LOCUS       NZ_CP072260             4148 bp    DNA     circular CON 28-MAR-2024
DEFINITION  Bacteroides caccae CL03T12C61 plasmid pBcacCL03T12-2, complete
            sequence.
ACCESSION   NZ_CP072260
VERSION     NZ_CP072260.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16451178
            Assembly: GCF_018292205.1
KEYWORDS    RefSeq.
SOURCE      Bacteroides caccae CL03T12C61
  ORGANISM  Bacteroides caccae CL03T12C61
            Bacteria; Bacteroidota; Bacteroidia; Bacteroidales; Bacteroidaceae;
            Bacteroides.
REFERENCE   1  (bases 1 to 4148)
  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 4148)
  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                     :: BcacCL03T12C61_pbv2
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 164x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_018292205.1-RS_2024_03_28
            Annotation Date                   :: 03/28/2024 06:46:16
            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)                     :: 4,594
            CDSs (total)                      :: 4,504
            Genes (coding)                    :: 4,387
            CDSs (with protein)               :: 4,387
            Genes (RNA)                       :: 90
            rRNAs                             :: 5, 5, 5 (5S, 16S, 23S)
            complete rRNAs                    :: 5, 5, 5 (5S, 16S, 23S)
            tRNAs                             :: 72
            ncRNAs                            :: 3
            Pseudo Genes (total)              :: 117
            CDSs (without protein)            :: 117
            Pseudo Genes (ambiguous residues) :: 0 of 117
            Pseudo Genes (frameshifted)       :: 42 of 117
            Pseudo Genes (incomplete)         :: 74 of 117
            Pseudo Genes (internal stop)      :: 31 of 117
            Pseudo Genes (multiple problems)  :: 25 of 117
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP072260.1.
            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..4148
                     /organism="Bacteroides caccae CL03T12C61"
                     /mol_type="genomic DNA"
                     /strain="CL03T12C61"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:997873"
                     /plasmid="pBcacCL03T12-2"
                     /geo_loc_name="USA: Boston"
                     /lat_lon="42.3361 N 71.1075 W"
                     /collection_date="2009-05"
     gene            1..1026
                     /locus_tag="INE72_RS22850"
                     /old_locus_tag="INE72_04551"
                     /db_xref="GeneID:75115726"
     CDS             1..1026
                     /locus_tag="INE72_RS22850"
                     /old_locus_tag="INE72_04551"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_008657007.1"
                     /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_005683051.1"
                     /db_xref="GeneID:75115726"
                     /translation="MKKKLPITKNKDVVVSWVYTWSKQQDMSIHEQRIVLRILEACQAE
                     LKGVKLKDYAGTKRKFEHGLWDVDAQMHVSDVIFSGRDYNEIIAALDSLAGRFFTYEDD
                     EEWWKCGFISNPKYKKHTGIITFRVSNDLWDVFTKFAKGYREFELNKALALPTGYSLRF
                     YMLMSGQVYPLDISLDNLKDRLGIPADKYKDKNGKDRIDNFEERVLKPAKAALDESCPY
                     TFNYVKVRENPNNKRSKVTGFRFYPVYQPQFRDEELEGKELQAKVTARYQIDSHVYEYL
                     RYSCGFTSEEINRNKETFITAQEKITDLIGELALLNGKSREKNNPKGWIINALKGKIKD
                     K"
