LOCUS       NZ_JALAUL010000016      2174 bp    DNA     linear   CON 26-JAN-2024
DEFINITION  Bacillus atrophaeus strain CK4F1-2 Contig_0000016, whole genome
            shotgun sequence.
ACCESSION   NZ_JALAUL010000016
VERSION     NZ_JALAUL010000016.1
KEYWORDS    WGS; RefSeq.
SOURCE      Bacillus atrophaeus
  ORGANISM  Bacillus atrophaeus
            Bacteria; Bacillota; Bacilli; Bacillales; Bacillaceae; Bacillus.
REFERENCE   1  (bases 1 to 2174)
  AUTHORS   Dunlap,C.
  TITLE     Crop Bioprotection Bacillus Genome Sequencing
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2174)
  AUTHORS   Dunlap,C.
  TITLE     Direct Submission
  JOURNAL   Submitted (24-FEB-2022) CBP, USDA-ARS-NCAUR, 1815 N. University St.,
            Peoria, IL 61604, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: CLC NGS Cell v. 21
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 219.01779805621194x
            Sequencing Technology             :: Illumina NovaSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/24/2024 02:32:00
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,147
            CDSs (total)                      :: 4,069
            Genes (coding)                    :: 3,904
            CDSs (with protein)               :: 3,904
            Genes (RNA)                       :: 78
            rRNAs                             :: 2, 1, 1 (5S, 16S, 23S)
            complete rRNAs                    :: 2, 1, 1 (5S, 16S, 23S)
            tRNAs                             :: 69
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 165
            CDSs (without protein)            :: 165
            Pseudo Genes (ambiguous residues) :: 0 of 165
            Pseudo Genes (frameshifted)       :: 97 of 165
            Pseudo Genes (incomplete)         :: 106 of 165
            Pseudo Genes (internal stop)      :: 39 of 165
            Pseudo Genes (multiple problems)  :: 66 of 165
            ##Genome-Annotation-Data-END##
            ##antiSMASH-Data-START##
            Version                           :: 8.dev-cf2fc5ee(changed)
            Run date                          :: 2025-09-13 02:35:49
            NOTE :: This is a single region extracted from a larger record!
            Orig. start                       :: 0
            Orig. end                         :: 2174
            ##antiSMASH-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            JALAUL010000016.1.
            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..2174
                     /db_xref="taxon:1452"
                     /isolation_source="soil"
                     /mol_type="genomic DNA"
                     /organism="Bacillus atrophaeus"
                     /strain="CK4F1-2"
                     /submitter_seqid="Contig_0000016"
     gene            complement(<1..>2174)
                     /locus_tag="MOE42_RS20515"
                     /old_locus_tag="MOE42_20460"
     region          1..2174
                     /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..2174
                     /SMILES="NC(CCC(=O)O)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..2174
                     /aStool="rule-based-clusters"
                     /category="NRPS"
                     /contig_edge="True"
                     /core_location="[<0:2174](-)"
                     /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(<1..2174)
                     /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"
     CDS             complement(<1..2174)
                     /GO_function="GO:0003824 - catalytic activity [Evidence
                     IEA]"
                     /NRPS_PKS="Domain: AMP-binding (1-216). E-value: 1.2e-54.
