LOCUS       NZ_AP023430             5501 bp    DNA     circular CON 16-JUN-2023
DEFINITION  Escherichia coli strain HUE1 plasmid pHFQ3, complete sequence.
ACCESSION   NZ_AP023430
VERSION     NZ_AP023430.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00241721
            Sequence Read Archive: DRR241416, DRR241417
            Assembly: GCF_014679325.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1
  AUTHORS   Munby,M., Fujiki,J., Aoki,K., Kawaguchi,C., Nakamura,K.,
            Nakamura,T., Sasaki,M., Sato,T., Usui,M., Sawa,H., Yokota,S.,
            Tamura,Y. and Iwano,H.
  TITLE     Whole-Genome Sequence of Escherichia coli, HUE1, isolated in
            Hokkaido, Japan
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5501)
  AUTHORS   Fujiki,J., Munby,M., Aoki,K., Kawaguchi,C., Nakamura,K.,
            Nakamura,T., Sasaki,M., Sato,T., Usui,M., Sawa,H., Yokota,S.,
            Tamura,Y. and Iwano,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (08-SEP-2020) Contact:Jumpei Fujiki Rakuno Gakuen
            University, Department of Veterinary Sciense; 582
            Bunkyodai-Midorimachi, Ebetsu, Hokkido 698501, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8-beta
            Genome Coverage                   :: 220x
            Sequencing Technology             :: Illumina MiSeq; Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/15/2023 02:42:42
            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)                     :: 4,605
            CDSs (total)                      :: 4,487
            Genes (coding)                    :: 4,252
            CDSs (with protein)               :: 4,252
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 235
            CDSs (without protein)            :: 235
            Pseudo Genes (ambiguous residues) :: 0 of 235
            Pseudo Genes (frameshifted)       :: 56 of 235
            Pseudo Genes (incomplete)         :: 165 of 235
            Pseudo Genes (internal stop)      :: 48 of 235
            Pseudo Genes (multiple problems)  :: 33 of 235
            Pseudo Genes (short protein)      :: 4 of 235
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP023430.1.
            Annotated at DFAST 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..5501
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="HUE1"
                     /isolation_source="urinary catheter"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pHFQ3"
                     /geo_loc_name="Japan"
                     /collection_date="2008"
     gene            144..>598
                     /locus_tag="IF662_RS22665"
                     /pseudo=""
     CDS             144..>598
                     /locus_tag="IF662_RS22665"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_086558267.1"
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /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="IS1 family transposase"
                     /name="IS1 family transposase"
     gene            <854..1102
                     /locus_tag="IF662_RS22670"
                     /old_locus_tag="RVB1_44490"
                     /pseudo=""
     CDS             <854..1102
                     /locus_tag="IF662_RS22670"
                     /old_locus_tag="RVB1_44490"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_076612230.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0004803 - transposase activity [Evidence IEA]"
                     /GO_process="GO:0006313 - DNA transposition [Evidence IEA]"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="IS1 family transposase"
                     /name="IS1 family transposase"
     gene            1216..2658
                     /locus_tag="IF662_RS22675"
                     /old_locus_tag="RVB1_44510"
     CDS             1216..2658
                     /locus_tag="IF662_RS22675"
                     /old_locus_tag="RVB1_44510"
                     /inference="COORDINATES: protein motif:HMM:NF013080.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="phosphoethanolamine transferase"
                     /protein_id="WP_190300595.1"
                     /translation="MTYLIIKYFISLLPFVFILTKNKITIFFCFLLAFISFFKIYFILF
                     EGFDLTEGIYLSILETNLDEVMNIKLIYFVIIAVSIISAILIITFIINLKNRIGVKKTH
                     IIRLLSVLFIIALLLKQFIFSINRGNIFRNFTESPSGFFLDSVREPLGTFLFFTAYALE
                     KNKYSNTEEDKALNKNITGFREPSSGLIVFIMGESSWKKRYSVYGYEKNTTKNISEIFL
                     KNEKGCVLNAFSAATVTRDSIPLTFSFAKPDNYNPLTKENSVFELARKQGYSTYWIGTQ
                     PLFGLYDSKYGYLTKGMFNENIIKSSDDNDIPSHLDDVLKRNRDMKLITLHLKGSHLIY
                     NNYDQIDKEQLKNTDEYDLTIHKTDRVINNIFNVLNKNNVPFVLIYTSDHGEVVNKGHG
                     LINGRSQIEIPLLAYSNDKYNVCESYTKLENKNSEITAQSNKLILLDMIGVSLDSDFIK
                     KESNDENMILGNGDIINYKNFN"
                     /name="phosphoethanolamine transferase"
     gene            complement(2933..3382)
                     /locus_tag="IF662_RS22680"
                     /old_locus_tag="RVB1_44520"
     CDS             complement(2933..3382)
                     /locus_tag="IF662_RS22680"
                     /old_locus_tag="RVB1_44520"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001229901.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DNA-binding protein"
                     /protein_id="WP_190300594.1"
                     /translation="MALVSISEAARLTGKSRTTVQAYIKQGKLTKSTDSAGSSKLDTSE
                     LLRVFGSFTGQQVGSEQPGITVQHLAGKSVQLTDQNLLHENYALKAEVELVKALLREKE
                     LLLNEKDKRNEDLKQALLLIESKLPTQPEPAMQAVTRKPWQFWKK"
                     /name="DNA-binding protein"
     gene            complement(3390..4352)
                     /locus_tag="IF662_RS22685"
                     /old_locus_tag="RVB1_44530"
     CDS             complement(3390..4352)
                     /locus_tag="IF662_RS22685"
                     /old_locus_tag="RVB1_44530"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001293214.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_072679208.1"
                     /translation="MSELVVFKANELAVSRYDLTEHETKLILFCVAKLNPSIENPTRDE
                     LTVKFSCTEYARSMGLSYENAWGRLNSATSDLFRRSVELIYPTGAVSKRIFNWTEYAEF
                     NREEQTVTLVFSSYIQPLLFHLKKFIKYNLEHVKSFENKYSMRIYEWLLKELSQRKTNR
                     VNIEISIKEFKFMLMLENNYPLYAELNRWILKPVSNDLNTYSNMKLAIAKRGRPADTLI
                     FQVELDRRIDLVTELTKDSIPSSKKTTKSAADTPESGLHSGLRKTLHDALMAKIQLTSF
                     EAKFLSDMQSKYDLNGSFSWLTPKQQATLEKILAKYGRI"
                     /name="replication initiation protein"
     gene            complement(4950..5327)
                     /gene="traD"
                     /locus_tag="IF662_RS22690"
                     /old_locus_tag="RVB1_44550"
     CDS             complement(4950..5327)
                     /gene="traD"
                     /locus_tag="IF662_RS22690"
                     /old_locus_tag="RVB1_44550"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000184721.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="conjugal transfer protein TraD"
                     /protein_id="WP_251003678.1"
                     /translation="MLILTDKADKTAQDIKTLSLLMKAEQAAEKAQEARAKAINLIQAE
                     KRAEARAARKARDHALYQSAGLLILAGLVDSQTGKPVDDTAALLGALASLNDLSRDNPT
