LOCUS       NZ_AP025237             5594 bp    DNA     circular CON 25-OCT-2023
DEFINITION  Phocaeicola vulgatus strain MG01-07 plasmid pMG01-07_2, complete
            sequence.
ACCESSION   NZ_AP025237
VERSION     NZ_AP025237.1
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  JOURNAL   Unpublished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 5594)
  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
            AP025237.1.
            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..5594
                     /organism="Phocaeicola vulgatus"
                     /mol_type="genomic DNA"
                     /strain="MG01-07"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:821"
                     /plasmid="pMG01-07_2"
                     /geo_loc_name="Japan"
                     /lat_lon="35.4234 N 136.7606 E"
                     /collection_date="2020-09-20"
     gene            397..645
                     /locus_tag="LPD80_RS20785"
                     /old_locus_tag="GAIMETA21S07_40100"
     CDS             397..645
                     /locus_tag="LPD80_RS20785"
                     /old_locus_tag="GAIMETA21S07_40100"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_008771457.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="AbrB/MazE/SpoVT family DNA-binding
                     domain-containing protein"
                     /protein_id="WP_005812783.1"
                     /translation="MVTNIIQIGNSKGIILPSEVLKQLRLSLKSAVSISLDGNNIVIKA
                     QPRQGWAEAAKRAHENGDDELLIPDVFEDEKFEDWTW"
                     /name="AbrB/MazE/SpoVT family DNA-binding domain-containing
                     protein"
     gene            639..959
                     /locus_tag="LPD80_RS20790"
                     /old_locus_tag="GAIMETA21S07_40110"
     CDS             639..959
                     /locus_tag="LPD80_RS20790"
                     /old_locus_tag="GAIMETA21S07_40110"
                     /EC_number="3.1.-.-"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005799262.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0003723 - RNA binding [Evidence IEA]; GO:0004521 - RNA
                     endonuclease activity [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 PemK/MazF family
                     toxin"
                     /protein_id="WP_005799262.1"
                     /translation="MVEQYEVYWVELDPTRGGEMAKTRPCVVVTPSDLNMYLTTVVIVP
                     ITSTIRNYPYRVLCSVAGREGEIATDQIRTVDKSRLKRKIGDLNFSEIKRLREVFQQMF
                     CE"
                     /name="type II toxin-antitoxin system PemK/MazF family
                     toxin"
     gene            996..1394
                     /locus_tag="LPD80_RS20795"
                     /old_locus_tag="GAIMETA21S07_40120"
     CDS             996..1394
                     /locus_tag="LPD80_RS20795"
                     /old_locus_tag="GAIMETA21S07_40120"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005799260.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_005799260.1"
                     /translation="MKPTDYIEWDNLKDIPFFLCQVVEDREKQDLDIYYLGKRVLHDYD
                     HVGHYLRTAVILFRRVKSRTADWVNLRNLWTLRNCVRENYNHGIGMNDLIFGENFDGDN
                     LDTLTPLTKKRFDFLCKRIKELDPYATI"
                     /name="hypothetical protein"
     gene            2036..2938
                     /locus_tag="LPD80_RS20800"
                     /old_locus_tag="GAIMETA21S07_40130"
     CDS             2036..2938
                     /locus_tag="LPD80_RS20800"
