Bradyrhizobium barranii subsp. barranii strain 323S2 plasmid pBb323S2d, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales; Nitrobacteraceae; Bradyrhizobium; Bradyrhizobium barranii.
Strains of Bradyrhizobium barranii sp. nov. associated with legumes native to Canada are symbionts of soybeans and belong to different subspecies (subsp. barranii subsp. nov. and subsp. apii subsp. nov.) and symbiovars (sv. glycinearum and sv. septentrionale)
Int J Syst Evol Microbiol 72 (10) (2022)
Soybeans inoculated with root zone soils of Canadian native legumes harbour diverse and novel Bradyrhizobium spp. that possess agricultural potential
Erratum:[Syst Appl Microbiol. 2017 Dec;40(8):517. PMID: 29113688]
Submitted (18-NOV-2021) ORDC, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, Ontario K1A 0C6, Canada
Submitted (19-JUN-2020) ORDC, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, Ontario K1A 0C6, Canada
REFSEQ INFORMATION: The reference sequence is identical to\nCP088277.1.\nBacteria and source DNA available from Eden S.P. Bromfield,\nAgriculture and Agri-Food Canada, 960 Carling Ave., Ottawa ON K1A\n0C6.\nThe annotation was added by the NCBI Prokaryotic Genome Annotation\nPipeline (PGAP). Information about PGAP can be found here:\nhttps://www.ncbi.nlm.nih.gov/genome/annotation_prok/\n\n##Genome-Assembly-Data-START##\nAssembly Date :: NOV-2021\nAssembly Method :: Flye v. v2.9\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 687.0x\nSequencing Technology :: PacBio Sequel\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 11/13/2022 12:54:39\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.3\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA;\n repeat_region\nGenes (total) :: 11,061\nCDSs (total) :: 10,995\nGenes (coding) :: 10,354\nCDSs (with protein) :: 10,354\nGenes (RNA) :: 66\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 56\nncRNAs :: 4\nPseudo Genes (total) :: 641\nCDSs (without protein) :: 641\nPseudo Genes (ambiguous residues) :: 0 of 641\nPseudo Genes (frameshifted) :: 332 of 641\nPseudo Genes (incomplete) :: 411 of 641\nPseudo Genes (internal stop) :: 43 of 641\nPseudo Genes (multiple problems) :: 133 of 641\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_076612082.1
GO:0004803 - transposase activity [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
IS3-like element ISRj2 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_011084489.1
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
DDE-type integrase/transposase/recombinase
COORDINATES: similar to AA sequence:RefSeq:WP_008967898.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
medium chain dehydrogenase/reductase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_057901383.1
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus and C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_007590565.1
COORDINATES: similar to AA sequence:RefSeq:WP_019863552.1
COORDINATES: similar to AA sequence:RefSeq:WP_031692132.1
COORDINATES: protein motif:HMM:TIGR00619.1
GO:0004527 - exonuclease activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]; GO:0006260 - DNA replication [Evidence IEA]
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF024867.2
COORDINATES: similar to AA sequence:RefSeq:WP_004174297.1
COORDINATES: similar to AA sequence:RefSeq:WP_007684537.1
COORDINATES: similar to AA sequence:RefSeq:WP_006023657.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913704.1
COORDINATES: similar to AA sequence:RefSeq:WP_020047573.1
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_009859417.1
COORDINATES: protein motif:HMM:NF014581.2
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_076612137.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_009859418.1
COORDINATES: similar to AA sequence:RefSeq:WP_018273651.1
GO:0043684 - type IV secretion system complex [Evidence IEA]
GO:0044097 - secretion by the type IV secretion system [Evidence IEA]
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_009859458.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: protein motif:HMM:NF019324.2
type II toxin-antitoxin system VapB family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_011931109.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564771.1
COORDINATES: similar to AA sequence:RefSeq:WP_011505049.1
COORDINATES: similar to AA sequence:RefSeq:WP_011505048.1
COORDINATES: similar to AA sequence:RefSeq:WP_011505047.1
COORDINATES: similar to AA sequence:RefSeq:WP_012319572.1
frameshifted; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_003537131.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013953029.1
incomplete; partial in the middle of a contig; missing N-terminus and C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011950655.1
COORDINATES: protein motif:HMM:NF024408.2
COORDINATES: similar to AA sequence:RefSeq:WP_006615047.1
TnpB, as the term is used for proteins encoded by IS66 family insertion elements, is considered an accessory protein, since TnpC, encoded by a neighboring gene, is a DDE family transposase; Derived by automated computational analysis using gene prediction method: Protein Homology.