                     WSDGKIRGQELLNSKKSDSTA"
                     /name="traD"
     Typing          complement(3391..4351)
                     /name="rep_cluster_1155"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="80.228"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 catttttaga taggcgcact tagtagtttc tctcacttcg tcagagaaac tgtgcgctcc
       61 tgctgagggc taaggtcatg gcatcttagg taatgatacc aacttactga tttggtgtat
      121 gatggtggtt ttgaggtgct cccgtggctt ccctttccat cagttgtccc tcctgttcag
      181 ctactgaagg cgtcgtgcgt aatggtaaaa gtactgccgg acatcagcgc tggctctgct
      241 ctcactgccg taaaacatgg cagctacagt tcacttacac cgcctctcag cccggtacac
      301 accagaaaat cattgatatg gccatgaatg gcgtcggatg tcgcgccagt gcacgcatta
      361 tgggtgtggg cctcaacacg attttacgac acttaaaaaa ctcaggccgc agtcggtaac
      421 ctcgcgcata caaccgggca gtgatgtcat tgtctgcgct gaaatggacg aacagtgggg
      481 ctacgtcggc gctaaatcac ggcagcgctg gctgttttac gcatatgaca ggatacgcag
      541 gatggtcgtg gcacacgtct ttggtgaacg tactatggcc acgctggagc gtcttctggg
      601 ggtcagtttg gagatcggaa atttttgtac gttaagcgca ttatttaacc aatcttagtt
      661 cgtaaggggt tgattttgcg tcagtggcta tcgcttttaa gttgtcgctc ttgcagtatc
      721 gcatttaggt tatccgatta aggtcaaacc tctgaaaatg ccgtatagcg cgggagtaca
      781 ccctattgct ataggtaagt ctgttcaaaa aacaggctta ccgtacaata attctctata
      841 tccaacctga ccccttctga gtctgctgtc accttttgat gtggtggtat ggatgacgga
      901 cggctggccg ctgtatgaat cacgtctgaa gggaaaactg cacgtcatca gcaagcgtta
      961 cacacagcga attgaacggc ataacctgaa tctgagacag catctggcaa ggctgggacg
     1021 gaagtcactg tcgttctcaa aatcggtgga actgcatgac aaggtcatcg ggcattatct
     1081 gaacataaaa cactatcagt aagttggagt cattaaccac cttccttagg caataaatat
     1141 tgcccgatta tttattaatc tgttaatctg ttaatctgtt aatcttctat gtgtcagaga
     1201 atttagccgg aaatcatgac ttacttaatt ataaaatatt tcatttccct tctacctttc
     1261 gtttttattc ttaccaaaaa caaaataacc atcttttttt gtttcttact ggcttttatt
     1321 tcatttttta aaatttactt tattcttttt gaaggttttg atttaactga gggcatatac
     1381 ttatcaattc ttgaaacaaa tctcgatgaa gttatgaata taaagttgat atacttcgta
     1441 ataatagccg tttcaattat ttcagcaata ttaattatta ctttcataat taatttgaaa
     1501 aataggattg gcgtaaaaaa aacgcatatc ataaggttat tatctgtttt atttatcata
     1561 gcgctattac ttaagcaatt tatttttagt attaatcgag gtaatatctt taggaacttt
     1621 actgagagcc catctggttt tttcttagat tcagttagag aacctttagg gacttttttg
     1681 ttcttcaccg cttatgcatt agaaaaaaat aagtattcaa atactgaaga agataaagca
     1741 ctaaacaaaa atattacagg gttcagagaa ccatcaagtg gcctcattgt tttcataatg
     1801 ggtgaatctt cttggaaaaa aagatattca gtttatgggt atgagaaaaa cacaacaaaa
     1861 aacatatcag aaatattctt aaaaaatgaa aaaggttgtg ttttaaatgc tttttctgct
     1921 gccaccgtaa ctagggattc gataccatta acgttttcat ttgccaagcc agataattat
     1981 aatccactaa ccaaagaaaa ctcagttttt gagctcgcaa gaaagcaagg gtactcaaca
     2041 tattggattg gcacgcaacc actgtttggt ttatacgatt caaaatacgg gtatctaacc
     2101 aaggggatgt ttaacgaaaa tataataaaa tcatcagatg acaatgacat accctctcat
     2161 cttgatgatg ttttaaaaag aaatagagac atgaaattaa tcactttaca cttgaaaggt
     2221 agtcatctaa tttataacaa ctatgaccaa attgataaag aacaactgaa aaacactgat
     2281 gagtacgacc taacaataca taaaacagat agagtaataa ataatatctt taacgtgcta
     2341 aataaaaaca acgttccttt cgttctaatt tacacatctg atcacggtga agtggttaat
     2401 aaagggcacg gtttaattaa tggtagatcg caaattgaaa taccattact agcttattcc
     2461 aatgataagt ataacgtatg cgaaagctat actaaactgg aaaataaaaa tagtgaaatc
     2521 acagcccaga gtaacaagct aatattattg gatatgattg gtgtgagttt ggatagtgac
     2581 ttcataaaaa aagagagtaa tgatgaaaat atgatactcg gcaatggtga tataattaac
     2641 tacaaaaact ttaattgatt aattattatt tatggatatg gtttacactt aaccatatcc
     2701 attgtcctta tgaaggtgga tgtcaatgtc accatattat ttttaaaaat agacatattt
     2761 actttttacc ataaagtcgc attatccgaa ccgccacccg cgcctcgcca caaaaatccg
     2821 gcgaaatggt caaaagcgcg ggttatccgc cccgaaaacg ggcggttttt gggttgccgg
     2881 tttgttatca gaatcgcggg aagggggtgg gccggtaaaa cccgccagag ggctattttt
     2941 tccagaattg ccagggtttt ctggtcaccg cctgcatggc aggttccggt tgtgtcggga
     3001 gtttggactc tatcagtaac aacgcttgct tgagatcctc gttgcgcttg tctttttcat
     3061 tgagtagtag ctctttttca cgcagcaatg cctttacgag ttctacttca gcttttaaag
     3121 catagttttc atgtagcaaa ttctggtcag ttaactgcac agatttgcct gccaagtgct
     3181 gcacagtgat gcctggttgt tcactgccaa cctgctgacc agtgaatgaa ccgaaaacac
     3241 gtagaagctc tgatgtgtct agttttgaag aacctgcgct atctgtactc ttggtcagtt
     3301 ttccctgctt aatgtatgcc tgtactgttg tgcggctttt tccagttagt cttgctgctt
     3361 cacttattga tactaaagcc atagatacct cagattcgtc cgtacttggc taaaattttc
     3421 tctaatgtgg cctgctgttt tggcgttagc cacgagaagg agccattcag gtcgtatttg
     3481 ctttgcatat cactcaaaaa cttagcttcg aagctggtta gctgaatttt tgccatgagt
     3541 gcatcgtgta atgtttttct tagtccacta tgtagaccag attctggtgt atcagctgct
     3601 gatttcgtcg tttttttaga tgatggaatt gagtctttag ttagctctgt cacaaggtcg
     3661 atccgtctgt ctaactcaac ctgaaatatt agcgtgtcgg ctgggcgacc tcgctttgca
     3721 atggctaact tcatattgct atatgtattt aagtcatttg aaactggctt tagaatccaa
     3781 cggttcagct ctgcatataa aggataatta ttttcaagca taagcataaa tttaaattct
     3841 ttgatgctta tctcaatatt tactctattt gttttccttt gtgatagctc ttttaataac
     3901 cattcatata tgcgcatcga atatttattt tcgaatgatt ttacatgttc taaattatat
     3961 ttaataaact tctttaaatg aaataacagc ggttggatgt atgagctaaa aactaacgtt
     4021 acagtttgtt cttctctatt gaactcagcg tattcagtcc agttgaaaat tcgttttgat
     4081 actgcacctg tagggtaaat taactctact gaccgtctaa ataggtcgct cgtggcactg
     4141 ttcaatcttc cccatgcatt ctcataactt aagcccatag atcgagcata ttcagtacat
     4201 gagaacttaa ctgtaagttc atctcgagtg ggattttcaa ttgaagggtt caactttgca
     4261 acgcaaaaca aaattaactt agtttcatgc tctgttaagt cataacggct taccgccaac
     4321 tcattcgctt taaagacgac caattctgac acttttatca cctccatgta gtggttttaa
     4381 attactacac taatcatatt catgtagcgg tttaaatcaa ctacattttt gtggctgtgg
     4441 ctgtggacta cctaattttt actacatctt ccgagatgcg aacctaattt ttactacatg
     4501 aaacctaatt tttactacat ttttcatttt ttttttttaa tgaaaacagt tacataaaaa
     4561 acctagaata aagaaagaat agaaaaagat aaaaaagaat agatcccagc cctgtggata
     4621 actgacctgc cttagccgat ttttcgatat gataaaagga tgtcgcaaac aaggtttgct
     4681 cctcttcaga acatacctta aaccccaaaa acactaagac agcaccctcg ccagctcggg
     4741 caacccgctg aacattcctt ttgtctccga ccatccggca cctgcatcgc tgttctttcc
     4801 gtaaaattca gttcgcttcg ctcacggctc tggcagggaa tggtggtaaa tggcactaca
     4861 ggcgcttttc atggattcat gcaaggaatc tacccatgaa acaagaaaag cccgtcacgg
     4921 gcttctcagg gcgttttatg acgggtcagc tatgcagtgc tgtctgactt cttgctgttc
     4981 agcagttcct gacctctgat tttcccgtct gaccacgtcg gattatcccg tgacaggtca
     5041 ttcagactgg ctaatgcacc cagcagggca gctgtatcat caaccggctt ccccgtctga
     5101 ctgtcaacca gtcccgccag gataagcagc ccggctgact ggtacagggc atggtcacgg
     5161 gctttacgtg cggctctggc ttcggcacgt ttttctgcct gtatcaggtt gatggctttt
     5221 gctctggctt cctgcgcttt ttctgcggcc tgttcagcct tcatcagcag ggacagcgtt
     5281 ttgatatcct gcgctgtttt atccgcttta tccgtcagta tcagcatgag tttctgctgt
     5341 tcattcggcg actttaagcc gcgaatatct gcactctgtc tgttgcccat tgttcctgct
     5401 tttcgctttt attcatgccc gtttatcctc tgaatgttaa cgggggaatt atgctcagtg
     5461 atgggcagcg gaggtcaaat tccactacaa tcctatctaa g
//
