LOCUS       NZ_AP027614             4073 bp    DNA     circular CON 04-APR-2024
DEFINITION  Escherichia coli strain LR-72 plasmid pLR-72_2, complete sequence.
ACCESSION   NZ_AP027614
VERSION     NZ_AP027614.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00562557
            Assembly: GCF_036498665.1
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  JOURNAL   Unpublished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 4073)
  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                   :: 162x
            Sequencing Technology :: MGI DNBSEQ-G400RS; ONT MinION Mk1c
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_036498665.1-RS_2024_04_04
            Annotation Date                   :: 04/04/2024 00:14:07
            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)                     :: 4,769
            CDSs (total)                      :: 4,647
            Genes (coding)                    :: 4,428
            CDSs (with protein)               :: 4,428
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 8 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 219
            CDSs (without protein)            :: 219
            Pseudo Genes (ambiguous residues) :: 0 of 219
            Pseudo Genes (frameshifted)       :: 73 of 219
            Pseudo Genes (incomplete)         :: 144 of 219
            Pseudo Genes (internal stop)      :: 42 of 219
            Pseudo Genes (multiple problems)  :: 39 of 219
            Pseudo Genes (short protein)      :: 4 of 219
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP027614.1.
            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..4073
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="LR-72"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pLR-72_2"
                     /geo_loc_name="Ecuador:Santo Domingo"
                     /collection_date="2019"
     gene            join(3872..4073,1..728)
                     /locus_tag="AABJ55_RS23790"
     CDS             join(3872..4073,1..728)
                     /locus_tag="AABJ55_RS23790"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001448734.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Abi family protein"
                     /protein_id="WP_000571803.1"
                     /translation="MIEMDMPNTIHYPHVIPFISQGKINAIKSTFGNNLSDRECYGIYI
                     WSQKASSAIYPLLQQLEVTLRNSIDKEATKLIGQKWWDNVYTDTSKSKHGDFIHNINKA
                     KRRYENEFKKKNPSMANTKIIAPHDDIIAHTDFYTWQAVLSDAFHTQSRSEASRALWPR
                     LTYRVLKGLDRSKDEGTARIDFLNELNEIRNYRNRLSHNDCIWIKIHSKNLQSAVETIR
                     EKINKIEGLIKTINPQVHLSLTKWGSFYHAKRICSQKEAELHLGKGIINSTTDEMNTIL
                     DQLYALTADGKLTGVVKRNTNNIAFHKF"
                     /name="Abi family protein"
     gene            1322..1915
                     /locus_tag="AABJ55_RS23795"
                     /old_locus_tag="VEE35_45360"
     CDS             1322..1915
                     /locus_tag="AABJ55_RS23795"
                     /old_locus_tag="VEE35_45360"
                     /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_012537770.1"
                     /translation="MSGRKFGRLPNWWARSSWLVNNVRSNEIGGGIASMKCLLALSVLI
                     DFHSRTASVSFTGMERLTGLSRPMIVKGVAKLEKDGLIKIDREMFVNSYELTVQPNDDR
                     WAKVPVDTIRKKLNTISNRGMAPFVALKLYLTIISLRYQSNNTVKVTHETLRSYTGVQP
                     NQIRFGLDVLYCSRLIHLQPKEDRESNIYEIIGL"
                     /name="hypothetical protein"
     gene            2688..2882
                     /locus_tag="AABJ55_RS23800"
                     /old_locus_tag="VEE35_45370"
     CDS             2688..2882
                     /locus_tag="AABJ55_RS23800"
                     /old_locus_tag="VEE35_45370"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /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_001041633.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQVRFETESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            3548..3661
                     /locus_tag="AABJ55_RS23805"
     CDS             3548..3661
                     /locus_tag="AABJ55_RS23805"
                     /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="replication initiation protein"
                     /protein_id="WP_071531573.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHALTPLAAATGN"
                     /name="replication initiation protein"
     Typing          complement(2174..2429)
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="93.411"
                     /coverage="89.0"
                     /evalue="2.67e-103"
     Typing          complement(2554..2652)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          complement(2964..3050)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.43e-38"
     Typing          3061..3620
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.204"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cgattgataa agaagcgaca aaactaatag gccaaaaatg gtgggataat gtatacaccg
       61 acacatcaaa aagcaaacac ggtgacttca tacataatat aaacaaagca aaaagaagat
      121 atgagaatga attcaagaaa aaaaacccat caatggcaaa taccaaaata attgcacctc
      181 atgatgacat cattgcacac acagattttt acacatggca agcggttttg agcgatgctt
      241 ttcatacaca atcaagatct gaagcatcaa gagccttatg gcccaggctc acctacagag
      301 tactgaaggg attagataga agcaaagatg aaggcacagc cagaattgat ttcttaaacg
      361 agctgaatga gatcagaaac tacagaaata ggttatcgca taatgattgc atatggataa
      421 aaatacactc taaaaatttg caatctgcag tagaaacaat aagagaaaaa ataaacaaaa
      481 tagaaggact gataaaaacg ataaacccac aggtacacct atcattaacg aagtggggtt
      541 ccttttatca cgccaaaaga atatgttctc aaaaagaggc cgaattgcat ctaggcaaag
      601 gaataatcaa tagcacaaca gatgagatga acacaattct agatcaacta tacgcactaa
      661 ctgctgacgg aaagctaacg ggtgttgtaa aacgaaatac caacaatatc gcatttcaca
      721 agttttagat cacaaaatag aaaaggcccg acagtttcct gtcgagcctc atccaaatct
      781 cttgccatta tcacctttcg gtggagcgtg gccttaatgt cattgtgaat ctataaaaat
      841 ttcacaatgc attaaagcga aagctcaagg cttcactgcc atacatgata catcatcatc
      901 aggaaaaaga gcaaactatt tcccatgatc acgccaaagc ttaccatcca ccatttacca
      961 atagatcaaa aaacacacaa caaaaataac taaaaacgcc gattaaacca gcattatcaa
     1021 atttacattt accagttaaa aaacgataaa aacaagataa catcatgttt tatatgggaa
     1081 aacaagcagc caccaaatat tgctttatct agatttattc taataagcgt atataaagtt
     1141 aaaacacaac aacttagtat gcgactggag gaccaattgg aaaccctcaa caatttgctg
     1201 gtaacgctaa cttccgcaaa gccggaggtt ttggtttctg ttgtatcttt aggtgcaatg
     1261 gttttcatgt atatgataat aaagctattt atatctctcc ttgaccgaaa atggggtaaa
     1321 aatgagcggt agaaaatttg gcaggcttcc aaactggtgg gcccgaagct catggcttgt
     1381 aaacaatgtt cgttcaaatg agataggggg cggcattgca tcaatgaaat gcttgttagc
