LOCUS       NZ_CP072247             2456 bp    DNA     circular CON 03-APR-2024
DEFINITION  Phocaeicola dorei strain CL06T03C03 plasmid pBdorCL06T03-1, complete
            sequence.
ACCESSION   NZ_CP072247
VERSION     NZ_CP072247.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16451185
            Assembly: GCF_018292105.1
KEYWORDS    RefSeq.
SOURCE      Phocaeicola dorei
  ORGANISM  Phocaeicola dorei
            Bacteria; Bacteroidota; Bacteroidia; Bacteroidales; Bacteroidaceae;
            Phocaeicola.
REFERENCE   1  (bases 1 to 2456)
  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 2456)
  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                     :: BdorCL06T03C03_pbv2
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 370x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_018292105.1-RS_2024_04_03
            Annotation Date                   :: 04/03/2024 05:58:31
            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)                     :: 4,858
            CDSs (total)                      :: 4,751
            Genes (coding)                    :: 4,624
            CDSs (with protein)               :: 4,624
            Genes (RNA)                       :: 107
            rRNAs                             :: 7, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 7, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 2
            Pseudo Genes (total)              :: 127
            CDSs (without protein)            :: 127
            Pseudo Genes (ambiguous residues) :: 0 of 127
            Pseudo Genes (frameshifted)       :: 52 of 127
            Pseudo Genes (incomplete)         :: 81 of 127
            Pseudo Genes (internal stop)      :: 25 of 127
            Pseudo Genes (multiple problems)  :: 27 of 127
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP072247.1.
            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..2456
                     /organism="Phocaeicola dorei"
                     /mol_type="genomic DNA"
                     /strain="CL06T03C03"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:357276"
                     /plasmid="pBdorCL06T03-1"
                     /geo_loc_name="USA: Boston"
                     /lat_lon="42.3361 N 71.1075 W"
                     /collection_date="2009-05"
     gene            166..1098
                     /locus_tag="INE79_RS23375"
                     /old_locus_tag="INE79_04687"
     CDS             166..1098
                     /locus_tag="INE79_RS23375"
                     /old_locus_tag="INE79_04687"
                     /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="mobilization protein"
                     /protein_id="WP_211479462.1"
                     /translation="MQYGDSTLKAAPIREGVIVIKQETTMQELQQFATVCKERFGIEAF
                     QIHIHKDEGYMNAKQWTPNLHAHVVFDWTQPNGKSVRLSRDDMAELQTIASETLGMERG
                     VSSDRKHLSAMQYKTECAKEQLQELSNDISSALDKHKDVQNQLLQLQKELRSIETKKNV
                     QKLISKASEKFYGLIGKTVNDREKDALKAKVKALEGENEQLSDRLGKAILEKEQNGTKA
                     FKAENDKEYYRQQMDNARTTSNRLRTENQELKTETKELKKELGKMKDLFNSEQLEALRH
                     HFPNISKAMEEGKDLLKQITRSRGFGMGM"
                     /name="mobilization protein"
     gene            1535..2125
                     /locus_tag="INE79_RS23380"
                     /old_locus_tag="INE79_04688"
     CDS             1535..2125
                     /locus_tag="INE79_RS23380"
                     /old_locus_tag="INE79_04688"
                     /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"
                     /translation="MENKKAVKLTDFQKNEENPFMKQAIEGIENHVVKKYKSNSGGDKR
                     AVVALADTETGEVFKTSFIRQIEVDEEQFTKLYLSNFAAFFDLSQAAIRVFGYFMTCMK
                     PKNDLIIFNRKKCLEYTKYKTDKAVYKGLAELVKAEIIARGPADNLWFINPLIVFNGDR
                     VTFAKTYVRKKTLAAQKKEEAEKRQLSLGFDEQ"
                     /name="replication/maintenance protein RepL"
     Typing          1503..2115
                     /name="rep_cluster_1868"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.701"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          191..1095
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.689"
                     /coverage="82.0"
                     /evalue="0.0"
ORIGIN
        1 atgtcggatg tccgtcaatt aactccagcg gcttgtattt tggtaactct cccgtatcgg
       61 tcggctaccg tttggtcagc aacaaaggta gtactttatt gtcgcaaatc caaatgtttt
      121 cccctttatt tgtgcattta cagaacattt gctaacttcg cacctatgca gtatggtgat
      181 agcacactaa aagccgcacc catacgagag ggagtaatag taatcaaaca agaaaccacc
      241 atgcaggaac tccagcagtt tgccacggtc tgcaaagaac gtttcggtat cgaagcattt
      301 caaatccata tacacaagga cgaaggatac atgaacgcaa agcaatggac acctaacctt
      361 catgcccatg tagttttcga ttggacgcag ccgaatggga aaagtgtgcg tttatcgcgt
      421 gatgacatgg cagaactcca aaccatagca tctgaaacac tgggcatgga acgtggcgtt
      481 tcttctgacc gcaaacactt atcggctatg cagtacaaga ccgaatgtgc gaaagaacag
      541 cttcaggaac tatcaaacga tatatccagt gcattagaca aacacaagga cgtacaaaac
      601 cagcttcttc agcttcagaa agaactacgt tccattgaaa caaagaagaa cgtccaaaaa
      661 ctcatttcta aggcttcaga gaagttttac ggcttgattg gaaaaacagt caacgatagg
      721 gaaaaggatg ccttaaaagc caaagtaaag gctttagagg gggaaaatga acagctatcc
      781 gatagactgg gaaaggctat acttgaaaaa gagcaaaacg gcacaaaggc attcaaagcc
      841 gagaatgaca aggagtatta tagacaacaa atggacaacg caaggacaac cagtaaccga
      901 ttaaggacgg agaaccaaga actaaagacc gaaaccaagg aattgaaaaa agaacttggt
      961 aagatgaaag acttgttcaa ttccgaacaa ctggaggctt taaggcatca tttcccaaac
     1021 atatcaaaag ctatggaaga ggggaaagac ctactcaagc aaatcaccag aagcagaggt
     1081 ttcggtatgg gtatgtaacc ccccccgccc ccaaaggggg agcgaccaaa cggcagcctc
     1141 tctcaatgga gtgttacgtc gttcggattc ggaagaaatt ttgcagggtt cggaaaacgg
     1201 ttgtgtgctt attctaaaaa agtttatggt gtggcgctcg tcgggacggg tggtcccgcc
     1261 ccttgccgct gggcgctccc cgaccgatga tttttaagtg actgattttg tgctgttttg
     1321 ggggtatatt aagaatagaa gaaatagaat aagttaagta cttgatacac aatatagggc
     1381 attttccata ttggaaattc tcattttcca atctagaaaa tactgatttc ctaatataat
     1441 actaaacagg aaaataatat ttcccttaat attgttttta tggaaaataa tagtttactt
     1501 tgtggagaat aatatttccc aaaaacacat caaaatggaa aataaaaaag cagttaagtt
     1561 aaccgatttt caaaagaacg aagaaaatcc ttttatgaaa caagctatag aaggtattga
     1621 aaatcatgtt gttaaaaagt ataagagtaa tagtggtggc gataagagag ccgtagtagc
     1681 tttagccgac actgaaactg gagaagtgtt taagacttcg tttatccgtc aaatagaagt
     1741 agatgaagaa caattcacta aattgtatct ttctaacttt gctgcattct ttgacctatc
     1801 acaagcagct attcgggttt ttggttactt tatgacctgc atgaaaccca aaaatgattt
     1861 aatcatcttc aatagaaaaa aatgcctaga atataccaaa tacaaaacag acaaagccgt
     1921 ttataaagga cttgcagaac ttgtaaaagc tgaaatcata gcccgaggac cagccgataa
     1981 tctttggttt attaatcctc tgatagtatt caatggtgac cgagtgacat ttgctaaaac
     2041 atacgttcgg aaaaagactt tagctgccca aaagaaagaa gaagcagaga aacgacaatt
     2101 atcacttggc tttgatgaac agtaacactc cattgagtga agctgccgtt tggtcgctcc
     2161 ccctttgggg gcgggggggg gatagataaa gttcctctat gtaaagttat aatgggggat
     2221 gaaaggcaag gttcgctaac cttaccccga ttgtttatgc ttcccagcat tcaatctatc
     2281 cccgtttatg ggtttctctt tcaccctaca aagataacct catgggggaa aaatgtccaa
     2341 gaatatgggg taaaaactat caagtcggta gaaaataagt atctttgaag tacattttta
     2401 gtagaggtac tggtatgcct agacgaagca gataggcaaa aataaagccg ctggag
//
