Bradyrhizobium elkanii USDA 61 plasmid pBel61, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales; Nitrobacteraceae; Bradyrhizobium.
Complete genome sequence of a soybean symbiont Bradyrhizobium elkanii strain USDA 61
Submitted (09-AUG-2013) Contact:Takakazu Kaneko Kyoto Sangyo University, Life Sciences; Motoyama,Kamigamo,Kita-Ku, Kyoto, Kyoto 603-8555, Japan
REFSEQ INFORMATION: The reference sequence is identical to\nAP013104.1.\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 Method :: SOAPdenovo\nGenome Coverage :: 309x\nSequencing Technology :: Illumina GAII\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/25/2023 03:53:10\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) :: 9,274\nCDSs (total) :: 9,211\nGenes (coding) :: 8,860\nCDSs (with protein) :: 8,860\nGenes (RNA) :: 63\nrRNAs :: 1, 1, 1 (5S, 16S, 23S)\ncomplete rRNAs :: 1, 1, 1 (5S, 16S, 23S)\ntRNAs :: 56\nncRNAs :: 4\nPseudo Genes (total) :: 352\nCDSs (without protein) :: 351\nPseudo Genes (ambiguous residues) :: 0 of 352\nPseudo Genes (frameshifted) :: 181 of 352\nPseudo Genes (incomplete) :: 238 of 352\nPseudo Genes (internal stop) :: 30 of 352\nPseudo Genes (multiple problems) :: 89 of 352\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_011505049.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011505048.1
COORDINATES: similar to AA sequence:RefSeq:WP_011505047.1
COORDINATES: protein motif:HMM:NF023228.2
COORDINATES: similar to AA sequence:RefSeq:WP_011930892.1
COORDINATES: similar to AA sequence:RefSeq:WP_006316160.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611540.1
GO:0004803 - transposase activity [Evidence IEA]
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012634672.1
COORDINATES: similar to AA sequence:RefSeq:WP_008121576.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_012654902.1
COORDINATES: similar to AA sequence:RefSeq:WP_008786797.1
COORDINATES: similar to AA sequence:RefSeq:WP_012648972.1
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_009859469.1
COORDINATES: similar to AA sequence:RefSeq:WP_018273792.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_018273791.1
plasmid mobilization relaxosome protein MobC
COORDINATES: similar to AA sequence:RefSeq:WP_009859472.1
relaxase/mobilization nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017266207.1
COORDINATES: similar to AA sequence:RefSeq:WP_008031862.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003170548.1
COORDINATES: protein motif:HMM:NF019291.2
GO:0003824 - catalytic activity [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]
GO:0006304 - DNA modification [Evidence IEA]
Eco57I restriction-modification methylase domain-containing protein
COORDINATES: protein motif:HMM:NF017519.2
YiiX/YebB-like N1pC/P60 family cysteine hydrolase
COORDINATES: protein motif:HMM:NF012493.2
helicase C-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF039739.1
COORDINATES: similar to AA sequence:RefSeq:WP_009734067.1
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: similar to AA sequence:RefSeq:WP_006022635.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_018317109.1
COORDINATES: similar to AA sequence:RefSeq:WP_006022633.1
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_014492143.1
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018269875.1
COORDINATES: similar to AA sequence:RefSeq:WP_006022630.1
COORDINATES: similar to AA sequence:RefSeq:WP_009734063.1
COORDINATES: similar to AA sequence:RefSeq:WP_007613480.1
COORDINATES: similar to AA sequence:RefSeq:WP_014493273.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612082.1
IS3-like element ISRj2 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_014492148.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003910 - DNA ligase (ATP) activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]; GO:0006281 - DNA repair [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007605926.1
COORDINATES: similar to AA sequence:RefSeq:WP_018269880.1
COORDINATES: similar to AA sequence:RefSeq:WP_009859187.1
COORDINATES: similar to AA sequence:RefSeq:WP_011087993.1
COORDINATES: similar to AA sequence:RefSeq:WP_043767036.1
COORDINATES: similar to AA sequence:RefSeq:WP_009797950.1
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_003290589.1
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_076612142.1
frameshifted; internal stop; 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_076612008.1
GO:0015074 - DNA integration [Evidence IEA]
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_013094623.1
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_076611133.1
COORDINATES: protein motif:HMM:NF024751.2
COORDINATES: protein motif:HMM:NF024954.2
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007591169.1
COORDINATES: similar to AA sequence:RefSeq:WP_011084470.1
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_008878011.1
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_011658829.1
COORDINATES: similar to AA sequence:RefSeq:WP_007605747.1
COORDINATES: protein motif:HMM:NF013677.2
COORDINATES: similar to AA sequence:RefSeq:WP_011084757.1
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_011090930.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611472.1
DDE-type integrase/transposase/recombinase
COORDINATES: similar to AA sequence:RefSeq:WP_007635327.1
COORDINATES: similar to AA sequence:RefSeq:WP_018273926.1
COORDINATES: similar to AA sequence:RefSeq:WP_007597078.1
COORDINATES: protein motif:HMM:NF013068.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [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_011631753.1
COORDINATES: similar to AA sequence:RefSeq:WP_018273693.1
COORDINATES: protein motif:HMM:NF025126.2
COORDINATES: similar to AA sequence:RefSeq:WP_019302861.1
catalyzes the isomerization of isopentenyl pyrophosphate to dimethylallyl diphosphate; frameshifted; internal stop; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
type 2 isopentenyl-diphosphate Delta-isomerase
COORDINATES: similar to AA sequence:RefSeq:WP_016845990.1
COORDINATES: similar to AA sequence:RefSeq:WP_026312707.1
COORDINATES: similar to AA sequence:RefSeq:WP_007605890.1
GO:0008299 - isoprenoid biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008838317.1
COORDINATES: similar to AA sequence:RefSeq:WP_018647446.1
COORDINATES: similar to AA sequence:RefSeq:WP_014497729.1
COORDINATES: similar to AA sequence:RefSeq:WP_014497730.1
GO:0020037 - heme binding [Evidence IEA]; GO:0005506 - iron ion binding [Evidence IEA]; GO:0016705 - oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003532617.1
COORDINATES: similar to AA sequence:RefSeq:WP_019303098.1
COORDINATES: similar to AA sequence:RefSeq:WP_015003371.1
COORDINATES: protein motif:HMM:NF012311.2
COORDINATES: similar to AA sequence:RefSeq:WP_012555266.1
COORDINATES: similar to AA sequence:RefSeq:WP_002719010.1
COORDINATES: similar to AA sequence:RefSeq:WP_018009154.1
type II toxin-antitoxin system PemK/MazF family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_004121362.1
type II toxin-antitoxin system prevent-host-death family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_012564774.1
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_015822436.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564771.1