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Conserved domains on  [gi|2018315368|gb|QTG40661|]
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ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit, partial (chloroplast) [Asparagopsis taxiformis]

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) ...
 1-92 1.22e-65

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: 204.17  E-value: 1.22e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315368   1 TATWTVVWTDLLTACDLYRAKAYKVDAVPNTSDQYFAYISYDIDLFEEGSIANLTASIIGNVFGFKAVKALRLEDMRIPV 80
Cdd:CHL00040   63 TGTWTTVWTDGLTSLDRYKGRCYRIEPVPGEENQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPP 142

                          90
                  ....*....|..
gi 2018315368  81 AYLKTFQGPATG 92
Cdd:CHL00040  143 AYLKTFQGPPHG 154
 
Name Accession Description Interval E-value
rbcL CHL00040
ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
 1-92 1.22e-65

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


Pssm-ID: 176981  Cd Length: 475  Bit Score: 204.17  E-value: 1.22e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315368   1 TATWTVVWTDLLTACDLYRAKAYKVDAVPNTSDQYFAYISYDIDLFEEGSIANLTASIIGNVFGFKAVKALRLEDMRIPV 80
Cdd:CHL00040   63 TGTWTTVWTDGLTSLDRYKGRCYRIEPVPGEENQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPP 142

                          90
                  ....*....|..
gi 2018315368  81 AYLKTFQGPATG 92
Cdd:CHL00040  143 AYLKTFQGPPHG 154
RuBisCO_large_I cd08212
Ribulose bisphosphate carboxylase large chain, Form I; Ribulose bisphosphate carboxylase ...
 1-92 7.05e-63

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: 196.49  E-value: 7.05e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315368   1 TATWTVVWTDLLTACDLYRAKAYKVDAVPNTSDQYFAYISYDIDLFEEGSIANLTASIIGNVFGFKAVKALRLEDMRIPV 80
Cdd:cd08212    41 TATWTVVWTDRLTALDRYKGKAYRVEPVPGEENQYFAYIAYPLDLFEEGSVANLTTSIVGNVFGFKALRALRLEDLRIPP 120

                          90
                  ....*....|..
gi 2018315368  81 AYLKTFQGPATG 92
Cdd:cd08212   121 AYVKTFQGPPHG 132
RuBisCO_large_N pfam02788
Ribulose bisphosphate carboxylase large chain, N-terminal domain; The N-terminal domain of ...
 1-82 6.68e-39

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: 125.40  E-value: 6.68e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315368   1 TATWTVVWTDLLTACDLYRAKAYKVDAVPNtsDQYFAYISYDIDLFEEGSIANLTASIIGNVFGFKAVKALRLEDMRIPV 80
Cdd:pfam02788  41 TGTWTEVWTLDDTFTKKLKAKVYEIDEVPG--GSYIVKIAYPLDLFEEGSIPQLLSSIAGNIFGMKAVKALRLEDIRFPP 118


                  ..
gi 2018315368  81 AY 82
Cdd:pfam02788 119 AY 120
 
Name Accession Description Interval E-value
rbcL CHL00040
ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
 1-92 1.22e-65

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


Pssm-ID: 176981  Cd Length: 475  Bit Score: 204.17  E-value: 1.22e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315368   1 TATWTVVWTDLLTACDLYRAKAYKVDAVPNTSDQYFAYISYDIDLFEEGSIANLTASIIGNVFGFKAVKALRLEDMRIPV 80
Cdd:CHL00040   63 TGTWTTVWTDGLTSLDRYKGRCYRIEPVPGEENQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPP 142

                          90
                  ....*....|..
gi 2018315368  81 AYLKTFQGPATG 92
Cdd:CHL00040  143 AYLKTFQGPPHG 154
RuBisCO_large_I cd08212
Ribulose bisphosphate carboxylase large chain, Form I; Ribulose bisphosphate carboxylase ...
 1-92 7.05e-63

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: 196.49  E-value: 7.05e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315368   1 TATWTVVWTDLLTACDLYRAKAYKVDAVPNTSDQYFAYISYDIDLFEEGSIANLTASIIGNVFGFKAVKALRLEDMRIPV 80
Cdd:cd08212    41 TATWTVVWTDRLTALDRYKGKAYRVEPVPGEENQYFAYIAYPLDLFEEGSVANLTTSIVGNVFGFKALRALRLEDLRIPP 120

                          90
                  ....*....|..
gi 2018315368  81 AYLKTFQGPATG 92
Cdd:cd08212   121 AYVKTFQGPPHG 132
rbcL PRK04208
ribulose bisophosphate carboxylase; Reviewed
 1-92 2.43e-57

ribulose bisophosphate carboxylase; Reviewed


Pssm-ID: 179787  Cd Length: 468  Bit Score: 182.41  E-value: 2.43e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315368   1 TATWTVVWTDLLTACDLYRAKAYKVDAVPNTSDQYFAYISYDIDLFEEGSIANLTASIIGNVFGFKAVKALRLEDMRIPV 80
Cdd:PRK04208   56 TGTWTTVWTDLLTDLDKYKAKAYRIEDVPGDDGSYYAFIAYPLDLFEEGSIPNLLASIAGNVFGFKAVKALRLEDIRFPV 135

                          90
                  ....*....|..
gi 2018315368  81 AYLKTFQGPATG 92
Cdd:PRK04208  136 AYVKTFKGPPFG 147
RuBisCO_large_I_II_III cd08206
Ribulose bisphosphate carboxylase large chain, Form I,II,III; Ribulose bisphosphate ...
 1-92 6.31e-51

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: 164.72  E-value: 6.31e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315368   1 TATWTVVWTDLLTACDLYRAKAYKVDAVPNtsDQYFAYISYDIDLFEEGSIANLTASIIGNVFGFKAVKALRLEDMRIPV 80
Cdd:cd08206    30 TGTWTTVWTDRLTATERLKAKVYRIDPVPD--GQYIAKIAYPLDLFEEGSVPNLLTSIIGNVFGMKAVKALRLEDFRFPP 107

                          90
                  ....*....|..
gi 2018315368  81 AYLKTFQGPATG 92
Cdd:cd08206   108 AYLKTFDGPSFG 119
RuBisCO_large_N pfam02788
Ribulose bisphosphate carboxylase large chain, N-terminal domain; The N-terminal domain of ...
 1-82 6.68e-39

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: 125.40  E-value: 6.68e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315368   1 TATWTVVWTDLLTACDLYRAKAYKVDAVPNtsDQYFAYISYDIDLFEEGSIANLTASIIGNVFGFKAVKALRLEDMRIPV 80
Cdd:pfam02788  41 TGTWTEVWTLDDTFTKKLKAKVYEIDEVPG--GSYIVKIAYPLDLFEEGSIPQLLSSIAGNIFGMKAVKALRLEDIRFPP 118


                  ..
gi 2018315368  81 AY 82
Cdd:pfam02788 119 AY 120
RuBisCO_large_III cd08213
Ribulose bisphosphate carboxylase large chain, Form III; Ribulose bisphosphate carboxylase ...
 1-92 1.49e-24

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: 94.76  E-value: 1.49e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315368   1 TATWTVVWTDLLTACDLYRAKAYKVDAVPNTsdqYFAYISYDIDLFEEGSIANLTASIIGNVFGFKAVKALRLEDMRIPV 80
Cdd:cd08213    30 IGTWTTLATLYPERAEKLKAKAYYFDGLGGS---YIVKVAYPLELFEEGNMPQLLSSIAGNIFGMKAVKNLRLEDIYFPE 106

                          90
                  ....*....|..
gi 2018315368  81 AYLKTFQGPATG 92
Cdd:cd08213   107 SYLREFKGPQFG 118
RuBisCO_large cd08148
Ribulose bisphosphate carboxylase large chain; Ribulose bisphosphate carboxylase (Rubisco) ...
 1-92 6.65e-23

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: 89.79  E-value: 6.65e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315368   1 TATWTVVWTdLLTACDLYRAKAYKVDavpNTSDQYFAYISYDIDLFEEGSIANLTASIIGNVFGFKAVKALRLEDMRIPV 80
Cdd:cd08148    27 TGTWTEVPT-TQEQLRRVKGRVYSVE---ELGKRYIVKIAYPVELFEPGNIPQILTVTAGNLFGLGALEAVRLEDLEFPE 102

                          90
                  ....*....|..
gi 2018315368  81 AYLKTFQGPATG 92
Cdd:cd08148   103 EYKKLFPGPKFG 114
PRK13475 PRK13475
ribulose-bisphosphate carboxylase;
39-91 2.43e-07

ribulose-bisphosphate carboxylase;


Pssm-ID: 184072  Cd Length: 443  Bit Score: 46.64  E-value: 2.43e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2018315368  39 ISYDIDLFE------EGSIANLTASIIGNVFGFKAVKALRLEDMRIPVAYLKTFQGPAT 91
Cdd:PRK13475   83 IAYPVELFDrniidgRAMIVSFLTLTIGNNQGMGDVEYAKMHDFYVPPRYLELFDGPST 141
RuBisCO_large_II cd08211
Ribulose bisphosphate carboxylase large chain, Form II; Ribulose bisphosphate carboxylase ...
 20-92 3.95e-06

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: 43.26  E-value: 3.95e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2018315368  20 AKAYKVDAvpntsDQYFAYISYDIDLFE------EGSIANLTASIIGNVFGFKAVKALRLEDMRIPVAYLKTFQGPATG 92
Cdd:cd08211    68 ALVYEIDE-----ARELMKIAYPVELFDrnltdgRAMVASFLTLIIGNNQGMGDVEYLKMHDFYVPESMLELFDGPSVN 141
RuBisCO_IV_RLP cd08205
Ribulose bisphosphate carboxylase like proteins, Rubisco-Form IV; Ribulose bisphosphate ...
 23-92 5.67e-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: 42.52  E-value: 5.67e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315368  23 YKVDAVPNTSDQYFAYISYDIDLFEeGSIANLTASIIGNVFGfkaVKALRLEDMRIPVAYLKTFQGPATG 92
Cdd:cd08205    52 EELEESEGKYGRARVTISYPLDNFG-GDLPQLLNTLFGNLSL---LPGIKLVDLELPDSLLAAFPGPRFG 117
 
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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