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Conserved domains on  [gi|9798652|dbj|BAB11747|]
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ribulose-1,5-bisphosphate carboxylase/oxygenase form I large subunit, partial [uncultured bacterium Hawaii Lohi chimney-6]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RuBisCO_large super family cl08232
Ribulose bisphosphate carboxylase large chain; Ribulose bisphosphate carboxylase (Rubisco) ...
 1-166 3.52e-112

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 PRK04208:

Pssm-ID: 471793  Cd Length: 468  Bit Score: 326.48  E-value: 3.52e-112
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9798652     1 ACYEGLRGGLDFTKDDENVNSQPFMRWRARFDFVQEAIEKAEAETGERKGHYLNVTAATSDEMMKRAEYAKEIGSPIIMH 80
Cdd:PRK04208 181 VVYEALRGGLDFTKDDENLNSQPFNRWRDRFLFVMEAIDKAEAETGERKGHYLNVTAPTMEEMYKRAEFAKELGSPIVMI 260

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9798652    81 DYLTGGFvCPNTQLAQWCQEQGMFVHIHRAMHAVLDRNPHHGIHFRVLTKVLRLSGGDHLHSGTVVGKLEGDREATLGWI 160
Cdd:PRK04208 261 DVVTAGW-TALQSLREWCRDNGLALHAHRAMHAAFTRNPNHGISFRVLAKLLRLIGVDHLHTGTVVGKLEGDRAEVLGYY 339


                 ....*.
gi 9798652   161 DIMRES 166
Cdd:PRK04208 340 DILRED 345
 
Name Accession Description Interval E-value
rbcL PRK04208
ribulose bisophosphate carboxylase; Reviewed
 1-166 3.52e-112

ribulose bisophosphate carboxylase; Reviewed


Pssm-ID: 179787  Cd Length: 468  Bit Score: 326.48  E-value: 3.52e-112
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9798652     1 ACYEGLRGGLDFTKDDENVNSQPFMRWRARFDFVQEAIEKAEAETGERKGHYLNVTAATSDEMMKRAEYAKEIGSPIIMH 80
Cdd:PRK04208 181 VVYEALRGGLDFTKDDENLNSQPFNRWRDRFLFVMEAIDKAEAETGERKGHYLNVTAPTMEEMYKRAEFAKELGSPIVMI 260

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9798652    81 DYLTGGFvCPNTQLAQWCQEQGMFVHIHRAMHAVLDRNPHHGIHFRVLTKVLRLSGGDHLHSGTVVGKLEGDREATLGWI 160
Cdd:PRK04208 261 DVVTAGW-TALQSLREWCRDNGLALHAHRAMHAAFTRNPNHGISFRVLAKLLRLIGVDHLHTGTVVGKLEGDRAEVLGYY 339


                 ....*.
gi 9798652   161 DIMRES 166
Cdd:PRK04208 340 DILRED 345
RuBisCO_large_I cd08212
Ribulose bisphosphate carboxylase large chain, Form I; Ribulose bisphosphate carboxylase ...
 1-166 4.09e-104

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: 305.50  E-value: 4.09e-104
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9798652    1 ACYEGLRGGLDFTKDDENVNSQPFMRWRARFDFVQEAIEKAEAETGERKGHYLNVTAATSDEMMKRAEYAKEIGSPIIMH 80
Cdd:cd08212 166 VVYECLRGGLDFTKDDENINSQPFMRWRDRFLFVAEAVNKAQAETGEVKGHYLNVTAGTMEEMYKRAEFAKELGSPIIMH 245

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9798652   81 DYLTgGFVCpNTQLAQWCQEQGMFVHIHRAMHAVLDRNPHHGIHFRVLTKVLRLSGGDHLHSGTVVGKLEGDREATLGWI 160
Cdd:cd08212 246 DLLT-GFTA-IQSLAKWCRDNGMLLHLHRAGHATYDRQKNHGIHFRVLAKWLRLSGVDHIHAGTVVGKLEGDPLVTLGFY 323


                ....*.
gi 9798652  161 DIMRES 166
Cdd:cd08212 324 DLLRDD 329
RuBisCO_large pfam00016
Ribulose bisphosphate carboxylase large chain, catalytic domain; The C-terminal domain of ...
 1-157 3.66e-84

