LOCUS       NZ_AP027561             4237 bp    DNA     circular CON 04-APR-2024
DEFINITION  Escherichia coli strain LR-58-1 plasmid pLR-58-1_8, complete
            sequence.
ACCESSION   NZ_AP027561
VERSION     NZ_AP027561.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00562503
            Assembly: GCF_036497325.1
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  JOURNAL   Unpublished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 4237)
  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                   :: 274x
            Sequencing Technology :: MGI DNBSEQ-G400RS; ONT MinION Mk1c
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_036497325.1-RS_2024_04_03
            Annotation Date                   :: 04/03/2024 23:57:35
            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)                     :: 5,032
            CDSs (total)                      :: 4,911
            Genes (coding)                    :: 4,681
            CDSs (with protein)               :: 4,681
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 230
            CDSs (without protein)            :: 230
            Pseudo Genes (ambiguous residues) :: 0 of 230
            Pseudo Genes (frameshifted)       :: 70 of 230
            Pseudo Genes (incomplete)         :: 161 of 230
            Pseudo Genes (internal stop)      :: 41 of 230
            Pseudo Genes (multiple problems)  :: 41 of 230
            Pseudo Genes (short protein)      :: 4 of 230
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP027561.1.
            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..4237
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="LR-58-1"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pLR-58-1_8"
                     /geo_loc_name="Ecuador:Santo Domingo"
                     /collection_date="2019"
     gene            join(3596..4237,1..72)
                     /locus_tag="AABJ65_RS25130"
     CDS             join(3596..4237,1..72)
                     /locus_tag="AABJ65_RS25130"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001590713.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type IV secretion system protein"
                     /protein_id="WP_001590713.1"
                     /translation="MNKKLIFSVLLCLFSFGSVAGIPVAIDASPEWAVEATRWTERLKQ
                     WSETARHYQSQIQAYKDQLATATGIRNIAAFTNELSNLQSELANIYKQGNSYISDFTSN
                     PEGALSSQAKNLFSKYGAFNMCSTGIESSDNLCKARIVSTAASIEQGNEINKQLSSAMS
                     QIQSLSNRIESSKDMKESQDLANALQAQSLKIQAIKMQYDVWDSKNRADAEMLKEQKYA
                     EYRLRQKNAKIPSFE"
                     /name="type IV secretion system protein"
     gene            1259..1774
                     /locus_tag="AABJ65_RS25135"
                     /old_locus_tag="VEE07_47920"
     CDS             1259..1774
                     /locus_tag="AABJ65_RS25135"
                     /old_locus_tag="VEE07_47920"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000097059.1"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA];
                     GO:0006276 - plasmid maintenance [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication/maintenance protein RepL"
                     /protein_id="WP_000097059.1"
                     /translation="MSSLSLQRYETNPFLELMTIPMKGKRIQVSRLGRDDNVLVNQNTG
                     EKFGTHVTTFKRVDSEQFVKLFTANIGLTFDLSSAGIKAFNVLLWAVQKQAFAKDQVLL
                     DSRALDDFLKSYDSLKLSYATLKRGINELEKAQIIAKTMRKGFYFINPNFVFNGDRIAF
                     TTLIERDC"
                     /name="replication/maintenance protein RepL"
     gene            1817..2245
                     /locus_tag="AABJ65_RS25140"
                     /old_locus_tag="VEE07_47930"
     CDS             1817..2245
                     /locus_tag="AABJ65_RS25140"
                     /old_locus_tag="VEE07_47930"
