LOCUS       NZ_AP027606             5053 bp    DNA     circular CON 04-APR-2024
DEFINITION  Escherichia coli strain LR-71-1 plasmid pLR-71-1_7, complete
            sequence.
ACCESSION   NZ_AP027606
VERSION     NZ_AP027606.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00562543
            Assembly: GCF_036498465.1
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  JOURNAL   Unpublished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 5053)
  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                   :: 84x
            Sequencing Technology :: MGI DNBSEQ-G400RS; ONT MinION Mk1c
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_036498465.1-RS_2024_04_04
            Annotation Date                   :: 04/04/2024 00:05:36
            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)                     :: 5,144
            CDSs (total)                      :: 5,026
            Genes (coding)                    :: 4,742
            CDSs (with protein)               :: 4,742
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 284
            CDSs (without protein)            :: 284
            Pseudo Genes (ambiguous residues) :: 0 of 284
            Pseudo Genes (frameshifted)       :: 78 of 284
            Pseudo Genes (incomplete)         :: 199 of 284
            Pseudo Genes (internal stop)      :: 46 of 284
            Pseudo Genes (multiple problems)  :: 38 of 284
            Pseudo Genes (short protein)      :: 3 of 284
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP027606.1.
            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..5053
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="LR-71-1"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pLR-71-1_7"
                     /geo_loc_name="Ecuador:Santo Domingo"
                     /collection_date="2019"
     gene            516..839
                     /locus_tag="AABJ98_RS25605"
                     /old_locus_tag="VEE28_49340"
     CDS             516..839
                     /locus_tag="AABJ98_RS25605"
                     /old_locus_tag="VEE28_49340"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /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_023139308.1"
                     /translation="MLTMWVTEDEHRRLLERCDGKQLAAWMRQTCLDEKPARAGKLPSL
                     SPALLRQLAGMGNNLNQIARQVNAGGGSGHDRVQVVAALMAIDAGLERLRHAVLEKDAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1048..>1482
                     /locus_tag="AABJ98_RS25610"
                     /pseudo=""
     CDS             1048..>1482
                     /locus_tag="AABJ98_RS25610"
                     /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            1517..2002
                     /locus_tag="AABJ98_RS25615"
                     /old_locus_tag="VEE28_49360"
     CDS             1517..2002
                     /locus_tag="AABJ98_RS25615"
                     /old_locus_tag="VEE28_49360"
                     /inference="COORDINATES: protein motif:HMM:NF016710.4"
                     /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_023139312.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQSTGEMLKAAFSEHEKSVRAELSESE
                     KRISAAILDHDRKLSSAMSQRTKGMVRMVSQTWLTIVLVSALLTASGASILWWQGQQIL
