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Conserved domains on  [gi|1787117973|ref|WP_157785715|]
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ribulose bisphosphate carboxylase small subunit, partial [Clostridium tunisiense]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PLN02289 super family cl42969
ribulose-bisphosphate carboxylase small chain
 1-96 1.83e-64

ribulose-bisphosphate carboxylase small chain


The actual alignment was detected with superfamily member PLN02289:

Pssm-ID: 215163 [Multi-domain]  Cd Length: 176  Bit Score: 192.39  E-value: 1.83e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1787117973   1 QLLKQIDFLLQNKWIPCLEFTLKNPYPYRENNRSPGYYDGRYWTMWKLPMFGCTDSVQVANELDEAVKAYPQGFVSIIGF 80
Cdd:PLN02289   80 ELAKEVDYLLRNKWVPCLEFELEHGFVYREHHRSPGYYDGRYWTMWKLPMFGCTDSAQVLKELEEAKKAYPNAFIRIIGF 159

                          90
                  ....*....|....*.
gi 1787117973  81 DNVRQVQLIAFIAYKP 96
Cdd:PLN02289  160 DNTRQVQCISFIAYKP 175
 
Name Accession Description Interval E-value
PLN02289 PLN02289
ribulose-bisphosphate carboxylase small chain
 1-96 1.83e-64

ribulose-bisphosphate carboxylase small chain


Pssm-ID: 215163 [Multi-domain]  Cd Length: 176  Bit Score: 192.39  E-value: 1.83e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1787117973   1 QLLKQIDFLLQNKWIPCLEFTLKNPYPYRENNRSPGYYDGRYWTMWKLPMFGCTDSVQVANELDEAVKAYPQGFVSIIGF 80
Cdd:PLN02289   80 ELAKEVDYLLRNKWVPCLEFELEHGFVYREHHRSPGYYDGRYWTMWKLPMFGCTDSAQVLKELEEAKKAYPNAFIRIIGF 159

                          90
                  ....*....|....*.
gi 1787117973  81 DNVRQVQLIAFIAYKP 96
Cdd:PLN02289  160 DNTRQVQCISFIAYKP 175
RuBisCO_small cd03527
Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit. Rubisco is a ...
 1-96 4.64e-42

Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit. Rubisco is a bifunctional enzyme catalyzes the initial steps of two opposing metabolic pathways: photosynthetic carbon fixation and the competing process of photorespiration. Rubisco Form I, present in plants and green algae, is composed of eight large and eight small subunits. The nearly identical small subunits are encoded by a family of nuclear genes. After translation, the small subunits are translocated across the chloroplast membrane, where an N-terminal signal peptide is cleaved off. While the large subunits contain the catalytic activities, it has been shown that the small subunits are important for catalysis by enhancing the catalytic rate through inducing conformational changes in the large subunits.


Pssm-ID: 239603  Cd Length: 99  Bit Score: 132.77  E-value: 4.64e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1787117973  1 QLLKQIDFLLQNKWIPCLEFTlknpypyrennrSPGYYDGRYWTMWKLPMFGCTDSVQVANELDEAVKAYPQGFVSIIGF 80
Cdd:cd03527   16 QIAKQIDYIISNGWAPCLEFT------------EPEHYDNRYWTMWKLPMFGCTDPAQVLREIEACRKAYPDHYVRVVGF 83

                         90
                 ....*....|....*.
gi 1787117973 81 DNVRQVQLIAFIAYKP 96
Cdd:cd03527   84 DNYKQSQCMSFIVHRP 99
RuBisCO_small pfam00101
Ribulose bisphosphate carboxylase, small chain;
1-96 3.48e-38

Ribulose bisphosphate carboxylase, small chain;


Pssm-ID: 425465  Cd Length: 97  Bit Score: 122.99  E-value: 3.48e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1787117973  1 QLLKQIDFLLQNKWIPCLEFTlKNPYPyrennrspgyyDGRYWTMWKLPMFGCTDSVQVANELDEAVKAYPQGFVSIIGF 80
Cdd:pfam00101 14 QIAKQVQYILSQGWIPGIEFT-DDPHP-----------RNRYWTMWKLPMFGCTDPAQVLAELEACRKAYPNHYIRLIGF 81

                         90
                 ....*....|....*.
gi 1787117973 81 DNVRQVQLIAFIAYKP 96
Cdd:pfam00101 82 DNYRQSQVMSFIVQRP 97
RbcS COG4451
Ribulose bisphosphate carboxylase small subunit [Carbohydrate transport and metabolism];
1-96 3.65e-25

Ribulose bisphosphate carboxylase small subunit [Carbohydrate transport and metabolism];


Pssm-ID: 443549  Cd Length: 102  Bit Score: 90.26  E-value: 3.65e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1787117973   1 QLLKQIDFLLQNKWIPCLEFTlknpypyreNNRSPGYYdgrYWTMWKLPMFGCTDSVQVANELDEAVKAYPQGFVSIIGF 80
Cdd:COG4451    18 EIVAQVRYLLAQGWAIGIEHA---------DDRRFRTT---YWQMWKLPMFDSTDEAEVLAELEACRKEHPGEYVRLIGI 85

                          90
                  ....*....|....*.
gi 1787117973  81 DNVRQVQLIAFIAYKP 96
Cdd:COG4451    86 DPKAKRRVLEFIVQRP 101
RuBisCO_small smart00961
Ribulose bisphosphate carboxylase, small chain; RuBisCO (ribulose-1,5-bisphosphate carboxylase ...
 1-96 9.84e-24

Ribulose bisphosphate carboxylase, small chain; RuBisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) is a bifunctional enzyme that catalyses both the carboxylation and oxygenation of ribulose-1,5-bisphosphate (RuBP), thus fixing carbon dioxide as the first step of the Calvin cycle. RuBisCO is the major protein in the stroma of chloroplasts, and in higher plants exists as a complex of 8 large and 8 small subunits. The function of the small subunit is unknown. While the large subunit is coded for by a single gene, the small subunit is coded for by several different genes, which are distributed in a tissue specific manner. They are transcriptionally regulated by light receptor phytochrome. which results in RuBisCO being more abundant during the day when it is required.


Pssm-ID: 198029  Cd Length: 96  Bit Score: 86.44  E-value: 9.84e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1787117973   1 QLLKQIDFLLQNKWIPCLEFTlknpypyrennrSPGYYDGRYWTmwKLPMFGCTDSVQVANELDEAVKAYPQGFVSIIGF 80
Cdd:smart00961 15 EIVAQVRYLLAQGYAIGVEHA------------DPRRFRTSSWQ--KLPMFGATDAAEVLAELEACLAEHPGEYVRLIGI 80

                          90
                  ....*....|....*.
gi 1787117973  81 DNVRQVQLIAFIAYKP 96
Cdd:smart00961 81 DPKAKRRVLEFIIQRP 96
 
Name Accession Description Interval E-value
PLN02289 PLN02289
ribulose-bisphosphate carboxylase small chain
 1-96 1.83e-64

ribulose-bisphosphate carboxylase small chain


Pssm-ID: 215163 [Multi-domain]  Cd Length: 176  Bit Score: 192.39  E-value: 1.83e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1787117973   1 QLLKQIDFLLQNKWIPCLEFTLKNPYPYRENNRSPGYYDGRYWTMWKLPMFGCTDSVQVANELDEAVKAYPQGFVSIIGF 80
Cdd:PLN02289   80 ELAKEVDYLLRNKWVPCLEFELEHGFVYREHHRSPGYYDGRYWTMWKLPMFGCTDSAQVLKELEEAKKAYPNAFIRIIGF 159

                          90
                  ....*....|....*.
gi 1787117973  81 DNVRQVQLIAFIAYKP 96
Cdd:PLN02289  160 DNTRQVQCISFIAYKP 175
RuBisCO_small cd03527
Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit. Rubisco is a ...
 1-96 4.64e-42

Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit. Rubisco is a bifunctional enzyme catalyzes the initial steps of two opposing metabolic pathways: photosynthetic carbon fixation and the competing process of photorespiration. Rubisco Form I, present in plants and green algae, is composed of eight large and eight small subunits. The nearly identical small subunits are encoded by a family of nuclear genes. After translation, the small subunits are translocated across the chloroplast membrane, where an N-terminal signal peptide is cleaved off. While the large subunits contain the catalytic activities, it has been shown that the small subunits are important for catalysis by enhancing the catalytic rate through inducing conformational changes in the large subunits.


Pssm-ID: 239603  Cd Length: 99  Bit Score: 132.77  E-value: 4.64e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1787117973  1 QLLKQIDFLLQNKWIPCLEFTlknpypyrennrSPGYYDGRYWTMWKLPMFGCTDSVQVANELDEAVKAYPQGFVSIIGF 80
Cdd:cd03527   16 QIAKQIDYIISNGWAPCLEFT------------EPEHYDNRYWTMWKLPMFGCTDPAQVLREIEACRKAYPDHYVRVVGF 83

                         90
                 ....*....|....*.
gi 1787117973 81 DNVRQVQLIAFIAYKP 96
Cdd:cd03527   84 DNYKQSQCMSFIVHRP 99
RuBisCO_small pfam00101
Ribulose bisphosphate carboxylase, small chain;
1-96 3.48e-38

Ribulose bisphosphate carboxylase, small chain;


Pssm-ID: 425465  Cd Length: 97  Bit Score: 122.99  E-value: 3.48e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1787117973  1 QLLKQIDFLLQNKWIPCLEFTlKNPYPyrennrspgyyDGRYWTMWKLPMFGCTDSVQVANELDEAVKAYPQGFVSIIGF 80
Cdd:pfam00101 14 QIAKQVQYILSQGWIPGIEFT-DDPHP-----------RNRYWTMWKLPMFGCTDPAQVLAELEACRKAYPNHYIRLIGF 81

                         90
                 ....*....|....*.
gi 1787117973 81 DNVRQVQLIAFIAYKP 96
Cdd:pfam00101 82 DNYRQSQVMSFIVQRP 97
RbcS COG4451
Ribulose bisphosphate carboxylase small subunit [Carbohydrate transport and metabolism];
1-96 3.65e-25

Ribulose bisphosphate carboxylase small subunit [Carbohydrate transport and metabolism];


Pssm-ID: 443549  Cd Length: 102  Bit Score: 90.26  E-value: 3.65e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1787117973   1 QLLKQIDFLLQNKWIPCLEFTlknpypyreNNRSPGYYdgrYWTMWKLPMFGCTDSVQVANELDEAVKAYPQGFVSIIGF 80
Cdd:COG4451    18 EIVAQVRYLLAQGWAIGIEHA---------DDRRFRTT---YWQMWKLPMFDSTDEAEVLAELEACRKEHPGEYVRLIGI 85

                          90
                  ....*....|....*.
gi 1787117973  81 DNVRQVQLIAFIAYKP 96
Cdd:COG4451    86 DPKAKRRVLEFIVQRP 101
RuBisCO_small smart00961
Ribulose bisphosphate carboxylase, small chain; RuBisCO (ribulose-1,5-bisphosphate carboxylase ...
 1-96 9.84e-24

Ribulose bisphosphate carboxylase, small chain; RuBisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) is a bifunctional enzyme that catalyses both the carboxylation and oxygenation of ribulose-1,5-bisphosphate (RuBP), thus fixing carbon dioxide as the first step of the Calvin cycle. RuBisCO is the major protein in the stroma of chloroplasts, and in higher plants exists as a complex of 8 large and 8 small subunits. The function of the small subunit is unknown. While the large subunit is coded for by a single gene, the small subunit is coded for by several different genes, which are distributed in a tissue specific manner. They are transcriptionally regulated by light receptor phytochrome. which results in RuBisCO being more abundant during the day when it is required.


Pssm-ID: 198029  Cd Length: 96  Bit Score: 86.44  E-value: 9.84e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1787117973   1 QLLKQIDFLLQNKWIPCLEFTlknpypyrennrSPGYYDGRYWTmwKLPMFGCTDSVQVANELDEAVKAYPQGFVSIIGF 80
Cdd:smart00961 15 EIVAQVRYLLAQGYAIGVEHA------------DPRRFRTSSWQ--KLPMFGATDAAEVLAELEACLAEHPGEYVRLIGI 80

                          90
                  ....*....|....*.
gi 1787117973  81 DNVRQVQLIAFIAYKP 96
Cdd:smart00961 81 DPKAKRRVLEFIIQRP 96
rbcS CHL00130
ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit; Reviewed
 1-96 2.33e-20

ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit; Reviewed


Pssm-ID: 177052  Cd Length: 138  Bit Score: 79.03  E-value: 2.33e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1787117973   1 QLLKQIDFLLQNKWIPCLEFTlKNPYPyrENNrspgyydgrYWTMWKLPMFGCTDSVQVANELDEAVKAYPQGFVSIIGF 80
Cdd:CHL00130   18 QIEKQIQYAISKGWALNVEWT-DDPHP--RNS---------YWELWGLPLFDVKDPAAVMFEINECRKQKPNGYIKVNAF 85

                          90
                  ....*....|....*...
gi 1787117973  81 DNVRQVQ--LIAFIAYKP 96
Cdd:CHL00130   86 DASRGVEscVLSFIVNRP 103
RuBisCO_small_like cd00307
Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit and related proteins. ...
 1-96 3.90e-14

Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit and related proteins. Rubisco is a bifunctional enzyme catalyzes the initial steps of two opposing metabolic pathways: photosynthetic carbon fixation and the competing process of photorespiration. Rubisco Form I, present in plants and green algae, is composed of eight large and eight small subunits. The nearly identical small subunits are encoded by a family of nuclear genes. After translation, the small subunits are translocated across the chloroplast membrane, where an N-terminal signal peptide is cleaved off. While the large subunits contain the catalytic activities, it has been shown that the small subunits are important for catalysis by enhancing the catalytic rate through inducing conformational changes in the large subunits. This superfamily also contains specific proteins from cyanobacteria. CcmM plays a role in a CO2 concentrating mechanism, which cyanobacteria need to to overcome the low specificity of their Rubisco and fusions to Rubisco activase, a type of chaperone, which promotes and maintains the catalytic activity of Rubisco. CcmM contains an N-terminal carbonic anhydrase fused to four copies of the Rubisco-small subunit domain


Pssm-ID: 238187  Cd Length: 84  Bit Score: 61.91  E-value: 3.90e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1787117973  1 QLLKQIDFLLQNKWIPCLEFTLKNpypyrennrspgyydgRYWTMWKLPMFGC--TDSVQVANELDEAVKAYPQGFVSII 78
Cdd:cd00307    3 DVVEQVRQLLAQGYKIGLEHADAR----------------RFRTSSWQSCGPIegRSEAQVLAALEACLAEHPGEYVRLI 66

                         90
                 ....*....|....*...
gi 1787117973 79 GFDNVRQVQLIAFIAYKP 96
Cdd:cd00307   67 GIDPKAKRRVLEIIIQRP 84
 
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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