LOCUS       NZ_AP027660             4634 bp    DNA     circular CON 04-APR-2024
DEFINITION  Escherichia coli strain PSJ-42 plasmid pPSJ-42_8, complete sequence.
ACCESSION   NZ_AP027660
VERSION     NZ_AP027660.1
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  JOURNAL   Unpublished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 4634)
  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
            AP027660.1.
            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..4634
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="PSJ-42"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pPSJ-42_8"
                     /geo_loc_name="Ecuador:Puyo"
                     /collection_date="2019"
     gene            378..1217
                     /locus_tag="AABK18_RS25100"
     CDS             378..1217
                     /locus_tag="AABK18_RS25100"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001354646.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001354646.1"
                     /translation="MLTLFIFFVLLIAACFFCFAPPRRGYDRNEIIPYKIKLSINKYRL
                     YIYSSGKVRQYLLFLVILSLYYSIAEPFKSELIKNISYSLMAAFIFDTGLNFSKENITK
                     GVISTRWHNDLYSSFERMKAINKIYYPSNKEINTEGLSKAITSSLFNDDANSFAKRDFR
                     LMWDLSSEKYLSYKEIIIRKGDKLDAVCLRFINDDYKFLVNFNRDEEVFKYFPSIMQPS
                     LKTYRALSRLVNSIKDPSRFKFTTESLEMELLEYLELRNELFNDIEEVMGSYAQRAP"
                     /name="hypothetical protein"
     gene            complement(1946..2179)
                     /locus_tag="AABK18_RS25105"
                     /old_locus_tag="VEE39_48020"
     CDS             complement(1946..2179)
                     /locus_tag="AABK18_RS25105"
                     /old_locus_tag="VEE39_48020"
                     /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_000137388.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHAVTQQNNA
                     ILNERVVNLSQQVQLLAGQVDRLSRLFITNNR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2186..2746)
                     /locus_tag="AABK18_RS25110"
                     /old_locus_tag="VEE39_48030"
     CDS             complement(2186..2746)
                     /locus_tag="AABK18_RS25110"
                     /old_locus_tag="VEE39_48030"
                     /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_000067488.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKQQLDTLSTTVSTQLSTTEAELSRQQKNLLWQVIKGRVLFPALTA
                     LSVTGGIFLGCWGLIQWQESRIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            complement(<2778..3434)
                     /locus_tag="AABK18_RS25115"
                     /pseudo=""
     CDS             complement(<2778..3434)
                     /locus_tag="AABK18_RS25115"
                     /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(3424..3747)
                     /locus_tag="AABK18_RS25120"
     CDS             complement(3424..3747)
                     /locus_tag="AABK18_RS25120"
                     /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_001677263.1"
                     /translation="MLTIRVSDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     SPPLLRHLAAIGNNLNQTARKVNSGHWSSIDRVHVVAALMAIEGELRQLRQAVREQGGR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3810..4001
                     /locus_tag="AABK18_RS25125"
