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Conserved domains on  [gi|1898807821|ref|NP_001269262|]
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tRNA-splicing endonuclease subunit Sen34 isoform 2 [Homo sapiens]

Protein Classification

tRNA-intron endonuclease family protein( domain architecture ID 17391175)

tRNA-intron endonuclease family protein similar to Homo sapiens tRNA-splicing endonuclease subunit Sen34, which constitutes one of the two catalytic subunit of the tRNA-splicing endonuclease complex, a complex responsible for identification and cleavage of the splice sites in pre-tRNA. It cleaves pre-tRNA at the 5'- and 3'-splice sites to release the intron

CATH:  3.40.1170.20
EC:  4.6.1.16
Gene Ontology:  GO:0000214|GO:0000379|GO:0006397|GO:0003676|GO:0016829|GO:0000213
PubMed:  22638584

Graphical summary

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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 ...
 218-297 1.09e-33

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: 118.74  E-value: 1.09e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1898807821 218 ELRYSIYRDLWERGFFLSAAGKFGGDFLVYPGDPLRFHAHYIAQCWAPEDTIPLQDLVAAGRLGTSVRKTLLLCSPQPDG 297
Cdd:cd22363     3 LLKYLVYKDLRSRGYVVKSGFKFGADFLVYPRGPGLYHAKYLVHVVPEDEELSWLELVRAGRLAHSVKKTLVLAVVDEEG 82
tolA super family cl35847
cell envelope integrity inner membrane protein TolA; Provisional
 87-169 9.05e-03

cell envelope integrity inner membrane protein TolA; Provisional


The actual alignment was detected with superfamily member PRK09510:

Pssm-ID: 236545 [Multi-domain]  Cd Length: 387  Bit Score: 37.48  E-value: 9.05e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1898807821  87 KRQQEESFQEQSALAAEARETRRQELLEkitegQAAKKQKLEQASGASSSQEAGSSQAAKEDETSDGQASGEQEEAGPSS 166
Cdd:PRK09510   86 QQQAEELQQKQAAEQERLKQLEKERLAA-----QEQKKQAEEAAKQAALKQKQAEEAAAKAAAAAKAKAEAEAKRAAAAA 160


                  ...
gi 1898807821 167 SQA 169
Cdd:PRK09510  161 KKA 163
 
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 ...
 218-297 1.09e-33

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: 118.74  E-value: 1.09e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1898807821 218 ELRYSIYRDLWERGFFLSAAGKFGGDFLVYPGDPLRFHAHYIAQCWAPEDTIPLQDLVAAGRLGTSVRKTLLLCSPQPDG 297
Cdd:cd22363     3 LLKYLVYKDLRSRGYVVKSGFKFGADFLVYPRGPGLYHAKYLVHVVPEDEELSWLELVRAGRLAHSVKKTLVLAVVDEEG 82
tRNA_int_endo pfam01974
tRNA intron endonuclease, catalytic C-terminal domain; Members of this family cleave pre tRNA ...
 217-297 3.55e-28

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: 104.26  E-value: 3.55e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1898807821 217 HELRYSIYRDLWERGFFLSAAGKFGGDFLVYPGDPLRFHAHYIAQCWAPEDTIPLQDLVAAGRLGTSVRKTLLLCSPQPD 296
Cdd:pfam01974   1 FWLKYLVYRDLRERGYVVKPGIKFGADFRVYGGGPGKGHSEYLVRVLSEDDPISLLDLLRAVRLAHSVRKELVLAIVDDE 80


                  .
gi 1898807821 297 G 297
Cdd:pfam01974  81 G 81
endA TIGR00324
tRNA-intron lyase; The enzyme catalyses the endonucleolytic cleavage of pre tRNA at the 5' and ...
 219-291 4.82e-17

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: 77.13  E-value: 4.82e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1898807821 219 LRYSIYRDLWERGFFLSAAGKFGGDFLVYPGDPLRFHAH--YIAQCWAPEDTIPLQDLVAAGRLGTSVRKTLLLC 291
Cdd:TIGR00324  80 RKYLVYKDLRDRGYVVKTGFKFGADFRLYERGPLRDHSHseYLVAIDDHDESIDLIDLSSGVRVAHGVKKKLVIA 154
SEN2 COG1676
tRNA splicing endonuclease subunit SEN34 [Translation, ribosomal structure and biogenesis]; ...
 218-297 3.39e-14

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: 69.47  E-value: 3.39e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1898807821 218 ELRYSIYRDLWERGFFLSAAGKFGGDFLVYPGDPLRF-HAHYIAQCWAPEDTIPLQDLVAAGRLGTSVRKTLLLCSPQPD 296
Cdd:COG1676    81 DRKYLVYRDLRDRGYVVKTGFKFGSDFRVYERGPGIEdHSPYLVHVVPEGTEFSPRELSRAVRLAHSVRKRMVFAVVDDE 160


                  .
gi 1898807821 297 G 297
Cdd:COG1676   161 G 161
PRK09300 PRK09300
tRNA splicing endonuclease; Reviewed
 218-289 1.69e-07

tRNA splicing endonuclease; Reviewed


Pssm-ID: 236460 [Multi-domain]  Cd Length: 330  Bit Score: 51.90  E-value: 1.69e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1898807821 218 ELRYSIYRDLWERGFFLSAAGKFGGDFLVYPG----DPLRfHAHYIAQCWAPEDTIPLQDLVAAGRLGTSVRKTLL 289
Cdd:PRK09300  237 DRKLAVYRDLRERGFVPKTGFKFGSDFRVYEGvesvEKLP-HSEYLVRVIPDDHEFSPRDLSRAVRLAHSVRKKMV 311
tolA PRK09510
cell envelope integrity inner membrane protein TolA; Provisional
 87-169 9.05e-03

cell envelope integrity inner membrane protein TolA; Provisional


Pssm-ID: 236545 [Multi-domain]  Cd Length: 387  Bit Score: 37.48  E-value: 9.05e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1898807821  87 KRQQEESFQEQSALAAEARETRRQELLEkitegQAAKKQKLEQASGASSSQEAGSSQAAKEDETSDGQASGEQEEAGPSS 166
Cdd:PRK09510   86 QQQAEELQQKQAAEQERLKQLEKERLAA-----QEQKKQAEEAAKQAALKQKQAEEAAAKAAAAAKAKAEAEAKRAAAAA 160


                  ...
gi 1898807821 167 SQA 169
Cdd:PRK09510  161 KKA 163
 
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 ...
 218-297 1.09e-33

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: 118.74  E-value: 1.09e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1898807821 218 ELRYSIYRDLWERGFFLSAAGKFGGDFLVYPGDPLRFHAHYIAQCWAPEDTIPLQDLVAAGRLGTSVRKTLLLCSPQPDG 297
Cdd:cd22363     3 LLKYLVYKDLRSRGYVVKSGFKFGADFLVYPRGPGLYHAKYLVHVVPEDEELSWLELVRAGRLAHSVKKTLVLAVVDEEG 82
tRNA_int_endo pfam01974
tRNA intron endonuclease, catalytic C-terminal domain; Members of this family cleave pre tRNA ...
 217-297 3.55e-28

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: 104.26  E-value: 3.55e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1898807821 217 HELRYSIYRDLWERGFFLSAAGKFGGDFLVYPGDPLRFHAHYIAQCWAPEDTIPLQDLVAAGRLGTSVRKTLLLCSPQPD 296
Cdd:pfam01974   1 FWLKYLVYRDLRERGYVVKPGIKFGADFRVYGGGPGKGHSEYLVRVLSEDDPISLLDLLRAVRLAHSVRKELVLAIVDDE 80


                  .
gi 1898807821 297 G 297
Cdd:pfam01974  81 G 81
endA TIGR00324
tRNA-intron lyase; The enzyme catalyses the endonucleolytic cleavage of pre tRNA at the 5' and ...
 219-291 4.82e-17

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: 77.13  E-value: 4.82e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1898807821 219 LRYSIYRDLWERGFFLSAAGKFGGDFLVYPGDPLRFHAH--YIAQCWAPEDTIPLQDLVAAGRLGTSVRKTLLLC 291
Cdd:TIGR00324  80 RKYLVYKDLRDRGYVVKTGFKFGADFRLYERGPLRDHSHseYLVAIDDHDESIDLIDLSSGVRVAHGVKKKLVIA 154
SEN2 COG1676
tRNA splicing endonuclease subunit SEN34 [Translation, ribosomal structure and biogenesis]; ...
 218-297 3.39e-14

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: 69.47  E-value: 3.39e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1898807821 218 ELRYSIYRDLWERGFFLSAAGKFGGDFLVYPGDPLRF-HAHYIAQCWAPEDTIPLQDLVAAGRLGTSVRKTLLLCSPQPD 296
Cdd:COG1676    81 DRKYLVYRDLRDRGYVVKTGFKFGSDFRVYERGPGIEdHSPYLVHVVPEGTEFSPRELSRAVRLAHSVRKRMVFAVVDDE 160


                  .
gi 1898807821 297 G 297
Cdd:COG1676   161 G 161
PRK09300 PRK09300
tRNA splicing endonuclease; Reviewed
 218-289 1.69e-07

tRNA splicing endonuclease; Reviewed


Pssm-ID: 236460 [Multi-domain]  Cd Length: 330  Bit Score: 51.90  E-value: 1.69e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1898807821 218 ELRYSIYRDLWERGFFLSAAGKFGGDFLVYPG----DPLRfHAHYIAQCWAPEDTIPLQDLVAAGRLGTSVRKTLL 289
Cdd:PRK09300  237 DRKLAVYRDLRERGFVPKTGFKFGSDFRVYEGvesvEKLP-HSEYLVRVIPDDHEFSPRDLSRAVRLAHSVRKKMV 311
PRK09300 PRK09300
tRNA splicing endonuclease; Reviewed
 212-275 1.03e-04

tRNA splicing endonuclease; Reviewed


Pssm-ID: 236460 [Multi-domain]  Cd Length: 330  Bit Score: 43.42  E-value: 1.03e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1898807821 212 AGRPAHELRYSIYRDLWERGFFLSAAgkfGGDFLVYP--GDPLRFHAHYIAQCWAPEDTIPLQDLV 275
Cdd:PRK09300   66 SLRPNFELRYLVYKDLRERGYYVQPG---DADFRVYPrgSGPGDGESKYRVRVVSERDPLPFSDLI 128
tolA PRK09510
cell envelope integrity inner membrane protein TolA; Provisional
 87-169 9.05e-03

cell envelope integrity inner membrane protein TolA; Provisional


Pssm-ID: 236545 [Multi-domain]  Cd Length: 387  Bit Score: 37.48  E-value: 9.05e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1898807821  87 KRQQEESFQEQSALAAEARETRRQELLEkitegQAAKKQKLEQASGASSSQEAGSSQAAKEDETSDGQASGEQEEAGPSS 166
Cdd:PRK09510   86 QQQAEELQQKQAAEQERLKQLEKERLAA-----QEQKKQAEEAAKQAALKQKQAEEAAAKAAAAAKAKAEAEAKRAAAAA 160


                  ...
gi 1898807821 167 SQA 169
Cdd:PRK09510  161 KKA 163
 
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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