LOCUS       NZ_CP083516             3888 bp    DNA     linear   CON 08-JAN-2024
DEFINITION  Escherichia coli strain elppa4 plasmid unnamed4, complete sequence.
ACCESSION   NZ_CP083516
VERSION     NZ_CP083516.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN21169127
            Assembly: GCF_020827655.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3888)
  AUTHORS   Huang,Y.T.
  TITLE     Genome sequencing and analysis
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3888)
  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                   :: 114x
            Sequencing Technology             :: Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/08/2024 05:40:40
            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)                     :: 5,308
            CDSs (total)                      :: 5,187
            Genes (coding)                    :: 4,971
            CDSs (with protein)               :: 4,971
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 216
            CDSs (without protein)            :: 216
            Pseudo Genes (ambiguous residues) :: 0 of 216
            Pseudo Genes (frameshifted)       :: 100 of 216
            Pseudo Genes (incomplete)         :: 128 of 216
            Pseudo Genes (internal stop)      :: 39 of 216
            Pseudo Genes (multiple problems)  :: 45 of 216
            Pseudo Genes (short protein)      :: 4 of 216
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP083516.1.
            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..3888
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="elppa4"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="unnamed4"
                     /geo_loc_name="Taiwan"
                     /lat_lon="24 N 120 E"
                     /collection_date="2019-08"
                     /collected_by="National Chung Cheng University"
     gene            31..784
                     /locus_tag="K9U07_RS26420"
                     /old_locus_tag="K9U07_26455"
                     /pseudo=""
     CDS             31..784
                     /locus_tag="K9U07_RS26420"
                     /old_locus_tag="K9U07_26455"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_416077.4"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="antitermination protein"
                     /name="antitermination protein"
     gene            1034..1228
                     /locus_tag="K9U07_RS26425"
                     /old_locus_tag="K9U07_26460"
     CDS             1034..1228
                     /locus_tag="K9U07_RS26425"
                     /old_locus_tag="K9U07_26460"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_309806.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001355891.1"
                     /translation="MLKQQDMTETAKVVFNELSIEPATVGEIAQNTYLSRERCQLILTQ
                     LVMAGLADYQFGCYRRLQQ"
                     /name="hypothetical protein"
     gene            1378..2430
                     /locus_tag="K9U07_RS26430"
                     /old_locus_tag="K9U07_26465"
     CDS             1378..2430
                     /locus_tag="K9U07_RS26430"
                     /old_locus_tag="K9U07_26465"
                     /EC_number="2.1.1.-"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000799668.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0008170 - N-methyltransferase activity [Evidence IEA]"
                     /GO_process="GO:0009307 - DNA restriction-modification
                     system [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="site-specific DNA-methyltransferase"
                     /protein_id="WP_039023677.1"
                     /translation="MKNTVKINSVDLINADCLHFIQSLPDDSIDLIVTDPPYFKVKPNG
