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Microbe : Bradyrhizobium diazoefficiens

Microbe Description

NBRC No. 14792
Scientific name Bradyrhizobium diazoefficiens
Synonymous name Rhizobium japonicum
Bradyrhizobium japonicum
History IFO 14792 <- USDA 110 (R. Griffin)
Other culture collection No.
Other No. USDA 110
Reference
Not assigned

Functional Potential >>Details

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TypePattern Component Gene CDS
Alanine racemization(NFUNC_0063)
RequireA
ALR
(NRULE_0228)
Alanine racemasebll4070
n-alkane hydroxylation(NFUNC_0008)
RequireA
CYP153
(NRULE_0041)
Cytochrome P450 CYP153blr1853 blr7242 blr7243
C
MMA
(NRULE_0027)
Multicomponent monooxygenase alpha subunitblr3677 blr3679
MMB
(NRULE_0028)
Multicomponent monooxygenase beta subunitblr3679 blr3677
FDR1
(NRULE_0032)
Oxygenase electron transfer componentblr2392 blr2895 blr3678 bll4816 blr7998 bll3766
MME
(NRULE_0033)
Multicomponent monooxygenase effector proteinblr3680
Participant 
RUBA
(NRULE_0039)
Rubredoxinbsl6935
 
FDX1
(NRULE_0034)
Putative Rieske-type ferredoxinblr3400 blr2983 bll5204 bll6221 bll6426 bll7609 blr7649 bll7906 blr2485 blr2390 blr0938 bll1070 blr1753 blr4922 blr3358
Aminoglycoside resistance (by aminoglycoside O-phosphotransferase)(NFUNC_0043)
RequireC
APH7
(NRULE_0157)
Hygromycin-B 7''-O-kinaseblr1035
Ampicillin resistance(NFUNC_0046)
RequireA
BLAA
(NRULE_0122)
Beta-lactamase class Abll0941
Participant 
BLAD
(NRULE_0125)
Beta-lactamase class Dbll5360
Anthranilate biosynthesis(NFUNC_0038)
RequireA
GLAT
(NRULE_0142)
Glutamine amidotransferasebll2091 blr2489
TRPE
(NRULE_0143)
Anthranilate synthase component Iblr2489
Arginine degradation(NFUNC_0074)
RequireA
ARGI
(NRULE_0239)
Arginasebll6122
Aromatic azo compounds degradation(NFUNC_0073)
RequireA
AZOR
(NRULE_0236)
FMN-dependent NADH-azoreductasebll3368 blr5106
Arsenical resistance(NFUNC_0004)
RequireD
ARSB2
(NRULE_0016)
Arsenite resistance protein ArsBbll3085
ARSC1
(NRULE_0017)
Arsenate reductasebll3084
E
ARSB2
(NRULE_0016)
Arsenite resistance protein ArsBbll3085
ARSC2
(NRULE_0018)
Arsenate reductasebll3086
Bacitracin resistance(NFUNC_0022)
RequireA
UPPP
(NRULE_0097)
Undecaprenyl-diphosphataseblr0716
Beta-lactam antibiotic resistance(NFUNC_0033)
RequireA
BLAA
(NRULE_0122)
Beta-lactamase class Abll0941
D
BLAD
(NRULE_0125)
Beta-lactamase class Dbll5360
Bioplastic degradation(NFUNC_0015)
RequireA
PHAZ1
(NRULE_0023)
Intracellular poly(3-hydroxyalkanoate) depolymeraseblr6703 blr0908
B
PHAZ2
(NRULE_0080)
Poly(3-hydroxyalkanoate) depolymerasebll4997 blr0899
Bioplastic synthesis(NFUNC_0001)
RequireA
PHAC1
(NRULE_0010)
Poly(3-hydroxyalkanoate) polymerasebll4360 blr3732
Participant 
PHAB
(NRULE_0011)
Acetoacetyl-CoA reductasebll0225 blr3725
 
PHAP1
(NRULE_0374)
Phasinbll5555 bll6129 bll7395 blr2887 blr3464 bll5155
Haloalkane degradation (conversion into hydroxyacid)(NFUNC_0010)
RequireA
DHAA
(NRULE_0050)
Haloalkane dehalogenaseblr1087
HAD
(NRULE_0051)
(S)-2-haloacid dehalogenaseblr7560 blr4364
B
DHAA
(NRULE_0050)
Haloalkane dehalogenaseblr1087
DEH
(NRULE_0075)
Haloacetate dehalogenasebll7497
Hygromycin resistance(NFUNC_0055)
RequireA
APH7
(NRULE_0157)
Hygromycin-B 7''-O-kinaseblr1035
Macrolide antibiotic resistance(NFUNC_0045)
RequireD
ERE
(NRULE_0168)
Erythromycin esterasebll4651
Metal-binding protein(NFUNC_0105)
RequireA
MOP
(NRULE_0322)
Putative molybdenum-binding proteinblr1895 bll1780 blr6644 bll6352 blr3917 blr3224 blr2437 blr6953
C
MODA
(NRULE_0324)
Molybdate ABC transporter substrate-binding proteinblr4797 blr6951 blr7099 blr8160
H
NIKR
(NRULE_0331)
Nickel-responsive transcriptional regulator NikRbll0699
Molybdate transport (ABC transporter)(NFUNC_0097)
RequireA
MODA
(NRULE_0324)
Molybdate ABC transporter substrate-binding proteinblr4797 blr7099 blr6951 blr8160
Participant 
MODB
(NRULE_0325)
Molybdate ABC transporter permease proteinblr8161 blr6952
 
MODC
(NRULE_0326)
Molybdate ABC transporter ATP-binding proteinblr8162 blr6953 bll1780
Nitrile hydratase(NFUNC_0002)
RequireA
NHAA
(NRULE_0001)
Nitrile hydratase subunit alphabll4498
NHAB
(NRULE_0002)
Nitrile hydratase subunit betabll4497
Participant 
P14K
(NRULE_0006)
Nitrile hydratase activator P14Kbll4496
 
COBW
(NRULE_0007)
CobW/P47K family proteinblr3261 bll7303 bll7768
Nitrogenase(NFUNC_0094)
RequireA
NIFD
(NRULE_0347)
Nitrogenase molybdenum-iron protein alpha chainblr1743
NIFK
(NRULE_0348)
Nitrogenase molybdenum-iron protein beta chainblr1744
VNFH
(NRULE_0353)
Nitrogenase reductaseblr1769
(R)-pantothenate biosynthesis(NFUNC_0030)
RequireA
PAND
(NRULE_0115)
Aspartate 1-decarboxylaseblr2096
PANB
(NRULE_0116)
3-methyl-2-oxobutanoate hydroxymethyltransferaseblr4048 blr2101
PANE
(NRULE_0117)
2-dehydropantoate 2-reductasebll6396 bll4604 bll0134 blr0117 blr0589 bll3147
PANC
(NRULE_0118)
Pantothenate synthetaseblr2102 blr5162
Penicillin resistance(NFUNC_0047)
RequireA
BLAA
(NRULE_0122)
Beta-lactamase class Abll0941
B
BLAD
(NRULE_0125)
Beta-lactamase class Dbll5360
Phenol degradation(NFUNC_0028)
RequireC
PHEA2
(NRULE_0084)
Aromatic ring hydroxylaseblr4222
Participant 
FDR1
(NRULE_0032)
Oxygenase electron transfer componentbll4816 bll3766 blr3678 blr2895 blr2392 blr7998
 
MME
(NRULE_0033)
Multicomponent monooxygenase effector proteinblr3680
 
FDX1
(NRULE_0034)
Putative Rieske-type ferredoxinblr2983 blr3358 blr3400 blr4922 bll5204 bll6221 bll6426 bll7609 blr7649 bll7906 blr2485 blr2390 blr1753 bll1070 blr0938
 
FADR1
(NRULE_0101)
NADH-dependent flavin reductaseblr7290 blr1238 blr2425 blr3324 blr3331 blr3398 bll3439 bll6095 bll7007
Pyrroloquinoline quinone biosynthesis(NFUNC_0020)
RequireA
PQQC
(NRULE_0092)
Pyrroloquinoline-quinone synthaseblr6737
Participant 
PQQA
(NRULE_0090)
Coenzyme PQQ synthesis protein Absr6735
 
PQQB
(NRULE_0091)
Coenzyme PQQ synthesis protein Bblr6736
 
PQQD
(NRULE_0093)
Coenzyme PQQ synthesis protein Dblr6738
 
PQQE
(NRULE_0094)
Coenzyme PQQ synthesis protein Eblr6739
Riboflavin biosynthesis(NFUNC_0058)
RequireA
RIBB
(NRULE_0200)
3,4-dihydroxy-2-butanone 4-phosphate synthaseblr2615
RIBA
(NRULE_0201)
GTP cyclohydrolase-2blr7237 blr2615
RIBD
(NRULE_0202)
Riboflavin biosynthesis protein RibDbll5031
RIBH
(NRULE_0203)
6,7-dimethyl-8-ribityllumazine synthasebll5029 bll7452
RIBE
(NRULE_0204)
Riboflavin synthasebll5030
Participant 
RIBF
(NRULE_0205)
Riboflavin biosynthesis protein RibFblr7480
Trehalose biosynthesis (from maltooligosaccharide)(NFUNC_0037)
RequireA
TREY
(NRULE_0140)
Maltooligosyl trehalose synthaseblr6771
TREZ
(NRULE_0141)
Malto-oligosyltrehalose trehalohydrolaseblr6770
Participant 
GLGX
(NRULE_0139)
Glycogen debranching enzymeblr6769
Trehalose biosynthesis (from maltose)(NFUNC_0034)
RequireB
TRES
(NRULE_0128)
Trehalose synthaseblr6767

Genomic Overview

BioProject IDPRJNA17
Locus_tag
INSDC entriesBA000040
Sequence statusComplete
Current status
Contig number1
Size(bp) 9,105,828
Gene 8,317
Finishing goal
Assembly method
Coverage
Technology
Reference
  • Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110. (DNA Res. 2002) PMID: 12597275
  • Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110 (supplement). (DNA Res. 2002) PMID: 12597279

Data Download

Genomic nucleotide sequence Nucleotide sequence of the coding regions Translation of the coding sequneces List of genes / ORFs
FASTA
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FASTA
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FASTA
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TSV
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2.7 MB 2.4 MB 1.6 MB 587.0 KB