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Conserved domains on  [gi|186523322|ref|NP_197122|]
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maize chloroplast splicing factor-like protein [Arabidopsis thaliana]

Protein Classification

YhbY family RNA-binding protein( domain architecture ID 10661237)

YhbY family RNA-binding protein similar to Arabidopsis thaliana CRS2-associated factors and CRM-domain containing factors

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CRS1_YhbY smart01103
Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function ...
 361-445 2.21e-18

Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly; GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome.


:

Pssm-ID: 198171  Cd Length: 84  Bit Score: 80.20  E-value: 2.21e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186523322   361 LTDEELTYLRNIAQPLPFHFVLGRNYGLQGLASAIVKLWEKCIIAKIAIKwGALNTNNEEMADELRYLTGGVLILRNKYL 440
Cdd:smart01103   1 LTGKQKRYLRSLAHHLKPVVQIGKNGLTEGVLEEIDEALEKHELIKVKVL-GNDREDRKEIAEELAEETGAELVQVIGKT 79


                   ....*
gi 186523322   441 IVLYR 445
Cdd:smart01103  80 IVLYR 84
CRS1_YhbY smart01103
Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function ...
 572-659 7.93e-18

Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly; GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome.


:

Pssm-ID: 198171  Cd Length: 84  Bit Score: 78.66  E-value: 7.93e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186523322   572 LTNEERECLRRIGLKMNSSLVLGRRGVFFGVMEGLHQHWKHREVAKVITMQKLFSRVVYTAKALETESNGVLISIeklkE 651
Cdd:smart01103   1 LTGKQKRYLRSLAHHLKPVVQIGKNGLTEGVLEEIDEALEKHELIKVKVLGNDREDRKEIAEELAEETGAELVQV----I 76


                   ....*...
gi 186523322   652 GHAILIYR 659
Cdd:smart01103  77 GKTIVLYR 84
CRS1_YhbY smart01103
Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function ...
 207-290 5.79e-14

Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly; GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome.


:

Pssm-ID: 198171  Cd Length: 84  Bit Score: 67.49  E-value: 5.79e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186523322   207 LDEGLLNRLRREASKMRKWVNVRKAGVTELVVNKIKSMWKLNELAMVRF-DVPLCRNMERAQEIIEmKTGGLVVLSKKEF 285
Cdd:smart01103   1 LTGKQKRYLRSLAHHLKPVVQIGKNGLTEGVLEEIDEALEKHELIKVKVlGNDREDRKEIAEELAE-ETGAELVQVIGKT 79


                   ....*
gi 186523322   286 LVVYR 290
Cdd:smart01103  80 IVLYR 84
COG4026 super family cl26606
Uncharacterized conserved protein, contains TOPRIM domain, potential nuclease [General ...
 465-561 1.47e-03

Uncharacterized conserved protein, contains TOPRIM domain, potential nuclease [General function prediction only];


The actual alignment was detected with superfamily member COG4026:

Pssm-ID: 443204 [Multi-domain]  Cd Length: 287  Bit Score: 41.25  E-value: 1.47e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186523322 465 LSRYQHFEETKREsdieLLEVVTNGKQLKETNKSgTLLEFQELQRKFGEMDPRNLETEAEKARLEKELKSQEHKLSILKS 544
Cdd:COG4026  124 LQNIPEYNELREE----LLELKEKIDEIAKEKEK-LTKENEELESELEELREEYKKLREENSILEEEFDNIKSEYSDLKS 198

                         90       100
                 ....*....|....*....|.
gi 186523322 545 KIE----KSNMELFKLNSLWK 561
Cdd:COG4026  199 RFEellkKRLLEVFSLEELWK 219
 
Name Accession Description Interval E-value
CRS1_YhbY smart01103
Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function ...
 361-445 2.21e-18

Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly; GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome.


