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Conserved domains on  [gi|499206294|ref|WP_010903834|]
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MULTISPECIES: RNA-binding domain-containing protein [Halobacterium]

Protein Classification

COG1931 family protein( domain architecture ID 10004954)

COG1931 family protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
COG1931 COG1931
Predicted RNA binding protein with dsRBD fold, UPF0201 family [General function prediction ...
 9-138 5.18e-55

Predicted RNA binding protein with dsRBD fold, UPF0201 family [General function prediction only];


:

Pssm-ID: 441534  Cd Length: 141  Bit Score: 168.90  E-value: 5.18e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499206294   9 VRVTAPVYPTEPDDRVADAILRLFPDATVTVEDD----RAVAETDTT--ASFREQLFDQRILDTAREQFQASQTDAGFSF 82
Cdd:COG1931    2 VRVEAPVRPTEDEDKVLDAIRNIFPEEELEIEEGggykRIVGESDLHslEKFHELLREQRILDTARSVLFKGIKGDTFSF 81

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 499206294  83 DLKKQAAFNGTVNFAVGNPDELGDLHVEVTVAEPaVQQFIDHLAPPTDGGEPLEDP 138
Cdd:COG1931   82 MLNKQAAFVGRVSFVVGEESPLGPIHVTVEVDDP-VERVIDWLAPPTEDGRPVDED 136
 
Name Accession Description Interval E-value
COG1931 COG1931
Predicted RNA binding protein with dsRBD fold, UPF0201 family [General function prediction ...
 9-138 5.18e-55

Predicted RNA binding protein with dsRBD fold, UPF0201 family [General function prediction only];


Pssm-ID: 441534  Cd Length: 141  Bit Score: 168.90  E-value: 5.18e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499206294   9 VRVTAPVYPTEPDDRVADAILRLFPDATVTVEDD----RAVAETDTT--ASFREQLFDQRILDTAREQFQASQTDAGFSF 82
Cdd:COG1931    2 VRVEAPVRPTEDEDKVLDAIRNIFPEEELEIEEGggykRIVGESDLHslEKFHELLREQRILDTARSVLFKGIKGDTFSF 81

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 499206294  83 DLKKQAAFNGTVNFAVGNPDELGDLHVEVTVAEPaVQQFIDHLAPPTDGGEPLEDP 138
Cdd:COG1931   82 MLNKQAAFVGRVSFVVGEESPLGPIHVTVEVDDP-VERVIDWLAPPTEDGRPVDED 136
PRK00447 PRK00447
hypothetical protein; Provisional
 7-137 1.08e-22

hypothetical protein; Provisional


Pssm-ID: 234766  Cd Length: 144  Bit Score: 86.65  E-value: 1.08e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499206294   7 VTVRVTAPVYPTEPDDRVADAILRLFPDATVTVED----DRAVAETDTTAS---FREQLFDQRILDTAREQFQASQTDAG 79
Cdd:PRK00447   3 VEVEVEAEVRPTEDEEKVKKAILNFFDFEKFEAEDegeyKILVGEARTLKSlqkLHRLLRGERILDTARKYLMKGIEGNE 82

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 499206294  80 FSFDLKKQAAFNGTVNFAVGNPDE-LGDlhVEVTVAEPAVQQFIDHLAPPTDGGEPLED 137
Cdd:PRK00447  83 ITFMVHKQAAYVGVLSFVDSDEESpLGP--ITITIRYKNPQEVIDWLAPRTARGVPLWE 139
RNA_binding pfam01877
RNA binding; PH1010 is composed of five alpha-helices (1-5) and eight beta-strands (1-8) with ...
 9-97 2.25e-06

RNA binding; PH1010 is composed of five alpha-helices (1-5) and eight beta-strands (1-8) with the following topology: beta-1, alpha-1, beta-2, beta-3, alpha-2, alpha-3, beta-4, beta-5, alpha-4, beta-6, alpha-5, beta-7, beta-8. The first six beta-strands (1-6) form a slightly twisted antiparallel beta-sheet and face five alpha-helices on one side. The last two beta-strands form an antiparallel beta-sheet in the C-terminus. PH1010 forms a characteriztic homodimer structure in the crystal. dimerization of the molecule is crucial for function. The structure resembles that of some ribosomal proteins such as the 50S ribosomal protein L5. Although the structure resembles that of the RRM-type RNA-binding domain of the ribosomal L5 protein, the residues involved in RNA-binding in the L5 protein are not conserved in this family. Despite this, these proteins bind to double-stranded RNA in a non-sequence specific manner.


Pssm-ID: 426487  Cd Length: 113  Bit Score: 43.69  E-value: 2.25e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499206294    9 VRVTAPVYPTEPDDRVADAILRLFPD----------------ATVTVEDDRAVAEtdttaSFREQLFDQRILDTAREQFQ 72
Cdd:pfam01877   2 IEVRAFVHATEDEEKVLEALSNFLPEeeeeeghygnpitileARLEKKDAKKFLK-----KLHELLREEDIKYLLDELDE 76

                          90       100
                  ....*....|....*....|....*
gi 499206294   73 ASQTDAGFSFDLKKQAAFNGTVNFA 97
Cdd:pfam01877  77 RVDENGKLYLRLDKQAAYLGKLSLS 101
 
Name Accession Description Interval E-value
COG1931 COG1931
Predicted RNA binding protein with dsRBD fold, UPF0201 family [General function prediction ...
 9-138 5.18e-55

Predicted RNA binding protein with dsRBD fold, UPF0201 family [General function prediction only];


Pssm-ID: 441534  Cd Length: 141  Bit Score: 168.90  E-value: 5.18e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499206294   9 VRVTAPVYPTEPDDRVADAILRLFPDATVTVEDD----RAVAETDTT--ASFREQLFDQRILDTAREQFQASQTDAGFSF 82
Cdd:COG1931    2 VRVEAPVRPTEDEDKVLDAIRNIFPEEELEIEEGggykRIVGESDLHslEKFHELLREQRILDTARSVLFKGIKGDTFSF 81

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 499206294  83 DLKKQAAFNGTVNFAVGNPDELGDLHVEVTVAEPaVQQFIDHLAPPTDGGEPLEDP 138
Cdd:COG1931   82 MLNKQAAFVGRVSFVVGEESPLGPIHVTVEVDDP-VERVIDWLAPPTEDGRPVDED 136
PRK00447 PRK00447
hypothetical protein; Provisional
 7-137 1.08e-22

hypothetical protein; Provisional


Pssm-ID: 234766  Cd Length: 144  Bit Score: 86.65  E-value: 1.08e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499206294   7 VTVRVTAPVYPTEPDDRVADAILRLFPDATVTVED----DRAVAETDTTAS---FREQLFDQRILDTAREQFQASQTDAG 79
Cdd:PRK00447   3 VEVEVEAEVRPTEDEEKVKKAILNFFDFEKFEAEDegeyKILVGEARTLKSlqkLHRLLRGERILDTARKYLMKGIEGNE 82

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 499206294  80 FSFDLKKQAAFNGTVNFAVGNPDE-LGDlhVEVTVAEPAVQQFIDHLAPPTDGGEPLED 137
Cdd:PRK00447  83 ITFMVHKQAAYVGVLSFVDSDEESpLGP--ITITIRYKNPQEVIDWLAPRTARGVPLWE 139
RNA_binding pfam01877
RNA binding; PH1010 is composed of five alpha-helices (1-5) and eight beta-strands (1-8) with ...
 9-97 2.25e-06

RNA binding; PH1010 is composed of five alpha-helices (1-5) and eight beta-strands (1-8) with the following topology: beta-1, alpha-1, beta-2, beta-3, alpha-2, alpha-3, beta-4, beta-5, alpha-4, beta-6, alpha-5, beta-7, beta-8. The first six beta-strands (1-6) form a slightly twisted antiparallel beta-sheet and face five alpha-helices on one side. The last two beta-strands form an antiparallel beta-sheet in the C-terminus. PH1010 forms a characteriztic homodimer structure in the crystal. dimerization of the molecule is crucial for function. The structure resembles that of some ribosomal proteins such as the 50S ribosomal protein L5. Although the structure resembles that of the RRM-type RNA-binding domain of the ribosomal L5 protein, the residues involved in RNA-binding in the L5 protein are not conserved in this family. Despite this, these proteins bind to double-stranded RNA in a non-sequence specific manner.


Pssm-ID: 426487  Cd Length: 113  Bit Score: 43.69  E-value: 2.25e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499206294    9 VRVTAPVYPTEPDDRVADAILRLFPD----------------ATVTVEDDRAVAEtdttaSFREQLFDQRILDTAREQFQ 72
Cdd:pfam01877   2 IEVRAFVHATEDEEKVLEALSNFLPEeeeeeghygnpitileARLEKKDAKKFLK-----KLHELLREEDIKYLLDELDE 76

                          90       100
                  ....*....|....*....|....*
gi 499206294   73 ASQTDAGFSFDLKKQAAFNGTVNFA 97
Cdd:pfam01877  77 RVDENGKLYLRLDKQAAYLGKLSLS 101
 
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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