LOCUS       NZ_CP042283             4148 bp    DNA     circular CON 10-JUN-2024
DEFINITION  Bacteroides xylanisolvens strain APCS1/XY plasmid pBXS1-2, complete
            sequence.
ACCESSION   NZ_CP042283
VERSION     NZ_CP042283.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN12372036
            Assembly: GCF_018279805.1
KEYWORDS    RefSeq.
SOURCE      Bacteroides xylanisolvens
  ORGANISM  Bacteroides xylanisolvens
            Bacteria; Bacteroidota; Bacteroidia; Bacteroidales; Bacteroidaceae;
            Bacteroides.
REFERENCE   1  (bases 1 to 4148)
  AUTHORS   Guerin,E., Shkoporov,A.N., Stockdale,S.R., Clooney,A.G., Daly,K.M.,
            Khokhlova,E.V., Draper,L.A., Ross,R. and Hill,C.
  TITLE     Antibiotic selective enrichment of a faecal fermentation facilitates
            the isolation of a novel crAss-like phage; crAss002
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4148)
  AUTHORS   Guerin,E., Shkoporov,A.N., Stockdale,S.R., Clooney,A.G., Daly,K.M.,
            Khokhlova,E.V., Draper,L.A., Ross,R. and Hill,C.
  TITLE     Direct Submission
  JOURNAL   Submitted (30-JUL-2019) Microbiology, University College Cork, Lab
            3.39, APC Microbiome Ireland, Bioscience Building, University
            College Cork, Cork, Cork T12 YT20, Ireland
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 26-JUL-2019
            Assembly Method                   :: SPAdes v. 3.13.1
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 43.0x
            Sequencing Technology :: Illumina HiSeq,; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_018279805.1-RS_2024_06_10
            Annotation Date                   :: 06/10/2024 03:54:55
            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)                     :: 5,261
            CDSs (total)                      :: 5,175
            Genes (coding)                    :: 5,067
            CDSs (with protein)               :: 5,067
            Genes (RNA)                       :: 86
            rRNAs                             :: 5, 5, 5 (5S, 16S, 23S)
            complete rRNAs                    :: 5, 5, 5 (5S, 16S, 23S)
            tRNAs                             :: 69
            ncRNAs                            :: 2
            Pseudo Genes (total)              :: 108
            CDSs (without protein)            :: 108
            Pseudo Genes (ambiguous residues) :: 0 of 108
            Pseudo Genes (frameshifted)       :: 34 of 108
            Pseudo Genes (incomplete)         :: 70 of 108
            Pseudo Genes (internal stop)      :: 25 of 108
            Pseudo Genes (multiple problems)  :: 19 of 108
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP042283.1.
            Bacteria and source DNA available from Colin Hill, APC Microbiome
            Ireland, University College Cork.
            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="APCS1/XY"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:371601"
                     /plasmid="pBXS1-2"
                     /geo_loc_name="Ireland:Cork"
                     /collection_date="2017-11"
     gene            216..467
                     /locus_tag="FQN58_RS26135"
                     /old_locus_tag="FQN58_26705"
     CDS             216..467
                     /locus_tag="FQN58_RS26135"
                     /old_locus_tag="FQN58_26705"
                     /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"
                     /translation="MEALSVREYRNNLAASFTKADNGEQVLIRRKNEIYALVKVGREDL
                     MITPELQARIDKAREEIKSGKCVTLKSSEDIDAYFDSL"
                     /name="hypothetical protein"
     gene            464..739
                     /locus_tag="FQN58_RS26140"
                     /old_locus_tag="FQN58_26710"
     CDS             464..739
                     /locus_tag="FQN58_RS26140"
                     /old_locus_tag="FQN58_26710"
                     /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"
                     /translation="MMYTIRVSDGVDKVIAKWKKSNPNLFKKYKKIYKELLEHPKTGLG
                     HPEALRGGGDITWSRHITAHDRIIYDIYEEVVEVYILEVEGHYNDK"
                     /name="type II toxin-antitoxin system YoeB family toxin"
     gene            750..947
                     /locus_tag="FQN58_RS26145"
                     /old_locus_tag="FQN58_26715"
     CDS             750..947
                     /locus_tag="FQN58_RS26145"
                     /old_locus_tag="FQN58_26715"
                     /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"
                     /translation="MVEYCVYWLENGEPMHEVFSSLAAAEMYSCAIRGKENIEWVEVSE
                     EETIDLDELEDMFPDDFCGV"
                     /name="hypothetical protein"
     gene            1140..1439
                     /gene="mbpA"
                     /locus_tag="FQN58_RS26570"
                     /old_locus_tag="FQN58_26720"
     CDS             1140..1439
                     /gene="mbpA"
                     /locus_tag="FQN58_RS26570"
                     /old_locus_tag="FQN58_26720"
                     /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"
                     /translation="MELRRNEKITFRCTELEKDALAEQAARCSLSVSEYCRSLSLGGRP
                     RERYTEEERQLLRDIAQLKGTLQRLNNYFGGRQYREVFEENRALITELKKILSR"
                     /name="mbpA"
     gene            1436..2230
                     /gene="mbpB"
                     /locus_tag="FQN58_RS26150"
                     /old_locus_tag="FQN58_26725"
     CDS             1436..2230
                     /gene="mbpB"
                     /locus_tag="FQN58_RS26150"
                     /old_locus_tag="FQN58_26725"
                     /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"
                     /translation="MIGKGKSISHGVAALEYDLAKEINGQAVATEIARHELYGCTGAEM
                     VQEMKPYHIDFPNVKNNCLRFEVSPSIEESATFTDADWAELGNDFMQRMGLANHQYIII
                     RHSGTESKKEQAHLHILANRVSLSGELYRDNWIGKKATEAANAIAKERNFVQSQDIGKV
                     NKAEIKEAMDGVLKKMQGFDFTKFKEELGKRGFKVREARASTGKLNGYYVTARSGTEYK
                     ASEIGKGYTLAHIERTQSKLKCNSMNISHGNKLTPGSGSFQR"
                     /name="mbpB"
     gene            2187..2639
                     /gene="mbpC"
                     /locus_tag="FQN58_RS26155"
                     /old_locus_tag="FQN58_26730"
     CDS             2187..2639
                     /gene="mbpC"
                     /locus_tag="FQN58_RS26155"
                     /old_locus_tag="FQN58_26730"
                     /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"
                     /translation="METNSHPEAAASNVKQGQYSPRKRKDTTPRVNPQLAVELVYQELK
                     RVEVYTKRIEDATARKVQIDGKSLESAENRLKNVLADFERQGYRMKNGGYVDKRISFYS
                     ILCAVISLLFACFMCYLWTDAAKDRDNYKQYYEYYQEQAREQKGNK"
