LOCUS       NZ_JARDXE010000068      1225 bp    DNA     linear   CON 01-APR-2024
DEFINITION  Rhodococcus qingshengii strain HQ HQ1_scaffold68, whole genome
            shotgun sequence.
ACCESSION   NZ_JARDXE010000068
VERSION     NZ_JARDXE010000068.1
KEYWORDS    WGS; RefSeq.
SOURCE      Rhodococcus qingshengii
  ORGANISM  Rhodococcus qingshengii
            Bacteria; Actinomycetota; Actinomycetes; Mycobacteriales;
            Nocardiaceae; Rhodococcus; Rhodococcus erythropolis group.
REFERENCE   1  (bases 1 to 1225)
  AUTHORS   Hu,J. and Xu,J.
  TITLE     A novel hydrolase synthesized by Rhodococcus erythropolis HQ is
            responsible for the detoxification of Zearalenone
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 1225)
  AUTHORS   Hu,J. and Xu,J.
  TITLE     Direct Submission
  JOURNAL   Submitted (23-FEB-2023) Grain and Oil Risk Assessment Laboratory,
            Jiangsu Academy of Agricultural Sciences, No. 50, Zhongling Street,
            nanjing 210014, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: MAY-2022
            Assembly Method                   :: ABySS v. 2.1.5
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Reference-guided Assembly         :: GCA_002079265.1
            Genome Coverage                   :: 470.0x
            Sequencing Technology             :: Illumina NovaSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_029076895.1-RS_2024_04_01
            Annotation Date                   :: 04/01/2024 06:35:53
            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)                     :: 6,927
            CDSs (total)                      :: 6,855
            Genes (coding)                    :: 6,768
            CDSs (with protein)               :: 6,768
            Genes (RNA)                       :: 72
            rRNAs                             :: 1, 1, 1 (5S, 16S, 23S)
            complete rRNAs                    :: 1, 1, 1 (5S, 16S, 23S)
            tRNAs                             :: 66
            ncRNAs                            :: 3
            Pseudo Genes (total)              :: 87
            CDSs (without protein)            :: 87
            Pseudo Genes (ambiguous residues) :: 0 of 87
            Pseudo Genes (frameshifted)       :: 33 of 87
            Pseudo Genes (incomplete)         :: 63 of 87
            Pseudo Genes (internal stop)      :: 12 of 87
            Pseudo Genes (multiple problems)  :: 18 of 87
            ##Genome-Annotation-Data-END##
            ##antiSMASH-Data-START##
            Version                           :: 8.dev-cf2fc5ee(changed)
            Run date                          :: 2025-09-12 19:34:22
            NOTE :: This is a single region extracted from a larger record!
            Orig. start                       :: 0
            Orig. end                         :: 1225
            ##antiSMASH-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            JARDXE010000068.1.
            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/
FEATURES             Location/Qualifiers
     cand_cluster    1..1225
                     /SMILES=""
                     /candidate_cluster_number="1"
                     /contig_edge="True"
                     /detection_rules="cds((PP-binding or NAD_binding_4) and
                     (AMP-binding or A-OX) and not alpha_am_amid)"
                     /kind="single"
                     /product="NRPS-like"
                     /protoclusters="1"
                     /tool="antismash"
     protocluster    1..1225
                     /aStool="rule-based-clusters"
                     /category="NRPS"
                     /contig_edge="True"
                     /core_location="[<0:1195](-)"
                     /cutoff="0"
                     /detection_rule="cds((PP-binding or NAD_binding_4) and
                     (AMP-binding or A-OX) and not alpha_am_amid)"
                     /neighbourhood="20000"
                     /product="NRPS-like"
                     /protocluster_number="1"
                     /tool="antismash"
     proto_core      complement(<1..1195)
                     /aStool="rule-based-clusters"
                     /tool="antismash"
                     /cutoff="0"
                     /detection_rule="cds((PP-binding or NAD_binding_4) and
                     (AMP-binding or A-OX) and not alpha_am_amid)"
                     /neighbourhood="20000"
                     /product="NRPS-like"
                     /protocluster_number="1"
     gene            complement(<1..1195)
                     /locus_tag="PXH69_RS34550"
                     /old_locus_tag="PXH69_34565"
     CDS             complement(<1..1195)
                     /NRPS_PKS="Domain: AMP-binding (0-257). E-value: 9.2e-65.