                     DNYTTIREQKRTQAMLSERNSGVQLSTCGEQRRRCVRVNPEAGRFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            2006..2221
                     /locus_tag="AABJ98_RS25620"
                     /old_locus_tag="VEE28_49370"
     CDS             2006..2221
                     /locus_tag="AABJ98_RS25620"
                     /old_locus_tag="VEE28_49370"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137421.1"
                     /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_023139311.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENSFAEWRTMSGLMQRENA
                     ALSERVTGLSRQVQSLSDQLRRLSKG"
                     /name="MbeD family mobilization/exclusion protein"
     gene            2350..2868
                     /locus_tag="AABJ98_RS25625"
                     /old_locus_tag="VEE28_49380"
     CDS             2350..2868
                     /locus_tag="AABJ98_RS25625"
                     /old_locus_tag="VEE28_49380"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016246513.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_172698723.1"
                     /translation="MKCFWACSVSVVLVMSFTVASAENITHTKPLARSDLYLTCKGYQV
                     KGASVINVEKPSYLEGTGEQIEFAIISLGDASDGLKVFFDSWSFSPFGLIESHVMHEHW
                     SLVHVGGRVSVKGEKIDYSFVDNQPQEGGSYKPKTGVFLYGCINSDKRPSWVEKIYTRT
                     GVFRGGIED"
                     /name="hypothetical protein"
     gene            3242..3682
                     /locus_tag="AABJ98_RS25630"
                     /old_locus_tag="VEE28_49390"
     CDS             3242..3682
                     /locus_tag="AABJ98_RS25630"
                     /old_locus_tag="VEE28_49390"
                     /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_023206709.1"
                     /translation="MSGIFLSLDDLQKLSVSARSEVMAIIAEGMDGNIFDDNGEGPTDL
                     SSLQSEKLVRGLSSKSRSVLKVILENSDASNGFWCEDLASELEVDVSDLTGVWSGLTRR
                     IRTVTGSPHAYLISWAWDDERQDYFGKMHPTTFKNCKKAVNI"
                     /name="hypothetical protein"
     gene            3900..4313
                     /locus_tag="AABJ98_RS25635"
                     /old_locus_tag="VEE28_49400"
     CDS             3900..4313
                     /locus_tag="AABJ98_RS25635"
                     /old_locus_tag="VEE28_49400"
                     /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_172698724.1"
                     /translation="MEIIKWASLSGVLLISACGVSQNEVNSANYGSKPIDNDAKVIGMI
                     KESLKDPDSLKVISITTPARGFSKYGFGSTEHGWFTTITYNAKNSYGGYVGAKSSTFVY
                     LNGDYKVAVPMSNGERVMLDKVSFSCKDNCQTK"
                     /name="hypothetical protein"
     gene            complement(4341..4496)
                     /locus_tag="AABJ98_RS25640"
                     /old_locus_tag="VEE28_49410"
     CDS             complement(4341..4496)
                     /locus_tag="AABJ98_RS25640"
                     /old_locus_tag="VEE28_49410"
                     /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_152913171.1"
                     /translation="MNSKQKCSHSNLEKEYYLGSATGDYKCLDCGEVGFGKDWPEKERS
                     KNDNEE"
                     /name="hypothetical protein"
     Typing          complement(4568..5053)
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="88.212"
                     /coverage="95.0"
                     /evalue="4.69e-163"
     Typing          830..2313
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.515"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 agtcctgtcg ggtttcgcca ccactgattt gagcgtccga ttctgtgatg cttgtcaggg
       61 gggcggagcc tatggaaaac cggcaactcc gggttcctct ctccgggcct ttcttcctgc
      121 gcacatgttc ttctgccgct tctcccctga atctgtggat aatgtagctt ccattcccgg
      181 gcatgctttc cccgctcgcc gcagccgaac gaccgagcgt agcgagtcag tgagcgagga
      241 agcggaatat caccggtcct gcattttctg cttacgcgcc cgccatggca ttacacctgc
      301 tttatgtggc atctatgcat tatgtttctg cgatgttaca tttttagcca gtatacactc
      361 cgctagcgct acgtgactgg ttcagggctg cgccccgaaa cccgctaaaa ccactgacgc
      421 gcctgcggct tgtccaacac cgcgccgacc gggaaaagat ttcccgcccg tcccggcgtt
      481 atcaggaggc cggattggca gacaaacgca gcaaaatgct cacgatgtgg gtgaccgaag
      541 atgagcaccg ccgtctgctg gagcgctgcg acggtaaaca gcttgcagcc tggatgcgcc
      601 agacgtgcct ggacgagaaa cccgcccgcg ccggcaagct tccctcgctc tcgccggcgc
      661 tgcttcgtca gcttgccggc atggggaaca acctcaacca gattgcccgg caggttaacg
      721 ccggtggtgg cagcgggcac gaccgcgtgc aggtcgtcgc cgcgctgatg gccatagatg
      781 ccggactcga gcggctgcgg catgctgtgc tggaaaagga tgcagacgat gatcgttaag
      841 tttcacccgc gagggcgcgg cggtggcgcc ggtccggtgg attatctgct ggggaaagac
      901 cgacagcgcg acggcgccac cgttctgcag gggaagccgg aagaagtcag ggagcttatc
      961 gacgcctcgc cctacgcaaa aaagtacaca tccggcgtcc tgtcctttgc cgaaaaggat
     1021 ttaccgcccg ggcagcgcga aaagctgatg gcgagctttg aacgggttct gatgcccgga
     1081 ctcgataaag accagtacag cgtgctgtgg gttgagcacc aggataaggg gcggctggag
     1141 ctgaacttcc tgatcccgaa cacggagctg ctgaccggca agcgtctcca gccgtattac
     1201 gaccgcgccg accgtccgcg cattgatgcc tggcagacca tcgtgaacgg caggctgggg
     1261 ctgcatgacc cgaacgcgcc tgaaaaccgg cgggcgctgg tcacgccgtc cgcgttgccg
     1321 gaaacgaagc aggaagccgc tcaggcaatt acacggggtt tactggcctt agcctcgtcc
     1381 ggggagctga aaacccgcca ggacgtcact gaggcgctgg aaagcgcagg ttttgaggtg
     1441 gtacgcacca caaaaagcag catcagcatt gccgacccgg acggggggcg aaacatccga
     1501 ctgaagggag ccatctatga acagtctttt aacgctggca aaggacttag agcagaaatc
     1561 gaaagcgcag cagcagagta ccggcgagat gctgaaagcc gcattcagcg agcacgagaa
     1621 gtctgtcaga gcggaactga gcgaaagcga gaagagaatc agcgccgcca tcctcgacca
     1681 cgaccggaag ctgtcctcag ccatgagcca gcgcacgaaa ggcatggtgc gtatggtcag
     1741 ccagacgtgg ctgaccatcg tcctggtgtc tgcactgctg acagcatcgg gcgcaagcat
     1801 tctgtggtgg caggggcagc agatactcga caattacacg accatccggg agcagaagcg
     1861 cacgcaggcc atgctgtccg agaggaacag cggcgtgcag ctctcgacct gcggagagca
     1921 gagacgccgc tgcgtgaggg tgaacccgga agcgggacgg ttcggagagg attcgagctg
     1981 gatgatactg gcggggaaat agcacatgac ggagctggaa aaacagttgc tgagcgcatt
     2041 agagcagcta cagcaggact actcgaaaag gctggacgag tgggagaact ccttcgcgga
     2101 atggcggacg atgtctggtc ttatgcaacg ggagaacgcg gcgctgagcg agcgcgtcac
     2161 gggcttgagc aggcaggtgc agagtttgag cgatcagctg cgccggttgt cgaaaggctg
     2221 aactcgattg aagcacacag gcagcaggag cgggcggcgc agcatcagaa aacgctggag
     2281 ctggaacgat cgcagcggca gaaaggtttt gagcttggaa tgtagttaat caatgaaaag
     2341 ggatgcgtta tgaagtgttt ctgggcttgc tcagtctcag tagttttggt tatgtcattt
     2401 acagtcgctt ctgcggagaa cattacacac acaaaaccgt tagccaggag cgacttatat
