LOCUS       NZ_CP053742             5238 bp    DNA     circular CON 13-JUN-2023
DEFINITION  Escherichia coli strain CP8-3_Sichuan plasmid pCP8-3-ColYe4449,
            complete sequence.
ACCESSION   NZ_CP053742
VERSION     NZ_CP053742.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14944002
            Assembly: GCF_013201235.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5238)
  AUTHORS   Li,R., Du,P., Zhang,P., Li,Y., Yang,X., Wang,Z., Wang,J. and Bai,L.
  TITLE     Comprehensive genomic understanding of coevolution of mcr genes in
            E. coli strains via nanopore sequencing
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5238)
  AUTHORS   Li,R., Li,Y., Zhang,P. and Bai,L.
  TITLE     Direct Submission
  JOURNAL   Submitted (18-MAY-2020) College of Veterinary Medicine (Institute of
            Comparative Medicine), Yangzhou University, Wenhui Road, Yangzhou,
            Jiangsu 225009, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 2019
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100x
            Sequencing Technology :: Illumina; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/13/2023 03:37:23
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,918
            CDSs (total)                      :: 4,800
            Genes (coding)                    :: 4,586
            CDSs (with protein)               :: 4,586
            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)              :: 214
            CDSs (without protein)            :: 214
            Pseudo Genes (ambiguous residues) :: 0 of 214
            Pseudo Genes (frameshifted)       :: 68 of 214
            Pseudo Genes (incomplete)         :: 150 of 214
            Pseudo Genes (internal stop)      :: 33 of 214
            Pseudo Genes (multiple problems)  :: 37 of 214
            Pseudo Genes (short protein)      :: 4 of 214
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP053742.1.
            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..5238
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="CP8-3_Sichuan"
                     /isolation_source="slaughterhouse"
                     /host="pig"
                     /db_xref="taxon:562"
                     /plasmid="pCP8-3-ColYe4449"
                     /geo_loc_name="China: Sichuan"
                     /collection_date="2016-07"
     gene            complement(join(4926..5238,1..14))
                     /locus_tag="HP430_RS24235"
                     /old_locus_tag="HP430_24300"
     CDS             complement(join(4926..5238,1..14))
                     /locus_tag="HP430_RS24235"
                     /old_locus_tag="HP430_24300"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006674374.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_003030983.1"
                     /translation="MEKRTKEIKIRLTETEHQRLLDRCDRTHLAEWLRQLGLGEHTSRK
                     RRVPDVAPELLRQVSGIGNNLNQIARRLNQTDSLTPSERASLLIVLTSLDRQLGDLLEQ
                     NRDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            300..704
                     /locus_tag="HP430_RS24240"
                     /old_locus_tag="HP430_24305"
     CDS             300..704
                     /locus_tag="HP430_RS24240"
                     /old_locus_tag="HP430_24305"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_019821692.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="TIR domain-containing protein"
                     /protein_id="WP_074468595.1"
                     /translation="MAREHKVFISHAWAYHDELESLRRLIDARPYFNAEYSEVSRNEPI
                     NSTNAPYIKSVLKRKILDSNILIGLAGIYASHSSWMEWELDTALANGIPVIGVVPRGAQ
                     RISTMVSTRAVEVVRWNTESIIAAIRRHAR"
                     /name="TIR domain-containing protein"
     gene            complement(722..1594)
                     /locus_tag="HP430_RS24245"
                     /old_locus_tag="HP430_24310"
     CDS             complement(722..1594)
                     /locus_tag="HP430_RS24245"
                     /old_locus_tag="HP430_24310"
                     /inference="COORDINATES: protein motif:HMM:NF033610.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF4231 domain-containing protein"
                     /protein_id="WP_112915697.1"
                     /translation="MKYPSLYDVTNKRSASYQKRYFFFLRLEYCILILNAVNAFLTYEK
                     KYIVALVLFSMLMLMMVLKIKKTSEQEWYKYRAITESIKTVSWKFSMRAEPFNDEDEVK
                     NINSLSEYLEDIVGGSEFISKTIDPKSVDESTVTDEMKGLRTLSFEQRRDFYVDGRIND
                     QRDWYVSKAQENKDAGKKWNICMFVIYALAFLCSLYNAYYSVPGSIIPISILTTIASSL
                     VGWIQVKRYSELSASYILTAHEIGVIKEQASYVSSESDFSSFIRDAETAFSREHTQWIA
                     RRVANRKPK"
                     /name="DUF4231 domain-containing protein"
     gene            complement(1591..2496)
                     /locus_tag="HP430_RS24250"
                     /old_locus_tag="HP430_24315"
     CDS             complement(1591..2496)
                     /locus_tag="HP430_RS24250"
                     /old_locus_tag="HP430_24315"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_019725130.1"
                     /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_113410844.1"
                     /translation="MNNAVLELFNDRLPHKPYFSDDLHFGVRIAGKERAILAKYIQFNQ
                     PHAMFWLGFDVDRAGAAIDWSDRNAPAPTLTITNPENGHAHLLYALETSIRTAPDGKMK
                     PLRYAAAVENALRKKLEADAGYSGLICKNPNHGHWKIAVWQPELYTLDWLADFLDLSAA
                     NDKEIVADYGLGRNCTLFDKTRKWAYRAIRQGWPEYEQWLQACYERASAYNLQFAVPLD
                     ENEVSGIAKSIAKWTSSKFSEESFSDFVKKTHTKKIQSKRGVLSGKSRRIGSLEDTRPW
                     DDLGISRRKYFYMKKNGEEK"
                     /name="replication initiation protein"
     gene            complement(2689..2973)
                     /gene="nadS"
                     /locus_tag="HP430_RS24255"
                     /old_locus_tag="HP430_24320"
     CDS             complement(2689..2973)
                     /gene="nadS"
                     /locus_tag="HP430_RS24255"
                     /old_locus_tag="HP430_24320"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000007431.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="NadS family protein"
                     /protein_id="WP_001697687.1"
                     /translation="MSFFDELKASLEEAVEIKNGVREPARVTRYELADVKAIRAQLNVS
                     QSEMAKVLGTSLDTIKSWETGRRNPTGLAAKVLATIQANPKFFQELAAH"
                     /name="nadS"
     gene            complement(2975..3307)
                     /locus_tag="HP430_RS24260"
                     /old_locus_tag="HP430_24325"
     CDS             complement(2975..3307)
                     /locus_tag="HP430_RS24260"
                     /old_locus_tag="HP430_24325"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015873600.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /protein_id="WP_000017531.1"
                     /translation="MSHAIEFIETPMFTRQIKQIATDEELRELQKTLIESPDKGDLIQK
                     TGGLRKIRMATGNQGKSGSVRVIYFLATAEVIYLVMAYPKSTKDSLTDAEKAALKTLTQ
                     QLKDEV"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            complement(3469..3693)
                     /locus_tag="HP430_RS24265"
                     /old_locus_tag="HP430_24330"
     CDS             complement(3469..3693)
                     /locus_tag="HP430_RS24265"
                     /old_locus_tag="HP430_24330"
                     /inference="COORDINATES: protein motif:HMM:NF016769.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_226939304.1"
                     /translation="MEKQLLSALESLQTSYEQQQQAWQDSYSSLQHMFEATSQALTHSD
                     RVCQHLSSQVESLRAQVESLSRNVSRLMR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(3763..4248)
                     /locus_tag="HP430_RS24270"
                     /old_locus_tag="HP430_24335"
     CDS             complement(3763..4248)
                     /locus_tag="HP430_RS24270"
                     /old_locus_tag="HP430_24335"
                     /inference="COORDINATES: protein motif:HMM:NF016710.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_139298759.1"
                     /translation="MSEILNLAKGFEEKSKQQAQDTEQSVKREFARLETSISAELQSSS
                     QSISNAIREQNGRLTGMLRASVSTAMAWIFLCFALLIGILSGIIWFQGTIITSRLSEMD
                     SYSQQLESLKAKSGAGVAIYSDDKHRNTYMVVLPKQAHGVETYTSTTDNTVVKYTAK"
                     /name="MbeB family mobilization protein"
     gene            complement(<4295..4717)
                     /locus_tag="HP430_RS24685"
                     /pseudo=""
     CDS             complement(<4295..4717)
                     /locus_tag="HP430_RS24685"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /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="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     Typing          4927..5119
                     /name="Col(Ye4449)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="81.026"
                     /coverage="100.0"
                     /evalue="4.02e-35"
     Typing          complement(3372..4936)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.659"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gttcgctttt ccataggctc cgctgagaaa aaattcgcac caccgtgaga atttttcgca
       61 gtggatgcag ggggtttcgg ggggcggcga gccccctgaa ccagtcacag gcggaacctc
      121 atagagggga cgctgtgtgt actggcttaa agtaatgtaa agtatgccag attctgtgct
      181 ggctgcaaaa acacagtccc tctaagagag gctgttatct gatataggtt cgagtgcaaa
      241 acggatcggc gcagaggtat aatgcgcgtt cataggggat tgagtaaaag gagcaatcag
      301 tggcaagaga acataaggtt tttattagtc atgcatgggc gtatcacgat gaactggaat
      361 cattaagaag attgattgac gctagaccct actttaatgc tgagtattcc gaagtcagca
      421 gaaatgaacc cataaattca accaacgcac cgtacataaa atccgttctc aaaagaaaga
      481 tactagattc taatatcttg attggtttag caggcatcta tgcatctcat agtagttgga
      541 tggagtggga gttagatact gcgctagcta acggaatacc tgttataggt gttgttccaa
      601 gaggtgcgca gcggatatct accatggttt caacaagagc agtagaagtt gttagatgga
      661 acactgaaag tattattgct gcaatccgcc gtcatgcgcg ataaaaaagg ggcggtgccc
      721 cttacttcgg ttttctgttg gccactcgtc tagcaatcca ttgggtatgc tctctcgaaa
      781 atgcagtttc cgcatctcta ataaatgagg agaaatcact ctcgcttgaa acatatgacg
      841 cctgttcttt tattacccct atttcatgcg cggtaagaat atacgaagcg gacagttcgc
      901 tatacctttt aacttgaatc caacctacta atgatgatgc tattgttgtc aaaatgctta
      961 ttggaattat gctacctgga actgaataat atgcattata aagtgaacat aagaacgcta
     1021 atgcatagat aacgaacata caaatgttcc attttttccc tgcatctttg ttttcttgag
     1081 ccttacttac ataccaatct ctttgatcat taatccttcc atctacataa aagtctctgc
     1141 gttgttcaaa tgatagggtt cgaagccctt tcatctcatc agtcaccgtg ctttcatcca
     1201 ctgacttagg atcaatagtt ttagatatga actcactacc accaacaatg tcctccagat
     1261 actctgataa tgagtttata tttttaacct catcttcatc attaaatggt tcagctctca
     1321 tggaaaactt ccatgagaca gtttttatcg attcagtaat cgccctgtat ttgtaccact
     1381 cttgttctga tgtttttttg atttttaaaa ccatcattaa cataagcatg gagaacagta
     1441 ctaatgcgac tatgtatttt ttttcataag ttaagaaagc attgaccgca ttaagtatca
     1501 aaatgcaata ttcaagcctt aaaaagaaga aatatctttt ctgatatgaa gcagatcttt
     1561 tatttgttac atcataaaga cttgggtatt tcatttttct tcaccattct ttttcatata
     1621 aaaatacttc cttctactta tgcccaaatc atcccacgga cgagtatcct ctaggctacc
     1681 tattcgtctt gattttcctg ataaaacacc tctctttgat tgaatttttt ttgtatgtgt
     1741 ctttttaaca aaatcgctga atgattcctc actaaatttt gatgaagtcc acttagcaat
     1801 acttttagct attccactaa cctcattttc atccagcggt actgcgaatt gcagattata
     1861 ggcgctggca cgctcatagc aggcttgcag ccactgctca tactcaggcc agccctgacg
     1921 gatggcgcgg tatgcccact tgcgggtttt gtcgaacaac gtgcagttac ggcctaagcc
     1981 gtagtcggcg acaatttcct tgtcgttcgc cgcactcagg tcgagaaagt cggccagcca
     2041 gtccagcgtg tagagttccg gctgccacac ggcaattttc cagtgaccgt ggttcggatt
     2101 tttgcagatt aaccccgaat accccgcgtc agcctctaat tttttacgca gcgcgttctc
     2161 cacggcggca gcgtagcgca gcggcttcat tttcccgtca ggtgcggtgc gtatcgaggt
     2221 ttccagcgcg tacagcaggt gcgcgtgtcc gttttccggg ttggtgatgg tcagcgtggg
     2281 cgcgggcgcg ttgcgatcgc tccagtcgat ggcggcaccg gcgcgatcga cgtcgaatcc
     2341 cagccagaac atggcgtgag gctgattgaa ctggatgtat ttcgccagaa tggcgcgttc
     2401 tttccctgca atgcgtacac caaagtgtaa atcatccgag aagtacggct tgtgcggtaa
     2461 gcggtcgttg aaaagttcga gtactgcgtt attcaattcg ccctgcgctt atggcgggct
     2521 gttgtctggc acgtttcatg tgctaatatc ctttcaaggt ttcgacctgg ccctggttat
     2581 catgtgcatc cgccaagatt gagcatgatt tccggggctt tgttttttct gttgccgtta
     2641 aattacacgc gaacggcctc gcctgtcgaa tccttctgtc acaacggctt agtgcgccgc
     2701 cagttcctgg aagaatttcg ggttcgcctg gatggttgcc agtaccttcg ccgccagtcc
     2761 ggtcgggtta cggcgtccgg tttcccagct cttgatggtg tcgaggctgg ttcccagcac
     2821 ttttgccatc tcgctctgag atacgttcag ctgtgccctg atggctttca cgtctgccag
     2881 ctcgtaacgg gtgacgcggg caggctctct gacgccgttt ttgatttcaa cggcttcttc
     2941 cagagatgct ttcagctcgt caaaaaaact catgtcacac ctcgtctttc agttgttggg
     3001 tcagcgtctt cagcgcggct ttttccgcgt ccgtcaggct gtctttggtg cttttcgggt
     3061 aggccatcac cagatagatc acctcggcgg tggccagaaa gtaaatcacc ctcacgctgc
     3121 cgctttttcc ctggttgccc gtcgccatcc tgattttgcg cagcccgccg gttttctgaa
     3181 tgagatcgcc tttgtccggc gactcaatca gcgtcttttg cagctccctg agttcttcat
     3241 ccgtggcgat ctgttttatc tgacgggtaa acatcggggt ctcgataaac tcaatcgcgt
     3301 gactcacggc tgtctcctgt ttttaacgga gtacatagta cacttaattc tgatttcgga
     3361 aaagcgatca catcgagggg ccatagtaac gagtcgtttt tttctgcggc tccggctctg
     3421 gctgctgctc acgcagcttc tcggcgtagg cgcggtcgtg ctgcctgatc aacgcatcaa
     3481 gcggctgacg ttcctgctca agctctcgac ctgcgcgcgc aagctctcta cctgactgct
     3541 caagtgctga cacacccggt cgctgtgcgt cagcgcctgt gaagtagcct cgaacatgtg
     3601 ctgcaagctg ctgtagctgt cctgccacgc ctgctgctgt tgctcgtagc ttgtctgtaa
     3661 gctctctaag gcgctcagaa gctgtttttc catctcggtc atcgttttgg tcatcctcgg
     3721 tgttaaaaac gcgctgtgtc gtttcagggc gctctgacgg ggttatttcg ccgtgtattt
     3781 cactacggtg ttgtcggtcg tcgatgtata ggtttccacg ccgtgcgcct gcttcggcag
     3841 caccaccatg taggtgttcc ggtgcttgtc gtcgctgtag atcgccacgc ccgcgccgct
     3901 tttcgctttc aggctctcca gctgttggct gtagctgtcc atctcgctca ggcgcgaggt
     3961 gatgatcgtg ccctgaaacc agattatccc gctcaggatg ccgatcagca gggcgaagca
     4021 gaggaatatc cacgccatcg ccgttgagac agaggctctg agcatgcccg tcagtctgcc
     4081 gttctgctcg cggatagcgt tgctgatgct ctgcgagctt gattgcagtt ccgcgctgat
     4141 agacgtctcc agcctcgcga actcgcgctt cacgctctgc tctgtatcct gcgcctgctg
     4201 cttcgatttc tcctcgaagc ccttcgccaa atttaaaatc tcgctcataa atcattcctt
     4261 tcagccggat atttcggccg ccgtccggat cggcaatgct gatgctgctt ttcgtttccc
     4321 gcgccacggt caggccatag ctttccagct gcgtcaccac gtcctgccgg ctgcggatca
     4381 cgccctgctg catcaggttc atcagcccgg cggtaatttt ctctgccgcc tgctgtttgt
     4441 cgcggggcag atcgctggcc tgcgtcagcg ggcggcgata agtcgggtcg ttcgggtcgc
     4501 gcagccccag ccggtcgttg gtcagggtct gccaggcgtt gacgcggggg cggtcggcgc
     4561 ggtcaaagta gggttgcagg cgttttccgc tctgcaattc gatgttcggg atgacaaaat
     4621 tcagctcaag ccgtcctttg tcgcggtgct ccacccacag gcaggcgtac tggtcgcggt
     4681 caaggccagt cagcagcgtg tgctcccatt catccatcag gcgtgatttc tcagcgtctg
     4741 caatgtccgg ctcctgaaat gacagcacac cggaggtgta agcgcgggca aaatcgcagc
     4801 catcgatcag ctcgcgtacg tgctcaggat tgccacgcag aacgctggcc tgttcgcgct
     4861 gccggtcttt tcccagcagg taatccaccg gcccgctgcc cgaacccgca ccccgcgaat
     4921 gaattttaac gatcacggtt ctgctccagc aggtcgccaa gctgacggtc gaggctagtc
     4981 agtacgatga gcagcgaggc acgttcagaa ggcgtcaggg aatcagtctg gttcaggcgg
     5041 cgggcaatct ggttcaggtt gttaccgatc ccgctgacct gtcgcagcag ttcgggcgcc
     5101 acatcgggca cacggcgctt gcgtgaagtg tgttcaccca gaccaagctg acgcagccac
     5161 tccgcaaggt gagtccggtc gcagcgatca agcaatcgct gatgctcggt ttcggtgagc
     5221 cggattttga tctctttc
//
