LOCUS       NZ_AP022538             5627 bp    DNA     circular CON 16-JUN-2023
DEFINITION  Escherichia coli strain THO-008 plasmid pTHO-008-2, complete
            sequence.
ACCESSION   NZ_AP022538
VERSION     NZ_AP022538.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00196006
            Sequence Read Archive: DRR199811
            Assembly: GCF_015139155.1
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-008 isolated
            from a patient
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5627)
  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                   :: 431x
            Sequencing Technology             :: Sequel; NextSeq 500
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/15/2023 04:34:51
            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)                     :: 5,058
            CDSs (total)                      :: 4,930
            Genes (coding)                    :: 4,729
            CDSs (with protein)               :: 4,729
            Genes (RNA)                       :: 128
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 201
            CDSs (without protein)            :: 201
            Pseudo Genes (ambiguous residues) :: 0 of 201
            Pseudo Genes (frameshifted)       :: 60 of 201
            Pseudo Genes (incomplete)         :: 146 of 201
            Pseudo Genes (internal stop)      :: 28 of 201
            Pseudo Genes (multiple problems)  :: 33 of 201
            Pseudo Genes (short protein)      :: 5 of 201
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP022538.1.
            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..5627
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="THO-008"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pTHO-008-2"
                     /geo_loc_name="Japan:Tokyo"
                     /collection_date="2018-06-07"
     gene            complement(102..293)
                     /locus_tag="JLF34_RS24960"
                     /old_locus_tag="THOESC008_P20010"
     CDS             complement(102..293)
                     /locus_tag="JLF34_RS24960"
                     /old_locus_tag="THOESC008_P20010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_000165985.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            357..680
                     /locus_tag="JLF34_RS24965"
                     /old_locus_tag="THOESC008_P20020"
     CDS             357..680
                     /locus_tag="JLF34_RS24965"
                     /old_locus_tag="THOESC008_P20020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_000955999.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            889..>1320
                     /locus_tag="JLF34_RS25385"
                     /pseudo=""
     CDS             889..>1320
                     /locus_tag="JLF34_RS25385"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /note="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="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            1358..1888
                     /locus_tag="JLF34_RS24975"
                     /old_locus_tag="THOESC008_P20030"
     CDS             1358..1888
                     /locus_tag="JLF34_RS24975"
                     /old_locus_tag="THOESC008_P20030"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001673158.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_200922427.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFRKLEESVNRELTSNE
                     SLIRNAINDHTTALKELLERYQKTTVDTMDAHWKTVLKMSVKRWLWLIIVSVLMFATTG
                     SLLWYQGMKINANMNILREQKESLEKLNSKTWGVRYHEDSNGRFLVLPKGMKAETNWTK
                     DNGKLNAVRLVQE"
                     /name="MbeB family mobilization protein"
     gene            1895..2128
                     /locus_tag="JLF34_RS24980"
                     /old_locus_tag="THOESC008_P20040"
     CDS             1895..2128
                     /locus_tag="JLF34_RS24980"
                     /old_locus_tag="THOESC008_P20040"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_000137437.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWENAFVELQKMFSLTQRDNA
                     MLNGRVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            2609..3661
                     /locus_tag="JLF34_RS24985"
                     /old_locus_tag="THOESC008_P20050"
     CDS             2609..3661
                     /locus_tag="JLF34_RS24985"
                     /old_locus_tag="THOESC008_P20050"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001557502.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001053268.1"
                     /translation="MNLQQRINKLPQLSSSFSFGKDIDNIHSFIFNETSKDKIEDLLRK
                     WVSGNQPCVFGKLASKKIKGLDFHLSIVNSPQLYNDDGHLFDFLRNERVRFKERARRGE
                     VSAHLIYFIHPQLAFARPSEELVDIQKYICSLHMPECYPIKEDVIYTESVPFQDKDGLK
                     IYKAGVNVFYSSAHRTRNHDRRIPGGILISVNAPGHFMRLAIEKGFYKDQEQALADIRN
                     MTIQSVGKGGYSHPEGISTTWHSESNLDRFGCPVHTGNSSYYSGFYHTDVLIPGELTKD
                     ERLLHEIENSDPMIFNWNVLFYVSLEEFPIDDPYYGEFIGIPVDDASMFFNSFQPRKFE
                     NKPLYEKEDD"
                     /name="hypothetical protein"
     gene            3663..4529
                     /locus_tag="JLF34_RS24990"
                     /old_locus_tag="THOESC008_P20060"
     CDS             3663..4529
                     /locus_tag="JLF34_RS24990"
                     /old_locus_tag="THOESC008_P20060"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001335763.1"
                     /GO_function="GO:0005215 - transporter activity [Evidence
                     IEA]"
                     /GO_process="GO:0055085 - transmembrane transport [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DMT family transporter"
                     /protein_id="WP_001335763.1"
                     /translation="MIKGMLFAFLAAFSWGAAIVMSKKGVEELDAGGVFFWQICSAVIL
                     SWIVLFIKRKKLPLNSKAILAYATGVFEPFLAYTFTLYGLYFISAGSASIIFSLESVFI
                     LVLSVLICSVKINSPQYFILFLIGAIVGSILVALPDISNGSNNIVGYCLVVAGVLSAAF
                     YVVISSRLIKSFEPITLLSGQLTFSLILSSLFIFISKSSIYLPLESVIIVFSSGILQYF
                     LAFCFYLNSLRWLPVHLAGIMLYFIPLVALFLSWLFLDEQFTFLQGVGFIVTVLSVYFL
                     NRKYSEE"
                     /name="DMT family transporter"
     Typing          4913..5100
                     /name="rep_cluster_2401"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="4.63e-94"
     Typing          671..2232
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.808"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ccccgacacc cgctaaaacc tgctgacgcg ccctgacggg cttgtcagct cccggcatcc
       61 gctcacagac aagctgtgac cgtctccggg agctgcatgt atcagagatt ttcaccgtca
      121 tccccgaaac gtgcgaggca gctgcggtaa agctcatcgg cgtggtcgtg aagcgattca
      181 caaatatcgg cctgttcatc tgcgtccagt tcgttgagct tctccagcag cgttaatgtc
