LOCUS       NZ_CP072218             4148 bp    DNA     circular CON 28-MAR-2024
DEFINITION  Bacteroides xylanisolvens strain CL11T00C03 plasmid
            pBxylCL11T00C03-2, complete sequence.
ACCESSION   NZ_CP072218
VERSION     NZ_CP072218.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16451198
            Assembly: GCF_018289135.1
KEYWORDS    RefSeq.
SOURCE      Bacteroides xylanisolvens
  ORGANISM  Bacteroides xylanisolvens
            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                     :: BxylCL11T00C03_pbv2
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 287x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_018289135.1-RS_2024_03_28
            Annotation Date                   :: 03/28/2024 06:58:33
            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)                     :: 5,394
            CDSs (total)                      :: 5,305
            Genes (coding)                    :: 5,172
            CDSs (with protein)               :: 5,172
            Genes (RNA)                       :: 89
            rRNAs                             :: 5, 5, 5 (5S, 16S, 23S)
            complete rRNAs                    :: 5, 5, 5 (5S, 16S, 23S)
            tRNAs                             :: 72
            ncRNAs                            :: 2
            Pseudo Genes (total)              :: 133
            CDSs (without protein)            :: 133
            Pseudo Genes (ambiguous residues) :: 0 of 133
            Pseudo Genes (frameshifted)       :: 28 of 133
            Pseudo Genes (incomplete)         :: 95 of 133
            Pseudo Genes (internal stop)      :: 22 of 133
            Pseudo Genes (multiple problems)  :: 10 of 133
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP072218.1.
            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.
            Bacteria available from Dr. Laurie Comstock, Brigham & Women's
            Hospital, 181 Longwood Avenue, Boston, MA 02115 USA.
            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 xylanisolvens"
                     /mol_type="genomic DNA"
                     /strain="CL11T00C03"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:371601"
                     /plasmid="pBxylCL11T00C03-2"
                     /geo_loc_name="USA: Boston"
                     /lat_lon="42.3361 N 71.1075 W"
                     /collection_date="2009-05"
     gene            40..1065
                     /locus_tag="INE92_RS26185"
                     /old_locus_tag="INE92_05222"
                     /db_xref="GeneID:69483913"
     CDS             40..1065
                     /locus_tag="INE92_RS26185"
                     /old_locus_tag="INE92_05222"
                     /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_004295509.1"
                     /db_xref="GeneID:69483913"
                     /translation="MKKKLPITKNKDVVVSWVYTWSKQQDMSIHEQRIVLRILEACQAE
                     LKGVKLKDYAGTKRKFEHGLWDVDAQMHVSDVIFSGRDYNEIIAALDSLAGRFFTYEDD
                     EEWWKCGFISNPKYKKRTGIITFRVSNDLWDVFTKFAKGYREFELNKALALPTGYSLRF
                     YMLMSGQVYPLDISLENLKDRLGIPADKYKDKNGKDRIDHFEERVLKPAKAALDESCPY
                     TFNYVKVRENPNNKRSKVTGFRFYPVYQPQFRDEELEGKELQAKVTARYQIDSHVYEYL
                     RYSCGFTSEEINRNKETFITAQEKITDLIGELALLNGKSREKNNPKGWIINALKGKIKD
                     K"
                     /name="replication initiation protein"