                     Score: 177.4. Matches aSDomain:
                     nrpspksdomains_MOE42_RS20515_AMP-binding.1"
                     /NRPS_PKS="Domain: PCP (318-386). E-value: 2.9e-25. Score:
                     80.2. Matches aSDomain: nrpspksdomains_MOE42_RS20515_PCP.1"
                     /NRPS_PKS="Domain: Condensation_LCL (401-681). E-value:
                     2.6e-108. Score: 353.5. Matches aSDomain:
                     nrpspksdomains_MOE42_RS20515_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: similar to AA
                     sequence:RefSeq:NP_389716.2"
                     /locus_tag="MOE42_RS20515"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /old_locus_tag="MOE42_20460"
                     /product="condensation domain-containing protein"
                     /protein_id="WP_268487120.1"
                     /sec_met_domain="AMP-binding (E-value: 3.9e-70, bitscore:
                     222.5, seeds: 400, tool: rule-based-clusters)"
                     /sec_met_domain="PP-binding (E-value: 2.6e-18, bitscore:
                     52.6, seeds: 164, tool: rule-based-clusters)"
                     /sec_met_domain="Condensation (E-value: 1.6e-95, bitscore:
                     305.7, seeds: 42, tool: rule-based-clusters)"
                     /transl_table=11
                     /translation="MVWQLFWWTLSGASAYLLPSGWEKDPALMAEAFTQERVTTAHFIP
                     AMLNSFLDQLEMETPERRDGLTTGLKRVFAGGELLTPQAAARFADLLPETSLIHGYGPT
                     EATVDAAFYVCDREKDSERLRLPIGKPVPGARLYILNPQMAVQPVGVIGELYIAGNGVA
                     RGYLNRPELTTERFLSDPFYPGERMYKTGDLARWLPDGQVEFLGRLDDQVKIRGYRIEP
                     GEIESALRNLEGVQEAAVITRADSGEAELCAYIQGRDKNDVRAQLALVLPSYMIPAHFV
                     QIDTWPITPSGKLDRKALPAPDGAAGQESYKAPRNLTEMKLAQLWEDVLKNGPVGITDD
                     FFDRGGHSLKATALISRIAKAFGVQVPLKDIFAQPTIEGLASVIRELEESPYAAIEPAE
                     KRDTYPVSSAQKRMYVLQQLEDGGVGYNMPAVLELEGKLDRKRMETAFQALISRHESLR
                     TSFETGNGGEPVQRIHHEVPFTVTEENSADAFVRPFDLSQAPLFRAGLVEETNERHVLL
                     VDMHHIISDGVSVNTLIREFGELYAGRKLEPLRIQYKDYAVWQQEFKKGDTYEKQESYW
                     LKQLGGEMPVLELPADEPRPAVRSFAGDKISFTLDQEVTSGLNRLARENGSTLYMVLLA
                     AYSALLSRLSGQEEIVVGSPIAGRPHEDLEPVLGMFVNTLALRTRPEGGKGFTDYLQEV
                     RQTALEAYEHQDYPFEELVEKLDVYRDTSR"
     CDS_motif       complement(3..92)
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_MOE42_RS20515_0010"
                     /evalue="1.00E-14"
                     /label="C67_LCL_14fromHMM"
                     /locus_tag="MOE42_RS20515"
                     /protein_end="724"
                     /protein_start="694"
                     /score="46.8"
                     /tool="antismash"
                     /translation="RQTALEAYEHQDYPFEELVEKLDVYRDTSR"
     aSDomain        complement(132..971)
                     /aSDomain="Condensation"
                     /aSTool="nrps_pks_domains"
                     /database="nrpspksdomains.hmm"
                     /detection="hmmscan"
                     /domain_id="nrpspksdomains_MOE42_RS20515_Condensation_LCL.1
                     "
                     /domain_subtypes="Condensation_LCL"
                     /evalue="2.60E-108"
                     /label="MOE42_RS20515_Condensation_LCL.1"
                     /locus_tag="MOE42_RS20515"
                     /protein_end="681"
                     /protein_start="401"
                     /score="353.5"
                     /specificity="C activity: active"
                     /specificity="Active site motif: HHIISDG"
                     /tool="antismash"
                     /translation="DTYPVSSAQKRMYVLQQLEDGGVGYNMPAVLELEGKLDRKRMETA
                     FQALISRHESLRTSFETGNGGEPVQRIHHEVPFTVTEENSADAFVRPFDLSQAPLFRAG
                     LVEETNERHVLLVDMHHIISDGVSVNTLIREFGELYAGRKLEPLRIQYKDYAVWQQEFK
                     KGDTYEKQESYWLKQLGGEMPVLELPADEPRPAVRSFAGDKISFTLDQEVTSGLNRLAR
                     ENGSTLYMVLLAAYSALLSRLSGQEEIVVGSPIAGRPHEDLEPVLGMFVNTLALRTRP"
     CDS_motif       complement(141..230)
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_MOE42_RS20515_0009"
                     /evalue="5.00E-16"
                     /label="C5_LCL_267-296"
                     /locus_tag="MOE42_RS20515"
                     /protein_end="678"
                     /protein_start="648"
