LOCUS       NZ_FOBB01000021         1895 bp    DNA     linear   CON 22-OCT-2024
DEFINITION  Chitinophaga rupis strain DSM 21039, whole genome shotgun sequence.
ACCESSION   NZ_FOBB01000021
VERSION     NZ_FOBB01000021.1
KEYWORDS    WGS; RefSeq.
SOURCE      Chitinophaga rupis
  ORGANISM  Chitinophaga rupis
            Bacteria; Bacteroidota; Chitinophagia; Chitinophagales;
            Chitinophagaceae; Chitinophaga.
REFERENCE   1
  AUTHORS   Varghese,N. and Submissions,S.
  TITLE     Direct Submission
  JOURNAL   Submitted (27-OCT-2016) DOE - JOINT GENOME INSTITUTE, LBNL, 2800
            Mitchell Drive, Walnut Creek, CA 94598, 94598, USA
COMMENT     ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_900109685.1-RS_2024_10_22
            Annotation Date                   :: 10/22/2024 15:41:43
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.8
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 6,474
            CDSs (total)                      :: 6,410
            Genes (coding)                    :: 6,392
            CDSs (with protein)               :: 6,392
            Genes (RNA)                       :: 64
            rRNAs                             :: 1, 2, 1 (5S, 16S, 23S)
            complete rRNAs                    :: 1, 1 (5S, 16S)
            partial rRNAs                     :: 1, 1 (16S, 23S)
            tRNAs                             :: 57
            ncRNAs                            :: 3
            Pseudo Genes (total)              :: 18
            CDSs (without protein)            :: 18
            Pseudo Genes (ambiguous residues) :: 0 of 18
            Pseudo Genes (frameshifted)       :: 4 of 18
            Pseudo Genes (incomplete)         :: 13 of 18
            Pseudo Genes (internal stop)      :: 2 of 18
            Pseudo Genes (multiple problems)  :: 1 of 18
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            ##antiSMASH-Data-START##
            Version                           :: 8.dev-cf2fc5ee(changed)
            Run date                          :: 2025-09-13 10:12:51
            NOTE :: This is a single region extracted from a larger record!
            Orig. start                       :: 0
            Orig. end                         :: 1895
            ##antiSMASH-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            FOBB01000021.1.
            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..1895
                     /db_xref="taxon:573321"
                     /mol_type="genomic DNA"
                     /note="contig: Ga0070597_121"
                     /organism="Chitinophaga rupis"
                     /strain="DSM 21039"
                     /type_material="type strain of Chitinophaga rupis"
     gene            complement(<1..>1895)
                     /locus_tag="BMZ54_RS32650"
                     /old_locus_tag="SAMN04488505_1211"
     region          1..1895
                     /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..1895
                     /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..1895
                     /aStool="rule-based-clusters"
                     /category="NRPS"
                     /contig_edge="True"
                     /core_location="[<0:1895](-)"
                     /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..1895)
                     /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..1895)
                     /GO_function="GO:0003824 - catalytic activity [Evidence
                     IEA]"
                     /NRPS_PKS="Domain: PCP (1-65). E-value: 3.2e-24. Score:
                     76.9. Matches aSDomain: nrpspksdomains_BMZ54_RS32650_PCP.1"
                     /NRPS_PKS="Domain: Condensation_LCL (82-379). E-value:
                     7e-103. Score: 335.7. Matches aSDomain:
                     nrpspksdomains_BMZ54_RS32650_Condensation_LCL.1"
                     /codon_start=1
                     /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: protein motif:HMM:NF012873.5"
                     /locus_tag="BMZ54_RS32650"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /old_locus_tag="SAMN04488505_1211"
                     /product="condensation domain-containing protein"
                     /protein_id="WP_143081228.1"
                     /sec_met_domain="PP-binding (E-value: 2.5e-16, bitscore:
                     46.3, seeds: 164, tool: rule-based-clusters)"
                     /sec_met_domain="Condensation (E-value: 6.1e-78, bitscore:
                     248.0, seeds: 42, tool: rule-based-clusters)"
                     /sec_met_domain="AMP-binding (E-value: 6.7e-22, bitscore:
