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Conserved domains on  [gi|260161135|emb|CAX62330|]
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pufM protein, partial [Chromatium weissei]

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

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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 ...
 1-238 5.02e-145

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 TIGR01115:

Pssm-ID: 447584  Cd Length: 305  Bit Score: 407.18  E-value: 5.02e-145
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260161135    1 MPEYQNIFNSVQVRSPAYPGVPLPKGSLPRLGKPLFSYWAGKIGDAQIGPLYLGFTGTLSLIFGFIALEIIGLNMLASVD 80
Cdd:TIGR01115   1 MAEYQNIFTQVQVRGPPHMGVPLPRGDFPRIGKPIFSYLLGKIGDAQIGPIYLGFTGIVSIVFGLMAIFIIGFNMLAQVG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260161135   81 WSPIELVKNLFWLALEPPAPSYGLSIPPLSEGGWWIMAGVFLTASIILWWVRTYKRAAALGMSQHLSWAFAAAIFFYLSL 160
Cdd:TIGR01115  81 WNPIQFFRQFFWLGLEPPSPEYGLSIPPLNEGGWWLIAGFFLTVSILLWWVRVYTRARALGMGTHLAWAFAAAIFLYLVL 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 260161135  161 GFIRPVMMGSWAEAVPFGIFPHLDWTAAFSIRYGNLYYNPFHMLSIAFLYGSALLFAMHGATILAVSRFGGDREIDQI 238
Cdd:TIGR01115 161 GFIRPVLMGSWSEAVPFGIFPHLDWTNAFSLRYGNLYYNPFHMLSIAFLYGSALLFAMHGATILAVSRFGGDRELEQI 238
 
Name Accession Description Interval E-value
pufM TIGR01115
photosynthetic reaction center M subunit; This model decribes the photosynthetic reaction ...
 1-238 5.02e-145

photosynthetic reaction center M subunit; This model decribes the photosynthetic reaction center M subunit in non-oxygenic photosynthetic bacteria. Reaction center is an integral membrane pigment-protein that carries out light-driven electron transfer reactions. At the core of reacion center is a collection light-harvesting cofactors and closely associated polypeptides. The core protein complex is made of L, M and H subunits. The common cofactors include bacterichlorophyll, bacteriopheophytins, ubiquinone and no-heme ferrous iron. The net result of electron tranfer reactions is the establishment of proton electrochemical gradient and production of reducing equivalents in form of NADH. Ultimately the process results in the reduction of C02 to carbohydrates(C6H12O6) In non-oxygenic organisms, the electron donor is some organic acid and not water. Much of our current functional understanding of photosynthesis comes from the structural determination, spectroscopic studies and mutational analysis on the reaction center of Rhodobacter sphaeroides. [Energy metabolism, Electron transport, Energy metabolism, Photosynthesis]


Pssm-ID: 273451  Cd Length: 305  Bit Score: 407.18  E-value: 5.02e-145
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260161135    1 MPEYQNIFNSVQVRSPAYPGVPLPKGSLPRLGKPLFSYWAGKIGDAQIGPLYLGFTGTLSLIFGFIALEIIGLNMLASVD 80
Cdd:TIGR01115   1 MAEYQNIFTQVQVRGPPHMGVPLPRGDFPRIGKPIFSYLLGKIGDAQIGPIYLGFTGIVSIVFGLMAIFIIGFNMLAQVG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260161135   81 WSPIELVKNLFWLALEPPAPSYGLSIPPLSEGGWWIMAGVFLTASIILWWVRTYKRAAALGMSQHLSWAFAAAIFFYLSL 160
Cdd:TIGR01115  81 WNPIQFFRQFFWLGLEPPSPEYGLSIPPLNEGGWWLIAGFFLTVSILLWWVRVYTRARALGMGTHLAWAFAAAIFLYLVL 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 260161135  161 GFIRPVMMGSWAEAVPFGIFPHLDWTAAFSIRYGNLYYNPFHMLSIAFLYGSALLFAMHGATILAVSRFGGDREIDQI 238
Cdd:TIGR01115 161 GFIRPVLMGSWSEAVPFGIFPHLDWTNAFSLRYGNLYYNPFHMLSIAFLYGSALLFAMHGATILAVSRFGGDRELEQI 238
PsbD COG5719
Photosystem II reaction center D2, PsbD [Energy production and conversion]; Photosystem II ...
 1-238 3.86e-134

