LOCUS       NZ_QZFU01000038         2861 bp    DNA     linear   CON 08-AUG-2024
DEFINITION  Nocardia panacis strain YIM PH 21724 NODE_664, whole genome shotgun
            sequence.
ACCESSION   NZ_QZFU01000038
VERSION     NZ_QZFU01000038.1
KEYWORDS    WGS; RefSeq.
SOURCE      Nocardia panacis
  ORGANISM  Nocardia panacis
            Bacteria; Actinomycetota; Actinomycetes; Mycobacteriales;
            Nocardiaceae; Nocardia.
REFERENCE   1  (bases 1 to 2861)
  AUTHORS   Miao,C.
  TITLE     YIM PH21274 draft genome
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2861)
  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                         :: 2861
            ##antiSMASH-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            QZFU01000038.1.
            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..2861
                     /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_664"
                     /type_material="type material of Nocardia panacis"
     region          1..2861
                     /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..2861
                     /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..2861
                     /aStool="rule-based-clusters"
                     /category="PKS"
                     /contig_edge="True"
                     /core_location="[5:>2861](+)"
                     /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      6..>2861
                     /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            6..>2861
                     /locus_tag="D5S18_RS27950"
                     /old_locus_tag="D5S18_27940"
     CDS             6..>2861
                     /NRPS_PKS="Domain: PKS_AT (195-494). E-value: 4.4e-106.
                     Score: 346.5. Matches aSDomain:
                     nrpspksdomains_D5S18_RS27950_PKS_AT.1"
                     /NRPS_PKS="Domain: PKS_DH (561-734). E-value: 5.4e-55.
                     Score: 178.2. Matches aSDomain:
                     nrpspksdomains_D5S18_RS27950_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_RS27950"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /old_locus_tag="D5S18_27940"
                     /product="type I polyketide synthase"
                     /protein_id="WP_282434897.1"
                     /sec_met_domain="mod_KS (E-value: 5.5e-42, bitscore: 130.1,
                     seeds: 217, tool: rule-based-clusters)"
                     /sec_met_domain="PKS_AT (E-value: 7.3e-108, bitscore:
                     346.5, seeds: 1682, tool: rule-based-clusters)"
                     /transl_table=11
                     /translation="MGHTQAAAGVAGVIKMVMAMRHGVLPPTLHADEPTPHVDWSSGGL
                     RLLTESTPWGEDGRTRRAAVSSFGISGTNAHVILEQTPAQEPVLEGEDDGQRTVIANAV
                     NAPAPLLISAKNKDGLKEQAQRLRSFLGDHPELDLGAVAYALVNDRAVFEYRAAVLGVD
                     RSDLLAGLDTLVGGGVAAGAVQGQAREGRMAFVFPGQGAQWEGMAAELLDSSPVFAGEI
                     RACATALAPYTDWSLEDVLRQVPGAACLDRVDVVQPVSFAVMVSLAALWRSYGVEPSMV
                     VGHSQGEIAAAYVAGALDLDDAARVVALRSKAILAVSGRGGMVAVSLPAEELTKRIERW
                     GDDISIAALNGPGLVVVSGGVSALTELLESLESDGVHARKIPVDYASHSAQMESIRATV
                     IEALTPIEPHSSKVPFYSTVTGDLLDTEALTAEYWYRSLRQTVLFEDATVVVLDQGCRA
                     LIEVSSHPVLTTAIRATIEAGDNSDSVSVLGSLRRGEGNLARFAMSLADAFVCGVGVDW
                     GRWFGAVRRGRVELPGYAFQHRRFWRESRSGGAGIQSVGLSRVDHPLVGAGVNLGDGRG
                     WLFTGRLSLDKHAWLADHAVSGTVLFPGTGFIEWALVASAQVGAGVVEELTVLKPLVLT
                     EHTAVQMQLTVGEVSGEGRRSFDIYSRPEHPSGAEAGQGQWTHHASGALVSGDAGAQEH
                     SELLAGSLWPPADATAVEIGSMYERLAGIGVVYGPAFQGVRAAWQHGDEVFAEVEMGEE
                     QAVQSGRFGIHPALLDAAFHVALDVLGVKSEPGRTPLPFSWSGVGVQGSGVSRLRVRVA
                     AVGPDAYRLTGWDESGEVVVSVEALTARAVDVAQLEAARGGHEDLYRRGWEQIQVRTGT
                     GADGLRVVTVGETDRVTITAGLAADRHSDLAALAESLVEGLPVPDVVVVPFTGAFADGD
                     ADLADGGLVSVVKANTYGLLGL"
     CDS_motif       9..68
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_D5S18_RS27950_0001"
                     /evalue="5.20E-01"
                     /label="PKSI-AT-mM_m3"
                     /locus_tag="D5S18_RS27950"
                     /protein_end="21"
                     /protein_start="1"
                     /score="3.5"
                     /tool="antismash"
                     /translation="GHTQAAAGVAGVIKMVMAMR"
     CDS_motif       588..641
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_D5S18_RS27950_0002"
                     /evalue="2.80E-09"
                     /label="PKSI-AT-mM_m1"
                     /locus_tag="D5S18_RS27950"
                     /protein_end="212"
                     /protein_start="194"
                     /score="28.6"
                     /tool="antismash"
                     /translation="FVFPGQGAQWEGMAAELL"
     aSDomain        591..1487
                     /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_RS27950_PKS_AT.1"
                     /evalue="4.40E-106"
                     /label="D5S18_RS27950_PKS_AT.1"
                     /locus_tag="D5S18_RS27950"
                     /protein_end="494"
                     /protein_start="195"
                     /score="346.5"
                     /specificity="substrate consensus: mmal"
                     /specificity="PKS signature: Methylmalonyl-CoA"
                     /specificity="Minowa: mmal"
                     /tool="antismash"
                     /translation="VFPGQGAQWEGMAAELLDSSPVFAGEIRACATALAPYTDWSLEDV
                     LRQVPGAACLDRVDVVQPVSFAVMVSLAALWRSYGVEPSMVVGHSQGEIAAAYVAGALD
                     LDDAARVVALRSKAILAVSGRGGMVAVSLPAEELTKRIERWGDDISIAALNGPGLVVVS
                     GGVSALTELLESLESDGVHARKIPVDYASHSAQMESIRATVIEALTPIEPHSSKVPFYS
                     TVTGDLLDTEALTAEYWYRSLRQTVLFEDATVVVLDQGCRALIEVSSHPVLTTAIRATI
                     EAGDNSDSVSVLGSLRRG"
     aSModule        591..2207
                     /domains="nrpspksdomains_D5S18_RS27950_PKS_AT.1"
                     /domains="nrpspksdomains_D5S18_RS27950_PKS_DH.1"
                     /incomplete
                     /locus_tags="D5S18_RS27950"
                     /starter_module
                     /tool="antismash"
                     /type="pks"
     CDS_motif       753..824
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_D5S18_RS27950_0003"
                     /evalue="2.40E-11"
                     /label="PKSI-AT-mM_m2"
                     /locus_tag="D5S18_RS27950"
                     /protein_end="273"
                     /protein_start="249"
                     /score="35.5"
                     /tool="antismash"
                     /translation="LDRVDVVQPVSFAVMVSLAALWRS"
     CDS_motif       828..938
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_D5S18_RS27950_0004"
                     /evalue="3.30E-19"
                     /label="PKSI-AT-mM_m3"
                     /locus_tag="D5S18_RS27950"
                     /protein_end="311"
                     /protein_start="274"
                     /score="60.6"
                     /tool="antismash"
                     /translation="GVEPSMVVGHSQGEIAAAYVAGALDLDDAARVVALRS"
     CDS_motif       1044..1082
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_D5S18_RS27950_0005"
                     /evalue="1.70E-03"
                     /label="PKSI-AT-M_m5"
                     /locus_tag="D5S18_RS27950"
                     /protein_end="359"
                     /protein_start="346"
                     /score="11.7"
                     /tool="antismash"
                     /translation="AALNGPGLVVVSG"
     CDS_motif       1152..1184
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_D5S18_RS27950_0006"
                     /evalue="1.90E-04"
                     /label="PKSI-AT-mM_m6"
                     /locus_tag="D5S18_RS27950"
                     /protein_end="393"
                     /protein_start="382"
                     /score="14.0"
                     /tool="antismash"
                     /translation="VDYASHSAQME"
     CDS_motif       1290..1337
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_D5S18_RS27950_0007"
                     /evalue="1.80E-03"
                     /label="PKSI-AT-mM_m8"
                     /locus_tag="D5S18_RS27950"
                     /protein_end="444"
                     /protein_start="428"
                     /score="10.9"
                     /tool="antismash"
                     /translation="LTAEYWYRSLRQTVLF"
     aSDomain        1689..2207
                     /ASF="catalytic triad H,G,P inconclusive"
                     /aSDomain="PKS_DH"
                     /aSTool="nrps_pks_domains"
                     /database="nrpspksdomains.hmm"
                     /detection="hmmscan"
                     /domain_id="nrpspksdomains_D5S18_RS27950_PKS_DH.1"
                     /evalue="5.40E-55"
                     /label="D5S18_RS27950_PKS_DH.1"
                     /locus_tag="D5S18_RS27950"
                     /protein_end="734"
                     /protein_start="561"
                     /score="178.2"
                     /tool="antismash"
                     /translation="HPLVGAGVNLGDGRGWLFTGRLSLDKHAWLADHAVSGTVLFPGTG
                     FIEWALVASAQVGAGVVEELTVLKPLVLTEHTAVQMQLTVGEVSGEGRRSFDIYSRPEH
                     PSGAEAGQGQWTHHASGALVSGDAGAQEHSELLAGSLWPPADATAVEIGSMYERLAGIG
                     VVYGPAFQGV"
     CDS_motif       1773..1847
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_D5S18_RS27950_0008"
                     /evalue="5.60E-11"
                     /label="PKSI-DH_m2"
                     /locus_tag="D5S18_RS27950"
                     /protein_end="614"
                     /protein_start="589"
                     /score="34.8"
                     /tool="antismash"
                     /translation="WLADHAVSGTVLFPGTGFIEWALVA"
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 tcgaacagac accggcgcag gaacccgtcc tcgaaggcga ggacgacggg cagcggacag
      301 tgatcgcgaa tgcagtgaat gccccagcac cactattgat ttcggcgaag aacaaggatg
      361 ggctcaagga gcaggcccag cgtttgcggt cgttccttgg cgatcacccg gagctggatc
      421 tcggtgctgt tgcatacgca ctggtcaacg atcgggctgt gttcgagtat cgggctgcgg
      481 tattgggcgt ggataggtcc gatctgctgg ccgggctgga caccctcgtg ggtggtgggg
      541 ttgcggcggg tgctgttcag ggacaggccc gtgaggggag aatggccttt gtctttcccg
      601 gccagggagc gcaatgggag ggtatggcag ccgagctgtt ggattcctcc ccggtgttcg
      661 ccggtgagat acgagcatgc gcaacagctc tcgccccgta tacggactgg tccttggagg
      721 acgttctacg gcaggtccca ggagcagctt gcctggatcg tgtcgatgtg gttcagccgg
      781 tctcgttcgc agtgatggtc tctctcgctg ccttatggcg atcgtacggt gtggagccgt
      841 cgatggtggt ggggcactca cagggagaaa tcgctgccgc gtatgtagcg ggagcgttgg
      901 acctcgacga cgcagctcgg gtcgtggcac tacgcagcaa agccatactt gcagtatcgg
      961 gccgaggggg aatggtcgcg gtttccttgc ctgcagaaga actcaccaaa cgtatcgagc
     1021 ggtggggcga tgacatttcg atagcggcat tgaacggccc aggtttagtg gtggtttccg
     1081 gtggagtgtc cgcactcact gaactgctcg aatccttgga atccgacggg gttcacgcgc
     1141 ggaagatacc ggtcgactat gcctcacatt ctgcccagat ggagtcgatc cgcgccacag
     1201 tgatcgaggc attgacgccg atcgaaccgc actcgagcaa ggtcccgttc tattccaccg
     1261 tcaccggcga tctgctcgat acagaggcgt tgacggcgga atactggtat cgcagcctcc
     1321 gtcaaacagt gttgttcgag gacgctaccg tcgtcgtgct cgaccaggga tgccgagcat
     1381 tgatcgaggt cagctcacat ccggtgttga ccacggcaat acgggcgacc attgaggctg
     1441 gtgacaacag cgattccgtc tcggtcctcg gttcactgcg ccgcggagaa ggcaaccttg
     1501 cacggttcgc aatgtcgctg gcggacgcgt ttgtgtgtgg ggtgggggtt gattggggtc
     1561 ggtggtttgg tgcggttcgc cggggccggg tggagcttcc tggttatgcg ttccagcatc
     1621 gccggttctg gcgcgagtca cggtcgggtg gagccggcat acagtcggtc ggcttgtcgc
     1681 gggtcgatca tccgcttgtg ggtgcgggtg tgaatctcgg ggatggccgg ggttggctat
     1741 tcaccggccg gttgtccctg gacaagcatg cgtggctggc cgatcacgca gtttcgggga
     1801 cagtgttgtt cccagggacc gggttcatcg agtgggcgtt ggtcgcgagt gcccaggtcg
     1861 gtgccggggt ggtcgaggaa ctgaccgtgc tgaagccgct ggtgttgacc gagcacacgg
     1921 ctgtgcagat gcaactcact gttggcgagg tgagcgggga ggggcgccgc agcttcgata
     1981 tctactcgcg gccggaacat ccttcagggg cggaagccgg gcaggggcag tggacacacc
     2041 acgccagcgg tgccctcgtc tcgggtgatg ccggtgctca agaacattcg gagttgttgg
     2101 cggggtcgct gtggccgcct gccgacgcca cggcggtgga gatcggttcg atgtatgagc
     2161 ggcttgcggg gatcggagtc gtttacggtc cggcgttcca gggtgtgcgc gcggcttggc
     2221 agcacggcga cgaggtcttc gccgaggtcg agatgggcga ggagcaggcc gtgcagagcg
     2281 gtcggttcgg tatacatccg gccttgctcg acgcggcgtt ccatgtcgcg ttggatgtgt
     2341 tgggtgtaaa gagtgagccg gggcggacgc cgctgccgtt ctcgtggtcg ggggtgggcg
     2401 tccaagggag cggtgtttcg cggttgcggg tgcgtgtggc ggctgtggga ccggatgctt
     2461 atcgactcac cggatgggac gagtcagggg aggtggtggt ttcggtcgag gcgttgactg
     2521 ctcgtgcggt cgatgtcgcg cagctcgagg ctgcccgtgg cggacatgag gatttgtatc
     2581 ggcgtggctg ggaacagatt caggtccgaa ctggtaccgg tgcggatggc ttgcgtgttg
     2641 tcacggtcgg ggagaccgat cgggtgacga tcaccgctgg tcttgccgct gatcgtcatt
     2701 ctgaccttgc tgcgttggcc gagtctctcg ttgaggggtt gccggtgccg gatgtggtgg
     2761 tggtgccgtt caccggtgcg tttgctgatg gcgatgctga tctcgcggat ggtgggttgg
     2821 tgtcggtggt gaaggcgaat acgtatgggt tgttgggttt g
//