                     /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_338381825.1"
                     /translation="MVPFDIGLSKNRVFACACRRLLEVVAGEQKWCFVRLLITTTWLEV
                     FMTKHDAIRISQLHQIFYDDDGLIDSEKNVTILYSIGFTVDEIAHFRNSTPNTVAGQLL
                     NARVKLGCASVSSLKPMILLRLLLNIKEIRFGFETDCK"
                     /name="hypothetical protein"
     gene            2333..2596
                     /locus_tag="AABJ65_RS25145"
                     /old_locus_tag="VEE07_47940"
     CDS             2333..2596
                     /locus_tag="AABJ65_RS25145"
                     /old_locus_tag="VEE07_47940"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001677227.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="EexN family lipoprotein"
                     /protein_id="WP_000717655.1"
                     /translation="MKKICTLLMSIFILSACGEDTKSSDWWLNHPKEATEKYKECKKSG
                     EDSVNCQNVKKVAGIIGRTYGPMLEILKAESAEYDKQHGLNR"
                     /name="EexN family lipoprotein"
     gene            2601..3599
                     /locus_tag="AABJ65_RS25150"
                     /old_locus_tag="VEE07_47950"
     CDS             2601..3599
                     /locus_tag="AABJ65_RS25150"
                     /old_locus_tag="VEE07_47950"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000012467.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type IV secretion system protein"
                     /protein_id="WP_000012467.1"
                     /translation="MSGFFEKFNSEVVSKIEEMTKPLQSQLGQDMLSLLSAGISVYILW
                     VGYQILAGKRQTPLQDLVWDLSKFAIILTFVSNADGYLTAAMDAIKSMKDGFLGKPVWA
                     TLDTMWSTTQLLADKVYAMDQSKYVSVEGGIGSMLVWGGSILIMSVAAVIYMLADVTMQ
                     LAILVAPIFIGCYMFGFTRVMFNNWLGILFSSVFTVIFAGVLVKIGTEFQTDMLSQISR
                     DANSTNILTMGAMAFVIGVLIAVFVWKSSSFAQQLAGAGVEGTLQGMALLGIGAAGMAV
                     EKTRNQMKRGTRTAAEWAGEKGEQKRASIGALGMEARRRASLEKARARNSA"
                     /name="type IV secretion system protein"
     Typing          2602..3404
                     /name="MPF_T"
                     /typing="mate-pair-formation"
                     /tool="MOB-suite"
                     /identity="89.552"
                     /coverage="91.0"
                     /evalue="1.15e-160"
ORIGIN
        1 atgttgaaag agcaaaagta tgctgagtat cgcctgcgtc agaaaaatgc aaagataccg
       61 agtttcgaat gatatgataa agctaaataa gctaaaagaa tgggtagata atcattggtc
      121 tagattgaat agtaccggtt ctacaccgcc gccactgtta atctcgctac caatcatagt
      181 tattgtttta agtgtggagc ttacgttaaa gctggttaat gctttaatgt attatggtac
      241 attgcaattt atcactgata aaattgaaaa gaggtttgtt cccagcggtg gtataaaaga
      301 aagactcctt tttacgttaa agctgttttg tattttactt ctgttattaa tagtaatgcg
      361 attttcaatg aagtaaaaaa taaaggtcat cgaatagatg gccttttcta ttctaaattc
      421 taaatataga gcctgcggca ggcacaggca aaaacatcgt ttttggacaa tctgattcaa
      481 atgttaacat ttgacatcgg attgtctatc ctgcattgct cttttgccga cctcaaaacc
      541 cctagcgtgt ttttgtttcc cgatctctag aaccaccgag ccgccacggt tccggcagcg
      601 ccttgagcgc aaccggaaac cgtctgggga gaaccccaga cccccatcgc tgtaacatcg
      661 acggtctacg accacctacc aaccgtgtgg ctacctgttc cgtgctaatg ggctttgcag
      721 ggggctggcg cggttcctgg cgacctgaaa gcccctggtt aggggtatcg gcgcgcctga
      781 cctcctgaaa ccctctgtaa gcatttttcg cgccttccat gccctgacgg gcatctaaag
      841 cccgtttcgt gcgtctgagc gcgttttaag agctaagacg actaaaacat taccaacacc
      901 tgaaaatcgc gttctggtgc tctggatggc ccacagaacg cattttcgaa cagaacagca
      961 acggcatttc tgacaacatg cgagaggtga tcccgctcgc cgcagcccca gcgaccgaac
     1021 gtagtgagcg agtgggcgag gaagcggaag agaattgata gccataattg agcacctacg
     1081 ctccttagtt aagaactaag aagggaaatt ctcggaaccc gcatgaatcc tagaaagtgg
     1141 tgatcaggat ctgtaccttg taagctcaga tccggtacct tgcaggctca aaaattgctt
     1201 gattttgagc ttatgaggat ttattgtgaa tctccaaagc ccaaaaaagg atgcaataat
     1261 gagctcgcta agcttacaga gatacgaaac aaacccgttt ttagagctta tgacgatccc
     1321 gatgaaaggg aaacggatac aagtatctcg tcttgggcgg gatgacaatg ttttggttaa
     1381 tcaaaacacg ggagaaaagt ttggaacaca tgtaaccact tttaagcgtg tagatagtga
     1441 gcaatttgtt aagttgttta ctgcgaatat tgggttaacg tttgatttat catcggcagg
     1501 aattaaagct tttaatgttc ttttatgggc tgttcaaaaa caagcctttg caaaggatca
     1561 ggttcttttg gattcaaggg ctcttgatga ctttttaaaa agctatgata gcttaaaact
     1621 tagttatgct acgttaaaga gaggaattaa cgagttagaa aaagctcaga ttatagcaaa
     1681 gacaatgcgt aaaggatttt attttataaa ccccaatttt gtatttaatg gagatcgaat
     1741 agcatttaca accctaattg agagggattg ttaatcgata gaacaataca atgcaggata
     1801 gacaatccga tgtcaaatgg taccattcga tatcggattg tccaaaaaca gggtttttgc
     1861 ctgtgcctgc cgcaggctac tagaagtagt cgcaggcgaa caaaagtggt gttttgttcg
     1921 cctgctaatc acaacaacct ggctagaggt ttttatgact aaacatgatg ctatacgcat
     1981 ttctcaactt catcaaattt tttacgatga tgatggatta attgattcag aaaagaacgt
     2041 gactatttta tacagtatag gatttacagt tgatgaaata gctcatttta gaaattcaac
     2101 accaaacaca gttgcgggtc agctattaaa tgcaagggtt aaattaggtt gcgcctcggt
     2161 ttcatcttta aagccaatga tcttattaag attgcttttg aacataaaag agattcgttt
     2221 tggattcgaa actgattgca aataatatag ttcaataggt atttttgctc ttgactagaa
     2281 ttacaattgc tgattgtatc agcaattgta atgtccatac gaggaatcaa agatgaaaaa
     2341 aatttgtacg ctcttaatgt ctattttcat tctttccgca tgtggtgaag atacaaaatc
     2401 atcagattgg tggcttaatc atcccaaaga agcgacggag aaatataagg agtgtaaaaa
     2461 gtcaggggaa gattctgtta attgtcaaaa tgttaaaaaa gttgccggaa ttattggtag
     2521 aacctatggc cctatgcttg aaatacttaa ggctgagtca gctgaatatg ataagcaaca
     2581 tggattgaac aggtgataac atgtctggtt tctttgaaaa gtttaatagc gaagttgtta
     2641 gtaaaatcga agagatgacc aaaccacttc aaagtcaatt aggtcaggat atgttatctc
     2701 ttctaagtgc aggtattagc gtttatatcc tctgggttgg ctatcaaata ttggcaggga
     2761 aacgccagac cccattacaa gatctcgtct gggatctatc aaaatttgcc attattttaa
     2821 cattcgtaag caatgctgat ggctatctga cggcagcaat ggatgctatt aaatctatga
     2881 aggatgggtt ccttggtaaa cctgtatggg caacgctaga taccatgtgg agtacaactc
     2941 agcttttggc tgacaaagtt tatgctatgg atcaatccaa atatgtgtca gttgaaggtg
     3001 gaatcgggtc aatgttggtt tggggaggaa gtatcctgat tatgtctgta gcggctgtta
     3061 tttacatgct tgccgatgta acaatgcagt tagctattct tgtagctccg atatttatcg
     3121 gttgttatat gtttggattc actagagtaa tgtttaataa ctggcttggt atattatttt
     3181 ctagtgtatt tactgttatt tttgctggag ttctcgtcaa aattggtacc gagtttcaaa
     3241 ctgatatgct tagtcagata tcgagagatg ctaactcaac aaatatttta acaatgggcg
     3301 caatggcatt tgtaattgga gttctgattg ctgtctttgt ctggaaatca tcgagtttcg
     3361 cgcagcagct tgccggtgca ggtgttgaag gtactcttca gggaatggct cttttaggga
     3421 ttggggctgc tggaatggcc gtagagaaaa cgagaaacca gatgaaacgt ggaacgcgaa
     3481 cagccgccga atgggcaggt gaaaaagggg agcagaaacg ggcttcaata ggcgcattgg
     3541 gaatggaagc aagaagacga gcatccctgg aaaaagcacg tgcgaggaat tcagcatgaa
     3601 caaaaaacta attttttcag tacttttgtg cttattttca tttggttctg tcgcaggtat
     3661 tccggttgct attgatgcca gtccggaatg ggctgttgaa gccacaagat ggacagaacg
     3721 actcaaacaa tggtctgaaa cagcgcggca ttatcaaagt cagattcagg catataaaga
     3781 ccagttagcc acggcaacag gtataaggaa tattgcggca ttcacaaatg aactaagtaa
     3841 cctacaatca gagctggcaa acatttataa gcaggggaac agttatattt ctgattttac
     3901 cagtaatcct gaaggtgcat taagtagtca ggcgaaaaat ctgttcagca agtatggtgc
     3961 ttttaatatg tgttctacag gcattgaaag ttctgataac ctttgtaagg ccagaatagt
     4021 ttcaacggcc gctagcattg aacagggaaa tgagataaat aagcagctat caagtgcaat
     4081 gtctcagatt cagagtttaa gtaaccgaat tgagtcttca aaggatatga aagaatccca
     4141 ggatttggct aacgcattgc aggcgcagtc gttaaaaata caggcaatta aaatgcagta
     4201 tgatgtatgg gatagtaaaa acagggctga tgcggaa
//
