LOCUS       NZ_JAFJXZ010000023      3136 bp    DNA     linear   CON 03-JUN-2024
DEFINITION  Paenibacillus polymyxa strain Hob6 Scaffold_23, whole genome shotgun
            sequence.
ACCESSION   NZ_JAFJXZ010000023
VERSION     NZ_JAFJXZ010000023.1
KEYWORDS    WGS; RefSeq.
SOURCE      Paenibacillus polymyxa
  ORGANISM  Paenibacillus polymyxa
            Bacteria; Bacillota; Bacilli; Bacillales; Paenibacillaceae;
            Paenibacillus.
REFERENCE   1  (bases 1 to 3136)
  AUTHORS   Mahmoud,M. and Jabaji,S.
  TITLE     Draft genome sequence of Paenibacillus polymyxa strain Hob6,
            isolated from hemp (Cannabis sative) seeds' oil
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3136)
  AUTHORS   Mahmoud,M. and Jabaji,S.
  TITLE     Direct Submission
  JOURNAL   Submitted (24-FEB-2021) Plant Science Departement, McGill
            University, 21111 Lakeshore, te-Anne-de-Bellevue, Quebec H9X 3V9,
            Canada
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 22-JUL-2020
            Assembly Method                   :: SPAdes v. 3.12.0; Medusa v. 1.6
            Genome Representation             :: Full
            Expected Final Version            :: No
            Reference-guided Assembly :: GCA_000507205.2; GCA_014706575.1;
            GCA_000164985.2; GCA_000597985.1; GCA_002893885.1
            Genome Coverage                   :: 266.29x
            Sequencing Technology             :: Illumina HiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_017589695.1-RS_2024_06_03
            Annotation Date                   :: 06/03/2024 02:57:45
            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)                     :: 5,275
            CDSs (total)                      :: 5,119
            Genes (coding)                    :: 5,024
            CDSs (with protein)               :: 5,024
            Genes (RNA)                       :: 156
            rRNAs                             :: 21, 9, 15 (5S, 16S, 23S)
            complete rRNAs                    :: 19, 2 (5S, 16S)
            partial rRNAs                     :: 2, 7, 15 (5S, 16S, 23S)
            tRNAs                             :: 107
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 95
            CDSs (without protein)            :: 95
            Pseudo Genes (ambiguous residues) :: 0 of 95
            Pseudo Genes (frameshifted)       :: 44 of 95
            Pseudo Genes (incomplete)         :: 63 of 95
            Pseudo Genes (internal stop)      :: 13 of 95
            Pseudo Genes (multiple problems)  :: 21 of 95
            ##Genome-Annotation-Data-END##
            ##antiSMASH-Data-START##
            Version                           :: 8.dev-cf2fc5ee(changed)
            Run date                          :: 2025-09-13 06:07:16
            NOTE :: This is a single region extracted from a larger record!
            Orig. start                       :: 0
            Orig. end                         :: 3136
            ##antiSMASH-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            JAFJXZ010000023.1.
            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..>1035)
                     /locus_tag="JYU28_RS26725"
     CDS             complement(<1..1035)
                     /NRPS_PKS="Domain: AMP-binding (70-340). E-value: 1.5e-66.
                     Score: 216.6. Matches aSDomain:
                     nrpspksdomains_JYU28_RS26725_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_013371211.1"
                     /locus_tag="JYU28_RS26725"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /product="AMP-binding protein"
                     /protein_id="WP_209950386.1"
                     /sec_met_domain="AMP-binding (E-value: 6.1e-60, bitscore:
                     189.9, seeds: 400, tool: rule-based-clusters)"
                     /transl_table=11
                     /translation="MTALYKPETMTRLAQHFAEIVRAIAYHPQQPLATLNMVTVEEKEQ
                     LIYGFGEVGVTDGAAVEAGALFHTYVEEQAQLVPDHVAVVYEEEQLTYRKLNERANQLA
                     RRLRNEGVGRESIVGILSERSVDMLVGVLAVWKAGGAYVPLDADYPSERIRFMLEDSGA
                     TVLLTQIGLQEQAQIWLGESRQALAGGQTEGELETAAGAETMERDSLNENLGSKSDSKS
                     DSEAASEPATGLRLHTVLALDDESLYTGDTTDVDHINEPHDLAYVIYTSGTTGRPKGVM
                     IEHRSLVNTAAAYRRDYRLNQFPVRLLQLASFSFDVFVGDIARTLYNGGTMVICPKDDR
                     IDFSR"
     source          1..3136
                     /collected_by="Mohannad Mahmoud, Suha Jabaji"
                     /collection_date="2019-11-18"
                     /db_xref="taxon:1406"
                     /host="Cannabis sativa"
                     /identified_by="Mohannad Mahmoud"
                     /isolation_source="commercial industrial hemp seed oil"
                     /mol_type="genomic DNA"
                     /organism="Paenibacillus polymyxa"
                     /strain="Hob6"
                     /submitter_seqid="Scaffold_23"
     region          1..3136
                     /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..3136
                     /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..3136
                     /aStool="rule-based-clusters"
                     /category="NRPS"
                     /contig_edge="True"
                     /core_location="[<1135:3132](-)"
                     /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(<1136..3132)
                     /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(16..825)
                     /aSDomain="AMP-binding"
                     /aSTool="nrps_pks_domains"
                     /database="nrpspksdomains.hmm"
                     /detection="hmmscan"
                     /domain_id="nrpspksdomains_JYU28_RS26725_AMP-binding.1"
                     /evalue="1.50E-66"
                     /label="JYU28_RS26725_AMP-binding.1"
                     /locus_tag="JYU28_RS26725"
                     /protein_end="340"
                     /protein_start="70"
                     /score="216.6"
                     /specificity="substrate consensus: X"
                     /tool="antismash"
                     /translation="VEEQAQLVPDHVAVVYEEEQLTYRKLNERANQLARRLRNEGVGRE
                     SIVGILSERSVDMLVGVLAVWKAGGAYVPLDADYPSERIRFMLEDSGATVLLTQIGLQE
                     QAQIWLGESRQALAGGQTEGELETAAGAETMERDSLNENLGSKSDSKSDSEAASEPATG
                     LRLHTVLALDDESLYTGDTTDVDHINEPHDLAYVIYTSGTTGRPKGVMIEHRSLVNTAA
                     AYRRDYRLNQFPVRLLQLASFSFDVFVGDIARTLYNGGTMVICPKDDR"
     CDS_motif       complement(184..243)
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_JYU28_RS26725_0003"
                     /evalue="4.80E-12"
                     /label="NRPS-A_a3"
                     /locus_tag="JYU28_RS26725"
                     /protein_end="284"
                     /protein_start="264"
                     /score="37.4"
                     /tool="antismash"
                     /translation="AYVIYTSGTTGRPKGVMIEH"
     CDS_motif       complement(598..639)
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_JYU28_RS26725_0002"
                     /evalue="4.10E-07"
                     /label="NRPS-A_a2"
                     /locus_tag="JYU28_RS26725"
                     /protein_end="146"
                     /protein_start="132"
                     /score="22.8"
                     /tool="antismash"
                     /translation="LAVWKAGGAYVPLD"
     CDS_motif       complement(850..897)
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_JYU28_RS26725_0001"
                     /evalue="9.50E+01"
                     /label="NRPS-A_a3"
                     /locus_tag="JYU28_RS26725"
                     /protein_end="62"
                     /protein_start="46"
                     /score="-2.9"
                     /tool="antismash"
                     /translation="IYGFGEVGVTDGAAVE"
     assembly_gap    1036..1135
                     /estimated_length=100
                     /gap_type="within scaffold"
                     /linkage_evidence="align genus"
     CDS             complement(<1136..3132)
                     /GO_function="GO:0003824 - catalytic activity [Evidence
                     IEA]"
                     /NRPS_PKS="Domain: PCP (150-217). E-value: 1.8e-25. Score:
                     80.9. Matches aSDomain: nrpspksdomains_JYU28_RS26730_PCP.1"
                     /NRPS_PKS="Domain: Condensation_LCL (235-426). E-value:
                     4.6e-56. Score: 182.0. Matches aSDomain:
                     nrpspksdomains_JYU28_RS26730_Condensation_LCL.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: similar to AA
                     sequence:RefSeq:WP_003336314.1"
                     /locus_tag="JYU28_RS26730"
                     /note="frameshifted; incomplete; missing N-terminus and
                     C-terminus; Derived by automated computational analysis
                     using gene prediction method: Protein Homology."
