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Conserved domains on  [gi|667667699|ref|NP_001288105|]
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tRNA-dihydrouridine(20) synthase [NAD(P)+]-like isoform 2 [Mus musculus]

Protein Classification

tRNA-dihydrouridine synthase family protein( domain architecture ID 14390137)

tRNA-dihydrouridine synthase family protein such as tRNA-dihydrouridine synthase, which catalyzes the synthesis of dihydrouridine, a modified base found in the D-loop of most tRNAs

CATH:  3.20.20.70
EC:  1.3.1.-
Gene Ontology:  GO:0017150|GO:0008033|GO:0050660|GO:0016491
PubMed:  26429968|30149704|34798057
SCOP:  4000080

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 ...
 1-139 2.96e-55

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: 181.15  E-value: 2.96e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 667667699   1 MGCPKEYSTKGGMGAALLSDPDKIEKILSTLVKGTHRPVTCKIRILPSLED-TLNLVKRIERTGISAIAVHGRNRDERPQ 79
Cdd:cd02801   88 MGCPSPKVTKGGAGAALLKDPELVAEIVRAVREAVPIPVTVKIRLGWDDEEeTLELAKALEDAGASALTVHGRTREQRYS 167

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 667667699  80 HPVSCEVIRAIAETLSIPVIANGGshdhIQQHVDIEDFRQATAASSVMVARAAMWNPSIF 139
Cdd:cd02801  168 GPADWDYIAEIKEAVSIPVIANGD----IFSLEDALRCLEQTGVDGVMIGRGALGNPWLF 223
DSRM_DUS2L cd19871
double-stranded RNA binding motif of tRNA-dihydrouridine(20) synthase [NAD(P)+]-like (DUS2L) ...
 256-323 6.07e-38

double-stranded RNA binding motif of tRNA-dihydrouridine(20) synthase [NAD(P)+]-like (DUS2L) and similar proteins; DUS2L (also known as dihydrouridine synthase 2 (DUS2), up-regulated in lung cancer protein 8 (URLC8), or tRNA-dihydrouridine synthase 2-like) catalyzes the synthesis of dihydrouridine, a modified base found in the D-loop of most tRNAs. It negatively regulates the activation of EIF2AK2/PKR. DUS2L contains an N-terminal FMN-binding domain and a C-terminal double-stranded RNA binding motif (DSRM) that is not sequence specific, but highly specific for dsRNAs of various origin and structure.


:

Pssm-ID: 380700  Cd Length: 68  Bit Score: 130.86  E-value: 6.07e-38
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 667667699 256 TPKMCLLEWCRREKLPQPVYETVQRTIDRMFCSVVTVAEQKYQSTLWDKSKKLAEQTAAIVCLRSQGL 323
Cdd:cd19871    1 TPKMILNEWCRKNKLPQPVYETVQRPSDRLFQSVVTVDGKKYTSSLWEKSKKLAEQAAAIVCLRALGL 68
 
Name Accession Description Interval E-value
DUS_like_FMN cd02801
Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze ...
 1-139 2.96e-55

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: 181.15  E-value: 2.96e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 667667699   1 MGCPKEYSTKGGMGAALLSDPDKIEKILSTLVKGTHRPVTCKIRILPSLED-TLNLVKRIERTGISAIAVHGRNRDERPQ 79
Cdd:cd02801   88 MGCPSPKVTKGGAGAALLKDPELVAEIVRAVREAVPIPVTVKIRLGWDDEEeTLELAKALEDAGASALTVHGRTREQRYS 167

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 667667699  80 HPVSCEVIRAIAETLSIPVIANGGshdhIQQHVDIEDFRQATAASSVMVARAAMWNPSIF 139
Cdd:cd02801  168 GPADWDYIAEIKEAVSIPVIANGD----IFSLEDALRCLEQTGVDGVMIGRGALGNPWLF 223
DSRM_DUS2L cd19871
double-stranded RNA binding motif of tRNA-dihydrouridine(20) synthase [NAD(P)+]-like (DUS2L) ...
 256-323 6.07e-38

double-stranded RNA binding motif of tRNA-dihydrouridine(20) synthase [NAD(P)+]-like (DUS2L) and similar proteins; DUS2L (also known as dihydrouridine synthase 2 (DUS2), up-regulated in lung cancer protein 8 (URLC8), or tRNA-dihydrouridine synthase 2-like) catalyzes the synthesis of dihydrouridine, a modified base found in the D-loop of most tRNAs. It negatively regulates the activation of EIF2AK2/PKR. DUS2L contains an N-terminal FMN-binding domain and a C-terminal double-stranded RNA binding motif (DSRM) that is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380700  Cd Length: 68  Bit Score: 130.86  E-value: 6.07e-38
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 667667699 256 TPKMCLLEWCRREKLPQPVYETVQRTIDRMFCSVVTVAEQKYQSTLWDKSKKLAEQTAAIVCLRSQGL 323
Cdd:cd19871    1 TPKMILNEWCRKNKLPQPVYETVQRPSDRLFQSVVTVDGKKYTSSLWEKSKKLAEQAAAIVCLRALGL 68
DusA COG0042
tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; ...
 1-165 2.64e-36

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: 134.07  E-value: 2.64e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 667667699   1 MGCPKEYSTKGGMGAALLSDPDKIEKILSTLVKGTHRPVTCKIRILPSlEDTLN---LVKRIERTGISAIAVHGRNRDER 77
Cdd:COG0042   95 MGCPVKKVTKGGAGAALLRDPELVAEIVKAVVEAVDVPVTVKIRLGWD-DDDENaleFARIAEDAGAAALTVHGRTREQR 173

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 667667699  78 PQHPVSCEVIRAIAETLSIPVIANGGshdhIQQHVDIEDFRQATAASSVMVARAAMWNPSIF------LKDGLRP---LE 148
Cdd:COG0042  174 YKGPADWDAIARVKEAVSIPVIGNGD----IFSPEDAKRMLEETGCDGVMIGRGALGNPWLFreidayLAGGEAPppsLE 249

                        170
                 ....*....|....*..
gi 667667699 149 EVMQKYIRYAVQYDNHY 165
Cdd:COG0042  250 EVLELLLEHLELLLEFY 266
Dus pfam01207
Dihydrouridine synthase (Dus); Members of this family catalyze the reduction of the 5,6-double ...
 1-211 4.47e-35

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: 130.91  E-value: 4.47e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 667667699    1 MGCPKEYSTKGGMGAALLSDPDKIEKILSTLVKGTHRPVTCKIRIL--PSLEDTLNLVKRIERTGISAIAVHGRNRDERP 78
Cdd:pfam01207  87 MGCPSKKVTRGGGGAALLRNPDLVAQIVKAVVKAVGIPVTVKIRIGwdDSHENAVEIAKIVEDAGAQALTVHGRTRAQNY 166

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 667667699   79 QHPVSCEVIRAIAETLSIPVIANGGshdhIQQHVDIEDFRQATAASSVMVARAAMWNPSIF-----LKDGLR----PLEE 149
Cdd:pfam01207 167 EGTADWDAIKQVKQAVSIPVIANGD----ITDPEDAQRCLAYTGADGVMIGRGALGNPWLFaeqhtVKTGEFgpspPLAE 242

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 667667699  150 VMQKyiryavqYDNHYTNTkyclcqmlrEQLESPQGRLLHAAQSSQEICEAFGLGAFYEETI 211
Cdd:pfam01207 243 EAEK-------VLRHLPYL---------EEFLGEDKGLRHARKHLAWYLKGFPGAAELRREL 288
nifR3_yhdG TIGR00737
putative TIM-barrel protein, nifR3 family; This model represents one branch of COG0042 ...
 1-139 2.13e-30

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: 118.62  E-value: 2.13e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 667667699    1 MGCPKEYSTKGGMGAALLSDPDKIEKILSTLVKGTHRPVTCKIRILPSlEDTLN---LVKRIERTGISAIAVHGRNRDER 77
Cdd:TIGR00737  96 MGCPVPKITKKGAGSALLRDPDLIGKIVKAVVDAVDIPVTVKIRIGWD-DAHINaveAARIAEDAGAQAVTLHGRTRAQG 174

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 667667699   78 PQHPVSCEVIRAIAETLSIPVIANGgshdhiqqhvDIEDFRQA------TAASSVMVARAAMWNPSIF 139
Cdd:TIGR00737 175 YSGEANWDIIARVKQAVRIPVIGNG----------DIFSPEDAkamletTGCDGVMIGRGALGNPWLF 232
PRK10415 PRK10415
tRNA-dihydrouridine synthase B; Provisional
 1-139 7.08e-21

tRNA-dihydrouridine synthase B; Provisional


Pssm-ID: 182440  Cd Length: 321  Bit Score: 91.96  E-value: 7.08e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 667667699   1 MGCPKEYSTKGGMGAALLSDPDKIEKILSTLVKGTHRPVTCKIRI--LPSLEDTLNLVKRIERTGISAIAVHGRNRDERP 78
Cdd:PRK10415  98 MGCPAKKVNRKLAGSALLQYPDLVKSILTEVVNAVDVPVTLKIRTgwAPEHRNCVEIAQLAEDCGIQALTIHGRTRACLF 177

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 667667699  79 QHPVSCEVIRAIAETLSIPVIANGgshdhiqqhvDIEDFRQA------TAASSVMVARAAMWNPSIF 139
Cdd:PRK10415 178 NGEAEYDSIRAVKQKVSIPVIANG----------DITDPLKAravldyTGADALMIGRAAQGRPWIF 234
DSRM smart00358
Double-stranded RNA binding motif;
257-320 2.05e-08

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 50.34  E-value: 2.05e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 667667699   257 PKMCLLEWCRREKLPqPVYETVQRT---IDRMFCSVVTVAEQKYQSTlWDKSKKLAEQTAAIVCLRS 320
Cdd:smart00358   1 PKSLLQELAQKRKLP-PEYELVKEEgpdHAPRFTVTVKVGGKRTGEG-EGSSKKEAKQRAAEAALRS 65
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 257-319 1.03e-07

Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training Putative motif shared by proteins that bind to dsRNA. At least some DSRM proteins seem to bind to specific RNA targets. Exemplified by Staufen, which is involved in localization of at least five different mRNAs in the early Drosophila embryo. Also by interferon-induced protein kinase in humans, which is part of the cellular response to dsRNA.