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: 249.20  E-value: 3.66e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9798652      1 ACYEGLRGGLDFTKDDENVNSQPFMRWRARFDFVQEAIEKAEAETGERKGHYLNVTAATSDEMMKRAEYAKEIGSPIIMH 80
Cdd:pfam00016  34 AVYEFLLGGLDFIKDDENINSQPFMPWRDRFLFVAEAIDRAQDETGEAKGHYLNITADDMEEMYRRAEFAKETGGVAVMV 113

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 9798652     81 DYLTGGFvCPNTQLAQWCQEQGMFVHIHRAMHAVLDRNPHHGIHFRVLTKVLRLSGGDHLHSGTV-VGKLEGDREATL 157
Cdd:pfam00016 114 DGLVIGP-TAITTLRRWFRDNGVILHYHRAGHGAVTRQSKHGISFRVLAKMARLAGADHLHTGTMgVGKLEGDPSDTL 190
RbcL COG1850
Ribulose 1,5-bisphosphate carboxylase, large subunit, or a RuBisCO-like protein [Carbohydrate ...
 1-165 7.81e-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: 211.57  E-value: 7.81e-68
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9798652    1 ACYEGLRGGLDFTKDDENVNSQPFMRWRARFDFVQEAIEKAEAETGERKGHYLNVTAATsDEMMKRAEYAKEIGSPIIMH 80
Cdd:COG1850 168 LVYELALGGVDFIKDDENLADQPFCPFEDRVRAVMEAIDRAEEETGEKKMYAFNITADT-DEMLRRADLAVELGANAVMV 246

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9798652   81 DYLTGGFvcpnTQLAQWCQEQ-GMFVHIHRAMHAVLDRNPHHGIHFRVLTKVLRLSGGDHLHSGTVVGKLEGDREATLGW 159
Cdd:COG1850 247 DVNTVGL----SAVQTLREEHiGLPIHAHRAGHGAFTRSPLHGISMRVLAKLWRLAGADHLHVGTPVGKMEGDDEEVLAI 322


                ....*.
gi 9798652  160 IDIMRE 165
Cdd:COG1850 323 ADALLQ 328
rubisco_III TIGR03326
ribulose bisphosphate carboxylase, type III; Members of this protein family are the archaeal, ...
 3-165 3.41e-47

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: 158.01  E-value: 3.41e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9798652      3 YEGLRGGLDFTKDDENVNSQPFMRWRARFDFVQEAIEKAEAETGERKGHYLNVTAATsDEMMKRAEYAKEIGSPIIMHDY 82
Cdd:TIGR03326 166 YELWSGGVDLLKDDENLTSQAFNRFEERVEKSLKVRDKVEAETGEKKSYLINITADV-REMERRAELVADLGGEYVMVDI 244

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9798652     83 LTGGFVCPNTqLAQWCQEQGMFVHIHRAMHAVLDRNPHHGIHFRVLTKVLRLSGGDHLHSGTV-VGKLEGDREATLGWID 161
Cdd:TIGR03326 245 VVAGWSALQY-VRERTEDLGLAIHAHRAMHAAFTRNPKHGISMFVLAKLYRLIGVDQLHTGTAgVGKLEGGNEDTKGIND 323


                  ....
gi 9798652    162 IMRE 165
Cdd:TIGR03326 324 FLRQ 327
 
Name Accession Description Interval E-value
rbcL PRK04208
ribulose bisophosphate carboxylase; Reviewed
 1-166 3.52e-112

ribulose bisophosphate carboxylase; Reviewed


Pssm-ID: 179787  Cd Length: 468  Bit Score: 326.48  E-value: 3.52e-112
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9798652     1 ACYEGLRGGLDFTKDDENVNSQPFMRWRARFDFVQEAIEKAEAETGERKGHYLNVTAATSDEMMKRAEYAKEIGSPIIMH 80
Cdd:PRK04208 181 VVYEALRGGLDFTKDDENLNSQPFNRWRDRFLFVMEAIDKAEAETGERKGHYLNVTAPTMEEMYKRAEFAKELGSPIVMI 260

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9798652    81 DYLTGGFvCPNTQLAQWCQEQGMFVHIHRAMHAVLDRNPHHGIHFRVLTKVLRLSGGDHLHSGTVVGKLEGDREATLGWI 160
Cdd:PRK04208 261 DVVTAGW-TALQSLREWCRDNGLALHAHRAMHAAFTRNPNHGISFRVLAKLLRLIGVDHLHTGTVVGKLEGDRAEVLGYY 339


                 ....*.
gi 9798652   161 DIMRES 166
Cdd:PRK04208 340 DILRED 345
rbcL CHL00040
ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
 1-165 2.36e-108