     gene            complement(1102..1332)
                     /locus_tag="INE92_RS26190"
                     /old_locus_tag="INE92_05223"
                     /db_xref="GeneID:69483914"
     CDS             complement(1102..1332)
                     /locus_tag="INE92_RS26190"
                     /old_locus_tag="INE92_05223"
                     /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_004295510.1"
                     /db_xref="GeneID:69483914"
                     /translation="MGTTEHEEPRFFFILNKGAKSGGEITHAVLNGSIVSKPAGWDAFH
                     GLALAREKLSSEEIQQQMKELGVEMEIVPLI"
                     /name="hypothetical protein"
     gene            complement(1352..1804)
                     /gene="mbpC"
                     /locus_tag="INE92_RS26195"
                     /old_locus_tag="INE92_05224"
                     /db_xref="GeneID:69483915"
     CDS             complement(1352..1804)
                     /gene="mbpC"
                     /locus_tag="INE92_RS26195"
                     /old_locus_tag="INE92_05224"
                     /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"
                     /db_xref="GeneID:69483915"
                     /translation="METNSHPEAAASNVKQGQYSPRKRKDTTPRVNPQLAVELVYQELK
                     RVEVYTKRIEDATARKVQIDGKSLESAENRLKNVLADFERQGYRMKNGGYVDKRISFYS
                     ILCAVISLLFACFMCYLWTDAAKDRDNYKQYYEYYQEQAREQKGNK"
                     /name="mbpC"
     gene            complement(1761..2555)
                     /gene="mbpB"
                     /locus_tag="INE92_RS26200"
                     /old_locus_tag="INE92_05225"
                     /db_xref="GeneID:69483916"
     CDS             complement(1761..2555)
                     /gene="mbpB"
                     /locus_tag="INE92_RS26200"
                     /old_locus_tag="INE92_05225"
                     /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"
                     /db_xref="GeneID:69483916"
                     /translation="MIGKGKSISHGVAALEYDLAKEINGQAVATEIARHELYGCTGAEM
                     VQEMKPYHIDFPNVKNNCLRFEVSPSIEESATFTDADWAELGNDFMQRMGLANHQYIII
                     RHSGTESKKEQAHLHILANRVSLSGELYRDNWIGKKATEAANAIAKERNFVQSQDIGKV
                     NKAEIKEAMDGVLKKMQGFDFTKFKEELGKRGFKVREARASTGKLNGYYVTARSGTEYK
                     ASEIGKGYTLAHIERTQSKLKCNSMNISHGNKLTPGSGSFQR"
                     /name="mbpB"
     gene            complement(2552..2851)
                     /gene="mbpA"
                     /locus_tag="INE92_RS27140"
                     /old_locus_tag="INE92_05226"
                     /db_xref="GeneID:79236272"
     CDS             complement(2552..2851)
                     /gene="mbpA"
                     /locus_tag="INE92_RS27140"
                     /old_locus_tag="INE92_05226"
                     /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"
                     /db_xref="GeneID:79236272"
                     /translation="MELRRNEKITFRCTELEKDALAEQAARCSLSVSEYCRSLSLGGRP
                     RERYTEEERQLLRDIAQLKGTLQRLNNYFGGRQYREVFEENRALITELKKILSR"
                     /name="mbpA"
     gene            complement(3044..3241)
                     /locus_tag="INE92_RS26205"
                     /old_locus_tag="INE92_05227"
                     /db_xref="GeneID:69483917"
     CDS             complement(3044..3241)
                     /locus_tag="INE92_RS26205"
                     /old_locus_tag="INE92_05227"
                     /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_004295503.1"
                     /db_xref="GeneID:69483917"
                     /translation="MVEYCVYWLENGEPMHEVFSSLAAAEMYSCAIRGKENIEWVEVSE
                     EETIDLDELEDMFPDDFCGV"
                     /name="hypothetical protein"
     gene            complement(3252..3527)
                     /locus_tag="INE92_RS26210"
                     /old_locus_tag="INE92_05228"
                     /db_xref="GeneID:69483918"
     CDS             complement(3252..3527)
                     /locus_tag="INE92_RS26210"
                     /old_locus_tag="INE92_05228"
                     /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:69483918"
                     /translation="MMYTIRVSDGVDKVIAKWKKSNPNLFKKYKKIYKELLEHPKTGLG
                     HPEALRGGGDITWSRHITAHDRIIYDIYEEVVEVYILEVEGHYNDK"
                     /name="type II toxin-antitoxin system YoeB family toxin"
     gene            complement(3524..3775)
                     /locus_tag="INE92_RS26215"
                     /old_locus_tag="INE92_05229"
                     /db_xref="GeneID:69483919"
     CDS             complement(3524..3775)
                     /locus_tag="INE92_RS26215"
                     /old_locus_tag="INE92_05229"
                     /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:69483919"
                     /translation="MEALSVREYRNNLAASFTKADNGEQVLIRRKNEIYALVKVGREDL
                     MITPELQARIDKAREEIKSGKCVTLKSSEDIDAYFDSL"
                     /name="hypothetical protein"
ORIGIN
        1 atgtggggat tgtgtatatt tgcagcaaat caatcgttta tgaaaaagaa actacctatt
       61 accaagaata aagatgttgt tgtttcatgg gtatatacat ggtcaaaaca gcaagacatg
      121 tccatacacg aacaaagaat agttcttcgc atactggaag cgtgccaagc tgaactaaag
      181 ggagtaaaac tgaaagatta tgcaggcacg aaacgcaagt ttgagcatgg actttgggat
      241 gttgatgcac aaatgcatgt atctgacgtt attttttccg gacgtgatta caatgaaatc
      301 atagccgcac tcgattcttt ggcaggacgt ttttttactt acgaagatga cgaggaatgg
      361 tggaagtgcg gatttatatc taacccaaaa tataaaaaac gcactggcat tataaccttt
      421 cgtgtgtcta acgacctttg ggatgtgttt accaagttcg ccaaggggta cagagaattt
      481 gagttaaaca aggctcttgc gctacctact gggtattccc ttaggtttta catgttaatg
      541 agtgggcagg tgtacccttt ggatatatcc cttgaaaact tgaaagaccg tcttggcata
      601 cctgcggaca aatacaagga caagaacgga aaagacagaa tagatcattt tgaggaaaga
      661 gttttgaaac cagcaaaggc tgcgcttgat gagagctgcc catacacttt caactacgtg
      721 aaagtgcgtg aaaacccaaa caacaaacgt agcaaggtga ccgggtttag gttctacccg
      781 gtctatcaac cacagttcag agatgaagaa ctggaaggga aagaattgca agcaaaggtt
      841 acagcacgat atcagataga cagccatgtg tacgagtacc tccgttattc ctgcggcttc
      901 acatcggaag agataaaccg gaacaaagag acattcataa cggcacaaga aaagataacc
      961 gaccttatcg gagaactggc tctcctaaac ggaaaatcac gagaaaagaa caatccgaaa
     1021 gggtggatta taaacgccct taaagggaaa atcaaggata agtaacaaga ttacccggct
     1081 gaaacactcc gggtaatctt gtcaaatcag aggaacgatt tccatttcta caccaagttc
     1141 tttcatctgc tgttgtattt cctcgctgct tagtttctct ctcgccagtg caagcccatg
     1201 aaaggcgtcc cagcctgccg gcttcgaaac gatactaccg tttaggacgg catgggtgat
     1261 ttcgccgccg gacttcgcac ccttgttcag tatgaagaag aaccggggtt cttcgtgttc
     1321 cgttgttccc ataattcgta aagttagatg tttatttatt ccccttttgt tcccttgcct
     1381 gctcttggta gtattcataa tactgcttgt agttgtcccg gtctttggct gcatccgtcc
