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Conserved domains on  [gi|469832013|dbj|BAN05210|]
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ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit, partial (chloroplast) [Moniliformopses sp. Blc-1]

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) ...
 1-173 4.47e-151

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: 426.04  E-value: 4.47e-151
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 469832013   1 VWTDGLTSLDRYKGRCYDIEPVAGEENQYIAYVAYPLDLFEEGSVTNLFTSIVGNVFGFKALRALRLEDLRIPPAYSKTF 80
Cdd:CHL00040  69 VWTDGLTSLDRYKGRCYRIEPVPGEENQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYLKTF 148

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 469832013  81 IGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFVAEALFKS 160
Cdd:CHL00040 149 QGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEAIYKA 228

                        170
                 ....*....|...
gi 469832013 161 QAETGEIKGHYLN 173
Cdd:CHL00040 229 QAETGEIKGHYLN 241
 
Name Accession Description Interval E-value
rbcL CHL00040
ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
 1-173 4.47e-151

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


Pssm-ID: 176981  Cd Length: 475  Bit Score: 426.04  E-value: 4.47e-151
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 469832013   1 VWTDGLTSLDRYKGRCYDIEPVAGEENQYIAYVAYPLDLFEEGSVTNLFTSIVGNVFGFKALRALRLEDLRIPPAYSKTF 80
Cdd:CHL00040  69 VWTDGLTSLDRYKGRCYRIEPVPGEENQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYLKTF 148

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 469832013  81 IGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFVAEALFKS 160
Cdd:CHL00040 149 QGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEAIYKA 228

                        170
                 ....*....|...
gi 469832013 161 QAETGEIKGHYLN 173
Cdd:CHL00040 229 QAETGEIKGHYLN 241
RuBisCO_large_I cd08212
Ribulose bisphosphate carboxylase large chain, Form I; Ribulose bisphosphate carboxylase ...
 1-173 4.03e-140

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: 397.18  E-value: 4.03e-140
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 469832013   1 VWTDGLTSLDRYKGRCYDIEPVAGEENQYIAYVAYPLDLFEEGSVTNLFTSIVGNVFGFKALRALRLEDLRIPPAYSKTF 80
Cdd:cd08212   47 VWTDRLTALDRYKGKAYRVEPVPGEENQYFAYIAYPLDLFEEGSVANLTTSIVGNVFGFKALRALRLEDLRIPPAYVKTF 126

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 469832013  81 IGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFVAEALFKS 160
Cdd:cd08212  127 QGPPHGIQVERDRLNKYGRPLLGCTIKPKLGLSAKNYGRVVYECLRGGLDFTKDDENINSQPFMRWRDRFLFVAEAVNKA 206

                        170
                 ....*....|...
gi 469832013 161 QAETGEIKGHYLN 173
Cdd:cd08212  207 QAETGEVKGHYLN 219
RbcL COG1850
Ribulose 1,5-bisphosphate carboxylase, large subunit, or a RuBisCO-like protein [Carbohydrate ...
 1-173 2.93e-77

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


Pssm-ID: 441455  Cd Length: 417  Bit Score: 235.83  E-value: 2.93e-77
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 469832013   1 VWTDGLTSLDRYKGRCYDIEPV---AGEENQYIAYVAYPLDLFEeGSVTNLFTSIVGNVFGFKALRALRLEDLRIPPAYS 77
Cdd:COG1850   47 VPTETDELRERLAARVYSIEELpevGGGYRRALVTIAYPLENFG-GNLPNLLSTVAGNLFGLKAVSGLRLLDLEFPESFL 125

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 469832013  78 KTFIGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFVAEAL 157
Cdd:COG1850  126 AAFPGPKFGIEGTRELLGVYDRPLLGTIIKPKVGLSPEETAELVYELALGGVDFIKDDENLADQPFCPFEDRVRAVMEAI 205

                        170
                 ....*....|....*.
gi 469832013 158 FKSQAETGEIKGHYLN 173
Cdd:COG1850  206 DRAEEETGEKKMYAFN 221
RuBisCO_large pfam00016
Ribulose bisphosphate carboxylase large chain, catalytic domain; The C-terminal domain of ...
 87-173 3.06e-55

