LOCUS       NZ_CP083509             2969 bp    DNA     linear   CON 08-JAN-2024
DEFINITION  Escherichia coli strain elppa5 plasmid unnamed6, complete sequence.
ACCESSION   NZ_CP083509
VERSION     NZ_CP083509.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN21169128
            Assembly: GCF_020827635.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2969)
  AUTHORS   Huang,Y.T.
  TITLE     Genome sequencing and analysis
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2969)
  AUTHORS   Huang,Y.T.
  TITLE     Direct Submission
  JOURNAL   Submitted (13-SEP-2021) Department of Computer Science and
            Information Engineering, National Chung Cheng University, No.168,
            Sec. 1, University Rd., Min-Hsiung Town, Chiayi City 621, Taiwan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: flye v. 2.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 59x
            Sequencing Technology             :: Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/08/2024 05:44:00
            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)                     :: 5,279
            CDSs (total)                      :: 5,157
            Genes (coding)                    :: 4,938
            CDSs (with protein)               :: 4,938
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 219
            CDSs (without protein)            :: 219
            Pseudo Genes (ambiguous residues) :: 0 of 219
            Pseudo Genes (frameshifted)       :: 79 of 219
            Pseudo Genes (incomplete)         :: 152 of 219
            Pseudo Genes (internal stop)      :: 42 of 219
            Pseudo Genes (multiple problems)  :: 50 of 219
            Pseudo Genes (short protein)      :: 4 of 219
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP083509.1.
            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..2969
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="elppa5"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="unnamed6"
                     /geo_loc_name="Taiwan"
                     /lat_lon="24 N 120 E"
                     /collection_date="2019-11"
                     /collected_by="National Chung Cheng University"
     gene            complement(122..1789)
                     /gene="ltrA"
                     /locus_tag="K9U08_RS26245"
                     /old_locus_tag="K9U08_26260"
     CDS             complement(122..1789)
                     /gene="ltrA"
                     /locus_tag="K9U08_RS26245"
                     /old_locus_tag="K9U08_26260"
                     /EC_number="2.7.7.49"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001748652.1"
                     /GO_function="GO:0003964 - RNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0000373 - Group II intron splicing
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="group II intron reverse transcriptase/maturase"
                     /protein_id="WP_012372796.1"
                     /translation="MNTHISVSTIPHPTGWHTIDWKACHARVRKLQLRIAKATRQQQWR
                     QVRELQRILTRSFSGKAVAVRRVTENTGKRTPGIDGKIWHTPKEKWEGICSLNLCGYRP
                     QPLRRIHIPKSNGKTRPLGIPTMRDRAMQALWLLALEPVSETTADHNSYGFRPMRSTHD
                     AIESIFLRMSQKVSPKWILEGDIKGCFDNISHDWLLSHIPMDRRLLKKWLKAGYMERGV
                     FNHTNSGTPQGGIISPVLANMALDGLEKELMQTFRKSGYHSAKHQVNYVRYADDFICSG
                     SSRELLENEVRPLIAAFMRERGLELSEEKTAITHIDKGFDFLGQNVRKYNGKMLIKPSK
                     KNLKNFLCKVREIIKRNPTLPAWKLIGQLNPVIRGWATYHRHVVAKETFNYVDTQIWRA
                     IWRWCVRRHPRKGLRWIAGRYFSFEGRRWIFKAITPEGKILTLFRAMETPIKRHIKIKG
                     EATPYTPGMEIYFERRLDLIWKGKSKKMKTVVQLWKRQGKHCPQCGQPITNQTGWNIHH
                     RIRKVMGGSDELTNLELLHPNCHRQLHSREAGAHRKHL"
                     /name="ltrA"
     gene            complement(<2518..2690)
                     /locus_tag="K9U08_RS26250"
                     /old_locus_tag="K9U08_26265"
                     /pseudo=""
     CDS             complement(<2518..2690)
                     /locus_tag="K9U08_RS26250"
                     /old_locus_tag="K9U08_26265"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052655.1"
                     /note="frameshifted; 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="hypothetical protein"
                     /name="hypothetical protein"
