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Conserved domains on  [gi|2234190668|dbj|BDG57003|]
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ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit, partial (chloroplast) [Myrica gale var. tomentosa]

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) ...
 1-199 3.64e-159

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: 447.61  E-value: 3.64e-159
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234190668   1 SVGFKAGVKDYKLTYYTPDYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYHIEP 80
Cdd:CHL00040   10 SVGFKAGVKDYKLTYYTPDYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYRIEP 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234190668  81 VAGEESQFIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPTSYVKTFQGPPHGIQVERDKLNKYGRPL 160
Cdd:CHL00040   90 VPGEENQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYLKTFQGPPHGIQVERDKLNKYGRPL 169

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 2234190668 161 LGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNS 199
Cdd:CHL00040  170 LGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNS 208
 
Name Accession Description Interval E-value
rbcL CHL00040
ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
 1-199 3.64e-159

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


Pssm-ID: 176981  Cd Length: 475  Bit Score: 447.61  E-value: 3.64e-159
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234190668   1 SVGFKAGVKDYKLTYYTPDYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYHIEP 80
Cdd:CHL00040   10 SVGFKAGVKDYKLTYYTPDYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYRIEP 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234190668  81 VAGEESQFIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPTSYVKTFQGPPHGIQVERDKLNKYGRPL 160
Cdd:CHL00040   90 VPGEENQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYLKTFQGPPHGIQVERDKLNKYGRPL 169

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 2234190668 161 LGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNS 199
Cdd:CHL00040  170 LGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNS 208
RuBisCO_large_I cd08212
Ribulose bisphosphate carboxylase large chain, Form I; Ribulose bisphosphate carboxylase ...
 14-199 1.46e-138

Ribulose bisphosphate carboxylase large chain, Form I; Ribulose bisphosphate carboxylase (Rubisco) plays an important role in the Calvin reductive pentose phosphate pathway. It catalyzes the primary CO2 fixation step. Rubisco is activated by carbamylation of an active site lysine, stabilized by a divalent cation, which then catalyzes the proton abstraction from the substrate ribulose 1,5 bisphosphate (RuBP) and leads to the formation of two molecules of 3-phosphoglycerate. Members of the Rubisco family can be divided into 4 subgroups, Form I-IV , which differ in their taxonomic distribution and subunit composition. Form I is the most abundant class, present in plants, algae, and bacteria, and forms large complexes composed of 8 large and 8 small subunits.


Pssm-ID: 173977  Cd Length: 450  Bit Score: 394.48  E-value: 1.46e-138
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234190668  14 TYYTPDYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYHIEPVAGEESQFIAYVA 93
Cdd:cd08212     1 GYWTPDYQPKDTDILAAFRITPQPGVDPEEAAAAVAGESSTATWTVVWTDRLTALDRYKGKAYRVEPVPGEENQYFAYIA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234190668  94 YPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPTSYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSA 173
Cdd:cd08212    81 YPLDLFEEGSVANLTTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGIQVERDRLNKYGRPLLGCTIKPKLGLSA 160

                         170       180
                  ....*....|....*....|....*.
gi 2234190668 174 KNYGRAVYECLRGGLDFTKDDENVNS 199
Cdd:cd08212   161 KNYGRVVYECLRGGLDFTKDDENINS 186
RbcL COG1850
Ribulose 1,5-bisphosphate carboxylase, large subunit, or a RuBisCO-like protein [Carbohydrate ...
 15-199 7.65e-78

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


Pssm-ID: 441455  Cd Length: 417  Bit Score: 238.53  E-value: 7.65e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234190668  15 YYTPDYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYHIEPV---AGEESQFIAY 91
Cdd:COG1850     2 YVDPDYIPDDDDILATYRITPETGVDPEEAAAAIAGEQSTGTWTEVPTETDELRERLAARVYSIEELpevGGGYRRALVT 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234190668  92 VAYPLDLFEeGSVTNMFTSIVGNVFGFKALRALRLEDLRIPTSYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGL 171
Cdd:COG1850    82 IAYPLENFG-GNLPNLLSTVAGNLFGLKAVSGLRLLDLEFPESFLAAFPGPKFGIEGTRELLGVYDRPLLGTIIKPKVGL 160

