LOCUS       NZ_AP027575             3372 bp    DNA     circular CON 04-APR-2024
DEFINITION  Escherichia coli strain LR-60 plasmid pLR-60_5, complete sequence.
ACCESSION   NZ_AP027575
VERSION     NZ_AP027575.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00562497
            Assembly: GCF_036497705.1
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  JOURNAL   Unpublished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 3372)
  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                   :: 107x
            Sequencing Technology :: MGI DNBSEQ-G400RS; ONT MinION Mk1c
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_036497705.1-RS_2024_04_04
            Annotation Date                   :: 04/04/2024 00:03:11
            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)                     :: 5,132
            CDSs (total)                      :: 5,013
            Genes (coding)                    :: 4,860
            CDSs (with protein)               :: 4,860
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 92
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 153
            CDSs (without protein)            :: 153
            Pseudo Genes (ambiguous residues) :: 0 of 153
            Pseudo Genes (frameshifted)       :: 59 of 153
            Pseudo Genes (incomplete)         :: 102 of 153
            Pseudo Genes (internal stop)      :: 30 of 153
            Pseudo Genes (multiple problems)  :: 34 of 153
            Pseudo Genes (short protein)      :: 4 of 153
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP027575.1.
            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..3372
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="LR-60"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pLR-60_5"
                     /geo_loc_name="Ecuador:Santo Domingo"
                     /collection_date="2019"
     gene            complement(896..1129)
                     /locus_tag="AABJ89_RS25640"
                     /old_locus_tag="VEE03_49150"
     CDS             complement(896..1129)
                     /locus_tag="AABJ89_RS25640"
                     /old_locus_tag="VEE03_49150"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137389.1"
                     /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_000137389.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHEVTQRNNA
                     ILNERVVILSQQVQRLAGQVDRLSRLFIANNS"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(1136..1696)
                     /locus_tag="AABJ89_RS25645"
                     /old_locus_tag="VEE03_49160"
     CDS             complement(1136..1696)
                     /locus_tag="AABJ89_RS25645"
                     /old_locus_tag="VEE03_49160"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000067488.1"
                     /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_000067487.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKKQLDTLSTTVSMQFSTTEAELSRQQKKLLWRVIKGRILFPALTA
                     LSVTGGIFLGCWGLMEWQESKIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            complement(<1728..2384)
                     /locus_tag="AABJ89_RS25650"
                     /pseudo=""
     CDS             complement(<1728..2384)
                     /locus_tag="AABJ89_RS25650"
                     /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(2374..2697)
                     /locus_tag="AABJ89_RS25655"
                     /old_locus_tag="VEE03_49170"
     CDS             complement(2374..2697)
                     /locus_tag="AABJ89_RS25655"
                     /old_locus_tag="VEE03_49170"
                     /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_024132211.1"
                     /translation="MLTIRVTDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     SPPLLRHLAAIGNNLNQTARKVNSGQWSSIDRVHVVAALMAIEGELRQLRQAVREQGVR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2761..2952
                     /locus_tag="AABJ89_RS25660"
                     /old_locus_tag="VEE03_49180"
     CDS             2761..2952
                     /locus_tag="AABJ89_RS25660"
                     /old_locus_tag="VEE03_49180"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165979.1"
                     /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_000165979.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNDLDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(3034..3114)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="87.805"
                     /coverage="93.0"
                     /evalue="8.68e-18"
     Typing          complement(814..2384)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.817"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 acatgggatc gtgcgatatg ccggatggtg aaaggttgga gggaacggca acaactcacc
       61 cctcccagtg aagggacggg tagtttgccg ctctcgatat gccggacgga gccaaggcca
      121 tcgatcacgg ggcgcgtcag tggaagaacc cgcgcctgcg tgacgtatgc gtcttcgccg
      181 caccatctca cccgtcacgc caccacatac cgggaactgc cgccaaggtc taactcaacc
      241 aatctagccg cgctacatac ggtttttgtg gcaactcatc aggtgtccgc tgtcgatgaa
      301 actctctgcg ccggtagcgg aactctcacg cgtgcggtcg ccgtcgtcac agctccccca
      361 accgcaaacg attctcgcaa atacgcaagt atctgcaaaa acaggttttt ttcggggttc
      421 ctgggagact gtgctgttga aaaattcttg aagaatacag aaggctcatg caaactgaat
      481 gaactggttt ctgttgtgga tctcaacagt ttccacagga acattgagga ggtcagagac
      541 ctcaatgaac ccgaaacagc tcgccttcct ggcgagctgt tttcgttcta cgcccgccga
      601 cgaaagatcg caagtgcaat aacgagattt ttcacgtctt tacgctcaaa aagtaaaaaa
      661 accatgtttt cccctggctg aatccccaaa aacgcgtgaa atgcgttttc aggatgttgc
      721 atagctatgc acaaatacgg cacacgattt gtttcgctcg ccccagccgt cgaactggtc
      781 aaaatggcaa gatttcgtca cttccccggt cacatctcca ttgatggccc actccgaacc
      841 cgtgccgcgc gttcctgtac ctcatgtctg taccgggcac gctcctgttc atcccttagc
      901 tgttgttcgc gataaataac cgactcaagc gatccacttg cccggctaat ctctgcacct
      961 gctgactcaa tatcacgacg cgctcgttca gtatcgcgtt gttccgttgc gtaacctcgt
     1021 gcatcttctg caattccgcg aaggcgctct cccactcgtt cagccgccgc atatagtcct
     1081 gttgcaaatg ctctaaggcg ttcagcaaat gcccttccag ttccgtcata ctcgtttact
     1141 ccctgaccag cctcacggcg ttcttgtcgc ccaccgtcca ggtgttttcc cctttcaccc
     1201 cgtccggcaa caccagaaat ttcccgttct cgccattgac gaacgtcacc ccccaggttt
     1261 ttgcctcgag tttcgccagc gtgttttcct gctctctgat agtcaggata tttttcgcaa
     1321 tcttgctttc ctgccactcc atcagccccc agcaccccag gaaaatgccg cccgtgacgc
     1381 tgagcgcggt cagcgccgga aacagtatcc gccctttgat cacccgccag agcagttttt
     1441 tctgctgccg ggacagttcg gcctctgtgg tgctgaactg catgctcacg gtggtgctca
     1501 gcgtatccag ttgctttttc acggatgttg tatgttcgct gatagcgtct ctgattttct
     1561 gcctgtttaa gctcaatgcc ttgtctacag actcttcgag cttcctgaac tcgctgttca
     1621 gcatgttctc ggtagaagcg gctcgctctt tcagtttctt ctcgaagtct gttcccattt
     1681 gtaaaagatt gctcatacag cgcccccttt agcctgagat tccgcccccc ctccgggtcg
     1741 gcaatactga tgctgctttt ggttgtcctc accacctcaa aacctgccgc tgtaagcgcc
     1801 tctgtgacat cctgacgcgt ttttattgct ccggcatggt aaagagcctc aagaccccgt
     1861 gtaatcgctt ctgcggcctc ctgtttcgct tttggcagat tatttggcgt gacaagcgtc
     1921 cgtctgttct ccggtgcgtt cgggtcacgc agcccgtaat gatgattaac cagcgtctgc
     1981 caggcattta tcctcggcct gtccgcgcgg tcgtagtacg gctggaggcg cttaccgctc
     2041 tgtagctcca tgttcgggat gacaaaattc agttcgagcc gccccttatc ctggtgttcc
     2101 acccagagaa tgctgtactg gtctttttcg agaccgggca taagaacacg ctcaaagctc
     2161 gtcatcactc tttcgcgttc acccggcggt aactccttct ccgcgaacga cagaacgcct
     2221 gaagtgtatt tcttcgagaa tggcgtggaa tcaatgagtt cccgcacttc ttccgggtta
     2281 ccccggagca ccgttgcgcc ttcgcggtta cgctcccgcc ccagcaggta atcgaccggg
     2341 ccacttccac cgcctttccc cctggcatga aatttaacta tcatcccgta ccccctgttc
     2401 cctgacagcc tgccgcaact ggcgcaattc accctcgatg gccatcagtg cggccaccac
     2461 atgaacccgg tcaatcgaag accactggcc gctgttcacc ttccgggctg tctggttcag
     2521 gttgttcccg atggcagcca gatgccgcag caatggcggc gatagtgtcg gcagttttcc
     2581 tgtgcgtgca accggctccc ccagacagac ccgccgcatc cattccgcca gccgtttacc
     2641 ctcgcagcgt tccagtaacc gggcgtgctc ctcatcggta acccgtatcg tgagcatctt
     2701 ctcgcgtttc atcggtatca ttccccctaa caaatccccc atacaaggag ccttaagacc
     2761 atgaccaaac aggaaaaaac agcccttaac atggctcgct ttatcagaag ccagacgcta
     2821 accctgctgg aaaaactcaa cgatctggac gcggacgaac aggcagacat ctgcgaatca
     2881 cttcacgacc acgccgacga actctaccgc agttgcctcg cacgcttcgg cgatgacggt
     2941 gaaagcaact gaaacatgca gctcccggag acgttcacag cttgcctgtg agcggatgcc
     3001 gggagcagac aagcccgcca gggcgcgtca gtgcgggtgt cggggcgcag ccctgaccca
     3061 gttcacagag cgatagcgat gtgtatactg gcttatctca ttttgcatcg gtgcagacat
     3121 ggatgggaag tgcaccatgt caggagtaaa aagccgcaca gatgtaaaaa cagcgcaccc
     3181 gataaacagc acacacgcgg acactggcac aggcgcgtaa gtgcacaatg cttgcatctg
     3241 tgactcttcc gcttcctcgc ccactcgctc actacgttcg gtcgctgggg ctgcggcgag
     3301 cggtgggatc actctcgttg tgatgcagat ccgttttttt ttttgcactg gagttatcag
     3361 gagttgcggt gc
//
