LOCUS       NZ_BMTZ01000055         2837 bp    DNA     linear   CON 02-SEP-2024
DEFINITION  Streptomyces variabilis strain JCM 4422 sequence55, whole genome
            shotgun sequence.
ACCESSION   NZ_BMTZ01000055
VERSION     NZ_BMTZ01000055.1
KEYWORDS    WGS; RefSeq; STANDARD_DRAFT.
SOURCE      Streptomyces variabilis
  ORGANISM  Streptomyces variabilis
            Bacteria; Actinomycetota; Actinomycetes; Kitasatosporales;
            Streptomycetaceae; Streptomyces; Streptomyces griseoincarnatus
            group.
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 2837)
  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                   :: 156X
            Sequencing Technology             :: Illumina HiSeq X Ten
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_014649935.1-RS_2024_09_02
            Annotation Date                   :: 09/02/2024 04:37:37
            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)                     :: 6,743
            CDSs (total)                      :: 6,668
            Genes (coding)                    :: 6,496
            CDSs (with protein)               :: 6,496
            Genes (RNA)                       :: 75
            rRNAs                             :: 2, 1, 1 (5S, 16S, 23S)
            complete rRNAs                    :: 1 (5S)
            partial rRNAs                     :: 1, 1, 1 (5S, 16S, 23S)
            tRNAs                             :: 68
            ncRNAs                            :: 3
            Pseudo Genes (total)              :: 172
            CDSs (without protein)            :: 172
            Pseudo Genes (ambiguous residues) :: 0 of 172
            Pseudo Genes (frameshifted)       :: 61 of 172
            Pseudo Genes (incomplete)         :: 147 of 172
            Pseudo Genes (internal stop)      :: 11 of 172
            Pseudo Genes (multiple problems)  :: 42 of 172
            ##Genome-Annotation-Data-END##
            ##antiSMASH-Data-START##
            Version                           :: 8.dev-cf2fc5ee(changed)
            Run date                          :: 2025-09-13 00:23:51
            NOTE :: This is a single region extracted from a larger record!
            Orig. start                       :: 0
            Orig. end                         :: 2837
            ##antiSMASH-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            BMTZ01000055.1.
            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..2837
                     /culture_collection="JCM:4422"
                     /db_xref="taxon:67372"
                     /mol_type="genomic DNA"
                     /organism="Streptomyces variabilis"
                     /strain="JCM 4422"
                     /submitter_seqid="sequence55"
                     /type_material="type strain of Streptomyces variabilis"
     region          1..2837
                     /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..2837
                     /SMILES="NC(C)C(=O)O"
                     /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..2837
                     /aStool="rule-based-clusters"
                     /category="NRPS"
                     /contig_edge="True"
                     /core_location="[27:>2837](+)"
                     /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      28..>2837
                     /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        28..927
                     /aSDomain="AMP-binding"
                     /aSTool="nrps_pks_domains"
                     /database="nrpspksdomains.hmm"
                     /detection="hmmscan"
                     /domain_id="nrpspksdomains_IE148_RS33230_AMP-binding.1"
                     /evalue="3.30E-69"
                     /label="IE148_RS33230_AMP-binding.1"
                     /locus_tag="IE148_RS33230"
                     /protein_end="300"
                     /protein_start="0"
                     /score="225.4"
                     /specificity="substrate consensus: Ala"
                     /tool="antismash"
                     /translation="MDPGYPGERVDFMVQDSGVSLVLRSVKDFPDGGRTDRVPVAGDGS
                     DVAYVIYTSGSTGRPKGVVIEHSQVVAMLSWAGRVFADGELSQTLAATSVSFDLSVFEI
                     FAPLSVGGTVHLVPDNALDLIAHPGRYADVTLVNTVPSVARELLAAGAIPPRARTVNLA
                     GEPLAPGLVAELYALPVIGVVNNLYGPSEDTTYSTHAVTAPGDARTPIGRPVDGTRVHV
                     LDGCLRPVVVGAVGELYLSGAGVTRGYHARPALTAQRYLPDPFSSEGGRMYRTGDLVRW
                     RPDGQLEYLGRADGQVKIR"
     aSModule        28..1455
                     /complete
                     /domains="nrpspksdomains_IE148_RS33230_AMP-binding.1"
                     /domains="nrpspksdomains_IE148_RS33230_PCP.1"
                     /locus_tags="IE148_RS33230"
                     /monomer_pairings="Ala -> Ala"
                     /starter_module
                     /tool="antismash"
                     /type="nrps"
     gene            28..>2837
                     /locus_tag="IE148_RS33230"
     CDS             28..>2837
                     /NRPS_PKS="Domain: AMP-binding (0-300). E-value: 3.3e-69.
                     Score: 225.4. Matches aSDomain:
                     nrpspksdomains_IE148_RS33230_AMP-binding.1"
                     /NRPS_PKS="Domain: PCP (408-476). E-value: 8.8e-23. Score:
                     72.3. Matches aSDomain: nrpspksdomains_IE148_RS33230_PCP.1"
                     /NRPS_PKS="Domain: Condensation_LCL (500-783). E-value:
                     9.2e-77. Score: 249.9. Matches aSDomain:
                     nrpspksdomains_IE148_RS33230_Condensation_LCL.1"
                     /codon_start=1
                     /gene_functions="biosynthetic (rule-based-clusters) NRPS:
                     AMP-binding"
                     /gene_functions="biosynthetic (rule-based-clusters) NRPS:
                     Condensation"
                     /gene_functions="biosynthetic-additional
                     (rule-based-clusters) PP-binding"
                     /gene_functions="biosynthetic-additional (smcogs)
                     SMCOG1002: AMP-dependent synthetase and ligase"
                     /gene_kind="biosynthetic"
                     /inference="COORDINATES: protein motif:HMM:NF012873.5"
                     /locus_tag="IE148_RS33230"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /product="amino acid adenylation domain-containing protein"
                     /protein_id="WP_246539281.1"
                     /sec_met_domain="AMP-binding (E-value: 7.8e-83, bitscore:
                     264.3, seeds: 400, tool: rule-based-clusters)"
                     /sec_met_domain="PP-binding (E-value: 4e-19, bitscore:
                     55.2, seeds: 164, tool: rule-based-clusters)"
                     /sec_met_domain="Condensation (E-value: 5.8e-63, bitscore:
                     198.8, seeds: 42, tool: rule-based-clusters)"
                     /transl_table=11
                     /translation="MDPGYPGERVDFMVQDSGVSLVLRSVKDFPDGGRTDRVPVAGDGS
                     DVAYVIYTSGSTGRPKGVVIEHSQVVAMLSWAGRVFADGELSQTLAATSVSFDLSVFEI
                     FAPLSVGGTVHLVPDNALDLIAHPGRYADVTLVNTVPSVARELLAAGAIPPRARTVNLA
                     GEPLAPGLVAELYALPVIGVVNNLYGPSEDTTYSTHAVTAPGDARTPIGRPVDGTRVHV
                     LDGCLRPVVVGAVGELYLSGAGVTRGYHARPALTAQRYLPDPFSSEGGRMYRTGDLVRW
                     RPDGQLEYLGRADGQVKIRGHRVELGEVEEVLRRHPHVSEAVVVARPDVTGSLRLVGYV
                     VADEAGGDVPSDLPSHARAWLPDFMVPSALVALREFPLLPNGKIDRSALPDPEPGADRA
                     SFRPPSGPAEELIARVWSELLGITGISADDDFFALGGHSLLATRLTHRLGEALGAHIPL
                     HLVFEHPTLTDLAAHLPEGTEQGRTPPITPLDRVPEPDGTLVLPTSPGQERLWVQCALD
                     PEANLAYHIRGAVHLHGPLDEDALVTALRHLARRHESLRTSLRQVDGELRQVVAPDPEV
                     PLLRTTNADWEAVIDAETRRHFDLSAGPLWHVTLVSAGPEHHVVVMSLHHAIADGWSLD
                     IILREIAQSYGALLHAPGSEAVSPAPVQYAEAAAWQRETAPENAEFWRSHLAGTTSAGL
                     PTDRPRPPRQTYRGDAVPLNLPQKALAGAARKAATTSFTVLATALAVVLVKLTDRYDVT
                     LGIPVAGRDHPDTAEVVGYLVDTLPLHLRPDPQATLAETLDVTRALVDDVRAHPRIPLE
                     ELLREARPHGDRGPLFQVLLAVNGTPPRYELAGLEMTPAPVPFRTTPYDLVVQAEERDG
                     RVTGHLLFNTDLFERSTAQLIADRLATAVHALADGPTLTVAEVDVRSVGEREWVAAVSA
                     GVPLAGG"
     CDS_motif       169..228
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_IE148_RS33230_0001"
                     /evalue="1.70E-11"
                     /label="NRPS-A_a3"
                     /locus_tag="IE148_RS33230"
                     /protein_end="67"
                     /protein_start="47"
                     /score="35.7"
                     /tool="antismash"
                     /translation="AYVIYTSGSTGRPKGVVIEH"
     CDS_motif       721..804
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_IE148_RS33230_0002"
                     /evalue="3.50E-14"
                     /label="NRPS-A_a6"
                     /locus_tag="IE148_RS33230"
                     /protein_end="259"
                     /protein_start="231"
                     /score="44.9"
                     /tool="antismash"
                     /translation="VGAVGELYLSGAGVTRGYHARPALTAQR"
     CDS_motif       892..957
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_IE148_RS33230_0003"
                     /evalue="3.20E-12"
                     /label="NRPS-A_a8"
                     /locus_tag="IE148_RS33230"
                     /protein_end="310"
                     /protein_start="288"
                     /score="38.3"
                     /tool="antismash"
                     /translation="YLGRADGQVKIRGHRVELGEVE"
     CDS_motif       994..1050
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_IE148_RS33230_0004"
                     /evalue="3.30E+00"
                     /label="C5_LCL_267-296"
                     /locus_tag="IE148_RS33230"
                     /protein_end="341"
                     /protein_start="322"
                     /score="0.4"
                     /tool="antismash"
                     /translation="VVVARPDVTGSLRLVGYVV"
     aSDomain        1252..1455
                     /aSDomain="PCP"
                     /aSTool="nrps_pks_domains"
                     /database="nrpspksdomains.hmm"
                     /detection="hmmscan"
                     /domain_id="nrpspksdomains_IE148_RS33230_PCP.1"
                     /evalue="8.80E-23"
                     /label="IE148_RS33230_PCP.1"
                     /locus_tag="IE148_RS33230"
                     /protein_end="476"
                     /protein_start="408"
                     /score="72.3"
                     /tool="antismash"
                     /translation="EELIARVWSELLGITGISADDDFFALGGHSLLATRLTHRLGEALG
                     AHIPLHLVFEHPTLTDLAAHLPE"
     aSDomain        1528..2376
                     /aSDomain="Condensation"
                     /aSTool="nrps_pks_domains"
                     /database="nrpspksdomains.hmm"
                     /detection="hmmscan"
                     /domain_id="nrpspksdomains_IE148_RS33230_Condensation_LCL.1
                     "
                     /domain_subtypes="Condensation_LCL"
                     /evalue="9.20E-77"
                     /label="IE148_RS33230_Condensation_LCL.1"
                     /locus_tag="IE148_RS33230"
                     /protein_end="783"
                     /protein_start="500"
                     /score="249.9"
                     /specificity="C activity: active"
                     /specificity="Active site motif: HHAIADG"
                     /tool="antismash"
                     /translation="LPTSPGQERLWVQCALDPEANLAYHIRGAVHLHGPLDEDALVTAL
                     RHLARRHESLRTSLRQVDGELRQVVAPDPEVPLLRTTNADWEAVIDAETRRHFDLSAGP
                     LWHVTLVSAGPEHHVVVMSLHHAIADGWSLDIILREIAQSYGALLHAPGSEAVSPAPVQ
                     YAEAAAWQRETAPENAEFWRSHLAGTTSAGLPTDRPRPPRQTYRGDAVPLNLPQKALAG
                     AARKAATTSFTVLATALAVVLVKLTDRYDVTLGIPVAGRDHPDTAEVVGYLVDTLPLHL
                     RP"
     CDS_motif       1594..1704
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_IE148_RS33230_0005"
                     /evalue="3.90E-14"
                     /label="C2_LCL_024-062"
                     /locus_tag="IE148_RS33230"
                     /protein_end="559"
                     /protein_start="522"
                     /score="45.0"
                     /tool="antismash"
                     /translation="AYHIRGAVHLHGPLDEDALVTALRHLARRHESLRTSL"
     CDS_motif       1897..1962
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_IE148_RS33230_0006"
                     /evalue="4.90E-09"
                     /label="C3_DCL_135-156"
                     /locus_tag="IE148_RS33230"
                     /protein_end="645"
                     /protein_start="623"
                     /score="28.7"
                     /tool="antismash"
                     /translation="LHHAIADGWSLDIILREIAQSY"
     CDS_motif       2278..2364
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_IE148_RS33230_0007"
                     /evalue="2.20E-11"
                     /label="C5_LCL_267-296"
                     /locus_tag="IE148_RS33230"
                     /protein_end="779"
                     /protein_start="750"
                     /score="36.1"
                     /tool="antismash"
                     /translation="DVTLGIPVAGRDHPDTAEVVGYLVDTLPL"
     CDS_motif       2431..2526
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_IE148_RS33230_0008"
                     /evalue="5.20E-05"
                     /label="C67_LCL_14fromHMM"
                     /locus_tag="IE148_RS33230"
                     /protein_end="833"
                     /protein_start="801"
                     /score="15.5"
                     /tool="antismash"
                     /translation="DVRAHPRIPLEELLREARPHGDRGPLFQVLLA"
ORIGIN
        1 ctgaagtcgg gtgcgggtta tgtgccgatg gatccgggtt atccgggtga gcgtgtcgac
       61 ttcatggtcc aggactcggg tgtctcgctg gtcttgaggt ctgtcaagga cttcccggac
      121 gggggccgca cggaccgggt gcccgtggcg ggggacgggt cggatgtggc gtatgtgatt
      181 tacacgtcgg gatccactgg tcgtccgaag ggggtggtga tcgagcactc ccaggtggtg
      241 gcgatgctgt cgtgggcggg ccgggtgttc gcggatgggg agttgtcgca gacgctggct
      301 gcgacgtcgg tgtcgttcga cctgtcggtg ttcgagatct tcgccccgct gtcggtgggc
      361 gggacggtcc atctcgtccc cgacaacgcg ctggatctga tcgcgcatcc gggccggtat