                     /name="replication initiation protein"
     gene            complement(1063..1293)
                     /locus_tag="INE72_RS22855"
                     /old_locus_tag="INE72_04552"
                     /db_xref="GeneID:75115727"
     CDS             complement(1063..1293)
                     /locus_tag="INE72_RS22855"
                     /old_locus_tag="INE72_04552"
                     /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_005683050.1"
                     /db_xref="GeneID:75115727"
                     /translation="MGTTEHEEPRFFFILNKGAKSGGEITHAVLNGSIVSKPAGWDAFH
                     GLALAKEKLSSEEIQQQMKELGVEMEIVPLI"
                     /name="hypothetical protein"
     gene            complement(1312..1764)
                     /gene="mbpC"
                     /locus_tag="INE72_RS22860"
                     /old_locus_tag="INE72_04553"
                     /db_xref="GeneID:75115728"
     CDS             complement(1312..1764)
                     /gene="mbpC"
                     /locus_tag="INE72_RS22860"
                     /old_locus_tag="INE72_04553"
                     /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_005683049.1"
                     /db_xref="GeneID:75115728"
                     /translation="METNSHPEAAASTVKQGQYSPRKRKDTAPKVNPQLAIELFFQEMG
                     RIEAYTKRIEDATSRKVQIDGKSLESAENRLKNVLSDFERQGYRMKNGGYVDKRISFYS
                     ILCAVISLLFACFMCYLWTDAAKDRDNYKQYYEYFQEQAREQKGNK"
                     /name="mbpC"
     gene            complement(1721..2515)
                     /gene="mbpB"
                     /locus_tag="INE72_RS22865"
                     /old_locus_tag="INE72_04554"
                     /db_xref="GeneID:75115729"
     CDS             complement(1721..2515)
                     /gene="mbpB"
                     /locus_tag="INE72_RS22865"
                     /old_locus_tag="INE72_04554"
                     /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_005683056.1"
                     /db_xref="GeneID:75115729"
                     /translation="MIGKGKSISHGTAALEYDLAKEIDGQTAAIEIARHELYGCTGAEM
                     VQEMKPYHADFPNVKNNCLRFEVSPSIEESATFTDADWAELGNDFMQRMGLANHQYIII
                     RHSGTESKKEQAHLHILANRVSLSGELYRDNWIGKKATEAANAIAKERNFVQSQDIGKA
                     NKAEIKEAMDDVLKKMQGFDLTKFKEELGRRGFKVREARASTGKLNGYYVTARSGTEYK
                     ASEIGKGYTLAHIERTQSKLKYNSMNISHGNKLTPGSGSFHR"
                     /name="mbpB"
     gene            complement(2512..2811)
                     /gene="mbpA"
                     /locus_tag="INE72_RS22870"
                     /old_locus_tag="INE72_04555"
                     /db_xref="GeneID:75115730"
     CDS             complement(2512..2811)
                     /gene="mbpA"
                     /locus_tag="INE72_RS22870"
                     /old_locus_tag="INE72_04555"
                     /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_005683055.1"
                     /db_xref="GeneID:75115730"
                     /translation="MEVRRNEKITFRCTRYEKLALAEQAARCSMSTSEYCRSLSLGGRP
                     RERYTEEERQLLRDIAQLKGTLQRLNNYFGGRQYREVFEENQALITELKKILSR"
                     /name="mbpA"
     gene            complement(3005..3202)
                     /locus_tag="INE72_RS22875"
                     /old_locus_tag="INE72_04556"
                     /db_xref="GeneID:75115731"
     CDS             complement(3005..3202)
                     /locus_tag="INE72_RS22875"
                     /old_locus_tag="INE72_04556"
                     /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_005683054.1"
                     /db_xref="GeneID:75115731"
                     /translation="MVEYCVYWLENGEPMHEVFSNLAAAEMYSCAIRGKENVEWVEVSE
                     EEAIDLDELEDMFPDDFCGV"
                     /name="hypothetical protein"
     gene            complement(3213..3488)
                     /locus_tag="INE72_RS22880"
                     /old_locus_tag="INE72_04557"
                     /db_xref="GeneID:75115732"
     CDS             complement(3213..3488)
                     /locus_tag="INE72_RS22880"
                     /old_locus_tag="INE72_04557"
                     /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"
                     /db_xref="GeneID:75115732"
                     /translation="MMYTIRVSDGVDKVIAKWKKSNPNLFKKYKKIYKELLEHPKTGLG
                     HPEALRGGGDITWSRHITAHDRIIYDIYEEVVEVYILEVEGHYNDK"
                     /name="type II toxin-antitoxin system YoeB family toxin"
     gene            complement(3485..3736)
                     /locus_tag="INE72_RS22885"
                     /old_locus_tag="INE72_04558"
                     /db_xref="GeneID:75115733"
     CDS             complement(3485..3736)
                     /locus_tag="INE72_RS22885"
                     /old_locus_tag="INE72_04558"
                     /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"
                     /db_xref="GeneID:75115733"
                     /translation="MEALSVREYRNNLAASFTKADNGEQVLIRRKNEIYALVKVGREDL
                     MITPELQARIDKAREEIKSGKCVTLKSSEDIDAYFDSL"
                     /name="hypothetical protein"
ORIGIN
        1 atgaaaaaga aactacctat taccaaaaac aaagatgttg ttgtttcatg ggtatataca
       61 tggtctaaac agcaagatat gtccatacac gaacaaagaa tagtacttcg tatcttggaa
      121 gcatgccagg cagaattgaa aggggtaaag ctgaaagatt atgcaggtac gaaacgcaaa
      181 tttgagcatg gactttggga tgttgatgca caaatgcatg tctcggacgt tattttttcc
      241 ggacgtgatt acaatgaaat catagccgca ctcgattctt tggcaggacg ttttttcact
      301 tacgaagatg acgaggagtg gtggaagtgc ggatttatat ctaatcccaa atataaaaaa
      361 cacactggca ttataacctt tcgtgtgtct aatgaccttt gggatgtgtt taccaagttc
      421 gccaaggggt acagagagtt tgaattaaac aaggctcttg cgctgcctac cgggtattcc
      481 cttaggtttt acatgctaat gagtgggcaa gtgtaccctt tggatatatc ccttgacaac
      541 ttgaaagacc gccttggcat accagcggac aagtacaagg acaagaacgg aaaagataga
      601 attgacaact tcgaggaaag ggttttaaaa cctgcaaagg ctgcgcttga tgagagttgc
      661 ccatacactt tcaactacgt gaaagtgcgt gaaaacccaa acaacaaacg tagcaaggtg
      721 accggattta ggttttaccc ggtctatcag ccacagttca gggatgaaga actggaaggg
      781 aaagaattgc aggcaaaggt tacagcacga tatcagatag acagccatgt atacgagtat
      841 ctccgttatt cctgcggttt cacatcggaa gagataaacc ggaacaaaga gacattcata
      901 acggcacaag aaaagataac cgaccttatc ggagaactgg ctctcctaaa cggaaaatca
      961 cgagaaaaga acaatccgaa agggtggatt ataaacgccc ttaaagggaa aatcaaggat
     1021 aagtaacagg attacccggc tgaaacactc cgggtaatct tgtcaaatca gaggaacgat
     1081 ttccatttct acaccaagtt ctttcatctg ctgttgtatt tcctcgctgc ttagtttctc
     1141 tttcgccagt gcaagcccat gaaaggcgtc ccagcctgcc ggcttcgaaa cgatactacc
     1201 gtttaggacg gcatgggtga tttcgccgcc ggacttcgca cccttgttca gtatgaagaa
     1261 gaaccggggt tcttcgtgtt ccgttgttcc cataattcgt aaagttagag tttatttgtt
     1321 tcccttttgt tcccttgcct gctcttggaa gtattcataa tactgcttgt agttgtcccg
     1381 gtctttggct gcatccgtcc aaagatagca catgaaacaa gcgaacaata gggagataac
     1441 agcacaaagg attgagtaga acgaaatccg tttgtccaca taaccgccgt ttttcattct
     1501 gtacccctgc cgttcaaagt ccgacaatac gttttttagg cgattttcgg cactttcgag
     1561 gcttttcccg tctatttgta cctttcggga tgttgcatcc tctatgcgct ttgtataggc
     1621 ttcaatacgt cccatttctt gaaaaaacag ttctatcgca agctgcgggt taacctttgg
     1681 tgctgtgtct tttcttttcc gggggctgta ctgtccctgc ttaacggtgg aagctgccgc
     1741 ttccgggtgt gagtttgttt ccatgagata tgttcattga gttatatttc agtttgcttt
     1801 gtgtccgctc gatatgggcg agagtgtagc ctttccctat ctcgctcgcc ttatactccg
     1861 taccgcttcg ggctgtgacg tagtagccgt taagttttcc ggtgcttgcc ctggcttccc
     1921 gaactttaaa acctctccta ccaagttctt ccttgaattt agtcaagtca aagccctgca
     1981 tcttcttcaa gacgtcgtcc atggcttcct tgatttccgc tttgttggct ttgccgatgt
     2041 cctgcgactg tacaaagttc cgttccttgg ctatggcgtt ggcggcttcc gttgcctttt
     2101 tccctatcca gttatcccgg tacagttccc cggaaaggga aacccggttt gccagtatat
     2161 gcaggtgggc ttgttctttt ttgctctccg taccgctgtg ccggatgatg atgtactggt
     2221 ggttcgccag ccccatgcgc tgcatgaagt cgttaccaag ttccgcccag tccgcatccg
     2281 taaaggtggc gctttcctct atcgaaggac tgacctcgaa acgtaggcaa ttgtttttta
     2341 cgttcggaaa atcagcgtgg tatggtttca tttcctgtac catttccgca cccgtacacc
     2401 cgtaaagttc atgccgggct atctcgatgg ctgctgtctg tccgtctatc tctttggcaa
     2461 ggtcatactc cagtgcagcc gtaccatgcg atatgctctt tcctttccct atcatcgtga
     2521 aagtattttt ttaagttcgg tgattagtgc ctgattctct tcaaatacct cccggtactg
     2581 gcgaccaccg aagtagttgt tcagccgttg gagcgttcct ttcaactggg ctatgtcccg
     2641 gagaagctgc cgttcctcct cggtgtacct ttcccttggg cgacctccaa gggacaaact
     2701 ccggcaatac tccgatgtgc tcatgctaca tcgggctgcc tgctccgcaa gtgccagctt
     2761 ttcataccgg gtacagcgga atgtaatctt ttcgttccgt cttacttcca tgtcacaaag
     2821 gtaatcttaa aatctttttg agcaaagcga gaaaagcaag aattgtccga caaggacact
     2881 tcttgctata tatacacatg ccgcatggga atacatccat gctaaccgcc cggcaaaaag
     2941 ccccggcgtg ttagaaaatc cccccacagc ctaacaattt ctaccccatt tctacccaag
     3001 gggattacac gccgcagaag tcatccggga acatgtcttc cagttcgtcc aaatcaatgg
     3061 cttcttcttc ggacacctcc acccattcaa cgttttcttt ccctcttatc gcacatgagt
     3121 acatctcggc ggcggcaagg ttagagaaca cctcgtgcat aggctcgccg ttctctaacc
     3181 agtaaacaca atattcgacc ataacagttt tatcatttat cgttgtaatg cccctctacc
     3241 tccaaaatat agacctctac cacttcctcg taaatgtcat agattatccg gtcatgggcg
     3301 gtgatgtgtc gagaccatgt aatatcccca ccgcccctta acgcttcggg atgcccaagc
     3361 ccagtcttag ggtgctctaa caattctttg tagattttct tatacttctt gaacaaattg
     3421 gggtttgatt tcttccattt ggcaatcacc ttatccaccc cgtcggaaac cctaattgtg
     3481 tacatcatag actgtcgaaa taagcgtcaa tatcctcact gcttttgagg gtaacacact
     3541 ttccggattt gatttcttcc cttgccttgt caatccttgc ttgcagctcc ggggttatca
     3601 tcaaatcttc acgaccaact tttaccaaag cgtaaatctc gtttttcctg cgaattagta
     3661 cctgctcgcc attgtcagct ttggtgaaag acgctgcgag gttgtttcgg tattctctta
     3721 ctgataatgc ttccatatct gtttgctttt aaattcagca caaagatagc tatattttaa
     3781 taaaatacaa actttttgta cacaaatgtg tacacgccat aaaaagccgc tcacagtcct
     3841 accgcccgtt ggttggtttt gctttgctct ttttccctat tgtttttctt tttccgacag
     3901 taaatcagcc atttaactct ataaatttcc cttgtctgtt ataagcatcg tctgtaatat
     3961 gctctatcac ttcttcgcaa atacccatga ataaagggat taaagtatga gtttccctac
     4021 attttgggag ttttaatcct acactttggg agtttttcac ctcactattc cctacacttt
     4081 gggagtttta cccttctttt tttgtttcaa tgtaggtttt atgtatattt gcagcaaatc
     4141 aatcgctt
//
