LOCUS       NZ_CP068045             6200 bp    DNA     circular CON 16-MAY-2024
DEFINITION  Escherichia coli strain XJW9B277 plasmid pXJW9B277-5, complete
            sequence.
ACCESSION   NZ_CP068045
VERSION     NZ_CP068045.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17245958
            Assembly: GCF_018988385.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6200)
  AUTHORS   He,W.Y., Zhang,X.X., Gao,G.L., Gao,M.Y., Zhong,F.G., Lv,L.C.,
            Cai,Z.P., Si,X.F., Yang,J. and Liu,J.H.
  TITLE     Clonal spread of Escherichia coli O101: H9-ST10 and O101: H9-ST167
            strains carrying fosA3 and blaCTX-M-14 among diarrheal calves in a
            Chinese farm, with Australian Chroicocephalus as the possible origin
            of E. coli O101: H9-ST10
  JOURNAL   Zool Res 42 (4), 461-468 (2021)
   PUBMED   34156173
REFERENCE   2  (bases 1 to 6200)
  AUTHORS   He,W.Y. and Liu,J.H.
  TITLE     Direct Submission
  JOURNAL   Submitted (08-JAN-2021) College of Veterinary Medicine, South China
            Agricultural University, Wushan, Tianhe District, Guangzhou,
            Guangdong 510642, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 12-DEC-2020
            Assembly Method :: SPAdes v. v3.8.7; Unicycler v. v0.4.7
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 200.0x
            Sequencing Technology :: Illumina MiniSeq; Oxford Nanopore's MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_018988385.1-RS_2024_05_16
            Annotation Date                   :: 05/16/2024 04:44:05
            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)                     :: 5,291
            CDSs (total)                      :: 5,172
            Genes (coding)                    :: 4,896
            CDSs (with protein)               :: 4,896
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 276
            CDSs (without protein)            :: 276
            Pseudo Genes (ambiguous residues) :: 0 of 276
            Pseudo Genes (frameshifted)       :: 83 of 276
            Pseudo Genes (incomplete)         :: 199 of 276
            Pseudo Genes (internal stop)      :: 54 of 276
            Pseudo Genes (multiple problems)  :: 53 of 276
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP068045.1.
            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..6200
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="XJW9B277"
                     /host="Bovine"
                     /db_xref="taxon:562"
                     /plasmid="pXJW9B277-5"
                     /geo_loc_name="China: Xinjiang"
                     /collection_date="2018-05-07"
     gene            complement(join(5795..6200,1..425))
                     /locus_tag="JJE78_RS26145"
                     /old_locus_tag="JJE78_26030"
     CDS             complement(join(5795..6200,1..425))
                     /locus_tag="JJE78_RS26145"
                     /old_locus_tag="JJE78_26030"
                     /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="APH(6)-I family aminoglycoside
                     O-phosphotransferase"
                     /protein_id="WP_001391758.1"
                     /translation="MPPVFPAHWHVSQPVLIADTFSSLVWKVSLPDGTPAIVKGLKPIE
                     DIADELRGADYLVWRNGRGAVRLLGRENNLMLLEYAGERMLSHIVAEHGDYQATEIAAE
                     LMAKLYAASEEPLPSALLPIRDRFAALFQRARDDQNAGCQTDYVHAAIIADQMMSNASE
                     LRGLHGDLHHENIMFSSRGWLVIDPVGLVGEVGFGAANMFYDPADRDDLCLDPRRIAQM
                     ADAFSRALDVDPRRLLDQAYAYGCLSAAWNADGEEEQRDLAIAAAIKQVRQTSY"
                     /name="APH(6)-I family aminoglycoside O-phosphotransferase"
     gene            complement(431..1234)
                     /gene="aph(3'')-Ib"
                     /locus_tag="JJE78_RS26150"
                     /old_locus_tag="JJE78_26035"
     ARG             complement(435..1234)
                     /name="aph(3'')-Ib"
                     /gene="aph(3'')-Ib"
                     /gene_name="aminoglycoside O-phosphotransferase
                     APH(3'')-Ib"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            complement(1295..2110)
                     /gene="sul2"
                     /locus_tag="JJE78_RS26155"
                     /old_locus_tag="JJE78_26040"
     ARG             complement(1299..2110)
                     /name="sul2"
                     /gene="sul2"
                     /gene_name="sulfonamide-resistant dihydropteroate synthase
                     Sul2"
                     /tool="amrfinderplus"
                     /drug_class="SULFONAMIDE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            complement(2570..2728)
                     /locus_tag="JJE78_RS26805"
     CDS             complement(2570..2728)
                     /locus_tag="JJE78_RS26805"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_032287700.1"
                     /translation="MHEPPVQSDRCALSGNYQLESNPERHDKTPLAAAISNRSAREDRL
                     RGLEVEA"
                     /name="hypothetical protein"
     gene            3299..3448
                     /locus_tag="JJE78_RS26160"
                     /old_locus_tag="JJE78_26045"
     CDS             3299..3448
                     /locus_tag="JJE78_RS26160"
                     /old_locus_tag="JJE78_26045"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001138880.1"
                     /translation="MPSEYDEQLDSTDTQLPGEYDLFDLMAQVTEENLHAPVDFGSPVG
                     REAL"
                     /name="hypothetical protein"
     gene            complement(4193..4633)
                     /locus_tag="JJE78_RS26165"
                     /old_locus_tag="JJE78_26050"
     CDS             complement(4193..4633)
                     /locus_tag="JJE78_RS26165"
                     /old_locus_tag="JJE78_26050"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011161230.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_005119689.1"
                     /translation="MAWHTVQETLKLTGKSRSQLYRDMAKGLVSYRTGKNDRREFETSE
                     LIRAYGELRTSETPKRHKEGHSKSVVSQAENAQLDVIQQKLDALQQTVTLMLEDKMARE
                     AENRLRNEEREQLQAEISRLADALAQEKKRGFWSRLFRSGSE"
                     /name="hypothetical protein"
     gene            4851..5240
                     /locus_tag="JJE78_RS26170"
                     /old_locus_tag="JJE78_26055"
     CDS             4851..5240
                     /locus_tag="JJE78_RS26170"
                     /old_locus_tag="JJE78_26055"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000102614.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000102614.1"
                     /translation="MSTELNSGTVGGFGHMGPNDPYNDGHSGSGSSGGSFNGGGNGGHD
                     NSSGSSYTASFGLITGRHPITVPGTKNINSVDLSAVINNIIHHEGARNNMYLDTANNVR
                     VGVTGTGWQCLATAGISAEGKRTFR"
                     /name="hypothetical protein"
     gene            5284..>5688
                     /locus_tag="JJE78_RS26175"
                     /old_locus_tag="JJE78_26060"
                     /pseudo=""
     CDS             5284..>5688
                     /locus_tag="JJE78_RS26175"
                     /old_locus_tag="JJE78_26060"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001120888.1"
                     /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="IS91 family transposase"
                     /name="IS91 family transposase"
     ARG             complement(5796..6199)
                     /name="APH(6)-Id"
                     /gene="APH(6)-Id"
                     /gene_name="APH(6)"
                     /tool="rgi"
                     /drug_class="aminoglycoside antibiotic"
                     /identity="99.25"
                     /coverage="48.2"
     ARG             complement(4..431)
                     /name="APH(6)-Id"
                     /gene="APH(6)-Id"
                     /gene_name="APH(6)"
                     /tool="rgi"
                     /drug_class="aminoglycoside antibiotic"
                     /identity="100.0"
                     /coverage="51.44"
     Typing          3091..3264
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.429"
                     /coverage="100.0"
                     /evalue="1.19e-84"
     Typing          complement(2562..3167)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.593"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 cctgcgtttt gatcatcgcg cgcccgctga aacaaagctg caaagcgatc ccggatcggg
       61 agaagggcag aaggcagggg ttcctcagat gcggcataca gcttcgccat tagttccgct
      121 gcaatttcgg tcgcctggta gtcgccgtgc tcggcaacga tgtgagagag cattcgctcc
      181 ccggcatatt cgagcaacat cagattgttc tcacgaccga gcaaccggac tgctcccctc
      241 ccattgcgcc ataccagata gtcggccccg cgcagttcat cagcaatgtc ttctataggt
      301 ttcaatccct tgacgattgc aggagtcccg tctggcaatg aaactttcca aacgaggctg
      361 gaaaaggtgt ccgcaatgag aacaggttgc gaaacgtgcc aatgagcagg aaaaacaggc
      421 ggcatgaaca tcaaccccaa gtcagagggt ccaatcgcag atagaaggca aggcgttcgc
      481 ggtcgggggc ttcgatcccc aatacattga ataggacagc gaaggcgcgc tctgcttcat
      541 ctggcgctgc ccagttctct tcggcgttag caatcatgag tgccaaatcg gcatagcgat
      601 ctgctgttcc gagccgccca aggtcgatca gacccgtgca ttgaagagtt ttagggtcca
      661 ccatgaagtt cggcatgcag ggatcaccat ggcaaacaac catatcggtg cgctcttggt
      721 cgagccgcac cggtagctct cgttcgacac gagccaaaag atcgagctgc ggcgtactct
      781 tgtcctcgtc cggtaagaag tcgggattga cggcattgcg ggacaccaca tcaacggcgc
      841 gtccgaacat tcgcgacagc ctgcgctcaa acggacattg atcaaccgat aggctgtgaa
      901 cagcgccaag ttgctgcccc attgacggcc acgctttgag caaatccgct ccagacagat
      961 cagccgccgg tactcccgga attgccgtta tcaccaagca tgcaccctcc tgttcctcct
     1021 gccagttgat gacctcgggg caagccacac ctcgaccttt gagccaaatg aggcggtcac
