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Conserved domains on  [gi|996063902|gb|AMK01648|]
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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) ...
 1-181 1.49e-133

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: 381.74  E-value: 1.49e-133
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063902   1 DDENINSQPFMRWRERFLNCMEGINRASAATGEVKGSYLNITGGTMEEVYKRAEYAKSVGSVIVMIDLVM-GYTAIQSIA 79
Cdd:CHL00040 202 DDENVNSQPFMRWRDRFLFCAEAIYKAQAETGEIKGHYLNATAGTCEEMYKRAVFARELGVPIVMHDYLTgGFTANTSLA 281

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063902  80 LWARENDMLLHLHRAGNSTYARQKNHGTNFRVICKWMRMSGVDHIHAGTVVGKLEGDPLMIKGFYDSLLATNLEVNLPCG 159
Cdd:CHL00040 282 HYCRDNGLLLHIHRAMHAVIDRQKNHGIHFRVLAKALRMSGGDHIHAGTVVGKLEGEREMTLGFVDLLRDDFIEKDRSRG 361

                        170       180
                 ....*....|....*....|..
gi 996063902 160 IFFEMTWASLRKCMPVASGGIH 181
Cdd:CHL00040 362 IYFTQDWVSLPGVLPVASGGIH 383
 
Name Accession Description Interval E-value
rbcL CHL00040
ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
 1-181 1.49e-133

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


Pssm-ID: 176981  Cd Length: 475  Bit Score: 381.74  E-value: 1.49e-133
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063902   1 DDENINSQPFMRWRERFLNCMEGINRASAATGEVKGSYLNITGGTMEEVYKRAEYAKSVGSVIVMIDLVM-GYTAIQSIA 79
Cdd:CHL00040 202 DDENVNSQPFMRWRDRFLFCAEAIYKAQAETGEIKGHYLNATAGTCEEMYKRAVFARELGVPIVMHDYLTgGFTANTSLA 281

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063902  80 LWARENDMLLHLHRAGNSTYARQKNHGTNFRVICKWMRMSGVDHIHAGTVVGKLEGDPLMIKGFYDSLLATNLEVNLPCG 159
Cdd:CHL00040 282 HYCRDNGLLLHIHRAMHAVIDRQKNHGIHFRVLAKALRMSGGDHIHAGTVVGKLEGEREMTLGFVDLLRDDFIEKDRSRG 361

                        170       180
                 ....*....|....*....|..
gi 996063902 160 IFFEMTWASLRKCMPVASGGIH 181
Cdd:CHL00040 362 IYFTQDWVSLPGVLPVASGGIH 383
RuBisCO_large_I cd08212
Ribulose bisphosphate carboxylase large chain, Form I; Ribulose bisphosphate carboxylase ...
 1-181 2.82e-125

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: 359.82  E-value: 2.82e-125
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063902   1 DDENINSQPFMRWRERFLNCMEGINRASAATGEVKGSYLNITGGTMEEVYKRAEYAKSVGSVIVMIDLVMGYTAIQSIAL 80
Cdd:cd08212  180 DDENINSQPFMRWRDRFLFVAEAVNKAQAETGEVKGHYLNVTAGTMEEMYKRAEFAKELGSPIIMHDLLTGFTAIQSLAK 259

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063902  81 WARENDMLLHLHRAGNSTYARQKNHGTNFRVICKWMRMSGVDHIHAGTVVGKLEGDPLMIKGFYDSLLATNLEVNLPCGI 160
Cdd:cd08212  260 WCRDNGMLLHLHRAGHATYDRQKNHGIHFRVLAKWLRLSGVDHIHAGTVVGKLEGDPLVTLGFYDLLRDDYIEKDRSRGI 339

                        170       180
                 ....*....|....*....|.
gi 996063902 161 FFEMTWASLRKCMPVASGGIH 181
Cdd:cd08212  340 FFTQDWASLPGVMPVASGGIH 360
RuBisCO_large pfam00016
Ribulose bisphosphate carboxylase large chain, catalytic domain; The C-terminal domain of ...
 1-181 9.98e-90

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: 264.22  E-value: 9.98e-90
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063902    1 DDENINSQPFMRWRERFLNCMEGINRASAATGEVKGSYLNITGGTMEEVYKRAEYAKSVGSVIVMID-LVMGYTAIQSIA 79
Cdd:pfam00016  48 DDENINSQPFMPWRDRFLFVAEAIDRAQDETGEAKGHYLNITADDMEEMYRRAEFAKETGGVAVMVDgLVIGPTAITTLR 127

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063902   80 LWARENDMLLHLHRAGNSTYARQKNHGTNFRVICKWMRMSGVDHIHAGTV-VGKLEGDPLmikgfyDSLLATNLEVNLPC 158
Cdd:pfam00016 128 RWFRDNGVILHYHRAGHGAVTRQSKHGISFRVLAKMARLAGADHLHTGTMgVGKLEGDPS------DTLRAYMLEEDRAR 201

                         170       180
                  ....*....|....*....|...
gi 996063902  159 GIFFEMTWASLRKCMPVASGGIH 181
Cdd:pfam00016 202 GPFFDQDWGGMPAVMPVASGGIH 224
RbcL COG1850
Ribulose 1,5-bisphosphate carboxylase, large subunit, or a RuBisCO-like protein [Carbohydrate ...
 1-181 3.68e-61

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


Pssm-ID: 441455  Cd Length: 417  Bit Score: 195.00  E-value: 3.68e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063902   1 DDENINSQPFMRWRERFLNCMEGINRASAATGEVKGSYLNITGgTMEEVYKRAEYAKSVGSVIVMID-LVMGYTAIQSIA 79
Cdd:COG1850  182 DDENLADQPFCPFEDRVRAVMEAIDRAEEETGEKKMYAFNITA-DTDEMLRRADLAVELGANAVMVDvNTVGLSAVQTLR 260

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063902  80 lwARENDMLLHLHRAGNSTYARQKNHGTNFRVICKWMRMSGVDHIHAGTVVGKLEGDPLMIKGFYDSLLAtnlevnlpcg 159
Cdd:COG1850  261 --EEHIGLPIHAHRAGHGAFTRSPLHGISMRVLAKLWRLAGADHLHVGTPVGKMEGDDEEVLAIADALLQ---------- 328

                        170       180
                 ....*....|....*....|..
gi 996063902 160 iffemTWASLRKCMPVASGGIH 181
Cdd:COG1850  329 -----PWGGLKPVFPVPSGGQH 345
 
Name Accession Description Interval E-value
rbcL CHL00040
ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
 1-181 1.49e-133

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


Pssm-ID: 176981  Cd Length: 475  Bit Score: 381.74  E-value: 1.49e-133
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063902   1 DDENINSQPFMRWRERFLNCMEGINRASAATGEVKGSYLNITGGTMEEVYKRAEYAKSVGSVIVMIDLVM-GYTAIQSIA 79
Cdd:CHL00040 202 DDENVNSQPFMRWRDRFLFCAEAIYKAQAETGEIKGHYLNATAGTCEEMYKRAVFARELGVPIVMHDYLTgGFTANTSLA 281

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063902  80 LWARENDMLLHLHRAGNSTYARQKNHGTNFRVICKWMRMSGVDHIHAGTVVGKLEGDPLMIKGFYDSLLATNLEVNLPCG 159
Cdd:CHL00040 282 HYCRDNGLLLHIHRAMHAVIDRQKNHGIHFRVLAKALRMSGGDHIHAGTVVGKLEGEREMTLGFVDLLRDDFIEKDRSRG 361

                        170       180
                 ....*....|....*....|..
gi 996063902 160 IFFEMTWASLRKCMPVASGGIH 181
Cdd:CHL00040 362 IYFTQDWVSLPGVLPVASGGIH 383
RuBisCO_large_I cd08212
Ribulose bisphosphate carboxylase large chain, Form I; Ribulose bisphosphate carboxylase ...
 1-181 2.82e-125

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: 359.82  E-value: 2.82e-125
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063902   1 DDENINSQPFMRWRERFLNCMEGINRASAATGEVKGSYLNITGGTMEEVYKRAEYAKSVGSVIVMIDLVMGYTAIQSIAL 80
Cdd:cd08212  180 DDENINSQPFMRWRDRFLFVAEAVNKAQAETGEVKGHYLNVTAGTMEEMYKRAEFAKELGSPIIMHDLLTGFTAIQSLAK 259

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063902  81 WARENDMLLHLHRAGNSTYARQKNHGTNFRVICKWMRMSGVDHIHAGTVVGKLEGDPLMIKGFYDSLLATNLEVNLPCGI 160
Cdd:cd08212  260 WCRDNGMLLHLHRAGHATYDRQKNHGIHFRVLAKWLRLSGVDHIHAGTVVGKLEGDPLVTLGFYDLLRDDYIEKDRSRGI 339

                        170       180
                 ....*....|....*....|.
gi 996063902 161 FFEMTWASLRKCMPVASGGIH 181
Cdd:cd08212  340 FFTQDWASLPGVMPVASGGIH 360
rbcL PRK04208
ribulose bisophosphate carboxylase; Reviewed
 1-181 1.40e-106

ribulose bisophosphate carboxylase; Reviewed


Pssm-ID: 179787  Cd Length: 468  Bit Score: 313.00  E-value: 1.40e-106
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063902   1 DDENINSQPFMRWRERFLNCMEGINRASAATGEVKGSYLNITGGTMEEVYKRAEYAKSVGSVIVMIDLVM-GYTAIQSIA 79
Cdd:PRK04208 195 DDENLNSQPFNRWRDRFLFVMEAIDKAEAETGERKGHYLNVTAPTMEEMYKRAEFAKELGSPIVMIDVVTaGWTALQSLR 274

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063902  80 LWARENDMLLHLHRAGNSTYARQKNHGTNFRVICKWMRMSGVDHIHAGTVVGKLEGDPLMIKGFYDSLLATNLEVNLPCG 159
Cdd:PRK04208 275 EWCRDNGLALHAHRAMHAAFTRNPNHGISFRVLAKLLRLIGVDHLHTGTVVGKLEGDRAEVLGYYDILREDFVPEDRSRG 354

                        170       180
                 ....*....|....*....|..
gi 996063902 160 IFFEMTWASLRKCMPVASGGIH 181
Cdd:PRK04208 355 IFFDQDWGSIKPVFPVASGGIH 376
RuBisCO_large_I_II_III cd08206
Ribulose bisphosphate carboxylase large chain, Form I,II,III; Ribulose bisphosphate ...
 1-181 3.07e-100

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: 294.91  E-value: 3.07e-100
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063902   1 DDENINSQPFMRWRERFLNCMEGINRASAATGEVKGSYLNITGGTMEEVYKRAEYAKSVGSVIVMIDLV-MGYTAIQSIA 79
Cdd:cd08206  167 DDENQNSQPFMRFEDRILFVAEAMDKAEAETGEAKGHYLNITADTPEEMIKRAEFAKELGSVIVMVDGVtAGWTAIQSAR 246

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063902  80 LWARENDMLLHLHRAGNSTYARQKNHGTNFRVICKWMRMSGVDHIHAGTVVGKLEGDPLMIKGFYDSLLATNLEVNLPcG 159
Cdd:cd08206  247 RWCPDNGLALHAHRAGHAAFTRQKNHGISMRVLAKLARLIGVDHIHTGTVVGKLEGDPSEVKGIADMLREDEVEGDLS-R 325

                        170       180
                 ....*....|....*....|..
gi 996063902 160 IFFEMTWASLRKCMPVASGGIH 181
Cdd:cd08206  326 IFFNQDWGGMKPVFPVASGGLH 347
RuBisCO_large pfam00016
Ribulose bisphosphate carboxylase large chain, catalytic domain; The C-terminal domain of ...
 1-181 9.98e-90

