LOCUS       NZ_AP027657             5093 bp    DNA     circular CON 04-APR-2024
DEFINITION  Escherichia coli strain PSJ-42 plasmid pPSJ-42_5, complete sequence.
ACCESSION   NZ_AP027657
VERSION     NZ_AP027657.1
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  JOURNAL   Unpublished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 5093)
  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
            AP027657.1.
            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..5093
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="PSJ-42"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pPSJ-42_5"
                     /geo_loc_name="Ecuador:Puyo"
                     /collection_date="2019"
     gene            join(3599..5093,1..665)
                     /gene="mobQ"
                     /locus_tag="AABK18_RS25020"
     CDS             join(3599..5093,1..665)
                     /gene="mobQ"
                     /locus_tag="AABK18_RS25020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016240513.1"
                     /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_219233555.1"
                     /translation="MAIYHLSMKIISRNSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMERRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIVLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAARLKKSSPFSSGFSRIPLMQWV
                     APEYSSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFETQWQQWGASGLAALRAQL
                     LKREEELRRKEQEDTERRRAERRAEQLRQNDNAVMDSGVLSAVVTGYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRARIFESVDLMRDRSGYICDRSEIGQRPPLQRVYSSA
                     TFEQLLTQVCQTWPQHTRNLRQPKTWPESFCLGEDRQPAMPSPVARKVDFTQGRLPPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPTADNSQLVINALTDKG
                     LRFAGYGEAVNHDADSPARPAPELMLFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRT
                     WDEWQREEYARTRVSDRKHERGWLL"
                     /name="mobQ"
     gene            918..1409
                     /locus_tag="AABK18_RS25025"
                     /old_locus_tag="VEE39_47890"
     CDS             918..1409
                     /locus_tag="AABK18_RS25025"
                     /old_locus_tag="VEE39_47890"
                     /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_032347463.1"
                     /translation="MAIGDDAIRDAFYLFTQQVAEMDNESLPKDVWGTPCFTYLMTRKQ
                     FNQMKVICQRNGWDVPTSPAIPITWSMFKHVLSARKSKDKLSWQECAEILATAFSVQSN
                     VYVSRDYSEQTIVLNASCRISVAGAGFFAMAIIDVSENNLAPVTAYHVTEAKCKAISRG
                     "
                     /name="hypothetical protein"
     gene            complement(1942..2634)
                     /locus_tag="AABK18_RS25030"
                     /old_locus_tag="VEE39_47900"
     CDS             complement(1942..2634)
                     /locus_tag="AABK18_RS25030"
                     /old_locus_tag="VEE39_47900"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001281399.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /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_044716251.1"
                     /translation="MSDLIAYKSNALVEASYKLTLQEQRFLLLCISRLKSGADAELQKT
                     MTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKDDEKREEFRWIQYRAQYAKG
                     EAKARITFSDAVMPYLTQLKGQFTRVVIKNISGLSSSYSIRIYELLQQFRSTGERIIAL
                     NDFRSMLGIENKYKQFRDLNKILIKPCITELNKKSDLVVTVETIKKGRTVAALHFRFKE
                     DKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(3166..3420)
                     /locus_tag="AABK18_RS25035"
                     /old_locus_tag="VEE39_47910"
     CDS             complement(3166..3420)
                     /locus_tag="AABK18_RS25035"
