LOCUS       NZ_CP075065             5128 bp    DNA     circular CON 14-JUN-2024
DEFINITION  Escherichia coli strain EC_J_9 plasmid pUN_J9_4, complete sequence.
ACCESSION   NZ_CP075065
VERSION     NZ_CP075065.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15684191
            Assembly: GCF_018415995.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5128)
  AUTHORS   Liu,Z.
  TITLE     Co-ocurrence of fosA7 in Escherichia coli
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5128)
  AUTHORS   Liu,Z.
  TITLE     Direct Submission
  JOURNAL   Submitted (31-JUL-2020) College of Veterinary Medicine, Northwest
            A&F University, No.3 Taicheng Road, Yangling, Shanxi 712100, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.48
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 80.0x
            Sequencing Technology             :: Illumina Hiseq, oxford nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_018415995.1-RS_2024_06_14
            Annotation Date                   :: 06/14/2024 05:23:42
            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)                     :: 5,155
            CDSs (total)                      :: 5,038
            Genes (coding)                    :: 4,819
            CDSs (with protein)               :: 4,819
            Genes (RNA)                       :: 117
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 219
            CDSs (without protein)            :: 219
            Pseudo Genes (ambiguous residues) :: 0 of 219
            Pseudo Genes (frameshifted)       :: 94 of 219
            Pseudo Genes (incomplete)         :: 136 of 219
            Pseudo Genes (internal stop)      :: 49 of 219
            Pseudo Genes (multiple problems)  :: 53 of 219
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP075065.1.
            Bacteria and source DNA available from xiaoping song , Traditional
            Chinese Veterinary Medicine Lab,College of vetrinary Medicine,
            Northwest A&F University.
            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..5128
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="EC_J_9"
                     /isolation_source="intestine"
                     /host="swine"
                     /db_xref="taxon:562"
                     /plasmid="pUN_J9_4"
                     /geo_loc_name="China:Yangling"
                     /collection_date="2016-10-11"
     gene            complement(join(4620..5128,1..166))
                     /locus_tag="H4F96_RS25195"
                     /old_locus_tag="H4F96_25205"
     CDS             complement(join(4620..5128,1..166))
                     /locus_tag="H4F96_RS25195"
                     /old_locus_tag="H4F96_25205"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001259273.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="NYN domain-containing protein"
                     /protein_id="WP_072644308.1"
                     /translation="MRTIVYVDGFNFYHGLVKRSGYKWLDLYKLFEEQLLPIRSRESQL
                     IQVKFFTAEIKAKFASRGELAHQAQQAYHRALVQIYGDNLQIIKGYYSERQECAMTFNE
                     GHPPSKTDRTTVWKLEEKQTDVRMALEMYRDAIRGEAEQLVLCTNDSDMIPPIEMIKAD
                     RPELKIGIVVPREQDTSRVISSLASLGDWSLPYVSYEALRLALLPDKVPTRRKPILKPN
                     HW"
