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Conserved domains on  [gi|226911088|gb|ACO91466|]
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photosystem II D1 protein, partial [Cylindrospermopsis raciborskii CHAB2379]

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 ...
 1-162 1.20e-119

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: 341.53  E-value: 1.20e-119
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226911088    1 GNNIISGAVVPSSNAIGLHFYPIWEAASLDEWLYNGGPYQLVIFHFLIGVACYLGREWELSFRLGMRPWICVAFSAPLAA 80
Cdd:TIGR01151  74 GNNIISGAVVPSSNAIGLHFYPIWEAASLDEWLYNGGPYQLIVFHFLLGVACYMGREWELSYRLGMRPWICVAYSAPVAA 153

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226911088   81 ATAVFLIYPIGQGSFSDGMPLGISGTFNFMIVFQAEHNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLVRETTETESQ 160
Cdd:TIGR01151 154 ATAVFLIYPIGQGSFSDGMPLGISGTFNFMIVFQAEHNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLIRETTENESA 233


                  ..
gi 226911088  161 NY 162
Cdd:TIGR01151 234 NY 235
 
Name Accession Description Interval E-value
psbA TIGR01151
photosystem II, DI subunit (also called Q(B)); This model describes the Photosystem II, DI ...
 1-162 1.20e-119

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: 341.53  E-value: 1.20e-119
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226911088    1 GNNIISGAVVPSSNAIGLHFYPIWEAASLDEWLYNGGPYQLVIFHFLIGVACYLGREWELSFRLGMRPWICVAFSAPLAA 80
Cdd:TIGR01151  74 GNNIISGAVVPSSNAIGLHFYPIWEAASLDEWLYNGGPYQLIVFHFLLGVACYMGREWELSYRLGMRPWICVAYSAPVAA 153

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226911088   81 ATAVFLIYPIGQGSFSDGMPLGISGTFNFMIVFQAEHNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLVRETTETESQ 160
Cdd:TIGR01151 154 ATAVFLIYPIGQGSFSDGMPLGISGTFNFMIVFQAEHNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLIRETTENESA 233


                  ..
gi 226911088  161 NY 162
Cdd:TIGR01151 234 NY 235
Photosystem-II_D1 cd09289
D1 subunit of photosystem II (PS II); Photosystem II (PS II), D2 subunit. PS II is a ...
 1-162 1.58e-114

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: 327.99  E-value: 1.58e-114
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226911088   1 GNNIISGAVVPSSNAIGLHFYPIWEAASLDEWLYNGGPYQLVIFHFLIGVACYLGREWELSFRLGMRPWICVAFSAPLAA 80
Cdd:cd09289   68 GNNIISGAVVPTSNAIGLHFYPIWEAASLDEWLYNGGPYQLIVLHFLLGVCCYMGREWELSYRLGMRPWIAVAYSAPVAA 147

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226911088  81 ATAVFLIYPIGQGSFSDGMPLGISGTFNFMIVFQAEHNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLVRETTETESQ 160
Cdd:cd09289  148 ATAVFLIYPIGQGSFSDGMPLGISGTFNFMIVFQAEHNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLIRETTENESA 227


                 ..
gi 226911088 161 NY 162
Cdd:cd09289  228 NA 229
PsbA COG5716
Photosystem II reaction center D1, PsbA [Energy production and conversion]; Photosystem II ...
 1-162 5.00e-101

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: 294.31  E-value: 5.00e-101
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226911088   1 GNNIISGAVVPSSNAIGLHFYPIWEAASLDEWLYNGGPYQLVIFHFLIGVACYLGREWELSFRLGMRPWICVAFSAPLAA 80
Cdd:COG5716   77 GNNLITAAVEPPSPAIGLHFYPIWEAASMDEWLYNGGPYQLIVFHFLIGIWAYWGRTWELSYRLGMRPWIAWAFAAPVAA 156

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226911088  81 ATAVFLIYPIGQGSFSDGMPLGISGTFNFMIVFQAEHNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLVRETTETESQ 160
Cdd:COG5716  157 ATSVGLVYPIGQGSFSEGVPLGIFGTFDFMLAFQADHNILMNPFHMLGVAGVYGGALLFAMHGSLVTSVLRRETTESESI 236