                     /old_locus_tag="VEE39_48050"
     CDS             3810..4001
                     /locus_tag="AABK18_RS25125"
                     /old_locus_tag="VEE39_48050"
                     /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_000165986.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(4090..4174)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.03e-37"
     Typing          complement(2..379)
                     /name="ColRNAI_rep_cluster_1857"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="83.0"
                     /evalue="0.0"
     Typing          4185..4634
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.363"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(1849..3434)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.811"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ggcccggtgt aggtcgttcg ctccaagctg ggctgtgtgc acgaaccccc cgttcagccc
       61 gaccgctgcg ccttatccgg taactatcgt cttgagtcca acccggaaag acacgtaaaa
      121 acgccactgg cagcagccat tggtaaccgt ttagaggagt tagtcttgaa gttatgcgcc
      181 ggttaaggct aaactgaaag gacagatttg gtggctgtgc tcctccaagc cagttacctt
      241 ggttcaaaga gttgctgctc tgagaacctt cgaaaagccg ccttgctggg cggttttttc
      301 gtttacggac aagactacct tcaggatcgt tagatctcaa gacaatcatg catagtgagc
      361 atacacagga gccgaacttg cttacactgt tcatcttttt tgttttatta atagctgcat
      421 gtttcttttg ttttgctcca ccacgaagag gatatgacag aaatgagatc attccataca
      481 aaataaaact atcaataaat aaatatcgcc tttacatata ctcatcggga aaggtaagac
      541 aatacctttt atttttagtt attttatcac tgtactactc catagcggaa ccatttaagt
      601 ctgagttaat aaaaaacata tcatattcac tgatggctgc atttattttt gatacagggc
      661 ttaattttag caaggagaat ataactaaag gggtgatttc aacaaggtgg cataatgacc
      721 tatattcatc atttgagaga atgaaagcaa ttaataaaat ttactaccca tccaacaaag
      781 agataaacac agaaggtcta tccaaagcca tcacatcatc tcttttcaat gatgacgcga
      841 actcgttcgc aaagagagat tttcgcttga tgtgggactt atcttctgaa aaatatcttt
      901 cctataaaga aataataata agaaaaggcg ataagcttga cgctgtatgc ttgagattta
      961 taaatgatga ctacaagttt ttagttaatt tcaacagaga tgaagaggtt ttcaaatact
     1021 ttccatctat aatgcaacct tcactcaaaa catatagagc gttatcaaga ctagtaaact
     1081 caatcaaaga tccttctaga tttaagttca cgacagagtc attagaaatg gagttactag
     1141 aatacttaga gttaagaaat gaattattca atgacataga agaagtaatg ggtagctatg
     1201 ctcagagggc accatagttc atgatagccc tcgatagtac ttacttatat ttttagagag
     1261 gtttaagtgt aagtagaggg agtaacacct ggtttttcag catccactcc aatgaatgct
     1321 gacaccgata cgcgataatt ctctttatcg tagcaaaatc atcctccaga ttgcggttga
     1381 gaataggttc atggtgcgca atacgattgc gcagttttct cacgggactt gttagcagta
     1441 atgcttcccc cccggggaca aacgacagag atatacaaca aaggcccgct gtatagagta
     1501 cagcgggcct ttgttgtttt aattcccgca attaaaatac tccgtattta ccataacgtc
     1561 gcattgcgcg taccgcttaa acgcgttcag cgcgatcacg gcagcagaca ggtaaaaaca
     1621 gcaacaaacc acccgaaaaa ctgccgcgat cgcgcctggt aaattttaac ctcatgcata
     1681 gttatgcgcg aaactgaatg acgatcagtt tcgcacgttc cagccgtcga acggggcaaa
     1741 atggggaggt ttggatattg ttaatgctaa tgtacgtaca ttaacattgg cgccatccgg
     1801 gtagggcgtg ccacaaactg gctcgatttc agggggcacc ccggtcacat ccccattgac
     1861 gggccacgcc agatccgcgc ttcgggttcc tgctcttcat gccagcgccg ggcaagctcc
     1921 tgcgcctgac gctcctgttc atcccttatc tgttgttcgt gataaataac cgactcaagc
