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Conserved domains on  [gi|419635906|ref|NP_001258692|]
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tRNA-dihydrouridine(20) synthase [NAD(P)+]-like isoform 2 [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 ...
 13-217 1.03e-67

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: 215.82  E-value: 1.03e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635906  13 KLILAPMVRVGTLPMRLLALDYGADIVYCEELIDLKMIQCKRVvnevlstvdfvapddRVVFRTCEREQNRVVFQMGG-- 90
Cdd:cd02801    1 KLILAPMVGVTDLPFRLLCRRYGADLVYTEMISAKALLRGNRK---------------RLRLLTRNPEERPLIVQLGGsd 65

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635906  91 ----------------------------------MGAALLSDPDKIEKILSTLVKGTRRPVTCKIRILPSLED-TLSLVK 135
Cdd:cd02801   66 petlaeaakiveelgadgidlnmgcpspkvtkggAGAALLKDPELVAEIVRAVREAVPIPVTVKIRLGWDDEEeTLELAK 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635906 136 RIERTGIAAIAVHGRKREERPQHPVSCEVIKAIADTLSIPVIANGGshdhIQQYSDIEDFRQATAASSVMVARAAMWNPS 215
Cdd:cd02801  146 ALEDAGASALTVHGRTREQRYSGPADWDYIAEIKEAVSIPVIANGD----IFSLEDALRCLEQTGVDGVMIGRGALGNPW 221


                 ..
gi 419635906 216 IF 217
Cdd:cd02801  222 LF 223
DSRM_DUS2L cd19871
double-stranded RNA binding motif of tRNA-dihydrouridine(20) synthase [NAD(P)+]-like (DUS2L) ...
 334-401 5.40e-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: 132.40  E-value: 5.40e-38
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 419635906 334 TPKMCLLEWCRREKLAQPVYETVQRPLDRLFSSIVTVAEQKYQSTLWDKSKKLAEQAAAIVCLRSQGL 401
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 ...
 13-217 1.03e-67

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: 215.82  E-value: 1.03e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635906  13 KLILAPMVRVGTLPMRLLALDYGADIVYCEELIDLKMIQCKRVvnevlstvdfvapddRVVFRTCEREQNRVVFQMGG-- 90
Cdd:cd02801    1 KLILAPMVGVTDLPFRLLCRRYGADLVYTEMISAKALLRGNRK---------------RLRLLTRNPEERPLIVQLGGsd 65

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635906  91 ----------------------------------MGAALLSDPDKIEKILSTLVKGTRRPVTCKIRILPSLED-TLSLVK 135
Cdd:cd02801   66 petlaeaakiveelgadgidlnmgcpspkvtkggAGAALLKDPELVAEIVRAVREAVPIPVTVKIRLGWDDEEeTLELAK 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635906 136 RIERTGIAAIAVHGRKREERPQHPVSCEVIKAIADTLSIPVIANGGshdhIQQYSDIEDFRQATAASSVMVARAAMWNPS 215
Cdd:cd02801  146 ALEDAGASALTVHGRTREQRYSGPADWDYIAEIKEAVSIPVIANGD----IFSLEDALRCLEQTGVDGVMIGRGALGNPW 221


                 ..
gi 419635906 216 IF 217
Cdd:cd02801  222 LF 223
DusA COG0042
tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; ...
 12-243 2.99e-38

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: 141.00  E-value: 2.99e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635906  12 NKLILAPMVRVGTLPMRLLALDYGADIVYCEelidlkMIQCKRVVNEVLSTVDFvapddrvvFRTCEREQNRVVfQ---- 87
Cdd:COG0042    7 NPLILAPMAGVTDRPFRRLCRELGAGLLYTE------MVSARALLHGNRKTRRL--------LDFDPEEHPVAV-Qlfgs 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635906  88 -----------------------MG---------GMGAALLSDPDKIEKILSTLVKGTRRPVTCKIRIL--PSLEDTLSL 133
Cdd:COG0042   72 dpeelaeaariaeelgadeidinMGcpvkkvtkgGAGAALLRDPELVAEIVKAVVEAVDVPVTVKIRLGwdDDDENALEF 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635906 134 VKRIERTGIAAIAVHGRKREERPQHPVSCEVIKAIADTLSIPVIANGGshdhIQQYSDIEDFRQATAASSVMVARAAMWN 213
Cdd:COG0042  152 ARIAEDAGAAALTVHGRTREQRYKGPADWDAIARVKEAVSIPVIGNGD----IFSPEDAKRMLEETGCDGVMIGRGALGN 227

                        250       260       270
                 ....*....|....*....|....*....|....*....
gi 419635906 214 PSIF------LKEGLRP---LEEVMQKYIRYAVQYDNHY 243
Cdd:COG0042  228 PWLFreidayLAGGEAPppsLEEVLELLLEHLELLLEFY 266
DSRM_DUS2L cd19871
double-stranded RNA binding motif of tRNA-dihydrouridine(20) synthase [NAD(P)+]-like (DUS2L) ...
 334-401 5.40e-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: 132.40  E-value: 5.40e-38
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 419635906 334 TPKMCLLEWCRREKLAQPVYETVQRPLDRLFSSIVTVAEQKYQSTLWDKSKKLAEQAAAIVCLRSQGL 401
Cdd:cd19871    1 TPKMILNEWCRKNKLPQPVYETVQRPSDRLFQSVVTVDGKKYTSSLWEKSKKLAEQAAAIVCLRALGL 68
Dus pfam01207
Dihydrouridine synthase (Dus); Members of this family catalyze the reduction of the 5,6-double ...
 15-248 1.44e-34

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


Pssm-ID: 426126  Cd Length: 309  Bit Score: 130.91  E-value: 1.44e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635906   15 ILAPMVRVGTLPMRLLALDYGA-DIVYCEelidlkmiqckrvvneVLSTVDFVAPDdRVVFRTC--EREQNRVVFQMGG- 90
Cdd:pfam01207   1 LLAPMAGVTDLPFRRLVREYGAgDLVYTE----------------MVTAKAQLRPE-KVRIRMLseLEEPTPLAVQLGGs 63

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635906   91 -----------------------------------MGAALLSDPDKIEKILSTLVKGTRRPVTCKIRIL--PSLEDTLSL 133
Cdd:pfam01207  64 dpallaeaaklvedrgadgidinmgcpskkvtrggGGAALLRNPDLVAQIVKAVVKAVGIPVTVKIRIGwdDSHENAVEI 143

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635906  134 VKRIERTGIAAIAVHGRKREERPQHPVSCEVIKAIADTLSIPVIANGGshdhIQQYSDIEDFRQATAASSVMVARAAMWN 213
Cdd:pfam01207 144 AKIVEDAGAQALTVHGRTRAQNYEGTADWDAIKQVKQAVSIPVIANGD----ITDPEDAQRCLAYTGADGVMIGRGALGN 219

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....
gi 419635906  214 PSIF-----LKEGLR----PLEEVMQKyiryavqYDNHYTNTKY 248
Cdd:pfam01207 220 PWLFaeqhtVKTGEFgpspPLAEEAEK-------VLRHLPYLEE 256
nifR3_yhdG TIGR00737
putative TIM-barrel protein, nifR3 family; This model represents one branch of COG0042 ...
 11-294 1.05e-29

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: 117.85  E-value: 1.05e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635906   11 HNKLILAPMVRVGTLPMRLLALDYGADIVYCEELIDLKMIQCkrvvNEVLSTVDFVAPDDR---VVFRTCER----EQNR 83
Cdd:TIGR00737   7 KSRVVLAPMAGVTDSPFRRLVAEYGAGLTVCEMVSSEAIVYD----SQRTMRLLDIAEDETpisVQLFGSDPdtmaEAAK 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635906   84 VVFQMG------------------GMGAALLSDPDKIEKILSTLVKGTRRPVTCKIRI--LPSLEDTLSLVKRIERTGIA 143
Cdd:TIGR00737  83 INEELGadiidinmgcpvpkitkkGAGSALLRDPDLIGKIVKAVVDAVDIPVTVKIRIgwDDAHINAVEAARIAEDAGAQ 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635906  144 AIAVHGRKREERPQHPVSCEVIKAIADTLSIPVIANGgshdhiqqysDIEDFRQA------TAASSVMVARAAMWNPSIF 217
Cdd:TIGR00737 163 AVTLHGRTRAQGYSGEANWDIIARVKQAVRIPVIGNG----------DIFSPEDAkamletTGCDGVMIGRGALGNPWLF 232

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635906  218 ------LKEGLR----PLEEVMQKYIRYAVQYDNHYTNTKycLCQMLREQLespqGRLLHAAQSSREICEAFGLGAFYEE 287
Cdd:TIGR00737 233 rqieqyLTTGKYkpppTFAEKLDAILRHLQLLADYYGESK--GLRIARKHI----AWYLKGFPGNAALRQTLNHASSFQE 306


                  ....*..
gi 419635906  288 TTQELDA 294
Cdd:TIGR00737 307 VKQLLDD 313
PRK10415 PRK10415
tRNA-dihydrouridine synthase B; Provisional
 12-217 2.62e-18

tRNA-dihydrouridine synthase B; Provisional


Pssm-ID: 182440  Cd Length: 321  Bit Score: 85.41  E-value: 2.62e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635906  12 NKLILAPMVRVGTLPMRLLALDYGADIVYCEELID-----------LKMIQCK----RVVNEVLSTVDFVAPDDRVvfrT 76
Cdd:PRK10415  10 NRLIAAPMAGITDRPFRTLCYEMGAGLTVSEMMSSnpqvwesdksrLRMVHIDepgiRTVQIAGSDPKEMADAARI---N 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635906  77 CEREQNRVVFQMGG---------MGAALLSDPDKIEKILSTLVKGTRRPVTCKIRI--LPSLEDTLSLVKRIERTGIAAI 145
Cdd:PRK10415  87 VESGAQIIDINMGCpakkvnrklAGSALLQYPDLVKSILTEVVNAVDVPVTLKIRTgwAPEHRNCVEIAQLAEDCGIQAL 166

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 419635906 146 AVHGRKREERPQHPVSCEVIKAIADTLSIPVIANGgshdhiqqysDIEDFRQA------TAASSVMVARAAMWNPSIF 217
Cdd:PRK10415 167 TIHGRTRACLFNGEAEYDSIRAVKQKVSIPVIANG----------DITDPLKAravldyTGADALMIGRAAQGRPWIF 234
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 335-397 3.21e-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: 3.21e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 419635906  335 PKMCLLEWCRREKLaQPVYETVQR---PLDRLFSSIVTVAEQKYQSTlWDKSKKLAEQAAAIVCLR 397
Cdd:pfam00035   1 PKSLLQEYAQKNGK-PPPYEYVSEegpPHSPKFTVTVKVDGKLYGSG-TGSSKKEAEQLAAEKALE 64
DSRM smart00358
Double-stranded RNA binding motif;
335-398 8.32e-08

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 49.18  E-value: 8.32e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 419635906   335 PKMCLLEWCRREKLaQPVYETVQR---PLDRLFSSIVTVAEQKYQSTlWDKSKKLAEQAAAIVCLRS 398
Cdd:smart00358   1 PKSLLQELAQKRKL-PPEYELVKEegpDHAPRFTVTVKVGGKRTGEG-EGSSKKEAKQRAAEAALRS 65
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
335-392 5.63e-05

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 44.32  E-value: 5.63e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 419635906 335 PKMCLLEWCRREKLAQPVYETVQR---PLDRLFSSIVTVAEQKYqSTLWDKSKKLAEQAAA 392
Cdd:COG0571  159 YKTALQEWLQARGLPLPEYEVVEEegpDHAKTFTVEVLVGGKVL-GEGTGRSKKEAEQAAA 218
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 335-396 1.17e-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: 1.17e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 419635906  335 PKMCLLEWCRREKLAQPVYETVQRPL---DRLFSSIVTVAEQKYqSTLWDKSKKLAEQAAAIVCL 396
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 ...
 13-217 1.03e-67

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: 215.82  E-value: 1.03e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635906  13 KLILAPMVRVGTLPMRLLALDYGADIVYCEELIDLKMIQCKRVvnevlstvdfvapddRVVFRTCEREQNRVVFQMGG-- 90
Cdd:cd02801    1 KLILAPMVGVTDLPFRLLCRRYGADLVYTEMISAKALLRGNRK---------------RLRLLTRNPEERPLIVQLGGsd 65

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635906  91 ----------------------------------MGAALLSDPDKIEKILSTLVKGTRRPVTCKIRILPSLED-TLSLVK 135
Cdd:cd02801   66 petlaeaakiveelgadgidlnmgcpspkvtkggAGAALLKDPELVAEIVRAVREAVPIPVTVKIRLGWDDEEeTLELAK 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635906 136 RIERTGIAAIAVHGRKREERPQHPVSCEVIKAIADTLSIPVIANGGshdhIQQYSDIEDFRQATAASSVMVARAAMWNPS 215
Cdd:cd02801  146 ALEDAGASALTVHGRTREQRYSGPADWDYIAEIKEAVSIPVIANGD----IFSLEDALRCLEQTGVDGVMIGRGALGNPW 221


                 ..
gi 419635906 216 IF 217
Cdd:cd02801  222 LF 223
DusA COG0042
tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; ...
 12-243 2.99e-38

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: 141.00  E-value: 2.99e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635906  12 NKLILAPMVRVGTLPMRLLALDYGADIVYCEelidlkMIQCKRVVNEVLSTVDFvapddrvvFRTCEREQNRVVfQ---- 87
Cdd:COG0042    7 NPLILAPMAGVTDRPFRRLCRELGAGLLYTE------MVSARALLHGNRKTRRL--------LDFDPEEHPVAV-Qlfgs 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635906  88 -----------------------MG---------GMGAALLSDPDKIEKILSTLVKGTRRPVTCKIRIL--PSLEDTLSL 133
Cdd:COG0042   72 dpeelaeaariaeelgadeidinMGcpvkkvtkgGAGAALLRDPELVAEIVKAVVEAVDVPVTVKIRLGwdDDDENALEF 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635906 134 VKRIERTGIAAIAVHGRKREERPQHPVSCEVIKAIADTLSIPVIANGGshdhIQQYSDIEDFRQATAASSVMVARAAMWN 213
Cdd:COG0042  152 ARIAEDAGAAALTVHGRTREQRYKGPADWDAIARVKEAVSIPVIGNGD----IFSPEDAKRMLEETGCDGVMIGRGALGN 227

                        250       260       270
                 ....*....|....*....|....*....|....*....
gi 419635906 214 PSIF------LKEGLRP---LEEVMQKYIRYAVQYDNHY 243
Cdd:COG0042  228 PWLFreidayLAGGEAPppsLEEVLELLLEHLELLLEFY 266
DSRM_DUS2L cd19871
double-stranded RNA binding motif of tRNA-dihydrouridine(20) synthase [NAD(P)+]-like (DUS2L) ...
 334-401 5.40e-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: 132.40  E-value: 5.40e-38
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 419635906 334 TPKMCLLEWCRREKLAQPVYETVQRPLDRLFSSIVTVAEQKYQSTLWDKSKKLAEQAAAIVCLRSQGL 401
Cdd:cd19871    1 TPKMILNEWCRKNKLPQPVYETVQRPSDRLFQSVVTVDGKKYTSSLWEKSKKLAEQAAAIVCLRALGL 68
Dus pfam01207
Dihydrouridine synthase (Dus); Members of this family catalyze the reduction of the 5,6-double ...
 15-248 1.44e-34

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


Pssm-ID: 426126  Cd Length: 309  Bit Score: 130.91  E-value: 1.44e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635906   15 ILAPMVRVGTLPMRLLALDYGA-DIVYCEelidlkmiqckrvvneVLSTVDFVAPDdRVVFRTC--EREQNRVVFQMGG- 90
Cdd:pfam01207   1 LLAPMAGVTDLPFRRLVREYGAgDLVYTE----------------MVTAKAQLRPE-KVRIRMLseLEEPTPLAVQLGGs 63

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635906   91 -----------------------------------MGAALLSDPDKIEKILSTLVKGTRRPVTCKIRIL--PSLEDTLSL 133
Cdd:pfam01207  64 dpallaeaaklvedrgadgidinmgcpskkvtrggGGAALLRNPDLVAQIVKAVVKAVGIPVTVKIRIGwdDSHENAVEI 143

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635906  134 VKRIERTGIAAIAVHGRKREERPQHPVSCEVIKAIADTLSIPVIANGGshdhIQQYSDIEDFRQATAASSVMVARAAMWN 213
Cdd:pfam01207 144 AKIVEDAGAQALTVHGRTRAQNYEGTADWDAIKQVKQAVSIPVIANGD----ITDPEDAQRCLAYTGADGVMIGRGALGN 219

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....
gi 419635906  214 PSIF-----LKEGLR----PLEEVMQKyiryavqYDNHYTNTKY 248
Cdd:pfam01207 220 PWLFaeqhtVKTGEFgpspPLAEEAEK-------VLRHLPYLEE 256
nifR3_yhdG TIGR00737
putative TIM-barrel protein, nifR3 family; This model represents one branch of COG0042 ...
 11-294 1.05e-29

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: 117.85  E-value: 1.05e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635906   11 HNKLILAPMVRVGTLPMRLLALDYGADIVYCEELIDLKMIQCkrvvNEVLSTVDFVAPDDR---VVFRTCER----EQNR 83
Cdd:TIGR00737   7 KSRVVLAPMAGVTDSPFRRLVAEYGAGLTVCEMVSSEAIVYD----SQRTMRLLDIAEDETpisVQLFGSDPdtmaEAAK 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635906   84 VVFQMG------------------GMGAALLSDPDKIEKILSTLVKGTRRPVTCKIRI--LPSLEDTLSLVKRIERTGIA 143
Cdd:TIGR00737  83 INEELGadiidinmgcpvpkitkkGAGSALLRDPDLIGKIVKAVVDAVDIPVTVKIRIgwDDAHINAVEAARIAEDAGAQ 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635906  144 AIAVHGRKREERPQHPVSCEVIKAIADTLSIPVIANGgshdhiqqysDIEDFRQA------TAASSVMVARAAMWNPSIF 217
Cdd:TIGR00737 163 AVTLHGRTRAQGYSGEANWDIIARVKQAVRIPVIGNG----------DIFSPEDAkamletTGCDGVMIGRGALGNPWLF 232

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635906  218 ------LKEGLR----PLEEVMQKYIRYAVQYDNHYTNTKycLCQMLREQLespqGRLLHAAQSSREICEAFGLGAFYEE 287
Cdd:TIGR00737 233 rqieqyLTTGKYkpppTFAEKLDAILRHLQLLADYYGESK--GLRIARKHI----AWYLKGFPGNAALRQTLNHASSFQE 306


                  ....*..
gi 419635906  288 TTQELDA 294
Cdd:TIGR00737 307 VKQLLDD 313
PRK10415 PRK10415
tRNA-dihydrouridine synthase B; Provisional
 12-217 2.62e-18

tRNA-dihydrouridine synthase B; Provisional


Pssm-ID: 182440  Cd Length: 321  Bit Score: 85.41  E-value: 2.62e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635906  12 NKLILAPMVRVGTLPMRLLALDYGADIVYCEELID-----------LKMIQCK----RVVNEVLSTVDFVAPDDRVvfrT 76
Cdd:PRK10415  10 NRLIAAPMAGITDRPFRTLCYEMGAGLTVSEMMSSnpqvwesdksrLRMVHIDepgiRTVQIAGSDPKEMADAARI---N 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635906  77 CEREQNRVVFQMGG---------MGAALLSDPDKIEKILSTLVKGTRRPVTCKIRI--LPSLEDTLSLVKRIERTGIAAI 145
Cdd:PRK10415  87 VESGAQIIDINMGCpakkvnrklAGSALLQYPDLVKSILTEVVNAVDVPVTLKIRTgwAPEHRNCVEIAQLAEDCGIQAL 166

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 419635906 146 AVHGRKREERPQHPVSCEVIKAIADTLSIPVIANGgshdhiqqysDIEDFRQA------TAASSVMVARAAMWNPSIF 217
Cdd:PRK10415 167 TIHGRTRACLFNGEAEYDSIRAVKQKVSIPVIANG----------DITDPLKAravldyTGADALMIGRAAQGRPWIF 234
PRK10550 PRK10550
tRNA dihydrouridine(16) synthase DusC;
90-240 4.79e-11

tRNA dihydrouridine(16) synthase DusC;


Pssm-ID: 236713  Cd Length: 312  Bit Score: 63.68  E-value: 4.79e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635906  90 GMGAALLSDPDKI---EKILSTLVKgTRRPVTCKIRI-LPSLEDTLSLVKRIERTGIAAIAVHGRKREE--RPQHpVSCE 163
Cdd:PRK10550 107 GGGATLLKDPELIyqgAKAMREAVP-AHLPVTVKVRLgWDSGERKFEIADAVQQAGATELVVHGRTKEDgyRAEH-INWQ 184

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635906 164 VIKAIADTLSIPVIANGgshdHIQQYSDIEDFRQATAASSVMVARAAMWNPS----IFLKEGLRPLEEVM---QKYIRYA 236
Cdd:PRK10550 185 AIGEIRQRLTIPVIANG----EIWDWQSAQQCMAITGCDAVMIGRGALNIPNlsrvVKYNEPRMPWPEVVallQKYTRLE 260


                 ....
gi 419635906 237 VQYD 240
Cdd:PRK10550 261 KQGD 264
DSRM_SF cd00048
double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ...
 341-396 1.04e-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: 1.04e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 419635906 341 EWCRREKLAQPVYETVQR--PLDRLFSSIVTVAEQKYQSTlwDKSKKLAEQAAAIVCL 396
Cdd:cd00048    2 ELCQKNKWPPPEYETVEEggPHNPRFTCTVTVNGQTFEGE--GKSKKEAKQAAAEKAL 57
DSRM_AtDRB-like cd19878
double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding proteins ...
 336-400 1.40e-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: 1.40e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 419635906 336 KMCLLEWCRREKLAQPVYETVQRPLDR--LFSSIVTVAEQKYQSTLWdKSKKLAEQAAAIVCLRSQG 400
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 ...
 335-397 1.50e-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: 1.50e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 419635906 335 PKMCLLEWCRREKLAQPVYETVQR---PLDRLFSSIVTVAEQKYqSTLWDKSKKLAEQAAAIVCLR 397
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 ...
 335-401 2.10e-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: 2.10e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635906 335 PKMCLLEWCRREKLAQPVYETVQR---PLDRLFSSIVTVAEQKYQSTLWDKSKKLAEQAAAIVCLRSQGL 401
Cdd:cd19870    4 PVSALMELCNKRKWGPPEFRLVEEsgpPHRKHFLFKVVVNGVEYQPSVASGNKKDAKAQAATVALQALGL 73
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 335-397 3.21e-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: 3.21e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 419635906  335 PKMCLLEWCRREKLaQPVYETVQR---PLDRLFSSIVTVAEQKYQSTlWDKSKKLAEQAAAIVCLR 397
Cdd:pfam00035   1 PKSLLQEYAQKNGK-PPPYEYVSEegpPHSPKFTVTVKVDGKLYGSG-TGSSKKEAEQLAAEKALE 64
DSRM smart00358
Double-stranded RNA binding motif;
335-398 8.32e-08

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 49.18  E-value: 8.32e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 419635906   335 PKMCLLEWCRREKLaQPVYETVQR---PLDRLFSSIVTVAEQKYQSTlWDKSKKLAEQAAAIVCLRS 398
Cdd:smart00358   1 PKSLLQELAQKRKL-PPEYELVKEegpDHAPRFTVTVKVGGKRTGEG-EGSSKKEAKQRAAEAALRS 65
PRK11815 PRK11815
tRNA dihydrouridine(20/20a) synthase DusA;
82-239 1.27e-06

tRNA dihydrouridine(20/20a) synthase DusA;


Pssm-ID: 236991 [Multi-domain]  Cd Length: 333  Bit Score: 50.13  E-value: 1.27e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635906  82 NRVvfQMGGMGAALLSDPDKIEKILSTLVKGTRRPVTCKIRI----LPSLEDTLSLVKRIERTGIAAIAVHGRK------ 151
Cdd:PRK11815 103 DRV--QNGRFGACLMAEPELVADCVKAMKDAVSIPVTVKHRIgiddQDSYEFLCDFVDTVAEAGCDTFIVHARKawlkgl 180

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635906 152 --REER--P--QHPVsceVIKAIADTLSIPVIANGG--SHDHIQ---QYSDiedfrqataasSVMVARAAMWNPSIFLK- 219
Cdd:PRK11815 181 spKENReiPplDYDR---VYRLKRDFPHLTIEINGGikTLEEAKehlQHVD-----------GVMIGRAAYHNPYLLAEv 246

                        170       180
                 ....*....|....*....|....*...
gi 419635906 220 ------EGLRPL--EEVMQKYIRYAVQY 239
Cdd:PRK11815 247 drelfgEPAPPLsrSEVLEAMLPYIERH 274
DHOD_DHPD_FMN cd02810
Dihydroorotate dehydrogenase (DHOD) and Dihydropyrimidine dehydrogenase (DHPD) FMN-binding ...
 92-219 4.20e-06

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: 48.12  E-value: 4.20e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635906  92 GAALLSDPDKIEKILSTLVKGTRRPVTCKIRILPSLEDTLSLVKRIERTGIAAI---------------AVHGRKREE-- 154
Cdd:cd02810  140 GRQLGQDPEAVANLLKAVKAAVDIPLLVKLSPYFDLEDIVELAKAAERAGADGLtaintisgrvvdlktVGPGPKRGTgg 219

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 419635906 155 ---RPQHPVSCEVIKAIADTLS--IPVIANGGshdhIQQYSDIEDFRQAtAASSVMVARAAMWN-PSIFLK 219
Cdd:cd02810  220 lsgAPIRPLALRWVARLAARLQldIPIIGVGG----IDSGEDVLEMLMA-GASAVQVATALMWDgPDVIRK 285
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
335-392 5.63e-05

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 44.32  E-value: 5.63e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 419635906 335 PKMCLLEWCRREKLAQPVYETVQR---PLDRLFSSIVTVAEQKYqSTLWDKSKKLAEQAAA 392
Cdd:COG0571  159 YKTALQEWLQARGLPLPEYEVVEEegpDHAKTFTVEVLVGGKVL-GEGTGRSKKEAEQAAA 218
DSRM_AtDRB-like_rpt1 cd19907
first double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding ...
 339-398 1.17e-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: 1.17e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 419635906 339 LLEWCRREKLAQPVYETVQRPLDR--LFSSIVTVAEQKYQSTLWDKSKKLAEQAAAIVCLRS 398
Cdd:cd19907    6 LQEYAQKSCLNLPVYACIREGPDHapRFRATVTFNGVIFESPPGFPTLKAAEHSAAEVALNS 67
DSRM_DGCR8_rpt1 cd19867
first double-stranded RNA binding motif of DiGeorge syndrome critical region 8 (DGCR8) and ...
 329-392 1.61e-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: 1.61e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 419635906 329 YPAQITPKMCLLEWCRREKLAQPVYETVQRP-LDRLFSSIVTVAEQKYQSTLwDKSKKLAEQAAA 392
Cdd:cd19867    2 NPDGKSPVCILHEYCQRVLKVQPEYNFTETEnAATPFSAEVFINGVEYGSGE-ASSKKLAKQKAA 65
FadH COG1902
2,4-dienoyl-CoA reductase or related NADH-dependent reductase, Old Yellow Enzyme (OYE) family ...
 126-214 2.47e-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: 43.23  E-value: 2.47e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635906 126 SLEDTLSLVKRIERTGIAAIAVHGRKREERPQHPVSC------EVIKAIADTLSIPVIANGGshdhIQQYSDIEDFRQAT 199
Cdd:COG1902  234 TLEESVELAKALEEAGVDYLHVSSGGYEPDAMIPTIVpegyqlPFAARIRKAVGIPVIAVGG----ITTPEQAEAALASG 309

                         90
                 ....*....|....*
gi 419635906 200 AASSVMVARAAMWNP 214
Cdd:COG1902  310 DADLVALGRPLLADP 324
OYE_like_FMN_family cd02803
Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme ...
 126-214 2.66e-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: 2.66e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635906 126 SLEDTLSLVKRIERTGIAAIAVHGRKREERPQHPVSCEVI--------KAIADTLSIPVIANGGSHDhiqqYSDIEDFRQ 197
Cdd:cd02803  226 TLEEAIEIAKALEEAGVDALHVSGGSYESPPPIIPPPYVPegyflelaEKIKKAVKIPVIAVGGIRD----PEVAEEILA 301

                         90
                 ....*....|....*..
gi 419635906 198 ATAASSVMVARAAMWNP 214
Cdd:cd02803  302 EGKADLVALGRALLADP 318
DHOD_1B_like cd04740
Dihydroorotate dehydrogenase (DHOD) class 1B FMN-binding domain. DHOD catalyzes the oxidation ...
 90-232 9.92e-04

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


Pssm-ID: 240091 [Multi-domain]  Cd Length: 296  Bit Score: 41.00  E-value: 9.92e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635906  90 GMGAALLSDPDKIEKILSTLVKGTRRPVTCKIRilPSLEDTLSLVKRIERTG---IAAI------AVHGRKReeRPQ--- 157
Cdd:cd04740  130 GGGMAFGTDPEAVAEIVKAVKKATDVPVIVKLT--PNVTDIVEIARAAEEAGadgLTLIntlkgmAIDIETR--KPIlgn 205

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 419635906 158 ----------HPVSCEVIKAIADTLSIPVIANGGshdhIQQYSDIEDFRQAtAASSVMVARAAMWNPSIFLKEgLRPLEE 227
Cdd:cd04740  206 vtgglsgpaiKPIALRMVYQVYKAVEIPIIGVGG----IASGEDALEFLMA-GASAVQVGTANFVDPEAFKEI-IEGLEA 279


                 ....*
gi 419635906 228 VMQKY 232
Cdd:cd04740  280 YLDEE 284
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 335-396 1.17e-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: 1.17e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 419635906  335 PKMCLLEWCRREKLAQPVYETVQRPL---DRLFSSIVTVAEQKYqSTLWDKSKKLAEQAAAIVCL 396
Cdd:TIGR02191 154 YKTALQEWAQARGKPLPEYRLIKEEGpdhDKEFTVEVSVNGEPY-GEGKGKSKKEAEQNAAKAAL 217
HisF cd04731
The cyclase subunit of imidazoleglycerol phosphate synthase (HisF). Imidazole glycerol ...
 163-217 5.41e-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: 5.41e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 419635906 163 EVIKAIADTLSIPVIANGGshdhiqqYSDIEDFRQATAASSVMVARAAmwnpSIF 217
Cdd:cd04731  183 ELIRAVSSAVNIPVIASGG-------AGKPEHFVEAFEEGGADAALAA----SIF 226
DSRM_EIF2AK2-like cd19875
double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 ...
 333-398 7.33e-03

double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 (EIF2AK2) and similar proteins; The family includes EIF2AK2 and adenosine deaminase domain-containing proteins, ADAD1 and ADAD2. EIF2AK2 (EC 2.7.11.1/EC 2.7.10.2; also known as interferon-induced, double-stranded RNA-activated protein kinase, eIF-2A protein kinase 2, interferon-inducible RNA-dependent protein kinase, P1/eIF-2A protein kinase, protein kinase RNA-activated (PKR), protein kinase R, tyrosine-protein kinase EIF2AK2, or p68 kinase) acts as an IFN-induced dsRNA-dependent serine/threonine-protein kinase which plays a key role in the innate immune response to viral infection and is also involved in the regulation of signal transduction, apoptosis, cell proliferation and differentiation. ADAD1 (also called testis nuclear RNA-binding protein (TENR)) and ADAD2 (also called testis nuclear RNA-binding protein-like (TENRL)) are phylogenetically related to a family of adenosine deaminases involved in RNA editing. ADAD1 plays an essential function in spermatid morphogenesis. It may be involved in testis-specific nuclear post-transcriptional processes such as heterogeneous nuclear RNA (hnRNA) packaging, alternative splicing, or nuclear/cytoplasmic transport of mRNAs. ADAD2 is a double-stranded RNA binding protein with unclear biological function. Members of this group contains varying numbers of double-stranded RNA binding motifs (DSRMs). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380704  Cd Length: 67  Bit Score: 34.93  E-value: 7.33e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 419635906 333 ITPKMCLLEWCRREKLAQPvYETVQR--PLDRLFSSIVTVAEQKYQSTLwDKSKKLAEQAAAIVCLRS 398
Cdd:cd19875    1 KNPVSALNEYCQKRGLSLE-FVDVSVgpDHCPGFTASATIDGIVFASAT-GTSKKEAKRAAAKLALKK 66
 
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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