     1081 gctctccagc gagctcaccg cggcgggaag caggtgcgat tttcgcgaag gcatgcccgt
     1141 caccacgtcg aaaaacaaaa tcaccagatt ctccgcctct gacaggcaac cagtcagaat
     1201 gcgattcacc aaaaaaaata ttagttcgat tcaatggagg ttccttcagt tttctgatga
     1261 agcgcgaata tagagaaata tcccgaatgt gcagttaacg aattcttgcg gtttctttca
     1321 gcgccgccaa taccgccagc ccgtcgcgca aggggcgcgg ctcgtgtgtg cggatgaagt
     1381 cagctccacc tgcggcggcg gcaagctctg cagcgagtgt cgcggccccg acatcccccg
     1441 gaccacggcc tgtgagcgcg cgcagaaagg atttgcgcga aacagacaga agcaccggca
     1501 aatcgaagcg cagccgcaat tcatcgaacc gcgccagcac cgagagcgag gtttcgggag
     1561 cagcccccag aaaaaacccc atgccgggat caaggacaag gcggttgcgt ttgataccgg
     1621 cacccgtcag cgccgcgatg cgcgcgtcaa agaacgccgc aatgtgatcc atgatgtcgc
     1681 cagcgggtgc ctcgcgccga tctgcctgcc cgtcttgcac cgaatgcata acgacgagtt
     1741 tggcagatga tttcgccaat tgcggataga acgcagcgtc tggaaaaccg cgaatatcat
     1801 tgagataggc cacaccacgc gacaaggcat aggcttgcgt cgcgggttga taactgtcga
     1861 gcgagacggg aatgccatct gccttgagcg cgtccagcac cggcgcgata cgcgcgattt
     1921 ctgtgtcgga cgaaacaggc gcggcgtcgg gattgctgga tgccggaccg aggtcgatca
     1981 catctgcccc ctcggccatc agcttacgcg cctgcgcaat ggctgcgtct ggcgccagat
     2041 accggcctcc atcggagaaa ctgtccgagg ttatgttgac gatgccgaaa atgatgagcg
     2101 atttattcat gggggcttct ataataataa taatcgagca tgagtctcat acggatgctc
     2161 gggtcgaaag ggaatcccca ggcgagtaac ctgtttgcgg tgatccgttt catgatgatg
     2221 tatctgtagc attttggaaa taaatatatc atctctcaat aagtagatat atttatcttt
     2281 tttgcttctt tggtgctgca agtcaccaat acgagggaaa cctgttacgg agcggtttaa
     2341 ccgtaatcaa cagtgactgg tgtcatgttc ggaagattaa ttgatagtaa tctacaaagg
     2401 atcttcttga gatccttttc aatgaatcgt aatctcttgc tctgtaaacg aaaaaaccgc
     2461 ctggggaggc ggtttgttcg aaggttaagt cagttgggga actgcttaac ccggtaacag
     2521 ggttcacgag accgccatta ccaaaactgt tctttcagtg tagccgcagt caggcctcta
     2581 cttcaagacc tcttaatcta tcttctcgtg cactcctgtt actaatggct gctgccagtg
     2641 gcgttttgtc gtgtctttcc gggttggact caagttgata gttaccggac aaggcgcagc
     2701 ggtcggactg aacggggggt tcgtgcatac agtccagctt ggagcgaact gccttcacgg
     2761 aactgagtgt caggcgtgga atgagaaacc gcggccataa cagcggaatg acaccggtaa
     2821 accgaaaggc aggaacagga gagcgcacga gggagctacc agggggaaac gcctgggatc
     2881 tttatagtcc tgtcgggttt cgccaccact gatttgagcg tcagattttg cgatgcttgt
     2941 caggggggcg gagcctatgg aaaaacggct tcgccgtggc cttatctctt ctttgctaag
     3001 tgtcttcctg gtatcttcca ggaaatttcc gtccccgtcc gtaagccggt accgctcgcc
     3061 gcagccgaac gaccgagcgt agcgagtcag tgagcgagga agcggaatat ctcctgtatc
     3121 gcatattctg ctgacgcgcc ggtgctgcct tttttctcct gccacatgaa gcacttcact
     3181 gattttcgca atcgtggcaa catagtaagc cagtatacac tccgctagcg ctacatgact
     3241 ggttcagggc tgcgccccga aacccgctaa caacctctca gctactggat atcaccccat
     3301 gccatctgaa tatgatgaac aactggattc gactgatacg cagcttcccg gcgaatatga
     3361 cctttttgat ttaatggcgc aggttactga agagaacctg catgcccctg tggattttgg
     3421 gtcgcctgtc ggccgggaag cgttatagct ttttcgcttg cccgcgtacg tggtaatact
     3481 ccggtattac cttttatttc tttattttca tgtaattaca gtggattttt aatacccggg
     3541 tattactcgt gaaaacgaaa tattcctttt ttttctttta attcatgcag ttgcgatgaa
     3601 aatcgcggct gcgttaggtg tatgaccatt ttgaggttga aaaataatca accatggcgg
