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Conserved domains on  [gi|28204218|gb|AAO36657|]
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putative ethanolamine utilization protein [Clostridium tetani E88]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
eut_PduT super family cl28668
PduT-like ethanolamine utilization protein; This gene shows up in ethanolamine utilization ...
 6-185 1.51e-87

PduT-like ethanolamine utilization protein; This gene shows up in ethanolamine utilization operons in which a proteinaceous coat organelle is also encoded. It is closely related to the PduT protein in propane-diol operons with the same structure.


The actual alignment was detected with superfamily member TIGR02526:

Pssm-ID: 131578 [Multi-domain]  Cd Length: 182  Bit Score: 254.80  E-value: 1.51e-87
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28204218     6 MKKALGLLEFNSISKGIETSDVLLKAAFVEVEILRQICPGKFLTIISGDVEEVKEAIDKAKSKDNKKLVESNIITSVHED 85
Cdd:TIGR02526   1 MKKSLGILEFRSISKGIEMSDVFLKAAFVEVFTLRPICPGKFLIILQGDSGEVKEAIQDAKEEAGKFLVSSYIIHSAHED 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28204218    86 ILKALKKRPIIK--EFNAIGVMEFSTVTSSLVALDIALKTSDIQLVKLVLGNGIAGKAYFIINGSVSSVEEGVKSAQNCV 163
Cdd:TIGR02526  81 ILAALKNKYSHKkvEVDAIGIMEISQVGSGLNALDEALKKSAIHLVKLTLGAGIGGKFVAIFTGEVSSVEEGMRILQETA 160

                         170       180
                  ....*....|....*....|..
gi 28204218   164 NSKRIVHSTVIPSPSKILLQNI 185
Cdd:TIGR02526 161 EPKKIIHHTVIPSPDELLKRNL 182
 
Name Accession Description Interval E-value
eut_PduT TIGR02526
PduT-like ethanolamine utilization protein; This gene shows up in ethanolamine utilization ...
 6-185 1.51e-87

PduT-like ethanolamine utilization protein; This gene shows up in ethanolamine utilization operons in which a proteinaceous coat organelle is also encoded. It is closely related to the PduT protein in propane-diol operons with the same structure.


Pssm-ID: 131578 [Multi-domain]  Cd Length: 182  Bit Score: 254.80  E-value: 1.51e-87
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28204218     6 MKKALGLLEFNSISKGIETSDVLLKAAFVEVEILRQICPGKFLTIISGDVEEVKEAIDKAKSKDNKKLVESNIITSVHED 85
Cdd:TIGR02526   1 MKKSLGILEFRSISKGIEMSDVFLKAAFVEVFTLRPICPGKFLIILQGDSGEVKEAIQDAKEEAGKFLVSSYIIHSAHED 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28204218    86 ILKALKKRPIIK--EFNAIGVMEFSTVTSSLVALDIALKTSDIQLVKLVLGNGIAGKAYFIINGSVSSVEEGVKSAQNCV 163
Cdd:TIGR02526  81 ILAALKNKYSHKkvEVDAIGIMEISQVGSGLNALDEALKKSAIHLVKLTLGAGIGGKFVAIFTGEVSSVEEGMRILQETA 160

                         170       180
                  ....*....|....*....|..
gi 28204218   164 NSKRIVHSTVIPSPSKILLQNI 185
Cdd:TIGR02526 161 EPKKIIHHTVIPSPDELLKRNL 182
BMC_PduT_repeat1 cd07053
1,2-propanediol utilization protein T (PduT), Bacterial Micro-Compartment (BMC) domain repeat ...
 9-84 1.75e-30

1,2-propanediol utilization protein T (PduT), Bacterial Micro-Compartment (BMC) domain repeat 1; PduT proteins are homologs of the carboxysome shell protein. They are encoded within the pdu operon and might be required for the formation of the outer shell of the bacterial pdu polyhedral organelles which are involved in coenzyme B12-dependent degradation of 1,2-propanediol. Although it has been suggested that PduT might form hexamers and further assemble into the flat facets of the polyhedral outer shell of pdu organelles at present no experimental evidence directly supports this view. PduT proteins contain two tandem BMC domains repeats. This CD contains repeat 1 (the first BMC domain of PduT) as well as carboxysome shell protein sequence homolog, EutM protein, are also included in this CD. They too might exist as hexamers and might play similar functional roles in the construction of the eut organelle outer shell which still remains poorly understood.


Pssm-ID: 132893  Cd Length: 76  Bit Score: 106.10  E-value: 1.75e-30
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 28204218   9 ALGLLEFNSISKGIETSDVLLKAAFVEVEILRQICPGKFLTIISGDVEEVKEAIDKAKSKDNKKLVESNIITSVHE 84
Cdd:cd07053   1 AIGLLELNSIAKGIEAADAMLKAANVELVLAKTICPGKYIIIVSGDVGAVQAAVDAGKEIGGKYVVDSFVLPNVHP 76
CcmK COG4577
Carboxysome shell and ethanolamine utilization microcompartment protein CcmL/EutN [Secondary ...
 6-89 6.06e-25

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


Pssm-ID: 443634  Cd Length: 86  Bit Score: 92.48  E-value: 6.06e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28204218   6 MKKALGLLEFNSISKGIETSDVLLKAAFVEVEILRQICPGKFLTIISGDVEEVKEAID--KAKSKDNKKLVESNIITSVH 83
Cdd:COG4577   1 MGKALGLIETKGLAAAIEAADAMLKAANVELVGYEKIGSGKVTVIVRGDVAAVKAAVDagAAAAERVGELVSSHVIPRPH 80


                ....*.
gi 28204218  84 EDILKA 89
Cdd:COG4577  81 PEVEAA 86
BMC pfam00936
BMC domain; Bacterial microcompartments are primitive organelles composed entirely of protein ...
 9-79 5.46e-18

BMC domain; Bacterial microcompartments are primitive organelles composed entirely of protein subunits. The prototypical bacterial microcompartment is the carboxysome, a protein shell for sequestering carbon fixation reactions. These proteins for hexameric structure.


Pssm-ID: 425954 [Multi-domain]  Cd Length: 74  Bit Score: 74.03  E-value: 5.46e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 28204218     9 ALGLLEFNSISKGIETSDVLLKAAFVEVEILRQICPGKFLTIISGDVEEVKEAIDKAKS--KDNKKLVESNII 79
Cdd:pfam00936   1 ALGLIETRGLAAGIEAADAMLKAANVELVGYELIGGGKVTVIITGDVAAVKAAVEAGVEaaERIGELVSSHVI 73
BMC smart00877
Bacterial microcompartments are primitive organelles composed entirely of protein subunits; ...
 9-82 3.94e-15

Bacterial microcompartments are primitive organelles composed entirely of protein subunits; The prototypical bacterial microcompartment is the carboxysome, a protein shell for sequestering carbon fixation reactions. These proteins for hexameric structure.


Pssm-ID: 197945  Cd Length: 75  Bit Score: 66.83  E-value: 3.94e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 28204218      9 ALGLLEFNSISKGIETSDVLLKAAFVEVEILRQICPGKFLTIISGDVEEVKEAIDKAKSK-DNKKLVESNIITSV 82
Cdd:smart00877   1 ALGIIETRGAAAAIEAADAALKAANVELVGYESIGGGKVTVIITGDVAAVRAAVEAGLEAaERLGLVSSHVIPRP 75
PRK15466 PRK15466
ethanolamine utilization microcompartment protein EutK;
6-63 6.74e-05

ethanolamine utilization microcompartment protein EutK;


Pssm-ID: 185363 [Multi-domain]  Cd Length: 166  Bit Score: 41.51  E-value: 6.74e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 28204218    6 MKKALGLLEFNSISKGIETSDVLLKAAFVEVEILRQICPGKFLTIISGDVEEVKEAID 63
Cdd:PRK15466   1 MINALGLLEVDGMVAAIDAADAMLKAANVRLLSHEVLDPGRLTLVVEGDLAACRAALD 58
 
Name Accession Description Interval E-value
eut_PduT TIGR02526
PduT-like ethanolamine utilization protein; This gene shows up in ethanolamine utilization ...
 6-185 1.51e-87

PduT-like ethanolamine utilization protein; This gene shows up in ethanolamine utilization operons in which a proteinaceous coat organelle is also encoded. It is closely related to the PduT protein in propane-diol operons with the same structure.


