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Conserved domains on  [gi|937904943|dbj|BAS79997|]
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Os02g0642300, partial [Oryza sativa Japonica Group]

Protein Classification

cytochrome b family protein( domain architecture ID 581032)

cytochrome b family protein such as formate dehydrogenase subunit gamma or cytochrome b, a component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex), a respiratory chain that generates an electrochemical potential coupled to ATP synthesis.

Gene Ontology:  GO:0046872|GO:0016491

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Cytochrome_b_N super family cl23723
Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit ...
 1-93 2.45e-37

Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria, cytochrome b6 is analogous to eukaryote cytochrome b, containing two chains: helices A-D are encoded by the petB gene and helices E-H are encoded by the petD gene in these organisms. Cytochrome b/b6 contains two bound hemes and two ubiquinol/ubiquinone binding sites. The C-terminal portion of cytochrome b is described in a separate CD.


The actual alignment was detected with superfamily member PLN02810:

Pssm-ID: 474033  Cd Length: 231  Bit Score: 125.32  E-value: 2.45e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937904943   1 QWIFGFVAFFFPRASPSVRKGVLPWHILFGLFVYILALATAELGFLEKLTFLQSSGLDKYGAEAFLVNFTALIVVLFGAS 80
Cdd:PLN02810 131 QWIYGFIVFFFPGGSTNLRSGSLPWHVLFGLFVYILAVGNAALGFLEKLTFLESGGLDKYGSEALLVNFTAIITILYGAF 210

                         90
                 ....*....|...
gi 937904943  81 VVVAAVSPARVEE 93
Cdd:PLN02810 211 VVLTALAQSPSDE 223
 
Name Accession Description Interval E-value
PLN02810 PLN02810
carbon-monoxide oxygenase
 1-93 2.45e-37

carbon-monoxide oxygenase


Pssm-ID: 178406  Cd Length: 231  Bit Score: 125.32  E-value: 2.45e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937904943   1 QWIFGFVAFFFPRASPSVRKGVLPWHILFGLFVYILALATAELGFLEKLTFLQSSGLDKYGAEAFLVNFTALIVVLFGAS 80
Cdd:PLN02810 131 QWIYGFIVFFFPGGSTNLRSGSLPWHVLFGLFVYILAVGNAALGFLEKLTFLESGGLDKYGSEALLVNFTAIITILYGAF 210

                         90
                 ....*....|...
gi 937904943  81 VVVAAVSPARVEE 93
Cdd:PLN02810 211 VVLTALAQSPSDE 223
Cyt_b561_ACYB-1_like cd08766
Plant cytochrome b(561), including the carbon monoxide oxygenase ACYB-1; Cytochrome b(561), as ...
 1-53 7.00e-23

Plant cytochrome b(561), including the carbon monoxide oxygenase ACYB-1; Cytochrome b(561), as found in plants, similar to the Arabidopsis thaliana ACYB-1 gene product, a cytochrome b561 isoform localized to the tonoplast. This protein might act as a ferric-chelate reductase, catalyzing the reduction of Fe(3+) to Fe(2+), and might be capable of trans-membrane electron transport from intracellular ascorbate to extracellular ferric chelates. It is assumed that this protein uses ascorbate as the electron donor. Belongs to the cytochrome b(561) family, which are secretory vesicle-specific electron transport proteins. Cytochromes b(561) are integral membrane proteins that bind two heme groups non-covalently, and may have six alpha-helical trans-membrane segments.


Pssm-ID: 176496  Cd Length: 144  Bit Score: 85.82  E-value: 7.00e-23
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 937904943   1 QWIFGFVAFFFPRASPSVRKGVLPWHILFGLFVYILALATAELGFLEKLTFLQ 53
Cdd:cd08766   92 QWLFGFVTFWFPGASRNTRAALLPWHVFLGLAIYYLAIATAETGLLEKLTFLQ 144
Cytochrom_B561 pfam03188
Eukaryotic cytochrome b561; Cytochrome b561 is a secretory vesicle-specific electron transport ...
 1-52 1.42e-16

Eukaryotic cytochrome b561; Cytochrome b561 is a secretory vesicle-specific electron transport protein. It is an integral membrane protein, that binds two heme groups non-covalently. This is a eukaryotic family. Members of the 'prokaryotic cytochrome b561' family can be found in Pfam: PF01292.


Pssm-ID: 427188  Cd Length: 137  Bit Score: 69.56  E-value: 1.42e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 937904943    1 QWIFGFVAFFFPRASPSVRKGVLPWHILFGLFVYILALATAELGFLEKLTFL 52
Cdd:pfam03188  86 QWVGGFVTFLFPGLSKRIRPLLLPLHVFFGLVIFVLAIVTALLGLLEKLIFQ 137
B561 smart00665
Cytochrome b-561 / ferric reductase transmembrane domain; Cytochrome b-561 recycles ascorbate ...
 1-45 2.20e-09

Cytochrome b-561 / ferric reductase transmembrane domain; Cytochrome b-561 recycles ascorbate for the generation of norepinephrine by dopamine-beta-hydroxylase in the chromaffin vesicles of the adrenal gland. It is a transmembrane heme protein with the two heme groups being bound to conserved histidine residues. A cytochrome b-561 homologue, termed Dcytb, is an iron-regulated ferric reductase in the duodenal mucosa. Other homologues of these are also likely to be ferric reductases. SDR2 is proposed to be important in regulating the metabolism of iron in the onset of neurodegenerative disorders.


Pssm-ID: 214769  Cd Length: 129  Bit Score: 50.69  E-value: 2.20e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 937904943     1 QWIFGFVAFFFPRASPSVRKGVLPWHILFGLFVYILALATAELGF 45
Cdd:smart00665  85 QWLSGFLRPLPPGLPSKYRSYLNPYHRFVGLAAFILAIVTIFLGL 129
 
Name Accession Description Interval E-value
PLN02810 PLN02810
carbon-monoxide oxygenase
 1-93 2.45e-37

carbon-monoxide oxygenase


Pssm-ID: 178406  Cd Length: 231  Bit Score: 125.32  E-value: 2.45e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937904943   1 QWIFGFVAFFFPRASPSVRKGVLPWHILFGLFVYILALATAELGFLEKLTFLQSSGLDKYGAEAFLVNFTALIVVLFGAS 80
Cdd:PLN02810 131 QWIYGFIVFFFPGGSTNLRSGSLPWHVLFGLFVYILAVGNAALGFLEKLTFLESGGLDKYGSEALLVNFTAIITILYGAF 210

                         90
                 ....*....|...
gi 937904943  81 VVVAAVSPARVEE 93
Cdd:PLN02810 211 VVLTALAQSPSDE 223
Cyt_b561_ACYB-1_like cd08766
Plant cytochrome b(561), including the carbon monoxide oxygenase ACYB-1; Cytochrome b(561), as ...
 1-53 7.00e-23

Plant cytochrome b(561), including the carbon monoxide oxygenase ACYB-1; Cytochrome b(561), as found in plants, similar to the Arabidopsis thaliana ACYB-1 gene product, a cytochrome b561 isoform localized to the tonoplast. This protein might act as a ferric-chelate reductase, catalyzing the reduction of Fe(3+) to Fe(2+), and might be capable of trans-membrane electron transport from intracellular ascorbate to extracellular ferric chelates. It is assumed that this protein uses ascorbate as the electron donor. Belongs to the cytochrome b(561) family, which are secretory vesicle-specific electron transport proteins. Cytochromes b(561) are integral membrane proteins that bind two heme groups non-covalently, and may have six alpha-helical trans-membrane segments.


Pssm-ID: 176496  Cd Length: 144  Bit Score: 85.82  E-value: 7.00e-23
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 937904943   1 QWIFGFVAFFFPRASPSVRKGVLPWHILFGLFVYILALATAELGFLEKLTFLQ 53
Cdd:cd08766   92 QWLFGFVTFWFPGASRNTRAALLPWHVFLGLAIYYLAIATAETGLLEKLTFLQ 144
PLN02680 PLN02680
carbon-monoxide oxygenase
 1-89 1.84e-21

carbon-monoxide oxygenase


Pssm-ID: 215365  Cd Length: 232  Bit Score: 84.47  E-value: 1.84e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937904943   1 QWIFGFVAFFFPRASPSVRKGVLPWHILFGLFVYILALATAELGFLEKLTFLQSSG-LDKYGAEAFLVNFTALIVVLFGA 79
Cdd:PLN02680 131 QWAAGFVTFWYPGGSRNSRASLLPWHVFFGIYIYALAVATATTGILEKATFLQSNKvISRYSTEAMLVNSLGILIVVLGG 210

                         90
                 ....*....|
gi 937904943  80 SVVVAAVSPA 89
Cdd:PLN02680 211 FVILAIVTPL 220
PLN02351 PLN02351
cytochromes b561 family protein
 1-88 9.83e-19

cytochromes b561 family protein


Pssm-ID: 215201  Cd Length: 242  Bit Score: 77.64  E-value: 9.83e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937904943   1 QWIFGFVAFFFPRASPSVRKGVLPWHILFGLFVYILALATAELGFLEKLTFLQSS-GLDKYGAEAFLVNFTALIVVLFGA 79
Cdd:PLN02351 134 QWLTGFMSFWHRGEMRTTRTTVLPWHVFLGLYTYGLAVATAETGLLEKLTFLQTKrNVSKHGSESMVVNGLGLGLALLSG 213


                 ....*....
gi 937904943  80 SVVVAAVSP 88
Cdd:PLN02351 214 IVILAAVLP 222
Cytochrom_B561 pfam03188
Eukaryotic cytochrome b561; Cytochrome b561 is a secretory vesicle-specific electron transport ...
 1-52 1.42e-16

Eukaryotic cytochrome b561; Cytochrome b561 is a secretory vesicle-specific electron transport protein. It is an integral membrane protein, that binds two heme groups non-covalently. This is a eukaryotic family. Members of the 'prokaryotic cytochrome b561' family can be found in Pfam: PF01292.


Pssm-ID: 427188  Cd Length: 137  Bit Score: 69.56  E-value: 1.42e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 937904943    1 QWIFGFVAFFFPRASPSVRKGVLPWHILFGLFVYILALATAELGFLEKLTFL 52
Cdd:pfam03188  86 QWVGGFVTFLFPGLSKRIRPLLLPLHVFFGLVIFVLAIVTALLGLLEKLIFQ 137
Cyt_b561_CG1275_like cd08764
Non-vertebrate eumetazoan cytochrome b(561); Cytochrome b(561), as found in non-vertebrate ...
 1-103 3.87e-15

Non-vertebrate eumetazoan cytochrome b(561); Cytochrome b(561), as found in non-vertebrate eumetazoans, similar to the Drosophila melanogaster CG1275 gene product. This protein might act as a ferric-chelate reductase, catalyzing the reduction of Fe(3+) to Fe(2+), such as associated with the transport of iron from the endosome to the cytoplasm. It is assumed that this protein uses ascorbate as the electron donor. Belongs to the cytochrome b(561) family, which are secretory vesicle-specific electron transport proteins. Cytochromes b(561) are integral membrane proteins that bind two heme groups non-covalently, and may have six alpha-helical trans-membrane segments.


Pssm-ID: 176494  Cd Length: 214  Bit Score: 67.36  E-value: 3.87e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937904943   1 QWIFGFVAFFFPRASPSVRKGVLPWHILFGLFVYILALATAELGFLEKLTFLQSSgLDKYGAEAFLVNFTALIVVLFGAS 80
Cdd:cd08764  111 QWVGGFVSFLFPGLPETLRAAYLPLHVFFGLFIFVLAVATALLGITEKAFFSLNK-YSNLPAEGVLGNFIGIVLVIFGGL 189

                         90       100
                 ....*....|....*....|....*
gi 937904943  81 VV--VAAVSPARVEEPHEYAPIPES 103
Cdd:cd08764  190 VVylVTEPDYKRIELPEEEELLIQN 214
B561 smart00665
Cytochrome b-561 / ferric reductase transmembrane domain; Cytochrome b-561 recycles ascorbate ...
 1-45 2.20e-09

Cytochrome b-561 / ferric reductase transmembrane domain; Cytochrome b-561 recycles ascorbate for the generation of norepinephrine by dopamine-beta-hydroxylase in the chromaffin vesicles of the adrenal gland. It is a transmembrane heme protein with the two heme groups being bound to conserved histidine residues. A cytochrome b-561 homologue, termed Dcytb, is an iron-regulated ferric reductase in the duodenal mucosa. Other homologues of these are also likely to be ferric reductases. SDR2 is proposed to be important in regulating the metabolism of iron in the onset of neurodegenerative disorders.


Pssm-ID: 214769  Cd Length: 129  Bit Score: 50.69  E-value: 2.20e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 937904943     1 QWIFGFVAFFFPRASPSVRKGVLPWHILFGLFVYILALATAELGF 45
Cdd:smart00665  85 QWLSGFLRPLPPGLPSKYRSYLNPYHRFVGLAAFILAIVTIFLGL 129
Cyt_b561_CYB561 cd08763
Vertebrate cytochrome b(561), CYB561 gene product; Cytochrome b(561), as found in vertebrates, ...
 1-51 1.45e-07

Vertebrate cytochrome b(561), CYB561 gene product; Cytochrome b(561), as found in vertebrates, which might act as a ferric-chelate reductase, catalyzing the reduction of Fe(3+) to Fe(2+), such as associated with the transport of iron from the endosome to the cytoplasm. It is assumed that this protein uses ascorbate as the electron donor. Belongs to the cytochrome b(561) family, which are secretory vesicle-specific electron transport proteins. Cytochromes b(561) are integral membrane proteins that bind two heme groups non-covalently, and may have six alpha-helical trans-membrane segments.


Pssm-ID: 176493  Cd Length: 143  Bit Score: 46.35  E-value: 1.45e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 937904943   1 QWIFGFVAFFFPRASPSVRKGVLPWHILFGLFVYILALATAELGFLEKLTF 51
Cdd:cd08763   92 QWLIGFSFFLFPGASFTLRSQYKPLHEFFGRALFLSSVGTSLLGLTEKLLF 142
Cyt_b561 cd08554
Eukaryotic cytochrome b(561); Cytochrome b(561) is a family of endosomal or secretory ...
 1-45 1.92e-07

Eukaryotic cytochrome b(561); Cytochrome b(561) is a family of endosomal or secretory vesicle-specific electron transport proteins. They are integral membrane proteins that bind two heme groups non-covalently, and may have six alpha-helical trans-membrane segments. This is an exclusively eukaryotic family. Members of the prokaryotic cytochrome b561 family are not deemed homologous.


Pssm-ID: 176489  Cd Length: 131  Bit Score: 45.74  E-value: 1.92e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 937904943   1 QWIFGFVAFFFPRASPSVRKGVLPWHILFGLFVYILALATAELGF 45
Cdd:cd08554   87 QFLSGFVLFLLPLLRLSYRSSLLPFHRFFGLAIFVLAIATILLGI 131
Cyt_b561_CYBRD1 cd08765
Vertebrate cytochrome b(561), CYBRD1 gene product; Duodenal cytochrome b or ferric-chelate ...
 1-51 2.06e-05

Vertebrate cytochrome b(561), CYBRD1 gene product; Duodenal cytochrome b or ferric-chelate reductase 3, a cytochrome b(561), as found in vertebrates, which might act as a ferric-chelate reductase, catalyzing the reduction of Fe(3+) to Fe(2+), such as associated with the transport of iron from the endosome to the cytoplasm. It is assumed that this protein uses ascorbate as the electron donor. This protein is expressed at the brush border of duodenal enterocytes and may play a role in the uptake of dietary Fe(3+), facilitating its transport into the mucosal cells. It may also be involved in the recycling of extracellular ascorbate in erythrocyte membranes, and act as a ferrireductase in epithelial cells of the respiratory system. Belongs to the cytochrome b(561) family, which are secretory vesicle-specific electron transport proteins. Cytochromes b(561) are integral membrane proteins that bind two heme groups non-covalently, and may have six alpha-helical trans-membrane segments.


Pssm-ID: 176495  Cd Length: 153  Bit Score: 40.65  E-value: 2.06e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 937904943   1 QWIFGFVAFFFPRASPSVRKGVLPWHILFGLFVYILALATAELGFLEKLTF 51
Cdd:cd08765   99 QLVLGISVYLLPVAPVRLRAALMPLHVYSGLFIFGTVIATALMGITEKLIF 149
 
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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