LOCUS       NZ_CP097184             4145 bp    DNA     circular CON 11-JUN-2024
DEFINITION  Escherichia coli strain SH21PTE31 plasmid pYUSHP31-3, complete
            sequence.
ACCESSION   NZ_CP097184
VERSION     NZ_CP097184.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN28157183
            Assembly: GCF_023370175.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4145)
  AUTHORS   Wang,J.
  TITLE     whole genome of E.coli SH21PTE31
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4145)
  AUTHORS   Wang,J.
  TITLE     Direct Submission
  JOURNAL   Submitted (08-MAY-2022) 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. 0.4.9
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology             :: Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_023370175.1-RS_2024_06_11
            Annotation Date                   :: 06/11/2024 04:53:37
            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)                     :: 4,805
            CDSs (total)                      :: 4,687
            Genes (coding)                    :: 4,459
            CDSs (with protein)               :: 4,459
            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)              :: 228
            CDSs (without protein)            :: 228
            Pseudo Genes (ambiguous residues) :: 0 of 228
            Pseudo Genes (frameshifted)       :: 60 of 228
            Pseudo Genes (incomplete)         :: 162 of 228
            Pseudo Genes (internal stop)      :: 40 of 228
            Pseudo Genes (multiple problems)  :: 30 of 228
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP097184.1.
            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="SH21PTE31"
                     /isolation_source="pig manure"
                     /db_xref="taxon:562"
                     /plasmid="pYUSHP31-3"
                     /geo_loc_name="China: Shanghai"
                     /lat_lon="30.40 N 120.52 E"
                     /collection_date="2021-07-15"
                     /collected_by="Jiang Yue"
     gene            join(<3988..4145,1..85)
                     /locus_tag="M4R35_RS23865"
                     /pseudo=""
     CDS             join(<3988..4145,1..85)
                     /locus_tag="M4R35_RS23865"
                     /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(123..1265)
                     /gene="wzz(fepE)"
                     /locus_tag="M4R35_RS23870"
     CDS             complement(123..1265)
                     /gene="wzz(fepE)"
                     /locus_tag="M4R35_RS23870"
                     /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            1460..1922
                     /locus_tag="M4R35_RS23875"
                     /pseudo=""
     CDS             1460..1922
                     /locus_tag="M4R35_RS23875"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_416498.2"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="transposase"
                     /name="transposase"
     gene            complement(<2071..2202)
                     /locus_tag="M4R35_RS23885"
                     /pseudo=""
     CDS             complement(<2071..2202)
                     /locus_tag="M4R35_RS23885"
                     /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(2510..2623)
                     /locus_tag="M4R35_RS23890"
     CDS             complement(2510..2623)
                     /locus_tag="M4R35_RS23890"
                     /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"
     gene            complement(3809..>3991)
                     /locus_tag="M4R35_RS23895"
                     /pseudo=""
     CDS             complement(3809..>3991)
                     /locus_tag="M4R35_RS23895"
                     /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"
     Typing          complement(2507..2892)
                     /name="rep_cluster_2373"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.373"
                     /coverage="90.0"
                     /evalue="1.04e-173"
ORIGIN
        1 gcacgtgatg cacggctgca tttgcctgaa gcccggcacc cttctggata cctttacgcc
       61 ggtgcgcgac gatttcctga aataaaaaaa ggcgctgaat cagcgccttt ttaatatcgt
      121 cgttactctg ttgctggcgt tacggccgtt atcggctctg gcaacggatt acgcgagagc
      181 attgcctcac gcagcagcac gctgccgcag gcaaacaggc cgcccagaat ccctgccagc
      241 agcacaatca gggctttgcc cggaccgtct tttttcaccg gcagtgacgg tgaaagctga
      301 tacctgaagg gttcaagctt cacgtcttcc acggacagtt tttgcaactg agtcagatag
      361 tattcacggt tctggaaatc cgcattcagc tcggccacgt ccttcagatt cttttcaatc
      421 tgcagctttt gcgcaatacc gtcagcaccc agcgccacgg agtagtcagg atcgtctttt
