LOCUS       NZ_JAQESL010000059      3232 bp    DNA     linear   CON 29-FEB-2024
DEFINITION  Coprococcus sp. AM97-35 AM97-35.Scaf59, whole genome shotgun
            sequence.
ACCESSION   NZ_JAQESL010000059
VERSION     NZ_JAQESL010000059.1
KEYWORDS    WGS; RefSeq.
SOURCE      Coprococcus sp. AM97-35
  ORGANISM  Coprococcus sp. AM97-35
            Bacteria; Bacillota; Clostridia; Lachnospirales; Lachnospiraceae;
            Coprococcus.
REFERENCE   1  (bases 1 to 3232)
  AUTHORS   Lin,X., Hu,T., Chen,J., Liang,H., Zhou,J., Wu,Z., Ye,C., Jin,X.,
            Xu,X., Zhang,W., Jing,X., Yang,T., Wang,J., Yang,H., Kristiansen,K.,
            Xiao,L. and Zou,Y.
  TITLE     The genomic landscape of reference genomes of cultivated human gut
            bacteria
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3232)
  AUTHORS   Zou,Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (30-NOV-2022) BGI Reaserch, BGI-Shenzhen, Beishan
            Industrial Zone, Shenzhen 518083, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: SOAPdenovo v. v2.04
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100x
            Sequencing Technology             :: MGI
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/29/2024 10:49:15
            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)                     :: 3,361
            CDSs (total)                      :: 3,321
            Genes (coding)                    :: 3,266
            CDSs (with protein)               :: 3,266
            Genes (RNA)                       :: 40
            rRNAs                             :: 1, 1 (16S, 23S)
            complete rRNAs                    :: 1, 1 (16S, 23S)
            tRNAs                             :: 34
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 55
            CDSs (without protein)            :: 55
            Pseudo Genes (ambiguous residues) :: 0 of 55
            Pseudo Genes (frameshifted)       :: 6 of 55
            Pseudo Genes (incomplete)         :: 54 of 55
            Pseudo Genes (internal stop)      :: 2 of 55
            Pseudo Genes (multiple problems)  :: 5 of 55
            ##Genome-Annotation-Data-END##
            ##antiSMASH-Data-START##
            Version                           :: 8.dev-cf2fc5ee(changed)
            Run date                          :: 2025-09-13 09:11:55
            NOTE :: This is a single region extracted from a larger record!
            Orig. start                       :: 0
            Orig. end                         :: 3232
            ##antiSMASH-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            JAQESL010000059.1.
            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
     region          1..3232
                     /candidate_cluster_numbers="1"
                     /contig_edge="True"
                     /product="lanthipeptide-class-ii"
                     /region_number="1"
                     /rules="cds(LANC_like and DUF4135)"
                     /tool="antismash"
     protocluster    1..3232
                     /aStool="rule-based-clusters"
                     /category="RiPP"
                     /contig_edge="True"
                     /core_location="[<0:2544](+)"
                     /cutoff="20000"
                     /detection_rule="cds(LANC_like and DUF4135)"
                     /neighbourhood="10000"
                     /product="lanthipeptide-class-ii"
                     /protocluster_number="1"
                     /tool="antismash"
     proto_core      <1..2544
                     /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            <1..2544
                     /gene="lanM"
                     /locus_tag="PG840_RS16500"
     CDS             <1..2544
                     /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="PG840_RS16500"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /product="type 2 lanthipeptide synthetase LanM"
                     /protein_id="WP_270613899.1"
                     /sec_met_domain="DUF4135 (E-value: 3.1e-74, bitscore:
                     237.4, seeds: 79, tool: rule-based-clusters)"
                     /sec_met_domain="LANC_like (E-value: 3.4e-40, bitscore:
                     124.9, seeds: 47, tool: rule-based-clusters)"
                     /transl_table=11
                     /translation="IYGNTFQKRVDSFTTMIKDKLFIENLFRKYPLLENILKINFHDFT
                     KLIYEIYKNYETDKLLIREKFNKDFGKIVNININLGDKHNGKTVAKVEFENGNLMYKPR
                     RLLSSNLYDELLRFIENKGVIDFKHYQSIVMQDYTWQEFVLYDADLTFAEAQRYYYRAG
                     VLLSLFLILKSTDMHHENIIVSGEYPMIIDTETILSAAIKDNMEITKGRSIEQSVLSTA
                     MLPINDSVYDINVSGLFFKEEFSKTIYYYSLIENKEKDFYYEKKAASTSLQKNIVFVNG
                     KIVGSEEVGEKLLEGFEAGAKCLLRNLEEFKKILGSSKYAQLEVRALLRGTQVYYTFIR
                     ECKKIETLKNKQKFDKILRILLKGFQPAEFGYLRVEEEIENLKKLDIPLFYTKLNDVNL
                     YSRNKVICNEYFKNSPLQNVLNGLSVFNEEMIKYQKHLIELSLFTFSCKESDINTESLL
                     IDKSIENKELQYILGKYAYEMLSYEVPMTDDSSLFYMAALNQECLRIDAVNAGIYMGGG
                     IIHFLYSYADVFKDETIKKYSKRLLKGIYNRYLIEKEKMDIKPFGIYEGYGGILYLSYN
                     YSRLNEDLEIDTIFQTMLIDVLDYYSTKSFDRKIDTDYINGIGSTILLLGKIYFEKTVD
                     RSIEQKLENLFEKYYEFLKISSIEDSIGIAHGLSGVSVVLSYIYRIFREEECLKLIETL
                     ITKEDQIIEKYLKTNTISYTWCRGMAGVLVSRCVIKENLEYISGNTYLKNYLQKKINKY
                     STKNIIESMMEVKNACLCHGIAGNIDAINYFNKVTGNSYKTDYFIDNIDSYNWFTNSKY
                     QFESFMLGKAGLMYSLLYQLEGNNVLSISALEIVK"
     source          1..3232
                     /collection_date="2014-02-01"
                     /country="China: Shenzhen"
                     /db_xref="taxon:2997953"
                     /host="Homo sapiens"
                     /isolation_source="fecal material [ENVO:00002003]"
                     /lat_lon="22.32 N 114.05 E"
                     /mol_type="genomic DNA"
                     /organism="Coprococcus sp. AM97-35"
                     /strain="AM97-35"
                     /submitter_seqid="AM97-35.Scaf59"
     cand_cluster    1..3232
                     /candidate_cluster_number="1"
                     /contig_edge="True"
                     /detection_rules="cds(LANC_like and DUF4135)"
                     /kind="single"
                     /product="lanthipeptide-class-ii"
                     /protoclusters="1"
                     /tool="antismash"
     gene            2576..>3232
                     /locus_tag="PG840_RS16505"
     CDS             2576..>3232
                     /GO_component="GO:0016020 - membrane [Evidence IEA]"
                     /GO_function="GO:0005524 - ATP binding [Evidence IEA]"
                     /GO_function="GO:0008233 - peptidase activity [Evidence
                     IEA]"
                     /GO_process="GO:0006508 - proteolysis [Evidence IEA]"
                     /codon_start=1
                     /gene_functions="biosynthetic-additional
                     (rule-based-clusters) Peptidase_C39"
                     /gene_kind="biosynthetic-additional"
                     /inference="COORDINATES: protein motif:HMM:NF015377.4"
                     /locus_tag="PG840_RS16505"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /product="cysteine peptidase family C39 domain-containing
                     protein"
                     /protein_id="WP_270613900.1"
                     /sec_met_domain="Peptidase_C39 (E-value: 3.7e-24, bitscore:
                     72.2, seeds: 36, tool: rule-based-clusters)"
                     /transl_table=11
                     /translation="MKKIKLIRQTTVSECGLCCVSMVAEYFGYVKPFNYYRQQYNPGRD
                     GISIKEMYLILCNIHLSPKVYNLDNIKEFYFDKKPYILLTKDNHYIVCVKRKQGFHLFD
                     PAKGKKRINLKDLEKISGGILISCDIDENFIKIKEKTSEFRHVKKFFLSILPTFICVSG
                     IALIGYFLALLIPKVIEAIINDILLRTEVNLDIILSKLLILMLIYLVISVLQNNLT"
     misc_feature    complement(2600..2613)
                     /note="TFBS match to PsrA, Oleic acid responsive regulator,
                     confidence: weak, score: 20.05"
                     /tool="antismash"
ORIGIN
