LOCUS       NZ_CP072248             5625 bp    DNA     circular CON 03-APR-2024
DEFINITION  Phocaeicola dorei strain CL06T03C03 plasmid pBdorCL06T03-2, complete
            sequence.
ACCESSION   NZ_CP072248
VERSION     NZ_CP072248.1
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 5625)
  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 5625)
  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
            CP072248.1.
            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..5625
                     /organism="Phocaeicola dorei"
                     /mol_type="genomic DNA"
                     /strain="CL06T03C03"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:357276"
                     /plasmid="pBdorCL06T03-2"
                     /geo_loc_name="USA: Boston"
                     /lat_lon="42.3361 N 71.1075 W"
                     /collection_date="2009-05"
     gene            1..1038
                     /locus_tag="INE79_RS23385"
                     /old_locus_tag="INE79_04689"
     CDS             1..1038
                     /locus_tag="INE79_RS23385"
                     /old_locus_tag="INE79_04689"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_008670426.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_211479465.1"
                     /translation="MDKGTINITNCKENPLKNGSKSLKKKAKVKIISHNFTRKLSEKNP
                     ESKLMKAYMDAHVCSNIYTVQGGKAHSHYCHRAFCPICQRIQTAQNIKKFLPIMKYLAS
                     EGREFYFVTLTLQNCVTSDVKVLRDFMRKCNRMWADGIRTKHKFRSLDISGVIKKECTY
                     HVVKKGLFSFHYHFHIIVDSLEAAKYVVAQWKKLHGCTVADARFQKYKKIEDLESAAIE
                     VFKYASKASVSRSKGRDGKEKVQINYRALDMIYTAMHGMQRMSSFGQFRTMIGDEALND
                     FRDEDLVLDVEGLNVDDGCYTWYMSVKDKVADWYNMETGEALCRYKVTRKDELLQDVYL
                     ENNSP"
                     /name="protein rep"
     gene            1107..1826
                     /locus_tag="INE79_RS23390"
                     /old_locus_tag="INE79_04690"
     CDS             1107..1826
                     /locus_tag="INE79_RS23390"
                     /old_locus_tag="INE79_04690"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_211479466.1"
                     /translation="MRVLNYVKFVFTVFFLGSFAVMGLTSCSNDESEVIENENPLLNAS
                     ITFKYDGSVYSYEMDNGELKCDDRTKSVIDFLWNCDDLVTYIHDDGSIEYFMSEEDCKD
                     AIFWERPELALSSVSRATEKERYYVTLRIYENAKYKGANRFYERIGNGIITLGDLTTLG
                     WGITSFKLNFINSLPPLLNETGVRFYAEKNLSGESIGYTTKGEKAISNFTSVPLRPGSS
                     ENWNDRVKSLKFGAGVY"
                     /name="hypothetical protein"
     gene            1888..2487
                     /locus_tag="INE79_RS23395"
                     /old_locus_tag="INE79_04691"
     CDS             1888..2487
                     /locus_tag="INE79_RS23395"
                     /old_locus_tag="INE79_04691"
                     /EC_number="5.2.1.8"
                     /inference="COORDINATES: protein motif:HMM:NF012478.4"
                     /GO_function="GO:0003755 - peptidyl-prolyl cis-trans
                     isomerase activity [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="FKBP-type peptidyl-prolyl cis-trans isomerase"
                     /protein_id="WP_211479467.1"
                     /translation="MKRKSFFVFLYICVIFFSSCEESDGINNDLRANWKDRNLFYIDSI
                     ADVAERNPASWKKILNYKLPPEGLGGNFYENSDYVYINILEEGDKNGKYPLYTDSVDVY
                     YKGSLIDKDVFDYNFMSDSDFDFRNPTRFAIGGDYGVIVGLSTALQRMRIGDRWMIYIS
                     ENLGYGEQEKEKIPSYSTLIFEVVLDDIIHPRFVKD"
                     /name="FKBP-type peptidyl-prolyl cis-trans isomerase"
     gene            complement(2561..3817)
                     /locus_tag="INE79_RS23400"
                     /old_locus_tag="INE79_04692"
     CDS             complement(2561..3817)
                     /locus_tag="INE79_RS23400"
                     /old_locus_tag="INE79_04692"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_008670432.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_211479468.1"
                     /translation="MAKTCIRVEACKIGSAERHNLRSKELDYIRPELTHRNEQWIERPI
                     TEVHQDITEKYKAATGQGLQKKATPIREGVIVISEDTTLRQLQNLAEKLEERFGVHAFQ
                     IYTHKDEGANVWDGREETWKPNYHAHIIFDWTDGHTGKTVKLNKHDMAEMQTITAECLN
                     MERGVSSDRKHLSAMQYKNQMETEKAGQLQKDIEQLNREYSTGTRQVNQVQEELNIARK
                     ELKSMKTDIHINEAKEAAAKAGKTVFNAVTSVFNVGEVKRQAKEIEELTKENYNLSFKN
                     QNLEGQLRTNTIAMQRAQETADRQIKAQAAKLKPITELFPEMENAEENIEELRTMGIQN
                     NDIRQLLTGKEIYYTGNLYDRDKRKSYPVKSIKIDIAKSRNGITTIWLNDTYFKTFLQE
                     LWNILQKTLGINRNKGMHL"
                     /name="hypothetical protein"
     gene            4207..4455
                     /locus_tag="INE79_RS23405"
                     /old_locus_tag="INE79_04693"
     CDS             4207..4455
                     /locus_tag="INE79_RS23405"
                     /old_locus_tag="INE79_04693"
                     /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_146352990.1"
                     /translation="MVTNIIQIGNSKGVILPSDLLKRLSLSLKSAVSVSLDGSSIVIKA
                     QPRQGWEEDAKRLHAEGGDELLIPDVFEDETFEDWTW"
                     /name="AbrB/MazE/SpoVT family DNA-binding domain-containing
                     protein"
     gene            4449..4769
                     /locus_tag="INE79_RS23410"
                     /old_locus_tag="INE79_04694"
     CDS             4449..4769
                     /locus_tag="INE79_RS23410"
                     /old_locus_tag="INE79_04694"
                     /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_211479463.1"
                     /translation="MVEQYEVYWVELDPTQGGEMAKTRPCVVVSPTGLNNHLKTVVVAP
                     VTSTIRNVSFRVRCFLAGKNGEIAADQLRAIDKSRIKRKIGELNNREIEELKKVFQQMF
                     CE"
                     /name="type II toxin-antitoxin system PemK/MazF family
                     toxin"
     gene            4766..4996
                     /locus_tag="INE79_RS23415"
                     /old_locus_tag="INE79_04695"
     CDS             4766..4996
                     /locus_tag="INE79_RS23415"
                     /old_locus_tag="INE79_04695"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_008670445.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_211479464.1"
                     /translation="MMEEKEKKPTCKDFAEYLRKCASAYAKRGSRELTDSREEYQDIFD
                     DLCQLHADFDHGANRIMSLKDMFIDFFDLKR"
                     /name="hypothetical protein"
     Typing          7..1019
                     /name="rep_cluster_870"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="88.856"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          complement(2595..3817)
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="85.784"
                     /coverage="98.0"
                     /evalue="0.0"
ORIGIN
        1 atggacaaag gtacaataaa tataaccaac tgcaaagaaa atccgttaaa aaacggttct
       61 aaaagtctta aaaaaaaggc taaagtaaaa atcatttccc ataattttac tcgaaaactt
      121 tcggaaaaga atccggaaag caaactgatg aaagcgtaca tggatgccca tgtgtgttca
      181 aatatctata ccgtgcaggg tggtaaggct cattcccatt actgccatcg ggctttctgt
      241 cctatttgtc agcgtatcca aacggcacaa aatataaaga agtttctccc gattatgaag
      301 tatctggctt cggaaggtag ggagttttat tttgtgacgc ttactttgca gaactgtgtt
      361 accagtgatg tgaaggtatt gcgcgatttt atgcgcaagt gtaaccggat gtgggctgac
      421 ggtataagga caaagcataa gtttcgctct cttgatatat cgggagtgat taagaaggaa
      481 tgtacctacc atgtagtaaa aaaagggttg ttttcgtttc attatcattt tcatattata
      541 gttgattcgt tggaagctgc taagtatgtg gtagcccagt ggaagaaatt gcatggttgt
      601 acagttgcgg atgctcgttt tcagaaatat aagaagatag aggatttgga gagtgcagcg
      661 atagaggttt ttaagtatgc ttcaaaggct tctgtttcac gttcaaaagg tcgtgacggt
      721 aaagagaagg ttcagataaa ttatagagca ctggatatga tttatactgc tatgcatggg
      781 atgcagcgta tgagtagttt tgggcagttc cgtactatga taggggatga agcattgaat
      841 gattttcggg atgaggattt ggttcttgat gtggaaggtt tgaatgtgga tgatggttgt
      901 tatacttggt atatgtctgt aaaagataag gtggctgatt ggtataatat ggaaacaggg
      961 gaagcattgt gccgttataa agtaacccga aaggatgagt tattgcagga tgtttatttg
     1021 gaaaacaatt caccttaaaa tattggcttg tataaaatat atatgtaatt ttgtagtatg
     1081 attgttttac tttaaatata aatattatga gagttttaaa ttatgtaaaa tttgtattta
     1141 ctgtcttctt tttgggaagt tttgcagtaa tgggcttgac ctcttgttct aatgatgaga
     1201 gtgaggttat agagaatgag aatccattgt taaatgcatc tattactttt aagtatgatg
     1261 gaagtgtgta ttcttatgag atggataatg gggaattgaa atgtgatgac agaacgaaat
     1321 ctgttataga ttttctgtgg aattgtgatg atttggtaac atatatccat gatgatggtt
     1381 ctattgaata ttttatgtca gaagaagatt gtaaagatgc tatattttgg gagcgtccag
     1441 agttagcgtt gtcttctgtt tcgagagcta cggaaaaaga aagatattat gttactttga
     1501 ggatttatga gaatgcgaaa tataaggggg caaatagatt ttatgaacgt attggcaatg
     1561 gaattattac tcttggtgat ttgacaacat taggttgggg tattacatct tttaaactta
     1621 atttcattaa tagtttgcct cctttattaa atgaaactgg agttagattt tatgctgaaa
     1681 agaatctttc gggtgagtca ataggatata ctacaaaagg cgaaaaagct attagtaatt
     1741 ttacgagtgt gcctttacgt ccggggtctt ctgaaaactg gaatgataga gtgaagtctt
     1801 taaaatttgg tgctggagtt tattaattag attttaatta tataatatgg gtaatttaga
     1861 aatgaattac ccatatatta tttgtttatg aagagaaaga gtttttttgt gtttctgtat
     1921 atttgtgtga ttttcttttc atcttgtgag gaaagtgatg gcataaataa tgatttaaga
     1981 gctaattgga aagatagaaa tcttttttat atagattcaa tagcggatgt ggctgagaga
     2041 aatccagcta gttggaaaaa aattttaaat tataagttac ctccggaggg gttaggaggt
     2101 aatttttatg agaatagtga ttatgtatac attaatatat tagaagaggg tgataagaat
     2161 ggaaagtacc ctttgtatac ggatagtgta gatgtatatt ataagggaag cttaatagat
     2221 aaagatgtat ttgattataa ttttatgagt gattcggatt ttgattttcg aaatccaaca
     2281 agatttgcga ttggtggaga ttatggagta attgtcggtt tatctacagc tttacagagg
     2341 atgagaattg gggataggtg gatgatatat attagtgaga atttaggata tggggaacag
     2401 gaaaaagaga aaatacctag ctattctact ttaatttttg aagttgtatt agatgatatt
     2461 attcatccga ggtttgtaaa agattgatta aagttttata tttaggtttg tttctaataa
     2521 actttttaag gaagtttgaa aggcaggtgt tagtatctgt ttatagatgc attcctttat
     2581 ttctatttat tcctaaagtt ttttgtagta tattccaaag ttcttgaagg aaagttttaa
     2641 agtaggtatc attaagccaa atggtagtaa taccattccg gcttttggcg atatctatct
     2701 ttatgctttt gaccgggtat gattttcttt tatccctgtc gtataggttg cctgtatagt
     2761 atatttcttt tcctgtaagg agttgccgga tatcgttgtt ttgtattccc atagttcgga
     2821 gttcttctat attttcctct gcgttttcca tttccggaaa cagttctgtt atgggtttga
     2881 gcttggctgc ctgtgctttt atttgcctgt cggctgtttc ctgtgctctt tgcatcgcaa
     2941 tagtgttagt tctaagctgt ccttccaagt tttggttttt gaaagagaga ttgtagtttt
     3001 cttttgtgag ctcttcgatt tctttggctt gtcgttttac ttcccctaca ttgaaaacac
     3061 ttgtaacggc attgaaaacg gtctttccgg cttttgctgc tgcttccttg gcttcgttaa
     3121 tgtggatatc ggttttcatg cttttgagtt ctttccgggc gatattgagt tcttcctgta
     3181 cttggttgac ctgtcgggtt cctgtggagt attcccggtt gagctgctcg atgtcttttt
     3241 gaagttgccc ggctttctcc gtttccatct ggtttttgta ttgcatggct gacaagtgtt
     3301 tccgatctga agaaacgcca cgttccatgt tcaagcactc ggctgttatg gtctgcatct
     3361 ccgccatgtc gtgtttgttc agcttaactg ttttcccggt atgtccgtcc gtccagtcga
     3421 agattatgtg cgcatgatag ttcggtttcc atgtttcttc cctaccgtcc catacgtttg
     3481 cgccttcatc tttatgggtg tatatttgga aagcgtgtac cccgaaacgt tcttccagct
     3541 tttcggctag gttctgaagc tgccggagtg tggtgtcctc gctgatcacg attactcctt
     3601 cccggattgg ggttgctttt ttttgcaagc cctgtccggt agctgccttg tatttttccg
     3661 ttatgtcttg gtgtacttca gtaattggac gttctatcca ctgttcgttg cggtgggtga
     3721 gttccggacg gatgtagtcc agttccttgc ttcttaggtt gtgccgttct gcgctgccga
     3781 ttttgcaggc ttccactctg atgcatgtct ttgccatatc gttaggtttt aggtgtgtat
     3841 gtctgttctg aagatgtggc gtgaaacgtc acatcgcacg gggtcaaggg gtgtcccctt
     3901 gcacacaacc cctttagggg ttagtgctat aaccttttgc aaaggtaaat cttccggatg
     3961 ggatttgcaa gcggtctgcc catacttaag aacagaagct ggataaaagg gaaaagagta
     4021 caaggcacga taaaaaatca tcggtcgggg agcgccgcac ggcaaggggg tgcaccagca
     4081 ctcccgacga gtgcatcggt tggctgagtt ctcggtaaaa aaggaaaaaa gttggctttt
     4141 cttttgataa tgttataact tcatatatct ttgtgttatg aaaatcaatt ttaaagttat
     4201 aacattatgg taacaaacat tattcagatt ggaaacagta agggagtcat acttccttct
     4261 gaccttttaa agaggcttag cctttcttta aagtctgccg tttctgtttc tttggacggt
     4321 agtagtatag tgataaaggc acaaccaaga caaggatggg aagaggatgc aaaacgactt
     4381 catgcagaag gtggtgatga gcttctgatt cctgatgttt tcgaagatga aacttttgaa
     4441 gactggacat ggtagaacaa tatgaagtgt actgggtgga gttggacccc actcaaggag
     4501 gtgagatggc taagacaaga ccatgtgtag tggttagtcc taccggtttg aataatcatt
     4561 taaaaactgt ggttgttgct ccggttacat ctaccattag gaatgtttct tttcgtgtgc
     4621 ggtgtttttt ggctgggaaa aatggagaga ttgcagcgga tcagttaagg gcaatagata
     4681 agagccgtat aaaacgaaag attggagaac ttaataacag ggaaatagag gaactgaaaa
     4741 aagtgttcca acaaatgttt tgtgaatgat ggaagaaaag gagaaaaaac ctacctgcaa
     4801 ggattttgca gagtatttaa ggaaatgtgc gagtgcctat gccaagcgtg gaagccggga
     4861 actaaccgac agccgggaag agtaccagga tatttttgac gatctgtgtc agcttcatgc
     4921 ggattttgac catggggcaa accggatcat gtctttaaaa gatatgttta tcgacttttt
     4981 tgacctgaag aggtaacact ccattgagtg aaggcagggt ttgtctttgt gtgctccccc
     5041 tttgggggac gggaggggga taagaaaaat accactggag atgtcggata tccgtcaatt
     5101 cactccagtg gtgttatttg caactctccc gtatcgttcg gcaagggttg tctttgtgta
     5161 cgacaaagat agtttttttt ccggaagtat ccttatttct gcggatttag ttgtgtattt
     5221 gtgtccggat tgcgcagccg ggggaatggg ggttagcccc catactggat aaattagaaa
     5281 gtttcgtggt aaatgcctta cagtatattg tgagtggggt cagcaataaa aaaactccga
     5341 gattcgcatc tgggagtttt ttattttaca tgtatagaaa tgctcgcttg catttctacc
     5401 ctcttttgag ggcaaagatg cagtgaatat agtaaaattt gtgttattac ggaaattgta
     5461 tcttcttttt ttgtagttgt ttggaggttt ggaatgaatt gcctactttt ggggtgagat
     5521 aaaaaacacg aagcccatcg gctcacaacc aatgggcttt gtatatgttt aacggcttcg
     5581 ctcttacttt tggacggttt gcagcgaaac cacaattata attac
//