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: 380.16  E-value: 3.86e-134
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260161135   1 MPEYQNIFNSVQVRSPAYPGVPLPKGSLPRLGKPLFSYWAGKIGDAQIGPLYLGFTGTLSLIFGFIALEIIGLNMLASVD 80
Cdd:COG5719    1 MALYQSIETKYQVRGGTLPGVPLPDGDEPRIGKPFFSYWLGDLGDFQVGPIYVGFFGVTSIFFGFLAIAIIGLNAAASVT 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260161135  81 WSPIELVKNLFWLALEPPAPSYGLSIPPLSEGGWWIMAGVFLTASIILWWVRTYKRAAALGMSQHLSWAFAAAIFFYLSL 160
Cdd:COG5719   81 WNPIQFVRQFFWLALEPPDPEYGLGLAPLAEGGWWQIATFFLTGSFLSWWLREYERARKLGMGTHVPWAFAAAIFLYLVL 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 260161135 161 GFIRPVMMGSWAEAVPFGIFPHLDWTAAFSIRYGNLYYNPFHMLSIAFLYGSALLFAMHGATILAVSRFGGDREIDQI 238
Cdd:COG5719  161 GVIRPLLMGSWGEAVPYGIFPHLDWTSNFSYRYGNFHYNPFHMLSITFLFGSTLLLAMHGATILAVSNPGGGREVKQI 238
Photo-RC_M cd09291
Subunit M of bacterial photosynthetic reaction center; Bacterial photosynthetic reaction ...
 12-238 7.35e-127

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: 360.97  E-value: 7.35e-127
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260161135  12 QVRSPAYPGVPLPKGSLPRLGKPLFSYWAGKIGDAQIGPLYLGFTGTLSLIFGFIALEIIGLNMLASVDWSPIELVKNLF 91
Cdd:cd09291    1 QVRGPADPGDPEPGDDLGRIGKPPFSYWLGKIGDAQIGPIYLGLWGVLSIIFGFIAIFIILFNMLAQVNWNPVQFLRQFF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260161135  92 WLALEPPAPSYGLSIPPLSEGGWWIMAGVFLTASIILWWVRTYKRAAALGMSQHLSWAFAAAIFFYLSLGFIRPVMMGSW 171
Cdd:cd09291   81 WLALEPPPPEYGLSIPPLNEGGWWLIAGFFLTLSILLWWIRTYTRAKALGMGTHLAWAFAAAIFLYLVIGFIRPVLMGSW 160

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 260161135 172 AEAVPFGIFPHLDWTAAFSIRYGNLYYNPFHMLSIAFLYGSALLFAMHGATILAVSRFGGDREIDQI 238
Cdd:cd09291  161 SEAVPFGIFPHLDWTNAFSIRYGNFYYNPFHMLSIAFLYGSTLLFAMHGATILAVSRFGGEREIEQI 227
Photo_RC pfam00124
Photosynthetic reaction centre protein;
51-238 4.47e-88

Photosynthetic reaction centre protein;


Pssm-ID: 425477  Cd Length: 260  Bit Score: 261.03  E-value: 4.47e-88
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260161135   51 LYLGFTGTLSLIFGFIALEIIGLNML--ASVDWSPIELVKNLFWLALEPPAPSYGLSIPPLSEGGWWIMAGVFLTASIIL 128
Cdd:pfam00124   1 FYVGFFGVLSIPTALLATFIIGIGFVaaPSVDWSPLLFGRNLITLAIEPPSPSYGLSFPPLWEGGLWQIITFHATIAFIS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260161135  129 WWVRTYKRAAALGMSQHLSWAFAAAIFFYLSLGFIRPVMMGSWAEAVPFGIFPHLDWTAAFSIRYGNLYYNPFHMLSIAF 208
Cdd:pfam00124  81 WWLREYEIARKLGMGPHIAWAFSAAIAAYLSLGLIRPILMGSWSEGFPLGIFPHLDWTSNFSYRYGNFLYNPFHMLGIAF 160

                         170       180       190
                  ....*....|....*....|....*....|
gi 260161135  209 LYGSALLFAMHGATILAVSRFGGDREIDQI 238
Cdd:pfam00124 161 LFGSALLLAMHGALVLSVLRPGGTREVESI 190
PRK14505 PRK14505
bifunctional photosynthetic reaction center subunit L/M; Provisional
 43-239 1.66e-42

bifunctional photosynthetic reaction center subunit L/M; Provisional


Pssm-ID: 172976  Cd Length: 643  Bit Score: 152.12  E-value: 1.66e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260161135  43 IGDAQIGPLYLGFTGTLSLIFGFIALEIIGLNMLASVDWSPIELVKNLFWLALEPPAPSYGLSIP-PLSEGGWWIMAGVF 121
Cdd:PRK14505 365 LGEGQVGPIYVGLWGVISFITFFASAFIILVDYGRQVEWNAIIYLREFWNLAVYPPPTEYGLSWNvPWDKGGAWLAATFF 444

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260161135 122 LTASIILWWVRTYKRAAALGMSQHLSWAFAAAIFFYLSLGFIRPVMMGSWAEAVPFGIFPHLDWTAAFSIRYGNLYYNPF 201
Cdd:PRK14505 445 LHISVLTWWARLYTRAKATGIGTHLAWGFASALSLYFVIYLFHPLALGNWSAAPGHGFRAILDWTNYVSIHWGNFYYNPF 524

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 260161135 202 HMLSIAFLYGSALLFAMHGATILAVSRFGGDREIDQIL 239
Cdd:PRK14505 525 HMLSIFFLLGSTLLLAMHGATIVATSKWKSEMEFTEMM 562
 
Name Accession Description Interval E-value
pufM TIGR01115
photosynthetic reaction center M subunit; This model decribes the photosynthetic reaction ...
 1-238 5.02e-145

photosynthetic reaction center M subunit; This model decribes the photosynthetic reaction center M subunit in non-oxygenic photosynthetic bacteria. Reaction center is an integral membrane pigment-protein that carries out light-driven electron transfer reactions. At the core of reacion center is a collection light-harvesting cofactors and closely associated polypeptides. The core protein complex is made of L, M and H subunits. The common cofactors include bacterichlorophyll, bacteriopheophytins, ubiquinone and no-heme ferrous iron. The net result of electron tranfer reactions is the establishment of proton electrochemical gradient and production of reducing equivalents in form of NADH. Ultimately the process results in the reduction of C02 to carbohydrates(C6H12O6) In non-oxygenic organisms, the electron donor is some organic acid and not water. Much of our current functional understanding of photosynthesis comes from the structural determination, spectroscopic studies and mutational analysis on the reaction center of Rhodobacter sphaeroides. [Energy metabolism, Electron transport, Energy metabolism, Photosynthesis]


Pssm-ID: 273451  Cd Length: 305  Bit Score: 407.18  E-value: 5.02e-145
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260161135    1 MPEYQNIFNSVQVRSPAYPGVPLPKGSLPRLGKPLFSYWAGKIGDAQIGPLYLGFTGTLSLIFGFIALEIIGLNMLASVD 80
Cdd:TIGR01115   1 MAEYQNIFTQVQVRGPPHMGVPLPRGDFPRIGKPIFSYLLGKIGDAQIGPIYLGFTGIVSIVFGLMAIFIIGFNMLAQVG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260161135   81 WSPIELVKNLFWLALEPPAPSYGLSIPPLSEGGWWIMAGVFLTASIILWWVRTYKRAAALGMSQHLSWAFAAAIFFYLSL 160
Cdd:TIGR01115  81 WNPIQFFRQFFWLGLEPPSPEYGLSIPPLNEGGWWLIAGFFLTVSILLWWVRVYTRARALGMGTHLAWAFAAAIFLYLVL 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 260161135  161 GFIRPVMMGSWAEAVPFGIFPHLDWTAAFSIRYGNLYYNPFHMLSIAFLYGSALLFAMHGATILAVSRFGGDREIDQI 238
Cdd:TIGR01115 161 GFIRPVLMGSWSEAVPFGIFPHLDWTNAFSLRYGNLYYNPFHMLSIAFLYGSALLFAMHGATILAVSRFGGDRELEQI 238
PsbD COG5719
Photosystem II reaction center D2, PsbD [Energy production and conversion]; Photosystem II ...
 1-238 3.86e-134

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: 380.16  E-value: 3.86e-134
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260161135   1 MPEYQNIFNSVQVRSPAYPGVPLPKGSLPRLGKPLFSYWAGKIGDAQIGPLYLGFTGTLSLIFGFIALEIIGLNMLASVD 80
Cdd:COG5719    1 MALYQSIETKYQVRGGTLPGVPLPDGDEPRIGKPFFSYWLGDLGDFQVGPIYVGFFGVTSIFFGFLAIAIIGLNAAASVT 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260161135  81 WSPIELVKNLFWLALEPPAPSYGLSIPPLSEGGWWIMAGVFLTASIILWWVRTYKRAAALGMSQHLSWAFAAAIFFYLSL 160
Cdd:COG5719   81 WNPIQFVRQFFWLALEPPDPEYGLGLAPLAEGGWWQIATFFLTGSFLSWWLREYERARKLGMGTHVPWAFAAAIFLYLVL 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 260161135 161 GFIRPVMMGSWAEAVPFGIFPHLDWTAAFSIRYGNLYYNPFHMLSIAFLYGSALLFAMHGATILAVSRFGGDREIDQI 238
Cdd:COG5719  161 GVIRPLLMGSWGEAVPYGIFPHLDWTSNFSYRYGNFHYNPFHMLSITFLFGSTLLLAMHGATILAVSNPGGGREVKQI 238
Photo-RC_M cd09291
Subunit M of bacterial photosynthetic reaction center; Bacterial photosynthetic reaction ...
 12-238 7.35e-127

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: 360.97  E-value: 7.35e-127
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260161135  12 QVRSPAYPGVPLPKGSLPRLGKPLFSYWAGKIGDAQIGPLYLGFTGTLSLIFGFIALEIIGLNMLASVDWSPIELVKNLF 91
Cdd:cd09291    1 QVRGPADPGDPEPGDDLGRIGKPPFSYWLGKIGDAQIGPIYLGLWGVLSIIFGFIAIFIILFNMLAQVNWNPVQFLRQFF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260161135  92 WLALEPPAPSYGLSIPPLSEGGWWIMAGVFLTASIILWWVRTYKRAAALGMSQHLSWAFAAAIFFYLSLGFIRPVMMGSW 171
Cdd:cd09291   81 WLALEPPPPEYGLSIPPLNEGGWWLIAGFFLTLSILLWWIRTYTRAKALGMGTHLAWAFAAAIFLYLVIGFIRPVLMGSW 160

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 260161135 172 AEAVPFGIFPHLDWTAAFSIRYGNLYYNPFHMLSIAFLYGSALLFAMHGATILAVSRFGGDREIDQI 238
Cdd:cd09291  161 SEAVPFGIFPHLDWTNAFSIRYGNFYYNPFHMLSIAFLYGSTLLFAMHGATILAVSRFGGEREIEQI 227
Photo_RC pfam00124
Photosynthetic reaction centre protein;
51-238 4.47e-88

Photosynthetic reaction centre protein;


Pssm-ID: 425477  Cd Length: 260  Bit Score: 261.03  E-value: 4.47e-88
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260161135   51 LYLGFTGTLSLIFGFIALEIIGLNML--ASVDWSPIELVKNLFWLALEPPAPSYGLSIPPLSEGGWWIMAGVFLTASIIL 128
Cdd:pfam00124   1 FYVGFFGVLSIPTALLATFIIGIGFVaaPSVDWSPLLFGRNLITLAIEPPSPSYGLSFPPLWEGGLWQIITFHATIAFIS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260161135  129 WWVRTYKRAAALGMSQHLSWAFAAAIFFYLSLGFIRPVMMGSWAEAVPFGIFPHLDWTAAFSIRYGNLYYNPFHMLSIAF 208
Cdd:pfam00124  81 WWLREYEIARKLGMGPHIAWAFSAAIAAYLSLGLIRPILMGSWSEGFPLGIFPHLDWTSNFSYRYGNFLYNPFHMLGIAF 160

                         170       180       190
                  ....*....|....*....|....*....|
gi 260161135  209 LYGSALLFAMHGATILAVSRFGGDREIDQI 238
Cdd:pfam00124 161 LFGSALLLAMHGALVLSVLRPGGTREVESI 190
PsbA COG5716
Photosystem II reaction center D1, PsbA [Energy production and conversion]; Photosystem II ...
 30-239 3.35e-81

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: 246.93  E-value: 3.35e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260161135  30 RLGKPLFSYWagKIGDAQIGP----LYLGFTGTLSLIFGFIALEIIGLNMLASVDWS----------PIELVKNLFWLAL 95
Cdd:COG5716    8 RTELPFFSSW--ERFCAWITStenrIYLGWFGVLMIPTLLTAFIIFGIAFLAAPPVDmdgirepvigSLLFGNNLITAAV 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260161135  96 EPPAPSYGLSIPP----------LSEGGWWIMAGVFLTASIILWWVRTYKRAAALGMSQHLSWAFAAAIFFYLSLGFIRP 165
Cdd:COG5716   86 EPPSPAIGLHFYPiweaasmdewLYNGGPYQLIVFHFLIGIWAYWGRTWELSYRLGMRPWIAWAFAAPVAAATSVGLVYP 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260161135 166 VMMGSWAEAVPFGIFPHLDWTAAFSIRYgNLYYNPFHMLSIAFLYGSALLFAMHGATILAVSR-------------FGGD 232
Cdd:COG5716  166 IGQGSFSEGVPLGIFGTFDFMLAFQADH-NILMNPFHMLGVAGVYGGALLFAMHGSLVTSVLRrettesesinagyFGGQ 244


                 ....*..
gi 260161135 233 REIDQIL 239
Cdd:COG5716  245 RELTYIV 251
PRK14505 PRK14505
bifunctional photosynthetic reaction center subunit L/M; Provisional
 43-239 1.66e-42

bifunctional photosynthetic reaction center subunit L/M; Provisional


Pssm-ID: 172976  Cd Length: 643  Bit Score: 152.12  E-value: 1.66e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260161135  43 IGDAQIGPLYLGFTGTLSLIFGFIALEIIGLNMLASVDWSPIELVKNLFWLALEPPAPSYGLSIP-PLSEGGWWIMAGVF 121
Cdd:PRK14505 365 LGEGQVGPIYVGLWGVISFITFFASAFIILVDYGRQVEWNAIIYLREFWNLAVYPPPTEYGLSWNvPWDKGGAWLAATFF 444

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260161135 122 LTASIILWWVRTYKRAAALGMSQHLSWAFAAAIFFYLSLGFIRPVMMGSWAEAVPFGIFPHLDWTAAFSIRYGNLYYNPF 201
Cdd:PRK14505 445 LHISVLTWWARLYTRAKATGIGTHLAWGFASALSLYFVIYLFHPLALGNWSAAPGHGFRAILDWTNYVSIHWGNFYYNPF 524

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 260161135 202 HMLSIAFLYGSALLFAMHGATILAVSRFGGDREIDQIL 239
Cdd:PRK14505 525 HMLSIFFLLGSTLLLAMHGATIVATSKWKSEMEFTEMM 562
Photo-RC_L cd09290
Subunit L of bacterial photosynthetic reaction center; Bacterial photosynthetic reaction ...
 32-235 1.21e-40

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: 140.27  E-value: 1.21e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260161135  32 GKPLFSYWagkigdaqIGPLYLGFTGTLSLIFGFIALEIIGlnmlasvdWSPI--ELVKNLFWLALEPPAPSYGLSIPPL 109
Cdd:cd09290   18 GGDLFDFW--------VGPFYVGFFGVVSIFFIILGVALII--------WEAVlgGPTWNIWAISINPPDLSYGLGAAPL 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260161135 110 SEGGWWIMAGVFLTASIILWWVRTYKRAAALGMSQHLSWAFAAAIFFYLSLGFIRPVMMGSWAEAVPFGIFPHLDWTAAF 189
Cdd:cd09290   82 TEGGLWQIITVCATGAFVSWALRQVEISRKLGMGYHVPIAFGVAISAYLTLQVIRPILMGAWGHGFPYGIMSHLDWVSNF 161

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 260161135 190 SIRYGNLYYNPFHMLSIAFLYGSALLFAMHGATILAVSRFGGDREI 235
Cdd:cd09290  162 GYQYLNFHYNPAHMIAITFLFTNTLALSMHGSLILSAANPKKGEPV 207
Photo_RC cd09223
D1, D2 subunits of photosystem II (PSII); M, L subunits of bacterial photosynthetic reaction ...
 112-238 1.26e-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.


Pssm-ID: 187745 [Multi-domain]  Cd Length: 199  Bit Score: 135.66  E-value: 1.26e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260161135 112 GGWWIMAGVFLTASIILWWVRTYKRAAALGMSQHLSWAFAAAIFFYLSLGFIRPVMMGSWAEAVPFGIFPHLDWTAAFSI 191
Cdd:cd09223   24 GGLWQIITFHALGAFISWMLRQVEIARKLGMGPHIAVAFSAPIASFFVLFLIRPIGQGSWSDAFPYGISSHLDWVNNFQY 103

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 260161135 192 RYGNLYYNPFHMLSIAFLYGSALLFAMHGATILAVSRFGGDREIDQI 238
Cdd:cd09223  104 EHNNWHYNPFHMLGVAFVFGGALLCAMHGALVLSVLNPEGEETEGQE 150
PRK14505 PRK14505
bifunctional photosynthetic reaction center subunit L/M; Provisional
 45-228 1.03e-22

bifunctional photosynthetic reaction center subunit L/M; Provisional


Pssm-ID: 172976  Cd Length: 643  Bit Score: 96.27  E-value: 1.03e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260161135  45 DAQIGPLYLGFTGTLSLIFGFIALEIIGLNMLASvdwspiELVKNLFWLALEPPAPSYGLSIPPLSEGGWWIMAGVFLTA 124
Cdd:PRK14505  61 DFWIGRFYVGLFGAISIIGIILGVAFYLYEGVVN------EGTFNILAMRIEPPPVSEGFNIDPAKPGFFWFLTMVAATI 134

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260161135 125 SIILWWVRTYKRAAALGMSQHLSWAFAAAIFFYLSLGFIRPVMMGSWAEAVPFGIFPHLDWTAAFSIRYGNLYYNPFHML 204
Cdd:PRK14505 135 AFIGWLLRQIDISLKLDMGMEVPIAFGAVVSSWITLQWLRPIAMGAWGHGFPLGITHHLDWVSNIGYQYYNFFYNPFHAI 214

                        170       180
                 ....*....|....*....|....
gi 260161135 205 SIAFLYGSALLFAMHGATILAVSR 228
Cdd:PRK14505 215 GITLLFASTLFLHMHGSAVLSEAK 238
Photosystem-II_D2 cd09288
D2 subunit of photosystem II (PS II); Photosystem II (PS II), D2 subunit. PS II is a ...
 112-223 3.93e-09

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: 55.76  E-value: 3.93e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260161135 112 GGWWIMAGVFLTASIILWWVRTYKRAAALGMSQHLSWAFAAAIFFYLSLGFIRPVMMGSWAEAVPFG---IFPHLDWTAA 188
Cdd:cd09288   95 GGLWTFVALHGAFGLIGFMLRQFEIARSVGIRPYNAIAFSGPIAVFVSVFLIYPLGQSGWFFAPSFGvaaIFRFILFFQG 174

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 260161135 189 FSirygNLYYNPFHMLSIAFLYGSALLFAMHGATI 223
Cdd:cd09288  175 FH----NWTLNPFHMMGVAGVLGAALLCAIHGATV 205
psbD CHL00004
photosystem II protein D2
 112-223 9.16e-08

photosystem II protein D2


Pssm-ID: 176949  Cd Length: 353  Bit Score: 51.78  E-value: 9.16e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260161135 112 GGWWIMAGVFLTASIILWWVRTYKRAAALGMSQHLSWAFAAAIFFYLSLGFIRPVMMGSWAEAVPFG---IFPHLDWTAA 188
Cdd:CHL00004 109 GGLWTFVALHGAFGLIGFMLRQFELARSVQLRPYNAIAFSGPIAVFVSVFLIYPLGQSGWFFAPSFGvaaIFRFILFFQG 188

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 260161135 189 FSirygNLYYNPFHMLSIAFLYGSALLFAMHGATI 223
Cdd:CHL00004 189 FH----NWTLNPFHMMGVAGVLGAALLCAIHGATV 219
PLN00056 PLN00056
photosystem Q(B) protein; Provisional
 55-223 2.05e-07

photosystem Q(B) protein; Provisional


Pssm-ID: 177687  Cd Length: 353  Bit Score: 50.90  E-value: 2.05e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260161135  55 FTGTLSLIFGFIALEIIGLNMLASVDWSPIELVKNLFWLALEPPAPSYGLSIPPLSEGGW---WIMAG-------VFLTA 124
Cdd:PLN00056  42 LTATSVFIIAFIAAPPVDIDGIREPVSGSLLYGNNIISGAIIPTSAAIGLHFYPIWEAASvdeWLYNGgpyelivLHFLL 121

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260161135 125 SIILWWVRTYKRAAALGMSQHLSWAFAAAIFFYLSLGFIRPVMMGSWAEAVPFGIFPHLDWTAAFSIRYgNLYYNPFHML 204
Cdd:PLN00056 122 GVACYMGREWELSFRLGMRPWIAVAYSAPVAAATAVFLIYPIGQGSFSDGMPLGISGTFNFMIVFQAEH-NILMHPFHML 200

                        170
                 ....*....|....*....
gi 260161135 205 SIAFLYGSALLFAMHGATI 223
Cdd:PLN00056 201 GVAGVFGGSLFSAMHGSLV 219
PLN00074 PLN00074
photosystem II D2 protein (PsbD); Provisional
 112-223 2.86e-07

photosystem II D2 protein (PsbD); Provisional


Pssm-ID: 215048  Cd Length: 353  Bit Score: 50.43  E-value: 2.86e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260161135 112 GGWWIMAGVFLTASIILWWVRTYKRAAALGMSQHLSWAFAAAIFFYLSLGFIRPVMMGSWAEAVPFGIFPHLDWTAAFSi 191
Cdd:PLN00074 109 GGLWTFVALHGAFGLIGFMLRQFELARSVQLRPYNAIAFSGPIAVFVSVFLIYPLGQSGWFFAPSFGVAAIFRFILFFQ- 187

                         90       100       110
                 ....*....|....*....|....*....|..
gi 260161135 192 RYGNLYYNPFHMLSIAFLYGSALLFAMHGATI 223
Cdd:PLN00074 188 GFHNWTLNPFHMMGVAGVLGAALLCAIHGATV 219
Photosystem-II_D1 cd09289
D1 subunit of photosystem II (PS II); Photosystem II (PS II), D2 subunit. PS II is a ...
 55-223 3.39e-07

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: 50.27  E-value: 3.39e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260161135  55 FTGTLSLIFGFIALEIIGLNMLASVDWSPIELVKNLFWLALEPPAPSYGLSIPPLSE----------GGWWIMAGVFLTA 124
Cdd:cd09289   36 LTATSVFIIAFIAAPPVDIDGIREPVSGSLLYGNNIISGAVVPTSNAIGLHFYPIWEaasldewlynGGPYQLIVLHFLL 115

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260161135 125 SIILWWVRTYKRAAALGMSQHLSWAFAAAIFFYLSLGFIRPVMMGSWAEAVPFGIFPHLDWTAAFSIRYgNLYYNPFHML 204
Cdd:cd09289  116 GVCCYMGREWELSYRLGMRPWIAVAYSAPVAAATAVFLIYPIGQGSFSDGMPLGISGTFNFMIVFQAEH-NILMHPFHML 194

                        170
                 ....*....|....*....
gi 260161135 205 SIAFLYGSALLFAMHGATI 223
Cdd:cd09289  195 GVAGVFGGSLFSAMHGSLV 213
 
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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