                     /score="51.0"
                     /tool="antismash"
                     /translation="EIVVGSPIAGRPHEDLEPVLGMFVNTLALR"
     CDS_motif       complement(240..293)
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_MOE42_RS20515_0008"
                     /evalue="8.50E-03"
                     /label="Cy4"
                     /locus_tag="MOE42_RS20515"
                     /protein_end="645"
                     /protein_start="627"
                     /score="9.3"
                     /tool="antismash"
                     /translation="TLYMVLLAAYSALLSRLS"
     CDS_motif       complement(489..521)
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_MOE42_RS20515_0007"
                     /evalue="8.90E-05"
                     /label="C4_LCL_164-176"
                     /locus_tag="MOE42_RS20515"
                     /protein_end="562"
                     /protein_start="551"
                     /score="15.1"
                     /tool="antismash"
                     /translation="QYKDYAVWQQE"
     CDS_motif       complement(552..617)
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_MOE42_RS20515_0006"
                     /evalue="2.00E-09"
                     /label="C3_LCL_132-143"
                     /locus_tag="MOE42_RS20515"
                     /protein_end="541"
                     /protein_start="519"
                     /score="29.9"
                     /tool="antismash"
                     /translation="MHHIISDGVSVNTLIREFGELY"
     CDS_motif       complement(792..899)
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_MOE42_RS20515_0005"
                     /evalue="1.80E-17"
                     /label="C2_LCL_024-062"
                     /locus_tag="MOE42_RS20515"
                     /protein_end="461"
                     /protein_start="425"
                     /score="55.7"
                     /tool="antismash"
                     /translation="YNMPAVLELEGKLDRKRMETAFQALISRHESLRTSF"
     aSDomain        complement(1017..1220)
                     /aSDomain="PCP"
                     /aSTool="nrps_pks_domains"
                     /database="nrpspksdomains.hmm"
                     /detection="hmmscan"
                     /domain_id="nrpspksdomains_MOE42_RS20515_PCP.1"
                     /evalue="2.90E-25"
                     /label="MOE42_RS20515_PCP.1"
                     /locus_tag="MOE42_RS20515"
                     /protein_end="386"
                     /protein_start="318"
                     /score="80.2"
                     /tool="antismash"
                     /translation="EMKLAQLWEDVLKNGPVGITDDFFDRGGHSLKATALISRIAKAFG
                     VQVPLKDIFAQPTIEGLASVIRE"
     aSModule        complement(1017..2171)
                     /complete
                     /domains="nrpspksdomains_MOE42_RS20515_AMP-binding.1"
                     /domains="nrpspksdomains_MOE42_RS20515_PCP.1"
                     /locus_tags="MOE42_RS20515"
                     /monomer_pairings="Glu -> Glu"
                     /starter_module
                     /tool="antismash"
                     /type="nrps"
     CDS_motif       complement(1275..1301)
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_MOE42_RS20515_0004"
                     /evalue="4.20E-02"
                     /label="NRPS-A_a10"
                     /locus_tag="MOE42_RS20515"
                     /protein_end="300"
                     /protein_start="291"
                     /score="6.7"
                     /tool="antismash"
                     /translation="GKLDRKALP"
     CDS_motif       complement(1497..1562)
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_MOE42_RS20515_0003"
                     /evalue="3.60E-13"
                     /label="NRPS-A_a8"
                     /locus_tag="MOE42_RS20515"
                     /protein_end="226"
                     /protein_start="204"
                     /score="41.3"
                     /tool="antismash"
                     /translation="FLGRLDDQVKIRGYRIEPGEIE"
     aSDomain        complement(1527..2171)
                     /aSDomain="AMP-binding"
                     /aSTool="nrps_pks_domains"
                     /database="nrpspksdomains.hmm"
                     /detection="hmmscan"
                     /domain_id="nrpspksdomains_MOE42_RS20515_AMP-binding.1"
                     /evalue="1.20E-54"
                     /label="MOE42_RS20515_AMP-binding.1"
                     /locus_tag="MOE42_RS20515"
                     /protein_end="216"
                     /protein_start="1"
                     /score="177.4"
                     /specificity="substrate consensus: Glu"
                     /tool="antismash"
                     /translation="VWQLFWWTLSGASAYLLPSGWEKDPALMAEAFTQERVTTAHFIPA
                     MLNSFLDQLEMETPERRDGLTTGLKRVFAGGELLTPQAAARFADLLPETSLIHGYGPTE
                     ATVDAAFYVCDREKDSERLRLPIGKPVPGARLYILNPQMAVQPVGVIGELYIAGNGVAR
                     GYLNRPELTTERFLSDPFYPGERMYKTGDLARWLPDGQVEFLGRLDDQVKIR"
     CDS_motif       complement(1644..1733)
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_MOE42_RS20515_0002"
                     /evalue="1.10E-18"
                     /label="NRPS-A_a6"
                     /locus_tag="MOE42_RS20515"
                     /protein_end="177"
                     /protein_start="147"
                     /score="59.2"
                     /tool="antismash"
                     /translation="PVGVIGELYIAGNGVARGYLNRPELTTERF"
     CDS_motif       complement(1956..2015)
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_MOE42_RS20515_0001"
                     /evalue="2.80E+01"
                     /label="C2_dual_024-063"
                     /locus_tag="MOE42_RS20515"
                     /protein_end="73"
                     /protein_start="53"
                     /score="-2.6"
                     /tool="antismash"
                     /translation="QLEMETPERRDGLTTGLKRV"
ORIGIN
        1 ttgcggcttg tgtcccgata aacgtccaac ttttcgacca gttcttcaaa tggataatcc
       61 tgatgttcat aagcttccag cgctgtctga cggacttcct gcaaatagtc tgtgaaaccc
      121 tttccgccct ccgggcgtgt ccgaagcgcc aacgtgttca caaacatgcc aagcacaggt
      181 tcaaggtctt catgcggacg gccggcgatc ggcgatccga ccacaatctc ctcttgcccg
      241 ctgaggcgtg acaaaagagc tgagtaggcc gcaagaagca ccatatacaa ggtgctgccg
      301 ttttcccgcg cgaggcggtt caggccggac gtgacttctt ggtccagagt aaatgagatc
      361 ttgtcaccgg cgaagcttcg caccgccgga cggggctcgt ccgccggcag ttcaagcaca
      421 ggcatctcgc cgccgagctg cttcagccaa taagattcct gcttctcata tgtgtctcct
      481 tttttgaatt cctgctgcca cacggcgtaa tctttgtatt ggatgcgcag cggctcaagt
      541 ttccgcccgg cgtacaattc tccaaattcc cgaatgagcg tattgactga gacgccgtca
      601 gaaatgatgt gatgcatgtc gaccaaaagg acatgccgct cgtttgtttc ttctacgagt
      661 cccgctctga aaagcggagc ctggctgaga tcaaagggac gtacaaacgc atcagccgag
      721 ttctcttcgg tcaccgtaaa cggcacctca tgatggatgc gctggaccgg ctcccctccg
      781 tttccggttt caaaggacgt ccggagcgac tcatggcggc tgatcagcgc ttggaaagcc
      841 gtctccatcc gtttgcggtc aagcttgcct tccagctcaa gcaccgcagg catattgtag
      901 ccgacgcctc catcttccag ctgctgaagg acatacatcc gtttttgcgc cgaggagacc
      961 ggataggtgt cccgcttttc ggccggttcg atcgccgcat acgggctttc ctccaactcg
     1021 cggatgacag aagccagccc ttctatggtc ggttgggcaa atatatcttt aagcggcact
     1081 tggacgccga atgccttggc gattcgggag atgagcgccg ttgcttttaa cgagtggccg
     1141 ccccggtcaa aaaagtcgtc cgtgataccg acaggaccgt ttttcagcac gtcttcccaa
     1201 agctgggcaa gcttcatctc ggtaaggttt cttggtgcct tgtatgattc ttgaccagct
     1261 gctccatcag gagcaggcaa agccttccgg tcaagcttcc cgcttggtgt gattggccat
     1321 gtgtcaattt gcacaaaatg agcggggatc atatagctgg gcagcacgag cgcaagctgt
     1381 gcccgcacgt cgtttttatc acgcccctgg atataagcgc atagctctgc ctccccgctg
     1441 tctgcgcggg tgataacggc tgcttcctgc acgccttcca agttccggag agctgattca
     1501 atttcgccgg gttcgatccg gtagccgcgg attttgactt gatcgtccaa acggccgagg
     1561 aactcaacct gcccgtccgg cagccagcgc gccagatctc ccgttttgta catccgttcc
     1621 ccaggataaa agggatcaga gagaaagcgt tccgtcgtta actcggggcg attcaggtag
     1681 cctctggcca caccattccc ggcgatatac agttcgccta tgacacccac aggctgaaca
     1741 gccatctgag ggttcaagat ataaagacgc gcgcccggca cgggctttcc gatcggaaga
     1801 cgcagccgtt cactgtcttt ttctctgtca cacacgtaaa atgccgcatc caccgtggct
     1861 tctgtcggcc cgtagccgtg gatcagagac gtctccggca agagatcagc aaatcgggcc
     1921 gctgcttggg gcgtgagcag ttcgcctccg gcgaataccc gtttaagacc tgtcgtgagc
     1981 ccgtcccttc gctcaggcgt ttccatctcc agctgatcta agaagctgtt cagcatcgca
     2041 ggaatgaagt gagccgttgt cacacgttcc tgcgtgaatg cctctgccat gagcgccgga
     2101 tctttttccc agccggacgg aagcagatag gccgaagcgc ctgagagtgt ccaccagaac
     2161 agctgccaga caga
//
