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Conserved domains on  [gi|57335298|emb|CAH04103|]
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ribulose 1,5-biphosphate carboxylase large subunit, partial [cyanobacterium BECID34]

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) ...
 1-82 4.51e-59

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: 186.83  E-value: 4.51e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57335298    1 FGDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQARNEGRSLAREGNDIIREAAKWSPELAVACELWKEIKFEFEAMD 80
Cdd:CHL00040 394 FGDDSVLQFGGGTLGHPWGNAPGAVANRVALEACVQARNEGRDLAREGNEIIREAAKWSPELAAACEVWKEIKFEFETTD 473


                 ..
gi 57335298   81 TV 82
Cdd:CHL00040 474 TL 475
 
Name Accession Description Interval E-value
rbcL CHL00040
ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
 1-82 4.51e-59

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


Pssm-ID: 176981  Cd Length: 475  Bit Score: 186.83  E-value: 4.51e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57335298    1 FGDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQARNEGRSLAREGNDIIREAAKWSPELAVACELWKEIKFEFEAMD 80
Cdd:CHL00040 394 FGDDSVLQFGGGTLGHPWGNAPGAVANRVALEACVQARNEGRDLAREGNEIIREAAKWSPELAAACEVWKEIKFEFETTD 473


                 ..
gi 57335298   81 TV 82
Cdd:CHL00040 474 TL 475
RuBisCO_large_I cd08212
Ribulose bisphosphate carboxylase large chain, Form I; Ribulose bisphosphate carboxylase ...
 1-80 7.82e-53

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: 169.91  E-value: 7.82e-53
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57335298   1 FGDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQARNEGRSLAREGNDIIREAAKWSPELAVACELWKEIKFEFEAMD 80
Cdd:cd08212 371 FGDDVVLQFGGGTIGHPWGIAAGATANRVALEAMVQARNEGRDLAREGPEILREAAKWSPELAAALETWKDIKFEFESTD 450
RuBisCO_large pfam00016
Ribulose bisphosphate carboxylase large chain, catalytic domain; The C-terminal domain of ...
 1-69 2.57e-22

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: 86.65  E-value: 2.57e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57335298     1 FGD-DSVLQFGGGTLGHPWGNAPGATANRVALEACVqarnEGRSLAREgndiireaAKWSPELAVACELW 69
Cdd:pfam00016 235 LGDsDVILQFGGGTFGHPDGPAAGAKANRQALEAWV----EGRDLEEY--------AKEHPELARAFESW 292
RbcL COG1850
Ribulose 1,5-bisphosphate carboxylase, large subunit, or a RuBisCO-like protein [Carbohydrate ...
 1-74 2.58e-20

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


Pssm-ID: 441455  Cd Length: 417  Bit Score: 82.52  E-value: 2.58e-20
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 57335298   1 FGDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQarneGRSLAregndiirEAAKWSPELAVACELWKEIKF 74
Cdd:COG1850 356 LGTDLILQAGGGIHGHPDGPAAGARALRQAWEAAVA----GIPLE--------EYAKTHPELAAALEKWGKKAP 417
 
Name Accession Description Interval E-value
rbcL CHL00040
ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
 1-82 4.51e-59

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


Pssm-ID: 176981  Cd Length: 475  Bit Score: 186.83  E-value: 4.51e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57335298    1 FGDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQARNEGRSLAREGNDIIREAAKWSPELAVACELWKEIKFEFEAMD 80
Cdd:CHL00040 394 FGDDSVLQFGGGTLGHPWGNAPGAVANRVALEACVQARNEGRDLAREGNEIIREAAKWSPELAAACEVWKEIKFEFETTD 473


                 ..
gi 57335298   81 TV 82
Cdd:CHL00040 474 TL 475
RuBisCO_large_I cd08212
Ribulose bisphosphate carboxylase large chain, Form I; Ribulose bisphosphate carboxylase ...
 1-80 7.82e-53

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: 169.91  E-value: 7.82e-53
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57335298   1 FGDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQARNEGRSLAREGNDIIREAAKWSPELAVACELWKEIKFEFEAMD 80
Cdd:cd08212 371 FGDDVVLQFGGGTIGHPWGIAAGATANRVALEAMVQARNEGRDLAREGPEILREAAKWSPELAAALETWKDIKFEFESTD 450
rbcL PRK04208
ribulose bisophosphate carboxylase; Reviewed
 1-82 2.87e-50

ribulose bisophosphate carboxylase; Reviewed


Pssm-ID: 179787  Cd Length: 468  Bit Score: 163.54  E-value: 2.87e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57335298    1 FGDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQARNEGRSLAREGNDIIREAAKWSPELAVACELWKEIKFEFEAMD 80
Cdd:PRK04208 387 FGDDVVLQFGGGTHGHPDGTAAGATANRVALEACVEARNEGRDIEKEGPDILEEAAKWSPELAAALEKWGEIKFEFDTVD 466


