BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 017515
(370 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3C4T|A Chain A, Structure Of Rnaseiiib And Dsrna Binding Domains Of Mouse
Dicer
Length = 265
Score = 96.3 bits (238), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 69/244 (28%), Positives = 116/244 (47%), Gaps = 17/244 (6%)
Query: 40 ENIINYNFKNKRLLEEALTHSSY---TDSTSYQRLEFIGDAALGLALSNYVFLAYPQLDP 96
E INY FKNK L +A TH+SY T + YQRLEF+GDA L ++ +++ Q P
Sbjct: 19 EKKINYRFKNKAYLLQAFTHASYHYNTITDXYQRLEFLGDAILDYLITKHLYEDPRQHSP 78
Query: 97 GQLSLLRAANISTEKLARVAVKHGFYKFVRHSAAALDDKVKEFAEAVSQEDNTAVYGGSI 156
G L+ LR+A ++ A +AVK+ ++K+ + + L + +F + +++ +
Sbjct: 79 GVLTDLRSALVNNTIFASLAVKYDYHKYFKAVSPELFHVIDDFVKFQLEKNEMQGMDSEL 138
Query: 157 K-------------APKVLADIVESIAAAIYVDIDFDLQKLWMIFRGLLEPIVTLEELQQ 203
+ PK + DI ES+A AIY+D L+ +W ++ +++P++
Sbjct: 139 RRSEEDEEKEEDIEVPKAMGDIFESLAGAIYMDSGMSLEVVWQVYYPMMQPLIEKFSANV 198
Query: 204 QPQPVTLLFKLCQKNGKQVDIKHWRKNRKNIASVYVDGSFVASASSEQKEIAKLNAAREA 263
PV L ++ + K + + + +V V G IAK AAR A
Sbjct: 199 PRSPVRELLEMEPETAKFSPAERTYDGKVRV-TVEVVGKGKFKGVGRSYRIAKSAAARRA 257
Query: 264 LEKL 267
L L
Sbjct: 258 LRSL 261
>pdb|2EB1|A Chain A, Crystal Structure Of The C-Terminal Rnase Iii Domain Of
Human Dicer
pdb|2EB1|B Chain B, Crystal Structure Of The C-Terminal Rnase Iii Domain Of
Human Dicer
pdb|2EB1|C Chain C, Crystal Structure Of The C-Terminal Rnase Iii Domain Of
Human Dicer
Length = 200
Score = 93.6 bits (231), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 53/173 (30%), Positives = 92/173 (53%), Gaps = 16/173 (9%)
Query: 40 ENIINYNFKNKRLLEEALTHSSY---TDSTSYQRLEFIGDAALGLALSNYVFLAYPQLDP 96
E INY FKNK L +A TH+SY T + YQRLEF+GDA L ++ +++ Q P
Sbjct: 12 EKKINYRFKNKAYLLQAFTHASYHYNTITDCYQRLEFLGDAILDYLITKHLYEDPRQHSP 71
Query: 97 GQLSLLRAANISTEKLARVAVKHGFYKFVRHSAAALDDKVKEFAEAVSQEDNTAVYGGSI 156
G L+ LR+A ++ A +AVK+ ++K+ + + L + +F + +++ +
Sbjct: 72 GVLTDLRSALVNNTIFASLAVKYDYHKYFKAVSPELFHVIDDFVQFQLEKNEMQGMDSEL 131
Query: 157 K-------------APKVLADIVESIAAAIYVDIDFDLQKLWMIFRGLLEPIV 196
+ PK + DI ES+A AIY+D L+ +W ++ ++ P++
Sbjct: 132 RRSEEDEEKEEDIEVPKAMGDIFESLAGAIYMDSGMSLETVWQVYYPMMRPLI 184
>pdb|3C4B|A Chain A, Structure Of Rnaseiiib And Dsrna Binding Domains Of Mouse
Dicer
Length = 265
Score = 89.0 bits (219), Expect = 4e-18, Method: Compositional matrix adjust.
Identities = 69/244 (28%), Positives = 111/244 (45%), Gaps = 17/244 (6%)
Query: 40 ENIINYNFKNKRLLEEALTHSSY---TDSTSYQRLEFIGDAALGLALSNYVFLAYPQLDP 96
E INY FKNK L +A TH+SY T + YQRLEF+GDA L ++ +++ Q P
Sbjct: 19 EKKINYRFKNKAYLLQAFTHASYHYNTITDXYQRLEFLGDAILDYLITKHLYEDPRQHSP 78
Query: 97 GQLSLLRAANISTEKLARVAVKHGFYKFVRHSAAALDDKVKEFAEAVSQEDNTAVYGGSI 156
G L+ LR+A ++ A +AVK+ ++K+ + + L + +F + +++ +
Sbjct: 79 GVLTDLRSALVNNTIFASLAVKYDYHKYFKAVSPELFHVIDDFVKFQLEKNEXQGXDSEL 138
Query: 157 K-------------APKVLADIVESIAAAIYVDIDFDLQKLWMIFRGLLEPIVTLEELQQ 203
+ PK DI ES+A AIY D L+ +W ++ +P++
Sbjct: 139 RRSEEDEEKEEDIEVPKAXGDIFESLAGAIYXDSGXSLEVVWQVYYPXXQPLIEKFSANV 198
Query: 204 QPQPVTLLFKLCQKNGKQVDIKHWRKNRKNIASVYVDGSFVASASSEQKEIAKLNAAREA 263
PV L + + K + + + +V V G IAK AAR A
Sbjct: 199 PRSPVRELLEXEPETAKFSPAERTYDGKVRV-TVEVVGKGKFKGVGRSYRIAKSAAARRA 257
Query: 264 LEKL 267
L L
Sbjct: 258 LRSL 261
>pdb|3N3W|A Chain A, 2.2 Angstrom Resolution Crystal Structure Of Nuclease
Domain Ribonuclase Iii (Rnc) From Campylobacter Jejuni
pdb|3N3W|B Chain B, 2.2 Angstrom Resolution Crystal Structure Of Nuclease
Domain Ribonuclase Iii (Rnc) From Campylobacter Jejuni
Length = 248