      421 gcggacgtga cgctggtgaa cacggtgccg tcggtggctc gggaactgct ggcggcgggt
      481 gcgatacctc ctcgggctcg gacggtgaac cttgcgggtg agccgttggc tccggggttg
      541 gtggcggagt tgtatgcgct tccggtgatc ggtgtggtga acaatctgta cgggccgagc
      601 gaggacacca cctactccac gcatgcggtc accgctcccg gtgacgcccg cacacccatc
      661 ggccggcccg tggacggcac acgagtgcat gtcctggacg ggtgtctgcg gccggtagtg
      721 gtaggtgcgg tgggggagct gtatctgtcg ggggccggtg tcacccgtgg ttatcacgcc
      781 cggcccgcac tgaccgccca gcggtacctt cccgacccgt tctcctcgga gggcggcagg
      841 atgtatcgga cgggggatct cgtgcgctgg cgtcctgacg ggcagttgga gtatctgggc
      901 cgggccgacg ggcaggtgaa gatccgcggt caccgtgtcg agctcggcga ggtcgaggag
      961 gtcctgcgcc ggcacccgca cgtctccgag gcggtggtcg tcgcccgccc ggacgtcacc
     1021 gggtcactgc ggctggtcgg ttacgttgtc gccgacgagg cgggcggtga cgtcccctcc
     1081 gacctgccct ctcacgcacg tgcctggctc ccggacttca tggtcccctc ggctctggtc
     1141 gccctgaggg agtttcccct cctccccaac gggaagatcg accgctccgc tctccccgac
     1201 cccgaacccg gcgcagaccg cgcctccttc cgccccccgt ccgggccggc cgaggaactg
     1261 atcgcccgcg tctggagcga actcctcggc atcaccggaa tcagcgcgga cgacgacttc
     1321 ttcgccctgg gcggccactc cctcctcgcc acccggctca cccaccggct cggcgaggcc
     1381 ctcggcgccc acataccgct ccacctcgtc ttcgaacacc ccaccctcac cgacctcgcc
     1441 gcccacctcc ccgaaggcac ggagcaaggg cgtacaccgc cgatcacccc gctcgaccgc
     1501 gtcccggaac cggacggcac actcgtgctg ccgacatcgc ccggtcagga acgcctgtgg
     1561 gtccagtgcg cgcttgaccc ggaggccaac ctcgcctacc acatcagggg cgccgtgcac
     1621 ctccacgggc cgttggacga ggacgccttg gtcaccgccc tccgtcacct cgcgcgccgc
     1681 catgagagct tgcgtacctc gctgcgccag gtcgacggcg agcttcgcca ggttgtggca
     1741 cccgatcccg aagtgccgct gctccgaacc accaacgccg actgggaagc ggtgatcgac
     1801 gccgaaaccc ggcggcactt cgacctctcc gccggccccc tctggcacgt cacgctcgtc
     1861 agcgccgggc ccgagcacca cgtcgtcgtc atgagcctgc atcacgccat cgccgacggt
     1921 tggtccctag acatcatcct ccgtgagatc gcccagagtt acggcgcact cctgcacgcc
     1981 cccggcagcg aagccgtctc gcccgcgccc gtgcagtacg ccgaagcagc agcctggcag
     2041 cgcgaaacgg cgccggagaa cgcggagttc tggcggtccc acctggcggg tactacctcg
     2101 gccggcctgc cgaccgaccg accccgtccc cctcggcaga cctaccgagg tgacgcggtc
     2161 ccactgaacc ttccgcagaa agcactggcc ggcgcggcac ggaaggcggc gaccacctcg
     2221 ttcaccgtcc tcgcgacagc ccttgccgtc gtcctcgtca agctcacgga ccggtacgac
     2281 gtgaccctcg gcattccagt cgccggccgc gaccacccgg acacggcgga ggtcgtgggc
     2341 tacctcgtcg acacgttgcc gctccatctg cgcccggatc cgcaggccac cctcgccgag
     2401 accctggacg tgacccgggc actcgtggac gacgtccgcg cccacccgcg catccccctc
     2461 gaggaactgc tccgcgaagc acgcccccac ggcgaccgcg gcccgctgtt ccaggtgttg
     2521 ctggccgtca acgggacgcc gccccgttac gaactggccg gcctggagat gaccccggct
     2581 cccgttccgt tccgcaccac cccttacgac ctggtcgtcc aggcggagga acgcgacggc
     2641 cgggtcaccg ggcacctgct cttcaacacc gacttgttcg agcgctccac cgcacagctc
     2701 atcgcggacc ggctcgccac cgcggtccac gccctggccg acggtcccac cctgactgtc
     2761 gccgaggtgg atgtgcggtc ggtgggggag cgcgagtggg tggccgcggt gtcggcgggt
     2821 gtgccgttgg cgggtgg
//
