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Conserved domains on  [gi|404244250|emb|CCJ32473|]
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ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit, partial [Vincetoxicum hirundinaria]

Protein Classification

RuBisCO large subunit( domain architecture ID 315)

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RuBisCO_large super family cl08232
Ribulose bisphosphate carboxylase large chain; Ribulose bisphosphate carboxylase (Rubisco) ...
 1-193 2.42e-155

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: 437.60  E-value: 2.42e-155
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404244250   1 YTPEYKTKDTDISAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYHIEPVPGEEDQFIGYVAYP 80
Cdd:CHL00040  25 YTPDYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYRIEPVPGEENQYIAYVAYP 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404244250  81 LDLFEEGSVTNMLTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGILVERDKLNKYGRPLLGCTIKPKLGLSAKN 160
Cdd:CHL00040 105 LDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYLKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKN 184

                        170       180       190
                 ....*....|....*....|....*....|...
gi 404244250 161 YGRAVYECLRGGLDFTKDDEKVNSQPFMRWRDR 193
Cdd:CHL00040 185 YGRAVYECLRGGLDFTKDDENVNSQPFMRWRDR 217
 
Name Accession Description Interval E-value
rbcL CHL00040
ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
 1-193 2.42e-155

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


Pssm-ID: 176981  Cd Length: 475  Bit Score: 437.60  E-value: 2.42e-155
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404244250   1 YTPEYKTKDTDISAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYHIEPVPGEEDQFIGYVAYP 80
Cdd:CHL00040  25 YTPDYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYRIEPVPGEENQYIAYVAYP 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404244250  81 LDLFEEGSVTNMLTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGILVERDKLNKYGRPLLGCTIKPKLGLSAKN 160
Cdd:CHL00040 105 LDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYLKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKN 184

                        170       180       190
                 ....*....|....*....|....*....|...
gi 404244250 161 YGRAVYECLRGGLDFTKDDEKVNSQPFMRWRDR 193
Cdd:CHL00040 185 YGRAVYECLRGGLDFTKDDENVNSQPFMRWRDR 217
RuBisCO_large_I cd08212
Ribulose bisphosphate carboxylase large chain, Form I; Ribulose bisphosphate carboxylase ...
 1-193 5.80e-145

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: 410.28  E-value: 5.80e-145
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404244250   1 YTPEYKTKDTDISAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYHIEPVPGEEDQFIGYVAYP 80
Cdd:cd08212    3 WTPDYQPKDTDILAAFRITPQPGVDPEEAAAAVAGESSTATWTVVWTDRLTALDRYKGKAYRVEPVPGEENQYFAYIAYP 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404244250  81 LDLFEEGSVTNMLTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGILVERDKLNKYGRPLLGCTIKPKLGLSAKN 160
Cdd:cd08212   83 LDLFEEGSVANLTTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGIQVERDRLNKYGRPLLGCTIKPKLGLSAKN 162

                        170       180       190
                 ....*....|....*....|....*....|...
gi 404244250 161 YGRAVYECLRGGLDFTKDDEKVNSQPFMRWRDR 193
Cdd:cd08212  163 YGRVVYECLRGGLDFTKDDENINSQPFMRWRDR 195
RbcL COG1850
Ribulose 1,5-bisphosphate carboxylase, large subunit, or a RuBisCO-like protein [Carbohydrate ...
 3-193 3.00e-81

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


Pssm-ID: 441455  Cd Length: 417  Bit Score: 247.00  E-value: 3.00e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404244250   3 PEYKTKDTDISAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYHIEPVP---GEEDQFIGYVAY 79
Cdd:COG1850    5 PDYIPDDDDILATYRITPETGVDPEEAAAAIAGEQSTGTWTEVPTETDELRERLAARVYSIEELPevgGGYRRALVTIAY 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404244250  80 PLDLFEeGSVTNMLTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGILVERDKLNKYGRPLLGCTIKPKLGLSAK 159
Cdd:COG1850   85 PLENFG-GNLPNLLSTVAGNLFGLKAVSGLRLLDLEFPESFLAAFPGPKFGIEGTRELLGVYDRPLLGTIIKPKVGLSPE 163

                        170       180       190
                 ....*....|....*....|....*....|....
gi 404244250 160 NYGRAVYECLRGGLDFTKDDEKVNSQPFMRWRDR 193
Cdd:COG1850  164 ETAELVYELALGGVDFIKDDENLADQPFCPFEDR 197
RuBisCO_large_N pfam02788
Ribulose bisphosphate carboxylase large chain, N-terminal domain; The N-terminal domain of ...
 3-120 4.96e-53

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: 165.46  E-value: 4.96e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404244250    3 PEYKTKDTDISAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYHIEPVPGeeDQFIGYVAYPLD 82
Cdd:pfam02788   5 LDYEPKDTDLLCAFRIEPAAGVSPEEAAAHVAAESSTGTWTEVWTLDDTFTKKLKAKVYEIDEVPG--GSYIVKIAYPLD 82

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 404244250   83 LFEEGSVTNMLTSIVGNVFGFKALRALRLEDLRIPPAY 120
Cdd:pfam02788  83 LFEEGSIPQLLSSIAGNIFGMKAVKALRLEDIRFPPAY 120
 
Name Accession Description Interval E-value
rbcL CHL00040
ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
 1-193 2.42e-155

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


Pssm-ID: 176981  Cd Length: 475  Bit Score: 437.60  E-value: 2.42e-155
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404244250   1 YTPEYKTKDTDISAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYHIEPVPGEEDQFIGYVAYP 80
Cdd:CHL00040  25 YTPDYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYRIEPVPGEENQYIAYVAYP 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404244250  81 LDLFEEGSVTNMLTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGILVERDKLNKYGRPLLGCTIKPKLGLSAKN 160
Cdd:CHL00040 105 LDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYLKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKN 184

                        170       180       190
                 ....*....|....*....|....*....|...
gi 404244250 161 YGRAVYECLRGGLDFTKDDEKVNSQPFMRWRDR 193
Cdd:CHL00040 185 YGRAVYECLRGGLDFTKDDENVNSQPFMRWRDR 217
RuBisCO_large_I cd08212
Ribulose bisphosphate carboxylase large chain, Form I; Ribulose bisphosphate carboxylase ...
 1-193 5.80e-145

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: 410.28  E-value: 5.80e-145
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404244250   1 YTPEYKTKDTDISAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYHIEPVPGEEDQFIGYVAYP 80
Cdd:cd08212    3 WTPDYQPKDTDILAAFRITPQPGVDPEEAAAAVAGESSTATWTVVWTDRLTALDRYKGKAYRVEPVPGEENQYFAYIAYP 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404244250  81 LDLFEEGSVTNMLTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGILVERDKLNKYGRPLLGCTIKPKLGLSAKN 160
Cdd:cd08212   83 LDLFEEGSVANLTTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGIQVERDRLNKYGRPLLGCTIKPKLGLSAKN 162

                        170       180       190
                 ....*....|....*....|....*....|...
gi 404244250 161 YGRAVYECLRGGLDFTKDDEKVNSQPFMRWRDR 193
Cdd:cd08212  163 YGRVVYECLRGGLDFTKDDENINSQPFMRWRDR 195
rbcL PRK04208
ribulose bisophosphate carboxylase; Reviewed
 1-193 5.45e-131

ribulose bisophosphate carboxylase; Reviewed


Pssm-ID: 179787  Cd Length: 468  Bit Score: 375.40  E-value: 5.45e-131
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404244250   1 YTPEYKTKDTDISAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYHIEPVPGEEDQFIGYVAYP 80
Cdd:PRK04208  18 WDPDYTPKDTDLLACFRITPQEGVDPEEAAAAVAAESSTGTWTTVWTDLLTDLDKYKAKAYRIEDVPGDDGSYYAFIAYP 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404244250  81 LDLFEEGSVTNMLTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGILVERDKLNKYGRPLLGCTIKPKLGLSAKN 160
Cdd:PRK04208  98 LDLFEEGSIPNLLASIAGNVFGFKAVKALRLEDIRFPVAYVKTFKGPPFGIQVERERLDKYGRPLLGTTPKPKLGLSAKN 177

                        170       180       190
                 ....*....|....*....|....*....|...
gi 404244250 161 YGRAVYECLRGGLDFTKDDEKVNSQPFMRWRDR 193
Cdd:PRK04208 178 YGRVVYEALRGGLDFTKDDENLNSQPFNRWRDR 210
RuBisCO_large_I_II_III cd08206
Ribulose bisphosphate carboxylase large chain, Form I,II,III; Ribulose bisphosphate ...
 10-193 2.60e-114

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: 331.12  E-value: 2.60e-114
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404244250  10 TDISAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYHIEPVPgeEDQFIGYVAYPLDLFEEGSV 89
Cdd:cd08206    1 TDLLAAFRMTPAEGVDPEEAAAAVAAESSTGTWTTVWTDRLTATERLKAKVYRIDPVP--DGQYIAKIAYPLDLFEEGSV 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404244250  90 TNMLTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGILVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECL 169
Cdd:cd08206   79 PNLLTSIIGNVFGMKAVKALRLEDFRFPPAYLKTFDGPSFGIQGEREILGKYGRPLLGTIVKPKLGLSPKEYARVVYEAL 158

                        170       180
                 ....*....|....*....|....
gi 404244250 170 RGGLDFTKDDEKVNSQPFMRWRDR 193
Cdd:cd08206  159 RGGLDFVKDDENQNSQPFMRFEDR 182
RuBisCO_large cd08148
Ribulose bisphosphate carboxylase large chain; Ribulose bisphosphate carboxylase (Rubisco) ...
 12-193 4.77e-83

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: 250.04  E-value: 4.77e-83
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404244250  12 ISAAFRVTPQPgVPPEEAGAAVAAESSTGTWTTVWTdGLTSLDRYKGRCYHIEPVPgeeDQFIGYVAYPLDLFEEGSVTN 91
Cdd:cd08148    1 VLATYRVHPEA-TPPEKAAEAIAAESSTGTWTEVPT-TQEQLRRVKGRVYSVEELG---KRYIVKIAYPVELFEPGNIPQ 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404244250  92 MLTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGILVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRG 171
Cdd:cd08148   76 ILTVTAGNLFGLGALEAVRLEDLEFPEEYKKLFPGPKFGIDGIRKLLGVYGRPLVGTIIKPKLGLNPKYTAEAAYAAALG 155

                        170       180
                 ....*....|....*....|..
gi 404244250 172 GLDFTKDDEKVNSQPFMRWRDR 193
Cdd:cd08148  156 GLDLIKDDETLTDQPFCPLRDR 177
RbcL COG1850
Ribulose 1,5-bisphosphate carboxylase, large subunit, or a RuBisCO-like protein [Carbohydrate ...
 3-193 3.00e-81

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


Pssm-ID: 441455  Cd Length: 417  Bit Score: 247.00  E-value: 3.00e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404244250   3 PEYKTKDTDISAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYHIEPVP---GEEDQFIGYVAY 79
Cdd:COG1850    5 PDYIPDDDDILATYRITPETGVDPEEAAAAIAGEQSTGTWTEVPTETDELRERLAARVYSIEELPevgGGYRRALVTIAY 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404244250  80 PLDLFEeGSVTNMLTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGILVERDKLNKYGRPLLGCTIKPKLGLSAK 159
Cdd:COG1850   85 PLENFG-GNLPNLLSTVAGNLFGLKAVSGLRLLDLEFPESFLAAFPGPKFGIEGTRELLGVYDRPLLGTIIKPKVGLSPE 163