                     Score: 210.7. Matches aSDomain:
                     nrpspksdomains_PXH69_RS34550_AMP-binding.1"
                     /codon_start=1
                     /gene_functions="biosynthetic (rule-based-clusters)
                     NRPS-like: AMP-binding"
                     /gene_functions="biosynthetic (rule-based-clusters)
                     NRPS-like: PP-binding"
                     /gene_functions="biosynthetic-additional (smcogs)
                     SMCOG1002: AMP-dependent synthetase and ligase"
                     /gene_kind="biosynthetic"
                     /inference="COORDINATES: protein motif:HMM:TIGR01733.1"
                     /locus_tag="PXH69_RS34550"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /old_locus_tag="PXH69_34565"
                     /product="AMP-binding protein"
                     /protein_id="WP_334556754.1"
                     /sec_met_domain="AMP-binding (E-value: 1.2e-83, bitscore:
                     267.1, seeds: 400, tool: rule-based-clusters)"
                     /sec_met_domain="PP-binding (E-value: 1.7e-08, bitscore:
                     21.2, seeds: 164, tool: rule-based-clusters)"
                     /transl_table=11
                     /translation="MIFTSGSTGRPKGVAVSHAAVVNQLRWKREVFGLDQDDAVLLKTA
                     STFDLSVWEFWSALVSGSRLVIAKVGGQQDPQYLLDVMSVSGVSTLHVVPSMLEALAAV
                     GGGVLPSGLRQVLAIGEALPADLARRVRVSNPGVRLFNLYGPTEAAVSVTSHEVTDGDV
                     SSVSIGSPEWNTQLLVLDSRLHPVPVGVAGELYLSGAQLARGYHGRVDLSAERFVANPY
                     GTAGSRMYRTGDVVSWSRSGELEYLGRSDFQVKLRGFRIELGEIEAALVAVDSVGRAVA
                     VVHEGAHAGEMLVAYVTASSGADVDVDVVREVLSAGLPSYMVPSQILVLDEFPLNINGK
                     IDRKLLPDPVFEKAEFRAPVTPVEEIVASVFADLLGVDRVGLDDDFFALGGNSLIATR"
     source          1..1225
                     /collection_date="2022-01"
                     /country="China: Anhui, Suzhou"
                     /db_xref="taxon:334542"
                     /isolation_source="Corn field soil"
                     /mol_type="genomic DNA"
                     /organism="Rhodococcus qingshengii"
                     /strain="HQ"
                     /submitter_seqid="HQ1_scaffold68"
     region          1..1225
                     /candidate_cluster_numbers="1"
                     /contig_edge="True"
                     /product="NRPS-like"
                     /region_number="1"
                     /rules="cds((PP-binding or NAD_binding_4) and (AMP-binding
                     or A-OX) and not alpha_am_amid)"
                     /tool="antismash"
     CDS_motif       complement(395..460)
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_PXH69_RS34550_0003"
                     /evalue="1.20E-12"
                     /label="NRPS-A_a8"
                     /locus_tag="PXH69_RS34550"
                     /protein_end="267"
                     /protein_start="245"
                     /score="39.6"
                     /tool="antismash"
                     /translation="YLGRSDFQVKLRGFRIELGEIE"
     aSDomain        complement(425..1195)
                     /aSDomain="AMP-binding"
                     /aSTool="nrps_pks_domains"
                     /database="nrpspksdomains.hmm"
                     /detection="hmmscan"
                     /domain_id="nrpspksdomains_PXH69_RS34550_AMP-binding.1"
                     /evalue="9.20E-65"
                     /label="PXH69_RS34550_AMP-binding.1"
                     /locus_tag="PXH69_RS34550"
                     /protein_end="257"
                     /protein_start="0"
                     /score="210.7"
                     /specificity="substrate consensus: X"
                     /tool="antismash"
                     /translation="MIFTSGSTGRPKGVAVSHAAVVNQLRWKREVFGLDQDDAVLLKTA
                     STFDLSVWEFWSALVSGSRLVIAKVGGQQDPQYLLDVMSVSGVSTLHVVPSMLEALAAV
                     GGGVLPSGLRQVLAIGEALPADLARRVRVSNPGVRLFNLYGPTEAAVSVTSHEVTDGDV
                     SSVSIGSPEWNTQLLVLDSRLHPVPVGVAGELYLSGAQLARGYHGRVDLSAERFVANPY
                     GTAGSRMYRTGDVVSWSRSGELEYLGRSDFQVKLR"
     CDS_motif       complement(545..634)
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_PXH69_RS34550_0002"
                     /evalue="1.10E-15"
                     /label="NRPS-A_a6"
                     /locus_tag="PXH69_RS34550"
                     /protein_end="217"
                     /protein_start="187"
                     /score="49.6"
                     /tool="antismash"
                     /translation="PVGVAGELYLSGAQLARGYHGRVDLSAERF"
     CDS_motif       complement(1142..1195)
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_PXH69_RS34550_0001"
                     /evalue="6.60E-09"
                     /label="NRPS-A_a3"
                     /locus_tag="PXH69_RS34550"
                     /protein_end="18"
                     /protein_start="0"
                     /score="27.9"
                     /tool="antismash"
                     /translation="MIFTSGSTGRPKGVAVSH"
ORIGIN
        1 ctcgtgtcgc gatcagcgaa ttaccaccga gtgcgaagaa atcgtcatcg agacccactc
       61 gatcgacacc cagcagatcc gcaaacaccg acgcgacgat ctcctccacc ggcgtcaccg
      121 gggcccgaaa ctcagccttc tcgaacaccg gatccggcaa caacttccga tcgatcttgc
      181 cgttgatatt gagagggaac tcatcgagca ccagaatctg cgacggcacc atgtacgagg
      241 gcagacccgc cgacaacacc tcacgcacaa cgtcgacatc gacgtcggcc ccggacgaag
      301 cagtgacata cgcaaccaac atctcaccag cgtgcgcacc ctcgtgcacg acagccaccg
      361 cccgacccac cgaatcaacg gcaaccaacg cggcctcgat ctcaccgagc tcgatcctga
      421 acccacgcaa cttcacctgg aaatcgctgc gccccaaata ctccaactca cccgaacgac
      481 tccacgacac cacatcgccc gtccgataca tacgcgaacc cgcagtgccg taaggattcg
      541 cgacgaaacg ttccgccgac aaatccaccc ggccgtgata cccacgagcc aactgcgcac
      601 ccgacagata caactcaccc gcaacaccca ccggaaccgg atgcaaccgc gaatccaaca
      661 ccaacagttg cgtattccac tccggcgacc cgatcgacac cgacgacaca tcaccatcgg
      721 tcacctcatg cgaagtcacc gaaaccgccg cctccgtcgg accatacaaa ttgaacaacc
      781 gcacaccagg attcgacaca cgtacacgcc gcgccagatc agcaggcaac gcctcaccga
      841 tcgccaacac ctgacgaagc cccgacggaa gaacaccacc cccaacagcc gccaacgcct
      901 ccaacatcga cggaaccaca tgcaacgtcg acacacccga cacagacatc acatcgagca
      961 ggtactgcgg atcctgctga ccgccgacct tcgcgatcac caaccgagaa cccgaaacca
     1021 acgcagacca aaactcccac accgacaaat cgaacgtcga cgcagtcttg agcaacaccg
     1081 catcatcctg atcaagaccg aaaacctcac gcttccaacg cagctgattc accacagctg
     1141 catgcgaaac cgccacaccc ttcggccgac ccgtcgaccc cgacgtgaaa atcacatacg
     1201 ccgtattccc cgaccgcaac ggcga
//