                     63.6, seeds: 400, tool: rule-based-clusters)"
                     /transl_table=11
                     /translation="MQQIWQEVLGISRVGVTDNFFELGGHSLKALRIFSAIHRRLQLNA
                     VLTDIFSYPTIRTFAIRLENAAATRHNSIPVQEPQSFYPVSYAQQRIWLLDNMEKAAAA
                     YNMPAGCYLTGIIQPLILEQAINALISRHEILRTGFIMQEDRLVQVIHAADTVHCKLNV
                     ISAQGKDDEQLAAMLTAAASTRFNLEEPLLFNATLVQLEQKKYVLLLNMHHIITDGWSA
                     EILLQELLRLYEAFVQEQPSPLAPLRIQYRDYAVWQQQGEGAAIIAAQQQYWLQQFAGE
                     LPVLALQTDRPRPAVKTYNGHTYYFQLDQPLAQQLKAFSQEQGATLFMTLLACVQVLLH
                     KYTAQHDLVIGTVTAGRDYKDLEDQAGMYANSLALRCRFNTEDTFATLLAQTKALVLDA
                     FAHQQYPFDKLVNELPLKRDTSRHPLFDVMVMLNGEQQATAPVAYYEPELPTSKFDITF
                     NFTVAGNSLTAALEYNTDLFDAARIALLAKHFNTLLTNILAAPGAVIQSYRLMPPDEQA
                     ALLRNGEQAAPFAAAQCLQEQLSLIAQQYPQRVAIVQGNESITYGELEARANRLAHLLR
                     RDYGVTPNTPVGLQGLRSPALLAGLWAILKAGGAYVPVDPAYPAARRQYLLTDSG"
     CDS_motif       complement(51..92)
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_BMZ54_RS32650_0008"
                     /evalue="2.80E-06"
                     /label="NRPS-A_a2"
                     /locus_tag="BMZ54_RS32650"
                     /protein_end="615"
                     /protein_start="601"
                     /score="20.3"
                     /tool="antismash"
                     /translation="WAILKAGGAYVPVD"
     CDS_motif       complement(603..713)
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_BMZ54_RS32650_0007"
                     /evalue="5.00E-18"
                     /label="C67_LCL_14fromHMM"
                     /locus_tag="BMZ54_RS32650"
                     /protein_end="431"
                     /protein_start="394"
                     /score="57.5"
                     /tool="antismash"
                     /translation="LVLDAFAHQQYPFDKLVNELPLKRDTSRHPLFDVMVM"
     aSDomain        complement(759..1649)
                     /aSDomain="Condensation"
                     /aSTool="nrps_pks_domains"
                     /database="nrpspksdomains.hmm"
                     /detection="hmmscan"
                     /domain_id="nrpspksdomains_BMZ54_RS32650_Condensation_LCL.1
                     "
                     /domain_subtypes="Condensation_LCL"
                     /evalue="7.00E-103"
                     /label="BMZ54_RS32650_Condensation_LCL.1"
                     /locus_tag="BMZ54_RS32650"
                     /protein_end="379"
                     /protein_start="82"
                     /score="335.7"
                     /specificity="C activity: active"
                     /specificity="Active site motif: HHIITDG"
                     /tool="antismash"
                     /translation="YPVSYAQQRIWLLDNMEKAAAAYNMPAGCYLTGIIQPLILEQAIN
                     ALISRHEILRTGFIMQEDRLVQVIHAADTVHCKLNVISAQGKDDEQLAAMLTAAASTRF
                     NLEEPLLFNATLVQLEQKKYVLLLNMHHIITDGWSAEILLQELLRLYEAFVQEQPSPLA
                     PLRIQYRDYAVWQQQGEGAAIIAAQQQYWLQQFAGELPVLALQTDRPRPAVKTYNGHTY
                     YFQLDQPLAQQLKAFSQEQGATLFMTLLACVQVLLHKYTAQHDLVIGTVTAGRDYKDLE
                     DQAGMYANSLALRCRF"
     CDS_motif       complement(768..857)
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_BMZ54_RS32650_0006"
                     /evalue="5.50E-10"
                     /label="C5_LCL_267-296"
                     /locus_tag="BMZ54_RS32650"
                     /protein_end="376"
                     /protein_start="346"
                     /score="31.7"
                     /tool="antismash"
                     /translation="DLVIGTVTAGRDYKDLEDQAGMYANSLALR"
     CDS_motif       complement(1065..1097)
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_BMZ54_RS32650_0005"
                     /evalue="4.00E+00"
                     /label="C1_starter_004-017"
                     /locus_tag="BMZ54_RS32650"
                     /protein_end="277"
                     /protein_start="266"
                     /score="1.4"
                     /tool="antismash"
                     /translation="IAAQQQYWLQQ"
     CDS_motif       complement(1116..1148)
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_BMZ54_RS32650_0004"
                     /evalue="1.20E-04"
                     /label="C4_LCL_164-176"
                     /locus_tag="BMZ54_RS32650"
                     /protein_end="260"
                     /protein_start="249"
                     /score="14.7"
                     /tool="antismash"
                     /translation="QYRDYAVWQQQ"