                     /old_locus_tag="GAIMETA21S07_40130"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005799258.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_225538865.1"
                     /translation="MKAYMDAHVCSNVYTVQGGKAHSHYCHRAFCPICQRIQTAQNVKK
                     FLPVMKYLASEGREFYFVTLTLQNCVTDDARVLRDFMRRCNRMWADGIRTKHKFRSLGI
                     SGVIKKECTYHVVKKDLFSFHYHFHIIVDSLEAAKYVVAQWKKLHGSTVADARFQKYKK
                     IEDFENAAIEVFKYASKASVSKSKGRDGKKKIQINYKALDMIYTAMHGMQRMSSFGQFR
                     TMIGDEALNDFRDEDLVLNIEGLNVEDGCYTWYMSVKDKVADWYNMETGEALCCYKVTR
                     KDELLQDIYLDEDIFPNSG"
                     /name="protein rep"
     gene            complement(2942..3403)
                     /locus_tag="LPD80_RS20805"
                     /old_locus_tag="GAIMETA21S07_40140"
     CDS             complement(2942..3403)
                     /locus_tag="LPD80_RS20805"
                     /old_locus_tag="GAIMETA21S07_40140"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005812785.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_005812785.1"
                     /translation="MNRIIHISLLISTVSLFLISNTGCVEKQGYYNHGEESIISLICDI
                     TWAGKKTTDENGSVWQGTYKFNKNGTYTRTNIEIDKQGNKKEANIYGQWSFGDPSFSTI
                     YFGGEHYWDIDELTKNKFSFYDRSGKFGDPFMNREYIELTPYQENNTTN"
                     /name="hypothetical protein"
     gene            3495..4265
                     /locus_tag="LPD80_RS20810"
                     /old_locus_tag="GAIMETA21S07_40150"
     CDS             3495..4265
                     /locus_tag="LPD80_RS20810"
                     /old_locus_tag="GAIMETA21S07_40150"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016274503.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_005799241.1"
                     /translation="MKKVMFMFISLLTVLGVCSCNDNEVIEPVVSDSVSDMEVLSRFVD
                     VNEITNEYYFNENKKTRALSYVTGSDWQDLEKVSPLSIEKYKNNLQVLNAQVASAISNP
                     NTAYVVFSVNGKTLVKKVKEDANFDFSVFRDVVTETRAVLPSLSINGGSQSTTGVFYDS
                     SRTLKMQVDLNASIQNNYYFFEVLNPNAKPSPDDNITTPESVAFSGTGPLWSNTFTWTS
                     YWDANVPGQGFKWEFKGKGTTPSFGFIANCTFSR"
                     /name="hypothetical protein"
     gene            complement(4335..5585)
                     /locus_tag="LPD80_RS20815"
     CDS             complement(4335..5585)
                     /locus_tag="LPD80_RS20815"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005799237.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="NBU/pMV158-type mobilization protein"
                     /protein_id="WP_005799237.1"
                     /translation="MAKTCIRVEACNIGSSERHNLRSKELDYIRPELTHRNEQWVECSI
                     AEVHRDITEKYKEATGQGLQKKATPIREGVIVISEETTIQQLQDLAEKLEERFGVHAFQ
                     IYTHKDEGANVWDGKEEAWKPNYHAHMIFDWTDGHTGKTVKLNRHDMAEMQTITAECLN
                     MERGVSSDKKHLSAMQYKNKMETEKAEQLQKDIEQLNRAYTAGTEKITTVQKELSTAQK
                     ELNSMKTDIHINEAKEAAAKAGKTVFNAVTSVFNVGEVKRQAKEIETLKKENYNLSFKN
                     QNLEGQLRTNNIEMRRVQETTDRQIKAEASKLKPITNLFPEMENAQENIEELQTMGIQN
                     KDIRQLLIGKEIYYTGNLYDKDKRKSYQVKNVKIDISKSQNGITTIWLNNIHFKNFLKE
                     LWNTLQKTLDNGNWLHR"
                     /name="NBU/pMV158-type mobilization protein"
     Typing          1890..2938
                     /name="rep_cluster_870"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.905"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(4339..5585)
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttttaggtgt gtatgtctgt ttagaagatg tggcgtgaaa cgtcacatcg cacggggtcg