                     WDNQWKGDEDYLKWLDHCLAQFWRVLKPAGSLYLFCGHRLASDIEIMMRERFNVLNHII
                     WAKPSGRWNGCNKESLRAYFPATERVLFAEHYHGPYRGKSDGYAAKERELKQHIMAPLI
                     SYFRNARAELGITAKQIAEATGKKNMVSHWFGASQWQLPNEADYRKLQALFSRIAAEKF
                     QEQQLEQPHHQLVASYDSLNRKYSELLDEFKSLRRYFSVSVSVPYTDVWTHKPVQFYPG
                     KHPCEKPADMLRQIINASSRPGDLVADFFMGSGSTIKAAMALGRRALGVELESERFNQT
                     VKEVSELVGK"
                     /name="site-specific DNA-methyltransferase"
     gene            2508..2843
                     /locus_tag="K9U07_RS26435"
                     /old_locus_tag="K9U07_26470"
     CDS             2508..2843
                     /locus_tag="K9U07_RS26435"
                     /old_locus_tag="K9U07_26470"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001120497.1"
                     /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="phage holin, lambda family"
                     /protein_id="WP_001120502.1"
                     /translation="MPHNPNTWPDWLELFQSWWRGDTPLGAVIMSIVMAGLRIAYFGGG
                     GGWKRKTLEILLCGALTLTFASALEYVGWPKSLSVAIGGGVGLIGVDAIRGAAMRVIGN
                     KFGSSKE"
                     /name="phage holin, lambda family"
     gene            2847..3323
                     /locus_tag="K9U07_RS26440"
                     /old_locus_tag="K9U07_26475"
     CDS             2847..3323
                     /locus_tag="K9U07_RS26440"
                     /old_locus_tag="K9U07_26475"
                     /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_001148534.1"
                     /translation="MQALNSQRKAFLDMVAWSEGTDNGRQPTRNHGYDVIVGGELFTDY
                     SDHPRKLVTLNPKLKSTAAGRYQLLSRWWDAYRKQLGLKDFSPESQDAVALQQIKERGA
                     LPMIDRGSIRQAIDRCSNIWASLPGAGYGQYEHKIGDLIARFKKAGGVVNEAEI"
                     /name="glycoside hydrolase family protein"
     gene            3307..3699
                     /locus_tag="K9U07_RS26445"
                     /old_locus_tag="K9U07_26480"
     CDS             3307..3699
                     /locus_tag="K9U07_RS26445"
                     /old_locus_tag="K9U07_26480"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001356320.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF2570 family protein"
                     /protein_id="WP_001766839.1"
                     /translation="MKLRYKLVIVAFVVTVIGSFIWSAGHYYSKYQHEKERADEAVRNA
                     ESATAITRNVLQSLQIVNTVLEANQHAKQQIALESQRTQEDIKVAVADDDCASRHVPAA
                     AADRLRKYANSLRTDSGGTVASKPDY"
                     /name="DUF2570 family protein"
ORIGIN
        1 taggcgtact ggcgtaagtg gagaacgagc atgaaccttg aagccttacc aaaatattac
       61 tccccaaaat ctccaaaatt gagcgatgac gcaccggcga caggctcagg tggtttaacg
      121 attacggatg tgatggctgc gcaggggatg gtgcagtcga aagcaccgct tgggtttgcc
      181 ttattcctgg caaaagttgg tgttcaggat cctcagtttg cgattgaagg tctgctcaat
      241 tacgcgatgg cactggataa cccgacattg aataaattga gtgaagaaac ccggttacag
      301 atcatccctt accttgtgaa ttttgccttt gctgattatt ccaggtctgc ggcaagtaag
      361 gctcgctgtg agcattgtgc tggtactgga tttcataatg tattgcgcga agtggtgaaa
      421 cactccagaa gcgggggaat ctgttatcaa ggaagagtgg gtgaaggaac tatgtcagca
      481 ttgtcatggt aagggagaag tcagcacagc gtgcagaggg tgtaagggta aaggtattgt
      541 cctggatgaa aaaaggaccc ggcttcatgg cacacctgtt tataagattt gtgggcgttg
      601 caatggaaac cggtttagcc gtttaccaac cacactggcg cggcatcatg tccagaagct
      661 ggtaccagac ctgacagatt atcagtggta caaaggatat gcagatgtca ttgataaact
      721 ggttacaaag tgctggcagg aagaagcata tgctgaggcg caattaagaa aagtgacgag
      781 ataaatgatt ttcgccgaag atggcgacat aatgcttgca tttttcaaaa aatatggata
      841 agatttttcc aacgatgggc tttgtatgtc taccgttgat aagatttaag aacccgccgc
      901 tgagcgggtt tttttgtgcc ttgatgttgg cagtacggta aacacgctgg tggtcgtgaa