Pssm-ID: 425434 [Multi-domain]  Cd Length: 66  Bit Score: 48.38  E-value: 1.03e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 667667699  257 PKMCLLEWCRREKlPQPVYETVQRT---IDRMFCSVVTVAEQKYQSTlWDKSKKLAEQTAAIVCLR 319
Cdd:pfam00035   1 PKSLLQEYAQKNG-KPPPYEYVSEEgppHSPKFTVTVKVDGKLYGSG-TGSSKKEAEQLAAEKALE 64
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
257-314 2.16e-05

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 45.09  E-value: 2.16e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 667667699 257 PKMCLLEWCRREKLPQPVYETVQRTI---DRMFCSVVTVAEQKYqSTLWDKSKKLAEQTAA 314
Cdd:COG0571  159 YKTALQEWLQARGLPLPEYEVVEEEGpdhAKTFTVEVLVGGKVL-GEGTGRSKKEAEQAAA 218
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 257-318 9.74e-05

ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. This enzyme cleaves double-stranded rRNA. It is involved in processing ribosomal RNA precursors. It is found even in minimal genones such as Mycoplasma genitalium and Buchnera aphidicola, and in some cases has been shown to be an essential gene. These bacterial proteins contain a double-stranded RNA binding motif (pfam00035) and a ribonuclease III domain (pfam00636). Eukaryotic homologs tend to be much longer proteins with additional domains, localized to the nucleus, and not included in this family. [Transcription, RNA processing]


Pssm-ID: 274024 [Multi-domain]  Cd Length: 220  Bit Score: 43.35  E-value: 9.74e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 667667699  257 PKMCLLEWCRREKLPQPVYETVQRT---IDRMFCSVVTVAEQKYqSTLWDKSKKLAEQTAAIVCL 318
Cdd:TIGR02191 154 YKTALQEWAQARGKPLPEYRLIKEEgpdHDKEFTVEVSVNGEPY-GEGKGKSKKEAEQNAAKAAL 217
 
Name Accession Description Interval E-value
DUS_like_FMN cd02801
Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze ...
 1-139 2.96e-55

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: 181.15  E-value: 2.96e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 667667699   1 MGCPKEYSTKGGMGAALLSDPDKIEKILSTLVKGTHRPVTCKIRILPSLED-TLNLVKRIERTGISAIAVHGRNRDERPQ 79
Cdd:cd02801   88 MGCPSPKVTKGGAGAALLKDPELVAEIVRAVREAVPIPVTVKIRLGWDDEEeTLELAKALEDAGASALTVHGRTREQRYS 167

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 667667699  80 HPVSCEVIRAIAETLSIPVIANGGshdhIQQHVDIEDFRQATAASSVMVARAAMWNPSIF 139
Cdd:cd02801  168 GPADWDYIAEIKEAVSIPVIANGD----IFSLEDALRCLEQTGVDGVMIGRGALGNPWLF 223
DSRM_DUS2L cd19871
double-stranded RNA binding motif of tRNA-dihydrouridine(20) synthase [NAD(P)+]-like (DUS2L) ...
 256-323 6.07e-38

double-stranded RNA binding motif of tRNA-dihydrouridine(20) synthase [NAD(P)+]-like (DUS2L) and similar proteins; DUS2L (also known as dihydrouridine synthase 2 (DUS2), up-regulated in lung cancer protein 8 (URLC8), or tRNA-dihydrouridine synthase 2-like) catalyzes the synthesis of dihydrouridine, a modified base found in the D-loop of most tRNAs. It negatively regulates the activation of EIF2AK2/PKR. DUS2L contains an N-terminal FMN-binding domain and a C-terminal double-stranded RNA binding motif (DSRM) that is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380700  Cd Length: 68  Bit Score: 130.86  E-value: 6.07e-38
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 667667699 256 TPKMCLLEWCRREKLPQPVYETVQRTIDRMFCSVVTVAEQKYQSTLWDKSKKLAEQTAAIVCLRSQGL 323
Cdd:cd19871    1 TPKMILNEWCRKNKLPQPVYETVQRPSDRLFQSVVTVDGKKYTSSLWEKSKKLAEQAAAIVCLRALGL 68
DusA COG0042
tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; ...
 1-165 2.64e-36

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: 134.07  E-value: 2.64e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 667667699   1 MGCPKEYSTKGGMGAALLSDPDKIEKILSTLVKGTHRPVTCKIRILPSlEDTLN---LVKRIERTGISAIAVHGRNRDER 77
Cdd:COG0042   95 MGCPVKKVTKGGAGAALLRDPELVAEIVKAVVEAVDVPVTVKIRLGWD-DDDENaleFARIAEDAGAAALTVHGRTREQR 173

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 667667699  78 PQHPVSCEVIRAIAETLSIPVIANGGshdhIQQHVDIEDFRQATAASSVMVARAAMWNPSIF------LKDGLRP---LE 148
Cdd:COG0042  174 YKGPADWDAIARVKEAVSIPVIGNGD----IFSPEDAKRMLEETGCDGVMIGRGALGNPWLFreidayLAGGEAPppsLE 249

                        170
                 ....*....|....*..
gi 667667699 149 EVMQKYIRYAVQYDNHY 165
Cdd:COG0042  250 EVLELLLEHLELLLEFY 266
Dus pfam01207
Dihydrouridine synthase (Dus); Members of this family catalyze the reduction of the 5,6-double ...
 1-211 4.47e-35

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: 130.91  E-value: 4.47e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 667667699    1 MGCPKEYSTKGGMGAALLSDPDKIEKILSTLVKGTHRPVTCKIRIL--PSLEDTLNLVKRIERTGISAIAVHGRNRDERP 78
Cdd:pfam01207  87 MGCPSKKVTRGGGGAALLRNPDLVAQIVKAVVKAVGIPVTVKIRIGwdDSHENAVEIAKIVEDAGAQALTVHGRTRAQNY 166

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 667667699   79 QHPVSCEVIRAIAETLSIPVIANGGshdhIQQHVDIEDFRQATAASSVMVARAAMWNPSIF-----LKDGLR----PLEE 149
Cdd:pfam01207 167 EGTADWDAIKQVKQAVSIPVIANGD----ITDPEDAQRCLAYTGADGVMIGRGALGNPWLFaeqhtVKTGEFgpspPLAE 242

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 667667699  150 VMQKyiryavqYDNHYTNTkyclcqmlrEQLESPQGRLLHAAQSSQEICEAFGLGAFYEETI 211
Cdd:pfam01207 243 EAEK-------VLRHLPYL---------EEFLGEDKGLRHARKHLAWYLKGFPGAAELRREL 288
nifR3_yhdG TIGR00737
putative TIM-barrel protein, nifR3 family; This model represents one branch of COG0042 ...
 1-139 2.13e-30

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: 118.62  E-value: 2.13e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 667667699    1 MGCPKEYSTKGGMGAALLSDPDKIEKILSTLVKGTHRPVTCKIRILPSlEDTLN---LVKRIERTGISAIAVHGRNRDER 77
Cdd:TIGR00737  96 MGCPVPKITKKGAGSALLRDPDLIGKIVKAVVDAVDIPVTVKIRIGWD-DAHINaveAARIAEDAGAQAVTLHGRTRAQG 174

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 667667699   78 PQHPVSCEVIRAIAETLSIPVIANGgshdhiqqhvDIEDFRQA------TAASSVMVARAAMWNPSIF 139
Cdd:TIGR00737 175 YSGEANWDIIARVKQAVRIPVIGNG----------DIFSPEDAkamletTGCDGVMIGRGALGNPWLF 232
PRK10415 PRK10415
tRNA-dihydrouridine synthase B; Provisional
 1-139 7.08e-21

tRNA-dihydrouridine synthase B; Provisional


Pssm-ID: 182440  Cd Length: 321  Bit Score: 91.96  E-value: 7.08e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 667667699   1 MGCPKEYSTKGGMGAALLSDPDKIEKILSTLVKGTHRPVTCKIRI--LPSLEDTLNLVKRIERTGISAIAVHGRNRDERP 78
Cdd:PRK10415  98 MGCPAKKVNRKLAGSALLQYPDLVKSILTEVVNAVDVPVTLKIRTgwAPEHRNCVEIAQLAEDCGIQALTIHGRTRACLF 177

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 667667699  79 QHPVSCEVIRAIAETLSIPVIANGgshdhiqqhvDIEDFRQA------TAASSVMVARAAMWNPSIF 139
Cdd:PRK10415 178 NGEAEYDSIRAVKQKVSIPVIANG----------DITDPLKAravldyTGADALMIGRAAQGRPWIF 234
PRK10550 PRK10550
tRNA dihydrouridine(16) synthase DusC;
2-162 2.60e-13

tRNA dihydrouridine(16) synthase DusC;


Pssm-ID: 236713  Cd Length: 312  Bit Score: 69.84  E-value: 2.60e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 667667699   2 GCPKEYSTKGGMGAALLSDPDKI---EKILSTLVKgTHRPVTCKIRI-LPSLEDTLNLVKRIERTGISAIAVHGRNRDE- 76
Cdd:PRK10550  97 GCPSKTVNGSGGGATLLKDPELIyqgAKAMREAVP-AHLPVTVKVRLgWDSGERKFEIADAVQQAGATELVVHGRTKEDg 175

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 667667699  77 -RPQHpVSCEVIRAIAETLSIPVIANGgshdHIQQHVDIEDFRQATAASSVMVARAAMWNPS----IFLKDGLRPLEEVM 151
Cdd:PRK10550 176 yRAEH-INWQAIGEIRQRLTIPVIANG----EIWDWQSAQQCMAITGCDAVMIGRGALNIPNlsrvVKYNEPRMPWPEVV 250

                        170
                 ....*....|....
gi 667667699 152 ---QKYIRYAVQYD 162
Cdd:PRK10550 251 allQKYTRLEKQGD 264
PRK11815 PRK11815
tRNA dihydrouridine(20/20a) synthase DusA;
2-161 3.81e-10

tRNA dihydrouridine(20/20a) synthase DusA;


Pssm-ID: 236991 [Multi-domain]  Cd Length: 333  Bit Score: 60.53  E-value: 3.81e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 667667699   2 GCPKEYSTKGGMGAALLSDPDKIEKILSTLVKGTHRPVTCKIRI----LPSLEDTLNLVKRIERTGISAIAVHGR----- 72
Cdd:PRK11815  99 GCPSDRVQNGRFGACLMAEPELVADCVKAMKDAVSIPVTVKHRIgiddQDSYEFLCDFVDTVAEAGCDTFIVHARkawlk 178

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 667667699  73 ------NRDERP-QHPVsceVIRAIAETLSIPVIANGG--SHDHIQQH---VDiedfrqataasSVMVARAAMWNPSIFL 140
Cdd:PRK11815 179 glspkeNREIPPlDYDR---VYRLKRDFPHLTIEINGGikTLEEAKEHlqhVD-----------GVMIGRAAYHNPYLLA 244

                        170       180       190
                 ....*....|....*....|....*....|
gi 667667699 141 K-------DGLRPL--EEVMQKYIRYAVQY 161
Cdd:PRK11815 245 EvdrelfgEPAPPLsrSEVLEAMLPYIERH 274
DSRM_SF cd00048
double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ...
 263-318 1.56e-09

double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 amino acid domain that adopts an alpha-beta-beta-beta-alpha fold. It is not sequence specific, but highly specific for double-stranded RNAs (dsRNAs) of various origin and structure. The DSRM domains are found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila Staufen protein, E. coli RNase III, RNase H1, and dsRNA dependent adenosine deaminases. They are involved in numerous cellular mechanisms ranging from localization and transport of messenger RNAs, through maturation and degradation of RNAs, to viral response and signal transduction. Some members harbor tandem DSRMs that act in small RNA biogenesis.


Pssm-ID: 380679 [Multi-domain]  Cd Length: 57  Bit Score: 53.44  E-value: 1.56e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 667667699 263 EWCRREKLPQPVYETVQRTID--RMFCSVVTVAEQKYQSTlwDKSKKLAEQTAAIVCL 318
Cdd:cd00048    2 ELCQKNKWPPPEYETVEEGGPhnPRFTCTVTVNGQTFEGE--GKSKKEAKQAAAEKAL 57
DSRM_SON-like cd19870
double-stranded RNA binding motif of protein SON and similar proteins; Protein SON (also known ...
 257-323 5.42e-09

double-stranded RNA binding motif of protein SON and similar proteins; Protein SON (also known as Bax antagonist selected in saccharomyces 1 (BASS1), negative regulatory element-binding protein (NRE-binding protein), or protein DBP-5, or SON3) is an RNA-binding protein which acts as an mRNA splicing cofactor by promoting efficient splicing of transcripts that possess weak splice sites. It specifically promotes splicing of many cell-cycle and DNA-repair transcripts that possess weak splice sites, such as TUBG1, KATNB1, TUBGCP2, AURKB, PCNT, AKT1, RAD23A, and FANCG. Members of this group contain a double-stranded RNA binding motif (DSRM) at the C-terminus. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380699  Cd Length: 75  Bit Score: 52.28  E-value: 5.42e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 667667699 257 PKMCLLEWCRREKLPQPVYETVQRT---IDRMFCSVVTVAEQKYQSTLWDKSKKLAEQTAAIVCLRSQGL 323
Cdd:cd19870    4 PVSALMELCNKRKWGPPEFRLVEESgppHRKHFLFKVVVNGVEYQPSVASGNKKDAKAQAATVALQALGL 73
DSRM_RNAse_III_family cd10845
double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase ...
 257-319 5.91e-09

double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase III (EC 3.1.26.3; also known as ribonuclease 3) digests double-stranded RNA formed within single-strand substrates, but not RNA-DNA hybrids. It is involved in the processing of rRNA precursors, viral transcripts, some mRNAs, and at least 1 tRNA (metY, a minor form of tRNA-init-Met). It cleaves the 30S primary rRNA transcript to yield the immediate precursors to the 16S and 23S rRNAs. The cleavage can occur in assembled 30S, 50S, and even 70S subunits and is influenced by the presence of ribosomal proteins. The RNase III family also includes the mitochondrion-specific ribosomal protein mL44 subfamily, which is composed of mitochondrial 54S ribosomal protein L3 (MRPL3) and mitochondrial 39S ribosomal protein L44 (MRPL44). Members of this family contain an RNase III domain and a C-terminal double-stranded RNA binding motif (DSRM). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380682 [Multi-domain]  Cd Length: 69  Bit Score: 52.11  E-value: 5.91e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 667667699 257 PKMCLLEWCRREKLPQPVYETVQRTI---DRMFCSVVTVAEQKYqSTLWDKSKKLAEQTAAIVCLR 319
Cdd:cd10845    3 YKTALQEYLQKRGLPLPEYELVEEEGpdhNKTFTVEVKVNGKVI-GEGTGRSKKEAEQAAAKAALE 67
DSRM smart00358
Double-stranded RNA binding motif;
257-320 2.05e-08

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 50.34  E-value: 2.05e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 667667699   257 PKMCLLEWCRREKLPqPVYETVQRT---IDRMFCSVVTVAEQKYQSTlWDKSKKLAEQTAAIVCLRS 320
Cdd:smart00358   1 PKSLLQELAQKRKLP-PEYELVKEEgpdHAPRFTVTVKVGGKRTGEG-EGSSKKEAKQRAAEAALRS 65
DSRM_AtDRB-like cd19878
double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding proteins ...
 258-322 3.28e-08

double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding proteins (AtDRBs)and similar proteins; This family includes a group of Arabidopsis thaliana double-stranded RNA-binding proteins (AtDRB1-5). They bind double-stranded RNA (dsRNA) and may be involved in RNA-mediated silencing. Members of this family contain two to three double-stranded RNA binding motifs (DSRMs). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380707 [Multi-domain]  Cd Length: 67  Bit Score: 49.82  E-value: 3.28e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 667667699 258 KMCLLEWCRREKLPQPVYETVQRTIDR--MFCSVVTVAEQKYQSTLWdKSKKLAEQTAAIVCLRSQG 322
Cdd:cd19878    2 KNLLQEYAQKKKIPLPKYESAKSGPSHqpTFVSTVIVLGVRFSSEGA-KNKKQAEQSAAKVALKELG 67
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 257-319 1.03e-07

Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training Putative motif shared by proteins that bind to dsRNA. At least some DSRM proteins seem to bind to specific RNA targets. Exemplified by Staufen, which is involved in localization of at least five different mRNAs in the early Drosophila embryo. Also by interferon-induced protein kinase in humans, which is part of the cellular response to dsRNA.


Pssm-ID: 425434 [Multi-domain]  Cd Length: 66  Bit Score: 48.38  E-value: 1.03e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 667667699  257 PKMCLLEWCRREKlPQPVYETVQRT---IDRMFCSVVTVAEQKYQSTlWDKSKKLAEQTAAIVCLR 319
Cdd:pfam00035   1 PKSLLQEYAQKNG-KPPPYEYVSEEgppHSPKFTVTVKVDGKLYGSG-TGSSKKEAEQLAAEKALE 64
DHOD_DHPD_FMN cd02810
Dihydroorotate dehydrogenase (DHOD) and Dihydropyrimidine dehydrogenase (DHPD) FMN-binding ...
 2-141 7.15e-07

Dihydroorotate dehydrogenase (DHOD) and Dihydropyrimidine dehydrogenase (DHPD) FMN-binding domain. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences and cellular location. Members of class 1 are cytosolic enzymes and multimers while class 2 enzymes are membrane associated and monomeric. The class 1 enzymes can be further divided into subtypes 1A and 1B which are homodimers and heterotetrameric proteins, respectively. DHPD catalyzes the first step in pyrimidine degradation: the NADPH-dependent reduction of uracil and thymine to the corresponding 5,6-dihydropyrimidines. DHPD contains two FAD, two FMN and eight [4Fe-4S] clusters, arranged in two electron transfer chains that pass its homodimeric interface twice. Two of the Fe-S clusters show a hitherto unobserved coordination involving a glutamine residue.


Pssm-ID: 239204 [Multi-domain]  Cd Length: 289  Bit Score: 50.43  E-value: 7.15e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 667667699   2 GCPKEystkgGMGAALLSDPDKIEKILSTLVKGTHRPVTCKIRILPSLEDTLNLVKRIERTGISAIAVHGR------NRD 75
Cdd:cd02810  133 SCPNV-----GGGRQLGQDPEAVANLLKAVKAAVDIPLLVKLSPYFDLEDIVELAKAAERAGADGLTAINTisgrvvDLK 207

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 667667699  76 ERPQ--------------HPVSCEVIRAIAETLS--IPVIANGGSHDhiQQHVDieDFRQAtAASSVMVARAAMWN-PSI 138
Cdd:cd02810  208 TVGPgpkrgtgglsgapiRPLALRWVARLAARLQldIPIIGVGGIDS--GEDVL--EMLMA-GASAVQVATALMWDgPDV 282


                 ...
gi 667667699 139 FLK 141
Cdd:cd02810  283 IRK 285
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
257-314 2.16e-05

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 45.09  E-value: 2.16e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 667667699 257 PKMCLLEWCRREKLPQPVYETVQRTI---DRMFCSVVTVAEQKYqSTLWDKSKKLAEQTAA 314
Cdd:COG0571  159 YKTALQEWLQARGLPLPEYEVVEEEGpdhAKTFTVEVLVGGKVL-GEGTGRSKKEAEQAAA 218
OYE_like_FMN_family cd02803
Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme ...
 48-136 5.96e-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: 44.49  E-value: 5.96e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 667667699  48 SLEDTLNLVKRIERTGISAIAVHGRNRDERPQHPVSCEVIRA--------IAETLSIPVIANGGshdhiqqHVDIEDFRQ 119
Cdd:cd02803  226 TLEEAIEIAKALEEAGVDALHVSGGSYESPPPIIPPPYVPEGyflelaekIKKAVKIPVIAVGG-------IRDPEVAEE 298

                         90       100
                 ....*....|....*....|
gi 667667699 120 ATA---ASSVMVARAAMWNP 136
Cdd:cd02803  299 ILAegkADLVALGRALLADP 318
DSRM_DGCR8_rpt1 cd19867
first double-stranded RNA binding motif of DiGeorge syndrome critical region 8 (DGCR8) and ...
 256-314 7.18e-05

first double-stranded RNA binding motif of DiGeorge syndrome critical region 8 (DGCR8) and similar proteins; DGCR8 is a component of the microprocessor complex that acts as an RNA- and heme-binding protein that is involved in the initial step of microRNA (miRNA) biogenesis. Within the microprocessor complex, DGCR8 functions as a molecular anchor necessary for the recognition of pri-miRNA at dsRNA-ssRNA junction and directs DROSHA to cleave 11bp away from the junction to release hairpin-shaped pre-miRNAs that are subsequently cut by the cytoplasmic DICER to generate mature miRNAs. DGCR8 contains two double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380696  Cd Length: 74  Bit Score: 40.78  E-value: 7.18e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 667667699 256 TPKMCLLEWCRREKLPQPVYETVQRTIDRM-FCSVVTVAEQKYQSTLwDKSKKLAEQTAA 314
Cdd:cd19867    7 SPVCILHEYCQRVLKVQPEYNFTETENAATpFSAEVFINGVEYGSGE-ASSKKLAKQKAA 65
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 257-318 9.74e-05

ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. This enzyme cleaves double-stranded rRNA. It is involved in processing ribosomal RNA precursors. It is found even in minimal genones such as Mycoplasma genitalium and Buchnera aphidicola, and in some cases has been shown to be an essential gene. These bacterial proteins contain a double-stranded RNA binding motif (pfam00035) and a ribonuclease III domain (pfam00636). Eukaryotic homologs tend to be much longer proteins with additional domains, localized to the nucleus, and not included in this family. [Transcription, RNA processing]


Pssm-ID: 274024 [Multi-domain]  Cd Length: 220  Bit Score: 43.35  E-value: 9.74e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 667667699  257 PKMCLLEWCRREKLPQPVYETVQRT---IDRMFCSVVTVAEQKYqSTLWDKSKKLAEQTAAIVCL 318
Cdd:TIGR02191 154 YKTALQEWAQARGKPLPEYRLIKEEgpdHDKEFTVEVSVNGEPY-GEGKGKSKKEAEQNAAKAAL 217
DSRM_AtDRB-like_rpt1 cd19907
first double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding ...
 261-320 1.48e-04

first double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding proteins (AtDRBs)and similar proteins; This family includes a group of Arabidopsis thaliana double-stranded RNA-binding proteins (AtDRB1-5). They bind double-stranded RNA (dsRNA) and may be involved in RNA-mediated silencing. Members of this family contain two to three double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380736 [Multi-domain]  Cd Length: 69  Bit Score: 39.77  E-value: 1.48e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 667667699 261 LLEWCRREKLPQPVYETVQRTIDR--MFCSVVTVAEQKYQSTLWDKSKKLAEQTAAIVCLRS 320
Cdd:cd19907    6 LQEYAQKSCLNLPVYACIREGPDHapRFRATVTFNGVIFESPPGFPTLKAAEHSAAEVALNS 67
DHOD_1B_like cd04740
Dihydroorotate dehydrogenase (DHOD) class 1B FMN-binding domain. DHOD catalyzes the oxidation ...
 3-154 2.25e-04

Dihydroorotate dehydrogenase (DHOD) class 1B FMN-binding domain. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences and cellular location. Members of class 1 are cytosolic enzymes and multimers while class 2 enzymes are membrane associated and monomeric. The class 1 enzymes can be further divided into subtypes 1A and 1B which are homodimers and heterotetrameric proteins, respectively.


Pssm-ID: 240091 [Multi-domain]  Cd Length: 296  Bit Score: 42.54  E-value: 2.25e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 667667699   3 CPkeySTKGGmGAALLSDPDKIEKILSTLVKGTHRPVTCKIRilPSLEDTLNLVKRIERTG---ISAI------AVHGRN 73
Cdd:cd04740  125 CP---NVKGG-GMAFGTDPEAVAEIVKAVKKATDVPVIVKLT--PNVTDIVEIARAAEEAGadgLTLIntlkgmAIDIET 198

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 667667699  74 RdeRPQ-------------HPVSCEVIRAIAETLSIPVIANGGshdhiqqhvdIEDFRQA-----TAASSVMVARAAMWN 135
Cdd:cd04740  199 R--KPIlgnvtgglsgpaiKPIALRMVYQVYKAVEIPIIGVGG----------IASGEDAleflmAGASAVQVGTANFVD 266

                        170       180
                 ....*....|....*....|.
gi 667667699 136 PSIFLK--DGlrpLEEVMQKY 154
Cdd:cd04740  267 PEAFKEiiEG---LEAYLDEE 284
FadH COG1902
2,4-dienoyl-CoA reductase or related NADH-dependent reductase, Old Yellow Enzyme (OYE) family ...
 48-136 3.95e-04

2,4-dienoyl-CoA reductase or related NADH-dependent reductase, Old Yellow Enzyme (OYE) family [Energy production and conversion];


Pssm-ID: 441506 [Multi-domain]  Cd Length: 365  Bit Score: 42.08  E-value: 3.95e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 667667699  48 SLEDTLNLVKRIERTGISAIAVHGRNRDERPQHPVSC------EVIRAIAETLSIPVIANGGshdhiqqhvdIEDFRQAT 121
Cdd:COG1902  234 TLEESVELAKALEEAGVDYLHVSSGGYEPDAMIPTIVpegyqlPFAARIRKAVGIPVIAVGG----------ITTPEQAE 303

                         90       100
                 ....*....|....*....|.
gi 667667699 122 A------ASSVMVARAAMWNP 136
Cdd:COG1902  304 AalasgdADLVALGRPLLADP 324
DHPD_FMN cd02940
Dihydropyrimidine dehydrogenase (DHPD) FMN-binding domain. DHPD catalyzes the first step in ...
 2-133 2.50e-03

Dihydropyrimidine dehydrogenase (DHPD) FMN-binding domain. DHPD catalyzes the first step in pyrimidine degradation: the NADPH-dependent reduction of uracil and thymine to the corresponding 5,6-dihydropyrimidines. DHPD contains two FAD, two FMN, and eight [4Fe-4S] clusters, arranged in two electron transfer chains that pass the dimer interface twice. Two of the Fe-S clusters show a hitherto unobserved coordination involving a glutamine residue.


Pssm-ID: 239244  Cd Length: 299  Bit Score: 39.19  E-value: 2.50e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 667667699   2 GCPKEYSTKGgMGAALLSDPDKIEKILSTLVKGTHRPVTCKIRilPSLEDTLNLVKRIER---TGISAI----AVHGRNR 74
Cdd:cd02940  135 SCPHGMPERG-MGAAVGQDPELVEEICRWVREAVKIPVIAKLT--PNITDIREIARAAKEggaDGVSAIntvnSLMGVDL 211

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 667667699  75 DERPQHP----------VSCEVIRAIA----------ETLSIPVIANGGshdhiqqhvdIEDFRQA-----TAASSVMVA 129
Cdd:cd02940  212 DGTPPAPgvegkttyggYSGPAVKPIAlravsqiaraPEPGLPISGIGG----------IESWEDAaefllLGASVVQVC 281


                 ....
gi 667667699 130 RAAM 133
Cdd:cd02940  282 TAVM 285
HisF COG0107
Imidazole glycerol phosphate synthase subunit HisF [Amino acid transport and metabolism]; ...
 84-139 5.54e-03

Imidazole glycerol phosphate synthase subunit HisF [Amino acid transport and metabolism]; Imidazole glycerol phosphate synthase subunit HisF is part of the Pathway/BioSystem: Histidine biosynthesis


Pssm-ID: 439877  Cd Length: 251  Bit Score: 38.08  E-value: 5.54e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 667667699  84 CEVIRAIAETLSIPVIANGGSHdhiqqhvDIEDFRQA---TAASSVMVAraamwnpSIF 139
Cdd:COG0107  184 LELTRAVSEAVSIPVIASGGAG-------TLEHFVEVfteGGADAALAA-------SIF 228
 
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.
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