LOCUS       NZ_CP072261             2764 bp    DNA     circular CON 28-MAR-2024
DEFINITION  Bacteroides caccae CL03T12C61 plasmid pBcacCL03T12-3, complete
            sequence.
ACCESSION   NZ_CP072261
VERSION     NZ_CP072261.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16451178
            Assembly: GCF_018292205.1
KEYWORDS    RefSeq.
SOURCE      Bacteroides caccae CL03T12C61
  ORGANISM  Bacteroides caccae CL03T12C61
            Bacteria; Bacteroidota; Bacteroidia; Bacteroidales; Bacteroidaceae;
            Bacteroides.
REFERENCE   1  (bases 1 to 2764)
  AUTHORS   Garcia-Bayona,L., Coyne,M.J. and Comstock,L.E.
  TITLE     Mobile Type VI secretion system loci of the gut Bacteroidales
            display extensive intra-ecosystem transfer, multi-species spread and
            geographical clustering
  JOURNAL   PLoS Genet 17 (4), e1009541 (2021)
   PUBMED   33901198
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 2764)
  AUTHORS   Coyne,M.J.
  TITLE     Direct Submission
  JOURNAL   Submitted (25-JAN-2021) Department of Medicine/Division of
            Infectious Diseases, Brigham & Women's Hospital, 181 Longwood
            Avenue, Boston, MA 02115, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 20-OCT-2020
            Assembly Method                   :: FALCON-Unzip v. 1.2.0
            Assembly Name                     :: BcacCL03T12C61_pbv2
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 164x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_018292205.1-RS_2024_03_28
            Annotation Date                   :: 03/28/2024 06:46:16
            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)                     :: 4,594
            CDSs (total)                      :: 4,504
            Genes (coding)                    :: 4,387
            CDSs (with protein)               :: 4,387
            Genes (RNA)                       :: 90
            rRNAs                             :: 5, 5, 5 (5S, 16S, 23S)
            complete rRNAs                    :: 5, 5, 5 (5S, 16S, 23S)
            tRNAs                             :: 72
            ncRNAs                            :: 3
            Pseudo Genes (total)              :: 117
            CDSs (without protein)            :: 117
            Pseudo Genes (ambiguous residues) :: 0 of 117
            Pseudo Genes (frameshifted)       :: 42 of 117
            Pseudo Genes (incomplete)         :: 74 of 117
            Pseudo Genes (internal stop)      :: 31 of 117
            Pseudo Genes (multiple problems)  :: 25 of 117
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP072261.1.
            Sequencing by the Institute for Genome Sciences, Genomics Resource
            Center, School of Medicine, University of Maryland, 801 W.
            Baltimore Street, Baltimore, MD 21201, USA. Gene calling method:
            Prodigal version 2.6.3. Annotated using a custom modification of
            Prokka version 1.14.6.
            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/
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..2764
                     /organism="Bacteroides caccae CL03T12C61"
                     /mol_type="genomic DNA"
                     /strain="CL03T12C61"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:997873"
                     /plasmid="pBcacCL03T12-3"
                     /geo_loc_name="USA: Boston"
                     /lat_lon="42.3361 N 71.1075 W"
                     /collection_date="2009-05"
     gene            1..1116
                     /locus_tag="INE72_RS22890"
                     /old_locus_tag="INE72_04559"
                     /db_xref="GeneID:75115734"
     CDS             1..1116
                     /locus_tag="INE72_RS22890"
                     /old_locus_tag="INE72_04559"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004295514.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid recombination protein"
                     /protein_id="WP_211480377.1"
                     /db_xref="GeneID:75115734"
                     /translation="MGATSIHVQAVKPGSEIHNFREKELDYVRPELSHLNESWVGDSIS
                     HRLESAKQRYLDTVGQKMQAKAAPIREGVIVIKQETTMQELQQFATVCKERFGIEAFQI
                     HIHKDEGYMNAKQWTPNLHAHVVFDWTQPNGKSVRLSRDDMAELQTIASETLGMERGVS
                     SDRKHLSAMQYKTECAKEQLQELFQELSNDISSALDKHKDVQNQLLQLQKELRSIETKK
                     NVQKLISKASEKFYGLIGKTVNDREKDALKAKVKALEGENEQLSDRLGKAILEKEQNGT
                     KAFKAENDKEYYRQQMDNARTTSNRLRTENQELKTETKELKKELGKMKDLFNSEQLEAL
                     RHHFPNISKAMEEGKDLLKQITRSRGFGMGM"
                     /name="plasmid recombination protein"
     gene            1554..2144
                     /locus_tag="INE72_RS22895"
                     /old_locus_tag="INE72_04560"
                     /db_xref="GeneID:75115735"
     CDS             1554..2144
                     /locus_tag="INE72_RS22895"
                     /old_locus_tag="INE72_04560"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004295513.1"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA];
                     GO:0006276 - plasmid maintenance [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication/maintenance protein RepL"
                     /protein_id="WP_004295513.1"
                     /db_xref="GeneID:75115735"
                     /translation="MENKKAVKLTDFQKNEENPFMKQAIEGIENHVVKKYKSNSGGDKR
                     AVVALADTETGEVFKTSFIRQIEVDEEQFTKLYLSNFAAFFDLSQAAIRVFGYFMTCMK
                     PKNDLIIFNRKKCLEYTKYKTDKAVYKGLAELVKAEIIARGPADNLWFINPLIVFNGDR
                     VTFAKTYVRKKTLAAQKKEEAEKRQLSLGFDEQ"
                     /name="replication/maintenance protein RepL"
     Typing          1522..2134
                     /name="rep_cluster_1868"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.701"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2..1113
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.226"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgggagcaa caagtattca tgtacaagca gtgaagccgg ggagtgagat tcacaacttt
       61 agggaaaaag agttggacta tgttcgtccc gaacttagtc atttgaatga aagctgggtt
      121 ggagatagca tctcccatcg gctggaaagt gcgaaacaaa gatatctcga tacggttggg
      181 cagaagatgc aggctaaagc cgcacccata cgagagggag taatagtaat caaacaagaa
      241 accaccatgc aggaactcca gcagtttgcc acggtctgca aagaacgttt cggtatcgaa
      301 gcatttcaaa tccatataca caaggacgaa ggatacatga acgcaaagca atggacacct
      361 aaccttcatg cccatgtagt tttcgattgg acgcagccga atgggaaaag tgtgcgttta
      421 tcgcgtgatg acatggcaga actccaaacc atagcatctg aaacactggg catggaacgt
      481 ggcgtttctt ctgaccgcaa acacttatcg gctatgcagt acaagaccga atgtgcgaaa
      541 gaacagcttc aggaactatt tcaggaacta tcaaacgata tatccagtgc attagacaaa
      601 cacaaggacg tacaaaacca gcttcttcag cttcagaaag aactacgttc cattgaaaca
      661 aagaagaacg tccaaaaact catttctaag gcttcagaga agttttacgg cttgattgga
      721 aaaacagtca acgataggga aaaggatgcc ttaaaagcca aagtaaaggc tttagagggg
      781 gaaaatgaac agctatccga tagactggga aaggctatac ttgaaaaaga gcaaaacggc
      841 acaaaggcat tcaaagccga gaatgacaag gagtattata gacaacaaat ggacaacgca
      901 aggacaacca gtaaccgatt aaggacggag aaccaagaac taaagaccga aaccaaggaa
      961 ttgaaaaaag aacttggtaa gatgaaagac ttgttcaatt ccgaacaact ggaggcttta
     1021 aggcatcatt tcccaaacat atcaaaagct atggaagagg ggaaagacct actcaagcaa
     1081 atcaccagaa gcagaggttt cggtatgggt atgtaacccc ccccgccccc aaagggggag
     1141 cgaccaaacg gcagcctctc tcaatggagt gttacgtcgt tcggattcgg aagaaatttt
     1201 gcagggttcg gaaaacggtt gtgtgcttat tctaaaaaaa gtttatggtg tggcgctcgt
     1261 cgggacgggt ggtcccgccc cttgccgctg ggcgctcccc gaccgatgat ttttaagtga
     1321 ctgattttgt gctgttttgg gggtatatta agaatagaag aaatagaata agttaagtac
     1381 ttgatacaca atatagggca ttttccatat tggaaattct cattttccaa tctagaaaat
     1441 actgatttcc taatataata ctaaacagga aaataatatt tcccttaata ttgtttttat
     1501 ggaaaataat agtttacttt gtggagaata atatttccca aaaacacatc aaaatggaaa
     1561 ataaaaaagc agttaagtta accgattttc aaaagaacga agaaaatcct tttatgaaac
     1621 aagctataga aggtattgaa aatcatgttg ttaaaaagta taagagtaat agtggtggcg
     1681 ataagagagc cgtagtagct ttagccgaca ctgaaactgg agaagtgttt aagacttcgt
     1741 ttatccgtca aatagaagta gatgaagaac aattcactaa attgtatctt tctaactttg
     1801 ctgcattctt tgacctatca caagcagcta ttcgggtttt tggttacttt atgacctgca
     1861 tgaaacccaa aaatgattta atcatcttca atagaaaaaa atgcctagaa tataccaaat
     1921 acaaaacaga caaagccgtt tataaaggac ttgcagaact tgtaaaagct gaaatcatag
     1981 cccgaggacc agccgataat ctttggttta ttaatcctct gatagtattc aatggtgacc
     2041 gagtgacatt tgctaaaaca tacgttcgga aaaagacttt agctgcccaa aagaaagaag
     2101 aagcagagaa acgacaatta tcacttggct ttgatgaaca gtaacactcc attgagtgaa
     2161 gctgccgttt ggtcgctccc cctttggggg cggggggggg gatagataaa gttcctctat
     2221 gtaaagttat aatgggggat gaaaggcaag gttcgctaac cttaccccga ttgtttatgc
     2281 ttcccagcat tcaatctatc cccgtttatg ggtttctctt tcaccctaca aagataacct
     2341 catgggggaa aaatgtccaa gaatatgggg taaaaactat caagtcggta gaaaataagt
     2401 atctttgaag tacattttta gtagaggtac tggtatgcct agacgaagca gataggcaaa
     2461 aataaagccg ctggagatgt cggatgtccg tcaattaact ccagcggctt gtattttggt
     2521 aactctcccg tatcggtcgg ctaccgtttg gtcagcaaca aaggtagtac tttattgtcg
     2581 caaatccaaa tgttttcccc tttatttgtg catttacaga acatttgcta acttcgcacc
     2641 tatgcagtat gtgtgatagc acactagcac cctaaagggt gcgtgtgtaa ggggacaagc
     2701 ccccttaacc ccctgtcagc cggctgtcac cggctgttat cgattgtcac aaaaatgtta
     2761 actt
//
