LOCUS       NZ_CP042281             5595 bp    DNA     circular CON 10-JUN-2024
DEFINITION  Bacteroides xylanisolvens strain APCS1/XY plasmid pBXS1-1, complete
            sequence.
ACCESSION   NZ_CP042281
VERSION     NZ_CP042281.1
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 5595)
  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  JOURNAL   Unpublished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 5595)
  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
            CP042281.1.
            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..5595
                     /organism="Bacteroides xylanisolvens"
                     /mol_type="genomic DNA"
                     /strain="APCS1/XY"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:371601"
                     /plasmid="pBXS1-1"
                     /geo_loc_name="Ireland:Cork"
                     /collection_date="2017-11"
     gene            631..1533
                     /locus_tag="FQN58_RS00005"
                     /old_locus_tag="FQN58_00010"
     CDS             631..1533
                     /locus_tag="FQN58_RS00005"
                     /old_locus_tag="FQN58_00010"
                     /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(1537..1998)
                     /locus_tag="FQN58_RS00010"
                     /old_locus_tag="FQN58_00015"
     CDS             complement(1537..1998)
                     /locus_tag="FQN58_RS00010"
                     /old_locus_tag="FQN58_00015"
                     /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            2090..2860
                     /locus_tag="FQN58_RS00015"
     CDS             2090..2860
                     /locus_tag="FQN58_RS00015"
                     /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            complement(2930..4180)
                     /locus_tag="FQN58_RS00020"
                     /old_locus_tag="FQN58_00025"
     CDS             complement(2930..4180)
                     /locus_tag="FQN58_RS00020"
                     /old_locus_tag="FQN58_00025"
                     /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            4586..4834
                     /locus_tag="FQN58_RS00025"
                     /old_locus_tag="FQN58_00030"
     CDS             4586..4834
                     /locus_tag="FQN58_RS00025"
                     /old_locus_tag="FQN58_00030"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_008771457.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /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"
     gene            4828..5148
                     /locus_tag="FQN58_RS00030"
                     /old_locus_tag="FQN58_00035"
     CDS             4828..5148
                     /locus_tag="FQN58_RS00030"
                     /old_locus_tag="FQN58_00035"
                     /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            5185..5583
                     /locus_tag="FQN58_RS00035"
                     /old_locus_tag="FQN58_00040"
     CDS             5185..5583
                     /locus_tag="FQN58_RS00035"
                     /old_locus_tag="FQN58_00040"
                     /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="exo-poly-alpha-D-galacturonosidase"
                     /protein_id="WP_212133340.1"
                     /translation="MKPTDYIEWDNLKDIPFFLCQVVEDREKQDLDIYYLGKRVLHDYD
                     HVGHYLRTAVILFRRVKSRTADWVNLRNLWTLRNCVRENYNHGIGMNDLIFGENFDEDN
                     LDTLTPLTKKRFDFLCKRIKELDPYATI"
                     /name="exo-poly-alpha-D-galacturonosidase"
     Typing          485..1533
                     /name="rep_cluster_870"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.81"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(2934..4180)
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tgaaggcagg gcttgtcttt gtgtgctccc cctttggggg acgggagggg gataagaaaa
       61 aaaaatacca ccggagatgt cggatatccg tcaattcact ccggtgtttt ttttgcaact
      121 ctcccgtatc gctcggcaag ggttgtcttt gtgtacggca aagatagttt tttttccgga
      181 agtatctttg tctgttgtgg atttagtagt gtatttgtgt cagaattgcg cagccggggg
      241 aatgggggcg agcccccata ctagataaac tagaaagttt cgtggtaaat gctttttgac
      301 ttgttatatg taggtttttt gaatgatgtt tggcggtttg gaatgaatta cctacttttg
      361 ggctgagaaa aaacgaaagc ccgaaggcag taaccaacgg gctttgtatt ttaagaatta
      421 gcaatcgttt gtgttcgttc ttggcggggc ggataccaaa cgaaagccac atcaaaattt
      481 catatgtgca aagatagaac aaatataacc aactgcaaag aaagtccgtt aaaaaacggt
      541 tctgatagtc ttaaaaaaaa ggctaaagta aaaatcatat cccataattt tactcgaaaa
      601 ctttcggaaa agaatccgga tagtaagctg atgaaagcat atatggatgc ccatgtgtgt
      661 tcaaatgttt atactgtgca gggaggtaag gcgcattccc attattgtca tcgggctttt
      721 tgtcctatct gtcagcgtat tcaaacggca caaaatgtaa agaagttcct tccggttatg
      781 aagtatttgg cttcggaagg cagagagttt tattttgtga cgcttacctt gcaaaattgt
      841 gtaaccgatg atgcaagggt attgcgagat ttcatgcgta gatgtaaccg gatgtgggct
      901 gatggtataa ggacgaaaca caagtttcgt tcacttggta tttcgggggt gattaagaag
      961 gagtgtacct atcatgtagt aaaaaaggat ttgttttcgt tccattatca ttttcatatt
     1021 attgttgatt cattggaagc tgcaaaatat gtagtagccc aatggaagaa attgcatggt
     1081 agtacggttg ctgatgcccg ttttcagaaa tataagaaga tagaggattt tgaaaatgca
     1141 gcgatagagg tttttaagta tgcttcaaag gcttctgtct caaaatcgaa aggtcgtgac
     1201 ggtaaaaaaa agattcagat aaattataag gctttggata tgatttatac tgccatgcat
     1261 gggatgcagc gcatgagtag tttcggacag ttccgcacca tgatcggaga tgaagcgttg
     1321 aatgatttta gagatgagga tttggttctt aatattgagg gattgaatgt tgaagatggt
     1381 tgttatactt ggtatatgtc tgtgaaagat aaggtggctg attggtataa tatggaaact
     1441 ggggaggcat tgtgttgtta taaggtcacc cggaaggatg aacttttgca ggatatttat
     1501 ttagatgagg atatttttcc taatagtggg tagttgttag tttgttgtat tgttttcttg
     1561 gtatggtgtg agttctatgt attctctatt catgaaagga tcgccaaatt ttccacttct
     1621 gtcatagaag gaaaatttgt ttttagttag ctcgtctatg tcccagtaat gttctccacc
     1681 aaaataaatg gtactgaaac ttggatcacc gaatgaccat tgtccgtaga tattggcttc
     1741 ttttttattt ccttgtttgt cgatttctat atttgtacgg gtatatgttc cgtttttatt
     1801 gaatttgtat gtaccttgcc agacactgcc gttttcgtct gttgtttttt taccagccca
     1861 tgtaatatca caaattaatg agattatgct ttcttctcca tggttgtagt atccttgttt
     1921 ttcaacacat ccggtgtttg aaataagaaa aagtgatact gttgaaataa gtaaagagat
     1981 atgtattatt ctattcatag ttaaatattt aatattcaat gcaaaaatag gagaaatttt
     2041 atatttttgg gcgaaacctt tatttattaa ctttaaaaaa ggaggattta tgaaaaaagt
     2101 aatgtttatg ttcatcagtc tactgactgt tttgggtgtt tgttcgtgta atgataatga
     2161 agtaatagaa cctgtggtta gtgattctgt atctgatatg gaggtcttat ctcgttttgt
     2221 tgatgtaaat gagattacaa atgaatacta tttcaatgag aataagaaaa cgagggcgtt
     2281 gtcttatgta acaggttcgg attggcagga tttagaaaaa gttagtcctt tgagtattga
     2341 gaaatataag aataacctgc aggttttaaa tgctcaagtg gcaagtgcta tttcaaatcc
     2401 taataccgct tatgttgttt tttctgtaaa tggaaagact ttggttaaaa aggtgaagga
     2461 ggatgctaat tttgattttt cagtatttag ggatgttgta acggaaacga gggctgttct
     2521 cccttctttg agtattaatg gaggttctca aagcactacc ggagtttttt acgattccag
     2581 tcgtacttta aagatgcaag ttgatttgaa tgcttcaata cagaataatt attatttctt
     2641 tgaagtatta aatcctaatg ctaaaccaag tccggatgat aatataacga cacctgaaag
