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Conserved domains on  [gi|110625595|ref|NP_079794|]
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tRNA-dihydrouridine(20) synthase [NAD(P)+]-like isoform 1 [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 ...
 13-252 1.84e-88

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: 270.52  E-value: 1.84e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595  13 KLILAPMVRVGTLPMRLLALDYGADIVYCEELIDLKMLQCKRVvnevlstvdfvapddRVVFRTCEREQSRVVFQMGTSD 92
Cdd:cd02801    1 KLILAPMVGVTDLPFRLLCRRYGADLVYTEMISAKALLRGNRK---------------RLRLLTRNPEERPLIVQLGGSD 65

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595  93 AERALAVARLVEN-DVAGIDVNMGCPKEYSTKGGMGAALLSDPDKIEKILSTLVKGTHRPVTCKIRILPSLED-TLNLVK 170
Cdd:cd02801   66 PETLAEAAKIVEElGADGIDLNMGCPSPKVTKGGAGAALLKDPELVAEIVRAVREAVPIPVTVKIRLGWDDEEeTLELAK 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595 171 RIERTGISAIAVHGRNRDERPQHPVSCEVIRAIAETLSIPVIANGGshdhIQQHVDIEDFRQATAASSVMVARAAMWNPS 250
Cdd:cd02801  146 ALEDAGASALTVHGRTREQRYSGPADWDYIAEIKEAVSIPVIANGD----IFSLEDALRCLEQTGVDGVMIGRGALGNPW 221


                 ..
gi 110625595 251 IF 252
Cdd:cd02801  222 LF 223
DSRM_DUS2L cd19871
double-stranded RNA binding motif of tRNA-dihydrouridine(20) synthase [NAD(P)+]-like (DUS2L) ...
 369-436 1.10e-37

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: 132.40  E-value: 1.10e-37
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 110625595 369 TPKMCLLEWCRREKLPQPVYETVQRTIDRMFCSVVTVAEQKYQSTLWDKSKKLAEQTAAIVCLRSQGL 436
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 ...
 13-252 1.84e-88

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: 270.52  E-value: 1.84e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595  13 KLILAPMVRVGTLPMRLLALDYGADIVYCEELIDLKMLQCKRVvnevlstvdfvapddRVVFRTCEREQSRVVFQMGTSD 92
Cdd:cd02801    1 KLILAPMVGVTDLPFRLLCRRYGADLVYTEMISAKALLRGNRK---------------RLRLLTRNPEERPLIVQLGGSD 65

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595  93 AERALAVARLVEN-DVAGIDVNMGCPKEYSTKGGMGAALLSDPDKIEKILSTLVKGTHRPVTCKIRILPSLED-TLNLVK 170
Cdd:cd02801   66 PETLAEAAKIVEElGADGIDLNMGCPSPKVTKGGAGAALLKDPELVAEIVRAVREAVPIPVTVKIRLGWDDEEeTLELAK 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595 171 RIERTGISAIAVHGRNRDERPQHPVSCEVIRAIAETLSIPVIANGGshdhIQQHVDIEDFRQATAASSVMVARAAMWNPS 250
Cdd:cd02801  146 ALEDAGASALTVHGRTREQRYSGPADWDYIAEIKEAVSIPVIANGD----IFSLEDALRCLEQTGVDGVMIGRGALGNPW 221


                 ..
gi 110625595 251 IF 252
Cdd:cd02801  222 LF 223
DusA COG0042
tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; ...
 12-284 1.49e-52

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: 179.90  E-value: 1.49e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595  12 NKLILAPMVRVGTLPMRLLALDYGADIVYCEelidlkMLQCKRVVNEVLSTVDFVAPDDrvvfrtcerEQSRVVFQMGTS 91
Cdd:COG0042    7 NPLILAPMAGVTDRPFRRLCRELGAGLLYTE------MVSARALLHGNRKTRRLLDFDP---------EEHPVAVQLFGS 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595  92 DAER-ALAVARLVENDVAGIDVNMGCPKEYSTKGGMGAALLSDPDKIEKILSTLVKGTHRPVTCKIRILPSlEDTLN--- 167
Cdd:COG0042   72 DPEElAEAARIAEELGADEIDINMGCPVKKVTKGGAGAALLRDPELVAEIVKAVVEAVDVPVTVKIRLGWD-DDDENale 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595 168 LVKRIERTGISAIAVHGRNRDERPQHPVSCEVIRAIAETLSIPVIANGGshdhIQQHVDIEDFRQATAASSVMVARAAMW 247
Cdd:COG0042  151 FARIAEDAGAAALTVHGRTREQRYKGPADWDAIARVKEAVSIPVIGNGD----IFSPEDAKRMLEETGCDGVMIGRGALG 226

