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Conserved domains on  [gi|844186839|gb|AKN00599|]
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ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit, partial (chloroplast) [Hyparrhenia aff. nubica TRK-2015]

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) ...
 1-167 6.85e-131

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: 374.42  E-value: 6.85e-131
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 844186839   1 GVKDYKLTYYTPEYETKETDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYHIEPVPGEAD 80
Cdd:CHL00040  16 GVKDYKLTYYTPDYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYRIEPVPGEEN 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 844186839  81 QYICYIAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPTYSKTFQGPPHGIQVERDKLNKYGRPLLGCTIK 160
Cdd:CHL00040  96 QYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYLKTFQGPPHGIQVERDKLNKYGRPLLGCTIK 175


                 ....*..
gi 844186839 161 PKLGLSA 167
Cdd:CHL00040 176 PKLGLSA 182
 
Name Accession Description Interval E-value
rbcL CHL00040
ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
 1-167 6.85e-131

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


Pssm-ID: 176981  Cd Length: 475  Bit Score: 374.42  E-value: 6.85e-131
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 844186839   1 GVKDYKLTYYTPEYETKETDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYHIEPVPGEAD 80
Cdd:CHL00040  16 GVKDYKLTYYTPDYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYRIEPVPGEEN 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 844186839  81 QYICYIAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPTYSKTFQGPPHGIQVERDKLNKYGRPLLGCTIK 160
Cdd:CHL00040  96 QYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYLKTFQGPPHGIQVERDKLNKYGRPLLGCTIK 175


                 ....*..
gi 844186839 161 PKLGLSA 167
Cdd:CHL00040 176 PKLGLSA 182
RuBisCO_large_I cd08212
Ribulose bisphosphate carboxylase large chain, Form I; Ribulose bisphosphate carboxylase ...
 8-167 2.88e-114

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: 331.31  E-value: 2.88e-114
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 844186839   8 TYYTPEYETKETDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYHIEPVPGEADQYICYIA 87
Cdd:cd08212    1 GYWTPDYQPKDTDILAAFRITPQPGVDPEEAAAAVAGESSTATWTVVWTDRLTALDRYKGKAYRVEPVPGEENQYFAYIA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 844186839  88 YPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPTYSKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSA 167
Cdd:cd08212   81 YPLDLFEEGSVANLTTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGIQVERDRLNKYGRPLLGCTIKPKLGLSA 160
RbcL COG1850
Ribulose 1,5-bisphosphate carboxylase, large subunit, or a RuBisCO-like protein [Carbohydrate ...
 9-167 1.05e-61

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


Pssm-ID: 441455  Cd Length: 417  Bit Score: 195.77  E-value: 1.05e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 844186839   9 YYTPEYETKETDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYHIEPVPGEA---DQYICY 85
Cdd:COG1850    2 YVDPDYIPDDDDILATYRITPETGVDPEEAAAAIAGEQSTGTWTEVPTETDELRERLAARVYSIEELPEVGggyRRALVT 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 844186839  86 IAYPLDLFEeGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPTYSKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGL 165
Cdd:COG1850   82 IAYPLENFG-GNLPNLLSTVAGNLFGLKAVSGLRLLDLEFPESFLAAFPGPKFGIEGTRELLGVYDRPLLGTIIKPKVGL 160


                 ..
gi 844186839 166 SA 167
Cdd:COG1850  161 SP 162
RuBisCO_large_N pfam02788
Ribulose bisphosphate carboxylase large chain, N-terminal domain; The N-terminal domain of ...
 8-129 8.89e-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: 168.55  E-value: 8.89e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 844186839    8 TYYTPEYETKETDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYHIEPVPGeaDQYICYIA 87
Cdd:pfam02788   1 DYVDLDYEPKDTDLLCAFRIEPAAGVSPEEAAAHVAAESSTGTWTEVWTLDDTFTKKLKAKVYEIDEVPG--GSYIVKIA 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 844186839   88 YPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPTY 129
Cdd:pfam02788  79 YPLDLFEEGSIPQLLSSIAGNIFGMKAVKALRLEDIRFPPAY 120
 
Name Accession Description Interval E-value
rbcL CHL00040
ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
 1-167 6.85e-131

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


Pssm-ID: 176981  Cd Length: 475  Bit Score: 374.42  E-value: 6.85e-131
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 844186839   1 GVKDYKLTYYTPEYETKETDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYHIEPVPGEAD 80
Cdd:CHL00040  16 GVKDYKLTYYTPDYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYRIEPVPGEEN 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 844186839  81 QYICYIAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPTYSKTFQGPPHGIQVERDKLNKYGRPLLGCTIK 160
Cdd:CHL00040  96 QYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYLKTFQGPPHGIQVERDKLNKYGRPLLGCTIK 175


                 ....*..
gi 844186839 161 PKLGLSA 167
Cdd:CHL00040 176 PKLGLSA 182
RuBisCO_large_I cd08212
Ribulose bisphosphate carboxylase large chain, Form I; Ribulose bisphosphate carboxylase ...
 8-167 2.88e-114

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: 331.31  E-value: 2.88e-114
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 844186839   8 TYYTPEYETKETDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYHIEPVPGEADQYICYIA 87
Cdd:cd08212    1 GYWTPDYQPKDTDILAAFRITPQPGVDPEEAAAAVAGESSTATWTVVWTDRLTALDRYKGKAYRVEPVPGEENQYFAYIA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 844186839  88 YPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPTYSKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSA 167
Cdd:cd08212   81 YPLDLFEEGSVANLTTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGIQVERDRLNKYGRPLLGCTIKPKLGLSA 160
rbcL PRK04208
ribulose bisophosphate carboxylase; Reviewed
 1-167 1.19e-105

ribulose bisophosphate carboxylase; Reviewed


Pssm-ID: 179787  Cd Length: 468  Bit Score: 309.91  E-value: 1.19e-105
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 844186839   1 GVKDYKLTYYTPEYETKETDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYHIEPVPGEAD 80
Cdd:PRK04208   9 GVKEYRQMYWDPDYTPKDTDLLACFRITPQEGVDPEEAAAAVAAESSTGTWTTVWTDLLTDLDKYKAKAYRIEDVPGDDG 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 844186839  81 QYICYIAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPTYSKTFQGPPHGIQVERDKLNKYGRPLLGCTIK 160
Cdd:PRK04208  89 SYYAFIAYPLDLFEEGSIPNLLASIAGNVFGFKAVKALRLEDIRFPVAYVKTFKGPPFGIQVERERLDKYGRPLLGTTPK 168


                 ....*..
gi 844186839 161 PKLGLSA 167
Cdd:PRK04208 169 PKLGLSA 175
RuBisCO_large_I_II_III cd08206
Ribulose bisphosphate carboxylase large chain, Form I,II,III; Ribulose bisphosphate ...
 19-167 6.96e-87

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: 260.25  E-value: 6.96e-87
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 844186839  19 TDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYHIEPVPgeADQYICYIAYPLDLFEEGSV 98
Cdd:cd08206    1 TDLLAAFRMTPAEGVDPEEAAAAVAAESSTGTWTTVWTDRLTATERLKAKVYRIDPVP--DGQYIAKIAYPLDLFEEGSV 78

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 844186839  99 TNMFTSIVGNVFGFKALRALRLEDLRIPPTYSKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSA 167
Cdd:cd08206   79 PNLLTSIIGNVFGMKAVKALRLEDFRFPPAYLKTFDGPSFGIQGEREILGKYGRPLLGTIVKPKLGLSP 147
RuBisCO_large cd08148
Ribulose bisphosphate carboxylase large chain; Ribulose bisphosphate carboxylase (Rubisco) ...
 21-167 8.16e-63

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: 8.16e-63
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 844186839  21 ILAAFRVTPQPgVPPEEAGAAVAAESSTGTWTTVWTdGLTSLDRYKGRCYHIEPVpgeADQYICYIAYPLDLFEEGSVTN 100
Cdd:cd08148    1 VLATYRVHPEA-TPPEKAAEAIAAESSTGTWTEVPT-TQEQLRRVKGRVYSVEEL---GKRYIVKIAYPVELFEPGNIPQ 75

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 844186839 101 MFTSIVGNVFGFKALRALRLEDLRIPPTYSKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSA 167
Cdd:cd08148   76 ILTVTAGNLFGLGALEAVRLEDLEFPEEYKKLFPGPKFGIDGIRKLLGVYGRPLVGTIIKPKLGLNP 142
RbcL COG1850
Ribulose 1,5-bisphosphate carboxylase, large subunit, or a RuBisCO-like protein [Carbohydrate ...
 9-167 1.05e-61

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


Pssm-ID: 441455  Cd Length: 417  Bit Score: 195.77  E-value: 1.05e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 844186839   9 YYTPEYETKETDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYHIEPVPGEA---DQYICY 85
Cdd:COG1850    2 YVDPDYIPDDDDILATYRITPETGVDPEEAAAAIAGEQSTGTWTEVPTETDELRERLAARVYSIEELPEVGggyRRALVT 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 844186839  86 IAYPLDLFEeGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPTYSKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGL 165
Cdd:COG1850   82 IAYPLENFG-GNLPNLLSTVAGNLFGLKAVSGLRLLDLEFPESFLAAFPGPKFGIEGTRELLGVYDRPLLGTIIKPKVGL 160


                 ..
gi 844186839 166 SA 167
Cdd:COG1850  161 SP 162
RuBisCO_large_N pfam02788
Ribulose bisphosphate carboxylase large chain, N-terminal domain; The N-terminal domain of ...
 8-129 8.89e-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: 168.55  E-value: 8.89e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 844186839    8 TYYTPEYETKETDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYHIEPVPGeaDQYICYIA 87
Cdd:pfam02788   1 DYVDLDYEPKDTDLLCAFRIEPAAGVSPEEAAAHVAAESSTGTWTEVWTLDDTFTKKLKAKVYEIDEVPG--GSYIVKIA 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 844186839   88 YPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPTY 129
Cdd:pfam02788  79 YPLDLFEEGSIPQLLSSIAGNIFGMKAVKALRLEDIRFPPAY 120
RuBisCO_large_III cd08213
Ribulose bisphosphate carboxylase large chain, Form III; Ribulose bisphosphate carboxylase ...
 19-167 6.07e-47

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: 157.55  E-value: 6.07e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 844186839  19 TDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYHIEpvpGEADQYICYIAYPLDLFEEGSV 98
Cdd:cd08213    1 DDLIAVFRIEPAEGISIEEAAGRVASESSIGTWTTLATLYPERAEKLKAKAYYFD---GLGGSYIVKVAYPLELFEEGNM 77

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 844186839  99 TNMFTSIVGNVFGFKALRALRLEDLRIPPTYSKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSA 167
Cdd:cd08213   78 PQLLSSIAGNIFGMKAVKNLRLEDIYFPESYLREFKGPQFGIEGVREILGIKDRPLLGTVPKPKVGLSP 146
RuBisCO_IV_RLP cd08205
Ribulose bisphosphate carboxylase like proteins, Rubisco-Form IV; Ribulose bisphosphate ...
 47-167 5.86e-24

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: 95.68  E-value: 5.86e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 844186839  47 STGTWTTVWTDGLTSLDRYKGRCYHIEPVPGEADQYICY---IAYPLDLFEeGSVTNMFTSIVGNVFGfkaLRALRLEDL 123
Cdd:cd08205   26 TVGTWTELPGETEEIRERHVGRVESIEELEESEGKYGRArvtISYPLDNFG-GDLPQLLNTLFGNLSL---LPGIKLVDL 101

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 844186839 124 RIPPTYSKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSA 167
Cdd:cd08205  102 ELPDSLLAAFPGPRFGIEGLRRLLGVHDRPLLGTIIKPSIGLSP 145
RLP_NonPhot cd08207
Ribulose bisphosphate carboxylase like proteins from nonphototrophic bacteria; Ribulose ...
 47-167 4.01e-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: 88.52  E-value: 4.01e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 844186839  47 STGTWTTV--WTDGLTslDRYKGRCYHIEPVPGEADQYI-------CY------IAYPLDLFeeG-SVTNMFTSIVGNVF 110
Cdd:cd08207   26 SSGTFIALpgETDELK--ERSAARVESIEELETAAQPSLprrasggPYtrarvtISFPLDNI--GtSLPNLLATVAGNLF 101

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 844186839 111 GFKALRALRLEDLRIPPTYSKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSA 167
Cdd:cd08207  102 ELRELSGLRLVDLGLPDEFAAAFPGPAFGIAGTRRLTGVEDRPLIGTIIKPSVGLTP 158
PRK13475 PRK13475
ribulose-bisphosphate carboxylase;
21-165 8.72e-17

ribulose-bisphosphate carboxylase;


Pssm-ID: 184072  Cd Length: 443  Bit Score: 76.30  E-value: 8.72e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 844186839  21 ILAAFRVTPQPGVPPEEAGAAVAAESSTGT-----WTTVWTDGLTSLdrykgrCYHIEPVPGeadqyICYIAYPLDLFE- 94
Cdd:PRK13475  24 ILCAYKMKPKAGHGYLEAAAHFAAESSTGTnvevsTTDDFTRGVDAL------VYEIDEARE-----LMKIAYPVELFDr 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 844186839  95 -----EGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPTYSKTFQGPPHGIqverDKLNKY-GRP------LLGCTIKPK 162
Cdd:PRK13475  93 niidgRAMIVSFLTLTIGNNQGMGDVEYAKMHDFYVPPRYLELFDGPSTDI----SDLWRVlGRPvkdggyIAGTIIKPK 168


                 ...
gi 844186839 163 LGL 165
Cdd:PRK13475 169 LGL 171
RuBisCO_large_II cd08211
Ribulose bisphosphate carboxylase large chain, Form II; Ribulose bisphosphate carboxylase ...
 21-165 6.97e-16

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: 73.69  E-value: 6.97e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 844186839  21 ILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTV-WTDGLT-SLDrykGRCYHIEpvpgEADQyICYIAYPLDLFE---- 94
Cdd:cd08211   23 VLVAYIMKPKAGYGYLATAAHFAAESSTGTNVEVsTTDDFTrGVD---ALVYEID----EARE-LMKIAYPVELFDrnlt 94

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 844186839  95 --EGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPTYSKTFQGPPHGIQVERDKLNKY---GRPLLGCTIKPKLGL 165
Cdd:cd08211   95 dgRAMVASFLTLIIGNNQGMGDVEYLKMHDFYVPESMLELFDGPSVNISDMWKVLGRPevdGGYIAGTIIKPKLGL 170
RLP_DK-MTP-1-P-enolase cd08209
2,3-diketo-5-methylthiopentyl-1-phosphate enolase; Ribulose bisphosphate carboxylase like ...
 49-167 4.93e-13

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: 65.42  E-value: 4.93e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 844186839  49 GTWTTVWTDGLTSLDRYKGRCYHIEPvpGEADQYICYIAYPLdlfeeGSVTNMFTSIVGNVFGFKALR-ALRLEDLRIPP 127
Cdd:cd08209   27 GSWTDLPALRQAQLQKHLGEVVSVEE--LEEGRGVITIAYPL-----INVSGDIPALLTTIFGKLSLDgKIKLVDLRLPE 99

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 844186839 128 TYSKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSA 167
Cdd:cd08209  100 EFGRAFPGPKFGIEGIRQRLGVHDRPLLMSIFKGVLGLDL 139
RuBisCO_large pfam00016
Ribulose bisphosphate carboxylase large chain, catalytic domain; The C-terminal domain of ...
 140-167 3.60e-11

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: 59.68  E-value: 3.60e-11
                          10        20
                  ....*....|....*....|....*...
gi 844186839  140 IQVERDKLNKYGRPLLGCTIKPKLGLSA 167
Cdd:pfam00016   1 IAVERRVLNKYGRPILGTIIKPKLGLSP 28
mtnW PRK09549
2,3-diketo-5-methylthiopentyl-1-phosphate enolase; Reviewed
 49-166 6.04e-10

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


Pssm-ID: 236560  Cd Length: 407  Bit Score: 56.56  E-value: 6.04e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 844186839  49 GTWTTVWTDGLTSLDRYKGRCYHIEPVPGEAD----QYICYIAYPldlfeEGSVTNMFTSIVGNVFGFKALRA-LRLEDL 123
Cdd:PRK09549  31 GSWTDLPHLEQEQLKKHKGNVVHVEELEEHERkgvkRGIIKIAYP-----LANFSPDLPAILTTTFGKLSLDGeVKLIDL 105

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 844186839 124 RIPPTYSKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLS 166
Cdd:PRK09549 106 TFSDELKRHFPGPKFGIDGIRNLLGVHDRPLLMSIFKGVIGRD 148
RLP_Photo cd08208
Ribulose bisphosphate carboxylase like proteins from phototrophic bacteria; Ribulose ...
 86-166 4.62e-09

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: 54.13  E-value: 4.62e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 844186839  86 IAYPLDLFEEgSVTNMFTSIVGN-VFGFKALRALRLEDLRIPPTYSKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLG 164
Cdd:cd08208   94 IAHPHGNFGP-KIPNLLSAVCGEgTFFSPGVPVVKLMDIHFPETYLADFEGPKFGIAGLRERLQAHDRPIFFGVIKPNIG 172


                 ..
gi 844186839 165 LS 166
Cdd:cd08208  173 LP 174
RLP_RrRLP cd08210
Ribulose bisphosphate carboxylase like proteins (RLPs) similar to R.rubrum RLP; RLP from ...
 62-167 1.50e-08

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: 52.63  E-value: 1.50e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 844186839  62 LDRYKGRCYHIEPVpgEADQYICYIAYPLDlfeegSVTNMFTSIVGNVFGFKAL-RALRLEDLRIPPTYSKTFQGPPHGI 140
Cdd:cd08210   42 RDNIVGRVESLEPA--GEGSYRARISYSVD-----TAGGELTQLLNVLFGNSSLqPGIRLVDFELPPSLLRRFPGPRFGI 114

                         90       100
                 ....*....|....*....|....*..
gi 844186839 141 QVERDKLNKYGRPLLGCTIKPkLGLSA 167
Cdd:cd08210  115 AGLRALLGIPERPLLCSALKP-QGLSA 140
 
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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