Score = 79.3 bits (194), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 70/260 (26%), Positives = 114/260 (43%), Gaps = 74/260 (28%)
Query: 39 VENIINYNFKNKRLLEEALTHSSYTDSTSYQRLEFIGDAALGLALSNYVFLAYPQLDPGQ 98
+E + Y FK+K LL ALTH S+ S + +RLEF+GDA L L + Y+F + + G
Sbjct: 31 LEQSLTYEFKDKNLLIHALTHKSFKKSYNNERLEFLGDAVLDLVVGEYLFHKFAKDAEGD 90
Query: 99 LSLLRAANISTEKLARVAVKHGFYKFVRHSAAALDDKVKEFAEAVSQEDNTAVYGGSIKA 158
LS LRAA ++ + A++A F+ S V++E+N G +
Sbjct: 91 LSKLRAALVNEKSFAKIANSLNLGDFILMS--------------VAEENN-----GGKEK 131
Query: 159 PKVLADIVESIAAAIYVDIDFDLQKLWMIFRGLLEPIVTLEELQQQPQPVTLLFKLCQKN 218
P +L+D +E+I AI+++ F+ K T+ +L +KN
Sbjct: 132 PSILSDALEAIIGAIHLEAGFEFAK-------------------------TIALRLIEKN 166
Query: 219 GKQVD----IKHWRKNRKNIA--------------------------SVYVDGSFVASAS 248
Q+D IK ++ + I ++ +DG +A A
Sbjct: 167 FPQIDAKILIKDYKTKLQEITQGKIGQTPQYETVRAFGPDHLKQFEIALMLDGKELARAI 226
Query: 249 SEQKEIAKLNAAREALEKLA 268
+ K+ A+ AA+ ALEKL
Sbjct: 227 AGSKKEAQQMAAKIALEKLG 246
Score = 33.1 bits (74), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 38/83 (45%), Gaps = 4/83 (4%)
Query: 281 FDDIDEKFEIEAAKQKLHELCGKKKWPKPSYKIEKDEGPSHDKKFMSAVQIATTDGVLFI 340
F ID K I+ K KL E+ K P Y+ + GP H K+F A+ + + I
Sbjct: 167 FPQIDAKILIKDYKTKLQEITQGKIGQTPQYETVRAFGPDHLKQFEIALMLDGKELARAI 226
Query: 341 TGDEKSRVKDAENSAASMMLRAL 363
G + K+A+ AA + L L
Sbjct: 227 AGSK----KEAQQMAAKIALEKL 245
>pdb|3O2R|A Chain A, Structural Flexibility In Region Involved In Dimer
Formation Of Nuclease Domain Of Ribonuclase Iii (Rnc)
From Campylobacter Jejuni
pdb|3O2R|C Chain C, Structural Flexibility In Region Involved In Dimer
Formation Of Nuclease Domain Of Ribonuclase Iii (Rnc)
From Campylobacter Jejuni
Length = 170
Score = 77.4 bits (189), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 48/145 (33%), Positives = 77/145 (53%), Gaps = 19/145 (13%)
Query: 39 VENIINYNFKNKRLLEEALTHSSYTDSTSYQRLEFIGDAALGLALSNYVFLAYPQLDPGQ 98
+E + Y FK+K LL ALTH S+ S + +RLEF+GDA L L + Y+F + + G
Sbjct: 31 LEQSLTYEFKDKNLLIHALTHKSFKKSYNNERLEFLGDAVLDLVVGEYLFHKFAKDAEGD 90
Query: 99 LSLLRAANISTEKLARVAVKHGFYKFVRHSAAALDDKVKEFAEAVSQEDNTAVYGGSIKA 158
LS LRAA ++ + A++A F+ S V++E+N G +
Sbjct: 91 LSKLRAALVNEKSFAKIANSLNLGDFILMS--------------VAEENN-----GGKEK 131
Query: 159 PKVLADIVESIAAAIYVDIDFDLQK 183
P +L+D +E+I AI+++ F+ K
Sbjct: 132 PSILSDALEAIIGAIHLEAGFEFAK 156
>pdb|3O2R|B Chain B, Structural Flexibility In Region Involved In Dimer
Formation Of Nuclease Domain Of Ribonuclase Iii (Rnc)
From Campylobacter Jejuni
pdb|3O2R|D Chain D, Structural Flexibility In Region Involved In Dimer
Formation Of Nuclease Domain Of Ribonuclase Iii (Rnc)
From Campylobacter Jejuni
Length = 144
Score = 73.2 bits (178), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 48/146 (32%), Positives = 77/146 (52%), Gaps = 20/146 (13%)
Query: 39 VENIINYNFKNKRLLEEALTHSSYTD-STSYQRLEFIGDAALGLALSNYVFLAYPQLDPG 97
+E + Y FK+K LL ALTH S+ S + +RLEF+GDA L L + Y+F + + G
Sbjct: 5 LEQSLTYEFKDKNLLIHALTHKSFXKKSYNNERLEFLGDAVLDLVVGEYLFHKFAKDAEG 64
Query: 98 QLSLLRAANISTEKLARVAVKHGFYKFVRHSAAALDDKVKEFAEAVSQEDNTAVYGGSIK 157
LS LRAA ++ + A++A F+ S V++E+N G +
Sbjct: 65 DLSKLRAALVNEKSFAKIANSLNLGDFILMS--------------VAEENN-----GGKE 105
Query: 158 APKVLADIVESIAAAIYVDIDFDLQK 183
P +L+D +E+I AI+++ F+ K
Sbjct: 106 KPSILSDALEAIIGAIHLEAGFEFAK 131
>pdb|1O0W|A Chain A, Crystal Structure Of Ribonuclease Iii (Tm1102) From
Thermotoga Maritima At 2.0 A Resolution
pdb|1O0W|B Chain B, Crystal Structure Of Ribonuclease Iii (Tm1102) From
Thermotoga Maritima At 2.0 A Resolution
Length = 252
Score = 72.0 bits (175), Expect = 5e-13, Method: Compositional matrix adjust.
Identities = 71/246 (28%), Positives = 112/246 (45%), Gaps = 53/246 (21%)
Query: 46 NFKNKRLLEEALTHSSYT---------DSTSYQRLEFIGDAALGLALSNYVFLAYPQLDP 96
NFKN+ LL AL HSSY D S ++LEF+GDA L L + ++ YP+ +
Sbjct: 31 NFKNEELLFRALCHSSYANEQNQAGRKDVESNEKLEFLGDAVLELFVCEILYKKYPEAEV 90
Query: 97 GQLSLLRAANISTEKLARVAVKHGFYKFVRHSAAALDDKVKEFAEAVSQEDNTAVYGGSI 156
G L+ +++A S E LA V+ K KF+ E+ T G
Sbjct: 91 GDLARVKSAAASEEVLAMVSRKMNLGKFLFLGKG---------------EEKT----GGR 131
Query: 157 KAPKVLADIVESIAAAIYVDIDFD-LQKLW---------MIFRG--LLEPIVTLEELQQQ 204
+LAD E++ AAIY+D ++ +++L+ I +G L + L+E+ Q
Sbjct: 132 DRDSILADAFEALLAAIYLDQGYEKIKELFEQEFEFYIEKIMKGEMLFDYKTALQEIVQS 191
Query: 205 PQ---PVTLLFKLCQKNGKQVDIKHWRKNRKNIASVYVDGSFVASASSEQKEIAKLNAAR 261
P +L + + +G +R + V V+G +A+ K+ A+ AAR
Sbjct: 192 EHKVPPEYILVRTEKNDG----------DRIFVVEVRVNGKTIATGKGRTKKEAEKEAAR 241
Query: 262 EALEKL 267
A EKL
Sbjct: 242 IAYEKL 247
>pdb|1YYK|A Chain A, Crystal Structure Of Rnase Iii From Aquifex Aeolicus
Complexed With Double-Stranded Rna At 2.5-Angstrom
Resolution
pdb|1YYK|B Chain B, Crystal Structure Of Rnase Iii From Aquifex Aeolicus
Complexed With Double-Stranded Rna At 2.5-Angstrom
Resolution
pdb|1YYW|A Chain A, Crystal Structure Of Rnase Iii From Aquifex Aeolicus
Complexed With Double Stranded Rna At 2.8-Angstrom
Resolution
pdb|1YYW|B Chain B, Crystal Structure Of Rnase Iii From Aquifex Aeolicus
Complexed With Double Stranded Rna At 2.8-Angstrom
Resolution
pdb|1YYW|C Chain C, Crystal Structure Of Rnase Iii From Aquifex Aeolicus
Complexed With Double Stranded Rna At 2.8-Angstrom
Resolution
pdb|1YYW|D Chain D, Crystal Structure Of Rnase Iii From Aquifex Aeolicus
Complexed With Double Stranded Rna At 2.8-Angstrom
Resolution
pdb|2NUE|A Chain A, Crystal Structure Of Rnase Iii From Aquifex Aeolicus
Complexed With Ds-Rna At 2.9-Angstrom Resolution
pdb|2NUE|B Chain B, Crystal Structure Of Rnase Iii From Aquifex Aeolicus
Complexed With Ds-Rna At 2.9-Angstrom Resolution
pdb|2NUF|A Chain A, Crystal Structure Of Rnase Iii From Aquifex Aeolicus
Complexed With Ds-Rna At 2.5-Angstrom Resolution
pdb|2NUF|B Chain B, Crystal Structure Of Rnase Iii From Aquifex Aeolicus
Complexed With Ds-Rna At 2.5-Angstrom Resolution
pdb|2NUG|A Chain A, Crystal Structure Of Rnase Iii From Aquifex Aeolicus
Complexed With Ds-Rna At 1.7-Angstrom Resolution
pdb|2NUG|B Chain B, Crystal Structure Of Rnase Iii From Aquifex Aeolicus
Complexed With Ds-Rna At 1.7-Angstrom Resolution
Length = 221
Score = 65.9 bits (159), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 51/188 (27%), Positives = 91/188 (48%), Gaps = 33/188 (17%)
Query: 39 VENIINYNFKNKRLLEEALTHSSYTDSTSYQRLEFIGDAALGLALSNYVFLAYPQLDPGQ 98
+E + Y FK+K LLE+ALTH SY+ Y+ LEF+GDA + + + + P G
Sbjct: 7 LEKKLGYTFKDKSLLEKALTHVSYSKKEHYETLEFLGDALVNFFIVDLLVQYSPNKREGF 66
Query: 99 LSLLRAANISTEKLARVAVKHGFYKFVRHSAAALDDKVKEFAEAVSQEDNTAVYGGSIKA 158
LS L+A IS E +A K +KF+R +++
Sbjct: 67 LSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINE------------------------ 102
Query: 159 PKVLADIVESIAAAIYV----DIDFDLQKLWMIFRGLLEPIVT-LEELQQQPQPVTLLFK 213
++ D+ E++ AA+Y+ D +F + + +F+ E I++ ++E + + T+L +
Sbjct: 103 -TIIGDVFEALWAAVYIDSGRDANFTRELFYKLFK---EDILSAIKEGRVKKDYKTILQE 158
Query: 214 LCQKNGKQ 221
+ QK K+
Sbjct: 159 ITQKRWKE 166
Score = 38.5 bits (88), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 24/70 (34%), Positives = 38/70 (54%), Gaps = 5/70 (7%)
Query: 297 LHELCGKKKWPKPSYKIEKDEGPSHDKKFMSAVQIATTDGVLFITGDEKSRVKDAENSAA 356
L E+ K+ +P Y++ EGP H KKF+ +I + G+ KS+ K+AE AA
Sbjct: 156 LQEITQKRWKERPEYRLISVEGPHHKKKFIVEAKIKEYRTL----GEGKSK-KEAEQRAA 210
Query: 357 SMMLRALRES 366
+++ L ES
Sbjct: 211 EELIKLLEES 220
>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
pdb|1YZ9|B Chain B, Crystal Structure Of Rnase Iii Mutant E110q From Aquifex
Aeolicus Complexed With Double Stranded Rna At 2.1-
Angstrom Resolution
Length = 221
Score = 64.3 bits (155), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 50/188 (26%), Positives = 91/188 (48%), Gaps = 33/188 (17%)
Query: 39 VENIINYNFKNKRLLEEALTHSSYTDSTSYQRLEFIGDAALGLALSNYVFLAYPQLDPGQ 98
+E + Y FK+K LLE+ALTH SY+ Y+ LEF+GDA + + + + P G
Sbjct: 7 LEKKLGYTFKDKSLLEKALTHVSYSKKEHYETLEFLGDALVNFFIVDLLVQYSPNKREGF 66
Query: 99 LSLLRAANISTEKLARVAVKHGFYKFVRHSAAALDDKVKEFAEAVSQEDNTAVYGGSIKA 158
LS L+A IS E +A K +KF+R +++
Sbjct: 67 LSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINE------------------------ 102
Query: 159 PKVLADIVESIAAAIYV----DIDFDLQKLWMIFRGLLEPIVT-LEELQQQPQPVTLLFK 213
++ D+ +++ AA+Y+ D +F + + +F+ E I++ ++E + + T+L +
Sbjct: 103 -TIIGDVFQALWAAVYIDSGRDANFTRELFYKLFK---EDILSAIKEGRVKKDYKTILQE 158
Query: 214 LCQKNGKQ 221
+ QK K+
Sbjct: 159 ITQKRWKE 166
Score = 38.5 bits (88), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 24/70 (34%), Positives = 38/70 (54%), Gaps = 5/70 (7%)
Query: 297 LHELCGKKKWPKPSYKIEKDEGPSHDKKFMSAVQIATTDGVLFITGDEKSRVKDAENSAA 356
L E+ K+ +P Y++ EGP H KKF+ +I + G+ KS+ K+AE AA
Sbjct: 156 LQEITQKRWKERPEYRLISVEGPHHKKKFIVEAKIKEYRTL----GEGKSK-KEAEQRAA 210
Query: 357 SMMLRALRES 366
+++ L ES
Sbjct: 211 EELIKLLEES 220
>pdb|1I4S|A Chain A, Crystal Structure Of Rnase Iii Endonuclease Domain From
Aquifex Aeolicus At 2.15 Angstrom Resolution
pdb|1I4S|B Chain B, Crystal Structure Of Rnase Iii Endonuclease Domain From
Aquifex Aeolicus At 2.15 Angstrom Resolution
Length = 147
Score = 63.9 bits (154), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 41/138 (29%), Positives = 66/138 (47%), Gaps = 25/138 (18%)
Query: 39 VENIINYNFKNKRLLEEALTHSSYTDSTSYQRLEFIGDAALGLALSNYVFLAYPQLDPGQ 98
+E + Y FK+K LLE+ALTH SY+ Y+ LEF+GDA + + + + P G
Sbjct: 7 LEKKLGYTFKDKSLLEKALTHVSYSKKEHYETLEFLGDALVNFFIVDLLVQYSPNKREGF 66
Query: 99 LSLLRAANISTEKLARVAVKHGFYKFVRHSAAALDDKVKEFAEAVSQEDNTAVYGGSIKA 158
LS L+A IS E +A K +KF+R +++
Sbjct: 67 LSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINE------------------------ 102
Query: 159 PKVLADIVESIAAAIYVD 176
++ D+ E++ AA+Y+D
Sbjct: 103 -TIIGDVFEALWAAVYID 119
>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
Score = 63.9 bits (154), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 50/188 (26%), Positives = 91/188 (48%), Gaps = 33/188 (17%)
Query: 39 VENIINYNFKNKRLLEEALTHSSYTDSTSYQRLEFIGDAALGLALSNYVFLAYPQLDPGQ 98
+E + Y FK+K LLE+ALTH SY+ Y+ LEF+GDA + + + + P G
Sbjct: 7 LEKKLGYTFKDKSLLEKALTHVSYSKKEHYETLEFLGDALVNFFIVDLLVQYSPNKREGF 66
Query: 99 LSLLRAANISTEKLARVAVKHGFYKFVRHSAAALDDKVKEFAEAVSQEDNTAVYGGSIKA 158
LS L+A IS E +A K +KF+R +++
Sbjct: 67 LSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINE------------------------ 102
Query: 159 PKVLADIVESIAAAIYV----DIDFDLQKLWMIFRGLLEPIVT-LEELQQQPQPVTLLFK 213
++ D+ +++ AA+Y+ D +F + + +F+ E I++ ++E + + T+L +
Sbjct: 103 -TIIGDVFKALWAAVYIDSGRDANFTRELFYKLFK---EDILSAIKEGRVKKDYKTILQE 158
Query: 214 LCQKNGKQ 221
+ QK K+
Sbjct: 159 ITQKRWKE 166
Score = 38.5 bits (88), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 24/70 (34%), Positives = 38/70 (54%), Gaps = 5/70 (7%)
Query: 297 LHELCGKKKWPKPSYKIEKDEGPSHDKKFMSAVQIATTDGVLFITGDEKSRVKDAENSAA 356
L E+ K+ +P Y++ EGP H KKF+ +I + G+ KS+ K+AE AA
Sbjct: 156 LQEITQKRWKERPEYRLISVEGPHHKKKFIVEAKIKEYRTL----GEGKSK-KEAEQRAA 210
Query: 357 SMMLRALRES 366
+++ L ES
Sbjct: 211 EELIKLLEES 220
>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
pdb|1YYO|B Chain B, Crystal Structure Of Rnase Iii Mutant E110k From Aquifex
Aeolicus Complexed With Double-stranded Rna At 2.9-
Angstrom Resolution
Length = 221
Score = 63.9 bits (154), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 50/188 (26%), Positives = 91/188 (48%), Gaps = 33/188 (17%)
Query: 39 VENIINYNFKNKRLLEEALTHSSYTDSTSYQRLEFIGDAALGLALSNYVFLAYPQLDPGQ 98
+E + Y FK+K LLE+ALTH SY+ Y+ LEF+GDA + + + + P G
Sbjct: 7 LEKKLGYTFKDKSLLEKALTHVSYSKKEHYETLEFLGDALVNFFIVDLLVQYSPNKREGF 66
Query: 99 LSLLRAANISTEKLARVAVKHGFYKFVRHSAAALDDKVKEFAEAVSQEDNTAVYGGSIKA 158
LS L+A IS E +A K +KF+R +++
Sbjct: 67 LSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINE------------------------ 102
Query: 159 PKVLADIVESIAAAIYV----DIDFDLQKLWMIFRGLLEPIVT-LEELQQQPQPVTLLFK 213
++ D+ +++ AA+Y+ D +F + + +F+ E I++ ++E + + T+L +
Sbjct: 103 -TIIGDVFKALWAAVYIDSGRDANFTRELFYKLFK---EDILSAIKEGRVKKDYKTILQE 158
Query: 214 LCQKNGKQ 221
+ QK K+
Sbjct: 159 ITQKRWKE 166
Score = 38.5 bits (88), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 24/70 (34%), Positives = 38/70 (54%), Gaps = 5/70 (7%)
Query: 297 LHELCGKKKWPKPSYKIEKDEGPSHDKKFMSAVQIATTDGVLFITGDEKSRVKDAENSAA 356
L E+ K+ +P Y++ EGP H KKF+ +I + G+ KS+ K+AE AA
Sbjct: 156 LQEITQKRWKERPEYRLISVEGPHHKKKFIVEAKIKEYRTL----GEGKSK-KEAEQRAA 210
Query: 357 SMMLRALRES 366
+++ L ES
Sbjct: 211 EELIKLLEES 220
>pdb|1JFZ|A Chain A, Crystal Structure Of Mn(Ii)-Complex Of Rnase Iii
Endonuclease Domain From Aquifex Aeolicus At 2.10
Angstrom Resolution
pdb|1JFZ|B Chain B, Crystal Structure Of Mn(Ii)-Complex Of Rnase Iii
Endonuclease Domain From Aquifex Aeolicus At 2.10
Angstrom Resolution
pdb|1JFZ|C Chain C, Crystal Structure Of Mn(Ii)-Complex Of Rnase Iii
Endonuclease Domain From Aquifex Aeolicus At 2.10
Angstrom Resolution
pdb|1JFZ|D Chain D, Crystal Structure Of Mn(Ii)-Complex Of Rnase Iii
Endonuclease Domain From Aquifex Aeolicus At 2.10
Angstrom Resolution
pdb|1RC5|A Chain A, Crystal Structure Of Mg(Ii)-Complex Of Rnase Iii
Endonuclease Domain From Aquifex Aeolicus At 2.30
Angstrom Resolution
pdb|1RC5|B Chain B, Crystal Structure Of Mg(Ii)-Complex Of Rnase Iii
Endonuclease Domain From Aquifex Aeolicus At 2.30
Angstrom Resolution
pdb|1RC5|C Chain C, Crystal Structure Of Mg(Ii)-Complex Of Rnase Iii
Endonuclease Domain From Aquifex Aeolicus At 2.30
Angstrom Resolution
pdb|1RC5|D Chain D, Crystal Structure Of Mg(Ii)-Complex Of Rnase Iii
Endonuclease Domain From Aquifex Aeolicus At 2.30
Angstrom Resolution
Length = 154
Score = 63.9 bits (154), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 41/138 (29%), Positives = 66/138 (47%), Gaps = 25/138 (18%)
Query: 39 VENIINYNFKNKRLLEEALTHSSYTDSTSYQRLEFIGDAALGLALSNYVFLAYPQLDPGQ 98
+E + Y FK+K LLE+ALTH SY+ Y+ LEF+GDA + + + + P G
Sbjct: 8 LEKKLGYTFKDKSLLEKALTHVSYSKKEHYETLEFLGDALVNFFIVDLLVQYSPNKREGF 67
Query: 99 LSLLRAANISTEKLARVAVKHGFYKFVRHSAAALDDKVKEFAEAVSQEDNTAVYGGSIKA 158
LS L+A IS E +A K +KF+R +++
Sbjct: 68 LSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINE------------------------ 103
Query: 159 PKVLADIVESIAAAIYVD 176
++ D+ E++ AA+Y+D
Sbjct: 104 -TIIGDVFEALWAAVYID 120
>pdb|2EZ6|A Chain A, Crystal Structure Of Aquifex Aeolicus Rnase Iii (d44n)
Complexed With Product Of Double-stranded Rna Processing
pdb|2EZ6|B Chain B, Crystal Structure Of Aquifex Aeolicus Rnase Iii (d44n)
Complexed With Product Of Double-stranded Rna Processing
Length = 221
Score = 63.9 bits (154), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 50/188 (26%), Positives = 91/188 (48%), Gaps = 33/188 (17%)
Query: 39 VENIINYNFKNKRLLEEALTHSSYTDSTSYQRLEFIGDAALGLALSNYVFLAYPQLDPGQ 98
+E + Y FK+K LLE+ALTH SY+ Y+ LEF+G+A + + + + P G
Sbjct: 7 LEKKLGYTFKDKSLLEKALTHVSYSKKEHYETLEFLGNALVNFFIVDLLVQYSPNKREGF 66
Query: 99 LSLLRAANISTEKLARVAVKHGFYKFVRHSAAALDDKVKEFAEAVSQEDNTAVYGGSIKA 158
LS L+A IS E +A K +KF+R +++
Sbjct: 67 LSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINE------------------------ 102
Query: 159 PKVLADIVESIAAAIYV----DIDFDLQKLWMIFRGLLEPIVT-LEELQQQPQPVTLLFK 213
++ D+ E++ AA+Y+ D +F + + +F+ E I++ ++E + + T+L +
Sbjct: 103 -TIIGDVFEALWAAVYIDSGRDANFTRELFYKLFK---EDILSAIKEGRVKKDYKTILQE 158
Query: 214 LCQKNGKQ 221
+ QK K+
Sbjct: 159 ITQKRWKE 166
Score = 38.5 bits (88), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 24/70 (34%), Positives = 38/70 (54%), Gaps = 5/70 (7%)
Query: 297 LHELCGKKKWPKPSYKIEKDEGPSHDKKFMSAVQIATTDGVLFITGDEKSRVKDAENSAA 356
L E+ K+ +P Y++ EGP H KKF+ +I + G+ KS+ K+AE AA
Sbjct: 156 LQEITQKRWKERPEYRLISVEGPHHKKKFIVEAKIKEYRTL----GEGKSK-KEAEQRAA 210
Query: 357 SMMLRALRES 366
+++ L ES
Sbjct: 211 EELIKLLEES 220
>pdb|2A11|A Chain A, Crystal Structure Of Nuclease Domain Of Ribonuclase Iii
From Mycobacterium Tuberculosis
Length = 242
Score = 55.5 bits (132), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 45/128 (35%), Positives = 65/128 (50%), Gaps = 20/128 (15%)
Query: 52 LLEEALTHSSYT----DSTSYQRLEFIGDAALGLALSNYVFLAYPQLDPGQLSLLRAANI 107
LL ALTH SY + +RLEF+GDA LGL +++ +F +P G L+ LRA+ +
Sbjct: 22 LLSLALTHRSYAYENGGLPTNERLEFLGDAVLGLTITDALFHRHPDRSEGDLAKLRASVV 81
Query: 108 STEKLARVAVKHGFYKFVRHSAAALDDKVKEFAEAVSQEDNTAVYGGSIKAPKVLADIVE 167
+T+ LA VA + H E NT GG+ K+ +LAD +E
Sbjct: 82 NTQALADVARRLCAEGLGVHVLLG------------RGEANT---GGADKS-SILADGME 125
Query: 168 SIAAAIYV 175
S+ AIY+
Sbjct: 126 SLLGAIYL 133
Score = 31.2 bits (69), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 14/38 (36%), Positives = 19/38 (50%), Gaps = 1/38 (2%)
Query: 294 KQKLHELCGKKKWPKPSYKIEKDEGPSHDKKFMSAVQI 331
K L EL + PSY + GP HDK+F + V +
Sbjct: 165 KTSLQELTAARGLGAPSYLVTS-TGPDHDKEFTAVVVV 201
>pdb|2LRS|A Chain A, The Second Dsrbd Domain From A. Thaliana Dicer-like 1
Length = 71
Score = 52.4 bits (124), Expect = 4e-07, Method: Composition-based stats.
Identities = 25/71 (35%), Positives = 43/71 (60%), Gaps = 2/71 (2%)
Query: 298 HELCGKKKWPKPSYKIEKDEGPSHDKKFMSAVQIATTDG--VLFITGDEKSRVKDAENSA 355
+++C +K WP PSY+ K+ GP+H K+F V++ T+D G+ VK A++SA
Sbjct: 1 NDICLRKNWPMPSYRCVKEGGPAHAKRFTFGVRVNTSDRGWTDECIGEPMPSVKKAKDSA 60
Query: 356 ASMMLRALRES 366
A ++L L ++
Sbjct: 61 AVLLLELLNKT 71
>pdb|3RV0|A Chain A, Crystal Structure Of K. Polysporus Dcr1 Without The
C-Terminal Dsrbd
pdb|3RV0|B Chain B, Crystal Structure Of K. Polysporus Dcr1 Without The
C-Terminal Dsrbd
pdb|3RV0|C Chain C, Crystal Structure Of K. Polysporus Dcr1 Without The
C-Terminal Dsrbd
pdb|3RV0|D Chain D, Crystal Structure Of K. Polysporus Dcr1 Without The
C-Terminal Dsrbd
Length = 341
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 38/142 (26%), Positives = 62/142 (43%), Gaps = 19/142 (13%)
Query: 36 VFYVENIINYNFKNKRLLE-EALTHSSYTDSTSYQRLEFIGDAALGLALSNYVFLAYPQL 94
V Y EN+ N F +K A + + S +RLEF+GD+ LG +S V+ +P
Sbjct: 96 VVYDENLENLAFMHKSFPNMNAHLNDAQKTQLSNERLEFLGDSWLGALVSYIVYTRFPSA 155
Query: 95 DPGQLSLLRAANISTEKLARVAVKHGFYKFVRHSAAALDDKVKEFAEAVSQEDNTAVYGG 154
+ G LS ++ + ++ L + K F K ++ + A VK+
Sbjct: 156 NEGMLSQMKESIVNNNNLFDWSTKLNFTKRLQGNIATPTRVVKD---------------- 199
Query: 155 SIKAPKVLADIVESIAAAIYVD 176
K K AD VE+ A+ +D
Sbjct: 200 --KMSKRYADCVEAYIGALVID 219
>pdb|2L2N|A Chain A, Backbone 1h, 13c, And 15n Chemical Shift Assignments For
The First Dsrbd Of Protein Hyl1
Length = 103
Score = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 32/76 (42%), Positives = 40/76 (52%), Gaps = 4/76 (5%)
Query: 294 KQKLHELCGKKKWPKPSYKIEKDEGPSHDKKFMSAVQIATTDGVLFITGDEKSRVKDAEN 353
K +L E K K P P Y+I K EGPSH F S V + DGV + + K AE
Sbjct: 20 KSRLQEYAQKYKLPTPVYEIVK-EGPSHKSLFQSTVIL---DGVRYNSLPGFFNRKAAEQ 75
Query: 354 SAASMMLRALRESTYL 369
SAA + LR L +S+ L
Sbjct: 76 SAAEVALRELAKSSEL 91
>pdb|3RV1|A Chain A, Crystal Structure Of The N-Terminal And Rnase Iii Domains
Of K. Polysporus Dcr1 E224q Mutant
pdb|3RV1|B Chain B, Crystal Structure Of The N-Terminal And Rnase Iii Domains
Of K. Polysporus Dcr1 E224q Mutant
Length = 246
Score = 42.4 bits (98), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 37/142 (26%), Positives = 62/142 (43%), Gaps = 19/142 (13%)
Query: 36 VFYVENIINYNFKNKRLLE-EALTHSSYTDSTSYQRLEFIGDAALGLALSNYVFLAYPQL 94
V Y EN+ N F +K A + + S +RLEF+GD+ LG +S V+ +P
Sbjct: 96 VVYDENLENLAFMHKSFPNMNAHLNDAQKTQLSNERLEFLGDSWLGALVSYIVYTRFPSA 155
Query: 95 DPGQLSLLRAANISTEKLARVAVKHGFYKFVRHSAAALDDKVKEFAEAVSQEDNTAVYGG 154
+ G LS ++ + ++ L + K F K ++ + A VK+
Sbjct: 156 NEGMLSQMKESIVNNNNLFDWSTKLNFTKRLQGNIATPTRVVKD---------------- 199
Query: 155 SIKAPKVLADIVESIAAAIYVD 176
K K AD V++ A+ +D
Sbjct: 200 --KMSKRYADCVQAYIGALVID 219
>pdb|3ADG|A Chain A, Structure Of Arabidopsis Hyl1 And Its Molecular
Implications For Mirna Processing
pdb|3ADI|A Chain A, Structure Of Arabidopsis Hyl1 And Its Molecular
Implications For Mirna Processing
pdb|3ADI|B Chain B, Structure Of Arabidopsis Hyl1 And Its Molecular
Implications For Mirna Processing
pdb|3ADI|C Chain C, Structure Of Arabidopsis Hyl1 And Its Molecular
Implications For Mirna Processing
Length = 73
Score = 41.2 bits (95), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 30/70 (42%), Positives = 36/70 (51%), Gaps = 4/70 (5%)
Query: 294 KQKLHELCGKKKWPKPSYKIEKDEGPSHDKKFMSAVQIATTDGVLFITGDEKSRVKDAEN 353
K +L E K K P P Y+I K EGPSH F S V + DGV + + K AE
Sbjct: 6 KSRLQEYAQKYKLPTPVYEIVK-EGPSHKSLFQSTVIL---DGVRYNSLPGFFNRKAAEQ 61
Query: 354 SAASMMLRAL 363
SAA + LR L
Sbjct: 62 SAAEVALREL 71
>pdb|3ADL|A Chain A, Structure Of Trbp2 And Its Molecule Implications For Mirna
Processing
Length = 88
Score = 38.5 bits (88), Expect = 0.006, Method: Composition-based stats.
Identities = 22/66 (33%), Positives = 33/66 (50%), Gaps = 6/66 (9%)
Query: 297 LHELCGKKKWPKPSYKIEKDEGPSHDKKFMSAVQIATTDGVLFI-TGDEKSRVKDAENSA 355
L EL +K W P Y + ++ GP+H K+F ++ FI G S+ N+A
Sbjct: 21 LQELVVQKGWRLPEYTVTQESGPAHRKEFTMTCRVER-----FIEIGSGTSKKLAKRNAA 75
Query: 356 ASMMLR 361
A M+LR
Sbjct: 76 AKMLLR 81
>pdb|2CPN|A Chain A, Solution Structure Of The Second Dsrbd Of Tar Rna-Binding
Protein 2
Length = 89
Score = 38.1 bits (87), Expect = 0.008, Method: Composition-based stats.
Identities = 22/66 (33%), Positives = 33/66 (50%), Gaps = 6/66 (9%)
Query: 297 LHELCGKKKWPKPSYKIEKDEGPSHDKKFMSAVQIATTDGVLFI-TGDEKSRVKDAENSA 355
L EL +K W P Y + ++ GP+H K+F ++ FI G S+ N+A
Sbjct: 22 LQELVVQKGWRLPEYTVTQESGPAHRKEFTMTCRVER-----FIEIGSGTSKKLAKRNAA 76
Query: 356 ASMMLR 361
A M+LR
Sbjct: 77 AKMLLR 82
>pdb|2FFL|A Chain A, Crystal Structure Of Dicer From Giardia Intestinalis
pdb|2FFL|B Chain B, Crystal Structure Of Dicer From Giardia Intestinalis
pdb|2FFL|C Chain C, Crystal Structure Of Dicer From Giardia Intestinalis
pdb|2FFL|D Chain D, Crystal Structure Of Dicer From Giardia Intestinalis
pdb|2QVW|A Chain A, Structure Of Giardia Dicer Refined Against Twinned Data
pdb|2QVW|B Chain B, Structure Of Giardia Dicer Refined Against Twinned Data
pdb|2QVW|C Chain C, Structure Of Giardia Dicer Refined Against Twinned Data
pdb|2QVW|D Chain D, Structure Of Giardia Dicer Refined Against Twinned Data
Length = 756
Score = 34.3 bits (77), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 35/65 (53%), Gaps = 6/65 (9%)
Query: 51 RLLEEALTHSSYTDSTSYQRLEFIGDAALGLALSNYVFLAYPQLDPGQLSLLRAANISTE 110
RLL+ ALT YQ+LE +GDA L +L+ ++ +P L G L+ +R + +
Sbjct: 636 RLLQIALT------PHVYQKLELLGDAFLKCSLALHLHALHPTLTEGALTRMRQSAETNS 689
Query: 111 KLARV 115
L R+
Sbjct: 690 VLGRL 694
Score = 32.0 bits (71), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 27/52 (51%), Gaps = 2/52 (3%)
Query: 61 SYTDSTSYQRLEFIGDAALGLALSNYVFLAYPQLDPGQLSLLRAANISTEKL 112
S+TD +QRLE +GDA LG ++ + +P G L L+ + E L
Sbjct: 329 SHTDV--FQRLELLGDAVLGFIVTARLLCLFPDASVGTLVELKMELVRNEAL 378
>pdb|1DI2|A Chain A, Crystal Structure Of A Dsrna-Binding Domain Complexed With
Dsrna: Molecular Basis Of Double-Stranded Rna-Protein
Interactions
pdb|1DI2|B Chain B, Crystal Structure Of A Dsrna-Binding Domain Complexed With
Dsrna: Molecular Basis Of Double-Stranded Rna-Protein
Interactions
Length = 69
Score = 32.0 bits (71), Expect = 0.53, Method: Composition-based stats.
Identities = 12/37 (32%), Positives = 20/37 (54%)
Query: 297 LHELCGKKKWPKPSYKIEKDEGPSHDKKFMSAVQIAT 333
L EL +K W P Y + ++ GP H ++F ++ T
Sbjct: 6 LQELAVQKGWRLPEYTVAQESGPPHKREFTITCRVET 42
>pdb|1STU|A Chain A, Double Stranded Rna Binding Domain
Length = 68
Score = 30.8 bits (68), Expect = 1.3, Method: Composition-based stats.
Identities = 20/70 (28%), Positives = 39/70 (55%), Gaps = 6/70 (8%)
Query: 296 KLHELCGKKKWPKPSYKIEKDEGPSHDKKFMSAVQIATTDGVLFITGDEKSRVKDAENSA 355
++HE+ G K+ +K+ ++EGP+H K F++A + + +T E + K ++ A
Sbjct: 4 QVHEI-GIKRNMTVHFKVLREEGPAHMKNFITACIVGS-----IVTEGEGNGKKVSKKRA 57
Query: 356 ASMMLRALRE 365
A ML L++
Sbjct: 58 AEKMLVELQK 67
>pdb|1EKZ|A Chain A, Nmr Structure Of The Complex Between The Third Dsrbd From
Drosophila Staufen And A Rna Hairpin
Length = 76
Score = 30.4 bits (67), Expect = 1.5, Method: Composition-based stats.
Identities = 24/84 (28%), Positives = 45/84 (53%), Gaps = 10/84 (11%)
Query: 282 DDIDEKFEIEAAKQKLHELCGKKKWPKPSYKIEKDEGPSHDKKFMSAVQIATTDGVLFIT 341
D+ D+K I ++HE+ G K+ +K+ ++EGP+H K F++A + + +T
Sbjct: 2 DEGDKKSPI----SQVHEI-GIKRNMTVHFKVLREEGPAHMKNFITACIVGS-----IVT 51
Query: 342 GDEKSRVKDAENSAASMMLRALRE 365
E + K ++ AA ML L++
Sbjct: 52 EGEGNGKKVSKKRAAEKMLVELQK 75
>pdb|1X47|A Chain A, Solution Structure Of Dsrm Domain In Dgcr8 Protein
Length = 98
Score = 29.3 bits (64), Expect = 4.1, Method: Composition-based stats.
Identities = 15/33 (45%), Positives = 20/33 (60%)
Query: 235 ASVYVDGSFVASASSEQKEIAKLNAAREALEKL 267
ASV +DG S ++ K++AK AAR LE L
Sbjct: 50 ASVTIDGVTYGSGTASSKKLAKNKAARATLEIL 82
>pdb|2YT4|A Chain A, Crystal Structure Of Human Dgcr8 Core
Length = 232
Score = 28.9 bits (63), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 29/58 (50%), Gaps = 8/58 (13%)
Query: 235 ASVYVDGSFVASASSEQKEIAKLNAAREALEKL--------AQSMPVNCDVCEIFDDI 284
ASV +DG S ++ K++AK AAR LE L ++ P + + E F+ I
Sbjct: 56 ASVTIDGVTYGSGTASSKKLAKNKAARATLEILIPDFVKQTSEEKPKDSEELEYFNHI 113
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.317 0.131 0.370
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,247,590
Number of Sequences: 62578
Number of extensions: 403641
Number of successful extensions: 1128
Number of sequences better than 100.0: 33
Number of HSP's better than 100.0 without gapping: 26
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1070
Number of HSP's gapped (non-prelim): 47
length of query: 370
length of database: 14,973,337
effective HSP length: 100
effective length of query: 270
effective length of database: 8,715,537
effective search space: 2353194990
effective search space used: 2353194990
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)