Bradyrhizobium septentrionale strain 1S1 plasmid pBs1S1b, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales; Nitrobacteraceae; Bradyrhizobium.
Bradyrhizobium septentrionale sp. nov. (sv. septentrionale) and Bradyrhizobium quebecense sp. nov. (sv. septentrionale) associated with legumes native to Canada possess rearranged symbiosis genes and numerous insertion sequences
Submitted (19-NOV-2021) ORDC, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, Ontario K1A 0C6, Canada
Submitted (17-SEP-2021) ORDC, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, Ontario K1A 0C6, Canada
REFSEQ INFORMATION: The reference sequence is identical to\nCP088287.1.\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 :: No\nGenome Coverage :: 386.0x\nSequencing Technology :: PacBio Sequel\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/20/2023 09:26:17\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.4\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 9,999\nCDSs (total) :: 9,929\nGenes (coding) :: 9,364\nCDSs (with protein) :: 9,364\nGenes (RNA) :: 70\nrRNAs :: 1, 1, 1 (5S, 16S, 23S)\ncomplete rRNAs :: 1, 1, 1 (5S, 16S, 23S)\ntRNAs :: 63\nncRNAs :: 4\nPseudo Genes (total) :: 566\nCDSs (without protein) :: 565\nPseudo Genes (ambiguous residues) :: 0 of 566\nPseudo Genes (frameshifted) :: 280 of 566\nPseudo Genes (incomplete) :: 386 of 566\nPseudo Genes (internal stop) :: 50 of 566\nPseudo Genes (multiple problems) :: 137 of 566\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
Root nodule from soybean plant inoculated with root zone soil from Amphicarpaea bracteata
type strain of Bradyrhizobium septentrionale
COORDINATES: similar to AA sequence:RefSeq:WP_014439177.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_002634692.1
GO:0016788 - hydrolase activity, acting on ester bonds [Evidence IEA]
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF012798.2
COORDINATES: similar to AA sequence:RefSeq:WP_008840754.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008840753.1
COORDINATES: similar to AA sequence:RefSeq:WP_007606460.1
GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0006974 - cellular response to DNA damage stimulus [Evidence IEA]; GO:0018142 - protein-DNA covalent cross-linking [Evidence IEA]
SOS response-associated peptidase family protein
COORDINATES: protein motif:HMM:NF024854.2
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009032021.1
frameshifted; 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_008137858.1
COORDINATES: similar to AA sequence:RefSeq:WP_010511758.1
COORDINATES: protein motif:HMM:NF024642.2
COORDINATES: similar to AA sequence:RefSeq:WP_039183842.1
IS1380-like element ISBdi2 family transposase
COORDINATES: protein motif:HMM:NF024754.2
COORDINATES: similar to AA sequence:RefSeq:WP_003571565.1
COORDINATES: similar to AA sequence:RefSeq:WP_012452317.1
COORDINATES: similar to AA sequence:RefSeq:WP_011084731.1
COORDINATES: similar to AA sequence:RefSeq:WP_011112984.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
5-methylcytosine-specific restriction system specificity protein McrC
COORDINATES: similar to AA sequence:RefSeq:WP_004545940.1
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF024117.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012789.2
COORDINATES: similar to AA sequence:RefSeq:WP_007674970.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003916 - DNA topoisomerase activity [Evidence IEA]
GO:0006265 - DNA topological change [Evidence IEA]
DDE-type integrase/transposase/recombinase
COORDINATES: similar to AA sequence:RefSeq:WP_011024495.1
GO:0003964 - RNA-directed DNA polymerase activity [Evidence IEA]
GO:0000373 - Group II intron splicing [Evidence IEA]
group II intron reverse transcriptase/maturase
COORDINATES: similar to AA sequence:RefSeq:WP_009800157.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611638.1
GO:0004803 - transposase activity [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011931032.1
COORDINATES: similar to AA sequence:RefSeq:WP_011931033.1
COORDINATES: similar to AA sequence:RefSeq:WP_011509865.1
COORDINATES: protein motif:HMM:NF037056.2
COORDINATES: similar to AA sequence:RefSeq:WP_018643590.1
sigma-70 family RNA polymerase sigma factor
COORDINATES: similar to AA sequence:RefSeq:WP_011663911.1
COORDINATES: similar to AA sequence:RefSeq:WP_009797621.1
COORDINATES: similar to AA sequence:RefSeq:WP_006018770.1
COORDINATES: similar to AA sequence:RefSeq:WP_012043454.1
COORDINATES: similar to AA sequence:RefSeq:WP_014492187.1
