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Conserved domains on  [gi|1095593149|gb|APA17119|]
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ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit, partial (chloroplast) [Colchicum boissieri]

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) ...
 2-171 3.23e-147

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: 416.03  E-value: 3.23e-147
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1095593149   2 VIGEDNQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYSKTFQGPPHGIQVERDKLNKYGRPL 81
Cdd:CHL00040   90 VPGEENQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYLKTFQGPPHGIQVERDKLNKYGRPL 169

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1095593149  82 LGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEAIYKAQAETGEIKGHYLNATAGTCEE 161
Cdd:CHL00040  170 LGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEAIYKAQAETGEIKGHYLNATAGTCEE 249

                         170
                  ....*....|
gi 1095593149 162 MIKKAVFARE 171
Cdd:CHL00040  250 MYKRAVFARE 259
 
Name Accession Description Interval E-value
rbcL CHL00040
ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
 2-171 3.23e-147

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


Pssm-ID: 176981  Cd Length: 475  Bit Score: 416.03  E-value: 3.23e-147
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1095593149   2 VIGEDNQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYSKTFQGPPHGIQVERDKLNKYGRPL 81
Cdd:CHL00040   90 VPGEENQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYLKTFQGPPHGIQVERDKLNKYGRPL 169

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1095593149  82 LGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEAIYKAQAETGEIKGHYLNATAGTCEE 161
Cdd:CHL00040  170 LGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEAIYKAQAETGEIKGHYLNATAGTCEE 249

                         170
                  ....*....|
gi 1095593149 162 MIKKAVFARE 171
Cdd:CHL00040  250 MYKRAVFARE 259
RuBisCO_large_I cd08212
Ribulose bisphosphate carboxylase large chain, Form I; Ribulose bisphosphate carboxylase ...
 2-171 7.24e-138

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: 391.40  E-value: 7.24e-138
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1095593149   2 VIGEDNQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYSKTFQGPPHGIQVERDKLNKYGRPL 81
Cdd:cd08212    68 VPGEENQYFAYIAYPLDLFEEGSVANLTTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGIQVERDRLNKYGRPL 147

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1095593149  82 LGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEAIYKAQAETGEIKGHYLNATAGTCEE 161
Cdd:cd08212   148 LGCTIKPKLGLSAKNYGRVVYECLRGGLDFTKDDENINSQPFMRWRDRFLFVAEAVNKAQAETGEVKGHYLNVTAGTMEE 227

                         170
                  ....*....|
gi 1095593149 162 MIKKAVFARE 171
Cdd:cd08212   228 MYKRAEFAKE 237
RbcL COG1850
Ribulose 1,5-bisphosphate carboxylase, large subunit, or a RuBisCO-like protein [Carbohydrate ...
 1-172 6.52e-78

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


Pssm-ID: 441455  Cd Length: 417  Bit Score: 237.76  E-value: 6.52e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1095593149   1 EVIGEDNQYIAYVAYPLDLFEeGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYSKTFQGPPHGIQVERDKLNKYGRP 80
Cdd:COG1850    70 EVGGGYRRALVTIAYPLENFG-GNLPNLLSTVAGNLFGLKAVSGLRLLDLEFPESFLAAFPGPKFGIEGTRELLGVYDRP 148

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1095593149  81 LLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEAIYKAQAETGEIKGHYLNATAGTcE 160
Cdd:COG1850   149 LLGTIIKPKVGLSPEETAELVYELALGGVDFIKDDENLADQPFCPFEDRVRAVMEAIDRAEEETGEKKMYAFNITADT-D 227

                         170
                  ....*....|..
gi 1095593149 161 EMIKKAVFAREW 172
Cdd:COG1850   228 EMLRRADLAVEL 239
RuBisCO_large pfam00016
Ribulose bisphosphate carboxylase large chain, catalytic domain; The C-terminal domain of ...
 67-171 1.10e-65

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: 202.59  E-value: 1.10e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1095593149  67 IQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEAIYKAQAETGE 146
Cdd:pfam00016   1 IAVERRVLNKYGRPILGTIIKPKLGLSPKNYARAVYEFLLGGLDFIKDDENINSQPFMPWRDRFLFVAEAIDRAQDETGE 80

                          90       100
                  ....*....|....*....|....*
gi 1095593149 147 IKGHYLNATAGTCEEMIKKAVFARE 171
Cdd:pfam00016  81 AKGHYLNITADDMEEMYRRAEFAKE 105
rubisco_III TIGR03326
ribulose bisphosphate carboxylase, type III; Members of this protein family are the archaeal, ...
 9-171 2.68e-48

