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Conserved domains on  [gi|51847685|gb|AAU10480|]
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PsbC, partial (chloroplast) [Ipomopsis tenuituba]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PSII super family cl08223
Photosystem II protein;
1-143 8.73e-113

Photosystem II protein;


The actual alignment was detected with superfamily member CHL00035:

Pssm-ID: 447585  Cd Length: 473  Bit Score: 327.06  E-value: 8.73e-113
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 51847685    1 AQGPTGLGKYLMRSPTGEVIFGGETMRFWDLRAPWLEPLRGPNGLDLSRLKKDIQPWQERRSAEYMTHAPLGSLNSVGGV 80
Cdd:CHL00035 331 AQGPTGLGKYLMRSPTGEIIFGGETMRFWDLRAPWLEPLRGPNGLDLSKLKKDIQPWQERRSAEYMTHAPLGSLNSVGGV 410

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 51847685   81 ATEINAVNYVSPRSWLATSHFVLAFFLFVGHLWHAGRARAAAAGFEKGIDRDFEPVLSMTPLN 143
Cdd:CHL00035 411 ATEINAVNYVSPRSWLATSHFVLGFFFFVGHLWHAGRARAAAAGFEKGIDRDFEPVLSMTPLN 473
 
Name Accession Description Interval E-value
psbC CHL00035
photosystem II 44 kDa protein
 1-143 8.73e-113

photosystem II 44 kDa protein


Pssm-ID: 214343  Cd Length: 473  Bit Score: 327.06  E-value: 8.73e-113
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 51847685    1 AQGPTGLGKYLMRSPTGEVIFGGETMRFWDLRAPWLEPLRGPNGLDLSRLKKDIQPWQERRSAEYMTHAPLGSLNSVGGV 80
Cdd:CHL00035 331 AQGPTGLGKYLMRSPTGEIIFGGETMRFWDLRAPWLEPLRGPNGLDLSKLKKDIQPWQERRSAEYMTHAPLGSLNSVGGV 410

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 51847685   81 ATEINAVNYVSPRSWLATSHFVLAFFLFVGHLWHAGRARAAAAGFEKGIDRDFEPVLSMTPLN 143
Cdd:CHL00035 411 ATEINAVNYVSPRSWLATSHFVLGFFFFVGHLWHAGRARAAAAGFEKGIDRDFEPVLSMTPLN 473
PsbC COG5718
Photosystem II reaction center chlorophyll a-binding protein CP43, PsbC [Energy production and ...
 1-143 6.58e-90

Photosystem II reaction center chlorophyll a-binding protein CP43, PsbC [Energy production and conversion]; Photosystem II reaction center chlorophyll a-binding protein CP43, PsbC is part of the Pathway/BioSystem: Photosystem II


Pssm-ID: 444428  Cd Length: 462  Bit Score: 268.61  E-value: 6.58e-90
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 51847685   1 AQGPTGLGKYLMRSPTGEVIFGGETMRFWDLRAPWLEPLRGPNGLDLSRLKKDIQPWQERRSAEYMTHAPLGSLNSVGGV 80
Cdd:COG5718 320 AQGPTGLGKYLMRSPTGEIIFGGETMRFWDFRGPWLEPLRGPNGLDLDKLQNDIQPWQVRRAAEYMTHAPLGSLNSVGGI 399

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 51847685  81 ATEINAVNYVSPRSWLATSHFVLAFFLFVGHLWHAGRARAAAAGFEKGIDRDFEPVLSMTPLN 143
Cdd:COG5718 400 ATEPNSVNFVSPRQWLASSHFVLAFFFLVGHLWHAGRARAAAAGFEKGIDRETEPALSMPDLD 462
psbC TIGR01153
photosystem II 44 kDa subunit reaction center protein (also called P6 protein, CP43), ...
 1-134 2.72e-77

photosystem II 44 kDa subunit reaction center protein (also called P6 protein, CP43), bacterial and chloroplast; This model describes the Photosystem II, 44kDa subunit (also called P6 protein, CP43) in bacterial and its equivalents in chloroplast of algae and higher plants. Photosystem II is in 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 44 kDa protein,DI, DII, Cyt.b, Cyt.f, iron-sulphur protein and others. Functinally 44 kDa subunit is imlicated in chlorophyll binding. 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 high resolution X-ray structural data is presently available, recently a 3D structure of the supercomplex has been described by cryo-electron microscopy. Besides 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: 213589  Cd Length: 432  Bit Score: 235.48  E-value: 2.72e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 51847685     1 AQGPTGLGKYLMRSPTGEVIFGGETMRFWDLRAPWLEPLRGPNGLDLSRLKKDIQPWQERRSAEYMTHAPLGSLNSVGGV 80
Cdd:TIGR01153 299 AQGPTGLGKYLMRSPTGEIIFGGETMRFWDFRGPWLEPLRGPNGLSLDKIQNDIQPWQVRRAAEYMTHAPNGSLNSVGGV 378