     1441 tctatccgtc ttgattgatt tccattcaag aacagcctca gtatcattta ccggaatgga
     1501 aagactgact ggactaagcc gccccatgat agtgaaagga gtagccaaac ttgagaaaga
     1561 tggtcttata aagatagata gagagatgtt tgttaactcc tatgaattaa cagtacagcc
     1621 aaatgatgat aggtgggcaa aagtaccagt agatactatc aggaaaaaac taaacaccat
     1681 atcgaacagg gggatggccc catttgtggc attaaaacta tatttaacaa ttataagcct
     1741 tcgttatcag tcaaataata ctgttaaggt gacacatgaa acactgagaa gctatacagg
     1801 tgtccagcca aaccagatta ggttcggctt agatgtactg tactgtagtc gcctgataca
     1861 tctgcaacca aaagaagata gagagtcaaa catctatgaa ataatcggcc tatgaggaaa
     1921 tgcatttacc ataacgtcgc attacgcgca ccgctaaaac gcactgaacg cgattctgac
     1981 gcagataccg caaaaagaga tgttttaccc agtgaaaacc gaaaaaatgc gtcaggatcg
     2041 ttttcagccc actgcatagc tatgcatgaa aatgaatgac gaacggtttg ggcgcatacg
     2101 gtgcccatga gacacatttt cggacatttt cagttcgtga atccctgact cattgctaca
     2161 tatctgaaca gacacccctg gcagcgcccc caggggcgtc ctgtaaaaaa acacaccgcg
     2221 ccgctagcag cacccctgat ataaaatgat gttttttata aaaatagtca gtaccacccc
     2281 tacaaagcgg tgtcggcgcg gtgttgtagc tgcgccggca ccgctttttt aaatatcgca
     2341 aagagagcaa gagaaactaa tttttcataa ctctctattt ataaagaaaa atcagcaaaa
     2401 acttgttttt gcgtggggtg tgggcatttc aggaatgaga acagactcgc gtttttccgg
     2461 agtatcagcg gaattattga ttaagaaaca ctcgacgcag agcgaaattt tatgcaacag
     2521 cggctgcact gcacagggat tatttatcag ttgatatgct gtgccatgat acgtcctaaa
     2581 aaaacaggac aggatgtgca attgtaatac cgtcgcccgc aacgtcttac aattaccagc
     2641 tgctcagggt ccccccgaca cccggaactg acggagaaca acggaaggtg aacaaacaac
     2701 aacaaactgc gctgaatatg gcgcgattta tcaaaagcca gagcctgaca ctgcttgaaa
     2761 aactggatgc tctggatgcc gacgaacagg cagccatgtg cgaacgactg cacgaactcg
     2821 cggaagaact ccagaacagc atccaggttc gctttgagac cgaaagtgaa acaggaacat
     2881 aacgaagctg ccgaaaacgc tcacggcttg tccgcgagcg ttttcggcag cagacaagcc
     2941 cgtcagggcg cgtcaggggg ttttagcggg tgtcggggcg cagccatgac ccagtcacgt
     3001 agcgatagcg gagtgtatac tggcttaacc atgcggcatc agtgcggatt gtatgaaaag
     3061 tgccccatgc cgggtgtgaa atgccgcaca gatgcgtaag gagaaaatgc acgtccaggc
     3121 gcttttccgc ttcctcgctc actgactcgc tacgctcggt cgttcggctg cggcgagcgg
     3181 tactgactca cacaaaaacg gtaacacagt tatccacaga atcaggggat aagaccggaa
     3241 agaacatgtg agcaacaagg caaagccagg acaaaaggcc gcgccgctgg cgtttttcca
     3301 taggctccgc ccccctgacg agcatcacaa aaaccgacgc tcaagtcaga ggtggcgaaa
     3361 cccgacagga ctataaagat accaggcgtt tccccctgga agctccctcg tgcgctctcc
     3421 tgttccgacc ctgccgctta ccggatacct gtccgccttt ctcccttcgg gaagcgtggc
     3481 gctttctcat agctcacgct gttggtatct cagttcggtg taggtcgttc gctccaagct
     3541 gggctgtgtg cacgaacccc ccgttcagcc cgaccgctgc gccttatccg gtaactatcg
     3601 tcttgagtcc aacccggtaa ggcacgcctt aacgccactg gcagcagcca ctggtaactg
     3661 atttagagga gtttgtcttg aagttatgca cctgttaagg ctaaactgaa agaacagatt
     3721 ttggtgactg cgctcctcca agccagttac cttggttcac agagcgccaa ctctttgaac
     3781 cttcgaaaaa ccgcccgcca aggcggtttt ttcgtttaac actctacaac tatccatacg
     3841 tgtatggcaa catccaatca ccactaagtg tatgatagag atggatatgc caaatacaat
     3901 tcattaccct catgtaatac catttatatc ccaaggaaaa ataaatgcta taaaaagcac
     3961 gtttggtaat aacctgtctg atagggagtg ctacgggata tatatatgga gccagaaagc
     4021 ctcatctgcc atatatccat tactgcaaca actcgaagtt actttgagaa act
//
