LOCUS       NZ_AP027683             5523 bp    DNA     circular CON 04-APR-2024
DEFINITION  Escherichia coli strain PSS-08-2 plasmid pPSS-08-2_4, complete
            sequence.
ACCESSION   NZ_AP027683
VERSION     NZ_AP027683.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00562531
            Assembly: GCF_036501305.1
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  JOURNAL   Unpublished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 5523)
  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                   :: 88x
            Sequencing Technology :: MGI DNBSEQ-G400RS; ONT MinION Mk1c
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_036501305.1-RS_2024_04_04
            Annotation Date                   :: 04/04/2024 00:34:07
            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)                     :: 5,114
            CDSs (total)                      :: 4,994
            Genes (coding)                    :: 4,739
            CDSs (with protein)               :: 4,739
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 255
            CDSs (without protein)            :: 255
            Pseudo Genes (ambiguous residues) :: 0 of 255
            Pseudo Genes (frameshifted)       :: 68 of 255
            Pseudo Genes (incomplete)         :: 178 of 255
            Pseudo Genes (internal stop)      :: 48 of 255
            Pseudo Genes (multiple problems)  :: 37 of 255
            Pseudo Genes (short protein)      :: 3 of 255
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP027683.1.
            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..5523
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="PSS-08-2"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pPSS-08-2_4"
                     /geo_loc_name="Ecuador:Puyo"
                     /collection_date="2019"
     gene            complement(join(5208..5523,1..62))
                     /locus_tag="AABK31_RS25520"
     CDS             complement(join(5208..5523,1..62))
                     /locus_tag="AABK31_RS25520"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002444123.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_061103833.1"
                     /translation="MARHTVTEAAKLAGVTRRTIYRHIKAGKLSATVTDDDNTVIETSE
                     LLRVYGALSQPEPEQVYTRSHENQPEYVTLLLAEMSQMRAQIETLTGKVDELQSKLALP
                     APKRDLSVVEWVALRRLKKDR"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(185..1558)
                     /locus_tag="AABK31_RS25525"
                     /old_locus_tag="VEE22_49520"
     CDS             complement(185..1558)
                     /locus_tag="AABK31_RS25525"
                     /old_locus_tag="VEE22_49520"
                     /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_139059186.1"
                     /translation="MEWELTRNQLLIQREVIRVMKNMHSQNWDIGHKYPVKPDDSDPYA
                     IRSEDGVLMIGRHVASNLTAEKAAFNRSKGNSIQPGKYSASQLTPLVLGEFLDGEGKQL
                     TAAQMFDLYDKETGFEKSGILSAEERESRRKCMEQRKQQGITGASVTDWEYVPAFKVKV
                     YRRPEWTELKGRLIAMYEEHKSYGSLEAGEGLRVALACEMVELVELAIERERQAVEQSG
                     EIETALDWCWLAVSNRLDGQNIEPLYLPLVDSVTGREVWRGVKVATDGFAYETTYNATG
                     AILSDAAAKRDNELSKMETSAQEYFERFQRPLPRHQWDIFWKGLLTANSQWSDLQFEWR
