LOCUS       NZ_BMTZ01000052         4356 bp    DNA     linear   CON 02-SEP-2024
DEFINITION  Streptomyces variabilis strain JCM 4422 sequence52, whole genome
            shotgun sequence.
ACCESSION   NZ_BMTZ01000052
VERSION     NZ_BMTZ01000052.1
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 4356)
  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                         :: 4356
            ##antiSMASH-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            BMTZ01000052.1.
            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..4356
                     /culture_collection="JCM:4422"
                     /db_xref="taxon:67372"
                     /mol_type="genomic DNA"
                     /organism="Streptomyces variabilis"
                     /strain="JCM 4422"
                     /submitter_seqid="sequence52"
                     /type_material="type strain of Streptomyces variabilis"
     region          1..4356
                     /candidate_cluster_numbers="1"
                     /contig_edge="True"
                     /product="butyrolactone"
                     /region_number="1"
                     /rules="AfsA"
                     /tool="antismash"
     cand_cluster    1..4356
                     /candidate_cluster_number="1"
                     /contig_edge="True"
                     /detection_rules="AfsA"
                     /kind="single"
                     /product="butyrolactone"
                     /protoclusters="1"
                     /tool="antismash"
     protocluster    1..4356
                     /aStool="rule-based-clusters"
                     /category="other"
                     /contig_edge="True"
                     /core_location="[990:1977](-)"
                     /cutoff="20000"
                     /detection_rule="AfsA"
                     /neighbourhood="5000"
                     /product="butyrolactone"
                     /protocluster_number="1"
                     /tool="antismash"
     proto_core      complement(991..1977)
                     /aStool="rule-based-clusters"
                     /tool="antismash"
                     /cutoff="20000"
                     /detection_rule="AfsA"
                     /neighbourhood="5000"
                     /product="butyrolactone"
                     /protocluster_number="1"
     gene            complement(125..775)
                     /locus_tag="IE148_RS33160"
                     /old_locus_tag="GCM10010287_66850"
     CDS             complement(125..775)
                     /codon_start=1
                     /gene_functions="regulatory (smcogs) SMCOG1057: TetR family
                     transcriptional regulator"
                     /gene_kind="regulatory"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007387458.1"
                     /locus_tag="IE148_RS33160"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /old_locus_tag="GCM10010287_66850"
                     /product="ScbR family autoregulator-binding transcription
                     factor"
                     /protein_id="WP_189366868.1"
                     /transl_table=11
                     /translation="MAEQERAIRTRRTILFAAAKVFQEHGYQAATISQILAEAGVTKGA
                     LYFHFPSKEDLAQEVLLSQNQDFFVPDRPSKIQEIVDMVLLHTYRLQTDPLVQAAVRLS
