LOCUS       NZ_AP027504             3126 bp    DNA     circular CON 04-APR-2024
DEFINITION  Escherichia coli strain LR-25 plasmid pLR-25_4, complete sequence.
ACCESSION   NZ_AP027504
VERSION     NZ_AP027504.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00562495
            Assembly: GCF_036495185.1
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  JOURNAL   Unpublished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 3126)
  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                   :: 64x
            Sequencing Technology :: MGI DNBSEQ-G400RS; ONT MinION Mk1c
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_036495185.1-RS_2024_04_04
            Annotation Date                   :: 04/04/2024 00:14:00
            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)                     :: 5,021
            CDSs (total)                      :: 4,903
            Genes (coding)                    :: 4,720
            CDSs (with protein)               :: 4,720
            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)              :: 183
            CDSs (without protein)            :: 183
            Pseudo Genes (ambiguous residues) :: 0 of 183
            Pseudo Genes (frameshifted)       :: 54 of 183
            Pseudo Genes (incomplete)         :: 118 of 183
            Pseudo Genes (internal stop)      :: 39 of 183
            Pseudo Genes (multiple problems)  :: 28 of 183
            Pseudo Genes (short protein)      :: 3 of 183
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP027504.1.
            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..3126
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="LR-25"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pLR-25_4"
                     /geo_loc_name="Ecuador:Santo Domingo"
                     /collection_date="2019"
     gene            205..399
                     /locus_tag="AABK20_RS25080"
                     /old_locus_tag="VEE02_48140"
     CDS             205..399
                     /locus_tag="AABK20_RS25080"
                     /old_locus_tag="VEE02_48140"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041624.1"
                     /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_024193633.1"
                     /translation="MNKQQQTVLNMAGFIKSQSLTLLEKLDALDADEQAAMCEKLHELA
                     EELQNSIQRRFEAENRTGI"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            869..982
                     /locus_tag="AABK20_RS25085"
     CDS             869..982
                     /locus_tag="AABK20_RS25085"
                     /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_071790583.1"
                     /translation="MHEPPVQSDYCALSGNYRLESNPERHDLSPLAAATGN"
                     /name="replication initiation protein"
     gene            1344..1487
                     /locus_tag="AABK20_RS25090"
                     /old_locus_tag="VEE02_48150"
     CDS             1344..1487
                     /locus_tag="AABK20_RS25090"
                     /old_locus_tag="VEE02_48150"
                     /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_016249640.1"
                     /translation="MNTKVLFVKKALKSITCATLSLLPALSRAVTELRSLSAARLKAGK
                     SF"
                     /name="hypothetical protein"
     gene            complement(1512..2264)
                     /locus_tag="AABK20_RS25095"
                     /old_locus_tag="VEE02_48160"
     CDS             complement(1512..2264)
                     /locus_tag="AABK20_RS25095"
                     /old_locus_tag="VEE02_48160"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001127762.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_016249639.1"
                     /translation="MDTTSLISSISVPRLSFYETFLGCATDQEKVGAYVAYQDLSGDFF
                     CLVQMIEVALRNAINNTIKANHGPAWYDSIPQTKKSQDLVLNAKQKALDECGVRYTDDD
                     VICRLTFGFWVYMLDAPYRDTQRPCYIWTPENKAKTFPHAKNPLGGGDMKVKALFDEFH
                     KVLLFRNRLFHHEPIWKKHHCKSHSQAINNMLKEFNFLMNALSIVSNEKKELIEFIGHD
                     RRFYERCTIEYVMGIIGRIKCRELKVAG"
                     /name="hypothetical protein"
     gene            complement(2723..3046)
                     /gene="mobA"
                     /locus_tag="AABK20_RS25100"
                     /old_locus_tag="VEE02_48170"
     CDS             complement(2723..3046)
                     /gene="mobA"
                     /locus_tag="AABK20_RS25100"
                     /old_locus_tag="VEE02_48170"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization protein MobA"
                     /protein_id="WP_000166966.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="mobA"
     Typing          complement(2..168)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="95.238"
                     /coverage="99.0"
                     /evalue="6.379999999999996e-69"
     Typing          435..938
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.528"
                     /coverage="95.0"
                     /evalue="8.27e-156"
     Typing          complement(2727..3046)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="2.17e-62"
ORIGIN
        1 ggtataacaa ttgcacatcc tgtcctgtca gcaagttcga attaccgaca aaggcacggc
       61 agttttttgg cagtgacagt gttgcctgac agaaataccc gttaaagcgt cagacggcag
      121 aataccggcg gcaaaactgt cgaaaagtgg tacgcgatat aatcacacga cgcagatgac
      181 agacagaacg gagaaaacag aaagatgaac aagcagcagc aaaccgtact taacatggca
      241 ggattcataa aaagccagag cctgacgctg ctcgaaaaac tggacgcact tgatgctgac
      301 gaacaggccg ccatgtgtga gaagctgcac gaactcgcgg aagaacttca gaacagcata
      361 cagagacgct ttgaagcgga aaatcgcacc gggatataac gcatccggac aggatgcaga
      421 acggcataga ggagcgtaag gagaaaatgt cacataaggc gctcttccgc ttcctcgctc
      481 actgactcgc tacgctcggt cgttcgactg cggcgagcgg tgtcagctca ctcaaaggcg
      541 gtaatgcggt tatccacaga atcaggggat aaagccggaa agaacatgtg agcaaaagac
      601 aaagacccag aagaagagca cgcaggaggc gtttttccat aggctccgcc cccctgacga
      661 gcatcacaaa aaccgacgct caagtcagag gtggcgaaac ccgacaggac ttaaagatac
      721 caggcgtttc cccctggtgg ctccctcgtg cgctctcctg ttcctgcctt tcggtttacc
      781 ggtgtcattc cgctgttatg gccgcgtttg tctcattcca cgcctgacac tcagttccgg
      841 gtaggcagtt cgctccaagc tggactgtat gcacgaaccc cccgttcagt ccgactactg
      901 cgccttatcc ggtaactatc gtcttgagtc caacccggaa aggcacgact tatcgccatt
      961 ggcagcagcc actggtaact gatttagagg agttagtctt gaagttacgt gccagttaag
     1021 gctaaactgg aataacaagt tttggtgact gcgctcctct taagccagtt accgcggttc
     1081 agaaacttgc cggttgctga accttcgaaa aaccaccttg ccgggtggtt ttttcgtttt
     1141 taagattacg atgggcgcga tatgaactca aggaaatccg taattaaatt ataaaacttc
     1201 gtgaattaat ggaaaaactg atgtgaatca gctatttatc cttaagattt gatgttagat
     1261 atggtataat taaccattca aatagatgga ataaaaagtc aacgctgcca ttagaacggc
     1321 ataagaaata gaggattatg aaaatgaata ctaaagttct ttttgtgaaa aaagctttga
     1381 aatcaattac ttgcgcaact ctttcgctct taccggcttt aagtcgcgca gtaacagagt
     1441 tacgtagcct ttcggctgcg cgacttaaag ccggtaagag cttttgattg tatcacattt
     1501 tcccttaaaa gtcaaccggc taccttaagc tccctgcact taatcctccc tataatcccc
     1561 ataacatact ctatcgtgca gcgttcataa aagcgcctat cgtgcccaat aaactcaata
     1621 agttcctttt tctcgttaga gacgatactc aaggcattca ttaaaaaatt gaactctttc
     1681 aacatattat ttatggcttg actatgcgac ttgcagtggt gttttttcca aataggctca
     1741 tggtgaaaaa gtcgattcct aaacaaaaga actttatgaa actcgtcaaa cagcgcttta
     1801 accttcatat cccccccacc caaaggattc ttcgcatgag gaaatgtttt tgccttgttc
     1861 tctggagtcc agatgtagca cggcctttgc gtatccctat atggggcatc taacatataa
     1921 acccaaaagc caaaggttag acggcaaata acatcatcat ccgtatacct tacgccacac
     1981 tcatctagtg ctttttgttt cgcatttaaa acaagatcct gagatttctt tgtttgaggt
     2041 atagagtcgt accaagcagg cccatgatta gctttgattg tattgtttat cgcattacgc
     2101 agagcaacct caatcatctg gacaagacaa aaaaaatcgc cagacagatc ttggtaggca
     2161 acgtatgccc caaccttttc ttgatcagta gcgcacccaa gaaatgtttc atagaaagat
     2221 aatcttggta cagaaattga gctaattaaa cttgttgtat ccatgaaaac tcacttatct
     2281 ctttactatg aatatttttc agactaccat tacaacattc gaggagcagg cgaactaccg
     2341 tttttctgtg tacctctaga gcgtaaaata taacaaaaaa gcccactaca gagtgggctt
     2401 ttttgttata tttatctata tgaaacaacc agttatagtt attgtttcat aataaggatt
     2461 gaatactctt cacaatccat aacatcagaa aatactttgc tgccaattta ccataactcc
     2521 ccttacgcgc accgctaaaa cgcgctgaac gcgattctgc cgcaaacacc gcaaaaagag
     2581 atgttttacc cagtgaaaac tggaaaaatg cgtcaggatc gttttcagct cactgcatag
     2641 ctatgcatga aagtgaatgg cgatcggttt gggggcttac ggcgttcata ccgtctgttt
     2701 tcgacagttt ctctccggga agctaatctg ccataagcct ggataacagg gcccggtgat
     2761 actccgtaat agcgatcagc acctccgcat actctctgtc cccgacacgc ttgccgtcga
     2821 taaagagttt tttctgtaac gcccccagtc tcataacttc tttcagtacc cgatcatcag
     2881 tcagtgagtt aactttctta ccgagagctg ccgcccgtaa aaaaccggaa acggtcttgc
     2941 cgcattcagc agcccttttt ctgatttcct ggtcttcttc tgccgtcaga cgaacagggc
     3001 gactgatagc ccgcctgcgc gtattacttc cacttcgttt tgtcataaaa catggctccg
     3061 tatctgacat ggggtgtcgg ggcaaagccc tgaccagggt aattgtaata gcgtgcatgc
     3121 atgcgc
//