      961 tactgacttt ttatcttgct ggctttttag acaagagtta ttggtatgtc atgttaacca
     1021 gaaggaaaaa ggcatgctaa aacagcaaga tatgacagaa acggcgaaag ttgtttttaa
     1081 tgaattaagc atcgaaccgg caacagtcgg ggagattgca caaaacacat atctttcacg
     1141 cgaacgctgt cagttaatac tgacccagtt ggttatggcg gggctggcag attaccagtt
     1201 cggctgttac agacgccttc agcaatgaag gacttttaat ttgtgaaaat gggcggctgg
     1261 tgggtgttgg tagcacctgc cagccattcg ctcatgctta ctggtcacaa gcgaaccacg
     1321 gcccactgct ttagcgcaaa agcagagtga gcctaccaga gttacgctta ctgatccatg
     1381 aaaaatactg taaaaataaa cagtgttgat ttaatcaacg ctgattgcct gcattttatt
     1441 cagtccctgc ctgatgattc cattgacctg attgttaccg atccgccgta cttcaaggtg
     1501 aaacccaacg gttgggacaa tcagtggaaa ggggacgaag attaccttaa gtggctggat
     1561 cactgtctgg cccagttctg gcgggtgctg aaacctgccg gaagccttta cctgttctgt
     1621 ggacatcgcc tggcatctga tattgagatc atgatgcgtg aacgtttcaa cgtgcttaac
     1681 catatcatct gggcgaagcc gtccggacgt tggaatgggt gtaataaaga aagtctgcgt
     1741 gcatattttc ctgccacaga gcgcgttctg tttgctgaac attaccatgg gccatatcgt
     1801 ggcaaaagtg acggctatgc ggcaaaagaa agggaactca agcagcacat aatggcaccg
     1861 ctgatatcgt atttcaggaa tgctcgtgcc gaactgggta taacggcaaa acaaattgcc
     1921 gaagccacag gtaagaaaaa tatggtttcc cactggtttg gtgccagtca gtggcagttg
     1981 ccgaatgagg ctgactaccg gaagttacag gcactgtttt cccgtatagc ggcagagaag
     2041 tttcaggaac agcaactgga acaaccacac caccagctgg tggcatctta tgattcactg
     2101 aatcgcaaat attctgaatt gctggatgag tttaaatcac tccggcgcta tttctccgta
     2161 tcagtctccg tgccttatac cgatgtctgg acgcataagc ccgttcagtt ctatccgggt
     2221 aaacatccgt gcgagaaacc ggcggatatg ctccggcaaa taatcaatgc cagtagtcga
     2281 ccaggcgatc tggttgctga tttctttatg ggatccggtt ccacaataaa agcagcaatg
     2341 gcgctggggc gtcgggcgtt aggtgttgaa cttgagtcag agcggtttaa tcagacggtg
     2401 aaagaggtaa gtgaactggt ggggaaataa ttctggtggc cacgttgcgt ggcctttttt
     2461 atttccaaca cagcacccgc aaatatcgcg aggtgagaga tgacgaaatg cctcataacc
     2521 caaatacctg gccggactgg ctggagttgt ttcagagctg gtggcgtgga gacacaccgc
     2581 tgggtgcagt gattatgtcg atcgttatgg ctggtttgcg catcgcctat tttggcggtg
     2641 gtggtggctg gaagcgaaaa acgctcgaga ttttgctatg tggcgctctg acgctgacct
     2701 ttgcatccgc tcttgagtat gtcggatggc ctaaatcgct ttctgttgcc attggtggtg
     2761 gcgtggggct gatcggtgtc gatgctattc gtggggctgc aatgcgagta atcggtaaca
     2821 aatttggtag ctcgaaggag taatttatgc aggcactaaa ttcccagcgt aaagctttcc
     2881 tggatatggt ggcatggtca gaaggaacgg ataacgggcg acaaccgaca cgtaaccacg
     2941 gttatgatgt tattgttggt ggcgaactgt tcactgatta ctccgatcac cctcgcaaac
     3001 ttgtcacgct aaaccccaaa ctcaaatcaa cagccgccgg acgttaccag cttctttcac
     3061 gctggtggga tgcttaccgt aaacagcttg gcctgaaaga tttttctcca gaaagccagg
     3121 acgctgtagc tctgcagcag attaaagagc gtggtgcttt accgatgatt gaccgcggca
     3181 gtattcgtca ggcaatcgac cgttgcagca atatctgggc gtcgttacct ggtgcaggtt
     3241 acggtcagta tgaacataaa atcggtgacc tgattgcccg atttaaaaaa gctggtgggg
     3301 tagtaaatga agctgagata taagctggtt attgttgcct tcgttgttac cgtcattggt
     3361 tccttcatct ggtctgccgg gcattactac agcaaatatc agcacgaaaa ggagcgtgct
     3421 gatgaggctg tacgaaatgc tgaatcagca actgccatta cccgtaacgt tctgcaatca
     3481 ctgcaaatcg tcaatacagt tctggaggct aaccagcatg caaaacagca gatcgcactg
     3541 gagtcacaga gaacccagga agatatcaaa gtggctgttg cggatgatga ttgtgcttca
     3601 cgtcatgtgc ctgctgccgc tgctgaccgg ttgcggaagt acgcgaacag tttacgtacc
     3661 gattccggcg gtaccgttgc cagcaagcct gactactgaa actccccagc cagtcattcc
     3721 cgagccgctg acctatgggg ccagtctgga tctgaatgtg agcctgcttt cggcgttggg
     3781 acaatgcaat attgacaaag cggggattcg aagtatcgag atgcgccgta acgctttgct
     3841 ggcagcagtc aaatagtccg gataaagaac aggaatatat ttatgccc
//
