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Conserved domains on  [gi|373884041|gb|AEY79353|]
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ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit, partial [Nostoc sp. PCC 6720]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RuBisCO_large super family cl08232
Ribulose bisphosphate carboxylase large chain; Ribulose bisphosphate carboxylase (Rubisco) ...
 1-99 2.89e-75

Ribulose bisphosphate carboxylase large chain; Ribulose bisphosphate carboxylase (Rubisco) plays an important role in the Calvin reductive pentose phosphate pathway. It catalyzes the primary CO2 fixation step. Rubisco is activated by carbamylation of an active site lysine, stabilized by a divalent cation, which then catalyzes the proton abstraction from the substrate ribulose 1,5 bisphosphate (RuBP) and leads to the formation of two molecules of 3-phosphoglycerate. Members of the Rubisco family can be divided into 4 subgroups, Form I-IV, which differ in their taxonomic distribution and subunit composition. Form I-III have Rubisco activity, while Form IV, also called Rubisco-like proteins (RLP), are missing critical active site residues and therefore do not catalyze CO2 fixation. They are believed to utilize a related enzymatic mechanism, but have divergent functions.


The actual alignment was detected with superfamily member CHL00040:

Pssm-ID: 471793  Cd Length: 475  Bit Score: 229.20  E-value: 2.89e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373884041   1 VASGGIHVWHMPALVEIFGDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQARNEGRNLAREGNDIIREAAKWSPELA 80
Cdd:CHL00040 377 VASGGIHVWHMPALTEIFGDDSVLQFGGGTLGHPWGNAPGAVANRVALEACVQARNEGRDLAREGNEIIREAAKWSPELA 456

                         90
                 ....*....|....*....
gi 373884041  81 VACELWKEIKFEFEAMDTV 99
Cdd:CHL00040 457 AACEVWKEIKFEFETTDTL 475
 
Name Accession Description Interval E-value
rbcL CHL00040
ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
 1-99 2.89e-75

ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit


Pssm-ID: 176981  Cd Length: 475  Bit Score: 229.20  E-value: 2.89e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373884041   1 VASGGIHVWHMPALVEIFGDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQARNEGRNLAREGNDIIREAAKWSPELA 80
Cdd:CHL00040 377 VASGGIHVWHMPALTEIFGDDSVLQFGGGTLGHPWGNAPGAVANRVALEACVQARNEGRDLAREGNEIIREAAKWSPELA 456

                         90
                 ....*....|....*....
gi 373884041  81 VACELWKEIKFEFEAMDTV 99
Cdd:CHL00040 457 AACEVWKEIKFEFETTDTL 475
RuBisCO_large_I cd08212
Ribulose bisphosphate carboxylase large chain, Form I; Ribulose bisphosphate carboxylase ...
 1-97 2.52e-67

Ribulose bisphosphate carboxylase large chain, Form I; Ribulose bisphosphate carboxylase (Rubisco) plays an important role in the Calvin reductive pentose phosphate pathway. It catalyzes the primary CO2 fixation step. Rubisco is activated by carbamylation of an active site lysine, stabilized by a divalent cation, which then catalyzes the proton abstraction from the substrate ribulose 1,5 bisphosphate (RuBP) and leads to the formation of two molecules of 3-phosphoglycerate. Members of the Rubisco family can be divided into 4 subgroups, Form I-IV , which differ in their taxonomic distribution and subunit composition. Form I is the most abundant class, present in plants, algae, and bacteria, and forms large complexes composed of 8 large and 8 small subunits.


Pssm-ID: 173977  Cd Length: 450  Bit Score: 208.05  E-value: 2.52e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373884041   1 VASGGIHVWHMPALVEIFGDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQARNEGRNLAREGNDIIREAAKWSPELA 80
Cdd:cd08212  354 VASGGIHVGQMHQLIEIFGDDVVLQFGGGTIGHPWGIAAGATANRVALEAMVQARNEGRDLAREGPEILREAAKWSPELA 433

                         90
                 ....*....|....*..
gi 373884041  81 VACELWKEIKFEFEAMD 97
Cdd:cd08212  434 AALETWKDIKFEFESTD 450
RuBisCO_large pfam00016
Ribulose bisphosphate carboxylase large chain, catalytic domain; The C-terminal domain of ...
 1-86 4.18e-32

Ribulose bisphosphate carboxylase large chain, catalytic domain; The C-terminal domain of RuBisCO large chain is the catalytic domain adopting a TIM barrel fold.


