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)
//