                 ..
gi 226911088 161 NY 162
Cdd:COG5716  237 NA 238
PLN00056 PLN00056
photosystem Q(B) protein; Provisional
 1-161 3.85e-98

photosystem Q(B) protein; Provisional


Pssm-ID: 177687  Cd Length: 353  Bit Score: 287.02  E-value: 3.85e-98
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226911088   1 GNNIISGAVVPSSNAIGLHFYPIWEAASLDEWLYNGGPYQLVIFHFLIGVACYLGREWELSFRLGMRPWICVAFSAPLAA 80
Cdd:PLN00056  74 GNNIISGAIIPTSAAIGLHFYPIWEAASVDEWLYNGGPYELIVLHFLLGVACYMGREWELSFRLGMRPWIAVAYSAPVAA 153

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226911088  81 ATAVFLIYPIGQGSFSDGMPLGISGTFNFMIVFQAEHNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLVRETTETESQ 160
Cdd:PLN00056 154 ATAVFLIYPIGQGSFSDGMPLGISGTFNFMIVFQAEHNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLIRETTENESA 233


                 .
gi 226911088 161 N 161
Cdd:PLN00056 234 N 234
Photo_RC pfam00124
Photosynthetic reaction centre protein;
1-161 1.58e-65

Photosynthetic reaction centre protein;


Pssm-ID: 425477  Cd Length: 260  Bit Score: 200.55  E-value: 1.58e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226911088    1 GNNIISGAVVPSSNAIGLHFYPIWeaasldewlyNGGPYQLVIFHFLIGVACYLGREWELSFRLGMRPWICVAFSAPLAA 80
Cdd:pfam00124  39 GRNLITLAIEPPSPSYGLSFPPLW----------EGGLWQIITFHATIAFISWWLREYEIARKLGMGPHIAWAFSAAIAA 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226911088   81 ATAVFLIYPIGQGSFSDGMPLGISGTFNFMIVFQAEH-NILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLVR-ETTETE 158
Cdd:pfam00124 109 YLSLGLIRPILMGSWSEGFPLGIFPHLDWTSNFSYRYgNFLYNPFHMLGIAFLFGSALLLAMHGALVLSVLRPgGTREVE 188


                  ...
gi 226911088  159 SQN 161
Cdd:pfam00124 189 SIN 191
 
Name Accession Description Interval E-value
psbA TIGR01151
photosystem II, DI subunit (also called Q(B)); This model describes the Photosystem II, DI ...
 1-162 1.20e-119

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: 341.53  E-value: 1.20e-119
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226911088    1 GNNIISGAVVPSSNAIGLHFYPIWEAASLDEWLYNGGPYQLVIFHFLIGVACYLGREWELSFRLGMRPWICVAFSAPLAA 80
Cdd:TIGR01151  74 GNNIISGAVVPSSNAIGLHFYPIWEAASLDEWLYNGGPYQLIVFHFLLGVACYMGREWELSYRLGMRPWICVAYSAPVAA 153

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226911088   81 ATAVFLIYPIGQGSFSDGMPLGISGTFNFMIVFQAEHNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLVRETTETESQ 160
Cdd:TIGR01151 154 ATAVFLIYPIGQGSFSDGMPLGISGTFNFMIVFQAEHNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLIRETTENESA 233


                  ..
gi 226911088  161 NY 162
Cdd:TIGR01151 234 NY 235
Photosystem-II_D1 cd09289
D1 subunit of photosystem II (PS II); Photosystem II (PS II), D2 subunit. PS II is a ...
 1-162 1.58e-114

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: 327.99  E-value: 1.58e-114
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226911088   1 GNNIISGAVVPSSNAIGLHFYPIWEAASLDEWLYNGGPYQLVIFHFLIGVACYLGREWELSFRLGMRPWICVAFSAPLAA 80
Cdd:cd09289   68 GNNIISGAVVPTSNAIGLHFYPIWEAASLDEWLYNGGPYQLIVLHFLLGVCCYMGREWELSYRLGMRPWIAVAYSAPVAA 147

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226911088  81 ATAVFLIYPIGQGSFSDGMPLGISGTFNFMIVFQAEHNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLVRETTETESQ 160
Cdd:cd09289  148 ATAVFLIYPIGQGSFSDGMPLGISGTFNFMIVFQAEHNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLIRETTENESA 227


                 ..
gi 226911088 161 NY 162
Cdd:cd09289  228 NA 229
PsbA COG5716
Photosystem II reaction center D1, PsbA [Energy production and conversion]; Photosystem II ...
 1-162 5.00e-101

