LOCUS       NZ_AP027567             5631 bp    DNA     circular CON 04-APR-2024
DEFINITION  Escherichia coli strain LR-58-2 plasmid pLR-58-2_4, complete
            sequence.
ACCESSION   NZ_AP027567
VERSION     NZ_AP027567.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00562499
            Assembly: GCF_036497485.1
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  JOURNAL   Unpublished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 5631)
  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                   :: 176x
            Sequencing Technology :: MGI DNBSEQ-G400RS; ONT MinION Mk1c
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_036497485.1-RS_2024_04_04
            Annotation Date                   :: 04/04/2024 00:14:44
            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)                     :: 5,432
            CDSs (total)                      :: 5,314
            Genes (coding)                    :: 5,113
            CDSs (with protein)               :: 5,113
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 201
            CDSs (without protein)            :: 201
            Pseudo Genes (ambiguous residues) :: 0 of 201
            Pseudo Genes (frameshifted)       :: 62 of 201
            Pseudo Genes (incomplete)         :: 144 of 201
            Pseudo Genes (internal stop)      :: 40 of 201
            Pseudo Genes (multiple problems)  :: 44 of 201
            Pseudo Genes (short protein)      :: 4 of 201
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP027567.1.
            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..5631
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="LR-58-2"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pLR-58-2_4"
                     /geo_loc_name="Ecuador:Santo Domingo"
                     /collection_date="2019"
     gene            10..330
                     /locus_tag="AABJ83_RS27090"
     CDS             10..330
                     /locus_tag="AABJ83_RS27090"
                     /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_187655770.1"
                     /translation="MDNRVSVFEKGESARRSRTTERSESVSEEAEERLNWHFLLTHLCG
                     ISHRTWRTFHTIRTDAEWLSQYTLRYRYVTGSGLRPDTPKVNGLTRPGGLVCSRHPLTD
                     KL"
                     /name="hypothetical protein"
     gene            complement(353..544)
                     /locus_tag="AABJ83_RS27095"
                     /old_locus_tag="VEE04_51610"
     CDS             complement(353..544)
                     /locus_tag="AABJ83_RS27095"
                     /old_locus_tag="VEE04_51610"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165975.1"
                     /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_000165975.1"
                     /translation="MTKQEKTALNMARFIRGQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENR"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            609..932
                     /locus_tag="AABJ83_RS27100"
                     /old_locus_tag="VEE04_51620"
     CDS             609..932
                     /locus_tag="AABJ83_RS27100"
                     /old_locus_tag="VEE04_51620"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_000955999.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1141..>1572
                     /locus_tag="AABJ83_RS27105"
                     /pseudo=""
     CDS             1141..>1572
                     /locus_tag="AABJ83_RS27105"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /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="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            1610..2140
                     /locus_tag="AABJ83_RS27110"
                     /old_locus_tag="VEE04_51630"
     CDS             1610..2140
                     /locus_tag="AABJ83_RS27110"
                     /old_locus_tag="VEE04_51630"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001673158.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_001673158.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFRKLEESVNRELTSNE
                     SLIRNAINDHTTALKELLERYQKTTVDTMDAHWKTVLKMSVKRWLWLIIVSVLMFATTG
                     SLLWYQGMKINANMNILREQKESLEKLNAKTWGVRYHEDSNGRFLVLPKGMKAETNWTK
                     DNGKLNAVRLVQE"
                     /name="MbeB family mobilization protein"
     gene            2147..2380
                     /locus_tag="AABJ83_RS27115"
                     /old_locus_tag="VEE04_51640"
     CDS             2147..2380
                     /locus_tag="AABJ83_RS27115"
                     /old_locus_tag="VEE04_51640"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_000137437.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWENAFVELQKMFSLTQRDNA
                     MLNGRVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            2861..3913
                     /locus_tag="AABJ83_RS27120"
                     /old_locus_tag="VEE04_51650"
     CDS             2861..3913
                     /locus_tag="AABJ83_RS27120"
                     /old_locus_tag="VEE04_51650"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001557502.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001053268.1"
                     /translation="MNLQQRINKLPQLSSSFSFGKDIDNIHSFIFNETSKDKIEDLLRK
                     WVSGNQPCVFGKLASKKIKGLDFHLSIVNSPQLYNDDGHLFDFLRNERVRFKERARRGE
                     VSAHLIYFIHPQLAFARPSEELVDIQKYICSLHMPECYPIKEDVIYTESVPFQDKDGLK
                     IYKAGVNVFYSSAHRTRNHDRRIPGGILISVNAPGHFMRLAIEKGFYKDQEQALADIRN
                     MTIQSVGKGGYSHPEGISTTWHSESNLDRFGCPVHTGNSSYYSGFYHTDVLIPGELTKD
                     ERLLHEIENSDPMIFNWNVLFYVSLEEFPIDDPYYGEFIGIPVDDASMFFNSFQPRKFE
                     NKPLYEKEDD"
                     /name="hypothetical protein"
     gene            3915..4781
                     /locus_tag="AABJ83_RS27125"
     CDS             3915..4781
                     /locus_tag="AABJ83_RS27125"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001335763.1"
                     /GO_function="GO:0005215 - transporter activity [Evidence
                     IEA]"
                     /GO_process="GO:0055085 - transmembrane transport [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DMT family transporter"
                     /protein_id="WP_001335763.1"
                     /translation="MIKGMLFAFLAAFSWGAAIVMSKKGVEELDAGGVFFWQICSAVIL
                     SWIVLFIKRKKLPLNSKAILAYATGVFEPFLAYTFTLYGLYFISAGSASIIFSLESVFI
                     LVLSVLICSVKINSPQYFILFLIGAIVGSILVALPDISNGSNNIVGYCLVVAGVLSAAF
                     YVVISSRLIKSFEPITLLSGQLTFSLILSSLFIFISKSSIYLPLESVIIVFSSGILQYF
                     LAFCFYLNSLRWLPVHLAGIMLYFIPLVALFLSWLFLDEQFTFLQGVGFIVTVLSVYFL
                     NRKYSEE"
                     /name="DMT family transporter"
     Typing          178..259
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.795"
                     /coverage="100.0"
                     /evalue="6.23e-34"
     Typing          5165..5352
                     /name="rep_cluster_2401"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="4.63e-94"
     Typing          923..2484
