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Conserved domains on  [gi|469735833|gb|AGH70663|]
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ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit, partial (chloroplast) [Gracilariopsis cf. lemaneiformis]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RuBisCO_small_like super family cl01843
Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit and related proteins. ...
 1-46 1.23e-29

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


The actual alignment was detected with superfamily member CHL00130:

Pssm-ID: 445577  Cd Length: 138  Bit Score: 100.22  E-value: 1.23e-29
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 469735833   1 MRLTQGTFSFLPDLTDEQITKQIEYAVSQNWSVNIEYTEDPHPRNN 46
Cdd:CHL00130   1 MRLTQGTFSFLPDLTDQQIEKQIQYAISKGWALNVEWTDDPHPRNS 46
 
Name Accession Description Interval E-value
rbcS CHL00130
ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit; Reviewed
 1-46 1.23e-29

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


Pssm-ID: 177052  Cd Length: 138  Bit Score: 100.22  E-value: 1.23e-29
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 469735833   1 MRLTQGTFSFLPDLTDEQITKQIEYAVSQNWSVNIEYTEDPHPRNN 46
Cdd:CHL00130   1 MRLTQGTFSFLPDLTDQQIEKQIQYAISKGWALNVEWTDDPHPRNS 46
RbcS COG4451
Ribulose bisphosphate carboxylase small subunit [Carbohydrate transport and metabolism];
1-46 1.18e-22

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


Pssm-ID: 443549  Cd Length: 102  Bit Score: 81.40  E-value: 1.18e-22
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 469735833   1 MRLTQGTFSFLPDLTDEQITKQIEYAVSQNWSVNIEYTEDPHPRNN 46
Cdd:COG4451    1 MSRTQETFSYLPPLLDAEIVAQVRYLLAQGWAIGIEHADDRRFRTT 46
RuBisCO_small cd03527
Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit. Rubisco is a ...
 3-45 1.24e-22

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: 81.53  E-value: 1.24e-22
                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 469735833  3 LTQGTFSFLPDLTDEQITKQIEYAVSQNWSVNIEYTEDPHPRN 45
Cdd:cd03527   1 RTFETFSYLPPLTDEQIAKQIDYIISNGWAPCLEFTEPEHYDN 43
RuBisCO_small pfam00101
Ribulose bisphosphate carboxylase, small chain;
5-45 5.09e-22

Ribulose bisphosphate carboxylase, small chain;


Pssm-ID: 425465  Cd Length: 97  Bit Score: 79.85  E-value: 5.09e-22
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 469735833   5 QGTFSFLPDLTDEQITKQIEYAVSQNWSVNIEYTEDPHPRN 45
Cdd:pfam00101  1 FETFSYLPPLTDEQIAKQVQYILSQGWIPGIEFTDDPHPRN 41
RuBisCO_small smart00961
Ribulose bisphosphate carboxylase, small chain; RuBisCO (ribulose-1,5-bisphosphate carboxylase ...
 4-46 1.03e-18

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: 71.41  E-value: 1.03e-18
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 469735833    4 TQGTFSFLPDLTDEQITKQIEYAVSQNWSVNIEYTEDPHPRNN 46
Cdd:smart00961  1 TQETFSYLPPLTDAEIVAQVRYLLAQGYAIGVEHADPRRFRTS 43
 
Name Accession Description Interval E-value
rbcS CHL00130
ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit; Reviewed
 1-46 1.23e-29

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


Pssm-ID: 177052  Cd Length: 138  Bit Score: 100.22  E-value: 1.23e-29
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 469735833   1 MRLTQGTFSFLPDLTDEQITKQIEYAVSQNWSVNIEYTEDPHPRNN 46
Cdd:CHL00130   1 MRLTQGTFSFLPDLTDQQIEKQIQYAISKGWALNVEWTDDPHPRNS 46
RbcS COG4451
Ribulose bisphosphate carboxylase small subunit [Carbohydrate transport and metabolism];
1-46 1.18e-22

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


Pssm-ID: 443549  Cd Length: 102  Bit Score: 81.40  E-value: 1.18e-22
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 469735833   1 MRLTQGTFSFLPDLTDEQITKQIEYAVSQNWSVNIEYTEDPHPRNN 46
Cdd:COG4451    1 MSRTQETFSYLPPLLDAEIVAQVRYLLAQGWAIGIEHADDRRFRTT 46
RuBisCO_small cd03527
Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit. Rubisco is a ...
 3-45 1.24e-22

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: 81.53  E-value: 1.24e-22
                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 469735833  3 LTQGTFSFLPDLTDEQITKQIEYAVSQNWSVNIEYTEDPHPRN 45
Cdd:cd03527   1 RTFETFSYLPPLTDEQIAKQIDYIISNGWAPCLEFTEPEHYDN 43
RuBisCO_small pfam00101
Ribulose bisphosphate carboxylase, small chain;
5-45 5.09e-22

Ribulose bisphosphate carboxylase, small chain;


Pssm-ID: 425465  Cd Length: 97  Bit Score: 79.85  E-value: 5.09e-22
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 469735833   5 QGTFSFLPDLTDEQITKQIEYAVSQNWSVNIEYTEDPHPRN 45
Cdd:pfam00101  1 FETFSYLPPLTDEQIAKQVQYILSQGWIPGIEFTDDPHPRN 41
RuBisCO_small smart00961
Ribulose bisphosphate carboxylase, small chain; RuBisCO (ribulose-1,5-bisphosphate carboxylase ...
 4-46 1.03e-18

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: 71.41  E-value: 1.03e-18
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 469735833    4 TQGTFSFLPDLTDEQITKQIEYAVSQNWSVNIEYTEDPHPRNN 46
Cdd:smart00961  1 TQETFSYLPPLTDAEIVAQVRYLLAQGYAIGVEHADPRRFRTS 43
PLN02289 PLN02289
ribulose-bisphosphate carboxylase small chain
 7-38 4.16e-06

ribulose-bisphosphate carboxylase small chain


Pssm-ID: 215163 [Multi-domain]  Cd Length: 176  Bit Score: 40.62  E-value: 4.16e-06
                         10        20        30
                 ....*....|....*....|....*....|..
gi 469735833   7 TFSFLPDLTDEQITKQIEYAVSQNWSVNIEYT 38
Cdd:PLN02289  69 TLSYLPDLTDEELAKEVDYLLRNKWVPCLEFE 100
LomR COG3637
Opacity protein LomR and related surface antigens [Cell wall/membrane/envelope biogenesis];
23-37 6.03e-03

Opacity protein LomR and related surface antigens [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442854 [Multi-domain]  Cd Length: 154  Bit Score: 31.87  E-value: 6.03e-03
                         10
                 ....*....|....*
gi 469735833  23 IEYAVSQNWSVNIEY 37
Cdd:COG3637  107 VEYALTDNWSLRLEY 121
RuBisCO_small_like cd00307
Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit and related proteins. ...
 16-40 7.53e-03

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: 30.71  E-value: 7.53e-03
                        10        20
                ....*....|....*....|....*
gi 469735833 16 DEQITKQIEYAVSQNWSVNIEYTED 40
Cdd:cd00307   1 SEDVVEQVRQLLAQGYKIGLEHADA 25
 
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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