     CDS_motif       complement(1197..1262)
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_BMZ54_RS32650_0003"
                     /evalue="5.40E-12"
                     /label="C3_LCL_132-143"
                     /locus_tag="BMZ54_RS32650"
                     /protein_end="233"
                     /protein_start="211"
                     /score="38.1"
                     /tool="antismash"
                     /translation="MHHIITDGWSAEILLQELLRLY"
     CDS_motif       complement(1476..1589)
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_BMZ54_RS32650_0002"
                     /evalue="8.30E-15"
                     /label="C2_LCL_024-062"
                     /locus_tag="BMZ54_RS32650"
                     /protein_end="140"
                     /protein_start="102"
                     /score="47.1"
                     /tool="antismash"
                     /translation="AAYNMPAGCYLTGIIQPLILEQAINALISRHEILRTGF"
     CDS_motif       complement(1608..1640)
                     /aSTool="nrps_pks_domains"
                     /database="abmotifs"
                     /detection="hmmscan"
                     /domain_id="nrpspksmotif_BMZ54_RS32650_0001"
                     /evalue="9.10E-03"
                     /label="C1_LCL_004-017"
                     /locus_tag="BMZ54_RS32650"
                     /protein_end="96"
                     /protein_start="85"
                     /score="8.8"
                     /tool="antismash"
                     /translation="SYAQQRIWLLD"
     aSDomain        complement(1701..1892)
                     /aSDomain="PCP"
                     /aSTool="nrps_pks_domains"
                     /database="nrpspksdomains.hmm"
                     /detection="hmmscan"
                     /domain_id="nrpspksdomains_BMZ54_RS32650_PCP.1"
                     /evalue="3.20E-24"
                     /label="BMZ54_RS32650_PCP.1"
                     /locus_tag="BMZ54_RS32650"
                     /protein_end="65"
                     /protein_start="1"
                     /score="76.9"
                     /tool="antismash"
                     /translation="QQIWQEVLGISRVGVTDNFFELGGHSLKALRIFSAIHRRLQLNAV
                     LTDIFSYPTIRTFAIRLEN"
ORIGIN
        1 ataccactgt ctgttagcag gtactggcgg cgggcagcgg ggtaagccgg atctaccggc
       61 acataagcgc cgccggcttt cagaatggcc cataagcctg cgagtaaagc agggctgcgc
      121 aagccctgca agcctaccgg cgtgttgggt gttaccccat aatcacggcg cagcaggtgg
      181 gccagccggt tagcgcgggc ttccagctcg ccgtaggtaa tactttcatt cccctgcaca
      241 atggccaccc gttgcgggta ttgctgtgca ataaggctca actgctcctg caggcattgt
      301 gcggctgcaa aaggtgctgc ctgttcgcca ttgcgtaata aagcagcctg ctcatccggc
      361 ggcattagcc ggtaagactg tataacagca cccggcgcgg ccaggatatt tgttagcaag
      421 gtgttgaaat gttttgccaa cagcgctatc cgggcagcat caaagaggtc tgtattatat
      481 tccagggcag cggttaagct atttcctgct accgtaaaat tgaaagtaat atcaaatttg
      541 ctggtgggca gttccggctc ataatacgca acaggcgcag tggcctgctg ctcaccgttc
      601 agcatcacca tcacatcaaa cagcggatgg cggctggtat cccttttaag cggcagctca
      661 ttcaccagct tatcaaaagg atactgctgg tgcgcaaaag cgtccagcac cagtgctttt
      721 gtttgagcaa gcaaagtggc aaaagtatct tccgtgttaa aacggcagcg cagggccagt
      781 gagttcgcat acatacctgc ctggtcttcc aggtccttat agtccctgcc ggcagttact
      841 gttcctatca ccaggtcatg ctgcgcagtg tatttatgca acaatacctg cacgcatgcc
      901 agcaaggtca taaaaagagt ggcgccctgt tcctggctga atgccttcag ctgctgcgcc
      961 agcggttgat ccagctgaaa ataataggta tggccgttat aggttttaac agcggggcgg
     1021 gggcggtctg tttgtaaagc cagcacaggc agctctcccg caaactgttg cagccagtat
     1081 tgctgctgtg cggcaataat agcagctcct tctccctgct gctgccatac ggcatagtcg
     1141 cggtactgga tgcgcaaggg cgctaacggt gatggttgtt cctgcacaaa ggcttcgtat
     1201 aaccgcaaca gctcctgtaa taatatttct gctgaccagc cgtctgtgat aatatgatgc
     1261 atgttgagca gcagcacata ttttttctgt tccagctgca cgagcgtggc attgaacagc
     1321 aagggctcct ccaggttaaa ccgggtggat gccgcagcag taagcatagc agccagctgc
     1381 tcatcatctt ttccctgggc ggatattacg ttcagcttac agtgaacagt atctgcagca
     1441 tggatcacct gcaccagcct gtcttcctgc attataaaac cggtgcgtaa gatctcgtgc
     1501 cggcttatca atgcattaat ggcctgctcc aatataagcg gctgtataat cccggtgaga
     1561 taacagccgg ccggcatatt atatgcggcg gcggcctttt ccatattatc cagtaaccag
     1621 atgcgctgct gtgcatagga aaccgggtaa aaagactgcg gttcctgcac agggatgctg
     1681 ttatgccttg tggcggcggc gttttccaac ctgattgcaa atgtgcgtat agttggatag
     1741 gaaaaaatat ctgtcagtac tgcgtttaat tgtaaacggc ggtgaatagc cgaaaagatg
     1801 cgcagcgctt tcagggaatg cccgcccagc tcaaaaaagt tatctgttac gcctacacgg
     1861 gaaataccca gcacctcctg ccagatctgc tgcag
//