     2701 tgttgctttt agtggaactg gaccgttatg gagtaacact ttcacttgga cttcgtattg
     2761 ggatgcaaat gtacctggtc aaggttttaa atgggagttt aaaggaaaag gtactactcc
     2821 ttcttttggt tttatagcta attgcacctt tagtcgttaa aaaatgaacg ggatttaatt
     2881 tgaattgcac ttctcaaaaa agagaagtgc aattcttttt agtgtctttc tatcggtgta
     2941 gccagttacc gttatctaaa gtcttttgta gtgtattcca aagttcttta agaaagtttt
     3001 taaagtggat gttatttagc caaattgtag taataccatt ctgacttttg gagatatcta
     3061 ttttcacgtt tttaacttgg tatgattttc tcttgtcttt atcgtaaagg tttccagtgt
     3121 agtatatttc ctttccaata agaagttgtc ggatatcttt attttgtatt cccatagttt
     3181 ggagttcctc tatattttcc tgtgcatttt ccatttccgg aaaaaggttg gttatgggtt
     3241 ttagtttgga tgcttctgcc tttatctgtc tgtcggttgt ttcctgtacc cttcgcatct
     3301 cgatgttgtt ggttcttaat tgtccttcta aattttgatt cttgaatgag aggttataat
     3361 tttctttttt gagggtttca atttctttgg cttgtcgttt tacttcccct acattaaaga
     3421 cgcttgtaac ggcattaaat acggtttttc cggcttttgc ggcagcttct ttggcttcgt
     3481 tgatgtgtat gtcggttttc atgctgttta gctctttttg tgccgtacta agttcctttt
     3541 ggactgtggt gattttctcg gttccggcag tgtatgccct gtttagttgc tcgatgtctt
     3601 tttgaagttg ttcagctttc tctgtttcca ttttgttttt gtattgcatg gccgacaagt
     3661 gtttcttgtc tgaagaaact ccacgttcca tgttgagaca ctccgctgtt atagtctgca
     3721 tctccgccat gtcgtgtctg ttcagcttta cagtttttcc tgtatggccg tccgtccagt
     3781 caaagatcat gtgcgcatga tagttcggtt tccatgcttc ttcctttccg tcccatacgt
     3841 ttgcgccttc atccttatgg gtgtagattt ggaaggcgtg cactccaaag cgttcttcca
     3901 gtttttcggc caagtcttga agctgctgga ttgtggtttc ctcgctgatt actattaccc
     3961 cttcccggat tggggtagct ttcttctgta atccttgtcc ggtggcttcc ttgtattttt
     4021 ccgttatgtc ccgatgtact tcggcaatgg aacattctac ccactgttcg ttgcggtgtg
     4081 tgagttccgg acggatgtag tcgagctcct tgcttcttaa gttgtgacgt tccgagctgc
     4141 ctatattgca ggcttccact ctgatacatg tctttgccat atctttaggt tttaggtgtg
     4201 tatgtctgtt tagaagatgt ggcgtgaaac gtcacatcgc acggggtcga ggggacaccc
     4261 ctcgcacaca acccctttag gggttatagt gtgctataac cttttgcaaa ggtaagcctt
     4321 ccggacggga tttgcaagcg ctctgccatg tgttccggat gtgcttggga acagaagccg
     4381 gacaaaaggg aaaaggacac aaggcacaat aaaaaatcat cggtcgggga gcgctgcacg
     4441 gcaagggggt gcaccaacac tcccgacgag tgcagccatt gacagggttc tcggtgaaaa
     4501 tggaaaaaag ttgtttttcc ttttgttatt gttataactt tatatatatt tgtatcgtga
     4561 taatcaatta taaagttata acattatggt aacgaatatt attcagattg gaaacagcaa
     4621 ggggataata cttccttccg aagtattgaa acagttgcgt ttgtccttga aatcggctgt
     4681 gagcatttct ttggacggga acaatattgt gataaaggca caaccacggc agggatgggc
     4741 ggaagctgcc aaacgtgccc atgagaatgg ggatgatgag ttgcttatcc ctgatgtgtt
     4801 tgaggatgaa aagtttgagg attggacatg gtagaacagt atgaagtgta ttgggtagag
     4861 ttagacccta cccgtggggg tgaaatggca aagacacggc catgtgtagt tgtcactcct
     4921 tcagatttga atatgtacct tacaacagta gtcattgttc cgataacctc aacgataaga
     4981 aattatcctt accgggttct gtgttctgta gccgggcgtg aaggagagat agccactgat
     5041 caaattcgca cggtggataa aagccggctg aaaagaaaga ttggagattt gaatttcagt
     5101 gagataaaaa ggttacgtga agtatttcag caaatgttct gtgaataatg gaaagtacgg
     5161 aaagaaaaat gcaaataaga cattatgaaa ccaactgact acatcgaatg ggataacctg
     5221 aaggatattc cattcttcct ctgtcaagta gtcgaggaca gagaaaaaca agatttggat
     5281 atttactatt tgggcaaacg tgtcttgcac gattacgacc atgtggggca ctatttgcgg
     5341 actgccgtta tcttgttccg cagggtaaag agccgcacag cagactgggt aaacctgcgt
     5401 aacctttgga cgctgcgcaa ctgtgtgcgt gagaactaca atcacggcat aggaatgaac
     5461 gaccttattt ttggggagaa tttcgatgaa gataatctcg atacgcttac accacttaca
     5521 aagaaacgct ttgatttttt gtgtaagcgg attaaggaac ttgacccata tgcaactatt
     5581 taacactcca ttgag
//