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


Pssm-ID: 176981  Cd Length: 475  Bit Score: 317.03  E-value: 2.36e-108
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9798652     1 ACYEGLRGGLDFTKDDENVNSQPFMRWRARFDFVQEAIEKAEAETGERKGHYLNVTAATSDEMMKRAEYAKEIGSPIIMH 80
Cdd:CHL00040 188 AVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEAIYKAQAETGEIKGHYLNATAGTCEEMYKRAVFARELGVPIVMH 267

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9798652    81 DYLTGGFVCpNTQLAQWCQEQGMFVHIHRAMHAVLDRNPHHGIHFRVLTKVLRLSGGDHLHSGTVVGKLEGDREATLGWI 160
Cdd:CHL00040 268 DYLTGGFTA-NTSLAHYCRDNGLLLHIHRAMHAVIDRQKNHGIHFRVLAKALRMSGGDHIHAGTVVGKLEGEREMTLGFV 346


                 ....*
gi 9798652   161 DIMRE 165
Cdd:CHL00040 347 DLLRD 351
RuBisCO_large_I cd08212
Ribulose bisphosphate carboxylase large chain, Form I; Ribulose bisphosphate carboxylase ...
 1-166 4.09e-104

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: 305.50  E-value: 4.09e-104
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9798652    1 ACYEGLRGGLDFTKDDENVNSQPFMRWRARFDFVQEAIEKAEAETGERKGHYLNVTAATSDEMMKRAEYAKEIGSPIIMH 80
Cdd:cd08212 166 VVYECLRGGLDFTKDDENINSQPFMRWRDRFLFVAEAVNKAQAETGEVKGHYLNVTAGTMEEMYKRAEFAKELGSPIIMH 245

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9798652   81 DYLTgGFVCpNTQLAQWCQEQGMFVHIHRAMHAVLDRNPHHGIHFRVLTKVLRLSGGDHLHSGTVVGKLEGDREATLGWI 160
Cdd:cd08212 246 DLLT-GFTA-IQSLAKWCRDNGMLLHLHRAGHATYDRQKNHGIHFRVLAKWLRLSGVDHIHAGTVVGKLEGDPLVTLGFY 323


                ....*.
gi 9798652  161 DIMRES 166
Cdd:cd08212 324 DLLRDD 329
RuBisCO_large_I_II_III cd08206
Ribulose bisphosphate carboxylase large chain, Form I,II,III; Ribulose bisphosphate ...
 1-165 2.71e-95

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: 281.82  E-value: 2.71e-95
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9798652    1 ACYEGLRGGLDFTKDDENVNSQPFMRWRARFDFVQEAIEKAEAETGERKGHYLNVTAATSDEMMKRAEYAKEIGSPIIMH 80
Cdd:cd08206 153 VVYEALRGGLDFVKDDENQNSQPFMRFEDRILFVAEAMDKAEAETGEAKGHYLNITADTPEEMIKRAEFAKELGSVIVMV 232

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9798652   81 DYLTGGFVCpNTQLAQWCQEQGMFVHIHRAMHAVLDRNPHHGIHFRVLTKVLRLSGGDHLHSGTVVGKLEGDREATLGWI 160
Cdd:cd08206 233 DGVTAGWTA-IQSARRWCPDNGLALHAHRAGHAAFTRQKNHGISMRVLAKLARLIGVDHIHTGTVVGKLEGDPSEVKGIA 311


                ....*
gi 9798652  161 DIMRE 165
Cdd:cd08206 312 DMLRE 316
RuBisCO_large pfam00016
Ribulose bisphosphate carboxylase large chain, catalytic domain; The C-terminal domain of ...
 1-157 3.66e-84

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: 249.20  E-value: 3.66e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9798652      1 ACYEGLRGGLDFTKDDENVNSQPFMRWRARFDFVQEAIEKAEAETGERKGHYLNVTAATSDEMMKRAEYAKEIGSPIIMH 80
Cdd:pfam00016  34 AVYEFLLGGLDFIKDDENINSQPFMPWRDRFLFVAEAIDRAQDETGEAKGHYLNITADDMEEMYRRAEFAKETGGVAVMV 113

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 9798652     81 DYLTGGFvCPNTQLAQWCQEQGMFVHIHRAMHAVLDRNPHHGIHFRVLTKVLRLSGGDHLHSGTV-VGKLEGDREATL 157
Cdd:pfam00016 114 DGLVIGP-TAITTLRRWFRDNGVILHYHRAGHGAVTRQSKHGISFRVLAKMARLAGADHLHTGTMgVGKLEGDPSDTL 190
RuBisCO_large cd08148
Ribulose bisphosphate carboxylase large chain; Ribulose bisphosphate carboxylase (Rubisco) ...
 1-165 1.79e-68

