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Conserved domains on  [gi|526849364|gb|AGR92417|]
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ribulose 1,5-bisphosphate carboxylase large subunit, partial (chloroplast) [Strychnos potatorum]

Protein Classification

RuBisCO large subunit( domain architecture ID 315)

large subunit of the ribulose bisphosphate carboxylase is part of the complex that catalyzes the primary event in carbon dioxide fixation, the carboxylation of D-ribulose 1,5-bisphosphate, as well as the oxidative fragmentation of the pentose substrate in the photorespiration process.

EC:  4.1.1.39
Gene Ontology:  GO:0016984
PubMed:  18294858

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RuBisCO_large super family cl08232
Ribulose bisphosphate carboxylase large chain; Ribulose bisphosphate carboxylase (Rubisco) ...
 1-193 9.87e-162

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: 453.78  E-value: 9.87e-162
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 526849364   1 TETKASVGFKAGVKEYKLTYYTPEYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRC 80
Cdd:CHL00040   5 TETKASVGFKAGVKDYKLTYYTPDYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRC 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 526849364  81 YHIEPVAGEEDQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPVAYVKTFQGPPHGIQVERDKLNK 160
Cdd:CHL00040  85 YRIEPVPGEENQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYLKTFQGPPHGIQVERDKLNK 164

                        170       180       190
                 ....*....|....*....|....*....|...
gi 526849364 161 YGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGL 193
Cdd:CHL00040 165 YGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGL 197
 
Name Accession Description Interval E-value
rbcL CHL00040
ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
 1-193 9.87e-162

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


Pssm-ID: 176981  Cd Length: 475  Bit Score: 453.78  E-value: 9.87e-162
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 526849364   1 TETKASVGFKAGVKEYKLTYYTPEYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRC 80
Cdd:CHL00040   5 TETKASVGFKAGVKDYKLTYYTPDYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRC 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 526849364  81 YHIEPVAGEEDQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPVAYVKTFQGPPHGIQVERDKLNK 160
Cdd:CHL00040  85 YRIEPVPGEENQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYLKTFQGPPHGIQVERDKLNK 164

                        170       180       190
                 ....*....|....*....|....*....|...
gi 526849364 161 YGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGL 193
Cdd:CHL00040 165 YGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGL 197
RuBisCO_large_I cd08212
Ribulose bisphosphate carboxylase large chain, Form I; Ribulose bisphosphate carboxylase ...
 19-193 8.78e-129

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: 369.45  E-value: 8.78e-129
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 526849364  19 TYYTPEYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYHIEPVAGEEDQYIAYVA 98
Cdd:cd08212    1 GYWTPDYQPKDTDILAAFRITPQPGVDPEEAAAAVAGESSTATWTVVWTDRLTALDRYKGKAYRVEPVPGEENQYFAYIA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 526849364  99 YPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPVAYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSA 178
Cdd:cd08212   81 YPLDLFEEGSVANLTTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGIQVERDRLNKYGRPLLGCTIKPKLGLSA 160

                        170
                 ....*....|....*
gi 526849364 179 KNYGRAVYECLRGGL 193
Cdd:cd08212  161 KNYGRVVYECLRGGL 175
RbcL COG1850
Ribulose 1,5-bisphosphate carboxylase, large subunit, or a RuBisCO-like protein [Carbohydrate ...
 20-193 5.65e-70

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


Pssm-ID: 441455  Cd Length: 417  Bit Score: 218.11  E-value: 5.65e-70
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 526849364  20 YYTPEYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYHIEPV---AGEEDQYIAY 96
Cdd:COG1850    2 YVDPDYIPDDDDILATYRITPETGVDPEEAAAAIAGEQSTGTWTEVPTETDELRERLAARVYSIEELpevGGGYRRALVT 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 526849364  97 VAYPLDLFEeGSVTNMFTSIVGNVFGFKALRALRLEDLRIPVAYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGL 176
Cdd:COG1850   82 IAYPLENFG-GNLPNLLSTVAGNLFGLKAVSGLRLLDLEFPESFLAAFPGPKFGIEGTRELLGVYDRPLLGTIIKPKVGL 160

                        170
                 ....*....|....*..
gi 526849364 177 SAKNYGRAVYECLRGGL 193
Cdd:COG1850  161 SPEETAELVYELALGGV 177
RuBisCO_large_N pfam02788
Ribulose bisphosphate carboxylase large chain, N-terminal domain; The N-terminal domain of ...
 19-140 6.48e-55

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: 170.09  E-value: 6.48e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 526849364   19 TYYTPEYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYHIEPVAGeeDQYIAYVA 98
Cdd:pfam02788   1 DYVDLDYEPKDTDLLCAFRIEPAAGVSPEEAAAHVAAESSTGTWTEVWTLDDTFTKKLKAKVYEIDEVPG--GSYIVKIA 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 526849364   99 YPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPVAY 140
Cdd:pfam02788  79 YPLDLFEEGSIPQLLSSIAGNIFGMKAVKALRLEDIRFPPAY 120
 
Name Accession Description Interval E-value
rbcL CHL00040
ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
 1-193 9.87e-162

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


Pssm-ID: 176981  Cd Length: 475  Bit Score: 453.78  E-value: 9.87e-162
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 526849364   1 TETKASVGFKAGVKEYKLTYYTPEYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRC 80
Cdd:CHL00040   5 TETKASVGFKAGVKDYKLTYYTPDYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRC 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 526849364  81 YHIEPVAGEEDQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPVAYVKTFQGPPHGIQVERDKLNK 160
Cdd:CHL00040  85 YRIEPVPGEENQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYLKTFQGPPHGIQVERDKLNK 164

                        170       180       190
                 ....*....|....*....|....*....|...
gi 526849364 161 YGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGL 193
Cdd:CHL00040 165 YGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGL 197
RuBisCO_large_I cd08212
Ribulose bisphosphate carboxylase large chain, Form I; Ribulose bisphosphate carboxylase ...
 19-193 8.78e-129

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: 369.45  E-value: 8.78e-129
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 526849364  19 TYYTPEYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYHIEPVAGEEDQYIAYVA 98
Cdd:cd08212    1 GYWTPDYQPKDTDILAAFRITPQPGVDPEEAAAAVAGESSTATWTVVWTDRLTALDRYKGKAYRVEPVPGEENQYFAYIA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 526849364  99 YPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPVAYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSA 178
Cdd:cd08212   81 YPLDLFEEGSVANLTTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGIQVERDRLNKYGRPLLGCTIKPKLGLSA 160

                        170
                 ....*....|....*
gi 526849364 179 KNYGRAVYECLRGGL 193
Cdd:cd08212  161 KNYGRVVYECLRGGL 175
rbcL PRK04208
ribulose bisophosphate carboxylase; Reviewed
 4-193 8.08e-122

ribulose bisophosphate carboxylase; Reviewed


Pssm-ID: 179787  Cd Length: 468  Bit Score: 352.29  E-value: 8.08e-122
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 526849364   4 KASVGFKAGVKEYKLTYYTPEYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYHI 83
Cdd:PRK04208   1 MAKERYDAGVKEYRQMYWDPDYTPKDTDLLACFRITPQEGVDPEEAAAAVAAESSTGTWTTVWTDLLTDLDKYKAKAYRI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 526849364  84 EPVAGEEDQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPVAYVKTFQGPPHGIQVERDKLNKYGR 163
Cdd:PRK04208  81 EDVPGDDGSYYAFIAYPLDLFEEGSIPNLLASIAGNVFGFKAVKALRLEDIRFPVAYVKTFKGPPFGIQVERERLDKYGR 160

                        170       180       190
                 ....*....|....*....|....*....|
gi 526849364 164 PLLGCTIKPKLGLSAKNYGRAVYECLRGGL 193
Cdd:PRK04208 161 PLLGTTPKPKLGLSAKNYGRVVYEALRGGL 190
RuBisCO_large_I_II_III cd08206
Ribulose bisphosphate carboxylase large chain, Form I,II,III; Ribulose bisphosphate ...
 30-193 1.94e-98

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: 291.06  E-value: 1.94e-98
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 526849364  30 TDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYHIEPVAgeEDQYIAYVAYPLDLFEEGSV 109
Cdd:cd08206    1 TDLLAAFRMTPAEGVDPEEAAAAVAAESSTGTWTTVWTDRLTATERLKAKVYRIDPVP--DGQYIAKIAYPLDLFEEGSV 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 526849364 110 TNMFTSIVGNVFGFKALRALRLEDLRIPVAYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECL 189
Cdd:cd08206   79 PNLLTSIIGNVFGMKAVKALRLEDFRFPPAYLKTFDGPSFGIQGEREILGKYGRPLLGTIVKPKLGLSPKEYARVVYEAL 158


                 ....
gi 526849364 190 RGGL 193
Cdd:cd08206  159 RGGL 162
RuBisCO_large cd08148
Ribulose bisphosphate carboxylase large chain; Ribulose bisphosphate carboxylase (Rubisco) ...
 32-193 2.37e-70

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: 217.68  E-value: 2.37e-70
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 526849364  32 ILAAFRVTPQPgVPPEEAGAAVAAESSTGTWTTVWTdGLTSLDRYKGRCYHIEPVAgeeDQYIAYVAYPLDLFEEGSVTN 111
Cdd:cd08148    1 VLATYRVHPEA-TPPEKAAEAIAAESSTGTWTEVPT-TQEQLRRVKGRVYSVEELG---KRYIVKIAYPVELFEPGNIPQ 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 526849364 112 MFTSIVGNVFGFKALRALRLEDLRIPVAYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRG 191
Cdd:cd08148   76 ILTVTAGNLFGLGALEAVRLEDLEFPEEYKKLFPGPKFGIDGIRKLLGVYGRPLVGTIIKPKLGLNPKYTAEAAYAAALG 155


                 ..
gi 526849364 192 GL 193
Cdd:cd08148  156 GL 157
RbcL COG1850
Ribulose 1,5-bisphosphate carboxylase, large subunit, or a RuBisCO-like protein [Carbohydrate ...
 20-193 5.65e-70

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


Pssm-ID: 441455  Cd Length: 417  Bit Score: 218.11  E-value: 5.65e-70
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 526849364  20 YYTPEYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYHIEPV---AGEEDQYIAY 96
Cdd:COG1850    2 YVDPDYIPDDDDILATYRITPETGVDPEEAAAAIAGEQSTGTWTEVPTETDELRERLAARVYSIEELpevGGGYRRALVT 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 526849364  97 VAYPLDLFEeGSVTNMFTSIVGNVFGFKALRALRLEDLRIPVAYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGL 176
Cdd:COG1850   82 IAYPLENFG-GNLPNLLSTVAGNLFGLKAVSGLRLLDLEFPESFLAAFPGPKFGIEGTRELLGVYDRPLLGTIIKPKVGL 160

                        170
                 ....*....|....*..
gi 526849364 177 SAKNYGRAVYECLRGGL 193
Cdd:COG1850  161 SPEETAELVYELALGGV 177
RuBisCO_large_N pfam02788
Ribulose bisphosphate carboxylase large chain, N-terminal domain; The N-terminal domain of ...
 19-140 6.48e-55

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: 170.09  E-value: 6.48e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 526849364   19 TYYTPEYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYHIEPVAGeeDQYIAYVA 98
Cdd:pfam02788   1 DYVDLDYEPKDTDLLCAFRIEPAAGVSPEEAAAHVAAESSTGTWTEVWTLDDTFTKKLKAKVYEIDEVPG--GSYIVKIA 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 526849364   99 YPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPVAY 140
Cdd:pfam02788  79 YPLDLFEEGSIPQLLSSIAGNIFGMKAVKALRLEDIRFPPAY 120
RuBisCO_large_III cd08213
Ribulose bisphosphate carboxylase large chain, Form III; Ribulose bisphosphate carboxylase ...
 30-193 5.87e-53

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: 174.11  E-value: 5.87e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 526849364  30 TDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYHIEPVAGeedQYIAYVAYPLDLFEEGSV 109
Cdd:cd08213    1 DDLIAVFRIEPAEGISIEEAAGRVASESSIGTWTTLATLYPERAEKLKAKAYYFDGLGG---SYIVKVAYPLELFEEGNM 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 526849364 110 TNMFTSIVGNVFGFKALRALRLEDLRIPVAYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECL 189
Cdd:cd08213   78 PQLLSSIAGNIFGMKAVKNLRLEDIYFPESYLREFKGPQFGIEGVREILGIKDRPLLGTVPKPKVGLSPEEHAEVAYEAL 157


                 ....
gi 526849364 190 RGGL 193
Cdd:cd08213  158 VGGV 161
RuBisCO_IV_RLP cd08205
Ribulose bisphosphate carboxylase like proteins, Rubisco-Form IV; Ribulose bisphosphate ...
 58-193 2.00e-26

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: 103.38  E-value: 2.00e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 526849364  58 STGTWTTVWTDGLTSLDRYKGRCYHIEPV---AGEEDQYIAYVAYPLDLFEeGSVTNMFTSIVGNVFGfkaLRALRLEDL 134
Cdd:cd08205   26 TVGTWTELPGETEEIRERHVGRVESIEELeesEGKYGRARVTISYPLDNFG-GDLPQLLNTLFGNLSL---LPGIKLVDL 101

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 526849364 135 RIPVAYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGL 193
Cdd:cd08205  102 ELPDSLLAAFPGPRFGIEGLRRLLGVHDRPLLGTIIKPSIGLSPEELAELAYELALGGI 160
RuBisCO_large pfam00016
Ribulose bisphosphate carboxylase large chain, catalytic domain; The C-terminal domain of ...
 151-193 1.51e-21

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: 88.96  E-value: 1.51e-21
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 526849364  151 IQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGL 193
Cdd:pfam00016   1 IAVERRVLNKYGRPILGTIIKPKLGLSPKNYARAVYEFLLGGL 43
RLP_NonPhot cd08207
Ribulose bisphosphate carboxylase like proteins from nonphototrophic bacteria; Ribulose ...
 58-193 4.93e-21

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: 88.91  E-value: 4.93e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 526849364  58 STGTWTTV--WTDGLTslDRYKGRCYHIEPVAGEEDQYIAY-------------VAYPLDLFeeG-SVTNMFTSIVGNVF 121
Cdd:cd08207   26 SSGTFIALpgETDELK--ERSAARVESIEELETAAQPSLPRrasggpytrarvtISFPLDNI--GtSLPNLLATVAGNLF 101

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 526849364 122 GFKALRALRLEDLRIPVAYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGL 193
Cdd:cd08207  102 ELRELSGLRLVDLGLPDEFAAAFPGPAFGIAGTRRLTGVEDRPLIGTIIKPSVGLTPEETAALVRQLAAAGI 173
PRK13475 PRK13475
ribulose-bisphosphate carboxylase;
32-192 1.01e-18

ribulose-bisphosphate carboxylase;


Pssm-ID: 184072  Cd Length: 443  Bit Score: 82.85  E-value: 1.01e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 526849364  32 ILAAFRVTPQPGVPPEEAGAAVAAESSTGT-----WTTVWTDGLTSLdrykgrCYHIEPVAGeedqyIAYVAYPLDLFE- 105
Cdd:PRK13475  24 ILCAYKMKPKAGHGYLEAAAHFAAESSTGTnvevsTTDDFTRGVDAL------VYEIDEARE-----LMKIAYPVELFDr 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 526849364 106 -----EGSVTNMFTSIVGNVFGFKALRALRLEDLRIPVAYVKTFQGPPHGIqverDKLNKY-GRP------LLGCTIKPK 173
Cdd:PRK13475  93 niidgRAMIVSFLTLTIGNNQGMGDVEYAKMHDFYVPPRYLELFDGPSTDI----SDLWRVlGRPvkdggyIAGTIIKPK 168

                        170
                 ....*....|....*....
gi 526849364 174 LGLSAKNYGRAVYECLRGG 192
Cdd:PRK13475 169 LGLRPEPFAEACYDFWLGG 187
RuBisCO_large_II cd08211
Ribulose bisphosphate carboxylase large chain, Form II; Ribulose bisphosphate carboxylase ...
 32-192 1.52e-17

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: 79.47  E-value: 1.52e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 526849364  32 ILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTV-WTDGLT-SLDrykGRCYHIEpvageEDQYIAYVAYPLDLFE---- 105
Cdd:cd08211   23 VLVAYIMKPKAGYGYLATAAHFAAESSTGTNVEVsTTDDFTrGVD---ALVYEID-----EARELMKIAYPVELFDrnlt 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 526849364 106 --EGSVTNMFTSIVGNVFGFKALRALRLEDLRIPVAYVKTFQGPPHGIQVERDKLNKY---GRPLLGCTIKPKLGLSAKN 180
Cdd:cd08211   95 dgRAMVASFLTLIIGNNQGMGDVEYLKMHDFYVPESMLELFDGPSVNISDMWKVLGRPevdGGYIAGTIIKPKLGLRPKP 174

                        170
                 ....*....|..
gi 526849364 181 YGRAVYECLRGG 192
Cdd:cd08211  175 FAEACYAFWLGG 186
RLP_DK-MTP-1-P-enolase cd08209
2,3-diketo-5-methylthiopentyl-1-phosphate enolase; Ribulose bisphosphate carboxylase like ...
 60-193 8.87e-16

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: 74.28  E-value: 8.87e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 526849364  60 GTWTTVWTDGLTSLDRYKGRCYHIEPvaGEEDQYIAYVAYPLdlfeeGSVTNMFTSIVGNVFGFKALR-ALRLEDLRIPV 138
Cdd:cd08209   27 GSWTDLPALRQAQLQKHLGEVVSVEE--LEEGRGVITIAYPL-----INVSGDIPALLTTIFGKLSLDgKIKLVDLRLPE 99

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 526849364 139 AYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGL 193
Cdd:cd08209  100 EFGRAFPGPKFGIEGIRQRLGVHDRPLLMSIFKGVLGLDLDDLAEQLREQALGGV 154
RLP_Photo cd08208
Ribulose bisphosphate carboxylase like proteins from phototrophic bacteria; Ribulose ...
 109-193 5.55e-11

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: 60.29  E-value: 5.55e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 526849364 109 VTNMFTSIVGN-VFGFKALRALRLEDLRIPVAYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYE 187
Cdd:cd08208  105 IPNLLSAVCGEgTFFSPGVPVVKLMDIHFPETYLADFEGPKFGIAGLRERLQAHDRPIFFGVIKPNIGLPPGEFAELGYQ 184


                 ....*.
gi 526849364 188 CLRGGL 193
Cdd:cd08208  185 SWLGGL 190
RLP_RrRLP cd08210
Ribulose bisphosphate carboxylase like proteins (RLPs) similar to R.rubrum RLP; RLP from ...
 73-193 1.32e-10

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: 59.17  E-value: 1.32e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 526849364  73 LDRYKGRCYHIEPVagEEDQYIAYVAYPLDlfeegSVTNMFTSIVGNVFGFKAL-RALRLEDLRIPVAYVKTFQGPPHGI 151
Cdd:cd08210   42 RDNIVGRVESLEPA--GEGSYRARISYSVD-----TAGGELTQLLNVLFGNSSLqPGIRLVDFELPPSLLRRFPGPRFGI 114

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 526849364 152 QVERDKLNKYGRPLLGCTIKPkLGLSAKNYGRAVYECLRGGL 193
Cdd:cd08210  115 AGLRALLGIPERPLLCSALKP-QGLSAAELAELAYAFALGGI 155
mtnW PRK09549
2,3-diketo-5-methylthiopentyl-1-phosphate enolase; Reviewed
 60-177 3.64e-09

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


Pssm-ID: 236560  Cd Length: 407  Bit Score: 55.01  E-value: 3.64e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 526849364  60 GTWTTVWTDGLTSLDRYKGRCYHIEPVAGEED----QYIAYVAYPldlfeEGSVTNMFTSIVGNVFGFKALRA-LRLEDL 134
Cdd:PRK09549  31 GSWTDLPHLEQEQLKKHKGNVVHVEELEEHERkgvkRGIIKIAYP-----LANFSPDLPAILTTTFGKLSLDGeVKLIDL 105

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 526849364 135 RIPVAYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLS 177
Cdd:PRK09549 106 TFSDELKRHFPGPKFGIDGIRNLLGVHDRPLLMSIFKGVIGRD 148
 
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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