                     /name="NYN domain-containing protein"
     gene            514..930
                     /locus_tag="H4F96_RS25200"
                     /old_locus_tag="H4F96_25210"
     CDS             514..930
                     /locus_tag="H4F96_RS25200"
                     /old_locus_tag="H4F96_25210"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001283459.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_057103209.1"
                     /translation="MSDQKNNLDLQKQTLESKWGKEALSMGWSAIPTSLFFLQGALNMT
                     PTTFNVLLHLIIHWWKPYDWPHPSQESIAVRMGVSSRTVQRSLQELENYGLLTKIRTSK
                     DNPKYKGRNIYDMSLLVKSLNILTPDLNAKLNEK"
                     /name="helix-turn-helix domain-containing protein"
     gene            1095..1358
                     /locus_tag="H4F96_RS25205"
                     /old_locus_tag="H4F96_25215"
     CDS             1095..1358
                     /locus_tag="H4F96_RS25205"
                     /old_locus_tag="H4F96_25215"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010891192.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein L"
                     /protein_id="WP_072644307.1"
                     /translation="MAVYTSETKKFLDSVSHDKTWWTSRYNPADDVPVSGIYRCTVCGK
                     EITSNKDDPFPPQNHHQHSQSQAIKWQLIVRTDTQGNGCGSK"
                     /name="protein L"
     gene            complement(1517..2209)
                     /locus_tag="H4F96_RS25210"
                     /old_locus_tag="H4F96_25220"
     CDS             complement(1517..2209)
                     /locus_tag="H4F96_RS25210"
                     /old_locus_tag="H4F96_25220"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000550475.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF3800 domain-containing protein"
                     /protein_id="WP_072644306.1"
                     /translation="MHLLYVDESGTPSDPTLNHFVLSGISVFEKQTHWIEQEMNAIAAR
                     FNADDPYERELHGSPMRGGRDGWKNFSFNDRKQAIKDCLALLTQKHRDIRIFACVVPKG
                     ALDGKDVITESFYQISSRFDMYLSRLHHQGATSRGVAIFDKSSTEKSIQSLARTFKDTG
                     YEYGKLRNFSEVPLFLDSKASRLIQLADLVSYSIFRKFEFNDDEFYKIIENRFDYHNGK
                     VHGLYVAH"
                     /name="DUF3800 domain-containing protein"
     gene            3436..3630
                     /locus_tag="H4F96_RS25215"
                     /old_locus_tag="H4F96_25225"
     CDS             3436..3630
                     /locus_tag="H4F96_RS25215"
                     /old_locus_tag="H4F96_25225"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /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_072644309.1"
                     /translation="MNKQQQIALNMARFIKSQSLTLLEKLDALDADEQATMCERLHELA
                     EELQNSIQVRFETESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          3331..3415
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="85.393"
                     /coverage="87.0"
                     /evalue="5.15e-16"
     Typing          complement(3707..3788)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.857"
                     /coverage="98.0"
                     /evalue="1.43e-25"
     Typing          4089..4612
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.604"
                     /coverage="99.0"
