NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1007892866|ref|NP_001308208|]
View 

tRNA-splicing endonuclease subunit Sen2 isoform 2 [Homo sapiens]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
tRNA-intron_lyase_C cd22363
catalytic C-terminal domain of the tRNA-intron lyase; This C-terminal catalytic domain of tRNA ...
 313-404 1.54e-28

catalytic C-terminal domain of the tRNA-intron lyase; This C-terminal catalytic domain of tRNA intron endonucleases cleaves pre tRNA at the 5' and 3' splice sites to release the intron (EC:3.1.27.9). It belongs to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI.


:

Pssm-ID: 411767  Cd Length: 91  Bit Score: 107.57  E-value: 1.54e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007892866 313 FRTTYMAYHYFRSKGWVPKVGLKYGTDLLLYRKGPPFYHASYSVIIELVDDhfegslrrPLSWKSLAALSRVSVNVSKEL 392
Cdd:cd22363     2 FLLKYLVYKDLRSRGYVVKSGFKFGADFLVYPRGPGLYHAKYLVHVVPEDE--------ELSWLELVRAGRLAHSVKKTL 73

                          90
                  ....*....|..
gi 1007892866 393 MLCYLIKPSTMT 404
Cdd:cd22363    74 VLAVVDEEGEVT 85
PRK09300 super family cl35808
tRNA splicing endonuclease; Reviewed
 277-345 5.12e-03

tRNA splicing endonuclease; Reviewed


The actual alignment was detected with superfamily member PRK09300:

Pssm-ID: 236460 [Multi-domain]  Cd Length: 330  Bit Score: 38.80  E-value: 5.12e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1007892866 277 EAFFLVyALGCLSIyyekEPLTIVKLWKAFTVVQPTFRTTYMAYHYFRSKGWVPKVGLKYGTDLLLYRK 345
Cdd:PRK09300  205 EAAYLL-ERGVLSV----EILDADEFVERAREVEGEFDRKLAVYRDLRERGFVPKTGFKFGSDFRVYEG 268
tRNA_int_endo_N super family cl46877
tRNA intron endonuclease, N-terminal domain; Members of this family cleave pre tRNA at the 5' ...
 41-68 9.12e-03

tRNA intron endonuclease, N-terminal domain; Members of this family cleave pre tRNA at the 5' and 3' splice sites to release the intron EC:3.1.27.9.


The actual alignment was detected with superfamily member pfam02778:

Pssm-ID: 397071  Cd Length: 67  Bit Score: 34.88  E-value: 9.12e-03
                          10        20
                  ....*....|....*....|....*...
gi 1007892866  41 RAEMINNNVIVRNAEDIEQLYGKGYFGK 68
Cdd:pfam02778   2 EGELSGDRVIVWDEEAARRLYERGYYGK 29
 
Name Accession Description Interval E-value
tRNA-intron_lyase_C cd22363
catalytic C-terminal domain of the tRNA-intron lyase; This C-terminal catalytic domain of tRNA ...
 313-404 1.54e-28

catalytic C-terminal domain of the tRNA-intron lyase; This C-terminal catalytic domain of tRNA intron endonucleases cleaves pre tRNA at the 5' and 3' splice sites to release the intron (EC:3.1.27.9). It belongs to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI.


Pssm-ID: 411767  Cd Length: 91  Bit Score: 107.57  E-value: 1.54e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007892866 313 FRTTYMAYHYFRSKGWVPKVGLKYGTDLLLYRKGPPFYHASYSVIIELVDDhfegslrrPLSWKSLAALSRVSVNVSKEL 392
Cdd:cd22363     2 FLLKYLVYKDLRSRGYVVKSGFKFGADFLVYPRGPGLYHAKYLVHVVPEDE--------ELSWLELVRAGRLAHSVKKTL 73

                          90
                  ....*....|..
gi 1007892866 393 MLCYLIKPSTMT 404
Cdd:cd22363    74 VLAVVDEEGEVT 85
tRNA_int_endo pfam01974
tRNA intron endonuclease, catalytic C-terminal domain; Members of this family cleave pre tRNA ...
 313-396 7.78e-17

tRNA intron endonuclease, catalytic C-terminal domain; Members of this family cleave pre tRNA at the 5' and 3' splice sites to release the intron EC:3.1.27.9.


Pssm-ID: 396521  Cd Length: 85  Bit Score: 74.99  E-value: 7.78e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007892866 313 FRTTYMAYHYFRSKGWVPKVGLKYGTDLLLYRKGPPFYHASYSVIIelVDDhfegslRRPLSWKSLAALSRVSVNVSKEL 392
Cdd:pfam01974   1 FWLKYLVYRDLRERGYVVKPGIKFGADFRVYGGGPGKGHSEYLVRV--LSE------DDPISLLDLLRAVRLAHSVRKEL 72


                  ....
gi 1007892866 393 MLCY 396
Cdd:pfam01974  73 VLAI 76
endA TIGR00324
tRNA-intron lyase; The enzyme catalyses the endonucleolytic cleavage of pre tRNA at the 5' and ...
 290-397 5.21e-13

tRNA-intron lyase; The enzyme catalyses the endonucleolytic cleavage of pre tRNA at the 5' and 3' splice sites to release the intron and produces two half tRNA molecules bearing 5' hydroxyl and 2', 3'-cyclic phosphate termini. The genes are homologous in Eucarya and Archea. The two yeast genes have been functionally studied and are two subunits of a heterotetramer enzyme in yeast the other two subunits of which have no known homologs. [Transcription, RNA processing]


Pssm-ID: 129424  Cd Length: 170  Bit Score: 66.73  E-value: 5.21e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007892866 290 IYYEKEPLTIVKLWKAFTVVQPTFRTTYMAYHYFRSKGWVPKVGLKYGTDLLLYRKGP--PFYHASYSVIIelvDDHfeg 367
Cdd:TIGR00324  55 IRSDSEPLSREELSDLARKVERGFMRKYLVYKDLRDRGYVVKTGFKFGADFRLYERGPlrDHSHSEYLVAI---DDH--- 128

                          90       100       110
                  ....*....|....*....|....*....|
gi 1007892866 368 slRRPLSWKSLAALSRVSVNVSKELMLCYL 397
Cdd:TIGR00324 129 --DESIDLIDLSSGVRVAHGVKKKLVIAYV 156
SEN2 COG1676
tRNA splicing endonuclease subunit SEN34 [Translation, ribosomal structure and biogenesis]; ...
 277-395 1.54e-12

tRNA splicing endonuclease subunit SEN34 [Translation, ribosomal structure and biogenesis]; tRNA splicing endonuclease subunit SEN34 is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 441282  Cd Length: 173  Bit Score: 65.61  E-value: 1.54e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007892866 277 EAFFLVYAlGCLSIYYEKEPLTIVKLWKAFTVVQPTFRTTYMAYHYFRSKGWVPKVGLKYGTDLLLYRKGP-PFYHASYS 355
Cdd:COG1676    45 EALYLLEK-GKLEVYDDGKELSFEELLEIARKVDPEFDRKYLVYRDLRDRGYVVKTGFKFGSDFRVYERGPgIEDHSPYL 123

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1007892866 356 VIIeLVDDHfegslrrPLSWKSLAALSRVSVNVSKELMLC 395
Cdd:COG1676   124 VHV-VPEGT-------EFSPRELSRAVRLAHSVRKRMVFA 155
PRK09300 PRK09300
tRNA splicing endonuclease; Reviewed
 277-345 5.12e-03

tRNA splicing endonuclease; Reviewed


Pssm-ID: 236460 [Multi-domain]  Cd Length: 330  Bit Score: 38.80  E-value: 5.12e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1007892866 277 EAFFLVyALGCLSIyyekEPLTIVKLWKAFTVVQPTFRTTYMAYHYFRSKGWVPKVGLKYGTDLLLYRK 345
Cdd:PRK09300  205 EAAYLL-ERGVLSV----EILDADEFVERAREVEGEFDRKLAVYRDLRERGFVPKTGFKFGSDFRVYEG 268
tRNA_int_endo_N pfam02778
tRNA intron endonuclease, N-terminal domain; Members of this family cleave pre tRNA at the 5' ...
 41-68 9.12e-03

tRNA intron endonuclease, N-terminal domain; Members of this family cleave pre tRNA at the 5' and 3' splice sites to release the intron EC:3.1.27.9.


Pssm-ID: 397071  Cd Length: 67  Bit Score: 34.88  E-value: 9.12e-03
                          10        20
                  ....*....|....*....|....*...
gi 1007892866  41 RAEMINNNVIVRNAEDIEQLYGKGYFGK 68
Cdd:pfam02778   2 EGELSGDRVIVWDEEAARRLYERGYYGK 29
 
Name Accession Description Interval E-value
tRNA-intron_lyase_C cd22363
catalytic C-terminal domain of the tRNA-intron lyase; This C-terminal catalytic domain of tRNA ...
 313-404 1.54e-28

catalytic C-terminal domain of the tRNA-intron lyase; This C-terminal catalytic domain of tRNA intron endonucleases cleaves pre tRNA at the 5' and 3' splice sites to release the intron (EC:3.1.27.9). It belongs to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI.


Pssm-ID: 411767  Cd Length: 91  Bit Score: 107.57  E-value: 1.54e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007892866 313 FRTTYMAYHYFRSKGWVPKVGLKYGTDLLLYRKGPPFYHASYSVIIELVDDhfegslrrPLSWKSLAALSRVSVNVSKEL 392
Cdd:cd22363     2 FLLKYLVYKDLRSRGYVVKSGFKFGADFLVYPRGPGLYHAKYLVHVVPEDE--------ELSWLELVRAGRLAHSVKKTL 73

                          90
                  ....*....|..
gi 1007892866 393 MLCYLIKPSTMT 404
Cdd:cd22363    74 VLAVVDEEGEVT 85
tRNA_int_endo pfam01974
tRNA intron endonuclease, catalytic C-terminal domain; Members of this family cleave pre tRNA ...
 313-396 7.78e-17

tRNA intron endonuclease, catalytic C-terminal domain; Members of this family cleave pre tRNA at the 5' and 3' splice sites to release the intron EC:3.1.27.9.


Pssm-ID: 396521  Cd Length: 85  Bit Score: 74.99  E-value: 7.78e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007892866 313 FRTTYMAYHYFRSKGWVPKVGLKYGTDLLLYRKGPPFYHASYSVIIelVDDhfegslRRPLSWKSLAALSRVSVNVSKEL 392
Cdd:pfam01974   1 FWLKYLVYRDLRERGYVVKPGIKFGADFRVYGGGPGKGHSEYLVRV--LSE------DDPISLLDLLRAVRLAHSVRKEL 72


                  ....
gi 1007892866 393 MLCY 396
Cdd:pfam01974  73 VLAI 76
endA TIGR00324
tRNA-intron lyase; The enzyme catalyses the endonucleolytic cleavage of pre tRNA at the 5' and ...
 290-397 5.21e-13

tRNA-intron lyase; The enzyme catalyses the endonucleolytic cleavage of pre tRNA at the 5' and 3' splice sites to release the intron and produces two half tRNA molecules bearing 5' hydroxyl and 2', 3'-cyclic phosphate termini. The genes are homologous in Eucarya and Archea. The two yeast genes have been functionally studied and are two subunits of a heterotetramer enzyme in yeast the other two subunits of which have no known homologs. [Transcription, RNA processing]


Pssm-ID: 129424  Cd Length: 170  Bit Score: 66.73  E-value: 5.21e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007892866 290 IYYEKEPLTIVKLWKAFTVVQPTFRTTYMAYHYFRSKGWVPKVGLKYGTDLLLYRKGP--PFYHASYSVIIelvDDHfeg 367
Cdd:TIGR00324  55 IRSDSEPLSREELSDLARKVERGFMRKYLVYKDLRDRGYVVKTGFKFGADFRLYERGPlrDHSHSEYLVAI---DDH--- 128

                          90       100       110
                  ....*....|....*....|....*....|
gi 1007892866 368 slRRPLSWKSLAALSRVSVNVSKELMLCYL 397
Cdd:TIGR00324 129 --DESIDLIDLSSGVRVAHGVKKKLVIAYV 156
SEN2 COG1676
tRNA splicing endonuclease subunit SEN34 [Translation, ribosomal structure and biogenesis]; ...
 277-395 1.54e-12

tRNA splicing endonuclease subunit SEN34 [Translation, ribosomal structure and biogenesis]; tRNA splicing endonuclease subunit SEN34 is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 441282  Cd Length: 173  Bit Score: 65.61  E-value: 1.54e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007892866 277 EAFFLVYAlGCLSIYYEKEPLTIVKLWKAFTVVQPTFRTTYMAYHYFRSKGWVPKVGLKYGTDLLLYRKGP-PFYHASYS 355
Cdd:COG1676    45 EALYLLEK-GKLEVYDDGKELSFEELLEIARKVDPEFDRKYLVYRDLRDRGYVVKTGFKFGSDFRVYERGPgIEDHSPYL 123

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1007892866 356 VIIeLVDDHfegslrrPLSWKSLAALSRVSVNVSKELMLC 395
Cdd:COG1676   124 VHV-VPEGT-------EFSPRELSRAVRLAHSVRKRMVFA 155
PRK09300 PRK09300
tRNA splicing endonuclease; Reviewed
 277-345 5.12e-03

tRNA splicing endonuclease; Reviewed


Pssm-ID: 236460 [Multi-domain]  Cd Length: 330  Bit Score: 38.80  E-value: 5.12e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1007892866 277 EAFFLVyALGCLSIyyekEPLTIVKLWKAFTVVQPTFRTTYMAYHYFRSKGWVPKVGLKYGTDLLLYRK 345
Cdd:PRK09300  205 EAAYLL-ERGVLSV----EILDADEFVERAREVEGEFDRKLAVYRDLRERGFVPKTGFKFGSDFRVYEG 268
tRNA_int_endo_N pfam02778
tRNA intron endonuclease, N-terminal domain; Members of this family cleave pre tRNA at the 5' ...
 41-68 9.12e-03

tRNA intron endonuclease, N-terminal domain; Members of this family cleave pre tRNA at the 5' and 3' splice sites to release the intron EC:3.1.27.9.


Pssm-ID: 397071  Cd Length: 67  Bit Score: 34.88  E-value: 9.12e-03
                          10        20
                  ....*....|....*....|....*...
gi 1007892866  41 RAEMINNNVIVRNAEDIEQLYGKGYFGK 68
Cdd:pfam02778   2 EGELSGDRVIVWDEEAARRLYERGYYGK 29
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH