LOCUS       NZ_AP023432             3555 bp    DNA     circular CON 16-JUN-2023
DEFINITION  Escherichia coli strain HUE1 plasmid pHFQ5, complete sequence.
ACCESSION   NZ_AP023432
VERSION     NZ_AP023432.1
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  JOURNAL   Unpublished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 3555)
  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
            AP023432.1.
            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..3555
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="HUE1"
                     /isolation_source="urinary catheter"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pHFQ5"
                     /geo_loc_name="Japan"
                     /collection_date="2008"
     gene            join(3491..3555,1..259)
                     /gene="mobA"
                     /locus_tag="IF662_RS22725"
     CDS             join(3491..3555,1..259)
                     /gene="mobA"
                     /locus_tag="IF662_RS22725"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization protein MobA"
                     /protein_id="WP_000166966.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="mobA"
     gene            complement(547..1161)
                     /locus_tag="IF662_RS22730"
     CDS             complement(547..1161)
                     /locus_tag="IF662_RS22730"
                     /inference="COORDINATES: protein motif:HMM:NF025107.2"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_052895292.1"
                     /translation="MSTKNAQKEQKKESLITTHWGDDATIHGWTAIPNSLLMLQGDLGI
                     GSTEMCILLNILMHQWPESGESISFPSIGTIASRIGVSKRTIQRGVSNLEALGILTRYQ
                     STRNDPLTNGANIFDSTPLKEYLNKKAKGITISNSNKKKERKKTGITPNIKLPRICPKC
                     LKTKATSHEEIVKFFGVRKTMAGEIINSYCKECRASEKDLF"
                     /name="helix-turn-helix domain-containing protein"
     gene            1482..2207
                     /locus_tag="IF662_RS22735"
                     /old_locus_tag="RVB1_44610"
     CDS             1482..2207
                     /locus_tag="IF662_RS22735"
                     /old_locus_tag="RVB1_44610"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001307201.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="NYN domain-containing protein"
                     /protein_id="WP_001427890.1"
                     /translation="MASMETEQQPQQTTEQIEVKTKRVQCFIDGYNLYHAIEETGNKAL
                     HWVDLKSLCKRYLPKNASIDNVFWFSAKPSHLSRAINENYQNYTNALTECGVDVIGGRF
                     KKKNVTCEADNGCGGVFHKHEEKESDVNLAISLVSGACNDEYDIAIIITADSDLCPPIK
                     YVRERFPNKELWLVAPPGRIRRATDLCSLSSRSMEIKNDALRACCMRDEFYKDGVLVAR
                     RPQEWRAVANTRQRRARSR"
                     /name="NYN domain-containing protein"
     gene            complement(3013..3207)
                     /locus_tag="IF662_RS22740"
                     /old_locus_tag="RVB1_44620"
     CDS             complement(3013..3207)
                     /locus_tag="IF662_RS22740"
                     /old_locus_tag="RVB1_44620"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041624.1"
                     /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_052895291.1"
                     /translation="MNKQQQTVLNMAGFIKSQSLRLLEKLDALDADEQAAMCEKLHELA
                     EELQNSIQTRFEAENRTGI"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          3243..3482
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="7.6e-123"
     Typing          complement(2454..2978)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.274"
                     /coverage="95.0"
                     /evalue="0.0"
ORIGIN
        1 agaagaagac caggaaatca gaaaaagggc tgctgaatgc ggcaagaccg tttccggttt
       61 tttacgggcg gcagctctcg gtaagaaagt taactcactg actgatgatc gggtactgaa
      121 agaagttatg aggctggggg cgttacagaa aaaactcttt atcgacggca agcgtgtcgg
      181 ggacagagag tatgcggagg tgctgatagc tattacggag tatcaccggg ccctgttatc
      241 caggcttatg gcagattagc ttcccggagg gaaactgtcg aaaacagacg gtatgaacgc
      301 cgtaagcccc caaaccgatc gccattcact ttcatacata gctatgcagt gagctgaaag
