LOCUS       NZ_AP023431             5498 bp    DNA     circular CON 16-JUN-2023
DEFINITION  Escherichia coli strain HUE1 plasmid pHFQ4, complete sequence.
ACCESSION   NZ_AP023431
VERSION     NZ_AP023431.1
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  JOURNAL   Unpublished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 5498)
  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
            AP023431.1.
            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..5498
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="HUE1"
                     /isolation_source="urinary catheter"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pHFQ4"
                     /geo_loc_name="Japan"
                     /collection_date="2008"
     gene            join(4566..5498,1..267)
                     /gene="tet(A)"
                     /locus_tag="IF662_RS22695"
     ARG             4567..5498
                     /name="tet(A)"
                     /gene="tet(A)"
                     /gene_name="major facilitator superfamily (MFS) antibiotic
                     efflux pump"
                     /tool="rgi"
                     /drug_class="tetracycline antibiotic"
                     /identity="99.68"
                     /coverage="73.35"
     gene            complement(299..1183)
                     /locus_tag="IF662_RS22700"
                     /old_locus_tag="RVB1_44560"
     CDS             complement(299..1183)
                     /locus_tag="IF662_RS22700"
                     /old_locus_tag="RVB1_44560"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000058717.1"
                     /GO_component="GO:0016020 - membrane [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="EamA family transporter"
                     /protein_id="WP_000058717.1"
                     /translation="MSLRTPDLLFTAIAPAIWGSTYIVTTQYLPNFSPMTVAMLRALPA
                     GLLLVMIVRQIPTGIWWMRIFILGALNISLFWSLLFISVYRLPGGVAATVGAVQPLMVV
                     FISAALLGSPIRLMAVLGAICGTAGVALLVLTPNAALDPVGVAAGLAGAVSMAFGTVLT
                     RKWQPPVPLLTFTAWQLAAGGLLLVPVALVFDPPIPMPTGTNVLGLAWLGLIGAGLTYF
                     LWFRGISRLEPTVVSLLGFLSPGTAVLLGWLFLDQTLSALQIIGVLLVIGSIWLGQRSN
                     RTPRARIACRKSP"
                     /name="EamA family transporter"
     gene            complement(1321..1713)
                     /locus_tag="IF662_RS22705"
     CDS             complement(1321..1713)
                     /locus_tag="IF662_RS22705"
                     /EC_number="3.-.-.-"
                     /inference="COORDINATES: protein motif:HMM:NF013053.2"
                     /GO_function="GO:0016787 - hydrolase activity [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="isochorismatase family cysteine hydrolase"
                     /protein_id="WP_001351729.1"
                     /translation="MLFPNFSLGEEYEHAPPATNRQISPYLPSGRFRTGLPVEGLAIER
                     GDLFYACPRASVFYGTALDADLRTRGVSTLVMAGISTTGVVLSSVAWASDADYDVRLVQ
                     DCCYDPDRDAHEALLRSGFGGRVQVV"
                     /name="isochorismatase family cysteine hydrolase"
     gene            <1717..3468
                     /locus_tag="IF662_RS22710"
                     /old_locus_tag="RVB1_44580"
                     /pseudo=""
     CDS             <1717..3468
                     /locus_tag="IF662_RS22710"
                     /old_locus_tag="RVB1_44580"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001138014.1"
                     /GO_function="GO:0004803 - transposase activity [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="Tn3-like element TnAs1 family transposase"
                     /name="Tn3-like element TnAs1 family transposase"
     gene            3526..3768
                     /locus_tag="IF662_RS22715"
                     /old_locus_tag="RVB1_44590"
     CDS             3526..3768
                     /locus_tag="IF662_RS22715"
                     /old_locus_tag="RVB1_44590"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000844627.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase"
                     /protein_id="WP_094888177.1"
                     /translation="MKTAALDLARERQAHEAGARTRATAHERTPQQERQKAAREAERGR
                     EAWTLGQGMKKPVAGCYGRLTGWKGGGDVVYMALL"
                     /name="relaxase"
     gene            complement(3810..4460)
                     /gene="tetR(A)"
                     /locus_tag="IF662_RS22720"
                     /old_locus_tag="RVB1_44600"
     CDS             complement(3810..4460)
                     /gene="tetR(A)"
                     /locus_tag="IF662_RS22720"
                     /old_locus_tag="RVB1_44600"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000164043.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="tetracycline resistance transcriptional repressor
                     TetR(A)"
                     /protein_id="WP_000164043.1"
                     /translation="MTKLQPNTVIRAALDLLNEVGVDGLTTRKLAERLGVQQPALYWHF
                     RNKRALLDALAEAMLAENHTHSVPRADDDWRSFLIGNARSFRQALLAYRDGARIHAGTR
                     PGAPQMETADAQLRFLCEAGFSAGDAVNALMTISYFTVGAVLEEQAGDSDAGERGGTVE
                     QAPLSPLLRAAIDAFDEAGPDAAFEQGLAVIVDGLAKRRLVVRNVEGPRKGDD"
                     /name="tetR(A)"
ORIGIN
        1 tcgggtggca tcggaatgcc ggcgctgcaa gcaatgttgt ccaggcaggt ggatgaggaa
       61 cgtcaggggc agctgcaagg ctcactggcg gcgctcacca gcctgacctc gatcgtcgga
      121 cccctcctct tcacggcgat ctatgcggct tctataacaa cgtggaacgg gtgggcatgg
      181 attgcaggcg ctgccctcta cttgctctgc ctgccggcgc tgcgtcgcgg gctttggagc
      241 ggcgcagggc aacgagccga tcgctgatcg tggaaacgat aggcctatgc catgcgggtc
      301 aaggcgactt ccggcaagct atacgcgccc taggagtgcg gttggaacgt tggcccagcc
      361 agatactccc gatcacgagc aggacgccga tgatttgaag cgcactcagc gtctgatcca
      421 agaacaacca tcctagcaac acggcggtcc ccgggctgag aaagcccagt aaggaaacaa
      481 ctgtaggttc gagtcgcgag atcccccgga accaaaggaa gtaggttaaa cccgctccga
      541 tcaggccgag ccacgccagg ccgagaacat tggttcctgt aggcatcggg attggcggat
      601 caaacactaa agctactgga acgagcagaa gtcctccggc cgccagttgc caggcggtaa
      661 aggtgagcag aggcacggga ggttgccact tgcgggtcag cacggttccg aacgccatgg
      721 aaaccgcccc cgccaggccc gctgcgacgc cgacaggatc tagcgctgcg tttggtgtca
      781 acaccaacag cgccacgccc gcagttccgc aaatagcccc caggaccgcc atcaatcgta
      841 tcgggctacc tagcagagcg gcagagatga acacgaccat cagcggctgc acagcgccta
      901 ccgtcgccgc gaccccgccc ggcaggcggt agaccgaaat aaacaacaag ctccagaata
      961 gcgaaatatt aagtgcgccg aggatgaaga tgcgcatcca ccagattccc gttggaatct
     1021 gtcggacgat catcacgagc aataaacccg ccggcaacgc ccgcagcatc gcgaccgtca
     1081 tcggtgagaa gttcggcagg tattgggtgg tgacaatgta ggtgctgccc caaatggcag
     1141 gtgctatcgc tgtgaacaat aaatcgggcg tgcgtaatga catgcgatta caagacctcc
     1201 gctacggcga tgggtttttg agagttgcag gcgccgcgat gaccgcaccc tgacttggac
     1261 tggccctgcc tcgcaccaat ccacctgcgg ctatggccgc gatcatgcga ggcccgaaaa
     1321 ttacacgacc tgtacacgtc cgccgaaccc ggaacgcaac agagcttcgt gggcatcccg
     1381 atccgggtcg tagcagcagt cctggaccaa acgcacgtcg tagtccgcat cactagccca
     1441 ggcgacgctt gaaagaacaa cgccggtggt gcttatcccg gccatgacaa gcgtgcttac
     1501 gccgcgcgtc cgaaggtcgg cgtcgagcgc cgtgccataa aagacgctgg ctcgcggaca
     1561 tgcatagaaa aggtcgcccc gttcgatcgc aagcccttcg acgggcagac cggtgcgaaa
     1621 tcgtccgctc gggagatacg gtgagatttg gcgattcgtc gccggcggcg catgttcata
     1681 ctcttcgccg agcgaaaagt tggggaacag cacgggccgg ccgcgcaagg cgtgctggca
     1741 gccgtgcaga ccctgcgtga gatgaacgcc gacaacctgc gcaaggtgcc ggccgatgca
     1801 cccacggcct tcatcaagcc gcgctggaag ccgctggtga tcaccccgga aggcctcgac
     1861 cggaaattct acgaaatctg cgccctgtcc gagctgaaga acgccctgcg ctccggcgac
     1921 atctgggtca agggctcgcg gcagttccgc gacttcgacg actacctgct gccggccgag
     1981 aagttcgccg cactcaagcg cgagcaggcc ctgcccctgg cgatcaaccc gaacagcgac
     2041 cagtacctgg aagagcgttt gcagctgctg gacgagcagt tggccaccgt cacccgcctg
     2101 gccaaggaca acgagctgcc cgatgccatc ctcaccgagt cagggctgaa aatcaccccg
     2161 ctggatgcgg cggtgccgga tcgggcgcag gcgctgatcg accaaaccag ccagttactg
     2221 ccgcgcatca agatcaccga actgctgatg gacgtggacg actggacggg cttcagccgc
     2281 cacttcaccc acttgaagga cggggccgag gccaaagaca ggacgttgct gctgtccgca
     2341 atcctcggtg atgcgatcaa cctcgggctg accaagatgg ccgagtcgag ccccggcctg
     2401 acctacgcca agctgtcctg gctgcaagcc tggcacatcc gcgacgaaac ctattcggcg
     2461 gccttggccg agctggtcaa ccaccagtat cgccacgcct ttgccgccca ctggggcgac
     2521 ggcacgacct catcctccga tggccagcgc ttccgcgcgg gtggccgggg cgagagcacc
     2581 gggcacgtca acccgaagta cggtagcgag ccgggacggc tgttctatac ccatatctcc
     2641 gaccagtacg cgccgttcag cacccgcgtg gtgaatgtcg gcgtccgcga ttccacctat
     2701 gtgctcgacg gcctgctgta ccacgagtcc gacctgcgga tcgaggagca ctacaccgac
     2761 acggccggct tcaccgatca cgtctttgcc ctgatgcacc tgctaggctt ccgcttcgcg
     2821 ccgcgcatcc gcgacctcgg cgaaaccaag ctgtacgtgc cgcagggcgt gcaagcctac
     2881 ccgacgttgc gcccgctgat cggcggcacc ctgaacatca agcacgtgcg tgcccactgg
     2941 gacgacatcc tgcgcctggc cagctcgatc aagcagggca ccgtcaccgc ctcgctgatg
     3001 ctgcgcaagc tcggcagcta cccgcgccag aacggactgg ccgtggccct gcgcgagctg
     3061 ggccggatcg agcgcacgct gttcatcctg gactggctgc aaagtgttga actgcgccgc
     3121 cgcgtgcatg ccggcctgaa caaaggtgag gcgcgcaact cgctggccag ggcggtgttc
     3181 ttcaaccgcc ttggggaaat cagggatcgg agcttcgagc agcagcgcta ccgggccagc
     3241 ggcctcaacc tggtgacggc ggctatcgtg ctgtggaaca cggtgtacct ggaacgcgcc
     3301 acccaggggt tggtcgaggc cggcaagccg gtggacggcg agctgctgca attcctgtcg
     3361 ccgctgggct gggagcacat caacctaacc ggcgattacg tctggcggca gagccgcaga
     3421 ctggaagacg ggaagtttcg gcccttacgg atgcccggaa aaccttagcg tacgattttt
     3481 tccgaattct gcgggctccc ctatctcatc tgcgcaaggc agaacgtgaa gacggccgcc
     3541 ctggacctcg cccgcgagcg ccaggcgcac gaggccggcg cgcggacccg cgccacggcc
     3601 cacgagcgga cgccgcagca ggagcgccag aaggccgcca gagaggccga gcgcggccgt
     3661 gaggcttgga cgctagggca gggcatgaaa aagcccgtag cgggctgcta cgggcgtctg
     3721 acggggtgga aagggggagg ggatgttgtc tacatggctc tgctgtagtg agtgggttgc
     3781 gctccggcag cggtcctgag cggtcctgat caatcgtcac cctttctcgg tccttcaacg
     3841 ttcctgacaa cgagcctcct tttcgccaat ccatcgacaa tcaccgcgag tccctgctcg
     3901 aacgctgcgt ccggaccggc ttcgtcgaag gcgtctatcg cggcccgcaa cagcggcgag
     3961 agcggagcct gttcaacggt gccgccgcgc tcgccggcat cgctgtcgcc ggcctgctcc
     4021 tcaagcacgg ccccaacagt gaagtagctg attgtcatca gcgcattgac ggcgtccccg
     4081 gccgaaaaac ccgcctcgca gaggaagcga agctgcgcgt cggccgtttc catctgcggt
     4141 gcgcccggtc gcgtgccggc atggatgcgc gcgccatcgc ggtaggcgag cagcgcctgc
     4201 ctgaagctgc gggcattccc gatcagaaat gagcgccagt cgtcgtcggc tctcggcacc
     4261 gaatgcgtat gattctccgc cagcatggct tcggccagtg cgtcgagcag cgcccgcttg
     4321 ttcctgaagt gccagtaaag cgccggctgc tgaaccccca accgttccgc cagtttgcgt
     4381 gtcgtcagac cgtctacgcc gacctcgttc aacaggtcca gggcggcacg gatcactgta
     4441 ttcggctgca actttgtcat gcttgacact ttatcactga taaacataat atgtccacca
     4501 acttatcagt gataaagaat ccgcgcgttc aatcggacca gcggaggctg gtccggaggc
     4561 cagacgtgaa acccaacaga cccctgatcg taattctgag cactgtcgcg ctcgacgctg
     4621 tcggcatcgg cctgattatg ccggtgctgc cgggcctcct gcgcgatctg gttcactcga
     4681 acgacgtcac cgcccactat ggcattctgc tggcgctgta tgcgttgatg caatttgcct
     4741 gcgcacctgt gctgggcgcg ctgtcggatc gtttcgggcg gcggccggtc ttgctcgtct
     4801 cgctggccgg cgctgctgtc gactacgcca tcatggcgac ggcgcctttc ctttgggttc
     4861 tctatatcgg gcggatcgtg gccggcatca ccggggcgac tggggcggta gccggcgctt
     4921 atattgccga tatcactgat ggcgatgagc gcgcgcggca cttcggcttc atgagcgcct
     4981 gtttcgggtt cgggatggtc gcgggacctg tgctcggtgg gctgatgggc ggtttctccc
     5041 cccacgctcc gttcttcgcc gcggcagcct tgaacggcct caatttcctg acgggctgtt
     5101 tccttttgcc ggagtcgcac aaaggcgaac gccggccgtt acgccgggag gctctcaacc
     5161 cgctcgcttc gttccggtgg gcccggggca tgaccgtcgt cgccgccctg atggcggtct
     5221 tcttcatcat gcaacttgtc ggacaggtgc cggccgcgct ttgggtcatt ttcggcgagg
     5281 atcgctttca ctgggacgcg accacgatcg gcatttcgct tgccgcattt ggcattctgc
     5341 attcactcgc ccaggcaatg atcaccggcc ctgtagccgc ccggctcggc gaaaggcggg
     5401 cactcatgct cggaatgatt gccgacggca caggctacat cctgcttgcc ttcgcgacac
     5461 ggggatggat ggcgttcccg atcatggtcc tgcttgct
//
