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Conserved domains on  [gi|516431175|ref|WP_017820230|]
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MULTISPECIES: nitrite reductase small subunit NirD [Vibrio]

Protein Classification

nitrite reductase (NAD(P)H) small subunit family protein( domain architecture ID 10131482)

NAD(P)H-dependent nitrite reductase small subunit family protein similar to NAD(P)H-dependent nitrite reductase small subunit NirD which is required for nitrite assimilation and contains a single Rieske [2Fe-2S] cluster binding domain involved in electron transfer

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Rieske_NirD cd03529
Assimilatory nitrite reductase (NirD) family, Rieske domain; Assimilatory nitrate and nitrite ...
 7-105 4.89e-56

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: 168.84  E-value: 4.89e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516431175   7 VKLCQLDDLMPFIGATVLIEGEHVALFYIPDSGVYAVQDWDPIGKAYVMSRGIVGDIDGEMCVASPLYKQHFSLKSGQCL 86
Cdd:cd03529    2 QTVCALDDLPPGSGVAALVGDTQIAIFRLPGREVYAVQNMDPHSRANVLSRGIVGDIGGEPVVASPLYKQHFSLKTGRCL 81

                         90
                 ....*....|....*....
gi 516431175  87 EDEAHCLKTWQVTVDDNQV 105
Cdd:cd03529   82 EDEDVSVATFPVRVEDGEV 100
 
Name Accession Description Interval E-value
Rieske_NirD cd03529
Assimilatory nitrite reductase (NirD) family, Rieske domain; Assimilatory nitrate and nitrite ...
 7-105 4.89e-56

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: 168.84  E-value: 4.89e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516431175   7 VKLCQLDDLMPFIGATVLIEGEHVALFYIPDSGVYAVQDWDPIGKAYVMSRGIVGDIDGEMCVASPLYKQHFSLKSGQCL 86
Cdd:cd03529    2 QTVCALDDLPPGSGVAALVGDTQIAIFRLPGREVYAVQNMDPHSRANVLSRGIVGDIGGEPVVASPLYKQHFSLKTGRCL 81

                         90
                 ....*....|....*....
gi 516431175  87 EDEAHCLKTWQVTVDDNQV 105
Cdd:cd03529   82 EDEDVSVATFPVRVEDGEV 100
Rieske_2 pfam13806
Rieske-like [2Fe-2S] domain;
7-105 7.53e-45

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


Pssm-ID: 433491 [Multi-domain]  Cd Length: 103  Bit Score: 140.77  E-value: 7.53e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516431175    7 VKLCQLDDLMPFIGATVLIEGEHVALFYIPDSGVYAVQDWDPIGKAYVMSRGIVGDIDGEMCVASPLYKQHFSLKSGQCL 86
Cdd:pfam13806   2 TPVCALDDLPPGTGVCALVGGRQVAVFRLEDGQVYAIDNRDPFSGANVLSRGIVGDLGGELVVASPLYKQHFDLKTGECL 81

                          90
                  ....*....|....*....
gi 516431175   87 EDEAHCLKTWQVTVDDNQV 105
Cdd:pfam13806  82 EDPEVSVPVYPVRVRDGNV 100
nirD_assim_sml TIGR02378
nitrite reductase [NAD(P)H], small subunit; This model describes NirD, the small subunit of ...
 5-105 1.75e-40

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: 129.74  E-value: 1.75e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516431175    5 TKVKLCQLDDLMPFIGATVLIEGEHVALFYIPDSGVYAVQDWDPIGKAYVMSRGIVGDIDGEMCVASPLYKQHFSLKSGQ 84
Cdd:TIGR02378   1 TWQDICAIDDIPEETGVCVLLGDTQIAIFRVPGDQVFAIQNMCPHKRAFVLSRGIVGDAQGELWVACPLHKRNFRLEDGR 80

                          90       100
                  ....*....|....*....|.
gi 516431175   85 CLEDEAHCLKTWQVTVDDNQV 105
Cdd:TIGR02378  81 CLEDDSGSVRTYEVRVEDGRV 101
nirD PRK09511
nitrite reductase small subunit NirD;
7-105 1.59e-33

nitrite reductase small subunit NirD;


Pssm-ID: 181921  Cd Length: 108  Bit Score: 112.05  E-value: 1.59e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516431175   7 VKLCQLDDLMPFIGATVLIEGEHVALFYiP--DSGVYAVQDWDPIGKAYVMSRGIVGDIDGEMCVASPLYKQHFSLKSGQ 84
Cdd:PRK09511   5 KDICKIDDILPGTGVCALVGDEQVAIFR-PyhDEQVFAISNIDPFFQASVLSRGLIAEHQGELWVASPLKKQRFRLSDGL 83

                         90       100
                 ....*....|....*....|.
gi 516431175  85 CLEDEAHCLKTWQVTVDDNQV 105
Cdd:PRK09511  84 CMEDEQFSVKHYDARVKDGVV 104
NirD COG2146
Ferredoxin subunit of nitrite reductase or a ring-hydroxylating dioxygenase [Inorganic ion ...
 5-106 2.52e-20

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: 78.34  E-value: 2.52e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516431175   5 TKVKLCQLDDLMPFIGATVLIEGEHVALFYiPDSGVYAVQDWDPIGKAYVmSRGIVgdiDGEmCVASPLYKQHFSLKSGQ 84
Cdd:COG2146    2 SEVKVCALDDLPEGGGVVVEVGGKQIAVFR-TDGEVYAYDNRCPHQGAPL-SEGIV---DGG-VVTCPLHGARFDLRTGE 75

                         90       100
                 ....*....|....*....|...
gi 516431175  85 CLEDEA-HCLKTWQVTVDDNQVC 106
Cdd:COG2146   76 CLGGPAtEPLKTYPVRVEDGDVY 98
 
Name Accession Description Interval E-value
Rieske_NirD cd03529
Assimilatory nitrite reductase (NirD) family, Rieske domain; Assimilatory nitrate and nitrite ...
 7-105 4.89e-56

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: 168.84  E-value: 4.89e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516431175   7 VKLCQLDDLMPFIGATVLIEGEHVALFYIPDSGVYAVQDWDPIGKAYVMSRGIVGDIDGEMCVASPLYKQHFSLKSGQCL 86
Cdd:cd03529    2 QTVCALDDLPPGSGVAALVGDTQIAIFRLPGREVYAVQNMDPHSRANVLSRGIVGDIGGEPVVASPLYKQHFSLKTGRCL 81

                         90
                 ....*....|....*....
gi 516431175  87 EDEAHCLKTWQVTVDDNQV 105
Cdd:cd03529   82 EDEDVSVATFPVRVEDGEV 100
Rieske_2 pfam13806
Rieske-like [2Fe-2S] domain;
7-105 7.53e-45

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


Pssm-ID: 433491 [Multi-domain]  Cd Length: 103  Bit Score: 140.77  E-value: 7.53e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516431175    7 VKLCQLDDLMPFIGATVLIEGEHVALFYIPDSGVYAVQDWDPIGKAYVMSRGIVGDIDGEMCVASPLYKQHFSLKSGQCL 86
Cdd:pfam13806   2 TPVCALDDLPPGTGVCALVGGRQVAVFRLEDGQVYAIDNRDPFSGANVLSRGIVGDLGGELVVASPLYKQHFDLKTGECL 81

                          90
                  ....*....|....*....
gi 516431175   87 EDEAHCLKTWQVTVDDNQV 105
Cdd:pfam13806  82 EDPEVSVPVYPVRVRDGNV 100
nirD_assim_sml TIGR02378
nitrite reductase [NAD(P)H], small subunit; This model describes NirD, the small subunit of ...
 5-105 1.75e-40

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: 129.74  E-value: 1.75e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516431175    5 TKVKLCQLDDLMPFIGATVLIEGEHVALFYIPDSGVYAVQDWDPIGKAYVMSRGIVGDIDGEMCVASPLYKQHFSLKSGQ 84
Cdd:TIGR02378   1 TWQDICAIDDIPEETGVCVLLGDTQIAIFRVPGDQVFAIQNMCPHKRAFVLSRGIVGDAQGELWVACPLHKRNFRLEDGR 80

                          90       100
                  ....*....|....*....|.
gi 516431175   85 CLEDEAHCLKTWQVTVDDNQV 105
Cdd:TIGR02378  81 CLEDDSGSVRTYEVRVEDGRV 101
nirD PRK09511
nitrite reductase small subunit NirD;
7-105 1.59e-33

nitrite reductase small subunit NirD;


Pssm-ID: 181921  Cd Length: 108  Bit Score: 112.05  E-value: 1.59e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516431175   7 VKLCQLDDLMPFIGATVLIEGEHVALFYiP--DSGVYAVQDWDPIGKAYVMSRGIVGDIDGEMCVASPLYKQHFSLKSGQ 84
Cdd:PRK09511   5 KDICKIDDILPGTGVCALVGDEQVAIFR-PyhDEQVFAISNIDPFFQASVLSRGLIAEHQGELWVASPLKKQRFRLSDGL 83

                         90       100
                 ....*....|....*....|.
gi 516431175  85 CLEDEAHCLKTWQVTVDDNQV 105
Cdd:PRK09511  84 CMEDEQFSVKHYDARVKDGVV 104
NirD COG2146
Ferredoxin subunit of nitrite reductase or a ring-hydroxylating dioxygenase [Inorganic ion ...
 5-106 2.52e-20

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: 78.34  E-value: 2.52e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516431175   5 TKVKLCQLDDLMPFIGATVLIEGEHVALFYiPDSGVYAVQDWDPIGKAYVmSRGIVgdiDGEmCVASPLYKQHFSLKSGQ 84
Cdd:COG2146    2 SEVKVCALDDLPEGGGVVVEVGGKQIAVFR-TDGEVYAYDNRCPHQGAPL-SEGIV---DGG-VVTCPLHGARFDLRTGE 75

                         90       100
                 ....*....|....*....|...
gi 516431175  85 CLEDEA-HCLKTWQVTVDDNQVC 106
Cdd:COG2146   76 CLGGPAtEPLKTYPVRVEDGDVY 98
Rieske_NirD_small_Bacillus cd03530
Small subunit of nitrite reductase (NirD) family, Rieske domain; composed of proteins similar ...
 6-105 1.17e-13

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: 61.47  E-value: 1.17e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516431175   6 KVKLCQLDDLMPFIGATVLIEGEHVALFYIPDSGVYAVQDWDPiGKAYVMSRGIVGDIdgemCVASPLYKQHFSLKSGQC 85
Cdd:cd03530    1 WIDIGALEDIPPRGARKVQTGGGEIAVFRTADDEVFALENRCP-HKGGPLSEGIVHGE----YVTCPLHNWVIDLETGEA 75

                         90       100
                 ....*....|....*....|
gi 516431175  86 LEDEAHCLKTWQVTVDDNQV 105
Cdd:cd03530   76 QGPDEGCVRTFPVKVEDGRV 95
Rieske_RO_ferredoxin cd03528
Rieske non-heme iron oxygenase (RO) family, Rieske ferredoxin component; composed of the ...
 6-106 2.84e-04

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: 37.08  E-value: 2.84e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516431175   6 KVKLCQLDDLMPFIGATVLIEGEHVALFYIPDsGVYAVQDWDPIGKAYvMSRGIVgdiDGEmCVASPLYKQHFSLKSGQC 85
Cdd:cd03528    1 WVRVCAVDELPEGEPKRVDVGGRPIAVYRVDG-EFYATDDLCTHGDAS-LSEGYV---EGG-VIECPLHGGRFDLRTGKA 74

                         90       100
                 ....*....|....*....|..
gi 516431175  86 LEDEA-HCLKTWQVTVDDNQVC 106
Cdd:cd03528   75 LSLPAtEPLKTYPVKVEDGDVY 96
Rieske cd03467
Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron ...
 7-105 1.41e-03

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: 35.16  E-value: 1.41e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516431175   7 VKLCQLDDLMPFIGATVLIEGEHVALFYIPDSGVYAvqdWDPI---GKAYVMSRGIVGDidgemCVASPLYKQHFSLKSG 83
Cdd:cd03467    2 VVVGALSELPPGGGRVVVVGGGPVVVVRREGGEVYA---LSNRcthQGCPLSEGEGEDG-----CIVCPCHGSRFDLRTG 73

                         90       100
                 ....*....|....*....|...
gi 516431175  84 QCLEDEA-HCLKTWQVTVDDNQV 105
Cdd:cd03467   74 EVVSGPApRPLPKYPVKVEGDGV 96
 
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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