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Conserved domains on  [gi|304556499|gb|ADM35606|]
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PsbA, partial (chloroplast) [uncultured Corallinales]

Protein Classification

photosynthetic reaction center family protein( domain architecture ID 607)

photosynthetic reaction center family protein is a subunit of a photosynthetic system that utilizes light-induced electron transfer to generate protons that power reactions such as the synthesis of ATP, similar to photosystem II protein D

Gene Ontology:  GO:0045156|GO:0009772|GO:0016168|GO:0046872
PubMed:  15313239|11115630

Graphical summary

 Zoom to residue level

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List of domain hits

 Name Accession Description Interval E-value
Photo_RC super family cl08220
D1, D2 subunits of photosystem II (PSII); M, L subunits of bacterial photosynthetic reaction ...
 1-196 1.61e-132

D1, D2 subunits of photosystem II (PSII); M, L subunits of bacterial photosynthetic reaction center; This protein superfamily contains the D1, D2 subunits of the photosystem II (PS II) and the M, L subunits of the bacterial photosynthetic reaction center (RC). These four proteins are highly homologous and share a common fold. PS II is a multi-subunit protein found in the photosynthetic membranes of plants, algae, and cyanobacteria. It utilizes light-induced electron transfer and water-splitting reactions to produce protons, electrons, and molecular oxygen. The protons generated are instrumental in ATP formation. Bacterial photosynthetic reaction center (RC) complex is found in photosynthetic bacteria, such as purple bacteria and other proteobacteria species. It couples light-induced electron transfer to proton pumping across the membrane by reactions of a quinone molecule (QB) that binds two electrons and two protons at the active site. Protons are translocated from the bacterial cytoplasm to the periplasmic space, generating an electrochemical gradient of protons (the protonmotive force) that can be used to power reactions such as the synthesis of ATP.


The actual alignment was detected with superfamily member TIGR01151:

Pssm-ID: 447584 [Multi-domain]  Cd Length: 360  Bit Score: 375.81  E-value: 1.61e-132
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304556499    1 IGWFGVLMIPTLLTATSVFIIAFVAAPPVDIDGIREPVAGSLLYGNNIISGAIIPSSAAIGIHFYPIWEAASLDEWLYNG 80
Cdd:TIGR01151  30 IGWFGVLMIPTLLTATSCFIIAFIAAPPVDIDGIREPVAGSLLYGNNIISGAVVPSSNAIGLHFYPIWEAASLDEWLYNG 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304556499   81 GPYELIVLHFLLGVCCYIGREWELSYRLGMRPWISVAFTAPVAAAAAVFLIYPIGQGSFSDGMPLGISGTFNFMLVFQAE 160
Cdd:TIGR01151 110 GPYQLIVFHFLLGVACYMGREWELSYRLGMRPWICVAYSAPVAAATAVFLIYPIGQGSFSDGMPLGISGTFNFMIVFQAE 189

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 304556499  161 HNILMHPFHQLGVAGVFGGSLFSAMHGSLVTSSLIR 196
Cdd:TIGR01151 190 HNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLIR 225
 
Name Accession Description Interval E-value
psbA TIGR01151
photosystem II, DI subunit (also called Q(B)); This model describes the Photosystem II, DI ...
 1-196 1.61e-132

photosystem II, DI subunit (also called Q(B)); This model describes the Photosystem II, DI subunit (also called Q(B)) in bacterial and its equivalents in chloroplast of algae and higher plants. Photosystem II is many ways functionally equivalent to bacterial reaction center. At the core of Photosystem II are several light harvesting cofactors including plastoquinones, pheophytins, phyloquinones etc. These cofactors are intimately associated with the polypeptides, which principally including subunits DI, DII, Cyt.b, Cyt.f and iron-sulphur protein. Together they participate in the electron transfer reactions that lead to the net production of the reducting equivalents in the form of NADPH, which are used for reduction of CO2 to carbohydrates(C6H1206). Phosystem II operates during oxygenic photosynthesis and principal electron donor is H2O. Although no structural data is presently available, a huge body of literature exits that describes function using a variety of biochemical and biophysical techniques. [Energy metabolism, Electron transport, Energy metabolism, Photosynthesis]


