LOCUS       NZ_AP027860             5270 bp    DNA     circular CON 04-APR-2024
DEFINITION  Escherichia coli strain 2017-19-1CC plasmid p2017-19-1CC_6, complete
            sequence.
ACCESSION   NZ_AP027860
VERSION     NZ_AP027860.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00562630
            Assembly: GCF_036506655.1
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  JOURNAL   Unpublished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 5270)
  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                   :: 523x
            Sequencing Technology :: MGI DNBSEQ-G400RS; ONT MinION Mk1c
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_036506655.1-RS_2024_04_04
            Annotation Date                   :: 04/04/2024 00:01:59
            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)                     :: 4,921
            CDSs (total)                      :: 4,796
            Genes (coding)                    :: 4,564
            CDSs (with protein)               :: 4,564
            Genes (RNA)                       :: 125
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 232
            CDSs (without protein)            :: 232
            Pseudo Genes (ambiguous residues) :: 0 of 232
            Pseudo Genes (frameshifted)       :: 61 of 232
            Pseudo Genes (incomplete)         :: 163 of 232
            Pseudo Genes (internal stop)      :: 47 of 232
            Pseudo Genes (multiple problems)  :: 36 of 232
            Pseudo Genes (short protein)      :: 4 of 232
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP027860.1.
            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..5270
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="2017-19-1CC"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p2017-19-1CC_6"
                     /geo_loc_name="Viet Nam:Thai Binh"
                     /collection_date="2017"
     gene            175..693
                     /locus_tag="AABJ85_RS24480"
                     /old_locus_tag="VEE77_47250"
     CDS             175..693
                     /locus_tag="AABJ85_RS24480"
                     /old_locus_tag="VEE77_47250"
                     /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="MbeB family mobilization protein"
                     /protein_id="WP_001749510.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFRKLGESVSEAVTSNE
                     TKIRDAIALFTASTEKSLEKHREGVKEAMMQHRKDVLKLAGNTGMMLLGIVFLLFTASG
                     GTLWYLGGRIQTNLEEIRKQEETLQKLNAKTWGVEFVQDGNRKFLVLPYGKSAEVIPFQ
                     GKEWVHLKE"
                     /name="MbeB family mobilization protein"
     gene            700..933
                     /locus_tag="AABJ85_RS24485"
                     /old_locus_tag="VEE77_47260"
     CDS             700..933
                     /locus_tag="AABJ85_RS24485"
                     /old_locus_tag="VEE77_47260"
                     /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_004026237.1"
                     /translation="MTELEIHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSEQTERLSQLYSENWR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            1333..1977
                     /locus_tag="AABJ85_RS24490"
                     /old_locus_tag="VEE77_47270"
     CDS             1333..1977
                     /locus_tag="AABJ85_RS24490"
                     /old_locus_tag="VEE77_47270"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001529705.1"
