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Conserved domains on  [gi|996063904|gb|AMK01649|]
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ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit, partial [phytoplankton environmental sample]

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) ...
 2-143 1.64e-104

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: 306.24  E-value: 1.64e-104
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063904   2 DDENINSQPFMRWRERFLDCMEGINRASAATGEVKGSYLNITGGTMEEVYKRAEYAKSVGSVIVMIDLVM-GYTAIQSIA 80
Cdd:CHL00040 202 DDENVNSQPFMRWRDRFLFCAEAIYKAQAETGEIKGHYLNATAGTCEEMYKRAVFARELGVPIVMHDYLTgGFTANTSLA 281

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 996063904  81 LWARENDMLLHLHRAGNSTYARQKNHGTNFRVICKWMRMSGVDHIHAGTVVGKLEGDPLMIKG 143
Cdd:CHL00040 282 HYCRDNGLLLHIHRAMHAVIDRQKNHGIHFRVLAKALRMSGGDHIHAGTVVGKLEGEREMTLG 344
 
Name Accession Description Interval E-value
rbcL CHL00040
ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
 2-143 1.64e-104

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


Pssm-ID: 176981  Cd Length: 475  Bit Score: 306.24  E-value: 1.64e-104
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063904   2 DDENINSQPFMRWRERFLDCMEGINRASAATGEVKGSYLNITGGTMEEVYKRAEYAKSVGSVIVMIDLVM-GYTAIQSIA 80
Cdd:CHL00040 202 DDENVNSQPFMRWRDRFLFCAEAIYKAQAETGEIKGHYLNATAGTCEEMYKRAVFARELGVPIVMHDYLTgGFTANTSLA 281

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 996063904  81 LWARENDMLLHLHRAGNSTYARQKNHGTNFRVICKWMRMSGVDHIHAGTVVGKLEGDPLMIKG 143
Cdd:CHL00040 282 HYCRDNGLLLHIHRAMHAVIDRQKNHGIHFRVLAKALRMSGGDHIHAGTVVGKLEGEREMTLG 344
RuBisCO_large_I cd08212
Ribulose bisphosphate carboxylase large chain, Form I; Ribulose bisphosphate carboxylase ...
 2-143 2.66e-100

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: 294.72  E-value: 2.66e-100
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063904   2 DDENINSQPFMRWRERFLDCMEGINRASAATGEVKGSYLNITGGTMEEVYKRAEYAKSVGSVIVMIDLVMGYTAIQSIAL 81
Cdd:cd08212  180 DDENINSQPFMRWRDRFLFVAEAVNKAQAETGEVKGHYLNVTAGTMEEMYKRAEFAKELGSPIIMHDLLTGFTAIQSLAK 259

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 996063904  82 WARENDMLLHLHRAGNSTYARQKNHGTNFRVICKWMRMSGVDHIHAGTVVGKLEGDPLMIKG 143
Cdd:cd08212  260 WCRDNGMLLHLHRAGHATYDRQKNHGIHFRVLAKWLRLSGVDHIHAGTVVGKLEGDPLVTLG 321
RuBisCO_large pfam00016
Ribulose bisphosphate carboxylase large chain, catalytic domain; The C-terminal domain of ...
 2-138 1.00e-74

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: 224.16  E-value: 1.00e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063904    2 DDENINSQPFMRWRERFLDCMEGINRASAATGEVKGSYLNITGGTMEEVYKRAEYAKSVGSVIVMID-LVMGYTAIQSIA 80
Cdd:pfam00016  48 DDENINSQPFMPWRDRFLFVAEAIDRAQDETGEAKGHYLNITADDMEEMYRRAEFAKETGGVAVMVDgLVIGPTAITTLR 127

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 996063904   81 LWARENDMLLHLHRAGNSTYARQKNHGTNFRVICKWMRMSGVDHIHAGTV-VGKLEGDP 138
Cdd:pfam00016 128 RWFRDNGVILHYHRAGHGAVTRQSKHGISFRVLAKMARLAGADHLHTGTMgVGKLEGDP 186
RbcL COG1850
Ribulose 1,5-bisphosphate carboxylase, large subunit, or a RuBisCO-like protein [Carbohydrate ...
 2-138 6.04e-52

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


Pssm-ID: 441455  Cd Length: 417  Bit Score: 169.58  E-value: 6.04e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063904   2 DDENINSQPFMRWRERFLDCMEGINRASAATGEVKGSYLNITGgTMEEVYKRAEYAKSVGSVIVMID-LVMGYTAIQSIA 80
Cdd:COG1850  182 DDENLADQPFCPFEDRVRAVMEAIDRAEEETGEKKMYAFNITA-DTDEMLRRADLAVELGANAVMVDvNTVGLSAVQTLR 260

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 996063904  81 lwARENDMLLHLHRAGNSTYARQKNHGTNFRVICKWMRMSGVDHIHAGTVVGKLEGDP 138
Cdd:COG1850  261 --EEHIGLPIHAHRAGHGAFTRSPLHGISMRVLAKLWRLAGADHLHVGTPVGKMEGDD 316
 
Name Accession Description Interval E-value
rbcL CHL00040
ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
 2-143 1.64e-104

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


Pssm-ID: 176981  Cd Length: 475  Bit Score: 306.24  E-value: 1.64e-104
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063904   2 DDENINSQPFMRWRERFLDCMEGINRASAATGEVKGSYLNITGGTMEEVYKRAEYAKSVGSVIVMIDLVM-GYTAIQSIA 80
Cdd:CHL00040 202 DDENVNSQPFMRWRDRFLFCAEAIYKAQAETGEIKGHYLNATAGTCEEMYKRAVFARELGVPIVMHDYLTgGFTANTSLA 281

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 996063904  81 LWARENDMLLHLHRAGNSTYARQKNHGTNFRVICKWMRMSGVDHIHAGTVVGKLEGDPLMIKG 143
Cdd:CHL00040 282 HYCRDNGLLLHIHRAMHAVIDRQKNHGIHFRVLAKALRMSGGDHIHAGTVVGKLEGEREMTLG 344
RuBisCO_large_I cd08212
Ribulose bisphosphate carboxylase large chain, Form I; Ribulose bisphosphate carboxylase ...
 2-143 2.66e-100

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: 294.72  E-value: 2.66e-100
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063904   2 DDENINSQPFMRWRERFLDCMEGINRASAATGEVKGSYLNITGGTMEEVYKRAEYAKSVGSVIVMIDLVMGYTAIQSIAL 81
Cdd:cd08212  180 DDENINSQPFMRWRDRFLFVAEAVNKAQAETGEVKGHYLNVTAGTMEEMYKRAEFAKELGSPIIMHDLLTGFTAIQSLAK 259

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 996063904  82 WARENDMLLHLHRAGNSTYARQKNHGTNFRVICKWMRMSGVDHIHAGTVVGKLEGDPLMIKG 143
Cdd:cd08212  260 WCRDNGMLLHLHRAGHATYDRQKNHGIHFRVLAKWLRLSGVDHIHAGTVVGKLEGDPLVTLG 321
rbcL PRK04208
ribulose bisophosphate carboxylase; Reviewed
 2-143 5.37e-88

ribulose bisophosphate carboxylase; Reviewed


Pssm-ID: 179787  Cd Length: 468  Bit Score: 263.69  E-value: 5.37e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063904   2 DDENINSQPFMRWRERFLDCMEGINRASAATGEVKGSYLNITGGTMEEVYKRAEYAKSVGSVIVMIDLVM-GYTAIQSIA 80
Cdd:PRK04208 195 DDENLNSQPFNRWRDRFLFVMEAIDKAEAETGERKGHYLNVTAPTMEEMYKRAEFAKELGSPIVMIDVVTaGWTALQSLR 274

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 996063904  81 LWARENDMLLHLHRAGNSTYARQKNHGTNFRVICKWMRMSGVDHIHAGTVVGKLEGDPLMIKG 143
Cdd:PRK04208 275 EWCRDNGLALHAHRAMHAAFTRNPNHGISFRVLAKLLRLIGVDHLHTGTVVGKLEGDRAEVLG 337
RuBisCO_large_I_II_III cd08206
Ribulose bisphosphate carboxylase large chain, Form I,II,III; Ribulose bisphosphate ...
 2-143 4.06e-83

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: 249.46  E-value: 4.06e-83
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063904   2 DDENINSQPFMRWRERFLDCMEGINRASAATGEVKGSYLNITGGTMEEVYKRAEYAKSVGSVIVMIDLV-MGYTAIQSIA 80
Cdd:cd08206  167 DDENQNSQPFMRFEDRILFVAEAMDKAEAETGEAKGHYLNITADTPEEMIKRAEFAKELGSVIVMVDGVtAGWTAIQSAR 246

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 996063904  81 LWARENDMLLHLHRAGNSTYARQKNHGTNFRVICKWMRMSGVDHIHAGTVVGKLEGDPLMIKG 143
Cdd:cd08206  247 RWCPDNGLALHAHRAGHAAFTRQKNHGISMRVLAKLARLIGVDHIHTGTVVGKLEGDPSEVKG 309
RuBisCO_large pfam00016
Ribulose bisphosphate carboxylase large chain, catalytic domain; The C-terminal domain of ...
 2-138 1.00e-74

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: 224.16  E-value: 1.00e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063904    2 DDENINSQPFMRWRERFLDCMEGINRASAATGEVKGSYLNITGGTMEEVYKRAEYAKSVGSVIVMID-LVMGYTAIQSIA 80
Cdd:pfam00016  48 DDENINSQPFMPWRDRFLFVAEAIDRAQDETGEAKGHYLNITADDMEEMYRRAEFAKETGGVAVMVDgLVIGPTAITTLR 127

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 996063904   81 LWARENDMLLHLHRAGNSTYARQKNHGTNFRVICKWMRMSGVDHIHAGTV-VGKLEGDP 138
Cdd:pfam00016 128 RWFRDNGVILHYHRAGHGAVTRQSKHGISFRVLAKMARLAGADHLHTGTMgVGKLEGDP 186
RbcL COG1850
Ribulose 1,5-bisphosphate carboxylase, large subunit, or a RuBisCO-like protein [Carbohydrate ...
 2-138 6.04e-52

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


Pssm-ID: 441455  Cd Length: 417  Bit Score: 169.58  E-value: 6.04e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063904   2 DDENINSQPFMRWRERFLDCMEGINRASAATGEVKGSYLNITGgTMEEVYKRAEYAKSVGSVIVMID-LVMGYTAIQSIA 80
Cdd:COG1850  182 DDENLADQPFCPFEDRVRAVMEAIDRAEEETGEKKMYAFNITA-DTDEMLRRADLAVELGANAVMVDvNTVGLSAVQTLR 260

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 996063904  81 lwARENDMLLHLHRAGNSTYARQKNHGTNFRVICKWMRMSGVDHIHAGTVVGKLEGDP 138
Cdd:COG1850  261 --EEHIGLPIHAHRAGHGAFTRSPLHGISMRVLAKLWRLAGADHLHVGTPVGKMEGDD 316
RuBisCO_large cd08148
Ribulose bisphosphate carboxylase large chain; Ribulose bisphosphate carboxylase (Rubisco) ...
 2-137 6.48e-46

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: 152.58  E-value: 6.48e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063904   2 DDENINSQPFMRWRERFLDCMEGINRASAATGEVKGSYLNITGGTmEEVYKRAEYAKSVGSVIVMID-LVMGYTAIQSIA 80
Cdd:cd08148  162 DDETLTDQPFCPLRDRITEVAAALDRVQEETGEKKLYAVNVTAGT-FEIIERAERALELGANMLMVDvLTAGFSALQALA 240

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 996063904  81 LwARENDMLLHLHRAGNSTYARQKNHGTNFRVICKWMRMSGVDHIHAGTVVGKLEGD 137
Cdd:cd08148  241 E-DFEIDLPIHVHRAMHGAVTRSKFHGISMLVLAKLLRMAGGDFIHTGTVVGKMALE 296
RuBisCO_large_III cd08213
Ribulose bisphosphate carboxylase large chain, Form III; Ribulose bisphosphate carboxylase ...
 2-137 1.22e-37

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: 132.13  E-value: 1.22e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063904   2 DDENINSQPFMRWRERFLDCMEGINRASAATGEVKGSYLNITGGTmEEVYKRAEYAKSVGSVIVMIDLVM-GYTAIQSIA 80
Cdd:cd08213  166 DDENLTSQPFNRFEERAKESLKARDKAEAETGERKAYLANITAPV-REMERRAELVADLGGKYVMIDVVVaGWSALQYLR 244

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 996063904  81 LWARENDMLLHLHRAGNSTYARQKNHGTNFRVICKWMRMSGVDHIHAGTVVGKLEGD 137
Cdd:cd08213  245 DLAEDYGLAIHAHRAMHAAFTRNPRHGISMLVLAKLYRLIGVDQLHIGTAVGKMEGD 301
RuBisCO_IV_RLP cd08205
Ribulose bisphosphate carboxylase like proteins, Rubisco-Form IV; Ribulose bisphosphate ...
 2-134 4.96e-17

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: 75.65  E-value: 4.96e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063904   2 DDENINSQPFMRWRERFLDCMEGINRASAATGEvKGSYL-NITGGTmEEVYKRAEYAKSVGSVIVMIDL-VMGYTAIQSI 79
Cdd:cd08205  165 DDELLADQPYAPFEERVRACMEAVRRANEETGR-KTLYApNITGDP-DELRRRADRAVEAGANALLINPnLVGLDALRAL 242

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 996063904  80 AlwaRENDMLLHLHRAGNSTYARQKNHGTNFRVICKWMRMSGVDHIHAGTVVGKL 134
Cdd:cd08205  243 A---EDPDLPIMAHPAFAGALSRSPDYGSHFLLLGKLMRLAGADAVIFPGPGGRF 294
RuBisCO_large_II cd08211
Ribulose bisphosphate carboxylase large chain, Form II; Ribulose bisphosphate carboxylase ...
 2-137 1.54e-15

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: 71.76  E-value: 1.54e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063904   2 DDENINSQPFMRWRERFLDCMEGINRASAATGEVKGSYLNITGGTMEEVYKRAEYAKSV-----GSVIVMID-LVMGYTA 75
Cdd:cd08211  191 NDEPQANQPFCPLKKVIPLVADAMRRAQDETGEAKLFSANITADDPDEMIARGEYILEAfgpnaGHVAFLVDgYVAGPAA 270

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 996063904  76 IQSialwAREN--DMLLHLHRAGNSTYARQKNH-GTNFRVICKWMRMSGVDHIHAGTV-VGKLEGD 137
Cdd:cd08211  271 VTT----ARRRfpDQFLHYHRAGHGAVTSPQSKrGYTAFVLSKMARLQGASGIHTGTMgFGKMEGE 332
RLP_NonPhot cd08207
Ribulose bisphosphate carboxylase like proteins from nonphototrophic bacteria; Ribulose ...
 2-137 8.15e-14

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: 66.95  E-value: 8.15e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063904   2 DDENINSQPFMRWRERFLDCMEGINRASAATGEvKGSY-LNITGGTmEEVYKRAEYAKSVGSVIVMIDL-VMGYTAIQSI 79
Cdd:cd08207  178 DDELLANPPYSPLDERVRAVMRVINDHAQRTGR-KVMYaFNITDDI-DEMRRNHDLVVEAGGTCVMVSLnSVGLSGLAAL 255

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 996063904  80 AlwaRENDMLLHLHRAGNSTYARQKNHGTNFRVICKWMRMSGVDHIHAGTVVGKL-EGD 137
Cdd:cd08207  256 R---RHSQLPIHGHRNGWGMLTRSPALGISFQAYQKLWRLAGVDHLHVNGLASKFwESD 311
PRK13475 PRK13475
ribulose-bisphosphate carboxylase;
2-138 1.53e-13

ribulose-bisphosphate carboxylase;


Pssm-ID: 184072  Cd Length: 443  Bit Score: 66.28  E-value: 1.53e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063904   2 DDENINSQPFMRWRERFLDCMEGINRASAATGEVKGSYLNITGGTMEEVYKRAEY-----AKSVGSVIVMID-LVMGYTA 75
Cdd:PRK13475 192 NDEPQGNQVFAPLKKTVPLVADAMKRAQDETGEAKLFSANITADDHYEMIARGEYiletfGENADHVAFLVDgYVAGPGA 271

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 996063904  76 IQSialwAREN--DMLLHLHRAGNSTYARQKN-HGTNFRVICKWMRMSGVDHIHAGTV-VGKLEGDP 138
Cdd:PRK13475 272 VTT----ARRQypDQYLHYHRAGHGAVTSPSSkRGYTAFVLSKMARLQGASGIHTGTMgYGKMEGEA 334
RLP_RrRLP cd08210
Ribulose bisphosphate carboxylase like proteins (RLPs) similar to R.rubrum RLP; RLP from ...
 2-67 5.64e-07

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: 47.23  E-value: 5.64e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 996063904   2 DDENINSQPFMRWRERFLDCMEGINRASAATGEvKGSYL-NITGGTMeEVYKRAEYAKSVGSVIVMI 67
Cdd:cd08210  160 DDHGLADQPFAPFEERVKACQEAVAEANAETGG-RTLYApNVTGPPT-QLLERARFAKEAGAGGVLI 224
 
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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