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Conserved domains on  [gi|1371471150|gb|AVR43676|]
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ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit, partial (chloroplast) [Ceramium gaditanum]

Protein Classification

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) ...
 1-124 8.64e-95

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: 280.44  E-value: 8.64e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1371471150   1 YKVDAVPNTSDQYFAYIAYDIDLFEEGSIANLTASIIGNVFGFKAVKALRLEDMRIPVAYLKTFQGPATGLVVERERMDK 80
Cdd:CHL00040   85 YRIEPVPGEENQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYLKTFQGPPHGIQVERDKLNK 164

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1371471150  81 FGRPFLGATVKPKLGLSGKNYGRVVYEGLRGGLDFLKDDENINS 124
Cdd:CHL00040  165 YGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNS 208
 
Name Accession Description Interval E-value
rbcL CHL00040
ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
 1-124 8.64e-95

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


Pssm-ID: 176981  Cd Length: 475  Bit Score: 280.44  E-value: 8.64e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1371471150   1 YKVDAVPNTSDQYFAYIAYDIDLFEEGSIANLTASIIGNVFGFKAVKALRLEDMRIPVAYLKTFQGPATGLVVERERMDK 80
Cdd:CHL00040   85 YRIEPVPGEENQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYLKTFQGPPHGIQVERDKLNK 164

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1371471150  81 FGRPFLGATVKPKLGLSGKNYGRVVYEGLRGGLDFLKDDENINS 124
Cdd:CHL00040  165 YGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNS 208
RuBisCO_large_I cd08212
Ribulose bisphosphate carboxylase large chain, Form I; Ribulose bisphosphate carboxylase ...
 1-124 6.06e-90

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: 267.37  E-value: 6.06e-90
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1371471150   1 YKVDAVPNTSDQYFAYIAYDIDLFEEGSIANLTASIIGNVFGFKAVKALRLEDMRIPVAYLKTFQGPATGLVVERERMDK 80
Cdd:cd08212    63 YRVEPVPGEENQYFAYIAYPLDLFEEGSVANLTTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGIQVERDRLNK 142

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1371471150  81 FGRPFLGATVKPKLGLSGKNYGRVVYEGLRGGLDFLKDDENINS 124
Cdd:cd08212   143 YGRPLLGCTIKPKLGLSAKNYGRVVYECLRGGLDFTKDDENINS 186
RbcL COG1850
Ribulose 1,5-bisphosphate carboxylase, large subunit, or a RuBisCO-like protein [Carbohydrate ...
 1-124 3.07e-53

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


Pssm-ID: 441455  Cd Length: 417  Bit Score: 171.89  E-value: 3.07e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1371471150   1 YKVDAVPNTSDQYFAYIAYDIDLFEeGSIANLTASIIGNVFGFKAVKALRLEDMRIPVAYLKTFQGPATGLVVERERMDK 80
Cdd:COG1850    66 EELPEVGGGYRRALVTIAYPLENFG-GNLPNLLSTVAGNLFGLKAVSGLRLLDLEFPESFLAAFPGPKFGIEGTRELLGV 144

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1371471150  81 FGRPFLGATVKPKLGLSGKNYGRVVYEGLRGGLDFLKDDENINS 124
Cdd:COG1850   145 YDRPLLGTIIKPKVGLSPEETAELVYELALGGVDFIKDDENLAD 188
rubisco_III TIGR03326
ribulose bisphosphate carboxylase, type III; Members of this protein family are the archaeal, ...
 11-124 1.01e-35

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: 126.04  E-value: 1.01e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1371471150  11 DQYFAYIAYDIDLFEEGSIANLTASIIGNVFGFKAVKALRLEDMRIPVAYLKTFQGPATGLVVERERMDKFGRPFLGATV 90
Cdd:TIGR03326  71 DGSIVRIAYPLGLFEEGNLPQLLSCIAGNIFGMKAVKGLRLLDFEFPAEFLRAFKGPQFGIEGVREILGIKDRPITATVP 150

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1371471150  91 KPKLGLSGKNYGRVVYEGLRGGLDFLKDDENINS 124
Cdd:TIGR03326 151 KPKVGLSTEEHAKVAYELWSGGVDLLKDDENLTS 184
RuBisCO_large_N pfam02788
Ribulose bisphosphate carboxylase large chain, N-terminal domain; The N-terminal domain of ...
 1-60 5.60e-28

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: 98.82  E-value: 5.60e-28
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1371471150   1 YKVDAVPNtsDQYFAYIAYDIDLFEEGSIANLTASIIGNVFGFKAVKALRLEDMRIPVAY 60
Cdd:pfam02788  63 YEIDEVPG--GSYIVKIAYPLDLFEEGSIPQLLSSIAGNIFGMKAVKALRLEDIRFPPAY 120
 
Name Accession Description Interval E-value
rbcL CHL00040
ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
 1-124 8.64e-95

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


Pssm-ID: 176981  Cd Length: 475  Bit Score: 280.44  E-value: 8.64e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1371471150   1 YKVDAVPNTSDQYFAYIAYDIDLFEEGSIANLTASIIGNVFGFKAVKALRLEDMRIPVAYLKTFQGPATGLVVERERMDK 80
Cdd:CHL00040   85 YRIEPVPGEENQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYLKTFQGPPHGIQVERDKLNK 164

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1371471150  81 FGRPFLGATVKPKLGLSGKNYGRVVYEGLRGGLDFLKDDENINS 124
Cdd:CHL00040  165 YGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNS 208
RuBisCO_large_I cd08212
Ribulose bisphosphate carboxylase large chain, Form I; Ribulose bisphosphate carboxylase ...
 1-124 6.06e-90

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: 267.37  E-value: 6.06e-90
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1371471150   1 YKVDAVPNTSDQYFAYIAYDIDLFEEGSIANLTASIIGNVFGFKAVKALRLEDMRIPVAYLKTFQGPATGLVVERERMDK 80
Cdd:cd08212    63 YRVEPVPGEENQYFAYIAYPLDLFEEGSVANLTTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGIQVERDRLNK 142

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1371471150  81 FGRPFLGATVKPKLGLSGKNYGRVVYEGLRGGLDFLKDDENINS 124
Cdd:cd08212   143 YGRPLLGCTIKPKLGLSAKNYGRVVYECLRGGLDFTKDDENINS 186
rbcL PRK04208
ribulose bisophosphate carboxylase; Reviewed
 1-124 1.06e-85

ribulose bisophosphate carboxylase; Reviewed


Pssm-ID: 179787  Cd Length: 468  Bit Score: 257.14  E-value: 1.06e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1371471150   1 YKVDAVPNTSDQYFAYIAYDIDLFEEGSIANLTASIIGNVFGFKAVKALRLEDMRIPVAYLKTFQGPATGLVVERERMDK 80
Cdd:PRK04208   78 YRIEDVPGDDGSYYAFIAYPLDLFEEGSIPNLLASIAGNVFGFKAVKALRLEDIRFPVAYVKTFKGPPFGIQVERERLDK 157

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1371471150  81 FGRPFLGATVKPKLGLSGKNYGRVVYEGLRGGLDFLKDDENINS 124
Cdd:PRK04208  158 YGRPLLGTTPKPKLGLSAKNYGRVVYEALRGGLDFTKDDENLNS 201
RuBisCO_large_I_II_III cd08206
Ribulose bisphosphate carboxylase large chain, Form I,II,III; Ribulose bisphosphate ...
 1-124 1.18e-75

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: 229.81  E-value: 1.18e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1371471150   1 YKVDAVPNtsDQYFAYIAYDIDLFEEGSIANLTASIIGNVFGFKAVKALRLEDMRIPVAYLKTFQGPATGLVVERERMDK 80
Cdd:cd08206    52 YRIDPVPD--GQYIAKIAYPLDLFEEGSVPNLLTSIIGNVFGMKAVKALRLEDFRFPPAYLKTFDGPSFGIQGEREILGK 129

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1371471150  81 FGRPFLGATVKPKLGLSGKNYGRVVYEGLRGGLDFLKDDENINS 124
Cdd:cd08206   130 YGRPLLGTIVKPKLGLSPKEYARVVYEALRGGLDFVKDDENQNS 173
RbcL COG1850
Ribulose 1,5-bisphosphate carboxylase, large subunit, or a RuBisCO-like protein [Carbohydrate ...
 1-124 3.07e-53

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


Pssm-ID: 441455  Cd Length: 417  Bit Score: 171.89  E-value: 3.07e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1371471150   1 YKVDAVPNTSDQYFAYIAYDIDLFEeGSIANLTASIIGNVFGFKAVKALRLEDMRIPVAYLKTFQGPATGLVVERERMDK 80
Cdd:COG1850    66 EELPEVGGGYRRALVTIAYPLENFG-GNLPNLLSTVAGNLFGLKAVSGLRLLDLEFPESFLAAFPGPKFGIEGTRELLGV 144

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1371471150  81 FGRPFLGATVKPKLGLSGKNYGRVVYEGLRGGLDFLKDDENINS 124
Cdd:COG1850   145 YDRPLLGTIIKPKVGLSPEETAELVYELALGGVDFIKDDENLAD 188
RuBisCO_large_III cd08213
Ribulose bisphosphate carboxylase large chain, Form III; Ribulose bisphosphate carboxylase ...
 13-124 5.06e-44

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: 147.92  E-value: 5.06e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1371471150  13 YFAYIAYDIDLFEEGSIANLTASIIGNVFGFKAVKALRLEDMRIPVAYLKTFQGPATGLVVERERMDKFGRPFLGATVKP 92
Cdd:cd08213    61 YIVKVAYPLELFEEGNMPQLLSSIAGNIFGMKAVKNLRLEDIYFPESYLREFKGPQFGIEGVREILGIKDRPLLGTVPKP 140

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1371471150  93 KLGLSGKNYGRVVYEGLRGGLDFLKDDENINS 124
Cdd:cd08213   141 KVGLSPEEHAEVAYEALVGGVDLVKDDENLTS 172
RuBisCO_large cd08148
Ribulose bisphosphate carboxylase large chain; Ribulose bisphosphate carboxylase (Rubisco) ...
 3-124 5.17e-43

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: 144.49  E-value: 5.17e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1371471150   3 VDAVPNTSDQYFAYIAYDIDLFEEGSIANLTASIIGNVFGFKAVKALRLEDMRIPVAYLKTFQGPATGLVVERERMDKFG 82
Cdd:cd08148    47 VYSVEELGKRYIVKIAYPVELFEPGNIPQILTVTAGNLFGLGALEAVRLEDLEFPEEYKKLFPGPKFGIDGIRKLLGVYG 126

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1371471150  83 RPFLGATVKPKLGLSGKNYGRVVYEGLRGGLDFLKDDENINS 124
Cdd:cd08148   127 RPLVGTIIKPKLGLNPKYTAEAAYAAALGGLDLIKDDETLTD 168
rubisco_III TIGR03326
ribulose bisphosphate carboxylase, type III; Members of this protein family are the archaeal, ...
 11-124 1.01e-35

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: 126.04  E-value: 1.01e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1371471150  11 DQYFAYIAYDIDLFEEGSIANLTASIIGNVFGFKAVKALRLEDMRIPVAYLKTFQGPATGLVVERERMDKFGRPFLGATV 90
Cdd:TIGR03326  71 DGSIVRIAYPLGLFEEGNLPQLLSCIAGNIFGMKAVKGLRLLDFEFPAEFLRAFKGPQFGIEGVREILGIKDRPITATVP 150

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1371471150  91 KPKLGLSGKNYGRVVYEGLRGGLDFLKDDENINS 124
Cdd:TIGR03326 151 KPKVGLSTEEHAKVAYELWSGGVDLLKDDENLTS 184
RuBisCO_large_N pfam02788
Ribulose bisphosphate carboxylase large chain, N-terminal domain; The N-terminal domain of ...
 1-60 5.60e-28

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: 98.82  E-value: 5.60e-28
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1371471150   1 YKVDAVPNtsDQYFAYIAYDIDLFEEGSIANLTASIIGNVFGFKAVKALRLEDMRIPVAY 60
Cdd:pfam02788  63 YEIDEVPG--GSYIVKIAYPLDLFEEGSIPQLLSSIAGNIFGMKAVKALRLEDIRFPPAY 120
RuBisCO_large pfam00016
Ribulose bisphosphate carboxylase large chain, catalytic domain; The C-terminal domain of ...
 71-124 2.43e-27

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: 102.05  E-value: 2.43e-27
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1371471150  71 LVVERERMDKFGRPFLGATVKPKLGLSGKNYGRVVYEGLRGGLDFLKDDENINS 124
Cdd:pfam00016   1 IAVERRVLNKYGRPILGTIIKPKLGLSPKNYARAVYEFLLGGLDFIKDDENINS 54
RLP_NonPhot cd08207
Ribulose bisphosphate carboxylase like proteins from nonphototrophic bacteria; Ribulose ...
 17-120 1.87e-21

Ribulose bisphosphate carboxylase like proteins from nonphototrophic bacteria; Ribulose bisphosphate carboxylase (Rubisco) plays an important role in the Calvin reductive pentose phosphate pathway. It catalyzes the primary CO2 fixation step. Rubisco is activated by carbamylation of an active site lysine, stabilized by a divalent cation, which then catalyzes the proton abstraction from the substrate ribulose 1,5 bisphosphate (RuBP) and leads to the formation of two molecules of 3-phosphoglycerate. Members of the Rubisco family can be divided into 4 subgroups, Form I-IV, which differ in their taxonomic distribution and subunit composition. Form I-III have Rubisco activity, while Form IV, also called Rubisco-like proteins (RLP), are missing critical active site residues and therefore do not catalyze CO2 fixation. They are believed to utilize a related enzymatic mechanism, but have divergent functions. The specific function of this subgroup is unknown.


Pssm-ID: 173972  Cd Length: 406  Bit Score: 87.75  E-value: 1.87e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1371471150  17 IAYDIDLFeeG-SIANLTASIIGNVFGFKAVKALRLEDMRIPVAYLKTFQGPATGLVVERERMDKFGRPFLGATVKPKLG 95
Cdd:cd08207    78 ISFPLDNI--GtSLPNLLATVAGNLFELRELSGLRLVDLGLPDEFAAAFPGPAFGIAGTRRLTGVEDRPLIGTIIKPSVG 155

                          90       100
                  ....*....|....*....|....*
gi 1371471150  96 LSGKNYGRVVYEGLRGGLDFLKDDE 120
Cdd:cd08207   156 LTPEETAALVRQLAAAGIDFIKDDE 180
RuBisCO_IV_RLP cd08205
Ribulose bisphosphate carboxylase like proteins, Rubisco-Form IV; Ribulose bisphosphate ...
 1-120 4.00e-21

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: 86.43  E-value: 4.00e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1371471150   1 YKVDAVPNTSDQYFAYIAYDIDLFEeGSIANLTASIIGNVFGfkaVKALRLEDMRIPVAYLKTFQGPATGLVVERERMDK 80
Cdd:cd08205    52 EELEESEGKYGRARVTISYPLDNFG-GDLPQLLNTLFGNLSL---LPGIKLVDLELPDSLLAAFPGPRFGIEGLRRLLGV 127

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1371471150  81 FGRPFLGATVKPKLGLSGKNYGRVVYEGLRGGLDFLKDDE 120
Cdd:cd08205   128 HDRPLLGTIIKPSIGLSPEELAELAYELALGGIDLIKDDE 167
PRK13475 PRK13475
ribulose-bisphosphate carboxylase;
17-120 4.70e-17

ribulose-bisphosphate carboxylase;


Pssm-ID: 184072  Cd Length: 443  Bit Score: 75.53  E-value: 4.70e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1371471150  17 IAYDIDLFE------EGSIANLTASIIGNVFGFKAVKALRLEDMRIPVAYLKTFQGPATGL-----VVERERMDkfGRPF 85
Cdd:PRK13475   83 IAYPVELFDrniidgRAMIVSFLTLTIGNNQGMGDVEYAKMHDFYVPPRYLELFDGPSTDIsdlwrVLGRPVKD--GGYI 160

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1371471150  86 LGATVKPKLGLSGKNYGRVVYEGLRGGlDFLKDDE 120
Cdd:PRK13475  161 AGTIIKPKLGLRPEPFAEACYDFWLGG-DFIKNDE 194
RLP_Photo cd08208
Ribulose bisphosphate carboxylase like proteins from phototrophic bacteria; Ribulose ...
 29-120 1.15e-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: 1.15e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1371471150  29 IANLTASIIGN-VFGFKAVKALRLEDMRIPVAYLKTFQGPATGLVVERERMDKFGRPFLGATVKPKLGLSGKNYGRVVYE 107
Cdd:cd08208   105 IPNLLSAVCGEgTFFSPGVPVVKLMDIHFPETYLADFEGPKFGIAGLRERLQAHDRPIFFGVIKPNIGLPPGEFAELGYQ 184

                          90
                  ....*....|...
gi 1371471150 108 GLRGGLDFLKDDE 120
Cdd:cd08208   185 SWLGGLDIAKDDE 197
RuBisCO_large_II cd08211
Ribulose bisphosphate carboxylase large chain, Form II; Ribulose bisphosphate carboxylase ...
 17-120 1.48e-16

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


Pssm-ID: 173976  Cd Length: 439  Bit Score: 74.07  E-value: 1.48e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1371471150  17 IAYDIDLFE------EGSIANLTASIIGNVFGFKAVKALRLEDMRIPVAYLKTFQGPATGLVVERERMDKF---GRPFLG 87
Cdd:cd08211    82 IAYPVELFDrnltdgRAMVASFLTLIIGNNQGMGDVEYLKMHDFYVPESMLELFDGPSVNISDMWKVLGRPevdGGYIAG 161

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1371471150  88 ATVKPKLGLSGKNYGRVVYEGLRGGlDFLKDDE 120
Cdd:cd08211   162 TIIKPKLGLRPKPFAEACYAFWLGG-DFIKNDE 193
RLP_RrRLP cd08210
Ribulose bisphosphate carboxylase like proteins (RLPs) similar to R.rubrum RLP; RLP from ...
 7-122 4.96e-12

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: 61.10  E-value: 4.96e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1371471150   7 PNTSDQYFAYIAYDIDlfeegSIANLTASIIGNVFGFKAVKA-LRLEDMRIPVAYLKTFQGPATGLVVERERMDKFGRPF 85
Cdd:cd08210    54 PAGEGSYRARISYSVD-----TAGGELTQLLNVLFGNSSLQPgIRLVDFELPPSLLRRFPGPRFGIAGLRALLGIPERPL 128

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1371471150  86 LGATVKPkLGLSGKNYGRVVYEGLRGGLDFLKDDENI 122
Cdd:cd08210   129 LCSALKP-QGLSAAELAELAYAFALGGIDIIKDDHGL 164
RLP_DK-MTP-1-P-enolase cd08209
2,3-diketo-5-methylthiopentyl-1-phosphate enolase; Ribulose bisphosphate carboxylase like ...
 50-120 1.32e-10

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: 56.94  E-value: 1.32e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1371471150  50 RLEDMRIPVAYLKTFQGPATGLVVERERMDKFGRPFLGATVKPKLGLSGKNYGRVVYEGLRGGLDFLKDDE 120
Cdd:cd08209    91 KLVDLRLPEEFGRAFPGPKFGIEGIRQRLGVHDRPLLMSIFKGVLGLDLDDLAEQLREQALGGVDLIKDDE 161
mtnW PRK09549
2,3-diketo-5-methylthiopentyl-1-phosphate enolase; Reviewed
 30-120 8.37e-05

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


Pssm-ID: 236560  Cd Length: 407  Bit Score: 40.38  E-value: 8.37e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1371471150  30 ANLTA---SIIGNVFGFKAVKA-LRLEDMRIPVAYLKTFQGPATGLVVERERMDKFGRPFLGATVKPKLGLSGKNYGRVV 105
Cdd:PRK09549   77 ANFSPdlpAILTTTFGKLSLDGeVKLIDLTFSDELKRHFPGPKFGIDGIRNLLGVHDRPLLMSIFKGVIGRDLDYLKEQL 156

                          90
                  ....*....|....*
gi 1371471150 106 YEGLRGGLDFLKDDE 120
Cdd:PRK09549  157 RDQALGGVDLVKDDE 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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