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Conserved domains on  [gi|446370367|ref|WP_000448222|]
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MULTISPECIES: nitrite reductase small subunit NirD [Staphylococcus]

Protein Classification

nitrite reductase (NAD(P)H) small subunit( domain architecture ID 10131486)

NAD(P)H-dependent nitrite reductase small subunit NirD is required for nitrite assimilation and consists of a Rieske domain, which is a [2Fe-2S] cluster binding domain involved in electron transfer. Assimilatory nitrate and nitrite reductases convert nitrate through nitrite to ammonium.

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Rieske_NirD_small_Bacillus cd03530
Small subunit of nitrite reductase (NirD) family, Rieske domain; composed of proteins similar ...
 6-103 2.97e-51

Small subunit of nitrite reductase (NirD) family, Rieske domain; composed of proteins similar to the Bacillus subtilis small subunit of assimilatory nitrite reductase containing a Rieske domain. The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. Assimilatory nitrate and nitrite reductases convert nitrate through nitrite to ammonium.


:

Pssm-ID: 239606 [Multi-domain]  Cd Length: 98  Bit Score: 156.23  E-value: 2.97e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446370367   6 KIKVTTIDELTPLIGKKVIVKGKEVGLFLTESGKIHAIHNICPHKQGPLSEGTVSGEYVFCPLHDQKIDLNTGIVQEPDE 85
Cdd:cd03530    1 WIDIGALEDIPPRGARKVQTGGGEIAVFRTADDEVFALENRCPHKGGPLSEGIVHGEYVTCPLHNWVIDLETGEAQGPDE 80

                         90
                 ....*....|....*...
gi 446370367  86 GCVDVYEVEVTDGNVYIC 103
Cdd:cd03530   81 GCVRTFPVKVEDGRVYLG 98
 
Name Accession Description Interval E-value
Rieske_NirD_small_Bacillus cd03530
Small subunit of nitrite reductase (NirD) family, Rieske domain; composed of proteins similar ...
 6-103 2.97e-51

Small subunit of nitrite reductase (NirD) family, Rieske domain; composed of proteins similar to the Bacillus subtilis small subunit of assimilatory nitrite reductase containing a Rieske domain. The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. Assimilatory nitrate and nitrite reductases convert nitrate through nitrite to ammonium.


Pssm-ID: 239606 [Multi-domain]  Cd Length: 98  Bit Score: 156.23  E-value: 2.97e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446370367   6 KIKVTTIDELTPLIGKKVIVKGKEVGLFLTESGKIHAIHNICPHKQGPLSEGTVSGEYVFCPLHDQKIDLNTGIVQEPDE 85
Cdd:cd03530    1 WIDIGALEDIPPRGARKVQTGGGEIAVFRTADDEVFALENRCPHKGGPLSEGIVHGEYVTCPLHNWVIDLETGEAQGPDE 80

                         90
                 ....*....|....*...
gi 446370367  86 GCVDVYEVEVTDGNVYIC 103
Cdd:cd03530   81 GCVRTFPVKVEDGRVYLG 98
NirD COG2146
Ferredoxin subunit of nitrite reductase or a ring-hydroxylating dioxygenase [Inorganic ion ...
 7-104 3.68e-30

Ferredoxin subunit of nitrite reductase or a ring-hydroxylating dioxygenase [Inorganic ion transport and metabolism, Secondary metabolites biosynthesis, transport and catabolism];


Pssm-ID: 441749 [Multi-domain]  Cd Length: 103  Bit Score: 103.00  E-value: 3.68e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446370367   7 IKVTTIDELTPLIGKKVIVKGKEVGLFLTEsGKIHAIHNICPHKQGPLSEGTVSGEYVFCPLHDQKIDLNTGIVQE-PDE 85
Cdd:COG2146    4 VKVCALDDLPEGGGVVVEVGGKQIAVFRTD-GEVYAYDNRCPHQGAPLSEGIVDGGVVTCPLHGARFDLRTGECLGgPAT 82