      361 cgatcctgcc gcatttttcc ggtttacccc ggggaaaaca tctatttttg cggtgtttgc
      421 ggcagaatcg cgttcagcgc gtttctgcgg tgcgcgtaat gagacgttat ggtaaatggg
      481 agcgttagaa acagtcccat ttacttgagt ggggggcagt tggccatata aaaaatggtc
      541 aactgtttaa aatagatctt tttcagaagc tcggcattct ttgcaatatg aatttattat
      601 ttccccagcc attgtttttc gcacgccaaa aaatttaaca atttcttcgt ggctggttgc
      661 tttagttttc aaacattttg ggcaaatgcg tggtaatttt atgttgggtg taattccggt
      721 tttctttctt tctttctttt tgttgctgtt gctaattgtt atgcctttag cttttttgtt
      781 taaatattct tttagaggag ttgagtcgaa tatattagcg ccattggtta gagggtcatt
      841 ccttgttgat tggtatctag ttaatatccc caatgcctct aggttactaa ccccgcgttg
      901 aattgttctt ttagatacac ctattcttga tgcaatggta ccaattgacg gaaaagatat
      961 tgactcccct gactcaggcc attgatgcat caatatattc agcagaatac acatctcagt
     1021 actcccaata ccaagatcac cttgcagcat aaggaggcta tttggtatag ccgtccaccc
     1081 atgtatggtt gcatcatctc cccagtgagt agtgattaat gactcttttt tttgttcttt
     1141 ctgtgcgttt tttgtgctca tagatgcttt tctcgcgaaa aaaaaatcaa aatgtgaaca
     1201 gttactacct aactactctt aatataagag tagttaggta gtaacatgta tcttttagga
     1261 tgacataaat gtcatccatt tgctcttttt ttatatagaa cttaagttga gtccactacc
     1321 taagagttat gctcttagtg gctatccaag tcgaggcttg gaagcgcatt gtacaaaatt
     1381 cttcctgtat tggatgcgtc catacagtgg tctgttaact gcggttaaga gacgcaaaaa
     1441 ggcctgcata tgcaggcctt tttgctatct agaggtcaaa aatggcaagt atggaaacag
     1501 agcagcaacc acaacaaact actgagcaaa tcgaagtaaa aacaaagcga gtgcagtgct
     1561 ttattgatgg gtataattta tatcatgcaa ttgaagagac tggtaataaa gctcttcatt
     1621 gggttgatct taaatcttta tgcaagagat accttcctaa aaatgcatct attgataatg
     1681 ttttttggtt ttccgctaag ccatcacatt tatcaagagc cataaatgaa aattatcaaa
     1741 attacaccaa cgctttaacc gaatgtggtg ttgatgttat cggtggacgt tttaaaaaaa
     1801 agaatgtaac gtgcgaagct gataatggat gtggtggagt tttccataag catgaagaaa
     1861 aagagtccga tgttaatttg gctataagtc tagtgtctgg tgcgtgtaat gatgagtatg
     1921 atatagccat tattatcact gcggattctg acttatgccc ccctattaaa tacgtaagag
     1981 agcgattccc taataaagag ctttggcttg tagctcctcc ggggagaatc aggcgagcga
     2041 cagatctctg ctctctgtca tcgagaagta tggagatcaa gaatgatgct ttgagagcct
     2101 gctgtatgcg tgatgagttc tacaaagatg gagtacttgt agccagaagg cctcaggaat
     2161 ggcgagctgt tgccaatacc aggcaaagaa gggctagaag tcgttaggct ttgttgacgc
     2221 agctagcgca aggagattaa tctaactagg ttgaaaacga aaaaaccgcc ttggcgggcg
     2281 gtttttcgaa ggttcataga gttggcgctc tttgaaccga ggtaactggc tttgaggagc
     2341 acagtcgcca aaacttgttc tttcagttta gccttatcag gtgcataact tcaagactca
     2401 actcctctaa atcagttacc aatggctgct gccagtggcg ttaagtcgtg tctttccggg
     2461 ttggactcaa gacgatagtt accggataag gcgcagcggt cgggctgaac ggggggttcg
     2521 tgcacacagc ccagcttgga gcgaacgacc tacaccgaac tgagatacca acagcgtgag
     2581 ctatgagaaa gcgccacgct tcccgaaggg agaaaggcgg acaggtatcc ggtaagcggc
     2641 agggtcggaa caggagagcg cacgagggag cttccagggg gaaacgcctg gtatctttat
     2701 agtcctgtcg ggtttcgcca cctctgactt gagcgtcgat ttttgtgatg ctcgtcaggg
     2761 gggcggagcc tatggaaaaa cggcatcggc gctggcttgt tccggtgctt tgctttttgc
     2821 tcacatgttc tttccggcgt tatcccctga ttctgtggat aaccgtatta ccgcctttga
     2881 gtgagctgac accgctcgcc gcagtcgaac gaccgagcgt agcgagtcag tgagcgagga
     2941 agcggaagag cgtctgacgt ggcattttct ccttacgctc cgctatgccg ttctgcatcc
     3001 tgtccgggtg cgttatatcc cggtgcgatt ttccgcttca aagcgtgtct gtatgctgtt
     3061 ctgaagttct tccgcgagtt cgtgcagctt ctcacacatg gcggcctgtt cgtcagcatc
     3121 aagtgcgtcc agtttttcga gcagcctcag gctctggctt tttatgaatc ccgccatgtt
     3181 gagtacggtt tgctgctgct tgttcatctt tctgttttct ccgttctttc tgtcatctgc
     3241 gttgtgtgat tatatcgagt accacttttc gactgtttta ccgccggtat tctgctgtct
     3301 gactctttga cgggcatttc tgtcagacaa cactgtcact gccaaaaaac tgccgtgctt
     3361 ttgtcggtaa ttcgagcttg ctgacaggac aggatgtgca attgttatac cgcgcataca
     3421 tgcacgctat tacaattacc ctggtcaggg ctttgccccg acacccatgt cagatacgga
     3481 gccatgtttt atgacaaaac gaagtggaag taatacgcgc aggcgggcta tcagtcgccc
     3541 tgttcgtctg acggc
//