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: 211.90  E-value: 1.79e-68
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9798652    1 ACYEGLRGGLDFTKDDENVNSQPFMRWRARFDFVQEAIEKAEAETGERKGHYLNVTAATsDEMMKRAEYAKEIGSPIIMH 80
Cdd:cd08148 148 AAYAAALGGLDLIKDDETLTDQPFCPLRDRITEVAAALDRVQEETGEKKLYAVNVTAGT-FEIIERAERALELGANMLMV 226

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9798652   81 DYLTGGFVCpNTQLAQWCqEQGMFVHIHRAMHAVLDRNPHHGIHFRVLTKVLRLSGGDHLHSGTVVGKLEGDREATLGWI 160
Cdd:cd08148 227 DVLTAGFSA-LQALAEDF-EIDLPIHVHRAMHGAVTRSKFHGISMLVLAKLLRMAGGDFIHTGTVVGKMALEREEALGIA 304


                ....*
gi 9798652  161 DIMRE 165
Cdd:cd08148 305 DALTD 309
RbcL COG1850
Ribulose 1,5-bisphosphate carboxylase, large subunit, or a RuBisCO-like protein [Carbohydrate ...
 1-165 7.81e-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: 211.57  E-value: 7.81e-68
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9798652    1 ACYEGLRGGLDFTKDDENVNSQPFMRWRARFDFVQEAIEKAEAETGERKGHYLNVTAATsDEMMKRAEYAKEIGSPIIMH 80
Cdd:COG1850 168 LVYELALGGVDFIKDDENLADQPFCPFEDRVRAVMEAIDRAEEETGEKKMYAFNITADT-DEMLRRADLAVELGANAVMV 246

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9798652   81 DYLTGGFvcpnTQLAQWCQEQ-GMFVHIHRAMHAVLDRNPHHGIHFRVLTKVLRLSGGDHLHSGTVVGKLEGDREATLGW 159
Cdd:COG1850 247 DVNTVGL----SAVQTLREEHiGLPIHAHRAGHGAFTRSPLHGISMRVLAKLWRLAGADHLHVGTPVGKMEGDDEEVLAI 322


                ....*.
gi 9798652  160 IDIMRE 165
Cdd:COG1850 323 ADALLQ 328
RuBisCO_large_III cd08213
Ribulose bisphosphate carboxylase large chain, Form III; Ribulose bisphosphate carboxylase ...
 3-166 1.79e-55

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: 179.51  E-value: 1.79e-55
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9798652    3 YEGLRGGLDFTKDDENVNSQPFMRWRARFDFVQEAIEKAEAETGERKGHYLNVTAATsDEMMKRAEYAKEIGSPIIMHDY 82
Cdd:cd08213 154 YEALVGGVDLVKDDENLTSQPFNRFEERAKESLKARDKAEAETGERKAYLANITAPV-REMERRAELVADLGGKYVMIDV 232

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9798652   83 LTGGFVCPNTqLAQWCQEQGMFVHIHRAMHAVLDRNPHHGIHFRVLTKVLRLSGGDHLHSGTVVGKLEGDREATLGWIDI 162
Cdd:cd08213 233 VVAGWSALQY-LRDLAEDYGLAIHAHRAMHAAFTRNPRHGISMLVLAKLYRLIGVDQLHIGTAVGKMEGDKEEVLRIADI 311


                ....
gi 9798652  163 MRES 166
Cdd:cd08213 312 LREQ 315
rubisco_III TIGR03326
ribulose bisphosphate carboxylase, type III; Members of this protein family are the archaeal, ...
 3-165 3.41e-47

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: 158.01  E-value: 3.41e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9798652      3 YEGLRGGLDFTKDDENVNSQPFMRWRARFDFVQEAIEKAEAETGERKGHYLNVTAATsDEMMKRAEYAKEIGSPIIMHDY 82
Cdd:TIGR03326 166 YELWSGGVDLLKDDENLTSQAFNRFEERVEKSLKVRDKVEAETGEKKSYLINITADV-REMERRAELVADLGGEYVMVDI 244

