LOCUS       NZ_AP025233             5594 bp    DNA     circular CON 25-OCT-2023
DEFINITION  Phocaeicola vulgatus strain MG01-03 plasmid pMG01-03_1, complete
            sequence.
ACCESSION   NZ_AP025233
VERSION     NZ_AP025233.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00405043
            Assembly: GCF_020885715.1
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  JOURNAL   Unpublished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, Life
            Science Research Center - Division of Anaerobe Research; 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 01:22:53
            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)                     :: 4,268
            CDSs (total)                      :: 4,164
            Genes (coding)                    :: 4,033
            CDSs (with protein)               :: 4,033
            Genes (RNA)                       :: 104
            rRNAs                             :: 7, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 7, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 81
            ncRNAs                            :: 2
            Pseudo Genes (total)              :: 131
            CDSs (without protein)            :: 131
            Pseudo Genes (ambiguous residues) :: 0 of 131
            Pseudo Genes (frameshifted)       :: 48 of 131
            Pseudo Genes (incomplete)         :: 95 of 131
            Pseudo Genes (internal stop)      :: 28 of 131
            Pseudo Genes (multiple problems)  :: 30 of 131
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP025233.1.
            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="MG01-03"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:821"
                     /plasmid="pMG01-03_1"
                     /geo_loc_name="Japan"
                     /lat_lon="35.4234 N 136.7606 E"
                     /collection_date="2020-09-20"
     gene            277..1527
                     /locus_tag="LPD79_RS21205"
                     /old_locus_tag="GAIMETA21S03_40820"
     CDS             277..1527
                     /locus_tag="LPD79_RS21205"
                     /old_locus_tag="GAIMETA21S03_40820"
                     /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"
     gene            complement(1597..2367)
                     /locus_tag="LPD79_RS21210"
                     /old_locus_tag="GAIMETA21S03_40830"
     CDS             complement(1597..2367)
                     /locus_tag="LPD79_RS21210"
                     /old_locus_tag="GAIMETA21S03_40830"
                     /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            2459..2920
                     /locus_tag="LPD79_RS21215"
                     /old_locus_tag="GAIMETA21S03_40840"
     CDS             2459..2920
                     /locus_tag="LPD79_RS21215"
                     /old_locus_tag="GAIMETA21S03_40840"
                     /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            complement(2924..3826)
                     /locus_tag="LPD79_RS21220"
                     /old_locus_tag="GAIMETA21S03_40850"
     CDS             complement(2924..3826)
                     /locus_tag="LPD79_RS21220"
                     /old_locus_tag="GAIMETA21S03_40850"
                     /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(4468..4866)
                     /locus_tag="LPD79_RS21225"
                     /old_locus_tag="GAIMETA21S03_40860"
     CDS             complement(4468..4866)
                     /locus_tag="LPD79_RS21225"
                     /old_locus_tag="GAIMETA21S03_40860"
                     /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            complement(4903..5223)
                     /locus_tag="LPD79_RS21230"
                     /old_locus_tag="GAIMETA21S03_40870"
     CDS             complement(4903..5223)
                     /locus_tag="LPD79_RS21230"
