LOCUS       NZ_CP043037             6731 bp    DNA     circular CON 26-APR-2024
DEFINITION  Escherichia coli strain XDL plasmid pXDL-4, complete sequence.
ACCESSION   NZ_CP043037
VERSION     NZ_CP043037.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN10691120
            Assembly: GCF_008949495.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6731)
  AUTHORS   Cui,Y., Quan,J., Liao,W., Zhao,D., Jiang,Y., Du,X., Zhao,F. and
            Yu,Y.
  TITLE     A new variant of mcr-1 identified from an extended-spectrum beta
            lactamase-producing Escherichia coli
  JOURNAL   J Glob Antimicrob Resist 18, 26-27 (2019)
   PUBMED   31154009
REFERENCE   2  (bases 1 to 6731)
  AUTHORS   Quan,J.
  TITLE     Direct Submission
  JOURNAL   Submitted (20-AUG-2019) Infectious Diseases, Sir Run Run Shaw
            Hospital, 3# East Qingchun Road, Hangzhou, Zhejiang 310016, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.7
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100x
            Sequencing Technology             :: PacBio RSII
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_008949495.1-RS_2024_04_26
            Annotation Date                   :: 04/26/2024 04:03:38
            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)                     :: 5,378
            CDSs (total)                      :: 5,262
            Genes (coding)                    :: 5,025
            CDSs (with protein)               :: 5,025
            Genes (RNA)                       :: 116
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 237
            CDSs (without protein)            :: 237
            Pseudo Genes (ambiguous residues) :: 0 of 237
            Pseudo Genes (frameshifted)       :: 105 of 237
            Pseudo Genes (incomplete)         :: 159 of 237
            Pseudo Genes (internal stop)      :: 51 of 237
            Pseudo Genes (multiple problems)  :: 65 of 237
            Pseudo Genes (short protein)      :: 4 of 237
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP043037.1.
            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..6731
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="XDL"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pXDL-4"
                     /geo_loc_name="China: Hangzhou"
                     /lat_lon="30.3 N 120.2 E"
                     /collection_date="2017-09-20"
                     /collected_by="Feng Zhao"
     gene            1..927
                     /locus_tag="EOV66_RS27245"
                     /old_locus_tag="EOV66_27260"
     CDS             1..927
                     /locus_tag="EOV66_RS27245"
                     /old_locus_tag="EOV66_27260"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001738986.1"
                     /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_024129980.1"
                     /translation="MSAALQYFDENLPHRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDSSVKA
                     LKYAAAIERSLCEKLCADVNYSGLICKNPFHLEWQVMEWREEAYTLGELADYLDLSASA
                     RRSIDKRYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLDAVIQRVEMYNASLPVPLSP
                     AECRAIGKSIAKYTHRNFTPETFAQYVADTHTPEIQAARGRKGGKIGGAKSKRGAVATS
                     ARTLKPWETLGISRAWYYQLKKRGLVE"
                     /name="replication initiation protein"
     gene            complement(1133..1408)
                     /locus_tag="EOV66_RS27250"
                     /old_locus_tag="EOV66_27265"
     CDS             complement(1133..1408)
                     /locus_tag="EOV66_RS27250"
                     /old_locus_tag="EOV66_27265"
                     /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            3359..3790
                     /locus_tag="EOV66_RS28105"
     CDS             3359..3790
                     /locus_tag="EOV66_RS28105"
                     /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_072276471.1"
                     /translation="MPVVFSTERNSRTLNLLLCKGPEEVLVGFVRQEDGLRPVLALPSP
                     DYSHLIVSTITENGVCLAGYGEAINHDADTPYPPEPHLMQFRLKGHHDRLLAAVHKPEE
                     MPDYLFRQLGFNQTWHEWKRDEQHRQQQRRPGHFRGMSM"
                     /name="hypothetical protein"
     gene            4022..5770
                     /gene="col"
                     /locus_tag="EOV66_RS27260"
                     /old_locus_tag="EOV66_27275"
     CDS             4022..5770
                     /gene="col"
                     /locus_tag="EOV66_RS27260"
                     /old_locus_tag="EOV66_27275"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012644886.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin-E9"
                     /protein_id="WP_073268826.1"
                     /translation="MSGGDGRGHNTGAHSTSGNINGGPTGLGVSGGASDGSGWSSENNP
                     WGGGSGSGIHWGGGSGRGNGGGNGNSGGGSGTGGNLSAVAAPVAFGFPALSTPGAGGLA
                     VSISASELSAAIAGIIAKLKKVNLKFTPFGVVLSSLIPSEIAKDDPNMMSKIVTSLPAD
                     DITESPVSSLPLDKATVNVNVRVVDDVKDERQNISVVSGVPMSVPVVDAKPTERPGVFT
                     ASIPGAPVLNISVNNSTPAVQTLSPGVTNNTDKDVRPAGFTQGGNTRDAVIRFPKDSGH
                     NAVYVSVSDVLSPDQVKQRQDEENRRQQEWDATHPVEAAERNYERARAELNQANEDVAR
                     NQERQAKAVQVYNSRKSELDAANKTLADAIAEIKQFNRFAHDPMAGGHRMWQMAGLKAQ
                     RAQTDVNNKQAAFDAAAKEKSDADAALSAAQERRKQKENKEKDAKDKLDKESKRNKPGK
                     ATGKGKPVGDKWLDDAGKDSGAPIPDRIADKLRDKEFKNFDDFRRKFWEEVSKDPELSK
                     QFNPGNKKRLSQGLAPRARNKDTVGGRRSFELHHDKPISQDGGVYDMDNLRITTPKRHI
                     DIHRGQ"
                     /name="col"
     gene            5773..6030
                     /locus_tag="EOV66_RS27265"
                     /old_locus_tag="EOV66_27280"
     CDS             5773..6030
                     /locus_tag="EOV66_RS27265"
                     /old_locus_tag="EOV66_27280"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000421100.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="bacteriocin immunity protein"
                     /protein_id="WP_000421100.1"
                     /translation="MELKNSISDYTETEFKKIIEDIINCEGDEKKQDDNLEHFISVTEH
                     PSGSDLIYYPEGNNDGSPEAVIKEIKEWRAANGKSGFKQG"
                     /name="bacteriocin immunity protein"
     gene            6092..6235
                     /locus_tag="EOV66_RS27270"
                     /old_locus_tag="EOV66_27285"
     CDS             6092..6235
                     /locus_tag="EOV66_RS27270"
