Citrus Sinensis ID: 041023

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300---
MDTNTNKYLLALVVFSLHSLQIQWSLVVAMEEAHQEEALISHLLQDLFVNEKAGDESESESLPNANNLDEEEILGYRFNNKNLLEEAFTDPSCPERFFSYERLEYVGDSVLNLLLTKEQFFLYPNLPPGSLTRLRSANVNTEKLARVAIKLGLHKYLRHNKPLLEEQIREFSEAILDYPLHSNGLVDAPKVLADIVESTIGAVFIDCNSSIDIVWKVFKELLKPMISPETLKTHPVTELYEVCQKNKLKVKFVDLWKESTAFHIFIEDQLLGRGAYAPKKEIAHNRAAKDALNNIERLLNEKR
cccccHHHHHHHHHcccccccHHHEEEEEcHHHHHHHHHHHHHHcccccccccccccccccccccccHHHHHHcccEEccHHHHHHHHccccccccccccccccHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHccccHHHHHHHHHccccHHHHcccccHHHHHHHHHHHHHccccccccccccccHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHccccccccccccccHHHHHHHHHccccccEEEEEEcccEEEEEEccEEEEEEEccccHHHHHHHHHHHHHHHHHHHHcccc
ccccHHHHHHHHHHHHHHHHHccccEEEcHHHHHHHHHHccccccccccccccccHHHHcccccHHHHHHHHHHccccccHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHccHHHHHHHHHHccHHHccEcccccHHHccHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHcHccccccccccHHHHHHHHHHHccccccEEEEEEEccccEEEEEcEEEEcccccccHHHHHHHHHHHHHHHHHHHHHccc
MDTNTNKYLLALVVFSLHSLQIQWSLVVAMEEAHQEEALISHLLQDLfvnekagdeseseslpnannldeeeilgyrfnnknlleeaftdpscperffsyerLEYVGDSVLNLLLtkeqfflypnlppgsltrlrsanvnTEKLARVAIKLGLHKYLRHNKPLLEEQIREFSEAILdyplhsnglvdapKVLADIVESTIGAVFIDCNSSIDIVWKVFKELLkpmispetlkthpvteLYEVCQKNKLKVKFVDLWKESTAFHIFIEdqllgrgayapkkeiaHNRAAKDALNNIERLLNEKR
MDTNTNKYLLALVVFSLHSLQIQWSLVVAMEEAHQEEALISHLLQDLFVNEKAGdeseseslpnannldeeEILGYRFNNKNLLEEAFTDPSCPERFFSYERLEYVGDSVLNLLLTKEQFFLYPNLPPGSLTRLRSANVNTEKLARVAIKLGLHKYLRHNKPLLEEQIREFSEAILDYPLHSNGLVDAPKVLADIVESTIGAVFIDCNSSIDIVWKVFKELLKPMispetlkthpvtELYEVCQKNKLKVKFVDLWKESTAFHIFIEDQLLGRGAYAPKKEiahnraakdalnnierllnekr
MDTNTNKYLLALVVFSLHSLQIQWSLVVAMEEAHQEEALISHLLQDLFVNEKAGDESESESLPNANNLDEEEILGYRFNNKNLLEEAFTDPSCPERFFSYERLEYVGDSVLNLLLTKEQFFLYPNLPPGSLTRLRSANVNTEKLARVAIKLGLHKYLRHNKPLLEEQIREFSEAILDYPLHSNGLVDAPKVLADIVESTIGAVFIDCNSSIDIVWKVFKELLKPMISPETLKTHPVTELYEVCQKNKLKVKFVDLWKESTAFHIFIEDQLLGRGAYAPKKEIAHNRAAKDALNNIERLLNEKR
******KYLLALVVFSLHSLQIQWSLVVAMEEAHQEEALISHLLQDLFV**********************EILGYRFNNKNLLEEAFTDPSCPERFFSYERLEYVGDSVLNLLLTKEQFFLYPNLPPGSLTRLRSANVNTEKLARVAIKLGLHKYLRHNKPLLEEQIREFSEAILDYPLHSNGLVDAPKVLADIVESTIGAVFIDCNSSIDIVWKVFKELLKPMISPETLKTHPVTELYEVCQKNKLKVKFVDLWKESTAFHIFIEDQLLGRGAYAPK************************
******K**LALVVFSLHSLQIQWSLVVAMEEAHQEEALISHLLQD********************NLDEEEILGYRFNNKNLLEEAFTDPSCPERFFSYERLEYVGDSVLNLLLTKEQFFLYPNLPPGSLTRLRSANVNTEKLARVAIKLGLHKYLRHNKPLLEEQIREFSEA***********VDAPKVLADIVESTIGAVFIDCNSSIDIVWKVFKELLKPMISPETLKTHPVTELYEVCQKNKLKVKFVDLWKESTAFHIFIEDQLL*************NRAAKDALNNI*RL*****
MDTNTNKYLLALVVFSLHSLQIQWSLVVAMEEAHQEEALISHLLQDLFVNE************NANNLDEEEILGYRFNNKNLLEEAFTDPSCPERFFSYERLEYVGDSVLNLLLTKEQFFLYPNLPPGSLTRLRSANVNTEKLARVAIKLGLHKYLRHNKPLLEEQIREFSEAILDYPLHSNGLVDAPKVLADIVESTIGAVFIDCNSSIDIVWKVFKELLKPMISPETLKTHPVTELYEVCQKNKLKVKFVDLWKESTAFHIFIEDQLLGRGAYAPKKEIAHNRAAKDALNNIERLLNEKR
*DTNTNKYLLALVVFSLHSLQIQWSLVVAMEEAHQEEALISHLLQDLFV***AGDESESESLPNANNLDEEEILGYRFNNKNLLEEAFTDPSCPERFFSYERLEYVGDSVLNLLLTKEQFFLYPNLPPGSLTRLRSANVNTEKLARVAIKLGLHKYLRHNKPLLEEQIREFSEAILDYPLHSNGLVDAPKVLADIVESTIGAVFIDCNSSIDIVWKVFKELLKPMISPETLKTHPVTELYEVCQKNKLKVKFVDLWKESTAFHIFIEDQLLGRGAYAPKKEIAHNR**KDALNNIERLL****
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MDTNTNKYLLALVVFSLHSLQIQWSLVVAMEEAHQEEALISHLLQDLFVNEKAGDESESESLPNANNLDEEEILGYRFNNKNLLEEAFTDPSCPERFFSYERLEYVGDSVLNLLLTKEQFFLYPNLPPGSLTRLRSANVNTEKLARVAIKLGLHKYLRHNKPLLEEQIREFSEAILDYPLHSNGLVDAPKVLADIVESTIGAVFIDCNSSIDIVWKVFKELLKPMISPETLKTHPVTELYEVCQKNKLKVKFVDLWKESTAFHIFIEDQLLGRGAYAPKKEIAHNRAAKDALNNIERLLNEKR
no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST ?

Original result of BLAST against SWISS-PROT Database

ID ?Alignment graph ?Length ? Definition ? RBH(Q2H) ? RBH(H2Q) ? Q cover ? H cover ? Identity ? E-value ?
Query303 2.2.26 [Sep-21-2011]
Q69KJ0299 Ribonuclease 3-like prote yes no 0.768 0.779 0.514 5e-63
Q8LMR2 1883 Endoribonuclease Dicer ho no no 0.752 0.121 0.467 2e-47
Q9LTQ0391 Ribonuclease 3-like prote no no 0.745 0.578 0.427 8e-46
Q9SP32 1909 Endoribonuclease Dicer ho no no 0.702 0.111 0.468 4e-44
Q6ATG6317 Ribonuclease 3-like prote no no 0.735 0.703 0.397 4e-40
Q5N870 1651 Endoribonuclease Dicer ho no no 0.745 0.136 0.385 2e-34
Q3EBC81388 Endoribonuclease Dicer ho no no 0.765 0.167 0.382 9e-34
Q7XD96 1637 Endoribonuclease Dicer ho no no 0.597 0.110 0.419 2e-32
Q9LXW7 1580 Endoribonuclease Dicer ho no no 0.775 0.148 0.371 2e-31
A7LFZ6 1657 Endoribonuclease Dicer ho no no 0.636 0.116 0.362 1e-28
>sp|Q69KJ0|RTL3_ORYSJ Ribonuclease 3-like protein 3 OS=Oryza sativa subsp. japonica GN=Os06g0358800 PE=2 SV=1 Back     alignment and function desciption
 Score =  241 bits (615), Expect = 5e-63,   Method: Compositional matrix adjust.
 Identities = 122/237 (51%), Positives = 165/237 (69%), Gaps = 4/237 (1%)

Query: 71  EEILGYRFNNKNLLEEAFTDPS--CPER-FFSYERLEYVGDSVLNLLLTKEQFFLYPNLP 127
           E +LGY F +K L+EEA T  S   P R   +YERLEY+GD+VL  ++++E F  Y  L 
Sbjct: 43  ESLLGYEFRDKALVEEALTHGSFYYPYRPGVTYERLEYLGDAVLTCVVSREVFLTYGQLQ 102

Query: 128 PGSLTRLRSANVNTEKLARVAIKLGLHKYLRHNKPLLEEQIREFSEAILDYPLHSNGLVD 187
           PG LTRLR+ANV+ EKLARVA+  GLH +LRH  P L+ QI +F E +  YP+HSNGL+D
Sbjct: 103 PGPLTRLRAANVDKEKLARVAVVHGLHHFLRHKAPNLDGQITDFIEELSMYPIHSNGLLD 162

Query: 188 APKVLADIVESTIGAVFIDCNSSIDIVWKVFKELLKPMISPETLKTHPVTELYEVCQKNK 247
            PKVL D+VES IGA++ D N + +IVW+VF++L  P+IS ETL  HPV+EL+E CQK +
Sbjct: 163 PPKVLCDVVESLIGAIYCDSNFNQEIVWQVFQKLADPLISLETLGKHPVSELFEFCQKTR 222