        1 atatatggaa atacttttca aaaacgagtg gactctttta caactatgat aaaagataaa
       61 ctattcattg aaaacttatt tcggaaatat ccattattag aaaatatttt gaaaatcaat
      121 tttcatgatt tcacaaagct aatttatgag atttataaaa actatgaaac agataaatta
      181 ttaataagag aaaaatttaa taaggatttt ggcaaaattg taaatattaa tattaattta
      241 ggggataagc ataatggtaa aacagtagca aaagtggagt ttgagaacgg gaatttaatg
      301 tataaaccaa gaagattatt aagtagcaat ttatatgatg aattattgcg gtttatagaa
      361 aataaaggag taattgattt taagcattac caatcaattg ttatgcaaga ttatacatgg
      421 caagaatttg ttctatatga tgctgactta acatttgcag aggcacaacg atattattat
      481 agagccggtg ttttattatc attattttta attcttaaat cgacagatat gcatcatgaa
      541 aatataattg tttcaggaga atatccaatg ataatagata cggagacaat attatcagca
      601 gccattaaag ataatatgga aattaccaag gggcgaagta ttgagcaaag tgtattatca
      661 actgcaatgt taccaataaa cgacagtgtt tatgacatta atgtttctgg tttgtttttt
      721 aaagaggaat tttctaaaac aatatattac tattcactaa tcgagaacaa agaaaaagat
      781 ttttattatg aaaaaaaagc agcatctaca agtttgcaaa aaaatatcgt atttgtgaat
      841 ggaaaaatag ttggaagtga agaggttggt gaaaagttat tagaaggatt tgaagctggc
      901 gcaaaatgtt tgttaagaaa cttggaagaa tttaaaaaaa ttctaggcag tagtaagtat
      961 gctcagttag aagttagagc tttattgcgt ggaacacagg tgtattatac atttattcgt
     1021 gaatgcaaaa aaattgaaac gctaaaaaac aaacaaaaat ttgataaaat tttgcgaatt
     1081 ttgttaaagg gatttcagcc agcagagttt gggtatctta gagttgaaga agaaatagaa
     1141 aatttaaaga aattggatat ccccttattt tatacaaaat tgaatgatgt taatttatat
     1201 agccgaaata aagttatttg caatgagtat tttaaaaatt cgccgttaca aaatgtgtta
     1261 aatgggcttt ctgtttttaa tgaagaaatg atcaagtacc aaaaacattt aattgagttg
     1321 agtttgttta cgttttcgtg taaagaaagt gacataaata cagagtctct attaattgat
     1381 aagtcaatag aaaacaaaga gttgcaatac atattgggaa aatatgccta tgagatgtta
     1441 agttatgaag tgccaatgac agatgattca agtttatttt atatggcagc attgaatcaa
     1501 gaatgtctta ggatagatgc cgttaatgct ggaatatata tgggaggggg aattattcat
     1561 tttttatatt cgtatgcaga tgtcttcaag gatgaaacaa ttaagaagta ttcaaagagg
     1621 ctattaaagg gaatttataa tagatatctt attgaaaaag aaaaaatgga tataaagcca
     1681 tttggaattt atgaaggata tggtggtatt ttatatttat catataatta ttcaaggcta
     1741 aatgaagatt tagaaataga tactattttt cagaccatgt taattgatgt actggattac
     1801 tatagtacaa aaagctttga tagaaagata gatacggatt atattaatgg tattggaagt
     1861 actatacttt tgttaggaaa aatatatttt gagaaaacag tagatagatc catagaacaa
     1921 aagctggaaa atttattcga aaaatattat gaatttttaa aaataagtag tatagaagat
     1981 tctataggga ttgcacatgg cctatcaggc gtttctgttg ttctttcgta tatataccga
     2041 atatttagag aagaagagtg cttaaagtta atagagactt taataacaaa agaggatcaa
     2101 ataatagaaa aatatttaaa aacaaataca ataagctata cgtggtgtag aggtatggca
     2161 ggagttcttg tttcaagatg tgtcataaaa gaaaatctag aatatatttc tggcaatacg
     2221 tatcttaaaa attatttaca gaaaaaaata aataaatata gtacgaaaaa tataatagaa
     2281 agtatgatgg aagtaaaaaa cgcttgttta tgtcatggaa ttgcaggaaa catagatgct
     2341 ataaattatt ttaataaggt tactggtaat tcatataaaa cagattattt tatagataat
     2401 atagattcgt ataattggtt tacaaattcg aaatatcaat ttgaatcatt tatgcttgga
     2461 aaagcaggat tgatgtatag tttattgtat caattagagg ggaataatgt attatctata
     2521 agcgcattag aaatagtcaa gtaatataca gtgataaaag agcatagagg gctacatgaa
     2581 aaaaattaaa ttaattagac aaacaacagt ttcggaatgc gggttgtgtt gtgtttctat
     2641 ggttgcagaa tactttggat atgtaaaacc ttttaattat tataggcaac aatataatcc
     2701 agggagagat gggatttcta taaaagaaat gtatttaatt ctgtgtaata tacatctatc
     2761 tcctaaagtt tataacttag acaatataaa ggaattttat ttcgataaaa aaccttatat
     2821 tcttttaaca aaagacaatc attatattgt atgcgttaaa agaaagcaag gatttcactt
     2881 atttgatccg gcaaaaggga aaaaaagaat aaatcttaaa gatttggaaa aaattagtgg
     2941 tggtattctt atatcatgcg atattgatga aaactttatt aaaataaaag aaaaaacaag
     3001 tgaatttcga catgtaaaaa aattcttttt aagtatattg ccaactttta tttgtgtttc
     3061 tggtattgct cttataggat actttttagc gttgctcatt cctaaagtaa ttgaggcaat
     3121 aataaatgat atattactta gaacagaggt aaatctagat attattttat caaaattatt
     3181 aattctaatg ttaatatatt tagttatatc tgtactacaa aataatctaa ca
//