                     /product="condensation domain-containing protein"
                     /pseudo=""
                     /sec_met_domain="AMP-binding (E-value: 9.6e-26, bitscore:
                     77.3, seeds: 400, tool: rule-based-clusters)"
                     /sec_met_domain="PP-binding (E-value: 3e-17, bitscore:
                     50.2, seeds: 164, tool: rule-based-clusters)"
                     /sec_met_domain="Condensation (E-value: 5.5e-48, bitscore:
                     150.6, seeds: 42, tool: rule-based-clusters)"
                     /transl_table=11
                     /translation="MKDPFAGGEAGYERMYRTGDLARWMPDGNIEYLGRIDHQVKIRGY
                     RIELGEVETQLLQVASVREAVVMARADETGQKHMVAYYVAGQELGASELRSELGRELPS
                     YMVPSYFVQLEQMPLSPNGKIDRKALPAPEGSLQSGADYVAPRTWVEVKLAHIWQEVLG
                     LTQVGVKENFFEIGGHSLRATTLASKIHKELNKPLPLRSIFEAPTIEQLAAVLEGLDQV
                     VYASIPVTEERSFYPLSSAQKRLYVLHQFDPSDVNYNMPSVLQVSGPLDVKRVEDVFRQ
                     LIDRHATLRTRFELVDNEPMQWIEDTVPFEVEYTKVQVESTTTATYTRISEEAQERVRQ
                     FIRPFDLKAAPLLRVGLVDLGVQGVGQESQHLLMLDMHHIVSDGVSMEVLTDEFVRLYG
                     GEELSPLRIQYKDYAVWQQSETHQEWMQVDGGTDR"
     gene            complement(<1136..>3136)
                     /locus_tag="JYU28_RS26730"
                     /pseudo=""
     aSDomain        complement(1853..2425)
                     /aSDomain="Condensation"
                     /aSTool="nrps_pks_domains"
                     /database="nrpspksdomains.hmm"
                     /detection="hmmscan"
                     /domain_id="nrpspksdomains_JYU28_RS26730_Condensation_LCL.1
                     "
                     /domain_subtypes="Condensation_LCL"
                     /evalue="4.60E-56"
                     /label="JYU28_RS26730_Condensation_LCL.1"
                     /locus_tag="JYU28_RS26730"
                     /protein_end="426"
                     /protein_start="235"
                     /score="182.0"
                     /specificity="C activity: active"
                     /specificity="Active site motif: HHIVSDG"
                     /tool="antismash"
                     /translation="YPLSSAQKRLYVLHQFDPSDVNYNMPSVLQVSGPLDVKRVEDVFR
                     QLIDRHATLRTRFELVDNEPMQWIEDTVPFEVEYTKVQVESTTTATYTRISEEAQERVR
                     QFIRPFDLKAAPLLRVGLVDLGVQGVGQESQHLLMLDMHHIVSDGVSMEVLTDEFVRLY
                     GGEELSPLRIQYKDYAVWQQSETHQEWM"
     CDS_motif       complement(1874..1906)
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_JYU28_RS26730_0004"
                     /evalue="1.60E-05"
                     /label="C4_LCL_164-176"
                     /locus_tag="JYU28_RS26730"
                     /protein_end="419"
                     /protein_start="408"
                     /score="17.4"
                     /tool="antismash"
                     /translation="QYKDYAVWQQS"
     CDS_motif       complement(1937..2002)
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_JYU28_RS26730_0003"
                     /evalue="1.30E-10"
                     /label="C3_LCL_132-143"
                     /locus_tag="JYU28_RS26730"
                     /protein_end="398"
                     /protein_start="376"
                     /score="33.7"
                     /tool="antismash"
                     /translation="MHHIVSDGVSMEVLTDEFVRLY"
     CDS_motif       complement(2252..2359)
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_JYU28_RS26730_0002"
                     /evalue="2.90E-15"
                     /label="C2_LCL_024-062"
                     /locus_tag="JYU28_RS26730"
                     /protein_end="293"
                     /protein_start="257"
                     /score="48.6"
                     /tool="antismash"
                     /translation="YNMPSVLQVSGPLDVKRVEDVFRQLIDRHATLRTRF"
     aSDomain        complement(2480..2680)
                     /aSDomain="PCP"
                     /aSTool="nrps_pks_domains"
                     /database="nrpspksdomains.hmm"
                     /detection="hmmscan"
                     /domain_id="nrpspksdomains_JYU28_RS26730_PCP.1"
                     /evalue="1.80E-25"
                     /label="JYU28_RS26730_PCP.1"
                     /locus_tag="JYU28_RS26730"
                     /protein_end="217"
                     /protein_start="150"
                     /score="80.9"
                     /tool="antismash"
                     /translation="EVKLAHIWQEVLGLTQVGVKENFFEIGGHSLRATTLASKIHKELN
                     KPLPLRSIFEAPTIEQLAAVLE"
     CDS_motif       complement(2972..3037)
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_JYU28_RS26730_0001"
                     /evalue="5.00E-13"
                     /label="NRPS-A_a8"
                     /locus_tag="JYU28_RS26730"
                     /protein_end="53"
                     /protein_start="31"
                     /score="40.8"
                     /tool="antismash"
                     /translation="YLGRIDHQVKIRGYRIELGEVE"
ORIGIN
        1 acggctaaaa tcaatccggt cgtctttcgg acaaatgacc atcgtgccgc cgttatagag
       61 cgtccgtgca atgtccccga cgaacacgtc gaaggagaag ctcgccagtt gcagcagtcg
      121 gactgggaat tggttcaggc gataatcccg gcgatacgcc gcagccgtat tcaccaggct
      181 gcgatgctcg atcatgacgc ccttcggccg tccggttgtc ccggatgtat agatcacata
      241 cgccaaatcg tgcggttcgt tgatgtgatc gacgtctgtc gtatctccgg tgtacagtga
      301 ctcatcgtcc aatgccaata cggtatgcag acgcagccct gttgccggtt cggatgctgc
      361 ttcgctgtca gacttcgaat ctgattttga gcctaagttt tcatttaggc tgtctctttc
      421 catcgtttca gcaccagccg ctgtttccaa ctcaccctca gtctgccctc cggccaaggc
      481 ctgtcggctt tccccaagcc atatctgtgc ttgctcctgt aagccgattt gggtcaacaa
      541 taccgtcgca ccactgtcct ccagcatgaa acgaatccgt tcagacggat agtctgcatc
      601 cagcggcaca taggcgcctc ccgccttcca caccgccagt acgccgacca gcatgtctac
      661 cgagcgttca ctcaaaatgc cgacaatcga ctcgcgtcca acgccttcat tccgcaatct
      721 ccgcgccaat tggttcgcgc gctcgttcag tttccggtaa gtgagctgct cctcctcgta
      781 caccaccgcc acatgatctg gtacaagctg tgcctgttct tccacatagg tatggaacag
      841 ggctcctgct tcaactgcag caccatccgt tactcccact tctccaaaac cgtagatgag
      901 ttgctccttt tcctcaacgg ttaccatatt caaagttgcc aggggctgtt gtggatggta
      961 tgcaatagct cgaacgattt ccgcaaaatg ctgtgccaat cgcgtcatgg tctcaggctt
     1021 gtacaacgcc gtgctnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     1081 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnntgcat
     1141 ctaaagtcag atcaaacttg gccgtatgat tttccagtgg ataggagctc aaggtcaaac
     1201 cttccagcag taactcctgt tgctccaagg ttttcaactc aaacatcgtg tcaaacagcg
     1261 catttcggct cgtatctctc gtcaaattca gctgttcaac cagttcttca aaaggatagt
     1321 cctgatgctc ataagcactg agcgcatgct ccttcacctc ttgcagataa tccagaaacg
     1381 ttttgtcgct ggacggataa ttgcgaatcg ccagcgtgtt aatgaagaca cccaccagat
     1441 tactgagctc cgcatgcggt cgtcctgcaa tcggcgtgcc gacgacaatg tcctcttggc
     1501 ccgtgtattt gtgcaagagc gtagtgtacg ccgccagcag caccatgtat agggtagcgc
     1561 ctgtttgcga agccagttct ttcaggcgtt cactaacctc acgctccaat gcaaattcga
     1621 tcgtatcccc tgccgtactc tgcaccgccg gacgggcaaa gtcggttgac agatccagta
     1681 caggcactcc gccccggaag gtgcccagcc agtacgcttc ctgacgctgc atccactcct
     1741 gatgggtttc gctttgctgc catacggcat agtctttgta ctgaatccgc aatggcgaca
     1801 gttcttcacc gccatacaag cggacaaact catcggtcag tacctccatc gacctgcatc
     1861 cactcctgat gggtttcgct ttgctgccat acggcatagt ctttgtactg aatccgcaat
     1921 ggcgacagtt cttcaccgcc atacaagcgg acaaactcat cggtcagtac ctccatcgac
     1981 acgccatccg aaacgatatg gtgcatgtcg agcatgagta aatgctggga ttcttgccct
     2041 actccttgga cacccagatc caccaagcct acccgcagca gcggtgcagc ttttagatca
     2101 aacggacgga taaactgccg tacccgttct tgtgcttcct cgctaatcct cgtgtacgta
     2161 gccgtagtcg tactctctac ctgtaccttc gtatattcca cctcgaatgg cacggtatcc
     2221 tcaatccatt gcatcggctc attgtctacc agctcaaagc gggtacgcaa ggttgcatga
     2281 cgatcaatta gttgacggaa cacgtcttct actcgtttca catccagcgg accgctcact
     2341 tgcagcactg acggcatgtt gtagttcaca tcacttggat caaactgatg cagtacatac
     2401 agtcgttttt gtgctgaaga taacgggtag aagctgcgtt cttctgttac cggaatggac
     2461 gcgtacacca cttgatccag accttccaga acggctgcca gttgttcaat cgtgggtgct
     2521 tcaaaaatac tgcgcagggg aagcggcttg ttcaactcct tgtgaatctt cgaggccagt
     2581 gtcgtcgccc gcagcgagtg tccgccaatc tcgaagaagt tttccttcac accgacctgc
     2641 gtgaggccca gcacctcctg ccaaatgtgt gccagtttca cttccaccca cgttcgcggt
     2701 gcgacataat cggctccgct ttgcaggctg ccttccggtg ctggtagggc cttgcggtca
     2761 atttttccat ttggactcag cggcatttgc tccagttgta caaagtagga cggcaccatg
     2821 tagcttggca gttcccggcc cagctcactt ctcagctcgc tggctcctag ctcttgcccc
     2881 gcgacatagt aggccaccat gtgtttttgg cccgtttcgt ctgcacgagc catgacaacc
     2941 gcttctcgca cggacgctac ttggagcagc tgcgtttcga cctcgcccag ctcaatccgg
     3001 tacccccgga ttttcacctg atggtcgatc cggcccaaat attcaatgtt gccgtccggc
     3061 atccatctcg ccaaatcgcc ggtgcggtac atccgctcat acccggcttc cccgccggca
     3121 aacggatctt tcacaa
//
