LOCUS       NZ_CP145514             3561 bp    DNA     circular CON 05-APR-2024
DEFINITION  Escherichia coli strain L1PEag1 plasmid pL1PEag1, complete sequence.
ACCESSION   NZ_CP145514
VERSION     NZ_CP145514.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN39710041
            Assembly: GCF_036870985.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3561)
  AUTHORS   Tenea,G.N.
  TITLE     Genome characterization of a multi-drug resistant Escherichia coli
            strain, L1PEag1, isolated from commercial cape gooseberry fruits
            (Physalis peruviana L.)
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3561)
  AUTHORS   Tenea,G.N.
  TITLE     Direct Submission
  JOURNAL   Submitted (06-FEB-2024) Biofood and Nutraceutics Research and
            Development Group, Technical University of the North, Ibarra
            Ecuador, Av 17 de Julio, Ibarra, Imbabura 100150, Ecuador
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: SPAdes v. 3.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 400.0x
            Sequencing Technology             :: Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_036870985.1-RS_2024_04_05
            Annotation Date                   :: 04/05/2024 16:48:04
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,676
            CDSs (total)                      :: 4,562
            Genes (coding)                    :: 4,437
            CDSs (with protein)               :: 4,437
            Genes (RNA)                       :: 114
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 125
            CDSs (without protein)            :: 125
            Pseudo Genes (ambiguous residues) :: 0 of 125
            Pseudo Genes (frameshifted)       :: 48 of 125
            Pseudo Genes (incomplete)         :: 80 of 125
            Pseudo Genes (internal stop)      :: 23 of 125
            Pseudo Genes (multiple problems)  :: 25 of 125
            Pseudo Genes (short protein)      :: 4 of 125
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP145514.1.
            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..3561
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="L1PEag1"
                     /isolation_source="cape gooseberry"
                     /db_xref="taxon:562"
                     /plasmid="pL1PEag1"
                     /geo_loc_name="Ecuador"
                     /lat_lon="0.21 N 78.7 W"
                     /collection_date="2023-06-24"
                     /collected_by="GNT"
     gene            217..627
                     /locus_tag="V3C55_RS23350"
                     /old_locus_tag="V3C55_23350"
     CDS             217..627
                     /locus_tag="V3C55_RS23350"
                     /old_locus_tag="V3C55_23350"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_415090.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF1398 domain-containing protein"
                     /protein_id="WP_012775990.1"
                     /translation="MAQVAIFKEIFDQVRKDLDCELFYSELKRHNVSHYIYYLATDNIH
                     IVLENDNTVLIKGLKKVVNVKFSRNTHLIETSYDRLKSREITFQQYRENLAKAGVFRWV
                     TNIHEHKRYYYTFDNSLLFTESIQNTTQIFPR"
                     /name="DUF1398 domain-containing protein"
     gene            917..1210
                     /gene="bor"
                     /locus_tag="V3C55_RS23355"
                     /old_locus_tag="V3C55_23355"
     CDS             917..1210
                     /gene="bor"
                     /locus_tag="V3C55_RS23355"
                     /old_locus_tag="V3C55_23355"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_309652.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="serum resistance lipoprotein Bor"
                     /protein_id="WP_000738492.1"
                     /translation="MKKMLLATALALLITGCAQQTFTVQNKPAAVAPKETITHHFFVSG
                     IGQKKTVDAAKICGGAENVVKTETQQTFVNGLLGFITLGIYTPLEARVYCSQ"
                     /name="bor"
     gene            complement(1301..1483)
                     /gene="rzoD"
                     /locus_tag="V3C55_RS23360"