IS66 family insertion sequence element accessory protein TnpB
COORDINATES: protein motif:HMM:NF013677.2
COORDINATES: similar to AA sequence:RefSeq:WP_011090936.1
IS21-like element ISFK1 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_011090937.1
IS21-like element ISFK1 family helper ATPase IstB
COORDINATES: similar to AA sequence:RefSeq:WP_011084505.1
COORDINATES: similar to AA sequence:RefSeq:WP_012354672.1
COORDINATES: similar to AA sequence:RefSeq:WP_012330183.1
COORDINATES: protein motif:HMM:NF012472.2
COORDINATES: similar to AA sequence:RefSeq:WP_042650430.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611592.1
GO:0015074 - DNA integration [Evidence IEA]
integrase core domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014989244.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611723.1
COORDINATES: similar to AA sequence:RefSeq:WP_011970376.1
COORDINATES: similar to AA sequence:RefSeq:WP_011983062.1
COORDINATES: similar to AA sequence:RefSeq:WP_018270224.1
COORDINATES: protein motif:HMM:NF012360.2
COORDINATES: similar to AA sequence:RefSeq:WP_018273679.1
COORDINATES: similar to AA sequence:RefSeq:WP_010562368.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012406695.1
COORDINATES: similar to AA sequence:RefSeq:WP_012976683.1
COORDINATES: similar to AA sequence:RefSeq:WP_012634672.1
COORDINATES: protein motif:HMM:NF017528.2
COORDINATES: similar to AA sequence:RefSeq:WP_009820056.1
COORDINATES: similar to AA sequence:RefSeq:WP_008840747.1
COORDINATES: similar to AA sequence:RefSeq:WP_017503702.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612116.1
COORDINATES: similar to AA sequence:RefSeq:WP_039183842.1
IS1380-like element ISBdi2 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_007601949.1
COORDINATES: protein motif:HMM:NF013698.2
COORDINATES: protein motif:HMM:NF025849.2
GO:0004842 - ubiquitin-protein transferase activity [Evidence IEA]
GO:0016567 - protein ubiquitination [Evidence IEA]
NEL-type E3 ubiquitin ligase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018493481.1
GO:0030170 - pyridoxal phosphate binding [Evidence IEA]
GO:0019346 - transsulfuration [Evidence IEA]
cystathionine gamma-synthase family protein
COORDINATES: protein motif:HMM:NF013068.2
COORDINATES: protein motif:HMM:NF025638.2
COORDINATES: similar to AA sequence:RefSeq:WP_011090958.1
COORDINATES: similar to AA sequence:RefSeq:WP_007594308.1
tripartite tricarboxylate transporter permease
COORDINATES: similar to AA sequence:RefSeq:WP_020655341.1
LysR substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008549358.1
GO:0003824 - catalytic activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018270231.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_013836279.1
COORDINATES: similar to AA sequence:RefSeq:WP_020095364.1
COORDINATES: protein motif:HMM:NF015411.2
NAD(P)-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007598741.1
COORDINATES: similar to AA sequence:RefSeq:WP_014766436.1
COORDINATES: similar to AA sequence:RefSeq:WP_011510130.1
COORDINATES: similar to AA sequence:RefSeq:WP_012335275.1
COORDINATES: similar to AA sequence:RefSeq:WP_018269639.1
COORDINATES: similar to AA sequence:RefSeq:WP_011508891.1
frameshifted; internal stop; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_076611419.1
IS630-like element ISRj1 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_008554630.1
COORDINATES: protein motif:HMM:NF014021.2
nucleotidyltransferase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007800792.1
COORDINATES: similar to AA sequence:RefSeq:WP_017992740.1
nucleotidyl transferase AbiEii/AbiGii toxin family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012479494.1