LOCUS       NZ_AP022546             3121 bp    DNA     circular CON 16-JUN-2023
DEFINITION  Escherichia coli strain THO-010 plasmid pTHO-010-6, complete
            sequence.
ACCESSION   NZ_AP022546
VERSION     NZ_AP022546.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00196008
            Sequence Read Archive: DRR199813
            Assembly: GCF_015139375.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1
  AUTHORS   Sekizuka,T., Katagiri,M., Asai,K. and Kuroda,M.
  TITLE     complete genome sequences of Escherichia coli str. THO-010 isolated
            from a patient
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3121)
  AUTHORS   Sekizuka,T., Katagiri,M., Asai,K. and Kuroda,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (03-FEB-2020) Contact:Tsuyoshi Sekizuka National Institute
            of Infectious Diseases, Pathogen Genomics Center; 1-23-1 Toyama,
            Shinjuku-ku, Tokyo 162-8640, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method :: flye v. 2.5; minimap v. 0.2-r124; racon v. 1.1.0;
            circlator v. 1.5.3; Pilon v. 1.18; SPAdes v. 3.11.1; A5-miseq v.
            20140604
            Genome Coverage                   :: 281x
            Sequencing Technology             :: Sequel; NextSeq 500
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/15/2023 04:46:30
            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)                     :: 5,340
            CDSs (total)                      :: 5,219
            Genes (coding)                    :: 4,998
            CDSs (with protein)               :: 4,998
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 221
            CDSs (without protein)            :: 221
            Pseudo Genes (ambiguous residues) :: 0 of 221
            Pseudo Genes (frameshifted)       :: 71 of 221
            Pseudo Genes (incomplete)         :: 158 of 221
            Pseudo Genes (internal stop)      :: 37 of 221
            Pseudo Genes (multiple problems)  :: 41 of 221
            Pseudo Genes (short protein)      :: 2 of 221
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP022546.1.
            Annotated by DFAST v.1.2.3 (https://dfast.nig.ac.jp).
            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..3121
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="THO-010"
                     /isolation_source="urethral catheter"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pTHO-010-6"
                     /geo_loc_name="Japan:Tokyo"
                     /collection_date="2018-06-20"
     gene            complement(739..1134)
                     /locus_tag="JLH08_RS26375"
                     /old_locus_tag="THOESC010_P60020"
     CDS             complement(739..1134)
                     /locus_tag="JLH08_RS26375"
                     /old_locus_tag="THOESC010_P60020"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001222910.1"
                     /translation="MRISNIDWLKKRIGFIRKLGEQTARQRQIIDLLDNEAGLTEQERK
                     LLHVLATAEKNELQAQENARKQANQKRMEGKTQRRERNHRLFLAAGLLIEAGLVDTKTG
                     ELRYPKDNILQKLKAIRLDLETSPDHH"
                     /name="hypothetical protein"
     gene            1314..2267
                     /locus_tag="JLH08_RS26380"
                     /old_locus_tag="THOESC010_P60030"
     CDS             1314..2267
                     /locus_tag="JLH08_RS26380"
                     /old_locus_tag="THOESC010_P60030"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016235474.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobA/MobL family protein"
                     /protein_id="WP_001360358.1"
                     /translation="MATYHLNVKFGGKGQAGNHADYIERKGEYEKRKDLEYSEHGNMPG
                     WARDNPSHFWQAADQFERANGSTYREIEIALPRELTPDQRIELVQDFVRQVAGERHAYS
                     FAIHNPKASIDGGEQPHAHIMMSQRINDGMERSPEQYFRRYNAKNPERGGAKKDSGNLT
                     PTQQKEQLRTLRASWSALQNEHLARHGHRVRVDHRSLEERGIKRTPERHFGFAASSRLD
                     HAQRREILQNRAQPLEHFLEKAHSVRHQFDAQVQQKELVKTLLQDVARERGHALTARIN
                     KTGEVEFERAPTRTRSNTRGHGMGIRDNSRGYDYER"
                     /name="MobA/MobL family protein"
     gene            2279..2809
                     /locus_tag="JLH08_RS26385"
                     /old_locus_tag="THOESC010_P60040"
     CDS             2279..2809
                     /locus_tag="JLH08_RS26385"
                     /old_locus_tag="THOESC010_P60040"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000168768.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000168766.1"