     2461 cttacctgta aaggttatca ggtgaagggg gcgtctgtaa ttaacgtcga gaaaccttct
     2521 taccttgaag gtacaggtga gcagattgag tttgcaatca tttctctcgg tgatgcatct
     2581 gatggactca aggttttttt tgattcatgg agtttttctc cttttggatt gattgaaagt
     2641 catgtaatgc atgagcactg gtctttagtt catgttgggg ggcgtgtttc agtcaagggt
     2701 gaaaagattg attattcatt tgtagataac cagccacagg agggtgggag ctataaaccc
     2761 aaaacaggtg tgttcctgta tggctgcatt aactctgata aaaggccatc ttgggtcgaa
     2821 aaaatctaca caagaacagg cgtgtttcga gggggcatag aagactaaaa tactgcgtac
     2881 agcatgaaaa ttcattgaac agagtgttag ttcattttcg tgcatggcta tgcatacacg
     2941 caaaacttat cagcgcgatt ccgggcggtt ttcggtgaga agacgggctc ttttgtggct
     3001 caggacggaa aaacgccctg aacgcgtctg agcggtgcgc ccaagggatg ttatggtaaa
     3061 tcagcccaaa atcatgagtc agatttttat atcttcccgg atggggatcg cagaacaatg
     3121 ggaaaataat ttgtgataaa acgattttaa tgtgtttgtt gatattagtc ttattgttta
     3181 atttcttcta atgtttagtc tgtgttagtc tttatctaac ttaactaaat ggagagaaga
     3241 catgagcgga atctttttgt cattggatga tttgcaaaag ctttcggtga gcgcacgtag
     3301 tgaggtgatg gctattatcg ctgaagggat ggacggtaat atttttgacg ataacggtga
     3361 agggccaacc gatctatcat ctctgcaatc agaaaaactt gtgcgtggtt tgagtagtaa
     3421 atctcgttct gtactgaaag ttattcttga gaatagcgat gcttccaacg gattctggtg
     3481 cgaagatctc gcttctgaac ttgaggtgga tgtctctgat ttaacaggag tgtggtcagg
     3541 cctcactcgt cgaatcagaa ccgttactgg ttcaccgcat gcttacctca tttcgtgggc
     3601 atgggacgat gaaaggcagg attattttgg aaagatgcat ccaactacct ttaaaaattg
     3661 caaaaaagca gtaaatatct aaaaaaaaag cccgcttaag cgggcttttt tgcttatctg
     3721 caagcatggc gaccgctaag agcatgagaa aggcatggcg ctgacggcga ggatgcttca
     3781 gaggtttgct ttagagaagt ttggcggccg gttcgtcgtc gagatgttat ggtaaatcta
     3841 tctataaatg tctatatagt ggatttccta tagttgtttg gaaaatgaca aggatatata
     3901 tggaaataat taagtgggct tcactgtctg gtgttctgtt aatatctgct tgtggtgttt
     3961 ctcagaacga agtaaatagt gctaattatg gttcaaaacc aatagataat gatgcgaaag
     4021 tgattggtat gattaaagag agtctaaaag atcctgattc tctaaaagtt atatcaataa
     4081 ccacccccgc cagaggtttt tctaagtatg gctttggctc tacagagcat ggctggttca
     4141 ctactatcac atataatgca aaaaactctt atggcggtta tgttggtgct aagtccagta
     4201 ctttcgttta cttaaacgga gattataaag tggcagtgcc aatgtctaat ggtgagaggg
     4261 ttatgttaga taaagtgtca ttttcatgta aagacaattg ccaaactaaa tgataaaaaa
     4321 ggccgcaata gcggcctttt ttattcttcg ttatcatttt tacttctttc tttttctggc
     4381 cagtccttcc caaaaccaac ctccccgcaa tccaaacatt tataatcgcc tgtggcgcta
     4441 cccaagtagt attctttttc aagatttgaa tgagaacatt tttgtttgct gttcactaca
     4501 gtcacctttg gatattcatt tattcgtgaa tgatttttat ctataccgac attgttaaat
     4561 gatggaaaga tcttcttgag atcctttttt tctacgcgta atcttcatga ctgtaaacga
     4621 aaaaaccacc ctggcaggtg gtttttcgaa ggttagttaa tcctggcaga ttctctaacc
     4681 gtggtaacag tcttgtgcga gacatgtcac caaatctgtc cttccagtgt agcctcagtc
     4741 aggccgccac ttcaagaact ctgaacacat ctctcgcaca aacctgttac cagtggctgc
     4801 tgccagtggc gttttgtcgt gtctttccgg gttggactca agacgatagt taccggataa
     4861 ggcgcagcag tcggactgaa cggggggttc gtgcatacag tccagcttgg agcgaactgc
     4921 ctacccggaa ctgagtgtca ggcgtggaat gagacaaacg cggccataac agcggaatga
     4981 caccggtaaa ccgaaaggca ggaacaggag agcgcacgag ggagccacca gggggaaacg
     5041 cctggtatct tta
//
