LOCUS       NZ_CP139847             3472 bp    DNA     linear   CON 21-DEC-2023
DEFINITION  Escherichia coli strain Nord58 plasmid pNORD58_6.
ACCESSION   NZ_CP139847
VERSION     NZ_CP139847.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN38610762
            Assembly: GCF_034422435.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3472)
  AUTHORS   Braun,S.D.
  TITLE     DRESI Project
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3472)
  AUTHORS   Braun,S.D.
  TITLE     Direct Submission
  JOURNAL   Submitted (04-DEC-2023) Optical Molecular Diagnostics and System
            Technology, Leibniz Institute of Photonic Technology, Albert
            Einstein Strasse 9, Jena 07745, Germany
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 17-MAR-2023
            Assembly Method                   :: Flye v. 2.9.1-b1780
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 61.0x
            Sequencing Technology             :: Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 12/21/2023 09:39:28
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,795
            CDSs (total)                      :: 5,664
            Genes (coding)                    :: 5,273
            CDSs (with protein)               :: 5,273
            Genes (RNA)                       :: 131
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 98
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 391
            CDSs (without protein)            :: 391
            Pseudo Genes (ambiguous residues) :: 0 of 391
            Pseudo Genes (frameshifted)       :: 225 of 391
            Pseudo Genes (incomplete)         :: 194 of 391
            Pseudo Genes (internal stop)      :: 62 of 391
            Pseudo Genes (multiple problems)  :: 78 of 391
            Pseudo Genes (short protein)      :: 3 of 391
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP139847.1.
            Bacteria and source DNA available from Leibniz-IPHT Jena.
            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/
FEATURES             Location/Qualifiers
     source          1..3472
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="Nord58"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pNORD58_6"
                     /geo_loc_name="Germany"
                     /collection_date="2017-05-12"
     gene            156..350
                     /locus_tag="U0535_RS28750"
                     /old_locus_tag="U0535_28750"
     CDS             156..350
                     /locus_tag="U0535_RS28750"
                     /old_locus_tag="U0535_28750"
                     /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(515..721)
                     /gene="ybcW"
                     /locus_tag="U0535_RS28755"
                     /old_locus_tag="U0535_28755"
     CDS             complement(515..721)
                     /gene="ybcW"
                     /locus_tag="U0535_RS28755"
                     /old_locus_tag="U0535_28755"
                     /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"
     gene            1007..1417
                     /locus_tag="U0535_RS28760"
                     /old_locus_tag="U0535_28760"
     CDS             1007..1417
                     /locus_tag="U0535_RS28760"
                     /old_locus_tag="U0535_28760"
                     /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            1707..2000
                     /gene="bor"
                     /locus_tag="U0535_RS28765"
                     /old_locus_tag="U0535_28765"
     CDS             1707..2000
                     /gene="bor"
                     /locus_tag="U0535_RS28765"
                     /old_locus_tag="U0535_28765"
                     /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(2091..2273)
                     /gene="rzoD"
                     /locus_tag="U0535_RS28770"
                     /old_locus_tag="U0535_28770"
     CDS             complement(2091..2273)
                     /gene="rzoD"
                     /locus_tag="U0535_RS28770"
                     /old_locus_tag="U0535_28770"
                     /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(2490..2966)
                     /locus_tag="U0535_RS28775"
                     /old_locus_tag="U0535_28775"
     CDS             complement(2490..2966)
                     /locus_tag="U0535_RS28775"
                     /old_locus_tag="U0535_28775"
                     /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(2950..3272)
                     /locus_tag="U0535_RS28780"
                     /old_locus_tag="U0535_28780"
                     /pseudo=""
     CDS             complement(2950..3272)
                     /locus_tag="U0535_RS28780"