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: 176.01  E-value: 3.06e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 469832013   87 IQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFVAEALFKSQAETGE 166
Cdd:pfam00016   1 IAVERRVLNKYGRPILGTIIKPKLGLSPKNYARAVYEFLLGGLDFIKDDENINSQPFMPWRDRFLFVAEAIDRAQDETGE 80


                  ....*..
gi 469832013  167 IKGHYLN 173
Cdd:pfam00016  81 AKGHYLN 87
rubisco_III TIGR03326
ribulose bisphosphate carboxylase, type III; Members of this protein family are the archaeal, ...
 8-173 7.99e-45

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: 152.23  E-value: 7.99e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 469832013    8 SLDRYKG---RCYDIEPVaGEEnqYIAYVAYPLDLFEEGSVTNLFTSIVGNVFGFKALRALRLEDLRIPPAYSKTFIGPP 84
Cdd:TIGR03326  52 DPERYKDlsaKVYDIEEH-GDG--SIVRIAYPLGLFEEGNLPQLLSCIAGNIFGMKAVKGLRLLDFEFPAEFLRAFKGPQ 128

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 469832013   85 HGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFVAEALFKSQAET 164
Cdd:TIGR03326 129 FGIEGVREILGIKDRPITATVPKPKVGLSTEEHAKVAYELWSGGVDLLKDDENLTSQAFNRFEERVEKSLKVRDKVEAET 208


                  ....*....
gi 469832013  165 GEIKGHYLN 173
Cdd:TIGR03326 209 GEKKSYLIN 217
 
Name Accession Description Interval E-value
rbcL CHL00040
ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
 1-173 4.47e-151

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


Pssm-ID: 176981  Cd Length: 475  Bit Score: 426.04  E-value: 4.47e-151
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 469832013   1 VWTDGLTSLDRYKGRCYDIEPVAGEENQYIAYVAYPLDLFEEGSVTNLFTSIVGNVFGFKALRALRLEDLRIPPAYSKTF 80
Cdd:CHL00040  69 VWTDGLTSLDRYKGRCYRIEPVPGEENQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYLKTF 148

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 469832013  81 IGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFVAEALFKS 160
Cdd:CHL00040 149 QGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEAIYKA 228

                        170
                 ....*....|...
gi 469832013 161 QAETGEIKGHYLN 173
Cdd:CHL00040 229 QAETGEIKGHYLN 241
RuBisCO_large_I cd08212
Ribulose bisphosphate carboxylase large chain, Form I; Ribulose bisphosphate carboxylase ...
 1-173 4.03e-140

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: 397.18  E-value: 4.03e-140
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 469832013   1 VWTDGLTSLDRYKGRCYDIEPVAGEENQYIAYVAYPLDLFEEGSVTNLFTSIVGNVFGFKALRALRLEDLRIPPAYSKTF 80
Cdd:cd08212   47 VWTDRLTALDRYKGKAYRVEPVPGEENQYFAYIAYPLDLFEEGSVANLTTSIVGNVFGFKALRALRLEDLRIPPAYVKTF 126

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 469832013  81 IGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFVAEALFKS 160
Cdd:cd08212  127 QGPPHGIQVERDRLNKYGRPLLGCTIKPKLGLSAKNYGRVVYECLRGGLDFTKDDENINSQPFMRWRDRFLFVAEAVNKA 206

                        170
                 ....*....|...
gi 469832013 161 QAETGEIKGHYLN 173
Cdd:cd08212  207 QAETGEVKGHYLN 219
rbcL PRK04208
ribulose bisophosphate carboxylase; Reviewed
 1-173 1.61e-126

ribulose bisophosphate carboxylase; Reviewed


Pssm-ID: 179787  Cd Length: 468  Bit Score: 363.46  E-value: 1.61e-126
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 469832013   1 VWTDGLTSLDRYKGRCYDIEPVAGEENQYIAYVAYPLDLFEEGSVTNLFTSIVGNVFGFKALRALRLEDLRIPPAYSKTF 80
Cdd:PRK04208  62 VWTDLLTDLDKYKAKAYRIEDVPGDDGSYYAFIAYPLDLFEEGSIPNLLASIAGNVFGFKAVKALRLEDIRFPVAYVKTF 141

