NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2018315342|gb|QTG40648|]
View 

ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit, partial (chloroplast) [Gigartinales sp.]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
RuBisCO_large super family cl08232
Ribulose bisphosphate carboxylase large chain; Ribulose bisphosphate carboxylase (Rubisco) ...
 1-186 5.73e-144

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: 408.32  E-value: 5.73e-144
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315342   1 ESSTATWTVVWTDLLTACDLYRAKAYKVDAVPNSSDQYFAYVAYDIDLFEEGSIPNLTASIIGNVFGFKAVKALRLEDMR 80
Cdd:CHL00040   60 ESSTGTWTTVWTDGLTSLDRYKGRCYRIEPVPGEENQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLR 139

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315342  81 IPVAYLKTFQGPATGIVCERERMDKFGRPFLGATVKPKLGLSGKNYGRVVYEGLKGGLDFLKDDENINSQPFMRWKERYL 160
Cdd:CHL00040  140 IPPAYLKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFL 219

                         170       180
                  ....*....|....*....|....*.
gi 2018315342 161 YAMEGVNRSIAATGEVKGHYLNVTSA 186
Cdd:CHL00040  220 FCAEAIYKAQAETGEIKGHYLNATAG 245
 
Name Accession Description Interval E-value
rbcL CHL00040
ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
 1-186 5.73e-144

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


Pssm-ID: 176981  Cd Length: 475  Bit Score: 408.32  E-value: 5.73e-144
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315342   1 ESSTATWTVVWTDLLTACDLYRAKAYKVDAVPNSSDQYFAYVAYDIDLFEEGSIPNLTASIIGNVFGFKAVKALRLEDMR 80
Cdd:CHL00040   60 ESSTGTWTTVWTDGLTSLDRYKGRCYRIEPVPGEENQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLR 139

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315342  81 IPVAYLKTFQGPATGIVCERERMDKFGRPFLGATVKPKLGLSGKNYGRVVYEGLKGGLDFLKDDENINSQPFMRWKERYL 160
Cdd:CHL00040  140 IPPAYLKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFL 219

                         170       180
                  ....*....|....*....|....*.
gi 2018315342 161 YAMEGVNRSIAATGEVKGHYLNVTSA 186
Cdd:CHL00040  220 FCAEAIYKAQAETGEIKGHYLNATAG 245
RuBisCO_large_I cd08212
Ribulose bisphosphate carboxylase large chain, Form I; Ribulose bisphosphate carboxylase ...
 1-186 4.99e-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: 392.56  E-value: 4.99e-138
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315342   1 ESSTATWTVVWTDLLTACDLYRAKAYKVDAVPNSSDQYFAYVAYDIDLFEEGSIPNLTASIIGNVFGFKAVKALRLEDMR 80
Cdd:cd08212    38 ESSTATWTVVWTDRLTALDRYKGKAYRVEPVPGEENQYFAYIAYPLDLFEEGSVANLTTSIVGNVFGFKALRALRLEDLR 117

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315342  81 IPVAYLKTFQGPATGIVCERERMDKFGRPFLGATVKPKLGLSGKNYGRVVYEGLKGGLDFLKDDENINSQPFMRWKERYL 160
Cdd:cd08212   118 IPPAYVKTFQGPPHGIQVERDRLNKYGRPLLGCTIKPKLGLSAKNYGRVVYECLRGGLDFTKDDENINSQPFMRWRDRFL 197

                         170       180
                  ....*....|....*....|....*.
gi 2018315342 161 YAMEGVNRSIAATGEVKGHYLNVTSA 186
Cdd:cd08212   198 FVAEAVNKAQAETGEVKGHYLNVTAG 223
RbcL COG1850
Ribulose 1,5-bisphosphate carboxylase, large subunit, or a RuBisCO-like protein [Carbohydrate ...
 1-184 4.25e-81