                     /translation="MASTEEGLLTLLLSVEHLKNTAIEQQKAVADTLAVARETLRGYRD
                     ISDSVVKQVSDEVRKGVQKTDIAGLMGERMTQDFQRLEETVAKMRANAEALNKDIATIH
                     HNVVKEYNTLNKYSLKWFIGVTVSFLVMFSLLGWFTKTLIDRNYTATEVVYQKIVDIEK
                     KLDKPATGKSRKN"
                     /name="hypothetical protein"
     Typing          1315..2264
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.685"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cgggttcatt gaggttttcg acctcctcaa tgttcctgtg gagtctgttg cggcgacaac
       61 ggaaaccagt tcattcagtt tgcatgaacc ttctgtattc ttcaagcatt accgaccgca
      121 cagcctcccc agaatcccga aaaaatcctg tttttgcaga tgattgcgtg tttgcaaaga
      181 ccgtttgcgg ttgggggagc tgtgacgacg gcaaccgcac gcgtgagagt tccgctaccg
      241 gcgcagagag tttcatcgac agcggacacc tgatgagttg ccacaaaaac cgtatgtagc
      301 gcggctagat tggttgagtt agaccttggc ggcagttccc ggtatgtggt ggcgtgacgg
      361 gtgagatggt gcggcgaaga cgcatacgtc acgcaggcgc gggttcttcc accgacgcgc
      421 cccgtgatcg atggccttgg ctccgtccgg catatcgaga gcggcaaact acccgtccct
      481 tcactgggag gggtgagttg ttgccgttcc ctccgacctt ccaccatcca gcatatcgca
      541 cgatcccatg agcaccgcaa caactgataa ctccagagca aaaaaaaaaa aaaggatctg
      601 catcatgtga gagtgatccc accgctcgcc gcagccccag cgaccgaacg tacgcaccta
      661 tgccagatcc gcgcgtagcg cgtcgcgaaa tcgaaaacat tgaacaccgg caggcaaacg
      721 caccaccacg cagcggaatt aatgatgatc tgggcttgtt tcaagatcga gcctgattgc
      781 cttaagtttc tgtaatatat tgtcttttgg gtatctcagt tcgcctgttt ttgtgtccac
      841 tagtccggcc tcgatcagta accccgccgc aagaaacagg cggtgattgc gttcccgtcg
      901 ttgtgttttc ccctccatcc gtttttggtt ggcctgtttg cgtgcgttct cctgtgcctg
      961 tagctcgttt ttttctgcgg ttgccaggac gtggagtagt ttgcgctcct gttctgttag
     1021 tccggcttcg ttatcgagca ggtcaatgat ctgcctctgt cgtgcggtct gttctccgag
     1081 cttcctgata aagccgattc gtttcttcaa ccagtcgatg ttgctgatgc gcatgtttgg
     1141 gatgctcctt ggtgtttttt gcggtgtgtt ggggttgtgc agtatatcgc ttgcggtggg
     1201 tgggtgcagg ggggtatctt ccgtgctaat tcgtaaaatt agcaggaagc gcacttatat
     1261 gtttcttcgc cgttggctca gaaacatgtg cgctcctgcg gagggctaac accgtggcaa
     1321 cctatcacct caatgtaaaa tttggcggca agggacaggc cggaaaccat gccgattaca
     1381 tcgaacgcaa aggcgagtac gagaaacgaa aagatctgga atactcagag cacgggaata
     1441 tgccaggctg ggcgcgagat aatccctccc atttctggca agcggctgat cagtttgaac
     1501 gtgcgaatgg ttcgacttat cgggagatcg aaatcgcctt gccgcgtgaa ctgacaccgg
     1561 atcagcgcat tgaactggtg caggattttg tgcgtcaggt agctggagaa cggcacgcct
     1621 atagctttgc cattcacaat ccaaaagcga gcattgacgg aggggaacag cctcatgcgc
     1681 atatcatgat gagccagcgt attaacgatg gtatggaacg ttcgccggaa cagtatttcc
     1741 ggcgttataa cgccaagaat cccgaacggg gaggcgcaaa aaaagattca ggcaatctga
     1801 caccgactca gcaaaaagag caattgcgga cgttacgggc gagctggtca gcgttacaga
     1861 acgagcattt agcgcgtcat ggtcacaggg tgcgcgttga ccatcgctca ctggaagaac
     1921 gcggaattaa acgcacgcca gaacggcatt tcggatttgc cgcctcatca cggcttgatc
     1981 atgcgcagcg ccgcgaaatc ctgcaaaacc gagcgcagcc gctcgaacat tttctagaga
     2041 aagcgcattc ggttcgccat caatttgatg cacaagttca gcaaaaagag ttagttaaaa
     2101 cgcttttaca ggacgtcgca cgggagcgag ggcacgcgct tacggcaaga ataaataaaa
     2161 caggtgaagt tgaatttgaa cgtgcgccaa cgcggacgcg gagtaacacg cgagggcacg
     2221 gcatgggcat tcgtgacaac tcacgcgggt acgactacga acgttaaaag gggactgtat
     2281 ggcgagtaca gaagaggggt tgctcacgct cttgttgtcc gttgagcatt tgaaaaacac
     2341 tgcgatagaa caacagaaag cggttgcaga cacgctggcg gtcgcaaggg aaacactgcg
     2401 ggggtatcgg gatatttctg acagtgttgt aaaacaggtt agcgatgaag tcagaaaagg
     2461 ggtacagaaa acggacattg cggggctgat gggtgagcgc atgacccagg attttcagcg
     2521 tcttgaagag actgtggcaa agatgagagc caacgcggag gcgcttaaca aggacattgc
     2581 gacaattcat cacaatgttg ttaaagaata caacacgctc aataaataca gtctgaaatg
     2641 gtttatcggt gttacggtca gttttctggt catgttctcg ttgcttggct ggtttaccaa
     2701 aacgttgatc gacaggaact acaccgcgac ggaggtcgtg tatcagaaaa ttgttgatat
     2761 tgaaaagaaa ctggacaaac cagcaacagg gaagagccgg aaaaactgac gcgcttcgct
     2821 tgtccaacgc ctcacgggac gcgaaaaaat tccgcgtccc gttcaccgtt ttctgatgag
     2881 aaagtttgcc gttttgaccc gttcggtgct cagatttggc gaaattgatt ccgaatcact
     2941 tttgtgaata gttatgcaag cccctggaaa cgtttctgac gcgttttttg aggtaggggt
     3001 gggggaaagc atggtttttt gatgttttga gcgtaaaagc gtgaaaaatc gcgttattgt
     3061 gcttgcgatc tttcgtcagg gagcgtagaa cgaaaaaagc ccgccgttag gcgagcttct
     3121 t
//
