS26_RS23150"
                     /old_locus_tag="IQS26_23160"
                     /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"
     gene            951..1274
                     /locus_tag="IQS26_RS23155"
                     /old_locus_tag="IQS26_23165"
     CDS             951..1274
                     /locus_tag="IQS26_RS23155"
                     /old_locus_tag="IQS26_23165"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /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_000955999.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1483..>1914
                     /locus_tag="IQS26_RS24970"
                     /pseudo=""
     CDS             1483..>1914
                     /locus_tag="IQS26_RS24970"
                     /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            1952..2461
                     /locus_tag="IQS26_RS23160"
                     /old_locus_tag="IQS26_23170"
     CDS             1952..2461
                     /locus_tag="IQS26_RS23160"
                     /old_locus_tag="IQS26_23170"
                     /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_205561673.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFRKLGESVSEAVTSNE
                     TKIRDAIALFTASTEKSLEKHREGVKEAMMQHRKDVLKLAGNTGMMLLGIVFLLFTASG
                     GTLWYLGGRIQTNLEEIRKQEETLQKLNAKTWGVEFVQDGNRKFLVLPYGKSAEVIPFQ
                     GKSGYI"
                     /name="MbeB family mobilization protein"
     gene            2476..2709
                     /locus_tag="IQS26_RS23165"
                     /old_locus_tag="IQS26_23175"
     CDS             2476..2709
                     /locus_tag="IQS26_RS23165"
                     /old_locus_tag="IQS26_23175"
                     /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_004026237.1"
                     /translation="MTELEIHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSEQTERLSQLYSENWR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(3103..4236)
                     /locus_tag="IQS26_RS23170"
                     /old_locus_tag="IQS26_23180"
     CDS             complement(3103..4236)
                     /locus_tag="IQS26_RS23170"
                     /old_locus_tag="IQS26_23180"
                     /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_072647583.1"
                     /translation="MKINSIQWPVTFFATSFGAGIFFLPQTVGPKVIGTHGTITILILS
                     SLVSLLGQFTFYRFILITDKKEYVSSAILFIGKKAANAISIAFLLSMLLIAIINITTMI
                     NIICFSLSLNGSERIFVSLIISATLGSSFIFFNSKIEHLASGIAFPSLLIVLFLSIYFY
                     SHPAHPHSTEIQNISTSNLLTLFPVVLFSFNFSPCIQRFAQNKKDTAGDLRFFMFGILL
                     ILIFISFIVFSLSNIFSPSDIKNMREINSDALSYSANVTKNSFVAYISILTMILITSGA
                     YTGTLTGVVDTIVSLGFKNKTLIVFVVSVITFIAGEANFEIIKVIAALSTPIIAITVFI
                     IPSAFFLKTNCNSIFRKIMMTLNLLIGIGICFLAIIL"
                     /name="hypothetical protein"
     gene            complement(4248..5138)
                     /locus_tag="IQS26_RS23175"
                     /old_locus_tag="IQS26_23185"
     CDS             complement(4248..5138)
                     /locus_tag="IQS26_RS23175"
                     /old_locus_tag="IQS26_23185"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015376142.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_021512263.1"
                     /translation="MPDLEIMPLQSPDFYKKNKRAIYEGYKCNCTKDWKKEDRFVVYKA
                     DCTGIDEIINTEISDDNIDTVIKLAEKYTSDKIIISGGHTVVNLNDRFSVSNEVEKSAK
                     FCIDYIIKSTHELNIKPDFLMEINDFYMEKSNGEDIDGGNIYRKLATSPYIIPEVINNY
                     IIEKQNQHNIKINCFYVSEKNMADRFKRHIKRKEKEKPFFKENNSVFMNVDGSSFEVIK
                     NNKPTCAAGNAATFRSIRYKISSNKTFDNYTSHIGVFPLCSMANVINGYKAAASFYSNF
                     NLPCLLIFFGTSCFK"
                     /name="hypothetical protein"
     gene            5315..5403
                     /locus_tag="IQS26_RS23180"
                     /old_locus_tag="IQS26_23190"
     tRNA            5315..5403
                     /locus_tag="IQS26_RS23180"
                     /old_locus_tag="IQS26_23190"
                     /product="tRNA-Lys"
                     /inference="COORDINATES: profile:tRNAscan-SE:2.0.12"
                     /note="Derived by automated computational analysis using
                     gene prediction method: tRNAscan-SE."
                     /anticodon=(pos:5349..5351,aa:Lys,seq:ctt)
                     /name="tRNA-Lys"
     Typing          523..610
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.753"
                     /coverage="100.0"
                     /evalue="1.48e-35"
     Typing          complement(2..499)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.012"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          1265..2445
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.462"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2443..2813
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.13"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tcgggctgaa cgggggttcg tgcacacagc ccagcttgga gcgaacgacc tacaccgaac
       61 tgagatacca acagcgtgag ctatgagaaa gcgccacgct tcccgaaggg agaaaggcgg
      121 agaggtatcc ggtaagcggc agggtcggaa caggagagcg cacgagggag cttccagggg
      181 gaaacgcctg gtatctttat agtcctgtcg ggtttcgcca cctctgactt gagcgtctgt
      241 ttttgtgatg ctcgtcaggg gggcggagcc tatggaaaaa cgccatcggc gtggcctttt
      301 tccggctctt ggtcttttgc tcacatgttc tttccggcct tatcccctga ttctgtggat
      361 aaccgcatta ccgtctttga gtgagctgat accgctcgcc gcagccgaac gaccgagcgt
      421 agcgagtcag tgagcgagga agcggaagag cgcctgatgc ggtatgttct ccttacgcat
      481 ctgtgcggca tttcacaccc ggcatggcgt gcttttcata caatccgcac tgatgccgca
      541 tagttaagcc agtatacact ccgctatcgc tacgtgactg ggtcagggct gcgccccgac
      601 accccctaaa acctgctgac gcgccctgac ggacttgtct gctcccggca tccgctcaca
      661 gacaagctgt gaccgtctcc gggagctgca tgtgtcagag gttttcaccg tcatccccga
      721 aacgtgcgag gcagctgcgg taaagctcat cggcgtggtc gtgaagcgat tcacagatgt
      781 ctgcctgttc atccgcgtcc agttcgttga gcttctccag cagcgttaat gtctggcttc
      841 ttataaagcg ggccatgtta agggcggttt tttcctgttt agtcactgat gcctccgtgt
      901 aaggggggat ttctgttcat ggggtaatga taccgatgaa acgcgagagg atgctcacga
      961 tacgggttac tgatgatgaa catgcacggt tactggaacg ctgtgagggt aaacagctgg
     1021 cggtatggat gcggcgggtc tgcctgggtg agccggttgc ccgttccggg aagctgccga
     1081 cactggcacc gccgttactg cgccagctgg ccgccatcgg gaataacctg aatcagacgg
     1141 cgaggaaggt gaacagcggg cagtggtctt ccggtgaccg ggttcaggtg gtggccgcac
     1201 tgatggccat cggggatgag ctgcgccggc tgcgtctggc cgtcagggaa cagggggcgc
     1261 gggatgatag ttaaatttca tgccagggga aaaggtggtg gcagtggtcc ggttgattac
     1321 ctgctgggga gggagcgtaa tcgcgaaggc gcaacggtgc ttcagggtaa tccggaagaa
     1381 gtccgggaac tcatcgatgc cacgccattt gcgaagaaat acacgtccgg tgttctgtcg
     1441 tttgcggaga aagaactgcc accgggagga cgtgaaaaag tgatggcgag ttttgagcgt
     1501 gtactgatgc ccggtctcga aaaaaatcag tacagcatcc tgtgggtgga gcaccaggac
     1561 aagggacggc ttgagctgaa ttttgtcatt ccgaacatgg agctacagac aggaaaacgc
     1621 ctccagccgt actacgaccg cgcagacagg cctagaattg atgcctggca gacgctggtg
     1681 aatcaccatt acgggctgca tgacccgaac gccccggaga accgccggac gctgaccctt
     1741 cctgataacc tgccggaaac gaaacaggca cttgctgaga gcgttacacg cggtatagac
     1801 gcactttacc atgccggaga gataaaaggc cgtcaggatg tgattcaggc gctcactgag
     1861 gcggggctgg aagtggtcag ggtgacgcga agcagtatca gcattgcaga tccgaacggc
     1921 gggaagaata tcaggctgaa aggagcattt tatgagcaat cttttgcaga cgggcgcgga
     1981 gttcgagaaa aagctgaaag agagagccga atctacagag aaaatgctga acgacgagtt
     2041 caggaagctc ggcgagtctg tcagcgaggc tgtgacctca aacgagacga aaatcagaga
     2101 cgctatagcc ctgttcacag cctcgacaga gaaatcgctg gaaaaacacc gggaaggggt
     2161 gaaagaggcg atgatgcagc acaggaagga cgtgttaaag ctggcaggga atacgggcat
     2221 gatgttactg gggatagtct ttctcctgtt taccgcgagt ggcgggacgc tctggtatct
     2281 tggcggacgg atacagacga acctggaaga aatcaggaag caggaagaga cattgcagaa
     2341 actgaacgcg aagacatggg gcgtggagtt tgtgcaggac gggaacagga aattccttgt
     2401 ccttccgtac gggaaatcag cggaggtgat tccctttcag ggaaagagtg ggtacatctg
     2461 aaggagtgac tcagagtgac ggagctggaa atacatttgc tgaacgcctt agagcagctg
     2521 caacaggact atatgcagcg gctgagcgaa tgggagagcg ccttcgtgga attgcagaag
     2581 atgttttcgc ttacgcaacg ggacaacgcg atgctgaacg agcgggtcat gcagttgagt
     2641 cagcaggtgc agcacttgag cgagcagaca gaacgcttga gccagttata cagcgagaac
     2701 tggagataag agaggaacgg ctgatacagg agcgcgaaca tgcgttatcc ctggaacggg
     2761 agcgtcagcc ggaaatacag gaacgcacgc tggatggtcc ttcgctggga tggtgaaacc
     2821 atgaaaaatg gcagcttcag tggattaaga ggggttaatg tggcctgtac catctggttg
     2881 cataggtatt catgcggtta aaatttatca ggcgcgatcg cggcagtttt tcgggtggtt
     2941 tgttgccatt tttacctgtc tgctgccgtg atcgcgctga acgcgtttta gcggtgcgtg
     3001 taatattgtc gttatgttaa atggtttgga tgatcccccc attttccaca tttggttgtg
     3061 acgattaaga taaactcgtc agaatatttg ggtgaggaat aatcataata tgatggctag
     3121 gaagcatatt ccaataccta tgagcaggtt caacgtcatc attatttttc taaaaatact
     3181 gttacaattt gtttttaaaa agaatgctga tgggataatg aatactgtta ttgctataat
     3241 tggggttgat aatgcagcaa taacttttat aatttcgaaa ttggcttcgc ctgctataaa
     3301 tgtgataaca gatacgacaa aaacgattaa tgttttgttt ttaaatccaa gggatactat
     3361 tgtatcaaca acgcctgtta gtgtacctgt atatgcaccg ctggtaatta aaatcattgt
     3421 taatatggaa atgtaagcaa cgaaactatt ttttgttacg ttggcgctat atgataatgc
     3481 atcgctgtta atctcgcgca tgttttttat gtctgaaggt gagaatatat tgcttaatga
     3541 gaacacgatg aatgagataa atattaaaat taatagtatc ccaaacatga aaaaacgtaa
     3601 atcaccggct gtatcttttt tgttttgagc aaagcgttgt atacatggtg aaaaattaaa
     3661 actaaataaa acaactggaa atagagtaag taaattactt gtactaatat tttgtatttc
     3721 tgtagaatgt ggatgtgctg gatgtgaata gaaatatata gataagaaca gtacaataag
     3781 caaagatgga aatgctattc ctgatgcgag atgctctatc tttgaattaa aaaagataaa
     3841 agaagaacca agggttgcag aaataatcag tgacacaaat attcgctctg aaccatttag
     3901 acttaggcta aagcaaataa tatttatcat tgttgttatg tttataattg ctattaacag
     3961 cattgataat aggaatgcaa tactgatagc atttgcggct ttttttccga taaataatat
     4021 ggcagaacta acgtattctt ttttgtctgt aattaaaatg aatctataaa atgtaaattg
     4081 ccctaataaa gataccaaag atgataaaat cagtattgtt attgttccgt gagttcctat
     4141 gactttgggg cctacagtct ggggtaggaa aaaaatccct gccccaaatg atgttgcaaa
     4201 gaatgttact ggccattgga tgctatttat cttcattttt gaacctttca tttgaagcat
     4261 gatgttccaa agaaaataag taaacatgga agattaaaat tactataaaa agatgctgct
     4321 gctttatagc cattaattac attagccatt gagcacaatg ggaatacacc tatgtgtgat
     4381 gtgtaattgt caaatgtctt gttcgatgaa attttatatc gaatcgagcg aaatgtagct
     4441 gcgttacctg ctgcacaagt cggtttgtta ttttttatca cttcaaatga tgaaccatcg
     4501 acattcataa aaacagagtt gttttcttta aaaaatggct tttctttttc ttttctttta
     4561 atgtgtcgtt taaaacgatc tgccatgttt ttttcactaa catagaaaca atttattttt
     4621 atattatgct gattctgttt ctctataata tagttattta ttacttctgg tattatatag
     4681 ggtgatgtgg ctagttttct ataaatatta ccaccatcga tatcttcgcc atttgatttt
     4741 tccatgtaga aatcatttat ttccatgagg aaatcaggtt ttatatttag ctcatgtgtt
     4801 gattttatta tgtagtcaat gcaaaattta gccgattttt caacttcatt actaactgaa
     4861 aaacggtcat tcaaattcac aacagtatgt ccaccagata taataatctt gtctgatgtg
     4921 tatttttcgg ctagttttat tacagtatct atgttgtcat ctgatatttc tgtgtttatt
     4981 atctcatcga ttcctgtgca atctgctttg tatacaacaa atctgtcttc ttttttccag
     5041 tcttttgtac aattacattt atagccctcg tatattgctc ttttgttttt tttataaaaa
     5101 tctgggcttt gtaagggcat tatttctagg tctggcatag ttatgcttcc tttgtcacaa
     5161 agaaaatatt ttgctaatta tgacttatac atatcaatga tagagatcat gttagtgttt
     5221 gatcattgat gtctccttta tttatgtgat gcgtctctat tttttctctt atagtgtctt
     5281 ggatgttatt tgttaaatat gtattgtttt ttgtggagag gtgggcgagt ggtctaagtc
     5341 agggctctct tgaggccata tgcgacaagc gtatcgtagg ttcgaatcct accctctccg
     5401 ccattttgtt gatcgtttcc cccaccattt gttgaattga gaggggtttt gaaaaaagat
     5461 caaaggatcc tcttgagatc ctttttttct gcgcgtaatc tgctgcctgt aaacaaaaaa
     5521 accaccgcta ccaacggtgg ttcgtttgcc ggaatcaaga gctaccaact ctttttcccg
     5581 aaggtaactg gcttggtgga gcgcagatac caaatattgt ccttctagtg tagcctcagt
     5641 taggccacca cttcaagaac tcttaatatc tcaatccacc ttgtccagtt accaatggct
     5701 gctgccagtg gcgttaaggc gtgtcttacc gggttggact caagacgata gttaccgga
//