                         90
                 ....*....|....*....
gi 446370367  86 GCVDVYEVEVTDGNVYICL 104
Cdd:COG2146   83 EPLKTYPVRVEDGDVYVDL 101
nirD_assim_sml TIGR02378
nitrite reductase [NAD(P)H], small subunit; This model describes NirD, the small subunit of ...
 6-104 1.35e-25

nitrite reductase [NAD(P)H], small subunit; This model describes NirD, the small subunit of nitrite reductase [NAD(P)H] (the assimilatory nitrite reductase), which associates with NirB, the large subunit (TIGR02374). In a few bacteria such as Klebsiella pneumoniae and in Fungi, the two regions are fused. [Central intermediary metabolism, Nitrogen metabolism]


Pssm-ID: 131431 [Multi-domain]  Cd Length: 105  Bit Score: 91.61  E-value: 1.35e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446370367    6 KIKVTTIDELTPLIGKKVIVKGKEVGLFLTESGKIHAIHNICPHKQG-PLSEGTVSGE----YVFCPLHDQKIDLNTGIV 80
Cdd:TIGR02378   2 WQDICAIDDIPEETGVCVLLGDTQIAIFRVPGDQVFAIQNMCPHKRAfVLSRGIVGDAqgelWVACPLHKRNFRLEDGRC 81

                          90       100
                  ....*....|....*....|....
gi 446370367   81 QEPDEGCVDVYEVEVTDGNVYICL 104
Cdd:TIGR02378  82 LEDDSGSVRTYEVRVEDGRVYVAL 105
Rieske_2 pfam13806
Rieske-like [2Fe-2S] domain;
7-102 4.67e-18

Rieske-like [2Fe-2S] domain;


Pssm-ID: 433491 [Multi-domain]  Cd Length: 103  Bit Score: 72.59  E-value: 4.67e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446370367    7 IKVTTIDELTPLIGKKVIVKGKEVGLFLTESGKIHAIHNICP-HKQGPLSEGTV---SGEY-VFCPLHDQKIDLNTGIVQ 81
Cdd:pfam13806   2 TPVCALDDLPPGTGVCALVGGRQVAVFRLEDGQVYAIDNRDPfSGANVLSRGIVgdlGGELvVASPLYKQHFDLKTGECL 81

                          90       100
                  ....*....|....*....|.
gi 446370367   82 EPDEGCVDVYEVEVTDGNVYI 102
Cdd:pfam13806  82 EDPEVSVPVYPVRVRDGNVEV 102
nirD PRK09511
nitrite reductase small subunit NirD;
7-102 4.52e-09

nitrite reductase small subunit NirD;


Pssm-ID: 181921  Cd Length: 108  Bit Score: 49.64  E-value: 4.52e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446370367   7 IKVTTIDELTPLIGKKVIVKGKEVGLFL-TESGKIHAIHNICPHKQGP-LSEGTVS---GE-YVFCPLHDQKIDLNTGIV 80
Cdd:PRK09511   5 KDICKIDDILPGTGVCALVGDEQVAIFRpYHDEQVFAISNIDPFFQASvLSRGLIAehqGElWVASPLKKQRFRLSDGLC 84

                         90       100
                 ....*....|....*....|..
gi 446370367  81 QEPDEGCVDVYEVEVTDGNVYI 102
Cdd:PRK09511  85 MEDEQFSVKHYDARVKDGVVQL 106
 
Name Accession Description Interval E-value
Rieske_NirD_small_Bacillus cd03530
Small subunit of nitrite reductase (NirD) family, Rieske domain; composed of proteins similar ...
 6-103 2.97e-51

Small subunit of nitrite reductase (NirD) family, Rieske domain; composed of proteins similar to the Bacillus subtilis small subunit of assimilatory nitrite reductase containing a Rieske domain. The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. Assimilatory nitrate and nitrite reductases convert nitrate through nitrite to ammonium.


Pssm-ID: 239606 [Multi-domain]  Cd Length: 98  Bit Score: 156.23  E-value: 2.97e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446370367   6 KIKVTTIDELTPLIGKKVIVKGKEVGLFLTESGKIHAIHNICPHKQGPLSEGTVSGEYVFCPLHDQKIDLNTGIVQEPDE 85
Cdd:cd03530    1 WIDIGALEDIPPRGARKVQTGGGEIAVFRTADDEVFALENRCPHKGGPLSEGIVHGEYVTCPLHNWVIDLETGEAQGPDE 80

                         90
                 ....*....|....*...
gi 446370367  86 GCVDVYEVEVTDGNVYIC 103
Cdd:cd03530   81 GCVRTFPVKVEDGRVYLG 98
NirD COG2146
Ferredoxin subunit of nitrite reductase or a ring-hydroxylating dioxygenase [Inorganic ion ...
 7-104 3.68e-30

Ferredoxin subunit of nitrite reductase or a ring-hydroxylating dioxygenase [Inorganic ion transport and metabolism, Secondary metabolites biosynthesis, transport and catabolism];


Pssm-ID: 441749 [Multi-domain]  Cd Length: 103  Bit Score: 103.00  E-value: 3.68e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446370367   7 IKVTTIDELTPLIGKKVIVKGKEVGLFLTEsGKIHAIHNICPHKQGPLSEGTVSGEYVFCPLHDQKIDLNTGIVQE-PDE 85
Cdd:COG2146    4 VKVCALDDLPEGGGVVVEVGGKQIAVFRTD-GEVYAYDNRCPHQGAPLSEGIVDGGVVTCPLHGARFDLRTGECLGgPAT 82

                         90
                 ....*....|....*....
gi 446370367  86 GCVDVYEVEVTDGNVYICL 104
Cdd:COG2146   83 EPLKTYPVRVEDGDVYVDL 101
nirD_assim_sml TIGR02378
nitrite reductase [NAD(P)H], small subunit; This model describes NirD, the small subunit of ...
 6-104 1.35e-25

nitrite reductase [NAD(P)H], small subunit; This model describes NirD, the small subunit of nitrite reductase [NAD(P)H] (the assimilatory nitrite reductase), which associates with NirB, the large subunit (TIGR02374). In a few bacteria such as Klebsiella pneumoniae and in Fungi, the two regions are fused. [Central intermediary metabolism, Nitrogen metabolism]


Pssm-ID: 131431 [Multi-domain]  Cd Length: 105  Bit Score: 91.61  E-value: 1.35e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446370367    6 KIKVTTIDELTPLIGKKVIVKGKEVGLFLTESGKIHAIHNICPHKQG-PLSEGTVSGE----YVFCPLHDQKIDLNTGIV 80
Cdd:TIGR02378   2 WQDICAIDDIPEETGVCVLLGDTQIAIFRVPGDQVFAIQNMCPHKRAfVLSRGIVGDAqgelWVACPLHKRNFRLEDGRC 81

                          90       100
                  ....*....|....*....|....
gi 446370367   81 QEPDEGCVDVYEVEVTDGNVYICL 104
Cdd:TIGR02378  82 LEDDSGSVRTYEVRVEDGRVYVAL 105
Rieske_NirD cd03529
Assimilatory nitrite reductase (NirD) family, Rieske domain; Assimilatory nitrate and nitrite ...
 7-103 3.47e-18

Assimilatory nitrite reductase (NirD) family, Rieske domain; Assimilatory nitrate and nitrite reductases convert nitrate through nitrite to ammonium. Members include bacterial and fungal proteins. The bacterial NirD contains a single Rieske domain while fungal proteins have a C-terminal Rieske domain in addition to several other domains. The fungal NirD is involved in nutrient acquisition, functioning at the soil/fungus interface to control nutrient exchange between the fungus and the host plant. The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. The Rieske [2Fe-2S] cluster is liganded to two histidine and two cysteine residues present in conserved sequences called Rieske motifs. In this family, only a few members contain these residues. Other members may have lost the ability to bind the Rieske [2Fe-2S] cluster.


Pssm-ID: 239605 [Multi-domain]  Cd Length: 103  Bit Score: 72.54  E-value: 3.47e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446370367   7 IKVTTIDELTPLIGKKVIVKGKEVGLFLTESGKIHAIHNICPHKQGP-LSEG---TVSGE-YVFCPLHDQKIDLNTGIVQ 81
Cdd:cd03529    2 QTVCALDDLPPGSGVAALVGDTQIAIFRLPGREVYAVQNMDPHSRANvLSRGivgDIGGEpVVASPLYKQHFSLKTGRCL 81

                         90       100
                 ....*....|....*....|..
gi 446370367  82 EPDEGCVDVYEVEVTDGNVYIC 103
Cdd:cd03529   82 EDEDVSVATFPVRVEDGEVYVK 103
Rieske_2 pfam13806
Rieske-like [2Fe-2S] domain;
7-102 4.67e-18

Rieske-like [2Fe-2S] domain;


Pssm-ID: 433491 [Multi-domain]  Cd Length: 103  Bit Score: 72.59  E-value: 4.67e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446370367    7 IKVTTIDELTPLIGKKVIVKGKEVGLFLTESGKIHAIHNICP-HKQGPLSEGTV---SGEY-VFCPLHDQKIDLNTGIVQ 81
Cdd:pfam13806   2 TPVCALDDLPPGTGVCALVGGRQVAVFRLEDGQVYAIDNRDPfSGANVLSRGIVgdlGGELvVASPLYKQHFDLKTGECL 81

                          90       100
                  ....*....|....*....|.
gi 446370367   82 EPDEGCVDVYEVEVTDGNVYI 102
Cdd:pfam13806  82 EDPEVSVPVYPVRVRDGNVEV 102
Rieske_RO_ferredoxin cd03528
Rieske non-heme iron oxygenase (RO) family, Rieske ferredoxin component; composed of the ...
 6-102 7.33e-18

Rieske non-heme iron oxygenase (RO) family, Rieske ferredoxin component; composed of the Rieske ferredoxin component of some three-component RO systems including biphenyl dioxygenase (BPDO) and carbazole 1,9a-dioxygenase (CARDO). The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable microorganisms to tolerate and even exclusively utilize aromatic compounds for growth. ROs consist of two or three components: reductase, oxygenase, and ferredoxin (in some cases) components. The ferredoxin component contains either a plant-type or Rieske-type [2Fe-2S] cluster. The Rieske ferredoxin component in this family carries an electron from the RO reductase component to the terminal RO oxygenase component. BPDO degrades biphenyls and polychlorinated biphenyls. BPDO ferredoxin (BphF) has structural features consistent with a minimal and perhaps archetypical Rieske protein in that the insertions that give other Rieske proteins unique structural features are missing. CARDO catalyzes dihydroxylation at the C1 and C9a positions of carbazole. Rieske ferredoxins are found as subunits of membrane oxidase complexes, cis-dihydrodiol-forming aromatic dioxygenases, bacterial assimilatory nitrite reductases, and arsenite oxidase. Rieske ferredoxins are also found as soluble electron carriers in bacterial dioxygenase and monooxygenase complexes.


