254780940

254780940

ribonuclease III

GeneID in NCBI database:8209962Locus tag:CLIBASIA_04195
Protein GI in NCBI database:254780940Protein Accession:YP_003065353.1
Gene range:+(929867, 930550)Protein Length:227aa
Gene description:ribonuclease III
COG prediction:none
KEGG prediction:rnc; ribonuclease III (EC:3.1.26.3); K03685 ribonuclease III [EC:3.1.26.3]
SEED prediction:Ribonuclease III (EC 3.1.26.3)
Pathway involved in KEGG:not defined
Subsystem involved in SEED:RNA processing and degradation, bacterial
sequencesequence profile

Prediction of Local Sequence Properties

SourceSummaryResult
scaler
NCBI Databasesequence
PSIPREDsecondary structure
SSPROsecondary structure
DISEMBLcoil and loop
DISEMBLflexible loop
SEGlow complexity
DISOPREDdisordered
DISEMBLmissing residues
DISPROdisordered
TMHMMnone TM-Helix
TOPPREDnone TM-Helix
HMMTOP1 TM-Helix
MEMSATnone TM-Helix
MEMSAT_SVMnone TM-Helix
PHOBIUSnone TM-Helix
SignalP_HMMno
SignalP_NNno
COILScoiled coil
70% MSAconservation map
90% MSAconservation map
  
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------
MSALRYSTLEKRIGYAFANRSLLEKALTHSSISHSYQESYERLEFLGDRILGLLISTLLFNHFDSAKEGELSVRFNSLVSAETCSQVARELDLASFIRVSSDLRKDVCSFMTSIQADVVESLIAALYLDGGIEVAGTFVDKYWKQRALKSGKFRRDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKREGIWT
cccccHHHHHHHHccccccHHHHHHHcccccccccccccHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHcHHHHHHHHHHccHHHHHccccHHHHccccccccHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHccccccEEEEEEEcccccccEEEEEEEEccEEEEEEEEccHHHHHHHHHHHHHHHHcccc
cccHHHHHHHHHHccccccHHHHHHHcEccccccccccccHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHccHHHHHHHHHHHcHHHHcEccHHHHHccHHHcHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHccccccEEEEEEEcccccccEEEEEEEEcccEccccccccHHHHHHHHHHHHHHHccccc
MSALRYSTLEKRIGYAFANRSLLEKALTHSSISHSYQESYERLEFLGDRILGLLISTLLFnhfdsakegeLSVRFNSLVSAETCSQVARELDLASFIRVSSDLRKDVCSFMTSIQADVVESLIAALYLDGGIEVAGTFVDKYWKQRALKSGKFRRDAKTELQEWAhakfgvtpeykvtfrsgpdhdprFTVVVEIsglapaqgmdcSKRAAEQVAAAEVLKREGIWT
MSALRYSTLEKRIGYAFANRSLLEKALTHSSISHSYQESYERLEFLGDRILGLLISTLLFNHFDSAKEGELSVRFNSLVSAETCSQVARELDLASFIRVSSDLRKDVCSFMTSIQADVVESLIAALYLDGGIEVAGTFVDKYWKQRALKSGKFRRDAKTelqewahakfgvtpeyKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAevlkregiwt
MSALRYSTLEKRIGYAFANRSLLEKALTHSSISHSYQESYERLEFLGDRILGLLISTLLFNHFDSAKEGELSVRFNSLVSAETCSQVARELDLASFIRVSSDLRKDVCSFMTSIQADVVESLIAALYLDGGIEVAGTFVDKYWKQRALKSGKFRRDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKREGIWT
****RYS*LEKRIGYAFANRSLLEKALTHSSISHSYQESYERLEFLGDRILGLLISTLLFNHFDSAKEGELSVRFNSLVSAETCSQVARELDLASFIRVSSDL****CSFMTSIQADVVESLIAALYLDGGIEVAGTFVDKYWKQRALKSGKFRRDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLA***********AEQVAAAEVLKREGIW*
MSALRYSTLEKRIGYAFANRSLLEKALTHSSISHSYQESYERLEFLGDRILGLLISTLLFNHFDSAKEGELSVRFNSLVSAETCSQVARELDLASFIRVSSDLRKDVCSFMTSIQADVVESLIAALYLDGGIEVAGTFVDKYWKQRALKSGKFRRDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKREGIWT
*SALRYSTLEKRIGYAFANRSLLEKALTHSSISHSYQESYERLEFLGDRILGLLISTLLFNHFDSAKEGELSVRFNSLVSAETCSQVARELDLASFIRVSSDLRKDVCSFMTSIQADVVESLIAALYLDGGIEVAGTFVDKYWKQRALKSGKFRRDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSK********AE*LKREGIWT
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MSALRYSTLEKRIGYAFANRSLLEKALTHSSISHSYQESYERLEFLGDRILGLLISTLLFNHFDSAKEGELSVRFNSLVSAETCSQVARELDLASFIRVSSDLRKDVCSFMTSIQADVVESLIAALYLDGGIEVAGTFVDKYWKQRALKSGKFRRDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKREGIWT
MSALRYSTLEKRIGYAFANRSLLEKALTHSSISHSYQESYERLEFLGDRILGLLISTLLFNHFDSAKEGELSVRFNSLVSAETCSQVARELDLASFIRVSSDLRKDVCSFMTSIQADVVESLIAALYLDGGIEVAGTFVDKYWKQRALKSGKFRRDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKREGIWT
MSALRYSTLEKRIGYAFANRSLLEKALTHSSISHSYQESYERLEFLGDRILGLLISTLLFNHFDSAKEGELSVRFNSLVSAETCSQVARELDLASFIRVSSDLRKDVCSFMTSIQADVVESLIAALYLDGGIEVAGTFVDKYWKQRALKSGKFRRDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKREGIWT

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

No hits with e-value below 0.05

Close Homologs Detected BLAST or PSI-BLAST in the First 2 Iterations

IdentityAlignment graphLength Definition Round E-value
Target227 ribonuclease III [Candidatus Liberibacter asiaticus str
315122353232 ribonuclease III [Candidatus Liberibacter solanacearum 1 3e-98
222085390239 ribonuclease III [Agrobacterium radiobacter K84] Length 1 4e-73
209548601239 ribonuclease III [Rhizobium leguminosarum bv. trifolii 1 3e-72
190891073239 ribonuclease III protein [Rhizobium etli CIAT 652] Leng 1 5e-72
86357028239 ribonuclease III [Rhizobium etli CFN 42] Length = 239 1 6e-72
241203889239 ribonuclease III [Rhizobium leguminosarum bv. trifolii 1 7e-72
116251277239 ribonuclease III [Rhizobium leguminosarum bv. viciae 38 1 9e-72
227821403239 ribonuclease III [Sinorhizobium fredii NGR234] Length = 1 2e-71
15964825238 ribonuclease III [Sinorhizobium meliloti 1021] Length = 1 2e-71
150395906238 ribonuclease III [Sinorhizobium medicae WSM419] Length 1 3e-71
>gi|315122353|ref|YP_004062842.1| ribonuclease III [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 232 Back     alignment and organism information
 Score =  362 bits (928), Expect = 3e-98,   Method: Compositional matrix adjust.
 Identities = 169/225 (75%), Positives = 200/225 (88%)

Query: 3   ALRYSTLEKRIGYAFANRSLLEKALTHSSISHSYQESYERLEFLGDRILGLLISTLLFNH 62
           +L+ S LE+RIGY F+N+ LL+KALTHSSI HS QE+YERLEFLGDR+LG+LIS LLF++
Sbjct: 8   SLKLSALERRIGYTFSNKYLLKKALTHSSICHSPQENYERLEFLGDRVLGILISKLLFDY 67

Query: 63  FDSAKEGELSVRFNSLVSAETCSQVARELDLASFIRVSSDLRKDVCSFMTSIQADVVESL 122
           FDSAKEGELS+RFNSLVSAETCSQVA+EL+L SFI VSSDLR +VC F+  IQADVVESL
Sbjct: 68  FDSAKEGELSIRFNSLVSAETCSQVAKELELDSFIYVSSDLRMEVCKFVKGIQADVVESL 127

Query: 123 IAALYLDGGIEVAGTFVDKYWKQRALKSGKFRRDAKTELQEWAHAKFGVTPEYKVTFRSG 182
           IAALYLDGGIE A +FV KYWK+R LK+G+FRRDAKTELQEWAHAKF VTP YK+  RSG
Sbjct: 128 IAALYLDGGIESASSFVTKYWKKRVLKNGEFRRDAKTELQEWAHAKFRVTPTYKIMLRSG 187