Pssm-ID: 130221 [Multi-domain]  Cd Length: 360  Bit Score: 375.81  E-value: 1.61e-132
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304556499    1 IGWFGVLMIPTLLTATSVFIIAFVAAPPVDIDGIREPVAGSLLYGNNIISGAIIPSSAAIGIHFYPIWEAASLDEWLYNG 80
Cdd:TIGR01151  30 IGWFGVLMIPTLLTATSCFIIAFIAAPPVDIDGIREPVAGSLLYGNNIISGAVVPSSNAIGLHFYPIWEAASLDEWLYNG 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304556499   81 GPYELIVLHFLLGVCCYIGREWELSYRLGMRPWISVAFTAPVAAAAAVFLIYPIGQGSFSDGMPLGISGTFNFMLVFQAE 160
Cdd:TIGR01151 110 GPYQLIVFHFLLGVACYMGREWELSYRLGMRPWICVAYSAPVAAATAVFLIYPIGQGSFSDGMPLGISGTFNFMIVFQAE 189

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 304556499  161 HNILMHPFHQLGVAGVFGGSLFSAMHGSLVTSSLIR 196
Cdd:TIGR01151 190 HNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLIR 225
Photosystem-II_D1 cd09289
D1 subunit of photosystem II (PS II); Photosystem II (PS II), D2 subunit. PS II is a ...
 1-196 2.40e-131

D1 subunit of photosystem II (PS II); Photosystem II (PS II), D2 subunit. PS II is a multi-subunit protein found in the photosynthetic membranes of plants, algae, and cyanobacteria. It utilizes light-induced electron transfer and water-splitting reactions to produce protons, electrons, and molecular oxygen. The protons generated are instrumental in ATP formation. Molecular dioxygen is released as a by-product. PS II can be described as containing two parts: the photochemical part and the catalytic part. The photochemical portion promotes the fast, efficient light-induced charge separation and stabilization that occur when light is absorbed by chlorophyll. The catalytic portion, where water is oxidized, involves a cluster of Mn ions close to a redox-active tyrosine residue. The Mn cluster and its ligands form a functional unit called the oxygen-evolving complex (OEC) or the water-oxidizing complex (WOC). The D1 and D2 subunits are a pair of interwined polypeptides. They contain all the cofactors involved directly in water oxidation and plastoquinone reduction. The D1 subunit contains the Mn cluster that constitutes the site of water oxidation. D1 and D2 are highly homologous and are also similar to the L and M proteins in bacterial photosynthetic reaction centers.


Pssm-ID: 187747  Cd Length: 338  Bit Score: 371.91  E-value: 2.40e-131
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304556499   1 IGWFGVLMIPTLLTATSVFIIAFVAAPPVDIDGIREPVAGSLLYGNNIISGAIIPSSAAIGIHFYPIWEAASLDEWLYNG 80
Cdd:cd09289   24 IGWFGVLMIPTLLTATSVFIIAFIAAPPVDIDGIREPVSGSLLYGNNIISGAVVPTSNAIGLHFYPIWEAASLDEWLYNG 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304556499  81 GPYELIVLHFLLGVCCYIGREWELSYRLGMRPWISVAFTAPVAAAAAVFLIYPIGQGSFSDGMPLGISGTFNFMLVFQAE 160
Cdd:cd09289  104 GPYQLIVLHFLLGVCCYMGREWELSYRLGMRPWIAVAYSAPVAAATAVFLIYPIGQGSFSDGMPLGISGTFNFMIVFQAE 183

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 304556499 161 HNILMHPFHQLGVAGVFGGSLFSAMHGSLVTSSLIR 196
Cdd:cd09289  184 HNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLIR 219
PLN00056 PLN00056
photosystem Q(B) protein; Provisional
 1-196 7.10e-116

photosystem Q(B) protein; Provisional


Pssm-ID: 177687  Cd Length: 353  Bit Score: 333.25  E-value: 7.10e-116
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304556499   1 IGWFGVLMIPTLLTATSVFIIAFVAAPPVDIDGIREPVAGSLLYGNNIISGAIIPSSAAIGIHFYPIWEAASLDEWLYNG 80
Cdd:PLN00056  30 IGWFGVLMIPTLLTATSVFIIAFIAAPPVDIDGIREPVSGSLLYGNNIISGAIIPTSAAIGLHFYPIWEAASVDEWLYNG 109

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304556499  81 GPYELIVLHFLLGVCCYIGREWELSYRLGMRPWISVAFTAPVAAAAAVFLIYPIGQGSFSDGMPLGISGTFNFMLVFQAE 160
Cdd:PLN00056 110 GPYELIVLHFLLGVACYMGREWELSFRLGMRPWIAVAYSAPVAAATAVFLIYPIGQGSFSDGMPLGISGTFNFMIVFQAE 189

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 304556499 161 HNILMHPFHQLGVAGVFGGSLFSAMHGSLVTSSLIR 196
Cdd:PLN00056 190 HNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLIR 225
PsbA COG5716
Photosystem II reaction center D1, PsbA [Energy production and conversion]; Photosystem II ...
 1-196 1.08e-110

Photosystem II reaction center D1, PsbA [Energy production and conversion]; Photosystem II reaction center D1, PsbA is part of the Pathway/BioSystem: Photosystem II


Pssm-ID: 444426  Cd Length: 356  Bit Score: 320.12  E-value: 1.08e-110
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304556499   1 IGWFGVLMIPTLLTATSVFIIAFVAAPPVDIDGIREPVAGSLLYGNNIISGAIIPSSAAIGIHFYPIWEAASLDEWLYNG 80
Cdd:COG5716   33 LGWFGVLMIPTLLTAFIIFGIAFLAAPPVDMDGIREPVIGSLLFGNNLITAAVEPPSPAIGLHFYPIWEAASMDEWLYNG 112

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304556499  81 GPYELIVLHFLLGVCCYIGREWELSYRLGMRPWISVAFTAPVAAAAAVFLIYPIGQGSFSDGMPLGISGTFNFMLVFQAE 160
Cdd:COG5716  113 GPYQLIVFHFLIGIWAYWGRTWELSYRLGMRPWIAWAFAAPVAAATSVGLVYPIGQGSFSEGVPLGIFGTFDFMLAFQAD 192

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 304556499 161 HNILMHPFHQLGVAGVFGGSLFSAMHGSLVTSSLIR 196
Cdd:COG5716  193 HNILMNPFHMLGVAGVYGGALLFAMHGSLVTSVLRR 228
Photo_RC pfam00124
Photosynthetic reaction centre protein;
1-196 9.00e-66

Photosynthetic reaction centre protein;


Pssm-ID: 425477  Cd Length: 260  Bit Score: 202.86  E-value: 9.00e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304556499    1 IGWFGVLMIPTLLTATSVFIIAFVAAPPVDIdgirepvaGSLLYGNNIISGAIIPSSAAIGIHFYPIWeaasldewlyNG 80
Cdd:pfam00124   3 VGFFGVLSIPTALLATFIIGIGFVAAPSVDW--------SPLLFGRNLITLAIEPPSPSYGLSFPPLW----------EG 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304556499   81 GPYELIVLHFLLGVCCYIGREWELSYRLGMRPWISVAFTAPVAAAAAVFLIYPIGQGSFSDGMPLGISGTFNFMLVFQAE 160
Cdd:pfam00124  65 GLWQIITFHATIAFISWWLREYEIARKLGMGPHIAWAFSAAIAAYLSLGLIRPILMGSWSEGFPLGIFPHLDWTSNFSYR 144

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 304556499  161 H-NILMHPFHQLGVAGVFGGSLFSAMHGSLVTSSLIR 196
Cdd:pfam00124 145 YgNFLYNPFHMLGIAFLFGSALLLAMHGALVLSVLRP 181
 
Name Accession Description Interval E-value
psbA TIGR01151
photosystem II, DI subunit (also called Q(B)); This model describes the Photosystem II, DI ...
 1-196 1.61e-132

photosystem II, DI subunit (also called Q(B)); This model describes the Photosystem II, DI subunit (also called Q(B)) in bacterial and its equivalents in chloroplast of algae and higher plants. Photosystem II is many ways functionally equivalent to bacterial reaction center. At the core of Photosystem II are several light harvesting cofactors including plastoquinones, pheophytins, phyloquinones etc. These cofactors are intimately associated with the polypeptides, which principally including subunits DI, DII, Cyt.b, Cyt.f and iron-sulphur protein. Together they participate in the electron transfer reactions that lead to the net production of the reducting equivalents in the form of NADPH, which are used for reduction of CO2 to carbohydrates(C6H1206). Phosystem II operates during oxygenic photosynthesis and principal electron donor is H2O. Although no structural data is presently available, a huge body of literature exits that describes function using a variety of biochemical and biophysical techniques. [Energy metabolism, Electron transport, Energy metabolism, Photosynthesis]


Pssm-ID: 130221 [Multi-domain]  Cd Length: 360  Bit Score: 375.81  E-value: 1.61e-132
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304556499    1 IGWFGVLMIPTLLTATSVFIIAFVAAPPVDIDGIREPVAGSLLYGNNIISGAIIPSSAAIGIHFYPIWEAASLDEWLYNG 80
Cdd:TIGR01151  30 IGWFGVLMIPTLLTATSCFIIAFIAAPPVDIDGIREPVAGSLLYGNNIISGAVVPSSNAIGLHFYPIWEAASLDEWLYNG 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304556499   81 GPYELIVLHFLLGVCCYIGREWELSYRLGMRPWISVAFTAPVAAAAAVFLIYPIGQGSFSDGMPLGISGTFNFMLVFQAE 160
Cdd:TIGR01151 110 GPYQLIVFHFLLGVACYMGREWELSYRLGMRPWICVAYSAPVAAATAVFLIYPIGQGSFSDGMPLGISGTFNFMIVFQAE 189

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 304556499  161 HNILMHPFHQLGVAGVFGGSLFSAMHGSLVTSSLIR 196
Cdd:TIGR01151 190 HNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLIR 225
Photosystem-II_D1 cd09289
D1 subunit of photosystem II (PS II); Photosystem II (PS II), D2 subunit. PS II is a ...
 1-196 2.40e-131

D1 subunit of photosystem II (PS II); Photosystem II (PS II), D2 subunit. PS II is a multi-subunit protein found in the photosynthetic membranes of plants, algae, and cyanobacteria. It utilizes light-induced electron transfer and water-splitting reactions to produce protons, electrons, and molecular oxygen. The protons generated are instrumental in ATP formation. Molecular dioxygen is released as a by-product. PS II can be described as containing two parts: the photochemical part and the catalytic part. The photochemical portion promotes the fast, efficient light-induced charge separation and stabilization that occur when light is absorbed by chlorophyll. The catalytic portion, where water is oxidized, involves a cluster of Mn ions close to a redox-active tyrosine residue. The Mn cluster and its ligands form a functional unit called the oxygen-evolving complex (OEC) or the water-oxidizing complex (WOC). The D1 and D2 subunits are a pair of interwined polypeptides. They contain all the cofactors involved directly in water oxidation and plastoquinone reduction. The D1 subunit contains the Mn cluster that constitutes the site of water oxidation. D1 and D2 are highly homologous and are also similar to the L and M proteins in bacterial photosynthetic reaction centers.


Pssm-ID: 187747  Cd Length: 338  Bit Score: 371.91  E-value: 2.40e-131
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304556499   1 IGWFGVLMIPTLLTATSVFIIAFVAAPPVDIDGIREPVAGSLLYGNNIISGAIIPSSAAIGIHFYPIWEAASLDEWLYNG 80
Cdd:cd09289   24 IGWFGVLMIPTLLTATSVFIIAFIAAPPVDIDGIREPVSGSLLYGNNIISGAVVPTSNAIGLHFYPIWEAASLDEWLYNG 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304556499  81 GPYELIVLHFLLGVCCYIGREWELSYRLGMRPWISVAFTAPVAAAAAVFLIYPIGQGSFSDGMPLGISGTFNFMLVFQAE 160
Cdd:cd09289  104 GPYQLIVLHFLLGVCCYMGREWELSYRLGMRPWIAVAYSAPVAAATAVFLIYPIGQGSFSDGMPLGISGTFNFMIVFQAE 183

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 304556499 161 HNILMHPFHQLGVAGVFGGSLFSAMHGSLVTSSLIR 196
Cdd:cd09289  184 HNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLIR 219
PLN00056 PLN00056
photosystem Q(B) protein; Provisional
 1-196 7.10e-116

photosystem Q(B) protein; Provisional


Pssm-ID: 177687  Cd Length: 353  Bit Score: 333.25  E-value: 7.10e-116
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304556499   1 IGWFGVLMIPTLLTATSVFIIAFVAAPPVDIDGIREPVAGSLLYGNNIISGAIIPSSAAIGIHFYPIWEAASLDEWLYNG 80
Cdd:PLN00056  30 IGWFGVLMIPTLLTATSVFIIAFIAAPPVDIDGIREPVSGSLLYGNNIISGAIIPTSAAIGLHFYPIWEAASVDEWLYNG 109

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304556499  81 GPYELIVLHFLLGVCCYIGREWELSYRLGMRPWISVAFTAPVAAAAAVFLIYPIGQGSFSDGMPLGISGTFNFMLVFQAE 160
Cdd:PLN00056 110 GPYELIVLHFLLGVACYMGREWELSFRLGMRPWIAVAYSAPVAAATAVFLIYPIGQGSFSDGMPLGISGTFNFMIVFQAE 189

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 304556499 161 HNILMHPFHQLGVAGVFGGSLFSAMHGSLVTSSLIR 196
Cdd:PLN00056 190 HNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLIR 225
PsbA COG5716
Photosystem II reaction center D1, PsbA [Energy production and conversion]; Photosystem II ...
 1-196 1.08e-110

Photosystem II reaction center D1, PsbA [Energy production and conversion]; Photosystem II reaction center D1, PsbA is part of the Pathway/BioSystem: Photosystem II


Pssm-ID: 444426  Cd Length: 356  Bit Score: 320.12  E-value: 1.08e-110
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304556499   1 IGWFGVLMIPTLLTATSVFIIAFVAAPPVDIDGIREPVAGSLLYGNNIISGAIIPSSAAIGIHFYPIWEAASLDEWLYNG 80
Cdd:COG5716   33 LGWFGVLMIPTLLTAFIIFGIAFLAAPPVDMDGIREPVIGSLLFGNNLITAAVEPPSPAIGLHFYPIWEAASMDEWLYNG 112

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304556499  81 GPYELIVLHFLLGVCCYIGREWELSYRLGMRPWISVAFTAPVAAAAAVFLIYPIGQGSFSDGMPLGISGTFNFMLVFQAE 160
Cdd:COG5716  113 GPYQLIVFHFLIGIWAYWGRTWELSYRLGMRPWIAWAFAAPVAAATSVGLVYPIGQGSFSEGVPLGIFGTFDFMLAFQAD 192

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 304556499 161 HNILMHPFHQLGVAGVFGGSLFSAMHGSLVTSSLIR 196
Cdd:COG5716  193 HNILMNPFHMLGVAGVYGGALLFAMHGSLVTSVLRR 228
psbA CHL00003
photosystem II protein D1
 1-196 4.20e-105

photosystem II protein D1


Pssm-ID: 176948  Cd Length: 338  Bit Score: 305.27  E-value: 4.20e-105
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304556499   1 IGWFGVLMIPTLLTATSVFIIAFVAAPPVDIDGIREPVAGSLLYGNNIISGAIIPSSAAIGIHFYPIWEAASLDEWLYNG 80
Cdd:CHL00003  24 IGWFGVLMIPTLLTATSVFIIAFIAAPPVDIDGIREPVSGSLLYGNNIISGAIIPSSAAIGLHFYPIWEAASVDEWLYNG 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304556499  81 GPYELIVLHFLLGVCCYIGREWELSYRLGMRPWISVAFTAPVAAAAAVFLIYPIGQGSFSDGMPLGISGTFNFMLVFQAE 160
Cdd:CHL00003 104 GPYELIVLHFLLGVACYMGREWELSFRLGMRPWIAVAYSAPVAAATAVFLIYPIGQGSFSDGMPLGISGTFNFMIVFQAE 183

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 304556499 161 HNILMHPFHQLGVAGVFGGSLFSAMHGSLVTSSLIR 196
Cdd:CHL00003 184 HNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLIR 219
Photo_RC pfam00124
Photosynthetic reaction centre protein;
1-196 9.00e-66

Photosynthetic reaction centre protein;


Pssm-ID: 425477  Cd Length: 260  Bit Score: 202.86  E-value: 9.00e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304556499    1 IGWFGVLMIPTLLTATSVFIIAFVAAPPVDIdgirepvaGSLLYGNNIISGAIIPSSAAIGIHFYPIWeaasldewlyNG 80
Cdd:pfam00124   3 VGFFGVLSIPTALLATFIIGIGFVAAPSVDW--------SPLLFGRNLITLAIEPPSPSYGLSFPPLW----------EG 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304556499   81 GPYELIVLHFLLGVCCYIGREWELSYRLGMRPWISVAFTAPVAAAAAVFLIYPIGQGSFSDGMPLGISGTFNFMLVFQAE 160
Cdd:pfam00124  65 GLWQIITFHATIAFISWWLREYEIARKLGMGPHIAWAFSAAIAAYLSLGLIRPILMGSWSEGFPLGIFPHLDWTSNFSYR 144

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 304556499  161 H-NILMHPFHQLGVAGVFGGSLFSAMHGSLVTSSLIR 196
Cdd:pfam00124 145 YgNFLYNPFHMLGIAFLFGSALLLAMHGALVLSVLRP 181
Photo_RC cd09223
D1, D2 subunits of photosystem II (PSII); M, L subunits of bacterial photosynthetic reaction ...
 76-196 4.01e-37

D1, D2 subunits of photosystem II (PSII); M, L subunits of bacterial photosynthetic reaction center; This protein superfamily contains the D1, D2 subunits of the photosystem II (PS II) and the M, L subunits of the bacterial photosynthetic reaction center (RC). These four proteins are highly homologous and share a common fold. PS II is a multi-subunit protein found in the photosynthetic membranes of plants, algae, and cyanobacteria. It utilizes light-induced electron transfer and water-splitting reactions to produce protons, electrons, and molecular oxygen. The protons generated are instrumental in ATP formation. Bacterial photosynthetic reaction center (RC) complex is found in photosynthetic bacteria, such as purple bacteria and other proteobacteria species. It couples light-induced electron transfer to proton pumping across the membrane by reactions of a quinone molecule (QB) that binds two electrons and two protons at the active site. Protons are translocated from the bacterial cytoplasm to the periplasmic space, generating an electrochemical gradient of protons (the protonmotive force) that can be used to power reactions such as the synthesis of ATP.


Pssm-ID: 187745 [Multi-domain]  Cd Length: 199  Bit Score: 127.57  E-value: 4.01e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304556499  76 WLYNGGPYELIVLHFLLGVCCYIGREWELSYRLGMRPWISVAFTAPVAAAAAVFLIYPIGQGSFSDGMPLGISGTFNFML 155
Cdd:cd09223   20 IGIAGGLWQIITFHALGAFISWMLRQVEIARKLGMGPHIAVAFSAPIASFFVLFLIRPIGQGSWSDAFPYGISSHLDWVN 99

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 304556499 156 VFQAEH-NILMHPFHQLGVAGVFGGSLFSAMHGSLVTSSLIR 196
Cdd:cd09223  100 NFQYEHnNWHYNPFHMLGVAFVFGGALLCAMHGALVLSVLNP 141
Photosystem-II_D2 cd09288
D2 subunit of photosystem II (PS II); Photosystem II (PS II), D2 subunit. PS II is a ...
 1-194 3.63e-25

D2 subunit of photosystem II (PS II); Photosystem II (PS II), D2 subunit. PS II is a multi-subunit protein found in the photosynthetic membranes of plants, algae, and cyanobacteria. It utilizes light-induced electron transfer and water-splitting reactions to produce protons, electrons, and molecular oxygen. The protons generated are instrumental in ATP formation. Molecular dioxygen is released as a by-product. PS II can be described as containing two parts: the photochemical part and the catalytic part. The photochemical portion promotes the fast, efficient light-induced charge separation and stabilization that occur when light is absorbed by chlorophyll. The catalytic portion, where water is oxidized, involves a cluster of Mn ions close to a redox-active tyrosine residue. The Mn cluster and its ligands form a functional unit called the oxygen-evolving complex (OEC) or the water-oxidizing complex (WOC). The D1 and D2 subunits are a pair of intertwined polypeptides. They contain all the cofactors involved directly in water oxidation and plastoquinone reduction. D1 and D2 are highly homologous and are also similar to the L and M proteins in bacterial photosynthetic reaction centers.


Pssm-ID: 187746  Cd Length: 339  Bit Score: 99.67  E-value: 3.63e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304556499   1 IGWFGVLMIPTLLTATSVFIIAFVAAPPVDIDGIrepvAGSLLYGNNIISGAIIPSSAAIGIHFYPIW--EA-ASLDEWL 77
Cdd:cd09288   17 VGWSGLLLFPCAYLALGGWFTGTTFVTSWYTHGL----ASSYLEGCNFLTAAVSTPANSMGHSLLLLWgpEAqGDFTRWC 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304556499  78 YNGGPYELIVLHFLLGVCCYIGREWELSYRLGMRPWISVAFTAPVAAAAAVFLIYPIGQGSFSDGMPLGISGTFNFMLVF 157
Cdd:cd09288   93 QLGGLWTFVALHGAFGLIGFMLRQFEIARSVGIRPYNAIAFSGPIAVFVSVFLIYPLGQSGWFFAPSFGVAAIFRFILFF 172

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 304556499 158 QAEHNILMHPFHQLGVAGVFGGSLFSAMHGSLVTSSL 194
Cdd:cd09288  173 QGFHNWTLNPFHMMGVAGVLGAALLCAIHGATVENTL 209
psbD CHL00004
photosystem II protein D2
 1-194 4.49e-22

photosystem II protein D2


Pssm-ID: 176949  Cd Length: 353  Bit Score: 91.45  E-value: 4.49e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304556499   1 IGWFGVLMIPTLLTATSVFIIAFVAAPPVDIDGIrepvAGSLLYGNNIISGAIIPSSAAIGIHFYPIW--EA-ASLDEWL 77
Cdd:CHL00004  31 VGWSGLLLFPCAYFALGGWFTGTTFVTSWYTHGL----ASSYLEGCNFLTAAVSTPANSLAHSLLLLWgpEAqGDFTRWC 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304556499  78 YNGGPYELIVLHFLLGVCCYIGREWELSYRLGMRPWISVAFTAPVAAAAAVFLIYPIGQGSFSDGMPLGISGTFNFMLVF 157
Cdd:CHL00004 107 QLGGLWTFVALHGAFGLIGFMLRQFELARSVQLRPYNAIAFSGPIAVFVSVFLIYPLGQSGWFFAPSFGVAAIFRFILFF 186

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 304556499 158 QAEHNILMHPFHQLGVAGVFGGSLFSAMHGSLVTSSL 194
Cdd:CHL00004 187 QGFHNWTLNPFHMMGVAGVLGAALLCAIHGATVENTL 223
PLN00074 PLN00074
photosystem II D2 protein (PsbD); Provisional
 1-194 9.81e-21

photosystem II D2 protein (PsbD); Provisional


Pssm-ID: 215048  Cd Length: 353  Bit Score: 87.80  E-value: 9.81e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304556499   1 IGWFGVLMIPTLLTATSVFIIAFVAAPPVDIDGIrepvAGSLLYGNNIISGAIIPSSAAIGIHFYPIW--EA-ASLDEWL 77
Cdd:PLN00074  31 VGWSGLLLFPCAYFALGGWFTGTTFVTSWYTHGL----ASSYLEGCNFLTAAVSTPANSLAHSLLLLWgpEAqGDFTRWC 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304556499  78 YNGGPYELIVLHFLLGVCCYIGREWELSYRLGMRPWISVAFTAPVAAAAAVFLIYPIGQGSFSDGMPLGISGTFNFMLVF 157
Cdd:PLN00074 107 QLGGLWTFVALHGAFGLIGFMLRQFELARSVQLRPYNAIAFSGPIAVFVSVFLIYPLGQSGWFFAPSFGVAAIFRFILFF 186

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 304556499 158 QAEHNILMHPFHQLGVAGVFGGSLFSAMHGSLVTSSL 194
Cdd:PLN00074 187 QGFHNWTLNPFHMMGVAGVLGAALLCAIHGATVENTL 223
Photo-RC_L cd09290
Subunit L of bacterial photosynthetic reaction center; Bacterial photosynthetic reaction ...
 80-192 1.12e-04

Subunit L of bacterial photosynthetic reaction center; Bacterial photosynthetic reaction center (RC) complex, subunit L. The bacterial photosynthetic reaction center couples light-induced electron transfer with pumping protons across the membrane using reactions involving a quinone molecule (QB) that binds two electrons and two protons at the active site. The reaction center consists of three membrane-bound subunits, designated L, M, and H, plus an additional extracellular cytochrome subunit. The L and M subunits are arranged around an axis of 2-fold rotational symmetry perpendicular to the membrane, forming a scaffold that maintains the cofactors in a precise configuration. The L and M subunits have both sequence and structural similarity, suggesting a common evolutionary origin. The L and M subunits bind noncovalently to the nine cofactors in 2-fold symmetric branches: four bacteriochlorophylls (Bchl), two bacteriopheophytins (Bphe), two ubiquinone molecules (QA and QB), and a non-heme iron. Two Bchls on the periplasmic side of the membrane form the 'special pair' or dimer which is the primary electron donor for the photosynthetic reactions. The electron transfer reaction proceeds from the dimer to an intermediate acceptor (PA), a primary quinone (QA), and a secondary quinone (QB). Protons are translocated from the bacterial cytoplasm to the periplasmic space, generating an electrochemical gradient of protons (the protonmotive force) that can be used to power reactions such as ATP synthesis. The RC complex is found in photosynthetic bacteria, such as purple bacteria and other proteobacteria species.


Pssm-ID: 187748  Cd Length: 273  Bit Score: 41.66  E-value: 1.12e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304556499  80 GGPYELIVLHFLLGVCCYIGREWELSYRLGMRPWISVAFTAPVAAAAAVFLIYPIGQGSFSDGMPLGISGTFNFMLVFQA 159
Cdd:cd09290   84 GGLWQIITVCATGAFVSWALRQVEISRKLGMGYHVPIAFGVAISAYLTLQVIRPILMGAWGHGFPYGIMSHLDWVSNFGY 163

                         90       100       110
                 ....*....|....*....|....*....|....
gi 304556499 160 EH-NILMHPFHQLGVAGVFGGSLFSAMHGSLVTS 192
Cdd:cd09290  164 QYlNFHYNPAHMIAITFLFTNTLALSMHGSLILS 197
PsbD COG5719
Photosystem II reaction center D2, PsbD [Energy production and conversion]; Photosystem II ...
 1-192 3.13e-04

Photosystem II reaction center D2, PsbD [Energy production and conversion]; Photosystem II reaction center D2, PsbD is part of the Pathway/BioSystem: Photosystem II


Pssm-ID: 444429  Cd Length: 316  Bit Score: 40.42  E-value: 3.13e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304556499   1 IGWFGVLMIPTLLTATsvFIIAFVAAPPVDIDGIREPVAGSLLygnniisgAIIPSSAAIGIHFYPIWEaasldewlynG 80
Cdd:COG5719   53 VGFFGVTSIFFGFLAI--AIIGLNAAASVTWNPIQFVRQFFWL--------ALEPPDPEYGLGLAPLAE----------G 112

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304556499  81 GPYELIVLHFLLGVCCYIGREWELSYRLGMRPWISVAFTAPVAAAAAVFLIYPIGQGSFSDGMPLGISG----TFNFMLV 156
Cdd:COG5719  113 GWWQIATFFLTGSFLSWWLREYERARKLGMGTHVPWAFAAAIFLYLVLGVIRPLLMGSWGEAVPYGIFPhldwTSNFSYR 192

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 304556499 157 FQaehNILMHPFHQLGVAGVFGGSLFSAMHGSLVTS 192
Cdd:COG5719  193 YG---NFHYNPFHMLSITFLFGSTLLLAMHGATILA 225
PRK14505 PRK14505
bifunctional photosynthetic reaction center subunit L/M; Provisional
 133-196 4.29e-04

bifunctional photosynthetic reaction center subunit L/M; Provisional


Pssm-ID: 172976  Cd Length: 643  Bit Score: 40.42  E-value: 4.29e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 304556499 133 PIGQGSFSDGMPLGISGTFNFMLVFQAEH-NILMHPFHQLGVAGVFGGSLFSAMHGSLVTSSLIR 196
Cdd:PRK14505 175 PIAMGAWGHGFPLGITHHLDWVSNIGYQYyNFFYNPFHAIGITLLFASTLFLHMHGSAVLSEAKR 239
Photo-RC_M cd09291
Subunit M of bacterial photosynthetic reaction center; Bacterial photosynthetic reaction ...
 1-187 1.75e-03

Subunit M of bacterial photosynthetic reaction center; Bacterial photosynthetic reaction center (RC) complex, subunit M. The bacterial photosynthetic reaction center couples light-induced electron transfer with pumping protons across the membrane using reactions involving a quinone molecule (QB) that binds two electrons and two protons at the active site. The reaction center consists of three membrane-bound subunits, designated L, M, and H, plus an additional extracellular cytochrome subunit. The L and M subunits are arranged around an axis of 2-fold rotational symmetry perpendicular to the membrane, forming a scaffold that maintains the cofactors in a precise configuration. The L and M subunits have both sequence and structural similarity, suggesting a common evolutionary origin. The L and M subunits bind noncovalently to the nine cofactors in 2-fold symmetric branches: four bacteriochlorophylls (Bchl), two bacteriopheophytins (Bphe), two ubiquinone molecules (QA and QB), and a non-heme iron. Two Bchls on the periplasmic side of the membrane form the 'special pair' or dimer which is the primary electron donor for the photosynthetic reactions. The electron transfer reaction proceeds from the dimer to an intermediate acceptor (PA), a primary quinone (QA), and a secondary quinone (QB). Protons are translocated from the bacterial cytoplasm to the periplasmic space, generating an electrochemical gradient of protons (the protonmotive force) that can be used to power reactions such as ATP synthesis. The RC complex is found in photosynthetic bacteria, such as purple bacteria and other proteobacteria species.


Pssm-ID: 187749  Cd Length: 297  Bit Score: 38.18  E-value: 1.75e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304556499   1 IGWFGVLMIPTLLTATsvFIIAFVAAPPVDIDgirePVAgsllYGNNIISGAIIPSSAAIGIHFYPiweaasldewLYNG 80
Cdd:cd09291   42 LGLWGVLSIIFGFIAI--FIILFNMLAQVNWN----PVQ----FLRQFFWLALEPPPPEYGLSIPP----------LNEG 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304556499  81 GPYELIVLHFLLGVCCYIGREWELSYRLGMRPWISVAFTAPVAAAAAVFLIYPIGQGSFSDGMPLGISGTFNFMLVFQAE 160
Cdd:cd09291  102 GWWLIAGFFLTLSILLWWIRTYTRAKALGMGTHLAWAFAAAIFLYLVIGFIRPVLMGSWSEAVPFGIFPHLDWTNAFSIR 181

                        170       180
                 ....*....|....*....|....*...
gi 304556499 161 H-NILMHPFHQLGVAGVFGGSLFSAMHG 187
Cdd:cd09291  182 YgNFYYNPFHMLSIAFLYGSTLLFAMHG 209
 
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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