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Conserved domains on  [gi|1606716822|gb|QBS17993|]
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ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit, partial (chloroplast) [uncultured Chlorophyta]

Protein Classification

RuBisCO large subunit( domain architecture ID 315)

large subunit of the ribulose bisphosphate carboxylase is part of the complex that catalyzes the primary event in carbon dioxide fixation, the carboxylation of D-ribulose 1,5-bisphosphate, as well as the oxidative fragmentation of the pentose substrate in the photorespiration process.

EC:  4.1.1.39
Gene Ontology:  GO:0016984
PubMed:  18294858

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) ...
 1-187 2.95e-161

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: 452.24  E-value: 2.95e-161
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1606716822   1 RLTYYTPDYQVKDTDILAAFRMTPQPGVPPEECGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYDLEPVKGEENQYIAY 80
Cdd:CHL00040   21 KLTYYTPDYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYRIEPVPGEENQYIAY 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1606716822  81 VAYPLDLFEEGSVTNLFTSIVGNVFGFKALRALRLEDLRISVAYAKTFQGPPHGIEVERDKLNKYGRPLLGCTIKPKLGL 160
Cdd:CHL00040  101 VAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYLKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGL 180

                         170       180
                  ....*....|....*....|....*..
gi 1606716822 161 SAKNYGRAVYECLRGGLDFTKDDENVN 187
Cdd:CHL00040  181 SAKNYGRAVYECLRGGLDFTKDDENVN 207
 
Name Accession Description Interval E-value
rbcL CHL00040
ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
 1-187 2.95e-161

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


Pssm-ID: 176981  Cd Length: 475  Bit Score: 452.24  E-value: 2.95e-161
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1606716822   1 RLTYYTPDYQVKDTDILAAFRMTPQPGVPPEECGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYDLEPVKGEENQYIAY 80
Cdd:CHL00040   21 KLTYYTPDYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYRIEPVPGEENQYIAY 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1606716822  81 VAYPLDLFEEGSVTNLFTSIVGNVFGFKALRALRLEDLRISVAYAKTFQGPPHGIEVERDKLNKYGRPLLGCTIKPKLGL 160
Cdd:CHL00040  101 VAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYLKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGL 180

                         170       180
                  ....*....|....*....|....*..
gi 1606716822 161 SAKNYGRAVYECLRGGLDFTKDDENVN 187
Cdd:CHL00040  181 SAKNYGRAVYECLRGGLDFTKDDENVN 207
RuBisCO_large_I cd08212
Ribulose bisphosphate carboxylase large chain, Form I; Ribulose bisphosphate carboxylase ...
 3-187 8.36e-148

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: 417.21  E-value: 8.36e-148
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1606716822   3 TYYTPDYQVKDTDILAAFRMTPQPGVPPEECGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYDLEPVKGEENQYIAYVA 82
Cdd:cd08212     1 GYWTPDYQPKDTDILAAFRITPQPGVDPEEAAAAVAGESSTATWTVVWTDRLTALDRYKGKAYRVEPVPGEENQYFAYIA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1606716822  83 YPLDLFEEGSVTNLFTSIVGNVFGFKALRALRLEDLRISVAYAKTFQGPPHGIEVERDKLNKYGRPLLGCTIKPKLGLSA 162
Cdd:cd08212    81 YPLDLFEEGSVANLTTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGIQVERDRLNKYGRPLLGCTIKPKLGLSA 160

                         170       180
                  ....*....|....*....|....*
gi 1606716822 163 KNYGRAVYECLRGGLDFTKDDENVN 187
Cdd:cd08212   161 KNYGRVVYECLRGGLDFTKDDENIN 185
RbcL COG1850
Ribulose 1,5-bisphosphate carboxylase, large subunit, or a RuBisCO-like protein [Carbohydrate ...
 4-185 3.62e-85

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


Pssm-ID: 441455  Cd Length: 417  Bit Score: 257.02  E-value: 3.62e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1606716822   4 YYTPDYQVKDTDILAAFRMTPQPGVPPEECGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYDLEPV---KGEENQYIAY 80
Cdd:COG1850     2 YVDPDYIPDDDDILATYRITPETGVDPEEAAAAIAGEQSTGTWTEVPTETDELRERLAARVYSIEELpevGGGYRRALVT 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1606716822  81 VAYPLDLFEeGSVTNLFTSIVGNVFGFKALRALRLEDLRISVAYAKTFQGPPHGIEVERDKLNKYGRPLLGCTIKPKLGL 160
Cdd:COG1850    82 IAYPLENFG-GNLPNLLSTVAGNLFGLKAVSGLRLLDLEFPESFLAAFPGPKFGIEGTRELLGVYDRPLLGTIIKPKVGL 160

                         170       180
                  ....*....|....*....|....*
gi 1606716822 161 SAKNYGRAVYECLRGGLDFTKDDEN 185
Cdd:COG1850   161 SPEETAELVYELALGGVDFIKDDEN 185
RuBisCO_large_N pfam02788
Ribulose bisphosphate carboxylase large chain, N-terminal domain; The N-terminal domain of ...
 3-124 1.78e-62

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: 188.96  E-value: 1.78e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1606716822   3 TYYTPDYQVKDTDILAAFRMTPQPGVPPEECGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYDLEPVKGEenQYIAYVA 82
Cdd:pfam02788   1 DYVDLDYEPKDTDLLCAFRIEPAAGVSPEEAAAHVAAESSTGTWTEVWTLDDTFTKKLKAKVYEIDEVPGG--SYIVKIA 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1606716822  83 YPLDLFEEGSVTNLFTSIVGNVFGFKALRALRLEDLRISVAY 124
Cdd:pfam02788  79 YPLDLFEEGSIPQLLSSIAGNIFGMKAVKALRLEDIRFPPAY 120
rubisco_III TIGR03326
ribulose bisphosphate carboxylase, type III; Members of this protein family are the archaeal, ...
 4-185 2.54e-53

ribulose bisphosphate carboxylase, type III; Members of this protein family are the archaeal, single chain, type III form of ribulose bisphosphate carboxylase, or RuBisCO. Members act is a three-step pathway for conversion of the sugar moiety of AMP to two molecules of 3-phosphoglycerate. Many of these species use ADP-dependent sugar kinases, which form AMP, for glycolysis. [Energy metabolism, Sugars]


Pssm-ID: 188307  Cd Length: 411  Bit Score: 174.96  E-value: 2.54e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1606716822   4 YYTPDYQVKDTDILAAFRMTPQPGVPPEECGAAVAAESSTGTWTTVWTdgLTSLDRYKGRCYDLEPVKGEENQYIAYVAY 83
Cdd:TIGR03326   2 FVDLNYEPSDDDLVCTFRITPAEGVSIEDAAGRVASESSIGTWTTLQP--WKDPERYKDLSAKVYDIEEHGDGSIVRIAY 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1606716822  84 PLDLFEEGSVTNLFTSIVGNVFGFKALRALRLEDLRISVAYAKTFQGPPHGIEVERDKLNKYGRPLLGCTIKPKLGLSAK 163
Cdd:TIGR03326  80 PLGLFEEGNLPQLLSCIAGNIFGMKAVKGLRLLDFEFPAEFLRAFKGPQFGIEGVREILGIKDRPITATVPKPKVGLSTE 159

                         170       180
                  ....*....|....*....|..
gi 1606716822 164 NYGRAVYECLRGGLDFTKDDEN 185
Cdd:TIGR03326 160 EHAKVAYELWSGGVDLLKDDEN 181
 
Name Accession Description Interval E-value
rbcL CHL00040
ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
 1-187 2.95e-161

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


Pssm-ID: 176981  Cd Length: 475  Bit Score: 452.24  E-value: 2.95e-161
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1606716822   1 RLTYYTPDYQVKDTDILAAFRMTPQPGVPPEECGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYDLEPVKGEENQYIAY 80
Cdd:CHL00040   21 KLTYYTPDYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYRIEPVPGEENQYIAY 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1606716822  81 VAYPLDLFEEGSVTNLFTSIVGNVFGFKALRALRLEDLRISVAYAKTFQGPPHGIEVERDKLNKYGRPLLGCTIKPKLGL 160
Cdd:CHL00040  101 VAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYLKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGL 180

                         170       180
                  ....*....|....*....|....*..
gi 1606716822 161 SAKNYGRAVYECLRGGLDFTKDDENVN 187
Cdd:CHL00040  181 SAKNYGRAVYECLRGGLDFTKDDENVN 207
RuBisCO_large_I cd08212
Ribulose bisphosphate carboxylase large chain, Form I; Ribulose bisphosphate carboxylase ...
 3-187 8.36e-148

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: 417.21  E-value: 8.36e-148
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1606716822   3 TYYTPDYQVKDTDILAAFRMTPQPGVPPEECGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYDLEPVKGEENQYIAYVA 82
Cdd:cd08212     1 GYWTPDYQPKDTDILAAFRITPQPGVDPEEAAAAVAGESSTATWTVVWTDRLTALDRYKGKAYRVEPVPGEENQYFAYIA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1606716822  83 YPLDLFEEGSVTNLFTSIVGNVFGFKALRALRLEDLRISVAYAKTFQGPPHGIEVERDKLNKYGRPLLGCTIKPKLGLSA 162
Cdd:cd08212    81 YPLDLFEEGSVANLTTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGIQVERDRLNKYGRPLLGCTIKPKLGLSA 160

                         170       180
                  ....*....|....*....|....*
gi 1606716822 163 KNYGRAVYECLRGGLDFTKDDENVN 187
Cdd:cd08212   161 KNYGRVVYECLRGGLDFTKDDENIN 185
rbcL PRK04208
ribulose bisophosphate carboxylase; Reviewed
 1-187 9.48e-136

ribulose bisophosphate carboxylase; Reviewed


Pssm-ID: 179787  Cd Length: 468  Bit Score: 387.34  E-value: 9.48e-136
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1606716822   1 RLTYYTPDYQVKDTDILAAFRMTPQPGVPPEECGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYDLEPVKGEENQYIAY 80
Cdd:PRK04208   14 RQMYWDPDYTPKDTDLLACFRITPQEGVDPEEAAAAVAAESSTGTWTTVWTDLLTDLDKYKAKAYRIEDVPGDDGSYYAF 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1606716822  81 VAYPLDLFEEGSVTNLFTSIVGNVFGFKALRALRLEDLRISVAYAKTFQGPPHGIEVERDKLNKYGRPLLGCTIKPKLGL 160
Cdd:PRK04208   94 IAYPLDLFEEGSIPNLLASIAGNVFGFKAVKALRLEDIRFPVAYVKTFKGPPFGIQVERERLDKYGRPLLGTTPKPKLGL 173

                         170       180
                  ....*....|....*....|....*..
gi 1606716822 161 SAKNYGRAVYECLRGGLDFTKDDENVN 187
Cdd:PRK04208  174 SAKNYGRVVYEALRGGLDFTKDDENLN 200
RuBisCO_large_I_II_III cd08206
Ribulose bisphosphate carboxylase large chain, Form I,II,III; Ribulose bisphosphate ...
 14-187 1.21e-116

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: 336.90  E-value: 1.21e-116
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1606716822  14 TDILAAFRMTPQPGVPPEECGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYDLEPVKgeENQYIAYVAYPLDLFEEGSV 93
Cdd:cd08206     1 TDLLAAFRMTPAEGVDPEEAAAAVAAESSTGTWTTVWTDRLTATERLKAKVYRIDPVP--DGQYIAKIAYPLDLFEEGSV 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1606716822  94 TNLFTSIVGNVFGFKALRALRLEDLRISVAYAKTFQGPPHGIEVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECL 173
Cdd:cd08206    79 PNLLTSIIGNVFGMKAVKALRLEDFRFPPAYLKTFDGPSFGIQGEREILGKYGRPLLGTIVKPKLGLSPKEYARVVYEAL 158

                         170
                  ....*....|....
gi 1606716822 174 RGGLDFTKDDENVN 187
Cdd:cd08206   159 RGGLDFVKDDENQN 172
RbcL COG1850
Ribulose 1,5-bisphosphate carboxylase, large subunit, or a RuBisCO-like protein [Carbohydrate ...
 4-185 3.62e-85

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


Pssm-ID: 441455  Cd Length: 417  Bit Score: 257.02  E-value: 3.62e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1606716822   4 YYTPDYQVKDTDILAAFRMTPQPGVPPEECGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYDLEPV---KGEENQYIAY 80
Cdd:COG1850     2 YVDPDYIPDDDDILATYRITPETGVDPEEAAAAIAGEQSTGTWTEVPTETDELRERLAARVYSIEELpevGGGYRRALVT 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1606716822  81 VAYPLDLFEeGSVTNLFTSIVGNVFGFKALRALRLEDLRISVAYAKTFQGPPHGIEVERDKLNKYGRPLLGCTIKPKLGL 160
Cdd:COG1850    82 IAYPLENFG-GNLPNLLSTVAGNLFGLKAVSGLRLLDLEFPESFLAAFPGPKFGIEGTRELLGVYDRPLLGTIIKPKVGL 160

                         170       180
                  ....*....|....*....|....*
gi 1606716822 161 SAKNYGRAVYECLRGGLDFTKDDEN 185
Cdd:COG1850   161 SPEETAELVYELALGGVDFIKDDEN 185
RuBisCO_large cd08148
Ribulose bisphosphate carboxylase large chain; Ribulose bisphosphate carboxylase (Rubisco) ...
 16-187 1.43e-80

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: 243.49  E-value: 1.43e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1606716822  16 ILAAFRMTPQPgVPPEECGAAVAAESSTGTWTTVWTdGLTSLDRYKGRCYDLEPVKgeeNQYIAYVAYPLDLFEEGSVTN 95
Cdd:cd08148     1 VLATYRVHPEA-TPPEKAAEAIAAESSTGTWTEVPT-TQEQLRRVKGRVYSVEELG---KRYIVKIAYPVELFEPGNIPQ 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1606716822  96 LFTSIVGNVFGFKALRALRLEDLRISVAYAKTFQGPPHGIEVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRG 175
Cdd:cd08148    76 ILTVTAGNLFGLGALEAVRLEDLEFPEEYKKLFPGPKFGIDGIRKLLGVYGRPLVGTIIKPKLGLNPKYTAEAAYAAALG 155

                         170
                  ....*....|..
gi 1606716822 176 GLDFTKDDENVN 187
Cdd:cd08148   156 GLDLIKDDETLT 167
RuBisCO_large_III cd08213
Ribulose bisphosphate carboxylase large chain, Form III; Ribulose bisphosphate carboxylase ...
 14-185 9.76e-65

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: 204.55  E-value: 9.76e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1606716822  14 TDILAAFRMTPQPGVPPEECGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYDLEpvkGEENQYIAYVAYPLDLFEEGSV 93
Cdd:cd08213     1 DDLIAVFRIEPAEGISIEEAAGRVASESSIGTWTTLATLYPERAEKLKAKAYYFD---GLGGSYIVKVAYPLELFEEGNM 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1606716822  94 TNLFTSIVGNVFGFKALRALRLEDLRISVAYAKTFQGPPHGIEVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECL 173
Cdd:cd08213    78 PQLLSSIAGNIFGMKAVKNLRLEDIYFPESYLREFKGPQFGIEGVREILGIKDRPLLGTVPKPKVGLSPEEHAEVAYEAL 157

                         170
                  ....*....|..
gi 1606716822 174 RGGLDFTKDDEN 185
Cdd:cd08213   158 VGGVDLVKDDEN 169
RuBisCO_large_N pfam02788
Ribulose bisphosphate carboxylase large chain, N-terminal domain; The N-terminal domain of ...
 3-124 1.78e-62