Pssm-ID: 459631  Cd Length: 292  Bit Score: 113.22  E-value: 4.18e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373884041    1 VASGGIHVWHMPALVEIFGD-DSVLQFGGGTLGHPWGNAPGATANRVALEACVqarnegrnlarEGNDIIREaAKWSPEL 79
Cdd:pfam00016 218 VASGGIHAGQMPGLFDNLGDsDVILQFGGGTFGHPDGPAAGAKANRQALEAWV-----------EGRDLEEY-AKEHPEL 285


                  ....*..
gi 373884041   80 AVACELW 86
Cdd:pfam00016 286 ARAFESW 292
RbcL COG1850
Ribulose 1,5-bisphosphate carboxylase, large subunit, or a RuBisCO-like protein [Carbohydrate ...
 1-91 5.88e-29

Ribulose 1,5-bisphosphate carboxylase, large subunit, or a RuBisCO-like protein [Carbohydrate transport and metabolism];


Pssm-ID: 441455  Cd Length: 417  Bit Score: 107.18  E-value: 5.88e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373884041   1 VASGGIHVWHMPALVEIFGDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQARNegrnlaregndiIREAAKWSPELA 80
Cdd:COG1850  339 VPSGGQHPGQVPELYDALGTDLILQAGGGIHGHPDGPAAGARALRQAWEAAVAGIP------------LEEYAKTHPELA 406

                         90
                 ....*....|.
gi 373884041  81 VACELWKEIKF 91
Cdd:COG1850  407 AALEKWGKKAP 417
salvage_mtnW TIGR03332
2,3-diketo-5-methylthiopentyl-1-phosphate enolase; Members of this family are the methionine ...
 1-86 2.06e-09

2,3-diketo-5-methylthiopentyl-1-phosphate enolase; Members of this family are the methionine salvage pathway enzyme 2,3-diketo-5-methylthiopentyl-1-phosphate enolase, a homolog of RuBisCO. This protein family seems restricted to Bacillus subtilis and close relatives, where two separate proteins carry the enolase and phosphatase activities that in other species occur in a single protein, MtnC (TIGR01691). [Amino acid biosynthesis, Aspartate family, Central intermediary metabolism, Sulfur metabolism]


Pssm-ID: 132375  Cd Length: 407  Bit Score: 52.53  E-value: 2.06e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373884041    1 VASGGIHVWHMPALVEIFGDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQARNegrnlaregndiIREAAKWSPELA 80
Cdd:TIGR03332 333 VPSAGIHPGMVPLIMRDFGIDHIINAGGGIHGHPNGAQGGGRAFRAAIDAVLEAKP------------LHEKAADDIDLK 400


                  ....*.
gi 373884041   81 VACELW 86
Cdd:TIGR03332 401 LALDKW 406
 
Name Accession Description Interval E-value
rbcL CHL00040
ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
 1-99 2.89e-75

ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit


Pssm-ID: 176981  Cd Length: 475  Bit Score: 229.20  E-value: 2.89e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373884041   1 VASGGIHVWHMPALVEIFGDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQARNEGRNLAREGNDIIREAAKWSPELA 80
Cdd:CHL00040 377 VASGGIHVWHMPALTEIFGDDSVLQFGGGTLGHPWGNAPGAVANRVALEACVQARNEGRDLAREGNEIIREAAKWSPELA 456

                         90
                 ....*....|....*....
gi 373884041  81 VACELWKEIKFEFEAMDTV 99
Cdd:CHL00040 457 AACEVWKEIKFEFETTDTL 475
RuBisCO_large_I cd08212
Ribulose bisphosphate carboxylase large chain, Form I; Ribulose bisphosphate carboxylase ...
 1-97 2.52e-67

Ribulose bisphosphate carboxylase large chain, Form I; Ribulose bisphosphate carboxylase (Rubisco) plays an important role in the Calvin reductive pentose phosphate pathway. It catalyzes the primary CO2 fixation step. Rubisco is activated by carbamylation of an active site lysine, stabilized by a divalent cation, which then catalyzes the proton abstraction from the substrate ribulose 1,5 bisphosphate (RuBP) and leads to the formation of two molecules of 3-phosphoglycerate. Members of the Rubisco family can be divided into 4 subgroups, Form I-IV , which differ in their taxonomic distribution and subunit composition. Form I is the most abundant class, present in plants, algae, and bacteria, and forms large complexes composed of 8 large and 8 small subunits.


Pssm-ID: 173977  Cd Length: 450  Bit Score: 208.05  E-value: 2.52e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373884041   1 VASGGIHVWHMPALVEIFGDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQARNEGRNLAREGNDIIREAAKWSPELA 80
Cdd:cd08212  354 VASGGIHVGQMHQLIEIFGDDVVLQFGGGTIGHPWGIAAGATANRVALEAMVQARNEGRDLAREGPEILREAAKWSPELA 433

                         90
                 ....*....|....*..
gi 373884041  81 VACELWKEIKFEFEAMD 97
Cdd:cd08212  434 AALETWKDIKFEFESTD 450
rbcL PRK04208
ribulose bisophosphate carboxylase; Reviewed
 1-99 8.97e-65

ribulose bisophosphate carboxylase; Reviewed


Pssm-ID: 179787  Cd Length: 468  Bit Score: 202.06  E-value: 8.97e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373884041   1 VASGGIHVWHMPALVEIFGDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQARNEGRNLAREGNDIIREAAKWSPELA 80
Cdd:PRK04208 370 VASGGIHPGHMPALLDIFGDDVVLQFGGGTHGHPDGTAAGATANRVALEACVEARNEGRDIEKEGPDILEEAAKWSPELA 449

                         90
                 ....*....|....*....
gi 373884041  81 VACELWKEIKFEFEAMDTV 99
Cdd:PRK04208 450 AALEKWGEIKFEFDTVDTL 468
RuBisCO_large_I_II_III cd08206
Ribulose bisphosphate carboxylase large chain, Form I,II,III; Ribulose bisphosphate ...
 1-86 3.45e-40

Ribulose bisphosphate carboxylase large chain, Form I,II,III; Ribulose bisphosphate carboxylase (Rubisco) plays an important role in the Calvin reductive pentose phosphate pathway. It catalyzes the primary CO2 fixation step. Rubisco is activated by carbamylation of an active site lysine, stabilized by a divalent cation, which then catalyzes the proton abstraction from the substrate ribulose 1,5 bisphosphate (RuBP) and leads to the formation of two molecules of 3-phosphoglycerate. Members of the Rubisco family can be divided into 4 subgroups, Form I-IV, which differ in their taxonomic distribution and subunit composition. Form I-III have Rubisco activity, while Form IV, also called Rubico-like proteins (RLP), are missing critical active site residues.


Pssm-ID: 173971  Cd Length: 414  Bit Score: 136.98  E-value: 3.45e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373884041   1 VASGGIHVWHMPALVEIFGDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQARnegrnlaregndIIREAAKWSPELA 80
Cdd:cd08206  341 VASGGLHPGRMPALIEILGDDVILQFGGGTHGHPDGPAAGAKANRQALEAWVQGR------------ILREYAKTHKELA 408


                 ....*.
gi 373884041  81 VACELW 86
Cdd:cd08206  409 AALEKW 414
RuBisCO_large pfam00016
Ribulose bisphosphate carboxylase large chain, catalytic domain; The C-terminal domain of ...
 1-86 4.18e-32

Ribulose bisphosphate carboxylase large chain, catalytic domain; The C-terminal domain of RuBisCO large chain is the catalytic domain adopting a TIM barrel fold.