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: 264.22  E-value: 9.98e-90
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063902    1 DDENINSQPFMRWRERFLNCMEGINRASAATGEVKGSYLNITGGTMEEVYKRAEYAKSVGSVIVMID-LVMGYTAIQSIA 79
Cdd:pfam00016  48 DDENINSQPFMPWRDRFLFVAEAIDRAQDETGEAKGHYLNITADDMEEMYRRAEFAKETGGVAVMVDgLVIGPTAITTLR 127

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063902   80 LWARENDMLLHLHRAGNSTYARQKNHGTNFRVICKWMRMSGVDHIHAGTV-VGKLEGDPLmikgfyDSLLATNLEVNLPC 158
Cdd:pfam00016 128 RWFRDNGVILHYHRAGHGAVTRQSKHGISFRVLAKMARLAGADHLHTGTMgVGKLEGDPS------DTLRAYMLEEDRAR 201

                         170       180
                  ....*....|....*....|...
gi 996063902  159 GIFFEMTWASLRKCMPVASGGIH 181
Cdd:pfam00016 202 GPFFDQDWGGMPAVMPVASGGIH 224
RbcL COG1850
Ribulose 1,5-bisphosphate carboxylase, large subunit, or a RuBisCO-like protein [Carbohydrate ...
 1-181 3.68e-61

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


Pssm-ID: 441455  Cd Length: 417  Bit Score: 195.00  E-value: 3.68e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063902   1 DDENINSQPFMRWRERFLNCMEGINRASAATGEVKGSYLNITGgTMEEVYKRAEYAKSVGSVIVMID-LVMGYTAIQSIA 79
Cdd:COG1850  182 DDENLADQPFCPFEDRVRAVMEAIDRAEEETGEKKMYAFNITA-DTDEMLRRADLAVELGANAVMVDvNTVGLSAVQTLR 260

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063902  80 lwARENDMLLHLHRAGNSTYARQKNHGTNFRVICKWMRMSGVDHIHAGTVVGKLEGDPLMIKGFYDSLLAtnlevnlpcg 159
Cdd:COG1850  261 --EEHIGLPIHAHRAGHGAFTRSPLHGISMRVLAKLWRLAGADHLHVGTPVGKMEGDDEEVLAIADALLQ---------- 328

                        170       180
                 ....*....|....*....|..
gi 996063902 160 iffemTWASLRKCMPVASGGIH 181
Cdd:COG1850  329 -----PWGGLKPVFPVPSGGQH 345
RuBisCO_large cd08148
Ribulose bisphosphate carboxylase large chain; Ribulose bisphosphate carboxylase (Rubisco) ...
 1-181 3.39e-52

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: 170.69  E-value: 3.39e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063902   1 DDENINSQPFMRWRERFLNCMEGINRASAATGEVKGSYLNITGGTmEEVYKRAEYAKSVGSVIVMID-LVMGYTAIQSIA 79
Cdd:cd08148  162 DDETLTDQPFCPLRDRITEVAAALDRVQEETGEKKLYAVNVTAGT-FEIIERAERALELGANMLMVDvLTAGFSALQALA 240

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063902  80 LwARENDMLLHLHRAGNSTYARQKNHGTNFRVICKWMRMSGVDHIHAGTVVGKLEGDPLMIKGFYDSLlatnlevnlpcg 159
Cdd:cd08148  241 E-DFEIDLPIHVHRAMHGAVTRSKFHGISMLVLAKLLRMAGGDFIHTGTVVGKMALEREEALGIADAL------------ 307

                        170       180
                 ....*....|....*....|..
gi 996063902 160 iffEMTWASLRKCMPVASGGIH 181
Cdd:cd08148  308 ---TDDWAGFKRVFPVASGGIH 326
RuBisCO_large_III cd08213
Ribulose bisphosphate carboxylase large chain, Form III; Ribulose bisphosphate carboxylase ...
 1-181 2.55e-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: 151.39  E-value: 2.55e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063902   1 DDENINSQPFMRWRERFLNCMEGINRASAATGEVKGSYLNITGGTmEEVYKRAEYAKSVGSVIVMIDLVM-GYTAIQSIA 79
Cdd:cd08213  166 DDENLTSQPFNRFEERAKESLKARDKAEAETGERKAYLANITAPV-REMERRAELVADLGGKYVMIDVVVaGWSALQYLR 244

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063902  80 LWARENDMLLHLHRAGNSTYARQKNHGTNFRVICKWMRMSGVDHIHAGTVVGKLEGDPLMIKGFYDsLLATNLEVNLPCG 159
Cdd:cd08213  245 DLAEDYGLAIHAHRAMHAAFTRNPRHGISMLVLAKLYRLIGVDQLHIGTAVGKMEGDKEEVLRIAD-ILREQKYKPDEED 323

                        170       180
                 ....*....|....*....|..
gi 996063902 160 IFFEMTWASLRKCMPVASGGIH 181
Cdd:cd08213  324 FHLAQDWGGIKPVFPVASGGLH 345
RuBisCO_large_II cd08211
Ribulose bisphosphate carboxylase large chain, Form II; Ribulose bisphosphate carboxylase ...
 1-180 4.69e-21

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


Pssm-ID: 173976  Cd Length: 439  Bit Score: 89.10  E-value: 4.69e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063902   1 DDENINSQPFMRWRERFLNCMEGINRASAATGEVKGSYLNITGGTMEEVYKRAEYAKSV-----GSVIVMID-LVMGYTA 74
Cdd:cd08211  191 NDEPQANQPFCPLKKVIPLVADAMRRAQDETGEAKLFSANITADDPDEMIARGEYILEAfgpnaGHVAFLVDgYVAGPAA 270

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063902  75 IQSialwAREN--DMLLHLHRAGNSTYARQKNH-GTNFRVICKWMRMSGVDHIHAGTV-VGKLEGDPlmikgfYDSLLAT 150
Cdd:cd08211  271 VTT----ARRRfpDQFLHYHRAGHGAVTSPQSKrGYTAFVLSKMARLQGASGIHTGTMgFGKMEGES------SDKVIAY 340

                        170       180       190
                 ....*....|....*....|....*....|
gi 996063902 151 NLEVNLPCGIFFEMTWASLRKCMPVASGGI 180
Cdd:cd08211  341 MIERDEAQGPLFNQKWYGMKPTTPIISGGM 370
RuBisCO_IV_RLP cd08205
Ribulose bisphosphate carboxylase like proteins, Rubisco-Form IV; Ribulose bisphosphate ...
 1-181 1.11e-20

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: 87.20  E-value: 1.11e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063902   1 DDENINSQPFMRWRERFLNCMEGINRASAATGEvKGSYL-NITGGTmEEVYKRAEYAKSVGSVIVMIDL-VMGYTAIQSI 78
Cdd:cd08205  165 DDELLADQPYAPFEERVRACMEAVRRANEETGR-KTLYApNITGDP-DELRRRADRAVEAGANALLINPnLVGLDALRAL 242

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063902  79 AlwaRENDMLLHLHRAGNSTYARQKNHGTNFRVICKWMRMSGVDHIHAGTVVGKLegdplmikGF-YDSLLATNLEVNLP 157
Cdd:cd08205  243 A---EDPDLPIMAHPAFAGALSRSPDYGSHFLLLGKLMRLAGADAVIFPGPGGRF--------PFsREECLAIARACRRP 311

                        170       180
                 ....*....|....*....|....
gi 996063902 158 cgiffemtWASLRKCMPVASGGIH 181
Cdd:cd08205  312 --------LGGIKPALPVPSGGMH 327
PRK13475 PRK13475
ribulose-bisphosphate carboxylase;
1-180 1.87e-19

ribulose-bisphosphate carboxylase;


Pssm-ID: 184072  Cd Length: 443  Bit Score: 84.39  E-value: 1.87e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063902   1 DDENINSQPFMRWRERFLNCMEGINRASAATGEVKGSYLNITGGTMEEVYKRAEY-----AKSVGSVIVMID-LVMGYTA 74
Cdd:PRK13475 192 NDEPQGNQVFAPLKKTVPLVADAMKRAQDETGEAKLFSANITADDHYEMIARGEYiletfGENADHVAFLVDgYVAGPGA 271

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063902  75 IQSialwAREN--DMLLHLHRAGNSTYARQKN-HGTNFRVICKWMRMSGVDHIHAGTV-VGKLEGDPlmikgfYDSLLAT 150
Cdd:PRK13475 272 VTT----ARRQypDQYLHYHRAGHGAVTSPSSkRGYTAFVLSKMARLQGASGIHTGTMgYGKMEGEA------DDRVIAY 341

                        170       180       190
                 ....*....|....*....|....*....|
gi 996063902 151 NLEVNLPCGIFFEMTWASLRKCMPVASGGI 180
Cdd:PRK13475 342 MIERDSAQGPFYHQEWYGMKPTTPIISGGM 371
RLP_NonPhot cd08207
Ribulose bisphosphate carboxylase like proteins from nonphototrophic bacteria; Ribulose ...
 1-179 1.79e-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: 70.03  E-value: 1.79e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063902   1 DDENINSQPFMRWRERFLNCMEGINRASAATGEvKGSY-LNITGGTmEEVYKRAEYAKSVGSVIVMIDL-VMGYTAIQSI 78
Cdd:cd08207  178 DDELLANPPYSPLDERVRAVMRVINDHAQRTGR-KVMYaFNITDDI-DEMRRNHDLVVEAGGTCVMVSLnSVGLSGLAAL 255

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063902  79 AlwaRENDMLLHLHRAGNSTYARQKNHGTNFRVICKWMRMSGVDHIHAGTVVGKL-EGDPLMIKGFYDSLlaTNLevnlp 157
Cdd:cd08207  256 R---RHSQLPIHGHRNGWGMLTRSPALGISFQAYQKLWRLAGVDHLHVNGLASKFwESDDSVIESARACL--TPL----- 325

                        170       180
                 ....*....|....*....|..
gi 996063902 158 cgiffemtWASLRKCMPVASGG 179
Cdd:cd08207  326 --------GGPDDAAMPVFSSG 339
RLP_RrRLP cd08210
Ribulose bisphosphate carboxylase like proteins (RLPs) similar to R.rubrum RLP; RLP from ...
 1-66 1.11e-06

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: 47.62  E-value: 1.11e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 996063902   1 DDENINSQPFMRWRERFLNCMEGINRASAATGEvKGSYL-NITGGTMeEVYKRAEYAKSVGSVIVMI 66
Cdd:cd08210  160 DDHGLADQPFAPFEERVKACQEAVAEANAETGG-RTLYApNVTGPPT-QLLERARFAKEAGAGGVLI 224
RLP_Photo cd08208
Ribulose bisphosphate carboxylase like proteins from phototrophic bacteria; Ribulose ...
 1-178 1.92e-03

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: 37.95  E-value: 1.92e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063902   1 DDENINSQPFMRWRERFLNCMEGINRASAATGEVKGSYLNITgGTMEEVYKRAEYAKSVGSVIVMID-LVMGYTAIQSIA 79
Cdd:cd08208  195 DDEMLADVDWCPLEERAALLGKARRRAEAETGVPKIYLANIT-DEVDRLMELHDVAVRNGANALLINaMPVGLSAVRMLR 273

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063902  80 LWARendMLLHLHRAGNSTYARQKNHGTNFRVICKWMRMSGVDHIhagtvvgklegdplMIKGFYDSLLATNLEVnLPCG 159
Cdd:cd08208  274 KHAQ---VPLIAHFPFIASFSRLEKYGIHSRVMTKLQRLAGLDVV--------------IMPGFGPRMMTPEEEV-LECV 335

                        170
                 ....*....|....*....
gi 996063902 160 IFFEMTWASLRKCMPVASG 178
Cdd:cd08208  336 IACLEPMGPIKPCLPVPGG 354
 
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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