                     /name="mbpC"
     gene            2659..2889
                     /locus_tag="FQN58_RS26160"
                     /old_locus_tag="FQN58_26735"
     CDS             2659..2889
                     /locus_tag="FQN58_RS26160"
                     /old_locus_tag="FQN58_26735"
                     /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"
                     /translation="MGTTEHEEPRFFFILNKGAKSGGEITHAVLNGSIVSKPAGWDAFH
                     GLALAREKLSSEEIQQQMKELGVEMEIVPLI"
                     /name="hypothetical protein"
     gene            complement(2926..3951)
                     /locus_tag="FQN58_RS26165"
                     /old_locus_tag="FQN58_26740"
     CDS             complement(2926..3951)
                     /locus_tag="FQN58_RS26165"
                     /old_locus_tag="FQN58_26740"
                     /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"
                     /translation="MKKKLPITKNKDVVVSWVYTWSKQQDMSIHEQRIVLRILEACQAE
                     LKGVKLKDYAGTKRKFEHGLWDVDAQMHVSDVIFSGRDYNEIIAALDSLAGRFFTYEDD
                     EEWWKCGFISNPKYKKRTGIITFRVSNDLWDVFTKFAKGYREFELNKALALPTGYSLRF
                     YMLMSGQVYPLDISLENLKDRLGIPADKYKDKNGKDRIDHFEERVLKPAKAALDESCPY
                     TFNYVKVRENPNNKRSKVTGFRFYPVYQPQFRDEELEGKELQAKVTARYQIDSHVYEYL
                     RYSCGFTSEEINRNKETFITAQEKITDLIGELALLNGKSREKNNPKGWIINALKGKIKD
                     K"
                     /name="replication initiation protein"
ORIGIN
        1 acgatgctta taacagacaa ggggaattta tagagctaag tggttgattt actgtcggaa
       61 aaagaaaaac gatagggaaa aagagcaaag caaaaccaac caacgggcgg taggattgga
      121 aacgggtttt tatggcgtgt acacgtttgt gtacaaaatg tttgtatttt attgaaatat
      181 agctatcttt gtgctgaatt taaaagcaaa cagatatgga agcattatca gtaagagaat
      241 accgtaacaa cctcgcagcg tctttcacca aagctgacaa tggcgagcag gtactaattc
      301 gcaggaaaaa cgagatttac gctttggtaa aagttggtcg tgaagatttg atgataaccc
      361 cggagctgca agcaaggatt gacaaggcaa gggaagaaat caaatccgga aagtgtgtta
      421 ccctcaaaag cagtgaggat attgacgctt atttcgatag tctatgatgt acacaattag
      481 ggtttccgac ggggtggata aggtgattgc caaatggaag aaatcaaacc ccaatttgtt
      541 caagaagtat aagaaaatct acaaagaatt gttagagcac cctaagactg ggcttgggca
      601 tcccgaagcg ttaaggggcg gtggggatat tacatggtct cgacacatta ccgcccatga
      661 ccggataatc tatgacattt acgaggaagt ggtagaggtc tacatcttgg aggtagaggg
      721 gcattacaac gataaatgat aaaactgtta tggtcgaata ttgtgtttac tggttagaga
      781 acggcgagcc tatgcacgag gtgttctctt ctcttgccgc cgccgagatg tactcatgtg
      841 cgataagagg gaaagaaaac attgaatggg tggaggtgtc cgaagaagaa accattgatt
      901 tggacgaact ggaagacatg ttcccggatg acttctgcgg cgtgtaatcc ccttgggtag
      961 aaatggggta gaatttgtta ggctgtgggg gattttctaa cacgccgggg ctttttgctg
     1021 ggcggttggc gtggatgtat tcccatgcgg catgtgtata tatagcaaga agtgtccttg
     1081 tcggacaatt cttgcttttc tcgctttgct caaaaagatt ttaagattac ctttgtggca
     1141 tggaactaag acggaacgaa aagattacat tccggtgtac cgaacttgaa aaggacgcac
     1201 ttgcggagca ggcagcccgg tgcagtctaa gcgtatcgga atactgccgg agtttgtccc
     1261 ttggggggcg cccaagggag aggtacaccg aggaggaacg gcagcttctc cgggacatag
     1321 cccagttgaa aggaacgctc caacggctga acaactactt cggtggtcgc cagtaccggg
     1381 aagtgttcga ggagaaccgg gcactaatta cagagctcaa aaaaatactc tcacgatgat
     1441 agggaaaggg aaaagcatat cacatggtgt ggcggcattg gagtacgacc tcgccaaaga
     1501 gataaacggg caggcagtag ccaccgagat agcccggcat gaactttatg ggtgtactgg
     1561 tgcggaaatg gtgcaggaaa tgaaaccgta tcacattgat tttccgaacg taaaaaacaa
     1621 ctgcctacgt ttcgaggtca gcccctcgat agaggaaagc gccaccttta cggatgcgga
     1681 ctgggcggaa cttggtaacg acttcatgca gcgcatgggg ttggcgaacc accagtacat
     1741 catcatccgg cacagcggta cggagagcaa gaaagagcaa gcccacctgc acatactggc
     1801 aaaccgggtt tccctttccg gggaactgta ccgggacaac tggataggga aaaaggcaac
     1861 ggaagccgcc aatgccatag ccaaggaacg gaactttgta cagtcgcagg acattggcaa
     1921 agtcaacaaa gcggaaatca aggaagccat ggacggcgta ttgaagaaga tgcagggctt
     1981 tgactttacc aaattcaagg aagaacttgg taagagaggt tttaaagtcc gggaagccag
     2041 ggcaagcacc gggaaactta acggctacta tgtcacagcc cgaagcggta cggagtataa
     2101 ggcaagcgag atagggaaag gctacactct cgcccatatc gagcggacac aaagcaaact
     2161 gaagtgcaac tcaatgaaca tatctcatgg aaacaaactc acacccggaa gcggcagctt
     2221 ccaacgttaa gcagggacag tacagccccc ggaaaagaaa agatacaacg ccaagggtaa
     2281 acccgcagct tgcggtagaa ctggtgtatc aagaactaaa gcgtgttgaa gtctatacga
     2341 agcgcataga ggacgcaaca gcccgaaagg tacaaataga cgggaaaagc cttgaaagtg
     2401 ccgaaaatcg cctaaaaaac gtgttggcgg actttgaacg gcaggggtac agaatgaaaa
     2461 acggcggtta tgtggacaaa cgaatttcgt tctactcaat cctttgtgct gttatctccc
     2521 tattgttcgc ttgtttcatg tgctatcttt ggacggatgc agccaaagac cgggacaact
     2581 acaagcagta ttatgaatac taccaagagc aggcaaggga acaaaagggg aataaataaa
     2641 catctaactt tacgaattat gggaacaacg gaacacgaag aaccccggtt cttcttcata
     2701 ctgaacaagg gtgcgaagtc cggcggcgaa atcacccatg ccgtcctaaa cggtagtatc
     2761 gtttcgaagc cggcaggctg ggacgccttt catgggcttg cactggcgag agagaaacta
     2821 agcagcgagg aaatacaaca gcagatgaaa gaacttggtg tagaaatgga aatcgttcct
     2881 ctgatttgac aagattaccc ggagtgtttc agccgggtaa tcttgttact tatccttgat
     2941 tttcccttta agggcgttta taatccaccc tttcggattg ttcttttctc gtgattttcc
     3001 gtttaggaga gccagttctc cgataaggtc ggttatcttt tcttgtgccg ttatgaatgt
     3061 ctctttgttc cggtttatct cttccgatgt gaagccgcag gaataacgga ggtactcgta
     3121 cacatggctg tctatctgat atcgtgctgt aacctttgct tgcaattctt tcccttccag
     3181 ttcttcatct ctgaactgtg gttgatagac cgggtagaac ctaaacccgg tcaccttgct
     3241 acgtttgttg tttgggtttt cacgcacttt cacgtagttg aaagtgtatg ggcagctctc
     3301 atcaagcgca gcctttgctg gtttcaaaac tctttcctca aaatgatcta ttctgtcttt
     3361 tccgttcttg tccttgtatt tgtccgcagg tatgccaaga cggtctttca agttttcaag
     3421 ggatatatcc aaagggtaca cctgcccact cattaacatg taaaacctaa gggaataccc
     3481 agtaggtagc gcaagagcct tgtttaactc aaattctctg taccccttgg cgaacttggt
     3541 aaacacatcc caaaggtcgt tagacacacg aaaggttata atgccagtgc gttttttata
     3601 ttttgggtta gatataaatc cgcacttcca ccattcctcg tcatcttcgt aagtaaaaaa
     3661 acgtcctgcc aaagaatcga gtgcggctat gatttcattg taatcacgtc cggaaaaaat
     3721 aacgtcagat acatgcattt gtgcatcaac atcccaaagt ccatgctcaa acttgcgttt
     3781 cgtgcctgca taatctttca gttttactcc ctttagttca gcttggcacg cttccagtat
     3841 gcgaagaact attctttgtt cgtgtatgga catgtcttgc tgttttgacc atgtatatac
     3901 ccatgaaaca acaacatctt tattcttggt aataggtagt ttctttttca taaacgattg
     3961 atttgctgca aatatacaca atccccacat taaaacaaaa aaagaggggt aaaactccca
     4021 aagtgtgggg actaatttac ttttaaactc ccaaagtgtg gggactaaac tcccaaagtg
     4081 tggggaaaca catgttctaa tccctttatt tatgggcgtt tgcgaagaag tgatagagca
     4141 tattacag
//