                     /old_locus_tag="VEE39_47910"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091747.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_032347465.1"
                     /translation="MSRTLEQKIAEAEARLQRLKAKSRSLDTAQKVVVGAALLAKVRKP
                     EEVQLRAWLLPFLRREVTRQADLNRIQPLIDELEALPER"
                     /name="hypothetical protein"
     Typing          complement(3425..3598)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.714"
                     /coverage="100.0"
                     /evalue="1.2e-79"
     Typing          3599..3957
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.611"
                     /coverage="100.0"
                     /evalue="1.82e-180"
     Typing          complement(1943..2634)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.711"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          4..656
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="90.367"
                     /coverage="99.0"
                     /evalue="9.03e-125"
     Typing          3513..5092
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.723"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 gtgaccgaag cgaaatcggc caacgcccgc cactgcaacg tgtttattcc tctgcgacct
       61 ttgagcaact gctgacgcag gtttgccaga catggccgca acatacccgc aatctccgcc
      121 agccgaagac atggccggag tctttctgtc ttggagaaga ccgccagcca gccatgccat
      181 caccggtggc aaggaaggtg gattttacgc aaggacgtct gccaccgacg ctgatgccgg
      241 taatgagttc tgtcgaccgg gaaacccgcc agcttcagct tttgctggtc atgggcgtgg
      301 atgactctct gggcggtgtt gtccggctta atggtacgct gtatcctgcg tttgccgtcc
      361 ccacagccga caacagccag ctggtaatca atgctctgac cgacaaaggt ttacgatttg
      421 ccggttatgg tgaagcggta aaccacgatg ctgacagtcc ggcacgccct gcgccagaac
      481 ttatgctgtt tcatctgaaa acccgtgagg caccgctttt tgctgccgtc aatacaccag
      541 aaaaacagcc ggatcatttg ttccgctcgc tgggttttaa tcgcacctgg gacgaatggc
      601 agcgcgagga atatgcacga acacgcgtct ccgacaggaa acatgagcgc ggctggttac
      661 tttaaagcac tttccgcata catatttttt atatgggcga aaacagaata attcgttttg
      721 agatagaaaa tttcaactct agttggtagc gcaacgaccg tgattcggca aacgggagaa
      781 agaccgcgca atagccgttt caggtatgat aataaagcga ttgctcagac attgaattat
      841 gctgagctgt cggcagtgga ataacgacgc gtgaagaccg tcataactaa aaaatgccgg
      901 ataaataagg aaaatcagtg gctattggcg atgatgctat ccgtgatgct ttttatcttt
      961 ttacacagca agtcgctgaa atggataatg aatcactccc taaagacgtc tggggaacac
     1021 cttgtttcac ttatttgatg actagaaaac aatttaacca aatgaaggtc atttgtcaga
     1081 ggaatggttg ggatgtaccc acatcaccgg cgatacctat cacttggagt atgttcaagc
     1141 atgtgctctc tgctcgaaaa tcgaaggata aattaagctg gcaagaatgc gcagaaatct
     1201 tggcaactgc tttttctgtg cagagtaatg tatacgttag cagagattat tcagagcaga
     1261 cgattgtact taatgcttct tgtcgcatca gcgttgcagg ggcaggattt ttcgcaatgg
     1321 cgattattga tgtctctgaa aataatttgg cccccgtaac tgcatatcat gtgacggagg
     1381 ccaaatgtaa agctatatcg cgagggtgat aggaaggacg cccatttaag cagctctcct
     1441 caatttaatg agaatgaacc ataacgccta aatatttccc ttcattgttt cctttcggat
     1501 ctagcagcat cggcggtttt ctgctgtcta tcaaatcgct aattgtttag gaacatcaat
     1561 gctcccactg ccgaacatta gaggatttct ccgtttatgg aatgttcttg cagtacattc
     1621 aatctacatc aattgtggct atagtacaat atttattgag cgcagctaag gctaaactcc
     1681 ccgcgaacag gggcttaaga tagggtgtgg aatgtcgcat tttgtgactt aggggcctca
     1741 tctgcctcaa ttagttttat ccgattggta ctggttgtta gcgtagagtg atgactatgg
     1801 tccaactgga acccaaacgc taaagatgct ttaaagctct ctaaagttat ttttacgcag
     1861 ttttcccctc tcttccatcg ccaccattac cagatgtaaa aaaatgcgcc agcgcgcgtt
     1921 ttagatgcct taaaatcgat tttagatcgt catcttgatc tgcttgtctt ccttgaatcg
     1981 aaaatgcagt gctgcaaccg tgcgcccctt cttgatcgtc tcaaccgtca caaccagatc
     2041 gcttttttta ttcagttccg tgatacaggg ttttattagt atcttattta agtctctgaa