Query: 183 PDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKREGIWT 227
           PDHDPRFTV+V++ GL   +G+DCSKR+AEQ+AAAE+L+REGIW+
Sbjct: 188 PDHDPRFTVMVDVLGLYSGKGIDCSKRSAEQMAAAEILRREGIWS 232


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|222085390|ref|YP_002543920.1| ribonuclease III [Agrobacterium radiobacter K84] Length = 239 Back     alignment and organism information
>gi|209548601|ref|YP_002280518.1| ribonuclease III [Rhizobium leguminosarum bv. trifolii WSM2304] Length = 239 Back     alignment and organism information
>gi|190891073|ref|YP_001977615.1| ribonuclease III protein [Rhizobium etli CIAT 652] Length = 239 Back     alignment and organism information
>gi|86357028|ref|YP_468920.1| ribonuclease III [Rhizobium etli CFN 42] Length = 239 Back     alignment and organism information
>gi|241203889|ref|YP_002974985.1| ribonuclease III [Rhizobium leguminosarum bv. trifolii WSM1325] Length = 239 Back     alignment and organism information
>gi|116251277|ref|YP_767115.1| ribonuclease III [Rhizobium leguminosarum bv. viciae 3841] Length = 239 Back     alignment and organism information
>gi|227821403|ref|YP_002825373.1| ribonuclease III [Sinorhizobium fredii NGR234] Length = 239 Back     alignment and organism information
>gi|15964825|ref|NP_385178.1| ribonuclease III [Sinorhizobium meliloti 1021] Length = 238 Back     alignment and organism information
>gi|150395906|ref|YP_001326373.1| ribonuclease III [Sinorhizobium medicae WSM419] Length = 238 Back     alignment and organism information

Conserved Domains in CDD Database
Detected by RPS-BLAST and HHsearch

Conserved Domains in CDD Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target227 ribonuclease III [Candidatus Liberibacter asiaticus str
PRK12371235 PRK12371, PRK12371, ribonuclease III; Reviewed 1e-111
TIGR02191220 TIGR02191, RNaseIII, ribonuclease III, bacterial 1e-67
PRK00102229 PRK00102, rnc, ribonuclease III; Reviewed 2e-59
KOG1817533 KOG1817, KOG1817, KOG1817, Ribonuclease [RNA processing 3e-26
PRK12372 413 PRK12372, PRK12372, ribonuclease III; Reviewed 1e-24
PRK14718 467 PRK14718, PRK14718, ribonuclease III; Provisional 4e-24
COG0571235 COG0571, Rnc, dsRNA-specific ribonuclease [Transcriptio 1e-58
smart00535129 smart00535, RIBOc, Ribonuclease III family 2e-31
cd00593133 cd00593, RIBOc, RIBOc 2e-29
pfam0063696 pfam00636, Ribonuclease_3, RNase3 domain 4e-21
KOG0701 1606 KOG0701, KOG0701, KOG0701, dsRNA-specific nuclease Dice 1e-07
KOG1817 533 KOG1817, KOG1817, KOG1817, Ribonuclease [RNA processing 2e-06
KOG0701 1606 KOG0701, KOG0701, KOG0701, dsRNA-specific nuclease Dice 1e-04
KOG07011606 KOG0701, KOG0701, KOG0701, dsRNA-specific nuclease Dice 5e-04
cd0004868 cd00048, DSRM, Double-stranded RNA binding motif 6e-15
smart0035867 smart00358, DSRM, Double-stranded RNA binding motif 3e-13
pfam0003566 pfam00035, dsrm, Double-stranded RNA binding motif 2e-12
KOG3732 339 KOG3732, KOG3732, KOG3732, Staufen and related double-s 4e-04
>gnl|CDD|171444 PRK12371, PRK12371, ribonuclease III; Reviewed Back     alignment and domain information
>gnl|CDD|162755 TIGR02191, RNaseIII, ribonuclease III, bacterial Back     alignment and domain information
>gnl|CDD|178863 PRK00102, rnc, ribonuclease III; Reviewed Back     alignment and domain information
>gnl|CDD|37028 KOG1817, KOG1817, KOG1817, Ribonuclease [RNA processing and modification] Back     alignment and domain information
>gnl|CDD|183478 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|30916 COG0571, Rnc, dsRNA-specific ribonuclease [Transcription] Back     alignment and domain information
>gnl|CDD|128808 smart00535, RIBOc, Ribonuclease III family Back     alignment and domain information
>gnl|CDD|29697 cd00593, RIBOc, RIBOc Back     alignment and domain information
>gnl|CDD|144289 pfam00636, Ribonuclease_3, RNase3 domain Back     alignment and domain information
>gnl|CDD|35920 KOG0701, KOG0701, KOG0701, dsRNA-specific nuclease Dicer and related ribonucleases [RNA processing and modification] Back     alignment and domain information
>gnl|CDD|37028 KOG1817, KOG1817, KOG1817, Ribonuclease [RNA processing and modification] Back     alignment and domain information
>gnl|CDD|35920 KOG0701, KOG0701, KOG0701, dsRNA-specific nuclease Dicer and related ribonucleases [RNA processing and modification] Back     alignment and domain information
>gnl|CDD|35920 KOG0701, KOG0701, KOG0701, dsRNA-specific nuclease Dicer and related ribonucleases [RNA processing and modification] Back     alignment and domain information
>gnl|CDD|28930 cd00048, DSRM, Double-stranded RNA binding motif Back     alignment and domain information
>gnl|CDD|128652 smart00358, DSRM, Double-stranded RNA binding motif Back     alignment and domain information
>gnl|CDD|143824 pfam00035, dsrm, Double-stranded RNA binding motif Back     alignment and domain information
>gnl|CDD|38936 KOG3732, KOG3732, KOG3732, Staufen and related double-stranded-RNA-binding proteins [Intracellular trafficking, secretion, and vesicular transport, Transcription] Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 227 ribonuclease III [Candidatus Liberibacter asiaticus str
TIGR02191228 RNaseIII ribonuclease III; InterPro: IPR011907 This fam 100.0
PRK12371235 ribonuclease III; Reviewed 100.0
PRK00102228 rnc ribonuclease III; Reviewed 100.0
COG0571235 Rnc dsRNA-specific ribonuclease [Transcription] 100.0
PRK12372 425 ribonuclease III; Reviewed 100.0
KOG1817533 consensus 100.0
KOG3769333 consensus 99.91
KOG07011606 consensus 99.81
smart00535129 RIBOc Ribonuclease III family. 100.0
cd00593133 RIBOc RIBOc. Ribonuclease III C terminal domain. This g 100.0
pfam0063696 Ribonuclease_3 RNase3 domain. 99.89
KOG0701 1606 consensus 99.84
KOG1817 533 consensus 99.8
COG1939132 Ribonuclease III family protein [Replication, recombina 97.77
cd0004868 DSRM Double-stranded RNA binding motif. Binding is not 99.64
smart0035867 DSRM Double-stranded RNA binding motif. 99.6
KOG3732 339 consensus 99.33
pfam0003566 dsrm Double-stranded RNA binding motif. Putative motif 99.33
KOG3732 339 consensus 99.05
KOG2777 542 consensus 98.3
KOG4334 650 consensus 98.15
KOG3792 816 consensus 92.3
KOG3792 816 consensus 91.45
KOG2334477 consensus 95.2
>TIGR02191 RNaseIII ribonuclease III; InterPro: IPR011907 This family consists almost exclusively of bacterial examples of ribonuclease III (RNase III) Back     alignment and domain information
>PRK12371 ribonuclease III; Reviewed Back     alignment and domain information
>PRK00102 rnc ribonuclease III; Reviewed Back     alignment and domain information
>COG0571 Rnc dsRNA-specific ribonuclease [Transcription] Back     alignment and domain information
>PRK12372 ribonuclease III; Reviewed Back     alignment and domain information
>KOG1817 consensus Back     alignment and domain information
>KOG3769 consensus Back     alignment and domain information
>KOG0701 consensus Back     alignment and domain information
>smart00535 RIBOc Ribonuclease III family Back     alignment and domain information
>cd00593 RIBOc RIBOc Back     alignment and domain information
>pfam00636 Ribonuclease_3 RNase3 domain Back     alignment and domain information
>KOG0701 consensus Back     alignment and domain information
>KOG1817 consensus Back     alignment and domain information
>COG1939 Ribonuclease III family protein [Replication, recombination, and repair] 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
>KOG3732 consensus Back     alignment and domain information
>pfam00035 dsrm Double-stranded RNA binding motif Back     alignment and domain information
>KOG3732 consensus Back     alignment and domain information
>KOG2777 consensus Back     alignment and domain information
>KOG4334 consensus Back     alignment and domain information
>KOG3792 consensus Back     alignment and domain information
>KOG3792 consensus Back     alignment and domain information
>KOG2334 consensus Back     alignment and domain information

