LOCUS       NZ_AP027559             5631 bp    DNA     circular CON 04-APR-2024
DEFINITION  Escherichia coli strain LR-58-1 plasmid pLR-58-1_6, complete
            sequence.
ACCESSION   NZ_AP027559
VERSION     NZ_AP027559.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00562503
            Assembly: GCF_036497325.1
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  JOURNAL   Unpublished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                   :: 274x
            Sequencing Technology :: MGI DNBSEQ-G400RS; ONT MinION Mk1c
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_036497325.1-RS_2024_04_03
            Annotation Date                   :: 04/03/2024 23:57:35
            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)                     :: 5,032
            CDSs (total)                      :: 4,911
            Genes (coding)                    :: 4,681
            CDSs (with protein)               :: 4,681
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 230
            CDSs (without protein)            :: 230
            Pseudo Genes (ambiguous residues) :: 0 of 230
            Pseudo Genes (frameshifted)       :: 70 of 230
            Pseudo Genes (incomplete)         :: 161 of 230
            Pseudo Genes (internal stop)      :: 41 of 230
            Pseudo Genes (multiple problems)  :: 41 of 230
            Pseudo Genes (short protein)      :: 4 of 230
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP027559.1.
            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-58-1"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pLR-58-1_6"
                     /geo_loc_name="Ecuador:Santo Domingo"
                     /collection_date="2019"
     gene            complement(join(5536..5631,1..243))
                     /locus_tag="AABJ65_RS25075"
     CDS             complement(join(5536..5631,1..243))
                     /locus_tag="AABJ65_RS25075"
                     /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="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_001405931.1"
                     /translation="MKRERMLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSG
                     KLPTLAPPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVR
                     EQGARDDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            293..484
                     /locus_tag="AABJ65_RS25080"
                     /old_locus_tag="VEE07_47800"
     CDS             293..484
                     /locus_tag="AABJ65_RS25080"
                     /old_locus_tag="VEE07_47800"
                     /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            complement(507..827)
                     /locus_tag="AABJ65_RS25085"
                     /old_locus_tag="VEE07_47810"
     CDS             complement(507..827)
                     /locus_tag="AABJ65_RS25085"
                     /old_locus_tag="VEE07_47810"
                     /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(1687..2553)
                     /locus_tag="AABJ65_RS25090"
     CDS             complement(1687..2553)
                     /locus_tag="AABJ65_RS25090"
                     /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"
     gene            complement(2555..3607)
                     /locus_tag="AABJ65_RS25095"
                     /old_locus_tag="VEE07_47830"
     CDS             complement(2555..3607)
                     /locus_tag="AABJ65_RS25095"
                     /old_locus_tag="VEE07_47830"
                     /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            complement(3981..5546)
                     /locus_tag="AABJ65_RS25100"
     CDS             complement(3981..5546)
                     /locus_tag="AABJ65_RS25100"
                     /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="nuclease"
                     /protein_id="WP_000635805.1"
                     /translation="MIVKFHARGKGGGSGPVDYLLGRERNREGATVLQGNPEEVRELID
                     ATPFAKKYTSGVLSFAEKELPPGGREKVMASFERVLMPGLEKNQYSILWVEHQDKGRLE
                     LNFVIPNMELQTGKRLQPYYDRADRPRIDAWQTLVNHHYGLHDPNAPENRRTLTLPDNL
                     PETKQALAEGVTRGIDALYHAGEIKGRQDVIQALTEAGLEVVRVTRSSISIADPNGGRN
                     IRLKGAFYEQSFTDGRGVREKAERESRIYRENAERRVQEARRICKQGTDLKRIFNQERY
                     QRPYNSPERTAGEVSENDRRYDGRALENRTENERETLAVADYRLSTDVCHDRESAVVPG
                     HEDKREYEYSPRAERESGEAEREDMGRALSRGQQRTFSGVAEGDESRNELDEGQRQTER
                     SETGAGVTEHDGAGKTFAERIRATATGLYAAAERMGERLRGIAENVFAYATGQRDAERA
                     SHAVESAGAALERADRTLEPVIQREQEIRDERLMQEREHELSLERERQPEIQERTLDGP
                     SLGW"
                     /name="nuclease"
     Typing          complement(579..660)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.795"
                     /coverage="100.0"
                     /evalue="6.23e-34"
     Typing          complement(1117..1304)
                     /name="rep_cluster_2401"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="4.63e-94"
     Typing          complement(2..261)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.701"
                     /coverage="100.0"
                     /evalue="3.08e-50"
     Typing          complement(3985..5546)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gtcaccggaa gaccactgcc cgctgttcac cttcctcgct gtctggttaa ggttattccc
       61 gatggcggcc agctgacgca gtaacggcgg tgccagtgtc ggcagcttcc cggaacgggc
      121 aaccggctca cccaggcaga cccgccgcat ccataccgcc agttgtttac cctcacagcg
      181 ttccagtaac cgggcatgtt catcatcagt aacccgtatc gtgagcatcc tctcgcgttt
      241 catcggtatc attaccccca tgaacagaac ccccccttac acggaggcat cagtgaccaa
      301 acaggaaaaa accgccctta acatggcccg cttcatcaga ggccagacat taacgctgct
      361 ggagaagctc aacgaactgg acgcggatga acaggcagac atctgtgaat cgcttcacga
      421 ccacgccgat gagctttacc gcagttgcct cgcacgcttc ggggatgacg gtgaaaaccg
      481 ctgacacatg cagctcccgg agacggtcac agcttgtctg tgagcggatg ccgggagcag
      541 acaagcccgc cagggcgcgt caggccgttg acctttgggg tgtcggggcg cagccctgac
      601 ccagtcacgt agcgatagcg gagtgtatac tggcttaacc attcggcatc agtgcggatt
      661 gtatgaaaag tgcgccatgt ccggtgtgaa atgccgcaca gatgcgtaag gagaaaatgc
      721 cagttcaggc gctcttccgc ttcctcgctc actgactcgc tacgctcggt cgttcggctg
      781 cggcgagcgg actctccttt ctcaaaaacg ctaaccctgt tatccacaga acccggggat
      841 aaaccaggaa agaacatgtg cgcaaaaaac gaaaccccgg gaaaggccgc gccggaggcg
      901 ctttttccat aggctccgcc cccctgacgg acttcacaaa acagacactt tttcggtgca
      961 tctgtgggag ccttgcggct caaccatgaa atccgccagc ggtggcgaaa cccgacgtgg
     1021 cttaaagatc atcaccgttt ccggtgaatc gctccctcct gcgcccccac gttcccgcca
     1081 tatcgattac cggatacctt ttccgccttt ctcccttacg ggacacgtgg cgctttctca
     1141 tagctcacgt cttctggtat ctcggggcga cttaggcagt tcgctccggg ctgggctgta
     1201 tgcaggaacc ccccgttcag cccgactgct gcgccttctc cggtaactgt tctcttgggt
     1261 ccaacccgga aaagacacca caaagcgcca ctggcagcag ccattggtaa aagtcatgtg
     1321 cgagatattt agagagtact tgaagtggct gccggagtgc ggctacacta gaagaacaat
     1381 tttggtgact cgtctcgcat aagacagtta cctggttaag cagtctgcaa gctgacttaa
     1441 ccttcgatca aaccgccctg caaggcggtt ttttcgttta caggcagcag attacgcgca
     1501 gaaaaaaagg atctcaagag gatcctttga tctttttgtt acaaacgtct ctatttgact
     1561 cccctgagag cgttttagcg cgcctctgac ccccttggtt acattccgac accagaaacg
     1621 ctcccgtttt ttacgtgcat ttggcacggt atcgatggag gccggggggc aatcctgaac
     1681 agaatgttac tcctctgagt attttctgtt aagaaaatat acacttagca cagttacaat
     1741 aaatcctacc ccctgtaaga atgtgaattg ttcatccaaa aacaaccatg acaaaaataa
     1801 tgcaactagc ggaataaagt acaacattat ccctgccaaa tgaactggga gccaacgcaa
     1861 ggagttcaag taaaaacaaa aagctaaaaa atattgtaat attccagatg aaaaaacaat
     1921 aatcacggat tccaacggaa gataaattga tgatttagat ataaaaataa agagcgatga
     1981 cagtataagg gagaatgtca actgtccgct caataatgtg ataggctcaa acgatttaat
     2041 aaggcgagac gatataacaa cataaaatgc tgccgataac acaccggcaa caacaagaca
     2101 atatccaaca atattattcg atccattact gatgtctggc aaggctacca aaatactgcc
     2161 aacaattgca cctataagga acaatataaa atattgcggg gaattaattt taactgagca
     2221 aataagaaca gacaacacca atataaacac tgattcaagt gaaaaaataa ttgatgcgct
     2281 tcctgctgaa ataaaataaa gtccgtagag tgtaaaagta tacgctaaga atggttcaaa
     2341 aacgcctgtc gcataagcaa gtatcgcttt tgagtttaat gggagttttt ttctttttat
     2401 aaaaagaact atccaagata gtattactgc actacaaatc tgccagaaaa acacccctcc
     2461 ggcatctagt tcttcaactc cttttttgct cattacgata gctgcccccc atgagaacgc
     2521 tgctaaaaaa gcaaaaagca ttcctttaat catattaatc atcctctttc tcataaaggg
     2581 gtttgttttc aaatttcctt ggttgaaagg agttaaaaaa catagatgca tcatctacag
     2641 gaataccaat aaactctcca taataaggat catctatagg aaactcttct aatgaaacat
     2701 aaaacaatac attccagttg aagatcattg gatcactatt ttctatttca tggagcaatc
     2761 tttcatcctt agttaattct cctggaatta atacatcagt atgataaaaa ccgctgtaat
     2821 aagaactatt accggtgtgc actgggcatc caaaacgatc caaattagat tctgaatgcc
     2881 atgttgtaga aatcccttcc ggatgtgaat acccaccctt accaacagac tgaatagtca
     2941 tgttacgaat atccgctaac gcttgttctt gatctttata gaaacctttt tctatcgcca
     3001 gcctcataaa atgccccggg gcatttacag aaataagtat tccccctggt attcttctat
     3061 catgatttct tgttctatga gcagaagagt aaaaaacatt aacaccagcc ttatatattt
     3121 ttagcccatc tttatcctga aatggtacgc tttcagtata aataacatcc tcttttattg
     3181 gatagcactc tggcatatgc agcgaacaaa tatatttttg tatgtccact aactcttctg
     3241 atggacgagc aaaggcaagt tgtggatgaa taaaataaat gagatgcgca ctgacctctc
     3301 ctcttcttgc gcgttcttta aaacgaactc tttcattacg caaaaaatca aacaaatgac
     3361 catcatcatt atatagttgg gggctattta caatagataa atggaaatca agccctttaa
     3421 ttttcttgct tgccaattta ccaaatacac agggctgatt gcctgacacc cattttctta
     3481 gtaaatcttc aattttatct ttagaagttt cgttaaagat aaatgaatga atattatcaa
     3541 tatcttttcc aaatgaaaaa ctggatgata attgtggaag tttatttata cgttgttgaa
     3601 gattcatgaa agctcccaca agacacctca tatatttttt tatatactga aactacatta
     3661 tatttattac cggcgtaaaa cgaaataatt tattatcgtt accgatattt taaaaaaatc
     3721 attatttgca cagtgttcga gttgttagta tcactccttc ctgaaaatcc gctccattta
     3781 ccataacgtc gcattgtacg caccgccaaa acgcgttcgg tgcgatcacg gcagcagaca
     3841 ggtaaaaatg gcaacaaacc acccgaaaaa ctgccgcgat cgcacctgat aaattttaac
     3901 cgcatgaata cctatgcaac cagatgctac aggccacatt agcccgcctt aatccactga
     3961 acacgtcatt tttcatggtt tcaccatccc agcgaagggc catccagtgt ccgctcctgg
     4021 atttccggct gacgctcccg ctccagagat aactcatgtt cgcgttcctg catcagccgt
     4081 tcatccctta tctcctgttc tcgctgtata actggctcaa gcgttctgtc cgctcgctca
     4141 agtgctgcac ctgctgactc aactgcatga ctcgcccgtt cagcatcgcg ttgtcccgtt
     4201 gcgtaagcga aaacattttc tgcaattcca cgaaggcgtt ctcccattcg ttcagccgct
     4261 gcatatagtc ctgttgcagt tgctctaatg cgttcagcaa atgtctttcc agctccgtca
     4321 tgctctgtca ctcctgcacc agtctcactg cgttcagttt gccgttgtcc ttcgtccagt
     4381 tcgtttcggc tttcatcccc ttcggcaaca ccagaaaacg tccgttgctg tcctcgtgat
     4441 aacgcacgcc ccatgtcttc gcgttcagct tctccagact ctctttctgc tcgcggagaa
     4501 tattcatatt cgcgtttatc ttcatgccct ggtaccacag cagactcccg gtcgtggcaa
     4561 acatcagtac tgagacgata atcagccaca gccagcgttt cacgctcatt ttcagtacgg
     4621 ttttccagtg cgcgtccatc gtatcgacgg tcgttttctg atacctctcc agcagttctt
     4681 tcagggctgt tgtatggtcg ttgatagcgt tcctgattaa agattcgttt gaggtcagtt
     4741 ccctgtttac agattcttcg agcttcctga actcgtcgtt cagcattttc tctgtagatt
     4801 cggctctctc tttcagcttt ttctcgaact ccgcgcccgt ctgtaaaaga ttgctcataa
     4861 aacgctcctt tcagtctgat attcctcccg ccgttcgggt ctgcaatgct gatactgctt
     4921 cgcgtcaccc tgaccacttc aagccccgcc tctgtgagcg cctgaatcac atcctgacgg
     4981 ccttttatct ctccggcatg gtaaagcgcg tctatcccgc gtgtgacgcc ctcagcaagc
     5041 gcctgtttcg tttccggcag gttatcagga agggtcagcg tccggcggtt ctccggggcg
     5101 ttggggtcat gcagaccgta atggtgattc accagcgtct gccaggcatc aattctcggc
     5161 ctgtctgccc ggtcgtagta cggctggagg cgttttccgg tctgtagctc catgttcgga
     5221 atgacaaaat tcagctcaag ccgtcccttg tcctggtgct ccacccacag gatgctgtac
     5281 tgattttttt cgagaccggg catcagtaca cgctcaaagc tcgccatcac tttttcacgt
     5341 cctcccggtg gcagctcctt ctccgcgaac gacagcacac cagacgtgta tttcttcgca
     5401 aatggcgtgg catcgatgag ttcccggacc tcttccggat tcccctgaag caccgttgcc
     5461 ccttcccggt tacgctccct tcccagcagg taatcaaccg gaccactgcc accacctttt
     5521 cccctggcat gaaacttaac tatcatcccg cgccccctgt tccctgaccg ccagacgcag
     5581 ccggcgcagc tcatccccga tggccatcag tgcggccacc acctgaaccc g
//
