LOCUS       NZ_CP063504             5264 bp    DNA     circular CON 17-JUN-2023
DEFINITION  Escherichia coli strain EH09-18-41 plasmid pEH09-18-41_1, complete
            sequence.
ACCESSION   NZ_CP063504
VERSION     NZ_CP063504.1
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 5264)
  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  JOURNAL   Unpublished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 5264)
  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
            CP063504.1.
            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..5264
                     /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_1"
                     /geo_loc_name="Laos"
                     /collection_date="2018"
                     /collected_by="Institute for Infectious Diseases Bern"
     gene            complement(761..1180)
                     /locus_tag="IQS19_RS23180"
                     /old_locus_tag="IQS19_23185"
     CDS             complement(761..1180)
                     /locus_tag="IQS19_RS23180"
                     /old_locus_tag="IQS19_23185"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016247941.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Exc2 family lipoprotein"
                     /protein_id="WP_001254967.1"
                     /translation="MRRTGNKLCLIAMITATVALTACTPKGSVEQHTRHYVYASDDGFD
                     PNFSTQKADTTRMMVPFFRQFWDMGAKDKATGKSRSDVQQRIQQFHSQEFLNSLRGTTQ
                     FAGTDYRSKDLTPKKSRLLADTISAVYLDGYEGRQ"
                     /name="Exc2 family lipoprotein"
     gene            complement(1261..1698)
                     /locus_tag="IQS19_RS23185"
                     /old_locus_tag="IQS19_23190"
     CDS             complement(1261..1698)
                     /locus_tag="IQS19_RS23185"
                     /old_locus_tag="IQS19_23190"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001405929.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001405929.1"
                     /translation="MGHCHFMAWHTLRDALKMTGRSRSQFYRDMRAGLVSYRTGRDGRR
                     EFETSELIRAYGELKQNETPERHSEGHAENPHDQQTERILRELNELKQCLTLMLEDKQA
                     QDMDRRRQEAEREQLQNEIAQLRQALELEKKRGFWSRLFGR"
                     /name="hypothetical protein"
     gene            1958..3526
                     /gene="cea"
                     /locus_tag="IQS19_RS23190"
                     /old_locus_tag="IQS19_23195"
     CDS             1958..3526
                     /gene="cea"
                     /locus_tag="IQS19_RS23190"
                     /old_locus_tag="IQS19_23195"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000447006.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="pore-forming bacteriocin colicin E1"
                     /protein_id="WP_000447006.1"
                     /translation="METAVAYYKDGVPYDDKGQVIITLLNGTPDGSGSGGGGGKGGSKS
                     ESSAAIHATAKWSTAQLKKTQAEQAARAKAAAEAQAKAKANRDALTQRLKDIVNEALRH
                     NASRTPSATELAHANNAAMQAEAERLRLAKAEEKARKEAEAAEKAFQEAEQRRKEIERE
                     KAETERQLKLAEAEEKRLAALSEEAKAVEIAQKKLSAAQSEVVKMDGEIKTLNSRLSSS
                     IHARDAEMKTLAGKRNELAQASAKYKELDELVKKLSPRANDPLQNRPFFEATRRRVGAG
