LOCUS       NZ_CP139132             4145 bp    DNA     circular CON 06-DEC-2023
DEFINITION  Escherichia coli strain YZ22PE165 plasmid pYUYZPE165-2, complete
            sequence.
ACCESSION   NZ_CP139132
VERSION     NZ_CP139132.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN38245693
            Assembly: GCF_034059795.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4145)
  AUTHORS   Wang,J.
  TITLE     tet(X4)-positive Escherichia coli strains in Yangzhou
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4145)
  AUTHORS   Wang,J.
  TITLE     Direct Submission
  JOURNAL   Submitted (14-NOV-2023) Key Laboratory of Prevention and Control of
            Biological Hazard Factors (Animal Origin) for Agrifood Safety and
            Quality, Ministry of Agriculture of China, Yangzhou University,
            No.48 Wenhui East Road, Yangzhou, Jiangsu 225009, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.5.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100x
            Sequencing Technology             :: Illumina; Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 12/05/2023 23:23:39
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,736
            CDSs (total)                      :: 4,616
            Genes (coding)                    :: 4,404
            CDSs (with protein)               :: 4,404
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 212
            CDSs (without protein)            :: 212
            Pseudo Genes (ambiguous residues) :: 0 of 212
            Pseudo Genes (frameshifted)       :: 57 of 212
            Pseudo Genes (incomplete)         :: 148 of 212
            Pseudo Genes (internal stop)      :: 36 of 212
            Pseudo Genes (multiple problems)  :: 29 of 212
            Pseudo Genes (short protein)      :: 4 of 212
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP139132.1.
            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..4145
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="YZ22PE165"
                     /isolation_source="Pig farm"
                     /host="pig"
                     /db_xref="taxon:562"
                     /plasmid="pYUYZPE165-2"
                     /geo_loc_name="China: Yangzhou"
                     /lat_lon="32.27 N 119.29 E"
                     /collection_date="2022-06-02"
                     /collected_by="Jiang Yue"
     gene            complement(join(3997..4145,1..>34))
                     /locus_tag="SIY76_RS23635"
                     /pseudo=""
     CDS             complement(join(3997..4145,1..>34))
                     /locus_tag="SIY76_RS23635"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007798797.1"
                     /note="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="NINE protein"
                     /name="NINE protein"
     gene            <31..273
                     /locus_tag="SIY76_RS23640"
                     /pseudo=""
     CDS             <31..273
                     /locus_tag="SIY76_RS23640"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_003862821.1"
                     /note="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="cupin domain-containing protein"
                     /name="cupin domain-containing protein"
     gene            complement(311..1453)
                     /gene="wzz(fepE)"
                     /locus_tag="SIY76_RS23645"
     CDS             complement(311..1453)
                     /gene="wzz(fepE)"
                     /locus_tag="SIY76_RS23645"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010435173.1"
                     /GO_component="GO:0016020 - membrane [Evidence IEA]"
                     /GO_process="GO:0009103 - lipopolysaccharide biosynthetic
                     process [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="LPS O-antigen length regulator Wzz(fepE)"
                     /protein_id="WP_021544858.1"
                     /translation="MSAMDFKKNTDLDFPRYATPAVSTKEIDLLGLLDVLLAAKKRIVT
                     IVLAFAVVGLAIAFLIPQKWTSKAVITPAEQTQWNTLRQMMVTLQVLDVDAKVSRGDVF
                     NLFIKKFQSQSLLEEYMKTSPYVMSQLEGTEVDPLELHRAVVNIAEKMKATDNTQVKDA
                     DKAPYTSWTLSFTAPTAGDAQTVLEGYINYISRIVEQETMENIRNQITLKTKVVQQQLE
                     LDRVRLTNIHNTNLQRLNYSLEVANAAGIKKPVYSNGQAVKDDPDYSVALGADGIAQKL
                     QIEKNLKDVAELNADFQNREYYLTQLQKLSVEDVKLEPFRYQLSPSLPVKKDGPGKALI
                     VLLAGILGGLFACGSVLLREAMLSRNPLPEPITAVTPATE"
                     /name="wzz(fepE)"
     gene            1648..2031
                     /locus_tag="SIY76_RS23650"
     CDS             1648..2031
                     /locus_tag="SIY76_RS23650"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_003117291.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS5/IS1182 family transposase"
                     /protein_id="WP_021544857.1"
                     /translation="MSHQLTFADSEFSSKRRQTRKEIFLSRMEQILPWQNMVEVIEPFY
                     PKAGNGRRPYPLETMLRIHCMQHWYNLSDGAIEDALYEIASMRLFARLHESQHPGQGGA
                     PISHHQATVRLRESQIQGVAEKR"
                     /name="IS5/IS1182 family transposase"
     gene            1994..2110
                     /locus_tag="SIY76_RS23655"
     CDS             1994..2110
                     /locus_tag="SIY76_RS23655"
                     /inference="COORDINATES: protein motif:HMM:NF013752.3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001407452.1"
                     /translation="MKARYKGLLKNDNQLAMLFTLANLFRADQMIRQWERSH"
                     /name="hypothetical protein"
     gene            complement(<2259..2390)
                     /locus_tag="SIY76_RS23660"
                     /pseudo=""
     CDS             complement(<2259..2390)
                     /locus_tag="SIY76_RS23660"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_013578013.1"
                     /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="zinc-ribbon domain-containing protein"
                     /name="zinc-ribbon domain-containing protein"
     gene            complement(2698..2811)
                     /locus_tag="SIY76_RS23665"
     CDS             complement(2698..2811)
                     /locus_tag="SIY76_RS23665"
                     /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="replication initiation protein"
                     /protein_id="WP_071778980.1"
                     /translation="MHEPPVQSDRCVFSGNYRLESKPERHDKAPLAAATGN"
                     /name="replication initiation protein"
     Typing          complement(2695..3080)
                     /name="rep_cluster_2373"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.373"
                     /coverage="90.0"
                     /evalue="1.04e-173"
ORIGIN
        1 caaatccacc aaggaagaat gctaagaaag atgatggcgg tggaggtcaa ttttgagcag
       61 ggtgcgattg gcccgatgca caatcacccg catgaacagc ttacctatgt gctctccggg
      121 gagttcgagt ttacgatagg tgaagaaaag cagatcgtga cggcgggcga tacgctctat
      181 aaagcgccgc acgtgatgca cggctgcatt tgcctgaagc ccggcaccct tctggatacc
      241 tttacgccgg tgcgcgacga tttcctgaaa taaaaaaagg cgctgaatca gcgccttttt
      301 aatatcgtcg ttactctgtt gctggcgtta cggccgttat cggctctggc aacggattac
      361 gcgagagcat tgcctcacgc agcagcacgc tgccgcaggc aaacaggccg cccagaatcc
      421 ctgccagcag cacaatcagg gctttgcccg gaccgtcttt tttcaccggc agtgacggtg
      481 aaagctgata cctgaagggt tcaagcttca cgtcttccac ggacagtttt tgcaactgag
      541 tcagatagta ttcacggttc tggaaatccg cattcagctc ggccacgtcc ttcagattct
      601 tttcaatctg cagcttttgc gcaataccgt cagcacccag cgccacggag tagtcaggat
      661 cgtcttttac cgcctgtccg ttgctgtaaa ccggcttctt aatgcctgcc gcgttcgcca
      721 cttccagcga atagttgagg cgctgcaggt tggtgttgtg gatattggtc agacgcacgc
      781 gatccagctc cagctgctgc tgaacgactt tcgttttcag cgtgatctgg ttacggatat
      841 tttccatcgt ctcctgctca acaatgcggg agatatagtt gatgtaacct tccagaaccg
      901 tctgcgcgtc tcccgccgtc ggggcggtaa agctcagcgt ccatgaggta tacggcgctt
      961 tgtctgcgtc tttaacctgc gtgttatctg tcgctttcat tttctcagca atattcacca
