LOCUS       NZ_AP025238             4306 bp    DNA     circular CON 25-OCT-2023
DEFINITION  Phocaeicola vulgatus strain MG01-07 plasmid pMG01-07_3, complete
            sequence.
ACCESSION   NZ_AP025238
VERSION     NZ_AP025238.1
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  JOURNAL   Unpublished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 4306)
  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
            AP025238.1.
            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..4306
                     /organism="Phocaeicola vulgatus"
                     /mol_type="genomic DNA"
                     /strain="MG01-07"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:821"
                     /plasmid="pMG01-07_3"
                     /geo_loc_name="Japan"
                     /lat_lon="35.4234 N 136.7606 E"
                     /collection_date="2020-09-20"
     gene            join(4171..4306,1..50)
                     /locus_tag="LPD80_RS20820"
     CDS             join(4171..4306,1..50)
                     /locus_tag="LPD80_RS20820"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007560600.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_007560600.1"
                     /translation="MKKIIVHFKKEEFERVKNAISILAKFSEIYAPHIDKANSILSFRV
                     DDENETTEEQQCNSRQ"
                     /name="hypothetical protein"
     gene            1..1005
                     /locus_tag="LPD80_RS20825"
                     /old_locus_tag="GAIMETA21S07_40160"
     CDS             1..1005
                     /locus_tag="LPD80_RS20825"
                     /old_locus_tag="GAIMETA21S07_40160"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007560598.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_007755890.1"
                     /translation="MMKTKQQKNNSVTVVNKDQIQSYIMTTAKYDFSVYEKRILYRIVE
                     MAQGELQGVRFATDCKKIEHTLFDTVHITMPIASLLNGESDENYTRVKQALLSLQKKIF
                     TYEDEKEWISISIIALPKIKKRSSVVSFQIDSHIWDCCLDFSKGFRKYELATAMKFKSV
                     YSMRFYELLSGQKTKLIYPLEQLKEMFKVQDKYAKTNDFVRKVIEPAKNELDELSPYTF
                     EWSANKEGKKIVSFNFYPIFKPEHRDAELYKKELQKQTGLSWDLGRQVISYLKTSLEFS
                     DKEIKNNRDLFVTAQMELPDIMTELAILRGKSRTKTNPKGWIINALKGKIKDK"
                     /name="replication initiation protein"
     gene            complement(1044..1274)
                     /locus_tag="LPD80_RS20830"
                     /old_locus_tag="GAIMETA21S07_40170"
     CDS             complement(1044..1274)
                     /locus_tag="LPD80_RS20830"
                     /old_locus_tag="GAIMETA21S07_40170"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005683050.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_007560596.1"
                     /translation="MGTAEHEEPRFFFILNKGAKSGGEITHAVLNGSIVSKPAGWDAFH
                     GLVLAKEKLSSEEIQRQMKELGVEMEIVPLI"
                     /name="hypothetical protein"
     gene            complement(1294..1746)
                     /gene="mbpC"
                     /locus_tag="LPD80_RS20835"
                     /old_locus_tag="GAIMETA21S07_40180"
     CDS             complement(1294..1746)
                     /gene="mbpC"
                     /locus_tag="LPD80_RS20835"
