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Conserved domains on  [gi|515242|pdb|1RLD|T]
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Chain T, Ribulose 1,5 Bisphosphate Carboxylase/oxygenase (small Chain)

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
 1-120 2.14e-89

ribulose-bisphosphate carboxylase small chain


The actual alignment was detected with superfamily member PLN02289:

Pssm-ID: 215163 [Multi-domain]  Cd Length: 176  Bit Score: 256.33  E-value: 2.14e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1RLD_T         1 MQVWPPINKKKYETLSYLPDLSQEQLLSEVEYLLKNGWVPCLEFETEHGFVYRENNKSPGYYDGRYWTMWKLPMFGCTDA 80
Cdd:PLN02289  56 MQVWPPIGKKKFETLSYLPDLTDEELAKEVDYLLRNKWVPCLEFELEHGFVYREHHRSPGYYDGRYWTMWKLPMFGCTDS 135

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
1RLD_T        81 TQVLAEVEEAKKAYPQAWIRIIGFDNVRQVQCISFIAYKP 120
Cdd:PLN02289 136 AQVLKELEEAKKAYPNAFIRIIGFDNTRQVQCISFIAYKP 175
 
Name Accession Description Interval E-value
PLN02289 PLN02289
ribulose-bisphosphate carboxylase small chain
 1-120 2.14e-89

ribulose-bisphosphate carboxylase small chain


Pssm-ID: 215163 [Multi-domain]  Cd Length: 176  Bit Score: 256.33  E-value: 2.14e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1RLD_T         1 MQVWPPINKKKYETLSYLPDLSQEQLLSEVEYLLKNGWVPCLEFETEHGFVYRENNKSPGYYDGRYWTMWKLPMFGCTDA 80
Cdd:PLN02289  56 MQVWPPIGKKKFETLSYLPDLTDEELAKEVDYLLRNKWVPCLEFELEHGFVYREHHRSPGYYDGRYWTMWKLPMFGCTDS 135

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
1RLD_T        81 TQVLAEVEEAKKAYPQAWIRIIGFDNVRQVQCISFIAYKP 120
Cdd:PLN02289 136 AQVLKELEEAKKAYPNAFIRIIGFDNTRQVQCISFIAYKP 175
RuBisCO_small cd03527
Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit. Rubisco is a ...
 10-120 1.33e-57

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: 173.21  E-value: 1.33e-57
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1RLD_T       10 KKYETLSYLPDLSQEQLLSEVEYLLKNGWVPCLEFETehgfvyrennksPGYYDGRYWTMWKLPMFGCTDATQVLAEVEE 89
Cdd:cd03527   1 RTFETFSYLPPLTDEQIAKQIDYIISNGWAPCLEFTE------------PEHYDNRYWTMWKLPMFGCTDPAQVLREIEA 68

                        90       100       110
                ....*....|....*....|....*....|.
1RLD_T       90 AKKAYPQAWIRIIGFDNVRQVQCISFIAYKP 120
Cdd:cd03527  69 CRKAYPDHYVRVVGFDNYKQSQCMSFIVHRP 99
RuBisCO_small pfam00101
Ribulose bisphosphate carboxylase, small chain;
12-120 8.34e-56

Ribulose bisphosphate carboxylase, small chain;


Pssm-ID: 425465  Cd Length: 97  Bit Score: 168.44  E-value: 8.34e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1RLD_T         12 YETLSYLPDLSQEQLLSEVEYLLKNGWVPCLEFETEHGFvyrennkspgyyDGRYWTMWKLPMFGCTDATQVLAEVEEAK 91
Cdd:pfam00101   1 FETFSYLPPLTDEQIAKQVQYILSQGWIPGIEFTDDPHP------------RNRYWTMWKLPMFGCTDPAQVLAELEACR 68

                          90       100
                  ....*....|....*....|....*....
1RLD_T         92 KAYPQAWIRIIGFDNVRQVQCISFIAYKP 120
Cdd:pfam00101  69 KAYPNHYIRLIGFDNYRQSQVMSFIVQRP 97
RbcS COG4451
Ribulose bisphosphate carboxylase small subunit [Carbohydrate transport and metabolism];
11-120 3.39e-38

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


Pssm-ID: 443549  Cd Length: 102  Bit Score: 124.16  E-value: 3.39e-38
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1RLD_T       11 KYETLSYLPDLSQEQLLSEVEYLLKNGWVPCLEF-ETEHgfvYRENnkspgyydgrYWTMWKLPMFGCTDATQVLAEVEE 89
Cdd:COG4451   4 TQETFSYLPPLLDAEIVAQVRYLLAQGWAIGIEHaDDRR---FRTT----------YWQMWKLPMFDSTDEAEVLAELEA 70

                        90       100       110
                ....*....|....*....|....*....|.
1RLD_T       90 AKKAYPQAWIRIIGFDNVRQVQCISFIAYKP 120
Cdd:COG4451  71 CRKEHPGEYVRLIGIDPKAKRRVLEFIVQRP 101
RuBisCO_small smart00961
Ribulose bisphosphate carboxylase, small chain; RuBisCO (ribulose-1,5-bisphosphate carboxylase ...
 11-120 3.44e-36

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: 119.18  E-value: 3.44e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1RLD_T          11 KYETLSYLPDLSQEQLLSEVEYLLKNGWVPCLEFEtehgfvyrennkSPGYYDGRYWTmwKLPMFGCTDATQVLAEVEEA 90
Cdd:smart00961   1 TQETFSYLPPLTDAEIVAQVRYLLAQGYAIGVEHA------------DPRRFRTSSWQ--KLPMFGATDAAEVLAELEAC 66

                           90       100       110
                   ....*....|....*....|....*....|
1RLD_T          91 KKAYPQAWIRIIGFDNVRQVQCISFIAYKP 120
Cdd:smart00961  67 LAEHPGEYVRLIGIDPKAKRRVLEFIIQRP 96
 
Name Accession Description Interval E-value
PLN02289 PLN02289
ribulose-bisphosphate carboxylase small chain
 1-120 2.14e-89

ribulose-bisphosphate carboxylase small chain


Pssm-ID: 215163 [Multi-domain]  Cd Length: 176  Bit Score: 256.33  E-value: 2.14e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1RLD_T         1 MQVWPPINKKKYETLSYLPDLSQEQLLSEVEYLLKNGWVPCLEFETEHGFVYRENNKSPGYYDGRYWTMWKLPMFGCTDA 80
Cdd:PLN02289  56 MQVWPPIGKKKFETLSYLPDLTDEELAKEVDYLLRNKWVPCLEFELEHGFVYREHHRSPGYYDGRYWTMWKLPMFGCTDS 135

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
1RLD_T        81 TQVLAEVEEAKKAYPQAWIRIIGFDNVRQVQCISFIAYKP 120
Cdd:PLN02289 136 AQVLKELEEAKKAYPNAFIRIIGFDNTRQVQCISFIAYKP 175
RuBisCO_small cd03527
Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit. Rubisco is a ...
 10-120 1.33e-57

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: 173.21  E-value: 1.33e-57
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1RLD_T       10 KKYETLSYLPDLSQEQLLSEVEYLLKNGWVPCLEFETehgfvyrennksPGYYDGRYWTMWKLPMFGCTDATQVLAEVEE 89
Cdd:cd03527   1 RTFETFSYLPPLTDEQIAKQIDYIISNGWAPCLEFTE------------PEHYDNRYWTMWKLPMFGCTDPAQVLREIEA 68

                        90       100       110
                ....*....|....*....|....*....|.
1RLD_T       90 AKKAYPQAWIRIIGFDNVRQVQCISFIAYKP 120
Cdd:cd03527  69 CRKAYPDHYVRVVGFDNYKQSQCMSFIVHRP 99
RuBisCO_small pfam00101
Ribulose bisphosphate carboxylase, small chain;
12-120 8.34e-56

Ribulose bisphosphate carboxylase, small chain;


Pssm-ID: 425465  Cd Length: 97  Bit Score: 168.44  E-value: 8.34e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1RLD_T         12 YETLSYLPDLSQEQLLSEVEYLLKNGWVPCLEFETEHGFvyrennkspgyyDGRYWTMWKLPMFGCTDATQVLAEVEEAK 91
Cdd:pfam00101   1 FETFSYLPPLTDEQIAKQVQYILSQGWIPGIEFTDDPHP------------RNRYWTMWKLPMFGCTDPAQVLAELEACR 68

                          90       100
                  ....*....|....*....|....*....
1RLD_T         92 KAYPQAWIRIIGFDNVRQVQCISFIAYKP 120
Cdd:pfam00101  69 KAYPNHYIRLIGFDNYRQSQVMSFIVQRP 97
RbcS COG4451
Ribulose bisphosphate carboxylase small subunit [Carbohydrate transport and metabolism];
11-120 3.39e-38

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


Pssm-ID: 443549  Cd Length: 102  Bit Score: 124.16  E-value: 3.39e-38
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1RLD_T       11 KYETLSYLPDLSQEQLLSEVEYLLKNGWVPCLEF-ETEHgfvYRENnkspgyydgrYWTMWKLPMFGCTDATQVLAEVEE 89
Cdd:COG4451   4 TQETFSYLPPLLDAEIVAQVRYLLAQGWAIGIEHaDDRR---FRTT----------YWQMWKLPMFDSTDEAEVLAELEA 70

                        90       100       110
                ....*....|....*....|....*....|.
1RLD_T       90 AKKAYPQAWIRIIGFDNVRQVQCISFIAYKP 120
Cdd:COG4451  71 CRKEHPGEYVRLIGIDPKAKRRVLEFIVQRP 101
RuBisCO_small smart00961
Ribulose bisphosphate carboxylase, small chain; RuBisCO (ribulose-1,5-bisphosphate carboxylase ...
 11-120 3.44e-36

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: 119.18  E-value: 3.44e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1RLD_T          11 KYETLSYLPDLSQEQLLSEVEYLLKNGWVPCLEFEtehgfvyrennkSPGYYDGRYWTmwKLPMFGCTDATQVLAEVEEA 90
Cdd:smart00961   1 TQETFSYLPPLTDAEIVAQVRYLLAQGYAIGVEHA------------DPRRFRTSSWQ--KLPMFGATDAAEVLAELEAC 66

                           90       100       110
                   ....*....|....*....|....*....|
1RLD_T          91 KKAYPQAWIRIIGFDNVRQVQCISFIAYKP 120
Cdd:smart00961  67 LAEHPGEYVRLIGIDPKAKRRVLEFIIQRP 96
rbcS CHL00130
ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit; Reviewed
 11-120 3.95e-29

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


Pssm-ID: 177052  Cd Length: 138  Bit Score: 102.53  E-value: 3.95e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1RLD_T        11 KYETLSYLPDLSQEQLLSEVEYLLKNGWVPCLEF-ETEHGfvyrENNkspgyydgrYWTMWKLPMFGCTDATQVLAEVEE 89
Cdd:CHL00130   4 TQGTFSFLPDLTDQQIEKQIQYAISKGWALNVEWtDDPHP----RNS---------YWELWGLPLFDVKDPAAVMFEINE 70

                         90       100       110
                 ....*....|....*....|....*....|...
1RLD_T        90 AKKAYPQAWIRIIGFDNVRQVQ--CISFIAYKP 120
Cdd:CHL00130  71 CRKQKPNGYIKVNAFDASRGVEscVLSFIVNRP 103
RuBisCO_small_like cd00307
Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit and related proteins. ...
 24-120 2.27e-17

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: 70.77  E-value: 2.27e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1RLD_T       24 EQLLSEVEYLLKNGWVPCLEFETEHgfvyrennkspgyydgRYWTMWKLPMFGC--TDATQVLAEVEEAKKAYPQAWIRI 101
Cdd:cd00307   2 EDVVEQVRQLLAQGYKIGLEHADAR----------------RFRTSSWQSCGPIegRSEAQVLAALEACLAEHPGEYVRL 65

                        90
                ....*....|....*....
1RLD_T      102 IGFDNVRQVQCISFIAYKP 120
Cdd:cd00307  66 IGIDPKAKRRVLEIIIQRP 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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