LOCUS       NZ_AP027950             4145 bp    DNA     circular CON 25-JUN-2023
DEFINITION  Escherichia coli strain VE-F10 plasmid pVE-F10_4, complete sequence.
ACCESSION   NZ_AP027950
VERSION     NZ_AP027950.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00587229
            Assembly: GCF_030161935.2
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1
  AUTHORS   Suzuki,M., Vu,T.M.H. and Kasuga,I.
  TITLE     Whole genome sequencing of colistin-resistant Escherichia coli
            isolated from Vietnam
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4145)
  AUTHORS   Suzuki,M., Vu,T.M.H. and Kasuga,I.
  TITLE     Direct Submission
  JOURNAL   Submitted (05-APR-2023) Contact:Masato Suzuki National Institute of
            Infectious Diseases, Antimicrobial Resistance Research Center; 4-2-1
            Aobacho, Higashimurayama, Tokyo 189-0002, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.5.0
            Genome Coverage                   :: 232x
            Sequencing Technology             :: Illumina MiSeq; ONT MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/23/2023 18:03:22
            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)                     :: 4,869
            CDSs (total)                      :: 4,747
            Genes (coding)                    :: 4,544
            CDSs (with protein)               :: 4,544
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 203
            CDSs (without protein)            :: 203
            Pseudo Genes (ambiguous residues) :: 0 of 203
            Pseudo Genes (frameshifted)       :: 63 of 203
            Pseudo Genes (incomplete)         :: 134 of 203
            Pseudo Genes (internal stop)      :: 42 of 203
            Pseudo Genes (multiple problems)  :: 37 of 203
            Pseudo Genes (short protein)      :: 4 of 203
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP027950.1.
            Annotated by DFAST https://dfast.ddbj.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..4145
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="VE-F10"
                     /db_xref="taxon:562"
                     /plasmid="pVE-F10_4"
                     /geo_loc_name="Viet Nam:Hanoi"
                     /lat_lon="20.95712843 N 105.82005564 E"
                     /collection_date="2020-07-03"
     gene            127..1269
                     /gene="wzz(fepE)"
                     /locus_tag="QQK65_RS24305"
                     /old_locus_tag="VEF10_46630"
     CDS             127..1269
                     /gene="wzz(fepE)"
                     /locus_tag="QQK65_RS24305"
                     /old_locus_tag="VEF10_46630"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010435173.1"
                     /GO_component="GO:0016020 - membrane [Evidence IEA]"
                     /GO_process="GO:0009103 - lipopolysaccharide biosynthetic
                     process [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="LPS O-antigen length regulator Wzz(fepE)"
                     /protein_id="WP_021544858.1"
                     /translation="MSAMDFKKNTDLDFPRYATPAVSTKEIDLLGLLDVLLAAKKRIVT
                     IVLAFAVVGLAIAFLIPQKWTSKAVITPAEQTQWNTLRQMMVTLQVLDVDAKVSRGDVF
                     NLFIKKFQSQSLLEEYMKTSPYVMSQLEGTEVDPLELHRAVVNIAEKMKATDNTQVKDA
                     DKAPYTSWTLSFTAPTAGDAQTVLEGYINYISRIVEQETMENIRNQITLKTKVVQQQLE
                     LDRVRLTNIHNTNLQRLNYSLEVANAAGIKKPVYSNGQAVKDDPDYSVALGADGIAQKL
                     QIEKNLKDVAELNADFQNREYYLTQLQKLSVEDVKLEPFRYQLSPSLPVKKDGPGKALI
                     VLLAGILGGLFACGSVLLREAMLSRNPLPEPITAVTPATE"
                     /name="wzz(fepE)"
     gene            complement(1307..>1549)
                     /locus_tag="QQK65_RS24310"
                     /old_locus_tag="VEF10_46640"
                     /pseudo=""
     CDS             complement(1307..>1549)
                     /locus_tag="QQK65_RS24310"
                     /old_locus_tag="VEF10_46640"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_003862821.1"
