LOCUS       NZ_AP027582             5423 bp    DNA     circular CON 04-APR-2024
DEFINITION  Escherichia coli strain LR-62-2 plasmid pLR-62-2_6, complete
            sequence.
ACCESSION   NZ_AP027582
VERSION     NZ_AP027582.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00562545
            Assembly: GCF_036497865.1
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  JOURNAL   Unpublished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 5423)
  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                   :: 39x
            Sequencing Technology :: MGI DNBSEQ-G400RS; ONT MinION Mk1c
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_036497865.1-RS_2024_04_04
            Annotation Date                   :: 04/04/2024 00:18:12
            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)                     :: 5,347
            CDSs (total)                      :: 5,231
            Genes (coding)                    :: 5,030
            CDSs (with protein)               :: 5,030
            Genes (RNA)                       :: 116
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 201
            CDSs (without protein)            :: 201
            Pseudo Genes (ambiguous residues) :: 0 of 201
            Pseudo Genes (frameshifted)       :: 69 of 201
            Pseudo Genes (incomplete)         :: 137 of 201
            Pseudo Genes (internal stop)      :: 35 of 201
            Pseudo Genes (multiple problems)  :: 39 of 201
            Pseudo Genes (short protein)      :: 4 of 201
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP027582.1.
            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..5423
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="LR-62-2"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pLR-62-2_6"
                     /geo_loc_name="Ecuador:Santo Domingo"
                     /collection_date="2019"
     gene            37..195
                     /locus_tag="AABK23_RS26600"
     CDS             37..195
                     /locus_tag="AABK23_RS26600"
                     /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_071529495.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDKAPLAAATGNWTRWIEIL
                     RVLEVVA"
                     /name="replication initiation protein"
     gene            complement(509..1312)
                     /locus_tag="AABK23_RS26605"
                     /old_locus_tag="VEE29_50930"
     CDS             complement(509..1312)
                     /locus_tag="AABK23_RS26605"
                     /old_locus_tag="VEE29_50930"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000510993.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000510993.1"
                     /translation="MGIFSQIGSALLNCISKPVDALCEWAKEPLKDREYRREEASKESE
                     HKRNMDVLTAKKRVEHELRMSELNAEYELREKEKTLEVDLEVRRVREIEKAVAEIQEWR
                     KSQELERMERTTAAIARYKEQLTKLNIEVINSIGNMQLDLKERAQKFVYEKAVQYKRLQ
                     DEATEEAMNDLIRIEEKFGDNERAKDILIRAVDTKMGNVIDTSTRFLEELNRDIVSLNQ
                     SIDRLTNQGQKFIESHLERFHIVDATSSLYITGDEKERLLLKNIN"
                     /name="hypothetical protein"
     gene            complement(1299..1775)
                     /locus_tag="AABK23_RS26610"
                     /old_locus_tag="VEE29_50940"
     CDS             complement(1299..1775)
                     /locus_tag="AABK23_RS26610"
                     /old_locus_tag="VEE29_50940"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000897048.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_252099277.1"
                     /translation="MNDFKLSSSELPEILAALREARECLVSRSINEDPQLYSALFLYEK
                     NEGLLSLSFEREYSIFINSNLECILRKVSDIKDKKQGKLQKIMNEFVRFKYSSSDSCAD
                     LLFLSGKLEQIRKIYEVFDRDRNRLEFLNYMMKKERVIFEREFERLLGEKNGDF"
                     /name="hypothetical protein"
     gene            complement(1841..2452)
                     /locus_tag="AABK23_RS26615"
                     /old_locus_tag="VEE29_50950"
     CDS             complement(1841..2452)
                     /locus_tag="AABK23_RS26615"
                     /old_locus_tag="VEE29_50950"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000130481.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000130481.1"
                     /translation="MTDKTTDIKMALENMIRFRDTIERLGGSMAKEFDVETKGKRTYSM
                     NNDMSDLYNVISRAVEASGADHSINEKLTNVLKRELVDYVSIAHLKTKLSVLYEFEKNY
                     LQLIAEYKEEIKFASSLQEDLRKERAKFFSETLKEVHQTLNESQVDNEVASKWIKELVG
                     SYTKSLDLSGGLVEEHTLDTIACIRAEAKLNKPSIEPGNN"
                     /name="hypothetical protein"
     gene            complement(2785..3018)
                     /locus_tag="AABK23_RS26620"
                     /old_locus_tag="VEE29_50960"
     CDS             complement(2785..3018)
                     /locus_tag="AABK23_RS26620"
                     /old_locus_tag="VEE29_50960"
                     /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_000137438.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWESAFVELQKMFSLTQRDNA
                     MLNEQVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(3025..3543)
                     /locus_tag="AABK23_RS26625"
                     /old_locus_tag="VEE29_50970"
     CDS             complement(3025..3543)
                     /locus_tag="AABK23_RS26625"
                     /old_locus_tag="VEE29_50970"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001447511.1"
                     /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_087451033.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTETMLNDEFSKLEKSVSKAVTSNE
                     TKIKDAIALFTTSTEESLEKHREGVKEAMMQHRKDVLKLAGNTGMMLLGMVIFLFTVSG
                     GTLWYLGGRIQANLEEIRIQEETLQKLNAKTWGVEFVQDGRRKFLVIPQGKSATVIPYQ
                     GKDWVQLTE"
                     /name="MbeB family mobilization protein"
     gene            complement(<3581..4243)
                     /locus_tag="AABK23_RS26630"
                     /pseudo=""
     CDS             complement(<3581..4243)
                     /locus_tag="AABK23_RS26630"
                     /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            complement(4221..4544)
                     /locus_tag="AABK23_RS26635"
                     /old_locus_tag="VEE29_50980"
     CDS             complement(4221..4544)
                     /locus_tag="AABK23_RS26635"
                     /old_locus_tag="VEE29_50980"
                     /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_000955989.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRICLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIERELRSLRQVVREHGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            4609..4800
                     /locus_tag="AABK23_RS26640"
                     /old_locus_tag="VEE29_50990"
     CDS             4609..4800
                     /locus_tag="AABK23_RS26640"
                     /old_locus_tag="VEE29_50990"
                     /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_000165990.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGGDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(4879..4963)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.674"
                     /coverage="100.0"
                     /evalue="6.569999999999999e-34"
     Typing          5..146
                     /name="rep_cluster_2370"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="97.203"
                     /coverage="94.0"
                     /evalue="2.03e-61"
     Typing          4987..5423
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.85"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(2682..4231)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="90.267"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 agttcggtgt aggtcgttcg ctccaagctg ggctgtgtgc acgaaccccc cgttcagccc
       61 gaccgctgcg ccttatccgg taactatcgt cttgagtcca acccggtaag acacgacaaa
      121 gcgccactgg cagcagccac tggtaactgg acaaggtgga ttgagatatt aagagttctt
      181 gaagtggtgg cctaactgcg gctacactag aaggacagta tttggtatct gtgctccacc
      241 aagccagtta ccttcggaag aaagagttgg tagctctaga ttccggcaaa caaaccaccg
      301 ttggtagcgg tggttttttt gtttacaggc agcagattac gcgcagaaaa aaaggatcac
      361 aagaggatcc ttgaatcttt tcactcccac tcccaggtca tagccatagc gctcagtttt
      421 caaccacaag acaaaaacta atgattagca accgcaagaa caaacaatgc gaccattaaa
      481 aataatgatc gctattactc acaaaatact aattaatatt tttcagcaac aatcgttctt
      541 tctcatcacc tgtaatatat aaagaagatg tcgcatcaac aatatgaaaa cgctccaaat
      601 gactttcaat gaatttttgt ccttgattag tcagcctatc aatactttgg tttaaactaa
      661 caatatctct atttaattct tccaaaaacc gagttgacgt atcaataaca ttccccatct
      721 tagtatcaac tgcacgaatt aaaatatctt tagctctttc attatcacca aacttttcct
      781 caatccttat aagatcattc atagcctctt cagttgcttc atcttgcagg cgcttatatt
      841 gtacagcttt ctcatagaca aatttctgtg cgcgctcctt taaatcaagc tgcatgttcc
      901 caatagagtt aatcacttct atatttaatt tcgttaattg ctccttgtaa cgtgcaatag
      961 ctgctgttgt tcgctccatc ctctcaagtt cctgtgactt tctccattcc tggatctcag
     1021 ctactgcttt ttctatttcg cgaacgcgac gaacctctag atcaacttca agagttttct
     1081 ctttttctct cagctcatat tcagcattca attcactcat tctgagttca tgttcaacac
     1141 gtttcttggc cgtcaagaca tccatgttgc gcttatgttc agactccttt gaagcctcct
     1201 ctcttctata ttccctatct ttcaatggtt ctttagccca ttcacagagt gcatcaacag
     1261 gcttactaat acaattaagc aaagcgctac caatctgact aaaaatcccc atttttttca
     1321 cctaaaagcc gttcaaactc tctttcaaaa ataacacgtt ctttcttcat catatagtta
     1381 agaaattcaa gtctatttct atccctatca aagacttcat atattttacg tatctgttca
     1441 agtttaccac tcaaaaacaa aagatccgca caagaatcgc tgcttgaata tttaaacctc
     1501 acaaattcat tcattatttt ttgcagttta ccctgctttt tatcttttat atcagaaact
     1561 ttcctcaata tgcactctaa attggagtta ataaaaatag agtattctct ctcaaatgaa
     1621 agacttagca acccttcatt tttttcatat aaaaataatg ccgaatataa ctgaggatct
     1681 tcattgatgc tgcgcgatac aaggcattcc cttgcctctc gtaaagcagc caatatctca
     1741 ggaagttccg acgaagacaa tttaaagtca ttcactttac gttctaatat agccacaaga
     1801 acataaagca aactatttat atgtctaccc ccggccataa ttagttattg cccggctcaa
     1861 tagatggttt atttaattta gcctcagcgc gaatacaagc aattgtatct aatgtatgct
     1921 cttcaacaag gcctccgctt agatccaagc ttttggtata actaccaaca agttctttaa
     1981 tccattttga tgccacttca ttatcaactt gagattcatt tagagtttga tgaacctctt
     2041 ttaatgtctc agaaaagaat ttagcacgtt ctttacgtaa atcctcttgc aaagaggaag
     2101 caaattttat ttcttcctta tattctgcga taagctgcaa ataattcttt tcaaactcat
     2161 ataatacaga caatttggtt tttagatgcg caatgctgac ataatcaact aattctcttt
     2221 tcaagacatt tgtcaatttt tcattaattg aatgatcggc accagacgct tcaacagccc
     2281 gtgatattac attatataaa tcactcatat cgttattcat agaataagta cgttttcctt
     2341 tggtctcaac atcaaactct ttcgccatag aacctcccaa tctctctata gtgtcacgaa
     2401 atctgatcat gttttctaaa gccattttaa tatcggtcgt tttatctgtc atgacttagg
     2461 cctaactcat ctatttacca taacgtcgca ttacgcgcac cgctaaaacg cgttcagcgc
     2521 gatcacggca gcagacaggt aaaaatggca acaaaccacc cgaaaaactg ccgcgatcgc
     2581 gcctgataaa ttttaaccgc atgaatacct atgcaaccag atggtacaga ccacattagc
     2641 ccgtcttaat ccacttaacc tgccattttt catagtttca ccatcccagt gaaggaccat
     2701 ccagtgtgcg ttcctgtatt tccagctggc gttcccgctc cagggataac tcatgttcgc
     2761 gttcctgtat cagccgttcg tcccttatct cctgttctcg ctgtataact ggctcaagcg
     2821 ttctgtccgc tcgctcaagt gctgcacctg ctgactcaac tgcatgacct gctcgttcag
     2881 catcgcgttg tcccgttgcg taagcgaaaa cattttctgc aattccacga aggcgctctc
     2941 ccattcgttc agccgctgca tatagtcctg ttgcagttgc tctaatgcgt tcagcaaatg
     3001 tctttccagc tccgtcactc tgtgtcactc cgtcagttgt acccagtcct tcccctgata
     3061 gggaatcacc gttgccgatt tcccctgcgg gatgaccaga aatttccttc tcccgtcctg
     3121 cacaaactcc acgccccatg tcttcgcgtt cagtttctgc aatgtttctt cctgtatcct
     3181 gatttcttcc aggttcgcct gtatccgccc gccaagatac cagagcgtcc cgccactcac
     3241 ggtaaacagg aaaatgacca tccccagtaa catcatgccc gtattccctg ccagctttaa
     3301 cacgtccttc ctgtgctgca tcatcgcctc tttcacccct tcccggtgtt tttccagcga
     3361 ttcctctgtc gacgttgtga acagggctat agcgtctttg attttcgtct cgtttgaggt
     3421 cacagccttg cttacagatt tttcgagctt gctgaactcg tcgttcagca ttgtctctgt
     3481 agattcggct ctctctttca gctttttctc gaactccgcg cccgtctgta aaagattgct
     3541 cataaaatgc tcctttcagc ctgatattct tcccaccgtt cgggtctgca atgctgatac
     3601 tgcttcgcgt caccctgacc acttcaagcc ccgcctctgt gagcgcctga atcacatcct
     3661 gacggccttt tatctccccg acatgataaa gagcgtctat cccgcgtgtg acgctctcag
     3721 caagcgcctg tttcgtttcc ggcaggttat cagagagagt cagtatccgg cggttctccg
     3781 gggcgttggg gtcatgcagc ccgtaatggt gattcaccag tgtctgccag gcatcaattc
     3841 tcggcctgtc tgcccggtcg tagtacggct ggaggcgttt tccggtctgt agctccatat
     3901 tcggaatgac aaaattcagc tcaagccgtc ccttgtcctg gtgctccacc cacaggatgc
     3961 tgtactgatt tttttcgaga ccgggcatca gtacacgctc aaagctcgcc atcacttttt
     4021 cacgccctcc cggcggcagc tccttctccg cgaacgacag aacacctgac gtgtatttct
     4081 tcgcaaatgg cgtggcatcg atgagttccc ggacttcttc cggatcaccc tgaagcaccg
     4141 ttgccccttc ccggttacgc tcccttccca gcaggtaatc aaccggacca ctgccaccgc
     4201 cttttcccct ggcatgaaac ttaactatca tcccgcgctc catgttccct gacgacctgc
     4261 cgtaagctgc gcaactctct ctcgatggcc atcagtgcgg ccaccacctg aacccggtca
     4321 ccggaagacc actgcccgct gttcaccttc ctcgccgtct gattcaggtt attcccgatg
     4381 gcagccagct ggcgcagtaa cggcggtgcc agtgtcggca gcttcccgga acgggcaacc
     4441 ggctcaccca ggcagatccg ccgcatccat accgccagct gtttaccctc acagcgttcc
     4501 agtaaccgtg catgttcatc atcagtaacc cgtatcgtga gcatcctctc gcgtttcatc
     4561 ggtatcatta ccccatgaac agaaatcccc ccttacacgg aggcatcagt gactaaacag
     4621 gaaaaaaccg cccttaacat ggcccgcttt ataagaagcc agacattaac gctgctggag
     4681 aagctcaacg aactggacgc agatgaacag gccgatattt gtgaatcact tcacgaccac
     4741 gccgacgagc tttaccgcag ctgcctcgca cgcttcgggg gtgacggtga aaacctctga
     4801 cacatacagc tcccggagac ggtcacagct tgtctgtgag cggatgccgg gagcagacaa
     4861 gcccgtcagg gcgcgtcagg gggtttcggg gcgaagccct gaaccagtca cgtagcgata
     4921 gcggagtgta tactggctta accatgcggc attagtgcag attgtatgaa aagtgcgcca
     4981 tgccgggtgt gaaatgccgc acagatgcgt aaggagaaaa tgcagcttcc gacgctcttc
     5041 cgcttcctcg ctcactgact cgctacgctc ggtcgttcgg ctgcggcgag cggtatcagc
     5101 tcactcaaag gcggtaataa ggttatccac agaatcaggg gataacgccg gaaagaacat
     5161 gtgcgcaaaa ggcaaaggcc gggagaaagg ccacgccgat ggcgtttttc cataggctcc
     5221 gcccccctga cgagcatcac aaaaatcgac gctcaagtca gaggtggcga aacccgacag
     5281 gactataaag ataccaggcg tttccccctg gaagctccct cgtgcgctct cctgttccga
     5341 ccctgccgct taccggatac ctgtccgcct ttctcccttc gggaagcgtg gcgctttctc
     5401 atagctcacg ctgttggtat ctc
//