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*.
gi 110625595 248 NPSIF------LKDGLRP---LEEVMQKYIRYAVQYDNHYTNTKYC 284
Cdd:COG0042  227 NPWLFreidayLAGGEAPppsLEEVLELLLEHLELLLEFYGERRGL 272
Dus pfam01207
Dihydrouridine synthase (Dus); Members of this family catalyze the reduction of the 5,6-double ...
 15-324 6.41e-52

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: 178.29  E-value: 6.41e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595   15 ILAPMVRVGTLPMRLLALDYGA-DIVYCEelidlkmlqckrvvneVLSTVDFVAPDdRVVFRTC--EREQSRVVFQMGTS 91
Cdd:pfam01207   1 LLAPMAGVTDLPFRRLVREYGAgDLVYTE----------------MVTAKAQLRPE-KVRIRMLseLEEPTPLAVQLGGS 63

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595   92 DAERALAVARLVEN-DVAGIDVNMGCPKEYSTKGGMGAALLSDPDKIEKILSTLVKGTHRPVTCKIRIL--PSLEDTLNL 168
Cdd:pfam01207  64 DPALLAEAAKLVEDrGADGIDINMGCPSKKVTRGGGGAALLRNPDLVAQIVKAVVKAVGIPVTVKIRIGwdDSHENAVEI 143

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595  169 VKRIERTGISAIAVHGRNRDERPQHPVSCEVIRAIAETLSIPVIANGGshdhIQQHVDIEDFRQATAASSVMVARAAMWN 248
Cdd:pfam01207 144 AKIVEDAGAQALTVHGRTRAQNYEGTADWDAIKQVKQAVSIPVIANGD----ITDPEDAQRCLAYTGADGVMIGRGALGN 219

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595  249 PSIF-----LKDGLR----PLEEVMQKyiryavqYDNHYTNTkyclcqmlrEQLESPQGRLLHAAQSSQEICEAFGLGAF 319
Cdd:pfam01207 220 PWLFaeqhtVKTGEFgpspPLAEEAEK-------VLRHLPYL---------EEFLGEDKGLRHARKHLAWYLKGFPGAAE 283


                  ....*
gi 110625595  320 YEETI 324
Cdd:pfam01207 284 LRREL 288
nifR3_yhdG TIGR00737
putative TIM-barrel protein, nifR3 family; This model represents one branch of COG0042 ...
 11-252 1.62e-42

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: 153.67  E-value: 1.62e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595   11 HNKLILAPMVRVGTLPMRLLALDYGADIVYCEelidlkMLQCKRVVNEVLSTvdfvapddRVVFRTCEREQSRVVfQMGT 90
Cdd:TIGR00737   7 KSRVVLAPMAGVTDSPFRRLVAEYGAGLTVCE------MVSSEAIVYDSQRT--------MRLLDIAEDETPISV-QLFG 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595   91 SDAERALAVARLVENDVAG-IDVNMGCPKEYSTKGGMGAALLSDPDKIEKILSTLVKGTHRPVTCKIRILPSlEDTLN-- 167
Cdd:TIGR00737  72 SDPDTMAEAAKINEELGADiIDINMGCPVPKITKKGAGSALLRDPDLIGKIVKAVVDAVDIPVTVKIRIGWD-DAHINav 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595  168 -LVKRIERTGISAIAVHGRNRDERPQHPVSCEVIRAIAETLSIPVIANGgshdhiqqhvDIEDFRQA------TAASSVM 240
Cdd:TIGR00737 151 eAARIAEDAGAQAVTLHGRTRAQGYSGEANWDIIARVKQAVRIPVIGNG----------DIFSPEDAkamletTGCDGVM 220

                         250
                  ....*....|..
gi 110625595  241 VARAAMWNPSIF 252
Cdd:TIGR00737 221 IGRGALGNPWLF 232
DSRM_DUS2L cd19871
double-stranded RNA binding motif of tRNA-dihydrouridine(20) synthase [NAD(P)+]-like (DUS2L) ...
 369-436 1.10e-37

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: 132.40  E-value: 1.10e-37
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 110625595 369 TPKMCLLEWCRREKLPQPVYETVQRTIDRMFCSVVTVAEQKYQSTLWDKSKKLAEQTAAIVCLRSQGL 436
Cdd:cd19871    1 TPKMILNEWCRKNKLPQPVYETVQRPSDRLFQSVVTVDGKKYTSSLWEKSKKLAEQAAAIVCLRALGL 68
PRK10415 PRK10415
tRNA-dihydrouridine synthase B; Provisional
 12-252 1.10e-30