                     /evalue="7.85e-161"
ORIGIN
        1 tgatctcagc agtaaagaac ttcacctgaa tcaactgtga ctctcttgat cttatcggaa
       61 gtagttgttc ttcaaagagt ttatagagat ctaaccactt atatcccgaa cgcttaacca
      121 atccgtgata aaaattaaac ccatctacgt aaactattgt tctcatttta tttcgcgcat
      181 aaaaaaaccg cctctaaagg cggttttaac aacaaaaact aacgttagca aacagtttaa
      241 gttgtagttc ctcagggtta aaactaaccg agagggcggt ttcaagctcc tgaaggaaga
      301 cgcgtaactt aatcgctgcc cacctaaagg gaggtttaga gcctcaaggg agctgcgtaa
      361 cttaatcgcg ctaccaagag gtgagtgtag attaagtata gttaaatata atgatattat
      421 aagcgcgatg gtgtcgtact aattatatga attaatttac caacctgcta agctgaagtc
      481 ttctatgaag acttcagctt agcaggttgg tatatgtcag atcaaaaaaa taatttagac
      541 cttcaaaaac agacacttga atctaaatgg gggaaggagg cgttaagcat gggatggtca
      601 gccattccta catccctttt cttcctgcag ggcgcactca atatgacccc cacaacattc
      661 aatgtgctac ttcatctaat catccactgg tggaaaccct atgattggcc acatccatct
      721 caagagagca tcgcggttag aatgggagtt tcatcaagaa cagttcaacg ctcactccaa
      781 gaacttgaaa attacggatt gcttacaaaa attcgtacaa gcaaggacaa ccctaagtac
      841 aaagggcgaa acatttacga tatgtctctt ttagttaagt cactaaacat tcttacgcca
      901 gaccttaatg ccaaactgaa cgaaaagtaa ccataaaata attttaaaaa tcagaccatt
      961 acagcttata tttaccatag catctctatt ttagcgtttt tcaatcatcg ccagatgatt
     1021 gaaaaacgct aaaaaaaacc aaacttataa aaaggatccc cctccgccct atacattttg
     1081 gaaaggaaag gcaaatggct gtatacacct ctgagactaa aaaattttta gacagtgttt
     1141 ctcacgataa aacttggtgg acatcacgat ataacccagc tgacgatgta ccggtatcag
     1201 ggatctatcg ttgtactgtt tgcggaaaag agataactag caataaagat gacccgtttc
     1261 cgccgcaaaa ccatcatcaa cacagccaaa gtcaggcaat caagtggcaa ttaattgtca
     1321 gaacagatac gcaaggaaat ggttgtggtt ctaaataact caaaagccct taggggcttt
     1381 tttgtaccta gcggtcagac ggattaaaca taacatccgt tgtacgctac gcatgaaaaa
     1441 gcccgcgtag cgggcttcgc gtcgatggtc acaaggaact cttacttata gatagtgcgt
     1501 attcacaact attccattag tgggctacgt aaagcccgtg aactttacca ttatggtagt
     1561 caaagcgatt ctctatgatt ttgtagaact catcatcatt gaactcaaac ttcctgaaaa
     1621 ttgagtacga cacaagatca gcaagctgaa tcagccttga cgctttggaa tccaaaaata
     1681 aaggtacttc agagaagttg cgaagttttc catactcata tccagtatct ttaaacgtac
     1741 gggcaagaga ttgaatactt ttttctgtcg acgatttatc aaaaatggcc acccctcgag
     1801 acgttgctcc ttggtgatgt aagcgactta aatacatgtc gaaacgagac gatatttgat
     1861 aaaaagactc tgttattaca tccttcccat ctaaggctcc cttgggtaca acacatgcaa
     1921 atatgcgaat atcccgatgc ttttgagtaa ggagtgctaa gcaatctttg atcgcttgtt
     1981 ttctgtcatt gaaagaaaaa tttttccagc catctcgtcc acctctcatc ggtgaaccat
     2041 gcaattctct ttcatacggg tcatcagcat taaatcgagc cgcaattgca ttcatctctt
     2101 gctctatcca gtgagtttgc ttttcaaata ctgatatacc agaaaggaca aaatgattaa
     2161 gagtagggtc tgatggtgta ccagactcat caacgtacaa gagatgcatc taagactcct
     2221 taaacgaaaa aggccgcgca aatgcgcggc ctttttatga attaggcaag ccagtgcgat
     2281 aaacatcgca tacaccgcta tgggcagcga actgactcaa tatcaatgat aacaggcaag
     2341 tgcatattta cccaaataat ttatacacac accatagcca tgagcaatca aataacataa
     2401 attcaatcag atagtttctt caccgtcatt ctgatttacc ataacatctg ttgcgtgcac
     2461 catctcagac gccctcaggg catttctgcg ccctccagcc tatttccggc atctttccct