                         170       180
                  ....*....|....*....|....*...
gi 2234190668 172 SAKNYGRAVYECLRGGLDFTKDDENVNS 199
Cdd:COG1850   161 SPEETAELVYELALGGVDFIKDDENLAD 188
RuBisCO_large_N pfam02788
Ribulose bisphosphate carboxylase large chain, N-terminal domain; The N-terminal domain of ...
 14-135 2.32e-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: 168.93  E-value: 2.32e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234190668  14 TYYTPDYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYHIEPVAGEesQFIAYVA 93
Cdd:pfam02788   1 DYVDLDYEPKDTDLLCAFRIEPAAGVSPEEAAAHVAAESSTGTWTEVWTLDDTFTKKLKAKVYEIDEVPGG--SYIVKIA 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 2234190668  94 YPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPTSY 135
Cdd:pfam02788  79 YPLDLFEEGSIPQLLSSIAGNIFGMKAVKALRLEDIRFPPAY 120
rubisco_III TIGR03326
ribulose bisphosphate carboxylase, type III; Members of this protein family are the archaeal, ...
 15-199 5.11e-49

ribulose bisphosphate carboxylase, type III; Members of this protein family are the archaeal, single chain, type III form of ribulose bisphosphate carboxylase, or RuBisCO. Members act is a three-step pathway for conversion of the sugar moiety of AMP to two molecules of 3-phosphoglycerate. Many of these species use ADP-dependent sugar kinases, which form AMP, for glycolysis. [Energy metabolism, Sugars]


Pssm-ID: 188307  Cd Length: 411  Bit Score: 164.17  E-value: 5.11e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234190668  15 YYTPDYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTdgLTSLDRYKG---RCYHIEPVaGEESqfIAY 91
Cdd:TIGR03326   2 FVDLNYEPSDDDLVCTFRITPAEGVSIEDAAGRVASESSIGTWTTLQP--WKDPERYKDlsaKVYDIEEH-GDGS--IVR 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234190668  92 VAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPTSYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGL 171
Cdd:TIGR03326  77 IAYPLGLFEEGNLPQLLSCIAGNIFGMKAVKGLRLLDFEFPAEFLRAFKGPQFGIEGVREILGIKDRPITATVPKPKVGL 156

                         170       180
                  ....*....|....*....|....*...
gi 2234190668 172 SAKNYGRAVYECLRGGLDFTKDDENVNS 199
Cdd:TIGR03326 157 STEEHAKVAYELWSGGVDLLKDDENLTS 184
 
Name Accession Description Interval E-value
rbcL CHL00040
ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
 1-199 3.64e-159

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


Pssm-ID: 176981  Cd Length: 475  Bit Score: 447.61  E-value: 3.64e-159
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234190668   1 SVGFKAGVKDYKLTYYTPDYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYHIEP 80
Cdd:CHL00040   10 SVGFKAGVKDYKLTYYTPDYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYRIEP 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234190668  81 VAGEESQFIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPTSYVKTFQGPPHGIQVERDKLNKYGRPL 160
Cdd:CHL00040   90 VPGEENQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYLKTFQGPPHGIQVERDKLNKYGRPL 169

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 2234190668 161 LGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNS 199
Cdd:CHL00040  170 LGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNS 208
RuBisCO_large_I cd08212
Ribulose bisphosphate carboxylase large chain, Form I; Ribulose bisphosphate carboxylase ...
 14-199 1.46e-138

Ribulose bisphosphate carboxylase large chain, Form I; Ribulose bisphosphate carboxylase (Rubisco) plays an important role in the Calvin reductive pentose phosphate pathway. It catalyzes the primary CO2 fixation step. Rubisco is activated by carbamylation of an active site lysine, stabilized by a divalent cation, which then catalyzes the proton abstraction from the substrate ribulose 1,5 bisphosphate (RuBP) and leads to the formation of two molecules of 3-phosphoglycerate. Members of the Rubisco family can be divided into 4 subgroups, Form I-IV , which differ in their taxonomic distribution and subunit composition. Form I is the most abundant class, present in plants, algae, and bacteria, and forms large complexes composed of 8 large and 8 small subunits.


