LOCUS       NZ_AP027509             3948 bp    DNA     circular CON 04-APR-2024
DEFINITION  Escherichia coli strain LR-27 plasmid pLR-27_3, complete sequence.
ACCESSION   NZ_AP027509
VERSION     NZ_AP027509.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00562507
            Assembly: GCF_036495405.1
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  JOURNAL   Unpublished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 3948)
  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                   :: 122x
            Sequencing Technology :: MGI DNBSEQ-G400RS; ONT MinION Mk1c
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_036495405.1-RS_2024_04_04
            Annotation Date                   :: 04/04/2024 00:15:57
            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)                     :: 4,813
            CDSs (total)                      :: 4,693
            Genes (coding)                    :: 4,414
            CDSs (with protein)               :: 4,414
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 279
            CDSs (without protein)            :: 279
            Pseudo Genes (ambiguous residues) :: 0 of 279
            Pseudo Genes (frameshifted)       :: 77 of 279
            Pseudo Genes (incomplete)         :: 189 of 279
            Pseudo Genes (internal stop)      :: 59 of 279
            Pseudo Genes (multiple problems)  :: 41 of 279
            Pseudo Genes (short protein)      :: 3 of 279
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP027509.1.
            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..3948
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="LR-27"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pLR-27_3"
                     /geo_loc_name="Ecuador:Santo Domingo"
                     /collection_date="2019"
     gene            52..1173
                     /locus_tag="AABK22_RS24025"
                     /old_locus_tag="VEE09_46040"
     CDS             52..1173
                     /locus_tag="AABK22_RS24025"
                     /old_locus_tag="VEE09_46040"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012088418.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF262 domain-containing protein"
                     /protein_id="WP_038999331.1"
                     /translation="MFGHIIDTPLEENDDEYSDDDLFKISSWGADLSFRELISRYDDDE
                     LVKPELQRNYVWDKPEASRFIDSILLGLPIPSIFLAKTKDEKLLIIDGYQRFMTVRDYV
                     KGIFTKDNSIFKLSRTEKIHEKWRGKSFLELTDDERRKIRNTTIHAIIFMQQQPKTGDT
                     SLFQIFERINSSGRSLLPQEIRNCVYQGPINSLLFELNNNNKWRKLWGSERRDDRMRDL
                     EFILRFFALSDHYIQHSDNPPSRISLKKYLNQFMELANNESKISDFRHRFNSTIDYIFD
                     NFGLSAFHNYQKEQGKWIPAFSPTIYDSIMISTDEALRRGIKLPTPEDAKEAKKLLLEN
                     QEYQNLLYQETMRTPNIKARVSLMFEAVFHEDW"
                     /name="DUF262 domain-containing protein"
     gene            1180..1755
                     /locus_tag="AABK22_RS24030"
                     /old_locus_tag="VEE09_46050"
     CDS             1180..1755
                     /locus_tag="AABK22_RS24030"
                     /old_locus_tag="VEE09_46050"
                     /inference="COORDINATES: protein motif:HMM:NF037889.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="HEPN domain-containing protein"