Query: 248 LKVKFV-DLWKESTAFHIFIEDQLLGRGAYAPKKEIAHNRAAKDALNNIERLLNEKR 303
             VK V D W ++    + I+ +++GR  YA KKEIA NRAAK AL+ ++  L + +
Sbjct: 223 RGVKIVKDEWDKNLTVEVLIDGEMVGRATYAQKKEIAQNRAAKAALDKLKETLGQSQ 279
Cleaves double-stranded RNA (dsRNA).
Oryza sativa subsp. japonica (taxid: 39947)
EC: 3EC: .EC: 1EC: .EC: 2EC: 6EC: .EC: -
>sp|Q8LMR2|DCL1_ORYSJ Endoribonuclease Dicer homolog 1 OS=Oryza sativa subsp. japonica GN=DCL1 PE=3 SV=1 Back     alignment and function description
>sp|Q9LTQ0|RTL2_ARATH Ribonuclease 3-like protein 2 OS=Arabidopsis thaliana GN=RTL2 PE=1 SV=1 Back     alignment and function description
>sp|Q9SP32|DCL1_ARATH Endoribonuclease Dicer homolog 1 OS=Arabidopsis thaliana GN=DCL1 PE=1 SV=2 Back     alignment and function description
>sp|Q6ATG6|RTL2_ORYSJ Ribonuclease 3-like protein 2 OS=Oryza sativa subsp. japonica GN=Os05g0271300 PE=2 SV=2 Back     alignment and function description
>sp|Q5N870|DCL3A_ORYSJ Endoribonuclease Dicer homolog 3a OS=Oryza sativa subsp. japonica GN=DCL3A PE=2 SV=1 Back     alignment and function description
>sp|Q3EBC8|DCL2_ARATH Endoribonuclease Dicer homolog 2 OS=Arabidopsis thaliana GN=At3g03300 PE=1 SV=2 Back     alignment and function description
>sp|Q7XD96|DCL3B_ORYSJ Endoribonuclease Dicer homolog 3b OS=Oryza sativa subsp. japonica GN=DCL3B PE=2 SV=2 Back     alignment and function description
>sp|Q9LXW7|DCL3_ARATH Endoribonuclease Dicer homolog 3 OS=Arabidopsis thaliana GN=DCL3 PE=1 SV=2 Back     alignment and function description
>sp|A7LFZ6|DCL4_ORYSJ Endoribonuclease Dicer homolog 4 OS=Oryza sativa subsp. japonica GN=DCL4 PE=2 SV=1 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query303
224064945303 predicted protein [Populus trichocarpa] 0.831 0.831 0.719 1e-100
359485630287 PREDICTED: ribonuclease 3-like protein 3 0.818 0.864 0.645 2e-87
147770295287 hypothetical protein VITISV_005321 [Viti 0.818 0.864 0.641 5e-86
357462175 565 Endoribonuclease Dicer-like protein [Med 0.841 0.451 0.603 6e-86
255589974259 dicer-1, putative [Ricinus communis] gi| 0.788 0.922 0.611 1e-84
357462179322 Ribonuclease 3-like protein [Medicago tr 0.755 0.711 0.606 8e-78
449493233275 PREDICTED: ribonuclease 3-like protein 3 0.739 0.814 0.634 3e-76
357462157 783 Endoribonuclease Dicer-like protein [Med 0.749 0.289 0.614 7e-76
449453708275 PREDICTED: ribonuclease 3-like protein 3 0.739 0.814 0.629 2e-75
240255863264 protein RNAse II-like 1 [Arabidopsis tha 0.759 0.871 0.538 4e-62
>gi|224064945|ref|XP_002301611.1| predicted protein [Populus trichocarpa] gi|222843337|gb|EEE80884.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
 Score =  371 bits (953), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 185/257 (71%), Positives = 211/257 (82%), Gaps = 5/257 (1%)

Query: 51  EKAGDESESESLPNANN----LDE-EEILGYRFNNKNLLEEAFTDPSCPERFFSYERLEY 105
           E + D SE  S     +    LDE EEIL Y+F +K LLEEA T  S  ++ FSYERLEY
Sbjct: 33  ESSDDRSEVASGKQTTDWVTDLDEVEEILHYKFKSKKLLEEALTHASFSDQCFSYERLEY 92

Query: 106 VGDSVLNLLLTKEQFFLYPNLPPGSLTRLRSANVNTEKLARVAIKLGLHKYLRHNKPLLE 165
           VGDSVLNLL TKEQ+FLYP+LPPG LTRLRSANV+TEKLARVAIK  LH+YLRH  PLLE
Sbjct: 93  VGDSVLNLLFTKEQYFLYPDLPPGPLTRLRSANVDTEKLARVAIKHKLHRYLRHKMPLLE 152

Query: 166 EQIREFSEAILDYPLHSNGLVDAPKVLADIVESTIGAVFIDCNSSIDIVWKVFKELLKPM 225
           EQIREFS+AILDYPLHSNGLV+ PK LADIVE+ IGAVFID N SID+VWK+FK+LL+P+
Sbjct: 153 EQIREFSQAILDYPLHSNGLVETPKALADIVEAAIGAVFIDSNFSIDVVWKIFKDLLEPI 212

Query: 226 ISPETLKTHPVTELYEVCQKNKLKVKFVDLWKESTAFHIFIEDQLLGRGAYAPKKEIAHN 285
           IS ETLK HPVTELYEVCQK  LKVKFVDLWKE+ AF +FI+DQ +GRG Y  KKEIAHN
Sbjct: 213 ISQETLKVHPVTELYEVCQKRNLKVKFVDLWKENMAFDVFIDDQFVGRGTYGLKKEIAHN 272

Query: 286 RAAKDALNNIERLLNEK 302
           RAAK+ALNNI ++L+EK
Sbjct: 273 RAAKNALNNIRKILSEK 289

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|359485630|ref|XP_002270948.2| PREDICTED: ribonuclease 3-like protein 3-like [Vitis vinifera] gi|297739192|emb|CBI28843.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|147770295|emb|CAN62473.1| hypothetical protein VITISV_005321 [Vitis vinifera] Back     alignment and taxonomy information
>gi|357462175|ref|XP_003601369.1| Endoribonuclease Dicer-like protein [Medicago truncatula] gi|355490417|gb|AES71620.1| Endoribonuclease Dicer-like protein [Medicago truncatula] Back     alignment and taxonomy information
>gi|255589974|ref|XP_002535144.1| dicer-1, putative [Ricinus communis] gi|223523936|gb|EEF27239.1| dicer-1, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|357462179|ref|XP_003601371.1| Ribonuclease 3-like protein [Medicago truncatula] gi|355490419|gb|AES71622.1| Ribonuclease 3-like protein [Medicago truncatula] Back     alignment and taxonomy information
>gi|449493233|ref|XP_004159229.1| PREDICTED: ribonuclease 3-like protein 3-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|357462157|ref|XP_003601360.1| Endoribonuclease Dicer-like protein [Medicago truncatula] gi|355490408|gb|AES71611.1| Endoribonuclease Dicer-like protein [Medicago truncatula] Back     alignment and taxonomy information
>gi|449453708|ref|XP_004144598.1| PREDICTED: ribonuclease 3-like protein 3-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|240255863|ref|NP_680697.4| protein RNAse II-like 1 [Arabidopsis thaliana] gi|332658200|gb|AEE83600.1| protein RNAse II-like 1 [Arabidopsis thaliana] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query303
TAIR|locus:504955425264 RTL1 "RNAse II-like 1" [Arabid 0.821 0.943 0.509 5.5e-61
TAIR|locus:2092409391 RTL2 "RNAse THREE-like protein 0.742 0.575 0.429 7.9e-46
UNIPROTKB|Q8LMR2 1883 DCL1 "Endoribonuclease Dicer h 0.762 0.122 0.469 3.4e-43
TAIR|locus:20977051388 DCL2 "dicer-like 2" [Arabidops 0.788 0.172 0.376 1.2e-34
TAIR|locus:2153333 957 RTL3 "RNAse THREE-like protein 0.528 0.167 0.425 4.7e-30
TAIR|locus:2149259 1702 DCL4 "dicer-like 4" [Arabidops 0.666 0.118 0.376 3.8e-28
UNIPROTKB|A7LFZ6 1657 DCL4 "Endoribonuclease Dicer h 0.646 0.118 0.358 9.8e-28
TIGR_CMR|CHY_1444235 CHY_1444 "ribonuclease III" [C 0.316 0.408 0.415 7.9e-24
FB|FBgn00390162249 Dcr-1 "Dicer-1" [Drosophila me 0.567 0.076 0.368 6.2e-22
ZFIN|ZDB-GENE-030131-34451865 dicer1 "Dicer1, Dcr-1 homolog 0.749 0.121 0.285 4.4e-19
TAIR|locus:504955425 RTL1 "RNAse II-like 1" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 624 (224.7 bits), Expect = 5.5e-61, P = 5.5e-61
 Identities = 129/253 (50%), Positives = 175/253 (69%)

Query:    50 NEKAGDESESESLPNANNLDEEEILGYRFNNKNLLEEAFTDPS-CPERFFSYERLEYVGD 108
             N K    ++ + L    +L  E+IL Y+F +K+LL +AFTD S   ++  SYE LE +GD
Sbjct:    14 NTKTIGSADPDQLMEIESL--EKILNYKFKDKSLLLKAFTDASYVDDKSESYELLELLGD 71

Query:   109 SVLNLLLTKEQFFLYPNLPPGSLTRLRSANVNTEKLARVAIKLGLHKYLRHNKPLLEEQI 168
             S+LN+ +  +   LYP   PG LT+LR+ NV+TEKLARVA+   L+ YLRH KPLLEEQI
Sbjct:    72 SILNMGIIYDFIKLYPKEAPGPLTKLRAVNVDTEKLARVAVNHQLYSYLRHKKPLLEEQI 131

Query:   169 REFSEAILDYPLHSNGLVDAPKVLADIVESTIGAVFIDCNSSIDIVWKVFKELLKPMISP 228
              EF EA+  YPLHSNGL+  PKVLADIVESTIGA+F+DCNS+ + VWKV K LL+P+I  
Sbjct:   132 LEFVEAMEKYPLHSNGLLKVPKVLADIVESTIGAIFMDCNST-ETVWKVIKPLLEPIIHL 190

Query:   229 ETLKTHPVTELYEVCQKNKLKVKFVDLWKESTAFHIFIEDQLLGRGAYAPKKEIAHNRAA 288
             + +K+HP+TEL E+CQK  LK+   D W+E+  +   IED+ +G G +  KKE A N AA
Sbjct:   191 DKMKSHPMTELNEMCQKRNLKLTSKDTWEENQTYCFHIEDKFVGCGHHPVKKETARNFAA 250

Query:   289 KDALNNIERLLNE 301
             K+A++N  +   +
Sbjct:   251 KNAIDNFAKFFGD 263
GO:0003723 "RNA binding" evidence=IEA;ISS
GO:0004525 "ribonuclease III activity" evidence=IEA;ISS
GO:0005737 "cytoplasm" evidence=ISM
GO:0006396 "RNA processing" evidence=IEA;ISS
TAIR|locus:2092409 RTL2 "RNAse THREE-like protein 2" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
UNIPROTKB|Q8LMR2 DCL1 "Endoribonuclease Dicer homolog 1" [Oryza sativa Japonica Group (taxid:39947)] Back     alignment and assigned GO terms
TAIR|locus:2097705 DCL2 "dicer-like 2" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2153333 RTL3 "RNAse THREE-like protein 3" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2149259 DCL4 "dicer-like 4" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
UNIPROTKB|A7LFZ6 DCL4 "Endoribonuclease Dicer homolog 4" [Oryza sativa Japonica Group (taxid:39947)] Back     alignment and assigned GO terms
TIGR_CMR|CHY_1444 CHY_1444 "ribonuclease III" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)] Back     alignment and assigned GO terms
FB|FBgn0039016 Dcr-1 "Dicer-1" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-030131-3445 dicer1 "Dicer1, Dcr-1 homolog (Drosophila)" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries ?

