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Conserved domains on  [gi|930159655|gb|ALF41179|]
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ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit, partial (chloroplast) [Populus sp. BIOUG24049-D06]

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) ...
 1-182 3.01e-142

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: 404.09  E-value: 3.01e-142
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 930159655   1 GVGFKAGVKEYKLNYYTPEYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYDIEP 80
Cdd:CHL00040  10 SVGFKAGVKDYKLTYYTPDYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYRIEP 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 930159655  81 VAGEENQFIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYTKTFQGPPHGIQVERDKLNKYGRPL 160
Cdd:CHL00040  90 VPGEENQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYLKTFQGPPHGIQVERDKLNKYGRPL 169

                        170       180
                 ....*....|....*....|..
gi 930159655 161 LGCTIKPKLGLSAKNYGRAVYE 182
Cdd:CHL00040 170 LGCTIKPKLGLSAKNYGRAVYE 191
 
Name Accession Description Interval E-value
rbcL CHL00040
ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
 1-182 3.01e-142

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


Pssm-ID: 176981  Cd Length: 475  Bit Score: 404.09  E-value: 3.01e-142
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 930159655   1 GVGFKAGVKEYKLNYYTPEYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYDIEP 80
Cdd:CHL00040  10 SVGFKAGVKDYKLTYYTPDYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYRIEP 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 930159655  81 VAGEENQFIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYTKTFQGPPHGIQVERDKLNKYGRPL 160
Cdd:CHL00040  90 VPGEENQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYLKTFQGPPHGIQVERDKLNKYGRPL 169

                        170       180
                 ....*....|....*....|..
gi 930159655 161 LGCTIKPKLGLSAKNYGRAVYE 182
Cdd:CHL00040 170 LGCTIKPKLGLSAKNYGRAVYE 191
RuBisCO_large_I cd08212
Ribulose bisphosphate carboxylase large chain, Form I; Ribulose bisphosphate carboxylase ...
 15-182 3.76e-122

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: 352.11  E-value: 3.76e-122
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 930159655  15 YYTPEYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYDIEPVAGEENQFIAYVAY 94
Cdd:cd08212    2 YWTPDYQPKDTDILAAFRITPQPGVDPEEAAAAVAGESSTATWTVVWTDRLTALDRYKGKAYRVEPVPGEENQYFAYIAY 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 930159655  95 PLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYTKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAK 174
Cdd:cd08212   82 PLDLFEEGSVANLTTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGIQVERDRLNKYGRPLLGCTIKPKLGLSAK 161


                 ....*...
gi 930159655 175 NYGRAVYE 182
Cdd:cd08212  162 NYGRVVYE 169
RbcL COG1850
Ribulose 1,5-bisphosphate carboxylase, large subunit, or a RuBisCO-like protein [Carbohydrate ...
 14-182 2.48e-67

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


Pssm-ID: 441455  Cd Length: 417  Bit Score: 210.80  E-value: 2.48e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 930159655  14 NYYTPEYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYDIEPV---AGEENQFIA 90
Cdd:COG1850    1 DYVDPDYIPDDDDILATYRITPETGVDPEEAAAAIAGEQSTGTWTEVPTETDELRERLAARVYSIEELpevGGGYRRALV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 930159655  91 YVAYPLDLFEeGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYTKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLG 170
Cdd:COG1850   81 TIAYPLENFG-GNLPNLLSTVAGNLFGLKAVSGLRLLDLEFPESFLAAFPGPKFGIEGTRELLGVYDRPLLGTIIKPKVG 159

                        170
                 ....*....|..
gi 930159655 171 LSAKNYGRAVYE 182
Cdd:COG1850  160 LSPEETAELVYE 171
RuBisCO_large_N pfam02788
Ribulose bisphosphate carboxylase large chain, N-terminal domain; The N-terminal domain of ...
 14-135 1.94e-54

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: 1.94e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 930159655   14 NYYTPEYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYDIEPVAGEenQFIAYVA 93
Cdd:pfam02788   1 DYVDLDYEPKDTDLLCAFRIEPAAGVSPEEAAAHVAAESSTGTWTEVWTLDDTFTKKLKAKVYEIDEVPGG--SYIVKIA 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 930159655   94 YPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAY 135
Cdd:pfam02788  79 YPLDLFEEGSIPQLLSSIAGNIFGMKAVKALRLEDIRFPPAY 120
 
Name Accession Description Interval E-value
rbcL CHL00040
ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
 1-182 3.01e-142

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


Pssm-ID: 176981  Cd Length: 475  Bit Score: 404.09  E-value: 3.01e-142
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 930159655   1 GVGFKAGVKEYKLNYYTPEYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYDIEP 80
Cdd:CHL00040  10 SVGFKAGVKDYKLTYYTPDYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYRIEP 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 930159655  81 VAGEENQFIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYTKTFQGPPHGIQVERDKLNKYGRPL 160
Cdd:CHL00040  90 VPGEENQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYLKTFQGPPHGIQVERDKLNKYGRPL 169

                        170       180
                 ....*....|....*....|..
gi 930159655 161 LGCTIKPKLGLSAKNYGRAVYE 182
Cdd:CHL00040 170 LGCTIKPKLGLSAKNYGRAVYE 191
RuBisCO_large_I cd08212
Ribulose bisphosphate carboxylase large chain, Form I; Ribulose bisphosphate carboxylase ...
 15-182 3.76e-122

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: 352.11  E-value: 3.76e-122
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 930159655  15 YYTPEYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYDIEPVAGEENQFIAYVAY 94
Cdd:cd08212    2 YWTPDYQPKDTDILAAFRITPQPGVDPEEAAAAVAGESSTATWTVVWTDRLTALDRYKGKAYRVEPVPGEENQYFAYIAY 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 930159655  95 PLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYTKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAK 174
Cdd:cd08212   82 PLDLFEEGSVANLTTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGIQVERDRLNKYGRPLLGCTIKPKLGLSAK 161


                 ....*...
gi 930159655 175 NYGRAVYE 182
Cdd:cd08212  162 NYGRVVYE 169
rbcL PRK04208
ribulose bisophosphate carboxylase; Reviewed
 3-182 2.47e-115

ribulose bisophosphate carboxylase; Reviewed


Pssm-ID: 179787  Cd Length: 468  Bit Score: 335.34  E-value: 2.47e-115
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 930159655   3 GFKAGVKEYKLNYYTPEYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYDIEPVA 82
Cdd:PRK04208   5 RYDAGVKEYRQMYWDPDYTPKDTDLLACFRITPQEGVDPEEAAAAVAAESSTGTWTTVWTDLLTDLDKYKAKAYRIEDVP 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 930159655  83 GEENQFIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYTKTFQGPPHGIQVERDKLNKYGRPLLG 162
Cdd:PRK04208  85 GDDGSYYAFIAYPLDLFEEGSIPNLLASIAGNVFGFKAVKALRLEDIRFPVAYVKTFKGPPFGIQVERERLDKYGRPLLG 164

                        170       180
                 ....*....|....*....|
gi 930159655 163 CTIKPKLGLSAKNYGRAVYE 182
Cdd:PRK04208 165 TTPKPKLGLSAKNYGRVVYE 184
RuBisCO_large_I_II_III cd08206
Ribulose bisphosphate carboxylase large chain, Form I,II,III; Ribulose bisphosphate ...
 25-182 2.57e-94

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: 279.89  E-value: 2.57e-94
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 930159655  25 TDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYDIEPVAgeENQFIAYVAYPLDLFEEGSV 104
Cdd:cd08206    1 TDLLAAFRMTPAEGVDPEEAAAAVAAESSTGTWTTVWTDRLTATERLKAKVYRIDPVP--DGQYIAKIAYPLDLFEEGSV 78

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 930159655 105 TNMFTSIVGNVFGFKALRALRLEDLRIPPAYTKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYE 182
Cdd:cd08206   79 PNLLTSIIGNVFGMKAVKALRLEDFRFPPAYLKTFDGPSFGIQGEREILGKYGRPLLGTIVKPKLGLSPKEYARVVYE 156
RbcL COG1850
Ribulose 1,5-bisphosphate carboxylase, large subunit, or a RuBisCO-like protein [Carbohydrate ...
 14-182 2.48e-67

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


Pssm-ID: 441455  Cd Length: 417  Bit Score: 210.80  E-value: 2.48e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 930159655  14 NYYTPEYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYDIEPV---AGEENQFIA 90
Cdd:COG1850    1 DYVDPDYIPDDDDILATYRITPETGVDPEEAAAAIAGEQSTGTWTEVPTETDELRERLAARVYSIEELpevGGGYRRALV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 930159655  91 YVAYPLDLFEeGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYTKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLG 170
Cdd:COG1850   81 TIAYPLENFG-GNLPNLLSTVAGNLFGLKAVSGLRLLDLEFPESFLAAFPGPKFGIEGTRELLGVYDRPLLGTIIKPKVG 159

                        170
                 ....*....|..
gi 930159655 171 LSAKNYGRAVYE 182
Cdd:COG1850  160 LSPEETAELVYE 171
RuBisCO_large cd08148
Ribulose bisphosphate carboxylase large chain; Ribulose bisphosphate carboxylase (Rubisco) ...
 27-182 8.08e-65

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: 203.04  E-value: 8.08e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 930159655  27 ILAAFRVTPQPgVPPEEAGAAVAAESSTGTWTTVWTdGLTSLDRYKGRCYDIEPVAgeeNQFIAYVAYPLDLFEEGSVTN 106
Cdd:cd08148    1 VLATYRVHPEA-TPPEKAAEAIAAESSTGTWTEVPT-TQEQLRRVKGRVYSVEELG---KRYIVKIAYPVELFEPGNIPQ 75

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 930159655 107 MFTSIVGNVFGFKALRALRLEDLRIPPAYTKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYE 182
Cdd:cd08148   76 ILTVTAGNLFGLGALEAVRLEDLEFPEEYKKLFPGPKFGIDGIRKLLGVYGRPLVGTIIKPKLGLNPKYTAEAAYA 151
RuBisCO_large_N pfam02788
Ribulose bisphosphate carboxylase large chain, N-terminal domain; The N-terminal domain of ...
 14-135 1.94e-54

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: 1.94e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 930159655   14 NYYTPEYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYDIEPVAGEenQFIAYVA 93
Cdd:pfam02788   1 DYVDLDYEPKDTDLLCAFRIEPAAGVSPEEAAAHVAAESSTGTWTEVWTLDDTFTKKLKAKVYEIDEVPGG--SYIVKIA 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 930159655   94 YPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAY 135
Cdd:pfam02788  79 YPLDLFEEGSIPQLLSSIAGNIFGMKAVKALRLEDIRFPPAY 120
RuBisCO_large_III cd08213
Ribulose bisphosphate carboxylase large chain, Form III; Ribulose bisphosphate carboxylase ...
 25-182 2.45e-51

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: 169.49  E-value: 2.45e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 930159655  25 TDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYDIEPVAGeenQFIAYVAYPLDLFEEGSV 104
Cdd:cd08213    1 DDLIAVFRIEPAEGISIEEAAGRVASESSIGTWTTLATLYPERAEKLKAKAYYFDGLGG---SYIVKVAYPLELFEEGNM 77

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 930159655 105 TNMFTSIVGNVFGFKALRALRLEDLRIPPAYTKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYE 182
Cdd:cd08213   78 PQLLSSIAGNIFGMKAVKNLRLEDIYFPESYLREFKGPQFGIEGVREILGIKDRPLLGTVPKPKVGLSPEEHAEVAYE 155
RuBisCO_IV_RLP cd08205
Ribulose bisphosphate carboxylase like proteins, Rubisco-Form IV; Ribulose bisphosphate ...
 53-182 1.30e-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: 97.99  E-value: 1.30e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 930159655  53 STGTWTTVWTDGLTSLDRYKGRCYDIEPV---AGEENQFIAYVAYPLDLFEeGSVTNMFTSIVGNVFGfkaLRALRLEDL 129
Cdd:cd08205   26 TVGTWTELPGETEEIRERHVGRVESIEELeesEGKYGRARVTISYPLDNFG-GDLPQLLNTLFGNLSL---LPGIKLVDL 101

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 930159655 130 RIPPAYTKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYE 182
Cdd:cd08205  102 ELPDSLLAAFPGPRFGIEGLRRLLGVHDRPLLGTIIKPSIGLSPEELAELAYE 154
RLP_NonPhot cd08207
Ribulose bisphosphate carboxylase like proteins from nonphototrophic bacteria; Ribulose ...
 53-182 4.35e-19

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: 83.13  E-value: 4.35e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 930159655  53 STGTWTTV--WTDGLTslDRYKGRCYDIEPVAGEENQFIAY-------------VAYPLDLFeeG-SVTNMFTSIVGNVF 116
Cdd:cd08207   26 SSGTFIALpgETDELK--ERSAARVESIEELETAAQPSLPRrasggpytrarvtISFPLDNI--GtSLPNLLATVAGNLF 101

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 930159655 117 GFKALRALRLEDLRIPPAYTKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYE 182
Cdd:cd08207  102 ELRELSGLRLVDLGLPDEFAAAFPGPAFGIAGTRRLTGVEDRPLIGTIIKPSVGLTPEETAALVRQ 167
PRK13475 PRK13475
ribulose-bisphosphate carboxylase;
27-182 8.35e-19

ribulose-bisphosphate carboxylase;


Pssm-ID: 184072  Cd Length: 443  Bit Score: 82.46  E-value: 8.35e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 930159655  27 ILAAFRVTPQPGVPPEEAGAAVAAESSTGT-----WTTVWTDGLTSLdrykgrCYDIEPVAGeenqfIAYVAYPLDLFE- 100
Cdd:PRK13475  24 ILCAYKMKPKAGHGYLEAAAHFAAESSTGTnvevsTTDDFTRGVDAL------VYEIDEARE-----LMKIAYPVELFDr 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 930159655 101 -----EGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYTKTFQGPPHGIqverDKLNKY-GRP------LLGCTIKPK 168
Cdd:PRK13475  93 niidgRAMIVSFLTLTIGNNQGMGDVEYAKMHDFYVPPRYLELFDGPSTDI----SDLWRVlGRPvkdggyIAGTIIKPK 168

                        170
                 ....*....|....
gi 930159655 169 LGLSAKNYGRAVYE 182
Cdd:PRK13475 169 LGLRPEPFAEACYD 182
RuBisCO_large_II cd08211
Ribulose bisphosphate carboxylase large chain, Form II; Ribulose bisphosphate carboxylase ...
 27-182 5.97e-18

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: 80.24  E-value: 5.97e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 930159655  27 ILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTV-WTDGLT-SLDrykGRCYDIEpvagEENQfIAYVAYPLDLFE---- 100
Cdd:cd08211   23 VLVAYIMKPKAGYGYLATAAHFAAESSTGTNVEVsTTDDFTrGVD---ALVYEID----EARE-LMKIAYPVELFDrnlt 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 930159655 101 --EGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYTKTFQGPPHGIQVERDKLNKY---GRPLLGCTIKPKLGLSAKN 175
Cdd:cd08211   95 dgRAMVASFLTLIIGNNQGMGDVEYLKMHDFYVPESMLELFDGPSVNISDMWKVLGRPevdGGYIAGTIIKPKLGLRPKP 174


                 ....*..
gi 930159655 176 YGRAVYE 182
Cdd:cd08211  175 FAEACYA 181
RuBisCO_large pfam00016
Ribulose bisphosphate carboxylase large chain, catalytic domain; The C-terminal domain of ...
 146-182 1.06e-17

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: 78.17  E-value: 1.06e-17
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 930159655  146 IQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYE 182
Cdd:pfam00016   1 IAVERRVLNKYGRPILGTIIKPKLGLSPKNYARAVYE 37
RLP_DK-MTP-1-P-enolase cd08209
2,3-diketo-5-methylthiopentyl-1-phosphate enolase; Ribulose bisphosphate carboxylase like ...
 55-182 5.65e-15

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: 71.58  E-value: 5.65e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 930159655  55 GTWTTVWTDGLTSLDRYKGRCYDIEPvaGEENQFIAYVAYPLdlfeeGSVTNMFTSIVGNVFGFKALR-ALRLEDLRIPP 133
Cdd:cd08209   27 GSWTDLPALRQAQLQKHLGEVVSVEE--LEEGRGVITIAYPL-----INVSGDIPALLTTIFGKLSLDgKIKLVDLRLPE 99

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 930159655 134 AYTKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYE 182
Cdd:cd08209  100 EFGRAFPGPKFGIEGIRQRLGVHDRPLLMSIFKGVLGLDLDDLAEQLRE 148
RLP_RrRLP cd08210
Ribulose bisphosphate carboxylase like proteins (RLPs) similar to R.rubrum RLP; RLP from ...
 68-182 1.36e-09

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: 56.09  E-value: 1.36e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 930159655  68 LDRYKGRCYDIEPVagEENQFIAYVAYPLDlfeegSVTNMFTSIVGNVFGFKAL-RALRLEDLRIPPAYTKTFQGPPHGI 146
Cdd:cd08210   42 RDNIVGRVESLEPA--GEGSYRARISYSVD-----TAGGELTQLLNVLFGNSSLqPGIRLVDFELPPSLLRRFPGPRFGI 114

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 930159655 147 QVERDKLNKYGRPLLGCTIKPkLGLSAKNYGRAVYE 182
Cdd:cd08210  115 AGLRALLGIPERPLLCSALKP-QGLSAAELAELAYA 149
RLP_Photo cd08208
Ribulose bisphosphate carboxylase like proteins from phototrophic bacteria; Ribulose ...
 53-182 1.41e-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: 56.06  E-value: 1.41e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 930159655  53 STGTWTTVWTDGLTSLdRYKGRCYDIEPVAGEENQFiayvaYPLDLFEEGSVT------------------NMFTSIVGN 114
Cdd:cd08208   42 STAQWRRVGVDEDFRP-RFAAKVIDLEVIEELEQLS-----YPVKHSETGPVHacrvtiahphgnfgpkipNLLSAVCGE 115

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 930159655 115 -VFGFKALRALRLEDLRIPPAYTKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYE 182
Cdd:cd08208  116 gTFFSPGVPVVKLMDIHFPETYLADFEGPKFGIAGLRERLQAHDRPIFFGVIKPNIGLPPGEFAELGYQ 184
mtnW PRK09549
2,3-diketo-5-methylthiopentyl-1-phosphate enolase; Reviewed
 55-172 7.47e-09

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


Pssm-ID: 236560  Cd Length: 407  Bit Score: 53.86  E-value: 7.47e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 930159655  55 GTWTTVWTDGLTSLDRYKGRCYDIEPVAGEEN----QFIAYVAYPldlfeEGSVTNMFTSIVGNVFGFKALRA-LRLEDL 129
Cdd:PRK09549  31 GSWTDLPHLEQEQLKKHKGNVVHVEELEEHERkgvkRGIIKIAYP-----LANFSPDLPAILTTTFGKLSLDGeVKLIDL 105

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 930159655 130 RIPPAYTKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLS 172
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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