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: 161.09  E-value: 2.68e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1095593149   9 YIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYSKTFQGPPHGIQVERDKLNKYGRPLLGCTIKP 88
Cdd:TIGR03326  73 SIVRIAYPLGLFEEGNLPQLLSCIAGNIFGMKAVKGLRLLDFEFPAEFLRAFKGPQFGIEGVREILGIKDRPITATVPKP 152

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1095593149  89 KLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEAIYKAQAETGEIKGHYLNATAGTcEEMIKKAVF 168
Cdd:TIGR03326 153 KVGLSTEEHAKVAYELWSGGVDLLKDDENLTSQAFNRFEERVEKSLKVRDKVEAETGEKKSYLINITADV-REMERRAEL 231


                  ...
gi 1095593149 169 ARE 171
Cdd:TIGR03326 232 VAD 234
 
Name Accession Description Interval E-value
rbcL CHL00040
ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
 2-171 3.23e-147

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


Pssm-ID: 176981  Cd Length: 475  Bit Score: 416.03  E-value: 3.23e-147
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1095593149   2 VIGEDNQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYSKTFQGPPHGIQVERDKLNKYGRPL 81
Cdd:CHL00040   90 VPGEENQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYLKTFQGPPHGIQVERDKLNKYGRPL 169

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1095593149  82 LGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEAIYKAQAETGEIKGHYLNATAGTCEE 161
Cdd:CHL00040  170 LGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEAIYKAQAETGEIKGHYLNATAGTCEE 249

                         170
                  ....*....|
gi 1095593149 162 MIKKAVFARE 171
Cdd:CHL00040  250 MYKRAVFARE 259
RuBisCO_large_I cd08212
Ribulose bisphosphate carboxylase large chain, Form I; Ribulose bisphosphate carboxylase ...
 2-171 7.24e-138

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: 391.40  E-value: 7.24e-138
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1095593149   2 VIGEDNQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYSKTFQGPPHGIQVERDKLNKYGRPL 81
Cdd:cd08212    68 VPGEENQYFAYIAYPLDLFEEGSVANLTTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGIQVERDRLNKYGRPL 147

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1095593149  82 LGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEAIYKAQAETGEIKGHYLNATAGTCEE 161
Cdd:cd08212   148 LGCTIKPKLGLSAKNYGRVVYECLRGGLDFTKDDENINSQPFMRWRDRFLFVAEAVNKAQAETGEVKGHYLNVTAGTMEE 227

                         170
                  ....*....|
gi 1095593149 162 MIKKAVFARE 171
Cdd:cd08212   228 MYKRAEFAKE 237
rbcL PRK04208
ribulose bisophosphate carboxylase; Reviewed
 1-171 3.69e-125

ribulose bisophosphate carboxylase; Reviewed


Pssm-ID: 179787  Cd Length: 468  Bit Score: 359.99  E-value: 3.69e-125
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1095593149   1 EVIGEDNQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYSKTFQGPPHGIQVERDKLNKYGRP 80
Cdd:PRK04208   82 DVPGDDGSYYAFIAYPLDLFEEGSIPNLLASIAGNVFGFKAVKALRLEDIRFPVAYVKTFKGPPFGIQVERERLDKYGRP 161

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1095593149  81 LLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEAIYKAQAETGEIKGHYLNATAGTCE 160
Cdd:PRK04208  162 LLGTTPKPKLGLSAKNYGRVVYEALRGGLDFTKDDENLNSQPFNRWRDRFLFVMEAIDKAEAETGERKGHYLNVTAPTME 241

                         170
                  ....*....|.
gi 1095593149 161 EMIKKAVFARE 171
Cdd:PRK04208  242 EMYKRAEFAKE 252
RuBisCO_large_I_II_III cd08206
Ribulose bisphosphate carboxylase large chain, Form I,II,III; Ribulose bisphosphate ...
 6-171 7.11e-117

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: 7.11e-117
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1095593149   6 DNQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYSKTFQGPPHGIQVERDKLNKYGRPLLGCT 85
Cdd:cd08206    59 DGQYIAKIAYPLDLFEEGSVPNLLTSIIGNVFGMKAVKALRLEDFRFPPAYLKTFDGPSFGIQGEREILGKYGRPLLGTI 138

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1095593149  86 IKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEAIYKAQAETGEIKGHYLNATAGTCEEMIKK 165
Cdd:cd08206   139 VKPKLGLSPKEYARVVYEALRGGLDFVKDDENQNSQPFMRFEDRILFVAEAMDKAEAETGEAKGHYLNITADTPEEMIKR 218


