LOCUS       NZ_QZFU01000037         2918 bp    DNA     linear   CON 08-AUG-2024
DEFINITION  Nocardia panacis strain YIM PH 21724 NODE_657, whole genome shotgun
            sequence.
ACCESSION   NZ_QZFU01000037
VERSION     NZ_QZFU01000037.1
KEYWORDS    WGS; RefSeq.
SOURCE      Nocardia panacis
  ORGANISM  Nocardia panacis
            Bacteria; Actinomycetota; Actinomycetes; Mycobacteriales;
            Nocardiaceae; Nocardia.
REFERENCE   1  (bases 1 to 2918)
  AUTHORS   Miao,C.
  TITLE     YIM PH21274 draft genome
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2918)
  AUTHORS   Miao,C.
  TITLE     Direct Submission
  JOURNAL   Submitted (19-SEP-2018) Yunnan University, Yunnan Institute of
            Microbiology, 121, Kunming 650091, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: SPAdes v. 3.5.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 29.0x
            Sequencing Technology             :: Illumina HiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_003598715.1-RS_2024_08_08
            Annotation Date                   :: 08/08/2024 03:06:18
            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)                     :: 6,880
            CDSs (total)                      :: 6,804
            Genes (coding)                    :: 6,707
            CDSs (with protein)               :: 6,707
            Genes (RNA)                       :: 76
            rRNAs                             :: 4, 5, 4 (5S, 16S, 23S)
            complete rRNAs                    :: 2, 1, 1 (5S, 16S, 23S)
            partial rRNAs                     :: 2, 4, 3 (5S, 16S, 23S)
            tRNAs                             :: 60
            ncRNAs                            :: 3
            Pseudo Genes (total)              :: 97
            CDSs (without protein)            :: 97
            Pseudo Genes (ambiguous residues) :: 0 of 97
            Pseudo Genes (frameshifted)       :: 32 of 97
            Pseudo Genes (incomplete)         :: 82 of 97
            Pseudo Genes (internal stop)      :: 7 of 97
            Pseudo Genes (multiple problems)  :: 22 of 97
            CRISPR Arrays                     :: 6
            ##Genome-Annotation-Data-END##
            ##antiSMASH-Data-START##
            Version                           :: 8.dev-cf2fc5ee(changed)
            Run date                          :: 2025-09-12 20:26:29
            NOTE :: This is a single region extracted from a larger record!
            Orig. start                       :: 0
            Orig. end                         :: 2918
            ##antiSMASH-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            QZFU01000037.1.
            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..2918
                     /collection_date="2015-05-12"
                     /db_xref="taxon:2340916"
                     /geo_loc_name="China"
                     /isolation_source="soil"
                     /mol_type="genomic DNA"
                     /organism="Nocardia panacis"
                     /strain="YIM PH 21724"
                     /submitter_seqid="NODE_657"
                     /type_material="type material of Nocardia panacis"
     region          1..2918
                     /candidate_cluster_numbers="1"
                     /contig_edge="True"
                     /product="T1PKS"
                     /region_number="1"
                     /rules="cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or
                     hyb_KS or itr_KS or tra_KS))"
                     /tool="antismash"
     cand_cluster    1..2918
                     /SMILES=""
                     /candidate_cluster_number="1"
                     /contig_edge="True"
                     /detection_rules="cds(PKS_AT and (PKS_KS or ene_KS or
                     mod_KS or hyb_KS or itr_KS or tra_KS))"
                     /kind="single"
                     /product="T1PKS"
                     /protoclusters="1"
                     /tool="antismash"
     protocluster    1..2918
                     /aStool="rule-based-clusters"
                     /category="PKS"
                     /contig_edge="True"
                     /core_location="[41:>2918](+)"
                     /cutoff="20000"
                     /detection_rule="cds(PKS_AT and (PKS_KS or ene_KS or mod_KS
                     or hyb_KS or itr_KS or tra_KS))"
                     /neighbourhood="20000"
                     /product="T1PKS"
                     /protocluster_number="1"
                     /tool="antismash"
     proto_core      42..>2918
                     /aStool="rule-based-clusters"
                     /tool="antismash"
                     /cutoff="20000"
                     /detection_rule="cds(PKS_AT and (PKS_KS or ene_KS or mod_KS
                     or hyb_KS or itr_KS or tra_KS))"
                     /neighbourhood="20000"
                     /product="T1PKS"
                     /protocluster_number="1"
     gene            42..>2918
                     /locus_tag="D5S18_RS27945"
                     /old_locus_tag="D5S18_27935"
     CDS             42..>2918
                     /NRPS_PKS="Domain: PKS_AT (179-478). E-value: 1.1e-104.
                     Score: 342.0. Matches aSDomain:
                     nrpspksdomains_D5S18_RS27945_PKS_AT.1"
                     /NRPS_PKS="Domain: PKS_DH (545-721). E-value: 1.1e-56.
                     Score: 183.7. Matches aSDomain:
                     nrpspksdomains_D5S18_RS27945_PKS_DH.1"
                     /codon_start=1
                     /gene_functions="biosynthetic (rule-based-clusters) T1PKS:
                     mod_KS"
                     /gene_functions="biosynthetic (rule-based-clusters) T1PKS:
                     PKS_AT"
                     /gene_functions="biosynthetic-additional (smcogs)
                     SMCOG1021: malonyl CoA-acyl carrier protein transacylase"
                     /gene_kind="biosynthetic"
                     /inference="COORDINATES: protein motif:HMM:NF012901.4"
                     /locus_tag="D5S18_RS27945"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /old_locus_tag="D5S18_27935"
                     /product="type I polyketide synthase"
                     /protein_id="WP_239004051.1"
                     /sec_met_domain="mod_KS (E-value: 2.4e-33, bitscore: 101.6,
                     seeds: 217, tool: rule-based-clusters)"
                     /sec_met_domain="PKS_AT (E-value: 1.8e-106, bitscore:
                     342.0, seeds: 1682, tool: rule-based-clusters)"
                     /transl_table=11
                     /translation="MIKMVMAMRHGVLPPTLHADEPTPHVDWSSGGLRLLTESTPWGED
                     GRTRRAAVSSFGISGTNAHVILEQAPALEGADSQPNVVPVNAVNTLVPLLISAKNKEGL
                     EEQAQRLRSFLSDQPELDLGVVAYALANERAVFEYRAVVLGADRSDLLAGLETVAAGGD
                     SANVVRGQARGGKVAFVFPGQGAQWAGMGAALLDFSPVFAEQVRACAAALAGYVDWSLE
                     DALRQVPGAADLDRVDVVQPLSFAVMVSLAALWRSYGVEPSMVVGHSQGEIAAAYVAGA
                     LSLEDAARVVALRSKALLEVSGRGGMVAVSLPVEQLADRIRRWGEAISIAALNGPGSVV
                     VSGEVTALGELLESLEADGVHTREIPVDYASHSAQMETIRDTVIESLAPIRPRLSVVPF
                     YSTVTGGLFDTNGLTAEYWYRSLRQTVLFQDATAVVLGQGCRALIEVSSHPVLKTAVQA
                     TIEVGADGDAAAVLGSLRRDDGGLHRFATSLAEAFTCGVGVDWGRWFGPVRPGRVELPG
                     YAFQHRRFWLGSRSSAGDAASVGLSRVDHPFVGAGVALGDGRGWLFTGRLSLQVHGWLA
                     DHAVLGTVLFPGTGFLEWAFAAGGRVGAEVVEDLTVQAPLVLAEHGAVQMQLCLGEADA
                     HGRRPFDIYSRPESSGGTETGPWTHHATGVLSTNEVGGRGSSESLAQELFVGSAWPPAG
                     AVSADIDALYERLAGIGVVYGPAFQGLRAAWRRGEEVFAEVEIDQEHAEESRRFGLHPA
                     LFDSAFHVALDVLGAGDEPGRTPLLFSWSRVTLHVPGATRLRVRVVGVGADGYRLTGWD
                     DSGELVVTVETLIARPVDTAALAIARGNHEDLYRLGWEQLDPQQIGGQQIRAGSEGNAL
                     RVAVIEQTDHIASSTNFTTNLTGDLASDLAADCYADVGELVDAVAGGLPVPDVVVVPFT
                     GAFADGDADLADGGLVSVVKANTYGLLGL"
     CDS_motif       576..629
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_D5S18_RS27945_0001"
                     /evalue="5.00E-09"
                     /label="PKSI-AT-mM_m1"
                     /locus_tag="D5S18_RS27945"
                     /protein_end="196"
                     /protein_start="178"
