LOCUS       NZ_FZOF01000076         3900 bp    DNA     linear   CON 02-JAN-2025
DEFINITION  Actinacidiphila glaucinigra strain CGMCC 4.1858, whole genome
            shotgun sequence.
ACCESSION   NZ_FZOF01000076
VERSION     NZ_FZOF01000076.1
KEYWORDS    WGS; RefSeq.
SOURCE      Actinacidiphila glaucinigra
  ORGANISM  Actinacidiphila glaucinigra
            Bacteria; Bacillati; Actinomycetota; Actinomycetes;
            Kitasatosporales; Streptomycetaceae; Actinacidiphila.
REFERENCE   1
  AUTHORS   Varghese,N. and Submissions,S.
  TITLE     Direct Submission
  JOURNAL   Submitted (20-JUN-2017) DOE - JOINT GENOME INSTITUTE, LBNL, 2800
            Mitchell Drive, Walnut Creek, CA 94598, USA
COMMENT     ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_900188405.1-RS_2025_01_02
            Annotation Date                   :: 01/02/2025 02:14:37
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.9
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 8,793
            CDSs (total)                      :: 8,707
            Genes (coding)                    :: 8,547
            CDSs (with protein)               :: 8,547
            Genes (RNA)                       :: 86
            rRNAs                             :: 5, 3, 2 (5S, 16S, 23S)
            complete rRNAs                    :: 5, 1 (5S, 16S)
            partial rRNAs                     :: 2, 2 (16S, 23S)
            tRNAs                             :: 73
            ncRNAs                            :: 3
            Pseudo Genes (total)              :: 160
            CDSs (without protein)            :: 160
            Pseudo Genes (ambiguous residues) :: 0 of 160
            Pseudo Genes (frameshifted)       :: 47 of 160
            Pseudo Genes (incomplete)         :: 136 of 160
            Pseudo Genes (internal stop)      :: 6 of 160
            Pseudo Genes (multiple problems)  :: 29 of 160
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            ##antiSMASH-Data-START##
            Version                           :: 8.dev-cf2fc5ee(changed)
            Run date                          :: 2025-09-13 04:25:11
            NOTE :: This is a single region extracted from a larger record!
            Orig. start                       :: 0
            Orig. end                         :: 3900
            ##antiSMASH-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            FZOF01000076.1.
            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..3900
                     /db_xref="taxon:235986"
                     /mol_type="genomic DNA"
                     /note="contig: Ga0079895_176"
                     /organism="Actinacidiphila glaucinigra"
                     /strain="CGMCC 4.1858"
                     /type_material="type strain of Streptomyces glauciniger"
     region          1..3900
                     /candidate_cluster_numbers="1"
                     /contig_edge="True"
                     /product="lanthipeptide-class-ii"
                     /region_number="1"
                     /rules="cds(LANC_like and DUF4135)"
                     /tool="antismash"
     cand_cluster    1..3900
                     /candidate_cluster_number="1"
                     /contig_edge="True"
                     /detection_rules="cds(LANC_like and DUF4135)"