      481 accgcctgtc cgttgctgta aaccggcttc ttaatgcctg ccgcgttcgc cacttccagc
      541 gaatagttga ggcgctgcag gttggtgttg tggatattgg tcagacgcac gcgatccagc
      601 tccagctgct gctgaacgac tttcgttttc agcgtgatct ggttacggat attttccatc
      661 gtctcctgct caacaatgcg ggagatatag ttgatgtaac cttccagaac cgtctgcgcg
      721 tctcccgccg tcggggcggt aaagctcagc gtccatgagg tatacggcgc tttgtctgcg
      781 tctttaacct gcgtgttatc tgtcgctttc attttctcag caatattcac caccgcgcga
      841 tgcagctcca gcgggtctac ctcggtgcct tccagctgag acatcacgta cggggaggtt
      901 ttcatgtact cttcgagcag cgactgcgac tgaaactttt tgatgaacag gttaaacacg
      961 tctccacggc tcaccttcgc gtcgacgtcc agcacctgca gcgtcaccat catctggcgc
     1021 agcgtgttcc actgcgtctg ctcggccggc gtgatcacgg ctttactggt ccatttttgc
     1081 gggattaaaa acgcaatggc caaccctact acggcgaacg ccaggacgat cgtcacaata
     1141 cgttttttgg ctgccagaag tacgtctaac aaccccagga gatctatctc tttggtgctt
     1201 accgccggag tggcataacg gggaaaatcg aggtccgtgt ttttcttgaa atccatcgct
     1261 gacataaccg ttcttctttt tggagcgcag taaatttctg cctgattggt tgcagtggtc
     1321 ggatgataca agaaagtaag aataatctga acgccagatt gatctatctg tagaccgact
     1381 atcagattta gggaaggtgc gaacaagtcc ctgatatgag atcatgtttg tcatctggag
     1441 ccatggaaca gggttcatca tgagtcatca acttaccttc gccgacagtg aattcagcag
     1501 taagcgccgt cagaccagaa aagagatttt cttgtcccgc atggagcaga ttctgccatg
     1561 gcaaaacatg gtggaagtca tcgagccgtt ttaccccaag gctggtaatg gccggcgacc
     1621 ttatccgctg gaaaccatgc tacgcattca ctgcatgcag cattggtaca acctgagcga
     1681 tggcgcgatc gaagatgctc tgtacgaaat cgcctccatg cgtctgtttg cccggttaca
     1741 tgaaagccag catccgggcc aaggtggagc acccatttcg catcatcaag cgacagttcg
     1801 gcttcgtgaa agccagatac aaggggttgc tgaaaaacga taaccaactg gcgatgttat
     1861 tcacgctggc caacctgttt cgggcggacc aaatgatacg tcagtgggag agatctcact
     1921 aaaaactggg aataacgcct taaatggcga agaaacggtc taaataggct gattcaaggc
     1981 atttacggga gaaaaaaatc ggctcaaaca tgaagaaatg aaatgactga gtcaaccgag
     2041 aagaatttcc ccgcttattc gcaccttccc taatagcgcg gctgcgattc tacttttttc
     2101 acctgaacct gaagaggcgt ttgtggctcc gcagtgtggg catgactttg ctgtttcgtg
     2161 tatttccttg ccgcatcctc ggcagtaaac cattgaactc attttttatc ctcgagctta
     2221 tttttagttg ggatgcataa tatccgatgt tttataacga tatgcatcct atatgctcgg
     2281 gtgggataga tttccattat ggtgaaggat cttcttgaga tcctttctgt agcgtcgtaa
     2341 tctcttgctc agtaaacgaa aaaaccgccc agcaaggcgg tttttcgaag gttctcagag
     2401 ctgcaactct ttgaaccgtg gtaactggct tatgaggagc gcagtaacca aatctgttct
     2461 ttcagtttag ccttaacagg cgcataactt caagactaac tcctctaaat cagttaccag
     2521 tggctgctgc cagtggcgct ttgtcgtgtc tttccggctt ggactcaagt cgatagttac
     2581 cggagaagac gcagcggtcg gactgaacgg ggggttcgtg catacagtcc agcttggagc
     2641 gaactgccta cccggaactg agtgtcaggc gtggaatgag ataaacgcgg ccataacagc
     2701 ggaatgacac cggtaaaccg aaaggcagga acaggagagc gcacgaggga gccaccaggg
     2761 ggaaacgcct ggtatcttta agtcctgtcg ggtttcgcca ccactgattt gagcgtcaga
     2821 ttctgtgatg cttgtcaggg gggcggagcc tatggaaaac cggcaacgcc gcggcctttt
     2881 cttttgcctc tcgatcctct ctcattgcct gtgccttaat gtctccgttc cctccgctcg
     2941 ccgcagccga acgaccgagc gtagcgagtc agtgagcgag gaagcggaat atccccggac
     3001 ttatcttcgg caccgtacgc gccagtgctg cattttttaa tacgatgcag gatagggcta
     3061 acgccgcaaa gtgacgtcac ctgacgttcc tggattacaa aggttaaagc agcggacagg
     3121 aaatgttttg tgcccacagc tatgctggct tattcacaaa acagcgggac aagatgtgtt
     3181 tttggagtac cgccggcccg ctaaagactc ctggttagct cccgcatgtt tgctatcttt
     3241 ttgctaccat tttgctactt ttttgctatc tccagagtct tctggtcttt cggttgctat
     3301 ccttttgcta cttttttgct atcaaaatgc tacctctccc ttcttgcaat aaatgaccaa
     3361 ggcacgttag cgatgtatac atcgccgcgc cgcaagggtg ccccttccga atcccgttca
     3421 tcactgcgtg ctgattcatc cacgttaaat ccgaccccct tagcaataaa tccagccatg
     3481 cctgacggcc tggccaacgc ctcacggccg cacagtaaac tgcacacccg tgaggcgtta
     3541 ttcgtgaggt tcagtggtgc ttttgggcgt ccagccggat tttagccgct aaaatcccgg
     3601 ccatgcatgt gtgtgcatag ccatgcagac gcgccagaat catcaggcgc gttttttcac
     3661 gatataggca cagggaagtg tcggaaacag gcaggaagac ccagaaacgc cctgagagcc
     3721 tctcaggcgg tgcacgcaac ggatgttatg gtaaatctgc ctcacagact ggtacaaaaa
     3781 aagccccgca gggctttttt gctatgagtt agccatattt tcttgcgaat ttttcatcgg
     3841 aatcgcatag ataaataata aactcaataa acgcgatgat cgcgggtatg aatgtccagc
     3901 aaaaaattag atacaggaat ccctgtccta ttttacctaa gtaaaattta tgtacgccaa
     3961 atccaccaag gaagaatgct aagaaagatg atggcggtgg aggtcaattt tgagcagggt
     4021 gcgattggcc cgatgcacaa tcacccgcat gaacagctta cctatgtgct ctccggggag
     4081 ttcgagttta cgataggtga agaaaagcag atcgtgacgg cgggcgatac gctctataaa
     4141 gcgcc
//