     1021 ccgcgcgatg cagctccagc gggtctacct cggtgccttc cagctgagac atcacgtacg
     1081 gggaggtttt catgtactct tcgagcagcg actgcgactg aaactttttg atgaacaggt
     1141 taaacacgtc tccacggctc accttcgcgt cgacgtccag cacctgcagc gtcaccatca
     1201 tctggcgcag cgtgttccac tgcgtctgct cggccggcgt gatcacggct ttactggtcc
     1261 atttttgcgg gattaaaaac gcaatggcca accctactac ggcgaacgcc aggacgatcg
     1321 tcacaatacg ttttttggct gccagaagta cgtctaacaa ccccaggaga tctatctctt
     1381 tggtgcttac cgccggagtg gcataacggg gaaaatcgag gtccgtgttt ttcttgaaat
     1441 ccatcgctga cataaccgtt cttctttttg gagcgcagta aatttctgcc tgattggttg
     1501 cagtggtcgg atgatacaag aaagtaagaa taatctgaac gccagattga tctatctgta
     1561 gaccgactat cagatttagg gaaggtgcga acaagtccct gatatgagat catgtttgtc
     1621 atctggagcc atggaacagg gttcatcatg agtcatcaac ttaccttcgc cgacagtgaa
     1681 ttcagcagta agcgccgtca gaccagaaaa gagattttct tgtcccgcat ggagcagatt
     1741 ctgccatggc aaaacatggt ggaagtcatc gagccgtttt accccaaggc tggtaatggc
     1801 cggcgacctt atccgctgga aaccatgcta cgcattcact gcatgcagca ttggtacaac
     1861 ctgagcgatg gcgcgatcga agatgctctg tacgaaatcg cctccatgcg tctgtttgcc
     1921 cggttacatg aaagccagca tccgggccaa ggtggagcac ccatttcgca tcatcaagcg
     1981 acagttcggc ttcgtgaaag ccagatacaa ggggttgctg aaaaacgata accaactggc
     2041 gatgttattc acgctggcca acctgtttcg ggcggaccaa atgatacgtc agtgggagag
     2101 atctcactaa aaactgggaa taacgcctta aatggcgaag aaacggtcta aataggctga
     2161 ttcaaggcat ttacgggaga aaaaaatcgg ctcaaacatg aagaaatgaa atgactgagt
     2221 caaccgagaa gaatttcccc gcttattcgc accttcccta atagcgcggc tgcgattcta
     2281 cttttttcac ctgaacctga agaggcgttt gtggctccgc agtgtgggca tgactttgct
     2341 gtttcgtgta tttccttgcc gcatcctcgg cagtaaacca ttgaactcat tttttatcct
     2401 cgagcttatt tttagttggg atgcataata tccgatgttt tataacgata tgcatcctat
     2461 atgctcgggt gggatagatt tccattatgg tgaaggatct tcttgagatc ctttctgtag
     2521 cgtcgtaatc tcttgctcag taaacgaaaa aaccgcccag caaggcggtt tttcgaaggt
     2581 tctcagagct gcaactcttt gaaccgtggt aactggctta tgaggagcgc agtaaccaaa
     2641 tctgttcttt cagtttagcc ttaacaggcg cataacttca agactaactc ctctaaatca
     2701 gttaccagtg gctgctgcca gtggcgcttt gtcgtgtctt tccggcttgg actcaagtcg
     2761 atagttaccg gagaagacgc agcggtcgga ctgaacgggg ggttcgtgca tacagtccag
     2821 cttggagcga actgcctacc cggaactgag tgtcaggcgt ggaatgagat aaacgcggcc
     2881 ataacagcgg aatgacaccg gtaaaccgaa aggcaggaac aggagagcgc acgagggagc
     2941 caccaggggg aaacgcctgg tatctttaag tcctgtcggg tttcgccacc actgatttga
     3001 gcgtcagatt ctgtgatgct tgtcaggggg gcggagccta tggaaaaccg gcaacgccgc
     3061 ggccttttct tttgcctctc gatcctctct cattgcctgt gccttaatgt ctccgttccc
     3121 tccgctcgcc gcagccgaac gaccgagcgt agcgagtcag tgagcgagga agcggaatat
     3181 ccccggactt atcttcggca ccgtacgcgc cagtgctgca ttttttaata cgatgcagga
     3241 tagggctaac gccgcaaagt gacgtcacct gacgttcctg gattacaaag gttaaagcag
     3301 cggacaggaa atgttttgtg cccacagcta tgctggctta ttcacaaaac agcgggacaa
     3361 gatgtgtttt tggagtaccg ccggcccgct aaagactcct ggttagctcc cgcatgtttg
     3421 ctatcttttt gctaccattt tgctactttt ttgctatctc cagagtcttc tggtctttcg
     3481 gttgctatcc ttttgctact tttttgctat caaaatgcta cctctccctt cttgcaataa
     3541 atgaccaagg cacgttagcg atgtatacat cgccgcgccg caagggtgcc ccttccgaat
     3601 cccgttcatc actgcgtgct gattcatcca cgttaaatcc gaccccctta gcaataaatc
     3661 cagccatgcc tgacggcctg gccaacgcct cacggccgca cagtaaactg cacacccgtg
     3721 aggcgttatt cgtgaggttc agtggtgctt ttgggcgtcc agccggattt tagccgctaa
     3781 aatcccggcc atgcatgtgt gtgcatagcc atgcagacgc gccagaatca tcaggcgcgt
     3841 tttttcacga tataggcaca gggaagtgtc ggaaacaggc aggaagaccc agaaacgccc
     3901 tgagagcctc tcaggcggtg cacgcaacgg atgttatggt aaatctgcct cacagactgg
     3961 tacaaaaaaa gccccgcagg gcttttttgc tatgagttag ccatattttc ttgcgaattt
     4021 ttcatcggaa tcgcatagat aaataataaa ctcaataaac gcgatgatcg cgggtatgaa
     4081 tgtccagcaa aaaattagat acaggaatcc ctgtcctatt ttacctaagt aaaatttatg
     4141 tacgc
//