                     /old_locus_tag="EOV66_27285"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000724569.1"
                     /GO_component="GO:0019867 - outer membrane [Evidence IEA]"
                     /GO_process="GO:0019835 - cytolysis [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin release lysis protein"
                     /protein_id="WP_001314446.1"
                     /translation="MKKITGIILLLLAVIILAACQANYIRDVQGGTVSPSSTAEVTGLA
                     TQ"
                     /name="colicin release lysis protein"
     BGC             1..6731
                     /name="RiPP-like"
                     /gene="RiPP-like"
                     /tool="antismash"
     Typing          complement(1410..1588)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.778"
                     /coverage="100.0"
                     /evalue="7.47e-67"
     Typing          complement(1589..1935)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="86.436"
                     /coverage="100.0"
                     /evalue="2.04e-100"
     Typing          2..927
                     /name="rep_cluster_2131"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.935"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgagcgccg cgcttcaata cttcgacgaa aatttacccc accgtcccta tcacacggat
       61 gatctcgctt ttggtcttcg catctccggc aaagggcgtg cgcttcttgc gcggtacatc
      121 cagcagaacc agcctcatgc gcagttctgg ctggtttttg acgttgaccg cgagggggca
      181 gcgattgact ggagtgaccg gaacgctccc gcgccgaaca tcaccgtaaa aaatcctgtg
      241 aacggtcatg ctcacctgct ctacgcgctc aatatcgccg tgagaaccgc gccggacagc
      301 tcggttaagg cgctgaaata cgccgctgcg attgaacgtt cgctgtgtga gaaactttgt
      361 gctgatgtga actacagcgg actgatttgt aaaaatccgt tccacctgga atggcaggtg
      421 atggagtggc gagaggaagc ctataccctc ggtgaactgg ctgattatct cgatttgagt
      481 gcctcagcgc gccgtagcat cgataaacgt tacgggatgg ggcgaaactg ccacctgttc
      541 gaaatgacgc gcaaatgggc ttacagggcg attcgtcagg gctggccagc attctcacag
      601 tggcttgatg ccgtgattca gcgtgtcgaa atgtacaacg catcgcttcc cgttccgctt
      661 tctccggctg aatgtcgggc tattggcaag agcattgcga aatacacgca caggaacttc
      721 acgccggaaa ctttcgcaca gtatgtggct gatacgcaca cgccagaaat tcaggctgca
      781 cgtggtcgca agggcgggaa aattggaggt gctaagtcta agcgtggtgc tgttgccaca
      841 tctgcgcgaa cgttgaaacc gtgggagact cttggaatta gccgcgcctg gtattaccaa
      901 ctgaaaaaac gaggtcttgt agagtagacc aaataaaacc tatatcagat aacagcgctt
      961 ttttgagctg ttggcgtttg gtggcttttt cgtttcctcc ctgcaatggt gcggctttcc
     1021 gcgtgattga ggttgtagcg ctcgccgcag tctcatgacc gagcgtagcg agcgaatgag
     1081 cgaggaagcg caaaggcgtc cggtggtgta tgtggctctt acgcgccggg gcttagtggt
     1141 tctgcggttt cgccggtggt ctgggtagct tctccagctc gttaatcagc ggttgtagtc
     1201 ggttcatatc ggcctgtctt gtgacttcct ttcgcagaaa ctggagcagg aacgctcgca
     1261 gttgcgcttc ttccggcctc cgtaccctcg ccagcatggc agcccccaca atgacttttt
     1321 gcgccgtgtc caggctccgg ctcttcgcct tcaggcgctg taatctggcc tcagcttcgg
     1381 caatcttctg ttcgagcgtt ctgctcatga tgtaactccg tacgcgatga aaaatcgtat
     1441 tttagcgcgt cactggtagt tgcaaaactg aactggcata atgcacgggc tatcacgaag
     1501 tgcgcactta tacaatcttc acttcgtttt cgattgtgtg cggcctgcgt ggctgaaaag
     1561 aaaacggcaa aaaggcatta cggcagaaat ggcgatttat catctcagca tgaaaatcat
     1621 ttcgcgaaaa aacggctaca gtgccgttgc ttctgctgcc tttaccgttc ggctctgtca
     1681 acccgatgac cgtaccggat aatcccacga ttacacccgt acgttgattg cggtctcatc
     1741 tcacccctgc gaaaatgcac cgtccctggt gtgtttgaac cgttccgttc tctggaatgc
     1801 ggttcgagaa gccgaacagc gccggaaact ccgccagctg gcaaaaggag attgaacttc
     1861 cattcccgcg aggccgcacg gaggccgttc tcgcttttgt ccgggaaact tttggtcagt
     1921 ccgggccatg attgccgatg tggcgttccc atcattatgg aatggaccaa ccgcccatgc
     1981 cacacatcat gctcacgagg gagctgtcga agatttcgca ggaaggtcag ggactggaac
     2041 gaccgggcac cgccgagacg agtggcgcgc atcatggccc tgaccatgcg aacagagcgc
     2101 ttgcgaacgc ccggctacca ggaagagata gaccatcgtt catacgagcg tcagatggac
     2161 tggagaaagc gcgcgggcct tccacctcgg aaagctgcct gtgcgatgga aaaacggggc
     2221 attggaaaca gaaacgcggt gagcagaaga aaccgcctga ttagacagcc ttaacctgga
     2281 aatacaggtt tcccgccaca aggctggcag tcatccaggt acaggagaac gtgcggaaac
     2341 gggaaactca gcgatgccgc acgtcgtgca gcggaagccc cttaatctga ctattcccgc
     2401 ccgcgaatgc ctcagcggat accctgcgga attcattgcc acaactgccc gcaggaatgc
     2461 gggaacgcat gggagatgac accggagttc gtggcgatga acgggaaggc aaaacgacat
     2521 caaacgtgag gggaatgcgc tggtgaaaag agcgggatat tctcgaaaaa gagatgaccg
     2581 gaactctaga aaagcccgtc cggtagcgtc catcctgtca gagcttcccc tgatgacatg
     2641 ggctgaaccg aataccgcaa aagacaactc cgcttctgga aactcgagaa acagattgaa
     2701 tctcttctcc cacctacagg ccgtgaaaga acgggacatt cccgcccgtc gtccacggcc
     2761 tttgaaacgc agtggatacg tggatttcgc cgggaatggc agagctgaag acagcaaacg
     2821 gagcgcaggc cgaagcggaa agcgcgccgg aaggaacagg aatatgggac gcacgggcct
     2881 aaccacccat gataacatcc gaggggatcg cctgacctga gccgtgaaag tcgttcggca
     2941 ttagccgggg ttattacggg ctggggcggc cagagagcgg gcagggaacg ctacactgat
     3001 gcctagagta acagagggag aattcgggtg atgagacgat gttagcgtta tgaattaaca
     3061 ttcaggaacc tgtgaatgtt atacctgtcg ccaggcgggg ctgtgatggt ctcggataat
     3121 acgtgaggga atgccagaat ctcatagcgg acgactgagc ctcgcgtgtg agaatgtatc
     3181 ggtccggcat gttactggaa ggaacagagc cagttggccc ctcttacggt tttccggcgc
     3241 tgccgcatca ctggccggat aattttttat ttcagcgacg accggcaggc ccgtagcctc
     3301 tccgctgccg tctgcgcacc gggtggacgt caccgcttat gcggcaccgg agcaactcat
     3361 gcccgttgta ttttcgacag agcgaaacag caggacgctg aatctgctgt tgtgcaaagg
     3421 gccggaggaa gtgcttgtcg gatttgtgcg tcaggaggac gggctgcgtc ccgttcttgc
     3481 gcttccgtcg ccggattaca gtcatctgat agtcagcacc atcacggaga acggggtatg
     3541 cctggcaggt tacggagaag ctataaacca tgatgcggat actccgtacc caccggaacc
     3601 gcacctgatg cagttccggc tcaaaggcca tcatgacagg cttttggctg ctgtccacaa
     3661 accggaagag atgccggatt atctcttccg tcaactcggt tttaatcaga cctggcatga
     3721 gtggaagcgg gacgaacagc acaggcaaca acaacgccgc cccgggcact tccggggtat
     3781 gagtatgtga tatccggggc tgccccccga accctaccaa cacatcacgg gccacaaaat
     3841 tttttgtggt ccgctctgcg ttttctaagt gttatccctc ctgacttcta aaaaattttc
     3901 cacctgaact tgacagaaaa aacgatgacg ggtacttttt gatctgtaca taaaaccagt
     3961 ggttttatgt acagtattaa tcatgtaatt aattgtttta acgcttaaaa gagggacttt
     4021 tatgagcggt ggagatggac gcggccataa cacgggcgcg catagcacaa gtggtaacat
     4081 taatggtggc ccgaccgggc ttggtgtaag tggtggtgct tctgatggtt caggatggag
     4141 ttcggaaaat aacccgtggg gtggtggttc cggtagcggc attcactggg gaggtggctc