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: 294.31  E-value: 5.00e-101
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226911088   1 GNNIISGAVVPSSNAIGLHFYPIWEAASLDEWLYNGGPYQLVIFHFLIGVACYLGREWELSFRLGMRPWICVAFSAPLAA 80
Cdd:COG5716   77 GNNLITAAVEPPSPAIGLHFYPIWEAASMDEWLYNGGPYQLIVFHFLIGIWAYWGRTWELSYRLGMRPWIAWAFAAPVAA 156

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226911088  81 ATAVFLIYPIGQGSFSDGMPLGISGTFNFMIVFQAEHNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLVRETTETESQ 160
Cdd:COG5716  157 ATSVGLVYPIGQGSFSEGVPLGIFGTFDFMLAFQADHNILMNPFHMLGVAGVYGGALLFAMHGSLVTSVLRRETTESESI 236


                 ..
gi 226911088 161 NY 162
Cdd:COG5716  237 NA 238
PLN00056 PLN00056
photosystem Q(B) protein; Provisional
 1-161 3.85e-98

photosystem Q(B) protein; Provisional


Pssm-ID: 177687  Cd Length: 353  Bit Score: 287.02  E-value: 3.85e-98
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226911088   1 GNNIISGAVVPSSNAIGLHFYPIWEAASLDEWLYNGGPYQLVIFHFLIGVACYLGREWELSFRLGMRPWICVAFSAPLAA 80
Cdd:PLN00056  74 GNNIISGAIIPTSAAIGLHFYPIWEAASVDEWLYNGGPYELIVLHFLLGVACYMGREWELSFRLGMRPWIAVAYSAPVAA 153

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226911088  81 ATAVFLIYPIGQGSFSDGMPLGISGTFNFMIVFQAEHNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLVRETTETESQ 160
Cdd:PLN00056 154 ATAVFLIYPIGQGSFSDGMPLGISGTFNFMIVFQAEHNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLIRETTENESA 233


                 .
gi 226911088 161 N 161
Cdd:PLN00056 234 N 234
psbA CHL00003
photosystem II protein D1
 1-162 1.10e-91

photosystem II protein D1


Pssm-ID: 176948  Cd Length: 338  Bit Score: 269.83  E-value: 1.10e-91
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226911088   1 GNNIISGAVVPSSNAIGLHFYPIWEAASLDEWLYNGGPYQLVIFHFLIGVACYLGREWELSFRLGMRPWICVAFSAPLAA 80
Cdd:CHL00003  68 GNNIISGAIIPSSAAIGLHFYPIWEAASVDEWLYNGGPYELIVLHFLLGVACYMGREWELSFRLGMRPWIAVAYSAPVAA 147

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226911088  81 ATAVFLIYPIGQGSFSDGMPLGISGTFNFMIVFQAEHNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLVRETTETESQ 160
Cdd:CHL00003 148 ATAVFLIYPIGQGSFSDGMPLGISGTFNFMIVFQAEHNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLIRETTENESA 227


                 ..
gi 226911088 161 NY 162
Cdd:CHL00003 228 NL 229
Photo_RC pfam00124
Photosynthetic reaction centre protein;
1-161 1.58e-65

Photosynthetic reaction centre protein;


Pssm-ID: 425477  Cd Length: 260  Bit Score: 200.55  E-value: 1.58e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226911088    1 GNNIISGAVVPSSNAIGLHFYPIWeaasldewlyNGGPYQLVIFHFLIGVACYLGREWELSFRLGMRPWICVAFSAPLAA 80
Cdd:pfam00124  39 GRNLITLAIEPPSPSYGLSFPPLW----------EGGLWQIITFHATIAFISWWLREYEIARKLGMGPHIAWAFSAAIAA 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226911088   81 ATAVFLIYPIGQGSFSDGMPLGISGTFNFMIVFQAEH-NILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLVR-ETTETE 158
Cdd:pfam00124 109 YLSLGLIRPILMGSWSEGFPLGIFPHLDWTSNFSYRYgNFLYNPFHMLGIAFLFGSALLLAMHGALVLSVLRPgGTREVE 188


                  ...
gi 226911088  159 SQN 161
Cdd:pfam00124 189 SIN 191
Photo_RC cd09223
D1, D2 subunits of photosystem II (PSII); M, L subunits of bacterial photosynthetic reaction ...
 32-160 2.03e-48

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: 155.30  E-value: 2.03e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226911088  32 WLYNGGPYQLVIFHFLIGVACYLGREWELSFRLGMRPWICVAFSAPLAAATAVFLIYPIGQGSFSDGMPLGISGTFNFMI 111
Cdd:cd09223   20 IGIAGGLWQIITFHALGAFISWMLRQVEIARKLGMGPHIAVAFSAPIASFFVLFLIRPIGQGSWSDAFPYGISSHLDWVN 99

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 226911088 112 VFQAEH-NILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLVRETTETESQ 160
Cdd:cd09223  100 NFQYEHnNWHYNPFHMLGVAFVFGGALLCAMHGALVLSVLNPEGEETEGQ 149
Photosystem-II_D2 cd09288
D2 subunit of photosystem II (PS II); Photosystem II (PS II), D2 subunit. PS II is a ...
 1-153 3.93e-30

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: 111.61  E-value: 3.93e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226911088   1 GNNIISGAVVPSSNAIGLHFYPIW--EA-ASLDEWLYNGGPYQLVIFHFLIGVACYLGREWELSFRLGMRPWICVAFSAP 77
Cdd:cd09288   57 GCNFLTAAVSTPANSMGHSLLLLWgpEAqGDFTRWCQLGGLWTFVALHGAFGLIGFMLRQFEIARSVGIRPYNAIAFSGP 136

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 226911088  78 LAAATAVFLIYPIGQGSFSDGMPLGISGTFNFMIVFQAEHNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLVRE 153
Cdd:cd09288  137 IAVFVSVFLIYPLGQSGWFFAPSFGVAAIFRFILFFQGFHNWTLNPFHMMGVAGVLGAALLCAIHGATVENTLFED 212
psbD CHL00004
photosystem II protein D2
 1-150 1.95e-28

photosystem II protein D2


Pssm-ID: 176949  Cd Length: 353  Bit Score: 107.63  E-value: 1.95e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226911088   1 GNNIISGAVVPSSNAIGLHFYPIW--EA-ASLDEWLYNGGPYQLVIFHFLIGVACYLGREWELSFRLGMRPWICVAFSAP 77
Cdd:CHL00004  71 GCNFLTAAVSTPANSLAHSLLLLWgpEAqGDFTRWCQLGGLWTFVALHGAFGLIGFMLRQFELARSVQLRPYNAIAFSGP 150

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 226911088  78 LAAATAVFLIYPIGQGSFSDGMPLGISGTFNFMIVFQAEHNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSL 150
Cdd:CHL00004 151 IAVFVSVFLIYPLGQSGWFFAPSFGVAAIFRFILFFQGFHNWTLNPFHMMGVAGVLGAALLCAIHGATVENTL 223
PLN00074 PLN00074
photosystem II D2 protein (PsbD); Provisional
 1-153 9.26e-28

photosystem II D2 protein (PsbD); Provisional


Pssm-ID: 215048  Cd Length: 353  Bit Score: 105.52  E-value: 9.26e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226911088   1 GNNIISGAVVPSSNAIGLHFYPIW--EA-ASLDEWLYNGGPYQLVIFHFLIGVACYLGREWELSFRLGMRPWICVAFSAP 77
Cdd:PLN00074  71 GCNFLTAAVSTPANSLAHSLLLLWgpEAqGDFTRWCQLGGLWTFVALHGAFGLIGFMLRQFELARSVQLRPYNAIAFSGP 150

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 226911088  78 LAAATAVFLIYPIGQGSFSDGMPLGISGTFNFMIVFQAEHNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLVRE 153
Cdd:PLN00074 151 IAVFVSVFLIYPLGQSGWFFAPSFGVAAIFRFILFFQGFHNWTLNPFHMMGVAGVLGAALLCAIHGATVENTLFED 226
Photo-RC_L cd09290
Subunit L of bacterial photosynthetic reaction center; Bacterial photosynthetic reaction ...
 36-148 2.52e-10

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: 57.07  E-value: 2.52e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226911088  36 GGPYQLVIFHFLIGVACYLGREWELSFRLGMRPWICVAFSAPLAAATAVFLIYPIGQGSFSDGMPLGISGTFNFMIVFQA 115
Cdd:cd09290   84 GGLWQIITVCATGAFVSWALRQVEISRKLGMGYHVPIAFGVAISAYLTLQVIRPILMGAWGHGFPYGIMSHLDWVSNFGY 163

                         90       100       110
                 ....*....|....*....|....*....|....
gi 226911088 116 EH-NILMHPFHMLGVAGVFGGSLFSAMHGSLVTS 148
Cdd:cd09290  164 QYlNFHYNPAHMIAITFLFTNTLALSMHGSLILS 197
PsbD COG5719
Photosystem II reaction center D2, PsbD [Energy production and conversion]; Photosystem II ...
 33-148 6.78e-09

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: 53.13  E-value: 6.78e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226911088  33 LYNGGPYQLVIFHFLIGVACYLGREWELSFRLGMRPWICVAFSAPLAAATAVFLIYPIGQGSFSDGMPLGISG----TFN 108
Cdd:COG5719  109 LAEGGWWQIATFFLTGSFLSWWLREYERARKLGMGTHVPWAFAAAIFLYLVLGVIRPLLMGSWGEAVPYGIFPhldwTSN 188

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 226911088 109 FMIVFQaehNILMHPFHMLGVAGVFGGSLFSAMHGSLVTS 148
Cdd:COG5719  189 FSYRYG---NFHYNPFHMLSITFLFGSTLLLAMHGATILA 225
PRK14505 PRK14505
bifunctional photosynthetic reaction center subunit L/M; Provisional
 34-156 8.86e-09

bifunctional photosynthetic reaction center subunit L/M; Provisional


Pssm-ID: 172976  Cd Length: 643  Bit Score: 53.13  E-value: 8.86e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226911088  34 YNGGPYQLVIFHFLIGVAC------YLGREWELSFRLGMRPWICVAFSAPLAAATAVFLIYPIGQGSFSDGMPLGISGTF 107
Cdd:PRK14505 114 FNIDPAKPGFFWFLTMVAAtiafigWLLRQIDISLKLDMGMEVPIAFGAVVSSWITLQWLRPIAMGAWGHGFPLGITHHL 193

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 226911088 108 NFM--IVFQAeHNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLVRETTE 156
Cdd:PRK14505 194 DWVsnIGYQY-YNFFYNPFHAIGITLLFASTLFLHMHGSAVLSEAKRNISD 243
Photo-RC_M cd09291
Subunit M of bacterial photosynthetic reaction center; Bacterial photosynthetic reaction ...
 8-143 1.94e-07

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: 48.96  E-value: 1.94e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226911088   8 AVVPSSNAIGLHFYPiweaasldewLYNGGPYQLVIFHFLIGVACYLGREWELSFRLGMRPWICVAFSAPLAAATAVFLI 87
Cdd:cd09291   83 ALEPPPPEYGLSIPP----------LNEGGWWLIAGFFLTLSILLWWIRTYTRAKALGMGTHLAWAFAAAIFLYLVIGFI 152

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 226911088  88 YPIGQGSFSDGMPLGISGTFNFMIVFQAEH-NILMHPFHMLGVAGVFGGSLFSAMHG 143
Cdd:cd09291  153 RPVLMGSWSEAVPFGIFPHLDWTNAFSIRYgNFYYNPFHMLSIAFLYGSTLLFAMHG 209
PRK14505 PRK14505
bifunctional photosynthetic reaction center subunit L/M; Provisional
 8-149 2.05e-03

bifunctional photosynthetic reaction center subunit L/M; Provisional


Pssm-ID: 172976  Cd Length: 643  Bit Score: 37.72  E-value: 2.05e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226911088   8 AVVPSSNAIGLHFYPIWEaasldewlyNGGPYQLVIFHFLIGVACYLGREWELSFRLGMRPWICVAFSAPLAAATAVFLI 87
Cdd:PRK14505 416 AVYPPPTEYGLSWNVPWD---------KGGAWLAATFFLHISVLTWWARLYTRAKATGIGTHLAWGFASALSLYFVIYLF 486

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 226911088  88 YPIGQGSFSDGMPLGISGTFNFMIVFQAE-HNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSS 149
Cdd:PRK14505 487 HPLALGNWSAAPGHGFRAILDWTNYVSIHwGNFYYNPFHMLSIFFLLGSTLLLAMHGATIVAT 549
 
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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