Pssm-ID: 131578 [Multi-domain]  Cd Length: 182  Bit Score: 254.80  E-value: 1.51e-87
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28204218     6 MKKALGLLEFNSISKGIETSDVLLKAAFVEVEILRQICPGKFLTIISGDVEEVKEAIDKAKSKDNKKLVESNIITSVHED 85
Cdd:TIGR02526   1 MKKSLGILEFRSISKGIEMSDVFLKAAFVEVFTLRPICPGKFLIILQGDSGEVKEAIQDAKEEAGKFLVSSYIIHSAHED 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28204218    86 ILKALKKRPIIK--EFNAIGVMEFSTVTSSLVALDIALKTSDIQLVKLVLGNGIAGKAYFIINGSVSSVEEGVKSAQNCV 163
Cdd:TIGR02526  81 ILAALKNKYSHKkvEVDAIGIMEISQVGSGLNALDEALKKSAIHLVKLTLGAGIGGKFVAIFTGEVSSVEEGMRILQETA 160

                         170       180
                  ....*....|....*....|..
gi 28204218   164 NSKRIVHSTVIPSPSKILLQNI 185
Cdd:TIGR02526 161 EPKKIIHHTVIPSPDELLKRNL 182
BMC_PduT_repeat1 cd07053
1,2-propanediol utilization protein T (PduT), Bacterial Micro-Compartment (BMC) domain repeat ...
 9-84 1.75e-30

1,2-propanediol utilization protein T (PduT), Bacterial Micro-Compartment (BMC) domain repeat 1; PduT proteins are homologs of the carboxysome shell protein. They are encoded within the pdu operon and might be required for the formation of the outer shell of the bacterial pdu polyhedral organelles which are involved in coenzyme B12-dependent degradation of 1,2-propanediol. Although it has been suggested that PduT might form hexamers and further assemble into the flat facets of the polyhedral outer shell of pdu organelles at present no experimental evidence directly supports this view. PduT proteins contain two tandem BMC domains repeats. This CD contains repeat 1 (the first BMC domain of PduT) as well as carboxysome shell protein sequence homolog, EutM protein, are also included in this CD. They too might exist as hexamers and might play similar functional roles in the construction of the eut organelle outer shell which still remains poorly understood.


Pssm-ID: 132893  Cd Length: 76  Bit Score: 106.10  E-value: 1.75e-30
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 28204218   9 ALGLLEFNSISKGIETSDVLLKAAFVEVEILRQICPGKFLTIISGDVEEVKEAIDKAKSKDNKKLVESNIITSVHE 84
Cdd:cd07053   1 AIGLLELNSIAKGIEAADAMLKAANVELVLAKTICPGKYIIIVSGDVGAVQAAVDAGKEIGGKYVVDSFVLPNVHP 76
BMC_PduT_repeat2 cd07054
1,2-propanediol utilization protein T (PduT), Bacterial Micro-Compartment (BMC) domain repeat ...
 101-177 1.63e-27

1,2-propanediol utilization protein T (PduT), Bacterial Micro-Compartment (BMC) domain repeat 2; PduT proteins are homologs of the carboxysome shell protein. They are encoded within the pdu operon and might be required for the formation of the outer shell of the bacterial pdu polyhedral organelles which are involved in coenzyme B12-dependent degradation of 1,2-propanediol. Although it has been suggested that PduT might form hexamers and further assemble into the flat facets of the polyhedral outer shell of pdu organelles, at present no experimental evidence directly supports this view. PduT proteins contain two tandem BMC domains repeats. This CD contains repeat 2 (the second BMC domain of PduT) as well as carboxysome shell protein sequence homolog, EutM protein, are also included in this CD. They too might exist as hexamers and might play similar functional roles in the construction of the eut organelle outer shell which still remains poorly understood.


Pssm-ID: 132894  Cd Length: 78  Bit Score: 98.78  E-value: 1.63e-27
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 28204218 101 AIGVMEFSTVTSSLVALDIALKTSDIQLVKLVLGNGIAGKAYFIINGSVSSVEEGVKSAQNCVN-SKRIVHSTVIPSP 177
Cdd:cd07054   1 ALGVIETFSVASGIVAADAALKAADVQLIEIRLAMGIGGKSFVVLTGDVSAVEAAVEAAEAVVGeKGLLVDSVVIPSP 78
CcmK COG4577
Carboxysome shell and ethanolamine utilization microcompartment protein CcmL/EutN [Secondary ...
 6-89 6.06e-25

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


Pssm-ID: 443634  Cd Length: 86  Bit Score: 92.48  E-value: 6.06e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28204218   6 MKKALGLLEFNSISKGIETSDVLLKAAFVEVEILRQICPGKFLTIISGDVEEVKEAID--KAKSKDNKKLVESNIITSVH 83
Cdd:COG4577   1 MGKALGLIETKGLAAAIEAADAMLKAANVELVGYEKIGSGKVTVIVRGDVAAVKAAVDagAAAAERVGELVSSHVIPRPH 80


                ....*.
gi 28204218  84 EDILKA 89
Cdd:COG4577  81 PEVEAA 86
BMC pfam00936
BMC domain; Bacterial microcompartments are primitive organelles composed entirely of protein ...
 9-79 5.46e-18

BMC domain; Bacterial microcompartments are primitive organelles composed entirely of protein subunits. The prototypical bacterial microcompartment is the carboxysome, a protein shell for sequestering carbon fixation reactions. These proteins for hexameric structure.


