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Conserved domains on  [gi|419635745|ref|NP_001258691|]
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tRNA-dihydrouridine(20) synthase [NAD(P)+]-like isoform 1 [Homo sapiens]

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 3.89e-91

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: 277.07  E-value: 3.89e-91
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635745  13 KLILAPMVRVGTLPMRLLALDYGADIVYCEELIDLKMIQCKRVvnevlstvdfvapddRVVFRTCEREQNRVVFQMGTSD 92
Cdd:cd02801    1 KLILAPMVGVTDLPFRLLCRRYGADLVYTEMISAKALLRGNRK---------------RLRLLTRNPEERPLIVQLGGSD 65

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635745  93 AERALAVARLVEN-DVAGIDVNMGCPKQYSTKGGMGAALLSDPDKIEKILSTLVKGTRRPVTCKIRILPSLED-TLSLVK 170
Cdd:cd02801   66 PETLAEAAKIVEElGADGIDLNMGCPSPKVTKGGAGAALLKDPELVAEIVRAVREAVPIPVTVKIRLGWDDEEeTLELAK 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635745 171 RIERTGIAAIAVHGRKREERPQHPVSCEVIKAIADTLSIPVIANGGshdhIQQYSDIEDFRQATAASSVMVARAAMWNPS 250
Cdd:cd02801  146 ALEDAGASALTVHGRTREQRYSGPADWDYIAEIKEAVSIPVIANGD----IFSLEDALRCLEQTGVDGVMIGRGALGNPW 221


                 ..
gi 419635745 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 7.01e-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: 132.78  E-value: 7.01e-38
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 419635745 369 TPKMCLLEWCRREKLAQPVYETVQRPLDRLFSSIVTVAEQKYQSTLWDKSKKLAEQAAAIVCLRSQGL 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 3.89e-91

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: 277.07  E-value: 3.89e-91
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635745  13 KLILAPMVRVGTLPMRLLALDYGADIVYCEELIDLKMIQCKRVvnevlstvdfvapddRVVFRTCEREQNRVVFQMGTSD 92
Cdd:cd02801    1 KLILAPMVGVTDLPFRLLCRRYGADLVYTEMISAKALLRGNRK---------------RLRLLTRNPEERPLIVQLGGSD 65

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635745  93 AERALAVARLVEN-DVAGIDVNMGCPKQYSTKGGMGAALLSDPDKIEKILSTLVKGTRRPVTCKIRILPSLED-TLSLVK 170
Cdd:cd02801   66 PETLAEAAKIVEElGADGIDLNMGCPSPKVTKGGAGAALLKDPELVAEIVRAVREAVPIPVTVKIRLGWDDEEeTLELAK 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635745 171 RIERTGIAAIAVHGRKREERPQHPVSCEVIKAIADTLSIPVIANGGshdhIQQYSDIEDFRQATAASSVMVARAAMWNPS 250
Cdd:cd02801  146 ALEDAGASALTVHGRTREQRYSGPADWDYIAEIKEAVSIPVIANGD----IFSLEDALRCLEQTGVDGVMIGRGALGNPW 221


                 ..
gi 419635745 251 IF 252
Cdd:cd02801  222 LF 223
DusA COG0042
tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; ...
 12-278 3.06e-54

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: 184.53  E-value: 3.06e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635745  12 NKLILAPMVRVGTLPMRLLALDYGADIVYCEelidlkMIQCKRVVNEVLSTVDFvapddrvvFRTCEREQNRVVfQMGTS 91
Cdd:COG0042    7 NPLILAPMAGVTDRPFRRLCRELGAGLLYTE------MVSARALLHGNRKTRRL--------LDFDPEEHPVAV-QLFGS 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635745  92 DAER-ALAVARLVENDVAGIDVNMGCPkqyS---TKGGMGAALLSDPDKIEKILSTLVKGTRRPVTCKIRIL--PSLEDT 165
Cdd:COG0042   72 DPEElAEAARIAEELGADEIDINMGCP---VkkvTKGGAGAALLRDPELVAEIVKAVVEAVDVPVTVKIRLGwdDDDENA 148

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635745 166 LSLVKRIERTGIAAIAVHGRKREERPQHPVSCEVIKAIADTLSIPVIANGGshdhIQQYSDIEDFRQATAASSVMVARAA 245
Cdd:COG0042  149 LEFARIAEDAGAAALTVHGRTREQRYKGPADWDAIARVKEAVSIPVIGNGD----IFSPEDAKRMLEETGCDGVMIGRGA 224

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|..
gi 419635745 246 MWNPSIF------LKEGLRP---LEEVMQKYIRYAVQYDNHY 278
Cdd:COG0042  225 LGNPWLFreidayLAGGEAPppsLEEVLELLLEHLELLLEFY 266
Dus pfam01207
Dihydrouridine synthase (Dus); Members of this family catalyze the reduction of the 5,6-double ...
 15-283 3.29e-53