                  ....*.
gi 1095593149 166 AVFARE 171
Cdd:cd08206   219 AEFAKE 224
RuBisCO_large cd08148
Ribulose bisphosphate carboxylase large chain; Ribulose bisphosphate carboxylase (Rubisco) ...
 8-171 3.65e-88

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: 262.36  E-value: 3.65e-88
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1095593149   8 QYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYSKTFQGPPHGIQVERDKLNKYGRPLLGCTIK 87
Cdd:cd08148    56 RYIVKIAYPVELFEPGNIPQILTVTAGNLFGLGALEAVRLEDLEFPEEYKKLFPGPKFGIDGIRKLLGVYGRPLVGTIIK 135

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1095593149  88 PKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEAIYKAQAETGEIKGHYLNATAGTcEEMIKKAV 167
Cdd:cd08148   136 PKLGLNPKYTAEAAYAAALGGLDLIKDDETLTDQPFCPLRDRITEVAAALDRVQEETGEKKLYAVNVTAGT-FEIIERAE 214


                  ....
gi 1095593149 168 FARE 171
Cdd:cd08148   215 RALE 218
RbcL COG1850
Ribulose 1,5-bisphosphate carboxylase, large subunit, or a RuBisCO-like protein [Carbohydrate ...
 1-172 6.52e-78

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


Pssm-ID: 441455  Cd Length: 417  Bit Score: 237.76  E-value: 6.52e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1095593149   1 EVIGEDNQYIAYVAYPLDLFEeGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYSKTFQGPPHGIQVERDKLNKYGRP 80
Cdd:COG1850    70 EVGGGYRRALVTIAYPLENFG-GNLPNLLSTVAGNLFGLKAVSGLRLLDLEFPESFLAAFPGPKFGIEGTRELLGVYDRP 148

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1095593149  81 LLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEAIYKAQAETGEIKGHYLNATAGTcE 160
Cdd:COG1850   149 LLGTIIKPKVGLSPEETAELVYELALGGVDFIKDDENLADQPFCPFEDRVRAVMEAIDRAEEETGEKKMYAFNITADT-D 227

                         170
                  ....*....|..
gi 1095593149 161 EMIKKAVFAREW 172
Cdd:COG1850   228 EMLRRADLAVEL 239
RuBisCO_large pfam00016
Ribulose bisphosphate carboxylase large chain, catalytic domain; The C-terminal domain of ...
 67-171 1.10e-65

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: 202.59  E-value: 1.10e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1095593149  67 IQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEAIYKAQAETGE 146
Cdd:pfam00016   1 IAVERRVLNKYGRPILGTIIKPKLGLSPKNYARAVYEFLLGGLDFIKDDENINSQPFMPWRDRFLFVAEAIDRAQDETGE 80

                          90       100
                  ....*....|....*....|....*
gi 1095593149 147 IKGHYLNATAGTCEEMIKKAVFARE 171
Cdd:pfam00016  81 AKGHYLNITADDMEEMYRRAEFAKE 105
RuBisCO_large_III cd08213
Ribulose bisphosphate carboxylase large chain, Form III; Ribulose bisphosphate carboxylase ...
 9-166 3.09e-62

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: 197.23  E-value: 3.09e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1095593149   9 YIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYSKTFQGPPHGIQVERDKLNKYGRPLLGCTIKP 88
Cdd:cd08213    61 YIVKVAYPLELFEEGNMPQLLSSIAGNIFGMKAVKNLRLEDIYFPESYLREFKGPQFGIEGVREILGIKDRPLLGTVPKP 140

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1095593149  89 KLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEAIYKAQAETGEIKGHYLNATAgTCEEMIKKA 166
Cdd:cd08213   141 KVGLSPEEHAEVAYEALVGGVDLVKDDENLTSQPFNRFEERAKESLKARDKAEAETGERKAYLANITA-PVREMERRA 217
rubisco_III TIGR03326
ribulose bisphosphate carboxylase, type III; Members of this protein family are the archaeal, ...
 9-171 2.68e-48

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: 161.09  E-value: 2.68e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1095593149   9 YIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYSKTFQGPPHGIQVERDKLNKYGRPLLGCTIKP 88
Cdd:TIGR03326  73 SIVRIAYPLGLFEEGNLPQLLSCIAGNIFGMKAVKGLRLLDFEFPAEFLRAFKGPQFGIEGVREILGIKDRPITATVPKP 152

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1095593149  89 KLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEAIYKAQAETGEIKGHYLNATAGTcEEMIKKAVF 168
Cdd:TIGR03326 153 KVGLSTEEHAKVAYELWSGGVDLLKDDENLTSQAFNRFEERVEKSLKVRDKVEAETGEKKSYLINITADV-REMERRAEL 231


                  ...
gi 1095593149 169 ARE 171
Cdd:TIGR03326 232 VAD 234
RuBisCO_IV_RLP cd08205
Ribulose bisphosphate carboxylase like proteins, Rubisco-Form IV; Ribulose bisphosphate ...
 1-171 1.36e-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: 126.88  E-value: 1.36e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1095593149   1 EVIGEDNQYIAYVAYPLDLFEeGSVTNMFTSIVGNVFGfkaLRALRLEDLRIPPAYSKTFQGPPHGIQVERDKLNKYGRP 80
Cdd:cd08205    56 ESEGKYGRARVTISYPLDNFG-GDLPQLLNTLFGNLSL---LPGIKLVDLELPDSLLAAFPGPRFGIEGLRRLLGVHDRP 131

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1095593149  81 LLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEAIYKAQAETGEIKGHYLNATAGTcE 160
Cdd:cd08205   132 LLGTIIKPSIGLSPEELAELAYELALGGIDLIKDDELLADQPYAPFEERVRACMEAVRRANEETGRKTLYAPNITGDP-D 210

                         170
                  ....*....|.
gi 1095593149 161 EMIKKAVFARE 171
Cdd:cd08205   211 ELRRRADRAVE 221
PRK13475 PRK13475
ribulose-bisphosphate carboxylase;
13-171 5.30e-31

ribulose-bisphosphate carboxylase;


Pssm-ID: 184072  Cd Length: 443  Bit Score: 115.97  E-value: 5.30e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1095593149  13 VAYPLDLFE------EGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYSKTFQGPPHGIqverDKLNKY-GRP----- 80
Cdd:PRK13475   83 IAYPVELFDrniidgRAMIVSFLTLTIGNNQGMGDVEYAKMHDFYVPPRYLELFDGPSTDI----SDLWRVlGRPvkdgg 158

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1095593149  81 -LLGCTIKPKLGLSAKNYGRAVYECLRGGlDFTKDDENVNSQPFMRWRDRFLFCAEAIYKAQAETGEIKGHYLNATAGTC 159
Cdd:PRK13475  159 yIAGTIIKPKLGLRPEPFAEACYDFWLGG-DFIKNDEPQGNQVFAPLKKTVPLVADAMKRAQDETGEAKLFSANITADDH 237

                         170
                  ....*....|..
gi 1095593149 160 EEMIKKAVFARE 171
Cdd:PRK13475  238 YEMIARGEYILE 249
RuBisCO_large_II cd08211
Ribulose bisphosphate carboxylase large chain, Form II; Ribulose bisphosphate carboxylase ...
 3-171 2.20e-30

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: 114.14  E-value: 2.20e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1095593149   3 IGEDNQyIAYVAYPLDLFE------EGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYSKTFQGPPHGIQVERDKLNK 76
Cdd:cd08211    73 IDEARE-LMKIAYPVELFDrnltdgRAMVASFLTLIIGNNQGMGDVEYLKMHDFYVPESMLELFDGPSVNISDMWKVLGR 151

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1095593149  77 Y---GRPLLGCTIKPKLGLSAKNYGRAVYECLRGGlDFTKDDENVNSQPFMRWRDRFLFCAEAIYKAQAETGEIKGHYLN 153
Cdd:cd08211   152 PevdGGYIAGTIIKPKLGLRPKPFAEACYAFWLGG-DFIKNDEPQANQPFCPLKKVIPLVADAMRRAQDETGEAKLFSAN 230

                         170
                  ....*....|....*...
gi 1095593149 154 ATAGTCEEMIKKAVFARE 171
Cdd:cd08211   231 ITADDPDEMIARGEYILE 248
RLP_RrRLP cd08210
Ribulose bisphosphate carboxylase like proteins (RLPs) similar to R.rubrum RLP; RLP from ...
 5-171 3.38e-27

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: 104.63  E-value: 3.38e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1095593149   5 EDNQYIAYVAYPLDlfeegSVTNMFTSIVGNVFGFKAL-RALRLEDLRIPPAYSKTFQGPPHGIQVERDKLNKYGRPLLG 83
Cdd:cd08210    56 GEGSYRARISYSVD-----TAGGELTQLLNVLFGNSSLqPGIRLVDFELPPSLLRRFPGPRFGIAGLRALLGIPERPLLC 130

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1095593149  84 CTIKPkLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEAIYKAQAETGeikGH--YLNATAGTCEE 161
Cdd:cd08210   131 SALKP-QGLSAAELAELAYAFALGGIDIIKDDHGLADQPFAPFEERVKACQEAVAEANAETG---GRtlYAPNVTGPPTQ 206

                         170
                  ....*....|
gi 1095593149 162 MIKKAVFARE 171
Cdd:cd08210   207 LLERARFAKE 216
RLP_NonPhot cd08207
Ribulose bisphosphate carboxylase like proteins from nonphototrophic bacteria; Ribulose ...
 13-145 8.45e-27

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: 104.31  E-value: 8.45e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1095593149  13 VAYPLDLFeeG-SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYSKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLG 91
Cdd:cd08207    78 ISFPLDNI--GtSLPNLLATVAGNLFELRELSGLRLVDLGLPDEFAAAFPGPAFGIAGTRRLTGVEDRPLIGTIIKPSVG 155

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1095593149  92 LSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEAIYKAQAETG 145
Cdd:cd08207   156 LTPEETAALVRQLAAAGIDFIKDDELLANPPYSPLDERVRAVMRVINDHAQRTG 209
RuBisCO_large_N pfam02788
Ribulose bisphosphate carboxylase large chain, N-terminal domain; The N-terminal domain of ...
 6-56 1.88e-25

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: 94.20  E-value: 1.88e-25
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1095593149   6 DNQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAY 56
Cdd:pfam02788  70 GGSYIVKIAYPLDLFEEGSIPQLLSSIAGNIFGMKAVKALRLEDIRFPPAY 120
RLP_DK-MTP-1-P-enolase cd08209
2,3-diketo-5-methylthiopentyl-1-phosphate enolase; Ribulose bisphosphate carboxylase like ...
 1-145 4.87e-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: 82.75  E-value: 4.87e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1095593149   1 EVIG----EDNQYIAYVAYPLdlfeeGSVTNMFTSIVGNVFGFKALR-ALRLEDLRIPPAYSKTFQGPPHGIQVERDKLN 75
Cdd:cd08209    46 EVVSveelEEGRGVITIAYPL-----INVSGDIPALLTTIFGKLSLDgKIKLVDLRLPEEFGRAFPGPKFGIEGIRQRLG 120

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1095593149  76 KYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEAIYKAQAETG 145
Cdd:cd08209   121 VHDRPLLMSIFKGVLGLDLDDLAEQLREQALGGVDLIKDDEILFDNPLAPALERIRACRPVLQEVYEQTG 190
RLP_Photo cd08208
Ribulose bisphosphate carboxylase like proteins from phototrophic bacteria; Ribulose ...
 25-155 5.97e-19

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: 82.64  E-value: 5.97e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1095593149  25 VTNMFTSIVGN-VFGFKALRALRLEDLRIPPAYSKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYE 103
Cdd:cd08208   105 IPNLLSAVCGEgTFFSPGVPVVKLMDIHFPETYLADFEGPKFGIAGLRERLQAHDRPIFFGVIKPNIGLPPGEFAELGYQ 184

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1095593149 104 CLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEAIYKAQAETGEIKGHYLNAT 155
Cdd:cd08208   185 SWLGGLDIAKDDEMLADVDWCPLEERAALLGKARRRAEAETGVPKIYLANIT 236
mtnW PRK09549
2,3-diketo-5-methylthiopentyl-1-phosphate enolase; Reviewed
 13-167 6.01e-13

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


Pssm-ID: 236560  Cd Length: 407  Bit Score: 65.41  E-value: 6.01e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1095593149  13 VAYPldlfeEGSVTNMFTSIVGNVFGFKALRA-LRLEDLRIPPAYSKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLG 91
Cdd:PRK09549   72 IAYP-----LANFSPDLPAILTTTFGKLSLDGeVKLIDLTFSDELKRHFPGPKFGIDGIRNLLGVHDRPLLMSIFKGVIG 146

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1095593149  92 LSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEAIYKAQAETGEIKGHYLNATAGTCE--EMIKKAV 167
Cdd:PRK09549  147 RDLDYLKEQLRDQALGGVDLVKDDEILFENALTPFEKRIVAGKEVLQEVYETTGHKTLYAVNLTGRTFElkEKAKRAA 224
 
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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