Homologous Structures in PDB Database
Detected by PSI-BLAST, RPS-BLAST and HHsearch

Homologous Structures Detected by PSI-BLAST against Nonredundant Database

IdentityAlignment graphLength Definition E-value
Target227 ribonuclease III [Candidatus Liberibacter asiaticus str
3n3w_A248 2.2 Angstrom Resolution Crystal Structure Of Nuclea 2e-35
1o0w_A252 Crystal Structure Of Ribonuclease Iii (Tm1102) From 1e-31
1yz9_A221 Crystal Structure Of Rnase Iii Mutant E110q From Aq 1e-28
1yyk_A221 Crystal Structure Of Rnase Iii From Aquifex Aeolicu 1e-28
1rc7_A220 Crystal Structure Of Rnase Iii Mutant E110k From Aq 1e-28
1yyo_A221 Crystal Structure Of Rnase Iii Mutant E110k From Aq 1e-28
2ez6_A221 Crystal Structure Of Aquifex Aeolicus Rnase Iii (D4 8e-28
3c4t_A265 Structure Of Rnaseiiib And Dsrna Binding Domains Of 1e-23
3c4b_A265 Structure Of Rnaseiiib And Dsrna Binding Domains Of 1e-22
2a11_A242 Crystal Structure Of Nuclease Domain Of Ribonuclase 7e-17
3o2r_D144 Structural Flexibility In Region Involved In Dimer 2e-17
3o2r_A170 Structural Flexibility In Region Involved In Dimer 2e-17
1jfz_A154 Crystal Structure Of Mn(Ii)-Complex Of Rnase Iii En 2e-14
1i4s_A147 Crystal Structure Of Rnase Iii Endonuclease Domain 2e-14
2eb1_A200 Crystal Structure Of The C-Terminal Rnase Iii Domai 5e-15
2khx_A85 Drosha Double-Stranded Rna Binding Motif Length = 8 1e-07
2l3j_A 236 The Solution Structure Of The Adar2 Dsrbm-Rna Compl 2e-07
2l3j_A236 The Solution Structure Of The Adar2 Dsrbm-Rna Compl 1e-05
2l3c_A74 Solution Structure Of Adar2 Dsrbm1 Bound To Lsl Rna 2e-07
2b7t_A73 Structure Of Adar2 Dsrbm1 Length = 73 2e-07
1uhz_A89 Solution Structure Of Dsrna Binding Domain In Stauf 3e-07
2cpn_A89 Solution Structure Of The Second Dsrbd Of Tar Rna-B 4e-07
1x49_A97 Solution Structure Of The First Dsrm Domain In Inte 5e-07
3adl_A88 Structure Of Trbp2 And Its Molecule Implications Fo 1e-06
2dmy_A97 Solution Structure Of Dsrm Domain In Spermatid Peri 5e-06
1x48_A88 Solution Structure Of The Second Dsrm Domain In Int 7e-06
1di2_A69 Crystal Structure Of A Dsrna-Binding Domain Complex 1e-05
2b7v_A71 Structure Of Adar2 Dsrbm2 Length = 71 1e-05
1x47_A98 Solution Structure Of Dsrm Domain In Dgcr8 Protein 3e-04
2yt4_A 232 Crystal Structure Of Human Dgcr8 Core Length = 232 8e-04
2dix_A84 Solution Structure Of The Dsrm Domain Of Protein Ac 9e-04
1qu6_A179 Structure Of The Double-Stranded Rna-Binding Domain 0.001
2l2n_A103 Backbone 1h, 13c, And 15n Chemical Shift Assignment 0.002
3adg_A73 Structure Of Arabidopsis Hyl1 And Its Molecular Imp 0.002
>gi|297343244|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
 Score =  153 bits (386), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 76/226 (33%), Positives = 124/226 (54%), Gaps = 6/226 (2%)

Query: 1   MSALRYSTLEKRIGYAFANRSLLEKALTHSSISHSYQESYERLEFLGDRILGLLISTLLF 60
           M  +    LE+ + Y F +++LL  ALTH S   SY  + ERLEFLGD +L L++   LF
Sbjct: 25  MKNI--EKLEQSLTYEFKDKNLLIHALTHKSFKKSY--NNERLEFLGDAVLDLVVGEYLF 80

Query: 61  NHFDSAKEGELSVRFNSLVSAETCSQVARELDLASFIRVSSDLRKDVCSFMTSIQADVVE 120
           + F    EG+LS    +LV+ ++ +++A  L+L  FI +S     +      SI +D +E
Sbjct: 81  HKFAKDAEGDLSKLRAALVNEKSFAKIANSLNLGDFILMSVAEENNGGKEKPSILSDALE 140

Query: 121 SLIAALYLDGGIEVAGTFVDKYWKQRALKSGKFR--RDAKTELQEWAHAKFGVTPEYKVT 178
           ++I A++L+ G E A T   +  ++   +       +D KT+LQE    K G TP+Y+  
Sbjct: 141 AIIGAIHLEAGFEFAKTIALRLIEKNFPQIDAKILIKDYKTKLQEITQGKIGQTPQYETV 200

Query: 179 FRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKREG 224
              GPDH  +F + + + G   A+ +  SK+ A+Q+AA   L++ G
Sbjct: 201 RAFGPDHLKQFEIALMLDGKELARAIAGSKKEAQQMAAKIALEKLG 246