      241 tggcttctga taaagcgggc catgttaagg gcggtttttt cctgtttagt cactgatgcc
      301 tccgtgtaag ggggatttct gttcatgggg taatgatacc gatgaaacgc gagaggatgc
      361 tcacaatacg ggttactgat gatgaacatg cccggttact tgaacgctgt gagggtaaac
      421 aactggcggt atggatgcgg cgggtctgcc tgggggagcc ggttgcccgt tccggaaaac
      481 tgccgacact ggcaccgccg ttactgcgtc agctggccgc catcggaaat aacctgaatc
      541 agacagcccg taaggtgaac agcgggcagt ggtcttccgg tgaccgggtt caggtggtgg
      601 ccgcactgat ggccatcggg gatgagctgc gccggctgcg tctggccgtc agggaacagg
      661 gggcgcggga tgatagttaa atttcatgcc aggggaaaag gtggtggcag tggtccggtt
      721 gattacctgc tggggaggga gcgtaaccgc gaaggcgcaa cggtgcttca gggtaatccg
      781 gaagaagtcc gggaactcat cgatgccacg ccatttgcga agaaatacac gtccggtgtt
      841 ctgtcgttcg cggagaagga gctgccgccg ggaggacgtg aaaaagtgat ggcgagcttt
      901 gagcgtgtac tgatgcccgg tctcgaaaaa aatcagtaca gcatcctgtg ggtggagcac
      961 caggacaagg gacggcttga gctgaatttt gtcattccga acatggagct acagaccgga
     1021 aaacgcctcc agccgtacta cgaccgcgca gacaggccta gaattgatgc ctggcagacg
     1081 ctggtgaatc accattacgg gctgcatgac ccgaacgccc cggagaaccg ccggacgctg
     1141 acccttcctg ataacctgcc ggaaacgaaa caggcgcttg ctgagggcgt cacacgcggg
     1201 atagacgcgc tttaccatgc cggagagata aaaggccgtc aggatgtgat tcaggcgctc
     1261 acagaggcgg ggcttgaagt ggtcagggtg acgcgaagca gtatcagcat tgcagacccg
     1321 aacggcggga ggaatatcag actgaaagga gcgttttatg agcaatcttt tacagacggg
     1381 cgcggagttc gagaaaaagc tgaaagagag agccgaatct acagagaaaa tgctgaacga
     1441 cgagttcagg aagctcgaag aatctgtaaa cagggaactg acctcaaacg aatctttaat
     1501 caggaacgct atcaacgacc atacaacagc cctgaaagaa ctgctggaga ggtatcagaa
     1561 aacgaccgtc gatacgatgg acgcgcactg gaaaaccgta ctgaaaatga gcgtgaaacg
     1621 ctggctgtgg ctgattatcg tctcagtact gatgtttgcc acgaccggga gtctgctgtg
     1681 gtaccagggc atgaagataa acgcgaatat gaatattctc cgcgagcaga aagagagtct
     1741 ggagaagctg aactcgaaga catggggcgt gcgttatcac gaggacagca acggacgttt
     1801 tctggtgttg ccgaagggga tgaaagccga aacgaactgg acgaaggaca acggcaaact
     1861 gaacgcagtg agactggtgc aggagtgaca gagcatgacg gagctggaaa gacatttgct
     1921 gaacgcatta gagcaactgc aacaggacta tatgcagcgg ctgaacgaat gggagaacgc
     1981 cttcgtggaa ttgcagaaaa tgttttcgct tacgcaacgg gacaacgcga tgctgaacgg
     2041 gcgagtcatg cagttgagtc agcaggtgca gcacttgagc gagcggacag aacgcttgag
     2101 ccagttatac agcgagaaca ggagataagg gatgaacggc tgatgcagga acgcgaacat
     2161 gagttatctc tggagcggga gcgtcagccg gaaatccagg agcggacact ggatggccct
     2221 tcgctgggat ggtgaaacca tgaaaaatga cgtgttcagt ggattaaggc gggctaatgt
     2281 ggcctgtagc atctggttgc ataggtattc atgcggttaa aatttatcag gtgcgatcgc
     2341 ggcagttttt cgggtggttt gttgccattt ttacctgtct gctgccgtga tcgcaccgaa
     2401 cgcgttttgg cggtgcgtac aatgcgacgt tatggtaaat ggagcggatt ttcaggaagg
     2461 agtgatacta acaactcgaa cactgtgcaa ataatgattt ttttaaaata tcggtaacga
     2521 taataaatta tttcgtttta cgccggtaat aaatataatg tagtttcagt atataaaaaa
     2581 atatatgagg tgtcttgtgg gagctttcat gaatcttcaa caacgtataa ataaactacc
     2641 acaattatca tccagttttt catttggaaa agatattgat aatattcatt catttatctt
     2701 taacgaaact tctaaagata aaattgaaga tttactaaga aaatgggtgt caggcaatca
     2761 gccctgtgta tttggtaaat tggcaagcaa gaaaattaaa gggcttgatt tccatttatc
     2821 tattgtaaat agcccccaac tatataatga tgatggtcat ttgtttgatt ttttgcgtaa
     2881 tgaaagagtt cgttttaaag aacgcgcaag aagaggagag gtcagtgcgc atctcattta