tRNA-dihydrouridine synthase B; Provisional


Pssm-ID: 182440  Cd Length: 321  Bit Score: 121.23  E-value: 1.10e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595  12 NKLILAPMVRVGTLPMRLLALDYGADIVyceelidlkmlqckrvVNEVLSTVDFVAPDDRVVFRTCEREQSRV-VFQMGT 90
Cdd:PRK10415  10 NRLIAAPMAGITDRPFRTLCYEMGAGLT----------------VSEMMSSNPQVWESDKSRLRMVHIDEPGIrTVQIAG 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595  91 SDAERALAVARL-VENDVAGIDVNMGCPKEYSTKGGMGAALLSDPDKIEKILSTLVKGTHRPVTCKIRI--LPSLEDTLN 167
Cdd:PRK10415  74 SDPKEMADAARInVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKSILTEVVNAVDVPVTLKIRTgwAPEHRNCVE 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595 168 LVKRIERTGISAIAVHGRNRDERPQHPVSCEVIRAIAETLSIPVIANGgshdhiqqhvDIEDFRQA------TAASSVMV 241
Cdd:PRK10415 154 IAQLAEDCGIQALTIHGRTRACLFNGEAEYDSIRAVKQKVSIPVIANG----------DITDPLKAravldyTGADALMI 223

                        250
                 ....*....|.
gi 110625595 242 ARAAMWNPSIF 252
Cdd:PRK10415 224 GRAAQGRPWIF 234
DSRM smart00358
Double-stranded RNA binding motif;
370-433 1.37e-08

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 51.49  E-value: 1.37e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 110625595   370 PKMCLLEWCRREKLPqPVYETVQRT---IDRMFCSVVTVAEQKYQSTlWDKSKKLAEQTAAIVCLRS 433
Cdd:smart00358   1 PKSLLQELAQKRKLP-PEYELVKEEgpdHAPRFTVTVKVGGKRTGEG-EGSSKKEAKQRAAEAALRS 65
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 370-432 6.62e-08

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: 49.54  E-value: 6.62e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 110625595  370 PKMCLLEWCRREKlPQPVYETVQRT---IDRMFCSVVTVAEQKYQSTlWDKSKKLAEQTAAIVCLR 432
Cdd:pfam00035   1 PKSLLQEYAQKNG-KPPPYEYVSEEgppHSPKFTVTVKVDGKLYGSG-TGSSKKEAEQLAAEKALE 64
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
370-427 3.02e-05

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 45.09  E-value: 3.02e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 110625595 370 PKMCLLEWCRREKLPQPVYETVQRTI---DRMFCSVVTVAEQKYqSTLWDKSKKLAEQTAA 427
Cdd:COG0571  159 YKTALQEWLQARGLPLPEYEVVEEEGpdhAKTFTVEVLVGGKVL-GEGTGRSKKEAEQAAA 218
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 370-431 1.25e-04

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: 1.25e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 110625595  370 PKMCLLEWCRREKLPQPVYETVQRT---IDRMFCSVVTVAEQKYqSTLWDKSKKLAEQTAAIVCL 431
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 ...
 13-252 1.84e-88

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: 270.52  E-value: 1.84e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595  13 KLILAPMVRVGTLPMRLLALDYGADIVYCEELIDLKMLQCKRVvnevlstvdfvapddRVVFRTCEREQSRVVFQMGTSD 92
Cdd:cd02801    1 KLILAPMVGVTDLPFRLLCRRYGADLVYTEMISAKALLRGNRK---------------RLRLLTRNPEERPLIVQLGGSD 65

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595  93 AERALAVARLVEN-DVAGIDVNMGCPKEYSTKGGMGAALLSDPDKIEKILSTLVKGTHRPVTCKIRILPSLED-TLNLVK 170
Cdd:cd02801   66 PETLAEAAKIVEElGADGIDLNMGCPSPKVTKGGAGAALLKDPELVAEIVRAVREAVPIPVTVKIRLGWDDEEeTLELAK 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595 171 RIERTGISAIAVHGRNRDERPQHPVSCEVIRAIAETLSIPVIANGGshdhIQQHVDIEDFRQATAASSVMVARAAMWNPS 250
Cdd:cd02801  146 ALEDAGASALTVHGRTREQRYSGPADWDYIAEIKEAVSIPVIANGD----IFSLEDALRCLEQTGVDGVMIGRGALGNPW 221


                 ..
gi 110625595 251 IF 252
Cdd:cd02801  222 LF 223
DusA COG0042
tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; ...
 12-284 1.49e-52

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: 179.90  E-value: 1.49e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595  12 NKLILAPMVRVGTLPMRLLALDYGADIVYCEelidlkMLQCKRVVNEVLSTVDFVAPDDrvvfrtcerEQSRVVFQMGTS 91
Cdd:COG0042    7 NPLILAPMAGVTDRPFRRLCRELGAGLLYTE------MVSARALLHGNRKTRRLLDFDP---------EEHPVAVQLFGS 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595  92 DAER-ALAVARLVENDVAGIDVNMGCPKEYSTKGGMGAALLSDPDKIEKILSTLVKGTHRPVTCKIRILPSlEDTLN--- 167
Cdd:COG0042   72 DPEElAEAARIAEELGADEIDINMGCPVKKVTKGGAGAALLRDPELVAEIVKAVVEAVDVPVTVKIRLGWD-DDDENale 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595 168 LVKRIERTGISAIAVHGRNRDERPQHPVSCEVIRAIAETLSIPVIANGGshdhIQQHVDIEDFRQATAASSVMVARAAMW 247
Cdd:COG0042  151 FARIAEDAGAAALTVHGRTREQRYKGPADWDAIARVKEAVSIPVIGNGD----IFSPEDAKRMLEETGCDGVMIGRGALG 226

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*.
gi 110625595 248 NPSIF------LKDGLRP---LEEVMQKYIRYAVQYDNHYTNTKYC 284
Cdd:COG0042  227 NPWLFreidayLAGGEAPppsLEEVLELLLEHLELLLEFYGERRGL 272
Dus pfam01207
Dihydrouridine synthase (Dus); Members of this family catalyze the reduction of the 5,6-double ...
 15-324 6.41e-52

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: 178.29  E-value: 6.41e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595   15 ILAPMVRVGTLPMRLLALDYGA-DIVYCEelidlkmlqckrvvneVLSTVDFVAPDdRVVFRTC--EREQSRVVFQMGTS 91
Cdd:pfam01207   1 LLAPMAGVTDLPFRRLVREYGAgDLVYTE----------------MVTAKAQLRPE-KVRIRMLseLEEPTPLAVQLGGS 63

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595   92 DAERALAVARLVEN-DVAGIDVNMGCPKEYSTKGGMGAALLSDPDKIEKILSTLVKGTHRPVTCKIRIL--PSLEDTLNL 168
Cdd:pfam01207  64 DPALLAEAAKLVEDrGADGIDINMGCPSKKVTRGGGGAALLRNPDLVAQIVKAVVKAVGIPVTVKIRIGwdDSHENAVEI 143

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595  169 VKRIERTGISAIAVHGRNRDERPQHPVSCEVIRAIAETLSIPVIANGGshdhIQQHVDIEDFRQATAASSVMVARAAMWN 248
Cdd:pfam01207 144 AKIVEDAGAQALTVHGRTRAQNYEGTADWDAIKQVKQAVSIPVIANGD----ITDPEDAQRCLAYTGADGVMIGRGALGN 219

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595  249 PSIF-----LKDGLR----PLEEVMQKyiryavqYDNHYTNTkyclcqmlrEQLESPQGRLLHAAQSSQEICEAFGLGAF 319
Cdd:pfam01207 220 PWLFaeqhtVKTGEFgpspPLAEEAEK-------VLRHLPYL---------EEFLGEDKGLRHARKHLAWYLKGFPGAAE 283


                  ....*
gi 110625595  320 YEETI 324
Cdd:pfam01207 284 LRREL 288
nifR3_yhdG TIGR00737
putative TIM-barrel protein, nifR3 family; This model represents one branch of COG0042 ...
 11-252 1.62e-42

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: 153.67  E-value: 1.62e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595   11 HNKLILAPMVRVGTLPMRLLALDYGADIVYCEelidlkMLQCKRVVNEVLSTvdfvapddRVVFRTCEREQSRVVfQMGT 90
Cdd:TIGR00737   7 KSRVVLAPMAGVTDSPFRRLVAEYGAGLTVCE------MVSSEAIVYDSQRT--------MRLLDIAEDETPISV-QLFG 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595   91 SDAERALAVARLVENDVAG-IDVNMGCPKEYSTKGGMGAALLSDPDKIEKILSTLVKGTHRPVTCKIRILPSlEDTLN-- 167
Cdd:TIGR00737  72 SDPDTMAEAAKINEELGADiIDINMGCPVPKITKKGAGSALLRDPDLIGKIVKAVVDAVDIPVTVKIRIGWD-DAHINav 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595  168 -LVKRIERTGISAIAVHGRNRDERPQHPVSCEVIRAIAETLSIPVIANGgshdhiqqhvDIEDFRQA------TAASSVM 240
Cdd:TIGR00737 151 eAARIAEDAGAQAVTLHGRTRAQGYSGEANWDIIARVKQAVRIPVIGNG----------DIFSPEDAkamletTGCDGVM 220

                         250
                  ....*....|..
gi 110625595  241 VARAAMWNPSIF 252
Cdd:TIGR00737 221 IGRGALGNPWLF 232
DSRM_DUS2L cd19871
double-stranded RNA binding motif of tRNA-dihydrouridine(20) synthase [NAD(P)+]-like (DUS2L) ...
 369-436 1.10e-37

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: 132.40  E-value: 1.10e-37
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 110625595 369 TPKMCLLEWCRREKLPQPVYETVQRTIDRMFCSVVTVAEQKYQSTLWDKSKKLAEQTAAIVCLRSQGL 436
Cdd:cd19871    1 TPKMILNEWCRKNKLPQPVYETVQRPSDRLFQSVVTVDGKKYTSSLWEKSKKLAEQAAAIVCLRALGL 68
PRK10415 PRK10415
tRNA-dihydrouridine synthase B; Provisional
 12-252 1.10e-30

tRNA-dihydrouridine synthase B; Provisional


Pssm-ID: 182440  Cd Length: 321  Bit Score: 121.23  E-value: 1.10e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595  12 NKLILAPMVRVGTLPMRLLALDYGADIVyceelidlkmlqckrvVNEVLSTVDFVAPDDRVVFRTCEREQSRV-VFQMGT 90
Cdd:PRK10415  10 NRLIAAPMAGITDRPFRTLCYEMGAGLT----------------VSEMMSSNPQVWESDKSRLRMVHIDEPGIrTVQIAG 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595  91 SDAERALAVARL-VENDVAGIDVNMGCPKEYSTKGGMGAALLSDPDKIEKILSTLVKGTHRPVTCKIRI--LPSLEDTLN 167
Cdd:PRK10415  74 SDPKEMADAARInVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKSILTEVVNAVDVPVTLKIRTgwAPEHRNCVE 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595 168 LVKRIERTGISAIAVHGRNRDERPQHPVSCEVIRAIAETLSIPVIANGgshdhiqqhvDIEDFRQA------TAASSVMV 241
Cdd:PRK10415 154 IAQLAEDCGIQALTIHGRTRACLFNGEAEYDSIRAVKQKVSIPVIANG----------DITDPLKAravldyTGADALMI 223

                        250
                 ....*....|.
gi 110625595 242 ARAAMWNPSIF 252
Cdd:PRK10415 224 GRAAQGRPWIF 234
PRK10550 PRK10550
tRNA dihydrouridine(16) synthase DusC;
13-275 2.91e-17

tRNA dihydrouridine(16) synthase DusC;


Pssm-ID: 236713  Cd Length: 312  Bit Score: 82.55  E-value: 2.91e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595  13 KLILAPMVRV-GTLPMRLLAL--DYgadivyceeliDLKMLQCKRVVNEVLSTVDF--VAPDDRVVFRTCEREQSRVVF- 86
Cdd:PRK10550   2 RVLLAPMEGVlDSLVRELLTEvnDY-----------DLCITEFLRVVDQLLPVKVFhrLCPELHNASRTPSGTLVRIQLl 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595  87 -QMGTSDAERAlavARLVENDVAGIDVNMGCPKEYSTKGGMGAALLSDPDKI---EKILSTLVKgTHRPVTCKIRI-LPS 161
Cdd:PRK10550  71 gQYPQWLAENA---ARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIyqgAKAMREAVP-AHLPVTVKVRLgWDS 146

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595 162 LEDTLNLVKRIERTGISAIAVHGRNRDE--RPQHpVSCEVIRAIAETLSIPVIANGgshdHIQQHVDIEDFRQATAASSV 239
Cdd:PRK10550 147 GERKFEIADAVQQAGATELVVHGRTKEDgyRAEH-INWQAIGEIRQRLTIPVIANG----EIWDWQSAQQCMAITGCDAV 221

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|...
gi 110625595 240 MVARAAMWNPS----IFLKDGLRPLEEVM---QKYIRYAVQYD 275
Cdd:PRK10550 222 MIGRGALNIPNlsrvVKYNEPRMPWPEVVallQKYTRLEKQGD 264
PRK11815 PRK11815
tRNA dihydrouridine(20/20a) synthase DusA;
84-274 7.78e-13

tRNA dihydrouridine(20/20a) synthase DusA;


Pssm-ID: 236991 [Multi-domain]  Cd Length: 333  Bit Score: 69.39  E-value: 7.78e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595  84 VVFQMGTSD-AERALAvARLVENdvAG---IDVNMGCPKEYSTKGGMGAALLSDPDKIEKILSTLVKGTHRPVTCKIRI- 158
Cdd:PRK11815  67 VALQLGGSDpADLAEA-AKLAED--WGydeINLNVGCPSDRVQNGRFGACLMAEPELVADCVKAMKDAVSIPVTVKHRIg 143

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595 159 ---LPSLEDTLNLVKRIERTGISAIAVHGR-----------NRDERP-QHPVsceVIRAIAETLSIPVIANGG--SHDHI 221
Cdd:PRK11815 144 iddQDSYEFLCDFVDTVAEAGCDTFIVHARkawlkglspkeNREIPPlDYDR---VYRLKRDFPHLTIEINGGikTLEEA 220

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 110625595 222 QQH---VDiedfrqataasSVMVARAAMWNPSIFLK-------DGLRPL--EEVMQKYIRYAVQY 274
Cdd:PRK11815 221 KEHlqhVD-----------GVMIGRAAYHNPYLLAEvdrelfgEPAPPLsrSEVLEAMLPYIERH 274
DHOD_DHPD_FMN cd02810
Dihydroorotate dehydrogenase (DHOD) and Dihydropyrimidine dehydrogenase (DHPD) FMN-binding ...
 84-254 7.27e-11

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: 63.14  E-value: 7.27e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595  84 VVFQMGTSDAERALAVARLVENDVAGID-VNMGCPKEystkgGMGAALLSDPDKIEKILSTLVKGTHRPVTCKIRILPSL 162
Cdd:cd02810  101 LIASVGGSSKEDYVELARKIERAGAKALeLNLSCPNV-----GGGRQLGQDPEAVANLLKAVKAAVDIPLLVKLSPYFDL 175

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595 163 EDTLNLVKRIERTGISAIAVHGR------NRDERPQ--------------HPVSCEVIRAIAETLS--IPVIANGGSHDh 220
Cdd:cd02810  176 EDIVELAKAAERAGADGLTAINTisgrvvDLKTVGPgpkrgtgglsgapiRPLALRWVARLAARLQldIPIIGVGGIDS- 254

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 110625595 221 iQQHVDieDFRQAtAASSVMVARAAMWN-PSIFLK 254
Cdd:cd02810  255 -GEDVL--EMLMA-GASAVQVATALMWDgPDVIRK 285
DSRM_SF cd00048
double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ...
 376-431 1.80e-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: 1.80e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 110625595 376 EWCRREKLPQPVYETVQRTID--RMFCSVVTVAEQKYQSTlwDKSKKLAEQTAAIVCL 431
Cdd:cd00048    2 ELCQKNKWPPPEYETVEEGGPhnPRFTCTVTVNGQTFEGE--GKSKKEAKQAAAEKAL 57
DSRM_RNAse_III_family cd10845
double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase ...
 370-432 3.82e-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: 52.88  E-value: 3.82e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 110625595 370 PKMCLLEWCRREKLPQPVYETVQRTI---DRMFCSVVTVAEQKYqSTLWDKSKKLAEQTAAIVCLR 432
Cdd:cd10845    3 YKTALQEYLQKRGLPLPEYELVEEEGpdhNKTFTVEVKVNGKVI-GEGTGRSKKEAEQAAAKAALE 67
DSRM_SON-like cd19870
double-stranded RNA binding motif of protein SON and similar proteins; Protein SON (also known ...
 370-436 5.04e-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: 52.67  E-value: 5.04e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595 370 PKMCLLEWCRREKLPQPVYETVQRT---IDRMFCSVVTVAEQKYQSTLWDKSKKLAEQTAAIVCLRSQGL 436
Cdd:cd19870    4 PVSALMELCNKRKWGPPEFRLVEESgppHRKHFLFKVVVNGVEYQPSVASGNKKDAKAQAATVALQALGL 73
DSRM smart00358
Double-stranded RNA binding motif;
370-433 1.37e-08

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 51.49  E-value: 1.37e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 110625595   370 PKMCLLEWCRREKLPqPVYETVQRT---IDRMFCSVVTVAEQKYQSTlWDKSKKLAEQTAAIVCLRS 433
Cdd:smart00358   1 PKSLLQELAQKRKLP-PEYELVKEEgpdHAPRFTVTVKVGGKRTGEG-EGSSKKEAKQRAAEAALRS 65
DSRM_AtDRB-like cd19878
double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding proteins ...
 371-435 4.31e-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: 4.31e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 110625595 371 KMCLLEWCRREKLPQPVYETVQRTIDR--MFCSVVTVAEQKYQSTLWdKSKKLAEQTAAIVCLRSQG 435
Cdd:cd19878    2 KNLLQEYAQKKKIPLPKYESAKSGPSHqpTFVSTVIVLGVRFSSEGA-KNKKQAEQSAAKVALKELG 67
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 370-432 6.62e-08