                     /score="27.9"
                     /tool="antismash"
                     /translation="FVFPGQGAQWAGMGAALL"
     aSDomain        579..1475
                     /ASF="Methylmalonyl-CoA specific"
                     /ASF="found active site serine: True, scaffold matched
                     GHGE: True"
                     /aSDomain="PKS_AT"
                     /aSTool="nrps_pks_domains"
                     /database="nrpspksdomains.hmm"
                     /detection="hmmscan"
                     /domain_id="nrpspksdomains_D5S18_RS27945_PKS_AT.1"
                     /evalue="1.10E-104"
                     /label="D5S18_RS27945_PKS_AT.1"
                     /locus_tag="D5S18_RS27945"
                     /protein_end="478"
                     /protein_start="179"
                     /score="342.0"
                     /specificity="substrate consensus: mmal"
                     /specificity="PKS signature: Methylmalonyl-CoA"
                     /specificity="Minowa: mmal"
                     /tool="antismash"
                     /translation="VFPGQGAQWAGMGAALLDFSPVFAEQVRACAAALAGYVDWSLEDA
                     LRQVPGAADLDRVDVVQPLSFAVMVSLAALWRSYGVEPSMVVGHSQGEIAAAYVAGALS
                     LEDAARVVALRSKALLEVSGRGGMVAVSLPVEQLADRIRRWGEAISIAALNGPGSVVVS
                     GEVTALGELLESLEADGVHTREIPVDYASHSAQMETIRDTVIESLAPIRPRLSVVPFYS
                     TVTGGLFDTNGLTAEYWYRSLRQTVLFQDATAVVLGQGCRALIEVSSHPVLKTAVQATI
                     EVGADGDAAAVLGSLRRD"
     aSModule        579..2204
                     /domains="nrpspksdomains_D5S18_RS27945_PKS_AT.1"
                     /domains="nrpspksdomains_D5S18_RS27945_PKS_DH.1"
                     /incomplete
                     /locus_tags="D5S18_RS27945"
                     /starter_module
                     /tool="antismash"
                     /type="pks"
     CDS_motif       741..812
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_D5S18_RS27945_0002"
                     /evalue="1.40E-10"
                     /label="PKSI-AT-mM_m2"
                     /locus_tag="D5S18_RS27945"
                     /protein_end="257"
                     /protein_start="233"
                     /score="33.2"
                     /tool="antismash"
                     /translation="LDRVDVVQPLSFAVMVSLAALWRS"
     CDS_motif       816..926
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_D5S18_RS27945_0003"
                     /evalue="5.90E-20"
                     /label="PKSI-AT-mM_m3"
                     /locus_tag="D5S18_RS27945"
                     /protein_end="295"
                     /protein_start="258"
                     /score="63.0"
                     /tool="antismash"
                     /translation="GVEPSMVVGHSQGEIAAAYVAGALSLEDAARVVALRS"
     CDS_motif       1032..1070
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_D5S18_RS27945_0004"
                     /evalue="1.60E-03"
                     /label="PKSI-AT-M_m5"
                     /locus_tag="D5S18_RS27945"
                     /protein_end="343"
