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Conserved domains on  [gi|1102132855|gb|APC26176|]
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ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit, partial (plastid) [Rufodorsia intermedia]

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) ...
 1-53 6.37e-34

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: 119.04  E-value: 6.37e-34
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1102132855   1 MSPQTETKASVGFKAGVKEYKLTYYTPEYETKDTDILAAFRVTPQPGVPPEEA 53
Cdd:CHL00040    1 MSPQTETKASVGFKAGVKDYKLTYYTPDYETKDTDILAAFRVTPQPGVPPEEA 53
 
Name Accession Description Interval E-value
rbcL CHL00040
ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
 1-53 6.37e-34

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


Pssm-ID: 176981  Cd Length: 475  Bit Score: 119.04  E-value: 6.37e-34
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1102132855   1 MSPQTETKASVGFKAGVKEYKLTYYTPEYETKDTDILAAFRVTPQPGVPPEEA 53
Cdd:CHL00040    1 MSPQTETKASVGFKAGVKDYKLTYYTPDYETKDTDILAAFRVTPQPGVPPEEA 53
RuBisCO_large_I cd08212
Ribulose bisphosphate carboxylase large chain, Form I; Ribulose bisphosphate carboxylase ...
 23-53 2.50e-16

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: 70.15  E-value: 2.50e-16
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1102132855  23 TYYTPEYETKDTDILAAFRVTPQPGVPPEEA 53
Cdd:cd08212     1 GYWTPDYQPKDTDILAAFRITPQPGVDPEEA 31
RuBisCO_large_N pfam02788
Ribulose bisphosphate carboxylase large chain, N-terminal domain; The N-terminal domain of ...
 23-53 1.58e-09

Ribulose bisphosphate carboxylase large chain, N-terminal domain; The N-terminal domain of RuBisCO large chain adopts a ferredoxin-like fold.


Pssm-ID: 426983  Cd Length: 120  Bit Score: 48.75  E-value: 1.58e-09
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1102132855  23 TYYTPEYETKDTDILAAFRVTPQPGVPPEEA 53
Cdd:pfam02788   1 DYVDLDYEPKDTDLLCAFRIEPAAGVSPEEA 31
 
Name Accession Description Interval E-value
rbcL CHL00040
ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
 1-53 6.37e-34

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


Pssm-ID: 176981  Cd Length: 475  Bit Score: 119.04  E-value: 6.37e-34
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1102132855   1 MSPQTETKASVGFKAGVKEYKLTYYTPEYETKDTDILAAFRVTPQPGVPPEEA 53
Cdd:CHL00040    1 MSPQTETKASVGFKAGVKDYKLTYYTPDYETKDTDILAAFRVTPQPGVPPEEA 53
rbcL PRK04208
ribulose bisophosphate carboxylase; Reviewed
 8-53 8.01e-19

ribulose bisophosphate carboxylase; Reviewed


Pssm-ID: 179787  Cd Length: 468  Bit Score: 77.25  E-value: 8.01e-19
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1102132855   8 KASVGFKAGVKEYKLTYYTPEYETKDTDILAAFRVTPQPGVPPEEA 53
Cdd:PRK04208    1 MAKERYDAGVKEYRQMYWDPDYTPKDTDLLACFRITPQEGVDPEEA 46
RuBisCO_large_I cd08212
Ribulose bisphosphate carboxylase large chain, Form I; Ribulose bisphosphate carboxylase ...
 23-53 2.50e-16

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: 70.15  E-value: 2.50e-16
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1102132855  23 TYYTPEYETKDTDILAAFRVTPQPGVPPEEA 53
Cdd:cd08212     1 GYWTPDYQPKDTDILAAFRITPQPGVDPEEA 31
RuBisCO_large_N pfam02788
Ribulose bisphosphate carboxylase large chain, N-terminal domain; The N-terminal domain of ...
 23-53 1.58e-09

Ribulose bisphosphate carboxylase large chain, N-terminal domain; The N-terminal domain of RuBisCO large chain adopts a ferredoxin-like fold.


Pssm-ID: 426983  Cd Length: 120  Bit Score: 48.75  E-value: 1.58e-09
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1102132855  23 TYYTPEYETKDTDILAAFRVTPQPGVPPEEA 53
Cdd:pfam02788   1 DYVDLDYEPKDTDLLCAFRIEPAAGVSPEEA 31
RuBisCO_large_I_II_III cd08206
Ribulose bisphosphate carboxylase large chain, Form I,II,III; Ribulose bisphosphate ...
 34-53 1.29e-06

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: 42.61  E-value: 1.29e-06
                          10        20
                  ....*....|....*....|
gi 1102132855  34 TDILAAFRVTPQPGVPPEEA 53
Cdd:cd08206     1 TDLLAAFRMTPAEGVDPEEA 20
 
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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