                     /protein_id="WP_052244190.1"
                     /translation="MNNTESMKILRDCCDELNDIRKLVSDLDDSNKAVGYINKYAIIRA
                     TGSIEFAFKKIIADKVEHGCHDQIKNFIKRKIRESAHNPRLGTIESVLTDFDPKWQKKF
                     NEKIALENKIALDESLKKLVTERNSFAHGRDANIGIDEIIENYLNGQKVIAILDETVHF
                     LYDEPGAEEKLTTTKRHKRRRKKRKKRK"
                     /name="HEPN domain-containing protein"
     gene            complement(2851..3051)
                     /locus_tag="AABK22_RS24035"
     CDS             complement(2851..3051)
                     /locus_tag="AABK22_RS24035"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000166333.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="antitoxin VbhA family protein"
                     /protein_id="WP_038999327.1"
                     /translation="MARSSDPRQRTEGFRKAEASLRLEGMDPAGTPLYENIKERVISGD
                     ITYEQGRAEILAHYQKRANGH"
                     /name="antitoxin VbhA family protein"
     gene            3626..3739
                     /locus_tag="AABK22_RS24040"
     CDS             3626..3739
                     /locus_tag="AABK22_RS24040"
                     /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_072038508.1"
                     /translation="MHEPPVQSDCCVLSGNYRLESNPERHDKAPLAAATGI"
                     /name="replication initiation protein"
     Typing          3365..3743
                     /name="rep_cluster_2373"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.538"
                     /coverage="88.0"
                     /evalue="1.74e-171"
ORIGIN
        1 taaataaagc atgatatctt tattacgtct cccaataaaa aaggatatat tatgtttggc
       61 catatcattg acactccatt agaagaaaat gacgatgaat atagtgatga cgacctattt
      121 aagatatctt catggggcgc cgatttaagc tttagagaat taatctcaag atacgacgat
      181 gatgaactgg taaagcctga actacaaaga aattacgtct gggataaacc agaggcatct
      241 agatttatag attccatact attaggcctt cctatcccaa gtatattcct agcaaaaaca
      301 aaagatgaaa agctattaat cattgatggt tatcagcgtt ttatgacggt aagggattat
      361 gtaaaaggaa tatttaccaa agataattcc attttcaagt tatcaagaac tgaaaaaata
      421 catgaaaaat ggagaggaaa atccttctta gaacttacag atgatgaaag aaggaaaata
      481 agaaacacta ccattcacgc cataatattc atgcagcaac aacctaaaac aggagataca
      541 agtttattcc agatatttga aagaataaac tcaagcggca ggagtctcct cccccaagaa
      601 ataagaaact gcgtttacca aggaccaatt aactccttac tattcgaatt gaataataac
      661 aataaatgga gaaaactatg gggctctgaa cgtagagatg atcgaatgcg tgatttagag
      721 tttatattac gcttctttgc actttcagat cattacatac aacatagcga caacccgcca
      781 tctcgcatat ccttaaaaaa atacctcaat caattcatgg agttagctaa caacgaatcg
      841 aagatatccg attttagaca tcgttttaat tcaactatag attacatttt tgataatttt
      901 ggattatctg cttttcacaa ctatcaaaaa gaacaaggaa aatggattcc agctttcagt
      961 ccaactatat atgacagcat aatgatatct acagatgagg cgctacgcag aggaataaaa
     1021 ctcccaacgc ccgaggatgc aaaagaagca aagaaattac ttcttgaaaa tcaagaatac
     1081 caaaaccttt tgtatcaaga aacaatgaga actccaaata taaaagcacg agtttccctt
     1141 atgtttgaag ctgtttttca tgaagactgg taaatgtaaa tgaacaatac tgagtcaatg
     1201 aagatattgc gcgactgctg tgatgagtta aatgatataa gaaaactagt ttctgacctt
     1261 gatgactcaa acaaagctgt tggttacata aataaatatg caataatcag agctacaggc
