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Conserved domains on  [gi|359269865|dbj|BAL27683|]
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ribulose-1,5-bisphosphate carboxylase/oxygenase, partial (chloroplast) [prasinophyte sp. 78-G2]

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) ...
 1-160 1.32e-138

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: 393.68  E-value: 1.32e-138
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359269865   1 VWTDGLTQLDRYKGRCYDIEPVPGEDNQFIAYVAYPLDLFEEGSVTNLFTSIVGNVFGFKALRALRLEDLRIPVAYCKTF 80
Cdd:CHL00040  69 VWTDGLTSLDRYKGRCYRIEPVPGEENQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYLKTF 148

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359269865  81 QGAPHGIQVERDKLNKYGRGLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFVAEAIYKS 160
Cdd:CHL00040 149 QGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEAIYKA 228
 
Name Accession Description Interval E-value
rbcL CHL00040
ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
 1-160 1.32e-138

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


Pssm-ID: 176981  Cd Length: 475  Bit Score: 393.68  E-value: 1.32e-138
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359269865   1 VWTDGLTQLDRYKGRCYDIEPVPGEDNQFIAYVAYPLDLFEEGSVTNLFTSIVGNVFGFKALRALRLEDLRIPVAYCKTF 80
Cdd:CHL00040  69 VWTDGLTSLDRYKGRCYRIEPVPGEENQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYLKTF 148

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359269865  81 QGAPHGIQVERDKLNKYGRGLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFVAEAIYKS 160
Cdd:CHL00040 149 QGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEAIYKA 228
RuBisCO_large_I cd08212
Ribulose bisphosphate carboxylase large chain, Form I; Ribulose bisphosphate carboxylase ...
 1-160 3.46e-129

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: 369.06  E-value: 3.46e-129
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359269865   1 VWTDGLTQLDRYKGRCYDIEPVPGEDNQFIAYVAYPLDLFEEGSVTNLFTSIVGNVFGFKALRALRLEDLRIPVAYCKTF 80
Cdd:cd08212   47 VWTDRLTALDRYKGKAYRVEPVPGEENQYFAYIAYPLDLFEEGSVANLTTSIVGNVFGFKALRALRLEDLRIPPAYVKTF 126

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359269865  81 QGAPHGIQVERDKLNKYGRGLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFVAEAIYKS 160
Cdd:cd08212  127 QGPPHGIQVERDRLNKYGRPLLGCTIKPKLGLSAKNYGRVVYECLRGGLDFTKDDENINSQPFMRWRDRFLFVAEAVNKA 206
RbcL COG1850
Ribulose 1,5-bisphosphate carboxylase, large subunit, or a RuBisCO-like protein [Carbohydrate ...
 1-157 2.42e-68

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


Pssm-ID: 441455  Cd Length: 417  Bit Score: 212.72  E-value: 2.42e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359269865   1 VWTDGLTQLDRYKGRCYDIEPVP---GEDNQFIAYVAYPLDLFEeGSVTNLFTSIVGNVFGFKALRALRLEDLRIPVAYC 77
Cdd:COG1850   47 VPTETDELRERLAARVYSIEELPevgGGYRRALVTIAYPLENFG-GNLPNLLSTVAGNLFGLKAVSGLRLLDLEFPESFL 125

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359269865  78 KTFQGAPHGIQVERDKLNKYGRGLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFVAEAI 157
Cdd:COG1850  126 AAFPGPKFGIEGTRELLGVYDRPLLGTIIKPKVGLSPEETAELVYELALGGVDFIKDDENLADQPFCPFEDRVRAVMEAI 205
RuBisCO_large pfam00016
Ribulose bisphosphate carboxylase large chain, catalytic domain; The C-terminal domain of ...
 87-159 3.81e-44

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: 146.74  E-value: 3.81e-44
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 359269865   87 IQVERDKLNKYGRGLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFVAEAIYK 159
Cdd:pfam00016   1 IAVERRVLNKYGRPILGTIIKPKLGLSPKNYARAVYEFLLGGLDFIKDDENINSQPFMPWRDRFLFVAEAIDR 73
rubisco_III TIGR03326
ribulose bisphosphate carboxylase, type III; Members of this protein family are the archaeal, ...
 10-149 3.95e-37

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: 131.43  E-value: 3.95e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359269865   10 DRYKG---RCYDIEPVpGEDNqfIAYVAYPLDLFEEGSVTNLFTSIVGNVFGFKALRALRLEDLRIPVAYCKTFQGAPHG 86
Cdd:TIGR03326  54 ERYKDlsaKVYDIEEH-GDGS--IVRIAYPLGLFEEGNLPQLLSCIAGNIFGMKAVKGLRLLDFEFPAEFLRAFKGPQFG 130

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 359269865   87 IQVERDKLNKYGRGLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDR 149
Cdd:TIGR03326 131 IEGVREILGIKDRPITATVPKPKVGLSTEEHAKVAYELWSGGVDLLKDDENLTSQAFNRFEER 193
 
Name Accession Description Interval E-value
rbcL CHL00040
ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
 1-160 1.32e-138

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


Pssm-ID: 176981  Cd Length: 475  Bit Score: 393.68  E-value: 1.32e-138
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359269865   1 VWTDGLTQLDRYKGRCYDIEPVPGEDNQFIAYVAYPLDLFEEGSVTNLFTSIVGNVFGFKALRALRLEDLRIPVAYCKTF 80
Cdd:CHL00040  69 VWTDGLTSLDRYKGRCYRIEPVPGEENQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYLKTF 148

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359269865  81 QGAPHGIQVERDKLNKYGRGLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFVAEAIYKS 160
Cdd:CHL00040 149 QGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEAIYKA 228
RuBisCO_large_I cd08212
Ribulose bisphosphate carboxylase large chain, Form I; Ribulose bisphosphate carboxylase ...
 1-160 3.46e-129

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: 369.06  E-value: 3.46e-129
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359269865   1 VWTDGLTQLDRYKGRCYDIEPVPGEDNQFIAYVAYPLDLFEEGSVTNLFTSIVGNVFGFKALRALRLEDLRIPVAYCKTF 80
Cdd:cd08212   47 VWTDRLTALDRYKGKAYRVEPVPGEENQYFAYIAYPLDLFEEGSVANLTTSIVGNVFGFKALRALRLEDLRIPPAYVKTF 126

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359269865  81 QGAPHGIQVERDKLNKYGRGLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFVAEAIYKS 160
Cdd:cd08212  127 QGPPHGIQVERDRLNKYGRPLLGCTIKPKLGLSAKNYGRVVYECLRGGLDFTKDDENINSQPFMRWRDRFLFVAEAVNKA 206
rbcL PRK04208
ribulose bisophosphate carboxylase; Reviewed
 1-159 3.69e-116

ribulose bisophosphate carboxylase; Reviewed


Pssm-ID: 179787  Cd Length: 468  Bit Score: 336.49  E-value: 3.69e-116
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359269865   1 VWTDGLTQLDRYKGRCYDIEPVPGEDNQFIAYVAYPLDLFEEGSVTNLFTSIVGNVFGFKALRALRLEDLRIPVAYCKTF 80
Cdd:PRK04208  62 VWTDLLTDLDKYKAKAYRIEDVPGDDGSYYAFIAYPLDLFEEGSIPNLLASIAGNVFGFKAVKALRLEDIRFPVAYVKTF 141

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 359269865  81 QGAPHGIQVERDKLNKYGRGLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFVAEAIYK 159
Cdd:PRK04208 142 KGPPFGIQVERERLDKYGRPLLGTTPKPKLGLSAKNYGRVVYEALRGGLDFTKDDENLNSQPFNRWRDRFLFVMEAIDK 220
RuBisCO_large_I_II_III cd08206
Ribulose bisphosphate carboxylase large chain, Form I,II,III; Ribulose bisphosphate ...
 1-160 2.05e-105

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: 307.24  E-value: 2.05e-105
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359269865   1 VWTDGLTQLDRYKGRCYDIEPVPgeDNQFIAYVAYPLDLFEEGSVTNLFTSIVGNVFGFKALRALRLEDLRIPVAYCKTF 80
Cdd:cd08206   36 VWTDRLTATERLKAKVYRIDPVP--DGQYIAKIAYPLDLFEEGSVPNLLTSIIGNVFGMKAVKALRLEDFRFPPAYLKTF 113

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359269865  81 QGAPHGIQVERDKLNKYGRGLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFVAEAIYKS 160
Cdd:cd08206  114 DGPSFGIQGEREILGKYGRPLLGTIVKPKLGLSPKEYARVVYEALRGGLDFVKDDENQNSQPFMRFEDRILFVAEAMDKA 193
RuBisCO_large cd08148
Ribulose bisphosphate carboxylase large chain; Ribulose bisphosphate carboxylase (Rubisco) ...
 2-159 9.36e-74

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: 225.00  E-value: 9.36e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359269865   2 WTD---GLTQLDRYKGRCYDIEPVPgedNQFIAYVAYPLDLFEEGSVTNLFTSIVGNVFGFKALRALRLEDLRIPVAYCK 78
Cdd:cd08148   30 WTEvptTQEQLRRVKGRVYSVEELG---KRYIVKIAYPVELFEPGNIPQILTVTAGNLFGLGALEAVRLEDLEFPEEYKK 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359269865  79 TFQGAPHGIQVERDKLNKYGRGLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFVAEAIY 158
Cdd:cd08148  107 LFPGPKFGIDGIRKLLGVYGRPLVGTIIKPKLGLNPKYTAEAAYAAALGGLDLIKDDETLTDQPFCPLRDRITEVAAALD 186


                 .
gi 359269865 159 K 159
Cdd:cd08148  187 R 187
RbcL COG1850
Ribulose 1,5-bisphosphate carboxylase, large subunit, or a RuBisCO-like protein [Carbohydrate ...
 1-157 2.42e-68

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


Pssm-ID: 441455  Cd Length: 417  Bit Score: 212.72  E-value: 2.42e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359269865   1 VWTDGLTQLDRYKGRCYDIEPVP---GEDNQFIAYVAYPLDLFEeGSVTNLFTSIVGNVFGFKALRALRLEDLRIPVAYC 77
Cdd:COG1850   47 VPTETDELRERLAARVYSIEELPevgGGYRRALVTIAYPLENFG-GNLPNLLSTVAGNLFGLKAVSGLRLLDLEFPESFL 125

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359269865  78 KTFQGAPHGIQVERDKLNKYGRGLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFVAEAI 157
Cdd:COG1850  126 AAFPGPKFGIEGTRELLGVYDRPLLGTIIKPKVGLSPEETAELVYELALGGVDFIKDDENLADQPFCPFEDRVRAVMEAI 205
RuBisCO_large_III cd08213
Ribulose bisphosphate carboxylase large chain, Form III; Ribulose bisphosphate carboxylase ...
 1-159 7.47e-50

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: 164.87  E-value: 7.47e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359269865   1 VWTDGLTQLDRYKGRCYDIEPVPGEDnqfIAYVAYPLDLFEEGSVTNLFTSIVGNVFGFKALRALRLEDLRIPVAYCKTF 80
Cdd:cd08213   36 LATLYPERAEKLKAKAYYFDGLGGSY---IVKVAYPLELFEEGNMPQLLSSIAGNIFGMKAVKNLRLEDIYFPESYLREF 112

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 359269865  81 QGAPHGIQVERDKLNKYGRGLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFVAEAIYK 159
Cdd:cd08213  113 KGPQFGIEGVREILGIKDRPLLGTVPKPKVGLSPEEHAEVAYEALVGGVDLVKDDENLTSQPFNRFEERAKESLKARDK 191
RuBisCO_large pfam00016
Ribulose bisphosphate carboxylase large chain, catalytic domain; The C-terminal domain of ...
 87-159 3.81e-44

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: 146.74  E-value: 3.81e-44
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 359269865   87 IQVERDKLNKYGRGLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFVAEAIYK 159
Cdd:pfam00016   1 IAVERRVLNKYGRPILGTIIKPKLGLSPKNYARAVYEFLLGGLDFIKDDENINSQPFMPWRDRFLFVAEAIDR 73
rubisco_III TIGR03326
ribulose bisphosphate carboxylase, type III; Members of this protein family are the archaeal, ...
 10-149 3.95e-37

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: 131.43  E-value: 3.95e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359269865   10 DRYKG---RCYDIEPVpGEDNqfIAYVAYPLDLFEEGSVTNLFTSIVGNVFGFKALRALRLEDLRIPVAYCKTFQGAPHG 86
Cdd:TIGR03326  54 ERYKDlsaKVYDIEEH-GDGS--IVRIAYPLGLFEEGNLPQLLSCIAGNIFGMKAVKGLRLLDFEFPAEFLRAFKGPQFG 130

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 359269865   87 IQVERDKLNKYGRGLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDR 149
Cdd:TIGR03326 131 IEGVREILGIKDRPITATVPKPKVGLSTEEHAKVAYELWSGGVDLLKDDENLTSQAFNRFEER 193
RuBisCO_large_N pfam02788
Ribulose bisphosphate carboxylase large chain, N-terminal domain; The N-terminal domain of ...
 1-76 1.46e-34

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: 117.31  E-value: 1.46e-34
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 359269865    1 VWTDGLTQLDRYKGRCYDIEPVPGEdnQFIAYVAYPLDLFEEGSVTNLFTSIVGNVFGFKALRALRLEDLRIPVAY 76
Cdd:pfam02788  47 VWTLDDTFTKKLKAKVYEIDEVPGG--SYIVKIAYPLDLFEEGSIPQLLSSIAGNIFGMKAVKALRLEDIRFPPAY 120
RuBisCO_IV_RLP cd08205
Ribulose bisphosphate carboxylase like proteins, Rubisco-Form IV; Ribulose bisphosphate ...
 8-157 1.30e-29

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: 110.70  E-value: 1.30e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359269865   8 QLDRYKGRCYDIEPVP---GEDNQFIAYVAYPLDLFEeGSVTNLFTSIVGNVFGfkaLRALRLEDLRIPVAYCKTFQGAP 84
Cdd:cd08205   40 IRERHVGRVESIEELEeseGKYGRARVTISYPLDNFG-GDLPQLLNTLFGNLSL---LPGIKLVDLELPDSLLAAFPGPR 115

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 359269865  85 HGIQVERDKLNKYGRGLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFVAEAI 157
Cdd:cd08205  116 FGIEGLRRLLGVHDRPLLGTIIKPSIGLSPEELAELAYELALGGIDLIKDDELLADQPYAPFEERVRACMEAV 188
RLP_NonPhot cd08207
Ribulose bisphosphate carboxylase like proteins from nonphototrophic bacteria; Ribulose ...
 33-157 2.07e-22

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: 91.60  E-value: 2.07e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359269865  33 VAYPLDLFeeG-SVTNLFTSIVGNVFGFKALRALRLEDLRIPVAYCKTFQGAPHGIQVERDKLNKYGRGLLGCTIKPKLG 111
Cdd:cd08207   78 ISFPLDNI--GtSLPNLLATVAGNLFELRELSGLRLVDLGLPDEFAAAFPGPAFGIAGTRRLTGVEDRPLIGTIIKPSVG 155

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 359269865 112 LSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFVAEAI 157
Cdd:cd08207  156 LTPEETAALVRQLAAAGIDFIKDDELLANPPYSPLDERVRAVMRVI 201
RuBisCO_large_II cd08211
Ribulose bisphosphate carboxylase large chain, Form II; Ribulose bisphosphate carboxylase ...
 15-160 2.23e-19

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: 83.32  E-value: 2.23e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359269865  15 RCYDIEpvpgEDNQfIAYVAYPLDLFE------EGSVTNLFTSIVGNVFGFKALRALRLEDLRIPVAYCKTFQGAPHGIQ 88
Cdd:cd08211   69 LVYEID----EARE-LMKIAYPVELFDrnltdgRAMVASFLTLIIGNNQGMGDVEYLKMHDFYVPESMLELFDGPSVNIS 143

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 359269865  89 VERDKLNKY---GRGLLGCTIKPKLGLSAKNYGRAVYECLRGGlDFTKDDENVNSQPFMRWRDRFLFVAEAIYKS 160
Cdd:cd08211  144 DMWKVLGRPevdGGYIAGTIIKPKLGLRPKPFAEACYAFWLGG-DFIKNDEPQANQPFCPLKKVIPLVADAMRRA 217
RLP_RrRLP cd08210
Ribulose bisphosphate carboxylase like proteins (RLPs) similar to R.rubrum RLP; RLP from ...
 9-157 2.54e-18

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: 79.97  E-value: 2.54e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359269865   9 LDRYKGRCYDIEPVpgEDNQFIAYVAYPLDLFEeGSVTNLFTSIVGNVfgfKALRALRLEDLRIPVAYCKTFQGAPHGIQ 88
Cdd:cd08210   42 RDNIVGRVESLEPA--GEGSYRARISYSVDTAG-GELTQLLNVLFGNS---SLQPGIRLVDFELPPSLLRRFPGPRFGIA 115

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 359269865  89 VERDKLNKYGRGLLGCTIKPkLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFVAEAI 157
Cdd:cd08210  116 GLRALLGIPERPLLCSALKP-QGLSAAELAELAYAFALGGIDIIKDDHGLADQPFAPFEERVKACQEAV 183
PRK13475 PRK13475
ribulose-bisphosphate carboxylase;
33-160 8.31e-18

ribulose-bisphosphate carboxylase;


Pssm-ID: 184072  Cd Length: 443  Bit Score: 79.00  E-value: 8.31e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359269865  33 VAYPLDLFE------EGSVTNLFTSIVGNVFGFKALRALRLEDLRIPVAYCKTFQGAPHGIQVERDKLN---KYGRGLLG 103
Cdd:PRK13475  83 IAYPVELFDrniidgRAMIVSFLTLTIGNNQGMGDVEYAKMHDFYVPPRYLELFDGPSTDISDLWRVLGrpvKDGGYIAG 162

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 359269865 104 CTIKPKLGLSAKNYGRAVYECLRGGlDFTKDDENVNSQPFMRWRDRFLFVAEAIYKS 160
Cdd:PRK13475 163 TIIKPKLGLRPEPFAEACYDFWLGG-DFIKNDEPQGNQVFAPLKKTVPLVADAMKRA 218
RLP_DK-MTP-1-P-enolase cd08209
2,3-diketo-5-methylthiopentyl-1-phosphate enolase; Ribulose bisphosphate carboxylase like ...
 2-136 2.09e-17

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: 77.74  E-value: 2.09e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359269865   2 WTDGLT----QLDRYKGRCYDIEPvpGEDNQFIAYVAYPLdlfeeGSVTNLFTSIVGNVFGFKALR-ALRLEDLRIPVAY 76
Cdd:cd08209   29 WTDLPAlrqaQLQKHLGEVVSVEE--LEEGRGVITIAYPL-----INVSGDIPALLTTIFGKLSLDgKIKLVDLRLPEEF 101

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 359269865  77 CKTFQGAPHGIQVERDKLNKYGRGLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDE 136
Cdd:cd08209  102 GRAFPGPKFGIEGIRQRLGVHDRPLLMSIFKGVLGLDLDDLAEQLREQALGGVDLIKDDE 161
RLP_Photo cd08208
Ribulose bisphosphate carboxylase like proteins from phototrophic bacteria; Ribulose ...
 45-136 4.11e-13

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: 65.69  E-value: 4.11e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359269865  45 VTNLFTSIVGN-VFGFKALRALRLEDLRIPVAYCKTFQGAPHGIQVERDKLNKYGRGLLGCTIKPKLGLSAKNYGRAVYE 123
Cdd:cd08208  105 IPNLLSAVCGEgTFFSPGVPVVKLMDIHFPETYLADFEGPKFGIAGLRERLQAHDRPIFFGVIKPNIGLPPGEFAELGYQ 184

                         90
                 ....*....|...
gi 359269865 124 CLRGGLDFTKDDE 136
Cdd:cd08208  185 SWLGGLDIAKDDE 197
mtnW PRK09549
2,3-diketo-5-methylthiopentyl-1-phosphate enolase; Reviewed
 2-136 1.72e-10

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


Pssm-ID: 236560  Cd Length: 407  Bit Score: 58.10  E-value: 1.72e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359269865   2 WTDgL-----TQLDRYKGRCYDIEPVPG----EDNQFIAYVAYPldlfeEGSVTNLFTSIVGNVFGFKALRA-LRLEDLR 71
Cdd:PRK09549  33 WTD-LphleqEQLKKHKGNVVHVEELEEherkGVKRGIIKIAYP-----LANFSPDLPAILTTTFGKLSLDGeVKLIDLT 106

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 359269865  72 IPVAYCKTFQGAPHGIQVERDKLNKYGRGLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDE 136
Cdd:PRK09549 107 FSDELKRHFPGPKFGIDGIRNLLGVHDRPLLMSIFKGVIGRDLDYLKEQLRDQALGGVDLVKDDE 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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