                     KIREEKQKQVTASETRINRINADITQIQKAISQVSNNRNAGIARVHEAEENLKKAQNNL
                     LNSQIKDAVDATVSFYQTLTEKYGEKYSKMAQELADKSKGKKIGNVNEALAAFEKYKDV
                     LNKKFSKADRDAIFNALASVKYDDWAKHLDQFAKYLKITGHVSFGYDVVSDILKIKDTG
                     DWKPLFLTLEKKAADAGVSYVVALLFSLLAGTTLGIWGIAIVTGILCSYIDKNKLNTIN
                     EVLGI"
                     /name="cea"
     gene            complement(3523..3864)
                     /locus_tag="IQS19_RS23195"
                     /old_locus_tag="IQS19_23200"
     CDS             complement(3523..3864)
                     /locus_tag="IQS19_RS23195"
                     /old_locus_tag="IQS19_23200"
                     /inference="COORDINATES: protein motif:HMM:NF015489.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin E1 immunity protein"
                     /protein_id="WP_000058760.1"
                     /translation="MSLRYYIKNILFGLYCTLIYIYLITKNSEGYYFLVSDKMLYAIVI
                     STILCPYSKYAIEYIAFNFIKKDFFERRKNLNNAPVAKLNLFMLYNLLCLVLAIPFGLL
                     GLFISIKNN"
                     /name="colicin E1 immunity protein"
     gene            3912..4049
                     /locus_tag="IQS19_RS23200"
                     /old_locus_tag="IQS19_23205"
     CDS             3912..4049
                     /locus_tag="IQS19_RS23200"
                     /old_locus_tag="IQS19_23205"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001405930.1"
                     /GO_component="GO:0019867 - outer membrane [Evidence IEA]"
                     /GO_process="GO:0019835 - cytolysis [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin release lysis protein"
                     /protein_id="WP_001405930.1"
                     /translation="MRKRFFVGIFAINLLVGCQANYIRDVQGGTIAPSSSSKLTGIAVQ
                     "
                     /name="colicin release lysis protein"
     gene            complement(5061..5255)
                     /locus_tag="IQS19_RS23205"
                     /old_locus_tag="IQS19_23210"
     CDS             complement(5061..5255)
                     /locus_tag="IQS19_RS23205"
                     /old_locus_tag="IQS19_23210"
                     /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_052923731.1"
                     /translation="MNKQQQTALNMARFIKSQSLALLEKLDALDADEQAAMCERLHELA
                     EELQNSIQVRFEAESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          28..126
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="6.22e-45"
     Typing          251..506
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.512"
                     /coverage="89.0"
                     /evalue="1.21e-116"
     Typing          4904..4985
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="98.0"
                     /evalue="1.39e-35"
     Typing          complement(4335..4890)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.699"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 ttctccgtca gtaccgggtg tcgggtggac cctgaccagg tggtaattgt aagacgttgc
       61 gggcgacggt attacaattg cacatcctgt cctgtttttt taggacgtat catggcacag
      121 catatcaact gataaataat ccctgtgcag tgcagccgct gttgcataaa atttcgctct
      181 gcgtcgagtg tttcttaatc aataattccg ctgatactcc ggaaaaacgc gagtctgttc
      241 tcatgcctga aatgcccaca ccccacgcaa aaacaatttt ttgctgattt ttctttataa
      301 atagagagtt atgacaaatt agttcttctt gctctctttg tgatatttaa aaaagcggtg
      361 tcggcgcggt gttgtagctg cgccaacacc gctttttagg ggtggtactg actattttca
      421 taaaaaacat cattttatat taggggtgct gctagcggcg cggtgtgttt ttttacagga
      481 cgcccctggg ggcgctgcta ggggtgtctg ttcagatatg tagcaatgag tcagggattc
      541 acgaactgaa aatgtccgaa aatgtgtctc atgggcaccg tatgcgccca aaccgatcgc
      601 cattcacttt catgcatagc tatgcagtga gctgaaagcg atcctgacgc atttttccgg
      661 ttttcgcttg gtaaaacatc tctttttgcg gtgttcgcgg cagaatcgcg ttcagcgcgt
      721 tttagcggtg cgtacaatta agggattatg gtaaatccac ttactgtctg ccctcgtagc
      781 catcgagata aaccgcagaa atcgtgtcag ccagcagcct ggattttttc ggggtaaggt
      841 ctttgctgcg gtaatcagta cccgcaaatt gagttgtgcc ccggagtgag tttaaaaatt
      901 cctggctgtg aaactgctga atgcgttgtt gcacatcact ccgtgatttt cctgtcgctt
      961 tatctttagc tcccatatcc cagaactgcc gaaaaaaagg caccatcatt cgtgttgtgt
     1021 cggctttttg ggtggaaaag ttgggatcaa aaccgtcatc agaagcatat acgtaatgcc
     1081 gggtatgttg ttccacgctg ccctttgggg tacaggctgt gagagctact gttgctgtta
     1141 tcatggcgat aagacaaagt ttgtttccgg tacgtctcat gagtgtctcc ctaccttaaa
     1201 gtatttattc tcggtgagtt attatccgaa gactatttta tcatcagtct ctgacagcgt
     1261 tcagcgaccg aacaacctgg accagaatcc ccgtttcttt tccagttcca gtgcctgcct
     1321 gagctgggct atctcatttt gtagctgttc ccgttctgct tcctggcgtc tgcgatccat
     1381 atcctgtgcc tgtttatcct caagcatcag cgtcaggcat tgtttcagct cattcagctc
     1441 ccggagaatg cgttctgtct gctgatcatg tggattttct gcatgtccct cactgtgcct
     1501 ttctggtgtc tcattctgct ttaattcgcc gtatgcccgg atcagttcac tggtttcaaa
     1561 ctcccgtcgt ccgtccctgc cggtacggta actgacaagg cctgcgcgca tatcacggta
     1621 aaactgtgaa cgcgatctgc ctgtcatttt tagtgcgtcc cggagtgtgt gccatgccat
     1681 aaagtgacag tgtcccatag atgtctcatc tcatagtttc agtaaaacat aatgaggtct
     1741 gagaacggta atgtttgtgc tggtttttgt ggcatcgggc gagaatagcg cgtggtgtga
     1801 aagactgttt ttttgatcgt tttcacaaaa atggaagtcc acagtcttga cagggaaaat
     1861 gcagcggcgt agcttttatg ctgtatataa aaccagtggt tatatgtaca gcatttattt
     1921 ttaacttatt gttttaaaag tcaaagagga ttttataatg gaaaccgcgg tagcgtacta
     1981 taaagatggt gttccttatg atgataaggg acaggtaatt attactcttt tgaatggtac
     2041 tcctgacggg agtggctctg gcggcggagg tggaaaagga ggcagtaaaa gtgaaagttc
     2101 tgcagctatt catgcaactg ctaaatggtc tactgctcaa ttaaagaaaa cacaggcaga
     2161 gcaggctgcc cgggcaaaag ctgcagcgga agcacaggcg aaagcaaagg caaacaggga
     2221 tgcgctgact cagcgcctga aggatatcgt gaatgaggct cttcgtcaca atgcctcacg
     2281 tacgccttca gcaacagagc ttgctcatgc taataatgca gctatgcagg cggaagcaga
     2341 gcgtttgcgc cttgcgaaag cagaagaaaa agcccgtaaa gaagcggaag cagcagaaaa
     2401 ggcttttcag gaagcagaac aacgacgtaa agagattgaa cgggagaagg ctgaaacaga
     2461 acgccagttg aaactggctg aagctgaaga gaaacgactg gctgcattga gtgaagaagc
     2521 taaagctgtt gagatcgccc aaaaaaaact ttctgctgca caatctgaag tggtgaaaat
     2581 ggatggagag attaagactc tcaattctcg tttaagctcc agtatccatg cccgtgatgc
     2641 agaaatgaaa acgctcgctg gaaaacgaaa tgaactggct caggcatccg ctaaatataa
     2701 agaactggat gagctggtca aaaaactatc accaagagcc aatgatccgc ttcagaaccg
     2761 tccttttttt gaagcaacca gacgacgggt tggggccggt aagattagag aagaaaaaca
     2821 aaaacaggta acagcatcag aaacacgtat taaccggata aatgctgata taactcagat
     2881 ccagaaggct atttctcagg tcagtaataa tcgtaatgcc ggtatcgctc gtgttcatga
     2941 agctgaagaa aatttgaaaa aagcacagaa taatctcctt aattcacaga ttaaggatgc
     3001 tgttgatgca acagttagct tttatcaaac gctgactgaa aaatatggtg aaaaatattc
     3061 gaaaatggca caggaacttg ctgataagtc taaaggtaag aaaatcggca atgtgaatga
     3121 agctctcgct gcttttgaaa aatacaagga tgttttaaat aagaaattca gcaaagccga
     3181 tcgtgatgct atttttaatg cgttggcatc ggtgaagtat gatgactggg ctaaacattt
     3241 agatcagttt gccaagtact tgaagattac ggggcatgtt tcttttggat atgatgtggt
     3301 atctgatatc ctaaaaatta aggatacagg tgactggaag ccactatttc ttacattaga
     3361 gaagaaagct gcagatgcag gggtgagtta tgttgttgct ttacttttta gcttgcttgc
     3421 tggaactaca ttaggtattt ggggtattgc tattgttaca ggaattctat gctcctatat
     3481 tgataagaat aaacttaata ctataaatga ggtgttaggg atttaattat tctttattga
     3541 tataaaaagt cctagcaatc caaatgggat tgctaggacc aaacaaagta gattatatag
     3601 cataaatagg tttaattttg ctacgggggc gttatttagg ttttttcttc tttcgaaaaa
     3661 atctttcttt atgaagttaa aagctatgta ttcaatagca tattttgaat atggacatag
     3721 aatagtgctt atcactattg catatagcat cttatctgac acaaggaaat aatacccttc
     3781 gctgtttttt gttataaggt atatatatat aagtgtgcag tacaggccaa ataaaatatt
     3841 ttttatgtag tatcttaagc tcataaatta aacctcgcca tatattcttt tcattttata
     3901 aggatcgagt tatgaggaaa agattttttg tgggaatatt cgcgataaac ctccttgttg
     3961 gatgtcaggc taactatata cgtgatgttc agggagggac catcgcacca tcctcctctt
     4021 ctaaactgac ggggatcgcg gttcagtaga aaagatcaaa ggatcttctt gagatccttt
     4081 ttttctgcgc gtaatctgct gcttgcaaac aaaaaaacca ccgctaccaa cggtggtttg
     4141 tttgccggat caagagctac caactctttt tccgaaggta actggcttca gcagagcgca
     4201 gataccaaat actgtccttc tagtgtagcc gtagtcgggc cactacttca agaactctgt
     4261 agcaccgttt gtgccatcat cgctctgcta atccggttac cagtggctgc tgccagtggc
     4321 gttaaggcgt gccttaccgg gttggactca agacgatagt taccggataa ggcgcagcgg
     4381 tcgggctgaa cggggggttc gtgcacacag cccagcttgg agcgaacgac ctacaccgaa
     4441 ctgagatacc aacagcgtga gctatgagaa agcgccacgc ttcccgaagg gagaaaggcg
     4501 gacaggtatc cggtaagcgg cagggtcgga acaggagagc gcacgaggga gcttccaggg
     4561 ggaaacgcct ggtatcttta tagtcctgtc gggtttcgcc acctctgact tgagcgtcta
     4621 tttttgtgat gctcgtcagg ggggcggagc ctatggaaaa acgcctgcta cgtggccttc
     4681 ttcctgttcc tggtcttttg ctcacatgtt ctttccggcc ttatcccctg attctgtgga
     4741 taactgtgtt accgtttttg tgtgagtcag taccgctcgc cgcagtcgaa cgaccgagcg
     4801 tagcgagtca gtgagcgagg aagcggaaaa gcgcctggac gtgcattttc tccttacgca
     4861 tctgtgcggc atttcacacc cggcatggcg tacttttcat acaatccgca ctgatgccgc
     4921 atggttaagc cagtatacac tccgctatcg ctacgtgact gggtcatggc tgcgccccga
     4981 caccccctga cgcgccctgg cgggcttgtc tgctgccgaa aacgctcgcg gacaagccgt
     5041 gagcgcctcc gtcagcttcg ttatgttcct gtttcacttt cggcctcaaa gcgaacctgg
     5101 atgctgttct ggagttcttc cgcgagttcg tgcagtcgtt cgcacatggc cgcctgttcg
     5161 tcggcatcca gagcatccag tttttcaagc agtgccaggc tctggctttt gataaatcgc
     5221 gccatattca gcgcagtttg ttgctgtttg ttcaccttcc gttg
//
