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Conserved domains on  [gi|1492536847|ref|WP_120797302|]
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carboxysome peptide B [Thiocapsa rosea]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
EutN_CcmL super family cl01889
Ethanolamine utilisation protein and carboxysome structural protein domain family; Beside the ...
 1-80 4.09e-38

Ethanolamine utilisation protein and carboxysome structural protein domain family; Beside the Escherichia coli ethanolamine utilization protein EutN and the Synechocystis sp. carboxysome (beta-type) structural protein CcmL, this family also includes alpha-type carboxysome structural proteins CsoS4A and CsoS4B (previously known as OrfA and OrfB), propanediol utilizationprotein PduN, and some hypothetical homologous of various bacterial microcompartments. The carboxysome, a polyhedral organelle, participates in carbon fixation by sequestering enzymes. It is the prototypical bacterial microcompartment. Its enzymatic components, ribulose bisphosphate carboxylase/oxygenase(RuBisCO) and carbonic anhydrase (CA), are surrounded by a polyhedral protein shell. Similarly, the ethanolamine utilization (eut) microcompartment, and the 1,2-propanediol utilization (pdu) microcompartment encapsulate the enzymes necessary for the process of cobalamin-dependent ethanolamine degradation, and coenzyme B12-dependent degradation of 1,2-propanediol, respectively, within its polyhedral protein shells. It is interesting that both carboxysome structural proteins CcmL and CsoS4A assemble as pentamers in the crystal structures, which might constitute the twelve pentameric vertices of a regular icosahedral carboxysome. However, the reported EutN structure is hexameric rather than pentameric. The absence of pentamers in Eut microcompartments might lead to less-regular icosahedral shell shapes. Due to the lack of structure evidence, the functional roles of the CsoS4A adjacent paralog, CsoS4B, and propanediol utilization protein PduN are not yet clear.


The actual alignment was detected with superfamily member TIGR02704:

Pssm-ID: 445597  Cd Length: 80  Bit Score: 122.27  E-value: 4.09e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1492536847  1 MEIRQVIGSLVCTHRITGLGHWDLRLLQDTKGKQYVATDPVDARPGDWVFVVSGSAARYAMGNAAILTDLTIGGIIDHWE 80
Cdd:TIGR02704  1 MEIMRVMSDLVCTRRIPGLKNASLRVLRDAKGKISVAVDPVGAPEGKWVFTASGSAARFACPDPSILTDLTIGGIIDHWT 80
 
Name Accession Description Interval E-value
carboxysome_B TIGR02704
carboxysome peptide B; This model distinguishes one of two closely related paralogs encoded by ...
 1-80 4.09e-38

carboxysome peptide B; This model distinguishes one of two closely related paralogs encoded by nearby genes in the carboxysome operons of a number of cyanobacteria and chemoautotrophic bacteria. More distantly related proteins, also belonging to pfam03319, participate in other types of shell such as the ethanolamine degradation organelle. [Central intermediary metabolism, One-carbon metabolism]


Pssm-ID: 131751  Cd Length: 80  Bit Score: 122.27  E-value: 4.09e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1492536847  1 MEIRQVIGSLVCTHRITGLGHWDLRLLQDTKGKQYVATDPVDARPGDWVFVVSGSAARYAMGNAAILTDLTIGGIIDHWE 80
Cdd:TIGR02704  1 MEIMRVMSDLVCTRRIPGLKNASLRVLRDAKGKISVAVDPVGAPEGKWVFTASGSAARFACPDPSILTDLTIGGIIDHWT 80
CcmL COG4576
Carboxysome shell and ethanolamine utilization microcompartment protein CcmK/EutM [Secondary ...
 1-80 1.77e-30

Carboxysome shell and ethanolamine utilization microcompartment protein CcmK/EutM [Secondary metabolites biosynthesis, transport and catabolism, Energy production and conversion];


Pssm-ID: 443633  Cd Length: 90  Bit Score: 103.34  E-value: 1.77e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1492536847  1 MEIRQVIGSLVCTHRITGLGHWDLRLLQDT------KGKQYVATDPVDARPGDWVFVVSGSAARYAMGNAAILTDLTIGG 74
Cdd:COG4576    1 MQLARVIGTVVATRKHPSLEGLKLLVVQPLdldgepTGEPVVAVDTVGAGVGEWVLVVSGSAARQAFGDKDAPVDAAIVG 80


                 ....*.
gi 1492536847 75 IIDHWE 80
Cdd:COG4576   81 IIDEVE 86
EutN_CcmL pfam03319
Ethanolamine utilization protein EutN/carboxysome; The crystal structure of EutN contains a ...
 1-77 2.55e-28

Ethanolamine utilization protein EutN/carboxysome; The crystal structure of EutN contains a central five-stranded beta-barrel, with an alpha-helix at the open end of this barrel (PDB:2HD3). The structure also contains three additional beta-strands, which help the formation of a tight hexamer, with a hole in the center. this suggests that EutN forms a pore, with an opening of 26 Angstrom in diameter on one face and 14 Angstrom on the other face. EutN is involved in the cobalamin-dependent degradation of ethanolamine.


Pssm-ID: 427242  Cd Length: 83  Bit Score: 97.54  E-value: 2.55e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1492536847  1 MEIRQVIGSLVCTHRITGLGHWDLRLLQD------TKGKQYVATDPVDARPGDWVFVVSGSAARYAMGNAAILTDLTIGG 74
Cdd:pfam03319  1 MQIAKVIGTVVSTRKDPSLKGLKLLVVQPldeegkPTGEPLVAVDTVGAGIGEWVLVVTGSAARQAAGDKDAPVDAAIVG 80


                 ...
gi 1492536847 75 IID 77
Cdd:pfam03319 81 IID 83
EutN_CcmL cd01614
Ethanolamine utilisation protein and carboxysome structural protein domain family; Beside the ...
 1-77 1.13e-27

Ethanolamine utilisation protein and carboxysome structural protein domain family; Beside the Escherichia coli ethanolamine utilization protein EutN and the Synechocystis sp. carboxysome (beta-type) structural protein CcmL, this family also includes alpha-type carboxysome structural proteins CsoS4A and CsoS4B (previously known as OrfA and OrfB), propanediol utilizationprotein PduN, and some hypothetical homologous of various bacterial microcompartments. The carboxysome, a polyhedral organelle, participates in carbon fixation by sequestering enzymes. It is the prototypical bacterial microcompartment. Its enzymatic components, ribulose bisphosphate carboxylase/oxygenase(RuBisCO) and carbonic anhydrase (CA), are surrounded by a polyhedral protein shell. Similarly, the ethanolamine utilization (eut) microcompartment, and the 1,2-propanediol utilization (pdu) microcompartment encapsulate the enzymes necessary for the process of cobalamin-dependent ethanolamine degradation, and coenzyme B12-dependent degradation of 1,2-propanediol, respectively, within its polyhedral protein shells. It is interesting that both carboxysome structural proteins CcmL and CsoS4A assemble as pentamers in the crystal structures, which might constitute the twelve pentameric vertices of a regular icosahedral carboxysome. However, the reported EutN structure is hexameric rather than pentameric. The absence of pentamers in Eut microcompartments might lead to less-regular icosahedral shell shapes. Due to the lack of structure evidence, the functional roles of the CsoS4A adjacent paralog, CsoS4B, and propanediol utilization protein PduN are not yet clear.


Pssm-ID: 133473  Cd Length: 83  Bit Score: 96.05  E-value: 1.13e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1492536847  1 MEIRQVIGSLVCTHRITGLGHWDLRLLQDT------KGKQYVATDPVDARPGDWVFVVSGSAARYAMGNAAILTDLTIGG 74
Cdd:cd01614    1 MLIARVIGTVVATRKHPSLAGKKLLVVQPLdgegkpKGEPLVAVDPVGAGVGEWVLVATGSAARQAFGDKDVPIDAAIIG 80


                 ...
gi 1492536847 75 IID 77
Cdd:cd01614   81 IID 83
PRK15448 PRK15448
ethanolamine utilization microcompartment protein EutN;
1-77 9.58e-11

ethanolamine utilization microcompartment protein EutN;


Pssm-ID: 185345  Cd Length: 95  Bit Score: 53.44  E-value: 9.58e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1492536847  1 MEIRQVIGSLVCTHRITGLGHWDLRLLQ------DTKGKQYVATDPVDARPGDWVFVVSGSAARYAMGNAAILTDLTIGG 74
Cdd:PRK15448   1 MKLAVVTGQIVCTVRHHGLAHDKLLMVEmidpqgNPDGQCAVAIDNIGAGTGEWVLLVSGSSARQAHKSETSPVDLCVIG 80


                 ...
gi 1492536847 75 IID 77
Cdd:PRK15448  81 IVD 83
 
Name Accession Description Interval E-value
carboxysome_B TIGR02704
carboxysome peptide B; This model distinguishes one of two closely related paralogs encoded by ...
 1-80 4.09e-38

carboxysome peptide B; This model distinguishes one of two closely related paralogs encoded by nearby genes in the carboxysome operons of a number of cyanobacteria and chemoautotrophic bacteria. More distantly related proteins, also belonging to pfam03319, participate in other types of shell such as the ethanolamine degradation organelle. [Central intermediary metabolism, One-carbon metabolism]


Pssm-ID: 131751  Cd Length: 80  Bit Score: 122.27  E-value: 4.09e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1492536847  1 MEIRQVIGSLVCTHRITGLGHWDLRLLQDTKGKQYVATDPVDARPGDWVFVVSGSAARYAMGNAAILTDLTIGGIIDHWE 80
Cdd:TIGR02704  1 MEIMRVMSDLVCTRRIPGLKNASLRVLRDAKGKISVAVDPVGAPEGKWVFTASGSAARFACPDPSILTDLTIGGIIDHWT 80
CcmL COG4576
Carboxysome shell and ethanolamine utilization microcompartment protein CcmK/EutM [Secondary ...
 1-80 1.77e-30

Carboxysome shell and ethanolamine utilization microcompartment protein CcmK/EutM [Secondary metabolites biosynthesis, transport and catabolism, Energy production and conversion];


Pssm-ID: 443633  Cd Length: 90  Bit Score: 103.34  E-value: 1.77e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1492536847  1 MEIRQVIGSLVCTHRITGLGHWDLRLLQDT------KGKQYVATDPVDARPGDWVFVVSGSAARYAMGNAAILTDLTIGG 74
Cdd:COG4576    1 MQLARVIGTVVATRKHPSLEGLKLLVVQPLdldgepTGEPVVAVDTVGAGVGEWVLVVSGSAARQAFGDKDAPVDAAIVG 80


                 ....*.
gi 1492536847 75 IIDHWE 80
Cdd:COG4576   81 IIDEVE 86
EutN_CcmL pfam03319
Ethanolamine utilization protein EutN/carboxysome; The crystal structure of EutN contains a ...
 1-77 2.55e-28

Ethanolamine utilization protein EutN/carboxysome; The crystal structure of EutN contains a central five-stranded beta-barrel, with an alpha-helix at the open end of this barrel (PDB:2HD3). The structure also contains three additional beta-strands, which help the formation of a tight hexamer, with a hole in the center. this suggests that EutN forms a pore, with an opening of 26 Angstrom in diameter on one face and 14 Angstrom on the other face. EutN is involved in the cobalamin-dependent degradation of ethanolamine.


Pssm-ID: 427242  Cd Length: 83  Bit Score: 97.54  E-value: 2.55e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1492536847  1 MEIRQVIGSLVCTHRITGLGHWDLRLLQD------TKGKQYVATDPVDARPGDWVFVVSGSAARYAMGNAAILTDLTIGG 74
Cdd:pfam03319  1 MQIAKVIGTVVSTRKDPSLKGLKLLVVQPldeegkPTGEPLVAVDTVGAGIGEWVLVVTGSAARQAAGDKDAPVDAAIVG 80


                 ...
gi 1492536847 75 IID 77
Cdd:pfam03319 81 IID 83
EutN_CcmL cd01614
Ethanolamine utilisation protein and carboxysome structural protein domain family; Beside the ...
 1-77 1.13e-27

Ethanolamine utilisation protein and carboxysome structural protein domain family; Beside the Escherichia coli ethanolamine utilization protein EutN and the Synechocystis sp. carboxysome (beta-type) structural protein CcmL, this family also includes alpha-type carboxysome structural proteins CsoS4A and CsoS4B (previously known as OrfA and OrfB), propanediol utilizationprotein PduN, and some hypothetical homologous of various bacterial microcompartments. The carboxysome, a polyhedral organelle, participates in carbon fixation by sequestering enzymes. It is the prototypical bacterial microcompartment. Its enzymatic components, ribulose bisphosphate carboxylase/oxygenase(RuBisCO) and carbonic anhydrase (CA), are surrounded by a polyhedral protein shell. Similarly, the ethanolamine utilization (eut) microcompartment, and the 1,2-propanediol utilization (pdu) microcompartment encapsulate the enzymes necessary for the process of cobalamin-dependent ethanolamine degradation, and coenzyme B12-dependent degradation of 1,2-propanediol, respectively, within its polyhedral protein shells. It is interesting that both carboxysome structural proteins CcmL and CsoS4A assemble as pentamers in the crystal structures, which might constitute the twelve pentameric vertices of a regular icosahedral carboxysome. However, the reported EutN structure is hexameric rather than pentameric. The absence of pentamers in Eut microcompartments might lead to less-regular icosahedral shell shapes. Due to the lack of structure evidence, the functional roles of the CsoS4A adjacent paralog, CsoS4B, and propanediol utilization protein PduN are not yet clear.


Pssm-ID: 133473  Cd Length: 83  Bit Score: 96.05  E-value: 1.13e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1492536847  1 MEIRQVIGSLVCTHRITGLGHWDLRLLQDT------KGKQYVATDPVDARPGDWVFVVSGSAARYAMGNAAILTDLTIGG 74
Cdd:cd01614    1 MLIARVIGTVVATRKHPSLAGKKLLVVQPLdgegkpKGEPLVAVDPVGAGVGEWVLVATGSAARQAFGDKDVPIDAAIIG 80


                 ...
gi 1492536847 75 IID 77
Cdd:cd01614   81 IID 83
carboxysome_A TIGR02703
carboxysome peptide A; This model distinguishes one of two closely related paralogs encoded by ...
 1-80 7.36e-21

carboxysome peptide A; This model distinguishes one of two closely related paralogs encoded by nearby genes in the carboxysome operons of a number of cyanobacteria and chemoautotrophic bacteria. More distantly related proteins, also belonging to pfam03319, participate in other types of shell such as the ethanolamine degradation organelle. [Central intermediary metabolism, One-carbon metabolism]


Pssm-ID: 131750  Cd Length: 81  Bit Score: 78.80  E-value: 7.36e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1492536847  1 MEIRQVIGSLVCTHRITGLGHWDLRLLQDTKG-KQYVATDPVDARPGDWVFVVSGSAARYAMGNAAILTDLTIGGIIDHW 79
Cdd:TIGR02703  1 MKIMQVEKTLVSTNRIADMGHKPLLVVWEKPGgARQVAVDAIGCKPGDWVLCVGSSAAREAAGSKSYPSDLTIVGIIDHW 80


                 .
gi 1492536847 80 E 80
Cdd:TIGR02703 81 E 81
PRK15448 PRK15448
ethanolamine utilization microcompartment protein EutN;
1-77 9.58e-11

ethanolamine utilization microcompartment protein EutN;


Pssm-ID: 185345  Cd Length: 95  Bit Score: 53.44  E-value: 9.58e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1492536847  1 MEIRQVIGSLVCTHRITGLGHWDLRLLQ------DTKGKQYVATDPVDARPGDWVFVVSGSAARYAMGNAAILTDLTIGG 74
Cdd:PRK15448   1 MKLAVVTGQIVCTVRHHGLAHDKLLMVEmidpqgNPDGQCAVAIDNIGAGTGEWVLLVSGSSARQAHKSETSPVDLCVIG 80


                 ...
gi 1492536847 75 IID 77
Cdd:PRK15448  81 IVD 83
 
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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