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ccgggttctg tggataacag ggttagcgtt tttgagaaag gagagtccgc tcgccgcagc
       61 cgaacgaccg agcgtagcga gtcagtgagc gaggaagcgg aagagcgcct gaactggcat
      121 tttctcctta cgcatctgtg cggcatttca caccggacat ggcgcacttt tcatacaatc
      181 cgcactgatg ccgaatggtt aagccagtat acactccgct atcgctacgt gactgggtca
      241 gggctgcgcc ccgacacccc aaaggtcaac ggcctgacgc gccctggcgg gcttgtctgc
      301 tcccggcatc cgctcacaga caagctgtga ccgtctccgg gagctgcatg tgtcagcggt
      361 tttcaccgtc atccccgaag cgtgcgaggc aactgcggta aagctcatcg gcgtggtcgt
      421 gaagcgattc acagatgtct gcctgttcat ccgcgtccag ttcgttgagc ttctccagca
      481 gcgttaatgt ctggcctctg atgaagcggg ccatgttaag ggcggttttt tcctgtttgg
      541 tcactgatgc ctccgtgtaa gggggggttc tgttcatggg ggtaatgata ccgatgaaac
      601 gcgagaggat gctcacgata cgggttactg atgatgaaca tgcccggtta ctggaacgct
      661 gtgagggtaa acaactggcg gtatggatgc ggcgggtctg cctgggtgag ccggttgccc
      721 gttccgggaa gctgccgaca ctggcaccgc cgttactgcg tcagctggcc gccatcggga
      781 ataaccttaa ccagacagcg aggaaggtga acagcgggca gtggtcttcc ggtgaccggg
      841 ttcaggtggt ggccgcactg atggccatcg gggatgagct gcgccggctg cgtctggcgg
      901 tcagggaaca gggggcgcgg gatgatagtt aagtttcatg ccaggggaaa aggtggtggc
      961 agtggtccgg ttgattacct gctgggaagg gagcgtaacc gggaaggggc aacggtgctt
     1021 caggggaatc cggaagaggt ccgggaactc atcgatgcca cgccatttgc gaagaaatac
     1081 acgtctggtg tgctgtcgtt cgcggagaag gagctgccac cgggaggacg tgaaaaagtg
     1141 atggcgagct ttgagcgtgt actgatgccc ggtctcgaaa aaaatcagta cagcatcctg
     1201 tgggtggagc accaggacaa gggacggctt gagctgaatt ttgtcattcc gaacatggag
     1261 ctacagaccg gaaaacgcct ccagccgtac tacgaccggg cagacaggcc gagaattgat
     1321 gcctggcaga cgctggtgaa tcaccattac ggtctgcatg accccaacgc cccggagaac
     1381 cgccggacgc tgacccttcc tgataacctg ccggaaacga aacaggcgct tgctgagggc
     1441 gtcacacgcg ggatagacgc gctttaccat gccggagaga taaaaggccg tcaggatgtg
     1501 attcaggcgc tcacagaggc ggggcttgaa gtggtcaggg tgacgcgaag cagtatcagc
     1561 attgcagacc cgaacggcgg gaggaatatc agactgaaag gagcgtttta tgagcaatct
     1621 tttacagacg ggcgcggagt tcgagaaaaa gctgaaagag agagccgaat ctacagagaa
     1681 aatgctgaac gacgagttca ggaagctcga agaatctgta aacagggaac tgacctcaaa
     1741 cgaatcttta atcaggaacg ctatcaacga ccatacaaca gccctgaaag aactgctgga
     1801 gaggtatcag aaaacgaccg tcgatacgat ggacgcgcac tggaaaaccg tactgaaaat
     1861 gagcgtgaaa cgctggctgt ggctgattat cgtctcagta ctgatgtttg ccacgaccgg
     1921 gagtctgctg tggtaccagg gcatgaagat aaacgcgaat atgaatattc tccgcgagca
     1981 gaaagagagt ctggagaagc tgaacgcgaa gacatggggc gtgcgttatc acgaggacag
     2041 caacggacgt tttctggtgt tgccgaaggg gatgaaagcc gaaacgaact ggacgaagga
     2101 caacggcaaa ctgaacgcag tgagactggt gcaggagtga cagagcatga cggagctgga
     2161 aagacatttg ctgaacgcat tagagcaact gcaacaggac tatatgcagc ggctgaacga
     2221 atgggagaac gccttcgtgg aattgcagaa aatgttttcg cttacgcaac gggacaacgc
     2281 gatgctgaac gggcgagtca tgcagttgag tcagcaggtg cagcacttga gcgagcggac
     2341 agaacgcttg agccagttat acagcgagaa caggagataa gggatgaacg gctgatgcag
     2401 gaacgcgaac atgagttatc tctggagcgg gagcgtcagc cggaaatcca ggagcggaca
     2461 ctggatggcc cttcgctggg atggtgaaac catgaaaaat gacgtgttca gtggattaag
     2521 gcgggctaat gtggcctgta gcatctggtt gcataggtat tcatgcggtt aaaatttatc
     2581 aggtgcgatc gcggcagttt ttcgggtggt ttgttgccat ttttacctgt ctgctgccgt
     2641 gatcgcaccg aacgcgtttt ggcggtgcgt acaatgcgac gttatggtaa atggagcgga
     2701 ttttcaggaa ggagtgatac taacaactcg aacactgtgc aaataatgat ttttttaaaa
     2761 tatcggtaac gataataaat tatttcgttt tacgccggta ataaatataa tgtagtttca
     2821 gtatataaaa aaatatatga ggtgtcttgt gggagctttc atgaatcttc aacaacgtat
     2881 aaataaactt ccacaattat catccagttt ttcatttgga aaagatattg ataatattca
     2941 ttcatttatc tttaacgaaa cttctaaaga taaaattgaa gatttactaa gaaaatgggt
     3001 gtcaggcaat cagccctgtg tatttggtaa attggcaagc aagaaaatta aagggcttga
     3061 tttccattta tctattgtaa atagccccca actatataat gatgatggtc atttgtttga
     3121 ttttttgcgt aatgaaagag ttcgttttaa agaacgcgca agaagaggag aggtcagtgc
     3181 gcatctcatt tattttattc atccacaact tgcctttgct cgtccatcag aagagttagt
     3241 ggacatacaa aaatatattt gttcgctgca tatgccagag tgctatccaa taaaagagga
     3301 tgttatttat actgaaagcg taccatttca ggataaagat gggctaaaaa tatataaggc
     3361 tggtgttaat gttttttact cttctgctca tagaacaaga aatcatgata gaagaatacc
     3421 agggggaata cttatttctg taaatgcccc ggggcatttt atgaggctgg cgatagaaaa
     3481 aggtttctat aaagatcaag aacaagcgtt agcggatatt cgtaacatga ctattcagtc
     3541 tgttggtaag ggtgggtatt cacatccgga agggatttct acaacatggc attcagaatc
     3601 taatttggat cgttttggat gcccagtgca caccggtaat agttcttatt acagcggttt
     3661 ttatcatact gatgtattaa ttccaggaga attaactaag gatgaaagat tgctccatga
     3721 aatagaaaat agtgatccaa tgatcttcaa ctggaatgta ttgttttatg tttcattaga
     3781 agagtttcct atagatgatc cttattatgg agagtttatt ggtattcctg tagatgatgc
     3841 atctatgttt tttaactcct ttcaaccaag gaaatttgaa aacaaacccc tttatgagaa
     3901 agaggatgat taatatgatt aaaggaatgc tttttgcttt tttagcagcg ttctcatggg
     3961 gggcagctat cgtaatgagc aaaaaaggag ttgaagaact agatgccgga ggggtgtttt
     4021 tctggcagat ttgtagtgca gtaatactat cttggatagt tctttttata aaaagaaaaa
     4081 aactcccatt aaactcaaaa gcgatacttg cttatgcgac aggcgttttt gaaccattct
     4141 tagcgtatac ttttacactc tacggacttt attttatttc agcaggaagc gcatcaatta
     4201 ttttttcact tgaatcagtg tttatattgg tgttgtctgt tcttatttgc tcagttaaaa
     4261 ttaattcccc gcaatatttt atattgttcc ttataggtgc aattgttggc agtattttgg
     4321 tagccttgcc agacatcagt aatggatcga ataatattgt tggatattgt cttgttgttg
     4381 ccggtgtgtt atcggcagca ttttatgttg ttatatcgtc tcgccttatt aaatcgtttg
     4441 agcctatcac attattgagc ggacagttga cattctccct tatactgtca tcgctcttta
     4501 tttttatatc taaatcatca atttatcttc cgttggaatc cgtgattatt gttttttcat
     4561 ctggaatatt acaatatttt ttagcttttt gtttttactt gaactccttg cgttggctcc
     4621 cagttcattt ggcagggata atgttgtact ttattccgct agttgcatta tttttgtcat
     4681 ggttgttttt ggatgaacaa ttcacattct tacagggggt aggatttatt gtaactgtgc
     4741 taagtgtata ttttcttaac agaaaatact cagaggagta acattctgtt caggattgcc
     4801 ccccggcctc catcgatacc gtgccaaatg cacgtaaaaa acgggagcgt ttctggtgtc
     4861 ggaatgtaac caagggggtc agaggcgcgc taaaacgctc tcaggggagt caaatagaga
     4921 cgtttgtaac aaaaagatca aaggatcctc ttgagatcct ttttttctgc gcgtaatctg
     4981 ctgcctgtaa acgaaaaaac cgccttgcag ggcggtttga tcgaaggtta agtcagcttg
     5041 cagactgctt aaccaggtaa ctgtcttatg cgagacgagt caccaaaatt gttcttctag
     5101 tgtagccgca ctccggcagc cacttcaagt actctctaaa tatctcgcac atgactttta
     5161 ccaatggctg ctgccagtgg cgctttgtgg tgtcttttcc gggttggacc caagagaaca
     5221 gttaccggag aaggcgcagc agtcgggctg aacggggggt tcctgcatac agcccagccc
     5281 ggagcgaact gcctaagtcg ccccgagata ccagaagacg tgagctatga gaaagcgcca
     5341 cgtgtcccgt aagggagaaa ggcggaaaag gtatccggta atcgatatgg cgggaacgtg
     5401 ggggcgcagg agggagcgat tcaccggaaa cggtgatgat ctttaagcca cgtcgggttt
     5461 cgccaccgct ggcggatttc atggttgagc cgcaaggctc ccacagatgc accgaaaaag
     5521 tgtctgtttt gtgaagtccg tcaggggggc ggagcctatg gaaaaagcgc ctccggcgcg
     5581 gcctttcccg gggtttcgtt ttttgcgcac atgttctttc ctggtttatc c
//