                     LDELAHGVNRGESFIHWDNLLQERLEKAQAQGELLPHIVPAETSGVLVGAYTGIQSLSQ
                     ALSKHQDLSTRVTALLRHLLPSIAVPSILASVDMSQDRMLKLHADMTAQAQTQ"
     gene            complement(991..1977)
                     /locus_tag="IE148_RS33165"
                     /old_locus_tag="GCM10010287_66860"
     CDS             complement(991..1977)
                     /GO_function="GO:0016740 - transferase activity [Evidence
                     IEA]"
                     /codon_start=1
                     /gene_functions="biosynthetic (rule-based-clusters)
                     butyrolactone: AfsA"
                     /gene_kind="biosynthetic"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_008406753.1"
                     /locus_tag="IE148_RS33165"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /old_locus_tag="GCM10010287_66860"
                     /product="ScbA/BarX family gamma-butyrolactone biosynthesis
                     protein"
                     /protein_id="WP_189366869.1"
                     /sec_met_domain="AfsA (E-value: 4.8e-26, bitscore: 78.9,
                     seeds: 34, tool: rule-based-clusters)"
                     /transl_table=11
                     /translation="MSANTLRVEPATLGTQYAETDHRAAARPAAPRHPSLTTTVPKEFV
                     HRAGVAEVMLTGWERADECRFAVSAQWPRGHIFFTSVNGCHDPLIAAETLRQIGSLLAH
                     AEYGVPLGHHFLMWDLSLTVRPEHLLVGGAPASLDIDVVCEDVKMRRESLAGLRYTTVM
                     RRAGQVVATGGASFTCMTSKVYQRLRADRLDGAGPQLALTAPAAPQNVGRVSPTDVVLT
                     PVGRPGRWQLRVDTRHPVLFEHPVDHIPGMMLLEAARQAAVAAVGEDAMPLSITGEFSR
                     YAELDTPCVIEARRLPRTDQGHVVQVSGRQDGEAVFCSTVTVAAPGT"
     misc_feature    complement(2541..2558)
                     /note="TFBS match to ArcA, Repressor of carbon oxidation,
                     confidence: weak, score: 14.67"
                     /tool="antismash"
     misc_feature    2561..2570
                     /note="TFBS match to ToxT, Regulator of MSHA biosynthesis,
                     confidence: weak, score: 15.27"
                     /tool="antismash"
     gene            2669..3286
                     /locus_tag="IE148_RS33170"
                     /old_locus_tag="GCM10010287_66870"
     CDS             2669..3286
                     /codon_start=1
                     /gene_functions="regulatory (smcogs) SMCOG1057: TetR family
                     transcriptional regulator"
                     /gene_kind="regulatory"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_018554475.1"
                     /locus_tag="IE148_RS33170"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /old_locus_tag="GCM10010287_66870"
                     /product="ScbR family autoregulator-binding transcription
                     factor"
                     /protein_id="WP_189366871.1"
                     /transl_table=11
                     /translation="MVMQVRAARTRRALIVAAAEVFADEGYVKASLPLICRRAGVSPGA
                     LHFHFASKDALAATVEGAAVDSAQELAGRCRAAAATALESLVDTASALMLAMAADPVVR
                     AGFRLSGDPSRKGPAQLFTWWNASVCELVRHARDAGELARDVSPDDAAAVIVAATVGSG
                     TLAGWDEDWLSAGRAQRLWAFVLPRLAAPPGPAPGGEGEGLP"
     misc_feature    3421..3430
                     /note="TFBS match to ToxT, Regulator of MSHA biosynthesis,
                     confidence: weak, score: 13.63"