Pssm-ID: 459631  Cd Length: 292  Bit Score: 113.22  E-value: 4.18e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373884041    1 VASGGIHVWHMPALVEIFGD-DSVLQFGGGTLGHPWGNAPGATANRVALEACVqarnegrnlarEGNDIIREaAKWSPEL 79
Cdd:pfam00016 218 VASGGIHAGQMPGLFDNLGDsDVILQFGGGTFGHPDGPAAGAKANRQALEAWV-----------EGRDLEEY-AKEHPEL 285


                  ....*..
gi 373884041   80 AVACELW 86
Cdd:pfam00016 286 ARAFESW 292
RbcL COG1850
Ribulose 1,5-bisphosphate carboxylase, large subunit, or a RuBisCO-like protein [Carbohydrate ...
 1-91 5.88e-29

Ribulose 1,5-bisphosphate carboxylase, large subunit, or a RuBisCO-like protein [Carbohydrate transport and metabolism];


Pssm-ID: 441455  Cd Length: 417  Bit Score: 107.18  E-value: 5.88e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373884041   1 VASGGIHVWHMPALVEIFGDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQARNegrnlaregndiIREAAKWSPELA 80
Cdd:COG1850  339 VPSGGQHPGQVPELYDALGTDLILQAGGGIHGHPDGPAAGARALRQAWEAAVAGIP------------LEEYAKTHPELA 406

                         90
                 ....*....|.
gi 373884041  81 VACELWKEIKF 91
Cdd:COG1850  407 AALEKWGKKAP 417
RuBisCO_large cd08148
Ribulose bisphosphate carboxylase large chain; Ribulose bisphosphate carboxylase (Rubisco) ...
 1-47 5.26e-22

Ribulose bisphosphate carboxylase large chain; Ribulose bisphosphate carboxylase (Rubisco) plays an important role in the Calvin reductive pentose phosphate pathway. It catalyzes the primary CO2 fixation step. Rubisco is activated by carbamylation of an active site lysine, stabilized by a divalent cation, which then catalyzes the proton abstraction from the substrate ribulose 1,5 bisphosphate (RuBP) and leads to the formation of two molecules of 3-phosphoglycerate. Members of the Rubisco family can be divided into 4 subgroups, Form I-IV, which differ in their taxonomic distribution and subunit composition. Form I-III have Rubisco activity, while Form IV, also called Rubisco-like proteins (RLP), are missing critical active site residues and therefore do not catalyze CO2 fixation. They are believed to utilize a related enzymatic mechanism, but have divergent functions.


Pssm-ID: 173969  Cd Length: 366  Bit Score: 87.87  E-value: 5.26e-22
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 373884041   1 VASGGIHVWHMPALVEIFGDDSVLQFGGGTLGHPWGNAPGATANRVA 47
Cdd:cd08148  320 VASGGIHPGLVPGILRDFGIDVILQAGGGIHGHPDGTVAGARAMRQA 366
RuBisCO_large_III cd08213
Ribulose bisphosphate carboxylase large chain, Form III; Ribulose bisphosphate carboxylase ...
 1-86 3.28e-18

Ribulose bisphosphate carboxylase large chain, Form III; Ribulose bisphosphate carboxylase (Rubisco) plays an important role in the Calvin reductive pentose phosphate pathway. It catalyzes the primary CO2 fixation step. Rubisco is activated by carbamylation of an active site lysine, stabilized by a divalent cation, which then catalyzes the proton abstraction from the substrate ribulose 1,5 bisphosphate (RuBP) and leads to the formation of two molecules of 3-phosphoglycerate. Members of the Rubisco family can be divided into 4 subgroups, Form I-IV , which differ in their taxonomic distribution and subunit composition. Form III is only found in archaea and forms large subunit oligomers (dimers or decamers) that do not include small subunits.


Pssm-ID: 173978  Cd Length: 412  Bit Score: 77.43  E-value: 3.28e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373884041   1 VASGGIHVWHMPALVEIFGDDSVLQFGGGTLGHPWGNAPGATANRVALEACVqarnEGRNLaregndiiREAAKWSPELA 80
Cdd:cd08213  339 VASGGLHPGLVPDVIDILGKDIVIQVGGGVHGHPDGTRAGAKAVRQAIEAAL----EGISL--------DEYAKDHKELA 406


                 ....*.
gi 373884041  81 VACELW 86
Cdd:cd08213  407 RALEKW 412
mtnW PRK09549
2,3-diketo-5-methylthiopentyl-1-phosphate enolase; Reviewed
 1-86 1.29e-12

2,3-diketo-5-methylthiopentyl-1-phosphate enolase; Reviewed


Pssm-ID: 236560  Cd Length: 407  Bit Score: 61.95  E-value: 1.29e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373884041   1 VASGGIHVWHMPALVEIFGDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQARNegrnlaregndiIREAAKWSPELA 80
Cdd:PRK09549 328 VPSAGIHPGLVPLLIRDFGKDVVINAGGGIHGHPNGAQGGGKAFRAAIDAVLQGKP------------LHEAAEDDENLH 395