                        170       180       190
                 ....*....|....*....|....*....|....
gi 404244250 160 NYGRAVYECLRGGLDFTKDDEKVNSQPFMRWRDR 193
Cdd:COG1850  164 ETAELVYELALGGVDFIKDDENLADQPFCPFEDR 197
RuBisCO_large_III cd08213
Ribulose bisphosphate carboxylase large chain, Form III; Ribulose bisphosphate carboxylase ...
 10-193 1.94e-61

Ribulose bisphosphate carboxylase large chain, Form III; Ribulose bisphosphate carboxylase (Rubisco) plays an important role in the Calvin reductive pentose phosphate pathway. It catalyzes the primary CO2 fixation step. Rubisco is activated by carbamylation of an active site lysine, stabilized by a divalent cation, which then catalyzes the proton abstraction from the substrate ribulose 1,5 bisphosphate (RuBP) and leads to the formation of two molecules of 3-phosphoglycerate. Members of the Rubisco family can be divided into 4 subgroups, Form I-IV , which differ in their taxonomic distribution and subunit composition. Form III is only found in archaea and forms large subunit oligomers (dimers or decamers) that do not include small subunits.


Pssm-ID: 173978  Cd Length: 412  Bit Score: 196.07  E-value: 1.94e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404244250  10 TDISAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYHIEpvpGEEDQFIGYVAYPLDLFEEGSV 89
Cdd:cd08213    1 DDLIAVFRIEPAEGISIEEAAGRVASESSIGTWTTLATLYPERAEKLKAKAYYFD---GLGGSYIVKVAYPLELFEEGNM 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404244250  90 TNMLTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGILVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECL 169
Cdd:cd08213   78 PQLLSSIAGNIFGMKAVKNLRLEDIYFPESYLREFKGPQFGIEGVREILGIKDRPLLGTVPKPKVGLSPEEHAEVAYEAL 157

                        170       180
                 ....*....|....*....|....
gi 404244250 170 RGGLDFTKDDEKVNSQPFMRWRDR 193
Cdd:cd08213  158 VGGVDLVKDDENLTSQPFNRFEER 181
RuBisCO_large_N pfam02788
Ribulose bisphosphate carboxylase large chain, N-terminal domain; The N-terminal domain of ...
 3-120 4.96e-53

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: 165.46  E-value: 4.96e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404244250    3 PEYKTKDTDISAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYHIEPVPGeeDQFIGYVAYPLD 82
Cdd:pfam02788   5 LDYEPKDTDLLCAFRIEPAAGVSPEEAAAHVAAESSTGTWTEVWTLDDTFTKKLKAKVYEIDEVPG--GSYIVKIAYPLD 82

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 404244250   83 LFEEGSVTNMLTSIVGNVFGFKALRALRLEDLRIPPAY 120
Cdd:pfam02788  83 LFEEGSIPQLLSSIAGNIFGMKAVKALRLEDIRFPPAY 120
RuBisCO_large pfam00016
Ribulose bisphosphate carboxylase large chain, catalytic domain; The C-terminal domain of ...
 131-193 1.08e-38

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: 134.03  E-value: 1.08e-38
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 404244250  131 ILVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDEKVNSQPFMRWRDR 193
Cdd:pfam00016   1 IAVERRVLNKYGRPILGTIIKPKLGLSPKNYARAVYEFLLGGLDFIKDDENINSQPFMPWRDR 63
RuBisCO_IV_RLP cd08205
Ribulose bisphosphate carboxylase like proteins, Rubisco-Form IV; Ribulose bisphosphate ...
 38-193 2.25e-34

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: 124.57  E-value: 2.25e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404244250  38 STGTWTTVWTDGLTSLDRYKGRCYHIEPVP---GEEDQFIGYVAYPLDLFEeGSVTNMLTSIVGNVFGfkaLRALRLEDL 114
Cdd:cd08205   26 TVGTWTELPGETEEIRERHVGRVESIEELEeseGKYGRARVTISYPLDNFG-GDLPQLLNTLFGNLSL---LPGIKLVDL 101

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 404244250 115 RIPPAYVKTFQGPPHGILVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDEKVNSQPFMRWRDR 193
Cdd:cd08205  102 ELPDSLLAAFPGPRFGIEGLRRLLGVHDRPLLGTIIKPSIGLSPEELAELAYELALGGIDLIKDDELLADQPYAPFEER 180
RLP_NonPhot cd08207
Ribulose bisphosphate carboxylase like proteins from nonphototrophic bacteria; Ribulose ...
 38-193 1.73e-28

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: 109.32  E-value: 1.73e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404244250  38 STGTWTTV--WTDGLTslDRYKGRCYHIEPVPGEEDQFIGY-------------VAYPLDLFeeG-SVTNMLTSIVGNVF 101
Cdd:cd08207   26 SSGTFIALpgETDELK--ERSAARVESIEELETAAQPSLPRrasggpytrarvtISFPLDNI--GtSLPNLLATVAGNLF 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404244250 102 GFKALRALRLEDLRIPPAYVKTFQGPPHGILVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDEK 181
Cdd:cd08207  102 ELRELSGLRLVDLGLPDEFAAAFPGPAFGIAGTRRLTGVEDRPLIGTIIKPSVGLTPEETAALVRQLAAAGIDFIKDDEL 181

                        170
                 ....*....|..
gi 404244250 182 VNSQPFMRWRDR 193
Cdd:cd08207  182 LANPPYSPLDER 193
PRK13475 PRK13475
ribulose-bisphosphate carboxylase;
12-192 6.07e-24

ribulose-bisphosphate carboxylase;


Pssm-ID: 184072  Cd Length: 443  Bit Score: 97.49  E-value: 6.07e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404244250  12 ISAAFRVTPQPGVPPEEAGAAVAAESSTGT-----WTTVWTDGLTSLdrykgrCYHIEPVpgEEDQFIgyvAYPLDLFE- 85
Cdd:PRK13475  24 ILCAYKMKPKAGHGYLEAAAHFAAESSTGTnvevsTTDDFTRGVDAL------VYEIDEA--RELMKI---AYPVELFDr 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404244250  86 -----EGSVTNMLTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGIlverDKLNKY-GRP------LLGCTIKPK 153
Cdd:PRK13475  93 niidgRAMIVSFLTLTIGNNQGMGDVEYAKMHDFYVPPRYLELFDGPSTDI----SDLWRVlGRPvkdggyIAGTIIKPK 168

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 404244250 154 LGLSAKNYGRAVYECLRGGlDFTKDDEKVNSQPFMRWRD 192
Cdd:PRK13475 169 LGLRPEPFAEACYDFWLGG-DFIKNDEPQGNQVFAPLKK 206
RuBisCO_large_II cd08211
Ribulose bisphosphate carboxylase large chain, Form II; Ribulose bisphosphate carboxylase ...
 37-187 7.34e-23

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: 94.49  E-value: 7.34e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404244250  37 SSTGTWTTV-WTDGLT-SLDrykGRCYHIEpvpgEEDQFIgYVAYPLDLFE------EGSVTNMLTSIVGNVFGFKALRA 108
Cdd:cd08211   48 SSTGTNVEVsTTDDFTrGVD---ALVYEID----EARELM-KIAYPVELFDrnltdgRAMVASFLTLIIGNNQGMGDVEY 119

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404244250 109 LRLEDLRIPPAYVKTFQGPPHGILVERDKLNKY---GRPLLGCTIKPKLGLSAKNYGRAVYECLRGGlDFTKDDEKVNSQ 185
Cdd:cd08211  120 LKMHDFYVPESMLELFDGPSVNISDMWKVLGRPevdGGYIAGTIIKPKLGLRPKPFAEACYAFWLGG-DFIKNDEPQANQ 198


                 ..
gi 404244250 186 PF 187
Cdd:cd08211  199 PF 200
RLP_DK-MTP-1-P-enolase cd08209
2,3-diketo-5-methylthiopentyl-1-phosphate enolase; Ribulose bisphosphate carboxylase like ...
 40-180 3.23e-19

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: 83.91  E-value: 3.23e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404244250  40 GTWTTVWTDGLTSLDRYKGRCYHIEPvpGEEDQFIGYVAYPLdlfeeGSVTNMLTSIVGNVFGFKALR-ALRLEDLRIPP 118
Cdd:cd08209   27 GSWTDLPALRQAQLQKHLGEVVSVEE--LEEGRGVITIAYPL-----INVSGDIPALLTTIFGKLSLDgKIKLVDLRLPE 99

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 404244250 119 AYVKTFQGPPHGILVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDE 180
Cdd:cd08209  100 EFGRAFPGPKFGIEGIRQRLGVHDRPLLMSIFKGVLGLDLDDLAEQLREQALGGVDLIKDDE 161
RLP_RrRLP cd08210
Ribulose bisphosphate carboxylase like proteins (RLPs) similar to R.rubrum RLP; RLP from ...
 53-193 1.52e-17

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: 78.82  E-value: 1.52e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404244250  53 LDRYKGRCYHIEPVpgEEDQFIGYVAYPLDlfeegSVTNMLTSIVGNVFGFKAL-RALRLEDLRIPPAYVKTFQGPPHGI 131
Cdd:cd08210   42 RDNIVGRVESLEPA--GEGSYRARISYSVD-----TAGGELTQLLNVLFGNSSLqPGIRLVDFELPPSLLRRFPGPRFGI 114

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 404244250 132 LVERDKLNKYGRPLLGCTIKPkLGLSAKNYGRAVYECLRGGLDFTKDDEKVNSQPFMRWRDR 193
Cdd:cd08210  115 AGLRALLGIPERPLLCSALKP-QGLSAAELAELAYAFALGGIDIIKDDHGLADQPFAPFEER 175
RLP_Photo cd08208
Ribulose bisphosphate carboxylase like proteins from phototrophic bacteria; Ribulose ...
 38-180 1.94e-15

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: 73.39  E-value: 1.94e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404244250  38 STGTWTTVWTDGLTSLdRYKGRCYHIEPVPGEEDQFigyvaYPLDLFEEGSVT------------------NMLTSIVGN 99
Cdd:cd08208   42 STAQWRRVGVDEDFRP-RFAAKVIDLEVIEELEQLS-----YPVKHSETGPVHacrvtiahphgnfgpkipNLLSAVCGE 115

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404244250 100 -VFGFKALRALRLEDLRIPPAYVKTFQGPPHGILVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKD 178
Cdd:cd08208  116 gTFFSPGVPVVKLMDIHFPETYLADFEGPKFGIAGLRERLQAHDRPIFFGVIKPNIGLPPGEFAELGYQSWLGGLDIAKD 195


                 ..
gi 404244250 179 DE 180
Cdd:cd08208  196 DE 197
mtnW PRK09549
2,3-diketo-5-methylthiopentyl-1-phosphate enolase; Reviewed
 40-180 1.77e-13

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


Pssm-ID: 236560  Cd Length: 407  Bit Score: 67.73  E-value: 1.77e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404244250  40 GTWTTVWTDGLTSLDRYKGRCYHIEPVPGEEDQFIGY----VAYPldlfeEGSVTNMLTSIVGNVFGFKALRA-LRLEDL 114
Cdd:PRK09549  31 GSWTDLPHLEQEQLKKHKGNVVHVEELEEHERKGVKRgiikIAYP-----LANFSPDLPAILTTTFGKLSLDGeVKLIDL 105

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 404244250 115 RIPPAYVKTFQGPPHGILVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDE 180
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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