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 469832013  81 IGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFVAEALFKS 160
Cdd:PRK04208 142 KGPPFGIQVERERLDKYGRPLLGTTPKPKLGLSAKNYGRVVYEALRGGLDFTKDDENLNSQPFNRWRDRFLFVMEAIDKA 221

                        170
                 ....*....|...
gi 469832013 161 QAETGEIKGHYLN 173
Cdd:PRK04208 222 EAETGERKGHYLN 234
RuBisCO_large_I_II_III cd08206
Ribulose bisphosphate carboxylase large chain, Form I,II,III; Ribulose bisphosphate ...
 1-173 2.54e-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: 335.36  E-value: 2.54e-116
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 469832013   1 VWTDGLTSLDRYKGRCYDIEPVAgeENQYIAYVAYPLDLFEEGSVTNLFTSIVGNVFGFKALRALRLEDLRIPPAYSKTF 80
Cdd:cd08206   36 VWTDRLTATERLKAKVYRIDPVP--DGQYIAKIAYPLDLFEEGSVPNLLTSIIGNVFGMKAVKALRLEDFRFPPAYLKTF 113

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 469832013  81 IGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFVAEALFKS 160
Cdd:cd08206  114 DGPSFGIQGEREILGKYGRPLLGTIVKPKLGLSPKEYARVVYEALRGGLDFVKDDENQNSQPFMRFEDRILFVAEAMDKA 193

                        170
                 ....*....|...
gi 469832013 161 QAETGEIKGHYLN 173
Cdd:cd08206  194 EAETGEAKGHYLN 206
RuBisCO_large cd08148
Ribulose bisphosphate carboxylase large chain; Ribulose bisphosphate carboxylase (Rubisco) ...
 2-173 5.99e-86

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: 256.58  E-value: 5.99e-86
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 469832013   2 WTD---GLTSLDRYKGRCYDIEPVAgeeNQYIAYVAYPLDLFEEGSVTNLFTSIVGNVFGFKALRALRLEDLRIPPAYSK 78
Cdd:cd08148   30 WTEvptTQEQLRRVKGRVYSVEELG---KRYIVKIAYPVELFEPGNIPQILTVTAGNLFGLGALEAVRLEDLEFPEEYKK 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 469832013  79 TFIGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFVAEALF 158
Cdd:cd08148  107 LFPGPKFGIDGIRKLLGVYGRPLVGTIIKPKLGLNPKYTAEAAYAAALGGLDLIKDDETLTDQPFCPLRDRITEVAAALD 186

                        170
                 ....*....|....*
gi 469832013 159 KSQAETGEIKGHYLN 173
Cdd:cd08148  187 RVQEETGEKKLYAVN 201
RbcL COG1850
Ribulose 1,5-bisphosphate carboxylase, large subunit, or a RuBisCO-like protein [Carbohydrate ...
 1-173 2.93e-77

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


Pssm-ID: 441455  Cd Length: 417  Bit Score: 235.83  E-value: 2.93e-77
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 469832013   1 VWTDGLTSLDRYKGRCYDIEPV---AGEENQYIAYVAYPLDLFEeGSVTNLFTSIVGNVFGFKALRALRLEDLRIPPAYS 77
Cdd:COG1850   47 VPTETDELRERLAARVYSIEELpevGGGYRRALVTIAYPLENFG-GNLPNLLSTVAGNLFGLKAVSGLRLLDLEFPESFL 125

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 469832013  78 KTFIGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFVAEAL 157
Cdd:COG1850  126 AAFPGPKFGIEGTRELLGVYDRPLLGTIIKPKVGLSPEETAELVYELALGGVDFIKDDENLADQPFCPFEDRVRAVMEAI 205

                        170
                 ....*....|....*.
gi 469832013 158 FKSQAETGEIKGHYLN 173
Cdd:COG1850  206 DRAEEETGEKKMYAFN 221
RuBisCO_large_III cd08213
Ribulose bisphosphate carboxylase large chain, Form III; Ribulose bisphosphate carboxylase ...
 1-173 3.09e-59

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: 189.52  E-value: 3.09e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 469832013   1 VWTDGLTSLDRYKGRCYDIEPVAGeenQYIAYVAYPLDLFEEGSVTNLFTSIVGNVFGFKALRALRLEDLRIPPAYSKTF 80
Cdd:cd08213   36 LATLYPERAEKLKAKAYYFDGLGG---SYIVKVAYPLELFEEGNMPQLLSSIAGNIFGMKAVKNLRLEDIYFPESYLREF 112

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 469832013  81 IGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFVAEALFKS 160
Cdd:cd08213  113 KGPQFGIEGVREILGIKDRPLLGTVPKPKVGLSPEEHAEVAYEALVGGVDLVKDDENLTSQPFNRFEERAKESLKARDKA 192

                        170
                 ....*....|...
gi 469832013 161 QAETGEIKGHYLN 173
Cdd:cd08213  193 EAETGERKAYLAN 205
RuBisCO_large pfam00016
Ribulose bisphosphate carboxylase large chain, catalytic domain; The C-terminal domain of ...
 87-173 3.06e-55

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: 176.01  E-value: 3.06e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 469832013   87 IQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFVAEALFKSQAETGE 166
Cdd:pfam00016   1 IAVERRVLNKYGRPILGTIIKPKLGLSPKNYARAVYEFLLGGLDFIKDDENINSQPFMPWRDRFLFVAEAIDRAQDETGE 80


                  ....*..
gi 469832013  167 IKGHYLN 173
Cdd:pfam00016  81 AKGHYLN 87
rubisco_III TIGR03326
ribulose bisphosphate carboxylase, type III; Members of this protein family are the archaeal, ...
 8-173 7.99e-45

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: 152.23  E-value: 7.99e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 469832013    8 SLDRYKG---RCYDIEPVaGEEnqYIAYVAYPLDLFEEGSVTNLFTSIVGNVFGFKALRALRLEDLRIPPAYSKTFIGPP 84
Cdd:TIGR03326  52 DPERYKDlsaKVYDIEEH-GDG--SIVRIAYPLGLFEEGNLPQLLSCIAGNIFGMKAVKGLRLLDFEFPAEFLRAFKGPQ 128

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 469832013   85 HGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFVAEALFKSQAET 164
Cdd:TIGR03326 129 FGIEGVREILGIKDRPITATVPKPKVGLSTEEHAKVAYELWSGGVDLLKDDENLTSQAFNRFEERVEKSLKVRDKVEAET 208


                  ....*....
gi 469832013  165 GEIKGHYLN 173
Cdd:TIGR03326 209 GEKKSYLIN 217
RuBisCO_IV_RLP cd08205
Ribulose bisphosphate carboxylase like proteins, Rubisco-Form IV; Ribulose bisphosphate ...
 9-166 1.04e-34

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: 124.57  E-value: 1.04e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 469832013   9 LDRYKGRCYDIEPV---AGEENQYIAYVAYPLDLFEeGSVTNLFTSIVGNVFGfkaLRALRLEDLRIPPAYSKTFIGPPH 85
Cdd:cd08205   41 RERHVGRVESIEELeesEGKYGRARVTISYPLDNFG-GDLPQLLNTLFGNLSL---LPGIKLVDLELPDSLLAAFPGPRF 116

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 469832013  86 GIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFVAEALFKSQAETG 165
Cdd:cd08205  117 GIEGLRRLLGVHDRPLLGTIIKPSIGLSPEELAELAYELALGGIDLIKDDELLADQPYAPFEERVRACMEAVRRANEETG 196


                 .
gi 469832013 166 E 166
Cdd:cd08205  197 R 197
RuBisCO_large_N pfam02788
Ribulose bisphosphate carboxylase large chain, N-terminal domain; The N-terminal domain of ...
 1-76 1.09e-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: 118.08  E-value: 1.09e-34
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 469832013    1 VWTDGLTSLDRYKGRCYDIEPVAGEenQYIAYVAYPLDLFEEGSVTNLFTSIVGNVFGFKALRALRLEDLRIPPAY 76
Cdd:pfam02788  47 VWTLDDTFTKKLKAKVYEIDEVPGG--SYIVKIAYPLDLFEEGSIPQLLSSIAGNIFGMKAVKALRLEDIRFPPAY 120
RuBisCO_large_II cd08211
Ribulose bisphosphate carboxylase large chain, Form II; Ribulose bisphosphate carboxylase ...
 15-173 1.35e-26

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: 104.12  E-value: 1.35e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 469832013  15 RCYDIEpvagEENQyIAYVAYPLDLFE------EGSVTNLFTSIVGNVFGFKALRALRLEDLRIPPAYSKTFIGPPHGIQ 88
Cdd:cd08211   69 LVYEID----EARE-LMKIAYPVELFDrnltdgRAMVASFLTLIIGNNQGMGDVEYLKMHDFYVPESMLELFDGPSVNIS 143

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 469832013  89 VERDKLNKY---GRPLLGCTIKPKLGLSAKNYGRAVYECLRGGlDFTKDDENVNSQPFMRWRDRFLFVAEALFKSQAETG 165
Cdd:cd08211  144 DMWKVLGRPevdGGYIAGTIIKPKLGLRPKPFAEACYAFWLGG-DFIKNDEPQANQPFCPLKKVIPLVADAMRRAQDETG 222


                 ....*...
gi 469832013 166 EIKGHYLN 173
Cdd:cd08211  223 EAKLFSAN 230
RLP_NonPhot cd08207
Ribulose bisphosphate carboxylase like proteins from nonphototrophic bacteria; Ribulose ...
 33-165 1.84e-26

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: 103.16  E-value: 1.84e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 469832013  33 VAYPLDLFeeG-SVTNLFTSIVGNVFGFKALRALRLEDLRIPPAYSKTFIGPPHGIQVERDKLNKYGRPLLGCTIKPKLG 111
Cdd:cd08207   78 ISFPLDNI--GtSLPNLLATVAGNLFELRELSGLRLVDLGLPDEFAAAFPGPAFGIAGTRRLTGVEDRPLIGTIIKPSVG 155

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 469832013 112 LSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFVAEALFKSQAETG 165
Cdd:cd08207  156 LTPEETAALVRQLAAAGIDFIKDDELLANPPYSPLDERVRAVMRVINDHAQRTG 209
PRK13475 PRK13475
ribulose-bisphosphate carboxylase;
17-173 3.56e-26

ribulose-bisphosphate carboxylase;


Pssm-ID: 184072  Cd Length: 443  Bit Score: 102.88  E-value: 3.56e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 469832013  17 YDIEPVAGeenqyIAYVAYPLDLFE------EGSVTNLFTSIVGNVFGFKALRALRLEDLRIPPAYSKTFIGPPHGIqve 90
Cdd:PRK13475  72 YEIDEARE-----LMKIAYPVELFDrniidgRAMIVSFLTLTIGNNQGMGDVEYAKMHDFYVPPRYLELFDGPSTDI--- 143

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 469832013  91 rDKLNKY-GRP------LLGCTIKPKLGLSAKNYGRAVYECLRGGlDFTKDDENVNSQPFMRWRDRFLFVAEALFKSQAE 163
Cdd:PRK13475 144 -SDLWRVlGRPvkdggyIAGTIIKPKLGLRPEPFAEACYDFWLGG-DFIKNDEPQGNQVFAPLKKTVPLVADAMKRAQDE 221

                        170
                 ....*....|
gi 469832013 164 TGEIKGHYLN 173
Cdd:PRK13475 222 TGEAKLFSAN 231
RLP_RrRLP cd08210
Ribulose bisphosphate carboxylase like proteins (RLPs) similar to R.rubrum RLP; RLP from ...
 9-165 8.57e-24

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: 95.38  E-value: 8.57e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 469832013   9 LDRYKGRCYDIEPVagEENQYIAYVAYPLDLFEeGSVTNLFTSIVGNVfgfKALRALRLEDLRIPPAYSKTFIGPPHGIQ 88
Cdd:cd08210   42 RDNIVGRVESLEPA--GEGSYRARISYSVDTAG-GELTQLLNVLFGNS---SLQPGIRLVDFELPPSLLRRFPGPRFGIA 115

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 469832013  89 VERDKLNKYGRPLLGCTIKPkLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFVAEALFKSQAETG 165
Cdd:cd08210  116 GLRALLGIPERPLLCSALKP-QGLSAAELAELAYAFALGGIDIIKDDHGLADQPFAPFEERVKACQEAVAEANAETG 191
RLP_DK-MTP-1-P-enolase cd08209
2,3-diketo-5-methylthiopentyl-1-phosphate enolase; Ribulose bisphosphate carboxylase like ...
 2-165 3.83e-19

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: 83.14  E-value: 3.83e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 469832013   2 WTDGLTS----LDRYKGRCYDIEPvaGEENQYIAYVAYPLdlfeeGSVTNLFTSIVGNVFGFKALR-ALRLEDLRIPPAY 76
Cdd:cd08209   29 WTDLPALrqaqLQKHLGEVVSVEE--LEEGRGVITIAYPL-----INVSGDIPALLTTIFGKLSLDgKIKLVDLRLPEEF 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 469832013  77 SKTFIGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFVAEA 156
Cdd:cd08209  102 GRAFPGPKFGIEGIRQRLGVHDRPLLMSIFKGVLGLDLDDLAEQLREQALGGVDLIKDDEILFDNPLAPALERIRACRPV 181


                 ....*....
gi 469832013 157 LFKSQAETG 165
Cdd:cd08209  182 LQEVYEQTG 190
RLP_Photo cd08208
Ribulose bisphosphate carboxylase like proteins from phototrophic bacteria; Ribulose ...
 45-173 1.83e-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: 78.40  E-value: 1.83e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 469832013  45 VTNLFTSIVGN-VFGFKALRALRLEDLRIPPAYSKTFIGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYE 123
Cdd:cd08208  105 IPNLLSAVCGEgTFFSPGVPVVKLMDIHFPETYLADFEGPKFGIAGLRERLQAHDRPIFFGVIKPNIGLPPGEFAELGYQ 184

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 469832013 124 CLRGGLDFTKDDENVNSQPFMRWRDRFLFVAEALFKSQAETGEIKGHYLN 173
Cdd:cd08208  185 SWLGGLDIAKDDEMLADVDWCPLEERAALLGKARRRAEAETGVPKIYLAN 234
mtnW PRK09549
2,3-diketo-5-methylthiopentyl-1-phosphate enolase; Reviewed
 2-165 2.85e-13

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


Pssm-ID: 236560  Cd Length: 407  Bit Score: 66.57  E-value: 2.85e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 469832013   2 WTDgLTSLDR-----YKGRCYDIEPVAGEEN----QYIAYVAYPldlfeEGSVTNLFTSIVGNVFGFKALRA-LRLEDLR 71
Cdd:PRK09549  33 WTD-LPHLEQeqlkkHKGNVVHVEELEEHERkgvkRGIIKIAYP-----LANFSPDLPAILTTTFGKLSLDGeVKLIDLT 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 469832013  72 IPPAYSKTFIGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFL 151
Cdd:PRK09549 107 FSDELKRHFPGPKFGIDGIRNLLGVHDRPLLMSIFKGVIGRDLDYLKEQLRDQALGGVDLVKDDEILFENALTPFEKRIV 186

                        170
                 ....*....|....
gi 469832013 152 FVAEALFKSQAETG 165
Cdd:PRK09549 187 AGKEVLQEVYETTG 200
 
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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