                     /protein_start="330"
                     /score="11.8"
                     /tool="antismash"
                     /translation="AALNGPGSVVVSG"
     CDS_motif       1140..1172
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_D5S18_RS27945_0005"
                     /evalue="1.90E-04"
                     /label="PKSI-AT-mM_m6"
                     /locus_tag="D5S18_RS27945"
                     /protein_end="377"
                     /protein_start="366"
                     /score="14.0"
                     /tool="antismash"
                     /translation="VDYASHSAQME"
     CDS_motif       1278..1325
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_D5S18_RS27945_0006"
                     /evalue="1.90E-03"
                     /label="PKSI-AT-mM_m8"
                     /locus_tag="D5S18_RS27945"
                     /protein_end="428"
                     /protein_start="412"
                     /score="10.9"
                     /tool="antismash"
                     /translation="LTAEYWYRSLRQTVLF"
     aSDomain        1677..2204
                     /ASF="catalytic triad H,G,P inconclusive"
                     /aSDomain="PKS_DH"
                     /aSTool="nrps_pks_domains"
                     /database="nrpspksdomains.hmm"
                     /detection="hmmscan"
                     /domain_id="nrpspksdomains_D5S18_RS27945_PKS_DH.1"
                     /evalue="1.10E-56"
                     /label="D5S18_RS27945_PKS_DH.1"
                     /locus_tag="D5S18_RS27945"
                     /protein_end="721"
                     /protein_start="545"
                     /score="183.7"
                     /tool="antismash"
                     /translation="HPFVGAGVALGDGRGWLFTGRLSLQVHGWLADHAVLGTVLFPGTG
                     FLEWAFAAGGRVGAEVVEDLTVQAPLVLAEHGAVQMQLCLGEADAHGRRPFDIYSRPES
                     SGGTETGPWTHHATGVLSTNEVGGRGSSESLAQELFVGSAWPPAGAVSADIDALYERLA
                     GIGVVYGPAFQGL"
     CDS_motif       1761..1838
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_D5S18_RS27945_0007"
                     /evalue="2.90E-10"
                     /label="PKSI-DH_m2"
                     /locus_tag="D5S18_RS27945"
                     /protein_end="599"
                     /protein_start="573"
                     /score="32.6"
                     /tool="antismash"
                     /translation="WLADHAVLGTVLFPGTGFLEWAFAAG"
ORIGIN
        1 ccaatatcgg tcacactcag gcggctgcgg gggtggctgg tgtgatcaag atggtgatgg
       61 cgatgcggca tggggtgctg ccgccgacgt tgcatgcgga tgagccgact ccgcatgtgg
      121 attggtcgag tggtggattg cggttgttga ccgagtccac tccgtggggc gaggacgggc
      181 gaacccgacg agcagcggtg tcctcgttcg gtatcagcgg taccaacgca catgtcattc
      241 tcgaacaggc acccgccctt gaaggcgcgg acagccagcc gaacgtagtc cctgtgaatg
      301 ccgtgaatac tctggtgccg ctgttgattt cggcgaagaa caaggaaggg ctcgaggagc
      361 aggcacagcg tttacggtcg ttcctttctg atcagccgga gctcgatctc ggtgtggtgg
      421 cttatgccct agccaacgag cgggcggtgt tcgagtatcg ggctgtggta ctcggtgcgg
