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Conserved domains on  [gi|1184125035|gb|ARJ55534|]
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photosystem II 32 kDa protein, partial (chloroplast) [Riccia billardierei]

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 ...
 1-184 1.50e-131

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: 372.73  E-value: 1.50e-131
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1184125035   1 MTATLERRESASIWGRFCDWITSTENRLYIGWFGVLMIPTLLTATSVFIIAFIAAPPVBIDGIREPVSGSLLYGNNIISG 80
Cdd:TIGR01151   1 MTATLQRRESASLWERFCEWITSTENRLYIGWFGVLMIPTLLTATSCFIIAFIAAPPVDIDGIREPVAGSLLYGNNIISG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1184125035  81 AIIPTSAAIGLHFYPIWEAASVDEWLYNGGPY*LIVLHFLLGVACYMGREWELSYRLGMRPWIAVAYSAPVAAATAVFLI 160
Cdd:TIGR01151  81 AVVPSSNAIGLHFYPIWEAASLDEWLYNGGPYQLIVFHFLLGVACYMGREWELSYRLGMRPWICVAYSAPVAAATAVFLI 160

                         170       180
                  ....*....|....*....|....
gi 1184125035 161 YPIGQGSFSDGMPLGISGTFNFMI 184
Cdd:TIGR01151 161 YPIGQGSFSDGMPLGISGTFNFMI 184
 
Name Accession Description Interval E-value
psbA TIGR01151
photosystem II, DI subunit (also called Q(B)); This model describes the Photosystem II, DI ...
 1-184 1.50e-131

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: 372.73  E-value: 1.50e-131
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1184125035   1 MTATLERRESASIWGRFCDWITSTENRLYIGWFGVLMIPTLLTATSVFIIAFIAAPPVBIDGIREPVSGSLLYGNNIISG 80
Cdd:TIGR01151   1 MTATLQRRESASLWERFCEWITSTENRLYIGWFGVLMIPTLLTATSCFIIAFIAAPPVDIDGIREPVAGSLLYGNNIISG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1184125035  81 AIIPTSAAIGLHFYPIWEAASVDEWLYNGGPY*LIVLHFLLGVACYMGREWELSYRLGMRPWIAVAYSAPVAAATAVFLI 160
Cdd:TIGR01151  81 AVVPSSNAIGLHFYPIWEAASLDEWLYNGGPYQLIVFHFLLGVACYMGREWELSYRLGMRPWICVAYSAPVAAATAVFLI 160

                         170       180
                  ....*....|....*....|....
gi 1184125035 161 YPIGQGSFSDGMPLGISGTFNFMI 184
Cdd:TIGR01151 161 YPIGQGSFSDGMPLGISGTFNFMI 184
Photosystem-II_D1 cd09289
D1 subunit of photosystem II (PS II); Photosystem II (PS II), D2 subunit. PS II is a ...
 7-184 8.23e-127

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: 359.97  E-value: 8.23e-127
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1184125035   7 RRESASIWGRFCDWITSTENRLYIGWFGVLMIPTLLTATSVFIIAFIAAPPVBIDGIREPVSGSLLYGNNIISGAIIPTS 86
Cdd:cd09289     1 RRESASLWERFCAWITSTENRLYIGWFGVLMIPTLLTATSVFIIAFIAAPPVDIDGIREPVSGSLLYGNNIISGAVVPTS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1184125035  87 AAIGLHFYPIWEAASVDEWLYNGGPY*LIVLHFLLGVACYMGREWELSYRLGMRPWIAVAYSAPVAAATAVFLIYPIGQG 166
Cdd:cd09289    81 NAIGLHFYPIWEAASLDEWLYNGGPYQLIVLHFLLGVCCYMGREWELSYRLGMRPWIAVAYSAPVAAATAVFLIYPIGQG 160

                         170
                  ....*....|....*...
gi 1184125035 167 SFSDGMPLGISGTFNFMI 184
Cdd:cd09289   161 SFSDGMPLGISGTFNFMI 178
PLN00056 PLN00056
photosystem Q(B) protein; Provisional
 1-184 1.95e-119

photosystem Q(B) protein; Provisional


Pssm-ID: 177687  Cd Length: 353  Bit Score: 341.72  E-value: 1.95e-119
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1184125035   1 MTATLERRESASIWGRFCDWITSTENRLYIGWFGVLMIPTLLTATSVFIIAFIAAPPVBIDGIREPVSGSLLYGNNIISG 80
Cdd:PLN00056    1 MTAILERRESESLWGRFCNWITSTENRLYIGWFGVLMIPTLLTATSVFIIAFIAAPPVDIDGIREPVSGSLLYGNNIISG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1184125035  81 AIIPTSAAIGLHFYPIWEAASVDEWLYNGGPY*LIVLHFLLGVACYMGREWELSYRLGMRPWIAVAYSAPVAAATAVFLI 160
Cdd:PLN00056   81 AIIPTSAAIGLHFYPIWEAASVDEWLYNGGPYELIVLHFLLGVACYMGREWELSFRLGMRPWIAVAYSAPVAAATAVFLI 160

                         170       180
                  ....*....|....*....|....
gi 1184125035 161 YPIGQGSFSDGMPLGISGTFNFMI 184
Cdd:PLN00056  161 YPIGQGSFSDGMPLGISGTFNFMI 184
PsbA COG5716
Photosystem II reaction center D1, PsbA [Energy production and conversion]; Photosystem II ...
 1-184 3.24e-105

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: 305.87  E-value: 3.24e-105
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1184125035   1 MTATLERRES---ASIWGRFCDWITSTENRLYIGWFGVLMIPTLLTATSVFIIAFIAAPPVBIDGIREPVSGSLLYGNNI 77
Cdd:COG5716     1 MTTTLQRRTElpfFSSWERFCAWITSTENRIYLGWFGVLMIPTLLTAFIIFGIAFLAAPPVDMDGIREPVIGSLLFGNNL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1184125035  78 ISGAIIPTSAAIGLHFYPIWEAASVDEWLYNGGPY*LIVLHFLLGVACYMGREWELSYRLGMRPWIAVAYSAPVAAATAV 157
Cdd:COG5716    81 ITAAVEPPSPAIGLHFYPIWEAASMDEWLYNGGPYQLIVFHFLIGIWAYWGRTWELSYRLGMRPWIAWAFAAPVAAATSV 160

                         170       180
                  ....*....|....*....|....*..
gi 1184125035 158 FLIYPIGQGSFSDGMPLGISGTFNFMI 184
Cdd:COG5716   161 GLVYPIGQGSFSEGVPLGIFGTFDFML 187
Photo_RC pfam00124
Photosynthetic reaction centre protein;
28-184 1.41e-55

Photosynthetic reaction centre protein;


Pssm-ID: 425477  Cd Length: 260  Bit Score: 176.28  E-value: 1.41e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1184125035  28 LYIGWFGVLMIPTLLTATSVFIIAFIAAPPVBIdgirepvsGSLLYGNNIISGAIIPTSAAIGLHFYPIWeaasvdewly 107
Cdd:pfam00124   1 FYVGFFGVLSIPTALLATFIIGIGFVAAPSVDW--------SPLLFGRNLITLAIEPPSPSYGLSFPPLW---------- 62

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1184125035 108 NGGPY*LIVLHFLLGVACYMGREWELSYRLGMRPWIAVAYSAPVAAATAVFLIYPIGQGSFSDGMPLGISGTFNFMI 184
Cdd:pfam00124  63 EGGLWQIITFHATIAFISWWLREYEIARKLGMGPHIAWAFSAAIAAYLSLGLIRPILMGSWSEGFPLGIFPHLDWTS 139
 
Name Accession Description Interval E-value
psbA TIGR01151
photosystem II, DI subunit (also called Q(B)); This model describes the Photosystem II, DI ...
 1-184 1.50e-131

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: 372.73  E-value: 1.50e-131
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1184125035   1 MTATLERRESASIWGRFCDWITSTENRLYIGWFGVLMIPTLLTATSVFIIAFIAAPPVBIDGIREPVSGSLLYGNNIISG 80
Cdd:TIGR01151   1 MTATLQRRESASLWERFCEWITSTENRLYIGWFGVLMIPTLLTATSCFIIAFIAAPPVDIDGIREPVAGSLLYGNNIISG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1184125035  81 AIIPTSAAIGLHFYPIWEAASVDEWLYNGGPY*LIVLHFLLGVACYMGREWELSYRLGMRPWIAVAYSAPVAAATAVFLI 160
Cdd:TIGR01151  81 AVVPSSNAIGLHFYPIWEAASLDEWLYNGGPYQLIVFHFLLGVACYMGREWELSYRLGMRPWICVAYSAPVAAATAVFLI 160

                         170       180
                  ....*....|....*....|....
gi 1184125035 161 YPIGQGSFSDGMPLGISGTFNFMI 184
Cdd:TIGR01151 161 YPIGQGSFSDGMPLGISGTFNFMI 184
Photosystem-II_D1 cd09289
D1 subunit of photosystem II (PS II); Photosystem II (PS II), D2 subunit. PS II is a ...
 7-184 8.23e-127

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: 359.97  E-value: 8.23e-127
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1184125035   7 RRESASIWGRFCDWITSTENRLYIGWFGVLMIPTLLTATSVFIIAFIAAPPVBIDGIREPVSGSLLYGNNIISGAIIPTS 86
Cdd:cd09289     1 RRESASLWERFCAWITSTENRLYIGWFGVLMIPTLLTATSVFIIAFIAAPPVDIDGIREPVSGSLLYGNNIISGAVVPTS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1184125035  87 AAIGLHFYPIWEAASVDEWLYNGGPY*LIVLHFLLGVACYMGREWELSYRLGMRPWIAVAYSAPVAAATAVFLIYPIGQG 166
Cdd:cd09289    81 NAIGLHFYPIWEAASLDEWLYNGGPYQLIVLHFLLGVCCYMGREWELSYRLGMRPWIAVAYSAPVAAATAVFLIYPIGQG 160

                         170
                  ....*....|....*...
gi 1184125035 167 SFSDGMPLGISGTFNFMI 184
Cdd:cd09289   161 SFSDGMPLGISGTFNFMI 178
PLN00056 PLN00056
photosystem Q(B) protein; Provisional
 1-184 1.95e-119

photosystem Q(B) protein; Provisional


Pssm-ID: 177687  Cd Length: 353  Bit Score: 341.72  E-value: 1.95e-119
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1184125035   1 MTATLERRESASIWGRFCDWITSTENRLYIGWFGVLMIPTLLTATSVFIIAFIAAPPVBIDGIREPVSGSLLYGNNIISG 80
Cdd:PLN00056    1 MTAILERRESESLWGRFCNWITSTENRLYIGWFGVLMIPTLLTATSVFIIAFIAAPPVDIDGIREPVSGSLLYGNNIISG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1184125035  81 AIIPTSAAIGLHFYPIWEAASVDEWLYNGGPY*LIVLHFLLGVACYMGREWELSYRLGMRPWIAVAYSAPVAAATAVFLI 160
Cdd:PLN00056   81 AIIPTSAAIGLHFYPIWEAASVDEWLYNGGPYELIVLHFLLGVACYMGREWELSFRLGMRPWIAVAYSAPVAAATAVFLI 160

                         170       180
                  ....*....|....*....|....
gi 1184125035 161 YPIGQGSFSDGMPLGISGTFNFMI 184
Cdd:PLN00056  161 YPIGQGSFSDGMPLGISGTFNFMI 184
PsbA COG5716
Photosystem II reaction center D1, PsbA [Energy production and conversion]; Photosystem II ...
 1-184 3.24e-105

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: 305.87  E-value: 3.24e-105
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1184125035   1 MTATLERRES---ASIWGRFCDWITSTENRLYIGWFGVLMIPTLLTATSVFIIAFIAAPPVBIDGIREPVSGSLLYGNNI 77
Cdd:COG5716     1 MTTTLQRRTElpfFSSWERFCAWITSTENRIYLGWFGVLMIPTLLTAFIIFGIAFLAAPPVDMDGIREPVIGSLLFGNNL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1184125035  78 ISGAIIPTSAAIGLHFYPIWEAASVDEWLYNGGPY*LIVLHFLLGVACYMGREWELSYRLGMRPWIAVAYSAPVAAATAV 157
Cdd:COG5716    81 ITAAVEPPSPAIGLHFYPIWEAASMDEWLYNGGPYQLIVFHFLIGIWAYWGRTWELSYRLGMRPWIAWAFAAPVAAATSV 160

                         170       180
                  ....*....|....*....|....*..
gi 1184125035 158 FLIYPIGQGSFSDGMPLGISGTFNFMI 184
Cdd:COG5716   161 GLVYPIGQGSFSEGVPLGIFGTFDFML 187
psbA CHL00003
photosystem II protein D1
 7-184 2.51e-101

photosystem II protein D1


Pssm-ID: 176948  Cd Length: 338  Bit Score: 295.26  E-value: 2.51e-101
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1184125035   7 RRESASIWGRFCDWITSTENRLYIGWFGVLMIPTLLTATSVFIIAFIAAPPVBIDGIREPVSGSLLYGNNIISGAIIPTS 86
Cdd:CHL00003    1 RRESTSLWGRFCNWITSTENRLYIGWFGVLMIPTLLTATSVFIIAFIAAPPVDIDGIREPVSGSLLYGNNIISGAIIPSS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1184125035  87 AAIGLHFYPIWEAASVDEWLYNGGPY*LIVLHFLLGVACYMGREWELSYRLGMRPWIAVAYSAPVAAATAVFLIYPIGQG 166
Cdd:CHL00003   81 AAIGLHFYPIWEAASVDEWLYNGGPYELIVLHFLLGVACYMGREWELSFRLGMRPWIAVAYSAPVAAATAVFLIYPIGQG 160

                         170
                  ....*....|....*...
gi 1184125035 167 SFSDGMPLGISGTFNFMI 184
Cdd:CHL00003  161 SFSDGMPLGISGTFNFMI 178
Photo_RC pfam00124
Photosynthetic reaction centre protein;
28-184 1.41e-55

Photosynthetic reaction centre protein;


Pssm-ID: 425477  Cd Length: 260  Bit Score: 176.28  E-value: 1.41e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1184125035  28 LYIGWFGVLMIPTLLTATSVFIIAFIAAPPVBIdgirepvsGSLLYGNNIISGAIIPTSAAIGLHFYPIWeaasvdewly 107
Cdd:pfam00124   1 FYVGFFGVLSIPTALLATFIIGIGFVAAPSVDW--------SPLLFGRNLITLAIEPPSPSYGLSFPPLW---------- 62

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1184125035 108 NGGPY*LIVLHFLLGVACYMGREWELSYRLGMRPWIAVAYSAPVAAATAVFLIYPIGQGSFSDGMPLGISGTFNFMI 184
Cdd:pfam00124  63 EGGLWQIITFHATIAFISWWLREYEIARKLGMGPHIAWAFSAAIAAYLSLGLIRPILMGSWSEGFPLGIFPHLDWTS 139
Photosystem-II_D2 cd09288
D2 subunit of photosystem II (PS II); Photosystem II (PS II), D2 subunit. PS II is a ...
 19-184 2.56e-17

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: 78.10  E-value: 2.56e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1184125035  19 DWItSTENRLYIGWFGVLMIPTLLTATSVFIIAFIAAPPVBIDGIrepvSGSLLYGNNIISGAIIPTSAAIGLHFYPIW- 97
Cdd:cd09288     7 DWL-RRDRFVFVGWSGLLLFPCAYLALGGWFTGTTFVTSWYTHGL----ASSYLEGCNFLTAAVSTPANSMGHSLLLLWg 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1184125035  98 -EA-ASVDEWLYNGGPY*LIVLHFLLGVACYMGREWELSYRLGMRPWIAVAYSAPVAAATAVFLIYPIGQGSFSDGMPLG 175
Cdd:cd09288    82 pEAqGDFTRWCQLGGLWTFVALHGAFGLIGFMLRQFEIARSVGIRPYNAIAFSGPIAVFVSVFLIYPLGQSGWFFAPSFG 161


                  ....*....
gi 1184125035 176 ISGTFNFMI 184
Cdd:cd09288   162 VAAIFRFIL 170
psbD CHL00004
photosystem II protein D2
 19-184 1.72e-14

photosystem II protein D2


Pssm-ID: 176949  Cd Length: 353  Bit Score: 70.27  E-value: 1.72e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1184125035  19 DWItSTENRLYIGWFGVLMIPTLLTATSVFIIAFIAAPPVBIDGIrepvSGSLLYGNNIISGAIIPTSAAIGLHFYPIW- 97
Cdd:CHL00004   21 DWL-RRDRFVFVGWSGLLLFPCAYFALGGWFTGTTFVTSWYTHGL----ASSYLEGCNFLTAAVSTPANSLAHSLLLLWg 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1184125035  98 -EA-ASVDEWLYNGGPY*LIVLHFLLGVACYMGREWELSYRLGMRPWIAVAYSAPVAAATAVFLIYPIGQGSFSDGMPLG 175
Cdd:CHL00004   96 pEAqGDFTRWCQLGGLWTFVALHGAFGLIGFMLRQFELARSVQLRPYNAIAFSGPIAVFVSVFLIYPLGQSGWFFAPSFG 175


                  ....*....
gi 1184125035 176 ISGTFNFMI 184
Cdd:CHL00004  176 VAAIFRFIL 184
PLN00074 PLN00074
photosystem II D2 protein (PsbD); Provisional
 1-184 2.28e-13

photosystem II D2 protein (PsbD); Provisional


Pssm-ID: 215048  Cd Length: 353  Bit Score: 67.00  E-value: 2.28e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1184125035   1 MTATLER--RESASIWGRFCDWITStENRLYIGWFGVLMIPTLLTATSVFIIAFIAAPPVBIDGIrepvSGSLLYGNNII 78
Cdd:PLN00074    1 MTIALGKftKDENDLFDIMDDWLRR-DRFVFVGWSGLLLFPCAYFALGGWFTGTTFVTSWYTHGL----ASSYLEGCNFL 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1184125035  79 SGAIIPTSAAIGLHFYPIW--EA-ASVDEWLYNGGPY*LIVLHFLLGVACYMGREWELSYRLGMRPWIAVAYSAPVAAAT 155
Cdd:PLN00074   76 TAAVSTPANSLAHSLLLLWgpEAqGDFTRWCQLGGLWTFVALHGAFGLIGFMLRQFELARSVQLRPYNAIAFSGPIAVFV 155

                         170       180
                  ....*....|....*....|....*....
gi 1184125035 156 AVFLIYPIGQGSFSDGMPLGISGTFNFMI 184
Cdd:PLN00074  156 SVFLIYPLGQSGWFFAPSFGVAAIFRFIL 184
 
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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