     3661 gtgatttacg caggttaagg ggagatcgtg acaaaaaaag cgttcctcac tgtatcgttc
     3721 atgcctgcat gaacgggtta ttcttcctga ctacagaatt acatcgctcc ttcagttcat
     3781 acatcacttt tacatcactt atacatcact tttacatcat tccttcagct catacgtcac
     3841 tttcatcctc tgtgccattt gtacatcacc cccttcctga acgtgctgac agcgggtttt
     3901 ccggctgcgc cggcaacgct tcacggccac gcaataaatt gcgtccccgt tcaccgtttt
     3961 cggatgggaa gaacgccgga aacaggactt accccggctg aatggtgtga atttccgcgc
     4021 tatgcacttg tgcgcatact catgcatgcc gtaaaaacag agcctgcgcg tttctggcgg
     4081 gttttcgggt ggtttgttgc ctgttttacc ggtttcccgt cagaaacgcc ctgagggcct
     4141 ctcaggcggt gctgataaca gatgttatgg taaatcagag tcacctgcac tgttactctg
     4201 aaccggagcg aaacagccgc gaccagaatc cccgcttttt ttcctgtgcc agcgcgtcag
     4261 ccagacggct aatttcggcc tgtagttgtt ccctctcctc atttcgcagg cggttttctg
     4321 cttcccgcgc catcttgtct tcaagcatta gggtaacagt ctgctgcaga gcgtccagtt
     4381 tctgctgaat gacgtctagc tgagcatttt ccgcctggct aacgacagat ttggagtgtc
     4441 cctccttgtg cctttttggt gtctcagaag tgcgcagctc gccataggcc cgaatcagtt
     4501 cactggtctc gaactcccgg cgatcatttt ttcctgtgcg atagctgaca aggcctttag
     4561 ccatgtcacg atataattgc gagcgcgact ttcctgttaa tttcagtgtc tcttgaactg
     4621 tgtgccatgc cataaaagtg acagtgtctc ctgtgtgtac cgtattgtaa cagcagaaca
     4681 tattactgtt ttaacacaaa aggtctgagg ctgcccgtga ggcgtgaaaa atacacaaaa
     4741 aacctgttga cggtgtggtt ttgacgggcg tagtatttcg aatactgtat ataaacacat
     4801 tgttataaat acagtttttg ctgtttttaa aagtcaaaga ggataatttt atgagtacag
     4861 agttaaatag cggtactgtc ggtggttttg gtcacatggg accaaatgac ccctacaatg
     4921 atggtcatag cggctctgga agttcgggag gtagttttaa cggtggtggt aatggtggcc
     4981 atgataatag tagtggttca tcttatactg catcctttgg tctcatcact ggccgacacc
     5041 cgataactgt cccaggtacg aagaatatta attctgtcga tctttctgct gtcattaata
     5101 acattataca tcatgaaggt gcacgcaata acatgtacct agatactgcg aacaatgtaa
     5161 gagtgggagt gacgggcact ggctggcaat gtctagcaac ggcaggcatt tcggctgagg
     5221 gtaaaagaac tttccgctaa gcgatagact gtatgtaaac acagtattgc aaggacgcgg
     5281 aacatgcctc atgtggcggc caggacggcc agccgggatc gggatactgg tcgttaccag
     5341 agccaccgac ccgagcaaac ccttctctat cagatcgttg acgagtatta cccggcattc
     5401 gctgcgctta tggcagagca gggaaaggaa ttgccgggct atgtgcaacg ggaatttgaa
     5461 gaatttctcc aatgcgggcg gctggagcat ggctttctac gggttcgctg cgagtcttgc
     5521 cacgccgagc acctggtcgc tttcagctgt aagcgtcgcg gtttctgccc gagctgtggg
     5581 gcgcggcgga tggccgaaag tgccgccttg ctggttgatg aagtactgcc tgaacaaccc
     5641 atgcgtcagt gggtgttgag cttcccgttt cagctgcgtt tcctgtttgg ggtcgtttgc
     5701 gggaaggggc ggaatcctac gctaaggctt tggccagcga tattctccgg tgagattgat
     5761 gtgttcccag gggataggag aagtcgcttg atatctagta tgacgtctgt cgcacctgct
     5821 tgatcgcggc cgcgatagct agatcgcgtt gctcctcttc tccatccgcg ttccaagctg
     5881 cggaaaggca cccataagcg tacgcctggt cgagcaggcg acgcggatcg acgtccagcg
     5941 cacgagagaa tgcgtccgcc atctgtgcaa tgcgtctagg atcgagacaa aggtcgtctc
     6001 tgtcagccgg atcgtagaac atattggcgg cgccaaagcc cacttcaccg accagaccga
     6061 cgggatctat caccagccag ccgcgactgg agaacatgat gttttcatga tgcagatcgc
     6121 catgtagccc acgcagttcc gaggcattgc tcatcatttg atcggctata atcgccgcgt
     6181 ggacgtagtc agtttgacaa
//
