LOCUS       NZ_RYYV01000058         2825 bp    DNA     linear   CON 06-MAY-2024
DEFINITION  Dyella choica strain 4 M-K27 scaffold58, whole genome shotgun
            sequence.
ACCESSION   NZ_RYYV01000058
VERSION     NZ_RYYV01000058.1
KEYWORDS    WGS; RefSeq.
SOURCE      Dyella choica
  ORGANISM  Dyella choica
            Bacteria; Pseudomonadota; Gammaproteobacteria; Lysobacterales;
            Rhodanobacteraceae; Dyella.
REFERENCE   1  (bases 1 to 2825)
  AUTHORS   Qiu,L.-H. and Gao,Z.-H.
  TITLE     Dyella dinghuensis sp. nov. DHOA06 and Dyella choica sp. nov.
            4M-K27, isolated from forest soil
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2825)
  AUTHORS   Qiu,L.-H. and Gao,Z.-H.
  TITLE     Direct Submission
  JOURNAL   Submitted (21-DEC-2018) School of Life Sciences, Sun Yat-sen
            University, No. 135, Xinggang West Road, Guangzhou, Guangdong
            510275, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 2018
            Assembly Method                   :: Velvet v. 1.2.10
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 145.0x
            Sequencing Technology             :: Illumina Hiseq 4000
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_003977665.1-RS_2024_05_06
            Annotation Date                   :: 05/06/2024 01:53:55
            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)                     :: 4,733
            CDSs (total)                      :: 4,678
            Genes (coding)                    :: 4,648
            CDSs (with protein)               :: 4,648
            Genes (RNA)                       :: 55
            rRNAs                             :: 1, 1, 1 (5S, 16S, 23S)
            complete rRNAs                    :: 1, 1, 1 (5S, 16S, 23S)
            tRNAs                             :: 48
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 30
            CDSs (without protein)            :: 30
            Pseudo Genes (ambiguous residues) :: 0 of 30
            Pseudo Genes (frameshifted)       :: 9 of 30
            Pseudo Genes (incomplete)         :: 25 of 30
            Pseudo Genes (internal stop)      :: 5 of 30
            Pseudo Genes (multiple problems)  :: 9 of 30
            ##Genome-Annotation-Data-END##
            ##antiSMASH-Data-START##
            Version                           :: 8.dev-cf2fc5ee(changed)
            Run date                          :: 2025-09-13 03:37:17
            NOTE :: This is a single region extracted from a larger record!
            Orig. start                       :: 0
            Orig. end                         :: 2825
            ##antiSMASH-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            RYYV01000058.1.
            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
     CDS             complement(<1..1249)
                     /GO_function="GO:0003824 - catalytic activity [Evidence
                     IEA]"
                     /NRPS_PKS="Domain: Condensation_LCL (1-119). E-value:
                     6.3e-45. Score: 145.4. Matches aSDomain:
                     nrpspksdomains_EKH80_RS23920_Condensation_LCL.1"
                     /codon_start=2
                     /gene_functions="biosynthetic (rule-based-clusters) NRPS:
                     AMP-binding"
                     /gene_functions="biosynthetic (rule-based-clusters) NRPS:
                     Condensation"
                     /gene_functions="biosynthetic-additional (smcogs)
                     SMCOG1127: condensation domain-containing protein"
                     /gene_kind="biosynthetic"
                     /inference="COORDINATES: protein motif:HMM:NF012873.4"
                     /locus_tag="EKH80_RS23920"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /product="condensation domain-containing protein"
                     /protein_id="WP_158628939.1"
                     /sec_met_domain="Condensation (E-value: 5.1e-30, bitscore:
                     91.6, seeds: 42, tool: rule-based-clusters)"
                     /sec_met_domain="AMP-binding (E-value: 3.6e-28, bitscore:
                     85.3, seeds: 400, tool: rule-based-clusters)"
                     /transl_table=11
                     /translation="MKNSVIAAQIAYWQQHLAGLPEQLDLIVDFPRPASPSFRGADVSF
                     QLDADMHARLLQLAHDTQASLFMLLHAAVAVTLSRLGAGTDIPLGTVIAGRTDEALDEL
                     VGFFVNTLVLRTDVSGRPSFRELLKRVRQNNLAAYAHQDLPFERLVEIVNPTRALNRHP
                     LFQVMLSLQNNAGGRLELSGLTVAPQATGYSPAKFDLSFDFAEGRDAQGEKTLRGSLQY
                     ACDLYAPATAQQILQRLVRILEAVASDPDQCLERLDPLTAEEQAQLDAWNVTAQAVPGT
                     SMAQLFEQQAAATPEATALVCEDATLSYAELNGRANQLAHYLIADGIGAEDLVAIALPR
                     SSELIIAMLAVLKAGAAYLPLDASYPAERIAYMREDARPVRWLTRQAMTGRLAVDATEL
                     NLDSLQTGTFPRSNPDDG"
     gene            complement(<1..>1251)
                     /locus_tag="EKH80_RS23920"
     source          1..2825
                     /collected_by="Li-hong Qiu, Zeng-hong Gao"
                     /collection_date="2015-09-30"
                     /country="China: Guangdong Province, Dinghushan Biosphere
                     Reserve forest"
                     /db_xref="taxon:1927959"
                     /identified_by="Fang-hong Ou, Zeng-hong Gao, Li-hong Qiu"
                     /isolation_source="forest soil"
                     /lat_lon="23.17 N 112.53 E"
                     /mol_type="genomic DNA"
                     /organism="Dyella choica"
                     /strain="4 M-K27"
                     /submitter_seqid="scaffold58"
                     /type_material="type strain of Dyella choica"
     region          1..2825
                     /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..2825
                     /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..2825
                     /aStool="rule-based-clusters"
                     /category="NRPS"
                     /contig_edge="True"
                     /core_location="[<0:2823](-)"
                     /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..2823)
                     /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_motif       complement(163..204)
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_EKH80_RS23920_0003"
                     /evalue="1.70E-06"
                     /label="NRPS-A_a2"
                     /locus_tag="EKH80_RS23920"
                     /protein_end="362"
                     /protein_start="348"
                     /score="20.9"
                     /tool="antismash"
                     /translation="LAVLKAGAAYLPLD"
     CDS_motif       complement(736..855)
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_EKH80_RS23920_0002"
                     /evalue="1.50E-21"
                     /label="C67_LCL_14fromHMM"
                     /locus_tag="EKH80_RS23920"
                     /protein_end="171"
                     /protein_start="131"
                     /score="68.8"
                     /tool="antismash"
                     /translation="RQNNLAAYAHQDLPFERLVEIVNPTRALNRHPLFQVMLSL"
     aSDomain        complement(892..1245)
                     /aSDomain="Condensation"
                     /aSTool="nrps_pks_domains"
                     /database="nrpspksdomains.hmm"
                     /detection="hmmscan"
                     /domain_id="nrpspksdomains_EKH80_RS23920_Condensation_LCL.1
                     "
                     /domain_subtypes="Condensation_LCL"
                     /evalue="6.30E-45"
                     /label="EKH80_RS23920_Condensation_LCL.1"
                     /locus_tag="EKH80_RS23920"
                     /protein_end="119"
                     /protein_start="1"
                     /score="145.4"
                     /specificity="C activity: inactive"
                     /specificity="Active site motif: -------"
                     /tool="antismash"
                     /translation="KNSVIAAQIAYWQQHLAGLPEQLDLIVDFPRPASPSFRGADVSFQ
                     LDADMHARLLQLAHDTQASLFMLLHAAVAVTLSRLGAGTDIPLGTVIAGRTDEALDELV
                     GFFVNTLVLRTDVS"
     CDS_motif       complement(904..993)
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_EKH80_RS23920_0001"
                     /evalue="4.10E-14"
                     /label="C5_LCL_267-296"
                     /locus_tag="EKH80_RS23920"
                     /protein_end="115"
                     /protein_start="85"
                     /score="44.9"
                     /tool="antismash"
                     /translation="DIPLGTVIAGRTDEALDELVGFFVNTLVLR"
     assembly_gap    1252..1410
                     /estimated_length=159
                     /gap_type="within scaffold"
                     /linkage_evidence="paired-ends"
     aSDomain        complement(<1411..1892)
                     /aSDomain="Condensation"
                     /aSTool="nrps_pks_domains"
                     /database="nrpspksdomains.hmm"
                     /detection="hmmscan"
                     /domain_id="nrpspksdomains_EKH80_RS23635_Condensation_LCL.1
                     "
                     /domain_subtypes="Condensation_LCL"
                     /evalue="1.50E-57"
                     /label="EKH80_RS23635_Condensation_LCL.1"
                     /locus_tag="EKH80_RS23635"
                     /protein_end="471"
                     /protein_start="310"
                     /score="186.8"
                     /specificity="C activity: active"
                     /specificity="Active site motif: HHIASDG"
                     /tool="antismash"
                     /translation="GHIPLSFAQQRLWFLQQFAEADSAYNLPLALRLQGALDVAALQMA
                     LNDLLQRHESLRTIFSDGEEGARQIVLDKATLSFEQIACDANELAQHLRTCAGYRFELT
                     HELPVRAWLFALSHDEHVLLLQVHHIASDGWSWRPLFRDLGVAYAARREGRVPAWQP"
     CDS             complement(<1411..2823)
                     /GO_function="GO:0003824 - catalytic activity [Evidence
                     IEA]"
                     /NRPS_PKS="Domain: PCP (228-293). E-value: 1.1e-29. Score:
                     94.4. Matches aSDomain: nrpspksdomains_EKH80_RS23635_PCP.1"
                     /NRPS_PKS="Domain: Condensation_LCL (310-471). E-value:
                     1.5e-57. Score: 186.8. Matches aSDomain:
                     nrpspksdomains_EKH80_RS23635_Condensation_LCL.1"
                     /codon_start=2
                     /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: protein motif:HMM:NF012873.4"
                     /locus_tag="EKH80_RS23635"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /old_locus_tag="EKH80_23630"
                     /product="condensation domain-containing protein"
                     /protein_id="WP_148110439.1"
                     /sec_met_domain="AMP-binding (E-value: 1.9e-50, bitscore:
                     158.6, seeds: 400, tool: rule-based-clusters)"
                     /sec_met_domain="PP-binding (E-value: 3.6e-19, bitscore:
                     56.4, seeds: 164, tool: rule-based-clusters)"
                     /sec_met_domain="Condensation (E-value: 1.2e-42, bitscore:
                     133.1, seeds: 42, tool: rule-based-clusters)"
                     /transl_table=11