Original result of BLAST against SWISS-PROT

ID ?Name ?Annotated EC number ?Identity ?Query coverage ?Hit coverage ?RBH(Q2H) ?RBH(H2Q) ?
Q69KJ0RTL3_ORYSJ3, ., 1, ., 2, 6, ., -0.51470.76890.7792yesno

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

Prediction LevelEC numberConfidence of Prediction
3rd Layer3.1.260.691

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Your Input:
fgenesh4_pg.C_LG_II002055
hypothetical protein (303 aa)
(Populus trichocarpa)
Predicted Functional Partners:
gw1.VII.3631.1
hypothetical protein (351 aa)
•       0.437
fgenesh4_pm.C_LG_X000986
hypothetical protein (932 aa)
      • 0.424

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query303
COG0571235 COG0571, Rnc, dsRNA-specific ribonuclease [Transcr 4e-39
cd00593133 cd00593, RIBOc, RIBOc 1e-38
TIGR02191220 TIGR02191, RNaseIII, ribonuclease III, bacterial 2e-38
PRK00102229 PRK00102, rnc, ribonuclease III; Reviewed 2e-36
smart00535129 smart00535, RIBOc, Ribonuclease III family 6e-36
pfam0063691 pfam00636, Ribonuclease_3, Ribonuclease III domain 1e-24
PRK12371235 PRK12371, PRK12371, ribonuclease III; Reviewed 6e-13
PRK12372 413 PRK12372, PRK12372, ribonuclease III; Reviewed 9e-13
PRK14718 467 PRK14718, PRK14718, ribonuclease III; Provisional 2e-12
pfam0003566 pfam00035, dsrm, Double-stranded RNA binding motif 7e-06
smart0035867 smart00358, DSRM, Double-stranded RNA binding moti 1e-04
>gnl|CDD|223644 COG0571, Rnc, dsRNA-specific ribonuclease [Transcription] Back     alignment and domain information 
 Score =  136 bits (346), Expect = 4e-39
 Identities = 73/235 (31%), Positives = 109/235 (46%), Gaps = 33/235 (14%)

Query: 71  EEILGYRFNNKNLLEEAFTDPSC---PERFFSYERLEYVGDSVLNLLLTKEQFFLYPNLP 127
           E+ LGY F +K LLE+A T  S     +   + ERLE++GD+VL L++ +  F  YPNLP
Sbjct: 12  EKKLGYTFKDKELLEQALTHRSYANEHKAVENNERLEFLGDAVLGLVVAEYLFKKYPNLP 71

Query: 128 PGSLTRLRSANVNTEKLARVAIKLGLHKYLRHNKPLLEEQIREFSEAILDYPLHSNGLVD 187
            G L++LR+A V+ E LA +A +LGL  YLR  K   +   R                  
Sbjct: 72  EGELSKLRAALVSEESLAEIARELGLGDYLRLGKGEEKSGGR-----------------R 114

Query: 188 APKVLADIVESTIGAVFIDCNSSIDIVWKVFKELLKPMISPETLKTH---PVTELYEVCQ 244
              +LAD  E+ IGA+++D  S ++   K   +L  P +           P T L E+ Q
Sbjct: 115 RESILADAFEALIGAIYLD--SGLEAARKFILKLFLPRLEEIDAGDQFKDPKTRLQELLQ 172

Query: 245 KNKLKV---KFVDLWKESTA----FHIFIEDQLLGRGAYAPKKEIAHNRAAKDAL 292
              L +   + V     +        + +  + LG G     K+ A   AA+ AL
Sbjct: 173 AQGLVLPEYRLVKEEGPAHDKEFTVEVAVGGKELGTG-KGRSKKEAEQAAAEQAL 226

Length = 235
>gnl|CDD|238333 cd00593, RIBOc, RIBOc Back     alignment and domain information
>gnl|CDD|233772 TIGR02191, RNaseIII, ribonuclease III, bacterial Back     alignment and domain information
>gnl|CDD|234633 PRK00102, rnc, ribonuclease III; Reviewed Back     alignment and domain information
>gnl|CDD|197778 smart00535, RIBOc, Ribonuclease III family Back     alignment and domain information
>gnl|CDD|216036 pfam00636, Ribonuclease_3, Ribonuclease III domain Back     alignment and domain information
>gnl|CDD|171444 PRK12371, PRK12371, ribonuclease III; Reviewed Back     alignment and domain information
>gnl|CDD|237081 PRK12372, PRK12372, ribonuclease III; Reviewed Back     alignment and domain information
>gnl|CDD|173181 PRK14718, PRK14718, ribonuclease III; Provisional Back     alignment and domain information
>gnl|CDD|215670 pfam00035, dsrm, Double-stranded RNA binding motif Back     alignment and domain information
>gnl|CDD|214634 smart00358, DSRM, Double-stranded RNA binding motif Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 303
COG0571235 Rnc dsRNA-specific ribonuclease [Transcription] 100.0
PRK12371235 ribonuclease III; Reviewed 100.0
PRK14718 467 ribonuclease III; Provisional 100.0
PRK12372 413 ribonuclease III; Reviewed 100.0
PRK00102229 rnc ribonuclease III; Reviewed 100.0
TIGR02191220 RNaseIII ribonuclease III, bacterial. This family 100.0
KOG1817533 consensus Ribonuclease [RNA processing and modific 100.0
PF14622128 Ribonucleas_3_3: Ribonuclease-III-like; PDB: 1O0W_ 99.97
smart00535129 RIBOc Ribonuclease III family. 99.96
cd00593133 RIBOc RIBOc. Ribonuclease III C terminal domain. T 99.95
PF00636114 Ribonuclease_3: Ribonuclease III domain; InterPro: 99.9
KOG3769333 consensus Ribonuclease III domain proteins [Transl 99.89
KOG07011606 consensus dsRNA-specific nuclease Dicer and relate 99.62
KOG0701 1606 consensus dsRNA-specific nuclease Dicer and relate 99.62
KOG1817 533 consensus Ribonuclease [RNA processing and modific 99.6
PHA03103183 double-strand RNA-binding protein; Provisional 99.3
PHA02701183 ORF020 dsRNA-binding PKR inhibitor; Provisional 99.29
PF0003567 dsrm: Double-stranded RNA binding motif; InterPro: 99.24
cd0004868 DSRM Double-stranded RNA binding motif. Binding is 99.19
smart0035867 DSRM Double-stranded RNA binding motif. 99.17
PF1470980 DND1_DSRM: double strand RNA binding domain from D 98.3
KOG3732 339 consensus Staufen and related double-stranded-RNA- 98.26
COG1939132 Ribonuclease III family protein [Replication, reco 97.93
KOG3732 339 consensus Staufen and related double-stranded-RNA- 97.88
KOG4334 650 consensus Uncharacterized conserved protein, conta 96.72
KOG2777 542 consensus tRNA-specific adenosine deaminase 1 [RNA 96.39
PF11469120 Ribonucleas_3_2: Ribonuclease III; InterPro: IPR02 91.02
PF0336890 Dicer_dimer: Dicer dimerisation domain; InterPro: 88.0
>COG0571 Rnc dsRNA-specific ribonuclease [Transcription] Back     alignment and domain information 
Probab=100.00  E-value=1.3e-51  Score=365.00  Aligned_cols=212  Identities=35%  Similarity=0.503  Sum_probs=192.6

Q ss_pred             CccH-HHhcCCccCCHHHHHHhhcCCCCCCC---CCChhHHHHhhHHHHHHHHHHHHHHhCCCCChhchHHHHHhhcChH
Q 041023           67 NLDE-EEILGYRFNNKNLLEEAFTDPSCPER---FFSYERLEYVGDSVLNLLLTKEQFFLYPNLPPGSLTRLRSANVNTE  142 (303)
Q Consensus        67 ~l~~-e~~lgy~F~~~~LL~~AlTh~S~~~~---~~~~erLEfLGDavL~~~v~~~l~~~~p~~~~g~Lt~lr~~lvsn~  142 (303)
                      .+.. ++.+||+|+|++||.+||||+||.+.   ..+|||||||||+||+++|+++||++||+.+||.||.+|+.+||+.
T Consensus         7 ~~~~l~~~lg~~f~~~~lL~~AltH~S~~~e~~~~~~nERLEFLGDavL~l~vae~Lf~~yP~~~EG~Ls~~ra~lV~~~   86 (235)
T COG0571           7 KLEALEKKLGYTFKDKELLEQALTHRSYANEHKAVENNERLEFLGDAVLGLVVAEYLFKKYPNLPEGELSKLRAALVSEE   86 (235)
T ss_pred             HHHHHHHHhCCCcCCHHHHHHHhcCcchhccccCCcchHHHHhhHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHH
Confidence            3556 99999999999999999999999752   4689999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHcCchhhhhcCCcchHHHHHHHHHHhhcCCCCCCCCCCCchhHHHHHHHHhhhhcccCCCCHHHHHHHHHHhh
Q 041023          143 KLARVAIKLGLHKYLRHNKPLLEEQIREFSEAILDYPLHSNGLVDAPKVLADIVESTIGAVFIDCNSSIDIVWKVFKELL  222 (303)
Q Consensus       143 ~La~~a~~~gL~~~i~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~k~laD~fEAliGAIylD~G~~~~~v~~~i~~ll  222 (303)
                      +|+.+|..+||++|++.++++.                 ..+++..++++||+|||+|||||+|+|+  +.+++|+.+++
T Consensus        87 ~La~ia~~l~l~~~l~lg~ge~-----------------~~gg~~~~silaD~~EAligAiylD~g~--~~~~~~i~~l~  147 (235)
T COG0571          87 SLAEIARELGLGDYLRLGKGEE-----------------KSGGRRRESILADAFEALIGAIYLDSGL--EAARKFILKLF  147 (235)
T ss_pred             HHHHHHHHhCccchhhccCChh-----------------hcCCCCchhHHHHHHHHHHHHHHHhCCh--HHHHHHHHHHH
Confidence            9999999999999999998753                 1467788999999999999999999997  89999999999


Q ss_pred             cccCCCCc---ccCCCccHHHHHHHhCCCcceEEEee-------cceeEEEEEECCEEEEEEEeccchHHHHHHHHHHHH
Q 041023          223 KPMISPET---LKTHPVTELYEVCQKNKLKVKFVDLW-------KESTAFHIFIEDQLLGRGAYAPKKEIAHNRAAKDAL  292 (303)
Q Consensus       223 ~~~l~~~~---~~~~Pk~~Lqe~~q~~~~~~~~~~~~-------~~~~~v~V~i~~~~ig~G~g~skk~~Ae~~AA~~AL  292 (303)
                      .|.+....   ...|||++||||+|.+++..|.|++.       ++.|+++|.++|..+|+|.|.|+|+ |||.||++||
T Consensus       148 ~~~~~~~~~~~~~~D~Kt~LQe~~q~~~~~~p~Y~~v~~~g~~h~~~F~v~v~v~~~~~g~G~G~skk~-AEq~AA~~al  226 (235)
T COG0571         148 LPRLEEIDAGDQFKDPKTRLQELLQAQGLVLPEYRLVKEEGPAHDKEFTVEVAVGGKELGTGKGRSKKE-AEQAAAEQAL  226 (235)
T ss_pred             HHHHhhccccccccChhHHHHHHHHhcCCCCCeEEEeeccCCCCCceEEEEEEECCeeEEEecccCHHH-HHHHHHHHHH
Confidence            99876432   34799999999999999999988764       3468999999999999999999996 9999999999


Q ss_pred             HHHHhh
Q 041023          293 NNIERL  298 (303)
Q Consensus       293 ~~l~~~  298 (303)
                      +.+...
T Consensus       227 ~~l~~~  232 (235)
T COG0571         227 KKLGVK  232 (235)
T ss_pred             HHhccc
Confidence            998754

>PRK12371 ribonuclease III; Reviewed Back     alignment and domain information
>PRK14718 ribonuclease III; Provisional Back     alignment and domain information
>PRK12372 ribonuclease III; Reviewed Back     alignment and domain information
>PRK00102 rnc ribonuclease III; Reviewed Back     alignment and domain information
>TIGR02191 RNaseIII ribonuclease III, bacterial Back     alignment and domain information
>KOG1817 consensus Ribonuclease [RNA processing and modification] Back     alignment and domain information
>PF14622 Ribonucleas_3_3: Ribonuclease-III-like; PDB: 1O0W_A 2A11_A 3N3W_B Back     alignment and domain information
>smart00535 RIBOc Ribonuclease III family Back     alignment and domain information
>cd00593 RIBOc RIBOc Back     alignment and domain information
>PF00636 Ribonuclease_3: Ribonuclease III domain; InterPro: IPR000999 Prokaryotic ribonuclease III (3 Back     alignment and domain information
>KOG3769 consensus Ribonuclease III domain proteins [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>KOG0701 consensus dsRNA-specific nuclease Dicer and related ribonucleases [RNA processing and modification] Back     alignment and domain information
>KOG0701 consensus dsRNA-specific nuclease Dicer and related ribonucleases [RNA processing and modification] Back     alignment and domain information
>KOG1817 consensus Ribonuclease [RNA processing and modification] Back     alignment and domain information
>PHA03103 double-strand RNA-binding protein; Provisional Back     alignment and domain information
>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional Back     alignment and domain information
>PF00035 dsrm: Double-stranded RNA binding motif; InterPro: IPR001159 The DsRBD domain is found in a variety of RNA-binding proteins with different structures and exhibiting a diversity of functions [] Back     alignment and domain information
>cd00048 DSRM Double-stranded RNA binding motif Back     alignment and domain information
>smart00358 DSRM Double-stranded RNA binding motif Back     alignment and domain information
>PF14709 DND1_DSRM: double strand RNA binding domain from DEAD END PROTEIN 1 Back     alignment and domain information
>KOG3732 consensus Staufen and related double-stranded-RNA-binding proteins [Intracellular trafficking, secretion, and vesicular transport; Transcription] Back     alignment and domain information
>COG1939 Ribonuclease III family protein [Replication, recombination, and repair] Back     alignment and domain information
>KOG3732 consensus Staufen and related double-stranded-RNA-binding proteins [Intracellular trafficking, secretion, and vesicular transport; Transcription] Back     alignment and domain information
>KOG4334 consensus Uncharacterized conserved protein, contains double-stranded RNA-binding motif and WW domain [General function prediction only] Back     alignment and domain information
>KOG2777 consensus tRNA-specific adenosine deaminase 1 [RNA processing and modification] Back     alignment and domain information
>PF11469 Ribonucleas_3_2: Ribonuclease III; InterPro: IPR021568 This archaeal family of proteins has no known function Back     alignment and domain information
>PF03368 Dicer_dimer: Dicer dimerisation domain; InterPro: IPR005034 This domain is found in members of the Dicer protein family of dsRNA nucleases Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query303
3c4t_A265 Structure Of Rnaseiiib And Dsrna Binding Domains Of 4e-20
2eb1_A200 Crystal Structure Of The C-Terminal Rnase Iii Domai 2e-19
3c4b_A265 Structure Of Rnaseiiib And Dsrna Binding Domains Of 3e-18
3n3w_A248 2.2 Angstrom Resolution Crystal Structure Of Nuclea 8e-13
3o2r_D144 Structural Flexibility In Region Involved In Dimer 1e-12
3o2r_A170 Structural Flexibility In Region Involved In Dimer 2e-11
1yyk_A221 Crystal Structure Of Rnase Iii From Aquifex Aeolicu 3e-11
1yz9_A221 Crystal Structure Of Rnase Iii Mutant E110q From Aq 6e-11
1yyo_A221 Crystal Structure Of Rnase Iii Mutant E110k From Aq 9e-11
1rc7_A220 Crystal Structure Of Rnase Iii Mutant E110k From Aq 1e-10
2ez6_A221 Crystal Structure Of Aquifex Aeolicus Rnase Iii (d4 1e-10
1i4s_A147 Crystal Structure Of Rnase Iii Endonuclease Domain 2e-09
1jfz_A154 Crystal Structure Of Mn(Ii)-Complex Of Rnase Iii En 2e-09
2a11_A242 Crystal Structure Of Nuclease Domain Of Ribonuclase 5e-09
1o0w_A252 Crystal Structure Of Ribonuclease Iii (Tm1102) From 4e-07
2ffl_A 756 Crystal Structure Of Dicer From Giardia Intestinali 7e-07
3rv0_A341 Crystal Structure Of K. Polysporus Dcr1 Without The 7e-05
3rv1_A246 Crystal Structure Of The N-Terminal And Rnase Iii D 7e-04
>pdb|3C4T|A Chain A, Structure Of Rnaseiiib And Dsrna Binding Domains Of Mouse Dicer Length = 265 Back     alignment and structure 
Iteration: 1

