LOCUS       NZ_CP047879             6430 bp    DNA     circular CON 25-JUN-2024
DEFINITION  Escherichia coli strain LD22-1 plasmid pLD22-1-6kb, complete
            sequence.
ACCESSION   NZ_CP047879
VERSION     NZ_CP047879.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13829591
            Assembly: GCF_009913415.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6430)
  AUTHORS   Li,R. and Wang,Z.
  TITLE     Prevalence of plasmid Mediated Colistin Resistance Gene mcr-1 in E.
            coli from Deer in China
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6430)
  AUTHORS   Lu,X.
  TITLE     Direct Submission
  JOURNAL   Submitted (15-JAN-2020) Colloege of Veterinary Medicine, Yangzhou
            University, Shuangqiao Street, YangZhou, JiangSu 225000, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: DEC-2018
            Assembly Method                   :: Unicycler v. V0.4.4
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology :: Illumina HiSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_009913415.1-RS_2024_06_25
            Annotation Date                   :: 06/25/2024 02:15:25
            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)                     :: 5,051
            CDSs (total)                      :: 4,934
            Genes (coding)                    :: 4,755
            CDSs (with protein)               :: 4,755
            Genes (RNA)                       :: 117
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 179
            CDSs (without protein)            :: 179
            Pseudo Genes (ambiguous residues) :: 0 of 179
            Pseudo Genes (frameshifted)       :: 67 of 179
            Pseudo Genes (incomplete)         :: 113 of 179
            Pseudo Genes (internal stop)      :: 43 of 179
            Pseudo Genes (multiple problems)  :: 39 of 179
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP047879.1.
            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..6430
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="LD22-1"
                     /isolation_source="feces"
                     /db_xref="taxon:562"
                     /plasmid="pLD22-1-6kb"
                     /geo_loc_name="China: Dafeng"
                     /lat_lon="32.56 N 120.42 E"
                     /collection_date="2018-08"
                     /collected_by="Xiaoyu Lu"
     gene            complement(join(6351..6430,1..115))
                     /locus_tag="GUU87_RS24940"
                     /old_locus_tag="GUU87_24940"
     CDS             complement(join(6351..6430,1..115))
                     /locus_tag="GUU87_RS24940"
                     /old_locus_tag="GUU87_24940"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_001041636.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADVQAAMCERLHELA
                     EELQNSIQVHFEAENETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(909..1619)
                     /locus_tag="GUU87_RS24945"
                     /old_locus_tag="GUU87_24945"
     CDS             complement(909..1619)
                     /locus_tag="GUU87_RS24945"
                     /old_locus_tag="GUU87_24945"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000967646.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000967645.1"
                     /translation="MLYWKKMPSLWIGNRIAEFSDLDTAKAIAALKIYLTFCLFCKESD
                     SGHRTVELTFSNLCEIASLSRSLVNEGLKILYAKELIKNISPTARKKIYTVDVLENHND
                     GWCKLPFKGVVDEDKKISAFQSMHNRYPFELLALQTYMYLLYARDNNSDYTLARKKTIC
                     KKLKCKLPELNKAITYLIHIGLLDRVVKKSIENIPLEMFHDSYYFYIKTGSKSALTYRR
                     KSEPPVIPEADLPF"
                     /name="hypothetical protein"
     gene            complement(2033..2548)
                     /locus_tag="GUU87_RS24950"
                     /old_locus_tag="GUU87_24950"
     CDS             complement(2033..2548)
                     /locus_tag="GUU87_RS24950"
                     /old_locus_tag="GUU87_24950"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000675351.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type III toxin-antitoxin system ToxN/AbiQ family
                     toxin"
                     /protein_id="WP_000675351.1"
                     /translation="MKFYTISSRYIEYLKGFEDKVPNSEDPNYQNPKAFIGIVLEIQGH
                     KYLAPLTSPKPWHSTIKESSPSFFKLHENGVPENQLGLINLKFMIPIIEAEVSLLDLNG
                     MPNTAYKRMLYKQLQFIRVNSDKIAEKSELLRKLVLQGKMQGTCNFSLLEEKYRDFGKE
                     ANDTEEGE"
                     /name="type III toxin-antitoxin system ToxN/AbiQ family
                     toxin"
     gene            complement(3153..3284)
                     /locus_tag="GUU87_RS25730"
     CDS             complement(3153..3284)
                     /locus_tag="GUU87_RS25730"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001422066.1"
                     /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_071525238.1"
                     /translation="MHDPPVQSDRCALSGNYHLESNPERHDLSPLAAAIGKGCTRDY"
                     /name="replication initiation protein"
     gene            <3854..4438
                     /locus_tag="GUU87_RS24955"
                     /old_locus_tag="GUU87_24955"
                     /pseudo=""
     CDS             <3854..4438
                     /locus_tag="GUU87_RS24955"
                     /old_locus_tag="GUU87_24955"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001697689.1"
                     /note="internal stop; incomplete; partial in the middle of
                     a contig; missing N-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /name="replication initiation protein"
     gene            4435..6114
                     /locus_tag="GUU87_RS24960"
                     /old_locus_tag="GUU87_24960"
     CDS             4435..6114
                     /locus_tag="GUU87_RS24960"
                     /old_locus_tag="GUU87_24960"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000598747.1"
                     /GO_function="GO:0005524 - ATP binding [Evidence IEA];
                     GO:0016887 - ATP hydrolysis activity [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="AAA family ATPase"
                     /protein_id="WP_001774712.1"
                     /translation="MIKVQLPTREHRLHELNLNYGDVVFFIGQNGSGKSSLLNNLFQKI