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


Pssm-ID: 441455  Cd Length: 417  Bit Score: 246.23  E-value: 4.25e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315342   1 ESSTATWTVVWTDLLTACDLYRAKAYKVDAVPNSS---DQYFAYVAYDIDLFEeGSIPNLTASIIGNVFGFKAVKALRLE 77
Cdd:COG1850    38 EQSTGTWTEVPTETDELRERLAARVYSIEELPEVGggyRRALVTIAYPLENFG-GNLPNLLSTVAGNLFGLKAVSGLRLL 116

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315342  78 DMRIPVAYLKTFQGPATGIVCERERMDKFGRPFLGATVKPKLGLSGKNYGRVVYEGLKGGLDFLKDDENINSQPFMRWKE 157
Cdd:COG1850   117 DLEFPESFLAAFPGPKFGIEGTRELLGVYDRPLLGTIIKPKVGLSPEETAELVYELALGGVDFIKDDENLADQPFCPFED 196

                         170       180
                  ....*....|....*....|....*..
gi 2018315342 158 RYLYAMEGVNRSIAATGEVKGHYLNVT 184
Cdd:COG1850   197 RVRAVMEAIDRAEEETGEKKMYAFNIT 223
rubisco_III TIGR03326
ribulose bisphosphate carboxylase, type III; Members of this protein family are the archaeal, ...
 1-185 8.87e-51

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: 168.41  E-value: 8.87e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315342   1 ESSTATWTVV--WTDLLTACDLyRAKAYKVDAVpnsSDQYFAYVAYDIDLFEEGSIPNLTASIIGNVFGFKAVKALRLED 78
Cdd:TIGR03326  38 ESSIGTWTTLqpWKDPERYKDL-SAKVYDIEEH---GDGSIVRIAYPLGLFEEGNLPQLLSCIAGNIFGMKAVKGLRLLD 113

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315342  79 MRIPVAYLKTFQGPATGIVCERERMDKFGRPFLGATVKPKLGLSGKNYGRVVYEGLKGGLDFLKDDENINSQPFMRWKER 158
Cdd:TIGR03326 114 FEFPAEFLRAFKGPQFGIEGVREILGIKDRPITATVPKPKVGLSTEEHAKVAYELWSGGVDLLKDDENLTSQAFNRFEER 193

                         170       180
                  ....*....|....*....|....*..
gi 2018315342 159 YLYAMEGVNRSIAATGEVKGHYLNVTS 185
Cdd:TIGR03326 194 VEKSLKVRDKVEAETGEKKSYLINITA 220
RuBisCO_large pfam00016
Ribulose bisphosphate carboxylase large chain, catalytic domain; The C-terminal domain of ...
 96-186 8.39e-49

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: 159.83  E-value: 8.39e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315342  96 IVCERERMDKFGRPFLGATVKPKLGLSGKNYGRVVYEGLKGGLDFLKDDENINSQPFMRWKERYLYAMEGVNRSIAATGE 175
Cdd:pfam00016   1 IAVERRVLNKYGRPILGTIIKPKLGLSPKNYARAVYEFLLGGLDFIKDDENINSQPFMPWRDRFLFVAEAIDRAQDETGE 80

                          90
                  ....*....|.
gi 2018315342 176 VKGHYLNVTSA 186
Cdd:pfam00016  81 AKGHYLNITAD 91
 
Name Accession Description Interval E-value
rbcL CHL00040
ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
 1-186 5.73e-144

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


Pssm-ID: 176981  Cd Length: 475  Bit Score: 408.32  E-value: 5.73e-144
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315342   1 ESSTATWTVVWTDLLTACDLYRAKAYKVDAVPNSSDQYFAYVAYDIDLFEEGSIPNLTASIIGNVFGFKAVKALRLEDMR 80
Cdd:CHL00040   60 ESSTGTWTTVWTDGLTSLDRYKGRCYRIEPVPGEENQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLR 139

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315342  81 IPVAYLKTFQGPATGIVCERERMDKFGRPFLGATVKPKLGLSGKNYGRVVYEGLKGGLDFLKDDENINSQPFMRWKERYL 160
Cdd:CHL00040  140 IPPAYLKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFL 219

                         170       180
                  ....*....|....*....|....*.
gi 2018315342 161 YAMEGVNRSIAATGEVKGHYLNVTSA 186
Cdd:CHL00040  220 FCAEAIYKAQAETGEIKGHYLNATAG 245
RuBisCO_large_I cd08212
Ribulose bisphosphate carboxylase large chain, Form I; Ribulose bisphosphate carboxylase ...
 1-186 4.99e-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: 392.56  E-value: 4.99e-138
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315342   1 ESSTATWTVVWTDLLTACDLYRAKAYKVDAVPNSSDQYFAYVAYDIDLFEEGSIPNLTASIIGNVFGFKAVKALRLEDMR 80
Cdd:cd08212    38 ESSTATWTVVWTDRLTALDRYKGKAYRVEPVPGEENQYFAYIAYPLDLFEEGSVANLTTSIVGNVFGFKALRALRLEDLR 117

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315342  81 IPVAYLKTFQGPATGIVCERERMDKFGRPFLGATVKPKLGLSGKNYGRVVYEGLKGGLDFLKDDENINSQPFMRWKERYL 160
Cdd:cd08212   118 IPPAYVKTFQGPPHGIQVERDRLNKYGRPLLGCTIKPKLGLSAKNYGRVVYECLRGGLDFTKDDENINSQPFMRWRDRFL 197

                         170       180
                  ....*....|....*....|....*.
gi 2018315342 161 YAMEGVNRSIAATGEVKGHYLNVTSA 186
Cdd:cd08212   198 FVAEAVNKAQAETGEVKGHYLNVTAG 223
rbcL PRK04208
ribulose bisophosphate carboxylase; Reviewed
 1-186 2.98e-129

ribulose bisophosphate carboxylase; Reviewed


Pssm-ID: 179787  Cd Length: 468  Bit Score: 370.78  E-value: 2.98e-129
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315342   1 ESSTATWTVVWTDLLTACDLYRAKAYKVDAVPNSSDQYFAYVAYDIDLFEEGSIPNLTASIIGNVFGFKAVKALRLEDMR 80
Cdd:PRK04208   53 ESSTGTWTTVWTDLLTDLDKYKAKAYRIEDVPGDDGSYYAFIAYPLDLFEEGSIPNLLASIAGNVFGFKAVKALRLEDIR 132

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315342  81 IPVAYLKTFQGPATGIVCERERMDKFGRPFLGATVKPKLGLSGKNYGRVVYEGLKGGLDFLKDDENINSQPFMRWKERYL 160
Cdd:PRK04208  133 FPVAYVKTFKGPPFGIQVERERLDKYGRPLLGTTPKPKLGLSAKNYGRVVYEALRGGLDFTKDDENLNSQPFNRWRDRFL 212

                         170       180
                  ....*....|....*....|....*.
gi 2018315342 161 YAMEGVNRSIAATGEVKGHYLNVTSA 186
Cdd:PRK04208  213 FVMEAIDKAEAETGERKGHYLNVTAP 238
RuBisCO_large_I_II_III cd08206
Ribulose bisphosphate carboxylase large chain, Form I,II,III; Ribulose bisphosphate ...
 1-186 3.62e-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: 338.06  E-value: 3.62e-117
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315342   1 ESSTATWTVVWTDLLTACDLYRAKAYKVDAVPNssDQYFAYVAYDIDLFEEGSIPNLTASIIGNVFGFKAVKALRLEDMR 80
Cdd:cd08206    27 ESSTGTWTTVWTDRLTATERLKAKVYRIDPVPD--GQYIAKIAYPLDLFEEGSVPNLLTSIIGNVFGMKAVKALRLEDFR 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315342  81 IPVAYLKTFQGPATGIVCERERMDKFGRPFLGATVKPKLGLSGKNYGRVVYEGLKGGLDFLKDDENINSQPFMRWKERYL 160
Cdd:cd08206   105 FPPAYLKTFDGPSFGIQGEREILGKYGRPLLGTIVKPKLGLSPKEYARVVYEALRGGLDFVKDDENQNSQPFMRFEDRIL 184

                         170       180
                  ....*....|....*....|....*.
gi 2018315342 161 YAMEGVNRSIAATGEVKGHYLNVTSA 186
Cdd:cd08206   185 FVAEAMDKAEAETGEAKGHYLNITAD 210
RbcL COG1850
Ribulose 1,5-bisphosphate carboxylase, large subunit, or a RuBisCO-like protein [Carbohydrate ...
 1-184 4.25e-81

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


Pssm-ID: 441455  Cd Length: 417  Bit Score: 246.23  E-value: 4.25e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315342   1 ESSTATWTVVWTDLLTACDLYRAKAYKVDAVPNSS---DQYFAYVAYDIDLFEeGSIPNLTASIIGNVFGFKAVKALRLE 77
Cdd:COG1850    38 EQSTGTWTEVPTETDELRERLAARVYSIEELPEVGggyRRALVTIAYPLENFG-GNLPNLLSTVAGNLFGLKAVSGLRLL 116

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315342  78 DMRIPVAYLKTFQGPATGIVCERERMDKFGRPFLGATVKPKLGLSGKNYGRVVYEGLKGGLDFLKDDENINSQPFMRWKE 157
Cdd:COG1850   117 DLEFPESFLAAFPGPKFGIEGTRELLGVYDRPLLGTIIKPKVGLSPEETAELVYELALGGVDFIKDDENLADQPFCPFED 196

                         170       180
                  ....*....|....*....|....*..
gi 2018315342 158 RYLYAMEGVNRSIAATGEVKGHYLNVT 184
Cdd:COG1850   197 RVRAVMEAIDRAEEETGEKKMYAFNIT 223
RuBisCO_large_III cd08213
Ribulose bisphosphate carboxylase large chain, Form III; Ribulose bisphosphate carboxylase ...
 1-184 4.11e-64

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: 202.62  E-value: 4.11e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315342   1 ESSTATWTVVWTDLLTACDLYRAKAYKVDAVPNSsdqYFAYVAYDIDLFEEGSIPNLTASIIGNVFGFKAVKALRLEDMR 80
Cdd:cd08213    27 ESSIGTWTTLATLYPERAEKLKAKAYYFDGLGGS---YIVKVAYPLELFEEGNMPQLLSSIAGNIFGMKAVKNLRLEDIY 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315342  81 IPVAYLKTFQGPATGIVCERERMDKFGRPFLGATVKPKLGLSGKNYGRVVYEGLKGGLDFLKDDENINSQPFMRWKERYL 160
Cdd:cd08213   104 FPESYLREFKGPQFGIEGVREILGIKDRPLLGTVPKPKVGLSPEEHAEVAYEALVGGVDLVKDDENLTSQPFNRFEERAK 183

                         170       180
                  ....*....|....*....|....
gi 2018315342 161 YAMEGVNRSIAATGEVKGHYLNVT 184
Cdd:cd08213   184 ESLKARDKAEAETGERKAYLANIT 207
RuBisCO_large cd08148
Ribulose bisphosphate carboxylase large chain; Ribulose bisphosphate carboxylase (Rubisco) ...
 1-184 6.79e-64

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: 200.73  E-value: 6.79e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315342   1 ESSTATWTVVWTdLLTACDLYRAKAYKVDavpNSSDQYFAYVAYDIDLFEEGSIPNLTASIIGNVFGFKAVKALRLEDMR 80
Cdd:cd08148    24 ESSTGTWTEVPT-TQEQLRRVKGRVYSVE---ELGKRYIVKIAYPVELFEPGNIPQILTVTAGNLFGLGALEAVRLEDLE 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315342  81 IPVAYLKTFQGPATGIVCERERMDKFGRPFLGATVKPKLGLSGKNYGRVVYEGLKGGLDFLKDDENINSQPFMRWKERYL 160
Cdd:cd08148   100 FPEEYKKLFPGPKFGIDGIRKLLGVYGRPLVGTIIKPKLGLNPKYTAEAAYAAALGGLDLIKDDETLTDQPFCPLRDRIT 179