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: 49.54  E-value: 6.62e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 110625595  370 PKMCLLEWCRREKlPQPVYETVQRT---IDRMFCSVVTVAEQKYQSTlWDKSKKLAEQTAAIVCLR 432
Cdd:pfam00035   1 PKSLLQEYAQKNG-KPPPYEYVSEEgppHSPKFTVTVKVDGKLYGSG-TGSSKKEAEQLAAEKALE 64
DHOD_1B_like cd04740
Dihydroorotate dehydrogenase (DHOD) class 1B FMN-binding domain. DHOD catalyzes the oxidation ...
 89-267 6.83e-08

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: 54.09  E-value: 6.83e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595  89 GTSDAERALAVARLVENDVAGIDVNMGCPkeySTKGGmGAALLSDPDKIEKILSTLVKGTHRPVTCKIRilPSLEDTLNL 168
Cdd:cd04740   98 GSTVEEFVEVAEKLADAGADAIELNISCP---NVKGG-GMAFGTDPEAVAEIVKAVKKATDVPVIVKLT--PNVTDIVEI 171

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595 169 VKRIERTG---ISAI------AVHGRNRdeRPQ-------------HPVSCEVIRAIAETLSIPVIANGGshdhiqqhvd 226
Cdd:cd04740  172 ARAAEEAGadgLTLIntlkgmAIDIETR--KPIlgnvtgglsgpaiKPIALRMVYQVYKAVEIPIIGVGG---------- 239

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 110625595 227 IEDFRQA-----TAASSVMVARAAMWNPSIFLK--DGlrpLEEVMQKY 267
Cdd:cd04740  240 IASGEDAleflmAGASAVQVGTANFVDPEAFKEiiEG---LEAYLDEE 284
DHPD_FMN cd02940
Dihydropyrimidine dehydrogenase (DHPD) FMN-binding domain. DHPD catalyzes the first step in ...
 88-246 5.50e-06

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: 48.05  E-value: 5.50e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595  88 MGTSDAERALAVARLVENDVA-GIDVNMGCPKEYSTKGgMGAALLSDPDKIEKILSTLVKGTHRPVTCKIRilPSLEDTL 166
Cdd:cd02940  107 MCEYNKEDWTELAKLVEEAGAdALELNFSCPHGMPERG-MGAAVGQDPELVEEICRWVREAVKIPVIAKLT--PNITDIR 183

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595 167 NLVKRIER---TGISAI----AVHGRNRDERPQHP----------VSCEVIRAIA----------ETLSIPVIANGGshd 219
Cdd:cd02940  184 EIARAAKEggaDGVSAIntvnSLMGVDLDGTPPAPgvegkttyggYSGPAVKPIAlravsqiaraPEPGLPISGIGG--- 260

                        170       180       190
                 ....*....|....*....|....*....|..
gi 110625595 220 hiqqhvdIEDFRQA-----TAASSVMVARAAM 246
Cdd:cd02940  261 -------IESWEDAaefllLGASVVQVCTAVM 285
PRK07259 PRK07259
dihydroorotate dehydrogenase;
89-267 2.84e-05

dihydroorotate dehydrogenase;


Pssm-ID: 235982  Cd Length: 301  Bit Score: 45.91  E-value: 2.84e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595  89 GTSDAERALAVARLVEND-VAGIDVNMGCPkeySTKGGmGAALLSDPDKIEKILSTLVKGTHRPVTCKIRilPSLEDTLN 167
Cdd:PRK07259 100 GSTEEEYAEVAEKLSKAPnVDAIELNISCP---NVKHG-GMAFGTDPELAYEVVKAVKEVVKVPVIVKLT--PNVTDIVE 173

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595 168 LVKRIER---TGISAI------AVHGRNRdeRPQ-------------HPVSCEVIRAIAETLSIPVIANGGshdhiqqhv 225
Cdd:PRK07259 174 IAKAAEEagaDGLSLIntlkgmAIDIKTR--KPIlanvtgglsgpaiKPIALRMVYQVYQAVDIPIIGMGG--------- 242

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 110625595 226 dIEDFRQA-----TAASSVMVARAAMWNPSIFLK--DGlrpLEEVMQKY 267
Cdd:PRK07259 243 -ISSAEDAiefimAGASAVQVGTANFYDPYAFPKiiEG---LEAYLDKY 287
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
370-427 3.02e-05

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 45.09  E-value: 3.02e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 110625595 370 PKMCLLEWCRREKLPQPVYETVQRTI---DRMFCSVVTVAEQKYqSTLWDKSKKLAEQTAA 427
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 ...
 161-249 9.46e-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: 9.46e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595 161 SLEDTLNLVKRIERTGISAIAVHGRNRDERPQHPVSCEVIRA--------IAETLSIPVIANGGshdhiqqHVDIEDFRQ 232
Cdd:cd02803  226 TLEEAIEIAKALEEAGVDALHVSGGSYESPPPIIPPPYVPEGyflelaekIKKAVKIPVIAVGG-------IRDPEVAEE 298