Pssm-ID: 198171  Cd Length: 84  Bit Score: 80.20  E-value: 2.21e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186523322   361 LTDEELTYLRNIAQPLPFHFVLGRNYGLQGLASAIVKLWEKCIIAKIAIKwGALNTNNEEMADELRYLTGGVLILRNKYL 440
Cdd:smart01103   1 LTGKQKRYLRSLAHHLKPVVQIGKNGLTEGVLEEIDEALEKHELIKVKVL-GNDREDRKEIAEELAEETGAELVQVIGKT 79


                   ....*
gi 186523322   441 IVLYR 445
Cdd:smart01103  80 IVLYR 84
CRS1_YhbY smart01103
Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function ...
 572-659 7.93e-18

Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly; GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome.


Pssm-ID: 198171  Cd Length: 84  Bit Score: 78.66  E-value: 7.93e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186523322   572 LTNEERECLRRIGLKMNSSLVLGRRGVFFGVMEGLHQHWKHREVAKVITMQKLFSRVVYTAKALETESNGVLISIeklkE 651
Cdd:smart01103   1 LTGKQKRYLRSLAHHLKPVVQIGKNGLTEGVLEEIDEALEKHELIKVKVLGNDREDRKEIAEELAEETGAELVQV----I 76


                   ....*...
gi 186523322   652 GHAILIYR 659
Cdd:smart01103  77 GKTIVLYR 84
CRS1_YhbY pfam01985
CRS1 / YhbY (CRM) domain; Escherichia coli YhbY is associated with pre-50S ribosomal subunits, ...
 572-659 7.28e-17

CRS1 / YhbY (CRM) domain; Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localizes to the nucleolus, suggesting that an analogous activity may have been retained in plants. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome.


Pssm-ID: 460405  Cd Length: 84  Bit Score: 75.90  E-value: 7.28e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186523322  572 LTNEERECLRRIGLKMNSSLVLGRRGVFFGVMEGLHQHWKHREVAKVITMQKLFSRVVYTAKALETESNGVLISIeklkE 651
Cdd:pfam01985   1 LTSKERRYLRKLAHHLKPIVQIGKNGVTEGVVEEIHEALEARELIKVKVLKNCREDRKEIAEELAEKTGAEVVQV----I 76


                  ....*...
gi 186523322  652 GHAILIYR 659
Cdd:pfam01985  77 GRTIVLYR 84
CRS1_YhbY pfam01985
CRS1 / YhbY (CRM) domain; Escherichia coli YhbY is associated with pre-50S ribosomal subunits, ...
 361-445 1.08e-16

CRS1 / YhbY (CRM) domain; Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localizes to the nucleolus, suggesting that an analogous activity may have been retained in plants. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome.


Pssm-ID: 460405  Cd Length: 84  Bit Score: 75.51  E-value: 1.08e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186523322  361 LTDEELTYLRNIAQPLPFHFVLGRNYGLQGLASAIVKLWEKCIIAKIAIKWGALNTnNEEMADELRYLTGGVLILRNKYL 440
Cdd:pfam01985   1 LTSKERRYLRKLAHHLKPIVQIGKNGVTEGVVEEIHEALEARELIKVKVLKNCRED-RKEIAEELAEKTGAEVVQVIGRT 79


                  ....*
gi 186523322  441 IVLYR 445
Cdd:pfam01985  80 IVLYR 84
CRS1_YhbY smart01103
Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function ...
 207-290 5.79e-14

Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly; GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome.


Pssm-ID: 198171  Cd Length: 84  Bit Score: 67.49  E-value: 5.79e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186523322   207 LDEGLLNRLRREASKMRKWVNVRKAGVTELVVNKIKSMWKLNELAMVRF-DVPLCRNMERAQEIIEmKTGGLVVLSKKEF 285
Cdd:smart01103   1 LTGKQKRYLRSLAHHLKPVVQIGKNGLTEGVLEEIDEALEKHELIKVKVlGNDREDRKEIAEELAE-ETGAELVQVIGKT 79


                   ....*
gi 186523322   286 LVVYR 290
Cdd:smart01103  80 IVLYR 84
CRS1_YhbY pfam01985
CRS1 / YhbY (CRM) domain; Escherichia coli YhbY is associated with pre-50S ribosomal subunits, ...
 214-290 1.19e-13

CRS1 / YhbY (CRM) domain; Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localizes to the nucleolus, suggesting that an analogous activity may have been retained in plants. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome.


Pssm-ID: 460405  Cd Length: 84  Bit Score: 66.65  E-value: 1.19e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 186523322  214 RLRREASKMRKWVNVRKAGVTELVVNKIKSMWKLNELAMVRFdVPLCRN-MERAQEIIEMKTGGLVVLSKKEFLVVYR 290
Cdd:pfam01985   8 YLRKLAHHLKPIVQIGKNGVTEGVVEEIHEALEARELIKVKV-LKNCREdRKEIAEELAEKTGAEVVQVIGRTIVLYR 84
COG4026 COG4026
Uncharacterized conserved protein, contains TOPRIM domain, potential nuclease [General ...
 465-561 1.47e-03

Uncharacterized conserved protein, contains TOPRIM domain, potential nuclease [General function prediction only];


Pssm-ID: 443204 [Multi-domain]  Cd Length: 287  Bit Score: 41.25  E-value: 1.47e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186523322 465 LSRYQHFEETKREsdieLLEVVTNGKQLKETNKSgTLLEFQELQRKFGEMDPRNLETEAEKARLEKELKSQEHKLSILKS 544
Cdd:COG4026  124 LQNIPEYNELREE----LLELKEKIDEIAKEKEK-LTKENEELESELEELREEYKKLREENSILEEEFDNIKSEYSDLKS 198

                         90       100
                 ....*....|....*....|.
gi 186523322 545 KIE----KSNMELFKLNSLWK 561
Cdd:COG4026  199 RFEellkKRLLEVFSLEELWK 219
 
Name Accession Description Interval E-value
CRS1_YhbY smart01103
Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function ...
 361-445 2.21e-18

Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly; GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome.


Pssm-ID: 198171  Cd Length: 84  Bit Score: 80.20  E-value: 2.21e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186523322   361 LTDEELTYLRNIAQPLPFHFVLGRNYGLQGLASAIVKLWEKCIIAKIAIKwGALNTNNEEMADELRYLTGGVLILRNKYL 440
Cdd:smart01103   1 LTGKQKRYLRSLAHHLKPVVQIGKNGLTEGVLEEIDEALEKHELIKVKVL-GNDREDRKEIAEELAEETGAELVQVIGKT 79


                   ....*
gi 186523322   441 IVLYR 445
Cdd:smart01103  80 IVLYR 84
CRS1_YhbY smart01103
Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function ...
 572-659 7.93e-18

Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly; GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome.


Pssm-ID: 198171  Cd Length: 84  Bit Score: 78.66  E-value: 7.93e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186523322   572 LTNEERECLRRIGLKMNSSLVLGRRGVFFGVMEGLHQHWKHREVAKVITMQKLFSRVVYTAKALETESNGVLISIeklkE 651
Cdd:smart01103   1 LTGKQKRYLRSLAHHLKPVVQIGKNGLTEGVLEEIDEALEKHELIKVKVLGNDREDRKEIAEELAEETGAELVQV----I 76


                   ....*...
gi 186523322   652 GHAILIYR 659
Cdd:smart01103  77 GKTIVLYR 84
CRS1_YhbY pfam01985
CRS1 / YhbY (CRM) domain; Escherichia coli YhbY is associated with pre-50S ribosomal subunits, ...
 572-659 7.28e-17

CRS1 / YhbY (CRM) domain; Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localizes to the nucleolus, suggesting that an analogous activity may have been retained in plants. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome.


Pssm-ID: 460405  Cd Length: 84  Bit Score: 75.90  E-value: 7.28e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186523322  572 LTNEERECLRRIGLKMNSSLVLGRRGVFFGVMEGLHQHWKHREVAKVITMQKLFSRVVYTAKALETESNGVLISIeklkE 651
Cdd:pfam01985   1 LTSKERRYLRKLAHHLKPIVQIGKNGVTEGVVEEIHEALEARELIKVKVLKNCREDRKEIAEELAEKTGAEVVQV----I 76


                  ....*...
gi 186523322  652 GHAILIYR 659
Cdd:pfam01985  77 GRTIVLYR 84
CRS1_YhbY pfam01985
CRS1 / YhbY (CRM) domain; Escherichia coli YhbY is associated with pre-50S ribosomal subunits, ...
 361-445 1.08e-16

CRS1 / YhbY (CRM) domain; Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localizes to the nucleolus, suggesting that an analogous activity may have been retained in plants. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome.


Pssm-ID: 460405  Cd Length: 84  Bit Score: 75.51  E-value: 1.08e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186523322  361 LTDEELTYLRNIAQPLPFHFVLGRNYGLQGLASAIVKLWEKCIIAKIAIKWGALNTnNEEMADELRYLTGGVLILRNKYL 440
Cdd:pfam01985   1 LTSKERRYLRKLAHHLKPIVQIGKNGVTEGVVEEIHEALEARELIKVKVLKNCRED-RKEIAEELAEKTGAEVVQVIGRT 79


                  ....*
gi 186523322  441 IVLYR 445
Cdd:pfam01985  80 IVLYR 84
CRS1_YhbY smart01103
Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function ...
 207-290 5.79e-14

Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly; GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome.


Pssm-ID: 198171  Cd Length: 84  Bit Score: 67.49  E-value: 5.79e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186523322   207 LDEGLLNRLRREASKMRKWVNVRKAGVTELVVNKIKSMWKLNELAMVRF-DVPLCRNMERAQEIIEmKTGGLVVLSKKEF 285
Cdd:smart01103   1 LTGKQKRYLRSLAHHLKPVVQIGKNGLTEGVLEEIDEALEKHELIKVKVlGNDREDRKEIAEELAE-ETGAELVQVIGKT 79


                   ....*
gi 186523322   286 LVVYR 290
Cdd:smart01103  80 IVLYR 84
CRS1_YhbY pfam01985
CRS1 / YhbY (CRM) domain; Escherichia coli YhbY is associated with pre-50S ribosomal subunits, ...
 214-290 1.19e-13

CRS1 / YhbY (CRM) domain; Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localizes to the nucleolus, suggesting that an analogous activity may have been retained in plants. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome.


Pssm-ID: 460405  Cd Length: 84  Bit Score: 66.65  E-value: 1.19e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 186523322  214 RLRREASKMRKWVNVRKAGVTELVVNKIKSMWKLNELAMVRFdVPLCRN-MERAQEIIEMKTGGLVVLSKKEFLVVYR 290
Cdd:pfam01985   8 YLRKLAHHLKPIVQIGKNGVTEGVVEEIHEALEARELIKVKV-LKNCREdRKEIAEELAEKTGAEVVQVIGRTIVLYR 84
COG4026 COG4026
Uncharacterized conserved protein, contains TOPRIM domain, potential nuclease [General ...
 465-561 1.47e-03

Uncharacterized conserved protein, contains TOPRIM domain, potential nuclease [General function prediction only];


Pssm-ID: 443204 [Multi-domain]  Cd Length: 287  Bit Score: 41.25  E-value: 1.47e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186523322 465 LSRYQHFEETKREsdieLLEVVTNGKQLKETNKSgTLLEFQELQRKFGEMDPRNLETEAEKARLEKELKSQEHKLSILKS 544
Cdd:COG4026  124 LQNIPEYNELREE----LLELKEKIDEIAKEKEK-LTKENEELESELEELREEYKKLREENSILEEEFDNIKSEYSDLKS 198

                         90       100
                 ....*....|....*....|.
gi 186523322 545 KIE----KSNMELFKLNSLWK 561
Cdd:COG4026  199 RFEellkKRLLEVFSLEELWK 219
 
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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