                         170       180
                  ....*....|....*....|....
gi 2018315342 161 YAMEGVNRSIAATGEVKGHYLNVT 184
Cdd:cd08148   180 EVAAALDRVQEETGEKKLYAVNVT 203
rubisco_III TIGR03326
ribulose bisphosphate carboxylase, type III; Members of this protein family are the archaeal, ...
 1-185 8.87e-51

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: 168.41  E-value: 8.87e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315342   1 ESSTATWTVV--WTDLLTACDLyRAKAYKVDAVpnsSDQYFAYVAYDIDLFEEGSIPNLTASIIGNVFGFKAVKALRLED 78
Cdd:TIGR03326  38 ESSIGTWTTLqpWKDPERYKDL-SAKVYDIEEH---GDGSIVRIAYPLGLFEEGNLPQLLSCIAGNIFGMKAVKGLRLLD 113

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315342  79 MRIPVAYLKTFQGPATGIVCERERMDKFGRPFLGATVKPKLGLSGKNYGRVVYEGLKGGLDFLKDDENINSQPFMRWKER 158
Cdd:TIGR03326 114 FEFPAEFLRAFKGPQFGIEGVREILGIKDRPITATVPKPKVGLSTEEHAKVAYELWSGGVDLLKDDENLTSQAFNRFEER 193

                         170       180
                  ....*....|....*....|....*..
gi 2018315342 159 YLYAMEGVNRSIAATGEVKGHYLNVTS 185
Cdd:TIGR03326 194 VEKSLKVRDKVEAETGEKKSYLINITA 220
RuBisCO_large pfam00016
Ribulose bisphosphate carboxylase large chain, catalytic domain; The C-terminal domain of ...
 96-186 8.39e-49

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: 159.83  E-value: 8.39e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315342  96 IVCERERMDKFGRPFLGATVKPKLGLSGKNYGRVVYEGLKGGLDFLKDDENINSQPFMRWKERYLYAMEGVNRSIAATGE 175
Cdd:pfam00016   1 IAVERRVLNKYGRPILGTIIKPKLGLSPKNYARAVYEFLLGGLDFIKDDENINSQPFMPWRDRFLFVAEAIDRAQDETGE 80

                          90
                  ....*....|.
gi 2018315342 176 VKGHYLNVTSA 186
Cdd:pfam00016  81 AKGHYLNITAD 91
RuBisCO_large_N pfam02788
Ribulose bisphosphate carboxylase large chain, N-terminal domain; The N-terminal domain of ...
 1-85 4.33e-43

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: 139.66  E-value: 4.33e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315342   1 ESSTATWTVVWTDLLTACDLYRAKAYKVDAVPNssDQYFAYVAYDIDLFEEGSIPNLTASIIGNVFGFKAVKALRLEDMR 80
Cdd:pfam02788  38 ESSTGTWTEVWTLDDTFTKKLKAKVYEIDEVPG--GSYIVKIAYPLDLFEEGSIPQLLSSIAGNIFGMKAVKALRLEDIR 115


                  ....*
gi 2018315342  81 IPVAY 85
Cdd:pfam02788 116 FPPAY 120
RuBisCO_IV_RLP cd08205
Ribulose bisphosphate carboxylase like proteins, Rubisco-Form IV; Ribulose bisphosphate ...
 1-175 2.52e-27

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: 105.69  E-value: 2.52e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315342   1 ESSTATWTVVW--TDLLTACdlYRAKAYKVDAVPNSSDQYFAY---VAYDIDLFEeGSIPNLTASIIGNVFGfkaVKALR 75
Cdd:cd08205    24 EQTVGTWTELPgeTEEIRER--HVGRVESIEELEESEGKYGRArvtISYPLDNFG-GDLPQLLNTLFGNLSL---LPGIK 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315342  76 LEDMRIPVAYLKTFQGPATGIVCERERMDKFGRPFLGATVKPKLGLSGKNYGRVVYEGLKGGLDFLKDDENINSQPFMRW 155
Cdd:cd08205    98 LVDLELPDSLLAAFPGPRFGIEGLRRLLGVHDRPLLGTIIKPSIGLSPEELAELAYELALGGIDLIKDDELLADQPYAPF 177

