LOCUS       NZ_AP025239             2784 bp    DNA     circular CON 25-OCT-2023
DEFINITION  Phocaeicola vulgatus strain MG01-07 plasmid pMG01-07_4, complete
            sequence.
ACCESSION   NZ_AP025239
VERSION     NZ_AP025239.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00405044
            Assembly: GCF_020885775.1
KEYWORDS    RefSeq.
SOURCE      Phocaeicola vulgatus
  ORGANISM  Phocaeicola vulgatus
            Bacteria; Bacteroidota; Bacteroidia; Bacteroidales; Bacteroidaceae;
            Phocaeicola.
REFERENCE   1
  AUTHORS   Tanaka,K., Noguchi,H., Vu,H., Muto,Y., Hayashi,M. and Yamamoto,Y.
  TITLE     Complete genome sequences of three Phocaeicola vulgatus isolated
            from a healthy Japanese individual
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2784)
  AUTHORS   Tanaka,K., Noguchi,H., Vu,H., Muto,Y., Hayashi,M. and Yamamoto,Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (29-OCT-2021) Contact:Kaori Tanaka Gifu University;
            Yanagido, Gifu 501-1194, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler
            Genome Coverage                   :: 100x
            Sequencing Technology             :: Illumina Miseq; Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 10/25/2023 01:28:58
            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)                     :: 4,182
            CDSs (total)                      :: 4,072
            Genes (coding)                    :: 3,953
            CDSs (with protein)               :: 3,953
            Genes (RNA)                       :: 110
            rRNAs                             :: 7, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 7, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 2
            Pseudo Genes (total)              :: 119
            CDSs (without protein)            :: 119
            Pseudo Genes (ambiguous residues) :: 0 of 119
            Pseudo Genes (frameshifted)       :: 48 of 119
            Pseudo Genes (incomplete)         :: 84 of 119
            Pseudo Genes (internal stop)      :: 28 of 119
            Pseudo Genes (multiple problems)  :: 31 of 119
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP025239.1.
            Annotated by DFAST https://dfast.ddbj.nig.ac.jp/
            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..2784
                     /organism="Phocaeicola vulgatus"
                     /mol_type="genomic DNA"
                     /strain="MG01-07"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:821"
                     /plasmid="pMG01-07_4"
                     /geo_loc_name="Japan"
                     /lat_lon="35.4234 N 136.7606 E"
                     /collection_date="2020-09-20"
     gene            complement(514..1104)
                     /locus_tag="LPD80_RS20860"
                     /old_locus_tag="GAIMETA21S07_40230"
     CDS             complement(514..1104)
                     /locus_tag="LPD80_RS20860"
                     /old_locus_tag="GAIMETA21S07_40230"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_008670455.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_008670455.1"
                     /translation="MENKKVLKLTDFQKNEENPFMKQAIEGIENHVVKKYKSSTGSDKK
                     AVVAVADTDTGEVFKTSFIRQIEVDEEQFAKLYLANFAAFFNLSQSAIRVFGYILTCMK
                     PKNDMIIFDRRKCLEYTQYKSDKAIYKGLAELVQSEIIARGPNEYNWFINPLIVFNGDR
                     VSFTKTYVRKKTLAAQKKEEAEKRQLSLGFDEL"
                     /name="hypothetical protein"
     gene            complement(1576..2679)
                     /locus_tag="LPD80_RS20865"
                     /old_locus_tag="GAIMETA21S07_40240"
     CDS             complement(1576..2679)
                     /locus_tag="LPD80_RS20865"
                     /old_locus_tag="GAIMETA21S07_40240"
                     /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_005783389.1"
                     /translation="MGATSIHVQAVKPGSEIHNFREKELDYVRPELSHLNESWVGDSIS
                     HRLESAKQRYFDTVGQKMQTKAAPIREGVIVIKQETTMQELQQFAAVCKERFGIEAFQI
                     HIHKDEGYMNAKQWTPNLHAHVVFDWTQPNGKSVRLSRDDMAELQTIASEALGMERGVS
                     SDRKHLSAMQYKTECAKEQLQELSNDISSALDKHKDVQNQLLQLQKELRSIETKKNVQK
                     LISKASEKFYGLIGKTVNDREKDTLKAKIKALEGENEQLSDRLGKAILEKERNGTKVFK
                     AENDKEYYRQQMDNARTTSNRLRTENQELKTETKELKKELGKMKDLFNSEQLEALRHHF
                     PNISKAMEEGKDLLKQITRSRGFGMGM"
                     /name="plasmid recombination protein"
     Typing          complement(525..1104)
                     /name="rep_cluster_1868"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="80.479"
                     /coverage="95.0"
                     /evalue="2.71e-121"
     Typing          complement(1580..2679)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.64"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ctatcaccat actgcatagg tgcgaagtta gtgaatgttt tgtaaatgca caaataaagg
       61 ggaaaacatt tggatttgcg acaataaagt actacctttg ttgctgacca aacggtagct
      121 gaccgatacg ggagagttac caaaatacaa gccgctggag ttaattgacg gacatccgac
      181 atccccagcg gctttatttt tgcctatctg cttcgtctag gcataccagt acctctacta
      241 aaaatgtact tcaaagatac ttattttcta ccgacttgat agtttttacc ccatattctt
      301 ggacattttt cccccatgag gttatctttg tagggtgaaa gagaaaccca taaacgggga
      361 tagattgaat gctgggaagc ataaacaatc ggggtaaggt tagcgaacct tgcctttcat
      421 cccccattat aactttacat agaggaactt tatctatccc ccccccgccc ccaaaggggg
      481 agcgaccaaa cggcagcttc actcaatgga gtgttacagt tcatcaaaac caagtgataa
      541 ctgtcgtttc tctgcttctt ctttcttttg ggcagctaaa gtctttttcc gaacgtatgt
      601 ttttgtaaat gaaaccctat ccccattaaa gacaatcaac ggattaatga accaattata
      661 ttcgtttgga cctcttgcta tgatttcact ttgtacgagc tctgccaatc ctttgtatat
      721 ggctttgtct gatttgtatt gggtgtattc taagcatttt cgcctatcga aaattatcat
      781 atcattctta ggcttcatgc aagttagaat atacccgaaa acccgaatag ctgattgtga
      841 tagattgaaa aaagcggcaa aattcgcaag gtatagtttt gcaaattgct cttcatctac
      901 ttctatttgt cggataaacg aggttttgaa tacttctcct gtatctgtat cagcaacagc
      961 aactacagct tttttatcac ttcccgtact acttttgtat ttcttaacaa cgtgattttc
     1021 aatcccttca attgcttgtt tcataaaggg gttttcttcg tttttttgaa aatcggttaa
     1081 tttgagtact ttcttatttt ccataaacat tctatttagg caaatttgac tttctatata
     1141 tcggtgaaaa agtataattt gattttccac aaaggaatat ttaaatttcc attaatacaa
     1201 taaaaaagca aaatatattt tcctttttaa catctaatag gaaagagtga ctttctaata
     1261 tggaaaatct gattttccaa tatggaaaat accctatatt gagtatcaac tacttaactt
     1321 attctatttc ttaagttctt attataccct aaaaacggca tataatcaac tacttaaaaa
     1381 atcatcggtc ggggagcgcc cagcggcaag gggcgggacc acccgtcccg acgagcgccc
     1441 acaccataaa ctttttttcg aataagcaca caaccgtttt tcgaaccctg caaaatttct
     1501 tccgaacccg aacggcgtaa cactccattg agtgaagctg ccgtttggtc gctccccctt
     1561 tgggggcggg gggggttaca tacccatacc gaaacctctg cttctggtga tttgcttgag
     1621 taggtctttc ccctcttcca tagcttttga tatgtttggg aaatgatgcc ttaaagcctc
     1681 cagttgttcg gaattgaaca agtctttcat cttaccaagt tcttttttca attccttggt
     1741 ttcggtcttt agttcttggt tctccgttct tagtcggtta ctggttgtcc ttgcattgtc
     1801 catttgctgt ctataatact ccttgtcgtt ctcggctttg aatacctttg tgccgtttcg
     1861 ctctttttca agtatagcct ttcccagtct atcggatagc tgttcatttt ccccctctaa
     1921 agcctttatt ttggctttta aggtatcttt ttccctatcg ttaaccgttt tccctatcaa
     1981 gccgtaaaac ttctctgaag ccttagaaat gagtttttgg acgtttttct ttgtttcaat
     2041 ggaacgtagt tctttctgaa gctgaagaag ctggttttgc acgtccttgt gcttgtctaa
     2101 cgcactggat atatcgttgg atagttcctg aagctgttct ttcgcacatt cggtcttgta
     2161 ctgcatagcc gataagtgtt tgcgatcaga agaaacacca cgttccatgc ccagtgcttc
     2221 agatgctatg gtttggagtt ctgccatgtc atcacgcgat aaacgcacac tcttcccgtt
     2281 cggctgcgtc caatcgaaaa ctacatgggc gtgaaggtta ggtgtccatt gctttgcgtt
     2341 catgtatcct tcgtccttgt gtatatggat ttgaaacgct tcaataccga aacgttcctt
     2401 gcagaccgca gcgaattgct ggagttcctg catggtggtt tcttgcttga ttactattac
     2461 cccctcccgt atgggtgctg ctttagtctg catcttctgc ccaaccgtat cgaaatatct
     2521 ctgtttcgca ctctccagcc gatgggagat gctatctcca acccagcttt cattcaaatg
     2581 actaagttcc ggacgaacat agtccaactc tttttcccta aagttgtgaa tctcgctccc
     2641 cggcttcact gcttgtacat gaatacttgt tgctcccata agttaacatt tttgtgacaa
     2701 tcgataacag ccggtgacag ccggctgaca gggggttaag ggggcttgtc cccttacaca
     2761 cgtacccttt agggtgctag tgtg
//