                         90       100
                 ....*....|....*....|
gi 110625595 233 ATA---ASSVMVARAAMWNP 249
Cdd:cd02803  299 ILAegkADLVALGRALLADP 318
DSRM_DGCR8_rpt1 cd19867
first double-stranded RNA binding motif of DiGeorge syndrome critical region 8 (DGCR8) and ...
 369-427 9.48e-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: 9.48e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595 369 TPKMCLLEWCRREKLPQPVYETVQRTIDRM-FCSVVTVAEQKYQSTLwDKSKKLAEQTAA 427
Cdd:cd19867    7 SPVCILHEYCQRVLKVQPEYNFTETENAATpFSAEVFINGVEYGSGE-ASSKKLAKQKAA 65
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 370-431 1.25e-04

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: 1.25e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 110625595  370 PKMCLLEWCRREKLPQPVYETVQRT---IDRMFCSVVTVAEQKYqSTLWDKSKKLAEQTAAIVCL 431
Cdd:TIGR02191 154 YKTALQEWAQARGKPLPEYRLIKEEgpdHDKEFTVEVSVNGEPY-GEGKGKSKKEAEQNAAKAAL 217
DSRM_AtDRB-like_rpt1 cd19907
first double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding ...
 374-433 1.46e-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: 40.15  E-value: 1.46e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 110625595 374 LLEWCRREKLPQPVYETVQRTIDR--MFCSVVTVAEQKYQSTLWDKSKKLAEQTAAIVCLRS 433
Cdd:cd19907    6 LQEYAQKSCLNLPVYACIREGPDHapRFRATVTFNGVIFESPPGFPTLKAAEHSAAEVALNS 67
PRK08318 PRK08318
NAD-dependent dihydropyrimidine dehydrogenase subunit PreA;
84-155 1.78e-04

NAD-dependent dihydropyrimidine dehydrogenase subunit PreA;


Pssm-ID: 236237 [Multi-domain]  Cd Length: 420  Bit Score: 43.78  E-value: 1.78e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 110625595  84 VVFQMGTSDAERALAVARLVENDVA-GIDVNMGCPKEYSTKGgMGAALLSDPDKIEKILSTLVKGTHRPVTCK 155
Cdd:PRK08318 103 IASIMVECNEEEWKEIAPLVEETGAdGIELNFGCPHGMSERG-MGSAVGQVPELVEMYTRWVKRGSRLPVIVK 174
arch_FMN cd02911
Archeal FMN-binding domain. This family of archaeal proteins are part of the NAD(P)H-dependent ...
 91-245 3.86e-04

Archeal FMN-binding domain. This family of archaeal proteins are part of the NAD(P)H-dependent flavin oxidoreductase (oxidored) FMN-binding family that reduce a range of alternative electron acceptors. Most use FAD/FMN as a cofactor and NAD(P)H as electron donor. Some contain 4Fe-4S cluster to transfer electron from FAD to FMN. The specific function of this group is unknown.


Pssm-ID: 239237 [Multi-domain]  Cd Length: 233  Bit Score: 41.93  E-value: 3.86e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595  91 SDAERALAVARLVENDVAGIDVNMGCPKEYSTKGGMGAALLSDPDKIEKILSTLvKGTHRPVTCKIR--ILPsleDTLNL 168
Cdd:cd02911   82 SSLEPLLNAAALVAKNAAILEINAHCRQPEMVEAGAGEALLKDPERLSEFIKAL-KETGVPVSVKIRagVDV---DDEEL 157

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 110625595 169 VKRIERTGISAIAVHGRNrderPQHPVSCEVIRAIAETLSIpvIANGGShdhiqqhVDIEDFRQATA--ASSVMVARAA 245
Cdd:cd02911  158 ARLIEKAGADIIHVDAMD----PGNHADLKKIRDISTELFI--IGNNSV-------TTIESAKEMFSygADMVSVARAS 223
FadH COG1902
2,4-dienoyl-CoA reductase or related NADH-dependent reductase, Old Yellow Enzyme (OYE) family ...
 161-249 7.05e-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: 41.69  E-value: 7.05e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110625595 161 SLEDTLNLVKRIERTGISAIAVHGRNRDERPQHPVSC------EVIRAIAETLSIPVIANGGshdhiqqhvdIEDFRQAT 234
Cdd:COG1902  234 TLEESVELAKALEEAGVDYLHVSSGGYEPDAMIPTIVpegyqlPFAARIRKAVGIPVIAVGG----------ITTPEQAE 303

                         90       100
                 ....*....|....*....|.
gi 110625595 235 A------ASSVMVARAAMWNP 249
Cdd:COG1902  304 AalasgdADLVALGRPLLADP 324
 
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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