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Conserved domains on  [gi|1907082904|ref|XP_036012833|]
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tRNA-dihydrouridine(16/17) synthase [NAD(P)(+)]-like isoform X5 [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
TIM super family cl21457
TIM-like beta/alpha barrel domains; A large family of domains similar to triose phosphate ...
 3-66 5.59e-22

TIM-like beta/alpha barrel domains; A large family of domains similar to triose phosphate isomerase (TIM) which, in general, share an eight beta/alpha closed barrel structure.


The actual alignment was detected with superfamily member cd02801:

Pssm-ID: 473867 [Multi-domain]  Cd Length: 231  Bit Score: 91.79  E-value: 5.59e-22
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907082904   3 GTASWEHIKAVRKAVGIPVFANGNIQCLQDVERCIQDTGVQGVMSAEGNLHNPALFEGRSPAVW 66
Cdd:cd02801   168 GPADWDYIAEIKEAVSIPVIANGDIFSLEDALRCLEQTGVDGVMIGRGALGNPWLFREIKELLE 231
DUF702 super family cl38179
Domain of unknown function (DUF702); Members of this family are found in various putative zinc ...
 213-247 3.05e-04

Domain of unknown function (DUF702); Members of this family are found in various putative zinc finger proteins.


The actual alignment was detected with superfamily member pfam05142:

Pssm-ID: 461560 [Multi-domain]  Cd Length: 154  Bit Score: 40.43  E-value: 3.05e-04
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1907082904 213 CDQCGNPKGNRCVFNLCRGCCKKRAFretaDCPGH 247
Cdd:pfam05142   5 CQDCGNQAKKDCPHMRCRTCCKSRGF----DCPTH 35
 
Name Accession Description Interval E-value
DUS_like_FMN cd02801
Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze ...
 3-66 5.59e-22

Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also in some archaea. Most dihydrouridines are found in the D loop of t-RNAs. The role of dihydrouridine in tRNA is currently unknown, but may increase conformational flexibility of the tRNA. It is likely that different family members have different substrate specificities, which may overlap. 1VHN, a putative flavin oxidoreductase, has high sequence similarity to DUS. The enzymatic mechanism of 1VHN is not known at the present.


Pssm-ID: 239200 [Multi-domain]  Cd Length: 231  Bit Score: 91.79  E-value: 5.59e-22
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907082904   3 GTASWEHIKAVRKAVGIPVFANGNIQCLQDVERCIQDTGVQGVMSAEGNLHNPALFEGRSPAVW 66
Cdd:cd02801   168 GPADWDYIAEIKEAVSIPVIANGDIFSLEDALRCLEQTGVDGVMIGRGALGNPWLFREIKELLE 231
Dus pfam01207
Dihydrouridine synthase (Dus); Members of this family catalyze the reduction of the 5,6-double ...
 3-125 2.52e-21

Dihydrouridine synthase (Dus); Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also in some archae. Most dihydrouridines are found in the D loop of t-RNAs. The role of dihydrouridine in tRNA is currently unknown, but may increase conformational flexibility of the tRNA. It is likely that different family members have different substrate specificities, which may overlap. Dus 1 from Saccharomyces cerevisiae acts on pre-tRNA-Phe, while Dus 2 acts on pre-tRNA-Tyr and pre-tRNA-Leu. Dus 1 is active as a single subunit, requiring NADPH or NADH, and is stimulated by the presence of FAD. Some family members may be targeted to the mitochondria and even have a role in mitochondria.


Pssm-ID: 426126  Cd Length: 309  Bit Score: 91.62  E-value: 2.52e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907082904   3 GTASWEHIKAVRKAVGIPVFANGNIQCLQDVERCIQDTGVQGVMSAEGNLHNPALFEGRSPAVWELAE------EYLDIV 76
Cdd:pfam01207 168 GTADWDAIKQVKQAVSIPVIANGDITDPEDAQRCLAYTGADGVMIGRGALGNPWLFAEQHTVKTGEFGpspplaEEAEKV 247

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907082904  77 RQH-PC---------PLSYVRAHLFklWH-HTLQVHQQLREELAKVKTLEGVAAVSQALK 125
Cdd:pfam01207 248 LRHlPYleeflgedkGLRHARKHLA--WYlKGFPGAAELRRELNDVFDPVEALINLDAAL 305
DusA COG0042
tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; ...
 3-120 5.48e-18

tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; tRNA-dihydrouridine synthase is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 439812 [Multi-domain]  Cd Length: 310  Bit Score: 82.06  E-value: 5.48e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907082904   3 GTASWEHIKAVRKAVGIPVFANGNIQCLQDVERCIQDTGVQGVMSAEGNLHNPALF-------EGRSPA------VWELA 69
Cdd:COG0042   176 GPADWDAIARVKEAVSIPVIGNGDIFSPEDAKRMLEETGCDGVMIGRGALGNPWLFreidaylAGGEAPppsleeVLELL 255

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1907082904  70 EEYLDIVRQH---PCPLSYVRAHLFKLWHHtLQVHQQLREELAKVKTLEGVAAV 120
Cdd:COG0042   256 LEHLELLLEFygeRRGLRRMRKHLLWYFKG-LPGARELRRRLSKAKSLAELLEL 308
PRK10550 PRK10550
tRNA dihydrouridine(16) synthase DusC;
7-57 2.37e-05

tRNA dihydrouridine(16) synthase DusC;


Pssm-ID: 236713  Cd Length: 312  Bit Score: 45.19  E-value: 2.37e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1907082904   7 WEHIKAVRKAVGIPVFANGNIQCLQDVERCIQDTGVQGVMSAEGNLHNPAL 57
Cdd:PRK10550  183 WQAIGEIRQRLTIPVIANGEIWDWQSAQQCMAITGCDAVMIGRGALNIPNL 233
DUF702 pfam05142
Domain of unknown function (DUF702); Members of this family are found in various putative zinc ...
 213-247 3.05e-04

Domain of unknown function (DUF702); Members of this family are found in various putative zinc finger proteins.


Pssm-ID: 461560 [Multi-domain]  Cd Length: 154  Bit Score: 40.43  E-value: 3.05e-04
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1907082904 213 CDQCGNPKGNRCVFNLCRGCCKKRAFretaDCPGH 247
Cdd:pfam05142   5 CQDCGNQAKKDCPHMRCRTCCKSRGF----DCPTH 35
put_zinc_LRP1 TIGR01623
putative zinc finger domain, LRP1 type; This model represents a putative zinc finger domain ...
 212-247 3.95e-04

putative zinc finger domain, LRP1 type; This model represents a putative zinc finger domain found in plants. Arabidopsis thaliana has at least 10 distinct members. Proteins containing this domain, including LRP1, generally share the same size, about 300 amino acids, and architecture. This 43-residue domain, and a more C-terminal companion domain of similar size, appear as tightly conserved islands of sequence similarity. The remainder consists largely of low-complexity sequence. Several animal proteins have regions with matching patterns of Cys, Gly, and His residues. These are not included in the model but score between trusted and noise cutoffs.


Pssm-ID: 130684  Cd Length: 43  Bit Score: 37.57  E-value: 3.95e-04
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1907082904 212 KCDQCGNPKGNRCVFNLCRGCCKKRAFretaDCPGH 247
Cdd:TIGR01623   1 VCQDCGNQAKKECLFERCRTCCKSRGF----HCVTH 32
 
Name Accession Description Interval E-value
DUS_like_FMN cd02801
Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze ...
 3-66 5.59e-22

Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also in some archaea. Most dihydrouridines are found in the D loop of t-RNAs. The role of dihydrouridine in tRNA is currently unknown, but may increase conformational flexibility of the tRNA. It is likely that different family members have different substrate specificities, which may overlap. 1VHN, a putative flavin oxidoreductase, has high sequence similarity to DUS. The enzymatic mechanism of 1VHN is not known at the present.


Pssm-ID: 239200 [Multi-domain]  Cd Length: 231  Bit Score: 91.79  E-value: 5.59e-22
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907082904   3 GTASWEHIKAVRKAVGIPVFANGNIQCLQDVERCIQDTGVQGVMSAEGNLHNPALFEGRSPAVW 66
Cdd:cd02801   168 GPADWDYIAEIKEAVSIPVIANGDIFSLEDALRCLEQTGVDGVMIGRGALGNPWLFREIKELLE 231
Dus pfam01207
Dihydrouridine synthase (Dus); Members of this family catalyze the reduction of the 5,6-double ...
 3-125 2.52e-21

Dihydrouridine synthase (Dus); Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also in some archae. Most dihydrouridines are found in the D loop of t-RNAs. The role of dihydrouridine in tRNA is currently unknown, but may increase conformational flexibility of the tRNA. It is likely that different family members have different substrate specificities, which may overlap. Dus 1 from Saccharomyces cerevisiae acts on pre-tRNA-Phe, while Dus 2 acts on pre-tRNA-Tyr and pre-tRNA-Leu. Dus 1 is active as a single subunit, requiring NADPH or NADH, and is stimulated by the presence of FAD. Some family members may be targeted to the mitochondria and even have a role in mitochondria.


Pssm-ID: 426126  Cd Length: 309  Bit Score: 91.62  E-value: 2.52e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907082904   3 GTASWEHIKAVRKAVGIPVFANGNIQCLQDVERCIQDTGVQGVMSAEGNLHNPALFEGRSPAVWELAE------EYLDIV 76
Cdd:pfam01207 168 GTADWDAIKQVKQAVSIPVIANGDITDPEDAQRCLAYTGADGVMIGRGALGNPWLFAEQHTVKTGEFGpspplaEEAEKV 247

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907082904  77 RQH-PC---------PLSYVRAHLFklWH-HTLQVHQQLREELAKVKTLEGVAAVSQALK 125
Cdd:pfam01207 248 LRHlPYleeflgedkGLRHARKHLA--WYlKGFPGAAELRRELNDVFDPVEALINLDAAL 305
DusA COG0042
tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; ...
 3-120 5.48e-18

tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; tRNA-dihydrouridine synthase is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 439812 [Multi-domain]  Cd Length: 310  Bit Score: 82.06  E-value: 5.48e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907082904   3 GTASWEHIKAVRKAVGIPVFANGNIQCLQDVERCIQDTGVQGVMSAEGNLHNPALF-------EGRSPA------VWELA 69
Cdd:COG0042   176 GPADWDAIARVKEAVSIPVIGNGDIFSPEDAKRMLEETGCDGVMIGRGALGNPWLFreidaylAGGEAPppsleeVLELL 255

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1907082904  70 EEYLDIVRQH---PCPLSYVRAHLFKLWHHtLQVHQQLREELAKVKTLEGVAAV 120
Cdd:COG0042   256 LEHLELLLEFygeRRGLRRMRKHLLWYFKG-LPGARELRRRLSKAKSLAELLEL 308
PRK10550 PRK10550
tRNA dihydrouridine(16) synthase DusC;
7-57 2.37e-05

tRNA dihydrouridine(16) synthase DusC;


Pssm-ID: 236713  Cd Length: 312  Bit Score: 45.19  E-value: 2.37e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1907082904   7 WEHIKAVRKAVGIPVFANGNIQCLQDVERCIQDTGVQGVMSAEGNLHNPAL 57
Cdd:PRK10550  183 WQAIGEIRQRLTIPVIANGEIWDWQSAQQCMAITGCDAVMIGRGALNIPNL 233
OYE_like_FMN_family cd02803
Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme ...
 7-57 5.13e-05

Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme identified, however its true physiological role remains elusive to this day. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as electron acceptors in the catalytic reaction. Members of OYE family include trimethylamine dehydrogenase, 2,4-dienoyl-CoA reductase, enoate reductase, pentaerythriol tetranitrate reductase, xenobiotic reductase, and morphinone reductase.


Pssm-ID: 239201 [Multi-domain]  Cd Length: 327  Bit Score: 44.10  E-value: 5.13e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1907082904   7 WEHIKAVRKAVGIPVFANGNIQCLQDVERCIQDTGVQGVMSAEGNLHNPAL 57
Cdd:cd02803   270 LELAEKIKKAVKIPVIAVGGIRDPEVAEEILAEGKADLVALGRALLADPDL 320
DUF702 pfam05142
Domain of unknown function (DUF702); Members of this family are found in various putative zinc ...
 213-247 3.05e-04

Domain of unknown function (DUF702); Members of this family are found in various putative zinc finger proteins.


Pssm-ID: 461560 [Multi-domain]  Cd Length: 154  Bit Score: 40.43  E-value: 3.05e-04
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1907082904 213 CDQCGNPKGNRCVFNLCRGCCKKRAFretaDCPGH 247
Cdd:pfam05142   5 CQDCGNQAKKDCPHMRCRTCCKSRGF----DCPTH 35
put_zinc_LRP1 TIGR01623
putative zinc finger domain, LRP1 type; This model represents a putative zinc finger domain ...
 212-247 3.95e-04

putative zinc finger domain, LRP1 type; This model represents a putative zinc finger domain found in plants. Arabidopsis thaliana has at least 10 distinct members. Proteins containing this domain, including LRP1, generally share the same size, about 300 amino acids, and architecture. This 43-residue domain, and a more C-terminal companion domain of similar size, appear as tightly conserved islands of sequence similarity. The remainder consists largely of low-complexity sequence. Several animal proteins have regions with matching patterns of Cys, Gly, and His residues. These are not included in the model but score between trusted and noise cutoffs.


Pssm-ID: 130684  Cd Length: 43  Bit Score: 37.57  E-value: 3.95e-04
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1907082904 212 KCDQCGNPKGNRCVFNLCRGCCKKRAFretaDCPGH 247
Cdd:TIGR01623   1 VCQDCGNQAKKECLFERCRTCCKSRGF----HCVTH 32
TMP-TENI pfam02581
Thiamine monophosphate synthase; Thiamine monophosphate synthase (TMP) (EC:2.5.1.3) catalyzes ...
 1-48 9.64e-03

Thiamine monophosphate synthase; Thiamine monophosphate synthase (TMP) (EC:2.5.1.3) catalyzes the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5- (beta-hydroxyethyl)thiazole phosphate to yield thiamine phosphate. This Pfam family also includes the regulatory protein TENI, a protein from Bacillus subtilis that regulates the production of several extracellular enzymes by reducing alkaline protease production. While TenI shows high sequence similarity with thiamin phosphate synthase, the purified protein has no thiamin phosphate synthase activity. Instead, it is a thiazole tautomerase.


Pssm-ID: 426849 [Multi-domain]  Cd Length: 180  Bit Score: 36.37  E-value: 9.64e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1907082904   1 MAGTASWEHIKAVRKAVGIPVFANGNIQcLQDVERCIqDTGVQG--VMSA 48
Cdd:pfam02581 132 DAPPLGLEGLKAIAEAVEIPVVAIGGIT-PENVPEVI-EAGADGvaVVSA 179
 
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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