 Score = 95.1 bits (235), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 73/252 (28%), Positives = 123/252 (48%), Gaps = 34/252 (13%)
Query: 71  EEILGYRFNNKNLLEEAFTDPSCPERFFS--YERLEYVGDSVLNLLLTKEQFFLYPNLPP 128
           E+ + YRF NK  L +AFT  S      +  Y+RLE++GD++L+ L+TK  +       P
Sbjct: 19  EKKINYRFKNKAYLLQAFTHASYHYNTITDXYQRLEFLGDAILDYLITKHLYEDPRQHSP 78
Query: 129 GSLTRLRSANVNTEKLARVAIKLGLHKYLRHNKPLLEEQIREFSEAILDYPLHSNGL--- 185
           G LT LRSA VN    A +A+K   HKY +   P L   I +F    + + L  N +   
Sbjct: 79  GVLTDLRSALVNNTIFASLAVKYDYHKYFKAVSPELFHVIDDF----VKFQLEKNEMQGM 134
Query: 186 ----------------VDAPKVLADIVESTIGAVFIDCNSSIDIVWKVFKELLKPMIS-- 227
                           ++ PK + DI ES  GA+++D   S+++VW+V+  +++P+I   
Sbjct: 135 DSELRRSEEDEEKEEDIEVPKAMGDIFESLAGAIYMDSGMSLEVVWQVYYPMMQPLIEKF 194
Query: 228 PETLKTHPVTELYEVCQKNKLKVKFVDLWKESTAFHIFIEDQLLGRGAY---APKKEIAH 284
              +   PV EL E+  +     KF    +      + +  +++G+G +        IA 
Sbjct: 195 SANVPRSPVRELLEMEPET---AKFSPAERTYDG-KVRVTVEVVGKGKFKGVGRSYRIAK 250
Query: 285 NRAAKDALNNIE 296
           + AA+ AL +++
Sbjct: 251 SAAARRALRSLK 262
>pdb|2EB1|A Chain A, Crystal Structure Of The C-Terminal Rnase Iii Domain Of Human Dicer Length = 200 Back     alignment and structure
>pdb|3C4B|A Chain A, Structure Of Rnaseiiib And Dsrna Binding Domains Of Mouse Dicer Length = 265 Back     alignment and structure
>pdb|3N3W|A Chain A, 2.2 Angstrom Resolution Crystal Structure Of Nuclease Domain Ribonuclase Iii (Rnc) From Campylobacter Jejuni Length = 248 Back     alignment and structure
>pdb|3O2R|A Chain A, Structural Flexibility In Region Involved In Dimer Formation Of Nuclease Domain Of Ribonuclase Iii (Rnc) From Campylobacter Jejuni Length = 170 Back     alignment and structure
>pdb|1YYK|A Chain A, Crystal Structure Of Rnase Iii From Aquifex Aeolicus Complexed With Double-Stranded Rna At 2.5-Angstrom Resolution Length = 221 Back     alignment and structure
>pdb|1YZ9|A Chain A, Crystal Structure Of Rnase Iii Mutant E110q From Aquifex Aeolicus Complexed With Double Stranded Rna At 2.1- Angstrom Resolution Length = 221 Back     alignment and structure
>pdb|1YYO|A Chain A, Crystal Structure Of Rnase Iii Mutant E110k From Aquifex Aeolicus Complexed With Double-stranded Rna At 2.9- Angstrom Resolution Length = 221 Back     alignment and structure
>pdb|1RC7|A Chain A, Crystal Structure Of Rnase Iii Mutant E110k From Aquifex Aeolicus Complexed With Ds-Rna At 2.15 Angstrom Resolution Length = 220 Back     alignment and structure
>pdb|2EZ6|A Chain A, Crystal Structure Of Aquifex Aeolicus Rnase Iii (d44n) Complexed With Product Of Double-stranded Rna Processing Length = 221 Back     alignment and structure
>pdb|1I4S|A Chain A, Crystal Structure Of Rnase Iii Endonuclease Domain From Aquifex Aeolicus At 2.15 Angstrom Resolution Length = 147 Back     alignment and structure
>pdb|1JFZ|A Chain A, Crystal Structure Of Mn(Ii)-Complex Of Rnase Iii Endonuclease Domain From Aquifex Aeolicus At 2.10 Angstrom Resolution Length = 154 Back     alignment and structure
>pdb|2A11|A Chain A, Crystal Structure Of Nuclease Domain Of Ribonuclase Iii From Mycobacterium Tuberculosis Length = 242 Back     alignment and structure
>pdb|1O0W|A Chain A, Crystal Structure Of Ribonuclease Iii (Tm1102) From Thermotoga Maritima At 2.0 A Resolution Length = 252 Back     alignment and structure
>pdb|2FFL|A Chain A, Crystal Structure Of Dicer From Giardia Intestinalis Length = 756 Back     alignment and structure
>pdb|3RV0|A Chain A, Crystal Structure Of K. Polysporus Dcr1 Without The C-Terminal Dsrbd Length = 341 Back     alignment and structure
>pdb|3RV1|A Chain A, Crystal Structure Of The N-Terminal And Rnase Iii Domains Of K. Polysporus Dcr1 E224q Mutant Length = 246 Back     alignment and structure

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query303
3c4b_A265 Endoribonuclease dicer; RNAse, dsRNA binding prote 8e-69
3n3w_A248 Ribonuclease III; nuclease domain, ribonuclase III 1e-37
1o0w_A252 Ribonuclease III, RNAse III; TM1102, structural ge 2e-37
3rv0_A341 K. polysporus DCR1; RNAse III enzyme, RNA binding 3e-37
2nug_A221 Ribonuclease III, RNAse III; dsRNA, RNA interferen 2e-35
3o2r_A170 Ribonuclease III; structural genomics, center for 8e-32
2a11_A242 Ribonuclease III, RNAse III; nuclease domain, stru 9e-32
2qvw_A 756 GLP_546_48378_50642; dicer, RNAI,pseudo-merohedral 6e-30
2qvw_A756 GLP_546_48378_50642; dicer, RNAI,pseudo-merohedral 9e-26
3rv1_A246 K. polysporus DCR1; RNAse III enzyme, RNA binding 9e-29
1x49_A97 Interferon-induced, double-stranded RNA- activated 2e-05
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 3e-05
1x47_A98 DGCR8 protein; structural genomics, DSRM domain, N 8e-05
1qu6_A179 Protein kinase PKR; dsRNA-binding domain, solution 3e-04
>3c4b_A Endoribonuclease dicer; RNAse, dsRNA binding protein, ATP-binding, endonuclease, HEL hydrolase, nucleotide-binding, phosphoprotein, RN binding; HET: MSE; 1.68A {Mus musculus} PDB: 3c4t_A 2eb1_A Length = 265 Back     alignment and structure
 Score =  213 bits (545), Expect = 8e-69
 Identities = 69/251 (27%), Positives = 116/251 (46%), Gaps = 21/251 (8%)

Query: 66  NNLDE-EEILGYRFNNKNLLEEAFTDPSCPERFF--SYERLEYVGDSVLNLLLTKEQFFL 122
           +  +  E+ + YRF NK  L +AFT  S         Y+RLE++GD++L+ L+TK  +  
Sbjct: 13  SGFETFEKKINYRFKNKAYLLQAFTHASYHYNTITDCYQRLEFLGDAILDYLITKHLYED 72

Query: 123 YPNLPPGSLTRLRSANVNTEKLARVAIKLGLHKYLRHNKPLLEEQIREFSEAIL------ 176
                PG LT LRSA VN    A +A+K   HKY +   P L   I +F +  L      
Sbjct: 73  PRQHSPGVLTDLRSALVNNTIFASLAVKYDYHKYFKAVSPELFHVIDDFVKFQLEKNEMQ 132

Query: 177 ---------DYPLHSNGLVDAPKVLADIVESTIGAVFIDCNSSIDIVWKVFKELLKPMIS 227
                    +        ++ PK + DI ES  GA+++D   S+++VW+V+  +++P+I 
Sbjct: 133 GMDSELRRSEEDEEKEEDIEVPKAMGDIFESLAGAIYMDSGMSLEVVWQVYYPMMQPLIE 192

Query: 228 PETLK--THPVTELYEVCQKNKLKVKFVDLWKESTAFHIFIEDQLLGRGAYAPKKEIAHN 285
             +      PV EL E+  +          +       + +  +   +G       IA +
Sbjct: 193 KFSANVPRSPVRELLEMEPETAKFSPAERTYDGKVRVTVEVVGKGKFKGV-GRSYRIAKS 251

Query: 286 RAAKDALNNIE 296
            AA+ AL +++
Sbjct: 252 AAARRALRSLK 262
>3n3w_A Ribonuclease III; nuclease domain, ribonuclase III, IDP90862, csgid, structura genomics; 2.21A {Campylobacter jejuni subsp} Length = 248 Back     alignment and structure
>1o0w_A Ribonuclease III, RNAse III; TM1102, structural genomics, JCSG, PSI, protein structure initiative, joint center for structural genomics; 2.00A {Thermotoga maritima} SCOP: a.149.1.1 d.50.1.1 Length = 252 Back     alignment and structure
>3rv0_A K. polysporus DCR1; RNAse III enzyme, RNA binding protein; 2.29A {Vanderwaltozyma polyspora} Length = 341 Back     alignment and structure
>2nug_A Ribonuclease III, RNAse III; dsRNA, RNA interference, endonucleolytic cleavage, hydrolase/RNA complex; 1.70A {Aquifex aeolicus} SCOP: a.149.1.1 d.50.1.1 PDB: 1yyw_A 2nue_A 2nuf_A 1yyk_A 1yz9_A 1yyo_A 2ez6_A 1rc7_A 1i4s_A 1jfz_A 1rc5_A Length = 221 Back     alignment and structure
>3o2r_A Ribonuclease III; structural genomics, center for structural genomics of infec diseases, csgid, nuclease domain, ribonuclase III; HET: MLZ; 1.25A {Campylobacter jejuni subsp} PDB: 3o2r_B* Length = 170 Back     alignment and structure
>2a11_A Ribonuclease III, RNAse III; nuclease domain, structural genomic protein structure initiative; 2.10A {Mycobacterium tuberculosis} Length = 242 Back     alignment and structure
>2qvw_A GLP_546_48378_50642; dicer, RNAI,pseudo-merohedral twin, hydrolase; 3.00A {Giardia intestinalis} PDB: 2ffl_A Length = 756 Back     alignment and structure
>2qvw_A GLP_546_48378_50642; dicer, RNAI,pseudo-merohedral twin, hydrolase; 3.00A {Giardia intestinalis} PDB: 2ffl_A Length = 756 Back     alignment and structure
>3rv1_A K. polysporus DCR1; RNAse III enzyme, RNA binding protein; 1.98A {Vanderwaltozyma polyspora} Length = 246 Back     alignment and structure
>1x49_A Interferon-induced, double-stranded RNA- activated protein kinase; structure genomics, DSRM domain, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.50.1.1 Length = 97 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure
>1x47_A DGCR8 protein; structural genomics, DSRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.50.1.1 Length = 98 Back     alignment and structure
>1qu6_A Protein kinase PKR; dsRNA-binding domain, solution structure, transferase; NMR {Homo sapiens} SCOP: d.50.1.1 d.50.1.1 Length = 179 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query303
3n3w_A248 Ribonuclease III; nuclease domain, ribonuclase III 100.0
2nug_A221 Ribonuclease III, RNAse III; dsRNA, RNA interferen 100.0
3c4b_A265 Endoribonuclease dicer; RNAse, dsRNA binding prote 100.0
1o0w_A252 Ribonuclease III, RNAse III; TM1102, structural ge 100.0
2a11_A242 Ribonuclease III, RNAse III; nuclease domain, stru 100.0
3rv0_A341 K. polysporus DCR1; RNAse III enzyme, RNA binding 100.0
3o2r_A170 Ribonuclease III; structural genomics, center for 100.0
3rv1_A246 K. polysporus DCR1; RNAse III enzyme, RNA binding 100.0
2qvw_A756 GLP_546_48378_50642; dicer, RNAI,pseudo-merohedral 99.96
2qvw_A 756 GLP_546_48378_50642; dicer, RNAI,pseudo-merohedral 99.96
1u61_A138 Hypothetical protein; structural genomics, PSI, pr 99.87
2gsl_A137 Hypothetical protein; alpha-helical protein, struc 99.81
3adl_A88 RISC-loading complex subunit tarbp2; TRBP2, miRNA 99.5
1di2_A69 XLRBPA, double stranded RNA binding protein A; pro 99.48
3adg_A73 F21M12.9 protein; HYL1, miRNA processing mechanism 99.48
3adj_A76 F21M12.9 protein; HYL1, miRNA processing, RNA bind 99.47
1x47_A98 DGCR8 protein; structural genomics, DSRM domain, N 99.45
2cpn_A89 TAR RNA-binding protein 2; double-stranded RNA bin 99.44
1ekz_A76 DSRBDIII, maternal effect protein (staufen); struc 99.44
2khx_A85 Ribonuclease 3; drosha, RNA binding domain, hydrol 99.44
1uhz_A89 Staufen (RNA binding protein) homolog 2; DSRM, sta 99.43
2dix_A84 Interferon-inducible double stranded RNA- dependen 99.42
3llh_A90 RISC-loading complex subunit tarbp2; DSRBD, DSRM, 99.41
1t4n_A94 Ribonuclease III; DSRBD, RNA-binding, hydrolase; N 99.4
1t4o_A117 Ribonuclease III; RNT1P, DSRBD, RNA-binding, hydro 99.4
1x48_A88 Interferon-induced, double-stranded RNA- activated 99.4
2l2n_A103 Hyponastic leave 1; DSRBD, miRNA, RNA binding prot 99.39
1whq_A99 RNA helicase A; double-stranded RNA binding domain 99.36
1x49_A97 Interferon-induced, double-stranded RNA- activated 99.35
1whn_A128 Hypothetical protein riken cDNA 2310016K04; double 99.33
2b7t_A73 Double-stranded RNA-specific editase 1; RNA editin 99.3
1uil_A113 Double-stranded RNA-binding motif; structural geno 99.26
2dmy_A97 Spermatid perinuclear RNA-binding protein; DSRM do 99.26
2l33_A91 Interleukin enhancer-binding factor 3; structural 99.26
2ljh_A114 Double-stranded RNA-specific editase ADAR; DSRBD, 99.14
2yt4_A 232 Protein DGCR8; DSRBD, RNA binding domain, RNA bind 99.11
2b7v_A71 Double-stranded RNA-specific editase 1; RNA editin 99.08
1qu6_A179 Protein kinase PKR; dsRNA-binding domain, solution 99.06
3p1x_A75 Interleukin enhancer-binding factor 3; structural 98.97
1qu6_A179 Protein kinase PKR; dsRNA-binding domain, solution 98.74
2l3j_A236 Double-stranded RNA-specific editase 1; editing, d 98.56
2yt4_A232 Protein DGCR8; DSRBD, RNA binding domain, RNA bind 98.48
2l3j_A 236 Double-stranded RNA-specific editase 1; editing, d 98.42
2db2_A119 KIAA0890 protein; DSRM domain, structural genomics 93.01
1ztd_A133 Hypothetical protein PFU-631545-001; structural ge 91.86
2kou_A102 Dicer-like protein 4; ATP-binding, endonuclease, h 85.17
>3n3w_A Ribonuclease III; nuclease domain, ribonuclase III, IDP90862, csgid, structura genomics; 2.21A {Campylobacter jejuni subsp} Back     alignment and structure
Probab=100.00  E-value=2e-51  Score=369.01  Aligned_cols=215  Identities=28%  Similarity=0.412  Sum_probs=131.0

Q ss_pred             CCcCCccH-HHhcCCccCCHHHHHHhhcCCCCCCCCCChhHHHHhhHHHHHHHHHHHHHHhCCCCChhchHHHHHhhcCh
Q 041023           63 PNANNLDE-EEILGYRFNNKNLLEEAFTDPSCPERFFSYERLEYVGDSVLNLLLTKEQFFLYPNLPPGSLTRLRSANVNT  141 (303)
Q Consensus        63 ~~~~~l~~-e~~lgy~F~~~~LL~~AlTh~S~~~~~~~~erLEfLGDavL~~~v~~~l~~~~p~~~~g~Lt~lr~~lvsn  141 (303)
                      |....+.. |++|||+|+|++||.+||||+||... .+|||||||||+||+++|+++||.+||+.++|.|+.+|+.+|||
T Consensus        23 ~~~~~l~~le~~lgy~F~~~~LL~~AlTH~S~~~~-~~neRLefLGDavL~~~v~~~L~~~~p~~~eg~Ls~~r~~lVs~  101 (248)
T 3n3w_A           23 NAMKNIEKLEQSLTYEFKDKNLLIHALTHKSFKKS-YNNERLEFLGDAVLDLVVGEYLFHKFAKDAEGDLSKLRAALVNE  101 (248)
T ss_dssp             --CTTHHHHHHHHTCCCSSHHHHHHHTBCTTSBTT-BCSHHHHHHHHHHHHHHHHHHHHHHTTTCSCCCHHHHHHHHHSH
T ss_pred             ccHHHHHHHHHHHCCCCCCHHHHHHHhcCcCCCCC-CCcHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHCH
Confidence            34445888 99999999999999999999999863 79999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHcCchhhhhcCCcchHHHHHHHHHHhhcCCCCCCCCCCCchhHHHHHHHHhhhhcccCCCCHHHHHHHHHHh
Q 041023          142 EKLARVAIKLGLHKYLRHNKPLLEEQIREFSEAILDYPLHSNGLVDAPKVLADIVESTIGAVFIDCNSSIDIVWKVFKEL  221 (303)
Q Consensus       142 ~~La~~a~~~gL~~~i~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~k~laD~fEAliGAIylD~G~~~~~v~~~i~~l  221 (303)
                      ++|+.+|.++||+++|+.++++..                 .+....++++||+|||+|||||+|+|+  +.+++|+.++
T Consensus       102 ~~La~~a~~lgL~~~l~~~~~e~~-----------------~~g~~~~~~lad~fEAliGAiyld~G~--~~~~~~i~~~  162 (248)
T 3n3w_A          102 KSFAKIANSLNLGDFILMSVAEEN-----------------NGGKEKPSILSDALEAIIGAIHLEAGF--EFAKTIALRL  162 (248)
T ss_dssp             HHHHHHHHHTTGGGTCBCCHHHHH-----------------TTGGGCHHHHHHHHHHHHHHHHHHHCH--HHHHHHHHHH
T ss_pred             HHHHHHHHHcCcHHHhhcCchhhh-----------------cCCCCCccHHHHHHHHHHHHHHHHCCh--HHHHHHHHHH
Confidence            999999999999999998765311                 234567899999999999999999997  8999999999


Q ss_pred             hcccCCCCc---ccCCCccHHHHHHHhCCCcceEEEee-------cceeEEEEEECCEEEEEEEeccchHHHHHHHHHHH
Q 041023          222 LKPMISPET---LKTHPVTELYEVCQKNKLKVKFVDLW-------KESTAFHIFIEDQLLGRGAYAPKKEIAHNRAAKDA  291 (303)
Q Consensus       222 l~~~l~~~~---~~~~Pk~~Lqe~~q~~~~~~~~~~~~-------~~~~~v~V~i~~~~ig~G~g~skk~~Ae~~AA~~A  291 (303)
                      +.|.++...   ...|||+.||||||+++...|.|++.       .+.|+|+|+++|+.+|+|.|.|||+ ||++||+.|
T Consensus       163 ~~~~l~~~~~~~~~~dpks~LqE~~q~~~~~~p~Y~~~~~~Gp~h~~~F~v~v~v~g~~~~~G~G~SKK~-Aeq~AA~~A  241 (248)
T 3n3w_A          163 IEKNFPQIDAKILIKDYKTKLQEITQGKIGQTPQYETVRAFGPDHLKQFEIALMLDGKELARAIAGSKKE-AQQMAAKIA  241 (248)
T ss_dssp             HHHHCC--------------------------------------------------------------------------
T ss_pred             HHHHHHHhhccccccCHHHHHHHHHHHcCCCCCceEEeeccCCCCCceEEEEEEECCEEEEEeeeCCHHH-HHHHHHHHH
Confidence            999876532   35799999999999999888877653       2468999999999999999999996 999999999


