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Bifidobacterium pullorum subsp. gallinarum strain LMG 11586 Contig09, whole genome shotgun sequence

NCBI Reference Sequence: NZ_JGYX01000009.1

FASTA Graphics 

LOCUS       NZ_JGYX01000009         2726 bp    DNA     linear   CON 21-OCT-2024
DEFINITION  Bifidobacterium pullorum subsp. gallinarum strain LMG 11586
            Contig09, whole genome shotgun sequence.
ACCESSION   NZ_JGYX01000009 NZ_JGYX01000000
VERSION     NZ_JGYX01000009.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN02673435
            Assembly: GCF_000741215.1
KEYWORDS    WGS; RefSeq.
SOURCE      Bifidobacterium pullorum subsp. gallinarum
  ORGANISM  Bifidobacterium pullorum subsp. gallinarum
            Bacteria; Bacillati; Actinomycetota; Actinomycetes;
            Bifidobacteriales; Bifidobacteriaceae; Bifidobacterium.
REFERENCE   1  (bases 1 to 2726)
  AUTHORS   Lugli,G.A., Milani,C., Turroni,F., Duranti,S., Ferrario,C.,
            Viappiani,A., Mancabelli,L., Mangifesta,M., Taminiau,B.,
            Delcenserie,V., van Sinderen,D. and Ventura,M.
  TITLE     Investigation of the evolutionary development of the genus
            Bifidobacterium by comparative genomics
  JOURNAL   Appl Environ Microbiol 80 (20), 6383-6394 (2014)
   PUBMED   25107967
REFERENCE   2  (bases 1 to 2726)
  AUTHORS   Milani,C., Lugli,G.A., Duranti,S., Turroni,F., Bottacini,F.,
            Mangifesta,M., Sanchez,B., Viappiani,A., Mancabelli,L.,
            Taminiau,B., Delcenserie,V., Barrangou,R., Margolles,A., van
            Sinderen,D. and Ventura,M.
  TITLE     Genomic encyclopedia of type strains of the genus Bifidobacterium
  JOURNAL   Appl Environ Microbiol 80 (20), 6290-6302 (2014)
   PUBMED   25085493
REFERENCE   3  (bases 1 to 2726)
  AUTHORS   Ventura,M., Milani,C. and Lugli,G.A.
  TITLE     Direct Submission
  JOURNAL   Submitted (17-MAR-2014) Life Sciences, University of Parma, via
            Parco Area delle Scienze 11/A, Parma 43124, Italy
COMMENT     REFSEQ INFORMATION: The reference sequence is identical to
            JGYX01000009.1.
            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/
            
            ##Genome-Assembly-Data-START##
            Assembly Method       :: Mira v. 4.0
            Assembly Name         :: Bifgalrum
            Genome Coverage       :: 244.5x
            Sequencing Technology :: Ion Torrent
            ##Genome-Assembly-Data-END##
            
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_000741215.1-RS_2024_10_21
            Annotation Date                   :: 10/21/2024 21:30:25
            Annotation Pipeline               :: NCBI Prokaryotic Genome
                                                 Annotation Pipeline (PGAP)
            Annotation Method                 :: Best-placed reference protein
                                                 set; GeneMarkS-2+
            Annotation Software revision      :: 6.8
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 1,841
            CDSs (total)                      :: 1,778
            Genes (coding)                    :: 1,703
            CDSs (with protein)               :: 1,703
            Genes (RNA)                       :: 63
            rRNAs                             :: 2, 3, 2 (5S, 16S, 23S)
            complete rRNAs                    :: 2, 1, 1 (5S, 16S, 23S)
            partial rRNAs                     :: 2, 1 (16S, 23S)
            tRNAs                             :: 53
            ncRNAs                            :: 3
            Pseudo Genes (total)              :: 75
            CDSs (without protein)            :: 75
            Pseudo Genes (ambiguous residues) :: 0 of 75
            Pseudo Genes (frameshifted)       :: 25 of 75
            Pseudo Genes (incomplete)         :: 50 of 75
            Pseudo Genes (internal stop)      :: 6 of 75
            Pseudo Genes (multiple problems)  :: 6 of 75
            ##Genome-Annotation-Data-END##
FEATURES             Location/Qualifiers
     source          1..2726
                     /organism="Bifidobacterium pullorum subsp. gallinarum"
                     /mol_type="genomic DNA"
                     /submitter_seqid="Contig09"
                     /strain="LMG 11586"
                     /isolation_source="Chicken caecum"
                     /host="chicken"
                     /sub_species="gallinarum"
                     /type_material="type strain of Bifidobacterium gallinarum"
                     /db_xref="taxon:78344"
     gene            <1..421
                     /locus_tag="BIGA_RS08820"
                     /old_locus_tag="BIGA_1786"
     CDS             <1..421
                     /locus_tag="BIGA_RS08820"
                     /old_locus_tag="BIGA_1786"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_003831777.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=2
                     /transl_table=11
                     /product="IS3 family transposase"
                     /protein_id="WP_034259972.1"
                     /translation="DCHDGKIVAYTAGFHPNAELANRMLAEAAETLPDNARPVVHSDR
                     GCHYRWPGWLELMERYGLIRSMSAKGCSPDNAAAEGFFGRMKTESVYPEHWEKRTRDE
                     VLVLIDEYIHWYNHERIKQSLDWMSPVQYRQSQGMAA"
     gene            515..1564
                     /locus_tag="BIGA_RS08825"
                     /old_locus_tag="BIGA_1787"
     CDS             515..1564
                     /locus_tag="BIGA_RS08825"
                     /old_locus_tag="BIGA_1787"
                     /inference="COORDINATES: protein motif:HMM:NF037202.5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type ISP restriction/modification enzyme"
                     /protein_id="WP_161786284.1"
                     /translation="MVPSPDISWTAGFRQDFAKKKTKHPEQGKIVRSAYRPFAKQFLW
                     FDKQTNERTYLQPQLFPYPEAKNLQISIVLGSRQFSCLMTDVVPDIQLSFNAQCFPLY
                     WYEKLDDDSPEKYGLDFYEIRDRADSHGYVRHDAITDTALNVFRAAYPALSITKEDIF
                     YYVYGILHSSEYRRRFANNLTKELPRIPLARNFKAFEQAGRKLAKLHLNYEKVKPWDV
                     TEIGDPTNPGRTVRMTYPRKVKDPDTGKKVADLTVLQVAENLTIENIPLRAYEYVVNG
                     KTAIGWLIDRYQVTTDKKSGITNDPNDYSDDPRYIVDLVEKVIRVSVETVDIINGLPK
                     LDEIGKPANWPQEWN"
     gene            complement(1854..2177)
                     /locus_tag="BIGA_RS08830"
     CDS             complement(1854..2177)
                     /locus_tag="BIGA_RS08830"
                     /inference="COORDINATES: protein motif:HMM:NF036890.5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_033507983.1"
                     /translation="MGGNLPDASPYACSQWTVAGFNSPTQLKLRPLILSPEGLERVGW
                     TTGAAVPEEVDKLIAGRGWVVAVNTLAAMNPVCLRFDALGDPRWKSRKHVPLSWDWDE
                     KKQGR"
     gene            complement(2273..>2726)
                     /locus_tag="BIGA_RS08835"
                     /pseudo
     CDS             complement(2273..>2726)
                     /locus_tag="BIGA_RS08835"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012576493.1"
                     /note="frameshifted; incomplete; missing N-terminus;
                     Derived by automated computational analysis using gene
                     prediction method: Protein Homology."
                     /pseudo
                     /codon_start=2
                     /transl_table=11
                     /product="transposase"
CONTIG      join(JGYX01000009.1:1..2726)
//
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