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 51847685    81 ATEINAVNYVSPRSWLATSHFVLAFFLFVGHLWHAGRARAAAAGFEKGIDRDFE 134
Cdd:TIGR01153 379 ITEPNSVNFVSPRQWLAGSHFVLGFFFLVGHLWHAGRARAAAAGFEKGIDRKTE 432
PSII pfam00421
Photosystem II protein;
1-142 1.15e-43

Photosystem II protein;


Pssm-ID: 425673  Cd Length: 499  Bit Score: 149.58  E-value: 1.15e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 51847685     1 AQGPTGL--------GKYLMRSPTGEVIFGGETMRFWDLR--------APWLE-----------PL-RGPNGLDLSRLKK 52
Cdd:pfam00421 317 APAKGGLfrvgpmvnGDGLARSWLGHIIFGDETGRELDVRrmpnffetFPVVLvdkdgivradiPFrRGESKYSLEQLGV 396

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 51847685    53 DIQ-------------PWQERRsaeYMTHAPLGSLNSVGGVATEINAVNYVSPRSWLATSHFVLAFFLFVGHLWHAGRAR 119
Cdd:pfam00421 397 TVQfyggelngqtftdPWQVKR---YARHAQLGELFSFDRVTTESDGVFRSSPRGWLAFGHFCFALLFFFGHLWHGGRTL 473

                         170       180
                  ....*....|....*....|....*.
gi 51847685   120 AAAAG--FEKGIDRDFEP-VLSMTPL 142
Cdd:pfam00421 474 FRDVFagFEPGIDRQVEFgVFQKLGD 499
 
Name Accession Description Interval E-value
psbC CHL00035
photosystem II 44 kDa protein
 1-143 8.73e-113

photosystem II 44 kDa protein


Pssm-ID: 214343  Cd Length: 473  Bit Score: 327.06  E-value: 8.73e-113
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 51847685    1 AQGPTGLGKYLMRSPTGEVIFGGETMRFWDLRAPWLEPLRGPNGLDLSRLKKDIQPWQERRSAEYMTHAPLGSLNSVGGV 80
Cdd:CHL00035 331 AQGPTGLGKYLMRSPTGEIIFGGETMRFWDLRAPWLEPLRGPNGLDLSKLKKDIQPWQERRSAEYMTHAPLGSLNSVGGV 410

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 51847685   81 ATEINAVNYVSPRSWLATSHFVLAFFLFVGHLWHAGRARAAAAGFEKGIDRDFEPVLSMTPLN 143
Cdd:CHL00035 411 ATEINAVNYVSPRSWLATSHFVLGFFFFVGHLWHAGRARAAAAGFEKGIDRDFEPVLSMTPLN 473
PsbC COG5718
Photosystem II reaction center chlorophyll a-binding protein CP43, PsbC [Energy production and ...
 1-143 6.58e-90

Photosystem II reaction center chlorophyll a-binding protein CP43, PsbC [Energy production and conversion]; Photosystem II reaction center chlorophyll a-binding protein CP43, PsbC is part of the Pathway/BioSystem: Photosystem II


Pssm-ID: 444428  Cd Length: 462  Bit Score: 268.61  E-value: 6.58e-90
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 51847685   1 AQGPTGLGKYLMRSPTGEVIFGGETMRFWDLRAPWLEPLRGPNGLDLSRLKKDIQPWQERRSAEYMTHAPLGSLNSVGGV 80
Cdd:COG5718 320 AQGPTGLGKYLMRSPTGEIIFGGETMRFWDFRGPWLEPLRGPNGLDLDKLQNDIQPWQVRRAAEYMTHAPLGSLNSVGGI 399

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 51847685  81 ATEINAVNYVSPRSWLATSHFVLAFFLFVGHLWHAGRARAAAAGFEKGIDRDFEPVLSMTPLN 143
Cdd:COG5718 400 ATEPNSVNFVSPRQWLASSHFVLAFFFLVGHLWHAGRARAAAAGFEKGIDRETEPALSMPDLD 462
psbC TIGR01153
photosystem II 44 kDa subunit reaction center protein (also called P6 protein, CP43), ...
 1-134 2.72e-77

photosystem II 44 kDa subunit reaction center protein (also called P6 protein, CP43), bacterial and chloroplast; This model describes the Photosystem II, 44kDa subunit (also called P6 protein, CP43) in bacterial and its equivalents in chloroplast of algae and higher plants. Photosystem II is in 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 44 kDa protein,DI, DII, Cyt.b, Cyt.f, iron-sulphur protein and others. Functinally 44 kDa subunit is imlicated in chlorophyll binding. 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 high resolution X-ray structural data is presently available, recently a 3D structure of the supercomplex has been described by cryo-electron microscopy. Besides 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: 213589  Cd Length: 432  Bit Score: 235.48  E-value: 2.72e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 51847685     1 AQGPTGLGKYLMRSPTGEVIFGGETMRFWDLRAPWLEPLRGPNGLDLSRLKKDIQPWQERRSAEYMTHAPLGSLNSVGGV 80
Cdd:TIGR01153 299 AQGPTGLGKYLMRSPTGEIIFGGETMRFWDFRGPWLEPLRGPNGLSLDKIQNDIQPWQVRRAAEYMTHAPNGSLNSVGGV 378

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 51847685    81 ATEINAVNYVSPRSWLATSHFVLAFFLFVGHLWHAGRARAAAAGFEKGIDRDFE 134
Cdd:TIGR01153 379 ITEPNSVNFVSPRQWLAGSHFVLGFFFLVGHLWHAGRARAAAAGFEKGIDRKTE 432
PSII pfam00421
Photosystem II protein;
1-142 1.15e-43

Photosystem II protein;


Pssm-ID: 425673  Cd Length: 499  Bit Score: 149.58  E-value: 1.15e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 51847685     1 AQGPTGL--------GKYLMRSPTGEVIFGGETMRFWDLR--------APWLE-----------PL-RGPNGLDLSRLKK 52
Cdd:pfam00421 317 APAKGGLfrvgpmvnGDGLARSWLGHIIFGDETGRELDVRrmpnffetFPVVLvdkdgivradiPFrRGESKYSLEQLGV 396

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 51847685    53 DIQ-------------PWQERRsaeYMTHAPLGSLNSVGGVATEINAVNYVSPRSWLATSHFVLAFFLFVGHLWHAGRAR 119
Cdd:pfam00421 397 TVQfyggelngqtftdPWQVKR---YARHAQLGELFSFDRVTTESDGVFRSSPRGWLAFGHFCFALLFFFGHLWHGGRTL 473

                         170       180
                  ....*....|....*....|....*.
gi 51847685   120 AAAAG--FEKGIDRDFEP-VLSMTPL 142
Cdd:pfam00421 474 FRDVFagFEPGIDRQVEFgVFQKLGD 499
PS_antenn_a_b TIGR03041
chlorophyll a/b binding light-harvesting protein; This model represents a family of proteins ...
 91-114 1.94e-06

chlorophyll a/b binding light-harvesting protein; This model represents a family of proteins from the Cyanobacteria, closely homologous to and yet distinct from PbsC, a chlorophyll a antenna protein of photosystem II. Members are not univerally present in Cyanobacteria, while the family has several members per genome in Prochlorococcus marinus, with seven members in a strain adapted to low light conditions. These antenna proteins may deliver light energy to photosystem I and/or photosystem II. [Energy metabolism, Photosynthesis]


Pssm-ID: 213761  Cd Length: 321  Bit Score: 45.76  E-value: 1.94e-06
                          10        20
                  ....*....|....*....|....
gi 51847685    91 SPRSWLATSHFVLAFFLFVGHLWH 114
Cdd:TIGR03041 288 TSRAWLANVHFYLGFFFLQGHLWH 311
IsiA COG5742
Chlorophyll-binding protein PcbABC/IsiA [Energy production and conversion];
91-114 1.49e-05

Chlorophyll-binding protein PcbABC/IsiA [Energy production and conversion];


Pssm-ID: 444452  Cd Length: 346  Bit Score: 43.01  E-value: 1.49e-05
                        10        20
                ....*....|....*....|....
gi 51847685  91 SPRSWLATSHFVLAFFLFVGHLWH 114
Cdd:COG5742 298 TSRAWLANAHFYLGFFFLQGHLWH 321
psbB CHL00062
photosystem II 47 kDa protein
 91-114 1.53e-03

photosystem II 47 kDa protein


Pssm-ID: 214350  Cd Length: 504  Bit Score: 37.36  E-value: 1.53e-03
                         10        20
                 ....*....|....*....|....
gi 51847685   91 SPRSWLATSHFVLAFFLFVGHLWH 114
Cdd:CHL00062 446 SPRGWFTFGHASFALLFFFGHIWH 469
 
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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