                     /GO_function="GO:0004518 - nuclease activity [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Eco29kI family restriction endonuclease"
                     /protein_id="WP_011017202.1"
                     /translation="MHNKKFDRSEHVYRNDSFLELIKDAVRFFSGTPVHSLPPPERFQG
                     AGVYALYYTGHYSLYDEYSRINRLAYNLPIYVGKAVPAGWRQSRISDHETRAGSELSNR
                     IREHSRNIAKTSNLNLCDFSCRFVIFEATGSDMISTVEAALIKIYKPLWNTVVDGFGNH
                     TPGAGRFAQAKSDWDVIHPGREWAEKCTGVHSEPYFIEERIKQYFSKSNFT"
                     /name="Eco29kI family restriction endonuclease"
     gene            1977..3125
                     /locus_tag="AABJ85_RS24495"
                     /old_locus_tag="VEE77_47280"
     CDS             1977..3125
                     /locus_tag="AABJ85_RS24495"
                     /old_locus_tag="VEE77_47280"
                     /EC_number="2.1.1.37"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001529706.1"
                     /GO_function="GO:0003886 - DNA
                     (cytosine-5-)-methyltransferase activity [Evidence IEA];
                     GO:0008168 - methyltransferase activity [Evidence IEA];
                     GO:1904047 - S-adenosyl-L-methionine binding [Evidence
                     IEA]"
                     /GO_process="GO:0006304 - DNA modification [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DNA cytosine methyltransferase"
                     /protein_id="WP_040088069.1"
                     /translation="MRSLEIFSGAGGLAKGLELAGFQHVGFVELNKHACDSLRLNFDEE
                     KVFQGDIKNYDLSSIDKIDIVAGGPPCQPFSLGGKHKAHDDSRDMFPFAIKAIEVLQPK
                     AFIFENVKGLLRKSFADYFEYIILRLTYPCLSLSNVGDWRIHLDALRKARKDKHCGCTY
                     DVSFKLINAADYGVPQIRERVIIVGVRSDLNKKWSFPSVTHTQEKLLWEQHVTGDYWRK
                     HNIDAVIDKGISERLMKRFGIFPPSGKSWVTVRDALKNVPQPYESHGIGDHIFKDGARV
                     YPGHTGSYIDLPSKTLKAGAHGVPGGENMIRYEDGTVRYFTVYEGKLLQTFPREFLIAG
                     AWGEAMRQIGNAVPVLLAQKIGQQLYNLLNEEVEPLLCSNFN"
                     /name="DNA cytosine methyltransferase"
     gene            complement(3361..3519)
                     /locus_tag="AABJ85_RS24500"
     CDS             complement(3361..3519)
                     /locus_tag="AABJ85_RS24500"
                     /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_071791734.1"
                     /translation="MHEPPVQPDCCALPGNYRLESNPVRHALTPLAAAIGNWTRWIEIL
                     RVLEVVA"
                     /name="replication initiation protein"
     gene            complement(4189..4380)
                     /locus_tag="AABJ85_RS24505"
                     /old_locus_tag="VEE77_47290"
     CDS             complement(4189..4380)
                     /locus_tag="AABJ85_RS24505"
                     /old_locus_tag="VEE77_47290"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /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_000165985.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            4429..4767
                     /locus_tag="AABJ85_RS24510"
                     /old_locus_tag="VEE77_47300"
     CDS             4429..4767
                     /locus_tag="AABJ85_RS24510"
                     /old_locus_tag="VEE77_47300"
                     /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"
     Typing          4019..4104
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="8.58e-38"
     Typing          complement(3448..3993)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.526"
                     /coverage="98.0"
                     /evalue="0.0"
     Typing          7..1037
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="94.872"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          4758..5269
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="99.0"
                     /evalue="1.77e-108"
ORIGIN
        1 agagcgttac acgcggtata gacgcacttt accatgccgg agagataaaa ggccgtcagg
       61 atgtgattca ggcgctcaca gaggcggggc ttgaagtggt cagggtgacg cgaagcagta
      121 tcagcatttc agacccgaac ggcgggaaga atatcaggct gaaaggagca ttttatgagc
      181 aatcttttac agacgggcgc ggagttcgag aaaaagctga aagagagagc cgaatctaca
      241 gagaaaatgc tgaacgacga gttcaggaag ctcggcgagt ctgtcagcga ggctgtgacc
      301 tcaaacgaga cgaaaatcag agacgctata gccctgttca cagcctcgac agagaaatcg
      361 ctggaaaaac accgagaagg ggtgaaagag gcgatgatgc agcacaggaa ggacgtgtta
      421 aagctggcag ggaatacggg catgatgtta ctggggatag tctttctcct gtttaccgcg
      481 agtggcggga cgctctggta tcttggcgga cggatacaga cgaacctgga agaaatcagg
      541 aagcaggaag agacattgca gaaactgaac gcgaagacat ggggcgtgga gtttgtgcag
      601 gacgggaaca ggaaattcct tgtccttccg tacgggaaat cagcggaggt gattcccttt
      661 caggggaaag agtgggtaca tctgaaggag tgacacagag tgacagagct ggaaatacat
      721 ttgctgaacg ccttagagca gctgcaacag gactatatgc agcggctgag cgaatgggag
      781 agcgccttcg tggaattgca gaagatgttt tcgcttacgc aacgggacaa cgcgatgctg
      841 aacgagcggg tcatgcagtt gagtcagcag gtgcagcact tgagcgagca gacagaacgc
      901 ttgagccagt tatacagcga gaactggaga taagagagga acggctgata caggagcgcg
      961 aacatgcgtt atccctggaa cgggagcgtc agccggaaat acaggaacgc acgctggatg
     1021 gtccttcgct gggatggtga aaccatgaaa aatggcagct tcagtggatt aagaggggtt
     1081 aatgtggcct gtaccatctg gttgcatagg tattcatgcg gttaaaattt atcaggcgcg
     1141 atcgcggcag tttttcgggt ggtttgttgc catttttacc tgtctgctgc cgtgatcgcg
     1201 ctgaacgcgt tttagcggtg cgcgtaatga ggcgttatgg taaatgcgta tggttttggg
     1261 tatcagcttt atgatcgtat cataggtgat gttgagtagg agtgttaata taaaaacctt
     1321 tcggaaaaca taatgcacaa taagaaattt gatagatctg agcatgttta tagaaatgac
     1381 tctttcctag agttaataaa agatgccgtt cgttttttta gtggtacgcc tgttcattca
     1441 ttaccaccac cggaacggtt tcaaggtgct ggggtgtatg ctctttacta tacagggcat
     1501 tattcattat atgatgaata ctctcgtata aataggttgg catataacct tcctatttat
     1561 gttggcaagg ctgttcctgc tggttggcgt cagtctagaa ttagtgatca tgaaactagg
     1621 gctggttctg aactatctaa tagaattaga gaacatagcc gaaatatagc aaaaacatcg
     1681 aatctaaatt tgtgtgattt ttcatgtcgc tttgttatat ttgaggctac ggggtctgat
     1741 atgattagta cagttgaggc cgctcttatt aaaatttata agcctttgtg gaatacagtt
     1801 gttgatggct ttggaaatca tacccctggt gccgggcgat ttgcgcaagc taaatctgat
     1861 tgggatgtaa tacatcctgg cagggagtgg gctgagaaat gtacaggtgt tcattctgag
     1921 ccatacttta ttgaggagag aattaaacag tatttttcta agagtaattt tacataatga
     1981 gatcattaga gattttttca ggagccggcg gtttggctaa aggtctagag ttggcaggat
     2041 ttcagcatgt aggatttgtt gagttaaaca agcatgcatg tgattctttg cgacttaatt
     2101 ttgatgagga gaaggtattt cagggagata ttaaaaatta tgacctttca tctatagata
     2161 aaatagatat tgttgctggc gggcctccct gccaaccatt ttcattgggc ggaaaacata
     2221 aagctcatga tgactctagg gatatgttcc catttgcaat aaaagcaatt gaagtattgc
     2281 aaccaaaagc ttttattttt gaaaatgtta aagggttgct tagaaaatca tttgcggatt
     2341 attttgaata cataattctt cgtttgactt atccttgttt atcgttaagt aatgtaggtg
     2401 attggagaat acatctagat gcattaagaa aagctcgcaa ggataaacac tgtgggtgta
     2461 catatgatgt cagttttaaa ttgatcaatg cagctgatta tggagttcca caaattaggg
