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Conserved domains on  [gi|814969597|gb|AKE43717|]
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ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit, partial (chloroplast) [Tetrameles nudiflora]

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) ...
 1-145 9.07e-115

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: 332.44  E-value: 9.07e-115
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814969597   1 LNATAGTCEEMIKRAACARELGVPIVMHDYLTGGFTSNTSLAHYCRDNGLLLHIHRAMHAVIDRQKNHGIHFRVLAKALR 80
Cdd:CHL00040 240 LNATAGTCEEMYKRAVFARELGVPIVMHDYLTGGFTANTSLAHYCRDNGLLLHIHRAMHAVIDRQKNHGIHFRVLAKALR 319

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 814969597  81 MSGGDHVHSGTVVGKLEGERDITLGFVDLLRDDFIEKDRSRGIYFTQDWVSMPGVIPVASGGIHV 145
Cdd:CHL00040 320 MSGGDHIHAGTVVGKLEGEREMTLGFVDLLRDDFIEKDRSRGIYFTQDWVSLPGVLPVASGGIHV 384
 
Name Accession Description Interval E-value
rbcL CHL00040
ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
 1-145 9.07e-115

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


Pssm-ID: 176981  Cd Length: 475  Bit Score: 332.44  E-value: 9.07e-115
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814969597   1 LNATAGTCEEMIKRAACARELGVPIVMHDYLTGGFTSNTSLAHYCRDNGLLLHIHRAMHAVIDRQKNHGIHFRVLAKALR 80
Cdd:CHL00040 240 LNATAGTCEEMYKRAVFARELGVPIVMHDYLTGGFTANTSLAHYCRDNGLLLHIHRAMHAVIDRQKNHGIHFRVLAKALR 319

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 814969597  81 MSGGDHVHSGTVVGKLEGERDITLGFVDLLRDDFIEKDRSRGIYFTQDWVSMPGVIPVASGGIHV 145
Cdd:CHL00040 320 MSGGDHIHAGTVVGKLEGEREMTLGFVDLLRDDFIEKDRSRGIYFTQDWVSLPGVLPVASGGIHV 384
RuBisCO_large_I cd08212
Ribulose bisphosphate carboxylase large chain, Form I; Ribulose bisphosphate carboxylase ...
 1-145 1.15e-99

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: 293.18  E-value: 1.15e-99
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814969597   1 LNATAGTCEEMIKRAACARELGVPIVMHDYLTGgFTSNTSLAHYCRDNGLLLHIHRAMHAVIDRQKNHGIHFRVLAKALR 80
Cdd:cd08212  218 LNVTAGTMEEMYKRAEFAKELGSPIIMHDLLTG-FTAIQSLAKWCRDNGMLLHLHRAGHATYDRQKNHGIHFRVLAKWLR 296

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 814969597  81 MSGGDHVHSGTVVGKLEGERDITLGFVDLLRDDFIEKDRSRGIYFTQDWVSMPGVIPVASGGIHV 145
Cdd:cd08212  297 LSGVDHIHAGTVVGKLEGDPLVTLGFYDLLRDDYIEKDRSRGIFFTQDWASLPGVMPVASGGIHV 361
RuBisCO_large pfam00016
Ribulose bisphosphate carboxylase large chain, catalytic domain; The C-terminal domain of ...
 1-145 9.24e-67

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: 204.13  E-value: 9.24e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814969597    1 LNATAGTCEEMIKRAACARELGVPIVMHDYLTGGFTSNTSLAHYCRDNGLLLHIHRAMHAVIDRQKNHGIHFRVLAKALR 80
Cdd:pfam00016  86 LNITADDMEEMYRRAEFAKETGGVAVMVDGLVIGPTAITTLRRWFRDNGVILHYHRAGHGAVTRQSKHGISFRVLAKMAR 165

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 814969597   81 MSGGDHVHSGTV-VGKLEGERDitlgfvDLLRDDFIEKDRSRGIYFTQDWVSMPGVIPVASGGIHV 145
Cdd:pfam00016 166 LAGADHLHTGTMgVGKLEGDPS------DTLRAYMLEEDRARGPFFDQDWGGMPAVMPVASGGIHA 225
RbcL COG1850
Ribulose 1,5-bisphosphate carboxylase, large subunit, or a RuBisCO-like protein [Carbohydrate ...
 1-145 6.30e-42

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


Pssm-ID: 441455  Cd Length: 417  Bit Score: 143.39  E-value: 6.30e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814969597   1 LNATAGTcEEMIKRAACARELGVPIVMHDYLTGGFTSNTSLAHycRDNGLLLHIHRAMHAVIDRQKNHGIHFRVLAKALR 80
Cdd:COG1850  220 FNITADT-DEMLRRADLAVELGANAVMVDVNTVGLSAVQTLRE--EHIGLPIHAHRAGHGAFTRSPLHGISMRVLAKLWR 296

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 814969597  81 MSGGDHVHSGTVVGKLEGERDITLGFVDLLRddfiekdrsrgiyftQDWVSMPGVIPVASGGIHV 145
Cdd:COG1850  297 LAGADHLHVGTPVGKMEGDDEEVLAIADALL---------------QPWGGLKPVFPVPSGGQHP 346
rubisco_III TIGR03326
ribulose bisphosphate carboxylase, type III; Members of this protein family are the archaeal, ...
 2-144 2.19e-30

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: 112.94  E-value: 2.19e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814969597    2 NATAGTcEEMIKRAACARELGVPIVMHDYLTGGFTSNTSLAHYCRDNGLLLHIHRAMHAVIDRQKNHGIHFRVLAKALRM 81
Cdd:TIGR03326 217 NITADV-REMERRAELVADLGGEYVMVDIVVAGWSALQYVRERTEDLGLAIHAHRAMHAAFTRNPKHGISMFVLAKLYRL 295

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 814969597   82 SGGDHVHSGTV-VGKLEGERDITLGFVDLLRddfiekdrsrgiyftQDWVSMPGVIPVASGGIH 144
Cdd:TIGR03326 296 IGVDQLHTGTAgVGKLEGGNEDTKGINDFLR---------------QDWHHIKPVFPVASGGLH 344
 
Name Accession Description Interval E-value
rbcL CHL00040
ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
 1-145 9.07e-115

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


Pssm-ID: 176981  Cd Length: 475  Bit Score: 332.44  E-value: 9.07e-115
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814969597   1 LNATAGTCEEMIKRAACARELGVPIVMHDYLTGGFTSNTSLAHYCRDNGLLLHIHRAMHAVIDRQKNHGIHFRVLAKALR 80
Cdd:CHL00040 240 LNATAGTCEEMYKRAVFARELGVPIVMHDYLTGGFTANTSLAHYCRDNGLLLHIHRAMHAVIDRQKNHGIHFRVLAKALR 319

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 814969597  81 MSGGDHVHSGTVVGKLEGERDITLGFVDLLRDDFIEKDRSRGIYFTQDWVSMPGVIPVASGGIHV 145
Cdd:CHL00040 320 MSGGDHIHAGTVVGKLEGEREMTLGFVDLLRDDFIEKDRSRGIYFTQDWVSLPGVLPVASGGIHV 384
RuBisCO_large_I cd08212
Ribulose bisphosphate carboxylase large chain, Form I; Ribulose bisphosphate carboxylase ...
 1-145 1.15e-99

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: 293.18  E-value: 1.15e-99
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814969597   1 LNATAGTCEEMIKRAACARELGVPIVMHDYLTGgFTSNTSLAHYCRDNGLLLHIHRAMHAVIDRQKNHGIHFRVLAKALR 80
Cdd:cd08212  218 LNVTAGTMEEMYKRAEFAKELGSPIIMHDLLTG-FTAIQSLAKWCRDNGMLLHLHRAGHATYDRQKNHGIHFRVLAKWLR 296

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 814969597  81 MSGGDHVHSGTVVGKLEGERDITLGFVDLLRDDFIEKDRSRGIYFTQDWVSMPGVIPVASGGIHV 145
Cdd:cd08212  297 LSGVDHIHAGTVVGKLEGDPLVTLGFYDLLRDDYIEKDRSRGIFFTQDWASLPGVMPVASGGIHV 361
rbcL PRK04208
ribulose bisophosphate carboxylase; Reviewed
 1-145 5.06e-92

ribulose bisophosphate carboxylase; Reviewed


Pssm-ID: 179787  Cd Length: 468  Bit Score: 274.09  E-value: 5.06e-92
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814969597   1 LNATAGTCEEMIKRAACARELGVPIVMHDYLTGGFTSNTSLAHYCRDNGLLLHIHRAMHAVIDRQKNHGIHFRVLAKALR 80
Cdd:PRK04208 233 LNVTAPTMEEMYKRAEFAKELGSPIVMIDVVTAGWTALQSLREWCRDNGLALHAHRAMHAAFTRNPNHGISFRVLAKLLR 312

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 814969597  81 MSGGDHVHSGTVVGKLEGERDITLGFVDLLRDDFIEKDRSRGIYFTQDWVSMPGVIPVASGGIHV 145
Cdd:PRK04208 313 LIGVDHLHTGTVVGKLEGDRAEVLGYYDILREDFVPEDRSRGIFFDQDWGSIKPVFPVASGGIHP 377
RuBisCO_large_I_II_III cd08206
Ribulose bisphosphate carboxylase large chain, Form I,II,III; Ribulose bisphosphate ...
 1-145 6.13e-81

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: 244.07  E-value: 6.13e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814969597   1 LNATAGTCEEMIKRAACARELGVPIVMHDYLTGGFTSNTSLAHYCRDNGLLLHIHRAMHAVIDRQKNHGIHFRVLAKALR 80
Cdd:cd08206  205 LNITADTPEEMIKRAEFAKELGSVIVMVDGVTAGWTAIQSARRWCPDNGLALHAHRAGHAAFTRQKNHGISMRVLAKLAR 284

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 814969597  81 MSGGDHVHSGTVVGKLEGERDITLGFVDLLRDDFIEKDRSRgIYFTQDWVSMPGVIPVASGGIHV 145
Cdd:cd08206  285 LIGVDHIHTGTVVGKLEGDPSEVKGIADMLREDEVEGDLSR-IFFNQDWGGMKPVFPVASGGLHP 348
RuBisCO_large pfam00016
Ribulose bisphosphate carboxylase large chain, catalytic domain; The C-terminal domain of ...
 1-145 9.24e-67

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: 204.13  E-value: 9.24e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814969597    1 LNATAGTCEEMIKRAACARELGVPIVMHDYLTGGFTSNTSLAHYCRDNGLLLHIHRAMHAVIDRQKNHGIHFRVLAKALR 80
Cdd:pfam00016  86 LNITADDMEEMYRRAEFAKETGGVAVMVDGLVIGPTAITTLRRWFRDNGVILHYHRAGHGAVTRQSKHGISFRVLAKMAR 165

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 814969597   81 MSGGDHVHSGTV-VGKLEGERDitlgfvDLLRDDFIEKDRSRGIYFTQDWVSMPGVIPVASGGIHV 145
Cdd:pfam00016 166 LAGADHLHTGTMgVGKLEGDPS------DTLRAYMLEEDRARGPFFDQDWGGMPAVMPVASGGIHA 225
RuBisCO_large cd08148
Ribulose bisphosphate carboxylase large chain; Ribulose bisphosphate carboxylase (Rubisco) ...
 1-145 2.58e-57

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: 182.24  E-value: 2.58e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814969597   1 LNATAGTcEEMIKRAACARELGVPIVMHDYLTGGFTSNTSLAHYCRdNGLLLHIHRAMHAVIDRQKNHGIHFRVLAKALR 80
Cdd:cd08148  200 VNVTAGT-FEIIERAERALELGANMLMVDVLTAGFSALQALAEDFE-IDLPIHVHRAMHGAVTRSKFHGISMLVLAKLLR 277

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 814969597  81 MSGGDHVHSGTVVGKLEGERDITLGFVDLLRDdfiekdrsrgiyftqDWVSMPGVIPVASGGIHV 145
Cdd:cd08148  278 MAGGDFIHTGTVVGKMALEREEALGIADALTD---------------DWAGFKRVFPVASGGIHP 327
RbcL COG1850
Ribulose 1,5-bisphosphate carboxylase, large subunit, or a RuBisCO-like protein [Carbohydrate ...
 1-145 6.30e-42

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


Pssm-ID: 441455  Cd Length: 417  Bit Score: 143.39  E-value: 6.30e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814969597   1 LNATAGTcEEMIKRAACARELGVPIVMHDYLTGGFTSNTSLAHycRDNGLLLHIHRAMHAVIDRQKNHGIHFRVLAKALR 80
Cdd:COG1850  220 FNITADT-DEMLRRADLAVELGANAVMVDVNTVGLSAVQTLRE--EHIGLPIHAHRAGHGAFTRSPLHGISMRVLAKLWR 296

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 814969597  81 MSGGDHVHSGTVVGKLEGERDITLGFVDLLRddfiekdrsrgiyftQDWVSMPGVIPVASGGIHV 145
Cdd:COG1850  297 LAGADHLHVGTPVGKMEGDDEEVLAIADALL---------------QPWGGLKPVFPVPSGGQHP 346
RuBisCO_large_III cd08213
Ribulose bisphosphate carboxylase large chain, Form III; Ribulose bisphosphate carboxylase ...
 1-144 4.74e-41

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: 140.99  E-value: 4.74e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814969597   1 LNATAgTCEEMIKRAACARELGVPIVMHDYLTGGFTSNTSLAHYCRDNGLLLHIHRAMHAVIDRQKNHGIHFRVLAKALR 80
Cdd:cd08213  204 ANITA-PVREMERRAELVADLGGKYVMIDVVVAGWSALQYLRDLAEDYGLAIHAHRAMHAAFTRNPRHGISMLVLAKLYR 282

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 814969597  81 MSGGDHVHSGTVVGKLEGERDITLGFVDLLRDDFIEKDrSRGIYFTQDWVSMPGVIPVASGGIH 144
Cdd:cd08213  283 LIGVDQLHIGTAVGKMEGDKEEVLRIADILREQKYKPD-EEDFHLAQDWGGIKPVFPVASGGLH 345
rubisco_III TIGR03326
ribulose bisphosphate carboxylase, type III; Members of this protein family are the archaeal, ...
 2-144 2.19e-30

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: 112.94  E-value: 2.19e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814969597    2 NATAGTcEEMIKRAACARELGVPIVMHDYLTGGFTSNTSLAHYCRDNGLLLHIHRAMHAVIDRQKNHGIHFRVLAKALRM 81
Cdd:TIGR03326 217 NITADV-REMERRAELVADLGGEYVMVDIVVAGWSALQYVRERTEDLGLAIHAHRAMHAAFTRNPKHGISMFVLAKLYRL 295

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 814969597   82 SGGDHVHSGTV-VGKLEGERDITLGFVDLLRddfiekdrsrgiyftQDWVSMPGVIPVASGGIH 144
Cdd:TIGR03326 296 IGVDQLHTGTAgVGKLEGGNEDTKGINDFLR---------------QDWHHIKPVFPVASGGLH 344
PRK13475 PRK13475
ribulose-bisphosphate carboxylase;
2-143 6.43e-16

ribulose-bisphosphate carboxylase;


Pssm-ID: 184072  Cd Length: 443  Bit Score: 73.22  E-value: 6.43e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814969597   2 NATAGTCEEMIKRAACARELGVPIVMH-DYLTGGFTSNTSLAHYCRDN--GLLLHIHRAMHAVIDRQKN-HGIHFRVLAK 77
Cdd:PRK13475 231 NITADDHYEMIARGEYILETFGENADHvAFLVDGYVAGPGAVTTARRQypDQYLHYHRAGHGAVTSPSSkRGYTAFVLSK 310

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 814969597  78 ALRMSGGDHVHSGTV-VGKLEGERDitlgfvDLLRDDFIEKDRSRGIYFTQDWVSMPGVIPVASGGI 143
Cdd:PRK13475 311 MARLQGASGIHTGTMgYGKMEGEAD------DRVIAYMIERDSAQGPFYHQEWYGMKPTTPIISGGM 371
RuBisCO_large_II cd08211
Ribulose bisphosphate carboxylase large chain, Form II; Ribulose bisphosphate carboxylase ...
 2-143 2.19e-14

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: 68.68  E-value: 2.19e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814969597   2 NATAGTCEEMIKRAACARELGVPIVMH-----DYLTGGFTSNTSLAHYCRDNglLLHIHRAMHAVIDRQKNH-GIHFRVL 75
Cdd:cd08211  230 NITADDPDEMIARGEYILEAFGPNAGHvaflvDGYVAGPAAVTTARRRFPDQ--FLHYHRAGHGAVTSPQSKrGYTAFVL 307

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814969597  76 AKALRMSGGDHVHSGTV-VGKLEGE-RDITLGFVdllrddfIEKDRSRGIYFTQDWVSMPGVIPVASGGI 143
Cdd:cd08211  308 SKMARLQGASGIHTGTMgFGKMEGEsSDKVIAYM-------IERDEAQGPLFNQKWYGMKPTTPIISGGM 370
RuBisCO_IV_RLP cd08205
Ribulose bisphosphate carboxylase like proteins, Rubisco-Form IV; Ribulose bisphosphate ...
 6-145 5.29e-10

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: 56.00  E-value: 5.29e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814969597   6 GTCEEMIKRAACARELGVPIVMHDYLTGGFTSNTSLAhycRDNGLLLHIHRAMHAVIDRQKNHGIHFRVLAKALRMSGGD 85
Cdd:cd08205  207 GDPDELRRRADRAVEAGANALLINPNLVGLDALRALA---EDPDLPIMAHPAFAGALSRSPDYGSHFLLLGKLMRLAGAD 283

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 814969597  86 HVHSGTVVGKLEGERDITLGFVDLLRddfiekdrsrgiyftQDWVSMPGVIPVASGGIHV 145
Cdd:cd08205  284 AVIFPGPGGRFPFSREECLAIARACR---------------RPLGGIKPALPVPSGGMHP 328
RLP_NonPhot cd08207
Ribulose bisphosphate carboxylase like proteins from nonphototrophic bacteria; Ribulose ...
 9-88 6.06e-04

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: 38.44  E-value: 6.06e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814969597   9 EEMIKRAACARELGVPIVMHDYLTGGFTSntsLAHYCRDNGLLLHIHRAMHAVIDRQKNHGIHFRVLAKALRMSGGDHVH 88
Cdd:cd08207  223 DEMRRNHDLVVEAGGTCVMVSLNSVGLSG---LAALRRHSQLPIHGHRNGWGMLTRSPALGISFQAYQKLWRLAGVDHLH 299
 
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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