Pssm-ID: 425954 [Multi-domain]  Cd Length: 74  Bit Score: 74.03  E-value: 5.46e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 28204218     9 ALGLLEFNSISKGIETSDVLLKAAFVEVEILRQICPGKFLTIISGDVEEVKEAIDKAKS--KDNKKLVESNII 79
Cdd:pfam00936   1 ALGLIETRGLAAGIEAADAMLKAANVELVGYELIGGGKVTVIITGDVAAVKAAVEAGVEaaERIGELVSSHVI 73
BMC smart00877
Bacterial microcompartments are primitive organelles composed entirely of protein subunits; ...
 9-82 3.94e-15

Bacterial microcompartments are primitive organelles composed entirely of protein subunits; The prototypical bacterial microcompartment is the carboxysome, a protein shell for sequestering carbon fixation reactions. These proteins for hexameric structure.


Pssm-ID: 197945  Cd Length: 75  Bit Score: 66.83  E-value: 3.94e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 28204218      9 ALGLLEFNSISKGIETSDVLLKAAFVEVEILRQICPGKFLTIISGDVEEVKEAIDKAKSK-DNKKLVESNIITSV 82
Cdd:smart00877   1 ALGIIETRGAAAAIEAADAALKAANVELVGYESIGGGKVTVIITGDVAAVRAAVEAGLEAaERLGLVSSHVIPRP 75
BMC pfam00936
BMC domain; Bacterial microcompartments are primitive organelles composed entirely of protein ...
 101-175 1.30e-13

BMC domain; Bacterial microcompartments are primitive organelles composed entirely of protein subunits. The prototypical bacterial microcompartment is the carboxysome, a protein shell for sequestering carbon fixation reactions. These proteins for hexameric structure.


Pssm-ID: 425954 [Multi-domain]  Cd Length: 74  Bit Score: 62.85  E-value: 1.30e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 28204218   101 AIGVMEFSTVTSSLVALDIALKTSDIQLVKLVLGNGiaGKAYFIINGSVSSVEEGVKSAQNCVNS-KRIVHSTVIP 175
Cdd:pfam00936   1 ALGLIETRGLAAGIEAADAMLKAANVELVGYELIGG--GKVTVIITGDVAAVKAAVEAGVEAAERiGELVSSHVIP 74
BMC smart00877
Bacterial microcompartments are primitive organelles composed entirely of protein subunits; ...
 101-177 2.10e-13

Bacterial microcompartments are primitive organelles composed entirely of protein subunits; The prototypical bacterial microcompartment is the carboxysome, a protein shell for sequestering carbon fixation reactions. These proteins for hexameric structure.


Pssm-ID: 197945  Cd Length: 75  Bit Score: 62.20  E-value: 2.10e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 28204218    101 AIGVMEFSTVTSSLVALDIALKTSDIQLVKLVLGNGiaGKAYFIINGSVSSVEEGVKSAQNCVNSKRIVHSTVIPSP 177
Cdd:smart00877   1 ALGIIETRGAAAAIEAADAALKAANVELVGYESIGG--GKVTVIITGDVAAVRAAVEAGLEAAERLGLVSSHVIPRP 75
BMC cd06169
Bacterial Micro-Compartment (BMC) domain; Bacterial micro-compartments are primitive ...
 9-66 2.48e-09

Bacterial Micro-Compartment (BMC) domain; Bacterial micro-compartments are primitive protein-based organelles that sequester specific metabolic pathways in bacterial cells. The prototypical bacterial microcompartment is the carboxysome shell, a bacterial polyhedral organelle which increase the efficiency of CO2 fixation by encapsulating RuBisCO and carbonic anhydrase. They can be divided into two types: alpha-type carboxysomes (alpha-cyanobacteria and proteobacteria) and beta-type carboxysomes (beta-cyanobacteria). In addition to these proteins there are several homologous shell proteins including those found in pdu organelles involved in coenzyme B12-dependent degradation of 1,2-propanediol and eut organelles involved in the cobalamin-dependent degradation of ethanolamine. Structure evidence shows that several carboxysome shell proteins and their homologs (Csos1A, CcmK1,2,4, and PduU) exist as hexamers which might further assemble into extended, tightly packed layers hypothesized to represent the flat facets of the polyhedral organelles outer shell. Although it has been suggested that other homologous proteins in this family might also form hexamers and play similar functional roles in the construction of their corresponding organelle outer shell at present no experimental evidence directly supports this view.


Pssm-ID: 132884  Cd Length: 62  Bit Score: 51.11  E-value: 2.48e-09
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 28204218   9 ALGLLEFNSISKGIETSDVLLKAAFVEVEILRQICPGKFLT-IISGDVEEVKEAIDKAK 66
Cdd:cd06169   1 ALGLLEVRGLAAAIVAADAAVKAADVELVGIERAGGGGLVTlIIRGDVSAVKAAVEAAE 59
BMC_CcmK_like cd07045
Carbon dioxide concentrating mechanism K (CcmK)-like proteins, Bacterial Micro-Compartment ...
 9-90 1.09e-07

Carbon dioxide concentrating mechanism K (CcmK)-like proteins, Bacterial Micro-Compartment (BMC) domain; Bacterial micro-compartments are primitive protein-based organelles that sequester specific metabolic pathways in bacterial cells. The prototypical bacterial microcompartment is the carboxysome shell, a bacterial polyhedral organelle which increase the efficiency of CO2 fixation by encapsulating RuBisCO and carbonic anhydrase. They can be divided into two types: alpha-type carboxysomes (alpha-cyanobacteria and proteobacteria) and beta-type carboxysomes (beta-cyanobacteria). Potential functional differences between the two types are not yet fully understood. In addition to these proteins there are several homologous shell proteins including those found in pdu organelles involved in coenzyme B12-dependent degradation of 1,2-propanediol and eut organelles involved in the cobalamin-dependent degradation of ethanolamine. Structure evidence shows that several carboxysome shell proteins and their homologs (Csos1A, CcmK1,2,4, and PduU) exist as hexamers which might further assemble into extended, tightly packed layers hypothesized to represent the flat facets of the polyhedral organelles outer shell. Although it has been suggested that other homologous proteins in this family might also form hexamers and play similar functional roles in the construction of their corresponding organelle outer shells at present no experimental evidence directly supports this view.


Pssm-ID: 132885  Cd Length: 84  Bit Score: 47.54  E-value: 1.09e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28204218   9 ALGLLEFNSISKGIETSDVLLKAAFVEVEILRQICPGKFLTIISGDVEEVKEAID--KAKSKDNKKLVESNIITSVHEDI 86
Cdd:cd07045   1 ALGLIETRGLVAAIEAADAALKAANVTLVGYEKVGGGLVTVKITGDVAAVKAAVEagAAAAERIGELVSSHVIPRPHDEV 80


                ....
gi 28204218  87 LKAL 90
Cdd:cd07045  81 EKIL 84
BMC_PduT_repeat2 cd07054
1,2-propanediol utilization protein T (PduT), Bacterial Micro-Compartment (BMC) domain repeat ...
 9-82 8.25e-07

1,2-propanediol utilization protein T (PduT), Bacterial Micro-Compartment (BMC) domain repeat 2; PduT proteins are homologs of the carboxysome shell protein. They are encoded within the pdu operon and might be required for the formation of the outer shell of the bacterial pdu polyhedral organelles which are involved in coenzyme B12-dependent degradation of 1,2-propanediol. Although it has been suggested that PduT might form hexamers and further assemble into the flat facets of the polyhedral outer shell of pdu organelles, at present no experimental evidence directly supports this view. PduT proteins contain two tandem BMC domains repeats. This CD contains repeat 2 (the second BMC domain of PduT) as well as carboxysome shell protein sequence homolog, EutM protein, are also included in this CD. They too might exist as hexamers and might play similar functional roles in the construction of the eut organelle outer shell which still remains poorly understood.


Pssm-ID: 132894  Cd Length: 78  Bit Score: 44.85  E-value: 8.25e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 28204218   9 ALGLLEFNSISKGIETSDVLLKAAFV---EVEILRQICpGKFLTIISGDVEEVKEAIDKAKS--KDNKKLVESNIITSV 82
Cdd:cd07054   1 ALGVIETFSVASGIVAADAALKAADVqliEIRLAMGIG-GKSFVVLTGDVSAVEAAVEAAEAvvGEKGLLVDSVVIPSP 78
BMC cd06169
Bacterial Micro-Compartment (BMC) domain; Bacterial micro-compartments are primitive ...
 101-159 1.60e-06

Bacterial Micro-Compartment (BMC) domain; Bacterial micro-compartments are primitive protein-based organelles that sequester specific metabolic pathways in bacterial cells. The prototypical bacterial microcompartment is the carboxysome shell, a bacterial polyhedral organelle which increase the efficiency of CO2 fixation by encapsulating RuBisCO and carbonic anhydrase. They can be divided into two types: alpha-type carboxysomes (alpha-cyanobacteria and proteobacteria) and beta-type carboxysomes (beta-cyanobacteria). In addition to these proteins there are several homologous shell proteins including those found in pdu organelles involved in coenzyme B12-dependent degradation of 1,2-propanediol and eut organelles involved in the cobalamin-dependent degradation of ethanolamine. Structure evidence shows that several carboxysome shell proteins and their homologs (Csos1A, CcmK1,2,4, and PduU) exist as hexamers which might further assemble into extended, tightly packed layers hypothesized to represent the flat facets of the polyhedral organelles outer shell. Although it has been suggested that other homologous proteins in this family might also form hexamers and play similar functional roles in the construction of their corresponding organelle outer shell at present no experimental evidence directly supports this view.


Pssm-ID: 132884  Cd Length: 62  Bit Score: 43.79  E-value: 1.60e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 28204218 101 AIGVMEFSTVTSSLVALDIALKTSDIQLVKLVlGNGIAGKAYFIINGSVSSVEEGVKSA 159
Cdd:cd06169   1 ALGLLEVRGLAAAIVAADAAVKAADVELVGIE-RAGGGGLVTLIIRGDVSAVKAAVEAA 58
CcmK COG4577
Carboxysome shell and ethanolamine utilization microcompartment protein CcmL/EutN [Secondary ...
 100-178 1.93e-06

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


Pssm-ID: 443634  Cd Length: 86  Bit Score: 43.94  E-value: 1.93e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28204218 100 NAIGVMEFSTVTSSLVALDIALKTSDIQLVklvlGNGIAGKAYF--IINGSVSSVEEGVKSAQNCVNSK-RIVHSTVIPS 176
Cdd:COG4577   3 KALGLIETKGLAAAIEAADAMLKAANVELV----GYEKIGSGKVtvIVRGDVAAVKAAVDAGAAAAERVgELVSSHVIPR 78


                ..
gi 28204218 177 PS 178
Cdd:COG4577  79 PH 80
PRK15466 PRK15466
ethanolamine utilization microcompartment protein EutK;
6-63 6.74e-05

ethanolamine utilization microcompartment protein EutK;


Pssm-ID: 185363 [Multi-domain]  Cd Length: 166  Bit Score: 41.51  E-value: 6.74e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 28204218    6 MKKALGLLEFNSISKGIETSDVLLKAAFVEVEILRQICPGKFLTIISGDVEEVKEAID 63
Cdd:PRK15466   1 MINALGLLEVDGMVAAIDAADAMLKAANVRLLSHEVLDPGRLTLVVEGDLAACRAALD 58
BMC_PduT_repeat1 cd07053
1,2-propanediol utilization protein T (PduT), Bacterial Micro-Compartment (BMC) domain repeat ...
 101-178 1.93e-04

1,2-propanediol utilization protein T (PduT), Bacterial Micro-Compartment (BMC) domain repeat 1; PduT proteins are homologs of the carboxysome shell protein. They are encoded within the pdu operon and might be required for the formation of the outer shell of the bacterial pdu polyhedral organelles which are involved in coenzyme B12-dependent degradation of 1,2-propanediol. Although it has been suggested that PduT might form hexamers and further assemble into the flat facets of the polyhedral outer shell of pdu organelles at present no experimental evidence directly supports this view. PduT proteins contain two tandem BMC domains repeats. This CD contains repeat 1 (the first BMC domain of PduT) as well as carboxysome shell protein sequence homolog, EutM protein, are also included in this CD. They too might exist as hexamers and might play similar functional roles in the construction of the eut organelle outer shell which still remains poorly understood.


Pssm-ID: 132893  Cd Length: 76  Bit Score: 38.30  E-value: 1.93e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 28204218 101 AIGVMEFSTVTSSLVALDIALKTSDIQLVklVLGNGIAGKAYFIINGSVSSVEEGVKSAQNcVNSKRIVHSTVIPSPS 178
Cdd:cd07053   1 AIGLLELNSIAKGIEAADAMLKAANVELV--LAKTICPGKYIIIVSGDVGAVQAAVDAGKE-IGGKYVVDSFVLPNVH 75
BMC_CcmK cd07057
Carbon dioxide concentrating mechanism (CcmK); Bacterial Micro-Compartment (BMC) domain; ...
 9-86 4.22e-04

Carbon dioxide concentrating mechanism (CcmK); Bacterial Micro-Compartment (BMC) domain; CcmK1-4 and CcmL proteins found in Synechocystis sp. strain PCC 6803 make up the beta carboxysome shell. These CcmK proteins have been shown to form hexameric units, while the CcmL proteins have been shown to form pentameric units. Together these proteins further assemble into the flat facets of the polyhedral carboxysome shell. The structures suggest that the central pores and the gaps between hexamers limit the transport of metabolites into and out of the the carboxysome.


Pssm-ID: 132897  Cd Length: 88  Bit Score: 37.66  E-value: 4.22e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28204218   9 ALGLLEFNSISKGIETSDVLLKAAFVEVEILRQICPGKFLTIISGDVEEVKEA----IDKAKSKDNKKLVESNIITSVHE 84
Cdd:cd07057   1 AVGMIETLGFPAVLAAADAMVKAARVTLVGYEKIGSGRCTVIVRGDVAEVKAAveagIEAAERVHGGEVLSHTIIPRPHE 80


                ..
gi 28204218  85 DI 86
Cdd:cd07057  81 NL 82
BMC_PduA cd07059
1,2-propanediol utilization protein A (PduA), Bacterial Micro-Compartment (BMC) domain; PduA ...
 9-90 5.65e-04

1,2-propanediol utilization protein A (PduA), Bacterial Micro-Compartment (BMC) domain; PduA is encoded within the 1,2-propanediol utilization (pdu) operon along with other homologous carboxysome shell proteins PduB, B', J, K, T, and U. PduA is thought to be required for the formation of the outer shell of bacterial pdu polyhedral organelles which are involved in coenzyme B12-dependent degradation of 1,2-propanediol. Although it has been suggested that PduA might form hexamers and further assemble into the flat facets of the polyhedral outer shell of pdu organelles, like PduU does, at present no experimental evidence directly supports this view.


Pssm-ID: 132899  Cd Length: 85  Bit Score: 37.53  E-value: 5.65e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28204218   9 ALGLLEFNSISKGIETSDVLLKAAFVEVEILRQICPGKFLTIISGDVEEVKEAIDKAKSKDNK--KLVESNIITSVHEDI 86
Cdd:cd07059   1 ALGMIETKGLVGAIEAADAMVKAANVTLVGKEQIGGGLVTVMVRGDVGAVKAATDAGAAAAERvgELVSVHVIPRPHTEV 80


                ....
gi 28204218  87 LKAL 90
Cdd:cd07059  81 EKIL 84
BMC_PduK cd07056
1,2-propanediol utilization protein K (PduK), Bacterial Micro-Compartment (BMC) domain repeat ...
 101-177 5.71e-04

1,2-propanediol utilization protein K (PduK), Bacterial Micro-Compartment (BMC) domain repeat 1l; PduK proteins are homologs of the carboxysome shell protein. They are encoded within the pdu operon and might be required for the formation of the outer shell of the bacterial pdu polyhedral organelles which are involved in coenzyme B12-dependent degradation of 1,2-propanediol. Although it has been suggested that PduK might form hexamers and further assemble into the flat facets of the polyhedral outer shell of pdu organelles at present no experimental evidence directly supports this view.


Pssm-ID: 132896  Cd Length: 77  Bit Score: 37.00  E-value: 5.71e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 28204218 101 AIGVMEFSTVTSSLVALDIALKTSDIQLVKLVLGNGiAGKAYFIINGSVSSVEEGVKS-AQNCVNSKRIVHSTVIPSP 177
Cdd:cd07056   1 SLGLLEVSGLSGAIVVADRMAKTANVRLLGLENTKG-SGWMTVKISGDVAAVNAAIEAgKQTAGASDGYVASTVIARP 77
BMC_CsoS1 cd07058
Carboxysome Shell 1 (CsoS1); Bacterial Micro-Compartment (BMC) domain; The cso operon in ...
 9-90 1.50e-03

Carboxysome Shell 1 (CsoS1); Bacterial Micro-Compartment (BMC) domain; The cso operon in Halothiobacillus neapolitanus contains the genes involved in alpha carboxysome function including those for the carboxysome shell proteins: CsoS1A, CsoS1B, and CsoS1C. CsoS1A has been shown to form hexameric units which further assemble into the flat facets of the polyhedral carboxysome shell. The structures suggest that the central pores and the gaps between hexamers limit the transport of metabolites into and out of the the carboxysome. Although it has been suggested that other homologous proteins, CsoS1B and CsoS1C, in this family might also form hexamers and play similar functional roles in the construction of carboxysome outer shell at present no experimental evidence directly supports this view.


Pssm-ID: 132898  Cd Length: 88  Bit Score: 36.11  E-value: 1.50e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28204218   9 ALGLLEFNSISKGIETSDVLLKAAFVEVeILRQICPGKFLTII----SGDVEEVKEAIDKAKSKDNKKLVESNIITSVHE 84
Cdd:cd07058   3 ALGMIETRGLVPAIEAADAMTKAAEVRL-IGRQFVGGGYVTVLvrgeTGAVNAAVRAGADACERVGDGLVAAHIIARVHS 81


                ....*.
gi 28204218  85 DILKAL 90
Cdd:cd07058  82 EVENIL 87
BMC_PduU-EutS cd07046
1,2-propanediol utilization protein U (PduU)/ethanolamine utilization protein S (EutS), ...
 71-157 3.29e-03

1,2-propanediol utilization protein U (PduU)/ethanolamine utilization protein S (EutS), Bacterial Micro-Compartment (BMC) domain; PduU encapsulates several related enzymes within a shell composed of a few thousand protein subunits. PduU exists as a hexamer which might further assemble into the flat facets of the polyhedral outer shell of the pdu organelle. This proteinaceous noncarboxysome microcompartment is involved in coenzyme B12-dependent degradation of 1,2-propanediol. The core of PduU is related to the typical BMC domain and its natural oligomeric state is a cyclic hexamer. Unlike other typical BMC domain proteins, the 3D topology of PduU reveals a circular permuted variation on the typical BMC fold which leads to several unique features. The exact functions related to those unique features are still not clear. Another difference is the presence of a deep cavity on one side of the hexamer as well as an intermolecular six-stranded beta barrel that seems to block the central pore that is present in other BMC domain proteins. EutS proteins included in this CD are sequence homologs of PduU. They are encoded within eut operon and may be required for the formation of the outer shell of bacterial eut polyhedral organelles which are involved in the cobalamin-dependent degradation of ethanolamine. Although it has been suggested that EutS might also form hexamers and play similar functional roles in the construction of the eut organelle outer shell at present no experimental evidence directly supports this view.


Pssm-ID: 132886  Cd Length: 110  Bit Score: 35.69  E-value: 3.29e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28204218  71 KKLVESNIITSVHEDILKALKKRPIIKEfnAIGVMEFSTVTSSLVALDIALKTSDIQLVKLVLGNGIagkayFIINGSVS 150
Cdd:cd07046  11 KQITLAHLIANPDPEIYQKLGLNPGVDE--AIGILTITPSEAAIIAADIATKAADVEIGFLDRFSGA-----LVITGDVS 83


                ....*..
gi 28204218 151 SVEEGVK 157
Cdd:cd07046  84 EVESALE 90
BMC_like_2 cd07055
Bacterial Micro-Compartment (BMC)-like domain 2; BMC like 2 domains exist in cyanobacteria, ...
 9-69 6.69e-03

Bacterial Micro-Compartment (BMC)-like domain 2; BMC like 2 domains exist in cyanobacteria, proteobacteria, and actinobacteria and are homologs of carboxysome shell proteins. They might be encoded from putative organelles involved in unknown metabolic process. Although it has been suggested that these carboxysome shell protein homologs form hexamers and further assemble into the flat facets of the polyhedral bacterial organelles shell at present no experimental evidence exists to directly support this view.


Pssm-ID: 132895  Cd Length: 61  Bit Score: 33.59  E-value: 6.69e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 28204218   9 ALGLLEFNSISKgIETSDVLLKAAFVEVEILRQICPGKFLTI-ISGDVEEVKEAIDKAKSKD 69
Cdd:cd07055   1 AIGLMQGKVIDM-IYAADIAEKASGVFVSDIFGSCPQHMITLaIFGETSAVELAMREIEEDA 61
 
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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