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Conserved domains on  [gi|383875303|pdb|3AXM|Y]
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Chain Y, Ribulose bisphosphate carboxylase small chain, chloroplastic

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
 2-121 4.48e-92

ribulose-bisphosphate carboxylase small chain


The actual alignment was detected with superfamily member PLN02289:

Pssm-ID: 215163 [Multi-domain]  Cd Length: 176  Bit Score: 263.65  E-value: 4.48e-92
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3AXM_Y         2 MQVWPIEGIKKFETLSYLPPLTVEDLLKQIEYLLRSKWVPCLEFSKV-GFVYRENHRSPGYYDGRYWTMWKLPMFGCTDA 80
Cdd:PLN02289  56 MQVWPPIGKKKFETLSYLPDLTDEELAKEVDYLLRNKWVPCLEFELEhGFVYREHHRSPGYYDGRYWTMWKLPMFGCTDS 135

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
3AXM_Y        81 TQVLKELEEAKKAYPDAFVRIIGFDNVRQVQLISFIAYKPP 121
Cdd:PLN02289 136 AQVLKELEEAKKAYPNAFIRIIGFDNTRQVQCISFIAYKPP 176
 
Name Accession Description Interval E-value
PLN02289 PLN02289
ribulose-bisphosphate carboxylase small chain
 2-121 4.48e-92

ribulose-bisphosphate carboxylase small chain


Pssm-ID: 215163 [Multi-domain]  Cd Length: 176  Bit Score: 263.65  E-value: 4.48e-92
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3AXM_Y         2 MQVWPIEGIKKFETLSYLPPLTVEDLLKQIEYLLRSKWVPCLEFSKV-GFVYRENHRSPGYYDGRYWTMWKLPMFGCTDA 80
Cdd:PLN02289  56 MQVWPPIGKKKFETLSYLPDLTDEELAKEVDYLLRNKWVPCLEFELEhGFVYREHHRSPGYYDGRYWTMWKLPMFGCTDS 135

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
3AXM_Y        81 TQVLKELEEAKKAYPDAFVRIIGFDNVRQVQLISFIAYKPP 121
Cdd:PLN02289 136 AQVLKELEEAKKAYPNAFIRIIGFDNTRQVQCISFIAYKPP 176
RuBisCO_small cd03527
Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit. Rubisco is a ...
 11-120 5.26e-59

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: 177.06  E-value: 5.26e-59
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3AXM_Y       11 KKFETLSYLPPLTVEDLLKQIEYLLRSKWVPCLEFSKvgfvyrenhrsPGYYDGRYWTMWKLPMFGCTDATQVLKELEEA 90
Cdd:cd03527   1 RTFETFSYLPPLTDEQIAKQIDYIISNGWAPCLEFTE-----------PEHYDNRYWTMWKLPMFGCTDPAQVLREIEAC 69

                        90       100       110
                ....*....|....*....|....*....|
3AXM_Y       91 KKAYPDAFVRIIGFDNVRQVQLISFIAYKP 120
Cdd:cd03527  70 RKAYPDHYVRVVGFDNYKQSQCMSFIVHRP 99
RuBisCO_small pfam00101
Ribulose bisphosphate carboxylase, small chain;
13-120 3.42e-54

Ribulose bisphosphate carboxylase, small chain;


Pssm-ID: 425465  Cd Length: 97  Bit Score: 164.98  E-value: 3.42e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3AXM_Y         13 FETLSYLPPLTVEDLLKQIEYLLRSKWVPCLEFSKvgfvyrenhrsPGYYDGRYWTMWKLPMFGCTDATQVLKELEEAKK 92
Cdd:pfam00101   1 FETFSYLPPLTDEQIAKQVQYILSQGWIPGIEFTD-----------DPHPRNRYWTMWKLPMFGCTDPAQVLAELEACRK 69

                          90       100
                  ....*....|....*....|....*...
3AXM_Y         93 AYPDAFVRIIGFDNVRQVQLISFIAYKP 120
Cdd:pfam00101  70 AYPNHYIRLIGFDNYRQSQVMSFIVQRP 97
RbcS COG4451
Ribulose bisphosphate carboxylase small subunit [Carbohydrate transport and metabolism];
12-121 1.08e-38

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


Pssm-ID: 443549  Cd Length: 102  Bit Score: 125.70  E-value: 1.08e-38
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3AXM_Y       12 KFETLSYLPPLTVEDLLKQIEYLLRSKWVPCLEFskvgfvyrENHRSPGYYdgrYWTMWKLPMFGCTDATQVLKELEEAK 91
Cdd:COG4451   4 TQETFSYLPPLLDAEIVAQVRYLLAQGWAIGIEH--------ADDRRFRTT---YWQMWKLPMFDSTDEAEVLAELEACR 72

                        90       100       110
                ....*....|....*....|....*....|
3AXM_Y       92 KAYPDAFVRIIGFDNVRQVQLISFIAYKPP 121
Cdd:COG4451  73 KEHPGEYVRLIGIDPKAKRRVLEFIVQRPN 102
RuBisCO_small smart00961
Ribulose bisphosphate carboxylase, small chain; RuBisCO (ribulose-1,5-bisphosphate carboxylase ...
 12-120 1.31e-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: 120.33  E-value: 1.31e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3AXM_Y          12 KFETLSYLPPLTVEDLLKQIEYLLRSKWVPCLEFSkvgfvyrenhrSPGYYDGRYWTmwKLPMFGCTDATQVLKELEEAK 91
Cdd:smart00961   1 TQETFSYLPPLTDAEIVAQVRYLLAQGYAIGVEHA-----------DPRRFRTSSWQ--KLPMFGATDAAEVLAELEACL 67

                           90       100
                   ....*....|....*....|....*....
3AXM_Y          92 KAYPDAFVRIIGFDNVRQVQLISFIAYKP 120
Cdd:smart00961  68 AEHPGEYVRLIGIDPKAKRRVLEFIIQRP 96
 
Name Accession Description Interval E-value
PLN02289 PLN02289
ribulose-bisphosphate carboxylase small chain
 2-121 4.48e-92

ribulose-bisphosphate carboxylase small chain


Pssm-ID: 215163 [Multi-domain]  Cd Length: 176  Bit Score: 263.65  E-value: 4.48e-92
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3AXM_Y         2 MQVWPIEGIKKFETLSYLPPLTVEDLLKQIEYLLRSKWVPCLEFSKV-GFVYRENHRSPGYYDGRYWTMWKLPMFGCTDA 80
Cdd:PLN02289  56 MQVWPPIGKKKFETLSYLPDLTDEELAKEVDYLLRNKWVPCLEFELEhGFVYREHHRSPGYYDGRYWTMWKLPMFGCTDS 135

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
3AXM_Y        81 TQVLKELEEAKKAYPDAFVRIIGFDNVRQVQLISFIAYKPP 121
Cdd:PLN02289 136 AQVLKELEEAKKAYPNAFIRIIGFDNTRQVQCISFIAYKPP 176
RuBisCO_small cd03527
Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit. Rubisco is a ...
 11-120 5.26e-59

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: 177.06  E-value: 5.26e-59
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3AXM_Y       11 KKFETLSYLPPLTVEDLLKQIEYLLRSKWVPCLEFSKvgfvyrenhrsPGYYDGRYWTMWKLPMFGCTDATQVLKELEEA 90
Cdd:cd03527   1 RTFETFSYLPPLTDEQIAKQIDYIISNGWAPCLEFTE-----------PEHYDNRYWTMWKLPMFGCTDPAQVLREIEAC 69

                        90       100       110
                ....*....|....*....|....*....|
3AXM_Y       91 KKAYPDAFVRIIGFDNVRQVQLISFIAYKP 120
Cdd:cd03527  70 RKAYPDHYVRVVGFDNYKQSQCMSFIVHRP 99
RuBisCO_small pfam00101
Ribulose bisphosphate carboxylase, small chain;
13-120 3.42e-54

Ribulose bisphosphate carboxylase, small chain;


Pssm-ID: 425465  Cd Length: 97  Bit Score: 164.98  E-value: 3.42e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3AXM_Y         13 FETLSYLPPLTVEDLLKQIEYLLRSKWVPCLEFSKvgfvyrenhrsPGYYDGRYWTMWKLPMFGCTDATQVLKELEEAKK 92
Cdd:pfam00101   1 FETFSYLPPLTDEQIAKQVQYILSQGWIPGIEFTD-----------DPHPRNRYWTMWKLPMFGCTDPAQVLAELEACRK 69

                          90       100
                  ....*....|....*....|....*...
3AXM_Y         93 AYPDAFVRIIGFDNVRQVQLISFIAYKP 120
Cdd:pfam00101  70 AYPNHYIRLIGFDNYRQSQVMSFIVQRP 97
RbcS COG4451
Ribulose bisphosphate carboxylase small subunit [Carbohydrate transport and metabolism];
12-121 1.08e-38

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


Pssm-ID: 443549  Cd Length: 102  Bit Score: 125.70  E-value: 1.08e-38
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3AXM_Y       12 KFETLSYLPPLTVEDLLKQIEYLLRSKWVPCLEFskvgfvyrENHRSPGYYdgrYWTMWKLPMFGCTDATQVLKELEEAK 91
Cdd:COG4451   4 TQETFSYLPPLLDAEIVAQVRYLLAQGWAIGIEH--------ADDRRFRTT---YWQMWKLPMFDSTDEAEVLAELEACR 72

                        90       100       110
                ....*....|....*....|....*....|
3AXM_Y       92 KAYPDAFVRIIGFDNVRQVQLISFIAYKPP 121
Cdd:COG4451  73 KEHPGEYVRLIGIDPKAKRRVLEFIVQRPN 102
RuBisCO_small smart00961
Ribulose bisphosphate carboxylase, small chain; RuBisCO (ribulose-1,5-bisphosphate carboxylase ...
 12-120 1.31e-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: 120.33  E-value: 1.31e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3AXM_Y          12 KFETLSYLPPLTVEDLLKQIEYLLRSKWVPCLEFSkvgfvyrenhrSPGYYDGRYWTmwKLPMFGCTDATQVLKELEEAK 91
Cdd:smart00961   1 TQETFSYLPPLTDAEIVAQVRYLLAQGYAIGVEHA-----------DPRRFRTSSWQ--KLPMFGATDAAEVLAELEACL 67

                           90       100
                   ....*....|....*....|....*....
3AXM_Y          92 KAYPDAFVRIIGFDNVRQVQLISFIAYKP 120
Cdd:smart00961  68 AEHPGEYVRLIGIDPKAKRRVLEFIIQRP 96
rbcS CHL00130
ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit; Reviewed
 12-122 8.74e-29

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


Pssm-ID: 177052  Cd Length: 138  Bit Score: 101.76  E-value: 8.74e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3AXM_Y        12 KFETLSYLPPLTVEDLLKQIEYLLRSKWVPCLEFSKVGfvYRENHrspgyydgrYWTMWKLPMFGCTDATQVLKELEEAK 91
Cdd:CHL00130   4 TQGTFSFLPDLTDQQIEKQIQYAISKGWALNVEWTDDP--HPRNS---------YWELWGLPLFDVKDPAAVMFEINECR 72

                         90       100       110
                 ....*....|....*....|....*....|....*.
3AXM_Y        92 KAYPDAFVRIIGFDNVRQVQ--LISFIAYKP---PG 122
Cdd:CHL00130  73 KQKPNGYIKVNAFDASRGVEscVLSFIVNRPanePG 108
RuBisCO_small_like cd00307
Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit and related proteins. ...
 25-120 6.77e-18

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: 72.31  E-value: 6.77e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3AXM_Y       25 EDLLKQIEYLLRSKWVPCLEFSkvgfvyreNHRspgyydgRYWTMWKLPMFGC--TDATQVLKELEEAKKAYPDAFVRII 102
Cdd:cd00307   2 EDVVEQVRQLLAQGYKIGLEHA--------DAR-------RFRTSSWQSCGPIegRSEAQVLAALEACLAEHPGEYVRLI 66

                        90
                ....*....|....*...
3AXM_Y      103 GFDNVRQVQLISFIAYKP 120
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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