                         170       180
                  ....*....|....*....|
gi 2018315342 156 KERYLYAMEGVNRSIAATGE 175
Cdd:cd08205   178 EERVRACMEAVRRANEETGR 197
RLP_NonPhot cd08207
Ribulose bisphosphate carboxylase like proteins from nonphototrophic bacteria; Ribulose ...
 1-174 2.27e-25

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: 100.85  E-value: 2.27e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315342   1 ESSTATWTVV--WTDLLTACdlYRAKAYKVDAVPNSSDQYFAY-------------VAYDIDLFeeG-SIPNLTASIIGN 64
Cdd:cd08207    24 EQSSGTFIALpgETDELKER--SAARVESIEELETAAQPSLPRrasggpytrarvtISFPLDNI--GtSLPNLLATVAGN 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315342  65 VFGFKAVKALRLEDMRIPVAYLKTFQGPATGIVCERERMDKFGRPFLGATVKPKLGLSGKNYGRVVYEGLKGGLDFLKDD 144
Cdd:cd08207   100 LFELRELSGLRLVDLGLPDEFAAAFPGPAFGIAGTRRLTGVEDRPLIGTIIKPSVGLTPEETAALVRQLAAAGIDFIKDD 179

                         170       180       190
                  ....*....|....*....|....*....|
gi 2018315342 145 ENINSQPFMRWKERYLYAMEGVNRSIAATG 174
Cdd:cd08207   180 ELLANPPYSPLDERVRAVMRVINDHAQRTG 209
RuBisCO_large_II cd08211
Ribulose bisphosphate carboxylase large chain, Form II; Ribulose bisphosphate carboxylase ...
 1-186 1.09e-22

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: 93.72  E-value: 1.09e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315342   1 ESSTAT-WTVVWTDLLTACdlYRAKAYKVDAvpnssDQYFAYVAYDIDLFE------EGSIPNLTASIIGNVFGFKAVKA 73
Cdd:cd08211    47 ESSTGTnVEVSTTDDFTRG--VDALVYEIDE-----ARELMKIAYPVELFDrnltdgRAMVASFLTLIIGNNQGMGDVEY 119

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315342  74 LRLEDMRIPVAYLKTFQGPATGIVCERERMDKF---GRPFLGATVKPKLGLSGKNYGRVVYEGLKGGlDFLKDDENINSQ 150
Cdd:cd08211   120 LKMHDFYVPESMLELFDGPSVNISDMWKVLGRPevdGGYIAGTIIKPKLGLRPKPFAEACYAFWLGG-DFIKNDEPQANQ 198

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 2018315342 151 PFMRWKERYLYAMEGVNRSIAATGEVKGHYLNVTSA 186
Cdd:cd08211   199 PFCPLKKVIPLVADAMRRAQDETGEAKLFSANITAD 234
PRK13475 PRK13475
ribulose-bisphosphate carboxylase;
1-186 3.99e-22

ribulose-bisphosphate carboxylase;


Pssm-ID: 184072  Cd Length: 443  Bit Score: 92.09  E-value: 3.99e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315342   1 ESSTATWTVVWT--DLLTACDlyrAKAYKVDAVPNssdqyFAYVAYDIDLFE------EGSIPNLTASIIGNVFGFKAVK 72
Cdd:PRK13475   48 ESSTGTNVEVSTtdDFTRGVD---ALVYEIDEARE-----LMKIAYPVELFDrniidgRAMIVSFLTLTIGNNQGMGDVE 119

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315342  73 ALRLEDMRIPVAYLKTFQGPATGI-----VCERERMDkfGRPFLGATVKPKLGLSGKNYGRVVYEGLKGGlDFLKDDENI 147
Cdd:PRK13475  120 YAKMHDFYVPPRYLELFDGPSTDIsdlwrVLGRPVKD--GGYIAGTIIKPKLGLRPEPFAEACYDFWLGG-DFIKNDEPQ 196