     1321 agcatagagt ttgcttttaa aaaaataata gcagataaag ttgagcacgg atgccatgat
     1381 caaataaaaa acttcataaa aagaaaaata agagagtccg cacacaatcc gagattaggt
     1441 acaattgaaa gcgtccttac cgatttcgat ccaaaatggc agaaaaaatt caatgaaaaa
     1501 attgcgcttg agaataaaat tgcactggac gaatcattaa aaaaactagt gaccgaaaga
     1561 aacagctttg cacatggaag agatgcaaac attggaattg atgagataat tgaaaattac
     1621 ctcaacgggc aaaaagtaat cgcaatccta gatgaaacag tacacttctt gtacgatgaa
     1681 cctggggcgg aagagaaatt aacaaccaca aaacggcata aaagaagaag aaaaaaacgt
     1741 aaaaaaagga aatgataaaa caaaaaacca caacatcttt atgtaaaaat ttgactactt
     1801 ggtattttct agtaaaatac caataggaca caagcataag gtttcctttg agatctatgc
     1861 caaataaaag ccgccttacc agggtggctt tttttttggc atagaagtaa tattgttttc
     1921 ggacaatgcc ttggtggaat gcgacatcta ttttactgcg tatttgctat taaatagatc
     1981 tcactgcatg agttgtacgg gtggtgctgt taactcttct ctctcacagc aggaaacctt
     2041 gtgcttgtgt cctacgaaca caaacctcat agcggtattc aagggagata tgggggaaag
     2101 ttcctgcccg aatgcggtcg gcaaccgttg aggcagaaat catggtaatt cttattgctg
     2161 tgctgaactt actcgtagcg ctcctcgagc tgctattagc gttcaaataa tctaagtttt
     2221 cccaaagaag agaggctaac cacctctctt tcttaaacgc ccatatttaa cataacatcc
     2281 gttgcgtgca ccatctcaga cgccctcagg gcatttctgc gccctcctgc ctatttccgg
     2341 catctttccc tgtccatatc gtgaaaaaac gcgcctgatg atttctgcgc ggctgcatgg
     2401 ctatgcacgc aggtgaatgg cggtcgattt ggggtggatg ctggcatgaa agcctgcttt
     2461 ccggcgcata actcccccga taacggtgaa cgggtgcaca gtttactgtg cgaccgtgag
     2521 gcgttggcca ggccgtcagg catggcagaa tttactacca agcaggaggt cggatttaac
     2581 gtggataatc agcacgcagt gatgaacggg attcggaagg ggaacccttg cggcgcggcg
     2641 atgtatacat cgctaacgtg ccttactctt ttcacagcag agggtagcgg tagcaaacaa
     2701 gtagcaaata gatagcaaac aagtagcaaa tagatagcaa acaagtagca aacaagtagc
     2761 aaacagatag caaatacagg aaaagcctgg ccggagagag gccacgcctg tttttttgag
     2821 gaagcgatgg tacctagttt cctgtccgtg tcagtggccg ttcgcacgct tctggtaatg
     2881 agccagaatt tctgcccgtc cctgttcgta agtgatatcc ccggaaataa cccgctcctt
     2941 gatattttcg tacagcggcg ttccggcggg gtccatgcct tcaagcctca gcgacgcttc
     3001 cgctttgcgg aaaccctcag tacgttgtcg tggatcggag gacctggcca tcgatgttcc
     3061 tttgagctgt aagcgaataa ggcaggcggt aaagtaggcc tactttacat atcctgcccg
     3121 tactctgccg ttgtttatac gtgcagacga atgtgtaaac cggaaggaaa gtattgcagg
     3181 aaactgtgta atccggcggt aaagagaggg tacggcgcga cacgagccca atcaggcatc
     3241 gcagatcttc cgcttcctcg ctcactgact cgctacgctc ggccgttcgg ctgcggcgag
     3301 cggtaccggc agtccacctg gagttaccca cagattcggg ggtagcggaa ggagaaagag
     3361 gggaacagaa aaggccgcgg cgaagccgtt tttccatagg cttcgccccc ctgacaagca
     3421 tcacagaatc tgacgctcaa atcagtggtg gcgaaacccg acaggactat aaagatccca
     3481 ggcgtttccc cctggtagct ccctcgtgcg ctctcctgtt cctgccattc ggtttaccgg
     3541 tgtcattccg ctgttatggc cgcggtttct cattccacgc ctgacactca gttccgggaa
     3601 ggcagttcgc tccaagctgg actgtatgca cgaacccccc gttcagtccg actgctgcgt
     3661 cttatccggt aactatcgac ttgagtccaa cccggaaaga cacgacaaag cgccactggc
     3721 agcagccact ggtatctgat ttagaggagt tagtcttgaa gttatgcgcc tgttaaggct
     3781 aaactgaaag aacaagtttt ggtgactgcg ctcctccaag ccagttacct cggtttaacg
     3841 agcgccaact cgaaaaacct tagaaaaacc gcccgccaag gcggtttttt cttttctgac
     3901 aaaaagatac ccttacccag accactcgtc aatgtagagt ttttgcaa
//
