LOCUS       NZ_AP027712             4051 bp    DNA     circular CON 04-APR-2024
DEFINITION  Escherichia coli strain PSS-15 plasmid pPSS-15_3, complete sequence.
ACCESSION   NZ_AP027712
VERSION     NZ_AP027712.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00562533
            Assembly: GCF_036502285.1
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  JOURNAL   Unpublished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                   :: 179x
            Sequencing Technology :: MGI DNBSEQ-G400RS; ONT MinION Mk1c
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_036502285.1-RS_2024_04_04
            Annotation Date                   :: 04/04/2024 00:04:59
            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)                     :: 5,120
            CDSs (total)                      :: 4,996
            Genes (coding)                    :: 4,767
            CDSs (with protein)               :: 4,767
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 92
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 229
            CDSs (without protein)            :: 229
            Pseudo Genes (ambiguous residues) :: 0 of 229
            Pseudo Genes (frameshifted)       :: 77 of 229
            Pseudo Genes (incomplete)         :: 153 of 229
            Pseudo Genes (internal stop)      :: 35 of 229
            Pseudo Genes (multiple problems)  :: 33 of 229
            Pseudo Genes (short protein)      :: 3 of 229
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP027712.1.
            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="PSS-15"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pPSS-15_3"
                     /geo_loc_name="Ecuador:Puyo"
                     /collection_date="2019"
     gene            complement(261..464)
                     /locus_tag="AABJ97_RS25580"
                     /old_locus_tag="VEE23_49540"
     CDS             complement(261..464)
                     /locus_tag="AABJ97_RS25580"
                     /old_locus_tag="VEE23_49540"
                     /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(469..1608)
                     /locus_tag="AABJ97_RS25585"
                     /old_locus_tag="VEE23_49550"
     CDS             complement(469..1608)
                     /locus_tag="AABJ97_RS25585"
                     /old_locus_tag="VEE23_49550"
                     /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(2182..2448)
                     /locus_tag="AABJ97_RS25590"
                     /old_locus_tag="VEE23_49570"
     CDS             complement(2182..2448)
                     /locus_tag="AABJ97_RS25590"
                     /old_locus_tag="VEE23_49570"
                     /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(2673..2996)
                     /gene="mobA"
                     /locus_tag="AABJ97_RS25595"
                     /old_locus_tag="VEE23_49580"
     CDS             complement(2673..2996)
                     /gene="mobA"
                     /locus_tag="AABJ97_RS25595"
                     /old_locus_tag="VEE23_49580"
                     /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            3280..3474
                     /locus_tag="AABJ97_RS25600"
                     /old_locus_tag="VEE23_49590"
     CDS             3280..3474
                     /locus_tag="AABJ97_RS25600"
                     /old_locus_tag="VEE23_49590"
                     /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(3006..3245)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.755"
                     /coverage="100.0"
                     /evalue="7.66e-118"
     Typing          3510..4031
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.476"
                     /coverage="95.0"
                     /evalue="0.0"
     Typing          complement(2677..2996)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="3.08e-62"
ORIGIN
        1 actggcagca gccactggta accgaattag aggagttagc cttgaagtca tgcgcctgtt
       61 aaggctaaac tgaaagaaca agttttggtg actgcgctcc tccaagccag ttacctcggc
      121 tcaaagagtt ggtagctctg agaaccttcg aaaaaccgcc ctgcaaggcg gttttttcgt
      181 ttacacagca agagattacg acgagataga aaggatctca agttctcata tcataaaaac
      241 aagctgacac atccacgatg ttataccttt tgaatcgcta cagctttaaa ccctttatct
      301 gttttttcta atttaaacct aactaaaata cctttacata tatcgacatc atgccctaaa
      361 aacaaaaaat catcataccg aaagaaaaca tcacgtccac gctcacgcct tataaagcca
      421 taccctttaa catggtcata aaaattaaca aatccatttt ccatataatc acctatctgg