     2941 ttttattcat ccacaacttg cctttgctcg tccatcagaa gagttagtgg acatacaaaa
     3001 atatatttgt tcgctgcata tgccagagtg ctatccaata aaagaggatg ttatttatac
     3061 tgaaagcgta ccatttcagg ataaagatgg gctaaaaata tataaggctg gtgttaatgt
     3121 tttttactct tctgctcata gaacaagaaa tcatgataga agaataccag ggggaatact
     3181 tatttctgta aatgccccgg ggcattttat gaggctggcg atagaaaaag gtttctataa
     3241 agatcaagaa caagcgttag cggatattcg taacatgact attcagtctg ttggtaaggg
     3301 tgggtattca catccggaag ggatttctac aacatggcat tcagaatcta atttggatcg
     3361 ttttggatgc ccagtgcaca ccggtaatag ttcttattac agcggttttt atcatactga
     3421 tgtattaatt ccaggggaat taactaagga tgaaagattg ctccatgaaa tagaaaatag
     3481 tgatccaatg atcttcaact ggaatgtatt gttttatgtt tcattagaag agtttcctat
     3541 agatgatcct tattatggag agtttattgg tattcctgta gatgatgcat ctatgttttt
     3601 taactccttt caaccaagga aatttgaaaa caaacccctt tatgagaaag aggatgatta
     3661 atatgattaa aggaatgctt tttgcttttt tagcagcgtt ctcatggggg gcagctatcg
     3721 taatgagcaa aaaaggagtt gaagaactag atgccggagg ggtgtttttc tggcagattt
     3781 gtagtgcagt aatactatct tggatagttc tttttataaa aagaaaaaaa ctcccattaa
     3841 actcaaaagc gatacttgct tatgcgacag gcgtttttga accattctta gcgtatactt
     3901 ttacactcta cggactttat tttatttcag caggaagcgc atcaattatt ttttcacttg
     3961 aatcagtgtt tatattggtg ttgtctgttc ttatttgctc agttaaaatt aattccccgc
     4021 aatattttat attgttcctt ataggtgcaa ttgttggcag tattttggta gccttgccag
     4081 acatcagtaa tggatcgaat aatattgttg gatattgtct tgttgttgcc ggtgtgttat
     4141 cggcagcatt ttatgttgtt atatcgtctc gccttattaa atcgtttgag cctatcacat
     4201 tattgagcgg acagttgaca ttctccctta tactgtcatc gctctttatt tttatatcta
     4261 aatcatcaat ttatcttccg ttggaatccg tgattattgt tttttcatct ggaatattac
     4321 aatatttttt agctttttgt ttttacttga actccttgcg ttggctccca gttcatttgg
     4381 cagggataat gttgtacttt attccgctag ttgcattatt tttgtcatgg ttgtttttgg
     4441 atgaacaatt cacattctta cagggggtag gatttattgt aactgtgcta agtgtatatt
     4501 ttcttaacag aaaatactca gaggagtaac attctgttca ggattgcccc ccggcctcca
     4561 tcgataccgt gccaaatgca cgtaaaaaac gggagcgttt ctggtgtcgg aatgtaacca
     4621 agggggtcag aggcgcgcta aaacgctctc aggggagtca aatagagacg tttgtaacaa
     4681 aaagatcaaa ggatcctctt gagatccttt ttttctgcgc gtaatctgct gcctgtaaac
     4741 gaaaaaaccg ccttgcaggg cggtttgatc gaaggttaag tcagcttgca gactgcttaa
     4801 ccaggtaact gtcttatgcg agacgagtca ccaaaattgt tcttctagtg tagccgcact
     4861 ccggcagcca cttcaagtac tctctaaata tctcgcacat gacttttacc aatggctgct
     4921 gccagtggcg ctttgtggtg tcttttccgg gttggaccca agagaacagt taccggagaa
     4981 ggcgcagcag tcgggctgaa cggggggttc ctgcatacag cccagcccgg agcgaactgc
     5041 ctaagtcgcc ccgagatacc agaagacgtg agctatgaga aagcgccacg tgtcccgtaa
     5101 gggagaaagg cggaaaaggt atccggtaat cgatatggcg ggaacgtggg ggcgcaggag
     5161 ggagcgattc accggaaacg gtgatgatct ttaagccacg tcgggtttcg ccaccgctgg
     5221 cggatttcat ggttgagccg caaggctccc acagatgcac cgaaaaagtg tctgttttgt
     5281 gaagtccgtc aggggggcgg agcctatgga aaaagcgcct ccggcgcggc ctttcccggg
     5341 gtttcgtttt ttgcgcacat gttctttcct ggtttatccc cgggttctgt ggataacagg
     5401 gttagcgttt ttgagaaagg agagtccgct cgccgcagcc gaacgaccga gcgtagcgag
     5461 tcagtgagcg aggaagcgga agagcgcctg aactggcatt ttctccttac gcatctgtgc
     5521 ggcatttcac accggacatg gcgcactttt catacaatcc gcactgatgc cgaatggtta
     5581 agccagtata cactccgcta tcgctacgtg actgggtcag ggccgcg
//