     4201 cggtcgtggt aatggcgggg gtaatggcaa ttccggtggt ggctcgggaa caggcggtaa
     4261 tttgtcagca gtagctgcgc cagtggcatt tggttttccg gcgctttcca ctccaggagc
     4321 tggcggtctg gctgtcagta tttctgcaag cgaattatcg gcagctattg ctggtattat
     4381 tgctaaatta aaaaaagtaa atcttaaatt cactcctttt ggggttgtct tatcttcatt
     4441 aattccgtcg gaaatagcga aagatgaccc caatatgatg tcaaagattg tgacgtcatt
     4501 acccgcagat gatattactg aatcacctgt cagttcatta cctctcgata aggcaacagt
     4561 aaacgtaaat gttcgtgttg ttgatgatgt aaaagacgaa cgacagaata tttcggttgt
     4621 ttcaggtgtt ccgatgagtg ttccggtggt tgatgcaaaa cctaccgaac gtccaggtgt
     4681 ttttacggca tcaattccag gtgcacctgt tctgaatatt tcagttaata acagtacgcc
     4741 agcagtacag acattaagcc caggtgttac aaataatact gataaggatg ttcgcccggc
     4801 aggatttact cagggtggta ataccaggga tgcagttatt cgattcccga aggacagcgg
     4861 tcataatgcc gtatatgttt cagtgagtga tgttcttagt cctgaccagg taaaacaacg
     4921 tcaggatgaa gaaaatcgcc gtcagcagga atgggatgct acgcatccgg ttgaagcggc
     4981 tgagcgaaat tatgaacgcg cgcgtgcaga gctgaatcag gcaaatgaag atgttgccag
     5041 aaatcaggag cgacaggcta aagctgttca ggtttataat tcgcgtaaaa gcgaacttga
     5101 tgcagcgaat aaaactcttg ctgatgcaat agctgaaata aaacaattta atcgatttgc
     5161 ccatgaccca atggctggcg gtcacagaat gtggcaaatg gccgggctta aagctcagcg
     5221 ggcgcagacg gatgtaaata ataagcaggc tgcatttgat gctgctgcaa aagagaagtc
     5281 agatgctgat gctgcattaa gtgccgcgca ggagcgccgc aaacagaagg aaaataaaga
     5341 aaaggacgct aaggataaat tagataagga gagtaaacgg aataagccag ggaaggcgac
     5401 aggtaaaggt aaaccagttg gtgataaatg gctggatgat gcaggtaaag attcaggagc
     5461 gccaattcca gatcgcattg ctgataagtt gcgtgataaa gaatttaaaa acttcgacga
     5521 ttttcggaga aaattctggg aagaagtgtc gaaagatcct gagttaagta agcaatttaa
     5581 tccaggtaat aaaaaacgct tgagccaagg attagctcca cgggctagga ataaagatac
     5641 tgtcggtggg cgtcgctcat ttgagcttca tcacgacaag ccaatcagtc aggatggtgg
     5701 tgtttatgat atggacaacc tccgtatcac tacgccgaaa cgccatattg atattcacag
     5761 aggtcagtaa aaatggaact gaaaaacagc attagtgatt acactgaaac tgaattcaaa
     5821 aaaattattg aagacatcat caattgtgaa ggtgatgaaa aaaaacagga tgataacctc
     5881 gagcatttta taagtgttac tgagcatcct agtggttctg atctgattta ttacccagaa
     5941 ggtaataatg atggtagccc tgaagctgtt attaaagaga ttaaagaatg gcgagctgct
     6001 aacggtaagt caggatttaa acagggctga aatatgaatg ccagttgttt aaggatgaat
     6061 gactggcatt ctttcacaac aaggagtcgt tatgaaaaaa ataacaggga ttattttatt
     6121 gcttcttgca gtcattattc tggctgcatg tcaggcaaac tatatccggg atgttcaggg
     6181 cgggaccgta tctccgtcat caacagctga agtgaccgga ttagcaacgc agtaacccga
     6241 aatcctcttt gacaaaaaca aagcgtgtca ggctgattct gatgcgcttt tttttgaaat
     6301 gtcacaaaag ttccatgtgg gagatgggat ctaaaatccc tgtgcagaac cttccatccg
     6361 gtgggagaaa acttgtcatt ttgacctgtt cgccattcgg aacggtcgaa accgatcgcg
     6421 catcgctttc gtgcatagtt atgcagcgcc ctaaaaacga ttctgacgca tttttctggt
     6481 tcagcctggt gtttccttgt ctttttgcgt tttttgcgtc agaacgcgtc tgagagcgtt
     6541 ttaaggggta cgtacaacag gaattatggt aaatggatcg ggtttgcggg aaggatcgac
     6601 aggatttgcc gttgggtgta gtgtaagcga ctgaaaaaca aacgcccctg aaatcatgtc
     6661 cagatccggc aagattcaac atgaaataca gagggcgtgt aggtcgcata acccggagag
     6721 aatcgtaaca c
//