      481 aagtaatgcc acgagcttac gtctatatag ttttgcaaga ttcttattag tccgccctac
      541 tatatcaaaa tcatagagca tcctatctat tttcctaatc tgatcatcag ttaaaggcgg
      601 cgtaaactta tttagatagt gcttagccat caactttaat ttagatatct tgtaatcatc
      661 ataaactggc attatctcag aaagaatcgc cctcaattca accgcctgga catgcccaag
      721 cctcgacatt tgagcaacct tgccagagca tctattccat aaatcatggt actctttcgt
      781 atgacgttca taagcacctt gttttttaca tatataaact aagtacctga tataacgtct
      841 attttctttt gttaacttag gaacaccatg ctttacccac aacccagtga cactaagttt
      901 agaagacgaa tcttttgagt gctctatcgt tgtcttactt tcatttattg aaagtctgta
      961 ctgattcacc attccgtgaa cgagttttat tacttttgtt ttttcctctg atgaaagatc
     1021 cttatcagaa gatatagtaa tatcatctaa aagccttgaa tatgaaagcc ccatagactt
     1081 caatctatta tagagattat actcactatt aaaaaataaa agatttgcaa tataactaga
     1141 acagcaccca ccctgaggga ccttattatt caacgtcaca agttccgtta agcataaaga
     1201 aacatcagga gaaaaacgca ttaaattttt aaaaatagaa caaacatctt ttttactaat
     1261 gctgggataa aaattggtga tatcaagaca tataactgtt cttttcctag tatgaacagc
     1321 ggcattagat atataatcgc gaccacttaa cgccccatgc aaataatgag ggtaatcaat
     1381 tttctcaaaa atctctttat ttattttttt ttgaattcct ttcaaagatc tcttgggttc
     1441 aaaaatttgc ctttcttttt tattcttccc tgtttcaacc ttaaactgct tgtacgacat
     1501 cgatacagac ttgactatcc agtccaatct ttttctttct atgcctaaca tcgcagataa
     1561 agaatccaaa gatgcaacag gagttccatt aaacctgggt ttattcatga tgtttgagtt
     1621 aaaagtcgat tagttaaaaa gtttcgatac gtaatctatt actttaaaca taatcaagca
     1681 catagaaaac aaaaactgtg tttttttcag tgcctccaga gagccaacct ctcttttttt
     1741 cttcatctga ccgtctccag aacaagatga agagctcttg gttacgttaa tgttgatgtt
     1801 gataataaac atgatgcaac tcctattggt tatgaaattt tgccagacca gtaggaaagc
     1861 aaggaaaaac tctattggct ctttgggact tttaactcac attgccagac aatcgtcgct
     1921 attcttttag tgctgataca cgctcagggg cgttctcacc attaattagc ggccaggccg
     1981 gtcatgatct catgcgagat cgccttaaaa acaaggcatc ggtttccttg cgcaacatac
     2041 acgtaaccat ttgttaaaga gcgagagcca ggcgtggttc gcccgcttcg ctgattatta
     2101 taaagttttt tatctttctg tcaccaacaa gaaagcgcct tatcctgcca gcgataggct
     2161 aaaaggtatg cagcatgaga ttcaaatcaa ctcagctaca aaggccataa caacaatccc
     2221 aacctcagca tcggcactca ggataatttt tgaactagca tctcttaaat tctgaccgtc
     2281 aaaggttgct acttttttta aagaggcatc ccttaaaacc ttgccatcaa aagtcgctat
     2341 ttttctcgaa aaggcatctc ttaaggtttt accgtcaaac cgagcaacgg tttttaagtc
     2401 attgttttta ttgaaatatt catttctcac caatagtaat ttaaccaatt gtatttacca
     2461 taatccctta attgtacgca ccacagaatc gcgctcagcg cgattctgac acagacactg
     2521 caaaaagaga tgttttaccc taagaaaacc ggggaaatgc gtcaggatcg ttttcagctc
     2581 gctgcatagc tatgcatgaa agcgagtggt gatcactttg ggagcttaca gtgttcatac
     2641 cgtctgtttt cgacagtttt ctcccctgga agctaatctg ccataagcct ggataacagg
     2701 gcacggtgat actccgtaat agcgatcagc acctccgcat actccctgtc cccgacacgc
     2761 ttgccgtcga taaagagttt tttctgtaac gcccccagtc tcataacttc tttcagtacc
     2821 cgatcatcag tcagtgagtt aactttctta ccgagagctg ccgcccgtaa aaaaccggaa
     2881 acggtcttgc cgcattcagc agcccttttt ctgatttcct ggtcttcttc tgccgtcaga
     2941 cgaacagggc gactgatagc ccgcctgcgc gtattacttc cacttcgttt tgtcataaaa
     3001 catggctccg tatctgacat gggtgtcggg gcaaagccct gaccagggta attgtaatag
     3061 cgtgcatgta tgcgcggtat aacaattgca catcctgtcc tgtcagcaag ctcgaattac
     3121 cgacaaaggc acggcagttt tttggcagtg acagtgttgt ctgacagaaa tgcccgtcaa
     3181 agcgtcagac agcagaatac cgacggtaaa acagtcgaaa agtggtacgc gatataatca
     3241 cacaacgcag atgacagaaa gaacggagaa aacagaaaga tgaacaagca gcagcaaacc
     3301 gtactcaaca tggcaggatt cataaaaagc cagagcctga cgctgctcga aaaactggac
     3361 gcacttgatg ctgacgaaca ggccgccatg tgtgagaagc tgcacgaact cgcggaagaa
     3421 cttcagaaca gcatacagac acgctttgaa gcggaaaatc gcaccgggat ataacgcatc
     3481 cggacaggat gcagaacggc atagaggagc gtaaggagaa aatgtcacat aaggcgctct
     3541 tccgcttcct cgctcactga ctcgctacgc tcggtcgttc gactgcggcg agcggtgtca
     3601 gctcactcaa aggcggtaat acggttatcc acagaatcag gggataacgc cggaaagaac
     3661 atgtgagcaa aaagccgaag ccagggacaa aggccgcgcc gatggcgttt ttccataggc
     3721 tccgcccccc tgacgagcat cacaaaaacc gacgctcaag tcagaggtgg cgaaacccga
     3781 caggactata aagataccag gcgtttcccc ctggaagctc cctcgtgcgc tctcctgttc
     3841 cgaccctgcc gcttaccgga tacctgtccg cctttctccc ttcgggaaac gtggcgcttt
     3901 ctcatagctc acgctgttgg tatctcggcc cggtgtaggt cgttcgctcc aagctggact
     3961 gtatgcacga accccccgtt cagtccgacc gctgcgcctt atccggtaac tatcgacttg
     4021 aatccaaacc gagaagacac gacttatcgc c
//
