NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2438686390|ref|WP_271931852|]
View 

MULTISPECIES: photosystem II protein D2, partial [Microcystis]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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 ...
1-56 4.08e-39

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 cd09288:

Pssm-ID: 447584  Cd Length: 339  Bit Score: 130.49  E-value: 4.08e-39
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2438686390   1 DFVSQELRAAEDPEFETFYTKNILLNEGLRAWMAPQDQPHENFIFPEEVLPRGNAL 56
Cdd:cd09288   284 DFVSQEIRAAEDPEFETFYTKNILLNEGIRAWMAAQDQPHENLVFPEEVLPRGNAL 339
 
Name Accession Description Interval E-value
Photosystem-II_D2 cd09288
D2 subunit of photosystem II (PS II); Photosystem II (PS II), D2 subunit. PS II is a ...
1-56 4.08e-39

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: 130.49  E-value: 4.08e-39
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2438686390   1 DFVSQELRAAEDPEFETFYTKNILLNEGLRAWMAPQDQPHENFIFPEEVLPRGNAL 56
Cdd:cd09288   284 DFVSQEIRAAEDPEFETFYTKNILLNEGIRAWMAAQDQPHENLVFPEEVLPRGNAL 339
psbD CHL00004
photosystem II protein D2
1-56 5.32e-38

photosystem II protein D2


Pssm-ID: 176949  Cd Length: 353  Bit Score: 128.05  E-value: 5.32e-38
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2438686390   1 DFVSQELRAAEDPEFETFYTKNILLNEGLRAWMAPQDQPHENFIFPEEVLPRGNAL 56
Cdd:CHL00004  298 DFVSQEIRAAEDPEFETFYTKNILLNEGIRAWMAAQDQPHENLIFPEEVLPRGNAL 353
 
Name Accession Description Interval E-value
Photosystem-II_D2 cd09288
D2 subunit of photosystem II (PS II); Photosystem II (PS II), D2 subunit. PS II is a ...
1-56 4.08e-39

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: 130.49  E-value: 4.08e-39
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2438686390   1 DFVSQELRAAEDPEFETFYTKNILLNEGLRAWMAPQDQPHENFIFPEEVLPRGNAL 56
Cdd:cd09288   284 DFVSQEIRAAEDPEFETFYTKNILLNEGIRAWMAAQDQPHENLVFPEEVLPRGNAL 339
psbD CHL00004
photosystem II protein D2
1-56 5.32e-38

photosystem II protein D2


Pssm-ID: 176949  Cd Length: 353  Bit Score: 128.05  E-value: 5.32e-38
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2438686390   1 DFVSQELRAAEDPEFETFYTKNILLNEGLRAWMAPQDQPHENFIFPEEVLPRGNAL 56
Cdd:CHL00004  298 DFVSQEIRAAEDPEFETFYTKNILLNEGIRAWMAAQDQPHENLIFPEEVLPRGNAL 353
PLN00074 PLN00074
photosystem II D2 protein (PsbD); Provisional
1-56 6.20e-36

photosystem II D2 protein (PsbD); Provisional


Pssm-ID: 215048  Cd Length: 353  Bit Score: 122.46  E-value: 6.20e-36
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2438686390   1 DFVSQELRAAEDPEFETFYTKNILLNEGLRAWMAPQDQPHENFIFPEEVLPRGNAL 56
Cdd:PLN00074  298 DFVSQEIRAAEDPEFETFYTKNILLNEGIRAWMAAQDQPHENLIFPEEVLPRGNAL 353
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH