LOCUS       CP085523                5684 bp    DNA     circular BCT 31-OCT-2021
DEFINITION  Escherichia coli strain QH20-4D3-1 plasmid p4D31-6, complete
            sequence.
ACCESSION   CP085523
VERSION     CP085523.1
DBLINK      BioProject: PRJNA772555
            BioSample: SAMN22401922
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5684)
  AUTHORS   Wang,J. and Tang,B.
  TITLE     Emergence of colistin resistance gene mcr-1 in Escherichia coli from
            the broiler in Qinghai-Tibet plateau of China
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5684)
  AUTHORS   Wang,J. and Tang,B.
  TITLE     Direct Submission
  JOURNAL   Submitted (20-OCT-2021) Institute of Agro-product Safety and
            Nutrition, Zhejiang Academy of Agricultural Sciences, 198 Shiqiao
            Road, Hangzhou, Zhejiang 310021, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. SEP-2021
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology             :: Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 10/25/2021 12:01:18
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 5.3
            Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
            Genes (total)                     :: 5,407
            CDSs (total)                      :: 5,289
            Genes (coding)                    :: 4,847
            CDSs (with protein)               :: 4,847
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 442
            CDSs (without protein)            :: 442
            Pseudo Genes (ambiguous residues) :: 0 of 442
            Pseudo Genes (frameshifted)       :: 278 of 442
            Pseudo Genes (incomplete)         :: 179 of 442
            Pseudo Genes (internal stop)      :: 80 of 442
            Pseudo Genes (multiple problems)  :: 79 of 442
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            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/
FEATURES             Location/Qualifiers
     source          1..5684
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="QH20-4D3-1"
                     /isolation_source="feces"
                     /db_xref="taxon:562"
                     /plasmid="p4D31-6"
                     /geo_loc_name="China:Qinghai"
                     /collection_date="2020-07"
     gene            join(5585..5684,1..92)
                     /locus_tag="LJ051_27005"
     CDS             join(5585..5684,1..92)
                     /locus_tag="LJ051_27005"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /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="UDU17767.1"
                     /translation="MTKQEKTALNMARFIRGQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(1103..2170)
                     /locus_tag="LJ051_27010"
     CDS             complement(1103..2170)
                     /locus_tag="LJ051_27010"
                     /EC_number="3.1.21.-"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001009472.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="CfrBI family restriction endonuclease"
                     /protein_id="UDU17768.1"
                     /translation="MNFKDKNCFPNELIALAKISKNDVLDKFGTDVFKKVVYDVLTGKN
                     VREFTEILTRTRLLESNLSFFDFFVDKMKEGITPKQLYLYAKNALSNKSYVKSNQPVLE
                     WMVMMTNKQTQNVLRDEHGDGFDRLALRTQEEILKIKNGYEDKIGEISIGGQKVSLEDF
                     CYIILSLGSQTLTIRGSEKSLHGKYFEKLILGSLFTIMGFEYKEKIEEGLNAKCFTLST
                     RADDRESDATLVFNGKAIRVDIGFIGRGNTEISLDKVSRFRRMDDIGGVMHNISTMVIV
                     DVIGDRSRIVNMAEEIDGKVVAMSDPYWVAKVSSYISSKLNVDDLLEDKPQLKDIQSFI
                     SDALENVDLEKYIKL"
                     /name="CfrBI family restriction endonuclease"
     gene            2247..3377
                     /locus_tag="LJ051_27015"
     CDS             2247..3377
                     /locus_tag="LJ051_27015"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000216732.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="site-specific DNA-methyltransferase"
                     /protein_id="UDU17769.1"
                     /translation="MTVKNNYLNRGYLVTSTTQAKKIAKLHLEKLDLADKFSFGLPEVD
                     DRYHVWRVPLVATGHRIGEIVINSKTSTIDYKKSSKSPFLIKKAMEVVHTPKKVKKEKK
                     IISKSPLNNMLLQGNCAETLKKLPDESVNLVFTSPPYYNAKPEYSEYHTYDEYLSLLRS
                     VIKECHRVLSEGRFFVINVSPVLIRRASRNEASKRIAVPFDLHRLFIEEGYEFIDDIHW
                     VKPEGAGWALGRGRRFAADRNPLQYKPVPVTEYILVYRKKTDKLIDWNIRNHHSKEDVF
                     DSKIGDDYEKTNLWKINPSRNRKHPATFPYGLAERVIKYYSFKNDVILDPFAGSGTTAK
                     AAIDLGRRFVMCEISKQYIDLIIEGTMLGGDLKIIN"
                     /name="site-specific DNA-methyltransferase"
     gene            complement(3761..3994)
                     /locus_tag="LJ051_27020"
     CDS             complement(3761..3994)
                     /locus_tag="LJ051_27020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /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="UDU17765.1"
                     /translation="MTELETHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSEQTERLSQLYSENWR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(4001..4519)
                     /locus_tag="LJ051_27025"
     CDS             complement(4001..4519)
                     /locus_tag="LJ051_27025"
                     /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="UDU17766.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNNEFRRLGESVSEAVTSNE
                     TKIRDAIALFTASTEKSLEKHREGVKEAMMQHRKDVLKLAGNTGMMLLGIVFLLFTASG
                     GTLWYLGGRIQANLEEIRKQEETLQKLNAKTWGVEFVQDGNRKFLVLPYGKSAEVIPFQ
                     GKEWVHLKE"
                     /name="MbeB family mobilization protein"
     gene            complement(4497..5207)
                     /locus_tag="LJ051_27030"
                     /pseudo=""
     CDS             complement(4497..5207)
                     /locus_tag="LJ051_27030"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /note="incomplete; partial on complete genome; 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"
     gene            complement(5197..5520)
                     /locus_tag="LJ051_27035"
     CDS             complement(5197..5520)
                     /locus_tag="LJ051_27035"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /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="UDU17770.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGTR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     Typing          complement(178..257)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.67e-34"
     Typing          289..829
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.516"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(3658..5207)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.374"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aggcagatat ctgtgaatcg cttcacgacc acgccgatga gctttaccgc agctgcctcg
       61 cacgtttcgg ggatgacggt gaaaacctct gacacatgca gctcccggaa acggtcacag
      121 cttgtctgtg agcggatgcc gggagccgac aagcccgtca ggacgcgtca gcgggtttta
      181 gcgggtgtcg gggcgcagcc ctgacccagt cacgtagcga tagcggagtg tatactggct
      241 tacttattcg gcatcagggc gcattgtatg aaaagtgcac catgccgggt gtgaaatgcc
      301 gcacagatgc gtaaggagaa aatgcacgtc caggcgcttt tccgcttcct cgctcactga
      361 ctcgctgcgc tcggtcgttc gactgcggcg agcggagtct gcttgctcaa aaacggcaat
      421 acggttatcc acagaatcag gggataaggc cggaaagaac atgtgagcaa aaagacaaag
      481 ggcaaaaaag ccgcgccgct ggcgtttttt ccataggctc cgccccctga cgagcatcac
      541 aaaaatcgac gctcaagtca gaggtggcga aacccgacag gactataaag ataccaggcg
      601 tttccccctg gaagctccct cgtgcgctct cctgttccga ccctgccgct taccggatac
      661 ctctccgcct ttctcccttc gggaagcgtg gcgctttctc atagctcacg ctgttggtat
      721 ctcggctcgg tgtaggtcgt tcgctccaag ctgggctgtg tgcacgaacc ccccgttcag
      781 cccgaccgct gcgccttatc cggtaactat cgtcttgagt ccaacccgga aagacacgta
      841 aaaacgccac tggcagcagc cattggtaac cgggttagca gagcgagatt tataagttgg
      901 taacagagtt cttgaagtat cagcctgatt ctggctacac tagaagaaca agttttggtg
      961 gtctgcgctc tgcttaagcc agattacctg gttagataat ctgccaggat tagctaacct
     1021 ttgaaaaacc acctgccagg gtggtttttc tttatgtaga gattatgctt ttaataagca
     1081 cgcagtcaag gattacaatc tcttataatt taatgtattt ttccagatct acattctcta
     1141 atgcatcaga tataaaagac tgtatgtctt taagttgagg tttatcctct aaaagatcat
     1201 ctacattcag tttcgaacta atataggaag agacctttgc aacccaatac ggatcactca
     1261 tcgcaacaac tttaccatca atctcttcag ccatattaac tattctactt ctatcaccaa
     1321 taacgtcaac aataaccatt gtgcttatat tatgcatcac tccgccaata tcatccattc
     1381 gtctaaatct agatacttta tccaaactta tttctgtgtt acccctacca ataaaaccaa
     1441 tgtcaaccct aatcgccttc ccattaaaaa caagagtagc atcagactcc ctgtcatcag
     1501 ctcttgttga aagagtaaaa catttagcat ttaacccttc ttcaattttt tctttatatt
     1561 caaaacccat tattgtaaat aaagaaccga gtattagctt ttcaaaatat ttaccatgaa
     1621 gagatttctc agatccccta atagttaaag tttgcgaacc aagagataaa ataatatagc
     1681 aaaaatcttc taaagacacc ttttgcccac caatagatat ctctccaatt ttatcttcat
     1741 acccgttttt tattttaagt atttcttctt gcgtccttaa agcaagtcta tcaaaaccat
     1801 ccccatgctc atctcttaaa acattttggg tctgtttatt tgtcatcata accatccact
     1861 cgagaacagg ttgattagac ttaacataag acttgttcga taatgcattt tttgcataga
     1921 gataaagctg ctttggcgtt atcccttctt tcattttatc cacaaaaaag tcaaaaaaag
     1981 agagattgct ttctaacaat ctagtacgag ttagtatttc agtgaattcg cgaacatttt
     2041 tacctgttaa aacatcataa acaacctttt taaaaacatc cgttccgaac ttatctaaaa
     2101 catcattttt tgaaattttc gccaacgcta tgagttcgtt agggaaacaa tttttatcct
     2161 tgaaattcat atcctcacca tggacatagt aaaaatgaga tgctaagata gcaggttgta
     2221 tggtaacaga tcgatagtta ggaaaaatga cagttaaaaa caattactta aacagaggtt
     2281 atttggtaac ctctacgact caggcgaaaa aaatagcaaa gttgcaccta gagaaattag
     2341 acttagctga taaattttcc tttgggttac ctgaagtcga tgatcggtac catgtatggc
     2401 gtgtaccatt agtagcgaca ggccacagga ttggtgaaat agttataaat tcaaaaacgt
     2461 caactattga ttataagaaa agttcgaagt ctccatttct tattaagaaa gcaatggagg
     2521 ttgtccatac cccaaaaaag gtaaaaaaag aaaaaaaaat catatcaaag tcaccattaa
     2581 ataacatgtt actacaaggc aactgcgcgg agaccttgaa aaaattacct gatgaatcag
     2641 tgaacttagt attcacatca ccgccatatt acaatgccaa accagagtat tccgaatatc
     2701 atacatatga tgaatacctc tctctattgc gttcagtaat aaaagagtgc catagagttt
     2761 taagcgaagg tcgttttttc gtcatcaatg tctcgcccgt tttaataaga agggcgtcac
     2821 ggaatgaagc atcaaaaaga atagctgttc cttttgactt gcacaggtta tttatagaag
     2881 aaggctatga attcatagat gatatacatt gggttaaacc agaaggagct ggctgggctt
     2941 taggtagagg ccgtcgattc gcagctgacc gcaatccgtt gcaatataaa ccagtaccag
     3001 taactgagta cattcttgtt tacagaaaaa aaactgataa attaatagat tggaacataa
     3061 gaaaccatca tagcaaagag gatgtttttg actcaaaaat cggcgacgat tacgaaaaga
     3121 caaacctatg gaaaataaat ccatctcgta acagaaaaca tcctgctaca tttccatacg
     3181 gtctggcaga aagagttata aaatactatt ctttcaaaaa tgatgttatt ttagatcctt
     3241 ttgctggatc gggaacaaca gcaaaagcag caattgattt aggcagaaga tttgtgatgt
     3301 gtgagatatc aaagcagtat attgatctga tcatagaagg aaccatgcta ggtggtgatt
     3361 taaaaatcat aaattaatca aactttactg tggtaaaagc cgccttaagg cggcttattt
     3421 acgcgtcaac atcagccaca ttgtcgaatt taccataatc ccttaattgt acgcaccgcc
     3481 aaaacgcgtt cagcgcgatc acagcagcag acaggtgaaa atggcaacaa accacccgaa
     3541 aaactgccgc aatcgcgcct gataaatttt aaccgcatga atacctatgc aaccagatgg
     3601 tacagaccac attagcctgt cttaatccac ttaacctgcc atttttcatg gtttcaccat
     3661 cccagcgaag ggccatccag cgtgcgttcc tgtatttccg gctgacgctc ccgttccagg
     3721 gataacacat gttcgcgctc ctgtatcagc cgttcctctc ttatctccag ttctcgctgt
     3781 ataactggct caagcgttct gtctgctcgc tcaagtgctg cacctgctga ctcaactgca
     3841 tgacccgctc gttcagcatc gcgttgtccc gttgcgtaag cgaaaacatc ttctgcaatt
     3901 ccacgaaggc gctctcccat tcgctcagcc gctgcatata gtcctgttgc agctgctcta
     3961 aggcgttcag caaatgtgtt tccagctctg tcactctgtg tcactccttc agatgtaccc
     4021 actctttccc ctgaaaggga atcacctccg ctgatttccc gtacggaagg acaaggaatt
     4081 tcctgttccc gtcctgcaca aactccacgc cccatgtctt cgcgttcagt ttctgcaatg
     4141 tctcttcctg cttcctgatt tcttccaggt tcgcctgtat cctccctcca agataccaga
     4201 gcgtcccgcc actcgctgta aacaggagaa agactatccc cagtaacatc atgcccgtat
     4261 tccctgccag ctttaacacg tccttcctgt gctgcatcat cgcctctttc accccttccc
     4321 ggtgtttttc cagcgatttc tctgtcgagg ctgtgaacag ggctatagcg tctctgattt
     4381 tcgtctcgtt tgaggtcaca gcctcgctga cagactcgcc gagcctcctg aactcgttgt
     4441 tcagcatttt ctctgtagat tcggctctct ctttcagctt tttctcgaac tccgcgcccg
     4501 tctgtaaaag attgctcata aaatgctcct ttcagcctga tattcctccc gccgttcggg
     4561 tctgcaatgc tgatactgct tcgcgtcacc ctgaccactt caatccctgc ctccgtgagc
     4621 gcctgaatca catcctgacg gccttttatc tccccgacat gataaagagc gtctatcccg
     4681 cgtgtgacgc tctctgcaag cgcctgtttc gttttcggca ggttatcagg gagagtcagt
     4741 atccggcggt tctccggggc gttggggtca tgcagcccgt aatggtgatt aaccagcgtc
     4801 tgccaggcat caattctcgg cctgtctgcc cggtcgtagt acggctggag gcgttttccg
     4861 ctctgtagct ccatgttcgg aatgacaaaa ttcagctcaa gccgtccctt gtcctggtgc
     4921 tccacccaca ggatgctgta ctgatttttt tcgagaccgg gcatcagtac acgctcaaag
     4981 ctcgccatca ctttttcacg tcctcccggc ggcagctcct tctccgcgaa cgacagaaca
     5041 cctgacgtgt atttcttcgc aaatggcgtg gcatcgatga gttcccggac ttcttccgga
     5101 ttaccctgaa gcaccgttgc cccttcccgg ttacgctccc ttcccagcag gtaatcaacc
     5161 ggaccactgc caccaccttt tcccctggca tgaaatttaa ctatcatccc gcgtcccctg
     5221 ttccctgacg gccagacgca gccggcgcag ctcatccccg atggccatca gtgcggccac
     5281 tacctgaacc cggtcaccgg aagaccactg tccgctgttc accttcctcg ctgtctgatt
     5341 caggttattc ccgatggcgg ccagctgacg cagtaacggc ggtgccagtg tcggcagctt
     5401 cccggaacgg gcaaccggct cacccaggca gacccgccgc atccataccg ccagttgttt
     5461 accctcacag cgttccagta accgggcatg ttcatcatca gtaacccgta tcgtgagcat
     5521 cctctcgcgt ttcatcggta tcattacccc catgaacaga aatccccctt acacggaggc
     5581 atcagtgact aaacaggaaa aaaccgccct taacatggcc cgtttcatca gaggccagac
     5641 attaacgctg ctggagaaac ttaacgaact ggacgcagat gaac
//
