LOCUS       NZ_JAPWIK010000046      1886 bp    DNA     linear   CON 14-FEB-2024
DEFINITION  Rhodococcus qingshengii strain IEGM 766
            NODE_46_length_1886_cov_543.382851, whole genome shotgun sequence.
ACCESSION   NZ_JAPWIK010000046
VERSION     NZ_JAPWIK010000046.1
KEYWORDS    WGS; RefSeq.
SOURCE      Rhodococcus qingshengii
  ORGANISM  Rhodococcus qingshengii
            Bacteria; Actinomycetota; Actinomycetes; Mycobacteriales;
            Nocardiaceae; Rhodococcus; Rhodococcus erythropolis group.
REFERENCE   1  (bases 1 to 1886)
  AUTHORS   Krivoruchko,A.V. and Elkin,A.
  TITLE     Direct Submission
  JOURNAL   Submitted (15-DEC-2022) Lam, Institute of Ecology and Genetics of
            Microorganisms, Ural Branch of the Russian Academy of Sciences,
            Golev Str., 13, Perm, Perm Kray 614081, Russia
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 2022
            Assembly Method                   :: SPAdes v. 3.15.4
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 311x
            Sequencing Technology             :: Illumina NovaSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/14/2024 02:58:48
            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)                     :: 6,449
            CDSs (total)                      :: 6,385
            Genes (coding)                    :: 6,320
            CDSs (with protein)               :: 6,320
            Genes (RNA)                       :: 64
            rRNAs                             :: 1, 1, 5 (5S, 16S, 23S)
            complete rRNAs                    :: 1, 1 (5S, 16S)
            partial rRNAs                     :: 5 (23S)
            tRNAs                             :: 54
            ncRNAs                            :: 3
            Pseudo Genes (total)              :: 65
            CDSs (without protein)            :: 65
            Pseudo Genes (ambiguous residues) :: 0 of 65
            Pseudo Genes (frameshifted)       :: 17 of 65
            Pseudo Genes (incomplete)         :: 52 of 65
            Pseudo Genes (internal stop)      :: 6 of 65
            Pseudo Genes (multiple problems)  :: 9 of 65
            ##Genome-Annotation-Data-END##
            ##antiSMASH-Data-START##
            Version                           :: 8.dev-cf2fc5ee(changed)
            Run date                          :: 2025-09-13 05:17:55
            NOTE :: This is a single region extracted from a larger record!
            Orig. start                       :: 0
            Orig. end                         :: 1886
            ##antiSMASH-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            JAPWIK010000046.1.
            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
     CDS_motif       complement(<1..32)
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_O4271_RS32005_0005"
                     /evalue="2.10E-03"
                     /label="C1_LCL_004-017"
                     /locus_tag="O4271_RS32005"
                     /protein_end="628"
                     /protein_start="617"
                     /score="10.6"
                     /tool="antismash"
                     /translation="SLAQQRMWFLN"
     CDS             complement(<1..1884)
                     /NRPS_PKS="Domain: AMP-binding (11-422). E-value: 1.6e-101.
                     Score: 331.8. Matches aSDomain:
                     nrpspksdomains_O4271_RS32005_AMP-binding.1"
                     /NRPS_PKS="Domain: PCP (528-595). E-value: 2.3e-25. Score:
                     80.6. Matches aSDomain: nrpspksdomains_O4271_RS32005_PCP.1"
                     /codon_start=2
                     /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="O4271_RS32005"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /old_locus_tag="O4271_32005"
                     /product="amino acid adenylation domain-containing protein"
                     /protein_id="WP_269615185.1"
                     /sec_met_domain="AMP-binding (E-value: 7.8e-108, bitscore:
                     346.7, 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="MRGVDSTLSAWFDDAAARFGDRVAVRFGGESLSYGELSVRANRLA
                     RRLIAQGCGPESLVAVALPRSADLVVALLAVVKSGAGYLPVDPSYPADRVEFMLADAAP
                     VAAISWSGRELVLPAGLPVVDIDAVDLSEFDGSVVSDADRVAPLRSSNVAYVIYTSGST
                     GRPKGVQVPHTTVAKLFANTEGVYGFDESDVWTMFHSYAFDFSVWELWGPLLYGGTLVV
                     VDYVTSRSPEQFLELLAAERVTVLNQTPSAFYQLAEADRLASESGRAAELSLRWVVFGG
                     EALELRRLSDWYGRRGDFAPTLVNMYGITETTVHVSHRVLDAALAADASASVVGQAISG
                     LQVFVLDTRLAPVPVGVAGEMYVSGVQLARGYLGQAGLTSTRFVANPFNAGEVLYRTGD
                     VASWNSAGDLEYLGRADDQVKIRGFRIEIGEIESAVLADVSVAQTAVVVREDSPGDQRL
                     VAYVVPAAGVSVSVDDLRVSVGSLLPEYMVPSAFVVLDSIPLTVNGKLDRRALPVPSLQ
                     VAVFRAPTSVVEEVVAQTFADVLGVERVGLDDDFFALGGNSLIATQVTSRLGQALDASV
                     SVRELFEASTVEALAARLGSHVGGGSRAALTAQVRPVRVPLSLAQQRMWFLN"
     source          1..1886
                     /collected_by="M.I. Rychkova"
                     /collection_date="2001"
                     /country="Russia: Udmurt Republic"
                     /db_xref="taxon:334542"
                     /isolation_source="oil-polluted soil, oil-extracting
                     enterprise"
                     /mol_type="genomic DNA"
                     /organism="Rhodococcus qingshengii"
                     /strain="IEGM 766"
                     /submitter_seqid="NODE_46_length_1886_cov_543.382851"
     gene            complement(<1..>1886)
                     /locus_tag="O4271_RS32005"
                     /old_locus_tag="O4271_32005"
     region          1..1886
                     /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..1886
                     /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..1886
                     /aStool="rule-based-clusters"
                     /category="NRPS"
                     /contig_edge="True"
                     /core_location="[<0:1884](-)"
                     /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..1884)
                     /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"
     aSDomain        complement(99..299)
                     /aSDomain="PCP"
                     /aSTool="nrps_pks_domains"
                     /database="nrpspksdomains.hmm"
                     /detection="hmmscan"
                     /domain_id="nrpspksdomains_O4271_RS32005_PCP.1"
                     /evalue="2.30E-25"
                     /label="O4271_RS32005_PCP.1"
                     /locus_tag="O4271_RS32005"
                     /protein_end="595"
                     /protein_start="528"
                     /score="80.6"
                     /tool="antismash"
                     /translation="EEVVAQTFADVLGVERVGLDDDFFALGGNSLIATQVTSRLGQALD
                     ASVSVRELFEASTVEALAARLG"
     aSModule        complement(99..1850)
                     /complete
                     /domains="nrpspksdomains_O4271_RS32005_AMP-binding.1"
                     /domains="nrpspksdomains_O4271_RS32005_PCP.1"
                     /locus_tags="O4271_RS32005"
                     /monomer_pairings="Thr -> Thr"
                     /starter_module
                     /tool="antismash"
                     /type="nrps"
     CDS_motif       complement(588..653)
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_O4271_RS32005_0004"
                     /evalue="1.20E-12"
                     /label="NRPS-A_a8"
                     /locus_tag="O4271_RS32005"
                     /protein_end="432"
                     /protein_start="410"
                     /score="39.6"
                     /tool="antismash"
                     /translation="YLGRADDQVKIRGFRIEIGEIE"
     aSDomain        complement(618..1850)
                     /aSDomain="AMP-binding"
                     /aSTool="nrps_pks_domains"
                     /database="nrpspksdomains.hmm"
                     /detection="hmmscan"
                     /domain_id="nrpspksdomains_O4271_RS32005_AMP-binding.1"
                     /evalue="1.60E-101"
                     /label="O4271_RS32005_AMP-binding.1"
                     /locus_tag="O4271_RS32005"
                     /protein_end="422"
                     /protein_start="11"
                     /score="331.8"
                     /specificity="substrate consensus: Thr"
                     /tool="antismash"
                     /translation="FDDAAARFGDRVAVRFGGESLSYGELSVRANRLARRLIAQGCGPE
                     SLVAVALPRSADLVVALLAVVKSGAGYLPVDPSYPADRVEFMLADAAPVAAISWSGREL
                     VLPAGLPVVDIDAVDLSEFDGSVVSDADRVAPLRSSNVAYVIYTSGSTGRPKGVQVPHT
                     TVAKLFANTEGVYGFDESDVWTMFHSYAFDFSVWELWGPLLYGGTLVVVDYVTSRSPEQ
                     FLELLAAERVTVLNQTPSAFYQLAEADRLASESGRAAELSLRWVVFGGEALELRRLSDW
                     YGRRGDFAPTLVNMYGITETTVHVSHRVLDAALAADASASVVGQAISGLQVFVLDTRLA
                     PVPVGVAGEMYVSGVQLARGYLGQAGLTSTRFVANPFNAGEVLYRTGDVASWNSAGDLE
                     YLGRADDQVKIR"
     CDS_motif       complement(735..824)
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_O4271_RS32005_0003"
                     /evalue="3.30E-14"
                     /label="NRPS-A_a6"
                     /locus_tag="O4271_RS32005"
                     /protein_end="383"
                     /protein_start="353"
                     /score="45.0"
                     /tool="antismash"
                     /translation="PVGVAGEMYVSGVQLARGYLGQAGLTSTRF"
     CDS_motif       complement(1365..1424)
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_O4271_RS32005_0002"
                     /evalue="8.50E-11"
                     /label="NRPS-A_a3"
                     /locus_tag="O4271_RS32005"
                     /protein_end="173"
                     /protein_start="153"
                     /score="33.6"
                     /tool="antismash"
                     /translation="AYVIYTSGSTGRPKGVQVPH"
     CDS_motif       complement(1623..1664)
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_O4271_RS32005_0001"
                     /evalue="7.90E-04"
                     /label="NRPS-A_a2"
                     /locus_tag="O4271_RS32005"
                     /protein_end="87"
                     /protein_start="73"
                     /score="12.9"
                     /tool="antismash"
                     /translation="LAVVKSGAGYLPVD"
ORIGIN
        1 ggttgaggaa ccacatgcgc tgctgcgcca acgacaacgg aacccgaacc ggacgcacct
       61 gcgcagtcaa cgccgcacgt gaaccgccac cgacatgaga acccaaacga gcagccaacg
      121 cctccaccgt cgacgcctcg aacaactccc gcaccgacac cgaagcatcc aacgcctgac
      181 ccaaccgaga cgtcacctgc gtcgcaatca gcgaattacc accgagcgcg aagaaatcat
      241 catccaaacc aacacgctcg acgcccagaa catccgcaaa cgtctgcgca acaacctctt
      301 ccaccaccga cgtcggagca cggaacaccg caacctgcaa cgacggaacc ggcaacgccc
      361 gacgatccaa cttcccgttc accgtcaacg gaatcgaatc caacaccaca aacgccgacg
      421 gcaccatgta ctccggcaac aacgaaccca ccgacacccg aagatcgtcg accgaaacgc
      481 tcacacccgc agccggaacc acatacgcca ccaaccgctg atcacccgga gaatcctcac
      541 gaacaaccac cgccgtctgc gccaccgaca catccgccaa caccgcagac tcgatctcac
      601 cgatctcgat ccggaaacca cggatcttca cctgatcatc cgcgcgaccc agatactcca
      661 aatcaccagc actgttccac gacgcgacgt cacccgtgcg gtacaacacc tcgccggcat
      721 tgaacggatt cgccacaaac cgcgtcgacg tcaaccccgc ctgacccaga taaccccgag
      781 ccaactgaac accagagaca tacatctcac ccgcgacacc aacaggcacc ggagccaaac
      841 gcgtatcgag cacgaacacc tgcagacccg aaatagcctg acccacaaca ctcgccgacg
      901 catccgccgc caacgcagca tccaacacac gatggctcac atgcaccgtc gtctccgtga
      961 tgccgtacat gttcaccaac gtcggcgcga agtcaccgcg gcggccgtac caatccgaca
     1021 agcgacgcag ctcgagcgcc tcgccgccga aaacaaccca ccgcaacgac aactcagcag
     1081 cccgaccgga ttccgacgcc aaccgatcag cctcagccaa ctgatagaac gccgacggcg
     1141 tctgattgag caccgtcacc cgctcagcag caagcaactc caagaactgc tccggcgacc
     1201 gcgacgtcac ataatccaca accaccaacg tgccgccgta caacagcgga ccccacaact
     1261 cccacaccga gaagtcgaac gcataactgt ggaacatcgt ccacacatcg gattcgtcga
     1321 acccgtacac accctcggta ttcgcaaaca acttcgccac cgtcgtgtgc ggaacctgca
     1381 cacccttcgg gcgacccgtc gaacccgacg tgtaaatcac atacgcaaca ttcgacgacc
     1441 gcaacggcgc aacacgatcc gcatccgaaa ccaccgaacc atcgaactcc gacaaatcca
     1501 ccgcgtcgat atcaaccaca ggcaaaccag cgggcaacac caactcacgc ccggaccacg
     1561 aaatcgcagc caccggagca gcatcagcca acatgaactc gacacgatca gccggatacg
     1621 acggatccac cggcaaatac cccgcaccgg acttcaccac cgccaacaac gccaccacaa
     1681 gatccgccga ccgcggcaac gccaccgcca ccaacgactc cggaccacaa ccctgagcaa
     1741 tcaacctgcg cgccaaacga ttagcccgca ccgacaactc accatacgac aacgactcgc
     1801 caccgaaccg caccgcaacc cgatcaccaa accgcgcagc agcatcatcg aaccacgccg
     1861 acaacgtcga atccacacca cgatcg
//