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: 181.76  E-value: 3.29e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635745   15 ILAPMVRVGTLPMRLLALDYGA-DIVYCEelidlkmiqckrvvneVLSTVDFVAPDdRVVFRTC--EREQNRVVFQMGTS 91
Cdd:pfam01207   1 LLAPMAGVTDLPFRRLVREYGAgDLVYTE----------------MVTAKAQLRPE-KVRIRMLseLEEPTPLAVQLGGS 63

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635745   92 DAERALAVARLVEN-DVAGIDVNMGCPKQYSTKGGMGAALLSDPDKIEKILSTLVKGTRRPVTCKIRIL--PSLEDTLSL 168
Cdd:pfam01207  64 DPALLAEAAKLVEDrGADGIDINMGCPSKKVTRGGGGAALLRNPDLVAQIVKAVVKAVGIPVTVKIRIGwdDSHENAVEI 143

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635745  169 VKRIERTGIAAIAVHGRKREERPQHPVSCEVIKAIADTLSIPVIANGGshdhIQQYSDIEDFRQATAASSVMVARAAMWN 248
Cdd:pfam01207 144 AKIVEDAGAQALTVHGRTRAQNYEGTADWDAIKQVKQAVSIPVIANGD----ITDPEDAQRCLAYTGADGVMIGRGALGN 219

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....
gi 419635745  249 PSIF-----LKEGLR----PLEEVMQKyiryavqYDNHYTNTKY 283
Cdd:pfam01207 220 PWLFaeqhtVKTGEFgpspPLAEEAEK-------VLRHLPYLEE 256
nifR3_yhdG TIGR00737
putative TIM-barrel protein, nifR3 family; This model represents one branch of COG0042 ...
 11-329 2.16e-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: 153.29  E-value: 2.16e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635745   11 HNKLILAPMVRVGTLPMRLLALDYGADIVYCEelidlkMIQCKRVVNEVLSTvdfvapddRVVFRTCEREQNRVVfQMGT 90
Cdd:TIGR00737   7 KSRVVLAPMAGVTDSPFRRLVAEYGAGLTVCE------MVSSEAIVYDSQRT--------MRLLDIAEDETPISV-QLFG 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635745   91 SDAERALAVARLVENDVAG-IDVNMGCPKQYSTKGGMGAALLSDPDKIEKILSTLVKGTRRPVTCKIRI--LPSLEDTLS 167
Cdd:TIGR00737  72 SDPDTMAEAAKINEELGADiIDINMGCPVPKITKKGAGSALLRDPDLIGKIVKAVVDAVDIPVTVKIRIgwDDAHINAVE 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635745  168 LVKRIERTGIAAIAVHGRKREERPQHPVSCEVIKAIADTLSIPVIANGgshdhiqqysDIEDFRQA------TAASSVMV 241
Cdd:TIGR00737 152 AARIAEDAGAQAVTLHGRTRAQGYSGEANWDIIARVKQAVRIPVIGNG----------DIFSPEDAkamletTGCDGVMI 221

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635745  242 ARAAMWNPSIF------LKEGLR----PLEEVMQKYIRYAVQYDNHYTNTKycLCQMLREQLespqGRLLHAAQSSREIC 311
Cdd:TIGR00737 222 GRGALGNPWLFrqieqyLTTGKYkpppTFAEKLDAILRHLQLLADYYGESK--GLRIARKHI----AWYLKGFPGNAALR 295

                         330
                  ....*....|....*...
gi 419635745  312 EAFGLGAFYEETTQELDA 329
Cdd:TIGR00737 296 QTLNHASSFQEVKQLLDD 313
DSRM_DUS2L cd19871
double-stranded RNA binding motif of tRNA-dihydrouridine(20) synthase [NAD(P)+]-like (DUS2L) ...
 369-436 7.01e-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: 132.78  E-value: 7.01e-38
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 419635745 369 TPKMCLLEWCRREKLAQPVYETVQRPLDRLFSSIVTVAEQKYQSTLWDKSKKLAEQAAAIVCLRSQGL 436
Cdd:cd19871    1 TPKMILNEWCRKNKLPQPVYETVQRPSDRLFQSVVTVDGKKYTSSLWEKSKKLAEQAAAIVCLRALGL 68
PRK10415 PRK10415
tRNA-dihydrouridine synthase B; Provisional
 12-252 1.84e-29

tRNA-dihydrouridine synthase B; Provisional


Pssm-ID: 182440  Cd Length: 321  Bit Score: 117.76  E-value: 1.84e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635745  12 NKLILAPMVRVGTLPMRLLALDYGADIVyceelidlkmiqckrvVNEVLSTVDFVAPDDRVVFRTCEREQNRV-VFQMGT 90
Cdd:PRK10415  10 NRLIAAPMAGITDRPFRTLCYEMGAGLT----------------VSEMMSSNPQVWESDKSRLRMVHIDEPGIrTVQIAG 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635745  91 SDAERALAVARL-VENDVAGIDVNMGCPKQYSTKGGMGAALLSDPDKIEKILSTLVKGTRRPVTCKIRI--LPSLEDTLS 167
Cdd:PRK10415  74 SDPKEMADAARInVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKSILTEVVNAVDVPVTLKIRTgwAPEHRNCVE 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635745 168 LVKRIERTGIAAIAVHGRKREERPQHPVSCEVIKAIADTLSIPVIANGgshdhiqqysDIEDFRQA------TAASSVMV 241
Cdd:PRK10415 154 IAQLAEDCGIQALTIHGRTRACLFNGEAEYDSIRAVKQKVSIPVIANG----------DITDPLKAravldyTGADALMI 223

                        250
                 ....*....|.
gi 419635745 242 ARAAMWNPSIF 252
Cdd:PRK10415 224 GRAAQGRPWIF 234
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 370-432 3.50e-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: 50.31  E-value: 3.50e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 419635745  370 PKMCLLEWCRREKLaQPVYETVQR---PLDRLFSSIVTVAEQKYQSTlWDKSKKLAEQAAAIVCLR 432
Cdd:pfam00035   1 PKSLLQEYAQKNGK-PPPYEYVSEegpPHSPKFTVTVKVDGKLYGSG-TGSSKKEAEQLAAEKALE 64
DSRM smart00358
Double-stranded RNA binding motif;
370-433 8.56e-08

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 49.18  E-value: 8.56e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 419635745   370 PKMCLLEWCRREKLaQPVYETVQR---PLDRLFSSIVTVAEQKYQSTlWDKSKKLAEQAAAIVCLRS 433
Cdd:smart00358   1 PKSLLQELAQKRKL-PPEYELVKEegpDHAPRFTVTVKVGGKRTGEG-EGSSKKEAKQRAAEAALRS 65
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
370-427 6.22e-05

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 44.32  E-value: 6.22e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 419635745 370 PKMCLLEWCRREKLAQPVYETVQR---PLDRLFSSIVTVAEQKYqSTLWDKSKKLAEQAAA 427
Cdd:COG0571  159 YKTALQEWLQARGLPLPEYEVVEEegpDHAKTFTVEVLVGGKVL-GEGTGRSKKEAEQAAA 218
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 370-431 1.22e-03

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: 40.26  E-value: 1.22e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 419635745  370 PKMCLLEWCRREKLAQPVYETVQRPL---DRLFSSIVTVAEQKYqSTLWDKSKKLAEQAAAIVCL 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 3.89e-91

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: 277.07  E-value: 3.89e-91
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635745  13 KLILAPMVRVGTLPMRLLALDYGADIVYCEELIDLKMIQCKRVvnevlstvdfvapddRVVFRTCEREQNRVVFQMGTSD 92
Cdd:cd02801    1 KLILAPMVGVTDLPFRLLCRRYGADLVYTEMISAKALLRGNRK---------------RLRLLTRNPEERPLIVQLGGSD 65

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635745  93 AERALAVARLVEN-DVAGIDVNMGCPKQYSTKGGMGAALLSDPDKIEKILSTLVKGTRRPVTCKIRILPSLED-TLSLVK 170
Cdd:cd02801   66 PETLAEAAKIVEElGADGIDLNMGCPSPKVTKGGAGAALLKDPELVAEIVRAVREAVPIPVTVKIRLGWDDEEeTLELAK 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635745 171 RIERTGIAAIAVHGRKREERPQHPVSCEVIKAIADTLSIPVIANGGshdhIQQYSDIEDFRQATAASSVMVARAAMWNPS 250
Cdd:cd02801  146 ALEDAGASALTVHGRTREQRYSGPADWDYIAEIKEAVSIPVIANGD----IFSLEDALRCLEQTGVDGVMIGRGALGNPW 221


                 ..
gi 419635745 251 IF 252
Cdd:cd02801  222 LF 223
DusA COG0042
tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; ...
 12-278 3.06e-54

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: 184.53  E-value: 3.06e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635745  12 NKLILAPMVRVGTLPMRLLALDYGADIVYCEelidlkMIQCKRVVNEVLSTVDFvapddrvvFRTCEREQNRVVfQMGTS 91
Cdd:COG0042    7 NPLILAPMAGVTDRPFRRLCRELGAGLLYTE------MVSARALLHGNRKTRRL--------LDFDPEEHPVAV-QLFGS 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635745  92 DAER-ALAVARLVENDVAGIDVNMGCPkqyS---TKGGMGAALLSDPDKIEKILSTLVKGTRRPVTCKIRIL--PSLEDT 165
Cdd:COG0042   72 DPEElAEAARIAEELGADEIDINMGCP---VkkvTKGGAGAALLRDPELVAEIVKAVVEAVDVPVTVKIRLGwdDDDENA 148

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635745 166 LSLVKRIERTGIAAIAVHGRKREERPQHPVSCEVIKAIADTLSIPVIANGGshdhIQQYSDIEDFRQATAASSVMVARAA 245
Cdd:COG0042  149 LEFARIAEDAGAAALTVHGRTREQRYKGPADWDAIARVKEAVSIPVIGNGD----IFSPEDAKRMLEETGCDGVMIGRGA 224

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|..
gi 419635745 246 MWNPSIF------LKEGLRP---LEEVMQKYIRYAVQYDNHY 278
Cdd:COG0042  225 LGNPWLFreidayLAGGEAPppsLEEVLELLLEHLELLLEFY 266
Dus pfam01207
Dihydrouridine synthase (Dus); Members of this family catalyze the reduction of the 5,6-double ...
 15-283 3.29e-53

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: 181.76  E-value: 3.29e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635745   15 ILAPMVRVGTLPMRLLALDYGA-DIVYCEelidlkmiqckrvvneVLSTVDFVAPDdRVVFRTC--EREQNRVVFQMGTS 91
Cdd:pfam01207   1 LLAPMAGVTDLPFRRLVREYGAgDLVYTE----------------MVTAKAQLRPE-KVRIRMLseLEEPTPLAVQLGGS 63

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635745   92 DAERALAVARLVEN-DVAGIDVNMGCPKQYSTKGGMGAALLSDPDKIEKILSTLVKGTRRPVTCKIRIL--PSLEDTLSL 168
Cdd:pfam01207  64 DPALLAEAAKLVEDrGADGIDINMGCPSKKVTRGGGGAALLRNPDLVAQIVKAVVKAVGIPVTVKIRIGwdDSHENAVEI 143

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635745  169 VKRIERTGIAAIAVHGRKREERPQHPVSCEVIKAIADTLSIPVIANGGshdhIQQYSDIEDFRQATAASSVMVARAAMWN 248
Cdd:pfam01207 144 AKIVEDAGAQALTVHGRTRAQNYEGTADWDAIKQVKQAVSIPVIANGD----ITDPEDAQRCLAYTGADGVMIGRGALGN 219

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....
gi 419635745  249 PSIF-----LKEGLR----PLEEVMQKyiryavqYDNHYTNTKY 283
Cdd:pfam01207 220 PWLFaeqhtVKTGEFgpspPLAEEAEK-------VLRHLPYLEE 256
nifR3_yhdG TIGR00737
putative TIM-barrel protein, nifR3 family; This model represents one branch of COG0042 ...
 11-329 2.16e-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: 153.29  E-value: 2.16e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635745   11 HNKLILAPMVRVGTLPMRLLALDYGADIVYCEelidlkMIQCKRVVNEVLSTvdfvapddRVVFRTCEREQNRVVfQMGT 90
Cdd:TIGR00737   7 KSRVVLAPMAGVTDSPFRRLVAEYGAGLTVCE------MVSSEAIVYDSQRT--------MRLLDIAEDETPISV-QLFG 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635745   91 SDAERALAVARLVENDVAG-IDVNMGCPKQYSTKGGMGAALLSDPDKIEKILSTLVKGTRRPVTCKIRI--LPSLEDTLS 167
Cdd:TIGR00737  72 SDPDTMAEAAKINEELGADiIDINMGCPVPKITKKGAGSALLRDPDLIGKIVKAVVDAVDIPVTVKIRIgwDDAHINAVE 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635745  168 LVKRIERTGIAAIAVHGRKREERPQHPVSCEVIKAIADTLSIPVIANGgshdhiqqysDIEDFRQA------TAASSVMV 241
Cdd:TIGR00737 152 AARIAEDAGAQAVTLHGRTRAQGYSGEANWDIIARVKQAVRIPVIGNG----------DIFSPEDAkamletTGCDGVMI 221

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635745  242 ARAAMWNPSIF------LKEGLR----PLEEVMQKYIRYAVQYDNHYTNTKycLCQMLREQLespqGRLLHAAQSSREIC 311
Cdd:TIGR00737 222 GRGALGNPWLFrqieqyLTTGKYkpppTFAEKLDAILRHLQLLADYYGESK--GLRIARKHI----AWYLKGFPGNAALR 295

                         330
                  ....*....|....*...
gi 419635745  312 EAFGLGAFYEETTQELDA 329
Cdd:TIGR00737 296 QTLNHASSFQEVKQLLDD 313
DSRM_DUS2L cd19871
double-stranded RNA binding motif of tRNA-dihydrouridine(20) synthase [NAD(P)+]-like (DUS2L) ...
 369-436 7.01e-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: 132.78  E-value: 7.01e-38
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 419635745 369 TPKMCLLEWCRREKLAQPVYETVQRPLDRLFSSIVTVAEQKYQSTLWDKSKKLAEQAAAIVCLRSQGL 436
Cdd:cd19871    1 TPKMILNEWCRKNKLPQPVYETVQRPSDRLFQSVVTVDGKKYTSSLWEKSKKLAEQAAAIVCLRALGL 68
PRK10415 PRK10415
tRNA-dihydrouridine synthase B; Provisional
 12-252 1.84e-29

tRNA-dihydrouridine synthase B; Provisional


Pssm-ID: 182440  Cd Length: 321  Bit Score: 117.76  E-value: 1.84e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635745  12 NKLILAPMVRVGTLPMRLLALDYGADIVyceelidlkmiqckrvVNEVLSTVDFVAPDDRVVFRTCEREQNRV-VFQMGT 90
Cdd:PRK10415  10 NRLIAAPMAGITDRPFRTLCYEMGAGLT----------------VSEMMSSNPQVWESDKSRLRMVHIDEPGIrTVQIAG 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635745  91 SDAERALAVARL-VENDVAGIDVNMGCPKQYSTKGGMGAALLSDPDKIEKILSTLVKGTRRPVTCKIRI--LPSLEDTLS 167
Cdd:PRK10415  74 SDPKEMADAARInVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKSILTEVVNAVDVPVTLKIRTgwAPEHRNCVE 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635745 168 LVKRIERTGIAAIAVHGRKREERPQHPVSCEVIKAIADTLSIPVIANGgshdhiqqysDIEDFRQA------TAASSVMV 241
Cdd:PRK10415 154 IAQLAEDCGIQALTIHGRTRACLFNGEAEYDSIRAVKQKVSIPVIANG----------DITDPLKAravldyTGADALMI 223

                        250
                 ....*....|.
gi 419635745 242 ARAAMWNPSIF 252
Cdd:PRK10415 224 GRAAQGRPWIF 234
PRK10550 PRK10550
tRNA dihydrouridine(16) synthase DusC;
13-275 4.42e-17

tRNA dihydrouridine(16) synthase DusC;


Pssm-ID: 236713  Cd Length: 312  Bit Score: 81.78  E-value: 4.42e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635745  13 KLILAPMVRV-GTLPMRLLAL--DYgadivyceeliDLKMIQCKRVVNEVLSTVDF--VAPDDRVVFRTCEREQNRVVF- 86
Cdd:PRK10550   2 RVLLAPMEGVlDSLVRELLTEvnDY-----------DLCITEFLRVVDQLLPVKVFhrLCPELHNASRTPSGTLVRIQLl 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635745  87 -QMGTSDAERAlavARLVENDVAGIDVNMGCPKQYSTKGGMGAALLSDPDKI---EKILSTLVKgTRRPVTCKIRI-LPS 161
Cdd:PRK10550  71 gQYPQWLAENA---ARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIyqgAKAMREAVP-AHLPVTVKVRLgWDS 146

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635745 162 LEDTLSLVKRIERTGIAAIAVHGRKREE--RPQHpVSCEVIKAIADTLSIPVIANGgshdHIQQYSDIEDFRQATAASSV 239
Cdd:PRK10550 147 GERKFEIADAVQQAGATELVVHGRTKEDgyRAEH-INWQAIGEIRQRLTIPVIANG----EIWDWQSAQQCMAITGCDAV 221

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|...
gi 419635745 240 MVARAAMWNPS----IFLKEGLRPLEEVM---QKYIRYAVQYD 275
Cdd:PRK10550 222 MIGRGALNIPNlsrvVKYNEPRMPWPEVVallQKYTRLEKQGD 264
DHOD_DHPD_FMN cd02810
Dihydroorotate dehydrogenase (DHOD) and Dihydropyrimidine dehydrogenase (DHPD) FMN-binding ...
 84-254 3.85e-10

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: 60.83  E-value: 3.85e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635745  84 VVFQMGTSDAERALAVARLVENDVAGID-VNMGCPKqystkGGMGAALLSDPDKIEKILSTLVKGTRRPVTCKIRILPSL 162
Cdd:cd02810  101 LIASVGGSSKEDYVELARKIERAGAKALeLNLSCPN-----VGGGRQLGQDPEAVANLLKAVKAAVDIPLLVKLSPYFDL 175

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635745 163 EDTLSLVKRIERTGIAAI---------------AVHGRKREE-----RPQHPVSCEVIKAIADTLS--IPVIANGGshdh 220
Cdd:cd02810  176 EDIVELAKAAERAGADGLtaintisgrvvdlktVGPGPKRGTgglsgAPIRPLALRWVARLAARLQldIPIIGVGG---- 251

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 419635745 221 IQQYSDIEDFRQAtAASSVMVARAAMWN-PSIFLK 254
Cdd:cd02810  252 IDSGEDVLEMLMA-GASAVQVATALMWDgPDVIRK 285
PRK11815 PRK11815
tRNA dihydrouridine(20/20a) synthase DusA;
84-274 7.25e-10

tRNA dihydrouridine(20/20a) synthase DusA;


Pssm-ID: 236991 [Multi-domain]  Cd Length: 333  Bit Score: 60.53  E-value: 7.25e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635745  84 VVFQMGTSD-AERALAvARLVENdvAG---IDVNMGCPKQYSTKGGMGAALLSDPDKIEKILSTLVKGTRRPVTCKIRI- 158
Cdd:PRK11815  67 VALQLGGSDpADLAEA-AKLAED--WGydeINLNVGCPSDRVQNGRFGACLMAEPELVADCVKAMKDAVSIPVTVKHRIg 143

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635745 159 ---LPSLEDTLSLVKRIERTGIAAIAVHGRK--------REER--P--QHPVsceVIKAIADTLSIPVIANGG--SHDHI 221
Cdd:PRK11815 144 iddQDSYEFLCDFVDTVAEAGCDTFIVHARKawlkglspKENReiPplDYDR---VYRLKRDFPHLTIEINGGikTLEEA 220

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 419635745 222 Q---QYSDiedfrqataasSVMVARAAMWNPSIFLK-------EGLRPL--EEVMQKYIRYAVQY 274
Cdd:PRK11815 221 KehlQHVD-----------GVMIGRAAYHNPYLLAEvdrelfgEPAPPLsrSEVLEAMLPYIERH 274
DSRM_SF cd00048
double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ...
 376-431 1.14e-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: 54.21  E-value: 1.14e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 419635745 376 EWCRREKLAQPVYETVQR--PLDRLFSSIVTVAEQKYQSTlwDKSKKLAEQAAAIVCL 431
Cdd:cd00048    2 ELCQKNKWPPPEYETVEEggPHNPRFTCTVTVNGQTFEGE--GKSKKEAKQAAAEKAL 57
DSRM_AtDRB-like cd19878
double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding proteins ...
 371-435 1.51e-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: 51.36  E-value: 1.51e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 419635745 371 KMCLLEWCRREKLAQPVYETVQRPLDR--LFSSIVTVAEQKYQSTLWdKSKKLAEQAAAIVCLRSQG 435
Cdd:cd19878    2 KNLLQEYAQKKKIPLPKYESAKSGPSHqpTFVSTVIVLGVRFSSEGA-KNKKQAEQSAAKVALKELG 67
DSRM_RNAse_III_family cd10845
double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase ...
 370-432 1.59e-08

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: 51.34  E-value: 1.59e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 419635745 370 PKMCLLEWCRREKLAQPVYETVQR---PLDRLFSSIVTVAEQKYqSTLWDKSKKLAEQAAAIVCLR 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 2.19e-08

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: 51.13  E-value: 2.19e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635745 370 PKMCLLEWCRREKLAQPVYETVQR---PLDRLFSSIVTVAEQKYQSTLWDKSKKLAEQAAAIVCLRSQGL 436
Cdd:cd19870    4 PVSALMELCNKRKWGPPEFRLVEEsgpPHRKHFLFKVVVNGVEYQPSVASGNKKDAKAQAATVALQALGL 73
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 370-432 3.50e-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: 50.31  E-value: 3.50e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 419635745  370 PKMCLLEWCRREKLaQPVYETVQR---PLDRLFSSIVTVAEQKYQSTlWDKSKKLAEQAAAIVCLR 432
Cdd:pfam00035   1 PKSLLQEYAQKNGK-PPPYEYVSEegpPHSPKFTVTVKVDGKLYGSG-TGSSKKEAEQLAAEKALE 64
DHOD_1B_like cd04740
Dihydroorotate dehydrogenase (DHOD) class 1B FMN-binding domain. DHOD catalyzes the oxidation ...
 89-267 3.63e-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: 54.86  E-value: 3.63e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635745  89 GTSDAERALAVARLVENDVAGIDVNMGCPkqySTKGGmGAALLSDPDKIEKILSTLVKGTRRPVTCKIRilPSLEDTLSL 168
Cdd:cd04740   98 GSTVEEFVEVAEKLADAGADAIELNISCP---NVKGG-GMAFGTDPEAVAEIVKAVKKATDVPVIVKLT--PNVTDIVEI 171

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635745 169 VKRIERTG---IAAI------AVHGRKReeRPQ-------------HPVSCEVIKAIADTLSIPVIANGGshdhIQQYSD 226
Cdd:cd04740  172 ARAAEEAGadgLTLIntlkgmAIDIETR--KPIlgnvtgglsgpaiKPIALRMVYQVYKAVEIPIIGVGG----IASGED 245

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 419635745 227 IEDFRQAtAASSVMVARAAMWNPSIFLKEgLRPLEEVMQKY 267
Cdd:cd04740  246 ALEFLMA-GASAVQVGTANFVDPEAFKEI-IEGLEAYLDEE 284
DSRM smart00358
Double-stranded RNA binding motif;
370-433 8.56e-08

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 49.18  E-value: 8.56e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 419635745   370 PKMCLLEWCRREKLaQPVYETVQR---PLDRLFSSIVTVAEQKYQSTlWDKSKKLAEQAAAIVCLRS 433
Cdd:smart00358   1 PKSLLQELAQKRKL-PPEYELVKEegpDHAPRFTVTVKVGGKRTGEG-EGSSKKEAKQRAAEAALRS 65
PRK07259 PRK07259
dihydroorotate dehydrogenase;
89-267 1.02e-05

dihydroorotate dehydrogenase;


Pssm-ID: 235982  Cd Length: 301  Bit Score: 47.45  E-value: 1.02e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635745  89 GTSDAERALAVARLVEND-VAGIDVNMGCPkqySTKGGmGAALLSDPDKIEKILSTLVKGTRRPVTCKIRilPSLEDTLS 167
Cdd:PRK07259 100 GSTEEEYAEVAEKLSKAPnVDAIELNISCP---NVKHG-GMAFGTDPELAYEVVKAVKEVVKVPVIVKLT--PNVTDIVE 173

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635745 168 LVKRIERTGiA------------AIAVHGRKreerpqhPV--------SCEVIKAIA--------DTLSIPVIANGGshd 219
Cdd:PRK07259 174 IAKAAEEAG-AdglslintlkgmAIDIKTRK-------PIlanvtgglSGPAIKPIAlrmvyqvyQAVDIPIIGMGG--- 242

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 419635745 220 hIQQYSDIEDFRQAtAASSVMVARAAMWNPSIFLK--EGlrpLEEVMQKY 267
Cdd:PRK07259 243 -ISSAEDAIEFIMA-GASAVQVGTANFYDPYAFPKiiEG---LEAYLDKY 287
PRK08318 PRK08318
NAD-dependent dihydropyrimidine dehydrogenase subunit PreA;
84-181 1.20e-05

NAD-dependent dihydropyrimidine dehydrogenase subunit PreA;


Pssm-ID: 236237 [Multi-domain]  Cd Length: 420  Bit Score: 47.63  E-value: 1.20e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635745  84 VVFQMGTSDAERALAVARLVENDVA-GIDVNMGCPkQYSTKGGMGAALLSDPDKIEKILSTLVKGTRRPVTCKIRilPSL 162
Cdd:PRK08318 103 IASIMVECNEEEWKEIAPLVEETGAdGIELNFGCP-HGMSERGMGSAVGQVPELVEMYTRWVKRGSRLPVIVKLT--PNI 179

                         90
                 ....*....|....*....
gi 419635745 163 EDtlslvkrIERTGIAAIA 181
Cdd:PRK08318 180 TD-------IREPARAAKR 191
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
370-427 6.22e-05

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 44.32  E-value: 6.22e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 419635745 370 PKMCLLEWCRREKLAQPVYETVQR---PLDRLFSSIVTVAEQKYqSTLWDKSKKLAEQAAA 427
Cdd:COG0571  159 YKTALQEWLQARGLPLPEYEVVEEegpDHAKTFTVEVLVGGKVL-GEGTGRSKKEAEQAAA 218
DHPD_FMN cd02940
Dihydropyrimidine dehydrogenase (DHPD) FMN-binding domain. DHPD catalyzes the first step in ...
 88-180 1.06e-04

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: 44.20  E-value: 1.06e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635745  88 MGTSDAERALAVARLVENDVA-GIDVNMGCPKQYSTKGgMGAALLSDPDKIEKILSTLVKGTRRPVTCKIRilPSLEDTL 166
Cdd:cd02940  107 MCEYNKEDWTELAKLVEEAGAdALELNFSCPHGMPERG-MGAAVGQDPELVEEICRWVREAVKIPVIAKLT--PNITDIR 183

                         90
                 ....*....|....*..
gi 419635745 167 SLVKRIER---TGIAAI 180
Cdd:cd02940  184 EIARAAKEggaDGVSAI 200
DSRM_AtDRB-like_rpt1 cd19907
first double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding ...
 374-433 1.12e-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: 40.54  E-value: 1.12e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 419635745 374 LLEWCRREKLAQPVYETVQRPLDR--LFSSIVTVAEQKYQSTLWDKSKKLAEQAAAIVCLRS 433
Cdd:cd19907    6 LQEYAQKSCLNLPVYACIREGPDHapRFRATVTFNGVIFESPPGFPTLKAAEHSAAEVALNS 67
DSRM_DGCR8_rpt1 cd19867
first double-stranded RNA binding motif of DiGeorge syndrome critical region 8 (DGCR8) and ...
 364-427 1.74e-04

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: 40.01  E-value: 1.74e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 419635745 364 YPAQITPKMCLLEWCRREKLAQPVYETVQRP-LDRLFSSIVTVAEQKYQSTLwDKSKKLAEQAAA 427
Cdd:cd19867    2 NPDGKSPVCILHEYCQRVLKVQPEYNFTETEnAATPFSAEVFINGVEYGSGE-ASSKKLAKQKAA 65
OYE_like_FMN_family cd02803
Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme ...
 161-249 2.96e-04

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: 42.94  E-value: 2.96e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635745 161 SLEDTLSLVKRIERTGIAAIAVHGRKREERPQHPVSCEVI--------KAIADTLSIPVIANGGSHDhiqqYSDIEDFRQ 232
Cdd:cd02803  226 TLEEAIEIAKALEEAGVDALHVSGGSYESPPPIIPPPYVPegyflelaEKIKKAVKIPVIAVGGIRD----PEVAEEILA 301

                         90
                 ....*....|....*..
gi 419635745 233 ATAASSVMVARAAMWNP 249
Cdd:cd02803  302 EGKADLVALGRALLADP 318
FadH COG1902
2,4-dienoyl-CoA reductase or related NADH-dependent reductase, Old Yellow Enzyme (OYE) family ...
 161-249 3.17e-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: 42.85  E-value: 3.17e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635745 161 SLEDTLSLVKRIERTGIAAIAVHGRKREERPQHPVSC------EVIKAIADTLSIPVIANGGshdhIQQYSDIEDFRQAT 234
Cdd:COG1902  234 TLEESVELAKALEEAGVDYLHVSSGGYEPDAMIPTIVpegyqlPFAARIRKAVGIPVIAVGG----ITTPEQAEAALASG 309

                         90
                 ....*....|....*
gi 419635745 235 AASSVMVARAAMWNP 249
Cdd:COG1902  310 DADLVALGRPLLADP 324
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 370-431 1.22e-03

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: 40.26  E-value: 1.22e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 419635745  370 PKMCLLEWCRREKLAQPVYETVQRPL---DRLFSSIVTVAEQKYqSTLWDKSKKLAEQAAAIVCL 431
Cdd:TIGR02191 154 YKTALQEWAQARGKPLPEYRLIKEEGpdhDKEFTVEVSVNGEPY-GEGKGKSKKEAEQNAAKAAL 217
arch_FMN cd02911
Archeal FMN-binding domain. This family of archaeal proteins are part of the NAD(P)H-dependent ...
 91-245 2.11e-03

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: 39.62  E-value: 2.11e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635745  91 SDAERALAVARLVENDVAGIDVNMGCPKQYSTKGGMGAALLSDPDKIEKILSTLvKGTRRPVTCKIR--ILPsleDTLSL 168
Cdd:cd02911   82 SSLEPLLNAAALVAKNAAILEINAHCRQPEMVEAGAGEALLKDPERLSEFIKAL-KETGVPVSVKIRagVDV---DDEEL 157

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 419635745 169 VKRIERTGIAAIAVHGRKreerPQHPVSCEVIKAIADTLSIpvIANGGshdhiqqYSDIEDFRQATA--ASSVMVARAA 245
Cdd:cd02911  158 ARLIEKAGADIIHVDAMD----PGNHADLKKIRDISTELFI--IGNNS-------VTTIESAKEMFSygADMVSVARAS 223
HisF cd04731
The cyclase subunit of imidazoleglycerol phosphate synthase (HisF). Imidazole glycerol ...
 198-252 6.88e-03

The cyclase subunit of imidazoleglycerol phosphate synthase (HisF). Imidazole glycerol phosphate synthase (IGPS) catalyzes the fifth step of histidine biosynthesis, the formation of the imidazole ring. IGPS converts N1-(5'-phosphoribulosyl)-formimino-5-aminoimidazole-4-carboxamide ribonucleotide (PRFAR) to imidazole glycerol phosphate (ImGP) and 5'-(5-aminoimidazole-4-carboxamide) ribonucleotide (AICAR). This conversion involves two tightly coupled reactions in distinct active sites of IGPS. The two catalytic domains can be fused, like in fungi and plants, or peformed by a heterodimer (HisH-glutaminase and HisF-cyclase), like in bacteria.


Pssm-ID: 240082  Cd Length: 243  Bit Score: 38.22  E-value: 6.88e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 419635745 198 EVIKAIADTLSIPVIANGGshdhiqqYSDIEDFRQATAASSVMVARAAmwnpSIF 252
Cdd:cd04731  183 ELIRAVSSAVNIPVIASGG-------AGKPEHFVEAFEEGGADAALAA----SIF 226
 
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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