                 ....*.
gi 373884041  81 VACELW 86
Cdd:PRK09549 396 SALDIW 401
RLP_DK-MTP-1-P-enolase cd08209
2,3-diketo-5-methylthiopentyl-1-phosphate enolase; Ribulose bisphosphate carboxylase like ...
 1-86 4.08e-10

2,3-diketo-5-methylthiopentyl-1-phosphate enolase; Ribulose bisphosphate carboxylase like proteins (RLPs) similar to B. subtilis YkrW protein, have been identified as 2,3-diketo-5-methylthiopentyl-1-phosphate enolases. They catalyze the tautomerization of 2,3-diketo-5-methylthiopentane 1-phosphate (DK-MTP 1-P). This is an important step in the methionine salvage pathway in which 5-methylthio-D-ribose (MTR) derived from 5'-methylthioadenosine is converted to methionine.


Pssm-ID: 173974  Cd Length: 391  Bit Score: 54.63  E-value: 4.08e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373884041   1 VASGGIHVWHMPALVEIFGDDSVLQFGGGTLGHPWGNAPGATANRVALEACvqarnegrnlarEGNDIIREAAKWSPELA 80
Cdd:cd08209  317 VPSAGIHPGLVPQLLRDFGTDVILNAGGGIHGHPDGAAAGVRAFREAIDAV------------LAGESLEPAAIPDGPLK 384


                 ....*.
gi 373884041  81 VACELW 86
Cdd:cd08209  385 SALDKW 390
salvage_mtnW TIGR03332
2,3-diketo-5-methylthiopentyl-1-phosphate enolase; Members of this family are the methionine ...
 1-86 2.06e-09

2,3-diketo-5-methylthiopentyl-1-phosphate enolase; Members of this family are the methionine salvage pathway enzyme 2,3-diketo-5-methylthiopentyl-1-phosphate enolase, a homolog of RuBisCO. This protein family seems restricted to Bacillus subtilis and close relatives, where two separate proteins carry the enolase and phosphatase activities that in other species occur in a single protein, MtnC (TIGR01691). [Amino acid biosynthesis, Aspartate family, Central intermediary metabolism, Sulfur metabolism]


Pssm-ID: 132375  Cd Length: 407  Bit Score: 52.53  E-value: 2.06e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373884041    1 VASGGIHVWHMPALVEIFGDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQARNegrnlaregndiIREAAKWSPELA 80
Cdd:TIGR03332 333 VPSAGIHPGMVPLIMRDFGIDHIINAGGGIHGHPNGAQGGGRAFRAAIDAVLEAKP------------LHEKAADDIDLK 400


                  ....*.
gi 373884041   81 VACELW 86
Cdd:TIGR03332 401 LALDKW 406
RuBisCO_IV_RLP cd08205
Ribulose bisphosphate carboxylase like proteins, Rubisco-Form IV; Ribulose bisphosphate ...
 1-47 1.79e-06

Ribulose bisphosphate carboxylase like proteins, Rubisco-Form IV; Ribulose bisphosphate carboxylase (Rubisco) plays an important role in the Calvin reductive pentose phosphate pathway. It catalyzes the primary CO2 fixation step. Rubisco is activated by carbamylation of an active site lysine, stabilized by a divalent cation, which then catalyzes the proton abstraction from the substrate ribulose 1,5 bisphosphate (RuBP) and leads to the formation of two molecules of 3-phosphoglycerate. Members of the Rubisco family can be divided into 4 subgroups, Form I-IV, which differ in their taxonomic distribution and subunit composition. Form I-III have Rubisco activity, while Form IV, also called Rubisco-like proteins (RLP), are missing critical active site residues and therefore do not catalyze CO2 fixation. They are believed to utilize a related enzymatic mechanism, but have divergent functions, like for example 2,3-diketo-5-methylthiopentyl-1-phosphate enolase or 5-methylthio-d-ribulose 1-phosphate isomerase.


Pssm-ID: 173970  Cd Length: 367  Bit Score: 44.45  E-value: 1.79e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 373884041   1 VASGGIHVWHMPALVEIFGDDSVLQFGGGTLGHPWGNAPGATANRVA 47
Cdd:cd08205  321 VPSGGMHPGRVPELYRDYGPDVILLAGGGILGHPDGAAAGVRAFRQA 367
RLP_NonPhot cd08207
Ribulose bisphosphate carboxylase like proteins from nonphototrophic bacteria; Ribulose ...
 1-82 2.04e-05

Ribulose bisphosphate carboxylase like proteins from nonphototrophic bacteria; Ribulose bisphosphate carboxylase (Rubisco) plays an important role in the Calvin reductive pentose phosphate pathway. It catalyzes the primary CO2 fixation step. Rubisco is activated by carbamylation of an active site lysine, stabilized by a divalent cation, which then catalyzes the proton abstraction from the substrate ribulose 1,5 bisphosphate (RuBP) and leads to the formation of two molecules of 3-phosphoglycerate. Members of the Rubisco family can be divided into 4 subgroups, Form I-IV, which differ in their taxonomic distribution and subunit composition. Form I-III have Rubisco activity, while Form IV, also called Rubisco-like proteins (RLP), are missing critical active site residues and therefore do not catalyze CO2 fixation. They are believed to utilize a related enzymatic mechanism, but have divergent functions. The specific function of this subgroup is unknown.


Pssm-ID: 173972  Cd Length: 406  Bit Score: 41.14  E-value: 2.04e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373884041   1 VASGGIHVWHMPALVEIFGDDSVLQF-GGGTLGHPWGNAPGATANRVALEACVQARNegrnlaregndiIREAAKWSPEL 79
Cdd:cd08207  335 VFSSGQWGGQAPPTYRRLGSVDLLYLaGGGIMAHPDGPAAGVRSLRQAWEAAVAGVP------------LEEYAKTHPEL 402


                 ...
gi 373884041  80 AVA 82
Cdd:cd08207  403 ARA 405
PRK13475 PRK13475
ribulose-bisphosphate carboxylase;
3-84 2.26e-05

ribulose-bisphosphate carboxylase;


Pssm-ID: 184072  Cd Length: 443  Bit Score: 41.25  E-value: 2.26e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373884041   3 SGGIHVWHMPALVEIFGDDSVLQ-FGGGTLGHPWGNAPGATANRVALEACVQarnegrnlareGNDIIrEAAKWSPELAV 81
Cdd:PRK13475 368 SGGMNALRLPGFFDNLGHGNVINtAGGGAFGHIDGPAAGAKSLRQAYDCWKA-----------GADPI-EYAKEHKEFAR 435


                 ...
gi 373884041  82 ACE 84
Cdd:PRK13475 436 AFE 438
RuBisCO_large_II cd08211
Ribulose bisphosphate carboxylase large chain, Form II; Ribulose bisphosphate carboxylase ...
 3-84 3.82e-05

Ribulose bisphosphate carboxylase large chain, Form II; Ribulose bisphosphate carboxylase (Rubisco) plays an important role in the Calvin reductive pentose phosphate pathway. It catalyzes the primary CO2 fixation step. Rubisco is activated by carbamylation of an active site lysine, stabilized by a divalent cation, which then catalyzes the proton abstraction from the substrate ribulose 1,5 bisphosphate (RuBP) and leads to the formation of two molecules of 3-phosphoglycerate. Members of the Rubisco family can be divided into 4 subgroups, Form I-IV , which differ in their taxonomic distribution and subunit composition. Form II is mainly found in bacteria, and forms large subunit oligomers (dimers, tetramers, etc.) that do not include small subunits.


Pssm-ID: 173976  Cd Length: 439  Bit Score: 40.56  E-value: 3.82e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 373884041   3 SGGIHVWHMPALVEIFGDDSVLQ-FGGGTLGHPWGNAPGATANRVALEACVQarnegrnlareGNDIIrEAAKWSPELAV 81
Cdd:cd08211  367 SGGMNALRLPGFFENLGNGNVILtAGGGSFGHIDGPAAGAKSLRQAYDAWKQ-----------GVDVI-EYAKEHKELAR 434


                 ...
gi 373884041  82 ACE 84
Cdd:cd08211  435 AFE 437
 
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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