                     /translation="MLYGPTETTIQVATCAYTLQDPPQGITAAIGHPIWNTALHVLDTA
                     LQPVPPGVAGELYIAGACLARGYLRRPGLTAQRFIADPFAADGRRMYRSGDRVRWLADG
                     RLEYLGRTDEQVKIRGYRIELGEIEASLLRDPQVAQATVIVREDVPGNQQLVGYVVLGG
                     EAQTGSAATEALRQALAESLPEYMLPSAIVAIDALPLMPNGKLDRKALPAPVFTAPGIR
                     APRNEKEEALCALFAEVLGLERVGIDDNFFKLGGHSLLATRLVSRIRTALQVELPIRAL
                     FEAPSVAQLSGQMSAGQAVRTALRPVARTGHIPLSFAQQRLWFLQQFAEADSAYNLPLA
                     LRLQGALDVAALQMALNDLLQRHESLRTIFSDGEEGARQIVLDKATLSFEQIACDANEL
                     AQHLRTCAGYRFELTHELPVRAWLFALSHDEHVLLLQVHHIASDGWSWRPLFRDLGVAY
                     AARREGRVPAWQP"
     gene            complement(<1411..>2825)
                     /locus_tag="EKH80_RS23635"
                     /old_locus_tag="EKH80_23630"
     CDS_motif       complement(1449..1514)
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_EKH80_RS23635_0005"
                     /evalue="1.10E-10"
                     /label="C3_LCL_132-143"
                     /locus_tag="EKH80_RS23635"
                     /protein_end="458"
                     /protein_start="436"
                     /score="33.9"
                     /tool="antismash"
                     /translation="VHHIASDGWSWRPLFRDLGVAY"
     CDS_motif       complement(1713..1826)
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_EKH80_RS23635_0004"
                     /evalue="2.80E-20"
                     /label="C2_LCL_024-062"
                     /locus_tag="EKH80_RS23635"
                     /protein_end="370"
                     /protein_start="332"
                     /score="64.7"
                     /tool="antismash"
                     /translation="SAYNLPLALRLQGALDVAALQMALNDLLQRHESLRTIF"
     CDS_motif       complement(1845..1877)
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_EKH80_RS23635_0003"
                     /evalue="9.80E-04"
                     /label="C1_LCL_004-017"
                     /locus_tag="EKH80_RS23635"
                     /protein_end="326"
                     /protein_start="315"
                     /score="11.5"
                     /tool="antismash"
                     /translation="SFAQQRLWFLQ"
     aSDomain        complement(1944..2138)
                     /aSDomain="PCP"
                     /aSTool="nrps_pks_domains"
                     /database="nrpspksdomains.hmm"
                     /detection="hmmscan"
                     /domain_id="nrpspksdomains_EKH80_RS23635_PCP.1"
                     /evalue="1.10E-29"
                     /label="EKH80_RS23635_PCP.1"
                     /locus_tag="EKH80_RS23635"
                     /protein_end="293"
                     /protein_start="228"
                     /score="94.4"
                     /tool="antismash"
                     /translation="EEALCALFAEVLGLERVGIDDNFFKLGGHSLLATRLVSRIRTALQ
                     VELPIRALFEAPSVAQLSGQ"
     CDS_motif       complement(2436..2501)
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_EKH80_RS23635_0002"
                     /evalue="9.80E-13"
                     /label="NRPS-A_a8"
                     /locus_tag="EKH80_RS23635"
                     /protein_end="129"
                     /protein_start="107"
                     /score="39.9"
                     /tool="antismash"
                     /translation="YLGRTDEQVKIRGYRIELGEIE"
     CDS_motif       complement(2586..2675)
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_EKH80_RS23635_0001"
                     /evalue="9.00E-18"
                     /label="NRPS-A_a6"
                     /locus_tag="EKH80_RS23635"
                     /protein_end="79"
                     /protein_start="49"
                     /score="56.3"
                     /tool="antismash"
                     /translation="PPGVAGELYIAGACLARGYLRRPGLTAQRF"
ORIGIN
        1 ccgtcatcgg gattgctgcg agggaatgtc ccggtttgca ggctgtccag attcagttcg
       61 gtcgcgtcca cggccaggcg cccggtcatc gcttgccgtg tcaaccagcg caccgggcgg
      121 gcatcttccc gcatgtaggc aatgcgctcg gccggatagc tggcatccaa cggcagatag
      181 gcggcgccgg ccttgagcac ggcgagcatc gcgatgatca gttcgctcga acgcggcaag
      241 gcgatcgcca cgagatcctc ggccccgatg ccgtccgcga tcagataatg ggcgagctga
      301 ttggcacgcc cattgagttc tgcatagctc agcgtggcat cttcgcagac cagcgcggtg
      361 gcttcgggcg ttgcggcagc ctgctgctca aacaactgcg ccatgctcgt gccgggaacg
      421 gcctgggcgg tgacattcca ggcatccagt tgcgcctgtt cctctgcggt caatggatcg
      481 aggcgttcca ggcactggtc cggatcgctg gcaaccgctt cgagtatccg cactagccgc
      541 tgtaggatct gttgcgctgt agccggcgca tacaaatcgc aggcgtactg caggctgccg
      601 cgcaaagttt tctcaccttg cgcgtcgcgc ccttcggcaa agtcaaaact caggtcgaac
      661 ttggctgggc tgtagccggt tgcctgcggt gcgacggtga gaccggacag ttccaggcgt
      721 ccgccggcat tgttctgcag gctcagcatc acctggaaca gcggatgccg gttgagcgca
      781 cgagtgggat tgacgatttc caccagtcgc tcgaacggca gatcctggtg tgcataggcg
      841 gccagattgt tttgacggac ccgcttcagc agttcacgga agctgggacg gcctgataca
      901 tccgtgcgca gcaccagggt attgacgaag aagccgacca gctcatccag cgcttcgtcg
      961 gtgcgcccgg cgatgaccgt gccgagcgga atatccgtgc cggcgccgag tcgggacagg
     1021 gtcaccgcaa cagccgcatg caacagcatg aacagactgg cctgggtgtc atgcgccagt
     1081 tgcagcaggc gtgcatgcat gtctgcatcg agctggaagg agacgtccgc gccccggaag
     1141 ctggggctcg ccggacgcgg aaaatcgacg atcaagtcca actgctcggg aaggcccgcc
     1201 agatgctgtt gccaatacgc gatctgcgcg gcgatgacac tgttcttgtc gnnnnnnnnn
     1261 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     1321 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     1381 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn atggctgcca cgccgggacc cggccttccc
     1441 ggcgtgcggc ataagccacc cccaggtcgc ggaacaacgg ccgccatgac cagccatcac
     1501 tggcgatgtg atgcacttgc agcaatagca cgtgctcatc gtgcgacagc gcaaatagcc
     1561 atgcgcgcac gggcagttca tgggtcagct caaaccggta gccggcgcat gtcctgaggt
     1621 gctgcgccag ttcgttcgca tcgcaggcga tctgctcgaa cgaaagtgtc gccttgtcca
     1681 gcacgatctg ccgcgcgcct tcctcgccgt cgctgaagat agtgcgcagg ctttcatggc
     1741 gctgcagcag atcgttcaga gccatttgca acgccgcaac atccagcgcg ccttgcaggc
     1801 gcaaggccag cggcaggttg taggcgctgt cggcttcggc aaattgctgc aggaaccaca
     1861 gccgctgttg cgcgaaggac agcggtatgt gccccgtcct cgccacggga cgcaaggccg
     1921 tgcgtaccgc ctgcccggca gacatctgtc cgctcagttg cgccacgctg ggcgcttcaa
     1981 acaaagcgcg aatcggcagt tccacctgta aagcggtacg gatgcggctg accaggcgcg
     2041 tggccagcag ggagtggccg cccagcttga agaagttgtc gtcgatgcct acgcgctcca
     2101 ggccgagcac ttcggcaaac agtgcgcaga gagcttcttc tttctcgttg cgtggcgcgc
     2161 gtatgccggg tgccgtgaag accggcgcgg gaagcgcctt gcggtcgagt ttgccgttgg
     2221 gcatcaaggg cagcgcatca atcgctacga tggcggaggg cagcatgtac tcgggcaggg
     2281 attcggccag tgcttgacgc agcgcctcgg tcgccgcgct tcctgtttgg gcttccccgc
     2341 ccagcacgac atagccgacg agttgctggt tgcccggcac gtcctcacgc acgatcaccg
     2401 ttgcctgcgc gacttgcgga tcacgcagca agctggcttc gatttcgccc agttcaatgc
     2461 gatagccgcg gattttgacc tgttcatcgg tgcggcccag atactccagc cgtccgtctg
     2521 ccagccagcg cacccggtcg ccgctgcgat acatgcgccg gccatcggcg gcaaacggat
     2581 cggcgatgaa gcgttgcgcg gtcaggccgg gacggcgcag atagccgcgt gccagacagg
     2641 ctccggcgat gtacagctcg cccgccacac ccggcggtac cggctgcagg gccgtatcca
     2701 gcacatgcag cgcggtgttc cagatcggat gaccgatggc ggcagtgatt ccctgcggcg
     2761 gatcttgcag ggtgtaggcg cacgtggcca cctggatcgt ggtctcggtc gggccgtaca
     2821 gattg
//
