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Conserved domains on  [gi|2078124463|gb|KAG8573814|]
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hypothetical protein GDO81_012564 [Engystomops pustulosus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DUS_like_FMN cd02801
Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze ...
 313-411 9.84e-37

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: 134.16  E-value: 9.84e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2078124463 313 KLYLAPLTTCGNLPFRRICKRYGADITCGEMAMCTNLLQGQPSEWALMKRHHTEDLFGVQLEGAFPDTMTKCAELLNtSI 392
Cdd:cd02801     1 KLILAPMVGVTDLPFRLLCRRYGADLVYTEMISAKALLRGNRKRLRLLTRNPEERPLIVQLGGSDPETLAEAAKIVE-EL 79

                          90
                  ....*....|....*....
gi 2078124463 393 EVDFVDINVGCPIDLVYKK 411
Cdd:cd02801    80 GADGIDLNMGCPSPKVTKG 98
Zn_finger_prot super family cl44678
Putative zinc finger protein; This is a family of proteins predominantly found in Iridoviridae, ...
 55-161 7.56e-04

Putative zinc finger protein; This is a family of proteins predominantly found in Iridoviridae, which contains a zinc finger domain.


The actual alignment was detected with superfamily member pfam19242:

Pssm-ID: 437074  Cd Length: 268  Bit Score: 41.21  E-value: 7.56e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2078124463  55 TDSDQCNVGDENFAA--EPQSKKIKLDESVENQEKENKKVEEDKQDKKRARGQNK------SRPHVKYHQLEQ-QRLCPS 125
Cdd:pfam19242 109 TPSNELINGVLNYSLllPPSTPKREIKPTQPNKKRKNARGGATPPNSKPLGNPAKpngvsqQQQGPKRDSTQKpTRLCLS 188

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2078124463 126 IVQEcaSKCFFGDKCKFLHDpekYLSGKHEDIGPKC 161
Cdd:pfam19242 189 VLKQ--TKCFHGAQCRFAHR---YSDLKECNFGENC 219
 
Name Accession Description Interval E-value
DUS_like_FMN cd02801
Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze ...
 313-411 9.84e-37

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: 134.16  E-value: 9.84e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2078124463 313 KLYLAPLTTCGNLPFRRICKRYGADITCGEMAMCTNLLQGQPSEWALMKRHHTEDLFGVQLEGAFPDTMTKCAELLNtSI 392
Cdd:cd02801     1 KLILAPMVGVTDLPFRLLCRRYGADLVYTEMISAKALLRGNRKRLRLLTRNPEERPLIVQLGGSDPETLAEAAKIVE-EL 79

                          90
                  ....*....|....*....
gi 2078124463 393 EVDFVDINVGCPIDLVYKK 411
Cdd:cd02801    80 GADGIDLNMGCPSPKVTKG 98
DusA COG0042
tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; ...
 308-412 1.82e-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: 85.53  E-value: 1.82e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2078124463 308 IDFRGKLYLAPLTTCGNLPFRRICKRYGADITCGEMAMCTNLLQGQPSEWALMKRHHTEDLFGVQLEGAFPDTMTKCAEL 387
Cdd:COG0042     3 LELPNPLILAPMAGVTDRPFRRLCRELGAGLLYTEMVSARALLHGNRKTRRLLDFDPEEHPVAVQLFGSDPEELAEAARI 82

                          90       100
                  ....*....|....*....|....*
gi 2078124463 388 LNtSIEVDFVDINVGCPidlvYKKV 412
Cdd:COG0042    83 AE-ELGADEIDINMGCP----VKKV 102
nifR3_yhdG TIGR00737
putative TIM-barrel protein, nifR3 family; This model represents one branch of COG0042 ...
 306-411 1.85e-15

putative TIM-barrel protein, nifR3 family; This model represents one branch of COG0042 (Predicted TIM-barrel enzymes, possibly dehydrogenases, nifR3 family). This branch includes NifR3 itself, from Rhodobacter capsulatus. It excludes a broadly distributed but more sparsely populated subfamily that contains sll0926 from Synechocystis PCC6803, HI0634 from Haemophilus influenzae, and BB0225 from Borrelia burgdorferi. It also excludes a shorter and more distant archaeal subfamily.The function of nifR3, a member of this family, is unknown, but it is found in an operon with nitrogen-sensing two component regulators in Rhodobacter capsulatus.Members of this family show a distant relationship to alpha/beta (TIM) barrel enzymes such as dihydroorotate dehydrogenase and glycolate oxidase. [Unknown function, General]