                     /old_locus_tag="V3C55_23360"
     CDS             complement(1301..1483)
                     /gene="rzoD"
                     /locus_tag="V3C55_RS23360"
                     /old_locus_tag="V3C55_23360"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_309651.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="prophage lysis lipoprotein RzoD"
                     /protein_id="WP_012738274.1"
                     /translation="MLKLKMMLCVMMLPLVVVGCTSKQSVSQCVKPPPPPAWIMQPPPD
                     WQTPLNGIISPSERG"
                     /name="rzoD"
     gene            complement(1700..2176)
                     /locus_tag="V3C55_RS23365"
                     /old_locus_tag="V3C55_23365"
     CDS             complement(1700..2176)
                     /locus_tag="V3C55_RS23365"
                     /old_locus_tag="V3C55_23365"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_309649.1"
                     /GO_function="GO:0003796 - lysozyme activity [Evidence
                     IEA]"
                     /GO_process="GO:0016998 - cell wall macromolecule catabolic
                     process [Evidence IEA]; GO:0009253 - peptidoglycan
                     catabolic process [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="glycoside hydrolase family protein"
                     /protein_id="WP_000229403.1"
                     /translation="MVEINNQRKAFLDMLAWSEGTDNGRQKTRNHGYDVIVGGELFTDY
                     SDHPRKLVTLNPKLKSTGAGRYQLLSRWWDAYRKQLGLKDFSPKSQDAVALQQIKERGA
                     LPMIDRGDIRQAIDRCSNIWASLPGAGYGQFEHKADSLIAKFKEAGGTVREIDV"
                     /name="glycoside hydrolase family protein"
     gene            complement(2160..2483)
                     /locus_tag="V3C55_RS23370"
                     /old_locus_tag="V3C55_23370"
                     /pseudo=""
     CDS             complement(2160..2483)
                     /locus_tag="V3C55_RS23370"
                     /old_locus_tag="V3C55_23370"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015966862.1"
                     /GO_process="GO:0019835 - cytolysis [Evidence IEA]"
                     /note="internal stop; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="phage holin, lambda family"
                     /name="phage holin, lambda family"
     gene            2927..3121
                     /locus_tag="V3C55_RS23375"
                     /old_locus_tag="V3C55_23375"
     CDS             2927..3121
                     /locus_tag="V3C55_RS23375"
                     /old_locus_tag="V3C55_23375"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_001165309.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="YlcI/YnfO family protein"
                     /protein_id="WP_001421937.1"
                     /translation="MSTKNRTRRTTTRNIRFPNQMIEQINIALEQKGSGNFSAWVIEAC
                     RRRLTSEKRAYTSIKSDEE"
                     /name="YlcI/YnfO family protein"
     gene            complement(3286..3492)
                     /gene="ybcW"
                     /locus_tag="V3C55_RS23380"
                     /old_locus_tag="V3C55_23380"
     CDS             complement(3286..3492)
                     /gene="ybcW"
                     /locus_tag="V3C55_RS23380"
                     /old_locus_tag="V3C55_23380"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_309654.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein YbcW"
                     /protein_id="WP_001031427.1"
                     /translation="MNKEQSADDPSVDLIRVKNMLNSTISMSYPDVVIACIEHKVSLEA
                     FRAIEAALVKHDNNMKDYSLVVD"
                     /name="ybcW"
ORIGIN
        1 tttgagcacg ttggccttac atacatctgt cggttgtatt tccctccaga atgccagcag
       61 gaccgcactt tgttacgcaa ccaatactat taagtgaaaa cattcctaat atttgacata
      121 aatcatcaac aaaacacaag gaggtcagac cagattgaaa cgataaaaac gataatgcaa
      181 actacgcgcc ctcgtatcac atggaaggtt ttaccaatgg ctcaggttgc catttttaaa
      241 gaaatattcg atcaagtgcg aaaagattta gactgtgaat tgttttattc tgaactaaaa
      301 cgtcacaacg tctcacatta tatttactat ctagccacag ataatattca catcgtgtta
      361 gaaaacgata acaccgtgtt aataaaagga cttaaaaagg ttgtaaatgt taaattctca
      421 agaaacacgc atcttataga aacgtcctat gataggttga aatcaagaga aatcacattt
      481 cagcaataca gggaaaatct tgctaaagca ggagttttcc gatgggttac aaatatccat
      541 gaacataaaa gatattacta tacctttgat aattcattac tatttactga gagcattcag
      601 aacactacac aaatctttcc acgctaaatc ataacgtccg gtttcttccg tgtcagcacc
      661 ggggcgttgg cataatgcaa tacgtgtacg cgctaaaccc tgtgtgcatc gttttaatta
      721 ttcccggaca ctcccgcaga gaagttcccc gtcagggctg tggacatagt taatccggga
      781 atacaatgac gattcatcgc acctgacata cattaataaa tattaacaat atgaaatttc
      841 aactcattgt ttagggtttg tttaattttc tacacatacg attctgcgaa cttcaaaaag
      901 catcgggaat aacaccatga aaaaaatgct actcgctact gcgctggccc tgcttattac
      961 aggatgtgct caacagacgt ttactgttca aaacaaaccg gcagcagtag caccaaagga
     1021 aaccatcacc catcatttct tcgtttctgg aattgggcag aagaaaactg tcgatgcagc
     1081 caaaatttgt ggcggcgcag aaaatgttgt taaaacagaa acccagcaaa cattcgtaaa
     1141 tggattgctc ggttttatta ctttaggcat ttatactccg ctggaagcgc gtgtgtattg
     1201 ctcacaataa ttgcatgagt tgcccatcga tatgggcaac tctatctgca ctgctcatta
     1261 atatacttct gggttccttc cagttgtttt tgcatagtga tcagcctctc tctgagggtg
     1321 aaataatccc gttcagcggt gtctgccagt cggggggagg ctgcattatc cacgccggag
     1381 gcggtggtgg cttcacgcac tgactgacag actgctttga tgtgcaaccg acgacgacca
     1441 gcggcaacat catcacgcag agcatcattt tcagctttag catcagctaa ctccttcgtg
     1501 tattttgcat cgagcgcagc aacatcacgc tgacgcatct gcatgtcagt aattgccgcg
     1561 ttcgccagct tcagttctct ggcatttttg tcgcgctggg ctttgtaggt aatggcgtta
     1621 tcacggtaat gattaacagc ccatgacagg cagacgatga tgcagataac cagagcggag
     1681 ataatcgcgg tgactctgct catacatcaa tctctctgac cgttccgccc gcttctttga
     1741 attttgcaat caggctgtca gccttatgct cgaactgacc ataaccagcg cccggcagtg
     1801 aagcccagat attgctgcaa cggtcgattg cctgacggat atcaccacga tcaatcatag
     1861 gtaaagcgcc acgctcctta atctgctgca atgccacagc gtcctgactt ttcggagaga
     1921 agtctttcag gccaagctgc ttgcggtagg catcccacca acgggaaaga agctggtagc
     1981 gtccggcgcc tgttgatttg agttttgggt ttagcgtgac aagtttgcga gggtgatcgg
     2041 agtaatcagt aaatagctct ccgcctacaa tgacgtcata accatgattt ctggttttct
     2101 gacgtccgtt atcagttccc tccgaccacg ccagcatatc gaggaacgcc ttacgttgat
     2161 tattgatttc taccatcttc tactccggct tttttagcag cgaagcgttt gataagcgaa
     2221 ccaatcgagt cagtaccgat gtagccgata aacacgctcg ttatataagc gagattgcta
     2281 cttagtccgg cgaagtcgag aaggtcacga atgaactagg cgataatggc gcacatcgtt
     2341 gcgtcgatta ctgtttttgt aaacgcaccg ccattatatc tgccgcgaag gtacgccatt
     2401 gcaaacgcaa ggattgcccc gatgccttgt tcctttgccg cgagaatggc ggccaacagg
     2461 tcatgttttt ctggcatctt catgtcttac ccccaataag gggatttgct ctatttaatt
     2521 aggaataagg tcgattactg atagaacaaa tccaggctac tgtgtttagt aatcagattt
     2581 gttcgtgacc gatatgcacg ggcaaaacgg caggaggttg ttagcgcaaa aaaaaaattc
     2641 caaaaaaaaa attccaaaaa aaaaaagcga ctaacaaaca caatctgatg gccgcttacg
     2701 gttcactact cacgacgatg ttttttttgg tacctttttt ttcaccggaa aggacccgta
     2761 aagtgataat gattatcatc tacatatcac aacgtgcgtg gaggccatca aaccacgtca
     2821 aataatcaat tatgacgcag gtatcgtatt aattgatctg catcaactta acgtaaaaac
     2881 aacttcagac aatacaaatc agcgacactg aatacggggc aacctcatgt caacgaagaa
     2941 cagaacccgc agaacaacaa cccgcaacat ccgctttcct aaccaaatga ttgaacaaat
     3001 taacatcgct cttgagcaaa aagggtccgg gaatttctca gcctgggtca ttgaagcctg
     3061 ccgtcggaga ctaacgtcag aaaagagagc atatacatca attaaaagtg atgaagaatg
     3121 aacatcccgc gttcttccct ccgaacagga cgatattgta aattcactta attacgaggg
     3181 cattgcagta attgagttgc agttttacca ctttcctgac agtgacagac tgcgtgttgg
     3241 ctctgtcaca gactaaatag tttgaatgat tagcagttat ggtgatcagt caaccaccag
     3301 ggaataatcc ttcatattat tatcgtgctt caccaacgct gcctcaattg ctctgaatgc
     3361 ttccagagac accttatgtt ctatacatgc aattacaaca tcagggtaac tcatagaaat
     3421 ggtgctatta agcatatttt ttacacgaat cagatccacg gagggatcat cagcagattg
     3481 ttctttattc attttgtcgc tccatgcgct tgctcttcat ctagcggtta aaatattact
     3541 tcaaatcttt ctgtatgaag a
//