                     /kind="single"
                     /product="lanthipeptide-class-ii"
                     /protoclusters="1"
                     /tool="antismash"
     protocluster    1..3900
                     /aStool="rule-based-clusters"
                     /category="RiPP"
                     /contig_edge="True"
                     /core_location="[461:3332](+)"
                     /cutoff="20000"
                     /detection_rule="cds(LANC_like and DUF4135)"
                     /neighbourhood="10000"
                     /product="lanthipeptide-class-ii"
                     /protocluster_number="1"
                     /tool="antismash"
     proto_core      462..3332
                     /aStool="rule-based-clusters"
                     /tool="antismash"
                     /cutoff="20000"
                     /detection_rule="cds(LANC_like and DUF4135)"
                     /neighbourhood="10000"
                     /product="lanthipeptide-class-ii"
                     /protocluster_number="1"
     gene            462..3332
                     /gene="lanM"
                     /locus_tag="CHF15_RS43710"
                     /old_locus_tag="SAMN05216252_1761"
     CDS             462..3332
                     /GO_process="GO:0009403 - toxin biosynthetic process
                     [Evidence IEA]"
                     /GO_process="GO:0018193 - peptidyl-amino acid modification
                     [Evidence IEA]"
                     /codon_start=1
                     /gene="lanM"
                     /gene_functions="biosynthetic (rule-based-clusters)
                     lanthipeptide-class-ii: LANC_like"
                     /gene_functions="biosynthetic (rule-based-clusters)
                     lanthipeptide-class-ii: DUF4135"
                     /gene_functions="biosynthetic-additional (smcogs)
                     SMCOG1070: lanthionine synthetase C family protein"
                     /gene_kind="biosynthetic"
                     /inference="COORDINATES: protein motif:HMM:TIGR03897.1"
                     /locus_tag="CHF15_RS43710"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /old_locus_tag="SAMN05216252_1761"
                     /product="type 2 lanthipeptide synthetase LanM"
                     /protein_id="WP_179280274.1"
                     /sec_met_domain="DUF4135 (E-value: 4.4e-84, bitscore:
                     269.8, seeds: 79, tool: rule-based-clusters)"
                     /sec_met_domain="LANC_like (E-value: 6.2e-37, bitscore:
                     114.2, seeds: 47, tool: rule-based-clusters)"
                     /transl_table=11
                     /translation="MTHSQDRSSSEATYVTGDLHEVWHRLPGRAWPGEASDEDLALLGW
                     IGPLAVSAQEELRRRLGEACSETPLLDHSPAIFALPSARFLAMVKPMLVEELNATRSAR
                     EPDSPDTGFRGFEHFTASIREPETAVALLRKYPALARELVAEFDRWAASRLEFVTRLLT
                     DLPLLREKLAVTAASAADVEAVDFGAGDAHNGGRTVAVVSFRGGLKVVYKPRSLACDAA
                     FARFLDWLGDRGLTHRLRPARVLDCGTHGWSAHYAPAPCPDHNSLRRFYWRQGAFLAVF
                     HLLRGYDMHFQNQVAVGEDPVYFDLEALFHAESSDPGWLDDAEDVVARRLRDSVLAVGL
                     LPHRLVRTDEHGVRAMEMSGLAGGAAPGEFWAHPRTEYRDPGTDRMKPVPAFHPVGEYG
                     NRPTIAGHRHTPEEMADDLVSGFTHCYRLLLSQRPALSRSDGPLAQFSGVPVRAVLRDT
                     FQYRTVLTESWDPGLLTDPDRRHAHLGRLGHHNAGHPVKDSEWRQLACGDIPAFQTTPE
                     STDIADHHGILQRDFFKRAGTDLVRDRFASLSEEDLREQIWFIETSFTTRQEGGHLCTL
                     APSAPGSPAAALDSDLTLSAARAIGDQICDSVIRGEEGLVEWPSLRMVADRYWLVESGG
                     MGLDRGVSGIALFLAELGRSTGSDRYRSLAQDILTALLDPNDMPEPEELAGLEIGAYAE
                     LGGVLYLLTRAAEIWDAPELLGSAHRLVPAFAAAFDAPQPLDVATGVAGAALALVALQR
                     TDPSPQVLEAVRAAGAGLSDMAESGVPGFAHGLSGRAHALTAVACLTGDTVLLDRAAEA
                     RKRVNGMRLATASWCRGNAGLVMGEASSRWLVSGLEHQRPHGLDRVVAAVVQGVRNDSL
                     CHGTLGLVEALLTTSEYIGDAELRRVARDAAAGVAQRVLAGRVVTGVPRGTWTPGLLDG
                     AAGIGYGLLRTAAPHRVPNVLLMATP"
     misc_feature    3362..3373
                     /note="TFBS match to AfsR, Pleiotropic regulatory for
                     antibiotic production, confidence: medium, score: 19.75"
                     /tool="antismash"
     misc_feature    complement(3486..3498)
                     /note="TFBS match to MatP, Cell cycle regulator,
                     confidence: weak, score: 19.62"
                     /tool="antismash"
     misc_feature    complement(3504..3516)
                     /note="TFBS match to MatP, Cell cycle regulator,
                     confidence: weak, score: 19.46"
                     /tool="antismash"
     CDS             3532..3681
                     /gene="allorf_3532_3681"
                     /locus_tag="allorf_3532_3681"
                     /protein_id="allorf_3532_3681"
                     /tool="antismash"
                     /transl_table=1
                     /translation="MIDDLQTDVGDRELNELLPAGAAARRRGRERPPRWPVRRSPRCPL
                     RPGR"
     CDS_motif       3532..3591
                     /prepeptide="leader"
                     /note="peptide class: lanthipeptide"
                     /note="predicted sequence: MIDDLQTDVGDRELNELLPA"
                     /locus_tag="allorf_3532_3681_lanthipeptide"
                     /aSTool="lanthipeptides"
                     /tool="antismash"
     CDS_motif       3592..3681
                     /prepeptide="core"
                     /locus_tag="allorf_3532_3681_lanthipeptide"
                     /peptide="lanthipeptide"
                     /predicted_class="Class II"
                     /score="-4.10"
                     /molecular_weight="3402.9"
                     /monoisotopic_mass="3400.9"
                     /core_sequence="GAAARRRGRERPPRWPVRRSPRCPLRPGR"
                     /aSTool="lanthipeptides"
                     /tool="antismash"
                     /leader_sequence="MIDDLQTDVGDRELNELLPA"
                     /leader_location="[3531:3591](+)"
     CDS             3554..3697
                     /gene="allorf_3554_3697"
                     /locus_tag="allorf_3554_3697"
                     /protein_id="allorf_3554_3697"
                     /tool="antismash"
                     /transl_table=1
                     /translation="MWGTGNSTNFFPQGRQRGAGGESALPDGPFDARRDVRCAPAGERV
                     LS"
     CDS_motif       3554..3616
                     /prepeptide="leader"
                     /note="peptide class: lanthipeptide"
                     /note="predicted sequence: MWGTGNSTNFFPQGRQRGAGG"
                     /locus_tag="allorf_3554_3697_lanthipeptide"
                     /aSTool="lanthipeptides"
                     /tool="antismash"
     CDS_motif       3617..3697
                     /prepeptide="core"
                     /locus_tag="allorf_3554_3697_lanthipeptide"
                     /peptide="lanthipeptide"
                     /predicted_class="Class II"
                     /score="-7.00"
                     /molecular_weight="2749.0"
                     /monoisotopic_mass="2747.4"
                     /core_sequence="ESALPDGPFDARRDVRCAPAGERVLS"
                     /aSTool="lanthipeptides"
                     /tool="antismash"
                     /leader_sequence="MWGTGNSTNFFPQGRQRGAGG"
                     /leader_location="[3553:3616](+)"
                     /alternative_weights="2767.0"
     gene            3736..>3900
                     /locus_tag="CHF15_RS46330"
                     /old_locus_tag="SAMN05216252_1762"
                     /pseudo=""
     CDS             3736..>3900
                     /codon_start=1
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_018558646.1"
                     /locus_tag="CHF15_RS46330"
                     /note="incomplete; too short partial abutting assembly gap;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /old_locus_tag="SAMN05216252_1762"
                     /product="pyridoxamine 5'-phosphate oxidase family protein"
                     /pseudo=""
                     /transl_table=11
                     /translation="MSATPSAADAYASTDRTVPTRSRKRASYDRDLVHAILDADYLCHL
                     GFVRDGAPVV"
ORIGIN
        1 ccctgggtga cggacttggc ggcgggcttc gcgtacttac gcatgaaagt gcctctctct
       61 cgtaaacgat gtaccggcaa tggtccagca gcgctaatgc cgctggtttc cgtttcaccg
      121 gcgactgaag tcaagcacgg caatgacggg ctcaccagat gattcggtcc tcgccgaacc
      181 accatttcat ttgtccggat cacacacgga ttgccacgag tacgccgggt caatcctcgt
      241 tcctcacagc gctacggaac gacgtccgct atcgcgtgga cccgcgcttg tcccgtggag
      301 tgttgggttg tatagatgga catacccgcg ggcgtatgcg gcacccaggc cggatgcgtc
      361 gaatacctgg tacgcccttt ccattctcgc cgataccggc cggaattagt tgcacgcaag
      421 gccgtacccg cccttttgaa ttcaccttcc ggagtgagat tgtgacgcac agccaggacc
      481 gctcgtcctc ggaagccacc tacgtgacgg gcgacctcca tgaggtgtgg catcgtcttc
      541 caggccgcgc ttggccggga gaggcctccg acgaggacct ggcgctcttg ggctggatcg
      601 gcccgctcgc cgtctcggca caagaggagc tgcgccgacg gcttggtgag gcgtgttccg
      661 agacgcccct gctagaccac tcccccgcga tcttcgccct tccctccgcc cgcttcctgg
      721 ccatggtgaa gccgatgctg gtggaggagc tgaatgcgac gcggtccgcc cgcgagccgg
      781 acagtccgga cacgggattc cgggggttcg agcacttcac cgcctcgatc cgtgagccgg
      841 agaccgcggt cgccctgctg cggaagtatc cggcgcttgc cagggaattg gtagcggaat
      901 tcgatcgctg ggcagcgtct cgtctggaat tcgtgacgag gctgctgact gacctgcccc
      961 tgctccggga gaaactggcg gtgacggcgg cgtccgcggc cgatgtggaa gccgtcgact
     1021 tcggcgcggg agacgcccac aacgggggaa gaacggtggc cgtcgtctcc tttcgcggag
     1081 ggctcaaggt tgtctacaag ccccgctctc tcgcctgcga cgcagcgttc gcgcgattcc
     1141 tcgactggct tggcgaccga ggtctgacgc accgtctgcg gccggcacga gtcctcgact
     1201 gtggcactca cggatggtcg gcacactacg cgccggcccc atgcccagac cacaactccc
     1261 tgcggcgctt ctactggcgg caaggcgcct tcctcgccgt gttccacctg ctgcgcggct
     1321 acgacatgca cttccagaac caggtggcgg tcggcgaaga cccggtctac ttcgacctgg
     1381 aggctctgtt ccatgctgag tcctcggacc cgggctggct cgacgacgcg gaggacgtgg
     1441 tcgcgcggcg gctgcgcgac tccgtgctgg cagttggcct cctgccgcac cggctcgtcc
     1501 gcaccgacga acacggtgtt cgtgccatgg agatgagcgg tctagccggt ggtgcggcac
     1561 ccggtgagtt ctgggcccac ccccgcactg agtaccgcga tcccggtact gaccgtatga
     1621 aaccggtccc cgcgttccac ccagtcggag agtacggcaa ccgccccacc atcgcgggcc
     1681 atcgtcacac cccggaagag atggccgacg acctagtctc gggctttact cactgctatc
     1741 gcctactgct ctcgcagcgt ccggctctgt cgcggtccga cggcccgctg gcacagttct
     1801 ccggggtccc cgtgcgagcg gtgctgcgcg acaccttcca gtaccgcacc gtactcaccg
     1861 agtcctggga tccgggcctg ctcacggatc cggaccggcg ccacgcccac ctcgggcgcc
     1921 tcggacacca caacgccggg caccctgtca aggacagcga gtggcgccag ctcgcgtgcg
     1981 gagacatacc cgccttccag accaccccgg agagcaccga catcgcggac caccacggga
     2041 ttctgcagcg ggacttcttc aaacgcgctg gcacggacct tgtgcgggac cgcttcgcct
     2101 ccttgtcgga ggaggacttg cgggagcaga tctggttcat cgagacctcg ttcaccaccc
     2161 gccaggaggg cggccacctg tgtacgctgg ctccctccgc tcctggttcc ccggccgccg
     2221 cgctcgattc ggacctaacc ctctctgctg ccagagccat cggtgaccag atctgcgact
     2281 ctgtgatccg cggcgaggaa ggactcgtcg aatggccatc gctccgtatg gtggccgacc
     2341 gctactggct cgtggaatcc ggcggtatgg gtctcgaccg cggcgtcagc ggcattgcgc
     2401 tcttccttgc cgagctgggt cggtcgaccg ggtcggacag ataccggtcg ctggcccagg
     2461 acatcctcac cgctctgctg gaccccaacg acatgcccga gccggaggaa ttggcgggct
     2521 tggagatcgg ggcgtatgcc gaactgggcg gcgtccttta cctcctgacc cgggctgccg
     2581 agatctggga cgccccggaa ctcctgggtt ccgcccaccg gctcgtgccg gccttcgctg
     2641 cggccttcga cgcgccgcag cccctagatg tagcgactgg agtagccggg gcggcgcttg
     2701 ccctcgtggc cctccaacgg accgacccga gcccccaggt cctggaagcc gtccgggccg
     2761 ctggggcggg tctctccgac atggcggaat ccggcgtccc cgggttcgct catggcctgt
     2821 caggccgggc acacgcgctg actgctgtcg cttgcctgac cggcgatacg gtgctgctgg
     2881 accgggcggc cgaggcgcgc aagcgtgtca atggcatgcg tctcgctacc gcctcctggt
     2941 gccgggggaa cgcggggctc gtcatgggcg aggcgagcag tcgctggctc gtcagcggcc
     3001 tggaacacca gcggccccat gggctggacc gcgtcgtggc ggccgtggtc cagggggtcc
     3061 gcaacgactc gctctgccac ggcactctcg gactggtcga ggcgctcctc accacctccg
     3121 agtacatcgg cgacgcggag ttgcggcggg tcgcgcgcga cgcagcggca ggcgtcgccc
     3181 agcgggttct cgccggtcgg gtggtgaccg gcgttccccg aggcacgtgg acacccggac
     3241 tcttggacgg ggcggcgggg atcgggtatg gcctcctgag gaccgcggca ccgcatcgcg
     3301 tgccgaacgt cctgctgatg gccaccccat gagcgtcagg ggcagagcct cctatcggcg
     3361 gagacgtgaa cgccgactag tactccagta agacttctcc atttgccctg gtcaatggct
     3421 tgatgtcgcg aagttaagcg gggcacacgg gtgggacggc cttgcggagg acgtcccacc
     3481 cacgggtgac tgtggcacat gcagtgacag cggcgcggag agtccaccac tgtgatcgac
     3541 gatctacaga cggatgtggg ggaccgggaa ctcaacgaac ttcttcccgc aggggcggca
     3601 gcgcggcgcc gggggcgaga gcgccctccc cgatggcccg ttcgacgctc gccgcgatgt
     3661 ccgctgcgcc ccggccggtg aacgtgtact ctcctagcac aaaaagcatt atgcactagt
     3721 gcaaaggatc gcgccatgtc cgccacgccc tccgctgccg atgcgtacgc ttccaccgac
     3781 cgcaccgtcc ccacccgcag ccgcaagcgc gcctcgtacg accgcgacct ggtgcacgcg
     3841 atcctcgacg cggactacct ctgccacctc ggcttcgtcc gcgacggggc gccggtcgtg
//
