Bradyrhizobium quebecense strain 12S5 plasmid pBq12S5.
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-MAR-2021) ORDC, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, Ontario K1A 0C6, Canada
REFSEQ INFORMATION: The reference sequence is identical to\nCP088283.1.\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 :: 1421.0x\nSequencing Technology :: PacBio Sequel\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/20/2023 08:51:01\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) :: 8,252\nCDSs (total) :: 8,194\nGenes (coding) :: 7,898\nCDSs (with protein) :: 7,898\nGenes (RNA) :: 58\nrRNAs :: 1, 1, 1 (5S, 16S, 23S)\ncomplete rRNAs :: 1, 1, 1 (5S, 16S, 23S)\ntRNAs :: 51\nncRNAs :: 4\nPseudo Genes (total) :: 296\nCDSs (without protein) :: 296\nPseudo Genes (ambiguous residues) :: 0 of 296\nPseudo Genes (frameshifted) :: 179 of 296\nPseudo Genes (incomplete) :: 171 of 296\nPseudo Genes (internal stop) :: 44 of 296\nPseudo Genes (multiple problems) :: 88 of 296\n##Genome-Annotation-Data-END##
root nodule from soybean plant inoculated with root zone soil from Apios americana
COORDINATES: similar to AA sequence:RefSeq:WP_012564796.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012564795.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_010974883.1
COORDINATES: similar to AA sequence:RefSeq:WP_011931093.1
COORDINATES: similar to AA sequence:RefSeq:WP_011931094.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564791.1
COORDINATES: similar to AA sequence:RefSeq:WP_011931096.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012564790.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913795.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_011654735.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564786.1
type II toxin-antitoxin system YhaV family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_015822454.1
type II toxin-antitoxin system PrlF family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_010669065.1
COORDINATES: protein motif:HMM:NF012311.2
COORDINATES: similar to AA sequence:RefSeq:WP_010875309.1
COORDINATES: similar to AA sequence:RefSeq:WP_018273806.1
COORDINATES: similar to AA sequence:RefSeq:WP_009859458.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_009859459.1
type II toxin-antitoxin system VapB family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_011931109.1
COORDINATES: similar to AA sequence:RefSeq:WP_012653092.1
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_009859460.1
COORDINATES: similar to AA sequence:RefSeq:WP_018273801.1
COORDINATES: similar to AA sequence:RefSeq:WP_011505047.1
COORDINATES: similar to AA sequence:RefSeq:WP_018457241.1
COORDINATES: similar to AA sequence:RefSeq:WP_011930893.1
COORDINATES: similar to AA sequence:RefSeq:WP_009859465.1
COORDINATES: similar to AA sequence:RefSeq:WP_008121576.1
COORDINATES: similar to AA sequence:RefSeq:WP_011930896.1
COORDINATES: similar to AA sequence:RefSeq:WP_009859468.1
COORDINATES: similar to AA sequence:RefSeq:WP_011930898.1
COORDINATES: similar to AA sequence:RefSeq:WP_009859469.1
COORDINATES: similar to AA sequence:RefSeq:WP_009859470.1
COORDINATES: similar to AA sequence:RefSeq:WP_018273791.1
plasmid mobilization relaxosome protein MobC
COORDINATES: similar to AA sequence:RefSeq:WP_011930905.1
relaxase/mobilization nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_076611638.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_043766072.1
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_006893414.1
COORDINATES: similar to AA sequence:RefSeq:WP_018270152.1
nucleotidyl transferase AbiEii/AbiGii toxin family protein
COORDINATES: similar to AA sequence:RefSeq:WP_018270153.1
type IV toxin-antitoxin system AbiEi family antitoxin
Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
COORDINATES: similar to AA sequence:RefSeq:WP_012563543.1
COORDINATES: protein motif:HMM:NF012798.2
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [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_012112796.1
COORDINATES: protein motif:HMM:NF012789.2
COORDINATES: similar to AA sequence:RefSeq:WP_007068977.1
COORDINATES: similar to AA sequence:RefSeq:WP_014490982.1
GO:0007165 - signal transduction [Evidence IEA]
COORDINATES: protein motif:HMM:NF013594.2
GO:0004222 - metalloendopeptidase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF024949.2
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011084389.1
COORDINATES: similar to AA sequence:RefSeq:WP_018273520.1
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: similar to AA sequence:RefSeq:WP_076612405.1
COORDINATES: protein motif:HMM:NF024754.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018270029.1
COORDINATES: similar to AA sequence:RefSeq:WP_012590988.1
COORDINATES: similar to AA sequence:RefSeq:WP_009488473.1
COORDINATES: similar to AA sequence:RefSeq:WP_011266187.1
COORDINATES: similar to AA sequence:RefSeq:WP_015415381.1
COORDINATES: protein motif:HMM:NF024685.2
COORDINATES: similar to AA sequence:RefSeq:WP_009859433.1
COORDINATES: similar to AA sequence:RefSeq:WP_043767036.1
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF012521.2
COORDINATES: similar to AA sequence:RefSeq:WP_010508891.1
COORDINATES: similar to AA sequence:RefSeq:WP_015665180.1
COORDINATES: protein motif:HMM:NF014684.2
COORDINATES: similar to AA sequence:RefSeq:WP_011510130.1
COORDINATES: similar to AA sequence:RefSeq:WP_007599989.1
COORDINATES: similar to AA sequence:RefSeq:WP_011084670.1
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_076612338.1
COORDINATES: similar to AA sequence:RefSeq:WP_011511153.1
COORDINATES: similar to AA sequence:RefSeq:WP_018268867.1
COORDINATES: protein motif:HMM:NF020918.2
COORDINATES: similar to AA sequence:RefSeq:WP_011084489.1
COORDINATES: similar to AA sequence:RefSeq:WP_018327356.1
COORDINATES: similar to AA sequence:RefSeq:WP_015495987.1
COORDINATES: similar to AA sequence:RefSeq:WP_011508891.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011194944.1
COORDINATES: similar to AA sequence:RefSeq:WP_018328334.1
COORDINATES: protein motif:HMM:NF017528.2
COORDINATES: similar to AA sequence:RefSeq:WP_012975328.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611246.1
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_076612246.1
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_018099682.1
COORDINATES: protein motif:HMM:NF013677.2
COORDINATES: similar to AA sequence:RefSeq:WP_011511226.1
COORDINATES: protein motif:HMM:NF013786.2
GO:0008897 - holo-[acyl-carrier-protein] synthase activity [Evidence IEA]; GO:0000287 - magnesium ion binding [Evidence IEA]
4'-phosphopantetheinyl transferase superfamily protein
COORDINATES: similar to AA sequence:RefSeq:WP_043766079.1
COORDINATES: similar to AA sequence:RefSeq:WP_010913673.1
COORDINATES: similar to AA sequence:RefSeq:WP_018240773.1
COORDINATES: similar to AA sequence:RefSeq:WP_011501169.1
GO:0015074 - DNA integration [Evidence IEA]
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.
integrase core domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_076612082.1
COORDINATES: similar to AA sequence:RefSeq:WP_007792578.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611554.1
COORDINATES: similar to AA sequence:RefSeq:WP_018319411.1
ATP-binding cassette domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008878011.1
COORDINATES: similar to AA sequence:RefSeq:WP_008878010.1
COORDINATES: protein motif:HMM:NF012869.2
COORDINATES: similar to AA sequence:RefSeq:WP_076612008.1
COORDINATES: similar to AA sequence:RefSeq:WP_007068908.1
COORDINATES: similar to AA sequence:RefSeq:WP_006316161.1
COORDINATES: protein motif:HMM:NF003417.0
amino acid adenylation domain-containing protein
COORDINATES: protein motif:HMM:NF012711.2
COORDINATES: similar to AA sequence:RefSeq:WP_012554517.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611612.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611960.1
COORDINATES: similar to AA sequence:RefSeq:WP_010913867.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012778787.1
COORDINATES: protein motif:HMM:NF039194.1
COORDINATES: similar to AA sequence:RefSeq:WP_011082834.1
COORDINATES: similar to AA sequence:RefSeq:WP_014761245.1
COORDINATES: similar to AA sequence:RefSeq:WP_014989244.1
COORDINATES: similar to AA sequence:RefSeq:WP_019863552.1
COORDINATES: similar to AA sequence:RefSeq:WP_019856451.1
peptidase domain-containing ABC transporter
COORDINATES: similar to AA sequence:RefSeq:WP_020628969.1
HlyD family efflux transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_076611189.1
COORDINATES: similar to AA sequence:RefSeq:WP_011931067.1
COORDINATES: similar to AA sequence:RefSeq:WP_011931068.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011931069.1
GO:0043684 - type IV secretion system complex [Evidence IEA]
GO:0044097 - secretion by the type IV secretion system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011931070.1
COORDINATES: similar to AA sequence:RefSeq:WP_011931071.1
P-type conjugative transfer protein VirB9
COORDINATES: similar to AA sequence:RefSeq:WP_018409504.1
COORDINATES: similar to AA sequence:RefSeq:WP_011931074.1
COORDINATES: similar to AA sequence:RefSeq:WP_009859425.1
COORDINATES: similar to AA sequence:RefSeq:WP_018273833.1
COORDINATES: similar to AA sequence:RefSeq:WP_011931077.1
VirB4 family type IV secretion/conjugal transfer ATPase
COORDINATES: similar to AA sequence:RefSeq:WP_003526740.1
COORDINATES: similar to AA sequence:RefSeq:WP_011931079.1
COORDINATES: similar to AA sequence:RefSeq:WP_011931080.1
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009859431.1
GO:0016740 - transferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011931082.1
COORDINATES: similar to AA sequence:RefSeq:WP_007739926.1
COORDINATES: similar to AA sequence:RefSeq:WP_010915950.1
COORDINATES: similar to AA sequence:RefSeq:WP_008343560.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564801.1
COORDINATES: similar to AA sequence:RefSeq:WP_011931084.1
DUF3991 and toprim domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011931085.1