Q ss_pred             HHHHHhh
Q 041023          292 LNNIERL  298 (303)
Q Consensus       292 L~~l~~~  298 (303)
                      |+.|+.+
T Consensus       242 L~~L~~l  248 (248)
T 3n3w_A          242 LEKLGAL  248 (248)
T ss_dssp             -------
T ss_pred             HHHHHcC
Confidence            9998764
>2nug_A Ribonuclease III, RNAse III; dsRNA, RNA interference, endonucleolytic cleavage, hydrolase/RNA complex; 1.70A {Aquifex aeolicus} SCOP: a.149.1.1 d.50.1.1 PDB: 1yyw_A 2nue_A 2nuf_A 1yyk_A 1yz9_A 1yyo_A 2ez6_A 1rc7_A 1i4s_A 1jfz_A 1rc5_A Back     alignment and structure
>3c4b_A Endoribonuclease dicer; RNAse, dsRNA binding protein, ATP-binding, endonuclease, HEL hydrolase, nucleotide-binding, phosphoprotein, RN binding; HET: MSE; 1.68A {Mus musculus} PDB: 3c4t_A 2eb1_A Back     alignment and structure
>1o0w_A Ribonuclease III, RNAse III; TM1102, structural genomics, JCSG, PSI, protein structure initiative, joint center for structural genomics; 2.00A {Thermotoga maritima} SCOP: a.149.1.1 d.50.1.1 Back     alignment and structure
>2a11_A Ribonuclease III, RNAse III; nuclease domain, structural genomic protein structure initiative; 2.10A {Mycobacterium tuberculosis} Back     alignment and structure
>3rv0_A K. polysporus DCR1; RNAse III enzyme, RNA binding protein; 2.29A {Vanderwaltozyma polyspora} Back     alignment and structure
>3o2r_A Ribonuclease III; structural genomics, center for structural genomics of infec diseases, csgid, nuclease domain, ribonuclase III; HET: MLZ; 1.25A {Campylobacter jejuni subsp} PDB: 3o2r_B* Back     alignment and structure
>3rv1_A K. polysporus DCR1; RNAse III enzyme, RNA binding protein; 1.98A {Vanderwaltozyma polyspora} Back     alignment and structure
>2qvw_A GLP_546_48378_50642; dicer, RNAI,pseudo-merohedral twin, hydrolase; 3.00A {Giardia intestinalis} PDB: 2ffl_A Back     alignment and structure
>2qvw_A GLP_546_48378_50642; dicer, RNAI,pseudo-merohedral twin, hydrolase; 3.00A {Giardia intestinalis} PDB: 2ffl_A Back     alignment and structure
>1u61_A Hypothetical protein; structural genomics, PSI, protein STRU initiative, midwest center for structural genomics, MCSG, U function; 2.15A {Bacillus cereus} SCOP: a.149.1.1 Back     alignment and structure
>2gsl_A Hypothetical protein; alpha-helical protein, structural genomics, PSI, protein STR initiative; 2.60A {Fusobacterium nucleatum subsp} Back     alignment and structure
>3adl_A RISC-loading complex subunit tarbp2; TRBP2, miRNA processing, gene regulation-RNA complex; 2.20A {Homo sapiens} Back     alignment and structure
>1di2_A XLRBPA, double stranded RNA binding protein A; protein-RNA complex, protein-RNA interactions, RNA-bining protein; 1.90A {Xenopus laevis} SCOP: d.50.1.1 Back     alignment and structure
>3adg_A F21M12.9 protein; HYL1, miRNA processing mechanism, RNA binding protein, gene regulation; 1.70A {Arabidopsis thaliana} PDB: 3adi_A Back     alignment and structure
>3adj_A F21M12.9 protein; HYL1, miRNA processing, RNA binding protein, gene regulation; 3.00A {Arabidopsis thaliana} PDB: 2l2m_A Back     alignment and structure
>1x47_A DGCR8 protein; structural genomics, DSRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.50.1.1 Back     alignment and structure
>2cpn_A TAR RNA-binding protein 2; double-stranded RNA binding domain, DSRBD, DSRM., structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.50.1.1 Back     alignment and structure
>1ekz_A DSRBDIII, maternal effect protein (staufen); structure, protein/RNA, protein DSRBD, RNA hairpin; NMR {Drosophila melanogaster} SCOP: d.50.1.1 PDB: 1stu_A Back     alignment and structure
>2khx_A Ribonuclease 3; drosha, RNA binding domain, hydrolase, gene regulation, NUCL protein, gene regulation,nuclear protein; NMR {Homo sapiens} Back     alignment and structure
>1uhz_A Staufen (RNA binding protein) homolog 2; DSRM, staufen homolog 2, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.50.1.1 Back     alignment and structure
>2dix_A Interferon-inducible double stranded RNA- dependent protein kinase activator A; structure genomics, DSRM domain, hypothetical protein PRKRA; NMR {Homo sapiens} SCOP: d.50.1.1 Back     alignment and structure
>3llh_A RISC-loading complex subunit tarbp2; DSRBD, DSRM, microrna, RNA binding protein; 2.14A {Homo sapiens} Back     alignment and structure
>1t4n_A Ribonuclease III; DSRBD, RNA-binding, hydrolase; NMR {Saccharomyces cerevisiae} SCOP: d.50.1.1 Back     alignment and structure
>1t4o_A Ribonuclease III; RNT1P, DSRBD, RNA-binding, hydrolase; 2.50A {Saccharomyces cerevisiae} SCOP: d.50.1.1 PDB: 1t4l_B 2lbs_B Back     alignment and structure
>1x48_A Interferon-induced, double-stranded RNA- activated protein kinase; structure genomics, DSRM domain, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.50.1.1 Back     alignment and structure
>2l2n_A Hyponastic leave 1; DSRBD, miRNA, RNA binding protein, plant protein; NMR {Arabidopsis thaliana} Back     alignment and structure
>1whq_A RNA helicase A; double-stranded RNA binding domain, DSRBD, DSRM, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Mus musculus} SCOP: d.50.1.1 PDB: 2rs6_A Back     alignment and structure
>1x49_A Interferon-induced, double-stranded RNA- activated protein kinase; structure genomics, DSRM domain, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.50.1.1 Back     alignment and structure
>1whn_A Hypothetical protein riken cDNA 2310016K04; double-stranded RNA binding domain, DSRBD, DSRM, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.50.1.1 Back     alignment and structure
>2b7t_A Double-stranded RNA-specific editase 1; RNA editing, RNA-binding protein, hydrolase; NMR {Rattus norvegicus} SCOP: d.50.1.1 PDB: 2l3c_A Back     alignment and structure
>1uil_A Double-stranded RNA-binding motif; structural genomics, DSRM, riken structural genomics/proteomics initiative, RSGI RNA binding protein; NMR {Mus musculus} SCOP: d.50.1.1 PDB: 2rs7_A Back     alignment and structure
>2dmy_A Spermatid perinuclear RNA-binding protein; DSRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.50.1.1 Back     alignment and structure
>2l33_A Interleukin enhancer-binding factor 3; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, DRBM; NMR {Homo sapiens} Back     alignment and structure
>2ljh_A Double-stranded RNA-specific editase ADAR; DSRBD, DSRBM, editing, hydrolase; NMR {Drosophila melanogaster} Back     alignment and structure
>2yt4_A Protein DGCR8; DSRBD, RNA binding domain, RNA binding protein; 2.60A {Homo sapiens} Back     alignment and structure
>2b7v_A Double-stranded RNA-specific editase 1; RNA editing, RNA-binding protein, hydrolase; NMR {Rattus norvegicus} SCOP: d.50.1.1 PDB: 2l2k_B Back     alignment and structure
>1qu6_A Protein kinase PKR; dsRNA-binding domain, solution structure, transferase; NMR {Homo sapiens} SCOP: d.50.1.1 d.50.1.1 Back     alignment and structure
>3p1x_A Interleukin enhancer-binding factor 3; structural genomics, PSI-biology, protein structure initiati northeast structural genomics consortium, NESG; 1.90A {Homo sapiens} Back     alignment and structure
>1qu6_A Protein kinase PKR; dsRNA-binding domain, solution structure, transferase; NMR {Homo sapiens} SCOP: d.50.1.1 d.50.1.1 Back     alignment and structure
>2l3j_A Double-stranded RNA-specific editase 1; editing, dsRNA recognition, DSRBM, hydrolase-RNA complex; NMR {Rattus norvegicus} Back     alignment and structure
>2yt4_A Protein DGCR8; DSRBD, RNA binding domain, RNA binding protein; 2.60A {Homo sapiens} Back     alignment and structure
>2l3j_A Double-stranded RNA-specific editase 1; editing, dsRNA recognition, DSRBM, hydrolase-RNA complex; NMR {Rattus norvegicus} Back     alignment and structure
>2db2_A KIAA0890 protein; DSRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>1ztd_A Hypothetical protein PFU-631545-001; structural genomics, southeast collaboratory for structural genomics, secsg; 2.00A {Pyrococcus furiosus} SCOP: a.149.1.2 Back     alignment and structure
>2kou_A Dicer-like protein 4; ATP-binding, endonuclease, helicase, hydrolase, nuclease, nucleotide-binding, nucleus, RNA- binding; NMR {Arabidopsis thaliana} Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 303
d2nuga1148 a.149.1.1 (A:3-150) RNase III endonuclease catalyt 1e-21
d1o0wa1169 a.149.1.1 (A:-1-167) RNase III endonuclease cataly 4e-19
d1u61a_127 a.149.1.1 (A:) Hypothetical protein BC0111 {Bacill 1e-14
d1whna_128 d.50.1.1 (A:) tRNA-dihydrouridine synthase 2-like, 1e-07
d1x47a185 d.50.1.1 (A:8-92) Dgcr8 protein {Human (Homo sapie 4e-07
d1ekza_76 d.50.1.1 (A:) Staufen, domain III {Fruit fly (Dros 2e-05
d2cpna176 d.50.1.1 (A:150-225) TAR RNA-binding protein 2 {Hu 1e-04
d2dixa173 d.50.1.1 (A:7-79) Interferon-inducible double stra 1e-04
d1o0wa269 d.50.1.1 (A:168-236) RNase III, C-terminal domain 6e-04
d1whqa_99 d.50.1.1 (A:) ATP-dependent RNA helicase A, Dhx9 { 7e-04
d1qu6a190 d.50.1.1 (A:1-90) dsRNA-dependent protein kinase p 7e-04
d1uhza_89 d.50.1.1 (A:) staufen homolog 2 {Mouse (Mus muscul 0.001
d1t4oa_81 d.50.1.1 (A:) RNase III, C-terminal domain {Baker' 0.001
d1uila_113 d.50.1.1 (A:) ATP-dependent RNA helicase A, Dhx9 { 0.002
d1x49a185 d.50.1.1 (A:8-92) dsRNA-dependent protein kinase p 0.003
>d2nuga1 a.149.1.1 (A:3-150) RNase III endonuclease catalytic domain {Aquifex aeolicus [TaxId: 63363]} Length = 148 Back     information, alignment and structure

class: All alpha proteins
fold: RNase III domain-like
superfamily: RNase III domain-like
family: RNase III catalytic domain-like
domain: RNase III endonuclease catalytic domain
species: Aquifex aeolicus [TaxId: 63363]

 Score = 86.8 bits (214), Expect = 1e-21
 Identities = 44/156 (28%), Positives = 73/156 (46%), Gaps = 24/156 (15%)

Query: 71  EEILGYRFNNKNLLEEAFTDPSCPERFFSYERLEYVGDSVLNLLLTKEQFFLYPNLPPGS 130
           E+ LGY F +K+LLE+A T  S  ++   YE LE++GD+++N  +        PN   G 
Sbjct: 6   EKKLGYTFKDKSLLEKALTHVSYSKK-EHYETLEFLGDALVNFFIVDLLVQYSPNKREGF 64

Query: 131 LTRLRSANVNTEKLARVAIKLGLHKYLRHNKPLLEEQIREFSEAILDYPLHSNGLVDAPK 190
           L+ L++  ++ E    +A KL LHK++R  +  + E I                      
Sbjct: 65  LSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINETII--------------------- 103

Query: 191 VLADIVESTIGAVFIDCNSSIDIVWKVFKELLKPMI 226
              D+ E+   AV+ID     +   ++F +L K  I
Sbjct: 104 --GDVFEALWAAVYIDSGRDANFTRELFYKLFKEDI 137
>d1o0wa1 a.149.1.1 (A:-1-167) RNase III endonuclease catalytic domain {Thermotoga maritima [TaxId: 2336]} Length = 169 Back     information, alignment and structure
>d1u61a_ a.149.1.1 (A:) Hypothetical protein BC0111 {Bacillus cereus [TaxId: 1396]} Length = 127 Back     information, alignment and structure
>d1whna_ d.50.1.1 (A:) tRNA-dihydrouridine synthase 2-like, Dus2l (2310016k04Rik) {Mouse (Mus musculus) [TaxId: 10090]} Length = 128 Back     information, alignment and structure
>d1x47a1 d.50.1.1 (A:8-92) Dgcr8 protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85 Back     information, alignment and structure
>d1ekza_ d.50.1.1 (A:) Staufen, domain III {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 76 Back     information, alignment and structure
>d2cpna1 d.50.1.1 (A:150-225) TAR RNA-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 76 Back     information, alignment and structure
>d2dixa1 d.50.1.1 (A:7-79) Interferon-inducible double stranded RNA-dependent protein kinase activator A {Human (Homo sapiens) [TaxId: 9606]} Length = 73 Back     information, alignment and structure
>d1o0wa2 d.50.1.1 (A:168-236) RNase III, C-terminal domain {Thermotoga maritima [TaxId: 2336]} Length = 69 Back     information, alignment and structure
>d1whqa_ d.50.1.1 (A:) ATP-dependent RNA helicase A, Dhx9 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99 Back     information, alignment and structure
>d1qu6a1 d.50.1.1 (A:1-90) dsRNA-dependent protein kinase pkr {Human (Homo sapiens) [TaxId: 9606]} Length = 90 Back     information, alignment and structure
>d1uhza_ d.50.1.1 (A:) staufen homolog 2 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89 Back     information, alignment and structure
>d1t4oa_ d.50.1.1 (A:) RNase III, C-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81 Back     information, alignment and structure
>d1uila_ d.50.1.1 (A:) ATP-dependent RNA helicase A, Dhx9 {Mouse (Mus musculus) [TaxId: 10090]} Length = 113 Back     information, alignment and structure
>d1x49a1 d.50.1.1 (A:8-92) dsRNA-dependent protein kinase pkr {Mouse (Mus musculus) [TaxId: 10090]} Length = 85 Back     information, alignment and structure

Homologous Domains Detected by HHsearch ?

Original result of HHsearch against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query303
d2nuga1148 RNase III endonuclease catalytic domain {Aquifex a 100.0
d1o0wa1169 RNase III endonuclease catalytic domain {Thermotog 100.0
d1u61a_127 Hypothetical protein BC0111 {Bacillus cereus [TaxI 99.86
d1o0wa269 RNase III, C-terminal domain {Thermotoga maritima 99.51
d1x47a185 Dgcr8 protein {Human (Homo sapiens) [TaxId: 9606]} 99.46
d2cpna176 TAR RNA-binding protein 2 {Human (Homo sapiens) [T 99.44
d2nuga268 RNase III, C-terminal domain {Aquifex aeolicus [Ta 99.42
d1x48a176 dsRNA-dependent protein kinase pkr {Mouse (Mus mus 99.39
d1di2a_69 Double-stranded RNA-binding protein A, second dsRB 99.38
d2dixa173 Interferon-inducible double stranded RNA-dependent 99.37
d1qu6a289 dsRNA-dependent protein kinase pkr {Human (Homo sa 99.36
d1qu6a190 dsRNA-dependent protein kinase pkr {Human (Homo sa 99.36
d1x49a185 dsRNA-dependent protein kinase pkr {Mouse (Mus mus 99.35
d1uhza_89 staufen homolog 2 {Mouse (Mus musculus) [TaxId: 10 99.33
d1ekza_76 Staufen, domain III {Fruit fly (Drosophila melanog 99.33
d1whqa_99 ATP-dependent RNA helicase A, Dhx9 {Mouse (Mus mus 99.26
d1whna_128 tRNA-dihydrouridine synthase 2-like, Dus2l (231001 99.24
d1uila_113 ATP-dependent RNA helicase A, Dhx9 {Mouse (Mus mus 99.2
d1t4oa_81 RNase III, C-terminal domain {Baker's yeast (Sacch 99.17
d2b7va171 dsRNA-specific editase 1 {Rat (Rattus norvegicus) 99.01
d2b7ta173 dsRNA-specific editase 1 {Rat (Rattus norvegicus) 98.75
d2dmya184 Spermatid perinuclear RNA-binding protein {Human ( 98.65
d1ztda1124 Hypothetical protein PF0609 {Pyrococcus furiosus [ 90.98
>d2nuga1 a.149.1.1 (A:3-150) RNase III endonuclease catalytic domain {Aquifex aeolicus [TaxId: 63363]} Back     information, alignment and structure
class: All alpha proteins
fold: RNase III domain-like
superfamily: RNase III domain-like
family: RNase III catalytic domain-like
domain: RNase III endonuclease catalytic domain
species: Aquifex aeolicus [TaxId: 63363]

Probab=100.00  E-value=8.5e-38  Score=257.68  Aligned_cols=136  Identities=32%  Similarity=0.506  Sum_probs=126.7

Q ss_pred             ccH-HHhcCCccCCHHHHHHhhcCCCCCCCCCChhHHHHhhHHHHHHHHHHHHHHhCCCCChhchHHHHHhhcChHHHHH
Q 041023           68 LDE-EEILGYRFNNKNLLEEAFTDPSCPERFFSYERLEYVGDSVLNLLLTKEQFFLYPNLPPGSLTRLRSANVNTEKLAR  146 (303)
Q Consensus        68 l~~-e~~lgy~F~~~~LL~~AlTh~S~~~~~~~~erLEfLGDavL~~~v~~~l~~~~p~~~~g~Lt~lr~~lvsn~~La~  146 (303)
                      |+. |++|||+|+|++||.+||||+||.. ..+|||||||||++|+++++.|+|.+||+.++|.||.+|+.+|||++||.
T Consensus         2 l~~le~~igy~F~n~~LL~~Alth~S~~~-~~~~erLeflGDavl~~~v~~~l~~~~p~~~~g~lt~~r~~lvsn~~La~   80 (148)
T d2nuga1           2 LEQLEKKLGYTFKDKSLLEKALTHVSYSK-KEHYETLEFLGDALVNFFIVDLLVQYSPNKREGFLSPLKAYLISEEFFNL   80 (148)
T ss_dssp             HHHHHHHHTCCCSSHHHHHHHHBCTTTCS-SSCSHHHHHHHHHHHHHHHHHHHHHTCTTCCHHHHHHHHHHHTSHHHHHH
T ss_pred             HHHHHHHHCCccCCHHHHHHHhcCcCcCC-CcchHHHHHHHHHHHhhhhHHHHHhhCCCcchHHHHHHHHHhhhhhHhhh
Confidence            456 9999999999999999999999986 57999999999999999999999999999999999999999999999999


Q ss_pred             HHHHcCchhhhhcCCcchHHHHHHHHHHhhcCCCCCCCCCCCchhHHHHHHHHhhhhcccCCCCHHHHHHHHHHhhcccC
Q 041023          147 VAIKLGLHKYLRHNKPLLEEQIREFSEAILDYPLHSNGLVDAPKVLADIVESTIGAVFIDCNSSIDIVWKVFKELLKPMI  226 (303)
Q Consensus       147 ~a~~~gL~~~i~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~k~laD~fEAliGAIylD~G~~~~~v~~~i~~ll~~~l  226 (303)
                      +|.++||++|++.+++.                       ..++++||+|||+|||||+|+|.+.+.+++|+.+++.|.+
T Consensus        81 ~a~~lgl~~~i~~~~~~-----------------------~~~kilad~~EAiiGAiylD~g~~~~~~~~~i~~l~~~~i  137 (148)
T d2nuga1          81 LAQKLELHKFIRIKRGK-----------------------INETIIGDVFEALWAAVYIDSGRDANFTRELFYKLFKEDI  137 (148)
T ss_dssp             HHHTTTGGGTCBSCTTC-----------------------CCHHHHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHH
T ss_pred             HHHHhhHHHHHHhcccc-----------------------chhhhhHHHHHHHHHHhhhccCCCHHHHHHHHHHHHHHHH
Confidence            99999999999987542                       4579999999999999999999999999999999988765


Q ss_pred             C
Q 041023          227 S  227 (303)
Q Consensus       227 ~  227 (303)
                      .
T Consensus       138 ~  138 (148)
T d2nuga1         138 L  138 (148)
T ss_dssp             H
T ss_pred             H
Confidence            4
>d1u61a_ a.149.1.1 (A:) Hypothetical protein BC0111 {Bacillus cereus [TaxId: 1396]} Back     information, alignment and structure
>d1o0wa2 d.50.1.1 (A:168-236) RNase III, C-terminal domain {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d1x47a1 d.50.1.1 (A:8-92) Dgcr8 protein {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2cpna1 d.50.1.1 (A:150-225) TAR RNA-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2nuga2 d.50.1.1 (A:151-218) RNase III, C-terminal domain {Aquifex aeolicus [TaxId: 63363]} Back     information, alignment and structure
>d1x48a1 d.50.1.1 (A:8-83) dsRNA-dependent protein kinase pkr {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1di2a_ d.50.1.1 (A:) Double-stranded RNA-binding protein A, second dsRBD {Xenopus laevis [TaxId: 8355]} Back     information, alignment and structure
>d2dixa1 d.50.1.1 (A:7-79) Interferon-inducible double stranded RNA-dependent protein kinase activator A {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1qu6a2 d.50.1.1 (A:91-179) dsRNA-dependent protein kinase pkr {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1qu6a1 d.50.1.1 (A:1-90) dsRNA-dependent protein kinase pkr {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1x49a1 d.50.1.1 (A:8-92) dsRNA-dependent protein kinase pkr {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1uhza_ d.50.1.1 (A:) staufen homolog 2 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1ekza_ d.50.1.1 (A:) Staufen, domain III {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>d1whqa_ d.50.1.1 (A:) ATP-dependent RNA helicase A, Dhx9 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1whna_ d.50.1.1 (A:) tRNA-dihydrouridine synthase 2-like, Dus2l (2310016k04Rik) {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1uila_ d.50.1.1 (A:) ATP-dependent RNA helicase A, Dhx9 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1t4oa_ d.50.1.1 (A:) RNase III, C-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d2b7va1 d.50.1.1 (A:1-71) dsRNA-specific editase 1 {Rat (Rattus norvegicus) [TaxId: 10116]} Back     information, alignment and structure
>d2b7ta1 d.50.1.1 (A:1-73) dsRNA-specific editase 1 {Rat (Rattus norvegicus) [TaxId: 10116]} Back     information, alignment and structure
>d2dmya1 d.50.1.1 (A:8-91) Spermatid perinuclear RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1ztda1 a.149.1.2 (A:2-125) Hypothetical protein PF0609 {Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure