LOCUS       NZ_CP032070             6647 bp    DNA     circular CON 19-JUN-2023
DEFINITION  Escherichia coli strain E166 plasmid p.E166-P4, complete sequence.
ACCESSION   NZ_CP032070
VERSION     NZ_CP032070.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN09939624
            Assembly: GCF_018141225.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6647)
  AUTHORS   Zhuge,X.
  TITLE     Molecular Epidemiology and Zoonotic Risk of Avian-origin
            mcr-1-positive Extraintestinal Pathogenic Escherichia coli in China
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6647)
  AUTHORS   Zhuge,X.
  TITLE     Direct Submission
  JOURNAL   Submitted (30-AUG-2018) College of Veterinary Medicine, Nanjing
            Agricultural University, No.1, Weigang Road, Xuanwu District,
            Nanjing, Jiangsu 210095, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: ABySS v. 2.0.2
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 606.0x
            Sequencing Technology             :: Illumina HiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/19/2023 03:03:17
            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)                     :: 5,177
            CDSs (total)                      :: 5,061
            Genes (coding)                    :: 4,819
            CDSs (with protein)               :: 4,819
            Genes (RNA)                       :: 116
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 242
            CDSs (without protein)            :: 242
            Pseudo Genes (ambiguous residues) :: 0 of 242
            Pseudo Genes (frameshifted)       :: 93 of 242
            Pseudo Genes (incomplete)         :: 166 of 242
            Pseudo Genes (internal stop)      :: 53 of 242
            Pseudo Genes (multiple problems)  :: 62 of 242
            Pseudo Genes (short protein)      :: 4 of 242
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP032070.1.
            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..6647
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="E166"
                     /host="Avian"
                     /db_xref="taxon:562"
                     /plasmid="p.E166-P4"
                     /geo_loc_name="China"
                     /collection_date="2014"
     gene            1214..1441
                     /locus_tag="D2J89_RS25515"
                     /old_locus_tag="D2J89_27655"
     CDS             1214..1441
                     /locus_tag="D2J89_RS25515"
                     /old_locus_tag="D2J89_27655"
                     /inference="COORDINATES: protein motif:HMM:NF015489.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin E1 immunity protein"
                     /protein_id="WP_230498631.1"
                     /translation="MLYAIVISTILCPYSKYAIEHIAFNFIKKDFFERRKNLNNAPVAK
                     LNLFMLYNLLCLVLAIPFGLLGLFISIKNN"
                     /name="colicin E1 immunity protein"
     gene            complement(1438..3006)
                     /gene="cea"
                     /locus_tag="D2J89_RS26020"
                     /pseudo=""
     CDS             complement(1438..3006)
                     /gene="cea"
                     /locus_tag="D2J89_RS26020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000447006.1"
                     /note="internal stop; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="pore-forming bacteriocin colicin E1"
                     /name="cea"
     gene            3266..3703
                     /locus_tag="D2J89_RS25530"
                     /old_locus_tag="D2J89_27670"
     CDS             3266..3703
                     /locus_tag="D2J89_RS25530"
                     /old_locus_tag="D2J89_27670"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001405929.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001405929.1"
                     /translation="MGHCHFMAWHTLRDALKMTGRSRSQFYRDMRAGLVSYRTGRDGRR
                     EFETSELIRAYGELKQNETPERHSEGHAENPHDQQTERILRELNELKQCLTLMLEDKQA
                     QDMDRRRQEAEREQLQNEIAQLRQALELEKKRGFWSRLFGR"
                     /name="hypothetical protein"
     gene            3784..4203
                     /locus_tag="D2J89_RS25535"
                     /old_locus_tag="D2J89_27675"
     CDS             3784..4203
                     /locus_tag="D2J89_RS25535"
                     /old_locus_tag="D2J89_27675"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016247941.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Exc2 family lipoprotein"
                     /protein_id="WP_001254967.1"
                     /translation="MRRTGNKLCLIAMITATVALTACTPKGSVEQHTRHYVYASDDGFD
                     PNFSTQKADTTRMMVPFFRQFWDMGAKDKATGKSRSDVQQRIQQFHSQEFLNSLRGTTQ
                     FAGTDYRSKDLTPKKSRLLADTISAVYLDGYEGRQ"
                     /name="Exc2 family lipoprotein"
     gene            complement(4521..4754)
                     /locus_tag="D2J89_RS25540"
     CDS             complement(4521..4754)
                     /locus_tag="D2J89_RS25540"
                     /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="WP_000137445.1"
                     /translation="MTELETHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSEQTERLSQLYSENWR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(4761..5279)
                     /locus_tag="D2J89_RS25545"
     CDS             complement(4761..5279)
                     /locus_tag="D2J89_RS25545"
                     /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_000067500.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNNEFRRLGESVSEAVTSNE
                     TKIRDAIALFTASTEESLEKHREGVKEAMMQHRRDVLKLAGNTGMMLLGIVFLLFTASG
                     GTLWYLGGRIQANLEEIRKQEETLQKLNAKTWGVEFVQDGNRKFLVLPYGKSAEVIPFQ
                     GKEWVHLKE"
                     /name="MbeB family mobilization protein"
     gene            complement(<5317..5748)
                     /locus_tag="D2J89_RS26025"
                     /pseudo=""
     CDS             complement(<5317..5748)
                     /locus_tag="D2J89_RS26025"
                     /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"
     gene            complement(5957..6280)
                     /locus_tag="D2J89_RS25555"
                     /old_locus_tag="D2J89_27695"
     CDS             complement(5957..6280)
                     /locus_tag="D2J89_RS25555"
                     /old_locus_tag="D2J89_27695"
                     /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="WP_000955999.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            6344..6535
                     /locus_tag="D2J89_RS25560"
                     /old_locus_tag="D2J89_27700"
     CDS             6344..6535
                     /locus_tag="D2J89_RS25560"
                     /old_locus_tag="D2J89_27700"
                     /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="WP_000165985.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          72..630
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.365"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(4418..5967)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.473"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cccagtcacg tagcgatagc ggagtgtata ctggcttaac catgcggcat cagtgcggat
       61 tgtatgaaaa gtacgccatg ccgggtgtga aatgccgcac agatgcgtaa ggagaaaatg
      121 cacgtccagg cgcttttccg cttcctcgct cactgactcg ctacgctcgg tcgttcgact
      181 gcggcgagcg gtactgactc acacaaaaac ggtaacacag ttatccacag aatcagggga
      241 taaggccgga aagaacatgt gagcaaaaga ccagaaacag gaagaaggcc gcgtagcagg
      301 cgtttttcca taggctccgc ccccctgacg agcatcacaa aaatagacgc tcaagtcaga
      361 ggtggcgaaa cccgacagga ctataaagac accaggcgtt tccccctgga agctccctcg
      421 tgcgctctcc tgttccgacc ctgccgctta ccggatacct gtccgccttt ctcccttcgg
      481 gaagcgtggc gctttctcat agctcacgct gttggtatct cagttcggtg taggtcgttc
      541 gctccaagct gggctgtgtg cacgaacccc ccgttcagcc cgaccgctgc gccttatccg
      601 gtaactatcg tcttgagtcc aacccggtaa ggcacgcctt aacgccactg gcagcagcca
      661 ctggtaaccg gattagcaga gcgatgatgg cacaaacggt gctacagagt tcttgaagta
      721 gtggcccgac tacggctaca ctagaaggac agtatttggt atctgcgctc tgctgaagcc
      781 agttaccttc ggaaaaagag ttggtagctc ttgatccggc aaacaaacca ccgttggtag
      841 cggtggtttt tttgtttgca agcagcagat tacgcgcaga aaaaaaggat ctcaagaaga
      901 tcctttgatc ttttctactg aaccgcgatc cccgtcagtt tagaagagga ggatggtgcg
      961 atggtccctc cctgaacatc acgtatatag ttagcctgac atccaacaag gaggtttatc
     1021 gcgaatattc ccacaaaaaa tcttttcctc ataactcgat ccttataaaa tgaaaagaat
     1081 atatggcgag gtttaattta tgagcttaag atactacata aaaaatattt tatttggcct
     1141 gtactgcaca cttatatata tataccttat aacaaaaaac agcgaggggt attatttcct
     1201 tgtgtcagat aagatgctat atgcaatagt gataagcact attctatgtc catattcaaa
     1261 atatgctatt gaacacatag cttttaactt cataaagaaa gattttttcg aaagaagaaa
     1321 aaacctaaat aacgcccccg tagcaaaatt aaacctattt atgctatata atctactttg
     1381 tttggtccta gcaatcccat ttggattgct aggacttttt atatcaataa agaataatta
     1441 aatccctaac acctcattta tagtattaag tttattctta tcaatatagg agcatagaat
     1501 tcctgtaaca atagcaatac cccaaatacc taatgtagtt ccagcaagca agctaaaaag
     1561 taaagcaaca acataactca cccctgcatc tgcagctttc ttctctaatg taagaaatag
     1621 tggcttccag tcacctgtat ccttaatttt taggatatca gataccacat catatccaaa
     1681 agaaacatgc cccgtaatct tcaagtactt ggcaaactga tctaaatgtt tagcccagtc
     1741 atcatacttc accgatgcca acgcattaaa aatagcatca cgatcggctt tgctgaattt
     1801 cttatttaaa acatccttgt atttttcaaa agcagcgaga gcttcattca cattgccgat
     1861 tttcttacct ttagacttat cagcaagttc ctgtgccatt ttcgaatatt tttcaccata
     1921 tttttcagtc agcgtttgat aaaagctaac tgttgcatca acagcatcct taatctgtga
     1981 attaaggaga ttattctgtg cttttttcaa attttcttca gcttcatgaa cacgagcgat
     2041 accggcatta cgattattac tgacctgaga aatagccttc tggatctgag ttatatcagc
     2101 atttatccgg ttaatacgtg tttatgatgc tgttacctgt ttttgttttt cttctctaat
     2161 cttaccggcc ccaacccgtc gtctggttgc ttcaaaaaaa ggacggttct gaagcggatc
     2221 attggctctt ggtgatagtt ttttgaccag ctcatccagt tctttatatt tagcggatgc
     2281 ctgagccagt tcatttcgtt ttccagcgag cgttttcatt tctgcatcac gggcatggat
     2341 actggagctt aaacgagaat tgagagtctt aatctctcca tccattttca ccacttcaga
     2401 ttgtgcagca gaaagttttt tttgggcgat ctcaacagct ttagcttctt cactcaatgc
     2461 agccagtcgt ttctcttcag cttcagccag tttcaactgg cgttctgttt cagccttctc
     2521 ccgttcaatc tctttacgtc gttgttctgc ttcctgaaaa gccttttctg ctgcttccgc
     2581 ttctttacgg gctttttctt ctgctttcgc aaggcgcaaa cgctctgctt ccgcctgcat
     2641 agctgcatta ttagcatgag caagctctgt tgctgaaggc gtacgtgagg cattgtgacg
     2701 aagagcctca ttcacgatat ccttcaggcg ctgagtcagc gcatccctgt ttgcctttgc
     2761 tttcgcctgt gcttccgctg cagcttttgc ccgggcagcc tgctctgcct gtgttttctt
     2821 taattgagca gtagaccatt tagcagttgc atgaatagct gcagaacttt cacttttact
     2881 gcctcctttt ccacctccgc cgccagagcc actcccgtca ggagtaccat tcaaaagagt
     2941 aataattacc tgtcccttat catcataagg aacaccatct ttatagtacg ctaccgcggt
     3001 ttccattata aaatcctctt tgacttttaa aacaataagt taaaaataaa tactgtacat
     3061 ataaccactg gttttatata cagcataaaa gctacgccgc tgcattttcc ctgtcaagac
     3121 tgtggacttc catttttgtg aaaacgatca aaaaaacagt ctttcacacc acgcgctatt
     3181 ctcgcccgat gccacaaaaa ccagcacaaa cattaccgtt ctcagacctc attatgtttt
     3241 actgaaacta tgagatgaga catctatggg acactgtcac tttatggcat ggcacacact
     3301 ccgggacgca ctaaaaatga caggcagatc gcgttcacag ttttaccgtg atatgcgcgc
     3361 aggccttgtc agttaccgta ccggcaggga cggacgacgg gagtttgaaa ccagtgaact
     3421 gatccgggca tacggcgaat taaagcagaa tgagacacca gaaaggcaca gtgagggaca
     3481 tgcagaaaat ccacatgatc agcagacaga acgcattctc cgggagctga atgagctgaa
     3541 acaatgcctg acgctgatgc ttgaggataa acaggcacag gatatggatc gcagacgcca
     3601 ggaagcagaa cgggaacagc tacaaaatga gatagcccag ctcaggcagg cactggaact
     3661 ggaaaagaaa cggggattct ggtccaggtt gttcggtcgc tgaacgctgt cagagactga
     3721 tgataaaata gtcttcggat aataactcac cgagaataaa tactttaagg tagggagaca
     3781 ctcatgagac gtaccggaaa caaactttgt cttatcgcca tgataacagc aacagtagct
     3841 ctcacagcct gtaccccaaa gggcagcgtg gaacaacata cccggcatta cgtatatgct
     3901 tctgatgacg gttttgatcc caacttttcc acccaaaaag ccgacacaac acgaatgatg
     3961 gtgccttttt ttcggcagtt ctgggatatg ggagctaaag ataaagcgac aggaaaatca
     4021 cggagtgatg tgcaacaacg cattcagcag tttcacagcc aggaattttt aaactcactc
     4081 cggggcacaa ctcaatttgc gggtactgat taccgcagca aagaccttac cccgaaaaaa
     4141 tccaggctgc tggctgacac gatttctgcg gtttatctcg atggctacga gggcagacag
     4201 taagtggatt taccataatc ccttaattgt acgcaccgct aaaacgcgtt cagcgcgatc
     4261 acggcagcag acaggtaaaa atggcaacaa accacccgaa aaactgccgc gatcgcgcct
     4321 gataaatttt aaccgtatga atacctatgc aaccagaggg tacaggccac attaccccca
     4381 cttaatccac tgaagctgcc atttttcatg gtttcaccat cccagcgaag ggccatccag
     4441 cgtgcgttcc tgtatttccg gctgacgctc ccgttccagg gataacacat gttcgcgctc
     4501 ctgtatcagc cgttcctctc ttatctccag ttctcgctgt ataactggct caagcgttct
     4561 gtctgctcgc tcaagtgctg cacctgctga ctcaactgca tgacccgctc gttcagcatc
     4621 gcgttgtccc gttgcgtaag cgaaaacatc ttctgcaatt ccacgaaggc gctctcccat
     4681 tcgctcagcc gctgcatata gtcctgttgc agctgctcta aggcgttcag caaatgtgtt
     4741 tccagctctg tcactctgtg tcactccttc agatgtaccc actctttccc ctgaaaggga
     4801 atcacctccg ctgatttccc gtacggaagg acaaggaatt tcctgttccc gtcctgcaca
     4861 aactccacgc cccatgtctt cgcgttcagt ttctgcaatg tctcttcctg cttcctgatt
     4921 tcttccaggt tcgcctgtat cctccctcca agataccaga gcgtcccgcc actcgcggta
     4981 aacaggagaa agactatccc cagtaacatc atgcccgtat tccctgccag ctttaacacg
     5041 tccctcctgt gctgcatcat cgcctctttc accccttccc ggtgtttttc cagcgattcc
     5101 tctgtcgagg ctgtgaacag ggctatagcg tctctgattt tcgtctcgtt tgatgtcaca
     5161 gcctcgctta cagattcgcc gagcctcctg aactcgttgt tcagcatttt ctctgtagat
     5221 tcggctctct ctttcagctt tttctcgaac tccgcgcccg tctgcaaaag attgctcata
     5281 aaatgctcct ttcagcctga tattcttccc gccgttcgga tctgcaatgc tgatactgct
     5341 tcgcgtcacc ctgaccactt ccagccccgc ctcagtgagc gcctgaatca catcctgacg
     5401 gccttttatc tctccggcat ggtaaagtgc atctatacct cgcgtgacgc cctcagcaag
     5461 cgcctgtttc gtttcaggca ggttatcagg gagtgtcagc gtcctgcggt tctccggggc
     5521 gttcgggtca tgcagcccgt aatggtgatt caccagcgtc tgccaggcat caattctagg
     5581 cctgtctgcg cggtcgtagt acggctggag gcgttttccg gtctgtagct ccatgttcgg
     5641 aatgacaaaa ttcagctcaa gccgtccctt gtcctggtgc tccacccaca ggatgctgta
     5701 ctgatttttt tcgagaccgg gcatcagtac acgctcaaag ctcgccatca ctttttcacg
     5761 tcctcccggc ggcagctcct tctccgcgaa cgacagaaca ccggacgtgt atttcttcgc
     5821 aaatggcgtg gcatcgatga gttcccggac ttcttccgga ttaccctgaa gcaccgttgc
     5881 gccttcgcgg ttacgctccc tccccagcag gtaatcaacc ggaccactgc caccaccttt
     5941 tcccctggca tgaaatttaa ctatcatccc gcgccccctg ttccctgacg gccagacgca
     6001 gccggcgcag ctcatccccg atggccatca gtgcggccac cacctgaacc cggtcaccgg
     6061 aagaccactg cccgctgttc accttacggg ctgtctgatt caggttattt ccgatggcgg
     6121 ccagctgacg cagtaacggc ggtgccagtg tcggcagttt tccggaacgg gcaaccggct
     6181 cccccaggca gacccgccgc atccataccg ccagttgttt accctcacag cgttcaagta
     6241 accgggcatg ttcatcatca gtaacccgta ttgtgagcat cctctcgcgt ttcatcggta
     6301 tcattacccc atgaacagaa atccccctta cacggaggca tcagtgacta aacaggaaaa
     6361 aaccgccctt aacatggccc gctttatcag aagccagaca ttaacgctgc tggagaagct
     6421 caacgaactg gacgcagatg aacaggccga tatttgtgaa tcgcttcacg accacgccga
     6481 tgagctttac cgcagctgcc tcgcacgttt cggggatgac ggtgaaaacc tctgacacat
     6541 gcagctcccg gagacggtca cagcttgtct gtgagcggat gccgggagct gacaagcccg
     6601 tcagggcgcg tcagcaggtt ttagcgggtg tcggggcgca gccctga
//