>gi|27066029|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
>gi|83753776|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
gi|83753752|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
>gi|47168737|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
>gi|83753758|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
>gi|90109239|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
>gi|168177333|pdb|3C4T|A Chain A, Structure Of Rnaseiiib And Dsrna Binding Domains Of Mouse Dicer Length = 265 Back     alignment and structure
>gi|168177328|pdb|3C4B|A Chain A, Structure Of Rnaseiiib And Dsrna Binding Domains Of Mouse Dicer Length = 265 Back     alignment and structure
>gi|71042598|pdb|2A11|A Chain A, Crystal Structure Of Nuclease Domain Of Ribonuclase Iii From Mycobacterium Tuberculosis Length = 242 Back     alignment and structure
>gi|307448395|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
>gi|18158946|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
>gi|18158935|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
>gi|160285502|pdb|2EB1|A Chain A, Crystal Structure Of The C-Terminal Rnase Iii Domain Of Human Dicer Length = 200 Back     alignment and structure
>gi|289526478|pdb|2KHX|A Chain A, Drosha Double-Stranded Rna Binding Motif Length = 85 Back     alignment and structure
>gi|310689634|pdb|2L3J|A Chain A, The Solution Structure Of The Adar2 Dsrbm-Rna Complex Reveals A Sequence-Specific Read Out Of The Minor Groove Length = 236 Back     alignment and structure
>gi|310689634|pdb|2L3J|A Chain A, The Solution Structure Of The Adar2 Dsrbm-Rna Complex Reveals A Sequence-Specific Read Out Of The Minor Groove Length = 236 Back     alignment and structure
>gi|310689632|pdb|2L3C|A Chain A, Solution Structure Of Adar2 Dsrbm1 Bound To Lsl Rna Length = 74 Back     alignment and structure
>gi|93278801|pdb|2B7T|A Chain A, Structure Of Adar2 Dsrbm1 Length = 73 Back     alignment and structure
>gi|159163148|pdb|1UHZ|A Chain A, Solution Structure Of Dsrna Binding Domain In Staufen Homolog 2 Length = 89 Back     alignment and structure
>gi|159163844|pdb|2CPN|A Chain A, Solution Structure Of The Second Dsrbd Of Tar Rna-Binding Protein 2 Length = 89 Back     alignment and structure
>gi|159163524|pdb|1X49|A Chain A, Solution Structure Of The First Dsrm Domain In Interferon- Induced, Double-Stranded Rna-Activated Protein Kinase Length = 97 Back     alignment and structure
>gi|296863417|pdb|3ADL|A Chain A, Structure Of Trbp2 And Its Molecule Implications For Mirna P Length = 88 Back     alignment and structure
>gi|159164237|pdb|2DMY|A Chain A, Solution Structure Of Dsrm Domain In Spermatid Perinuclear Rna-Bind Protein Length = 97 Back     alignment and structure
>gi|159163523|pdb|1X48|A Chain A, Solution Structure Of The Second Dsrm Domain In Interferon- Induced, Double-Stranded Rna-Activated Protein Kinase Length = 88 Back     alignment and structure
>gi|6730350|pdb|1DI2|A Chain A, Crystal Structure Of A Dsrna-Binding Domain Complexed With Dsrna: Molecular Basis Of Double-Stranded Rna-Protein Interactions Length = 69 Back     alignment and structure
>gi|93278802|pdb|2B7V|A Chain A, Structure Of Adar2 Dsrbm2 Length = 71 Back     alignment and structure
>gi|159163522|pdb|1X47|A Chain A, Solution Structure Of Dsrm Domain In Dgcr8 Protein Length = 98 Back     alignment and structure
>gi|159795592|pdb|2YT4|A Chain A, Crystal Structure Of Human Dgcr8 Core Length = 232 Back     alignment and structure
>gi|159164135|pdb|2DIX|A Chain A, Solution Structure Of The Dsrm Domain Of Protein Activator Of The Interferon-Induced Protein Kinase Length = 84 Back     alignment and structure
>gi|159162913|pdb|1QU6|A Chain A, Structure Of The Double-Stranded Rna-Binding Domain Of The Protein Kinase Pkr Reveals The Molecular Basis Of Its Dsrna-Mediated Activation Length = 179 Back     alignment and structure
>gi|307776250|pdb|2L2N|A Chain A, Backbone 1h, 13c, And 15n Chemical Shift Assignments For The First Dsrbd Of Protein Hyl1 Length = 103 Back     alignment and structure
>gi|296863410|pdb|3ADG|A Chain A, Structure Of Arabidopsis Hyl1 And Its Molecular Implications Processing Length = 73 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target227 ribonuclease III [Candidatus Liberibacter asiaticus str
3n3w_A248 Ribonuclease III; nuclease domain, ribonuclase III, IDP 1e-51
1o0w_A252 Ribonuclease III, RNAse III; TM1102, structural genomic 4e-48
3c4b_A265 Endoribonuclease dicer; RNAse, dsRNA binding protein, A 2e-34
2nug_A221 Ribonuclease III, RNAse III; dsRNA, RNA interference, e 6e-34
2a11_A242 Ribonuclease III, RNAse III; nuclease domain, structura 7e-32
3o2r_A170 Ribonuclease III; structural genomics, center for struc 5e-33
2gsl_A137 Hypothetical protein; alpha-helical protein, structural 3e-19
1u61_A138 Hypothetical protein; structural genomics, PSI, protein 2e-17
2qvw_A 756 GLP_546_48378_50642; dicer, RNAI,pseudo-merohedral twin 2e-04
2khx_A85 Ribonuclease 3; drosha, RNA binding domain, hydrolase, 2e-17
3adj_A76 F21M12.9 protein; HYL1, miRNA processing, RNA binding p 4e-15
3adl_A88 RISC-loading complex subunit tarbp2; TRBP2, miRNA proce 1e-14
1qu6_A179 Protein kinase PKR; dsRNA-binding domain, solution stru 5e-14
1di2_A69 XLRBPA, double stranded RNA binding protein A; protein- 4e-13
2l2n_A103 Hyponastic leave 1; DSRBD, miRNA, RNA binding protein, 8e-13
3adg_A73 F21M12.9 protein; HYL1, miRNA processing mechanism, RNA 8e-13
2l33_A91 Interleukin enhancer-binding factor 3; structural genom 1e-12
2yt4_A 232 Protein DGCR8; DSRBD, RNA binding domain, RNA binding p 2e-12
2yt4_A232 Protein DGCR8; DSRBD, RNA binding domain, RNA binding p 8e-07
1t4o_A117 Ribonuclease III; RNT1P, DSRBD, RNA-binding, hydrolase; 2e-12
1ekz_A76 DSRBDIII, maternal effect protein (staufen); structure, 3e-12
2b7t_A73 Double-stranded RNA-specific editase 1; RNA editing, RN 4e-12
1x49_A97 Interferon-induced, double-stranded RNA- activated prot 9e-12
2dmy_A97 Spermatid perinuclear RNA-binding protein; DSRM domain, 2e-11
2b7v_A71 Double-stranded RNA-specific editase 1; RNA editing, RN 1e-10
1t4n_A94 Ribonuclease III; DSRBD, RNA-binding, hydrolase; NMR {S 2e-10
2l3j_A 236 Double-stranded RNA-specific editase 1; editing, dsRNA 5e-10
1x48_A88 Interferon-induced, double-stranded RNA- activated prot 5e-09
1whn_A128 Hypothetical protein riken cDNA 2310016K04; double-stra 5e-09
2dix_A84 Interferon-inducible double stranded RNA- dependent pro 5e-09
1x47_A98 DGCR8 protein; structural genomics, DSRM domain, NPPSFA 2e-08
2cpn_A89 TAR RNA-binding protein 2; double-stranded RNA binding 2e-08
1uil_A113 Double-stranded RNA-binding motif; structural genomics, 4e-08
1whq_A99 RNA helicase A; double-stranded RNA binding domain, DSR 6e-08
1uhz_A89 Staufen (RNA binding protein) homolog 2; DSRM, staufen 7e-08
1qu6_A179 Protein kinase PKR; dsRNA-binding domain, solution stru 4e-08
2l3j_A236 Double-stranded RNA-specific editase 1; editing, dsRNA 8e-10
>3n3w_A Ribonuclease III; nuclease domain, ribonuclase III, IDP90862, csgid, structura genomics; 2.21A {Campylobacter jejuni subsp} Length = 248 Back     alignment and structure
 Score =  198 bits (504), Expect = 1e-51
 Identities = 73/220 (33%), Positives = 121/220 (55%), Gaps = 4/220 (1%)

Query: 7   STLEKRIGYAFANRSLLEKALTHSSISHSYQESYERLEFLGDRILGLLISTLLFNHFDSA 66
             LE+ + Y F +++LL  ALTH S       + ERLEFLGD +L L++   LF+ F   
Sbjct: 29  EKLEQSLTYEFKDKNLLIHALTHKS--FKKSYNNERLEFLGDAVLDLVVGEYLFHKFAKD 86

Query: 67  KEGELSVRFNSLVSAETCSQVARELDLASFIRVSSDLRKDVCSFMTSIQADVVESLIAAL 126
            EG+LS    +LV+ ++ +++A  L+L  FI +S     +      SI +D +E++I A+
Sbjct: 87  AEGDLSKLRAALVNEKSFAKIANSLNLGDFILMSVAEENNGGKEKPSILSDALEAIIGAI 146

Query: 127 YLDGGIEVAGTFVDKYWKQR--ALKSGKFRRDAKTELQEWAHAKFGVTPEYKVTFRSGPD 184
           +L+ G E A T   +  ++    + +    +D KT+LQE    K G TP+Y+     GPD
Sbjct: 147 HLEAGFEFAKTIALRLIEKNFPQIDAKILIKDYKTKLQEITQGKIGQTPQYETVRAFGPD 206

Query: 185 HDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKREG 224
           H  +F + + + G   A+ +  SK+ A+Q+AA   L++ G
Sbjct: 207 HLKQFEIALMLDGKELARAIAGSKKEAQQMAAKIALEKLG 246


