LOCUS       NZ_BMSZ01000048         3166 bp    DNA     linear   CON 02-SEP-2024
DEFINITION  Streptomyces badius strain JCM 4350 sequence48, whole genome shotgun
            sequence.
ACCESSION   NZ_BMSZ01000048
VERSION     NZ_BMSZ01000048.1
KEYWORDS    WGS; RefSeq; STANDARD_DRAFT.
SOURCE      Streptomyces badius
  ORGANISM  Streptomyces badius
            Bacteria; Actinomycetota; Actinomycetes; Kitasatosporales;
            Streptomycetaceae; Streptomyces.
REFERENCE   1
  AUTHORS   Wu,L. and Ma,J.
  TITLE     The Global Catalogue of Microorganisms (GCM) 10K type strain
            sequencing project: providing services to taxonomists for standard
            genome sequencing and annotation
  JOURNAL   Int J Syst Evol Microbiol 69 (4), 895-898 (2019)
   PUBMED   30832757
REFERENCE   2  (bases 1 to 3166)
  AUTHORS   Sun,Q. and Ohkuma,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (09-SEP-2020) Contact:Qinglan Sun Institute of
            Microbiology, Chinese Academy of Sciences, WFCC-MIRCEN World Data
            Centre for Microorganisms (WDCM); No. 3, yard 1, Beichen W Rd, Ao
            Yun Cun, Chaoyang, Beijing, Beijing 1000101, China URL
            :http://www.wdcm.org/
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: BGI assembly pipeline
            Genome Coverage                   :: 154X
            Sequencing Technology             :: Illumina HiSeq X Ten
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_014649415.1-RS_2024_09_02
            Annotation Date                   :: 09/02/2024 03:57:07
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.8
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 6,894
            CDSs (total)                      :: 6,825
            Genes (coding)                    :: 6,582
            CDSs (with protein)               :: 6,582
            Genes (RNA)                       :: 69
            rRNAs                             :: 2 (23S)
            partial rRNAs                     :: 2 (23S)
            tRNAs                             :: 64
            ncRNAs                            :: 3
            Pseudo Genes (total)              :: 244
            CDSs (without protein)            :: 243
            Pseudo Genes (ambiguous residues) :: 0 of 244
            Pseudo Genes (frameshifted)       :: 70 of 244
            Pseudo Genes (incomplete)         :: 206 of 244
            Pseudo Genes (internal stop)      :: 7 of 244
            Pseudo Genes (multiple problems)  :: 38 of 244
            CRISPR Arrays                     :: 4
            ##Genome-Annotation-Data-END##
            ##antiSMASH-Data-START##
            Version                           :: 8.dev-cf2fc5ee(changed)
            Run date                          :: 2025-09-13 16:11:55
            NOTE :: This is a single region extracted from a larger record!
            Orig. start                       :: 0
            Orig. end                         :: 3166
            ##antiSMASH-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            BMSZ01000048.1.
            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
     gene            complement(<1..>720)
                     /locus_tag="IE135_RS33420"
     CDS             complement(<1..720)
                     /NRPS_PKS="Domain: AMP-binding (24-226). E-value: 8.2e-47.
                     Score: 151.6. Matches aSDomain:
                     nrpspksdomains_IE135_RS33420_AMP-binding.1"
                     /codon_start=1
                     /gene_functions="biosynthetic-additional
                     (rule-based-clusters) AMP-binding"
                     /gene_functions="biosynthetic-additional (smcogs)
                     SMCOG1002: AMP-dependent synthetase and ligase"
                     /gene_kind="biosynthetic-additional"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_018468694.1"
                     /locus_tag="IE135_RS33420"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /product="AMP-binding protein"
                     /protein_id="WP_199889940.1"
                     /sec_met_domain="AMP-binding (E-value: 9.9e-52, bitscore:
                     163.5, seeds: 400, tool: rule-based-clusters)"
                     /transl_table=11
                     /translation="MPALVLTSRATDGAVPGTADAPARVQVDGTDVLAQLETLSGDPVR
                     SVEVLPSHVAYVIYTSGSTGRPKGVAVPHGNVVALFGGTDGWFGFGTDDVWAWFHSFAF
                     DFSVWELWGALLHGGRLVVVPREVSRNPREVLDLLVTERVTVLNQTPSAFYQLMAAQSR
                     DPQLGQRLALRCVVFGGEALDPSRLRDWYTHHAADAPVLVNMYGITETTVHVSYKPLDE
                     TVVTADAGSVIGVGIPNL"
     source          1..3166
                     /culture_collection="JCM:4350"
                     /db_xref="taxon:1941"
                     /mol_type="genomic DNA"
                     /organism="Streptomyces badius"
                     /strain="JCM 4350"
                     /submitter_seqid="sequence48"
                     /type_material="type strain of Streptomyces badius"
     region          1..3166
                     /candidate_cluster_numbers="1"
                     /contig_edge="True"
                     /product="NRPS"
                     /region_number="1"
                     /rules="cds(Condensation and (AMP-binding or A-OX) and not
                     alpha_am_amid)"
                     /tool="antismash"
     cand_cluster    1..3166
                     /SMILES=""
                     /candidate_cluster_number="1"
                     /contig_edge="True"
                     /detection_rules="cds(Condensation and (AMP-binding or
                     A-OX) and not alpha_am_amid)"
                     /kind="single"
                     /product="NRPS"
                     /protoclusters="1"
                     /tool="antismash"
     protocluster    1..3166
                     /aStool="rule-based-clusters"
                     /category="NRPS"
                     /contig_edge="True"
                     /core_location="[<1355:3162](-)"
                     /cutoff="20000"
                     /detection_rule="cds(Condensation and (AMP-binding or A-OX)
                     and not alpha_am_amid)"
                     /neighbourhood="20000"
                     /product="NRPS"
                     /protocluster_number="1"
                     /tool="antismash"
     proto_core      complement(<1356..3162)
                     /aStool="rule-based-clusters"
                     /tool="antismash"
                     /cutoff="20000"
                     /detection_rule="cds(Condensation and (AMP-binding or A-OX)
                     and not alpha_am_amid)"
                     /neighbourhood="20000"
                     /product="NRPS"
                     /protocluster_number="1"
     aSDomain        complement(43..648)
                     /aSDomain="AMP-binding"
                     /aSTool="nrps_pks_domains"
                     /database="nrpspksdomains.hmm"
                     /detection="hmmscan"
                     /domain_id="nrpspksdomains_IE135_RS33420_AMP-binding.1"
                     /evalue="8.20E-47"
                     /label="IE135_RS33420_AMP-binding.1"
                     /locus_tag="IE135_RS33420"
                     /protein_end="226"
                     /protein_start="24"
                     /score="151.6"
                     /specificity="substrate consensus: Thr"
                     /tool="antismash"
                     /translation="VQVDGTDVLAQLETLSGDPVRSVEVLPSHVAYVIYTSGSTGRPKG
                     VAVPHGNVVALFGGTDGWFGFGTDDVWAWFHSFAFDFSVWELWGALLHGGRLVVVPREV
                     SRNPREVLDLLVTERVTVLNQTPSAFYQLMAAQSRDPQLGQRLALRCVVFGGEALDPSR
                     LRDWYTHHAADAPVLVNMYGITETTVHVSYKPLDETVVT"
     CDS_motif       complement(499..558)
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_IE135_RS33420_0001"
                     /evalue="1.70E-11"
                     /label="NRPS-A_a3"
                     /locus_tag="IE135_RS33420"
                     /protein_end="74"
                     /protein_start="54"
                     /score="35.7"
                     /tool="antismash"
                     /translation="AYVIYTSGSTGRPKGVAVPH"
     assembly_gap    721..820
                     /estimated_length=100
                     /gap_type="within scaffold"
                     /linkage_evidence="paired-ends"
     CDS             complement(<821..1321)
                     /codon_start=3
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /locus_tag="IE135_RS33425"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /product="hypothetical protein"
                     /protein_id="WP_199889941.1"
                     /transl_table=11
                     /translation="MADLLVHEHAPLTLAQQAADLAAETPLFTSLLNYRQNANAAQRLG
                     RSIAELNTGLDGVELLSAHERTNYPLTVSVDDTGEGFGLTVQAAAPIAAQTVCHLVSST
                     AEGVVAALEDESEGLLLGRVPVLGDAEQDRLVREWSGESRPVAEASLTELFAAQAVRTP
                     DATAV"
     gene            complement(<821..>1325)
                     /locus_tag="IE135_RS33425"
     assembly_gap    1326..1355
                     /estimated_length=30
                     /gap_type="within scaffold"
                     /linkage_evidence="paired-ends"
     aSDomain        complement(<1356..2050)
                     /aSDomain="Condensation"
                     /aSTool="nrps_pks_domains"
                     /database="nrpspksdomains.hmm"
                     /detection="hmmscan"
                     /domain_id="nrpspksdomains_IE135_RS35250_Condensation_Dual.
                     1"
                     /domain_subtypes="Condensation_Dual"
                     /evalue="4.10E-86"
                     /label="IE135_RS35250_Condensation_Dual.1"
                     /locus_tag="IE135_RS35250"
                     /protein_end="603"
                     /protein_start="370"
                     /score="280.9"
                     /specificity="C activity: active"
                     /specificity="Active site motif: HHLVQDH"
                     /tool="antismash"
                     /translation="DIYPLAPLQEGIFFHSVIGNENGADVYVLPTVLRFDSRERLDQFL
                     SVLQTAVDRHDTLRTGFAWEGLREPVQVVVRHAGIPVNEVNLKGAEGDLTQRLLDLCSP
                     SLDIRQAPLLRATVAAEPGSDRWLMVMQAHHLVQDHTAMGVLFAEVSALLRGDAEELAA
                     PVPFREFVAQARLGVSRAEHERFFGELLGGVSEPTAPFGLLDVHGDGSDVAEATAVLDT
                     GLAARLREQAR"
     CDS             complement(<1356..3162)
                     /GO_function="GO:0003824 - catalytic activity [Evidence
                     IEA]"
                     /NRPS_PKS="Domain: PCP (252-320). E-value: 1e-26. Score:
                     84.9. Matches aSDomain: nrpspksdomains_IE135_RS35250_PCP.1"
                     /NRPS_PKS="Domain: Condensation_Dual (370-603). E-value:
                     4.1e-86. Score: 280.9. Matches aSDomain:
                     nrpspksdomains_IE135_RS35250_Condensation_Dual.1"
                     /codon_start=3
                     /gene_functions="biosynthetic (rule-based-clusters) NRPS:
                     Condensation"
                     /gene_functions="biosynthetic (rule-based-clusters) NRPS:
                     AMP-binding"
                     /gene_functions="biosynthetic-additional
                     (rule-based-clusters) PP-binding"
                     /gene_functions="biosynthetic-additional (smcogs)
                     SMCOG1127: condensation domain-containing protein"
                     /gene_kind="biosynthetic"
                     /inference="COORDINATES: protein motif:HMM:NF012873.5"
                     /locus_tag="IE135_RS35250"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /product="condensation domain-containing protein"
                     /protein_id="WP_199889942.1"
                     /sec_met_domain="AMP-binding (E-value: 9.9e-20, bitscore:
                     58.0, seeds: 400, tool: rule-based-clusters)"
                     /sec_met_domain="PP-binding (E-value: 1.7e-16, bitscore:
                     48.4, seeds: 164, tool: rule-based-clusters)"
                     /sec_met_domain="Condensation (E-value: 4.8e-29, bitscore:
                     89.0, seeds: 42, tool: rule-based-clusters)"
                     /transl_table=11
                     /translation="MELAPTRSMARHPLFQIMLSLDTHADAVVDLPGLEAEVIASKDSA
                     AKFDLDLNVRERFDASGAPAGLRGTVVYAADLFDEATVAELVERFVRVLEAVTADPHQP
                     VSRIRILGNAELDRILTEWKHSAAGVPTRTVPVLDGAPQSGADAGGKVFVLDAALQPVP
                     VGVTGDLYVAGGLTDRGYEGRPGLTAERFVACPFETAGERMYRTGDVVRRRADGSLELV
                     GSAHQEHEANASTAAGEGQSARGRGPSSVQEEILSSVFAEMLDLPQVGVDDNFFELGGH
                     SLMAVKLVVRLRELGMPVSVRSLFATPTVAGLAAAVSAEGQSTVTVPENLIPTGGADLI
                     TPEMLPLVELTTEEIERISARVPGGAANIADIYPLAPLQEGIFFHSVIGNENGADVYVL
                     PTVLRFDSRERLDQFLSVLQTAVDRHDTLRTGFAWEGLREPVQVVVRHAGIPVNEVNLK
                     GAEGDLTQRLLDLCSPSLDIRQAPLLRATVAAEPGSDRWLMVMQAHHLVQDHTAMGVLF
                     AEVSALLRGDAEELAAPVPFREFVAQARLGVSRAEHERFFGELLGGVSEPTAPFGLLDV
                     HGDGSDVAEATAVLDTGLAARLREQAR"
     gene            complement(<1356..>3166)
                     /locus_tag="IE135_RS35250"
     CDS_motif       complement(1514..1555)
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_IE135_RS35250_0005"
                     /evalue="2.40E-06"
                     /label="C4_dual_169-182"
                     /locus_tag="IE135_RS35250"
                     /protein_end="549"
                     /protein_start="535"
                     /score="20.0"
                     /tool="antismash"
                     /translation="PFREFVAQARLGVS"
     CDS_motif       complement(1589..1651)
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_IE135_RS35250_0004"
                     /evalue="7.30E-07"
                     /label="C3_dual_135-156"
                     /locus_tag="IE135_RS35250"
                     /protein_end="524"
                     /protein_start="503"
                     /score="22.1"
                     /tool="antismash"
                     /translation="HHLVQDHTAMGVLFAEVSALL"
     CDS_motif       complement(1859..1972)
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_IE135_RS35250_0003"
                     /evalue="5.30E-15"
                     /label="C2_dual_024-063"
                     /locus_tag="IE135_RS35250"
                     /protein_end="434"
                     /protein_start="396"
                     /score="47.9"
                     /tool="antismash"
                     /translation="YVLPTVLRFDSRERLDQFLSVLQTAVDRHDTLRTGFAW"
     CDS_motif       complement(2006..2044)
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_IE135_RS35250_0002"
                     /evalue="8.10E-06"
                     /label="C1_dual_004-017"
                     /locus_tag="IE135_RS35250"
                     /protein_end="385"
                     /protein_start="372"
                     /score="18.3"
                     /tool="antismash"
                     /translation="YPLAPLQEGIFFH"
     aSDomain        complement(2201..2404)
                     /aSDomain="PCP"
                     /aSTool="nrps_pks_domains"
                     /database="nrpspksdomains.hmm"
                     /detection="hmmscan"
                     /domain_id="nrpspksdomains_IE135_RS35250_PCP.1"
                     /evalue="1.00E-26"
                     /label="IE135_RS35250_PCP.1"
                     /locus_tag="IE135_RS35250"
                     /protein_end="320"
                     /protein_start="252"
                     /score="84.9"
                     /tool="antismash"
                     /translation="EEILSSVFAEMLDLPQVGVDDNFFELGGHSLMAVKLVVRLRELGM
                     PVSVRSLFATPTVAGLAAAVSAE"
     CDS_motif       complement(2585..2674)
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_IE135_RS35250_0001"
                     /evalue="5.60E-11"
                     /label="NRPS-A_a6"
                     /locus_tag="IE135_RS35250"
                     /protein_end="192"
                     /protein_start="162"
                     /score="34.7"
                     /tool="antismash"
                     /translation="PVGVTGDLYVAGGLTDRGYEGRPGLTAERF"
     misc_feature    complement(2623..2625)
                     /note="tta leucine codon, possible target for bldA
                     regulation"
                     /tool="antismash"
ORIGIN
        1 caggttcggg atgcccacgc cgatcacact gcccgcgtcg gcggtgacca cagtttcgtc
       61 gaggggtttg tagctgacgt ggacggtggt ttcggtgatg ccgtacatgt tcaccagcac
      121 tggcgcgtcc gccgcgtggt gtgtgtacca gtcgcgcaag cgtgacgggt ccagtgcctc
      181 tccgccgaac accacacacc gcagtgccag ccgctgaccc agttgcgggt cccggctctg
      241 ggccgccatc agctggtaga acgccgaggg tgtctggttg agcacggtca cccgttcggt
      301 gaccagcagg tccagaacct cacgcgggtt gcgtgagacc tcgcgtggca cgaccacgag
      361 gcgtccgccg tgcagcagcg caccccacag ctcccacacc gagaagtcga acgcgaagga
      421 gtggaaccac gcccacacgt cgtccgtacc gaaaccgaac cagccatcgg tcccgccgaa
      481 cagcgcgacc acgttcccgt ggggaaccgc gacacccttc gggcgtcccg tcgaacccga
      541 cgtgtagatc acatacgcca cgtgcgacgg caggacctcg acagagcgaa ccggatcacc
      601 ggacagcgtc tccaactgtg ccagcacgtc ggtcccgtcc acctggactc gcgctggggc
      661 gtccgccgtt ccgggaacgg cgccgtccgt cgcccggctg gtcaggacca gggccggccg
      721 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
      781 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn accgcggtcg cgtcaggcgt
      841 gcgtactgcc tgggccgcga acagctctgt cagcgaagcc tccgccaccg ggcgggactc
      901 accgctccac tcccgcacca gacggtcctg ctccgcgtcg cccagaaccg gcacccggcc
      961 cagcagcaga ccctccgact cgtcctccag cgcagcgacc acaccctcgg ccgtggagct
     1021 gaccaggtgg cacaccgttt gcgcggcgat cggggcagcc gcctgcactg tcaggccgaa
     1081 gccttcgccg gtgtcgtcga ccgacaccgt cagcgggtag ttcgtccgct cgtgagccga
     1141 cagcagctcg accccgtcca ggccggtgtt gagttccgcg atcgacctgc ccagtcgctg
     1201 ggcggcgttg gcgttctgcc ggtagttgag gagggaggtg aacagtggcg tctcggccgc
     1261 gaggtcggcg gcctgttggg cgagggtgag gggggcgtgt tcgtggacga ggaggtcggc
     1321 gagctnnnnn nnnnnnnnnn nnnnnnnnnn nnnnntcgcg cctgttcccg cagtcgagcg
     1381 gcgagaccgg tgtccaggac agccgttgcc tcggcgacgt ccgagccgtc accgtgcaca
     1441 tccagcagcc cgaacggcgc cgtcggttca ctcacgccgc cgagcagctc cccgaagaac
     1501 cgctcgtgct ccgcgcgcga cacacccagg cgcgcctgcg ccacgaactc ccggaacggc
     1561 accggagcgg ccagttcctc cgcgtcaccg cggagcaacg cgctcacctc cgcgaagagg
     1621 acgcccatcg ccgtgtggtc ctggaccagg tgatgggcct gcatgaccat cagccagcgg
     1681 tcgctgccgg gctccgccgc gacagtggct cgcagtagcg gggcctgccg gatgtccagg
     1741 gacgggctgc acagatcgag gagcctctgc gtcaagtcac cttcagcacc cttgagattc
     1801 acctcattca caggaatccc ggcgtgccgg accacgacct gcaccggctc gcgcagcccc
     1861 tcccacgcga accccgtccg cagagtgtcg tgtcggtcca cggcagtctg gagcacgctc
     1921 aggaactggt cgagccgttc ccgggagtcg aaccgcagca ccgtcggcag cacgtacacg
     1981 tccgccccgt tctcgttgcc gatgacggag tggaagaaga tgccttcctg gaggggggcg
     2041 agggggtaga tgtcggcgat gttcgccgcg ccacccggca cgcgggccga gatccgctcg
     2101 atctcctccg tcgtcagctc gaccaggggc agcatttccg gagtgatgag gtcggcacca
     2161 cccgtgggga tcaggttctc cggcacggtc accgtgctct ggccctccgc gctgacggcg
     2221 gccgcgagcc cggccaccgt gggcgtcgcg aacaggctcc gcacgctcac gggcatgccc
     2281 agctcacgca ggcgtacgac gagcttgacg gccatgaggg agtgcccgcc gagctcgaag
     2341 aagttgtcgt cgacgccgac ctggggcagg tccagcatct ccgcgaacac cgagctcagg
     2401 atctcctcct gaacggacga aggaccacgt ccccgagcgg actgtccctc gccggcagcc
     2461 gtcgacgcgt tcgcctcgtg ctcttggtgt gcgctgccca cgagttccag gctgccgtcg
     2521 gcgcgccggc ggacgacgtc acccgtgcgg tacatccgct caccggcggt ctcgaacggg
     2581 cacgcgacga agcgctccgc cgtcaggccg gggcggccct cgtaaccgcg gtccgtcagg
     2641 ccacccgcga cgtacaggtc gcccgtgaca ccgacaggga ccggctggag cgccgcgtcg
     2701 agcacgaaca ccttgccgcc ggcgtccgct ccgctctgcg gggcgccgtc cagcacgggc
     2761 accgtgcggg tcgggacgcc cgccgcggag tgcttccact cggtcaggat ccggtccagc
     2821 tccgcgttgc cgaggatccg gatccggctc acgggctggt gcggatcggc cgtcacggcc
     2881 tccagtacgc gcacgaagcg ctcgacgagt tccgcgaccg tggcctcgtc gaacaggtcc
     2941 gcggcgtaga cgaccgtgcc acggagaccg gccggggccc cggaggcgtc gaaccgctcc
     3001 cgcacgttca ggtcgaggtc gaacttggcg gccgagtcct tgctcgcgat cacttcggcc
     3061 tcgagcccgg gcaggtccac gaccgcgtcc gcatgcgtgt ccaggctgag catgatctgg
     3121 aagagggggt ggcgtgccat ggagcgtgtg ggggcgagtt cttcga
//
