LOCUS       NZ_CP042284             4148 bp    DNA     circular CON 18-MAY-2024
DEFINITION  Parabacteroides distasonis strain APCS2/PD plasmid pPDS2-1, complete
            sequence.
ACCESSION   NZ_CP042284
VERSION     NZ_CP042284.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN12372652
            Assembly: GCF_018279895.1
KEYWORDS    RefSeq.
SOURCE      Parabacteroides distasonis
  ORGANISM  Parabacteroides distasonis
            Bacteria; Bacteroidota; Bacteroidia; Bacteroidales; Tannerellaceae;
            Parabacteroides.
REFERENCE   1  (bases 1 to 4148)
  AUTHORS   Guerin,E., Shkoporov,A.N., Stockdale,S.R., Khokhlova,E.V.,
            Clooney,A.G., Daly,K.M., Draper,L.A., Ross,R. and Hill,C.
  TITLE     Isolation and characterization of a novel gut bacteriophage
            targeting Parabacteroides distasonis; phage PDS1
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4148)
  AUTHORS   Guerin,E., Shkoporov,A.N., Stockdale,S.R., Khokhlova,E.V.,
            Clooney,A.G., Daly,K.M., 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 Institute, 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                   :: 54.0x
            Sequencing Technology :: Illumina HiSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_018279895.1-RS_2024_05_18
            Annotation Date                   :: 05/18/2024 03:34:39
            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)                     :: 4,509
            CDSs (total)                      :: 4,406
            Genes (coding)                    :: 4,336
            CDSs (with protein)               :: 4,336
            Genes (RNA)                       :: 103
            rRNAs                             :: 7, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 7, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 80
            ncRNAs                            :: 2
            Pseudo Genes (total)              :: 70
            CDSs (without protein)            :: 70
            Pseudo Genes (ambiguous residues) :: 0 of 70
            Pseudo Genes (frameshifted)       :: 19 of 70
            Pseudo Genes (incomplete)         :: 48 of 70
            Pseudo Genes (internal stop)      :: 17 of 70
            Pseudo Genes (multiple problems)  :: 12 of 70
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP042284.1.
            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="Parabacteroides distasonis"
                     /mol_type="genomic DNA"
                     /strain="APCS2/PD"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:823"
                     /plasmid="pPDS2-1"
                     /geo_loc_name="Ireland:Cork"
                     /collection_date="2017-11"
     gene            complement(join(3467..4148,1..344))
                     /locus_tag="FQN59_RS00005"
                     /old_locus_tag="FQN59_00005"
     CDS             complement(join(3467..4148,1..344))
                     /locus_tag="FQN59_RS00005"
                     /old_locus_tag="FQN59_00005"
                     /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"
     gene            757..1008
                     /locus_tag="FQN59_RS00010"
                     /old_locus_tag="FQN59_00010"
     CDS             757..1008
                     /locus_tag="FQN59_RS00010"
                     /old_locus_tag="FQN59_00010"
                     /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            1005..1280
                     /locus_tag="FQN59_RS00015"
                     /old_locus_tag="FQN59_00015"
     CDS             1005..1280
                     /locus_tag="FQN59_RS00015"
                     /old_locus_tag="FQN59_00015"
                     /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            1291..1488
                     /locus_tag="FQN59_RS00020"
                     /old_locus_tag="FQN59_00020"
     CDS             1291..1488
                     /locus_tag="FQN59_RS00020"
                     /old_locus_tag="FQN59_00020"
                     /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            1681..1980
                     /gene="mbpA"
                     /locus_tag="FQN59_RS22710"
                     /old_locus_tag="FQN59_00025"
     CDS             1681..1980
                     /gene="mbpA"
                     /locus_tag="FQN59_RS22710"
                     /old_locus_tag="FQN59_00025"
                     /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            1977..2771
                     /gene="mbpB"
                     /locus_tag="FQN59_RS00025"
                     /old_locus_tag="FQN59_00030"
     CDS             1977..2771
                     /gene="mbpB"
                     /locus_tag="FQN59_RS00025"
                     /old_locus_tag="FQN59_00030"
                     /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            2728..3180
                     /gene="mbpC"
                     /locus_tag="FQN59_RS00030"
                     /old_locus_tag="FQN59_00035"
     CDS             2728..3180
                     /gene="mbpC"
                     /locus_tag="FQN59_RS00030"
                     /old_locus_tag="FQN59_00035"
                     /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            3200..3430
                     /locus_tag="FQN59_RS00035"
                     /old_locus_tag="FQN59_00040"
     CDS             3200..3430
                     /locus_tag="FQN59_RS00035"
                     /old_locus_tag="FQN59_00040"
                     /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"
ORIGIN
        1 ttagatataa atccgcactt ccaccattcc tcgtcatctt cgtaagtaaa aaaacgtcct
       61 gccaaagaat cgagtgcggc tatgatttca ttgtaatcac gtccggaaaa aataacgtca
      121 gatacatgca tttgtgcatc aacatcccaa agtccatgct caaacttgcg tttcgtgcct
      181 gcataatctt tcagttttac tccctttagt tcagcttggc acgcttccag tatgcgaaga
      241 actattcttt gttcgtgtat ggacatgtct tgctgttttg accatgtata tacccatgaa
      301 acaacaacat ctttattctt ggtaataggt agtttctttt tcataaacga ttgatttgct
      361 gcaaatatac acaatcccca cattaaaaca aaaaaagagg ggtaaaactc ccaaagtgtg
      421 gggactaatt tacttttaaa ctcccaaagt gtggggacta aactcccaaa gtgtggggaa
      481 acacatgttc taatcccttt atttatgggc gtttgcgaag aagtgataga gcatattaca
      541 gacgatgctt ataacagaca aggggaattt atagagctaa gtggttgatt tactgtcgga
      601 aaaagaaaaa cgatagggaa aaagagcaaa gcaaaaccaa ccaacgggcg gtaggattgg
      661 aaacgggttt ttatggcgtg tacacgtttg tgtacaaaat gtttgtattt tattgaaata
      721 tagctatctt tgtgctgaat ttaaaagcaa acagatatgg aagcattatc agtaagagaa
      781 taccgtaaca acctcgcagc gtctttcacc aaagctgaca atggcgagca ggtactaatt
      841 cgcaggaaaa acgagattta cgctttggta aaagttggtc gtgaagattt gatgataacc
      901 ccggagctgc aagcaaggat tgacaaggca agggaagaaa tcaaatccgg aaagtgtgtt
      961 accctcaaaa gcagtgagga tattgacgct tatttcgata gtctatgatg tacacaatta
     1021 gggtttccga cggggtggat aaggtgattg ccaaatggaa gaaatcaaac cccaatttgt
     1081 tcaagaagta taagaaaatc tacaaagaat tgttagagca ccctaagact gggcttgggc
     1141 atcccgaagc gttaaggggc ggtggggata ttacatggtc tcgacacatt accgcccatg
     1201 accggataat ctatgacatt tacgaggaag tggtagaggt ctacatcttg gaggtagagg
     1261 ggcattacaa cgataaatga taaaactgtt atggtcgaat attgtgttta ctggttagag
     1321 aacggcgagc ctatgcacga ggtgttctct tctcttgccg ccgccgagat gtactcatgt
     1381 gcgataagag ggaaagaaaa cattgaatgg gtggaggtgt ccgaagaaga aaccattgat
     1441 ttggacgaac tggaagacat gttcccggat gacttctgcg gcgtgtaatc cccttgggta
     1501 gaaatggggt agaatttgtt aggctgtggg ggattttcta acacgccggg gctttttgct
     1561 gggcggttgg cgtggatgta ttcccatgcg gcatgtgtat atatagcaag aagtgtcctt
     1621 gtcggacaat tcttgctttt ctcgctttgc tcaaaaagat tttaagatta cctttgtggc
     1681 atggaactaa gacggaacga aaagattaca ttccggtgta ccgaacttga aaaggacgca
     1741 cttgcggagc aggcagcccg gtgcagtcta agcgtatcgg aatactgccg gagtttgtcc
     1801 cttggggggc gcccaaggga gaggtacacc gaggaggaac ggcagcttct ccgggacata
     1861 gcccagttga aaggaacgct ccaacggctg aacaactact tcggtggtcg ccagtaccgg
     1921 gaagtgttcg aggagaaccg ggcactaatt acagagctca aaaaaatact ctcacgatga
     1981 tagggaaagg gaaaagcata tcacatggtg tggcggcatt ggagtacgac ctcgccaaag
     2041 agataaacgg gcaggcagta gccaccgaga tagcccggca tgaactttat gggtgtactg
     2101 gtgcggaaat ggtgcaggaa atgaaaccgt atcacattga ttttccgaac gtaaaaaaca
     2161 actgcctacg tttcgaggtc agcccctcga tagaggaaag cgccaccttt acggatgcgg
     2221 actgggcgga acttggtaac gacttcatgc agcgcatggg gttggcgaac caccagtaca
     2281 tcatcatccg gcacagcggt acggagagca agaaagagca agcccacctg cacatactgg
     2341 caaaccgggt ttccctttcc ggggaactgt accgggacaa ctggataggg aaaaaggcaa
     2401 cggaagccgc caatgccata gccaaggaac ggaactttgt acagtcgcag gacattggca
     2461 aagtcaacaa agcggaaatc aaggaagcca tggacggcgt attgaagaag atgcagggct
     2521 ttgactttac caaattcaag gaagaacttg gtaagagagg ttttaaagtc cgggaagcca
     2581 gggcaagcac cgggaaactt aacggctact atgtcacagc ccgaagcggt acggagtata
     2641 aggcaagcga gatagggaaa ggctacactc tcgcccatat cgagcggaca caaagcaaac
     2701 tgaagtgcaa ctcaatgaac atatctcatg gaaacaaact cacacccgga agcggcagct
     2761 tccaacgtta agcagggaca gtacagcccc cggaaaagaa aagatacaac gccaagggta
     2821 aacccgcagc ttgcggtaga actggtgtat caagaactaa agcgtgttga agtctatacg
     2881 aagcgcatag aggacgcaac agcccgaaag gtacaaatag acgggaaaag ccttgaaagt
     2941 gccgaaaatc gcctaaaaaa cgtgttggcg gactttgaac ggcaggggta cagaatgaaa
     3001 aacggcggtt atgtggacaa acgaatttcg ttctactcaa tcctttgtgc tgttatctcc
     3061 ctattgttcg cttgtttcat gtgctatctt tggacggatg cagccaaaga ccgggacaac
     3121 tacaagcagt attatgaata ctaccaagag caggcaaggg aacaaaaggg gaataaataa
     3181 acatctaact ttacgaatta tgggaacaac ggaacacgaa gaaccccggt tcttcttcat
     3241 actgaacaag ggtgcgaagt ccggcggcga aatcacccat gccgtcctaa acggtagtat
     3301 cgtttcgaag ccggcaggct gggacgcctt tcatgggctt gcactggcga gagagaaact
     3361 aagcagcgag gaaatacaac agcagatgaa agaacttggt gtagaaatgg aaatcgttcc
     3421 tctgatttga caagattacc cggagtgttt cagccgggta atcttgttac ttatccttga
     3481 ttttcccttt aagggcgttt ataatccacc ctttcggatt gttcttttct cgtgattttc
     3541 cgtttaggag agccagttct ccgataaggt cggttatctt ttcttgtgcc gttatgaatg
     3601 tctctttgtt ccggtttatc tcttccgatg tgaagccgca ggaataacgg aggtactcgt
     3661 acacatggct gtctatctga tatcgtgctg taacctttgc ttgcaattct ttcccttcca
     3721 gttcttcatc tctgaactgt ggttgataga ccgggtagaa cctaaacccg gtcaccttgc
     3781 tacgtttgtt gtttgggttt tcacgcactt tcacgtagtt gaaagtgtat gggcagctct
     3841 catcaagcgc agcctttgct ggtttcaaaa ctctttcctc aaaatgatct attctgtctt
     3901 ttccgttctt gtccttgtat ttgtccgcag gtatgccaag acggtctttc aagttttcaa
     3961 gggatatatc caaagggtac acctgcccac tcattaacat gtaaaaccta agggaatacc
     4021 cagtaggtag cgcaagagcc ttgtttaact caaattctct gtaccccttg gcgaacttgg
     4081 taaacacatc ccaaaggtcg ttagacacac gaaaggttat aatgccagtg cgttttttat
     4141 attttggg
//