Pssm-ID: 173977  Cd Length: 450  Bit Score: 394.48  E-value: 1.46e-138
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234190668  14 TYYTPDYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYHIEPVAGEESQFIAYVA 93
Cdd:cd08212     1 GYWTPDYQPKDTDILAAFRITPQPGVDPEEAAAAVAGESSTATWTVVWTDRLTALDRYKGKAYRVEPVPGEENQYFAYIA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234190668  94 YPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPTSYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSA 173
Cdd:cd08212    81 YPLDLFEEGSVANLTTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGIQVERDRLNKYGRPLLGCTIKPKLGLSA 160

                         170       180
                  ....*....|....*....|....*.
gi 2234190668 174 KNYGRAVYECLRGGLDFTKDDENVNS 199
Cdd:cd08212   161 KNYGRVVYECLRGGLDFTKDDENINS 186
rbcL PRK04208
ribulose bisophosphate carboxylase; Reviewed
 3-199 8.21e-133

ribulose bisophosphate carboxylase; Reviewed


Pssm-ID: 179787  Cd Length: 468  Bit Score: 380.41  E-value: 8.21e-133
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234190668   3 GFKAGVKDYKLTYYTPDYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYHIEPVA 82
Cdd:PRK04208    5 RYDAGVKEYRQMYWDPDYTPKDTDLLACFRITPQEGVDPEEAAAAVAAESSTGTWTTVWTDLLTDLDKYKAKAYRIEDVP 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234190668  83 GEESQFIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPTSYVKTFQGPPHGIQVERDKLNKYGRPLLG 162
Cdd:PRK04208   85 GDDGSYYAFIAYPLDLFEEGSIPNLLASIAGNVFGFKAVKALRLEDIRFPVAYVKTFKGPPFGIQVERERLDKYGRPLLG 164

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 2234190668 163 CTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNS 199
Cdd:PRK04208  165 TTPKPKLGLSAKNYGRVVYEALRGGLDFTKDDENLNS 201
RuBisCO_large_I_II_III cd08206
Ribulose bisphosphate carboxylase large chain, Form I,II,III; Ribulose bisphosphate ...
 25-199 1.30e-107

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: 314.56  E-value: 1.30e-107
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234190668  25 TDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYHIEPVAgeESQFIAYVAYPLDLFEEGSV 104
Cdd:cd08206     1 TDLLAAFRMTPAEGVDPEEAAAAVAAESSTGTWTTVWTDRLTATERLKAKVYRIDPVP--DGQYIAKIAYPLDLFEEGSV 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234190668 105 TNMFTSIVGNVFGFKALRALRLEDLRIPTSYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECL 184
Cdd:cd08206    79 PNLLTSIIGNVFGMKAVKALRLEDFRFPPAYLKTFDGPSFGIQGEREILGKYGRPLLGTIVKPKLGLSPKEYARVVYEAL 158

                         170
                  ....*....|....*
gi 2234190668 185 RGGLDFTKDDENVNS 199
Cdd:cd08206   159 RGGLDFVKDDENQNS 173
RbcL COG1850
Ribulose 1,5-bisphosphate carboxylase, large subunit, or a RuBisCO-like protein [Carbohydrate ...
 15-199 7.65e-78

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


Pssm-ID: 441455  Cd Length: 417  Bit Score: 238.53  E-value: 7.65e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234190668  15 YYTPDYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYHIEPV---AGEESQFIAY 91
Cdd:COG1850     2 YVDPDYIPDDDDILATYRITPETGVDPEEAAAAIAGEQSTGTWTEVPTETDELRERLAARVYSIEELpevGGGYRRALVT 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234190668  92 VAYPLDLFEeGSVTNMFTSIVGNVFGFKALRALRLEDLRIPTSYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGL 171
Cdd:COG1850    82 IAYPLENFG-GNLPNLLSTVAGNLFGLKAVSGLRLLDLEFPESFLAAFPGPKFGIEGTRELLGVYDRPLLGTIIKPKVGL 160

                         170       180
                  ....*....|....*....|....*...
gi 2234190668 172 SAKNYGRAVYECLRGGLDFTKDDENVNS 199
Cdd:COG1850   161 SPEETAELVYELALGGVDFIKDDENLAD 188
RuBisCO_large cd08148
Ribulose bisphosphate carboxylase large chain; Ribulose bisphosphate carboxylase (Rubisco) ...
 27-199 2.36e-77

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: 235.78  E-value: 2.36e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234190668  27 ILAAFRVTPQPgVPPEEAGAAVAAESSTGTWTTVWTdGLTSLDRYKGRCYHIEPVAgeeSQFIAYVAYPLDLFEEGSVTN 106
Cdd:cd08148     1 VLATYRVHPEA-TPPEKAAEAIAAESSTGTWTEVPT-TQEQLRRVKGRVYSVEELG---KRYIVKIAYPVELFEPGNIPQ 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234190668 107 MFTSIVGNVFGFKALRALRLEDLRIPTSYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRG 186
Cdd:cd08148    76 ILTVTAGNLFGLGALEAVRLEDLEFPEEYKKLFPGPKFGIDGIRKLLGVYGRPLVGTIIKPKLGLNPKYTAEAAYAAALG 155

                         170
                  ....*....|...
gi 2234190668 187 GLDFTKDDENVNS 199
Cdd:cd08148   156 GLDLIKDDETLTD 168
RuBisCO_large_III cd08213
Ribulose bisphosphate carboxylase large chain, Form III; Ribulose bisphosphate carboxylase ...
 25-199 5.15e-60

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: 192.60  E-value: 5.15e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234190668  25 TDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYHIEPVAGeesQFIAYVAYPLDLFEEGSV 104
Cdd:cd08213     1 DDLIAVFRIEPAEGISIEEAAGRVASESSIGTWTTLATLYPERAEKLKAKAYYFDGLGG---SYIVKVAYPLELFEEGNM 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234190668 105 TNMFTSIVGNVFGFKALRALRLEDLRIPTSYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECL 184
Cdd:cd08213    78 PQLLSSIAGNIFGMKAVKNLRLEDIYFPESYLREFKGPQFGIEGVREILGIKDRPLLGTVPKPKVGLSPEEHAEVAYEAL 157

                         170
                  ....*....|....*
gi 2234190668 185 RGGLDFTKDDENVNS 199
Cdd:cd08213   158 VGGVDLVKDDENLTS 172
RuBisCO_large_N pfam02788
Ribulose bisphosphate carboxylase large chain, N-terminal domain; The N-terminal domain of ...
 14-135 2.32e-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: 168.93  E-value: 2.32e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234190668  14 TYYTPDYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYHIEPVAGEesQFIAYVA 93
Cdd:pfam02788   1 DYVDLDYEPKDTDLLCAFRIEPAAGVSPEEAAAHVAAESSTGTWTEVWTLDDTFTKKLKAKVYEIDEVPGG--SYIVKIA 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 2234190668  94 YPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPTSY 135
Cdd:pfam02788  79 YPLDLFEEGSIPQLLSSIAGNIFGMKAVKALRLEDIRFPPAY 120
rubisco_III TIGR03326
ribulose bisphosphate carboxylase, type III; Members of this protein family are the archaeal, ...
 15-199 5.11e-49

ribulose bisphosphate carboxylase, type III; Members of this protein family are the archaeal, single chain, type III form of ribulose bisphosphate carboxylase, or RuBisCO. Members act is a three-step pathway for conversion of the sugar moiety of AMP to two molecules of 3-phosphoglycerate. Many of these species use ADP-dependent sugar kinases, which form AMP, for glycolysis. [Energy metabolism, Sugars]


Pssm-ID: 188307  Cd Length: 411  Bit Score: 164.17  E-value: 5.11e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234190668  15 YYTPDYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTdgLTSLDRYKG---RCYHIEPVaGEESqfIAY 91
Cdd:TIGR03326   2 FVDLNYEPSDDDLVCTFRITPAEGVSIEDAAGRVASESSIGTWTTLQP--WKDPERYKDlsaKVYDIEEH-GDGS--IVR 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234190668  92 VAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPTSYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGL 171
Cdd:TIGR03326  77 IAYPLGLFEEGNLPQLLSCIAGNIFGMKAVKGLRLLDFEFPAEFLRAFKGPQFGIEGVREILGIKDRPITATVPKPKVGL 156

                         170       180
                  ....*....|....*....|....*...
gi 2234190668 172 SAKNYGRAVYECLRGGLDFTKDDENVNS 199
Cdd:TIGR03326 157 STEEHAKVAYELWSGGVDLLKDDENLTS 184
RuBisCO_IV_RLP cd08205
Ribulose bisphosphate carboxylase like proteins, Rubisco-Form IV; Ribulose bisphosphate ...
 53-195 9.13e-33

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: 120.33  E-value: 9.13e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234190668  53 STGTWTTVWTDGLTSLDRYKGRCYHIEPV---AGEESQFIAYVAYPLDLFEeGSVTNMFTSIVGNVFGfkaLRALRLEDL 129
Cdd:cd08205    26 TVGTWTELPGETEEIRERHVGRVESIEELeesEGKYGRARVTISYPLDNFG-GDLPQLLNTLFGNLSL---LPGIKLVDL 101

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2234190668 130 RIPTSYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDE 195
Cdd:cd08205   102 ELPDSLLAAFPGPRFGIEGLRRLLGVHDRPLLGTIIKPSIGLSPEELAELAYELALGGIDLIKDDE 167
RuBisCO_large pfam00016
Ribulose bisphosphate carboxylase large chain, catalytic domain; The C-terminal domain of ...
 146-199 8.25e-31

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: 114.00  E-value: 8.25e-31
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2234190668 146 IQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNS 199
Cdd:pfam00016   1 IAVERRVLNKYGRPILGTIIKPKLGLSPKNYARAVYEFLLGGLDFIKDDENINS 54
RLP_NonPhot cd08207
Ribulose bisphosphate carboxylase like proteins from nonphototrophic bacteria; Ribulose ...
 53-195 5.88e-27

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: 105.47  E-value: 5.88e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234190668  53 STGTWTTV--WTDGLTslDRYKGRCYHIEPVAGEESQFIAY-------------VAYPLDLFeeG-SVTNMFTSIVGNVF 116
Cdd:cd08207    26 SSGTFIALpgETDELK--ERSAARVESIEELETAAQPSLPRrasggpytrarvtISFPLDNI--GtSLPNLLATVAGNLF 101

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2234190668 117 GFKALRALRLEDLRIPTSYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDE 195
Cdd:cd08207   102 ELRELSGLRLVDLGLPDEFAAAFPGPAFGIAGTRRLTGVEDRPLIGTIIKPSVGLTPEETAALVRQLAAAGIDFIKDDE 180
PRK13475 PRK13475
ribulose-bisphosphate carboxylase;
27-195 4.19e-22

ribulose-bisphosphate carboxylase;


Pssm-ID: 184072  Cd Length: 443  Bit Score: 92.48  E-value: 4.19e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234190668  27 ILAAFRVTPQPGVPPEEAGAAVAAESSTGT-----WTTVWTDGLTSLdrykgrCYHIEPVAGeesqfIAYVAYPLDLFE- 100
Cdd:PRK13475   24 ILCAYKMKPKAGHGYLEAAAHFAAESSTGTnvevsTTDDFTRGVDAL------VYEIDEARE-----LMKIAYPVELFDr 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234190668 101 -----EGSVTNMFTSIVGNVFGFKALRALRLEDLRIPTSYVKTFQGPPHGIqverDKLNKY-GRP------LLGCTIKPK 168
Cdd:PRK13475   93 niidgRAMIVSFLTLTIGNNQGMGDVEYAKMHDFYVPPRYLELFDGPSTDI----SDLWRVlGRPvkdggyIAGTIIKPK 168

                         170       180
                  ....*....|....*....|....*..
gi 2234190668 169 LGLSAKNYGRAVYECLRGGlDFTKDDE 195
Cdd:PRK13475  169 LGLRPEPFAEACYDFWLGG-DFIKNDE 194
RLP_DK-MTP-1-P-enolase cd08209
2,3-diketo-5-methylthiopentyl-1-phosphate enolase; Ribulose bisphosphate carboxylase like ...
 55-195 6.12e-22

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: 91.61  E-value: 6.12e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234190668  55 GTWTTVWTDGLTSLDRYKGRCYHIEPvaGEESQFIAYVAYPLdlfeeGSVTNMFTSIVGNVFGFKALR-ALRLEDLRIPT 133
Cdd:cd08209    27 GSWTDLPALRQAQLQKHLGEVVSVEE--LEEGRGVITIAYPL-----INVSGDIPALLTTIFGKLSLDgKIKLVDLRLPE 99

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2234190668 134 SYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDE 195
Cdd:cd08209   100 EFGRAFPGPKFGIEGIRQRLGVHDRPLLMSIFKGVLGLDLDDLAEQLREQALGGVDLIKDDE 161
RuBisCO_large_II cd08211
Ribulose bisphosphate carboxylase large chain, Form II; Ribulose bisphosphate carboxylase ...
 27-195 7.45e-21

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: 89.10  E-value: 7.45e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234190668  27 ILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTV-WTDGLT-SLDrykGRCYHIEpvagEESQfIAYVAYPLDLFE---- 100
Cdd:cd08211    23 VLVAYIMKPKAGYGYLATAAHFAAESSTGTNVEVsTTDDFTrGVD---ALVYEID----EARE-LMKIAYPVELFDrnlt 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234190668 101 --EGSVTNMFTSIVGNVFGFKALRALRLEDLRIPTSYVKTFQGPPHGIQVERDKLNKY---GRPLLGCTIKPKLGLSAKN 175
Cdd:cd08211    95 dgRAMVASFLTLIIGNNQGMGDVEYLKMHDFYVPESMLELFDGPSVNISDMWKVLGRPevdGGYIAGTIIKPKLGLRPKP 174

                         170       180
                  ....*....|....*....|
gi 2234190668 176 YGRAVYECLRGGlDFTKDDE 195
Cdd:cd08211   175 FAEACYAFWLGG-DFIKNDE 193
RLP_Photo cd08208
Ribulose bisphosphate carboxylase like proteins from phototrophic bacteria; Ribulose ...
 104-195 7.85e-16

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: 74.55  E-value: 7.85e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234190668 104 VTNMFTSIVGN-VFGFKALRALRLEDLRIPTSYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYE 182
Cdd:cd08208   105 IPNLLSAVCGEgTFFSPGVPVVKLMDIHFPETYLADFEGPKFGIAGLRERLQAHDRPIFFGVIKPNIGLPPGEFAELGYQ 184

                          90
                  ....*....|...
gi 2234190668 183 CLRGGLDFTKDDE 195
Cdd:cd08208   185 SWLGGLDIAKDDE 197
RLP_RrRLP cd08210
Ribulose bisphosphate carboxylase like proteins (RLPs) similar to R.rubrum RLP; RLP from ...
 68-194 1.05e-14

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: 71.12  E-value: 1.05e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234190668  68 LDRYKGRCYHIEPVagEESQFIAYVAYPLDlfeegSVTNMFTSIVGNVFGFKAL-RALRLEDLRIPTSYVKTFQGPPHGI 146
Cdd:cd08210    42 RDNIVGRVESLEPA--GEGSYRARISYSVD-----TAGGELTQLLNVLFGNSSLqPGIRLVDFELPPSLLRRFPGPRFGI 114

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 2234190668 147 QVERDKLNKYGRPLLGCTIKPkLGLSAKNYGRAVYECLRGGLDFTKDD 194
Cdd:cd08210   115 AGLRALLGIPERPLLCSALKP-QGLSAAELAELAYAFALGGIDIIKDD 161
mtnW PRK09549
2,3-diketo-5-methylthiopentyl-1-phosphate enolase; Reviewed
 55-195 2.74e-14

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


Pssm-ID: 236560  Cd Length: 407  Bit Score: 70.04  E-value: 2.74e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234190668  55 GTWTTVWTDGLTSLDRYKGRCYHIEPVAGEES----QFIAYVAYPldlfeEGSVTNMFTSIVGNVFGFKALRA-LRLEDL 129
Cdd:PRK09549   31 GSWTDLPHLEQEQLKKHKGNVVHVEELEEHERkgvkRGIIKIAYP-----LANFSPDLPAILTTTFGKLSLDGeVKLIDL 105

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2234190668 130 RIPTSYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDE 195
Cdd:PRK09549  106 TFSDELKRHFPGPKFGIDGIRNLLGVHDRPLLMSIFKGVIGRDLDYLKEQLRDQALGGVDLVKDDE 171
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

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