       61 aggggacacc cctcgcacac aaccccttta ggggttatag tgtgctataa ccttttgcaa
      121 aggtaagcct tccggacggg atttgcaagc gctctgccat gtgttccgga tgtgcttggg
      181 aacagaagcc ggacaaaagg gaaaaggaca caaggcacaa taaaaaatca tcggtcgggg
      241 agcgctgcac ggcaaggggg tgcaccaaca ctcccgacga gtgcagccat tgacagggtt
      301 ctcggtgaaa atggaaaaaa gttgtttttc cttttgttat tgttataact ttacatatat
      361 ttgtatcgtg ataatcaatt ataaagttat aacattatgg taacgaatat tattcagatt
      421 ggaaacagca aggggataat acttccttcc gaagtattga aacagttgcg tttgtccttg
      481 aaatcggctg tgagcatttc tttggacggg aacaatattg tgataaaggc acaaccacgg
      541 cagggatggg cggaagctgc caaacgtgcc catgagaatg gggatgatga gttgcttatc
      601 cctgatgtgt ttgaggatga aaagtttgag gattggacat ggtagaacag tatgaagtgt
      661 attgggtaga gttagaccct acccgtgggg gtgaaatggc aaagacacgg ccatgtgtag
      721 ttgtcactcc ttcagatttg aatatgtacc ttacaacagt agtcattgtt ccgataacct
      781 caacgataag aaattatcct taccgggttc tgtgttctgt agccgggcgt gaaggagaga
      841 tagccactga tcaaattcgc acggtggata aaagccggct gaaaagaaag attggagatt
      901 tgaatttcag tgagataaaa aggttacgtg aagtgtttca gcaaatgttc tgtgaataat
      961 ggaaagtacg gaaagaaaaa tgcaaataag acattatgaa accaactgac tacatcgaat
     1021 gggataacct gaaggatatt ccattcttcc tctgtcaagt agtcgaggac agagaaaaac
     1081 aagatttgga tatttactat ttgggcaaac gtgtcttgca cgattacgac catgtggggc
     1141 actatttgcg gactgccgtt atcttgttcc gcagggtaaa gagccgcaca gcagactggg
     1201 taaacctgcg taacctttgg acgctgcgca actgtgtgcg tgagaactac aatcacggca
     1261 taggaatgaa cgaccttatt tttggggaga atttcgatgg agataatctc gatacgctta
     1321 caccacttac aaagaaacgc tttgattttt tgtgtaagcg gattaaggaa cttgacccat
     1381 atgcaactat ttaacactcc attgagtgaa ggcagggttt gtctttgtgt gctccccctt
     1441 tgggggacgg gagggggata agaaaaaaaa taccaccgga gatgtcggat atccgtcaat
     1501 tcactccggt gttttttttg caactctccc gtatcgctcg gcaagggttg tctttgtgta
     1561 cggcaaagat agtttttttt ccggaagtat ctttgtctgt tgtggattta gtagtgtatt
     1621 tgtgtcagaa ttgcgcagcc gggggaatgg gggcgagccc ccatactaga taaactagaa
     1681 agtttcgtgg taaatgcttt ttgacttgtt atatgtaggt tttttgaatg atgtttggcg
     1741 gtttggaatg aattacctac ttttgggctg agaaaaaacg aaagcccgaa ggcagtaacc
     1801 aacgggcttt gtattttaag aattagcaat cgtttgtgtt cgttcttggc ggggcggata
     1861 ccaaacgaaa gccacatcaa aatttcatat gtgcaaagat agaacaaata taaccaactg
     1921 caaagaaagt ccgttaaaaa acggttctga tagtcttaaa aaaaaggcta aagtaaaaat
     1981 catatcccat aattttactc gaaaactttc ggaaaagaat ccggatagta agctgatgaa
     2041 agcatatatg gatgcccatg tgtgttcaaa tgtttatact gtgcagggag gtaaggcgca
     2101 ttcccattat tgtcatcggg ctttttgtcc tatttgtcag cgtattcaaa cggcacaaaa
     2161 tgtaaagaag ttccttccgg ttatgaagta tttggcttcg gaaggcagag agttttattt
     2221 tgtgacgctt accttgcaaa attgtgtaac cgatgatgca agggtattgc gagatttcat
     2281 gcgtagatgt aaccggatgt gggctgatgg tataaggacg aaacacaagt ttcgttcact
     2341 tggtatttcg ggggtgatta agaaggagtg tacctatcat gtagtaaaaa aggatttgtt
     2401 ttcgttccat tatcattttc atattattgt tgattcattg gaagctgcaa aatatgtagt
     2461 agcccaatgg aagaaattgc atggtagtac ggttgctgat gcccgttttc agaaatataa
     2521 gaagatagag gattttgaaa atgcagcgat agaggttttt aagtatgctt caaaggcttc
     2581 tgtctcaaaa tcgaaaggtc gtgacggtaa aaaaaagatt cagataaatt ataaggcttt
     2641 ggatatgatt tatactgcca tgcatgggat gcagcgcatg agtagtttcg gacagttccg
     2701 caccatgatc ggagatgaag cgttgaatga ttttagagat gaggatttgg ttcttaatat
     2761 tgagggattg aatgttgaag atggttgtta tacttggtat atgtctgtga aagataaggt