     2521 aacgggtcat aattgttggt gttcgaagtg atttgaataa aaaatggtct tttccaagcg
     2581 taacgcatac tcaagaaaaa ttactgtggg aacagcatgt tactggtgac tattggcgaa
     2641 agcataatat tgatgcggtt atagataaag gtatttctga gcgtttaatg aaacgttttg
     2701 gtattttccc cccatcgggg aaaagctggg ttactgttag ggacgcatta aagaatgttc
     2761 ctcaaccata tgagtcacat ggtattggag atcatatctt taaagatggc gctcgagttt
     2821 atcctggtca tactggaagt tatatcgatt tgccttcaaa aacacttaag gctggcgctc
     2881 atggcgtacc tggaggtgaa aatatgatta ggtatgagga tgggactgtt cgttatttta
     2941 cggtttatga agggaagctt cttcagactt ttcctcgaga gtttctgatt gcaggagctt
     3001 ggggggaggc tatgaggcag attggtaatg cagttcctgt gttgctagct cagaagatag
     3061 gacagcaatt gtataactta ttgaatgaag aggttgagcc tttattgtgc tctaacttca
     3121 attaaaagtt tgtgtctcta tggtggtgat acagccatag aggcaatttg caaaaaaaga
     3181 tcaaaggatc ttcttgagat cctttttttc tgcgcgtaat ctgctgcctg taaacaaaaa
     3241 aaccaccgct accaacggtg gttcgtttgc cggaatcaag agctaccaac tctttttccc
     3301 gaaggtaact ggcttggtgg agcgcagata ccaaatactg tccttctagt gtagcctcag
     3361 ttaggccacc acttcaagaa ctcttaatat ctcaatccac cttgtccagt taccaatggc
     3421 tgctgccagt ggcgttaagg cgtgtcttac cgggttggac tcaagacgat agttaccggg
     3481 caaggcgcag cagtcgggct gaacgggggg ttcgtgcaca cagcccagct tggagcgaac
     3541 gacctacacc gaactgagat accaacagcg tgagctatga gaaagcgcca cgcttcccga
     3601 agggagaaag gcggacaggt atccggtaag cggcagggtc ggaacaggag agcgcacgag
     3661 ggagcttcca gggggaaacg cctggtatct ttatagtcct gtcgggtttc gccacctctg
     3721 acttgagcat ctgtttttgt gatgctcgtc aggggggcgg agcctatgga aaaacgccag
     3781 cggcgcggcc ttcttcctgt tcctggcctt ttgctcacat gtttcttttg gcgttatccc
     3841 ctgattctgt ggataaccgc atcaccgtct ttgagtgagc tgataccgct cgccgcagcc
     3901 gaacgaccga gcgtagcgag tcagtgagcg aggaagcgga agagcgcctg atgcggcatt
     3961 ttctccttac gcatctgtgc ggtatttcac accgtatatg gtgctctttt cttattatct
     4021 gcactgatgc cgcatggtta agccagtata cactccgcta tcgctacgtg actgggtcag
     4081 ggctgcgccc cgacacccgc taaaacctgc tgacgcgccc tgacgggctt gtctgctccc
     4141 ggcatccgct cacagacaag ctgtgaccgt ctccgggagc tgcatgtgtc agaggttttc
     4201 accgtcatcc ccgaaacgtg cgaggcagct gcggtaaagc tcatcggcgt ggtcgtgaag
     4261 cgattcacag atgtctgcct gttcatccgc gtccagttcg ttgagctttt ccagcagcgt
     4321 taatgtctgg cttctgataa agcgcgccat gttaagggct gttttttcct gtttagtcac
     4381 tgatgcctcc gtgtaagggg gatttctgtt catggggtaa tgataccgat gaaacgcgag
     4441 aggatgctca cgatacgggt tactgatgat gaacatgcca ggttacttga acgctgtgag
     4501 ggtaaacaac tggcggtatg gatgcggcgg gtctgcctgg gtgagccggt tgcccgttcc
     4561 gggaaactgc cgacactggc accgccgtta ctgcgtcagc tggccgccat cggaaataac
     4621 ctgaatcaga cagcccgtaa ggtgaacagc gggcagtggt cttccggtga ccgggttcag
     4681 gtagtggccg cactgatggc catcggggat gagctgcgcc ggctgcgtct ggccgtcagg
     4741 gaacaggggg cgcgggatga tagttaaatt tcatgccagg ggaaaaggtg gtggcagtgg
     4801 tccggttgat tacctgctgg ggagggagcg taaccgcgaa ggcgcaacgg tgcttcaggg
     4861 taatccggaa gaagtccggg aactcatcga tgccacgcca tttgcgaaga aatacacgtc
     4921 cggtgttctg tcgttcgcgg agaaggagct gccgccggga ggacgtgaaa aagtgatggc
     4981 gagctttgag cgtgtactga tgcccggtct cgaaaaaaat cagtacagca tcctgtgggt
     5041 ggagcaccag gacaagggac ggcttgagct gaattttgtc attccgaaca tggagctaca
     5101 gaccggaaaa cgtctccagc cgtactacga ccgcgcagac aggccgagaa ttgatgcctg
     5161 gcagacgctg gtgaatcacc attacggact gcatgacccc aacgccccgg agaaccgccg
     5221 gacgctgacc cttcctgata acctgccgga aacgaaacag gcacttgctg
//