     gene            2760..2966
                     /locus_tag="K9U08_RS26475"
     CDS             2760..2966
                     /locus_tag="K9U08_RS26475"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000547968.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="single-stranded DNA-binding protein"
                     /protein_id="WP_323809381.1"
                     /translation="MNIPQNFLPRTRQKILRSAPGQSFPAVAVMPHAAKVLKQVMVNTG
                     GNKEQVPAKRQNRGSRNSTDDGG"
                     /name="single-stranded DNA-binding protein"
ORIGIN
        1 ctctgattct gactactgca gtgttgtcct gtctgccggg tcgggtagca gcggcacatt
       61 gctgcgccgc cgccccccta agaacggagc gtgcgagttt ccccgcactc cgctcaagcc
      121 tttataagtg ctttcggtga gcaccggctt ccctgctgtg taactgtcgg tggcagttcg
      181 gatgtaacaa ctcgagattg gtcagttcgt cactgccgcc cataactttc ctgatccggt
      241 gatgtatatt ccatccggtc tggttggtta tgggttgtcc gcactgcgga cagtgtttcc
      301 cctgcctctt ccagagttga actactgtct tcatcttctt tgatttgcct ttccagatta
      361 gatccagacg acgttcaaag tagatttcca ttccgggggt gtatggtgtt gcttcgcctt
      421 tgatttttat atggcgcttt atcggtgttt ccattgcccg gaagagagtc agaattttcc
      481 cttccggggt tatggcttta aagatccagc gcctgccttc aaaggagaag tatcgtccgg
      541 cgatccaccg caatcctttt cgggggtgcc ttcttacaca ccatcgccat atagctcgcc
      601 agatttgggt gtcgacataa ttaaatgttt ctttcgccac gacgtgtcgg tgataggtag
      661 cccatccccg gattaccggg tttagctggc ctatcagttt ccatgccggg agcgtcggat
      721 tgcgtttaat tatttctctg actttacaga ggaagttctt caggtttttc ttcgacggtt
      781 taatcagcat tttaccgttg tacttcctga cgttctgccc taaaaagtcg aagcctttat
      841 ctatatgtgt aatcgcggtt ttttcttccg acagttccag ccctcgttcg cgcatgaaag
      901 ctgcaatcag tggtctgacc tcattttcca gcaattcacg ggagctgcct gaacagatga
      961 aatcatcagc atatctcaca taattcacct ggtgctttgc actgtgataa ccacttttcc
     1021 tgaacgtttg catcagttcc ttctccagtc cgtccagagc catgttggcg agaacagggg
     1081 atatgatgcc tccctgcggt gtcccgctgt tcgtatggtt aaacacgcct ctttccatgt
     1141 aacctgcttt caaccatttt ttaagcagtc tcctgtccat cggaatatgg gaaagcagcc
     1201 agtcatggct gatgttatcg aaacaccctt taatatcgcc ctccagtatc catttgggcg
     1261 atactttctg gctcatccgc agaaaaatgg actcaatggc gtcatgcgtg ctgcgcattg
     1321 gtctgaaacc atagctgtta tggtcagcag tggtctcgga tacgggttcc agagccagca
     1381 gccacagtgc ctgcatggcc cggtccctca ttgtgggtat gcccagcggt cgcgttttgc
     1441 cgtttgattt tgggatatgt attcgccgta gtggctgtgg cctgtaacca cacagattca
     1501 ggctgcatat tccttcccat ttctccttcg gtgtgtgcca tatttttccg tcaataccgg
     1561 gtgtcctttt accggtattt tcagttacac gcctgacagc cacggctttg ccggagaatg
     1621 agcgggtgag gatgcgctgt agttctctga cctgccgcca ttgttgctgt cgggttgcct
     1681 ttgcaatccg taactgtagc tttcgcaccc gggcatggca tgctttccag tctatggtgt
     1741 gccagcctgt cgggtggggt atcgtggaca cactgatgtg tgtattcatc tcgctgatat
     1801 ccttttgact gctttacagc ttttcatgca attaaagacc agacggaagt ctgcccgctt
     1861 tcgcgtcggg gaacctgccc cgtatcccgg tcattacaac cgggcatttg ctttttccgt
     1921 cctcctctgc ccgcaccgcc tacagtgttc cttacggttc acctgcctgt aaggcagcga
     1981 tacgggttta ccaggttccg cttaacatac agagggtcag ggcgggttct gtctcttcac
     2041 cgggggtctc tgcgcccatg tgctccctgt gcgcgaggta gcaaccggac cccgtacctt
     2101 ttggttcagg cctgtcagca tctttggcct gttgccgata acggtgttta tcaacagttc
     2161 acatgtgtta acccttctga ccagccttgc tctcctgcca catgatgctt gcagcaaggt
     2221 aaagcccctc acggggcttt acccgggctg acgcccggct ctcgttgtcc cgggagcttc
     2281 agaccccgcc gttgccggca gcgcctgtcc cggtaggcta cagctaatgg gatagctggt
     2341 tttatcaatg taaaacaata cgttaagcga cttcctgtcg cacgcgtacc ttcggctccc
     2401 ggctgcctgg cggcatccgg tcgtcaggcc cgactccgac aggcagctgc tggcgcaccc
     2461 gccagtctcc gccgaacccg ctggcgcggt ttcgggctgt tgctacggtc cgatgcgtga
     2521 aaaccccggg cttgcagcga ccgttccggt cgcgccgcct ctgtcgcgcc gtgacctgcg
     2581 ctcccggcat cccggcaaaa ggcgccggga tgtaaggcgc aacgccgttt cgcaaaccgc
     2641 gcttcacgtc gttgcggcgg gtccctgccc gttgttgtgt ccggtgccat tcaccagttt
     2701 aagcccctgt cgccgggggc atagacagcc acaaccgtct cctgccagtc cagggtgaaa
     2761 tgaacatccc gcaaaatttt ttgcccagaa cccggcaaaa aattttgcgg tctgcccccg
     2821 gacagtcgtt tccggccgtg gcagtgatgc cccatgcggc gaaggttctc aaacaggtga
     2881 tggtgaatac cggagggaac aaagagcagg tccccgcaaa acgtcaaaac cgcggctccc
     2941 gaaactcaac agatgatggg ggctgaaaa
//