                 ..
gi 57335298   81 TV 82
Cdd:PRK04208 467 TL 468
RuBisCO_large_I_II_III cd08206
Ribulose bisphosphate carboxylase large chain, Form I,II,III; Ribulose bisphosphate ...
 1-69 3.92e-28

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: 103.85  E-value: 3.92e-28
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 57335298   1 FGDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQARnegrslaregndIIREAAKWSPELAVACELW 69
Cdd:cd08206 358 LGDDVILQFGGGTHGHPDGPAAGAKANRQALEAWVQGR------------ILREYAKTHKELAAALEKW 414
RuBisCO_large pfam00016
Ribulose bisphosphate carboxylase large chain, catalytic domain; The C-terminal domain of ...
 1-69 2.57e-22

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: 86.65  E-value: 2.57e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57335298     1 FGD-DSVLQFGGGTLGHPWGNAPGATANRVALEACVqarnEGRSLAREgndiireaAKWSPELAVACELW 69
Cdd:pfam00016 235 LGDsDVILQFGGGTFGHPDGPAAGAKANRQALEAWV----EGRDLEEY--------AKEHPELARAFESW 292
RbcL COG1850
Ribulose 1,5-bisphosphate carboxylase, large subunit, or a RuBisCO-like protein [Carbohydrate ...
 1-74 2.58e-20

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


Pssm-ID: 441455  Cd Length: 417  Bit Score: 82.52  E-value: 2.58e-20
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 57335298   1 FGDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQarneGRSLAregndiirEAAKWSPELAVACELWKEIKF 74
Cdd:COG1850 356 LGTDLILQAGGGIHGHPDGPAAGARALRQAWEAAVA----GIPLE--------EYAKTHPELAAALEKWGKKAP 417
RuBisCO_large cd08148
Ribulose bisphosphate carboxylase large chain; Ribulose bisphosphate carboxylase (Rubisco) ...
 1-30 9.79e-12

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: 58.59  E-value: 9.79e-12
                        10        20        30
                ....*....|....*....|....*....|
gi 57335298   1 FGDDSVLQFGGGTLGHPWGNAPGATANRVA 30
Cdd:cd08148 337 FGIDVILQAGGGIHGHPDGTVAGARAMRQA 366
RuBisCO_large_III cd08213
Ribulose bisphosphate carboxylase large chain, Form III; Ribulose bisphosphate carboxylase ...
 1-69 2.20e-11

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: 57.40  E-value: 2.20e-11
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 57335298   1 FGDDSVLQFGGGTLGHPWGNAPGATANRVALEACVqarnEGRSLaregndiiREAAKWSPELAVACELW 69
Cdd:cd08213 356 LGKDIVIQVGGGVHGHPDGTRAGAKAVRQAIEAAL----EGISL--------DEYAKDHKELARALEKW 412
mtnW PRK09549
2,3-diketo-5-methylthiopentyl-1-phosphate enolase; Reviewed
 1-69 2.09e-09

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


Pssm-ID: 236560  Cd Length: 407  Bit Score: 51.93  E-value: 2.09e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 57335298    1 FGDDSVLQFGGGTLGHPWGNAPGATANRVALEACvqarNEGRSLaregndiiREAAKWSPELAVACELW 69
Cdd:PRK09549 345 FGKDVVINAGGGIHGHPNGAQGGGKAFRAAIDAV----LQGKPL--------HEAAEDDENLHSALDIW 401
RLP_DK-MTP-1-P-enolase cd08209
2,3-diketo-5-methylthiopentyl-1-phosphate enolase; Ribulose bisphosphate carboxylase like ...
 1-69 3.32e-07

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: 45.77  E-value: 3.32e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 57335298   1 FGDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQarneGRSLaregndiiREAAKWSPELAVACELW 69
Cdd:cd08209 334 FGTDVILNAGGGIHGHPDGAAAGVRAFREAIDAVLA----GESL--------EPAAIPDGPLKSALDKW 390
RLP_NonPhot cd08207
Ribulose bisphosphate carboxylase like proteins from nonphototrophic bacteria; Ribulose ...
 10-65 9.72e-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: 38.83  E-value: 9.72e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 57335298  10 GGGTLGHPWGNAPGATANRVALEACVQarneGRSLAregndiirEAAKWSPELAVA 65
Cdd:cd08207 362 GGGIMAHPDGPAAGVRSLRQAWEAAVA----GVPLE--------EYAKTHPELARA 405
 
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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