                     /tool="antismash"
     gene            3484..>4356
                     /locus_tag="IE148_RS33175"
     CDS             3484..>4356
                     /codon_start=1
                     /gene_functions="regulatory (smcogs) SMCOG1041:
                     transcriptional regulator, SARP family"
                     /gene_kind="regulatory"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005321575.1"
                     /locus_tag="IE148_RS33175"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /product="AfsR/SARP family transcriptional regulator"
                     /protein_id="WP_189366870.1"
                     /transl_table=11
                     /translation="MDIGILGSLAVGERGVSITPTAPKPRQVLALLALHADQVVTVGTL
                     TEELWGAAPPRSARPTLQTYILQLREHIACALRQGEGGGAGQRCAKDVLLTVPGGYLLK
                     GGQGASDLRDFERLAGLGYRAMDAGDYAGAAARLSEALELWTGPALADVHAGVHLATEI
                     RRLEESRLCALDQRIEADLRLGRHRELLAELTVLVSRYPTHESLCGQYMLALHRSGRRG
                     EALNAYRQLRARLVRSLGLEPSAALAKLQRSILVSGPAGAPAPPGMSAAGAPAPAGMSA
                     AGAPAPAGMS"
ORIGIN
        1 cgccgaggcg gcgcactggt acgcggctcg tctcgccggc cggggccggt cccgggcggg
       61 gcggggagcc gggccgggcg gcccggctgc ctgagccgcg ggccgggcgg gggaggctac
      121 tgggctactg ggtctgggct tgggctgtca tgtcggcgtg cagcttcagc atgcggtcct
      181 ggctcatgtc caccgaggcg aggatggagg ggaccgcgat gctgggcagc aggtggcgca
      241 gcagggcggt gacccttgtg ctgaggtcct ggtgcttgct gagggcctgg gagagggact
      301 ggatgcctgt gtaggcgccg acgaggacgc ccgaggtctc ggccggcacg atgtggggga
      361 gcagctcgcc ctgggcctgg gccttttcca gccgttcctg gagcaggttg tcccagtgga
      421 tgaacgactc gccgcggttg acgccgtggg ccagttcgtc cagggacagc cggaccgccg
      481 cctggaccag ggggtcggtc tgcaggcggt aggtgtgcag cagcaccatg tccacgatct
      541 cctggatctt ggacgggcgg tccggcacga agaagtcctg gttctgggag aggagcacct
      601 cctgggccag gtcctccttg gaggggaagt ggaagtagag cgcgcccttg gtgacgccgg
      661 cctccgcgag gatctgggag atcgtcgccg cctggtaccc gtgctcctgg aagaccttgg
      721 ccgcggcgaa caggatcgtc ctgcgtgtgc ggatggcccg ctcttgctca gccatgctgt
      781 cctccagtcg ttccacgtgc ccgggcgtac ccccgattgc aaaccatcca gtctgtattt
      841 taacagcccg tctccgtctg ccggtgatgg ccgccgtccg gaggagggga cccccggccg
      901 gaatcgcgcg gatcaggccg cgggcacacg tgcgggccgg ccggaaggcg ccgtccgcgc
      961 ccttccggcc ggcccgcggc cgtggcgggg tcaggtgccg ggcgccgcca cggtcacggt
     1021 ggagcagaag accgcctccc cgtcctgacg gccgctcacc tggacgacgt gcccctgatc
     1081 cgtgcgcggg aggcggcggg cctcgatcac gcagggcgtg tccagctcgg cgtagcggct
     1141 gaactccccg gtgatggaca ggggcatggc gtcctcgccg acggccgcca ccgcggcctg
     1201 ccgggcggcc tcgagcagca tcatgcccgg tatgtggtcc accgggtgct cgaagaggac
     1261 ggggtggcgg gtgtccaccc gcagctgcca gcggcccggc cggcccacgg gtgtcaggac
     1321 gacgtccgtc ggcgagacgc ggccgacgtt ctggggcgcc gccggagcgg tgagggcgag
     1381 ctgggggccg gcgccgtcca gccggtcggc acgcagccgc tggtagacct tggacgtcat
     1441 gcaggtgaag gaagcgccgc cggtcgcgac cacctgcccg gcgcggcgca tcaccgtcgt
     1501 gtagcgcagc ccggccaggc tctcccggcg catcttgacg tcctcgcaga cgacgtcgat
     1561 gtcgagggag gccggcgcgc cgccgacgag gaggtgttcg ggccgcaccg tgagcgacag
     1621 gtcccacatc aggaagtggt gaccgagcgg aaccccgtac tccgcgtggg ccagcagcga
     1681 accgatctgg cggagcgtct ccgccgcgat cagcgggtcg tggcagccgt tcacgctggt
     1741 gaagaagatg tgaccgcgag gccactgggc gctcacggcg aaccggcact cgtccgcgcg
     1801 ctcccagccg gtgagcatga cctcggcgac gccggcgcga tggacgaact ccttggggac
     1861 ggtggtggtc agagacggat ggcgcggtgc ggcgggtctc gccgccgccc ggtgatcggt
     1921 ctccgcgtac tgggtgccga gtgtcgcggg ctcgacgcgg agcgtgttcg cagacatcgc
     1981 ttgttccccc ttggccgcgt ggtgcggagg ttttgtgtgg gtcgctcagg ccgagaagat
     2041 acataccagc cggtttaatt tctagcggta tgagggactc cgctgtccgg gttttccgga
     2101 gtgatctata ccgttttgcc ggccgcccgc ttcggcggcc gaagaggcgc tccgggccgg
     2161 ctccctccct gcgggcgggt ggtccggaag gtgtccgcgg cgcgccgggg gaattgcggt
     2221 gacggcccgt ccgctcgtgc gggccccggc ggacaacgcc ggttccccca ggggttctcc
     2281 aggggttccc ggacgatttt ccgctgccgt ggacggcggt tcgcgcggga gcgggcgacg
     2341 ggagcgcgcg gctgccctgg gtgccccgtt cccccgcgcc gcggcggggc ggggcgccga
     2401 agggggcggg cgagggcggg cgggcggacg cctgccgtgc gccggccggg cgggcgccgg
     2461 gaagggcgca tccgggctcg agggcggctc gaaggcggct cgaggaaggc ctgatcgcgt
     2521 gagcggggca cttccgcccc gtaaaacaga cctatcatgc tgttttctga gaggggctcg
     2581 gcgtccggcc ggcctgcggg ggtgcgcgtg cacggcggac gtgcccgcgg cgggagcgga
     2641 ccggtccggc ccaggagggt gaagcgtgat ggtcatgcag gtacgggcgg cgcgcacgcg
     2701 ccgggcgctc atcgtcgcgg cggccgaggt cttcgccgac gagggctacg tcaaagcctc
     2761 cctgcccttg atctgcagac gggccggcgt gagtccgggg gccctgcatt tccacttcgc
     2821 cagcaaggac gccctggccg cgacggtgga gggcgcggcc gtggactcgg cgcaggagct
     2881 cgccggccgc tgtcgggccg cggccgcgac cgcgcttgag tcgctggtgg acaccgccag
     2941 cgccctcatg ctcgcgatgg ccgccgatcc cgtggtcagg gccgggttcc ggctgagcgg
     3001 cgacccttcc cgcaagggcc cggcgcagct gttcacgtgg tggaacgcct cggtgtgtga
     3061 actggtccgg cacgcgcggg acgcggggga actggcccgc gacgtctcgc ccgacgacgc
     3121 ggcggcggtg atcgtggccg ccacggtcgg ttccgggaca ctcgccgggt gggacgagga
     3181 ctggctctcg gccgggcgtg cgcaacggtt gtgggccttc gtcctgccgc gtctggcggc
     3241 accgcccgga ccggcccccg gcggtgaggg ggaggggctg ccttaaaggc ccgccgggcc
     3301 cgccgcgtcc ccggcgggcc gcgtggcggt ggcgtggtcc cggcggtggc tggagagcgg
     3361 ctcgagcggg gagggggtgt gcggtggggc cgctgaagcg cgttgacaaa ccgcatgcgc
     3421 tgttttttac tcgggcttct ggcacggcgt ttcacgaagc ctgcagcaga cgggggagac
     3481 agcgtggaca tcggcatact cggctcactg gccgtagggg agaggggcgt ttcgatcacg
     3541 ccgaccgccc ccaaaccacg gcaggtgctc gccctgctgg ccctgcacgc cgatcaggtc
     3601 gtgaccgtgg gcacgctgac cgaggagctc tggggcgcag cgccgccccg cagcgcgcgg
     3661 cccaccctgc agacgtacat cctccagctg cgcgagcaca tcgcctgcgc gctccggcag
     3721 ggcgagggcg gcggggcggg gcagcgctgc gccaaggacg tcctgctgac cgtccccggc
     3781 ggctacctgc tcaagggcgg gcagggcgcc agtgacctgc gggacttcga gcggctggcc
     3841 gggctcggct accgggccat ggacgccggg gactacgccg gggcagccgc ccggctgtcc
     3901 gaggcgctcg agctgtggac cgggcccgcg ctggccgacg tgcacgcggg cgtccacctg
     3961 gccaccgaga tcaggcggct cgaggagagc cggctgtgcg ccctcgacca gcgcatcgag
     4021 gccgacttga ggctcggccg gcaccgcgag ctgctcgccg aactgaccgt gctggtcagc
     4081 aggtacccca cccacgagag cctgtgcggc cagtacatgc tggccctgca ccgctcgggg
     4141 cgccggggcg aggcgctcaa cgcctaccgg cagctgcgcg cccggctggt gcgcagtctc
     4201 ggcctggagc cgtcggccgc actggccaag ctccagcgtt ccatcctggt gtccggtccg
     4261 gccggcgccc ccgcgccccc cggcatgtcc gccgccggcg cccccgcgcc cgccggcatg
     4321 tccgccgccg gcgcccccgc gcccgccggc atgtcc
//