Pssm-ID: 239604 [Multi-domain]  Cd Length: 98  Bit Score: 71.75  E-value: 7.33e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446370367   6 KIKVTTIDELTPLIGKKVIVKGKEVGLFLTEsGKIHAIHNICPHKQGPLSEGTVSGEYVFCPLHDQKIDLNTG-IVQEPD 84
Cdd:cd03528    1 WVRVCAVDELPEGEPKRVDVGGRPIAVYRVD-GEFYATDDLCTHGDASLSEGYVEGGVIECPLHGGRFDLRTGkALSLPA 79

                         90
                 ....*....|....*...
gi 446370367  85 EGCVDVYEVEVTDGNVYI 102
Cdd:cd03528   80 TEPLKTYPVKVEDGDVYV 97
Rieske cd03467
Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron ...
 8-102 8.76e-18

Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes. The Rieske domain can be divided into two subdomains, with an incomplete six-stranded, antiparallel beta-barrel at one end, and an iron-sulfur cluster binding subdomain at the other. The Rieske iron-sulfur center contains a [2Fe-2S] cluster, which is involved in electron transfer, and is liganded to two histidine and two cysteine residues present in conserved sequences called Rieske motifs. In RO systems, the N-terminal Rieske domain of the alpha subunit acts as an electron shuttle that accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron in the alpha subunit C-terminal domain to be used for catalysis.


Pssm-ID: 239550 [Multi-domain]  Cd Length: 98  Bit Score: 71.75  E-value: 8.76e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446370367   8 KVTTIDELTPLIGKKVIVKGKEVGLFLTESGKIHAIHNICPHKQGPLSEGTVSGEYVFCPLHDQKIDLNTGIVQE-PDEG 86
Cdd:cd03467    3 VVGALSELPPGGGRVVVVGGGPVVVVRREGGEVYALSNRCTHQGCPLSEGEGEDGCIVCPCHGSRFDLRTGEVVSgPAPR 82

                         90
                 ....*....|....*.
gi 446370367  87 CVDVYEVEVtDGNVYI 102
Cdd:cd03467   83 PLPKYPVKV-EGDGVV 97
Rieske pfam00355
Rieske [2Fe-2S] domain; The rieske domain has a [2Fe-2S] centre. Two conserved cysteines ...
 21-92 3.36e-15

Rieske [2Fe-2S] domain; The rieske domain has a [2Fe-2S] centre. Two conserved cysteines coordinate one Fe ion, while the other Fe ion is coordinated by two conserved histidines. In hyperthermophilic archaea there is a SKTPCX(2-3)C motif at the C-terminus. The cysteines in this motif form a disulphide bridge, which stabilizes the protein.


Pssm-ID: 425632 [Multi-domain]  Cd Length: 89  Bit Score: 64.68  E-value: 3.36e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446370367   21 KKVIVKGKEVGLFLTESGKIHAIHNICPHKQGPLSEGTVSGEYVF-CPLHDQKIDLNTGIVQEPDEGCVDVYE 92
Cdd:pfam00355  17 KVVEVGGEPLVVFRDEDGELYALEDRCPHRGAPLSEGKVNGGGRLeCPYHGWRFDGTGKVVKVPAPRPLKSYP 89
Rieske_AIFL_N cd03478
AIFL (apoptosis-inducing factor like) family, N-terminal Rieske domain; members of this family ...
 21-101 5.00e-14

AIFL (apoptosis-inducing factor like) family, N-terminal Rieske domain; members of this family show similarity to human AIFL, containing an N-terminal Rieske domain and a C-terminal pyridine nucleotide-disulfide oxidoreductase domain (Pyr_redox). The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. AIFL shares 35% homology with human AIF (apoptosis-inducing factor), mainly in the Pyr_redox domain. AIFL is predominantly localized to the mitochondria. AIFL induces apoptosis in a caspase-dependent manner.


Pssm-ID: 239560 [Multi-domain]  Cd Length: 95  Bit Score: 61.87  E-value: 5.00e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446370367  21 KKVIVKGKEVgLFLTESGKIHAIHNICPHKQGPLSEGTVSGEYVFCPLHDQKIDLNTG-IVQEPDEGCVDVYEVEVTDGN 99
Cdd:cd03478   15 KEVDVGDGKV-LLVRQGGEVHAIGAKCPHYGAPLAKGVLTDGRIRCPWHGACFNLRTGdIEDAPALDSLPCYEVEVEDGR 93


                 ..
gi 446370367 100 VY 101
Cdd:cd03478   94 VY 95
Rieske_T4moC cd03474
Toluene-4-monooxygenase effector protein complex (T4mo), Rieske ferredoxin subunit; The Rieske ...
 7-102 2.25e-11

Toluene-4-monooxygenase effector protein complex (T4mo), Rieske ferredoxin subunit; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. T4mo is a four-protein complex that catalyzes the NADH- and O2-dependent hydroxylation of toluene to form p-cresol. T4mo consists of an NADH oxidoreductase (T4moF), a diiron hydroxylase (T4moH), a catalytic effector protein (T4moD), and a Rieske ferredoxin (T4moC). T4moC contains a Rieske domain and functions as an obligate electron carrier between T4moF and T4moH. Rieske ferredoxins are found as subunits of membrane oxidase complexes, cis-dihydrodiol-forming aromatic dioxygenases, bacterial assimilatory nitrite reductases, and arsenite oxidase. Rieske ferredoxins are also found as soluble electron carriers in bacterial dioxygenase and monooxygenase complexes.


Pssm-ID: 239556 [Multi-domain]  Cd Length: 108  Bit Score: 55.42  E-value: 2.25e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446370367   7 IKVTTIDELTPLIGKKVIVKGKEVGLFLTESGKIHAIHNICPHKQGPLSEGTVSGEYVFCPLHDQKIDLNTGIVQEPDEG 86
Cdd:cd03474    2 TKVCSLDDVWEGEMELVDVDGEEVLLVAPEGGEFRAFQGICPHQEIPLAEGGFDGGVLTCRAHLWQFDADTGEGLNPRDC 81

                         90
                 ....*....|....*.
gi 446370367  87 CVDVYEVEVTDGNVYI 102
Cdd:cd03474   82 RLARYPVKVEGGDILV 97
Rieske_RO_Alpha_VanA_DdmC cd03532
Rieske non-heme iron oxygenase (RO) family, Vanillate-O-demethylase oxygenase (VanA) and ...
 13-102 1.34e-10

Rieske non-heme iron oxygenase (RO) family, Vanillate-O-demethylase oxygenase (VanA) and dicamba O-demethylase oxygenase (DdmC) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. Vanillate-O-demethylase is a heterodimeric enzyme consisting of a terminal oxygenase (VanA) and reductase (VanB) components. This enzyme reductively catalyzes the conversion of vanillate into protocatechuate and formaldehyde. Protocatechuate and vanillate are important intermediate metabolites in the degradation pathway of lignin-derived compounds such as ferulic acid and vanillin by soil microbes. DDmC is the oxygenase component of a three-component dicamba O-demethylase found in Pseudomonas maltophila, that catalyzes the conversion of a widely used herbicide called herbicide dicamba (2-methoxy-3,6-dichlorobenzoic acid) to DCSA (3,6-dichlorosalicylic acid).


Pssm-ID: 239608 [Multi-domain]  Cd Length: 116  Bit Score: 53.52  E-value: 1.34e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446370367  13 DELT-PLIGKKVIvkGKEVGLFLTESGKIHAIHNICPHKQGPLSEGTVSGEYVFCPLHDQKIDLNTGIVQEPDEG----- 86
Cdd:cd03532   13 DELGdKPLARTLL--GEPVVLYRTQDGRVAALEDRCPHRSAPLSKGSVEGGGLVCGYHGLEFDSDGRCVHMPGQErvpak 90

                         90
                 ....*....|....*..
gi 446370367  87 -CVDVYEVEVTDGNVYI 102
Cdd:cd03532   91 aCVRSYPVVERDALIWI 107
nirD PRK09511
nitrite reductase small subunit NirD;
7-102 4.52e-09

nitrite reductase small subunit NirD;


Pssm-ID: 181921  Cd Length: 108  Bit Score: 49.64  E-value: 4.52e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446370367   7 IKVTTIDELTPLIGKKVIVKGKEVGLFL-TESGKIHAIHNICPHKQGP-LSEGTVS---GE-YVFCPLHDQKIDLNTGIV 80
Cdd:PRK09511   5 KDICKIDDILPGTGVCALVGDEQVAIFRpYHDEQVFAISNIDPFFQASvLSRGLIAehqGElWVASPLKKQRFRLSDGLC 84

                         90       100
                 ....*....|....*....|..
gi 446370367  81 QEPDEGCVDVYEVEVTDGNVYI 102
Cdd:PRK09511  85 MEDEQFSVKHYDARVKDGVVQL 106
Rieske_RO_Alpha_N cd03469
Rieske non-heme iron oxygenase (RO) family, N-terminal Rieske domain of the oxygenase alpha ...
 27-104 1.90e-08

Rieske non-heme iron oxygenase (RO) family, N-terminal Rieske domain of the oxygenase alpha subunit; The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable microorganisms to tolerate and even exclusively utilize aromatic compounds for growth. ROs consist of two or three components: reductase, oxygenase, and ferredoxin (in some cases) components. The oxygenase component may contain alpha and beta subunits, with the beta subunit having a purely structural function. Some oxygenase components contain only an alpha subunit. The oxygenase alpha subunit has two domains, an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from the reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. Reduced pyridine nucleotide is used as the initial source of two electrons for dioxygen activation.


Pssm-ID: 239551 [Multi-domain]  Cd Length: 118  Bit Score: 47.97  E-value: 1.90e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446370367  27 GKEVGLFLTESGKIHAIHNICPHKQGPLSEGTVSGEYVF-CPLHDQKIDLN---TGIVQEPDEGCVD-------VYEVEV 95
Cdd:cd03469   23 GEPLVLVRDRDGEVRAFHNVCPHRGARLCEGRGGNAGRLvCPYHGWTYDLDgklVGVPREEGFPGFDkeklglrTVPVEE 102


                 ....*....
gi 446370367  96 TDGNVYICL 104
Cdd:cd03469  103 WGGLIFVNL 111
Rieske_RO_Alpha_KSH cd03531
The alignment model represents the N-terminal rieske iron-sulfur domain of KshA, the oxygenase ...
 27-70 2.56e-08

The alignment model represents the N-terminal rieske iron-sulfur domain of KshA, the oxygenase component of 3-ketosteroid 9-alpha-hydroxylase (KSH). The terminal oxygenase component of KSH is a key enzyme in the microbial steroid degradation pathway, catalyzing the 9 alpha-hydroxylation of 4-androstene-3,17-dione (AD) and 1,4-androstadiene-3,17-dione (ADD). KSH is a two-component class IA monooxygenase, with terminal oxygenase (KshA) and oxygenase reductase (KshB) components. KSH activity has been found in many actino- and proteo- bacterial genera including Rhodococcus, Nocardia, Arthrobacter, Mycobacterium, and Burkholderia.


Pssm-ID: 239607 [Multi-domain]  Cd Length: 115  Bit Score: 47.79  E-value: 2.56e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 446370367  27 GKEVGLFLTESGKIHAIHNICPHKQGPLSEGTVSGEYVFCPLHD 70
Cdd:cd03531   23 GTKLVVFADSDGALNVLDAYCRHMGGDLSQGTVKGDEIACPFHD 66
PRK09965 PRK09965
3-phenylpropionate dioxygenase ferredoxin subunit; Provisional
 7-102 8.44e-08

3-phenylpropionate dioxygenase ferredoxin subunit; Provisional


Pssm-ID: 170182 [Multi-domain]  Cd Length: 106  Bit Score: 46.31  E-value: 8.44e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446370367   7 IKVTTIDELTPliGKKV-IVKGKEVGLFLTEsGKIHAIHNICPHKQGPLSEGTVSGE-YVFCPLHDQKIDLNTGIVQ-EP 83
Cdd:PRK09965   4 IYACPVADLPE--GEALrVDTSPVIALFNVG-GEFYAIDDRCSHGNASLSEGYLEDDaTVECPLHAASFCLRTGKALcLP 80

                         90
                 ....*....|....*....
gi 446370367  84 DEGCVDVYEVEVTDGNVYI 102
Cdd:PRK09965  81 ATDPLRTYPVHVEGGDIFI 99
HcaE COG4638
Phenylpropionate dioxygenase or related ring-hydroxylating dioxygenase, large terminal subunit ...
 35-69 1.38e-06

Phenylpropionate dioxygenase or related ring-hydroxylating dioxygenase, large terminal subunit [Inorganic ion transport and metabolism, General function prediction only];


Pssm-ID: 443676 [Multi-domain]  Cd Length: 298  Bit Score: 44.59  E-value: 1.38e-06
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 446370367  35 TESGKIHAIHNICPHKQGPLSEGTVSGEYVFCPLH 69
Cdd:COG4638   57 DKDGEVRAFHNVCPHRGAPLSEGRGNGGRLVCPYH 91
Rieske_RO_Alpha_CMO cd03541
Rieske non-heme iron oxygenase (RO) family, Choline monooxygenase (CMO) subfamily, N-terminal ...
 36-69 9.57e-04

Rieske non-heme iron oxygenase (RO) family, Choline monooxygenase (CMO) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. CMO is a novel RO found in certain plants which catalyzes the first step in betaine synthesis. CMO is not found in animals or bacteria. In these organisms, the first step in betaine synthesis is catalyzed by either the membrane-bound choline dehydrogenase (CDH) or the soluble choline oxidase (COX).


Pssm-ID: 239614 [Multi-domain]  Cd Length: 118  Bit Score: 35.99  E-value: 9.57e-04
                         10        20        30
                 ....*....|....*....|....*....|....
gi 446370367  36 ESGKIHAIHNICPHKQGPLSEGTVSGEYVFCPLH 69
Cdd:cd03541   33 GNGKLHAFHNVCTHRASILACGSGKKSCFVCPYH 66
Rieske_RO_Alpha_Cao cd04337
Cao (chlorophyll a oxygenase) is a rieske non-heme iron-sulfur protein located within the ...
 32-90 1.04e-03

Cao (chlorophyll a oxygenase) is a rieske non-heme iron-sulfur protein located within the plastid-envelope inner and thylakoid membranes, that catalyzes the conversion of chlorophyllide a to chlorophyllide b. CAO is found not only in plants but also in chlorophytes and prochlorophytes. This domain represents the N-terminal rieske domain of the oxygenase alpha subunit. ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. Cao is closely related to several other plant RO's including Tic 55, a 55 kDa protein associated with protein transport through the inner chloroplast membrane; Ptc 52, a novel 52 kDa protein isolated from chloroplasts; and LLS1/Pao (Lethal-leaf spot 1/pheophorbide a oxygenase).


Pssm-ID: 239829 [Multi-domain]  Cd Length: 129  Bit Score: 35.93  E-value: 1.04e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 446370367  32 LFLTESGKIHAIHNICPHKQGPLSEGTVSGEYVFCPLHDQKIDLNTGIVQEPDEGCVDV 90
Cdd:cd04337   44 LFRDEDGTPGCIRDECAHRACPLSLGKVIEGRIQCPYHGWEYDGDGECTKMPSTKCLNV 102
PLN02281 PLN02281
chlorophyllide a oxygenase
 32-69 3.29e-03

chlorophyllide a oxygenase


Pssm-ID: 177920 [Multi-domain]  Cd Length: 536  Bit Score: 35.47  E-value: 3.29e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 446370367  32 LFLTESGKIHAIHNICPHKQGPLSEGTVSGEYVFCPLH 69
Cdd:PLN02281 247 IFRGEDGKPGCVRNTCAHRACPLDLGTVNEGRIQCPYH 284
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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