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: 188.96  E-value: 1.78e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1606716822   3 TYYTPDYQVKDTDILAAFRMTPQPGVPPEECGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYDLEPVKGEenQYIAYVA 82
Cdd:pfam02788   1 DYVDLDYEPKDTDLLCAFRIEPAAGVSPEEAAAHVAAESSTGTWTEVWTLDDTFTKKLKAKVYEIDEVPGG--SYIVKIA 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1606716822  83 YPLDLFEEGSVTNLFTSIVGNVFGFKALRALRLEDLRISVAY 124
Cdd:pfam02788  79 YPLDLFEEGSIPQLLSSIAGNIFGMKAVKALRLEDIRFPPAY 120
rubisco_III TIGR03326
ribulose bisphosphate carboxylase, type III; Members of this protein family are the archaeal, ...
 4-185 2.54e-53

ribulose bisphosphate carboxylase, type III; Members of this protein family are the archaeal, single chain, type III form of ribulose bisphosphate carboxylase, or RuBisCO. Members act is a three-step pathway for conversion of the sugar moiety of AMP to two molecules of 3-phosphoglycerate. Many of these species use ADP-dependent sugar kinases, which form AMP, for glycolysis. [Energy metabolism, Sugars]


Pssm-ID: 188307  Cd Length: 411  Bit Score: 174.96  E-value: 2.54e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1606716822   4 YYTPDYQVKDTDILAAFRMTPQPGVPPEECGAAVAAESSTGTWTTVWTdgLTSLDRYKGRCYDLEPVKGEENQYIAYVAY 83
Cdd:TIGR03326   2 FVDLNYEPSDDDLVCTFRITPAEGVSIEDAAGRVASESSIGTWTTLQP--WKDPERYKDLSAKVYDIEEHGDGSIVRIAY 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1606716822  84 PLDLFEEGSVTNLFTSIVGNVFGFKALRALRLEDLRISVAYAKTFQGPPHGIEVERDKLNKYGRPLLGCTIKPKLGLSAK 163
Cdd:TIGR03326  80 PLGLFEEGNLPQLLSCIAGNIFGMKAVKGLRLLDFEFPAEFLRAFKGPQFGIEGVREILGIKDRPITATVPKPKVGLSTE 159

                         170       180
                  ....*....|....*....|..
gi 1606716822 164 NYGRAVYECLRGGLDFTKDDEN 185
Cdd:TIGR03326 160 EHAKVAYELWSGGVDLLKDDEN 181
RuBisCO_IV_RLP cd08205
Ribulose bisphosphate carboxylase like proteins, Rubisco-Form IV; Ribulose bisphosphate ...
 16-184 9.63e-35

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: 125.34  E-value: 9.63e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1606716822  16 ILAAFRMTPqPGVPPEECGAAVAAESSTGTWTTVWTDGLTSLDRYKGRC---YDLEPVKGEENQYIAYVAYPLDLFEeGS 92
Cdd:cd08205     1 ITATYRIEA-PGADAEKKAEAIALEQTVGTWTELPGETEEIRERHVGRVesiEELEESEGKYGRARVTISYPLDNFG-GD 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1606716822  93 VTNLFTSIVGNVFGfkaLRALRLEDLRISVAYAKTFQGPPHGIEVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYEC 172
Cdd:cd08205    79 LPQLLNTLFGNLSL---LPGIKLVDLELPDSLLAAFPGPRFGIEGLRRLLGVHDRPLLGTIIKPSIGLSPEELAELAYEL 155

                         170
                  ....*....|..
gi 1606716822 173 LRGGLDFTKDDE 184
Cdd:cd08205   156 ALGGIDLIKDDE 167
RuBisCO_large pfam00016
Ribulose bisphosphate carboxylase large chain, catalytic domain; The C-terminal domain of ...
 135-187 3.21e-30

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: 111.68  E-value: 3.21e-30
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1606716822 135 IEVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVN 187
Cdd:pfam00016   1 IAVERRVLNKYGRPILGTIIKPKLGLSPKNYARAVYEFLLGGLDFIKDDENIN 53
RLP_NonPhot cd08207
Ribulose bisphosphate carboxylase like proteins from nonphototrophic bacteria; Ribulose ...
 28-184 1.80e-28

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: 109.32  E-value: 1.80e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1606716822  28 VPPEECGAAVAAESSTGTWTTV--WTDGLTslDRYKGRCYDLEPVKGEENQYIAY-------------VAYPLDLFeeG- 91
Cdd:cd08207    12 LDLERAAEVIAGEQSSGTFIALpgETDELK--ERSAARVESIEELETAAQPSLPRrasggpytrarvtISFPLDNI--Gt 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1606716822  92 SVTNLFTSIVGNVFGFKALRALRLEDLRISVAYAKTFQGPPHGIEVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYE 171
Cdd:cd08207    88 SLPNLLATVAGNLFELRELSGLRLVDLGLPDEFAAAFPGPAFGIAGTRRLTGVEDRPLIGTIIKPSVGLTPEETAALVRQ 167

                         170
                  ....*....|...
gi 1606716822 172 CLRGGLDFTKDDE 184
Cdd:cd08207   168 LAAAGIDFIKDDE 180
PRK13475 PRK13475
ribulose-bisphosphate carboxylase;
16-184 8.18e-26

ribulose-bisphosphate carboxylase;


Pssm-ID: 184072  Cd Length: 443  Bit Score: 102.49  E-value: 8.18e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1606716822  16 ILAAFRMTPQPGVPPEECGAAVAAESSTGT-----WTTVWTDGLTSLdrykgrCYDLEPVKGeenqyIAYVAYPLDLFE- 89
Cdd:PRK13475   24 ILCAYKMKPKAGHGYLEAAAHFAAESSTGTnvevsTTDDFTRGVDAL------VYEIDEARE-----LMKIAYPVELFDr 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1606716822  90 -----EGSVTNLFTSIVGNVFGFKALRALRLEDLRISVAYAKTFQGPPHGIeverDKLNKY-GRP------LLGCTIKPK 157
Cdd:PRK13475   93 niidgRAMIVSFLTLTIGNNQGMGDVEYAKMHDFYVPPRYLELFDGPSTDI----SDLWRVlGRPvkdggyIAGTIIKPK 168

                         170       180
                  ....*....|....*....|....*..
gi 1606716822 158 LGLSAKNYGRAVYECLRGGlDFTKDDE 184
Cdd:PRK13475  169 LGLRPEPFAEACYDFWLGG-DFIKNDE 194
RuBisCO_large_II cd08211
Ribulose bisphosphate carboxylase large chain, Form II; Ribulose bisphosphate carboxylase ...
 16-184 2.27e-24

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: 98.34  E-value: 2.27e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1606716822  16 ILAAFRMTPQPGVPPEECGAAVAAESSTGTWTTV-WTDGLT-SLDrykGRCYDLEpvkgEENQyIAYVAYPLDLFE---- 89
Cdd:cd08211    23 VLVAYIMKPKAGYGYLATAAHFAAESSTGTNVEVsTTDDFTrGVD---ALVYEID----EARE-LMKIAYPVELFDrnlt 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1606716822  90 --EGSVTNLFTSIVGNVFGFKALRALRLEDLRISVAYAKTFQGPPHGIEVERDKLNKY---GRPLLGCTIKPKLGLSAKN 164
Cdd:cd08211    95 dgRAMVASFLTLIIGNNQGMGDVEYLKMHDFYVPESMLELFDGPSVNISDMWKVLGRPevdGGYIAGTIIKPKLGLRPKP 174

                         170       180
                  ....*....|....*....|
gi 1606716822 165 YGRAVYECLRGGlDFTKDDE 184
Cdd:cd08211   175 FAEACYAFWLGG-DFIKNDE 193
RLP_DK-MTP-1-P-enolase cd08209
2,3-diketo-5-methylthiopentyl-1-phosphate enolase; Ribulose bisphosphate carboxylase like ...
 16-184 1.42e-21

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: 90.07  E-value: 1.42e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1606716822  16 ILAAFRMtpQPGVPPEECGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYDLEPvkGEENQYIAYVAYPLdlfeeGSVTN 95
Cdd:cd08209     1 IVATYRF--PDGADLEKKAEQIAVGLTVGSWTDLPALRQAQLQKHLGEVVSVEE--LEEGRGVITIAYPL-----INVSG 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1606716822  96 LFTSIVGNVFGFKALR-ALRLEDLRISVAYAKTFQGPPHGIEVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLR 174
Cdd:cd08209    72 DIPALLTTIFGKLSLDgKIKLVDLRLPEEFGRAFPGPKFGIEGIRQRLGVHDRPLLMSIFKGVLGLDLDDLAEQLREQAL 151