>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
>3c4b_A Endoribonuclease dicer; RNAse, dsRNA binding protein, ATP-binding, endonuclease, helicase, hydrolase, nucleotide-binding, phosphoprotein; HET: MSE; 1.68A {Mus musculus} PDB: 3c4t_A 2eb1_A Length = 265 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
>2a11_A Ribonuclease III, RNAse III; nuclease domain, structural genomics, PSI, protein structure initiative; 2.10A {Mycobacterium tuberculosis} Length = 242 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
>2gsl_A Hypothetical protein; alpha-helical protein, structural genomics, PSI, protein structure initiative; 2.60A {Fusobacterium nucleatum subsp} Length = 137 Back     alignment and structure
>1u61_A Hypothetical protein; structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG, unknown function; 2.15A {Bacillus cereus} SCOP: a.149.1.1 Length = 138 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
>2khx_A Ribonuclease 3; drosha, RNA binding domain, hydrolase, gene regulation, nuclear protein; NMR {Homo sapiens} Length = 85 Back     alignment and structure
>3adj_A F21M12.9 protein; HYL1, miRNA processing, RNA binding protein, gene regulation; 3.00A {Arabidopsis thaliana} PDB: 2l2m_A Length = 76 Back     alignment and structure
>3adl_A RISC-loading complex subunit tarbp2; TRBP2, miRNA processing, gene regulation-RNA complex; 2.20A {Homo sapiens} Length = 88 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
>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 Length = 69 Back     alignment and structure
>2l2n_A Hyponastic leave 1; DSRBD, miRNA, RNA binding protein, plant protein; NMR {Arabidopsis thaliana} Length = 103 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 Length = 73 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} Length = 91 Back     alignment and structure
>2yt4_A Protein DGCR8; DSRBD, RNA binding domain, RNA binding protein; 2.60A {Homo sapiens} Length = 232 Back     alignment and structure
>2yt4_A Protein DGCR8; DSRBD, RNA binding domain, RNA binding protein; 2.60A {Homo sapiens} Length = 232 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 Length = 117 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 Length = 76 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 Length = 73 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
>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 Length = 97 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 Length = 71 Back     alignment and structure
>1t4n_A Ribonuclease III; DSRBD, RNA-binding, hydrolase; NMR {Saccharomyces cerevisiae} SCOP: d.50.1.1 Length = 94 Back     alignment and structure
>2l3j_A Double-stranded RNA-specific editase 1; editing, dsRNA recognition, DSRBM, hydrolase-RNA complex; NMR {Rattus norvegicus} Length = 236 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 Length = 88 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 Length = 128 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 Length = 84 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
>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 Length = 89 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 Length = 113 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 Length = 99 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 Length = 89 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
>2l3j_A Double-stranded RNA-specific editase 1; editing, dsRNA recognition, DSRBM, hydrolase-RNA complex; NMR {Rattus norvegicus} Length = 236 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target227 ribonuclease III [Candidatus Liberibacter asiaticus str
1o0w_A252 Ribonuclease III, RNAse III; TM1102, structural genomic 100.0
3n3w_A248 Ribonuclease III; nuclease domain, ribonuclase III, IDP 100.0
2a11_A242 Ribonuclease III, RNAse III; nuclease domain, structura 100.0
2nug_A221 Ribonuclease III, RNAse III; dsRNA, RNA interference, e 100.0
3c4b_A265 Endoribonuclease dicer; RNAse, dsRNA binding protein, A 100.0
3o2r_A170 Ribonuclease III; structural genomics, center for struc 100.0
2gsl_A137 Hypothetical protein; alpha-helical protein, structural 99.9
2qvw_A756 GLP_546_48378_50642; dicer, RNAI,pseudo-merohedral twin 99.27
1u61_A138 Hypothetical protein; structural genomics, PSI, protein 99.9
2qvw_A 756 GLP_546_48378_50642; dicer, RNAI,pseudo-merohedral twin 99.48
2khx_A85 Ribonuclease 3; drosha, RNA binding domain, hydrolase, 99.74
1uhz_A89 Staufen (RNA binding protein) homolog 2; DSRM, staufen 99.69
2cpn_A89 TAR RNA-binding protein 2; double-stranded RNA binding 99.67
3adj_A76 F21M12.9 protein; HYL1, miRNA processing, RNA binding p 99.67
1whn_A128 Hypothetical protein riken cDNA 2310016K04; double-stra 99.66
3adl_A88 RISC-loading complex subunit tarbp2; TRBP2, miRNA proce 99.66
1di2_A69 XLRBPA, double stranded RNA binding protein A; protein- 99.64
2dix_A84 Interferon-inducible double stranded RNA- dependent pro 99.61
1x47_A98 DGCR8 protein; structural genomics, DSRM domain, NPPSFA 99.61
1uil_A113 Double-stranded RNA-binding motif; structural genomics, 99.6
2l2n_A103 Hyponastic leave 1; DSRBD, miRNA, RNA binding protein, 99.59
1x49_A97 Interferon-induced, double-stranded RNA- activated prot 99.59
1t4o_A117 Ribonuclease III; RNT1P, DSRBD, RNA-binding, hydrolase; 99.59
2yt4_A232 Protein DGCR8; DSRBD, RNA binding domain, RNA binding p 99.57
1t4n_A94 Ribonuclease III; DSRBD, RNA-binding, hydrolase; NMR {S 99.57
3adg_A73 F21M12.9 protein; HYL1, miRNA processing mechanism, RNA 99.57
1x48_A88 Interferon-induced, double-stranded RNA- activated prot 99.56
1whq_A99 RNA helicase A; double-stranded RNA binding domain, DSR 99.54
1qu6_A179 Protein kinase PKR; dsRNA-binding domain, solution stru 99.52
1ekz_A76 DSRBDIII, maternal effect protein (staufen); structure, 99.51
2b7v_A71 Double-stranded RNA-specific editase 1; RNA editing, RN 99.45
2dmy_A97 Spermatid perinuclear RNA-binding protein; DSRM domain, 99.4
2l33_A91 Interleukin enhancer-binding factor 3; structural genom 99.37
1qu6_A179 Protein kinase PKR; dsRNA-binding domain, solution stru 99.33
2b7t_A73 Double-stranded RNA-specific editase 1; RNA editing, RN 99.29
2l3j_A236 Double-stranded RNA-specific editase 1; editing, dsRNA 99.22
2yt4_A 232 Protein DGCR8; DSRBD, RNA binding domain, RNA binding p 99.14
2l3j_A 236 Double-stranded RNA-specific editase 1; editing, dsRNA 99.08
3htx_A 950 HEN1; HEN1, small RNA methyltransferase, protein-RNA co 97.22
2db2_A119 KIAA0890 protein; DSRM domain, structural genomics, NPP 92.8
2kou_A102 Dicer-like protein 4; ATP-binding, endonuclease, helica 90.94
>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
Probab=100.00  E-value=0  Score=409.13  Aligned_cols=221  Identities=32%  Similarity=0.421  Sum_probs=204.8

Q ss_pred             CCHHHHHHHHCCCCCCHHHHHHHCCCHHHCC-------CCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHH
Q ss_conf             5889999983696589899998424612126-------676654778874586886454787764104688789988888
Q gi|254780940|r    4 LRYSTLEKRIGYAFANRSLLEKALTHSSISH-------SYQESYERLEFLGDRILGLLISTLLFNHFDSAKEGELSVRFN   76 (227)
Q Consensus         4 ~~~~~l~~~lgy~f~~~~ll~~A~th~S~~~-------~~~~~~erLEflGDavL~~~v~~~l~~~~p~~~eG~lt~lr~   76 (227)
                      ..+++||++|||+|+|++||.+||||+||..       ....||||||||||+||+++|++|||.+||+.+||.||.+|+
T Consensus        19 ~~i~~le~~igy~F~n~~lL~~AlTH~S~~~~~~~~~~~~~~~~eRLEfLGDavL~~~v~~~l~~~~p~~~eg~lt~~r~   98 (252)
T 1o0w_A           19 KIVEEFQKETGINFKNEELLFRALCHSSYANEQNQAGRKDVESNEKLEFLGDAVLELFVCEILYKKYPEAEVGDLARVKS   98 (252)
T ss_dssp             HHHHHHHHHHCCCCSSHHHHHHHHBCHHHHHHHHHTTCTTCCCSHHHHHHHHHHHHHHHHHHHHHHCTTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHH
T ss_conf             99999999969843999999998067063444434334677547899998999999999999998688887131299999


Q ss_pred             HHHHHHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCHHHHHCCCCCCCCCC--CCCC
Q ss_conf             88744334545431387720010366312375313333326699999999641554220012210256431110--0013
Q gi|254780940|r   77 SLVSAETCSQVARELDLASFIRVSSDLRKDVCSFMTSIQADVVESLIAALYLDGGIEVAGTFVDKYWKQRALKS--GKFR  154 (227)
Q Consensus        77 ~lV~n~~La~~a~~lgl~~~l~~~~~~~~~~~~~~~~ilad~fEA~iGAiy~d~G~~~~~~~i~~~~~~~~~~~--~~~~  154 (227)
                      .+|||++|+.+|..+||++|++.+++...+....+++++||+|||+|||||+|+|++.|+.|+.+++.+.+...  ....
T Consensus        99 ~lv~~~~La~~a~~l~l~~~l~~~~~~~~~~~~~~~k~laD~fEAliGAiylD~g~~~~~~~v~~l~~~~l~~~~~~~~~  178 (252)
T 1o0w_A           99 AAASEEVLAMVSRKMNLGKFLFLGKGEEKTGGRDRDSILADAFEALLAAIYLDQGYEKIKELFEQEFEFYIEKIMKGEML  178 (252)
T ss_dssp             HHTSHHHHHHHHHHTTHHHHCBCCHHHHHTTGGGCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHTTCCC
T ss_pred             HHCCHHHHHHHHHHCCHHHHHHCCCCHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             98187879999997377998762870433377643348878999999999981680465899999999999887644300


Q ss_pred             CCHHHHHHHHHHCCCCCCCCCCEECCCCCCCCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHCC
Q ss_conf             4525889875320223333431010207788845999999999899999968989999999999999748
Q gi|254780940|r  155 RDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKREG  224 (227)
Q Consensus       155 ~dpK~~Lqe~~q~~~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~~AL~klg  224 (227)
                      .|||+.||||||+.+...|+|+++..+||+|.+.|.|+|+++|+.+|+|.|+|||+||+.||++||++|.
T Consensus       179 ~dpk~~L~e~~q~~~~~~p~y~~~~~~g~~~~~~f~v~v~i~~~~~~~G~G~SKK~Ae~~AA~~AL~~L~  248 (252)
T 1o0w_A          179 FDYKTALQEIVQSEHKVPPEYILVRTEKNDGDRIFVVEVRVNGKTIATGKGRTKKEAEKEAARIAYEKLL  248 (252)
T ss_dssp             SCHHHHHHHHHHHHHSSCCEEEEEEEECCTTSCEEEEEEEETTEEEEEEEESSHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCHHHHHHHHHCCCCCEEEEEEECCCCCCCEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHHH
T ss_conf             6755501787776405788558875116999951899999999999998848999999999999999998



>3n3w_A Ribonuclease III; nuclease domain, ribonuclase III, IDP90862, csgid, structura genomics; 2.21A {Campylobacter jejuni subsp} Back     alignment and structure
>2a11_A Ribonuclease III, RNAse III; nuclease domain, structural genomics, PSI, protein structure initiative; 2.10A {Mycobacterium tuberculosis} 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 Back     alignment and structure
>3c4b_A Endoribonuclease dicer; RNAse, dsRNA binding protein, ATP-binding, endonuclease, helicase, hydrolase, nucleotide-binding, phosphoprotein; HET: MSE; 1.68A {Mus musculus} PDB: 3c4t_A 2eb1_A 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
>2gsl_A Hypothetical protein; alpha-helical protein, structural genomics, PSI, protein structure initiative; 2.60A {Fusobacterium nucleatum subsp} 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 structure initiative, midwest center for structural genomics, MCSG, unknown function; 2.15A {Bacillus cereus} SCOP: a.149.1.1 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
>2khx_A Ribonuclease 3; drosha, RNA binding domain, hydrolase, 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
>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
>3adj_A F21M12.9 protein; HYL1, miRNA processing, RNA binding protein, gene regulation; 3.00A {Arabidopsis thaliana} PDB: 2l2m_A 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
>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
>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
>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
>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 Back     alignment and structure
>2l2n_A Hyponastic leave 1; DSRBD, miRNA, RNA binding protein, plant protein; NMR {Arabidopsis thaliana} 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
>1t4o_A Ribonuclease III; RNT1P, DSRBD, RNA-binding, hydrolase; 2.50A {Saccharomyces cerevisiae} SCOP: d.50.1.1 PDB: 1t4l_B Back     alignment and structure
>2yt4_A Protein DGCR8; DSRBD, RNA binding domain, RNA binding protein; 2.60A {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
>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
>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
>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 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
>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
>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
>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
>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
>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
>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
>3htx_A HEN1; HEN1, small RNA methyltransferase, protein-RNA complex; HET: SAH; 3.10A {Arabidopsis thaliana} 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
>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 Domains in SCOP and MMDB Database
Detected by RPS-BLAST and HHsearch

Homologous Domains in SCOP70 (Version1.75) Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 227 ribonuclease III [Candidatus Liberibacter asiaticus str
d1o0wa1169 a.149.1.1 (A:-1-167) RNase III endonuclease catalytic d 7e-25
d2nuga1148 a.149.1.1 (A:3-150) RNase III endonuclease catalytic do 2e-20
d1u61a_127 a.149.1.1 (A:) Hypothetical protein BC0111 {Bacillus ce 7e-18
d1o0wa269 d.50.1.1 (A:168-236) RNase III, C-terminal domain {Ther 2e-15
d1t4oa_81 d.50.1.1 (A:) RNase III, C-terminal domain {Baker's yea 4e-13
d2nuga268 d.50.1.1 (A:151-218) RNase III, C-terminal domain {Aqui 5e-13
d2b7ta173 d.50.1.1 (A:1-73) dsRNA-specific editase 1 {Rat (Rattus 1e-12
d2dmya184 d.50.1.1 (A:8-91) Spermatid perinuclear RNA-binding pro 2e-12
d1x47a185 d.50.1.1 (A:8-92) Dgcr8 protein {Human (Homo sapiens) [ 2e-11
d1qu6a190 d.50.1.1 (A:1-90) dsRNA-dependent protein kinase pkr {H 2e-11
d2b7va171 d.50.1.1 (A:1-71) dsRNA-specific editase 1 {Rat (Rattus 4e-11
d1x49a185 d.50.1.1 (A:8-92) dsRNA-dependent protein kinase pkr {M 2e-10
d1di2a_69 d.50.1.1 (A:) Double-stranded RNA-binding protein A, se 4e-10
d2cpna176 d.50.1.1 (A:150-225) TAR RNA-binding protein 2 {Human ( 5e-10
d1uila_113 d.50.1.1 (A:) ATP-dependent RNA helicase A, Dhx9 {Mouse 6e-10
d1ekza_76 d.50.1.1 (A:) Staufen, domain III {Fruit fly (Drosophil 8e-10
d2dixa173 d.50.1.1 (A:7-79) Interferon-inducible double stranded 4e-09
d1whna_128 d.50.1.1 (A:) tRNA-dihydrouridine synthase 2-like, Dus2 5e-09
d1x48a176 d.50.1.1 (A:8-83) dsRNA-dependent protein kinase pkr {M 7e-09
d1whqa_99 d.50.1.1 (A:) ATP-dependent RNA helicase A, Dhx9 {Mouse 1e-08
d1uhza_89 d.50.1.1 (A:) staufen homolog 2 {Mouse (Mus musculus) [ 4e-08
d1qu6a289 d.50.1.1 (A:91-179) dsRNA-dependent protein kinase pkr 2e-06
>d1o0wa1 a.149.1.1 (A:-1-167) RNase III endonuclease catalytic domain {Thermotoga maritima [TaxId: 2336]} Length = 169 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: Thermotoga maritima [TaxId: 2336]
 Score =  107 bits (268), Expect = 7e-25
 Identities = 46/145 (31%), Positives = 75/145 (51%), Gaps = 7/145 (4%)

Query: 9   LEKRIGYAFANRSLLEKALTHSSISHSYQ-------ESYERLEFLGDRILGLLISTLLFN 61
            +K  G  F N  LL +AL HSS ++          ES E+LEFLGD +L L +  +L+ 
Sbjct: 14  FQKETGINFKNEELLFRALCHSSYANEQNQAGRKDVESNEKLEFLGDAVLELFVCEILYK 73

Query: 62  HFDSAKEGELSVRFNSLVSAETCSQVARELDLASFIRVSSDLRKDVCSFMTSIQADVVES 121
            +  A+ G+L+   ++  S E  + V+R+++L  F+ +     K       SI AD  E+
Sbjct: 74  KYPEAEVGDLARVKSAAASEEVLAMVSRKMNLGKFLFLGKGEEKTGGRDRDSILADAFEA 133

Query: 122 LIAALYLDGGIEVAGTFVDKYWKQR 146
           L+AA+YLD G E      ++ ++  
Sbjct: 134 LLAAIYLDQGYEKIKELFEQEFEFY 158


>d2nuga1 a.149.1.1 (A:3-150) RNase III endonuclease catalytic domain {Aquifex aeolicus [TaxId: 63363]} Length = 148 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
>d1o0wa2 d.50.1.1 (A:168-236) RNase III, C-terminal domain {Thermotoga maritima [TaxId: 2336]} Length = 69 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
>d2nuga2 d.50.1.1 (A:151-218) RNase III, C-terminal domain {Aquifex aeolicus [TaxId: 63363]} Length = 68 Back     information, alignment and structure
>d2b7ta1 d.50.1.1 (A:1-73) dsRNA-specific editase 1 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 73 Back     information, alignment and structure
>d2dmya1 d.50.1.1 (A:8-91) Spermatid perinuclear RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 84 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
>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
>d2b7va1 d.50.1.1 (A:1-71) dsRNA-specific editase 1 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 71 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
>d1di2a_ d.50.1.1 (A:) Double-stranded RNA-binding protein A, second dsRBD {Xenopus laevis [TaxId: 8355]} Length = 69 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
>d1uila_ d.50.1.1 (A:) ATP-dependent RNA helicase A, Dhx9 {Mouse (Mus musculus) [TaxId: 10090]} Length = 113 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
>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
>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
>d1x48a1 d.50.1.1 (A:8-83) dsRNA-dependent protein kinase pkr {Mouse (Mus musculus) [TaxId: 10090]} Length = 76 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
>d1uhza_ d.50.1.1 (A:) staufen homolog 2 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89 Back     information, alignment and structure
>d1qu6a2 d.50.1.1 (A:91-179) dsRNA-dependent protein kinase pkr {Human (Homo sapiens) [TaxId: 9606]} Length = 89 Back     information, alignment and structure

Homologous Domains in SCOP70 (Version 1.75) Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target227 ribonuclease III [Candidatus Liberibacter asiaticus str
d1o0wa1169 RNase III endonuclease catalytic domain {Thermotoga mar 100.0
d2nuga1148 RNase III endonuclease catalytic domain {Aquifex aeolic 100.0
d1u61a_127 Hypothetical protein BC0111 {Bacillus cereus [TaxId: 13 99.89
d1o0wa269 RNase III, C-terminal domain {Thermotoga maritima [TaxI 99.73
d2cpna176 TAR RNA-binding protein 2 {Human (Homo sapiens) [TaxId: 99.68
d1uhza_89 staufen homolog 2 {Mouse (Mus musculus) [TaxId: 10090]} 99.68
d2nuga268 RNase III, C-terminal domain {Aquifex aeolicus [TaxId: 99.67
d1uila_113 ATP-dependent RNA helicase A, Dhx9 {Mouse (Mus musculus 99.63
d1qu6a190 dsRNA-dependent protein kinase pkr {Human (Homo sapiens 99.63
d1di2a_69 Double-stranded RNA-binding protein A, second dsRBD {Xe 99.63
d1x49a185 dsRNA-dependent protein kinase pkr {Mouse (Mus musculus 99.62
d1whna_128 tRNA-dihydrouridine synthase 2-like, Dus2l (2310016k04R 99.62
d2dixa173 Interferon-inducible double stranded RNA-dependent prot 99.61
d1x47a185 Dgcr8 protein {Human (Homo sapiens) [TaxId: 9606]} 99.61
d1whqa_99 ATP-dependent RNA helicase A, Dhx9 {Mouse (Mus musculus 99.58
d1qu6a289 dsRNA-dependent protein kinase pkr {Human (Homo sapiens 99.57
d1t4oa_81 RNase III, C-terminal domain {Baker's yeast (Saccharomy 99.56
d1x48a176 dsRNA-dependent protein kinase pkr {Mouse (Mus musculus 99.54
d1ekza_76 Staufen, domain III {Fruit fly (Drosophila melanogaster 99.54
d2dmya184 Spermatid perinuclear RNA-binding protein {Human (Homo 99.46
d2b7va171 dsRNA-specific editase 1 {Rat (Rattus norvegicus) [TaxI 99.45
d2b7ta173 dsRNA-specific editase 1 {Rat (Rattus norvegicus) [TaxI 99.31
>d2nuga1 a.149.1.1 (A:3-150) RNase III endonuclease catalytic domain {Aquifex aeolicus [TaxId: 63363]} Back     information, alignment and structure
>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
>d2cpna1 d.50.1.1 (A:150-225) TAR RNA-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1uhza_ d.50.1.1 (A:) staufen homolog 2 {Mouse (Mus musculus) [TaxId: 10090]} 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
>d1uila_ d.50.1.1 (A:) ATP-dependent RNA helicase A, Dhx9 {Mouse (Mus musculus) [TaxId: 10090]} 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
>d1di2a_ d.50.1.1 (A:) Double-stranded RNA-binding protein A, second dsRBD {Xenopus laevis [TaxId: 8355]} 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
>d1whna_ d.50.1.1 (A:) tRNA-dihydrouridine synthase 2-like, Dus2l (2310016k04Rik) {Mouse (Mus musculus) [TaxId: 10090]} 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
>d1x47a1 d.50.1.1 (A:8-92) Dgcr8 protein {Human (Homo sapiens) [TaxId: 9606]} 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
>d1qu6a2 d.50.1.1 (A:91-179) dsRNA-dependent protein kinase pkr {Human (Homo sapiens) [TaxId: 9606]} 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
>d1x48a1 d.50.1.1 (A:8-83) dsRNA-dependent protein kinase pkr {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
>d2dmya1 d.50.1.1 (A:8-91) Spermatid perinuclear RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} 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

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 227 ribonuclease III [Candidatus Liberibacter asiaticu
2a11_A_242 (A:) Ribonuclease III, RNAse III; nuclease domain, 1e-29
1o0w_A_1-177177 (A:1-177) Ribonuclease III, RNAse III; TM1102, str 1e-26
3c4b_A_1-199199 (A:1-199) Endoribonuclease dicer; RNAse, dsRNA bin 1e-26
2nug_A_1-148148 (A:1-148) Ribonuclease III, RNAse III; dsRNA, RNA 2e-26
2qvw_A_607-756150 (A:607-756) GLP_546_48378_50642; dicer, RNAI,pseud 3e-24
2gsl_A_137 (A:) Hypothetical protein; alpha-helical protein, 3e-21
2qvw_A_328-440113 (A:328-440) GLP_546_48378_50642; dicer, RNAI,pseud 2e-20
1u61_A_138 (A:) Hypothetical protein; structural genomics, PS 1e-17
1whn_A_128 (A:) Hypothetical protein riken cDNA 2310016K04; d 2e-16
1o0w_A_178-25275 (A:178-252) Ribonuclease III, RNAse III; TM1102, s 1e-15
2nug_A_149-22173 (A:149-221) Ribonuclease III, RNAse III; dsRNA, RN 2e-15
1t4o_A_117 (A:) Ribonuclease III; RNT1P, DSRBD, RNA-binding, 2e-15
1qu6_A_1-9292 (A:1-92) Protein kinase PKR; dsRNA-binding domain, 2e-15
1x49_A_97 (A:) Interferon-induced, double-stranded RNA- acti 3e-15
1x48_A_88 (A:) Interferon-induced, double-stranded RNA- acti 4e-15
1t4n_A_94 (A:) Ribonuclease III; DSRBD, RNA-binding, hydrola 5e-15
1qu6_A_93-17987 (A:93-179) Protein kinase PKR; dsRNA-binding domai 9e-15
2b7t_A_73 (A:) Double-stranded RNA-specific editase 1; RNA e 9e-15
1uil_A_113 (A:) Double-stranded RNA-binding motif; structural 1e-14
1uhz_A_89 (A:) Staufen (RNA binding protein) homolog 2; DSRM 1e-14
1ekz_A_76 (A:) DSRBDIII, maternal effect protein (staufen); 2e-14
1di2_A_69 (A:) XLRBPA, double stranded RNA binding protein A 2e-14
2yt4_A_22-10483 (A:22-104) Protein DGCR8; DSRBD, RNA binding domai 2e-14
2dix_A_84 (A:) Interferon-inducible double stranded RNA- dep 5e-14
2cpn_A_89 (A:) TAR RNA-binding protein 2; double-stranded RN 6e-14
2dmy_A_97 (A:) Spermatid perinuclear RNA-binding protein; DS 7e-14
2b7v_A_71 (A:) Double-stranded RNA-specific editase 1; RNA e 7e-14
1x47_A_98 (A:) DGCR8 protein; structural genomics, DSRM doma 1e-13
1whq_A_99 (A:) RNA helicase A; double-stranded RNA binding d 2e-13
2khx_A_29-8557 (A:29-85) Ribonuclease 3; drosha, RNA binding doma 6e-10
>2a11_A (A:) Ribonuclease III, RNAse III; nuclease domain, structural genomics, PSI, protein structure initiative; 2.10A {Mycobacterium tuberculosis}Length = 242 Back     alignment and structure
 Score =  124 bits (311), Expect = 1e-29
 Identities = 67/223 (30%), Positives = 99/223 (44%), Gaps = 7/223 (3%)

Query: 6   YSTLEKRIGYAFANRSLLEKALTHSSISHSYQE--SYERLEFLGDRILGLLISTLLFNHF 63
              L   +G    +  LL  ALTH S ++      + ERLEFLGD +LGL I+  LF+  
Sbjct: 7   RQPLLDALGVDLPDE-LLSLALTHRSYAYENGGLPTNERLEFLGDAVLGLTITDALFHRH 65

Query: 64  DSAKEGELSVRFNSLVSAETCSQVARELDLASFIRVSSDLRKDVCSFM---TSIQADVVE 120
               EG+L+    S+V+ +  + VAR L            R +  +     +SI AD +E
Sbjct: 66  PDRSEGDLAKLRASVVNTQALADVARRLCAEGLGVHVLLGRGEANTGGADKSSILADGME 125

Query: 121 SLIAALYLDGGIEVAGTFVDKYWKQRALKSGKF-RRDAKTELQEWAHAKFGVTPEYKVTF 179
           SL+ A+YL  G+E A   + + +      +             +   A  G+     +  
Sbjct: 126 SLLGAIYLQHGMEKAREVILRLFGPLLDAAPTLGAGLDWKTSLQELTAARGLGAPSYLVT 185

Query: 180 RSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKR 222
            +GPDHD  FT VV +       G+  SK+ AEQ AAA   K 
Sbjct: 186 STGPDHDKEFTAVVVVMDSEYGSGVGRSKKEAEQKAAAAAWKA 228


>1o0w_A (A:1-177) Ribonuclease III, RNAse III; TM1102, structural genomics, JCSG, PSI, protein structure initiative, joint center for structural genomics; 2.00A {Thermotoga maritima}Length = 177 Back     alignment and structure
>3c4b_A (A:1-199) Endoribonuclease dicer; RNAse, dsRNA binding protein, ATP-binding, endonuclease, helicase, hydrolase, nucleotide-binding, phosphoprotein; HET: MSE; 1.68A {Mus musculus} PDB: 3c4t_A 2eb1_ALength = 199 Back     alignment and structure
>2nug_A (A:1-148) Ribonuclease III, RNAse III; dsRNA, RNA interference, endonucleolytic cleavage, hydrolase/RNA complex; 1.70A {Aquifex aeolicus}Length = 148 Back     alignment and structure
>2qvw_A (A:607-756) GLP_546_48378_50642; dicer, RNAI,pseudo-merohedral twin, hydrolase; 3.00A {Giardia intestinalis} PDB: 2ffl_ALength = 150 Back     alignment and structure
>2gsl_A (A:) Hypothetical protein; alpha-helical protein, structural genomics, PSI, protein structure initiative; 2.60A {Fusobacterium nucleatum subsp}Length = 137 Back     alignment and structure
>2qvw_A (A:328-440) GLP_546_48378_50642; dicer, RNAI,pseudo-merohedral twin, hydrolase; 3.00A {Giardia intestinalis} PDB: 2ffl_ALength = 113 Back     alignment and structure
>1u61_A (A:) Hypothetical protein; structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG, unknown function; 2.15A {Bacillus cereus}Length = 138 Back     alignment and structure
>1whn_A (A:) Hypothetical protein riken cDNA 2310016K04; double-stranded RNA binding domain, DSRBD, DSRM, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus}Length = 128 Back     alignment and structure
>1o0w_A (A:178-252) Ribonuclease III, RNAse III; TM1102, structural genomics, JCSG, PSI, protein structure initiative, joint center for structural genomics; 2.00A {Thermotoga maritima}Length = 75 Back     alignment and structure
>2nug_A (A:149-221) Ribonuclease III, RNAse III; dsRNA, RNA interference, endonucleolytic cleavage, hydrolase/RNA complex; 1.70A {Aquifex aeolicus}Length = 73 Back     alignment and structure
>1t4o_A (A:) Ribonuclease III; RNT1P, DSRBD, RNA-binding, hydrolase; 2.50A {Saccharomyces cerevisiae}Length = 117 Back     alignment and structure
>1qu6_A (A:1-92) Protein kinase PKR; dsRNA-binding domain, solution structure, transferase; NMR {Homo sapiens}Length = 92 Back     alignment and structure
>1x49_A (A:) Interferon-induced, double-stranded RNA- activated protein kinase; structure genomics, DSRM domain, structural genomics, NPPSFA; NMR {Mus musculus}Length = 97 Back     alignment and structure
>1x48_A (A:) Interferon-induced, double-stranded RNA- activated protein kinase; structure genomics, DSRM domain, structural genomics, NPPSFA; NMR {Mus musculus}Length = 88 Back     alignment and structure
>1t4n_A (A:) Ribonuclease III; DSRBD, RNA-binding, hydrolase; NMR {Saccharomyces cerevisiae}Length = 94 Back     alignment and structure
>1qu6_A (A:93-179) Protein kinase PKR; dsRNA-binding domain, solution structure, transferase; NMR {Homo sapiens}Length = 87 Back     alignment and structure
>2b7t_A (A:) Double-stranded RNA-specific editase 1; RNA editing, RNA-binding protein, hydrolase; NMR {Rattus norvegicus}Length = 73 Back     alignment and structure
>1uil_A (A:) Double-stranded RNA-binding motif; structural genomics, DSRM, riken structural genomics/proteomics initiative, RSGI RNA binding protein; NMR {Mus musculus}Length = 113 Back     alignment and structure
>1uhz_A (A:) Staufen (RNA binding protein) homolog 2; DSRM, staufen homolog 2, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus}Length = 89 Back     alignment and structure
>1ekz_A (A:) DSRBDIII, maternal effect protein (staufen); structure, protein/RNA, protein DSRBD, RNA hairpin; NMR {Drosophila melanogaster}Length = 76 Back     alignment and structure
>1di2_A (A:) XLRBPA, double stranded RNA binding protein A; protein-RNA complex, protein-RNA interactions, RNA-bining protein; 1.90A {Xenopus laevis}Length = 69 Back     alignment and structure
>2yt4_A (A:22-104) Protein DGCR8; DSRBD, RNA binding domain, RNA binding protein; 2.60A {Homo sapiens}Length = 83 Back     alignment and structure
>2dix_A (A:) Interferon-inducible double stranded RNA- dependent protein kinase activator A; structure genomics, DSRM domain, hypothetical protein PRKRA; NMR {Homo sapiens}Length = 84 Back     alignment and structure
>2cpn_A (A:) TAR RNA-binding protein 2; double-stranded RNA binding domain, DSRBD, DSRM., structural genomics, NPPSFA; NMR {Homo sapiens}Length = 89 Back     alignment and structure
>2dmy_A (A:) Spermatid perinuclear RNA-binding protein; DSRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}Length = 97 Back     alignment and structure
>2b7v_A (A:) Double-stranded RNA-specific editase 1; RNA editing, RNA-binding protein, hydrolase; NMR {Rattus norvegicus}Length = 71 Back     alignment and structure
>1x47_A (A:) DGCR8 protein; structural genomics, DSRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}Length = 98 Back     alignment and structure
>1whq_A (A:) RNA helicase A; double-stranded RNA binding domain, DSRBD, DSRM, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Mus musculus}Length = 99 Back     alignment and structure
>2khx_A (A:29-85) Ribonuclease 3; drosha, RNA binding domain, hydrolase, gene regulation, nuclear protein; NMR {Homo sapiens}Length = 57 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target227 ribonuclease III [Candidatus Liberibacter asiaticus str
2a11_A_242 Ribonuclease III, RNAse III; nuclease domain, stru 100.0
3c4b_A_1-199199 Endoribonuclease dicer; RNAse, dsRNA binding prote 100.0
2nug_A_1-148148 Ribonuclease III, RNAse III; dsRNA, RNA interferen 100.0
1o0w_A_1-177