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Conserved domains on  [gi|2045472564|gb|QVV95892|]
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ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit, partial (plastid) [Yonagunia formosana]

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) ...
 1-186 3.42e-146

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: 414.10  E-value: 3.42e-146
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045472564   1 TWTVVWTDLLTACDLYRAKAYKVDAVPNSSEQYFAYISYDIDLFEEGSIANLTASIIGNVFGFKAVKALRLEDMRIPVAY 80
Cdd:CHL00040   65 TWTTVWTDGLTSLDRYKGRCYRIEPVPGEENQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAY 144

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045472564  81 LKTFQGPATGIIVERERMDKFGRPFLGATVKPKLGLSGKNYGRVVYEGLKGGLDFLKDDENINSQPFMRWKERFLYSMEG 160
Cdd:CHL00040  145 LKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEA 224

                         170       180
                  ....*....|....*....|....*.
gi 2045472564 161 VNRAIAATGEIKGHYMNVTAATMEDM 186
Cdd:CHL00040  225 IYKAQAETGEIKGHYLNATAGTCEEM 250
 
Name Accession Description Interval E-value
rbcL CHL00040
ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
 1-186 3.42e-146

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


Pssm-ID: 176981  Cd Length: 475  Bit Score: 414.10  E-value: 3.42e-146
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045472564   1 TWTVVWTDLLTACDLYRAKAYKVDAVPNSSEQYFAYISYDIDLFEEGSIANLTASIIGNVFGFKAVKALRLEDMRIPVAY 80
Cdd:CHL00040   65 TWTTVWTDGLTSLDRYKGRCYRIEPVPGEENQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAY 144

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045472564  81 LKTFQGPATGIIVERERMDKFGRPFLGATVKPKLGLSGKNYGRVVYEGLKGGLDFLKDDENINSQPFMRWKERFLYSMEG 160
Cdd:CHL00040  145 LKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEA 224

                         170       180
                  ....*....|....*....|....*.
gi 2045472564 161 VNRAIAATGEIKGHYMNVTAATMEDM 186
Cdd:CHL00040  225 IYKAQAETGEIKGHYLNATAGTCEEM 250
RuBisCO_large_I cd08212
Ribulose bisphosphate carboxylase large chain, Form I; Ribulose bisphosphate carboxylase ...
 1-186 1.76e-139

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: 396.41  E-value: 1.76e-139
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045472564   1 TWTVVWTDLLTACDLYRAKAYKVDAVPNSSEQYFAYISYDIDLFEEGSIANLTASIIGNVFGFKAVKALRLEDMRIPVAY 80
Cdd:cd08212    43 TWTVVWTDRLTALDRYKGKAYRVEPVPGEENQYFAYIAYPLDLFEEGSVANLTTSIVGNVFGFKALRALRLEDLRIPPAY 122

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045472564  81 LKTFQGPATGIIVERERMDKFGRPFLGATVKPKLGLSGKNYGRVVYEGLKGGLDFLKDDENINSQPFMRWKERFLYSMEG 160
Cdd:cd08212   123 VKTFQGPPHGIQVERDRLNKYGRPLLGCTIKPKLGLSAKNYGRVVYECLRGGLDFTKDDENINSQPFMRWRDRFLFVAEA 202

                         170       180
                  ....*....|....*....|....*.
gi 2045472564 161 VNRAIAATGEIKGHYMNVTAATMEDM 186
Cdd:cd08212   203 VNKAQAETGEVKGHYLNVTAGTMEEM 228
RbcL COG1850
Ribulose 1,5-bisphosphate carboxylase, large subunit, or a RuBisCO-like protein [Carbohydrate ...
 1-186 1.22e-79

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


Pssm-ID: 441455  Cd Length: 417  Bit Score: 242.77  E-value: 1.22e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045472564   1 TWTVVWTDLLTACDLYRAKAYKVDAVPNSS---EQYFAYISYDIDLFEeGSIANLTASIIGNVFGFKAVKALRLEDMRIP 77
Cdd:COG1850    43 TWTEVPTETDELRERLAARVYSIEELPEVGggyRRALVTIAYPLENFG-GNLPNLLSTVAGNLFGLKAVSGLRLLDLEFP 121

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045472564  78 VAYLKTFQGPATGIIVERERMDKFGRPFLGATVKPKLGLSGKNYGRVVYEGLKGGLDFLKDDENINSQPFMRWKERFLYS 157
Cdd:COG1850   122 ESFLAAFPGPKFGIEGTRELLGVYDRPLLGTIIKPKVGLSPEETAELVYELALGGVDFIKDDENLADQPFCPFEDRVRAV 201

                         170       180
                  ....*....|....*....|....*....
gi 2045472564 158 MEGVNRAIAATGEIKGHYMNVTaATMEDM 186
Cdd:COG1850   202 MEAIDRAEEETGEKKMYAFNIT-ADTDEM 229
RuBisCO_large pfam00016
Ribulose bisphosphate carboxylase large chain, catalytic domain; The C-terminal domain of ...
 91-186 3.36e-54

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: 173.70  E-value: 3.36e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045472564  91 IIVERERMDKFGRPFLGATVKPKLGLSGKNYGRVVYEGLKGGLDFLKDDENINSQPFMRWKERFLYSMEGVNRAIAATGE 170
Cdd:pfam00016   1 IAVERRVLNKYGRPILGTIIKPKLGLSPKNYARAVYEFLLGGLDFIKDDENINSQPFMPWRDRFLFVAEAIDRAQDETGE 80

                          90
                  ....*....|....*.
gi 2045472564 171 IKGHYMNVTAATMEDM 186
Cdd:pfam00016  81 AKGHYLNITADDMEEM 96
rubisco_III TIGR03326
ribulose bisphosphate carboxylase, type III; Members of this protein family are the archaeal, ...
 1-184 1.92e-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: 162.25  E-value: 1.92e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045472564   1 TWTVV--WTDLLTACDLyRAKAYKVDAVpnsSEQYFAYISYDIDLFEEGSIANLTASIIGNVFGFKAVKALRLEDMRIPV 78
Cdd:TIGR03326  43 TWTTLqpWKDPERYKDL-SAKVYDIEEH---GDGSIVRIAYPLGLFEEGNLPQLLSCIAGNIFGMKAVKGLRLLDFEFPA 118

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045472564  79 AYLKTFQGPATGIIVERERMDKFGRPFLGATVKPKLGLSGKNYGRVVYEGLKGGLDFLKDDENINSQPFMRWKERFLYSM 158
Cdd:TIGR03326 119 EFLRAFKGPQFGIEGVREILGIKDRPITATVPKPKVGLSTEEHAKVAYELWSGGVDLLKDDENLTSQAFNRFEERVEKSL 198

                         170       180
                  ....*....|....*....|....*.
gi 2045472564 159 EGVNRAIAATGEIKGHYMNVTAATME 184
Cdd:TIGR03326 199 KVRDKVEAETGEKKSYLINITADVRE 224
 
Name Accession Description Interval E-value
rbcL CHL00040
ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
 1-186 3.42e-146

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


Pssm-ID: 176981  Cd Length: 475  Bit Score: 414.10  E-value: 3.42e-146
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045472564   1 TWTVVWTDLLTACDLYRAKAYKVDAVPNSSEQYFAYISYDIDLFEEGSIANLTASIIGNVFGFKAVKALRLEDMRIPVAY 80
Cdd:CHL00040   65 TWTTVWTDGLTSLDRYKGRCYRIEPVPGEENQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAY 144

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045472564  81 LKTFQGPATGIIVERERMDKFGRPFLGATVKPKLGLSGKNYGRVVYEGLKGGLDFLKDDENINSQPFMRWKERFLYSMEG 160
Cdd:CHL00040  145 LKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEA 224

                         170       180
                  ....*....|....*....|....*.
gi 2045472564 161 VNRAIAATGEIKGHYMNVTAATMEDM 186
Cdd:CHL00040  225 IYKAQAETGEIKGHYLNATAGTCEEM 250
RuBisCO_large_I cd08212
Ribulose bisphosphate carboxylase large chain, Form I; Ribulose bisphosphate carboxylase ...
 1-186 1.76e-139

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: 396.41  E-value: 1.76e-139
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045472564   1 TWTVVWTDLLTACDLYRAKAYKVDAVPNSSEQYFAYISYDIDLFEEGSIANLTASIIGNVFGFKAVKALRLEDMRIPVAY 80
Cdd:cd08212    43 TWTVVWTDRLTALDRYKGKAYRVEPVPGEENQYFAYIAYPLDLFEEGSVANLTTSIVGNVFGFKALRALRLEDLRIPPAY 122

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045472564  81 LKTFQGPATGIIVERERMDKFGRPFLGATVKPKLGLSGKNYGRVVYEGLKGGLDFLKDDENINSQPFMRWKERFLYSMEG 160
Cdd:cd08212   123 VKTFQGPPHGIQVERDRLNKYGRPLLGCTIKPKLGLSAKNYGRVVYECLRGGLDFTKDDENINSQPFMRWRDRFLFVAEA 202

                         170       180
                  ....*....|....*....|....*.
gi 2045472564 161 VNRAIAATGEIKGHYMNVTAATMEDM 186
Cdd:cd08212   203 VNKAQAETGEVKGHYLNVTAGTMEEM 228
rbcL PRK04208
ribulose bisophosphate carboxylase; Reviewed
 1-186 9.17e-130

ribulose bisophosphate carboxylase; Reviewed


Pssm-ID: 179787  Cd Length: 468  Bit Score: 372.32  E-value: 9.17e-130
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045472564   1 TWTVVWTDLLTACDLYRAKAYKVDAVPNSSEQYFAYISYDIDLFEEGSIANLTASIIGNVFGFKAVKALRLEDMRIPVAY 80
Cdd:PRK04208   58 TWTTVWTDLLTDLDKYKAKAYRIEDVPGDDGSYYAFIAYPLDLFEEGSIPNLLASIAGNVFGFKAVKALRLEDIRFPVAY 137

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045472564  81 LKTFQGPATGIIVERERMDKFGRPFLGATVKPKLGLSGKNYGRVVYEGLKGGLDFLKDDENINSQPFMRWKERFLYSMEG 160
Cdd:PRK04208  138 VKTFKGPPFGIQVERERLDKYGRPLLGTTPKPKLGLSAKNYGRVVYEALRGGLDFTKDDENLNSQPFNRWRDRFLFVMEA 217

                         170       180
                  ....*....|....*....|....*.
gi 2045472564 161 VNRAIAATGEIKGHYMNVTAATMEDM 186
Cdd:PRK04208  218 IDKAEAETGERKGHYLNVTAPTMEEM 243
RuBisCO_large_I_II_III cd08206
Ribulose bisphosphate carboxylase large chain, Form I,II,III; Ribulose bisphosphate ...
 1-186 2.58e-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: 338.44  E-value: 2.58e-117
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045472564   1 TWTVVWTDLLTACDLYRAKAYKVDAVPNssEQYFAYISYDIDLFEEGSIANLTASIIGNVFGFKAVKALRLEDMRIPVAY 80
Cdd:cd08206    32 TWTTVWTDRLTATERLKAKVYRIDPVPD--GQYIAKIAYPLDLFEEGSVPNLLTSIIGNVFGMKAVKALRLEDFRFPPAY 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045472564  81 LKTFQGPATGIIVERERMDKFGRPFLGATVKPKLGLSGKNYGRVVYEGLKGGLDFLKDDENINSQPFMRWKERFLYSMEG 160
Cdd:cd08206   110 LKTFDGPSFGIQGEREILGKYGRPLLGTIVKPKLGLSPKEYARVVYEALRGGLDFVKDDENQNSQPFMRFEDRILFVAEA 189

                         170       180
                  ....*....|....*....|....*.
gi 2045472564 161 VNRAIAATGEIKGHYMNVTAATMEDM 186
Cdd:cd08206   190 MDKAEAETGEAKGHYLNITADTPEEM 215
RbcL COG1850
Ribulose 1,5-bisphosphate carboxylase, large subunit, or a RuBisCO-like protein [Carbohydrate ...
 1-186 1.22e-79

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


Pssm-ID: 441455  Cd Length: 417  Bit Score: 242.77  E-value: 1.22e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045472564   1 TWTVVWTDLLTACDLYRAKAYKVDAVPNSS---EQYFAYISYDIDLFEeGSIANLTASIIGNVFGFKAVKALRLEDMRIP 77
Cdd:COG1850    43 TWTEVPTETDELRERLAARVYSIEELPEVGggyRRALVTIAYPLENFG-GNLPNLLSTVAGNLFGLKAVSGLRLLDLEFP 121

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045472564  78 VAYLKTFQGPATGIIVERERMDKFGRPFLGATVKPKLGLSGKNYGRVVYEGLKGGLDFLKDDENINSQPFMRWKERFLYS 157
Cdd:COG1850   122 ESFLAAFPGPKFGIEGTRELLGVYDRPLLGTIIKPKVGLSPEETAELVYELALGGVDFIKDDENLADQPFCPFEDRVRAV 201

                         170       180
                  ....*....|....*....|....*....
gi 2045472564 158 MEGVNRAIAATGEIKGHYMNVTaATMEDM 186
Cdd:COG1850   202 MEAIDRAEEETGEKKMYAFNIT-ADTDEM 229
RuBisCO_large cd08148
Ribulose bisphosphate carboxylase large chain; Ribulose bisphosphate carboxylase (Rubisco) ...
 1-184 1.91e-62

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: 197.26  E-value: 1.91e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045472564   1 TWTVVWTdLLTACDLYRAKAYKVDavpNSSEQYFAYISYDIDLFEEGSIANLTASIIGNVFGFKAVKALRLEDMRIPVAY 80
Cdd:cd08148    29 TWTEVPT-TQEQLRRVKGRVYSVE---ELGKRYIVKIAYPVELFEPGNIPQILTVTAGNLFGLGALEAVRLEDLEFPEEY 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045472564  81 LKTFQGPATGIIVERERMDKFGRPFLGATVKPKLGLSGKNYGRVVYEGLKGGLDFLKDDENINSQPFMRWKERFLYSMEG 160
Cdd:cd08148   105 KKLFPGPKFGIDGIRKLLGVYGRPLVGTIIKPKLGLNPKYTAEAAYAAALGGLDLIKDDETLTDQPFCPLRDRITEVAAA 184

                         170       180
                  ....*....|....*....|....
gi 2045472564 161 VNRAIAATGEIKGHYMNVTAATME 184
Cdd:cd08148   185 LDRVQEETGEKKLYAVNVTAGTFE 208
RuBisCO_large_III cd08213
Ribulose bisphosphate carboxylase large chain, Form III; Ribulose bisphosphate carboxylase ...
 1-184 6.03e-61

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: 194.53  E-value: 6.03e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045472564   1 TWTVVWTDLLTACDLYRAKAYKVDAVPNSseqYFAYISYDIDLFEEGSIANLTASIIGNVFGFKAVKALRLEDMRIPVAY 80
Cdd:cd08213    32 TWTTLATLYPERAEKLKAKAYYFDGLGGS---YIVKVAYPLELFEEGNMPQLLSSIAGNIFGMKAVKNLRLEDIYFPESY 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045472564  81 LKTFQGPATGIIVERERMDKFGRPFLGATVKPKLGLSGKNYGRVVYEGLKGGLDFLKDDENINSQPFMRWKERFLYSMEG 160
Cdd:cd08213   109 LREFKGPQFGIEGVREILGIKDRPLLGTVPKPKVGLSPEEHAEVAYEALVGGVDLVKDDENLTSQPFNRFEERAKESLKA 188

                         170       180
                  ....*....|....*....|....
gi 2045472564 161 VNRAIAATGEIKGHYMNVTAATME 184
Cdd:cd08213   189 RDKAEAETGERKAYLANITAPVRE 212
RuBisCO_large pfam00016
Ribulose bisphosphate carboxylase large chain, catalytic domain; The C-terminal domain of ...
 91-186 3.36e-54

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: 173.70  E-value: 3.36e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045472564  91 IIVERERMDKFGRPFLGATVKPKLGLSGKNYGRVVYEGLKGGLDFLKDDENINSQPFMRWKERFLYSMEGVNRAIAATGE 170
Cdd:pfam00016   1 IAVERRVLNKYGRPILGTIIKPKLGLSPKNYARAVYEFLLGGLDFIKDDENINSQPFMPWRDRFLFVAEAIDRAQDETGE 80

                          90
                  ....*....|....*.
gi 2045472564 171 IKGHYMNVTAATMEDM 186
Cdd:pfam00016  81 AKGHYLNITADDMEEM 96
rubisco_III TIGR03326
ribulose bisphosphate carboxylase, type III; Members of this protein family are the archaeal, ...
 1-184 1.92e-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: 162.25  E-value: 1.92e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045472564   1 TWTVV--WTDLLTACDLyRAKAYKVDAVpnsSEQYFAYISYDIDLFEEGSIANLTASIIGNVFGFKAVKALRLEDMRIPV 78
Cdd:TIGR03326  43 TWTTLqpWKDPERYKDL-SAKVYDIEEH---GDGSIVRIAYPLGLFEEGNLPQLLSCIAGNIFGMKAVKGLRLLDFEFPA 118

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045472564  79 AYLKTFQGPATGIIVERERMDKFGRPFLGATVKPKLGLSGKNYGRVVYEGLKGGLDFLKDDENINSQPFMRWKERFLYSM 158
Cdd:TIGR03326 119 EFLRAFKGPQFGIEGVREILGIKDRPITATVPKPKVGLSTEEHAKVAYELWSGGVDLLKDDENLTSQAFNRFEERVEKSL 198

                         170       180
                  ....*....|....*....|....*.
gi 2045472564 159 EGVNRAIAATGEIKGHYMNVTAATME 184
Cdd:TIGR03326 199 KVRDKVEAETGEKKSYLINITADVRE 224
RuBisCO_large_N pfam02788
Ribulose bisphosphate carboxylase large chain, N-terminal domain; The N-terminal domain of ...
 1-80 2.72e-37

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: 125.02  E-value: 2.72e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045472564   1 TWTVVWTDLLTACDLYRAKAYKVDAVPNssEQYFAYISYDIDLFEEGSIANLTASIIGNVFGFKAVKALRLEDMRIPVAY 80
Cdd:pfam02788  43 TWTEVWTLDDTFTKKLKAKVYEIDEVPG--GSYIVKIAYPLDLFEEGSIPQLLSSIAGNIFGMKAVKALRLEDIRFPPAY 120
RuBisCO_IV_RLP cd08205
Ribulose bisphosphate carboxylase like proteins, Rubisco-Form IV; Ribulose bisphosphate ...
 16-184 1.95e-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: 1.95e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045472564  16 YRAKAYKVDAVPNSSEQYFAY---ISYDIDLFEeGSIANLTASIIGNVFGfkaVKALRLEDMRIPVAYLKTFQGPATGII 92
Cdd:cd08205    44 HVGRVESIEELEESEGKYGRArvtISYPLDNFG-GDLPQLLNTLFGNLSL---LPGIKLVDLELPDSLLAAFPGPRFGIE 119

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045472564  93 VERERMDKFGRPFLGATVKPKLGLSGKNYGRVVYEGLKGGLDFLKDDENINSQPFMRWKERFLYSMEGVNRAIAATGEIK 172
Cdd:cd08205   120 GLRRLLGVHDRPLLGTIIKPSIGLSPEELAELAYELALGGIDLIKDDELLADQPYAPFEERVRACMEAVRRANEETGRKT 199

                         170
                  ....*....|..
gi 2045472564 173 GHYMNVTAATME 184
Cdd:cd08205   200 LYAPNITGDPDE 211
PRK13475 PRK13475
ribulose-bisphosphate carboxylase;
37-186 1.26e-24

ribulose-bisphosphate carboxylase;


Pssm-ID: 184072  Cd Length: 443  Bit Score: 99.03  E-value: 1.26e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045472564  37 ISYDIDLFE------EGSIANLTASIIGNVFGFKAVKALRLEDMRIPVAYLKTFQGPATGI-----IVERERMDkfGRPF 105
Cdd:PRK13475   83 IAYPVELFDrniidgRAMIVSFLTLTIGNNQGMGDVEYAKMHDFYVPPRYLELFDGPSTDIsdlwrVLGRPVKD--GGYI 160

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045472564 106 LGATVKPKLGLSGKNYGRVVYEGLKGGlDFLKDDENINSQPFMRWKERFLYSMEGVNRAIAATGEIKGHYMNVTAATMED 185
Cdd:PRK13475  161 AGTIIKPKLGLRPEPFAEACYDFWLGG-DFIKNDEPQGNQVFAPLKKTVPLVADAMKRAQDETGEAKLFSANITADDHYE 239


                  .
gi 2045472564 186 M 186
Cdd:PRK13475  240 M 240
RLP_NonPhot cd08207
Ribulose bisphosphate carboxylase like proteins from nonphototrophic bacteria; Ribulose ...
 25-169 3.32e-24

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: 97.76  E-value: 3.32e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045472564  25 AVPNSSEQYFAY---ISYDIDLFeeG-SIANLTASIIGNVFGFKAVKALRLEDMRIPVAYLKTFQGPATGIIVERERMDK 100
Cdd:cd08207    63 PRRASGGPYTRArvtISFPLDNI--GtSLPNLLATVAGNLFELRELSGLRLVDLGLPDEFAAAFPGPAFGIAGTRRLTGV 140

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2045472564 101 FGRPFLGATVKPKLGLSGKNYGRVVYEGLKGGLDFLKDDENINSQPFMRWKERFLYSMEGVNRAIAATG 169
Cdd:cd08207   141 EDRPLIGTIIKPSVGLTPEETAALVRQLAAAGIDFIKDDELLANPPYSPLDERVRAVMRVINDHAQRTG 209
RuBisCO_large_II cd08211
Ribulose bisphosphate carboxylase large chain, Form II; Ribulose bisphosphate carboxylase ...
 18-186 8.65e-24

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: 96.80  E-value: 8.65e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045472564  18 AKAYKVDAvpnssEQYFAYISYDIDLFE------EGSIANLTASIIGNVFGFKAVKALRLEDMRIPVAYLKTFQGPATGI 91
Cdd:cd08211    68 ALVYEIDE-----ARELMKIAYPVELFDrnltdgRAMVASFLTLIIGNNQGMGDVEYLKMHDFYVPESMLELFDGPSVNI 142

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045472564  92 IVERERMDKF---GRPFLGATVKPKLGLSGKNYGRVVYEGLKGGlDFLKDDENINSQPFMRWKERFLYSMEGVNRAIAAT 168
Cdd:cd08211   143 SDMWKVLGRPevdGGYIAGTIIKPKLGLRPKPFAEACYAFWLGG-DFIKNDEPQANQPFCPLKKVIPLVADAMRRAQDET 221

                         170
                  ....*....|....*...
gi 2045472564 169 GEIKGHYMNVTAATMEDM 186
Cdd:cd08211   222 GEAKLFSANITADDPDEM 239
RLP_Photo cd08208
Ribulose bisphosphate carboxylase like proteins from phototrophic bacteria; Ribulose ...
 49-179 4.18e-20

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: 86.49  E-value: 4.18e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045472564  49 IANLTASIIGN-VFGFKAVKALRLEDMRIPVAYLKTFQGPATGIIVERERMDKFGRPFLGATVKPKLGLSGKNYGRVVYE 127
Cdd:cd08208   105 IPNLLSAVCGEgTFFSPGVPVVKLMDIHFPETYLADFEGPKFGIAGLRERLQAHDRPIFFGVIKPNIGLPPGEFAELGYQ 184

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2045472564 128 GLKGGLDFLKDDENINSQPFMRWKERFLYSMEGVNRAIAATGEIKGHYMNVT 179
Cdd:cd08208   185 SWLGGLDIAKDDEMLADVDWCPLEERAALLGKARRRAEAETGVPKIYLANIT 236
RLP_RrRLP cd08210
Ribulose bisphosphate carboxylase like proteins (RLPs) similar to R.rubrum RLP; RLP from ...
 27-184 1.35e-18

Ribulose bisphosphate carboxylase like proteins (RLPs) similar to R.rubrum RLP; RLP from Rhodospirillum rubrum plays a role in an uncharacterized sulfur salvage pathway and has been shown to catalyze a novel isomerization reaction that converts 5-methylthio-d-ribulose 1-phosphate to a 3:1 mixture of 1-methylthioxylulose 5-phosphate and 1-methylthioribulose 5-phosphate.


Pssm-ID: 173975  Cd Length: 364  Bit Score: 81.52  E-value: 1.35e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045472564  27 PNSSEQYFAYISYDIDlfeegSIANLTASIIGNVFGFKAVKA-LRLEDMRIPVAYLKTFQGPATGIIVERERMDKFGRPF 105
Cdd:cd08210    54 PAGEGSYRARISYSVD-----TAGGELTQLLNVLFGNSSLQPgIRLVDFELPPSLLRRFPGPRFGIAGLRALLGIPERPL 128

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045472564 106 LGATVKPkLGLSGKNYGRVVYEGLKGGLDFLKDDENINSQPFMRWKERFLYSMEGVNRAIAATGeikGH--YM-NVTAAT 182
Cdd:cd08210   129 LCSALKP-QGLSAAELAELAYAFALGGIDIIKDDHGLADQPFAPFEERVKACQEAVAEANAETG---GRtlYApNVTGPP 204


                  ..
gi 2045472564 183 ME 184
Cdd:cd08210   205 TQ 206
RLP_DK-MTP-1-P-enolase cd08209
2,3-diketo-5-methylthiopentyl-1-phosphate enolase; Ribulose bisphosphate carboxylase like ...
 70-140 8.94e-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: 59.64  E-value: 8.94e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2045472564  70 RLEDMRIPVAYLKTFQGPATGIIVERERMDKFGRPFLGATVKPKLGLSGKNYGRVVYEGLKGGLDFLKDDE 140
Cdd:cd08209    91 KLVDLRLPEEFGRAFPGPKFGIEGIRQRLGVHDRPLLMSIFKGVLGLDLDDLAEQLREQALGGVDLIKDDE 161
mtnW PRK09549
2,3-diketo-5-methylthiopentyl-1-phosphate enolase; Reviewed
 50-184 2.11e-05

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


Pssm-ID: 236560  Cd Length: 407  Bit Score: 43.84  E-value: 2.11e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2045472564  50 ANLTA---SIIGNVFGFKAVKA-LRLEDMRIPVAYLKTFQGPATGIIVERERMDKFGRPFLGATVKPKLGLSGKNYGRVV 125
Cdd:PRK09549   77 ANFSPdlpAILTTTFGKLSLDGeVKLIDLTFSDELKRHFPGPKFGIDGIRNLLGVHDRPLLMSIFKGVIGRDLDYLKEQL 156

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2045472564 126 YEGLKGGLDFLKDDENINSQPFMRWKERFLYSMEGVNRAIAATGEIKGHYMNVTAATME 184
Cdd:PRK09549  157 RDQALGGVDLVKDDEILFENALTPFEKRIVAGKEVLQEVYETTGHKTLYAVNLTGRTFE 215
 
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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