                         170
                  ....*....|
gi 1606716822 175 GGLDFTKDDE 184
Cdd:cd08209   152 GGVDLIKDDE 161
RLP_Photo cd08208
Ribulose bisphosphate carboxylase like proteins from phototrophic bacteria; Ribulose ...
 30-184 1.65e-17

Ribulose bisphosphate carboxylase like proteins from phototrophic 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: 173973  Cd Length: 424  Bit Score: 79.17  E-value: 1.65e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1606716822  30 PEECGAAVAAESSTGTWTTVWTDGLTSLdRYKGRCYDLEPVKGEENQYiayvaYPLDLFEEGSVT--------------- 94
Cdd:cd08208    30 PETAAAHFCSEQSTAQWRRVGVDEDFRP-RFAAKVIDLEVIEELEQLS-----YPVKHSETGPVHacrvtiahphgnfgp 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1606716822  95 ---NLFTSIVGN-VFGFKALRALRLEDLRISVAYAKTFQGPPHGIEVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVY 170
Cdd:cd08208   104 kipNLLSAVCGEgTFFSPGVPVVKLMDIHFPETYLADFEGPKFGIAGLRERLQAHDRPIFFGVIKPNIGLPPGEFAELGY 183

                         170
                  ....*....|....
gi 1606716822 171 ECLRGGLDFTKDDE 184
Cdd:cd08208   184 QSWLGGLDIAKDDE 197
RLP_RrRLP cd08210
Ribulose bisphosphate carboxylase like proteins (RLPs) similar to R.rubrum RLP; RLP from ...
 18-183 3.42e-15

Ribulose bisphosphate carboxylase like proteins (RLPs) similar to R.rubrum RLP; RLP from Rhodospirillum rubrum plays a role in an uncharacterized sulfur salvage pathway and has been shown to catalyze a novel isomerization reaction that converts 5-methylthio-d-ribulose 1-phosphate to a 3:1 mixture of 1-methylthioxylulose 5-phosphate and 1-methylthioribulose 5-phosphate.


Pssm-ID: 173975  Cd Length: 364  Bit Score: 72.27  E-value: 3.42e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1606716822  18 AAFRMTPQPGVPPEECGAAVAAESSTGTWTTVWTDGLTsLDRYKGRCYDLEPVkgEENQYIAYVAYPLDLFEeGSVTNLF 97
Cdd:cd08210     4 VTYRLVAASEAEAEARARGIALEQTVEMPLELVPDGYI-RDNIVGRVESLEPA--GEGSYRARISYSVDTAG-GELTQLL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1606716822  98 TSIVGNVfgfKALRALRLEDLRISVAYAKTFQGPPHGIEVERDKLNKYGRPLLGCTIKPkLGLSAKNYGRAVYECLRGGL 177
Cdd:cd08210    80 NVLFGNS---SLQPGIRLVDFELPPSLLRRFPGPRFGIAGLRALLGIPERPLLCSALKP-QGLSAAELAELAYAFALGGI 155


                  ....*.
gi 1606716822 178 DFTKDD 183
Cdd:cd08210   156 DIIKDD 161
mtnW PRK09549
2,3-diketo-5-methylthiopentyl-1-phosphate enolase; Reviewed
 36-184 2.89e-12

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


Pssm-ID: 236560  Cd Length: 407  Bit Score: 63.87  E-value: 2.89e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1606716822  36 AVAAESSTGTWTTVWTDGLTSLDRYKGRCYDLEPVKGEEN----QYIAYVAYPldlfeEGSVTNLFTSIVGNVFGFKALR 111
Cdd:PRK09549   23 QIALGLTVGSWTDLPHLEQEQLKKHKGNVVHVEELEEHERkgvkRGIIKIAYP-----LANFSPDLPAILTTTFGKLSLD 97

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1606716822 112 A-LRLEDLRISVAYAKTFQGPPHGIEVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDE 184
Cdd:PRK09549   98 GeVKLIDLTFSDELKRHFPGPKFGIDGIRNLLGVHDRPLLMSIFKGVIGRDLDYLKEQLRDQALGGVDLVKDDE 171
 
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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