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Conserved domains on  [gi|45549423|ref|NP_572950|]
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uncharacterized protein Dmel_CG1434, isoform A [Drosophila melanogaster]

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 ...
 25-266 6.48e-85

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: 260.50  E-value: 6.48e-85
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549423  25 KLILAPMVRVGTLPMRLLALEMGADIVYTEELVDIKLIKSIRRpnpalgtvdfvdpsdgTIVFRTCAQETSRLVLQMGTS 104
Cdd:cd02801   1 KLILAPMVGVTDLPFRLLCRRYGADLVYTEMISAKALLRGNRK----------------RLRLLTRNPEERPLIVQLGGS 64

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549423 105 DAGRALAVGKLLQR-DISGLDINMGCPKEFSIKGGMGAALLADPDKAAHILRTLCSGLDIPVTCKIRILPDVEG-TIDLV 182
Cdd:cd02801  65 DPETLAEAAKIVEElGADGIDLNMGCPSPKVTKGGAGAALLKDPELVAEIVRAVREAVPIPVTVKIRLGWDDEEeTLELA 144

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549423 183 QKLAATGIAAIGIHARTRDERPQHPAHPEVLRAVAQAVDIPIIANGGSKNmhcYDDLRKFQMECGADSVMVARAAQINVS 262
Cdd:cd02801 145 KALEDAGASALTVHGRTREQRYSGPADWDYIAEIKEAVSIPVIANGDIFS---LEDALRCLEQTGVDGVMIGRGALGNPW 221


                ....
gi 45549423 263 IFRP 266
Cdd:cd02801 222 LFRE 225
DSRM_DUS2L cd19871
double-stranded RNA binding motif of tRNA-dihydrouridine(20) synthase [NAD(P)+]-like (DUS2L) ...
 394-458 3.56e-27

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: 103.51  E-value: 3.56e-27
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 45549423 394 LPKTQLYVHAVKTGKSPPAYETQQC--DKLFRSICTYDGQRFSSSFWEKNKKQAEQGAALVALLHLG 458
Cdd:cd19871   1 TPKMILNEWCRKNKLPQPVYETVQRpsDRLFQSVVTVDGKKYTSSLWEKSKKLAEQAAAIVCLRALG 67
 
Name Accession Description Interval E-value
DUS_like_FMN cd02801
Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze ...
 25-266 6.48e-85

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: 260.50  E-value: 6.48e-85
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549423  25 KLILAPMVRVGTLPMRLLALEMGADIVYTEELVDIKLIKSIRRpnpalgtvdfvdpsdgTIVFRTCAQETSRLVLQMGTS 104
Cdd:cd02801   1 KLILAPMVGVTDLPFRLLCRRYGADLVYTEMISAKALLRGNRK----------------RLRLLTRNPEERPLIVQLGGS 64

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549423 105 DAGRALAVGKLLQR-DISGLDINMGCPKEFSIKGGMGAALLADPDKAAHILRTLCSGLDIPVTCKIRILPDVEG-TIDLV 182
Cdd:cd02801  65 DPETLAEAAKIVEElGADGIDLNMGCPSPKVTKGGAGAALLKDPELVAEIVRAVREAVPIPVTVKIRLGWDDEEeTLELA 144

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549423 183 QKLAATGIAAIGIHARTRDERPQHPAHPEVLRAVAQAVDIPIIANGGSKNmhcYDDLRKFQMECGADSVMVARAAQINVS 262
Cdd:cd02801 145 KALEDAGASALTVHGRTREQRYSGPADWDYIAEIKEAVSIPVIANGDIFS---LEDALRCLEQTGVDGVMIGRGALGNPW 221


                ....
gi 45549423 263 IFRP 266
Cdd:cd02801 222 LFRE 225
DusA COG0042
tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; ...
 24-286 1.39e-49

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: 171.43  E-value: 1.39e-49
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549423  24 NKLILAPMVRVGTLPMRLLALEMGADIVYTEelvdikliksirrpnpalgtvdFVdpSDGTIVFRTcaQETSRL------ 97
Cdd:COG0042   7 NPLILAPMAGVTDRPFRRLCRELGAGLLYTE----------------------MV--SARALLHGN--RKTRRLldfdpe 60

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549423  98 ----VLQMGTSDAGR-ALAVGKLLQRDISGLDINMGCPKEFSIKGGMGAALLADPDKAAHILRTLCSGLDIPVTCKIRIL 172
Cdd:COG0042  61 ehpvAVQLFGSDPEElAEAARIAEELGADEIDINMGCPVKKVTKGGAGAALLRDPELVAEIVKAVVEAVDVPVTVKIRLG 140

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549423 173 PD--VEGTIDLVQKLAATGIAAIGIHARTRDERPQHPAHPEVLRAVAQAVDIPIIANGGSKNmhcYDDLRKFQMECGADS 250
Cdd:COG0042 141 WDddDENALEFARIAEDAGAAALTVHGRTREQRYKGPADWDAIARVKEAVSIPVIGNGDIFS---PEDAKRMLEETGCDG 217

                       250       260       270       280
                ....*....|....*....|....*....|....*....|....*...
gi 45549423 251 VMVARAAQINVSIFR---------PEGLLPMDELIE---KYLRLCVDY 286
Cdd:COG0042 218 VMIGRGALGNPWLFReidaylaggEAPPPSLEEVLElllEHLELLLEF 265
Dus pfam01207
Dihydrouridine synthase (Dus); Members of this family catalyze the reduction of the 5,6-double ...
 27-275 1.88e-45

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: 160.57  E-value: 1.88e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549423    27 ILAPMVRVGTLPMRLLALEMGA-DIVYTEelvdikliksirrpnpALGTVDFVDPSDGTIVFRTCAQETSRLVLQMGTSD 105
Cdd:pfam01207   1 LLAPMAGVTDLPFRRLVREYGAgDLVYTE----------------MVTAKAQLRPEKVRIRMLSELEEPTPLAVQLGGSD 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549423   106 AGRALAVGKLL-QRDISGLDINMGCPKEFSIKGGMGAALLADPDKAAHILRTLCSGLDIPVTCKIRIL--PDVEGTIDLV 182
Cdd:pfam01207  65 PALLAEAAKLVeDRGADGIDINMGCPSKKVTRGGGGAALLRNPDLVAQIVKAVVKAVGIPVTVKIRIGwdDSHENAVEIA 144

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549423   183 QKLAATGIAAIGIHARTRDERPQHPAHPEVLRAVAQAVDIPIIANGGSKNMHcydDLRKFQMECGADSVMVARAAQINVS 262
Cdd:pfam01207 145 KIVEDAGAQALTVHGRTRAQNYEGTADWDAIKQVKQAVSIPVIANGDITDPE---DAQRCLAYTGADGVMIGRGALGNPW 221

                         250
                  ....*....|...
gi 45549423   263 IFRPEGLLPMDEL 275
Cdd:pfam01207 222 LFAEQHTVKTGEF 234
nifR3_yhdG TIGR00737
putative TIM-barrel protein, nifR3 family; This model represents one branch of COG0042 ...
 23-265 2.78e-35

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: 133.64  E-value: 2.78e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549423    23 RNKLILAPMVRVGTLPMRLLALEMGADIVYTEeLVDIKLIksIRRPNPALGTVDFVDpsdgtivfrtcaQETSRLVlQMG 102
Cdd:TIGR00737   7 KSRVVLAPMAGVTDSPFRRLVAEYGAGLTVCE-MVSSEAI--VYDSQRTMRLLDIAE------------DETPISV-QLF 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549423   103 TSD---AGRALAVGKLLQRDIsgLDINMGCPKEFSIKGGMGAALLADPDKAAHILRTLCSGLDIPVTCKIRILPDvEGTI 179
Cdd:TIGR00737  71 GSDpdtMAEAAKINEELGADI--IDINMGCPVPKITKKGAGSALLRDPDLIGKIVKAVVDAVDIPVTVKIRIGWD-DAHI 147

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549423   180 ---DLVQKLAATGIAAIGIHARTRDERPQHPAHPEVLRAVAQAVDIPIIANGgskNMHCYDDLRKFQMECGADSVMVARA 256
Cdd:TIGR00737 148 navEAARIAEDAGAQAVTLHGRTRAQGYSGEANWDIIARVKQAVRIPVIGNG---DIFSPEDAKAMLETTGCDGVMIGRG 224


                  ....*....
gi 45549423   257 AQINVSIFR 265
Cdd:TIGR00737 225 ALGNPWLFR 233
PRK10415 PRK10415
tRNA-dihydrouridine synthase B; Provisional
 23-265 4.32e-28

tRNA-dihydrouridine synthase B; Provisional


Pssm-ID: 182440  Cd Length: 321  Bit Score: 113.91  E-value: 4.32e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549423   23 RNKLILAPMVRVGTLPMRLLALEMGADIVYTEELvdikliksirRPNPAlgtvdfVDPSDGTIVFRTCAQETSRLVLQMG 102
Cdd:PRK10415   9 RNRLIAAPMAGITDRPFRTLCYEMGAGLTVSEMM----------SSNPQ------VWESDKSRLRMVHIDEPGIRTVQIA 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549423  103 TSDAGRALAVGKL-LQRDISGLDINMGCPKEFSIKGGMGAALLADPDKAAHILRTLCSGLDIPVTCKIRI--LPDVEGTI 179
Cdd:PRK10415  73 GSDPKEMADAARInVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKSILTEVVNAVDVPVTLKIRTgwAPEHRNCV 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549423  180 DLVQKLAATGIAAIGIHARTRDERPQHPAHPEVLRAVAQAVDIPIIANGGSKNMHcydDLRKFQMECGADSVMVARAAQI 259
Cdd:PRK10415 153 EIAQLAEDCGIQALTIHGRTRACLFNGEAEYDSIRAVKQKVSIPVIANGDITDPL---KARAVLDYTGADALMIGRAAQG 229


                 ....*.
gi 45549423  260 NVSIFR 265
Cdd:PRK10415 230 RPWIFR 235
DSRM_DUS2L cd19871
double-stranded RNA binding motif of tRNA-dihydrouridine(20) synthase [NAD(P)+]-like (DUS2L) ...
 394-458 3.56e-27

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: 103.51  E-value: 3.56e-27
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 45549423 394 LPKTQLYVHAVKTGKSPPAYETQQC--DKLFRSICTYDGQRFSSSFWEKNKKQAEQGAALVALLHLG 458
Cdd:cd19871   1 TPKMILNEWCRKNKLPQPVYETVQRpsDRLFQSVVTVDGKKYTSSLWEKSKKLAEQAAAIVCLRALG 67
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 395-457 7.98e-10

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: 54.54  E-value: 7.98e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 45549423   395 PKTQLYVHAVKTGKSPPAYETQQC----DKLFRSICTYDGQRFSSSfWEKNKKQAEQGAALVALLHL 457
Cdd:pfam00035   1 PKSLLQEYAQKNGKPPPYEYVSEEgpphSPKFTVTVKVDGKLYGSG-TGSSKKEAEQLAAEKALEKL 66
DSRM smart00358
Double-stranded RNA binding motif;
395-458 2.68e-07

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 47.64  E-value: 2.68e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 45549423    395 PKTQLYVHAVKTGKsPPAYETQQC-----DKLFRSICTYDGQRFSSsFWEKNKKQAEQGAALVALLHLG 458
Cdd:smart00358   1 PKSLLQELAQKRKL-PPEYELVKEegpdhAPRFTVTVKVGGKRTGE-GEGSSKKEAKQRAAEAALRSLK 67
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
395-458 2.50e-03

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 39.31  E-value: 2.50e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 45549423 395 PKTQL--YVHAvkTGKSPPAYETQQC-----DKLFRSICTYDGQRFSSSfWEKNKKQAEQGAALVALLHLG 458
Cdd:COG0571 159 YKTALqeWLQA--RGLPLPEYEVVEEegpdhAKTFTVEVLVGGKVLGEG-TGRSKKEAEQAAAKAALEKLG 226
 
Name Accession Description Interval E-value
DUS_like_FMN cd02801
Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze ...
 25-266 6.48e-85

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: 260.50  E-value: 6.48e-85
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549423  25 KLILAPMVRVGTLPMRLLALEMGADIVYTEELVDIKLIKSIRRpnpalgtvdfvdpsdgTIVFRTCAQETSRLVLQMGTS 104
Cdd:cd02801   1 KLILAPMVGVTDLPFRLLCRRYGADLVYTEMISAKALLRGNRK----------------RLRLLTRNPEERPLIVQLGGS 64

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549423 105 DAGRALAVGKLLQR-DISGLDINMGCPKEFSIKGGMGAALLADPDKAAHILRTLCSGLDIPVTCKIRILPDVEG-TIDLV 182
Cdd:cd02801  65 DPETLAEAAKIVEElGADGIDLNMGCPSPKVTKGGAGAALLKDPELVAEIVRAVREAVPIPVTVKIRLGWDDEEeTLELA 144

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549423 183 QKLAATGIAAIGIHARTRDERPQHPAHPEVLRAVAQAVDIPIIANGGSKNmhcYDDLRKFQMECGADSVMVARAAQINVS 262
Cdd:cd02801 145 KALEDAGASALTVHGRTREQRYSGPADWDYIAEIKEAVSIPVIANGDIFS---LEDALRCLEQTGVDGVMIGRGALGNPW 221


                ....
gi 45549423 263 IFRP 266
Cdd:cd02801 222 LFRE 225
DusA COG0042
tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; ...
 24-286 1.39e-49

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: 171.43  E-value: 1.39e-49
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549423  24 NKLILAPMVRVGTLPMRLLALEMGADIVYTEelvdikliksirrpnpalgtvdFVdpSDGTIVFRTcaQETSRL------ 97
Cdd:COG0042   7 NPLILAPMAGVTDRPFRRLCRELGAGLLYTE----------------------MV--SARALLHGN--RKTRRLldfdpe 60

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549423  98 ----VLQMGTSDAGR-ALAVGKLLQRDISGLDINMGCPKEFSIKGGMGAALLADPDKAAHILRTLCSGLDIPVTCKIRIL 172
Cdd:COG0042  61 ehpvAVQLFGSDPEElAEAARIAEELGADEIDINMGCPVKKVTKGGAGAALLRDPELVAEIVKAVVEAVDVPVTVKIRLG 140

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549423 173 PD--VEGTIDLVQKLAATGIAAIGIHARTRDERPQHPAHPEVLRAVAQAVDIPIIANGGSKNmhcYDDLRKFQMECGADS 250
Cdd:COG0042 141 WDddDENALEFARIAEDAGAAALTVHGRTREQRYKGPADWDAIARVKEAVSIPVIGNGDIFS---PEDAKRMLEETGCDG 217

                       250       260       270       280
                ....*....|....*....|....*....|....*....|....*...
gi 45549423 251 VMVARAAQINVSIFR---------PEGLLPMDELIE---KYLRLCVDY 286
Cdd:COG0042 218 VMIGRGALGNPWLFReidaylaggEAPPPSLEEVLElllEHLELLLEF 265
Dus pfam01207
Dihydrouridine synthase (Dus); Members of this family catalyze the reduction of the 5,6-double ...
 27-275 1.88e-45

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: 160.57  E-value: 1.88e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549423    27 ILAPMVRVGTLPMRLLALEMGA-DIVYTEelvdikliksirrpnpALGTVDFVDPSDGTIVFRTCAQETSRLVLQMGTSD 105
Cdd:pfam01207   1 LLAPMAGVTDLPFRRLVREYGAgDLVYTE----------------MVTAKAQLRPEKVRIRMLSELEEPTPLAVQLGGSD 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549423   106 AGRALAVGKLL-QRDISGLDINMGCPKEFSIKGGMGAALLADPDKAAHILRTLCSGLDIPVTCKIRIL--PDVEGTIDLV 182
Cdd:pfam01207  65 PALLAEAAKLVeDRGADGIDINMGCPSKKVTRGGGGAALLRNPDLVAQIVKAVVKAVGIPVTVKIRIGwdDSHENAVEIA 144

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549423   183 QKLAATGIAAIGIHARTRDERPQHPAHPEVLRAVAQAVDIPIIANGGSKNMHcydDLRKFQMECGADSVMVARAAQINVS 262
Cdd:pfam01207 145 KIVEDAGAQALTVHGRTRAQNYEGTADWDAIKQVKQAVSIPVIANGDITDPE---DAQRCLAYTGADGVMIGRGALGNPW 221

                         250
                  ....*....|...
gi 45549423   263 IFRPEGLLPMDEL 275
Cdd:pfam01207 222 LFAEQHTVKTGEF 234
nifR3_yhdG TIGR00737
putative TIM-barrel protein, nifR3 family; This model represents one branch of COG0042 ...
 23-265 2.78e-35

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: 133.64  E-value: 2.78e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549423    23 RNKLILAPMVRVGTLPMRLLALEMGADIVYTEeLVDIKLIksIRRPNPALGTVDFVDpsdgtivfrtcaQETSRLVlQMG 102
Cdd:TIGR00737   7 KSRVVLAPMAGVTDSPFRRLVAEYGAGLTVCE-MVSSEAI--VYDSQRTMRLLDIAE------------DETPISV-QLF 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549423   103 TSD---AGRALAVGKLLQRDIsgLDINMGCPKEFSIKGGMGAALLADPDKAAHILRTLCSGLDIPVTCKIRILPDvEGTI 179
Cdd:TIGR00737  71 GSDpdtMAEAAKINEELGADI--IDINMGCPVPKITKKGAGSALLRDPDLIGKIVKAVVDAVDIPVTVKIRIGWD-DAHI 147

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549423   180 ---DLVQKLAATGIAAIGIHARTRDERPQHPAHPEVLRAVAQAVDIPIIANGgskNMHCYDDLRKFQMECGADSVMVARA 256
Cdd:TIGR00737 148 navEAARIAEDAGAQAVTLHGRTRAQGYSGEANWDIIARVKQAVRIPVIGNG---DIFSPEDAKAMLETTGCDGVMIGRG 224


                  ....*....
gi 45549423   257 AQINVSIFR 265
Cdd:TIGR00737 225 ALGNPWLFR 233
PRK10415 PRK10415
tRNA-dihydrouridine synthase B; Provisional
 23-265 4.32e-28

tRNA-dihydrouridine synthase B; Provisional


Pssm-ID: 182440  Cd Length: 321  Bit Score: 113.91  E-value: 4.32e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549423   23 RNKLILAPMVRVGTLPMRLLALEMGADIVYTEELvdikliksirRPNPAlgtvdfVDPSDGTIVFRTCAQETSRLVLQMG 102
Cdd:PRK10415   9 RNRLIAAPMAGITDRPFRTLCYEMGAGLTVSEMM----------SSNPQ------VWESDKSRLRMVHIDEPGIRTVQIA 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549423  103 TSDAGRALAVGKL-LQRDISGLDINMGCPKEFSIKGGMGAALLADPDKAAHILRTLCSGLDIPVTCKIRI--LPDVEGTI 179
Cdd:PRK10415  73 GSDPKEMADAARInVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKSILTEVVNAVDVPVTLKIRTgwAPEHRNCV 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549423  180 DLVQKLAATGIAAIGIHARTRDERPQHPAHPEVLRAVAQAVDIPIIANGGSKNMHcydDLRKFQMECGADSVMVARAAQI 259
Cdd:PRK10415 153 EIAQLAEDCGIQALTIHGRTRACLFNGEAEYDSIRAVKQKVSIPVIANGDITDPL---KARAVLDYTGADALMIGRAAQG 229


                 ....*.
gi 45549423  260 NVSIFR 265
Cdd:PRK10415 230 RPWIFR 235
DSRM_DUS2L cd19871
double-stranded RNA binding motif of tRNA-dihydrouridine(20) synthase [NAD(P)+]-like (DUS2L) ...
 394-458 3.56e-27

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: 103.51  E-value: 3.56e-27
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 45549423 394 LPKTQLYVHAVKTGKSPPAYETQQC--DKLFRSICTYDGQRFSSSFWEKNKKQAEQGAALVALLHLG 458
Cdd:cd19871   1 TPKMILNEWCRKNKLPQPVYETVQRpsDRLFQSVVTVDGKKYTSSLWEKSKKLAEQAAAIVCLRALG 67
PRK10550 PRK10550
tRNA dihydrouridine(16) synthase DusC;
25-282 8.28e-11

tRNA dihydrouridine(16) synthase DusC;


Pssm-ID: 236713  Cd Length: 312  Bit Score: 62.91  E-value: 8.28e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549423   25 KLILAPMVRVGTLPMRLLALEMGA-DIVYTEEL--VDIKL-IKSIRRPNPALGTVDFVdPSdGTIVfrtcaqetsRLVL- 99
Cdd:PRK10550   2 RVLLAPMEGVLDSLVRELLTEVNDyDLCITEFLrvVDQLLpVKVFHRLCPELHNASRT-PS-GTLV---------RIQLl 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549423  100 ----QMGTSDAGRALAVGKLlqrdisGLDINMGCPKEFSIKGGMGAALLADPD---KAAHILRTLCSGlDIPVTCKIRIL 172
Cdd:PRK10550  71 gqypQWLAENAARAVELGSW------GVDLNCGCPSKTVNGSGGGATLLKDPEliyQGAKAMREAVPA-HLPVTVKVRLG 143

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549423  173 PDVEG----TIDLVQKLAATGIAaigIHARTRDE--RPQHpAHPEVLRAVAQAVDIPIIANGGSKNMHCYDDLRKfqmEC 246
Cdd:PRK10550 144 WDSGErkfeIADAVQQAGATELV---VHGRTKEDgyRAEH-INWQAIGEIRQRLTIPVIANGEIWDWQSAQQCMA---IT 216

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....
gi 45549423  247 GADSVMVARAAqINVS-----IFRPEGLLPMDE---LIEKYLRL 282
Cdd:PRK10550 217 GCDAVMIGRGA-LNIPnlsrvVKYNEPRMPWPEvvaLLQKYTRL 259
PRK11815 PRK11815
tRNA dihydrouridine(20/20a) synthase DusA;
97-257 1.03e-10

tRNA dihydrouridine(20/20a) synthase DusA;


Pssm-ID: 236991 [Multi-domain]  Cd Length: 333  Bit Score: 62.84  E-value: 1.03e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549423   97 LVLQMGTSDAGRALAVGKLLQRdiSGLD---INMGCPKEFSIKGGMGAALLADPDKAAHILRTLCSGLDIPVTCKIRI-- 171
Cdd:PRK11815  67 VALQLGGSDPADLAEAAKLAED--WGYDeinLNVGCPSDRVQNGRFGACLMAEPELVADCVKAMKDAVSIPVTVKHRIgi 144

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549423  172 --LPDVEGTIDLVQKLAATGIAAIGIHART-----------RDERPQHpaHPEVLRAVAQAVDIPIIANGGSKNM-HCYD 237
Cdd:PRK11815 145 ddQDSYEFLCDFVDTVAEAGCDTFIVHARKawlkglspkenREIPPLD--YDRVYRLKRDFPHLTIEINGGIKTLeEAKE 222

                        170       180
                 ....*....|....*....|
gi 45549423  238 DLRKFqmecgaDSVMVARAA 257
Cdd:PRK11815 223 HLQHV------DGVMIGRAA 236
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 395-457 7.98e-10

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: 54.54  E-value: 7.98e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 45549423   395 PKTQLYVHAVKTGKSPPAYETQQC----DKLFRSICTYDGQRFSSSfWEKNKKQAEQGAALVALLHL 457
Cdd:pfam00035   1 PKSLLQEYAQKNGKPPPYEYVSEEgpphSPKFTVTVKVDGKLYGSG-TGSSKKEAEQLAAEKALEKL 66
PyrD COG0167
Dihydroorotate dehydrogenase [Nucleotide transport and metabolism]; Dihydroorotate ...
 119-253 2.23e-09

Dihydroorotate dehydrogenase [Nucleotide transport and metabolism]; Dihydroorotate dehydrogenase is part of the Pathway/BioSystem: Pyrimidine biosynthesis


Pssm-ID: 439937 [Multi-domain]  Cd Length: 296  Bit Score: 58.55  E-value: 2.23e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549423 119 DISGLDINMGCP--KefsikgGMGAALLADPDKAAHILRTLCSGLDIPVTCKIRI-LPDVEGTIDLVQKLAATGIAAI-- 193
Cdd:COG0167 118 GADYLELNISCPntP------GGGRALGQDPEALAELLAAVKAATDKPVLVKLAPdLTDIVEIARAAEEAGADGVIAInt 191

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 45549423 194 ------GIHARTRDERPQH------PAHP---EVLRAVAQAV--DIPIIANGGsknMHCYDDLRKFqMECGADSVMV 253
Cdd:COG0167 192 tlgraiDLETRRPVLANEAgglsgpALKPialRMVREVAQAVggDIPIIGVGG---ISTAEDALEF-ILAGASAVQV 264
DHOD_1B_like cd04740
Dihydroorotate dehydrogenase (DHOD) class 1B FMN-binding domain. DHOD catalyzes the oxidation ...
 109-281 1.45e-07

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: 52.94  E-value: 1.45e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549423 109 ALAVGKLLQRDISGLDINMGCPkefSIKGGmGAALLADPDKAAHILRTLCSGLDIPVTCKIRilPDVEGTIDLVQKLA-- 186
Cdd:cd04740 105 VEVAEKLADAGADAIELNISCP---NVKGG-GMAFGTDPEAVAEIVKAVKKATDVPVIVKLT--PNVTDIVEIARAAEea 178

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549423 187 -ATGIAAI------GIHARTRdeRPQ---------HPA-HPEVLRAV---AQAVDIPIIANGGSKNmhcYDDLRKFqMEC 246
Cdd:cd04740 179 gADGLTLIntlkgmAIDIETR--KPIlgnvtgglsGPAiKPIALRMVyqvYKAVEIPIIGVGGIAS---GEDALEF-LMA 252

                       170       180       190
                ....*....|....*....|....*....|....*
gi 45549423 247 GADSVMVARAAQINVSIFRPEGllpmdELIEKYLR 281
Cdd:cd04740 253 GASAVQVGTANFVDPEAFKEII-----EGLEAYLD 282
DSRM smart00358
Double-stranded RNA binding motif;
395-458 2.68e-07

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 47.64  E-value: 2.68e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 45549423    395 PKTQLYVHAVKTGKsPPAYETQQC-----DKLFRSICTYDGQRFSSsFWEKNKKQAEQGAALVALLHLG 458
Cdd:smart00358   1 PKSLLQELAQKRKL-PPEYELVKEegpdhAPRFTVTVKVGGKRTGE-GEGSSKKEAKQRAAEAALRSLK 67
DSRM_AtDRB-like_rpt1 cd19907
first double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding ...
 396-457 4.47e-07

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: 47.09  E-value: 4.47e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 45549423 396 KTQLYVHAVKTGKSPPAYETQQCD----KLFRSICTYDGQRFSSSFWEKNKKQAEQGAALVALLHL 457
Cdd:cd19907   3 KSQLQEYAQKSCLNLPVYACIREGpdhaPRFRATVTFNGVIFESPPGFPTLKAAEHSAAEVALNSL 68
DSRM_AtDRB-like cd19878
double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding proteins ...
 396-458 1.12e-06

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: 45.97  E-value: 1.12e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 45549423 396 KTQLYVHAVKTGKSPPAYET----QQCDKLFRSICTYDGQRFSSSFWeKNKKQAEQGAALVALLHLG 458
Cdd:cd19878   2 KNLLQEYAQKKKIPLPKYESaksgPSHQPTFVSTVIVLGVRFSSEGA-KNKKQAEQSAAKVALKELG 67
DHPD_FMN cd02940
Dihydropyrimidine dehydrogenase (DHPD) FMN-binding domain. DHPD catalyzes the first step in ...
 122-258 1.28e-06

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


Pssm-ID: 239244  Cd Length: 299  Bit Score: 49.98  E-value: 1.28e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549423 122 GLDINMGCPKEFSIKGgMGAALLADPDKAAHILRTLCSGLDIPVTCKIRilPDVeGTIDLVQKLA----ATGIAAI---- 193
Cdd:cd02940 129 ALELNFSCPHGMPERG-MGAAVGQDPELVEEICRWVREAVKIPVIAKLT--PNI-TDIREIARAAkeggADGVSAIntvn 204

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549423 194 GIHARTRDERPQHP---------------AHPEVLRAVAQ-----AVDIPIIANGGSKNmhcYDDLRKFqMECGADSVMV 253
Cdd:cd02940 205 SLMGVDLDGTPPAPgvegkttyggysgpaVKPIALRAVSQiarapEPGLPISGIGGIES---WEDAAEF-LLLGASVVQV 280


                ....*
gi 45549423 254 ARAAQ 258
Cdd:cd02940 281 CTAVM 285
DSRM_SF cd00048
double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ...
 402-454 1.87e-06

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: 44.97  E-value: 1.87e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 45549423 402 HAVKTGKSPPAYETQQ----CDKLFRSICTYDGQRFSSSfwEKNKKQAEQGAALVAL 454
Cdd:cd00048   3 LCQKNKWPPPEYETVEeggpHNPRFTCTVTVNGQTFEGE--GKSKKEAKQAAAEKAL 57
OYE_like_FMN_family cd02803
Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme ...
 160-257 3.55e-06

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: 48.72  E-value: 3.55e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549423 160 GLDIPVTCKI---RILP---DVEGTIDLVQKLAATGIAAIGIHARTRDERPQHPAHPEV--------LRAVAQAVDIPII 225
Cdd:cd02803 206 GPDFPVGVRLsadDFVPgglTLEEAIEIAKALEEAGVDALHVSGGSYESPPPIIPPPYVpegyflelAEKIKKAVKIPVI 285

                        90       100       110
                ....*....|....*....|....*....|..
gi 45549423 226 ANGGsknMHCYDDLRKFQMECGADSVMVARAA 257
Cdd:cd02803 286 AVGG---IRDPEVAEEILAEGKADLVALGRAL 314
arch_FMN cd02911
Archeal FMN-binding domain. This family of archaeal proteins are part of the NAD(P)H-dependent ...
 104-257 1.74e-05

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: 46.17  E-value: 1.74e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549423 104 SDAGRALAVGKLLQRDISGLDINMGCPKEFSIKGGMGAALLADPDKAAHILRTLcSGLDIPVTCKIR--ILPDvegTIDL 181
Cdd:cd02911  82 SSLEPLLNAAALVAKNAAILEINAHCRQPEMVEAGAGEALLKDPERLSEFIKAL-KETGVPVSVKIRagVDVD---DEEL 157

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 45549423 182 VQKLAATGiaAIGIHARTRDERPQhpAHPEVLRAVAQavDIPIIANGGSKNmhcYDDLRKFqMECGADSVMVARAA 257
Cdd:cd02911 158 ARLIEKAG--ADIIHVDAMDPGNH--ADLKKIRDIST--ELFIIGNNSVTT---IESAKEM-FSYGADMVSVARAS 223
PRK07259 PRK07259
dihydroorotate dehydrogenase;
120-265 6.02e-05

dihydroorotate dehydrogenase;


Pssm-ID: 235982  Cd Length: 301  Bit Score: 44.76  E-value: 6.02e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549423  120 ISGLDINMGCPkefSIKGGmGAALLADPDKAAHILRTLCSGLDIPVTCKIRilPDVEGTIDL---VQKLAATGIAAI--- 193
Cdd:PRK07259 119 VDAIELNISCP---NVKHG-GMAFGTDPELAYEVVKAVKEVVKVPVIVKLT--PNVTDIVEIakaAEEAGADGLSLIntl 192

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549423  194 ---GIHARTRdeRP---------QHPA-HPEVLRAV---AQAVDIPIIANGGsknMHCYDDLRKFQMeCGADSVMVARAA 257
Cdd:PRK07259 193 kgmAIDIKTR--KPilanvtgglSGPAiKPIALRMVyqvYQAVDIPIIGMGG---ISSAEDAIEFIM-AGASAVQVGTAN 266


                 ....*...
gi 45549423  258 QINVSIFR 265
Cdd:PRK07259 267 FYDPYAFP 274
His_biosynth pfam00977
Histidine biosynthesis protein; Proteins involved in steps 4 and 6 of the histidine ...
 179-256 1.20e-04

Histidine biosynthesis protein; Proteins involved in steps 4 and 6 of the histidine biosynthesis pathway are contained in this family. Histidine is formed by several complex and distinct biochemical reactions catalyzed by eight enzymes. The enzymes in this Pfam entry are called His6 and His7 in eukaryotes and HisA and HisF in prokaryotes. The structure of HisA is known to be a TIM barrel fold. In some archaeal HisA proteins the TIM barrel is composed of two tandem repeats of a half barrel. This family belong to the common phosphate binding site TIM barrel family.


Pssm-ID: 425971  Cd Length: 228  Bit Score: 43.24  E-value: 1.20e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 45549423   179 IDLVQKLAATGIAAIGIHARTRDERPQHPAhPEVLRAVAQAVDIPIIANGGSKNMhcyDDLRKFQMEcGADSVMVARA 256
Cdd:pfam00977 149 VEWAKELEELGAGEILLTDIDRDGTLSGPD-LELTRELAEAVNIPVIASGGVGSL---EDLKELFTE-GVDGVIAGSA 221
DSRM_RNAse_III_family cd10845
double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase ...
 395-457 1.39e-04

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: 40.17  E-value: 1.39e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 45549423 395 PKTQLYVHAVKTGKSPPAYETQQC-----DKLFRSICTYDGQRFSSSfWEKNKKQAEQGAALVALLHL 457
Cdd:cd10845   3 YKTALQEYLQKRGLPLPEYELVEEegpdhNKTFTVEVKVNGKVIGEG-TGRSKKEAEQAAAKAALEKL 69
HisF COG0107
Imidazole glycerol phosphate synthase subunit HisF [Amino acid transport and metabolism]; ...
 211-264 1.51e-04

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


Pssm-ID: 439877  Cd Length: 251  Bit Score: 43.09  E-value: 1.51e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 45549423 211 EVLRAVAQAVDIPIIANGGSKNM-HCYDDLRkfqmECGADSVMVAraaqinvSIF 264
Cdd:COG0107 185 ELTRAVSEAVSIPVIASGGAGTLeHFVEVFT----EGGADAALAA-------SIF 228
FadH COG1902
2,4-dienoyl-CoA reductase or related NADH-dependent reductase, Old Yellow Enzyme (OYE) family ...
 174-257 8.57e-04

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


Pssm-ID: 441506 [Multi-domain]  Cd Length: 365  Bit Score: 41.31  E-value: 8.57e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45549423 174 DVEGTIDLVQKLAATGIAAIGIHARTRDERPQHPAHP------EVLRAVAQAVDIPIIANGGsknmhcYDDLRkfQMEC- 246
Cdd:COG1902 234 TLEESVELAKALEEAGVDYLHVSSGGYEPDAMIPTIVpegyqlPFAARIRKAVGIPVIAVGG------ITTPE--QAEAa 305

                        90
                ....*....|....*
gi 45549423 247 ----GADSVMVARAA 257
Cdd:COG1902 306 lasgDADLVALGRPL 320
HisF cd04731
The cyclase subunit of imidazoleglycerol phosphate synthase (HisF). Imidazole glycerol ...
 211-264 1.57e-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: 40.14  E-value: 1.57e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 45549423 211 EVLRAVAQAVDIPIIANGGSKNMhcyDDLRKFQMECGADSVMVAraaqinvSIF 264
Cdd:cd04731 183 ELIRAVSSAVNIPVIASGGAGKP---EHFVEAFEEGGADAALAA-------SIF 226
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
395-458 2.50e-03

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 39.31  E-value: 2.50e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 45549423 395 PKTQL--YVHAvkTGKSPPAYETQQC-----DKLFRSICTYDGQRFSSSfWEKNKKQAEQGAALVALLHLG 458
Cdd:COG0571 159 YKTALqeWLQA--RGLPLPEYEVVEEegpdhAKTFTVEVLVGGKVLGEG-TGRSKKEAEQAAAKAALEKLG 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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