                     /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="cupin domain-containing protein"
                     /name="cupin domain-containing protein"
     gene            <1546..1728
                     /locus_tag="QQK65_RS24315"
                     /pseudo=""
     CDS             <1546..1728
                     /locus_tag="QQK65_RS24315"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007798797.1"
                     /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="NINE protein"
                     /name="NINE protein"
     gene            2914..3027
                     /locus_tag="QQK65_RS24320"
     CDS             2914..3027
                     /locus_tag="QQK65_RS24320"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /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_071778980.1"
                     /translation="MHEPPVQSDRCVFSGNYRLESKPERHDKAPLAAATGN"
                     /name="replication initiation protein"
     gene            3335..>3466
                     /locus_tag="QQK65_RS24325"
                     /pseudo=""
     CDS             3335..>3466
                     /locus_tag="QQK65_RS24325"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_013578013.1"
                     /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="zinc-ribbon domain-containing protein"
                     /name="zinc-ribbon domain-containing protein"
     gene            complement(3615..3731)
                     /locus_tag="QQK65_RS24330"
     CDS             complement(3615..3731)
                     /locus_tag="QQK65_RS24330"
                     /inference="COORDINATES: protein motif:HMM:NF013752.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001407452.1"
                     /translation="MKARYKGLLKNDNQLAMLFTLANLFRADQMIRQWERSH"
                     /name="hypothetical protein"
     gene            complement(3694..4077)
                     /locus_tag="QQK65_RS24335"
                     /old_locus_tag="VEF10_46650"
     CDS             complement(3694..4077)
                     /locus_tag="QQK65_RS24335"
                     /old_locus_tag="VEF10_46650"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_003117291.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS5/IS1182 family transposase"
                     /protein_id="WP_021544857.1"
                     /translation="MSHQLTFADSEFSSKRRQTRKEIFLSRMEQILPWQNMVEVIEPFY
                     PKAGNGRRPYPLETMLRIHCMQHWYNLSDGAIEDALYEIASMRLFARLHESQHPGQGGA
                     PISHHQATVRLRESQIQGVAEKR"
                     /name="IS5/IS1182 family transposase"
     Typing          2643..3031
                     /name="rep_cluster_2373"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.153"
                     /coverage="91.0"
                     /evalue="1.04e-173"
ORIGIN
        1 ctaaatctga tagtcggtct acagatagat caatctggcg ttcagattat tcttactttc
       61 ttgtatcatc cgaccactgc aaccaatcag gcagaaattt actgcgctcc aaaaagaaga
      121 acggttatgt cagcgatgga tttcaagaaa aacacggacc tcgattttcc ccgttatgcc
      181 actccggcgg taagcaccaa agagatagat ctcctggggt tgttagacgt acttctggca
      241 gccaaaaaac gtattgtgac gatcgtcctg gcgttcgccg tagtagggtt ggccattgcg
      301 tttttaatcc cgcaaaaatg gaccagtaaa gccgtgatca cgccggccga gcagacgcag
      361 tggaacacgc tgcgccagat gatggtgacg ctgcaggtgc tggacgtcga cgcgaaggtg
      421 agccgtggag acgtgtttaa cctgttcatc aaaaagtttc agtcgcagtc gctgctcgaa
      481 gagtacatga aaacctcccc gtacgtgatg tctcagctgg aaggcaccga ggtagacccg
      541 ctggagctgc atcgcgcggt ggtgaatatt gctgagaaaa tgaaagcgac agataacacg
      601 caggttaaag acgcagacaa agcgccgtat acctcatgga cgctgagctt taccgccccg
      661 acggcgggag acgcgcagac ggttctggaa ggttacatca actatatctc ccgcattgtt
      721 gagcaggaga cgatggaaaa tatccgtaac cagatcacgc tgaaaacgaa agtcgttcag
      781 cagcagctgg agctggatcg cgtgcgtctg accaatatcc acaacaccaa cctgcagcgc
      841 ctcaactatt cgctggaagt ggcgaacgcg gcaggcatta agaagccggt ttacagcaac
      901 ggacaggcgg taaaagacga tcctgactac tccgtggcgc tgggtgctga cggtattgcg