                     GSQSSVYVLAHRKNTFSSDIIDFSNSEYKNAQGWIFNEIKGSQCRYRVNYDSQMVAIPI
                     VKLKNKVIARALSFVDSFKSNNNQPAELIKSEVDVLNMVFADAKLSIEFFLDDEANVMA
                     RNIKGENPDVYPISMLSDGEKSALIIASEIICADENTTIFLDEPERHMHRSIVSPLLSS
                     LMKYRRDCVFFVATHELSLPAFFDNVKVVNVKNCYFSEQREPIYWDFNVVEDYDELFNG
                     VDEQTKIDILGARDKVLFVEGVTSSLDRDLYSAIFPMVSVVSKQKCDLVELAVKGLRLN
                     DEIHRVSAFGIIDNDNKVQAKVDNLKKDFIFSLDVHSIESIYYHPRMIKFVIDFVKEAN
                     GIDNVDALFMEIHDFAIDAINEKRDHLCCRAVEKTIRADLMSAIPKQQDIKNRIKFNKE
                     IDIECYVNKEIAAFDAMIAERNLDALVSRYPIRETNLLAHVAKKCGFADRSRYELNVIR
                     TIKSNADARAFVLSLLGGLDEAILGCSDTENSPADTHTVFAM"
                     /name="AAA family ATPase"
     Typing          152..251
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.02"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          376..631
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="94.574"
                     /coverage="89.0"
                     /evalue="2.65e-108"
     Typing          complement(3117..3689)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.828"
                     /coverage="90.0"
                     /evalue="5.34e-173"
ORIGIN
        1 cacacatggc cgcctgtacg tcggcatcca gagcatccag tttttcaagc agtgtcaggc
       61 tctggctttt gataaatcgc gccatattca gcgcagtttg ttgctgtttg ttcaccttcc
      121 gttgttctcc gtcagtaccg ggtgtcgggt ggaccctgac taggtggtaa ttgtaagacg
      181 ttgcgggcga cggtattaca attgcacatc ctgtcctgtt ttttttagga cgtatcatgg
      241 cacagcatat caactgataa ataatccctg tgcagtgcag ccgctgttgc ataaaatttc
      301 gctctgcgtc gagtgtttct ttatcaataa ttccgctgat actccggaaa aacgcgagtc
      361 tgttctcatg cctgaaatgc ccacacccca cgcaaaaaca attttttgct gatttttctt
      421 tataaataga gagttatgac aaattagttt ctcttgctct ctttgtgata tttaaaaaag
      481 cggtgtcggc gcggctacaa caccgcgccg acaccgcttt gtaggggtgg tactgactat
      541 tttcataaaa aacatcattt tatattaggg gtgctgctag cggcgcggtg tgttttttta
      601 caggatgccc ctgggggcgc tgctaggggt gtctgttcag atatgtagca atgagtcagg
      661 gattcacgaa ctgaaaatgt ccgaaaatgt gtctcatggg caccgtatgc gcccaaaccg
      721 ttcgccattc actttcatgc atagctatgc agcgagctga aaacgatcct gacgcatttt
      781 ttcggtttac cttggggaaa acatctcttt ttgcggtatt tgcgtcagaa tcgcgttcag
      841 cgcgtttctg aggtgcgggc aacggatgtt atgttcaatc cgtgtgataa ttggtgtgga
      901 ataaacaatc aaaatggtaa gtcggcttct ggaataactg gcggttctga tttccttctg
      961 taggttagag cgctcttact gcctgttttt atatagaaat agtacgagtc atgaaacatc
     1021 tctagaggta tgttttctat ggattttttc acaactctat caagcaaacc tatatggata
     1081 aggtaggtga ttgctttgtt tagttcaggt aatttgcatt tcaatttttt gcatatggtc
     1141 tttttcctag ccagtgtgta gtcgctgtta ttatcacgag cgtaaagaag atacatgtaa
     1201 gtttgtaagg ctagtaactc aaagggatat ctgttgtgca tggattgaaa tgcacttatt
     1261 tttttgtcct cgtcgacaac tcctttaaat ggaagcttgc accatccatc attatgattt
     1321 tctagcacat ccacggtata aatctttttt cgtgcagtcg gcgatatgtt ttttatcagc
     1381 tcttttgcat aaagaatttt aaggccttcg ttcaccaagg aacggcttaa tgacgctatc
     1441 tcgcaaaggt tgctaaaggt taactcaacc gttctgtggc cagagtctga ctctttgcaa
     1501 aacaggcaga atgttaaata aatttttaat gccgctatag cttttgctgt atcaagatcg
     1561 ctgaattcag cgatcctatt tcctatccat agtgaaggca tttttttcca gtacagcatg
     1621 aatcacctca aggccaagtt ttgaaagatg aaatagacca atcccaatat agaaagtgag
     1681 agcacaaggt tagttattac cgctgcgact ttcgcaagtc tctcaaccag acacacgcct
     1741 ttctcaaaca tttttcaccc ctcgtaatcg cttcttgttg tttttattat ctcagggtgt
     1801 gaaggcgttg taacgccttc acaaaaatct atctagaaag ataaaagtga tgttaatttt
     1861 ttatcttgtt gtttttaacg gttttttatt tgagttttgg tatttgtatt aatcataata
     1921 tggttcaccg tgaactatgt atgtgagtcg aaccgttgag ttttgaatat tagacctgaa
     1981 tagtgtccaa gatcactcgg tttcggacac tattcaggat ggcaatgaag cgttactcgc
     2041 cttcttccgt gtcattagct tctttgccga aatctcggta tttttcttct aacagggaaa
     2101 aattacatgt tccttgcatt tttccttgca ggacgagctt ccttaaaagc tctgatttct
     2161 cagctatttt gtctgaattt acacgaataa actggagctg cttatagagc attctcttgt
     2221 aggcggtatt cggcataccg ttcaagtcaa gtaaggatac ttcggcttcg atgattggaa
     2281 tcatgaactt cagattaatc aatccgagct gattttcggg gacaccattt tcatggagct
     2341 taaagaagct aggcgatgat tctttaatag tgctatgcca tggctttggg gatgttaaag
     2401 gggctagata cttatgccct tgaatctcta acacaatgcc aatgaaagct ttcggattct
     2461 gatagttagg atcttcgcta ttgggaactt tgtcttcgaa tccctttagg tattcaatgt
     2521 atctgcttga tatagtgtaa aatttcattt ttttctcgta aaaaaggcga ctgtgtagtc
     2581 gcctctttta ctgtattact ttaaggtagt aaatgaccta aatttctagc tgcacttaag
     2641 gtagcaaatc acctgaattt ctagctgcac ttaaaggtag caaatcacct gaatttctag
     2701 ctgcacttaa ggtagcaaat cacctgaatt tctagctgca cttaaaggta gcaaatcacc
     2761 ttgattcgag tatacctgat cttcgcctag gcttacaact aggtaacttg cagctgtgta
     2821 gttgtagccc ttgccgctgt atcccctcaa aatgtcattt gaggcttttt taaagtactg
     2881 attccagagt tgactgtttt tttcatcagt tcagtgtggg ggggggtaag ttgggttatg
     2941 acatgaatca aaaaggatct gcttgagatc ctttttttct acgcgtaatc tcttgctctg
     3001 aaaacgaaaa aaccacctgg ggaggtggtt tttcgatggt tcagtaagtt ggggaacttc
     3061 tgaaccgtgg taacagggtg tacaagaccg ctgccaccaa attcgtcctt ccagtttagc
     3121 cgtagtttgg ttctaacttc aagaactctg catcagtaat ctcttgtaca ccccttacca
     3181 atggccgcag ccagtggcga taagtcgtgt ctttccgggt tggactcaag atgatagtta
     3241 ccggacaagg cgcagcggtc ggactgaacg ggggggtcgt gcatacagtc cagcttggag
     3301 cgaactgcct acccggaacc gagtgtcagg cgtggaatga gataaacgcg gccataacag
     3361 cggaatgaca ccggtaaacc gaaaggcagg aacaggagag cgcacgaggg agccaccagg
     3421 gggaaacgcc tggtatcttt aagtcctgtc gggtttcgcc accactgatt tgagcgtcag
     3481 attctgtgat gcttgtcagg ggggcggagc ctatggaaaa acgccagcgg cgcggccttt
     3541 tgccctggct ttgccttttt gctcacatgt tctttccggc cttatcccct gattctgtgg
     3601 ataaccgtat taccgtctct gagtgagctg ataccgctcg ccgcagccga acgaccgagc
     3661 gcagcgagtt agtgagcgag gaagcggaag agcgtaggca tttgcatttt ctccttacgc
     3721 atctgtgcgg catttcacac cgtcaatagc gcacttttca tacaatccgc actgataccg
     3781 catagttaag tcagtactca cagcgtcccc tctgcgaggt gccttctgtg actggttcag
     3841 ggggcttgcc gcccccctca aatatgcagc cgtcattgag aatgcgctgc gtaaaaaatt
     3901 gggcgccgat gcggggtatt cagggctaat ttgcgagaat ccgaaccacc tgcactggca
     3961 gatcaccgtt tggcagcctg agctctacac cctcgactga ttagccgact acctcgacct
     4021 tggcgcagct aatgaccgcg aaatcctacc ggactacggt ttaggccgta actgcaccct
     4081 cttcgataaa acccgcaagt gggcttaccg cgctatccac caaggctggc cgcagtatga
     4141 ccaatggcta caagcttgct ttgaacgcgc taaagcctac aacctgcagt tctccgcacc
     4201 tttagacgag aacgaagtca tgggtattgc caaaagtgta gctaagtgga ctaataaaaa
     4261 ttttacagag tcatcatttg atgattttat aaaaaagacc cattcggcag acatctaatc
     4321 tctatgtggg aaaaaaagta aaggaggagg taggccttca ttaaactctc catggattaa
     4381 tttaggaatt agtcgttcaa cgtattttag attaaaagct aaagagaaag gaaaatgata
     4441 aaagttcagt tacctactag agaacatcgt cttcatgagc ttaatcttaa ttatggcgat
     4501 gtcgtttttt ttattggtca gaatggtagt ggtaaatcca gcctattaaa taatcttttt
     4561 caaaaaatag gatctcaatc atcagtatat gttttagcgc atagaaaaaa tacattcagc
     4621 agcgacatta ttgatttcag taatagtgag tataaaaatg cgcagggatg gatttttaat
     4681 gaaattaaag gcagtcaatg tagatacaga gttaattatg actcacagat ggttgccata
     4741 cctatagtaa aattaaaaaa caaagtgata gccagggctt taagtttcgt agattcattt
     4801 aaatcaaata acaatcagcc ggcagagtta ataaagtcag aggttgatgt tctaaacatg
     4861 gtttttgctg atgccaaatt atctattgag ttctttctag atgatgaagc caacgttatg
     4921 gcaaggaata ttaaaggtga aaatcctgat gtttatccta tatcaatgct ttctgacggt
     4981 gaaaaaagtg cactaattat tgccagtgag attatttgcg ctgatgaaaa cacaactatt
     5041 ttcttagatg agcctgagcg acatatgcac agaagcattg tgtctccgct gctttcatct
     5101 ttaatgaaat atcgtagaga ttgtgttttt tttgttgcca cccacgagtt aagcttgcct
     5161 gcgttttttg ataacgtgaa agtggttaac gttaaaaact gctatttttc cgaacaaaga
     5221 gaaccgatat actgggattt caatgttgtt gaggattatg acgaattatt caatggtgtt
     5281 gatgagcaaa ctaaaataga tatacttggc gctagggata aggttctatt tgttgaaggt
     5341 gttacgtcta gccttgaccg tgatttatat tcggccatat ttcctatggt ttcagttgta
     5401 tctaaacaaa aatgtgattt ggttgaattg gcggtaaaag gcttgagact aaatgacgaa
     5461 attcatcgag tatcggcgtt tggtatcatt gataatgata acaaggtgca ggcgaaggtc
     5521 gataacttaa agaaagactt catttttagt ctcgacgttc attctattga gtcgatttat
     5581 tatcatccta gaatgattaa gtttgtcatt gactttgtaa aagaggctaa tgggatagat
     5641 aatgttgatg ccttatttat ggaaattcat gacttcgcta ttgatgccat aaatgaaaag
     5701 cgcgatcact tatgctgccg tgcagttgaa aaaacaataa gggcagactt aatgtcggcc
     5761 ataccaaaac agcaagatat taagaaccgc attaagttta ataaagaaat tgatattgaa
     5821 tgttatgtta ataaagaaat tgctgcattt gatgcaatga tcgcggaacg aaatttggat
     5881 gcgttagtct cacgctaccc tatccgagaa acaaatttgt tggcacatgt agctaaaaaa
     5941 tgtggttttg ccgatcgctc tagatatgag ttaaacgtga ttcgtacgat caagagtaat
     6001 gctgacgcta gagcatttgt tttatccctc ctcggagggt tagatgaagc tattttggga
     6061 tgttcagata cggaaaatag cccagctgat acccatacag tttttgctat gtgagactaa
     6121 acaacctata tcagataaca gccctgcttt tgcggggctt tttgtttgtg cgtgacttga
     6181 ccgcgatgta cgatagttgc tgtattaagt tagtatacac tccgctatcg ctacgtggct
     6241 gggtcagggc tgcgccccga cacccgttaa aacccgctga cgcgccctga cgggcttgtc
     6301 tgctgacgaa aatgctcacg ggcaagccgt gaccgccttc gtcagcttcg ttatgttcct
     6361 gtttcatttt cggcctcaaa gtgaacctgg atgctgttct ggagttcttc tgcgagttcg
     6421 tgcagtcgtt
//