                     /old_locus_tag="GAIMETA21S07_40180"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004295511.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="mobilization protein MbpC"
                     /protein_id="WP_004295511.1"
                     /translation="METNSHPEAAASNVKQGQYSPRKRKDTTPRVNPQLAVELVYQELK
                     RVEVYTKRIEDATARKVQIDGKSLESAENRLKNVLADFERQGYRMKNGGYVDKRISFYS
                     ILCAVISLLFACFMCYLWTDAAKDRDNYKQYYEYYQEQAREQKGNK"
                     /name="mbpC"
     gene            complement(1703..2497)
                     /gene="mbpB"
                     /locus_tag="LPD80_RS20840"
                     /old_locus_tag="GAIMETA21S07_40190"
     CDS             complement(1703..2497)
                     /gene="mbpB"
                     /locus_tag="LPD80_RS20840"
                     /old_locus_tag="GAIMETA21S07_40190"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007560590.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="mobilization protein MbpB"
                     /protein_id="WP_007560590.1"
                     /translation="MIGKGKSISHGVAALEYDLAKEINGQAVATEIARHELYGCTGAEM
                     VQEMKPYHIDFPNVKNNCLRFEVSPSIEESATFTDADWAELGNDFMQRMGLANHQYIII
                     RHSGTESKKEQAHLHILANRVSLSGELYRDNWIGKKATEAANAIAKERNFVQSQDIGKV
                     NKAEIKEAMDGVLKKMQGFDFTKFKEELGKRGFKVREARASTGKLNGYYVTARSGTEYK
                     ASEIGKGYTLAHIERTQSKLKCNSMNISHGNKLTPGSGSFQR"
                     /name="mbpB"
     gene            complement(2494..2793)
                     /gene="mbpA"
                     /locus_tag="LPD80_RS21050"
     CDS             complement(2494..2793)
                     /gene="mbpA"
                     /locus_tag="LPD80_RS21050"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004327437.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="mobilization protein MbpA"
                     /protein_id="WP_004327437.1"
                     /translation="MELRRNEKITFRCTELEKDALAEQAARCSLSVSEYCRSLSLGGRP
                     RERYTEEERQLLRDIAQLKGTLQRLNNYFGGRQYREVFEENRALITELKKILSR"
                     /name="mbpA"
     gene            complement(2975..3172)
                     /locus_tag="LPD80_RS20845"
                     /old_locus_tag="GAIMETA21S07_40200"
     CDS             complement(2975..3172)
                     /locus_tag="LPD80_RS20845"
                     /old_locus_tag="GAIMETA21S07_40200"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007209655.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_007209655.1"
                     /translation="MVEYCVYWLENGEPMHEVFSNLAAAEMYSCAIRGKENVEWVEVSE
                     EEAIDLDELKDMFPDDFCGV"
                     /name="hypothetical protein"
     gene            complement(3183..3458)
                     /locus_tag="LPD80_RS20850"
                     /old_locus_tag="GAIMETA21S07_40210"
     CDS             complement(3183..3458)
                     /locus_tag="LPD80_RS20850"
                     /old_locus_tag="GAIMETA21S07_40210"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004327436.1"
                     /GO_function="GO:0004519 - endonuclease activity [Evidence
                     IEA]"
                     /GO_process="GO:0006401 - RNA catabolic process [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system YoeB family toxin"
                     /protein_id="WP_004327436.1"
                     /translation="MMYTIRVSDGVDKVIAKWKKSNPNLFKKYKKIYKELLEHPKTGLG
                     HPEALRGGGDITWSRHITAHDRIIYDIYEEVVEVYILEVEGHYNDK"
                     /name="type II toxin-antitoxin system YoeB family toxin"
     gene            complement(3455..3706)
                     /locus_tag="LPD80_RS20855"
                     /old_locus_tag="GAIMETA21S07_40220"
     CDS             complement(3455..3706)
                     /locus_tag="LPD80_RS20855"
                     /old_locus_tag="GAIMETA21S07_40220"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004295507.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_004295507.1"
                     /translation="MEALSVREYRNNLAASFTKADNGEQVLIRRKNEIYALVKVGREDL
                     MITPELQARIDKAREEIKSGKCVTLKSSEDIDAYFDSL"
                     /name="hypothetical protein"
     Typing          2..1005
                     /name="rep_cluster_1019"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgatgaaaa cgaaacaaca gaagaacaac agtgtaacag tcgtcaataa agaccaaata
       61 caaagctata ttatgacgac agccaagtat gacttttccg tttatgagaa gcgcatactt
      121 tatagaattg tagaaatggc tcaaggtgaa ctccaaggag ttagatttgc aactgattgt
      181 aaaaaaatag aacacacact ttttgatacc gttcacatca caatgcctat tgcttcattg
      241 ctaaatggag aaagtgatga aaactacaca cgtgtaaaac aagcactgtt atctctacaa
      301 aagaaaatct ttacctatga ggatgaaaaa gaatggataa gcatttctat tattgcattg
      361 ccaaagataa agaagcgttc atctgttgta tcattccaaa tagactcaca catatgggac
      421 tgctgcttag atttttcaaa agggtttcgc aaatacgaat tagccactgc gatgaagttt
      481 aagagtgtat attctatgcg gttctacgaa cttttaagcg gtcagaaaac aaaactaatc
      541 tatccacttg aacagctcaa agaaatgttt aaagtacaag ataaatacgc aaagacaaac
      601 gattttgtcc ggaaagtaat tgaacctgca aaaaatgagc tggacgaact aagtccttat
      661 acattcgaat ggtccgcaaa caaggaaggg aaaaaaattg taagtttcaa cttctatcca
      721 atattcaagc cagagcatcg tgatgcagag ctatacaaaa aagagctaca aaagcaaacc
      781 gggctttcat gggatttagg taggcaagtg ataagttact taaaaacatc tttggagttc
      841 tccgataaag aaatcaaaaa caaccgggat ttatttgtaa cagcacaaat ggaacttcca
      901 gacatcatga cagaactcgc catacttaga ggaaaatcaa ggacaaaaac aaatccaaaa
      961 gggtggatta taaatgccct taaagggaaa atcaaggata agtgacaaga ttaccccggc
     1021 tgaaatatac cggggtaatc ttgtcaaatc agaggaacga tttccatttc tacaccaagc
     1081 tctttcatct gccgctgtat ttcctcgctg cttagtttct ctttcgccag tacaagccca
     1141 tgaaaggcgt cccagcctgc cggcttcgaa acgatactac cgtttaggac ggcatgggtg
     1201 atttcgccgc cggacttcgc acccttgttc agtatgaaga agaaccgggg ttcttcgtgt
     1261 tccgctgttc ccataattcg taaagttaga tgtttattta ttcccctttt gttcccttgc
     1321 ctgctcttgg tagtattcat aatactgctt gtagttgtcc cggtctttgg ctgcatccgt
     1381 ccaaagatag cacatgaaac aagcgaacaa tagggagata acagcacaaa ggattgagta
     1441 gaacgaaatt cgtttgtcca cataaccgcc gtttttcatt ctatacccct gccgttcaaa
     1501 gtccgccaat acgtttttta ggcgattttc ggcactttca aggcttttcc cgtctatttg
     1561 tacctttcgg gctgttgcgt cctctatgcg cttcgtatag acttcaacac gctttagttc
     1621 ttgatacacc agttctaccg caagctgcgg gtttaccctt ggcgttgtgt cttttctttt
     1681 ccgggggctg tactgtccct gcttaacgtt ggaagctgcc gcttccgggt gtgagtttgt