     2101 ttgtttgtat ttattttcaa tgcctaacat tgaacgaaag tcattaagag caataattct
     2161 ctctcccgta ctgcggaatt gctggagaag ttcgtatatt cttatactgt aactgcttga
     2221 taaacctgat atatttttta taacaacgcg cgtgaattgc cccttcagtt gcgtcagata
     2281 aggcattacc gcgtcagaga aggttattcg agccttggcc tcacctttag cgtactgtgc
     2341 gcgatactgg atccagcgga actcctcacg cttctcgtca tccttgagaa tgatcgacct
     2401 gtcccataaa cgatcgatcg cttcctgtaa ctgaacctcg gcatttttcc gccccatgtc
     2461 agggaatgaa tcaaaatatt ccgcggcggt aatggtcatt gttttttgca attcagcatc
     2521 agcaccagat ttcaatcgac tgatacacag caacagaaaa cgttgttcct gtagggtcag
     2581 tttgtagctg gcctcaacta gagcattcga cttgtaggca atcaagtccg acatacaaag
     2641 ctcccgttca aatgtggtga tactttaatg tgccccacaa ataagaaatg tggaatattt
     2701 ttttttatat cctcacattt ctgtgaataa caccttaaat tcctccacct ttaccttaaa
     2761 tccctccacc taaacacctt aaattcctcc acctttacct taaatccctc cacttataca
     2821 agtgtaatcc attgatttta ataatgaatt tcacccctaa aacaagtatt aaaaacaaga
     2881 tcttaaaaac aagatctaaa aacttaacgg cgagcctgtg gaaaacttag gatgccaaaa
     2941 agaaaaactc agtaaaaaca atgtgttgca aaaaagtaga attgcaaatt ccgaatactc
     3001 cccctccagc cctgtggaaa tccagtattc atgcgggttc agcgcgtatc acctgccgaa
     3061 aaaccgtgcg tatgtgctca acctggctac gggttcactt ccgcttcctc gctcactcgc
     3121 tcgctaacgc tcggtcgctg gggctgcggc gagcggacgg tgtaatcacc gttctggcag
     3181 tgcctccagc tcgtcaatca gtggctgtat cctgttcaag tcagcctgcc gtgtaacttc
     3241 tctccgcagg aacgggagca accaggcccg caactgcact tcctccggct ttctgacctt
     3301 tgccagcaat gctgcaccca caacgacctt ctgcgctgtg tccagactcc tgctcttcgc
     3361 cttcaggcgc tgcaatctgg cctcagcttc ggcaatcttc tgttcgagtg ttctgctcat
     3421 tccgtaactc cgtgcgcgat gaaaaatcgc attttagcgc gtcactggca gtttaaaaac
     3481 tgaactggca taatgcacgg cacatcacaa agtgcgcact tatacaatct ccactccgtt
     3541 tcgattgtgt gcgccctgcg gggctgaaag aaaacggcaa aaaggcatta cggcagaaat
     3601 ggcgatttat catctcagca tgaaaatcat ctccagaaac agcggctaca gcgccgtcgc
     3661 ttctgctgcc tatcgttccg gttcactgat gcttgatgag cgtacaggac tgactcatga
     3721 ctacacccgc aaaagcggtg tggctgaagc tgtgattctg acccccgcga cagcccctgc
     3781 ctggtgtacg aaccgtgccg aactctggaa tgccgttgag aaggccgaac gccggaagaa
     3841 ctcacaactt gcgcgggaaa ttgaactcgc catcccccgc gaactgccgc aggatgccgc
     3901 acgggaaacc gttctcgcct ttgtcagaga aaactttgtc agtcagggca tgattgctga
     3961 tgtggcgttc catcacatgg ataaaacaaa tccccatgcg cacatcatgc tgaccacgag
     4021 ggctgtcgga cctgctgggt tcggcggaaa ggtcagggac tggaacgacc ggacacatgc
     4081 cgagacgtgg cgggcatcat gggctgacca tgcaaacagg gcactggcga acgccggtta
     4141 tcaggaagag atagaccatc gttcatacga gcgacagggg cttgagaaaa cgcctggtat
     4201 tcacctcgga aagtctgcct gtgcgatgga aagacgcggt atcgaaacag aacgcggcga
     4261 acagaatcgt ctgattaaca ggcttaacct ggaaatacag atttcccgta ccgaactcag
     4321 gaacagcggg ctgacagagc ctgcccgccg tgtggctgac cttctgaata tcgtgcttcc
     4381 tgacaacgca acttcgtaca cactacgtga catcatcgaa gcgttgccga aggacagtaa
     4441 cgcggcatgg aaactcacca gtaatgccat gtcgatgatg gcagatatgc aggcgacacg
     4501 cagacgctgg gaagagctga acaccgaacg aaaggaagcg atgagccatg ctgccagact
     4561 gaaaaaatca tcgccttttt cgtccggttt ttcccgtatt cccctgatgc aatgggttgc
     4621 accggaatac agtagcgaac agggcaaaat ccagtcgctg agtcagcaaa tggaaaaatt
     4681 gcgacagcat taccggaagg tggagaaaca ggacattccc gcgagtcaga cggcatttga
     4741 aacacagtgg cagcagtggg gcgcatccgg ccttgcagct ctcagagccc agttgcttaa
     4801 acgtgaagag gaattgcgcc ggaaggagca ggaggataca gaacgtcgtc gcgcggagcg
     4861 acgggctgag cagctcaggc aaaatgacaa tgccgtcatg gattcagggg tactgagtgc
     4921 ggtcgtaacg gggtatggcg aggcccctat gcctggtaac ggggaaatga cctgttacct
     4981 tctgcttcac aaccgtaacg gagaatatac gctctggggg aacgaactgg agaaataccg
     5041 cgccagaatc tttgagagtg ttgatttaat gcgtgacagg agtggttata tct
//