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9798652     83 LTGGFVCPNTqLAQWCQEQGMFVHIHRAMHAVLDRNPHHGIHFRVLTKVLRLSGGDHLHSGTV-VGKLEGDREATLGWID 161
Cdd:TIGR03326 245 VVAGWSALQY-VRERTEDLGLAIHAHRAMHAAFTRNPKHGISMFVLAKLYRLIGVDQLHTGTAgVGKLEGGNEDTKGIND 323


                  ....
gi 9798652    162 IMRE 165
Cdd:TIGR03326 324 FLRQ 327
RuBisCO_IV_RLP cd08205
Ribulose bisphosphate carboxylase like proteins, Rubisco-Form IV; Ribulose bisphosphate ...
 2-165 4.38e-25

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: 98.76  E-value: 4.38e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9798652    2 CYEGLRGGLDFTKDDENVNSQPFMRWRARFDFVQEAIEKAEAETGERKGHYLNVTAATsDEMMKRAEYAKEIGSPIIMhd 81
Cdd:cd08205 152 AYELALGGIDLIKDDELLADQPYAPFEERVRACMEAVRRANEETGRKTLYAPNITGDP-DELRRRADRAVEAGANALL-- 228

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9798652   82 yltggfVCPNT-------QLAqwcQEQGMFVHIHRAMHAVLDRNPHHGIHFRVLTKVLRLSGGDHLHSGTVVGKLEGDRE 154
Cdd:cd08205 229 ------INPNLvgldalrALA---EDPDLPIMAHPAFAGALSRSPDYGSHFLLLGKLMRLAGADAVIFPGPGGRFPFSRE 299

                       170
                ....*....|.
gi 9798652  155 ATLGWIDIMRE 165
Cdd:cd08205 300 ECLAIARACRR 310
PRK13475 PRK13475
ribulose-bisphosphate carboxylase;
1-154 1.06e-22

ribulose-bisphosphate carboxylase;


Pssm-ID: 184072  Cd Length: 443  Bit Score: 92.86  E-value: 1.06e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9798652     1 ACYEGLRGGlDFTKDDENVNSQPFMRWRARFDFVQEAIEKAEAETGERKGHYLNVTAATSDEMMKRAEYAKEIGSPIIMH 80
Cdd:PRK13475 179 ACYDFWLGG-DFIKNDEPQGNQVFAPLKKTVPLVADAMKRAQDETGEAKLFSANITADDHYEMIARGEYILETFGENADH 257

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 9798652    81 -DYLTGGFVCpNTQLAQWCQEQ--GMFVHIHRAMH-AVLDRNPHHGIHFRVLTKVLRLSGGDHLHSGTV-VGKLEGDRE 154
Cdd:PRK13475 258 vAFLVDGYVA-GPGAVTTARRQypDQYLHYHRAGHgAVTSPSSKRGYTAFVLSKMARLQGASGIHTGTMgYGKMEGEAD 335
RuBisCO_large_II cd08211
Ribulose bisphosphate carboxylase large chain, Form II; Ribulose bisphosphate carboxylase ...
 1-154 7.19e-21

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: 87.94  E-value: 7.19e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9798652    1 ACYEGLRGGlDFTKDDENVNSQPFMRWRARFDFVQEAIEKAEAETGERKGHYLNVTAATSDEMMKRAEYAKEIGSPIIMH 80
Cdd:cd08211 178 ACYAFWLGG-DFIKNDEPQANQPFCPLKKVIPLVADAMRRAQDETGEAKLFSANITADDPDEMIARGEYILEAFGPNAGH 256

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9798652   81 -----DYLTGGFVCPNTQLAQWCQEqgmFVHIHRAMH-AVLDRNPHHGIHFRVLTKVLRLSGGDHLHSGTV-VGKLEGDR 153
Cdd:cd08211 257 vaflvDGYVAGPAAVTTARRRFPDQ---FLHYHRAGHgAVTSPQSKRGYTAFVLSKMARLQGASGIHTGTMgFGKMEGES 333


                .
gi 9798652  154 E 154
Cdd:cd08211 334 S 334
RLP_NonPhot cd08207
Ribulose bisphosphate carboxylase like proteins from nonphototrophic bacteria; Ribulose ...
 7-152 1.12e-17

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: 78.89  E-value: 1.12e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9798652    7 RGGLDFTKDDENVNSQPFMRWRARFDFVQEAIEKAEAETGERKGHYLNVTAATsDEMMKRAEYAKEIGSPIIMhdyltgg 86
Cdd:cd08207 170 AAGIDFIKDDELLANPPYSPLDERVRAVMRVINDHAQRTGRKVMYAFNITDDI-DEMRRNHDLVVEAGGTCVM------- 241

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 9798652   87 fVCPN----TQLAQWCQEQGMFVHIHRAMHAVLDRNPHHGIHFRVLTKVLRLSGGDHLHSGTVVGKL-EGD 152
Cdd:cd08207 242 -VSLNsvglSGLAALRRHSQLPIHGHRNGWGMLTRSPALGISFQAYQKLWRLAGVDHLHVNGLASKFwESD 311
RLP_RrRLP cd08210
Ribulose bisphosphate carboxylase like proteins (RLPs) similar to R.rubrum RLP; RLP from ...
 2-90 3.38e-14

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: 68.80  E-value: 3.38e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9798652    2 CYEGLRGGLDFTKDDENVNSQPFMRWRARFDFVQEAIEKAEAETGERKGHYLNVTaATSDEMMKRAEYAKEIGS------ 75
Cdd:cd08210 147 AYAFALGGIDIIKDDHGLADQPFAPFEERVKACQEAVAEANAETGGRTLYAPNVT-GPPTQLLERARFAKEAGAggvlia 225

                        90       100       110
                ....*....|....*....|....*....|....
gi 9798652   76 -------------------PIIMHDYLTGGFVCP 90
Cdd:cd08210 226 pgltgldtfrelaedfdflPILAHPAFAGAFVSS 259
RLP_Photo cd08208
Ribulose bisphosphate carboxylase like proteins from phototrophic bacteria; Ribulose ...
 3-138 2.24e-08

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: 52.20  E-value: 2.24e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9798652    3 YEGLRGGLDFTKDDENVNSQPFMRWRARFDFVQEAIEKAEAETGERKGHYLNVTAATsDEMMKRAEYAKEIGSPIIMHDY 82
Cdd:cd08208 183 YQSWLGGLDIAKDDEMLADVDWCPLEERAALLGKARRRAEAETGVPKIYLANITDEV-DRLMELHDVAVRNGANALLINA 261

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 9798652   83 LTGGFVCPNtQLAQWCQEQGMfvhIHRAMHAVLDRNPHHGIHFRVLTKVLRLSGGD 138
Cdd:cd08208 262 MPVGLSAVR-MLRKHAQVPLI---AHFPFIASFSRLEKYGIHSRVMTKLQRLAGLD 313
mtnW PRK09549
2,3-diketo-5-methylthiopentyl-1-phosphate enolase; Reviewed
 8-138 5.52e-07

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


Pssm-ID: 236560  Cd Length: 407  Bit Score: 48.08  E-value: 5.52e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9798652     8 GGLDFTKDDENVNSQPFMRWRARFDFVQEAIEKAEAETGERKGHYLNVTAATSdEMMKRAEYAKEIGSPIIMHDYLTGGF 87
Cdd:PRK09549 162 GGVDLVKDDEILFENALTPFEKRIVAGKEVLQEVYETTGHKTLYAVNLTGRTF-ELKEKAKRAAEAGADALLFNVFAYGL 240

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 9798652    88 vcpnTQLAQWCQEQGMFVHI--HRAMHAVLDRNPHHGI-HFRVLTKVLRLSGGD 138
Cdd:PRK09549 241 ----DVLQSLAEDPEIPVPImaHPAVSGAYTPSPLYGIsSPLLLGKLLRYAGAD 290
RLP_DK-MTP-1-P-enolase cd08209
2,3-diketo-5-methylthiopentyl-1-phosphate enolase; Ribulose bisphosphate carboxylase like ...
 8-166 2.63e-05

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: 43.08  E-value: 2.63e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9798652    8 GGLDFTKDDE----NVNSQPFMRWRArfdfVQEAIEKAEAETGERKGHYLNVTAATsDEMMKRAEYAKEIGSPIIMHDYL 83
Cdd:cd08209 152 GGVDLIKDDEilfdNPLAPALERIRA----CRPVLQEVYEQTGRRTLYAVNLTGPV-FTLKEKARRLVEAGANALLFNVF 226

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9798652   84 TGGFvcpnTQLAQWCQEQGMFVHI--HRAMHAVLDRNPHHGI-HFRVLTKVLRLSGGDHLHSGTVVGKLEGDREATLGWI 160
Cdd:cd08209 227 AYGL----DVLEALASDPEINVPIfaHPAFAGALYGSPDYGIaASVLLGTLMRLAGADAVLFPSPYGSVALSKEEALAIA 302


                ....*.
gi 9798652  161 DIMRES 166
Cdd:cd08209 303 EALRRG 308
 
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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