     1981 ggtcgacttg tccggctaat agctgcacct gctgactcaa gttcacgaca cgctcgttca
     2041 gtatcgcgtt gttctgttgc gtaaccgcgt gcatcttctg caattctgcg aaggcgctct
     2101 cccactcgtt cagccgccgc atatagtcct gttgcaaatg ctctaaggcg ttcagcaaat
     2161 gcccttccag ttccgtcata ctcgtttact ccctgaccag cctcacggcg ttcttgtcgc
     2221 ccaccgtcca ggtgttttcc cctttcaccc cgtccggcag caccagaaat ttcccgttct
     2281 cgccattgac gaacgtcacc ccccaggttt ttgcctcgag tttcgccagc gtgttttcct
     2341 gctctctgat ggtcaagata tttttcgcaa tcctgctttc ctgccactga atcagccccc
     2401 agcaccccag gaaaatgccg cccgtgacgc tgagcgcggt cagcgccgga aacagtaccc
     2461 gccctttgat cacctgccag agcaggtttt tctgctgccg ggacagttcg gcctctgtgg
     2521 tgctgagctg cgtgctcacg gtggtgctca gcgtatccag ttgctgtttc acggatgttg
     2581 tatgttcgct gatagcgtct ctgattttct gcctgtttaa gctcagtgcc ttgtctacag
     2641 actcttctag cttcctgaac tcgctgttca gcatgttctc ggtagaagcg gctcgctctt
     2701 tcagtttctt ctcgaagtct gttcccattt gtaaaagatt gctcatacag cgcccccttt
     2761 agcctgagat tccgcccccc ctccgggtcg gcaatactga tactgcttct ggttgtcctc
     2821 accacctcaa aacctgccgc tgtgagcgcc tcagtgacat cctgacgcgt ttttattgct
     2881 ccggcacggt aaagcgcctc aagaccccgt gtaatcgctt ctgcggcctc ctgtttcgct
     2941 tttggcagat tattcggtgt gacaagcgtc cgtctgttct ccggtgcgtt cgggtcacgc
     3001 agcccgtaat gatgattaac cagcgtctgc caggcattta tcctcggcct gtccgcacgg
     3061 tcgtagtacg gctggaggcg cttaccgctc tgtagttcca tgttcggaat gacaaaattc
     3121 agttcgagcc gccccttatc ctggtgttcc acccagagaa tgctgtactg gtctttttcg
     3181 agaccgggca taagaacacg ctcaaagctc gtcatcactc tttcgcgttc acccggcggt
     3241 aactccttct ccgcgaacga cagaacgcct gacgtgtatt tcttcgaaaa tggcgtggca
     3301 tcaatgagtt cccggatttc ttccgggtta ccccggagca ccgttgcgcc ttcgcggtta
     3361 cgctcccgcc ccagcaggta atcgaccggg ccacttccac cgcctttccc cctggcatga
     3421 aatttaacta tcatcccgtc ccccctgttc cctgacagcc tgccgcaact ggcgcaattc
     3481 accctcgatg gccatcagtg cggccaccac atgaacccgg tcaatcgaag accagtggcc
     3541 gctgttcacc ttccgggctg tctggttcag attgttcccg atggcagcca gatgccgcag
     3601 caatggcggc gatagtgtcg gcagttttcc tgtgcgcgca accggctccc ccagacagac
     3661 ccgccgcatc cattctgcca gtcgtttacc ctcgcagcgt tccagtaacc gggcgtgctc
     3721 ctcatcgcta acccgtatcg tgagcatctt ctcgcgtttc atcggtatca ttccccctaa
     3781 aaaatcccct attaaggagc cttaagacca tgaccaaaca ggaaaaaaca gcccttaaca
     3841 tggcccgctt tatcagaagc cagacgctga ccctgctgga aaaactcaac gagctggacg
     3901 cggacgaaca ggcagacatc tgcgaatcac ttcacgacca cgccgacgaa ctctaccgta
     3961 gttgcctcgc acgcttcggc gatgacggtg aaagcaactg aaacatgcag ctcccggaga
     4021 cgttcacagc ttgcctgtga gcggatgccg ggagcagaca agcccgtcag ggcgcgtcag
     4081 cgggttttag cgggtgtcgg ggcgcagccc tgacccagtc acgtagcgat agcggagtgt
     4141 atactggctt aactatgtgg catcagtgcg gattataaga aaagtgcacc atatgcggtg
     4201 tgaaataccg cacatatgcg taaggagaaa atgccgcatc aggcgctctt ccgcttcctc
     4261 gctcactgac tcgctacgct cggtcgttcg gctgcggcga gcggtatcag ctcactcaaa
     4321 gacggtgatg cggttatcca cagaatcagg ggataacgcc aaaagaaaca tgtgagcaaa
     4381 agaccaggaa caggaagaag gccgcgccgc tggcgttttt ccataggctc cgcccccctg
     4441 acgagcatca caaaaacaga cgctcaagtc agaggtggcg aaacccgaca ggactataaa
     4501 gataccaggc gtttccccct ggaagctccc tcgtgcgctc tcctgttccg accctgccgc
     4561 ttaccggata cctgtccgcc tttctccctt cgggaagcgt ggcgctttct catagctcac
     4621 gctgttggta tctc
//