     2821 ggctgattgg tataatatgg aaactgggga ggcattgtgt tgttataagg tcacccggaa
     2881 ggatgaactt ttgcaggata tttatttaga tgaggatatt tttcctaata gtgggtagtt
     2941 gttagtttgt tgtattgttt tcttggtatg gtgtgagttc tatgtattct ctattcatga
     3001 aaggatcgcc aaattttcca cttctgtcat agaaggaaaa tttgttttta gttagctcgt
     3061 ctatgtccca gtaatgttct ccaccaaaat aaatggtact gaaacttgga tcaccgaatg
     3121 accattgtcc gtagatattg gcttcttttt tatttccttg tttgtcgatt tctatatttg
     3181 tacgggtata tgttccgttt ttattgaatt tgtatgtacc ttgccagaca ctgccgtttt
     3241 cgtctgttgt ttttttacca gcccatgtaa tatcacaaat taatgagatt atgctttctt
     3301 ctccatggtt gtagtatcct tgtttttcaa cacatccggt gtttgaaata agaaaaagtg
     3361 atactgttga aataagtaaa gagatatgta ttattctatt catagttaaa tatttaatat
     3421 tcaatgcaaa aataggagaa attttatatt tttgggcgaa acctttattt attaacttta
     3481 aaaaaggagg atttatgaaa aaagtaatgt ttatgttcat cagtctactg actgttttgg
     3541 gtgtttgttc gtgtaatgat aatgaagtaa tagaacctgt ggttagtgat tctgtatctg
     3601 atatggaggt cttatctcgt tttgttgatg taaatgagat tacaaatgaa tactatttca
     3661 atgagaataa gaaaacgagg gcgttgtctt atgtaacagg ttcggattgg caggatttag
     3721 aaaaagttag tcctttgagt attgagaaat ataagaataa cctgcaggtt ttaaatgctc
     3781 aagtggcaag tgctatttca aatcctaata ccgcttatgt tgttttttct gtaaatggaa
     3841 agactttggt taaaaaggtg aaggaggatg ctaattttga tttttcagta tttagggatg
     3901 ttgtaacgga aacgagggct gttctccctt ctttgagtat taatggaggt tctcaaagca
     3961 ctaccggagt tttttacgat tccagtcgta ctttaaagat gcaagttgat ttgaatgctt
     4021 caatacagaa taattattat ttctttgaag tattaaatcc taatgctaaa ccaagtccgg
     4081 atgataatat aacgacacct gaaagtgttg cttttagtgg aactggaccg ttatggagta
     4141 acactttcac ttggacttcg tattgggatg caaatgtacc tggtcaaggt tttaaatggg
     4201 agtttaaagg aaaaggtact actccttctt ttggttttat agctaattgc acctttagtc
     4261 gttaaaaaat gaacgggatt taatttgaat tgcacttctc aaaaaagaga agtgcaattc
     4321 tttttagtgt ctttctatcg gtgtagccag ttaccgttat ctaaagtctt ttgtagtgta
     4381 ttccaaagtt ctttaagaaa gtttttaaag tggatgttat ttagccaaat tgtagtaata
     4441 ccattctgac ttttggagat atctattttc acgtttttaa cttggtatga ttttctcttg
     4501 tctttatcgt aaaggtttcc agtgtagtat atttcctttc caataagaag ttgtcggata
     4561 tctttatttt gtattcccat agtttggagt tcctctatat tttcctgtgc attttccatt
     4621 tccggaaaaa ggttggttat gggttttagt ttggatgctt ctgcctttat ctgtctgtcg
     4681 gttgtttcct gtacccttcg catctcgatg ttgttggttc ttaattgtcc ttctaaattt
     4741 tgattcttga atgagaggtt ataattttct tttttgaggg tttcaatttc tttggcttgt
     4801 cgttttactt cccctacatt aaagacgctt gtaacggcat taaatacggt ttttccggct
     4861 tttgcggcag cttctttggc ttcgttgatg tgtatgtcgg ttttcatgct gtttagctct
     4921 ttttgtgccg tactaagttc cttttggact gtggtgattt tctcggttcc ggcagtgtat
     4981 gccctgttta gttgctcgat gtctttttga agttgttcag ctttctctgt ttccattttg
     5041 tttttgtatt gcatggccga caagtgtttc ttgtctgaag aaactccacg ttccatgttg
     5101 agacactctg ctgttatagt ctgcatctcc gccatgtcgt gtctgttcag ctttacagtt
     5161 tttcctgtat ggccgtccgt ccagtcaaag atcatgtgcg catgatagtt cggtttccat
     5221 gcttcttcct ttccgtccca tacgtttgcg ccttcatcct tatgggtgta gatttggaag
     5281 gcgtgcactc caaagcgttc ttccagtttt tcggccaagt cttgaagctg ctggattgtg
     5341 gtttcctcgc tgattactat taccccttcc cggattgggg tagctttctt ctgtaatcct
     5401 tgtccggtgg cttccttgta tttttccgtt atgtcccggt gtacttcggc aatggaacat
     5461 tctacccact gttcgttgcg gtgtgtgagt tccggacgga tgtagtcgag ctccttgctt
     5521 cttaagttgt gacgttccga gctgcctata ttgcaggctt ccactctgat acatgtcttt
     5581 gccatatctt tagg
//