     2521 gtccatatcg tgaaaaaacg cgcctgatga tttctgcgca tctgcatggc tatgcacgaa
     2581 catgcctggc cggaatttta gcggctaaaa tcctgcgaac tgctcaaaag gctcgctgaa
     2641 ccccatcgat aacggtgaac gggtgcacag tttactgtgc ggtcgtgagg cgttgagcaa
     2701 cgagctttgc gaggcggtag gggttctgag agccagctgc aggctcagga gaaaacattc
     2761 tgttttcggg gcagataccg caaatgacgt cattttgcgg cgtctgccct atcctgcatc
     2821 gcaacgtcta aaggatgtga gtacaaacgc cagcactttg cgaatcctgc cctcgatctg
     2881 aacaaaagca aaatttcgta cgtacgaaat tcagggtatc aggctgcgcc tgatgaaatg
     2941 tttttggtgc cggcggtact ccaaaaacac atcttgtccg acagttttgt ggtgccggcg
     3001 aagcggcggt ggccacaaaa catttcctgt ccccatcgat tcattcgaga aacataagag
     3061 gcgaagaagg ggtcagtttg gagatcggaa atttttgtac gttaagcgca ttatttaacc
     3121 aatcttggtt cgtaaggggt tgattttgcg tcagtggcta tcgcttttaa gttgtcgctc
     3181 ttgcagtatc gcatttaggt tatccgatta aggtcaaacc tctgaaaatg ccgtatagcg
     3241 cgggagtaca ccctattgct ataggtaagt ctgttcaaaa aacaggctta ccgtacaata
     3301 attctctata tccaaactga cccctaaaga aacaggacag gatgtgcaat tgtaataccg
     3361 tcgcccgcaa cgtcttacaa ttaccacctg gtcagggtcc acccgacacc cggtactgac
     3421 ggagaacaac ggaaggtgaa caaacagcaa caaattgcgc tgaatatggc gcgatttatc
     3481 aaaagccaga gcctgacact acttgaaaaa ctggatgctc tggatgccga cgaacaggcg
     3541 accatgtgcg aacgactgca cgaactcgcg gaagagctcc agaacagcat ccaggttcgc
     3601 tttgagaccg aaagtgaaac agggacataa cgaagctgac ggaggcgctc acggcttgtc
     3661 cgcgagcgtt ttcggcagca gacaagcccg tcagggcgcg tcagtggggt tcggggcgaa
     3721 gccctgaacc agtcacgtag agatagcgga gtgtatacgg gcttaatcat gcagcatcag
     3781 tgcggattgt atgaaaagtt tgccatatcc ggagtgaaat gccgcacaga tgcgtaagga
     3841 gaatatgcct gttcaggcgc tcttccgctt cctcgctcac tgactcgcta cgctcggtcg
     3901 ttcggctgcg gcgagcggtg tctgctcact caaagatggt aatacagtta tccacagaat
     3961 ccgaggataa cgccggaaag aacatgtgag caacaagacg aaacccggaa aaaggcagcg
     4021 ccggtggcgt ttttccatag gcttcgcccc cctgacgagc atcacaaaaa tcgacgctca
     4081 agtcagaggt ggcgaaaccc gacaggactt aaagatacca ggcgtttccc cctggtggct
     4141 ccctcgtgcg ctctcctgtt cctgccattc ggtttaccgg tgtcactccg ctgttatggc
     4201 cgcgtttgtc tcattccacg cctgacactc agttccgggt aggcagttcg ctccaagctg
     4261 gactgtatgc acgaaccccc cgttcagtcc gactgctgcg ccttttccgg taactatcgt
     4321 cttgagtcca atccggaaag acacgactta tcgccactgg cagcagccat tggtaacagg
     4381 attcacggag cagagtagta gaagtgcttc tacagagttc ttgaagtgat ggcctgactg
     4441 cggctacact ggaaggacag ttttggtatc tgcgctccgt gaaagccagt taccttcgga
     4501 aaaaagagtt ggtagctctt gattccggca aacaaaccac cgttggtagc ggtggttttt
     4561 ttgtttgcag gacatgagat tacgacgaga gtaaaaggat cacaagaaga tccggctgtt
     4621 taccagtgat ttggcttcag tattggcttt cgcctagtgg ggactttatc tggcaataaa
     4681 gctaatctta aggcttcata ggatacatat ggcaagctcc aatcccctaa actagccaga
     4741 ctactaatca ctcgactagt atcttgttcc cttggcacta caattcctat ttttaactca
     4801 ggtcgatcgg cttttatcat ttctattggc ggtatcatat ctgagtcgtt agtacagaga
     4861 accaattgtt ctgcctcacc acggatcgca tcgcgataca tttctaaagc cattctaacg
     4921 tcggtctgct tttcttctaa cttccagacc gttgttctat ccgtttttga tggcggatgc
     4981 ccctcattaa aggtcattgc acattcctga cgctctgagt aataaccttt gattatctgt
     5041 aggttatcgc catagatctg tactaatgct cgatggtagg cttgctgagc ctggtgcgcc
     5101 aattcacccc gagaagcaaa ctttgctt
//