      481 atcggtcgga tttgctggcg gggttggaaa ccgttgctgc tggtggggat tcggcgaatg
      541 tggttcgggg acaagctcgt gggggcaagg tcgcgttcgt ctttcctggc caaggagcac
      601 agtgggctgg gatgggagct gcgttgctgg atttttcgcc ggtgttcgct gagcaggtac
      661 gggcgtgcgc ggccgcgttg gctggctatg tggattggtc gttggaggat gcgctgcgtc
      721 aggttccagg tgcggcggac ctggaccgtg tcgatgtggt gcaaccgctt tcgttcgcgg
      781 tgatggtgtc gttggcggcg ttgtggcgtt cgtacggggt ggaaccgtcg atggtggtgg
      841 ggcattcgca gggggagatc gctgctgcgt atgtggcggg tgcgctgagc cttgaggatg
      901 ccgcccgggt ggtggcgttg cgtagcaaag cattgctgga ggtgtcgggc cgcggtggga
      961 tggtcgcggt gtcgctgccg gtggaacaac tggccgaccg tattcggcgg tggggtgagg
     1021 cgatctcgat agcggcgttg aacgggcctg gctcggtggt ggtttccggt gaggtgactg
     1081 cgctgggcga gctgttggag tcgttggaag ccgatggggt ccatacccgt gaaattccgg
     1141 ttgactatgc ctcacattcg gcgcagatgg agacgatccg tgacacggtg atcgagtctt
     1201 tggctccgat ccggccgcgc ttgtcggtcg tgccgttcta ttcgacggtg actggtgggt
     1261 tgtttgatac caatgggctg actgcggagt attggtatcg cagcctacgc cagacggtgt
     1321 tattccagga cgcgactgct gttgtgctgg gccaaggttg tcgagcgttg atcgaggtca
     1381 gctcccatcc ggtgttgaag actgcggtac aagcgacaat cgaggtcggc gcggacggtg
     1441 acgcggcggc ggtactgggt tcgttgcgtc gtgacgatgg tgggctgcat cggtttgcta
     1501 cctcgttggc tgaggcgttc acctgtggtg tgggggtgga ttggggccga tggttcggtc
     1561 cggttcgccc ggggcgggtg gagcttcctg gttatgcgtt ccagcatcgc cggttttggc
     1621 tcgggtctcg ttcgagtgcc ggggatgcgg cgtcggtggg tttgtcgcgg gtcgatcatc
     1681 cgttcgtggg tgcgggcgtg gctctcgggg atggtcgggg gtggttgttt accggccggt
     1741 tgtcgttgca ggtgcatggg tggttggctg atcacgcagt gctgggcaca gtgttgtttc
     1801 ctgggacggg gttcctggag tgggcgttcg ctgctggggg cagggtcggg gccgaggttg
     1861 tcgaggatct gactgtccag gcaccgctgg tgttggctga gcacggtgcg gtgcagatgc
     1921 agttgtgcct gggtgaggcc gatgcccacg ggcgtcgtcc gttcgatatc tattcgcgtc
     1981 cggagtcttc cggggggact gagaccggtc cgtggacaca ccacgccacc ggggtcttgt
     2041 ccaccaatga ggttggtgga cgggggagtt cggaatcgct ggctcaggag ctgtttgtgg
     2101 gatcggcgtg gccgcccgct ggagcggtat cggcggatat cgacgcactg tatgagcgtt
     2161 tggccggaat cggggtggtc tatggtccgg ctttccaagg attgcgggcg gcgtggcgtc
     2221 gtggtgagga ggtgttcgcc gaggtcgaga tcgaccagga gcacgccgag gaaagtcgcc
     2281 ggttcgggtt gcatccggca ttgttcgatt ccgcgttcca cgtggcgttg gatgtgttgg
     2341 gtgccgggga tgagccgggg cggacaccgc tgctgttctc ttggtcgagg gtaactctgc
     2401 atgtaccggg cgccacgcgg ttgcgggtgc gtgtggtggg tgtcggagcc gatggctacc
     2461 gacttaccgg gtgggacgac tccggtgaac tggtggtcac ggtcgagacg ttgattgctc
     2521 gcccggtcga taccgccgcg ctcgcgatcg ctcgcggtaa ccacgaagac ctctatcgac
     2581 tcggctggga gcaattggac ccgcaacaga ttggcggaca acagatccgg gccggttctg
     2641 agggcaatgc cttgcgcgtt gccgttatcg agcagacgga ccacatcgcg tccagcacta
     2701 atttcactac taatctgact ggtgatttgg ctagtgatct cgctgcggac tgttacgcag
     2761 atgtgggcga gctcgttgat gctgtggccg gggggttgcc ggtgccggat gtggtggtgg
     2821 tgccgttcac cggtgcgttt gctgatggcg atgctgatct cgcggatggt gggttggtgt
     2881 cggtggtgaa ggcgaatacg tatgggttgt tgggtttg
//
