LOCUS       NZ_AP027526             4863 bp    DNA     circular CON 04-APR-2024
DEFINITION  Escherichia coli strain LR-33 plasmid pLR-33_3, complete sequence.
ACCESSION   NZ_AP027526
VERSION     NZ_AP027526.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00562513
            Assembly: GCF_036496145.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1
  AUTHORS   Hoang,H.T.T., Yamamoto,M., Calvopina,M., Bastidas-Caldes,C.,
            Khong,D.T., Nguyen,T.N. and Yamamoto,Y.
  TITLE     Comparative genome analysis of colistin-resistant Escherichia coli
            strains possessing mcr isolated in Ecuador and Vietnam
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4863)
  AUTHORS   Yamamoto,Y. and Hoang,H.T.T.
  TITLE     Direct Submission
  JOURNAL   Submitted (22-MAR-2023) Contact:Yoshimasa Yamamoto The United
            Graduate School of Drug Discovery and Medical Information Sciences,
            Gifu University; Yanagido 1-1, Gifu 501-1194, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Coverage                   :: 152x
            Sequencing Technology :: MGI DNBSEQ-G400RS; ONT MinION Mk1c
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_036496145.1-RS_2024_04_03
            Annotation Date                   :: 04/03/2024 23:48:30
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,800
            CDSs (total)                      :: 4,682
            Genes (coding)                    :: 4,488
            CDSs (with protein)               :: 4,488
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 194
            CDSs (without protein)            :: 194
            Pseudo Genes (ambiguous residues) :: 0 of 194
            Pseudo Genes (frameshifted)       :: 60 of 194
            Pseudo Genes (incomplete)         :: 126 of 194
            Pseudo Genes (internal stop)      :: 42 of 194
            Pseudo Genes (multiple problems)  :: 34 of 194
            Pseudo Genes (short protein)      :: 4 of 194
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP027526.1.
            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..4863
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="LR-33"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pLR-33_3"
                     /geo_loc_name="Ecuador:Santo Domingo"
                     /collection_date="2019"
     gene            265..1563
                     /locus_tag="AABJ50_RS23980"
                     /old_locus_tag="VEE12_45910"
     CDS             265..1563
                     /locus_tag="AABJ50_RS23980"
                     /old_locus_tag="VEE12_45910"
                     /inference="COORDINATES: protein motif:HMM:NF024700.4"
                     /GO_function="GO:0005524 - ATP binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="ATP-binding protein"
                     /protein_id="WP_097414638.1"
                     /translation="MMVNFSLSNAFSFMDAQNMSMLAVSSAKDDINLANVVSVSDVRIL
                     KSALIFGANASGKSNLMKTISLMKDIVLHSVQAIESSITKNVIPFLLDEDGPNKPSEME
                     MTFISDGVKYRYGLSIFQGKIKEEWLYYTPKSRETILFERDGLSIEVNKAAFSESNLFI
                     KEGIIQKTREDVPFVSVVAGFNGEHSKRVVNWFNNIVFLSGSNEGMFTAITMKLINESE
                     DFKAWLKKILPAFQINDIYLDEVAPDFPFGNIKTDDDNLKNLFSSIQNFAKNQKVFSLR
                     VVKKTASGEISVPIDFESEGTKKIVYLLGPIYNAMINGNLLLVDEFDSKFHTLLSKFLF
                     RIFHAQSEGLSQIIAAVQDVNLMNTDCFRRDQIWFVDKDIKSGSSHLYSLVEYKEKQRT
                     LKSSYGHDYLSGAFDAIPLFDNLDEFEKLMPEG"
                     /name="ATP-binding protein"
     gene            1636..2004
                     /locus_tag="AABJ50_RS23985"
                     /old_locus_tag="VEE12_45920"
     CDS             1636..2004
                     /locus_tag="AABJ50_RS23985"
                     /old_locus_tag="VEE12_45920"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_045626380.1"
                     /translation="MKTTDRFISVSFRYFHNVDDIGQSIDSWRVDGSLPDLIEKLVYLT
                     ANGITKVSSDGIFTNYTRFPDSAVNDFKCPDEISVDENWGVIKNIGGQKRRVAGFLKDN
                     VFYIVFFDKDHRFWKSRK"
                     /name="hypothetical protein"
     gene            complement(2241..2354)
                     /locus_tag="AABJ50_RS23990"
     CDS             complement(2241..2354)
                     /locus_tag="AABJ50_RS23990"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_032634168.1"
                     /translation="MHEPPVQSDCCALSGNYRLESNPERHAKAPLAAATGN"
                     /name="hypothetical protein"
     gene            2770..2961
                     /locus_tag="AABJ50_RS23995"
                     /old_locus_tag="VEE12_45930"
     CDS             2770..2961
                     /locus_tag="AABJ50_RS23995"
                     /old_locus_tag="VEE12_45930"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000166328.1"
                     /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_045265536.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELALDVEADLCEKLHDDA
                     EHLFRTLSSRLDELQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2961..3383
                     /locus_tag="AABJ50_RS24000"
                     /old_locus_tag="VEE12_45940"
     CDS             2961..3383
                     /locus_tag="AABJ50_RS24000"
                     /old_locus_tag="VEE12_45940"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005229777.1"
                     /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_045265535.1"
                     /translation="MARVSISEAARLVKVSRPTIYKMINSGKLSYTSVVKHGKAIKVID
                     TSELIRVFGSLDGVIDTVKYDVKSDAESTGVNSVGLHDLQHRIALLEAENDGLKGAVKA
                     RDEHIDSLRQAMQLLEHKHEPSSPPHSPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     Typing          complement(2242..2649)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.484"
                     /coverage="99.0"
                     /evalue="1.3e-157"
ORIGIN
        1 aatgctacaa agagaaacca tccccatcct gaaaccgagt gtaaagctag cactgctgag
       61 ctgacaactg cggctaaagg aaccatttgg tatagaaaaa atctcataga ccccctgcat
      121 ttagcttttt ttaacaagtg ttccataacg tgctatctat taaacgcacc tgttgtttta
      181 gaacgcttgt atgctatcct taagtcctga ttttgtcaat atttactcat tttgttgttt
      241 aaggatggcg taaggggtgt tcttatgatg gttaatttta gtctttctaa cgcattttcc
      301 tttatggatg ctcaaaatat gagcatgttg gcggtgtcat ccgcgaaaga cgacataaac
      361 ttggctaacg tggtttcagt gagtgatgtt cggatactga aatctgctct gatatttggg
      421 gctaacgcta gcgggaagtc taatctcatg aaaacaattt ctttaatgaa agatattgtt
      481 ttgcattccg tgcaagctat tgaaagtagc attacaaaga acgtaatacc gtttttgctt
      541 gatgaggatg gaccaaataa accatctgaa atggaaatga cttttatttc agatggggtt
      601 aaatatagat atggattgtc tatttttcag gggaaaataa aagaagaatg gttgtactac
      661 acaccaaaat caagagaaac cattctcttt gaaagagatg gtctttctat tgaggtaaat
      721 aaggcggctt ttagtgagtc aaaccttttt atcaaagaag ggattattca aaaaacaagg
      781 gaggatgttc catttgtttc ggttgttgct ggttttaatg gtgagcattc aaaacgagta
      841 gttaattggt ttaacaatat cgtattcctt tctggttcta atgaagggat gtttacagca
      901 attaccatga agttaataaa tgagtctgag gattttaagg cttggctaaa aaaaatactt
      961 ccagcattcc agattaatga tatttacctc gatgaggtcg cacctgattt tccatttgga
     1021 aatataaaaa cagatgatga taatttaaaa aatttattta gttcaataca aaattttgca
     1081 aaaaaccaga aggttttttc tcttagagta gtgaaaaaaa cagctagcgg tgagatttca
     1141 gtacctattg attttgagtc tgagggtact aaaaagatag tttatcttct tggtccaatc
     1201 tacaatgcca tgataaacgg taacttattg ttagttgatg agtttgattc taagtttcac
     1261 acccttttgt ctaagttttt gtttagaata ttccatgcgc aaagcgaggg gcttagccaa
     1321 ataatagctg ctgttcagga tgttaatcta atgaacactg attgttttag acgtgaccag
     1381 atttggtttg ttgataaaga tataaaatca ggaagtagtc atctctattc tttggttgag
     1441 tataaagaga agcagcgaac tttaaaatca tcgtatgggc atgattattt atctggtgca
     1501 tttgatgcta tcccattgtt tgataattta gatgaatttg aaaaacttat gcctgaggga
     1561 tgatttatgt caaagagagg ccgcggtctt cgtagctctt cgaggaaaga ggaaacaaaa
     1621 tcctcaaaga gcattatgaa aactacagat agatttattt ctgttagttt tagatatttt
     1681 cataacgtcg atgatattgg tcagtctatt gattcttgga gggttgacgg cagtttgcca
     1741 gatttaattg aaaagcttgt ttatcttaca gctaatggga taacaaaagt cagctctgat
     1801 ggtattttta ctaactacac tcgatttcca gattcagcag ttaatgattt taaatgccct
     1861 gatgaaatat cagttgatga gaactggggt gttataaaaa atataggagg ccagaaaaga
     1921 agggttgctg gttttttaaa ggataatgtg ttttatatag ttttttttga taaggatcat
     1981 cggttttgga agagcaggaa ataggcttag ttacgattgt actgtatgtt gaggcaagat
     2041 cttcttgaga tcactgtgtt ctcgtcgtaa tctctcgctc tgtaaacgaa aaaaccgcct
     2101 tggcgggcgg ttttttcgaa ggttccaaga gttggcgctc ttagaaccaa ggtaactggc
     2161 ttggaggagc gcagtaacca aaacttgttc tttcagttta gccttaaccg gcgcataact
     2221 tcaagactaa ctcctctaaa tcagttacca gtggctgctg ccagtggcgc ttttgcatgt
     2281 ctttccgggt tggactcaag acgatagtta ccggataagg cgcagcagtc ggactgaacg
     2341 gggggttcgt gcatacagtc cagcttggag cgaactgcct acccggaact gagtgtctgg
     2401 cgtggaatga gataaacgcg gccataacag cggaatggca ccggtaaacc gaaaggcagg
     2461 aacaggagag cgcacgaggg agccgcctat cagaaatgat aggtatcttt atagtcctgt
     2521 cgggtttcgc caccactgat ttgagcgtcc gtttctgtga tgcttgtcag gggggcggag
     2581 cctatggaaa aacggccgct gcgcggcctc ctcttttcct cctaccttga tcgctcggtt
     2641 ttctcgagct tttataagaa tggtcttgcc gctcgccgca gccgaacgac cggagcgtag
     2701 cgactgagtg agcgaggaag cggaaaagag actggtttta cactgagcac tgacgctctg
     2761 aggcttctta tgacgaaaca acagaaaaca gcgctgaaca tggctaaatt catccagaat
     2821 cagtctctgc tcctgctgga gaagcttaac gagcttgctc tcgatgtcga ggccgacctt
     2881 tgtgagaaac tccacgatga tgcggagcat cttttccgta cactgtcctc gagactggat
     2941 gaattacagg atggtaactg atggccagag tgtctattag tgaagcggca cggcttgtta
     3001 aggttagtcg ccccacaatt tacaagatga ttaacagtgg gaagttaagt tacacctctg
     3061 ttgtaaagca cggtaaggct attaaagtta ttgatacttc agagcttatt agagtgtttg
     3121 gttctcttga tggtgtcatc gatactgtaa aatatgatgt aaaaagtgac gcagaatcta
     3181 caggtgttaa cagcgttggt ttacatgatt tacaacatag aatcgcttta cttgaagctg
     3241 aaaacgatgg tcttaaaggg gctgttaagg ctcgagatga gcatattgat tcccttcgtc
     3301 aggctatgca gcttctggag cacaagcacg aaccttcttc accaccccat tccccgtggt
     3361 ggaaattctg gaaaaaatcc tgaccccgtc atgcttccgt tttcctctcc ggccatcccg
     3421 gggagttcct gaaccttccc aaaaatcgtc agatctctga acgctcctca ccactaaaaa
     3481 tacccacacc ccacgcaaaa ttaacatttt gcagatttgt atttaatatc agtgggttac
     3541 tttcctgaaa ttccgttttt taaattttat ttatatagat ccgactctat gacgagtcgt
     3601 catagagtcc ccggcgagtc gtcatagagt cggtaacgac tcaggactat aaaaacaata
     3661 agttaataac gacccgactc tagacacgac tccccgtttg gttgtttttt agactcggcg
     3721 actctgggta cgactctagt gaagattcgc cggtgaatcg tgtggtgagt cgtccggcga
     3781 cttgccataa cgtgattgcc ggccgtcgac gaacccgatt tctgaacgtg ctgaaaaccg
     3841 gttttccggc tgcgccggca acgcttcacg gccacgcaat aaattgcgtc cccgttcacc
     3901 gttttcggat gggaagaacg ccggaaacag gacttaccct ggctgaatgg cgtgaatttt
     3961 cgcgctatgc acttgcgtgc atactcatgc atgccgtaaa aacagagcct gcgcgtttct
     4021 ggcgggtttt cgggtggttt gttgcctgtt ttaccggttt cccgtcagaa acgccctgag
     4081 gccgttttag cggtgcgtac aattaggggg ttatgttaaa tccacaccag ctacagacgt
     4141 aaaaaaagcc ccgcagggct ttatatctat atatctgttc tcatccaatc ccatgtgtct
     4201 tgggtgagcc atcctgcgta ttctttggtt acaccaatca caagcaaggt gtcattattg
     4261 tccagatgcc tacgcaaacg atccgacagt tgttgcgctg tttctccggt tgatattagc
     4321 catgtggaat ctaaagggtg gcaccacccc ggcgattttt ttaactcatc atatagtgca
     4381 ttgtagtttt gacctgcttg attcaggtca taagagacac agtaaactga catagaacca
     4441 tcctctttaa tcaaatgtgg ggcagcccgt tagggctgca gtcacaactt acttcttctt
     4501 ttcacgatta attggaattt tgaacatccc accgtttgga cgggtgatcc gtttgccctt
     4561 tactgtgata taagggcgaa aaatgtatgc ctgagactcg tctgtctgca tggtgcattt
     4621 cctatttttc gccacatgag tgttgatttt tgctatcaaa attgtactgt agcaaccaac
     4681 aaatcttgtg gctggcttta tcaagctctt gaggtggtac tcaagtgccg catttgtgta
     4741 tggtttgtta cgggttagtt ctggtggtac aggctaaccc acttacttca aaaaacgtcg
     4801 tttttctcct ttcatgcgtc atttcctaga tgtttcttca ctgtatcagc tccgctgagc
     4861 ata
//