                     /old_locus_tag="GAIMETA21S03_40870"
                     /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            complement(5217..5465)
                     /locus_tag="LPD79_RS21235"
                     /old_locus_tag="GAIMETA21S03_40880"
     CDS             complement(5217..5465)
                     /locus_tag="LPD79_RS21235"
                     /old_locus_tag="GAIMETA21S03_40880"
                     /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"
     Typing          complement(2925..3973)
                     /name="rep_cluster_870"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.905"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          278..1524
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tggtgcaccc ccttgccgtg cagcgctccc cgaccgatga ttttttattg tgccttgtgt
       61 ccttttccct tttgtccggc ttctgttccc aagcacatcc ggaacacatg gcagagcgct
      121 tgcaaatccc gtccggaagg cttacctttg caaaaggtta tagcacacta taacccctaa
      181 aggggttgtg tgcgaggggt gtcccctcga ccccgtgcga tgtgacgttt cacgccacat
      241 cttctaaaca gacatacaca cctaaaacct aaagatatgg caaagacatg tatcagagtg
      301 gaagcctgca atataggcag ctcggaacgt cacaacttaa gaagcaagga gctcgactac
      361 atccgtccgg aactcacaca ccgcaacgaa cagtgggtag aatgttccat tgccgaagta
      421 caccgggaca taacggaaaa atacaaggaa gccaccggac aaggattaca gaagaaagct
      481 accccaatcc gggaaggggt aatagtaatc agcgaggaaa ccacaatcca gcagcttcaa
      541 gacttggccg aaaaactgga agaacgcttt ggagtgcacg ccttccaaat ctacacccat
      601 aaggatgaag gcgcaaacgt atgggacgga aaggaagaag catggaaacc gaactatcat
      661 gcgcacatga tctttgactg gacggacggc catacaggaa aaactgtaaa gctgaacaga
      721 cacgacatgg cggagatgca gactataaca gcagagtgtc tcaacatgga acgtggagtt
      781 tcttcagaca agaaacactt gtcggccatg caatacaaaa acaaaatgga aacagagaaa
      841 gctgaacaac ttcaaaaaga catcgagcaa ctaaacaggg catacactgc cggaaccgag
      901 aaaatcacca cagtccaaaa ggaacttagt acggcacaaa aagagctaaa cagcatgaaa
      961 accgacatac acatcaacga agccaaagaa gctgccgcaa aagccggaaa aaccgtattt
     1021 aatgccgtta caagcgtctt taatgtaggg gaagtaaaac gacaagccaa agaaattgaa
     1081 accctcaaaa aagaaaatta taacctctca ttcaagaatc aaaatttaga aggacaatta
     1141 agaaccaaca acatcgagat gcgaagggta caggaaacaa ccgacagaca gataaaggca
     1201 gaagcatcca aactaaaacc cataaccaac ctttttccgg aaatggaaaa tgcacaggaa
     1261 aatatagagg aactccaaac tatgggaata caaaataaag atatccgaca acttcttatt
     1321 ggaaaggaaa tatactacac tggaaacctt tacgataaag acaagagaaa atcataccaa
     1381 gttaaaaacg tgaaaataga tatctccaaa agtcagaatg gtattactac aatttggcta
     1441 aataacatcc actttaaaaa ctttcttaaa gaactttgga atacactaca aaagacttta
     1501 gataacggta actggctaca ccgatagaaa gacactaaaa agaattgcac ttctcttttt
     1561 tgagaagtgc aattcaaatt aaatcccgtt cattttttaa cgactaaagg tgcaattagc
     1621 tataaaacca aaagaaggag tagtaccttt tcctttaaac tcccatttaa aaccttgacc
     1681 aggtacattt gcatcccaat acgaagtcca agtgaaagtg ttactccata acggtccagt
     1741 tccactaaaa gcaacacttt caggtgtcgt tatattatca tccggacttg gtttagcatt
     1801 aggatttaat acttcaaaga aataataatt attctgtatt gaagcattca aatcaacttg
     1861 catctttaaa gtacgactgg aatcgtaaaa aactccggta gtgctttgag aacctccatt
     1921 aatactcaaa gaagggagaa cagccctcgt ttccgttaca acatccctaa atactgaaaa
     1981 atcaaaatta gcatcctcct tcaccttttt aaccaaagtc tttccattta cagaaaaaac
     2041 aacataagcg gtattaggat ttgaaatagc acttgccact tgagcattta aaacctgcag
     2101 gttattctta tatttctcaa tactcaaagg actaactttt tctaaatcct gccaatccga
     2161 acctgttaca taagacaacg ccctcgtttt cttattctca ttgaaatagt attcatttgt
     2221 aatctcattt acatcaacaa aacgagataa gacctccata tcagatacag aatcactaac
     2281 cacaggttct attacttcat tatcattaca cgaacaaaca cccaaaacag tcagtagact
     2341 gatgaacata aacattactt ttttcataaa tcctcctttt ttaaagttaa taaataaagg
     2401 tttcgcccaa aaatataaaa tttctcctat ttttgcattg aatattaaat atttaactat
     2461 gaatagaata atacatatct ctttacttat ttcaacagta tcactttttc ttatttcaaa
     2521 caccggatgt gttgaaaaac aaggatacta caaccatgga gaagaaagca taatctcatt
     2581 aatttgtgat attacatggg ctggtaaaaa aacaacagac gaaaacggca gtgtctggca
     2641 aggtacatac aaattcaata aaaacggaac atatacccgt acaaatatag aaatcgacaa
     2701 acaaggaaat aaaaaagaag ccaatatcta cggacaatgg tcattcggtg atccaagttt
     2761 cagtaccatt tattttggtg gagaacatta ctgggacata gacgagctaa ctaaaaacaa
     2821 attttccttc tatgacagaa gtggaaaatt tggcgatcct ttcatgaata gagaatacat
     2881 agaactcaca ccataccaag aaaacaatac aacaaactaa caactaccca ctattaggaa
     2941 aaatatcctc atctaaataa atatcctgca aaagttcatc cttccgggtg accttataac
     3001 aacacaatgc ctccccagtt tccatattat accaatcagc caccttatct ttcacagaca
     3061 tataccaagt ataacaacca tcttcaacat tcaatccctc aatattaaga accaaatcct
     3121 catctctaaa atcattcaac gcttcatctc cgatcatggt gcggaactgt ccgaaactac
     3181 tcatgcgctg catcccatgc atggcagtat aaatcatatc caaagcctta taatttatct
     3241 gaatcttttt tttaccgtca cgacctttcg attttgagac agaagccttt gaagcatact
     3301 taaaaacctc tatcgctgca ttttcaaaat cctctatctt cttatatttc tgaaaacggg
     3361 catcagcaac cgtactacca tgcaatttct tccattgggc tactacatat tttgcagctt
     3421 ccaatgaatc aacaataata tgaaaatgat aatggaacga aaacaaatcc ttttttacta
     3481 catgataggt acactccttc ttaatcaccc ccgaaatacc aagtgaacga aacttgtgtt
     3541 tcgtccttat accatcagcc cacatccggt tacatctacg catgaaatct cgcaataccc
     3601 ttgcatcatc ggttacacaa ttttgcaagg taagcgtcac aaaataaaac tctctgcctt
     3661 ccgaagccaa atacttcata accggaagga acttctttac attttgtgcc gtttgaatac
     3721 gctgacaaat aggacaaaaa gcccgatgac aataatggga atgcgcctta cctccctgca
     3781 cagtataaac atttgaacac acatgggcat ccatatatgc tttcatcagc ttactatccg
     3841 gattcttttc cgaaagtttt cgagtaaaat tatgggatat gatttttact ttagcctttt
     3901 ttttaagact atcagaaccg ttttttaacg gactttcttt gcagttggtt atatttgttc
     3961 tatctttgca catatgaaat tttgatgtgg ctttcgtttg gtatccgccc cgccaagaac
     4021 gaacacaaac gattgctaat tcttaaaata caaagcccgt tggttactgc cttcgggctt
     4081 tcgttttttc tcagcccaaa agtaggtaat tcattccaaa ccgccaaaca tcattcaaaa
     4141 aacctacata taacaagtca aaaagcattt accacgaaac tttctagttt atctagtatg
     4201 ggggctcgcc cccattcccc cggctgcgca attctgacac aaatacacta ctaaatccac
     4261 aacagacaaa gatacttccg gaaaaaaaac tatctttgcc gtacacaaag acaacccttg
     4321 ccgagcgata cgggagagtt gcaaaaaaaa caccggagtg aattgacgga tatccgacat
     4381 ctccggtggt attttttttc ttatccccct cccgtccccc aaagggggag cacacaaaga
     4441 caaaccctgc cttcactcaa tggagtgtta aatagttgca tatgggtcaa gttccttaat
     4501 ccgcttacac aaaaaatcaa agcgtttctt tgtaagtggt gtaagcgtat cgagattatc
     4561 tccatcgaaa ttctccccaa aaataaggtc gttcattcct atgccgtgat tgtagttctc
     4621 acgcacacag ttgcgcagcg tccaaaggtt acgcaggttt acccagtctg ctgtgcggct
     4681 ctttaccctg cggaacaaga taacggcagt ccgcaaatag tgccccacat ggtcgtaatc
     4741 gtgcaagaca cgtttgccca aatagtaaat atccaaatct tgtttttctc tgtcctcgac
     4801 tacttgacag aggaagaatg gaatatcctt caggttatcc cattcgatgt agtcagttgg
     4861 tttcataatg tcttatttgc atttttcttt ccgtactttc cattattcac agaacatttg
     4921 ctgaaacact tcacgtaacc tttttatctc actgaaattc aaatctccaa tctttctttt
     4981 cagccggctt ttatccaccg tgcgaatttg atcagtggct atctctcctt cacgcccggc
     5041 tacagaacac agaacccggt aaggataatt tcttatcgtt gaggttatcg gaacaatgac
     5101 tactgttgta aggtacatat tcaaatctga aggagtgaca actacacatg gccgtgtctt
     5161 tgccatttca cccccacggg tagggtctaa ctctacccaa tacacttcat actgttctac
     5221 catgtccaat cctcaaactt ttcatcctca aacacatcag ggataagcaa ctcatcatcc
     5281 ccattctcat gggcacgttt ggcagcttcc gcccatccct gccgtggttg tgcctttatc
     5341 acaatattgt tcccgtccaa agaaatgctc acagccgatt tcaaggacaa acgcaactgt
     5401 ttcaatactt cggaaggaag tattatcccc ttgctgtttc caatctgaat aatattcgtt
     5461 accataatgt tataacttta taattgatta tcacgataca aatatatgta aagttataac
     5521 aataacaaaa ggaaaaacaa cttttttcca ttttcaccga gaaccctgtc aatggctgca
     5581 ctcgtcggga gtgt
//