     1741 ttccatgaga tatgttcatt gagttgcact tcagtttgct ttgtgtccgc tcgatatggg
     1801 cgagagtgta gcctttccct atctcgcttg ccttatactc cgtaccgctt cgggctgtga
     1861 catagtagcc gttaagtttc ccggtgcttg ccctggcttc ccggacttta aaacctctct
     1921 taccaagttc ttccttgaat ttggtaaagt caaagccctg catcttcttc aatacgccgt
     1981 ccatggcttc cttgatttcc gctttgttga ctttgccaat gtcctgcgac tgtacaaagt
     2041 tccgttcctt ggctatggca ttggcggctt ccgttgcctt tttccctatc cagttgtccc
     2101 ggtacagttc cccggaaagg gaaacccggt ttgccagtat gtgcaggtgg gcttgctctt
     2161 tcttgctctc cgtaccgctg tgccggatga tgatgtactg gtggttcgcc aaccccatgc
     2221 gctgcatgaa gtcgttacca agttccgccc agtccgcatc cgtaaaggtg gcgctttcct
     2281 ctatcgaggg gctgacctcg aaacgtaggc agttgttttt tacgttcgga aaatcaatgt
     2341 gatacggttt catttcctgc accatttccg caccagtaca cccataaagt tcatgccggg
     2401 ctatctcggt ggctactgcc tgcccgttta tctctttggc gaggtcgtac tccaatgccg
     2461 ccacaccatg tgatatgctt ttccctttcc ctatcatcgt gagagtattt ttttgagctc
     2521 tgtaattagt gcccggttct cctcgaacac ttcccggtac tggcgaccac cgaagtagtt
     2581 gttcagccgt tggagcgttc ctttcaactg ggctatgtcc cggagaagct gccgttcctc
     2641 ctcggtgtac ctctcccttg ggcgcccccc aagggacaaa ctccggcagt attccgatac
     2701 gcttagactg caccgggctg cctgctccgc aagtgcgtcc ttttcaagtt cggtacatcg
     2761 gaatgtaatc ttttcgttcc gtcttagttc catgccacaa aggtaatctt aaaatctttt
     2821 tgagcaaagc gagaaaagca agaattgtcc gacaaggaca cttcttgcta tatatacaca
     2881 tgccgcatgg gaatacatcc acgccaaccg cccggcaaaa agcccaggca tgttagaaaa
     2941 tcccccacag cctaacaatt tctacccaag gggattacac gccgcagaag tcatccggga
     3001 acatgtcttt cagttcgtcc aaatcaatgg cttcttcttc ggacacctcc acccattcaa
     3061 cgttttcttt ccctcttatc gcacatgagt acatctcggc ggcggcaagg ttagagaaca
     3121 cctcgtgcat aggctcgccg ttctctaacc agtaaacaca atattcgacc ataacagttt
     3181 tatcatttat cgttgtaatg cccctctacc tccaaaatgt agacctctac cacttcctcg
     3241 taaatgtcat agattatccg gtcatgggcg gtaatgtgtc gagaccatgt aatatcccca
     3301 ccgcccctta acgcttcggg atgcccaagc ccagtcttag ggtgctctaa caattctttg
     3361 tagattttct tatacttctt gaacaaattg gggtttgatt tcttccattt ggcaatcacc
     3421 ttatccaccc cgtcggaaac cctaattgtg tacatcatag actgtcgaaa taagcatcaa
     3481 tatcctcact gcttttgagg gtaacacact ttccggattt gatttcttcc cttgccttgt
     3541 caatccttgc ttgcagttcc ggggttatca tcaaatcttc acgaccaact tttaccaaag
     3601 cgtaaatctc gtttttcctg cgaattagta cctgctcgcc attgtcagct ttggtgaaag
     3661 acgctgcgag gttgttacgg tattctctta ctgataatgc ttccatatct gtttgctttt
     3721 aaattcagta caaagatagc tatatttcaa taaaatacaa actttttgca cacaaatgtg
     3781 tacacgccat aaaaagccgt tcacagtcct accgcccgtt ggttggtttt gctttgcttt
     3841 tttcccctat tgtttttctt tttccgacag taaatcaacc acttatccgt aaaaaatcaa
     3901 tgacttgtta taaagcataa cttgtttata tgcttatcag cttttttttt taactaaaaa
     3961 ttatgctgaa atccaataac ttacacaatc tatttaacac attactacga ctttttgaat
     4021 gctatttaac acattactac gactttttga atgttatttt cccttccaaa tacgactttt
     4081 tgaatgttat tttgcatcat ctacgatttt catttgcaca agtcgtaatt acttattata
     4141 tttgcgcaac atactaataa tcaataaagg atgaagaaaa tcatagttca ttttaagaaa
     4201 gaagaatttg aaagggttaa aaacgcaatt tctatcctcg caaaattttc tgaaatatac
     4261 gctcctcaca tagataaagc caacagtatt ttatcctttc gtgtag
//
