LOCUS       NZ_JARDXE010000058      1881 bp    DNA     linear   CON 01-APR-2024
DEFINITION  Rhodococcus qingshengii strain HQ HQ1_scaffold58, whole genome
            shotgun sequence.
ACCESSION   NZ_JARDXE010000058
VERSION     NZ_JARDXE010000058.1
KEYWORDS    WGS; RefSeq.
SOURCE      Rhodococcus qingshengii
  ORGANISM  Rhodococcus qingshengii
            Bacteria; Actinomycetota; Actinomycetes; Mycobacteriales;
            Nocardiaceae; Rhodococcus; Rhodococcus erythropolis group.
REFERENCE   1  (bases 1 to 1881)
  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  JOURNAL   Unpublished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 1881)
  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                         :: 1881
            ##antiSMASH-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            JARDXE010000058.1.
            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
     source          1..1881
                     /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_scaffold58"
     gene            <1..>1881
                     /locus_tag="PXH69_RS34485"
                     /old_locus_tag="PXH69_34500"
     region          1..1881
                     /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"
     cand_cluster    1..1881
                     /SMILES="NC(C(O)C)C(=O)O"
                     /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..1881
                     /aStool="rule-based-clusters"
                     /category="NRPS"
                     /contig_edge="True"
                     /core_location="[4:>1881](+)"
                     /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      5..>1881
                     /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"
     CDS             5..>1881
                     /NRPS_PKS="Domain: AMP-binding (9-420). E-value: 1.5e-101.
                     Score: 331.9. Matches aSDomain:
                     nrpspksdomains_PXH69_RS34485_AMP-binding.1"
                     /NRPS_PKS="Domain: PCP (526-593). E-value: 2.3e-25. Score:
                     80.6. Matches aSDomain: nrpspksdomains_PXH69_RS34485_PCP.1"
                     /codon_start=3
                     /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: similar to AA
                     sequence:RefSeq:WP_019932726.1"
                     /locus_tag="PXH69_RS34485"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /old_locus_tag="PXH69_34500"
                     /product="amino acid adenylation domain-containing protein"
                     /protein_id="WP_156667390.1"
                     /sec_met_domain="AMP-binding (E-value: 7e-108, bitscore:
                     346.8, seeds: 400, tool: rule-based-clusters)"
                     /sec_met_domain="PP-binding (E-value: 1.5e-18, bitscore:
                     53.4, seeds: 164, tool: rule-based-clusters)"
                     /transl_table=11
                     /translation="MVDSTLSAWFDDAAARFGDRVAVRFGGESLSYGELSVRANRLARR
                     LIAQGCGPESLVAVALPRSADLVVALLAVVKSGAGYLPVDPSYPADRVEFMLADAAPVA
                     AISWSGRELVLPAGLPVVDIDAVDVSEFDGSVVSDADRVAPLRSSNVAYVIYTSGSTGR
                     PKGVQVPHTTVAKLFANTEGVYGFDESDVWTMFHSYAFDFSVWELWGPLLYGGTLVVVD
                     YVTSRSPEQFLELLAAERVTVLNQTPSAFYQLAEADRLASESGRAAELSLRWVVFGGEA
                     LELRRLSDWYGRRGDFAPTLVNMYGITETTVHVSHRVLDAALAADASASVVGQAISGLQ
                     VFVLDTRLAPVPVGVAGEMYVSGVQLARGYLGQAGLTSTRFVANPFNAGEVLYRTGDVA
                     SWNSAGDLEYLGRADDQVKIRGFRIEIGEIESAVLADVSVAQTAVVVREDSPGDQRLVA
                     YVVPAAGVSVSVDDLRVSVGSLLPEYMVPSAFVVLDSIPLTVNGKLDRRALPVPSLQVA
                     VFRAPTSVVEEVVAQTFADVLGVERVGLDDDFFALGGNSLIATQVTSRLGQALDASVSV
                     RELFEASTVEALAARLGSHVGGGSRAALTAQVRPVRVPLSLAQQRMWFLN"
     aSDomain        34..1266
                     /aSDomain="AMP-binding"
                     /aSTool="nrps_pks_domains"
                     /database="nrpspksdomains.hmm"
                     /detection="hmmscan"
                     /domain_id="nrpspksdomains_PXH69_RS34485_AMP-binding.1"
                     /evalue="1.50E-101"
                     /label="PXH69_RS34485_AMP-binding.1"
                     /locus_tag="PXH69_RS34485"
                     /protein_end="420"
                     /protein_start="9"
                     /score="331.9"
                     /specificity="substrate consensus: Thr"
                     /tool="antismash"
                     /translation="FDDAAARFGDRVAVRFGGESLSYGELSVRANRLARRLIAQGCGPE
                     SLVAVALPRSADLVVALLAVVKSGAGYLPVDPSYPADRVEFMLADAAPVAAISWSGREL
                     VLPAGLPVVDIDAVDVSEFDGSVVSDADRVAPLRSSNVAYVIYTSGSTGRPKGVQVPHT
                     TVAKLFANTEGVYGFDESDVWTMFHSYAFDFSVWELWGPLLYGGTLVVVDYVTSRSPEQ
                     FLELLAAERVTVLNQTPSAFYQLAEADRLASESGRAAELSLRWVVFGGEALELRRLSDW
                     YGRRGDFAPTLVNMYGITETTVHVSHRVLDAALAADASASVVGQAISGLQVFVLDTRLA
                     PVPVGVAGEMYVSGVQLARGYLGQAGLTSTRFVANPFNAGEVLYRTGDVASWNSAGDLE
                     YLGRADDQVKIR"
     aSModule        34..1785
                     /complete
                     /domains="nrpspksdomains_PXH69_RS34485_AMP-binding.1"
                     /domains="nrpspksdomains_PXH69_RS34485_PCP.1"
                     /locus_tags="PXH69_RS34485"
                     /monomer_pairings="Thr -> Thr"
                     /starter_module
                     /tool="antismash"
                     /type="nrps"
     CDS_motif       220..261
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_PXH69_RS34485_0001"
                     /evalue="7.90E-04"
                     /label="NRPS-A_a2"
                     /locus_tag="PXH69_RS34485"
                     /protein_end="85"
                     /protein_start="71"
                     /score="12.9"
                     /tool="antismash"
                     /translation="LAVVKSGAGYLPVD"
     CDS_motif       460..519
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_PXH69_RS34485_0002"
                     /evalue="8.50E-11"
                     /label="NRPS-A_a3"
                     /locus_tag="PXH69_RS34485"
                     /protein_end="171"
                     /protein_start="151"
                     /score="33.6"
                     /tool="antismash"
                     /translation="AYVIYTSGSTGRPKGVQVPH"
     CDS_motif       1060..1149
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_PXH69_RS34485_0003"
                     /evalue="3.30E-14"
                     /label="NRPS-A_a6"
                     /locus_tag="PXH69_RS34485"
                     /protein_end="381"
                     /protein_start="351"
                     /score="45.0"
                     /tool="antismash"
                     /translation="PVGVAGEMYVSGVQLARGYLGQAGLTSTRF"
     CDS_motif       1231..1296
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_PXH69_RS34485_0004"
                     /evalue="1.20E-12"
                     /label="NRPS-A_a8"
                     /locus_tag="PXH69_RS34485"
                     /protein_end="430"
                     /protein_start="408"
                     /score="39.6"
                     /tool="antismash"
                     /translation="YLGRADDQVKIRGFRIEIGEIE"
     aSDomain        1585..1785
                     /aSDomain="PCP"
                     /aSTool="nrps_pks_domains"
                     /database="nrpspksdomains.hmm"
                     /detection="hmmscan"
                     /domain_id="nrpspksdomains_PXH69_RS34485_PCP.1"
                     /evalue="2.30E-25"
                     /label="PXH69_RS34485_PCP.1"
                     /locus_tag="PXH69_RS34485"
                     /protein_end="593"
                     /protein_start="526"
                     /score="80.6"
                     /tool="antismash"
                     /translation="EEVVAQTFADVLGVERVGLDDDFFALGGNSLIATQVTSRLGQALD
                     ASVSVRELFEASTVEALAARLG"
     CDS_motif       1852..>1881
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_PXH69_RS34485_0005"
                     /evalue="2.10E-03"
                     /label="C1_LCL_004-017"
                     /locus_tag="PXH69_RS34485"
                     /protein_end="626"
                     /protein_start="615"
                     /score="10.6"
                     /tool="antismash"
                     /translation="SLAQQRMWFLN"
ORIGIN
        1 gtggtgtgga ttcgacgttg tcggcgtggt tcgatgatgc tgctgcgcgg tttggtgatc
       61 gggttgcggt gcggttcggt ggcgagtcgt tgtcgtatgg tgagttgtcg gtgcgggcta
      121 atcgtttggc gcgcaggttg attgctcagg gttgtggtcc ggagtcgttg gtggcggtgg
      181 cgttgccgcg gtcggcggat cttgtggtgg cgttgttggc ggtggtgaag tccggtgcgg
      241 ggtatttgcc ggtggatccg tcgtatccgg ctgatcgtgt cgagttcatg ttggctgatg
      301 ctgctccggt ggctgcgatt tcgtggtccg ggcgtgagtt ggtgttgccc gctggtttgc
      361 cggtggttga tatcgacgcg gtggatgtgt cggagttcga tggttcggtg gtttcggatg
      421 cggatcgtgt tgcgccgttg cggtcgtcga atgttgcgta tgtgatttac acgtcgggtt
      481 cgacgggtcg cccgaagggt gtgcaggttc cgcacacgac ggtggcgaag ttgtttgcga
      541 ataccgaggg tgtgtacggg ttcgacgaat ccgatgtgtg gacgatgttc cacagttatg
      601 cgttcgactt ctcggtgtgg gagttgtggg gtccgctgtt gtacggcggc acgttggtgg
      661 ttgtggatta tgtgacgtcg cggtcgccgg agcagttctt ggagttgctt gctgctgagc
      721 gggtgacggt gctcaatcag acgccgtcgg cgttctatca gttggccgag gctgatcggt
      781 tggcgtcgga atccggtcgg gctgctgagt tgtcgttgcg gtgggttgtt ttcggcggcg
      841 aggcgctcga gctgcgtcgc ttgtcggatt ggtacggccg ccgcggtgac ttcgcgccga
      901 cgttggtgaa catgtatggc atcacggaga cgacggtgca tgtgagccat cgtgtgttgg
      961 atgctgcgtt ggcggcggat gcgtcggcga gtgttgtggg tcaggctatt tcgggtctgc
     1021 aggtgttcgt gctcgatacg cgtttggctc cggtgcctgt tggtgtcgcg ggtgagatgt
     1081 atgtctctgg tgttcagttg gctcggggtt atctgggtca ggcggggttg acgtcgacgc
     1141 ggtttgtggc gaatccgttc aatgccggcg aggtgttgta ccgcacgggt gacgtcgcgt
     1201 cgtggaacag cgctggtgat ttggagtatc tgggtcgcgc ggatgatcag gtgaagatcc
     1261 gtggtttccg gatcgagatc ggtgagatcg agtctgcggt gttggcggat gtgtcggtgg
     1321 cgcagacggc ggtggttgtc cgtgaggatt ctccgggtga tcagcggttg gtggcgtatg
     1381 tggttccggc tgcgggtgtg agcgtttcgg tcgacgatct tcgggtgtcg gtgggttcgt
     1441 tgttgccgga gtacatggtg ccgtcggcgt ttgtggtgtt ggattcgatt ccgttgacgg
     1501 tgaacgggaa gttggatcgt cgggcgttgc cggttccgtc gttgcaggtt gcggtgttcc
     1561 gtgctccgac gtcggtggtg gaagaggttg ttgcgcagac gtttgcggat gttctgggcg
     1621 tcgagcgtgt tggtttggat gatgatttct tcgcgctcgg tggtaattcg ctgattgcga
     1681 cgcaggtgac gtctcggttg ggtcaggcgt tggatgcttc ggtgtcggtg cgggagttgt
     1741 tcgaggcgtc gacggtggag gcgttggctg ctcgtttggg ttctcatgtc ggtggcggtt
     1801 cacgtgcggc gttgactgcg caggtgcgtc cggttcgggt tccgttgtcg ttggcgcagc
     1861 agcgcatgtg gttcctcaac c
//