      961 caaaagctgc agattgaaaa gaatctgaag gacgtggccg agctgaatgc ggatttccag
     1021 aaccgtgaat actatctgac tcagttgcaa aaactgtccg tggaagacgt gaagcttgaa
     1081 cccttcaggt atcagctttc accgtcactg ccggtgaaaa aagacggtcc gggcaaagcc
     1141 ctgattgtgc tgctggcagg gattctgggc ggcctgtttg cctgcggcag cgtgctgctg
     1201 cgtgaggcaa tgctctcgcg taatccgttg ccagagccga taacggccgt aacgccagca
     1261 acagagtaac gacgatatta aaaaggcgct gattcagcgc ctttttttat ttcaggaaat
     1321 cgtcgcgcac cggcgtaaag gtatccagaa gggtgccggg cttcaggcaa atgcagccgt
     1381 gcatcacgtg cggcgcttta tagagcgtat cgcccgccgt cacgatctgc ttttcttcac
     1441 ctatcgtaaa ctcgaactcc ccggagagca cataggtaag ctgttcatgc gggtgattgt
     1501 gcatcgggcc aatcgcaccc tgctcaaaat tgacctccac cgccatcatc tttcttagca
     1561 ttcttccttg gtggatttgg cgtacataaa ttttacttag gtaaaatagg acagggattc
     1621 ctgtatctaa ttttttgctg gacattcata cccgcgatca tcgcgtttat tgagtttatt
     1681 atttatctat gcgattccga tgaaaaattc gcaagaaaat atggctaact catagcaaaa
     1741 aagccctgcg gggctttttt tgtaccagtc tgtgaggcag atttaccata acatccgttg
     1801 cgtgcaccgc ctgagaggct ctcagggcgt ttctgggtct tcctgcctgt ttccgacact
     1861 tccctgtgcc tatatcgtga aaaaacgcgc ctgatgattc tggcgcgtct gcatggctat
     1921 gcacacacat gcatggccgg gattttagcg gctaaaatcc ggctggacgc ccaaaagcac
     1981 cactgaacct cacgaataac gcctcacggg tgtgcagttt actgtgcggc cgtgaggcgt
     2041 tggccaggcc gtcaggcatg gctggattta ttgctaaggg ggtcggattt aacgtggatg
     2101 aatcagcacg cagtgatgaa cgggattcgg aaggggcacc cttgcggcgc ggcgatgtat
     2161 acatcgctaa cgtgccttgg tcatttattg caagaaggga gaggtagcat tttgatagca
     2221 aaaaagtagc aaaaggatag caaccgaaag accagaagac tctggagata gcaaagaagt
     2281 agcaaaatgg tagcaaaaag atagcaaaca tgcgggagct aaccaggagt ctttagtggg
     2341 ccggcggtac tccaaaaaca catcttgtcc cgctgttttg tgaataagcc agcatagctg
     2401 tgggcacaaa acatttcctg tccgctgctt taacctttgt aatccaggaa cgtcaggtga
     2461 cgtcactttg cggcgttagc cctatcctgc atcgtattaa aaaatgcagc actggcgcgt
     2521 acggtgccga agataagtcc ggggatattc cgcttcctcg ctcactgact cgctacgctc
     2581 ggtcgttcgg ctgcggcgag cggagggaac ggagacatta aggcacaggc aatgagagag
     2641 gatcgagagg caaaagaaaa ggccgcggcg ttgccggttt tccataggct ccgcccccct
     2701 gacaagcatc acagaatctg acgctcaaat cagtggtggc gaaacccgac aggacttaaa
     2761 gataccaggc gtttccccct ggtggctccc tcgtgcgctc tcctgttcct gcctttcggt
     2821 ttaccggtgt cattccgctg ttatggccgc gtttatctca ttccacgcct gacactcagt
     2881 tccgggtagg cagttcgctc caagctggac tgtatgcacg aaccccccgt tcagtccgac
     2941 cgctgcgtct tctccggtaa ctatcgactt gagtccaagc cggaaagaca cgacaaagcg
     3001 ccactggcag cagccactgg taactgattt agaggagtta gtcttgaagt tatgcgcctg
     3061 ttaaggctaa actgaaagaa cagatttggt tactgcgctc ctcataagcc agttaccacg
     3121 gttcaaagag ttgcagctct gagaaccttc gaaaaaccgc cttgctgggc ggttttttcg
     3181 tttactgagc aagagattac gacgctacag aaaggatctc aagaagatcc ttcaccataa
     3241 tggaaatcta tcccacccga gcatatagga tgcatatcgt tataaaacat cggatattat
     3301 gcatcccaac taaaaataag ctcgaggata aaaaatgagt tcaatggttt actgccgagg
     3361 atgcggcaag gaaatacacg aaacagcaaa gtcatgccca cactgcggag ccacaaacgc
     3421 ctcttcaggt tcaggtgaaa aaagtagaat cgcagccgcg ctattaggga aggtgcgaat
     3481 aagcggggaa attcttctcg gttgactcag tcatttcatt tcttcatgtt tgagccgatt
     3541 tttttctccc gtaaatgcct tgaatcagcc tatttagacc gtttcttcgc catttaaggc
     3601 gttattccca gtttttagtg agatctctcc cactgacgta tcatttggtc cgcccgaaac
     3661 aggttggcca gcgtgaataa catcgccagt tggttatcgt ttttcagcaa ccccttgtat
     3721 ctggctttca cgaagccgaa ctgtcgcttg atgatgcgaa atgggtgctc caccttggcc
     3781 cggatgctgg ctttcatgta accgggcaaa cagacgcatg gaggcgattt cgtacagagc
     3841 atcttcgatc gcgccatcgc tcaggttgta ccaatgctgc atgcagtgaa tgcgtagcat
     3901 ggtttccagc ggataaggtc gccggccatt accagccttg gggtaaaacg gctcgatgac
     3961 ttccaccatg ttttgccatg gcagaatctg ctccatgcgg gacaagaaaa tctcttttct
     4021 ggtctgacgg cgcttactgc tgaattcact gtcggcgaag gtaagttgat gactcatgat
     4081 gaaccctgtt ccatggctcc agatgacaaa catgatctca tatcagggac ttgttcgcac
     4141 cttcc
//