                     NAGLIYKEIGKMVIKGDLETMRQQVRGLMGQGLEAFPELADCTQEAGQKDWRGLTNGAG
                     KYVDVLGYPSTKASAWIQGVIADQLDGLEGLATVEANNKRIFLLAALTEERDQNTVWL"
                     /name="hypothetical protein"
     gene            complement(2363..2917)
                     /locus_tag="AABK31_RS25530"
                     /old_locus_tag="VEE22_49540"
     CDS             complement(2363..2917)
                     /locus_tag="AABK31_RS25530"
                     /old_locus_tag="VEE22_49540"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001273865.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="recombinase family protein"
                     /protein_id="WP_061103831.1"
                     /translation="MSNIGYVRVSSVQQNNERQLEGVELDRVFTETASGKNADRPQLNA
                     MLEYVREGDVIHVHELSRLGRNVRDLLTIIDAVKAKGASVNFHKEGIIAGAEETAASRM
                     MLNVFAAVSQMEREMMLERQAEGYAAAKAAGRRGARGNGKEIDRVGIVSALAAGESIRK
                     TAAQFGVSTQTVQRIKQEQAE"
                     /name="recombinase family protein"
     gene            complement(3159..3425)
                     /locus_tag="AABK31_RS25535"
     CDS             complement(3159..3425)
                     /locus_tag="AABK31_RS25535"
                     /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_061103830.1"
                     /translation="MTNYLIYNRNLFYDGREGMFSISLKIDLFGVKIFIFQPLTGHTFL
                     TRQGGCSKGAGERKRKRGKSSFQNRHIARLMIVPRKIELLANC"
                     /name="hypothetical protein"
     gene            3614..4000
                     /locus_tag="AABK31_RS25540"
                     /old_locus_tag="VEE22_49550"
     CDS             3614..4000
                     /locus_tag="AABK31_RS25540"
                     /old_locus_tag="VEE22_49550"
                     /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="DUF4156 domain-containing protein"
                     /protein_id="WP_139059185.1"
                     /translation="MMVSRILKISALISVAATLSGCAHMDEAASHVQVVNGNNAFTSQC
                     KMLGPVSDEQSEWSFATPGETQAQILINLRSQAYKLYGADTIALQSLGRTGFSTDSGSA
                     IALKCIRPELGSAEAPVHTVIDKQ"
                     /name="DUF4156 domain-containing protein"
     gene            4264..4617
                     /locus_tag="AABK31_RS25545"
                     /old_locus_tag="VEE22_49570"
     CDS             4264..4617
                     /locus_tag="AABK31_RS25545"
                     /old_locus_tag="VEE22_49570"
                     /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_159141169.1"
                     /translation="MRIRQIDKEELRDFIENDLLKSAKYKYATLKEITIDSVARNIHTI
                     VNKAILVEVAKKHIRKELEDQYPNPRDKNEAADKLIDQALQLMIVNENEGIHYQLKEQN
                     EKLERIAKRLESN"
                     /name="hypothetical protein"
ORIGIN
        1 tagatagtcc tacgagtgac cccagcaagt ttagccgcct cagtgacagt gtgacgcgcc
       61 atgtgacacc ctcaatttta tcaaccgtta tggttgtgat cagtagagac aagatcacaa
      121 gaatgtcaca gcgaattacc tatagcaaaa aatccttttt actgtacgga gtagaagcat
      181 ttaatcaaag ccagacagta ttttgatccc gttcctccgt cagagctgca agaaggaata
      241 tccgcttgtt gttggcctcc actgttgcca gcccttccaa cccatcaagc tgatcggcaa
      301 taactccctg aatccatgcg ctggctttcg tcgatggata gcccaacaca tcaacgtatt
      361 ttcccgcgcc gttcgtcagc cctcgccaat ccttttgccc tgcctcttgc gtacaatcag
      421 caagctcagg aaacgcctca agcccctgac ccatcaaccc tctgacttgc tggcgcatgg
      481 tctctaaatc acccttaatc accatttttc caatctcctt ataaatcaga cctgcattcc
      541 tccattcgaa ttgcagatcg ctccactggc tgttagccgt caataaccct ttccagaaaa
      601 tatcccactg gtgacgtggc agcggtctct ggaacctctc aaaatattcc tgtgcgcttg
      661 tttccatctt gcttagctca ttatcccttt tagcggctgc atcgcttaga atggctcctg
      721 ttgcgttata cgtggtctca tatgcaaaac catcagtagc aactttcacc cctcgccaca
      781 cttcccgccc ggtaacacta tcaaccaaag gcagatagag cggttctatg ttctgcccat
      841 cgagtcgatt cgatacagcc agccagcacc aatcaagcgc cgtctctatc tcacccgatt
      901 gctctacggc ttgccgttct ctctcaatag ccagctccac cagctccacc atttcgcaag
      961 caagcgccac tctcagccct tcaccagctt caagtgaacc gtagctttta tgttcctcgt
     1021 acatcgcaat taatcgcccc ttaagctctg tccactcagg gcggcgatac actttgactt
     1081 tgaaagctgg cacatattcc caatcagtaa cgctcgctcc ggtaatgcct tgttgcttgc
     1141 gctgttccat acacttacgt ctggattccc tttcctcagc ggataatatg cctgacttct
     1201 caaagcctgt ttccttgtcg taaaggtcaa acatctgcgc ggcggttaat tgcttgcctt
     1261 caccatctaa aaactcaccc aatacaagcg gcgttaactg tgatgcactg tatttaccag
     1321 gctgaataga gttaccctta ctacgattaa aagcggcttt ctctgctgtc aaattagatg
     1381 caacatgccg cccaatcatt aataccccat cttctgacct gatagcatag ggatcgctgt
     1441 catcaggttt aaccgggtat ttatgcccaa tatcccaatt ctggctgtgc atatttttca
     1501 taacccgaat cacttcgcgc tgaattaaaa gctgattcct cgttagctcc cattccatcg
     1561 cattagctgg cgcacctctc agcgtaccgc ctcgcttgaa atatcggatt atatgatccc
     1621 tcatgctccc atctgccacc cgttcgcctc tcgcgctgtt acgatatgca accgcctccc
     1681 tgttggcgtt ggctctgcgc ttgcattcca cgcagttccg attgttagcg tagcgcgtag
     1741 ttgtaccgca tttactgcaa ggcttgctct gataacaagc caccccatca acggaaaaaa
     1801 tatccttttt aaccatatct aaaatatcct ttttactgta tggggtagaa gcattttaat
     1861 gctctacgac gatattaatt attccacacc acaccgctct aacactttct ttctctgcca
     1921 ttcagctttt gaaagttcat gcttacaggt aacacaacgt ttcgaatttt tatatcgaac
     1981 cttaccaccg cacttcttac actcccgccc tgaataggta gacccaattt gataaaatgc
     2041 catatataga ccctccatga tccatagaaa aaataaaacc tgctccttgc tgctggttaa
     2101 caggacacaa tataaattca ttatacagga cacaaatcac tgtcacgtca ccagcaaaaa
     2161 gcctttaatt tccaaattgt taaagagcaa aaacacaaaa agccgcaatc caatcacttt
     2221 attttgtgat gaatatgcag cctctcgcac ttcctgatag accaattttc cggtatggcc
     2281 tcagataacc gcatatacta cgcaatcgtt ttcctaaatc aacaacaaag accggaattt
     2341 tcatcctgtc tttagtgatc actcactcgg cttgctcttg cttgatgcgc tgtactgtct
     2401 gtgtgcttac tccaaactgc gccgccgtct tgcgaatgct ttcacctgct gccagtgctg
     2461 acacaatgcc tacacggtcg atctcttttc cgttgcctct tgcacctctc cggcctgctg
     2521 ctttcgctgc tgcgtatcct tctgcctgac gttctaacat catctcccgt tccatctgtg
     2581 agactgctgc gaatacgttc aacatcatcc ggctggcggc tgtttcctcg gctccggcaa
     2641 tgatgccctc cttatggaaa ttcacgcttg cgcccttcgc tttcactgcg tcaatgatgg
     2701 ttagcagatc tctcacgtta cgccctaagc ggctcaattc gtggacgtgg ataacatcac
     2761 cctcacgcac atactcaagc atggcgttta gctgcggcct gtctgcattc ttgccgcttg
     2821 ctgtctcggt gaatacccgg tcaagctcaa caccttctaa ctggcgctcg ttgttctgct
     2881 gcacactact gacacgcaca taaccgatat tgctcattcc tgttctctca actgtagtga
     2941 tttagtatgt ggtgattata ggtgtgctga ttaaatcatt taatgctttt tcactacgat
     3001 ttattagctg ttttggtcgg cttattactg tggtgtttta gcgtactatt tcactacggc
     3061 tttacgttct gctggtgggt atgtatcacc ggttatcagc tctcttgctg taaccctgta
     3121 gtgcacccat agcaggtatc gaggtaagga gttcatactt agcaattagc caaaagctca
     3181 atctttcggg gaacgatcat caatctggcg atatgtcgat tttgaaaaga ggacttcccc
     3241 cttttgcgtt ttcgctctcc agcacccttg ctgcatccac cctgacgggt taaaaaagtg
     3301 tgtcctgtta atggttgaaa aataaaaatt ttcacgccaa aaagatcgat tttaaggctt
     3361 atggaaaaca tcccctccct gccgtcataa aataaattac ggttataaat caagtaatta
     3421 gtcatataat catatctgta acttatatga atatgatata agcctatgat tgataatcat
     3481 tttgatgggg taagaggtga tcggttagtg tcctgctaaa attaaatatc aacgtatgta
     3541 gatcggcatc aacagactca acataaacaa ccattaaaat gtgacgaatc tcaaataaaa
     3601 tggcgatata aaaatgatgg taagcagaat attaaaaatc agcgcattga tttccgtagc
     3661 agcaacacta agcggatgtg cacatatgga tgaggcagca agtcatgtgc aagtagttaa
     3721 tggaaacaat gccttcacat cccagtgcaa aatgcttggc ccagtaagcg atgaacaaag
     3781 tgaatggtca tttgcaaccc cgggagagac gcaagcccaa atactaatca acttgcgttc
     3841 tcaagcatat aaattatatg gcgcagatac tattgctctt caatcactag gacgtactgg
     3901 attttcaact gattctggta gtgcaatagc tttaaaatgt attcgcccag aattaggcag
     3961 cgcagaagca ccagttcata cagtgataga taaacaatga agcgatatat ctcattaata
     4021 attctgtgtg cgggactaac atcggtcaca aaagcccaca ctagtgagtg ggttatgatc
     4081 gctgaatcaa aagaccataa cactatagaa tatgcgaaac cagcaacatt tagacatgca
     4141 aatcatgaat caagagtgct aatacaagaa agtgtgtatg acaaaatcag ttaccaaata
     4201 gcgactatca gcgacagcgc atgtgatgtt tctttggtgg ataaaattta gttggagaaa
     4261 aaaatgagaa ttagacaaat agataaagaa gaactcagag attttataga gaatgatcta
     4321 ttaaagagtg ctaagtataa atatgcaaca ctaaaggaaa taactataga tagtgttgca
     4381 agaaacatac atacaatcgt taataaagcg attctagttg aggtagcaaa aaaacatata
     4441 cgtaaagagt tggaagatca gtatccaaat ccaagagata aaaatgaagc agcagacaaa
     4501 ttaattgatc aagcattgca attaatgata gtgaatgaaa acgagggaat acactatcaa
     4561 ctaaaagagc aaaacgagaa attagagcgg atagcgaaaa gactggaaag caactgacaa
     4621 cccccctttt ttcataggct ccgccctcct gccaagcatc acacaatctg acgctcaaag
     4681 caggagtggc gaaacctgac acagcttaaa gatccccacc gtttccgata ggtagctccc
     4741 tcgtgcgctc ctgtgttccc accttacagc ttagcccgtg tctttccgct gttatggccg
     4801 cgttttctca taccacgcct gacactgggt gctgcttagg tggttcgctc caagctggat
     4861 gatatgcacg aactccccgt ttcatccgac cattgcgcct actgggtaac taatctcttg
     4921 aatccaaccc caacagacac ggcaaagcgc cgtcaatggc aatagccatg tggtaacggt
     4981 tctttagtgc gggaactttt acgataggaa gctatgatga tagcttgatt gcttgatatc
     5041 ttgcgcgagg cgcaatacac tgaaagcacg ttttaggtag ctgttcccgc aaaagatgca
     5101 gttacccggt gcagagagcg ccaactcaaa gcaccttcga tcaaaccgcc cgccaaggcg
     5161 gttttttcgt ttctgagcaa gagattacgc cttacccctt cgatccgtca acgatccttt
     5221 ttcaagcgac gtaatgccac ccattcaaca acgctcaaat cacgctttgg tgcgggtaac
     5281 gccagcttgc tttgtagttc gtcaaccttc cctgtcagcg tttctatttg cgctcgcatt
     5341 tgtgacattt cagccaataa aagtgtgaca tattcaggct gattttcgtg tgatctggtg
     5401 tatacctgct ctggctctgg ttgtgacagc gcaccataaa cccgcagtaa ttcactggtc
     5461 tcgatcactg tattgtcatc atctgtcaca gtagctgaaa gctttccagc cttgatgtgt
     5521 cgg
//
