LOCUS       NZ_AP027661             4051 bp    DNA     circular CON 04-APR-2024
DEFINITION  Escherichia coli strain PSJ-42 plasmid pPSJ-42_9, complete sequence.
ACCESSION   NZ_AP027661
VERSION     NZ_AP027661.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00562565
            Assembly: GCF_036500485.1
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  JOURNAL   Unpublished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 4051)
  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                   :: 135x
            Sequencing Technology :: MGI DNBSEQ-G400RS; ONT MinION Mk1c
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_036500485.1-RS_2024_04_04
            Annotation Date                   :: 04/04/2024 00:14:17
            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)                     :: 5,040
            CDSs (total)                      :: 4,922
            Genes (coding)                    :: 4,743
            CDSs (with protein)               :: 4,743
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 179
            CDSs (without protein)            :: 179
            Pseudo Genes (ambiguous residues) :: 0 of 179
            Pseudo Genes (frameshifted)       :: 78 of 179
            Pseudo Genes (incomplete)         :: 115 of 179
            Pseudo Genes (internal stop)      :: 32 of 179
            Pseudo Genes (multiple problems)  :: 41 of 179
            Pseudo Genes (short protein)      :: 2 of 179
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP027661.1.
            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..4051
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="PSJ-42"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pPSJ-42_9"
                     /geo_loc_name="Ecuador:Puyo"
                     /collection_date="2019"
     gene            complement(424..627)
                     /locus_tag="AABK18_RS25130"
                     /old_locus_tag="VEE39_48060"
     CDS             complement(424..627)
                     /locus_tag="AABK18_RS25130"
                     /old_locus_tag="VEE39_48060"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000427298.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="retron Se72 family effector protein"
                     /protein_id="WP_000427298.1"
                     /translation="MENGFVNFYDHVKGYGFIRRERGRDVFFRYDDFLFLGHDVDICKG
                     ILVRFKLEKTDKGFKAVAIQKV"
                     /name="retron Se72 family effector protein"
     gene            complement(632..1771)
                     /locus_tag="AABK18_RS25135"
                     /old_locus_tag="VEE39_48070"
     CDS             complement(632..1771)
                     /locus_tag="AABK18_RS25135"
                     /old_locus_tag="VEE39_48070"
                     /EC_number="2.7.7.49"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000900598.1"
                     /GO_function="GO:0003964 - RNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="reverse transcriptase family protein"
                     /protein_id="WP_005761319.1"
                     /translation="MNKPRFNGTPVASLDSLSAMLGIERKRLDWIVKSVSMSYKQFKVE
                     TGKNKKERQIFEPKRSLKGIQKKINKEIFEKIDYPHYLHGALSGRDYISNAAVHTRKRT
                     VICLDITNFYPSISKKDVCSIFKNLMRFSPDVSLCLTELVTLNNKVPQGGCCSSYIANL
                     LFFNSEYNLYNRLKSMGLSYSRLLDDITISSDKDLSSEEKTKVIKLVHGMVNQYRLSIN
                     ESKTTIEHSKDSSSKLSVTGLWVKHGVPKLTKENRRYIRYLVYICKKQGAYERHTKEYH
                     DLWNRCSGKVAQMSRLGHVQAVELRAILSEIMPVYDDYKISKLKLMAKHYLNKFTPPLT
                     DDQIRKIDRMLYDFDIVGRTNKNLAKLYRRKLVALLPDR"
                     /name="reverse transcriptase family protein"
     gene            complement(2345..2611)
                     /locus_tag="AABK18_RS25140"
                     /old_locus_tag="VEE39_48090"
     CDS             complement(2345..2611)
                     /locus_tag="AABK18_RS25140"
                     /old_locus_tag="VEE39_48090"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001243419.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_224471576.1"
                     /translation="MVKLLLVRNEYFNKNNDLKTVARFDGKTLRDAFSRKIATFDGKVL
                     RDASLKKVATFDGQNLRDASSKIILSADAEVGIVVMAFVAELI"
                     /name="hypothetical protein"
     gene            complement(2836..3159)
                     /gene="mobA"
                     /locus_tag="AABK18_RS25145"
                     /old_locus_tag="VEE39_48100"
     CDS             complement(2836..3159)
                     /gene="mobA"
                     /locus_tag="AABK18_RS25145"
                     /old_locus_tag="VEE39_48100"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization protein MobA"
                     /protein_id="WP_000166966.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="mobA"
     gene            3443..3637
                     /locus_tag="AABK18_RS25150"
                     /old_locus_tag="VEE39_48110"
     CDS             3443..3637
                     /locus_tag="AABK18_RS25150"
                     /old_locus_tag="VEE39_48110"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041624.1"
                     /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_001041640.1"
                     /translation="MNKQQQTVLNMAGFIKSQSLTLLEKLDALDADEQAAMCEKLHELA
                     EELQNSIQTRFEAENRTGI"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(3169..3408)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.755"
                     /coverage="100.0"
                     /evalue="7.66e-118"
     Typing          3..184
                     /name="rep_cluster_2370"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.803"
                     /coverage="94.0"
                     /evalue="2.61e-65"
     Typing          3673..4051
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.288"
                     /coverage="95.0"
                     /evalue="1.05e-169"
     Typing          complement(2840..3159)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="3.08e-62"
ORIGIN
        1 acgtggcgct ttctcatagc tcacgctgtt ggtatctcgg cccggtgtag gtcgttcgct
       61 ccaagctgga ctgtatgcac gaaccccccg ttcagtccga ccgctgcgcc ttatccggta
      121 actatcgact tgaatccaaa ccgagaagac acgacttatc gccactggca gcagccactg
      181 gtaaccgaat tagaggagtt agccttgaag tcatgcgcct gttaaggcta aactgaaaga
      241 acaagttttg gtgactgcgc tcctccaagc cagttacctc ggctcaaaga gttggtagct
      301 ctgagaacct tcgaaaaacc gccctgcaag gcggtttttt cgtttacaca gcaagagatt
      361 acgacgagat agaaaggatc tcaagttctc atatcataaa aacaagctga cacatccacg
      421 atgttatacc ttttgaatcg ctacagcttt aaacccttta tctgtttttt ctaatttaaa
      481 cctaactaaa atacctttac atatatcgac atcatgccct aaaaacaaaa aatcatcata
      541 ccgaaagaaa acatcacgtc cacgctcacg ccttataaag ccataccctt taacatggtc
      601 ataaaaatta acaaatccat tttccatata atcacctatc tggaagtaat gccacgagct
      661 tacgtctata tagttttgca agattcttat tagtccgccc tactatatca aaatcataga
      721 gcatcctatc tattttccta atctgatcat cagttaaagg cggcgtaaac ttatttagat
      781 agtgcttagc catcaacttt aatttagata tcttgtaatc atcataaact ggcattatct
      841 cagaaagaat cgccctcaat tcaaccgcct ggacatgccc aagcctcgac atttgagcaa
      901 ccttgccaga gcatctattc cataaatcat ggtactcttt cgtatgacgt tcataagcac
      961 cttgtttttt acatatataa actaagtacc tgatataacg tctattttct tttgttaact
     1021 taggaacacc atgctttacc cacaacccag tgacactaag tttagaagac gaatcttttg
     1081 agtgctctat cgttgtctta ctttcattta ttgaaagtct gtactgattc accattccgt
     1141 gaacgagttt tattactttt gttttttcct ctgatgaaag atccttatca gaagatatag
     1201 taatatcatc taaaagcctt gaatatgaaa gccccataga cttcaatcta ttatagagat
     1261 tatactcact attaaaaaat aaaagatttg caatataact agaacagcac ccaccctgag
     1321 ggaccttatt attcaacgtc acaagttccg ttaagcataa agaaacatca ggagaaaaac
     1381 gcattaaatt tttaaaaata gaacaaacat cttttttact aatgctggga taaaaattgg
     1441 tgatatcaag acatataact gttcttttcc tagtatgaac agcggcatta gatatataat
     1501 cgcgaccact taacgcccca tgcaaataat gagggtaatc aattttctca aaaatctctt
     1561 tatttatttt tttttgaatt cctttcaaag atctcttggg ttcaaaaatt tgcctttctt
     1621 ttttattctt ccctgtttca accttaaact gcttgtacga catcgataca gacttgacta
     1681 tccagtccaa tctttttctt tctatgccta acatcgcaga taaagaatcc aaagatgcaa
     1741 caggagttcc attaaacctg ggtttattca tgatgtttga gttaaaagtc gattagttaa
     1801 aaagtttcga tacgtaatct attactttaa acataatcaa gcacatagaa aacaaaaact
     1861 gtgttttttt cagtgcctcc agagagccaa cctctctttt tttcttcatc tgaccgtctc
     1921 cagaacaaga tgaagagctc ttggttacgt taatgttgat gttgataata aacatgatgc
     1981 aactcctatt ggttatgaaa ttttgccaga ccagtaggaa agcaaggaaa aactctattg
     2041 gctctttggg acttttaact cacattgcca gacaatcgtc gctattcttt tagtgctgat
     2101 acacgctcag gggcgttctc accattaatt agcggccagg ccggtcatga tctcatgcga
     2161 gatcgcctta aaaacaaggc atcggtttcc ttgcgcaaca tacacgtaac catttgttaa
     2221 agagcgagag ccaggcgtgg ttcgcccgct tcgctgatta ttataaagtt ttttatcttt
     2281 ctgtcaccaa caagaaagcg ccttatcctg ccagcgatag gctaaaaggt atgcagcatg
     2341 agattcaaat caactcagct acaaaggcca taacaacaat cccaacctca gcatcggcac
     2401 tcaggataat ttttgaacta gcatctctta aattctgacc gtcaaaggtt gctacttttt
     2461 ttaaagaggc atcccttaaa accttgccat caaaagtcgc tatttttctc gaaaaggcat
     2521 ctcttaaggt tttaccgtca aaccgagcaa cggtttttaa gtcattgttt ttattgaaat
     2581 attcatttct caccaatagt aatttaacca attgtattta ccataatccc ttaattgtac
     2641 gcaccacaga atcgcgctca gcgcgattct gacacagaca ctgcaaaaag agatgtttta
     2701 ccctaagaaa accggggaaa tgcgtcagga tcgttttcag ctcgctgcat agctatgcat
     2761 gaaagcgagt ggtgatcact ttgggagctt acagtgttca taccgtctgt tttcgacagt
     2821 tttctcccct ggaagctaat ctgccataag cctggataac agggcacggt gatactccgt
     2881 aatagcgatc agcacctccg catactccct gtccccgaca cgcttgccgt cgataaagag
     2941 ttttttctgt aacgccccca gtctcataac ttctttcagt acccgatcat cagtcagtga
     3001 gttaactttc ttaccgagag ctgccgcccg taaaaaaccg gaaacggtct tgccgcattc
     3061 agcagccctt tttctgattt cctggtcttc ttctgccgtc agacgaacag ggcgactgat
     3121 agcccgcctg cgcgtattac ttccacttcg ttttgtcata aaacatggct ccgtatctga
     3181 catgggtgtc ggggcaaagc cctgaccagg gtaattgtaa tagcgtgcat gtatgcgcgg
     3241 tataacaatt gcacatcctg tcctgtcagc aagctcgaat taccgacaaa ggcacggcag
     3301 ttttttggca gtgacagtgt tgtctgacag aaatgcccgt caaagcgtca gacagcagaa
     3361 taccgacggt aaaacagtcg aaaagtggta cgcgatataa tcacacaacg cagatgacag
     3421 aaagaacgga gaaaacagaa agatgaacaa gcagcagcaa accgtactca acatggcagg
     3481 attcataaaa agccagagcc tgacgctgct cgaaaaactg gacgcacttg atgctgacga
     3541 acaggccgcc atgtgtgaga agctgcacga actcgcggaa gaacttcaga acagcataca
     3601 gacacgcttt gaagcggaaa atcgcaccgg gatataacgc atccggacag gatgcagaac
     3661 ggcatagagg agcgtaagga gaaaatgtca cataaggcgc tcttccgctt cctcgctcac
     3721 tgactcgcta cgctcggtcg ttcgactgcg gcgagcggtg tcagctcact caaaggcggt
     3781 aatacggtta tccacagaat caggggataa cgccggaaag aacatgtgag caaaaagccg
     3841 aagccaggga caaaggccgc gccgatggcg tttttccata ggctccgccc ccctgacgag
     3901 catcacaaaa accgacgctc aagtcagagg tggcgaaacc cgacaggact ataaagatac
     3961 caggcgtttc cccctggaag ctccctcgtg cgctctcctg ttccgaccct gccgcttacc
     4021 ggatacctgt ccgcctttct cccttcggga a
//