                     /old_locus_tag="U0535_28780"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015966862.1"
                     /GO_process="GO:0019835 - cytolysis [Evidence IEA]"
                     /note="frameshifted; 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"
ORIGIN
        1 attatcatct acatatcaca acgtgcgtgg aggccatcaa accacgtcaa ataatcaatt
       61 atgacgcagg tatcgtatta attgatctgc atcaacttaa cgtaaaaaca acttcagaca
      121 atacaaatca gcgacactga atacggggca acctcatgtc aacgaagaac agaacccgca
      181 gaacaacaac ccgcaacatc cgctttccta accaaatgat tgaacaaatt aacatcgctc
      241 ttgagcaaaa agggtccggg aatttctcag cctgggtcat tgaagcctgc cgtcggagac
      301 taacgtcaga aaagagagca tatacatcaa ttaaaagtga tgaagaatga acatcccgcg
      361 ttcttccctc cgaacaggac gatattgtaa attcacttaa ttacgagggc attgcagtaa
      421 ttgagttgca gttttaccac tttcctgaca gtgacagact gcgtgttggc tctgtcacag
      481 actaaatagt ttgaatgatt agcagttatg gtgatcagtc aaccaccagg gaataatcct
      541 tcatattatt atcgtgcttc accaacgctg cctcaattgc tctgaatgct tccagagaca
      601 ccttatgttc tatacatgca attacaacat cagggtaact catagaaatg gtgctattaa
      661 gcatattttt tacacgaatc agatccacgg agggatcatc agcagattgt tctttattca
      721 ttttgtcgct ccatgcgctt gctcttcatc tagcggttaa aatattactt caaatctttc
      781 tgtatgaaga tttgagcacg ttggccttac atacatctgt cggttgtatt tccctccaga
      841 atgccagcag gaccgcactt tgttacgcaa ccaatactat taagtgaaaa cattcctaat
      901 atttgacata aatcatcaac aaaacacaag gaggtcagac cagattgaaa cgataaaaac
      961 gataatgcaa actacgcgcc ctcgtatcac atggaaggtt ttaccaatgg ctcaggttgc
     1021 catttttaaa gaaatattcg atcaagtgcg aaaagattta gactgtgaat tgttttattc
     1081 tgaactaaaa cgtcacaacg tctcacatta tatttactat ctagccacag ataatattca
     1141 catcgtgtta gaaaacgata acaccgtgtt aataaaagga cttaaaaagg ttgtaaatgt
     1201 taaattctca agaaacacgc atcttataga aacgtcctat gataggttga aatcaagaga
     1261 aatcacattt cagcaataca gggaaaatct tgctaaagca ggagttttcc gatgggttac
     1321 aaatatccat gaacataaaa gatattacta tacctttgat aattcattac tatttactga
     1381 gagcattcag aacactacac aaatctttcc acgctaaatc ataacgtccg gtttcttccg
     1441 tgtcagcacc ggggcgttgg cataatgcaa tacgtgtacg cgctaaaccc tgtgtgcatc
     1501 gttttaatta ttcccggaca ctcccgcaga gaagttcccc gtcagggctg tggacatagt
     1561 taatccggga atacaatgac gattcatcgc acctgacata cattaataaa tattaacaat
     1621 atgaaatttc aactcattgt ttagggtttg tttaattttc tacacatacg attctgcgaa
     1681 cttcaaaaag catcgggaat aacaccatga aaaaaatgct actcgctact gcgctggccc
     1741 tgcttattac aggatgtgct caacagacgt ttactgttca aaacaaaccg gcagcagtag
     1801 caccaaagga aaccatcacc catcatttct tcgtttctgg aattgggcag aagaaaactg
     1861 tcgatgcagc caaaatttgt ggcggcgcag aaaatgttgt taaaacagaa acccagcaaa
     1921 cattcgtaaa tggattgctc ggttttatta ctttaggcat ttatactccg ctggaagcgc
     1981 gtgtgtattg ctcacaataa ttgcatgagt tgcccatcga tatgggcaac tctatctgca
     2041 ctgctcatta atatacttct gggttccttc cagttgtttt tgcatagtga tcagcctctc
     2101 tctgagggtg aaataatccc gttcagcggt gtctgccagt cggggggagg ctgcattatc
     2161 cacgccggag gcggtggtgg cttcacgcac tgactgacag actgctttga tgtgcaaccg
     2221 acgacgacca gcggcaacat catcacgcag agcatcattt tcagctttag catcagctaa
     2281 ctccttcgtg tattttgcat cgagcgcagc aacatcacgc tgacgcatct gcatgtcagt
     2341 aattgccgcg ttcgccagct tcagttctct ggcatttttg tcgcgctggg ctttgtaggt
     2401 aatggcgtta tcacggtaat gattaacagc ccatgacagg cagacgatga tgcagataac
     2461 cagagcggag ataatcgcgg tgactctgct catacatcaa tctctctgac cgttccgccc
     2521 gcttctttga attttgcaat caggctgtca gccttatgct cgaactgacc ataaccagcg
     2581 cccggcagtg aagcccagat attgctgcaa cggtcgattg cctgacggat atcaccacga
     2641 tcaatcatag gtaaagcgcc acgctcctta atctgctgca atgccacagc gtcctgactt
     2701 ttcggagaga agtctttcag gccaagctgc ttgcggtagg catcccacca acgggaaaga
     2761 agctggtagc gtccggcgcc tgttgatttg agttttgggt ttagcgtgac aagtttgcga
     2821 gggtgatcgg agtaatcagt aaatagctct ccgcctacaa tgacgtcata accatgattt
     2881 ctggttttct gacgtccgtt atcagttccc tccgaccacg ccagcatatc gaggaacgcc
     2941 ttacgttgat tattgatttc taccatcttc tactccggct tttttagcag cgaagcgttt
     3001 gataagcgaa ccaatcgagt cagtaccgat gtagccgata aacacgctcg ttatataagc
     3061 gagattgcta cttagtccgg cgaagtcgag aaggtcacga atgaactagg cgataatggc
     3121 gcacatcgtt gcgtcgatta ctgtttttgt aaacgcaccg ccattatatc tgccgcgaag
     3181 gtacgccatt gcaaacgcaa ggattgcccg atgccttgtt cctttgccgc gagaatggcg
     3241 gccaacaggt catgtttttc tggcatcttc atgtcttacc cccaataagg ggatttgctc
     3301 tatttaatta ggaataaggt cgattactga tagaacaaat ccaggctact gtgtttagta
     3361 atcagatttg ttcgtgaccg atatgcacgg gcaaaacggc aggaggttgt tagcgcaaaa
     3421 aaaaaattcc aaaaaaaaaa ttccaaaaaa aaaagcgact aacaaacaca at
//