Pssm-ID: 129820  Cd Length: 319  Bit Score: 77.02  E-value: 1.85e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2078124463 306 KTIDFRGKLYLAPLTTCGNLPFRRICKRYGADITCGEMAMCTNLLQGQPSEWALMKRHHTEDLFGVQLEGAFPDTMTKCA 385
Cdd:TIGR00737   2 GNIQLKSRVVLAPMAGVTDSPFRRLVAEYGAGLTVCEMVSSEAIVYDSQRTMRLLDIAEDETPISVQLFGSDPDTMAEAA 81

                          90       100
                  ....*....|....*....|....*.
gi 2078124463 386 ELlNTSIEVDFVDINVGCPIDLVYKK 411
Cdd:TIGR00737  82 KI-NEELGADIIDINMGCPVPKITKK 106
Dus pfam01207
Dihydrouridine synthase (Dus); Members of this family catalyze the reduction of the 5,6-double ...
 316-411 2.97e-10

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: 61.19  E-value: 2.97e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2078124463 316 LAPLTTCGNLPFRRICKRYGA-DITCGEMAMCTNLLQGQPSEWALMKRHHTEDLFGVQLEGAFPDTMTKCAELlNTSIEV 394
Cdd:pfam01207   2 LAPMAGVTDLPFRRLVREYGAgDLVYTEMVTAKAQLRPEKVRIRMLSELEEPTPLAVQLGGSDPALLAEAAKL-VEDRGA 80

                          90
                  ....*....|....*..
gi 2078124463 395 DFVDINVGCPIDLVYKK 411
Cdd:pfam01207  81 DGIDINMGCPSKKVTRG 97
PRK10415 PRK10415
tRNA-dihydrouridine synthase B; Provisional
 310-416 6.82e-08

tRNA-dihydrouridine synthase B; Provisional


Pssm-ID: 182440  Cd Length: 321  Bit Score: 53.82  E-value: 6.82e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2078124463 310 FRGKLYLAPLTTCGNLPFRRICKRYGADITCGEMamctnlLQGQPSEWALMKRH----HTED--LFGVQLEGAFPDTMTK 383
Cdd:PRK10415    8 LRNRLIAAPMAGITDRPFRTLCYEMGAGLTVSEM------MSSNPQVWESDKSRlrmvHIDEpgIRTVQIAGSDPKEMAD 81

                          90       100       110
                  ....*....|....*....|....*....|...
gi 2078124463 384 CAElLNTSIEVDFVDINVGCPIDLVYKKVSIEA 416
Cdd:PRK10415   82 AAR-INVESGAQIIDINMGCPAKKVNRKLAGSA 113
Zn_finger_prot pfam19242
Putative zinc finger protein; This is a family of proteins predominantly found in Iridoviridae, ...
 55-161 7.56e-04

Putative zinc finger protein; This is a family of proteins predominantly found in Iridoviridae, which contains a zinc finger domain.


Pssm-ID: 437074  Cd Length: 268  Bit Score: 41.21  E-value: 7.56e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2078124463  55 TDSDQCNVGDENFAA--EPQSKKIKLDESVENQEKENKKVEEDKQDKKRARGQNK------SRPHVKYHQLEQ-QRLCPS 125
Cdd:pfam19242 109 TPSNELINGVLNYSLllPPSTPKREIKPTQPNKKRKNARGGATPPNSKPLGNPAKpngvsqQQQGPKRDSTQKpTRLCLS 188

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2078124463 126 IVQEcaSKCFFGDKCKFLHDpekYLSGKHEDIGPKC 161
Cdd:pfam19242 189 VLKQ--TKCFHGAQCRFAHR---YSDLKECNFGENC 219
 
Name Accession Description Interval E-value
DUS_like_FMN cd02801
Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze ...
 313-411 9.84e-37

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: 134.16  E-value: 9.84e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2078124463 313 KLYLAPLTTCGNLPFRRICKRYGADITCGEMAMCTNLLQGQPSEWALMKRHHTEDLFGVQLEGAFPDTMTKCAELLNtSI 392
Cdd:cd02801     1 KLILAPMVGVTDLPFRLLCRRYGADLVYTEMISAKALLRGNRKRLRLLTRNPEERPLIVQLGGSDPETLAEAAKIVE-EL 79

                          90
                  ....*....|....*....
gi 2078124463 393 EVDFVDINVGCPIDLVYKK 411
Cdd:cd02801    80 GADGIDLNMGCPSPKVTKG 98
DusA COG0042
tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; ...
 308-412 1.82e-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: 85.53  E-value: 1.82e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2078124463 308 IDFRGKLYLAPLTTCGNLPFRRICKRYGADITCGEMAMCTNLLQGQPSEWALMKRHHTEDLFGVQLEGAFPDTMTKCAEL 387
Cdd:COG0042     3 LELPNPLILAPMAGVTDRPFRRLCRELGAGLLYTEMVSARALLHGNRKTRRLLDFDPEEHPVAVQLFGSDPEELAEAARI 82

                          90       100
                  ....*....|....*....|....*
gi 2078124463 388 LNtSIEVDFVDINVGCPidlvYKKV 412
Cdd:COG0042    83 AE-ELGADEIDINMGCP----VKKV 102
nifR3_yhdG TIGR00737
putative TIM-barrel protein, nifR3 family; This model represents one branch of COG0042 ...
 306-411 1.85e-15

putative TIM-barrel protein, nifR3 family; This model represents one branch of COG0042 (Predicted TIM-barrel enzymes, possibly dehydrogenases, nifR3 family). This branch includes NifR3 itself, from Rhodobacter capsulatus. It excludes a broadly distributed but more sparsely populated subfamily that contains sll0926 from Synechocystis PCC6803, HI0634 from Haemophilus influenzae, and BB0225 from Borrelia burgdorferi. It also excludes a shorter and more distant archaeal subfamily.The function of nifR3, a member of this family, is unknown, but it is found in an operon with nitrogen-sensing two component regulators in Rhodobacter capsulatus.Members of this family show a distant relationship to alpha/beta (TIM) barrel enzymes such as dihydroorotate dehydrogenase and glycolate oxidase. [Unknown function, General]


Pssm-ID: 129820  Cd Length: 319  Bit Score: 77.02  E-value: 1.85e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2078124463 306 KTIDFRGKLYLAPLTTCGNLPFRRICKRYGADITCGEMAMCTNLLQGQPSEWALMKRHHTEDLFGVQLEGAFPDTMTKCA 385
Cdd:TIGR00737   2 GNIQLKSRVVLAPMAGVTDSPFRRLVAEYGAGLTVCEMVSSEAIVYDSQRTMRLLDIAEDETPISVQLFGSDPDTMAEAA 81

                          90       100
                  ....*....|....*....|....*.
gi 2078124463 386 ELlNTSIEVDFVDINVGCPIDLVYKK 411
Cdd:TIGR00737  82 KI-NEELGADIIDINMGCPVPKITKK 106
Dus pfam01207
Dihydrouridine synthase (Dus); Members of this family catalyze the reduction of the 5,6-double ...
 316-411 2.97e-10

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: 61.19  E-value: 2.97e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2078124463 316 LAPLTTCGNLPFRRICKRYGA-DITCGEMAMCTNLLQGQPSEWALMKRHHTEDLFGVQLEGAFPDTMTKCAELlNTSIEV 394
Cdd:pfam01207   2 LAPMAGVTDLPFRRLVREYGAgDLVYTEMVTAKAQLRPEKVRIRMLSELEEPTPLAVQLGGSDPALLAEAAKL-VEDRGA 80

                          90
                  ....*....|....*..
gi 2078124463 395 DFVDINVGCPIDLVYKK 411
Cdd:pfam01207  81 DGIDINMGCPSKKVTRG 97
PRK10415 PRK10415
tRNA-dihydrouridine synthase B; Provisional
 310-416 6.82e-08

tRNA-dihydrouridine synthase B; Provisional


Pssm-ID: 182440  Cd Length: 321  Bit Score: 53.82  E-value: 6.82e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2078124463 310 FRGKLYLAPLTTCGNLPFRRICKRYGADITCGEMamctnlLQGQPSEWALMKRH----HTED--LFGVQLEGAFPDTMTK 383
Cdd:PRK10415    8 LRNRLIAAPMAGITDRPFRTLCYEMGAGLTVSEM------MSSNPQVWESDKSRlrmvHIDEpgIRTVQIAGSDPKEMAD 81

                          90       100       110
                  ....*....|....*....|....*....|...
gi 2078124463 384 CAElLNTSIEVDFVDINVGCPIDLVYKKVSIEA 416
Cdd:PRK10415   82 AAR-INVESGAQIIDINMGCPAKKVNRKLAGSA 113
Zn_finger_prot pfam19242
Putative zinc finger protein; This is a family of proteins predominantly found in Iridoviridae, ...
 55-161 7.56e-04

Putative zinc finger protein; This is a family of proteins predominantly found in Iridoviridae, which contains a zinc finger domain.


Pssm-ID: 437074  Cd Length: 268  Bit Score: 41.21  E-value: 7.56e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2078124463  55 TDSDQCNVGDENFAA--EPQSKKIKLDESVENQEKENKKVEEDKQDKKRARGQNK------SRPHVKYHQLEQ-QRLCPS 125
Cdd:pfam19242 109 TPSNELINGVLNYSLllPPSTPKREIKPTQPNKKRKNARGGATPPNSKPLGNPAKpngvsqQQQGPKRDSTQKpTRLCLS 188

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2078124463 126 IVQEcaSKCFFGDKCKFLHDpekYLSGKHEDIGPKC 161
Cdd:pfam19242 189 VLKQ--TKCFHGAQCRFAHR---YSDLKECNFGENC 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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