     1441 aaagatagca catgaaacaa gcgaacaata gggagataac agcacaaagg attgagtaga
     1501 acgaaattcg tttgtccaca taaccgccgt ttttcattct gtacccctgc cgttcaaagt
     1561 ccgccaacac gttttttagg cgattttcgg cactttcaag gcttttcccg tctatttgta
     1621 cctttcgggc tgttgcgtcc tctatgcgct tcgtatagac ttcaacacgc tttagttctt
     1681 gatacaccag ttctaccgca agctgcgggt ttacccttgg cgttgtatct tttcttttcc
     1741 gggggctgta ctgtccctgc ttaacgttgg aagctgccgc ttccgggtgt gagtttgttt
     1801 ccatgagata tgttcattga gttgcacttc agtttgcttt gtgtccgctc gatatgggcg
     1861 agagtgtagc ctttccctat ctcgcttgcc ttatactccg taccgcttcg ggctgtgaca
     1921 tagtagccgt taagtttccc ggtgcttgcc ctggcttccc ggactttaaa acctctctta
     1981 ccaagttctt ccttgaattt ggtaaagtca aagccctgca tcttcttcaa tacgccgtcc
     2041 atggcttcct tgatttccgc tttgttgact ttgccaatgt cctgcgactg tacaaagttc
     2101 cgttccttgg ctatggcatt ggcggcttcc gttgcctttt tccctatcca gttgtcccgg
     2161 tacagttccc cggaaaggga aacccggttt gccagtatgt gcaggtgggc ttgctctttc
     2221 ttgctctccg taccgctgtg ccggatgatg atgtactggt ggttcgccaa ccccatgcgc
     2281 tgcatgaagt cgttaccaag ttccgcccag tccgcatccg taaaggtggc gctttcctct
     2341 atcgaggggc tgacctcgaa acgtaggcag ttgtttttta cgttcggaaa atcaatgtga
     2401 tacggtttca tttcctgcac catttccgca ccagtacacc cataaagttc atgccgggct
     2461 atctcggtgg ctactgcctg cccgtttatc tctttggcga ggtcgtactc caatgccgcc
     2521 acaccatgtg atatgctttt ccctttccct atcatcgtga gagtattttt ttgagctctg
     2581 taattagtgc ccggttctcc tcgaacactt cccggtactg gcgaccaccg aagtagttgt
     2641 tcagccgttg gagcgttcct ttcaactggg ctatgtcccg gagaagctgc cgttcctcct
     2701 cggtgtacct ctcccttggg cgccccccaa gggacaaact ccggcagtat tccgatacgc
     2761 ttagactgca ccgggctgcc tgctccgcaa gtgcgtcctt ttcaagttcg gtacaccgga
     2821 atgtaatctt ttcgttccgt cttagttcca tgccacaaag gtaatcttaa aatctttttg
     2881 agcaaagcga gaaaagcaag aattgtccga caaggacact tcttgctata tatacacatg
     2941 ccgcatggga atacatccac gccaaccgcc cagcaaaaag ccccggcgtg ttagaaaatc
     3001 ccccacagcc taacaaattc taccccattt ctacccaagg ggattacacg ccgcagaagt
     3061 catccgggaa catgtcttcc agttcgtcca aatcaatggt ttcttcttcg gacacctcca
     3121 cccattcaat gttttctttc cctcttatcg cacatgagta catctcggcg gcggcaagag
     3181 aagagaacac ctcgtgcata ggctcgccgt tctctaacca gtaaacacaa tattcgacca
     3241 taacagtttt atcatttatc gttgtaatgc ccctctacct ccaagatgta gacctctacc
     3301 acttcctcgt aaatgtcata gattatccgg tcatgggcgg taatgtgtcg agaccatgta
     3361 atatccccac cgccccttaa cgcttcggga tgcccaagcc cagtcttagg gtgctctaac
     3421 aattctttgt agattttctt atacttcttg aacaaattgg ggtttgattt cttccatttg
     3481 gcaatcacct tatccacccc gtcggaaacc ctaattgtgt acatcataga ctatcgaaat
     3541 aagcgtcaat atcctcactg cttttgaggg taacacactt tccggatttg atttcttccc
     3601 ttgccttgtc aatccttgct tgcagctccg gggttatcat caaatcttca cgaccaactt
     3661 ttaccaaagc gtaaatctcg tttttcctgc gaattagtac ctgctcgcca ttgtcagctt
     3721 tggtgaaaga cgctgcgagg ttgttacggt attctcttac tgataatgct tccatatctg
     3781 tttgctttta aattcagcac aaagatagct atatttcaat aaaatacaaa cattttgtac
     3841 acaaacgtgt acacgccata aaaacccgtt tccaatccta ccgcccgttg gttggttttg
     3901 ctttgctctt tttccctatc gtttttcttt ttccgacagt aaatcaacca cttagctcta
     3961 taaattcccc ttgtctgtta taagcatcgt ctgtaatatg ctctatcact tcttcgcaaa
     4021 cgcccataaa taaagggatt agaacatgtg tttccccaca ctttgggagt ttagtcccca
     4081 cactttggga gtttaaaagt aaattagtcc ccacactttg ggagttttac ccctcttttt
     4141 ttgtttta
//
