LOCUS       NZ_AP027659             4732 bp    DNA     circular CON 04-APR-2024
DEFINITION  Escherichia coli strain PSJ-42 plasmid pPSJ-42_7, complete sequence.
ACCESSION   NZ_AP027659
VERSION     NZ_AP027659.1
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  JOURNAL   Unpublished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 4732)
  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
            AP027659.1.
            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..4732
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="PSJ-42"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pPSJ-42_7"
                     /geo_loc_name="Ecuador:Puyo"
                     /collection_date="2019"
     gene            join(4656..4732,1..199)
                     /locus_tag="AABK18_RS25080"
     CDS             join(4656..4732,1..199)
                     /locus_tag="AABK18_RS25080"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091757.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_039023505.1"
                     /translation="MSRTLEQKIAEAEARLQRLKAKSRSLDTAQKVIVGAAMLARVRRP
                     EEAQLRAFLLQFLRKEVTRQADMNRLQPLINELEKLPRPPAKPQNH"
                     /name="hypothetical protein"
     gene            complement(406..1341)
                     /locus_tag="AABK18_RS25085"
                     /old_locus_tag="VEE39_47990"
     CDS             complement(406..1341)
                     /locus_tag="AABK18_RS25085"
                     /old_locus_tag="VEE39_47990"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011666805.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_136700525.1"
                     /translation="MSAALQYFEENLPHRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDHEGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAVERSLCEKLCADVNYSGLICKNPFHLEWQVMEWREEAYTLDELADYLDLSASE
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPVFSQWLDAVIQRVEMYNASLPVPLSP
                     AECRAIGKSIAKYTHRNFTPETFAQYVATTHTPEIQAARGRKGGIAKGAGYEDKRSTAL
                     EMLVNGCTQKAIAEMLGVSDRTIRNWKSGK"
                     /name="replication initiation protein"
     gene            complement(<1873..2025)
                     /locus_tag="AABK18_RS25090"
                     /old_locus_tag="VEE39_48000"
                     /pseudo=""
     CDS             complement(<1873..2025)
                     /locus_tag="AABK18_RS25090"
                     /old_locus_tag="VEE39_48000"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_172690082.1"
                     /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="colicin-E9"
                     /name="colicin-E9"
     gene            complement(2258..4477)
                     /gene="mobQ"
                     /locus_tag="AABK18_RS25095"
                     /old_locus_tag="VEE39_48010"
     CDS             complement(2258..4477)
                     /gene="mobQ"
                     /locus_tag="AABK18_RS25095"
                     /old_locus_tag="VEE39_48010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001029330.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobQ family relaxase"
                     /protein_id="WP_103809171.1"
                     /translation="MAIYHLSMKIISRKNGYSAVASAAYRSGSVIPDDRTGLTHDYTRK
                     RGVDDAVILTPVNAPSWCGDRSVLWNAVEKAEQRRDSQLAREIELAIPREISREAARET
                     VLAFVRENFVSRGMIADVAFHHMDRTNPHAHIMLTTRAVGETGFAGKVRDWNDRALAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKAPGLHLGKAACAMEKRGMETERGEQ
                     NRLINSLNLEIQVSRTRLAVIQVQENVRKRELSDAARRAAEALNLTIPAANASADTLRE
                     FIATLPQECGNAWEMTPEFVAMNGKANDIKREGNALVKERDILEKEMTGLRKARPVASI
                     LSELPLMTWAEPEYRKRQLRFWKLEKQIESLLRTYRAVKERDIPARRQAFETQWNTWIS
                     PGMAELKEKLSAREAERRREEAEAEARRKEQEYDARLKHHDNHRLSRETALAGVITGLG
                     RAREPGTGRITRYMMLSNRAGEFTVWGDELAHYPQSVHDPVNVYLSPGGAVMVSDIREG
                     MPESHETMARPERVRMYSGATVRHVLEQMRQGWPSYGFPALPHHWPDNFYFSDDRRPVA
                     SPLPSAHRVDVTAYAAPEQLMPVVFSTERNSRTLNLLLCKGPEEVLVGFVRQEDGLRPV
                     LALPSPDYSHLIVSTITENGVCLAGYGEAINHDADTPYPPEPHLMQFRLKGHHDRLLAA
                     VHKPEEMPDYLFRQLGFNQTWHEWKRDEQHRQQQRRPGHFRGMSM"
                     /name="mobQ"
     Typing          4120..4478
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.056"
                     /coverage="100.0"
                     /evalue="3.94e-177"
     Typing          4479..4649
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="95.93"
                     /coverage="97.0"
                     /evalue="5.74e-73"
     Typing          complement(407..1341)
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.415"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(2262..4477)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="94.723"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ggacacggcg caaaaagtca ttgtgggggc tgccatgctg gcgagggtac ggaggccgga
       61 agaagcgcaa ctgcgagcgt tcctgctcca gttcctgcga aaggaagtca caagacaggc
      121 cgatatgaac cggctacaac cgctgattaa cgagctggag aagctaccca gaccacctgc
      181 gaaaccgcag aaccactaag ccccggcgcg taagtgccac atgcaccacc ggacgccttt
      241 gcgcttcctc gctcattcgc tcgctacgct cggtcatgag actgcggcga gcgcttccac
      301 cgcaatcacg aggaaaccag cgccattgct ggacggaacc ggaaaaacca caggaacacc
      361 aaaagctcaa aaaagcgccg aaaaggcgct gttatctgat ataggctatt ttccgctttt
      421 ccagtttcga atagtgcgat cggaaacacc taacatttca gctatagcct tttgagtaca
      481 cccattcacc aacatttcca gcgcggtgct gcgcttatcc tcatagccag cccctttggc
      541 tataccacct ttacggcctc gggcagcttg aatttccggc gtgtgcgttg tcgccacata
      601 ctgtgcgaaa gtttccggcg taaagttcct gtgcgtgtat ttcgctatgc tcttgccaat
      661 agcccgacat tcagccggag aaagcggaac gggaagtgat gcgttgtaca tttcgacacg
      721 ctggatcacg gcatcaagcc attgtgagaa tacaggccag ccctgacgaa tcgccctgta
      781 agcccatttg cgcgtcattt cgaacaggtg gcagtttcgc cccatcccgt aatgtttatc
      841 gatgctacga cgctctgagg cgctcaaatc gagataatct gccagttcat cgagggtata
      901 ggcttcctcg cgccactcca tcacctgcca ttccaggtgg aacggatttt tgcaaatcag
      961 tccgctgtag ttcacatcag cacaaagttt ctcacacagc gaacgttcaa ccgctgcggc
     1021 atatttcagc gccttaaccg acgcatcagg cgcggttctc acggcgatat tgagtgcata
     1081 gagcaggtga gcgtgtccgt tcacaggatt tttaacggtg atgttcggcg cgggggcgtt
     1141 ccggtcgctc cagtcaatcg ctgccccctc gtggtcaacg tcaaaaacca gccagaactg
     1201 cgcatgaggc tggttctgct ggatgtaccg cgcaagaagc gcacgccctt tgccggagat
     1261 gcgaaggccg aaagcgagat catccgtgtg atagggacga tgaggtaaat tttcttcgaa
     1321 gtattgaagc gcggcgctca tgtgttacga ttccttccag gttatcgacc gacctcgccc
     1381 ctgtattctc gtgacaatct tggcggagag acacgaattt caggggcgtt tgtttttcag
     1441 tcgcttacac tacacccaac ggcaaactct gtcgattatt ccccaaaacc cgatccattt
     1501 accataactc ccgttgtacg taccccttaa aacgctctca gacgcgttct gacgcaaaaa
     1561 acgcaaaaag acaaggaaac accaggctga accagaaaaa tgcgtcagaa tcgtttttag
     1621 ggcgctgcat aactatgcac gaaagcgatg cgcgatcggt ttcgaccgtt ccgaatggcg
     1681 aacaggtcaa aatgacaagt tttctcccac cggatggaag gttctgcaca gggattttag
     1741 atcccatctc ccacatggaa tttttgtgac acttcaaaaa aaagcgcgtc agaatcagcc
     1801 tgacacgctt tgttcttgtc aaagaggatt tcgggttact gcgttgctaa tccggtcagt
     1861 tcagctgagg ataccggaac caccacccca cgggttattt tccgaactcc acccggaacc
     1921 atcagaagca ccaccaccta caccaagccc ggtcgggcca ccattaatgt taccacttgt
     1981 gctatgcgcg cccgtgttat ggccgcgtcc atcgccaccg ctcataaaaa ttccctcttt
     2041 taagcgttaa aacaattaat tacacgatta atactgtaca taaaaccact ggttttatgt
     2101 acagatcaaa aagtacccgt catcgttttt tctgtcaagt tcaggtggaa aattttttag
     2161 aaatcaggag ggataacact tagaaaacgc agagcggacc acaaaaaatt ttgtggcccg
     2221 tgatgtgttg gtagggttcg gggggctgcc ccggatatca catactcatg ccccggaagt
     2281 gcccggggcg gcgttgttgt tgcctgtgct gttcgtcccg cttccactca tgccaggtct
     2341 gattaaaacc gagttgacgg aagagataat ccggcatctc ttccggtttg tggacagcag
     2401 ccaaaagcct gtcatgatgg cctttgagcc ggaactgcat caggtgcggt tccggtgggt
     2461 acggagtatc cgcatcatgg tttatagctt ctccgtaacc tgccaggcat accccgttct
     2521 ccgtgatggt gctgactatc agatgactgt aatccggcga cggaagcgca agaacgggac
     2581 gcagcccgtc ctcctggcgc acaaatccga caagcacttc ctccggccct ttgcacaaca
     2641 gcagattcag cgtcctgctg tttcgctctg tcgaaaatac aacgggcatg agttgctccg
     2701 gtgccgcata agcggtgacg tccacccggt gcgcagacgg cagcggagag gctacgggcc
     2761 tgcggtcgtc gctgaaataa aaattatccg gccagtgatg cggcagcgcc ggaaaaccgt
     2821 aagagggcca cccctggcgc atctgttcca gtacatgccg gaccgtcgca ccggaataca
     2881 ttctcacacg ctcaggccgc gccatcgtct catgagattc tggcattccc tcacgtatat
     2941 ccgagaccat cacagccccg cctggcgaca ggtaaacatt caccgggtca tgaacactct
     3001 gggggtaatg cgccagctca tcaccccata ccgtgaattc tccggctctg ttactcagca
     3061 tcatgtagcg ggttatcctg cccgttcccg gctctctggc acgccccagc cccgtaataa
     3121 ccccggctaa tgccgtttca cggctcaggc gatggttatc atggtgtttc agccgtgcgt
     3181 catattcctg ttccttccgg cgcgcttccg cttcggcttc ctccctgcgc cgctccgctt
     3241 cccgtgctga cagtttttct ttcagctctg ccattcccgg cgaaatccac gtattccact
     3301 gcgtttcaaa ggcctgacga cgggcgggaa tgtcccgttc tttcacggcc ctgtaggtgc
     3361 ggagaagaga ttcaatctgt ttctcgagtt tccagaagcg gagttgtctt ttgcggtatt
     3421 ccggttcagc ccatgtcatc aggggaagct ctgacaggat ggacgctacc ggacgggctt
     3481 ttctgagtcc ggtcatctct ttttcgagaa tatcccgctc tttcaccagc gcattcccct
     3541 cacgtttgat gtcgtttgcc ttcccgttca tcgccacgaa ctccggtgtc atctcccatg
     3601 cgttcccgca ttcctgcggc agtgtggcaa tgaattcccg cagggtatcc gctgaggcat
     3661 tcgcggcggg aatggtcaga ttaagggctt ccgctgcacg acgtgcggca tcgctgagtt
     3721 cccgtttccg cacgttctcc tgtacctgga tgactgccag ccttgtgcgg gaaacctgta
     3781 tttccaggtt aaggctgtta atcagacggt tctgctcacc gcgttctgtt tccattcccc
     3841 gtttttccat cgcacaggca gcctttccga ggtgaaggcc gggcgctttc tccagtccct
     3901 gacgctcgta tgaacgatgg tctatctctt cctggtagcc ggcgttcgca agcgctctgt
     3961 tcgcatggtc agcccatgat gcgcgccacg tctcggcgag tgcccggtcg ttccagtccc
     4021 tgacctttcc tgcaaatccc gtttccccga cagctctcgt ggtcagcatg atgtgcgcat
     4081 ggggattggt ccggtccatg tgatggaacg ccacatcggc aatcatgccc cgactgacaa
     4141 agttttcccg gacaaaagcg agaacggtct cccgtgcggc ctcgcgggaa atctcacggg
     4201 gaatggcaag ttcaatctcc cttgccagct gggagtcccg gcgctgttcg gctttctcga
     4261 ccgcattcca gagaacggaa cggtcaccac accaggacgg tgcattcaca ggggtgagaa
     4321 tgaccgcatc atcaacgccg cgtttacggg tgtaatcgtg ggttaatccg gtacgatcat
     4381 cgggtatgac agagccggaa cggtaggcag cagaagcaac ggcactgtag ccgttttttc
     4441 gcgaaatgat tttcatgctt agatgataaa tcgccatttc ttccgtaatg cctttttgcc
     4501 gttttctttc agccccgcag ggcgcacaca atcgaaacga agtgaagatt gtataagtgc
     4561 gcacttcgtg atgtgccgtg cattatgcca gttcggtttt gcaactacca gtgacgcgct
     4621 aaaatgcgat ttttcaccgc gcacggagtc acgaaatgag cagaacactc gaacagaaga
     4681 ttgccgaagc tgaggccaga ttacagcgcc tgaaggcgaa gagccggagc ct
//