COORDINATES: similar to AA sequence:RefSeq:WP_007606466.1
GO:0045027 - DNA end binding [Evidence IEA]
GO:0006303 - double-strand break repair via nonhomologous end joining [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076612082.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
IS3-like element ISRj2 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_011510130.1
IS1380-like element ISNha3 family transposase
COORDINATES: protein motif:HMM:NF041399.1
COORDINATES: similar to AA sequence:RefSeq:WP_011578756.1,RefSeq:WP_012452059.1
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_011090936.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611419.1
COORDINATES: similar to AA sequence:RefSeq:WP_018273859.1
COORDINATES: similar to AA sequence:RefSeq:WP_019863552.1
COORDINATES: similar to AA sequence:RefSeq:WP_006022633.1
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: protein motif:HMM:NF024908.2
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014857744.1
COORDINATES: similar to AA sequence:RefSeq:WP_004111509.1
COORDINATES: similar to AA sequence:RefSeq:WP_012335275.1
COORDINATES: similar to AA sequence:RefSeq:WP_006611535.1
COORDINATES: similar to AA sequence:RefSeq:WP_018268148.1
COORDINATES: similar to AA sequence:RefSeq:WP_018321970.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612067.1
COORDINATES: similar to AA sequence:RefSeq:WP_018273923.1
GO:0008270 - zinc ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011511274.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612068.1
COORDINATES: similar to AA sequence:RefSeq:WP_011511276.1
GO:0004386 - helicase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018269971.1
COORDINATES: similar to AA sequence:RefSeq:WP_018273947.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_015341784.1
COORDINATES: similar to AA sequence:RefSeq:WP_015341783.1
COORDINATES: similar to AA sequence:RefSeq:WP_011578806.1
COORDINATES: similar to AA sequence:RefSeq:WP_012553005.1
COORDINATES: similar to AA sequence:RefSeq:WP_012318773.1
type II toxin-antitoxin system PemK/MazF family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_018043438.1
COORDINATES: similar to AA sequence:RefSeq:WP_011194944.1
COORDINATES: similar to AA sequence:RefSeq:WP_007692751.1
type II toxin-antitoxin system VapB family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_008834278.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_013650748.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913701.1
COORDINATES: similar to AA sequence:RefSeq:WP_006205756.1
COORDINATES: similar to AA sequence:RefSeq:WP_003518550.1
GO:0016740 - transferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012649102.1
COORDINATES: similar to AA sequence:RefSeq:WP_011505223.1
COORDINATES: similar to AA sequence:RefSeq:WP_010892446.1
COORDINATES: similar to AA sequence:RefSeq:WP_012650638.1
COORDINATES: similar to AA sequence:RefSeq:WP_010892444.1
GO:0009291 - unidirectional conjugation [Evidence IEA]
P-type conjugative transfer protein TrbJ
COORDINATES: similar to AA sequence:RefSeq:WP_020048155.1
P-type conjugative transfer protein TrbL
COORDINATES: similar to AA sequence:RefSeq:WP_018482029.1
COORDINATES: similar to AA sequence:RefSeq:WP_018240861.1
P-type conjugative transfer protein TrbG
COORDINATES: similar to AA sequence:RefSeq:WP_013650735.1
COORDINATES: similar to AA sequence:RefSeq:WP_020046771.1
IncP-type conjugal transfer protein TrbI
COORDINATES: similar to AA sequence:RefSeq:WP_011993001.1
autoinducer binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007591169.1
COORDINATES: similar to AA sequence:RefSeq:WP_018273055.1
GO:0015074 - DNA integration [Evidence IEA]
integrase core domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008969630.1
GO:0042597 - periplasmic space [Evidence IEA]
Spy/CpxP family protein refolding chaperone
COORDINATES: similar to AA sequence:RefSeq:WP_007601711.1
COORDINATES: similar to AA sequence:RefSeq:WP_011086257.1
GO:0015116 - sulfate transmembrane transporter activity [Evidence IEA]
GO:0008272 - sulfate transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011086250.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_018455636.1
COORDINATES: similar to AA sequence:RefSeq:WP_007609935.1
COORDINATES: similar to AA sequence:RefSeq:WP_007604914.1
COORDINATES: similar to AA sequence:RefSeq:WP_018456570.1
COORDINATES: similar to AA sequence:RefSeq:WP_007674970.1,RefSeq:WP_018268369.1
frameshifted; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.