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 2018315342 148 NSQPFMRWKERYLYAMEGVNRSIAATGEVKGHYLNVTSA 186
Cdd:PRK13475  197 GNQVFAPLKKTVPLVADAMKRAQDETGEAKLFSANITAD 235
RLP_Photo cd08208
Ribulose bisphosphate carboxylase like proteins from phototrophic bacteria; Ribulose ...
 54-184 2.70e-21

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: 89.57  E-value: 2.70e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315342  54 IPNLTASIIGN-VFGFKAVKALRLEDMRIPVAYLKTFQGPATGIVCERERMDKFGRPFLGATVKPKLGLSGKNYGRVVYE 132
Cdd:cd08208   105 IPNLLSAVCGEgTFFSPGVPVVKLMDIHFPETYLADFEGPKFGIAGLRERLQAHDRPIFFGVIKPNIGLPPGEFAELGYQ 184

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2018315342 133 GLKGGLDFLKDDENINSQPFMRWKERYLYAMEGVNRSIAATGEVKGHYLNVT 184
Cdd:cd08208   185 SWLGGLDIAKDDEMLADVDWCPLEERAALLGKARRRAEAETGVPKIYLANIT 236
RLP_RrRLP cd08210
Ribulose bisphosphate carboxylase like proteins (RLPs) similar to R.rubrum RLP; RLP from ...
 32-186 2.41e-17

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: 78.05  E-value: 2.41e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315342  32 PNSSDQYFAYVAYDIDlfeegSIPNLTASIIGNVFGFKAVKA-LRLEDMRIPVAYLKTFQGPATGIVCERERMDKFGRPF 110
Cdd:cd08210    54 PAGEGSYRARISYSVD-----TAGGELTQLLNVLFGNSSLQPgIRLVDFELPPSLLRRFPGPRFGIAGLRALLGIPERPL 128

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2018315342 111 LGATVKPkLGLSGKNYGRVVYEGLKGGLDFLKDDENINSQPFMRWKERYLYAMEGVNRSIAATGevkGHYL---NVTSA 186
Cdd:cd08210   129 LCSALKP-QGLSAAELAELAYAFALGGIDIIKDDHGLADQPFAPFEERVKACQEAVAEANAETG---GRTLyapNVTGP 203
RLP_DK-MTP-1-P-enolase cd08209
2,3-diketo-5-methylthiopentyl-1-phosphate enolase; Ribulose bisphosphate carboxylase like ...
 11-145 1.85e-11

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: 61.57  E-value: 1.85e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315342  11 WTDL--LTACDLYRAKAyKVDAVPNSSDQYF-AYVAY-DIDLfeEGSIPnltaSIIGNVFG-FKAVKALRLEDMRIPVAY 85
Cdd:cd08209    29 WTDLpaLRQAQLQKHLG-EVVSVEELEEGRGvITIAYpLINV--SGDIP----ALLTTIFGkLSLDGKIKLVDLRLPEEF 101

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2018315342  86 LKTFQGPATGIVCERERMDKFGRPFLGATVKPKLGLSGKNYGRVVYEGLKGGLDFLKDDE 145
Cdd:cd08209   102 GRAFPGPKFGIEGIRQRLGVHDRPLLMSIFKGVLGLDLDDLAEQLREQALGGVDLIKDDE 161
mtnW PRK09549
2,3-diketo-5-methylthiopentyl-1-phosphate enolase; Reviewed
 75-145 2.47e-05

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


Pssm-ID: 236560  Cd Length: 407  Bit Score: 43.84  E-value: 2.47e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2018315342  75 RLEDMRIPVAYLKTFQGPATGIVCERERMDKFGRPFLGATVKPKLGLSGKNYGRVVYEGLKGGLDFLKDDE 145
Cdd:PRK09549  101 KLIDLTFSDELKRHFPGPKFGIDGIRNLLGVHDRPLLMSIFKGVIGRDLDYLKEQLRDQALGGVDLVKDDE 171
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH