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= 044799
(304 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4DZS|A Chain A, Crystal Structure Of Yeast Puf4p Rna Binding Domain In
Complex With Ho-4be Mutant Rna
pdb|4DZS|B Chain B, Crystal Structure Of Yeast Puf4p Rna Binding Domain In
Complex With Ho-4be Mutant Rna
Length = 357
Score = 81.6 bits (200), Expect = 5e-16, Method: Compositional matrix adjust.
Identities = 78/293 (26%), Positives = 126/293 (43%), Gaps = 59/293 (20%)
Query: 31 NALLAQPDYDIVLLGKTEGGSLFLQKMLSGKDSTITYKIFEAVYKYPFDLMTDGYGCHL- 89
+A+L Q I L K + G FLQK L S IFE Y +LMTD +G +L
Sbjct: 27 DAVLDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLI 86
Query: 90 --------------------------------ARSMQKLIKLLVGSPCISLVISAAYRRF 117
R++QKLI+ + +V+ + R
Sbjct: 87 QKLLEEVTTEQRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSL--RP 144
Query: 118 KDMMFSKE--ASSVIIKCLETLDEQKNEVLYLAAMNHFRELATHVRGCVSLNNFINEMRG 175
+ SK+ + VI KCL+ L + + ++ A + ++ATH GC L ++
Sbjct: 145 YTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTT 204
Query: 176 PRRGGLLDLISSHAEFLSKDPSGNYVVQHVLGLGDLK----YSEKICSLLKGKFEELSLL 231
+ L D + + + L+ DP GNYVVQ+++ K Y+ KI LLK + ELS+
Sbjct: 205 EQCDNLCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIH 264
Query: 232 RCGSHLVEKYQRPSIFTP------------------CQHKYGNFVIQQALRVT 266
+ GS+++EK + +I + YGN+V+Q AL ++
Sbjct: 265 KFGSNVIEKILKTAIVSEPMILEILNNGGETGIQSLLNDSYGNYVLQTALDIS 317
>pdb|3BWT|A Chain A, Crystal Structure Of The Rna Binding Domain Of Puf4 From
Saccharomyces Cerevisiae
Length = 333
Score = 81.3 bits (199), Expect = 6e-16, Method: Compositional matrix adjust.
Identities = 78/293 (26%), Positives = 126/293 (43%), Gaps = 59/293 (20%)
Query: 31 NALLAQPDYDIVLLGKTEGGSLFLQKMLSGKDSTITYKIFEAVYKYPFDLMTDGYGCHL- 89
+A+L Q I L K + G FLQK L S IFE Y +LMTD +G +L
Sbjct: 5 DAVLDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLI 64
Query: 90 --------------------------------ARSMQKLIKLLVGSPCISLVISAAYRRF 117
R++QKLI+ + +V+ + R
Sbjct: 65 QKLLEEVTTEQRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSL--RP 122
Query: 118 KDMMFSKE--ASSVIIKCLETLDEQKNEVLYLAAMNHFRELATHVRGCVSLNNFINEMRG 175
+ SK+ + VI KCL+ L + + ++ A + ++ATH GC L ++
Sbjct: 123 YTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTT 182
Query: 176 PRRGGLLDLISSHAEFLSKDPSGNYVVQHVLGLGDLK----YSEKICSLLKGKFEELSLL 231
+ L D + + + L+ DP GNYVVQ+++ K Y+ KI LLK + ELS+
Sbjct: 183 EQCDNLCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIH 242
Query: 232 RCGSHLVEKYQRPSIFTP------------------CQHKYGNFVIQQALRVT 266
+ GS+++EK + +I + YGN+V+Q AL ++
Sbjct: 243 KFGSNVIEKILKTAIVSEPMILEILNNGGETGIQSLLNDSYGNYVLQTALDIS 295
>pdb|3BX2|A Chain A, Puf4 Rna Binding Domain Bound To Ho Endonuclease Rna 3'
Utr Recognition Sequence
pdb|3BX2|B Chain B, Puf4 Rna Binding Domain Bound To Ho Endonuclease Rna 3'
Utr Recognition Sequence
Length = 335
Score = 81.3 bits (199), Expect = 7e-16, Method: Compositional matrix adjust.
Identities = 78/293 (26%), Positives = 126/293 (43%), Gaps = 59/293 (20%)
Query: 31 NALLAQPDYDIVLLGKTEGGSLFLQKMLSGKDSTITYKIFEAVYKYPFDLMTDGYGCHL- 89
+A+L Q I L K + G FLQK L S IFE Y +LMTD +G +L
Sbjct: 5 DAVLDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLI 64
Query: 90 --------------------------------ARSMQKLIKLLVGSPCISLVISAAYRRF 117
R++QKLI+ + +V+ + R
Sbjct: 65 QKLLEEVTTEQRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSL--RP 122
Query: 118 KDMMFSKE--ASSVIIKCLETLDEQKNEVLYLAAMNHFRELATHVRGCVSLNNFINEMRG 175
+ SK+ + VI KCL+ L + + ++ A + ++ATH GC L ++
Sbjct: 123 YTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTT 182
Query: 176 PRRGGLLDLISSHAEFLSKDPSGNYVVQHVLGLGDLK----YSEKICSLLKGKFEELSLL 231
+ L D + + + L+ DP GNYVVQ+++ K Y+ KI LLK + ELS+
Sbjct: 183 EQCDNLCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIH 242
Query: 232 RCGSHLVEKYQRPSIFTP------------------CQHKYGNFVIQQALRVT 266
+ GS+++EK + +I + YGN+V+Q AL ++
Sbjct: 243 KFGSNVIEKILKTAIVSEPMILEILNNGGETGIQSLLNDSYGNYVLQTALDIS 295
>pdb|3BX3|A Chain A, Puf4 T650cC724R MUTANT BOUND TO COX17 RNA 3' UTR
Recognition Sequence
pdb|3BX3|B Chain B, Puf4 T650cC724R MUTANT BOUND TO COX17 RNA 3' UTR
Recognition Sequence
Length = 335
Score = 80.1 bits (196), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 78/293 (26%), Positives = 126/293 (43%), Gaps = 59/293 (20%)
Query: 31 NALLAQPDYDIVLLGKTEGGSLFLQKMLSGKDSTITYKIFEAVYKYPFDLMTDGYGCHL- 89
+A+L Q I L K + G FLQK L S IFE Y +LMTD +G +L
Sbjct: 5 DAVLDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLI 64
Query: 90 --------------------------------ARSMQKLIKLLVGSPCISLVISAAYRRF 117
R++QKLI+ + +V+ + R
Sbjct: 65 QKLLEEVTTEQRIVLTKISSPHFVEISLNPHGCRALQKLIECIKTDEEAQIVVDSL--RP 122
Query: 118 KDMMFSKE--ASSVIIKCLETLDEQKNEVLYLAAMNHFRELATHVRGCVSLNNFINEMRG 175
+ SK+ + VI KCL+ L + + ++ A + ++ATH GC L ++
Sbjct: 123 YTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCRVLQRCLDHGTT 182
Query: 176 PRRGGLLDLISSHAEFLSKDPSGNYVVQHVLGLGDLK----YSEKICSLLKGKFEELSLL 231
+ L D + + + L+ DP GNYVVQ+++ K Y+ KI LLK + ELS+
Sbjct: 183 EQCDNLCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIH 242
Query: 232 RCGSHLVEKYQRPSIFTP------------------CQHKYGNFVIQQALRVT 266
+ GS+++EK + +I + YGN+V+Q AL ++
Sbjct: 243 KFGSNVIEKILKTAIVSEPMILEILNNGGETGIQSLLNDSYGNYVLQTALDIS 295
>pdb|3Q0Q|A Chain A, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio2 In Complex With P38alpha Nrea
pdb|3Q0R|A Chain A, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio2 In Complex With P38alpha Nreb
pdb|3Q0S|A Chain A, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio2 In Complex With Erk2 Nre
Length = 351
Score = 61.6 bits (148), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 66/293 (22%), Positives = 113/293 (38%), Gaps = 59/293 (20%)
Query: 41 IVLLGKTEGGSLFLQKMLSGKDSTITYKIFEAVYKYPFDLMTDGYGCHLARSM------- 93
IV + + GS F+Q+ L +F + + + LMTD +G ++ +
Sbjct: 26 IVEFSQDQHGSRFIQQKLERATPAERQMVFNEILQAAYQLMTDVFGNYVIQKFFEFGSLD 85
Query: 94 QKLI-----------------------KLLVGSPCISLVISAAYRRFKDMMF----SKEA 126
QKL K L VIS + + +
Sbjct: 86 QKLALATRIRGHVLPLALQMYGCRVIQKALESISSDQQVISEMVKELDGHVLKCVKDQNG 145
Query: 127 SSVIIKCLETLDEQKNEVLYLAAMNHFRELATHVRGCVSLNNFINEMRGPRRGGLLDLIS 186
+ V+ KC+E + Q + + A L+TH GC + + + +L+ +
Sbjct: 146 NHVVQKCIECVQPQSLQFIIDAFKGQVFVLSTHPYGCRVIQRILEHCTAEQTLPILEELH 205
Query: 187 SHAEFLSKDPSGNYVVQHVLGLGDLKYSEKICSLLKGKFEELSLLRCGSHLVEKY----- 241
H E L +D GNYV+QHVL G + KI S ++GK LS + S++VEK
Sbjct: 206 QHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGKVLALSQHKFASNVVEKCVTHAS 265
Query: 242 -----------------QRPSIFTPCQHKYGNFVIQQALRVTKGFQMTERNII 277
+++T + +Y N+V+Q+ + + + Q R II
Sbjct: 266 RAERALLIDEVCCQNDGPHSALYTMMKDQYANYVVQKMIDMAEPAQ---RKII 315
>pdb|3GVO|A Chain A, Structure And Rna Binding Of The Mouse Pumilio-2 Puf
Domain
pdb|3GVT|A Chain A, Structure And Rna Binding Of The Mouse Pumilio-2 Puf
Domain
pdb|3GVT|B Chain B, Structure And Rna Binding Of The Mouse Pumilio-2 Puf
Domain
Length = 351
Score = 60.5 bits (145), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 66/294 (22%), Positives = 115/294 (39%), Gaps = 63/294 (21%)
Query: 41 IVLLGKTEGGSLFLQKMLSGKDSTITYKIFEAVYKYPFDLMTDGYGCHLARSMQKLI--- 97
IV + + GS F+Q+ L +F + + + LMTD +G ++ +QK
Sbjct: 28 IVEFSQDQHGSRFIQQKLERATPAERQIVFNEILQAAYQLMTDVFGNYV---IQKFFEFG 84
Query: 98 ----KLLVGSPCISLVISAAYRRFKDMMFSKEASS------------------------- 128
KL + + V+ A + + + K S
Sbjct: 85 SLDQKLALATRIRGHVLPLALQMYGCRVIQKALESISSDQQSEMVKELDGHVLKCVKDQN 144
Query: 129 ---VIIKCLETLDEQKNEVLYLAAMNHFRELATHVRGCVSLNNFINEMRGPRRGGLLDLI 185
V+ KC+E + Q + + A L+TH GC + + + +L+ +
Sbjct: 145 GNHVVQKCIECVQPQSLQFIIDAFKGQVFVLSTHPYGCRVIQRILEHCTAEQTLPILEEL 204
Query: 186 SSHAEFLSKDPSGNYVVQHVLGLGDLKYSEKICSLLKGKFEELSLLRCGSHLVEKY---- 241
H E L +D GNYV+QHVL G + KI S ++GK LS + S++VEK
Sbjct: 205 HQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGKVLALSQHKFASNVVEKCVTHA 264
Query: 242 ------------------QRPSIFTPCQHKYGNFVIQQALRVTKGFQMTERNII 277
+++T + +Y N+V+Q+ + + + Q R II
Sbjct: 265 SRAERALLIDEVCCQNDGPHSALYTMMKDQYANYVVQKMIDMAEPAQ---RKII 315
>pdb|3H3D|X Chain X, Drosophila Pumilio Rna Binding Domain (Puf Domain)
pdb|3H3D|Y Chain Y, Drosophila Pumilio Rna Binding Domain (Puf Domain)
Length = 323
Score = 58.9 bits (141), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 61/285 (21%), Positives = 111/285 (38%), Gaps = 57/285 (20%)
Query: 41 IVLLGKTEGGSLFLQKMLSGKDSTITYKIFEAVYKYPFDLMTDGYGCHLARSMQKLI--- 97
IV + + GS F+Q+ L + +F + + LMTD +G ++ +QK
Sbjct: 28 IVEFSQDQHGSRFIQQKLERATAAEKQMVFSEILAAAYSLMTDVFGNYV---IQKFFEFG 84
Query: 98 ----KLLVGSPCISLVISAAYRRFKDMMFSKEASS------------------------- 128
K +G V+ A + + + K S
Sbjct: 85 TPEQKNTLGMQVKGHVLQLALQMYGCRVIQKALESISPEQQQEIVHELDGHVLKCVKDQN 144
Query: 129 ---VIIKCLETLDEQKNEVLYLAAMNHFRELATHVRGCVSLNNFINEMRGPRRGGLLDLI 185
V+ KC+E +D + + A L+TH GC + + + +LD +
Sbjct: 145 GNHVVQKCIECVDPVALQFIINAFKGQVYSLSTHPYGCRVIQRILEHCTAEQTTPILDEL 204
Query: 186 SSHAEFLSKDPSGNYVVQHVLGLGDLKYSEKICSLLKGKFEELSLLRCGSHLVEK----- 240
H E L +D GNYV+QHVL G + + + ++GK LS + S++VEK
Sbjct: 205 HEHTEQLIQDQYGNYVIQHVLEHGKQEDKSILINSVRGKVLVLSQHKFASNVVEKCVTHA 264
Query: 241 --------------YQRPSIFTPCQHKYGNFVIQQALRVTKGFQM 271
+ ++ + +Y N+V+Q+ + V++ Q+
Sbjct: 265 TRGERTGLIDEVCTFNDNALHVMMKDQYANYVVQKMIDVSEPTQL 309
Score = 32.3 bits (72), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 41/199 (20%), Positives = 82/199 (41%), Gaps = 22/199 (11%)
Query: 22 SIGPGTYGKNALLAQPDYDIVLLGKTEGGSLFLQKMLSGKDSTITYKIFEAVYKYPFDLM 81
SI P + ++ + D ++ K + G+ +QK + D I A + L
Sbjct: 119 SISPEQ--QQEIVHELDGHVLKCVKDQNGNHVVQKCIECVDPVALQFIINAFKGQVYSLS 176
Query: 82 TDGYGCHLARSMQKLIKLLVGSPCISLVISAAYRRFKDMMFSKEASSVIIKCLETLDEQK 141
T YGC R +Q++++ + ++ + + ++ + + VI LE ++
Sbjct: 177 THPYGC---RVIQRILEHCTAEQ-TTPILDELHEHTEQLIQDQYGNYVIQHVLEHGKQED 232
Query: 142 NEVLYLAAMNHFRELATH------VRGCVSLNNFINEMRGPRRGGLLDLISSHAE----F 191
+L + L+ H V CV+ + RG R GL+D + + +
Sbjct: 233 KSILINSVRGKVLVLSQHKFASNVVEKCVT-----HATRG-ERTGLIDEVCTFNDNALHV 286
Query: 192 LSKDPSGNYVVQHVLGLGD 210
+ KD NYVVQ ++ + +
Sbjct: 287 MMKDQYANYVVQKMIDVSE 305
>pdb|1IB2|A Chain A, Crystal Structure Of A Pumilio-Homology Domain
pdb|1M8Z|A Chain A, Crystal Structure Of A Pumilio-Homology Domain
pdb|1M8W|A Chain A, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Nre1-19 Rna
pdb|1M8W|B Chain B, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Nre1-19 Rna
pdb|1M8X|A Chain A, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Nre1-14 Rna
pdb|1M8X|B Chain B, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Nre1-14 Rna
pdb|1M8Y|A Chain A, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Nre2-10 Rna
pdb|1M8Y|B Chain B, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Nre2-10 Rna
pdb|3Q0L|A Chain A, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With P38alpha Nrea
pdb|3Q0L|B Chain B, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With P38alpha Nrea
pdb|3Q0M|A Chain A, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With P38alpha Nreb
pdb|3Q0M|B Chain B, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With P38alpha Nreb
pdb|3Q0N|A Chain A, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Erk2 Nre
pdb|3Q0N|B Chain B, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Erk2 Nre
pdb|3Q0O|A Chain A, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Erk2 Nre
pdb|3Q0O|B Chain B, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Erk2 Nre
pdb|3Q0P|A Chain A, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Hunchback Nre
pdb|3Q0P|B Chain B, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Hunchback Nre
Length = 349
Score = 55.5 bits (132), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 53/240 (22%), Positives = 97/240 (40%), Gaps = 26/240 (10%)
Query: 50 GSLFLQKMLSGKDSTITYKIFEAVYKYPFDLMTDGYGCHLARSMQKLIKLLVGSPCISLV 109
G+ +QK + E + + L YGC R +QK ++ + +V
Sbjct: 71 GNYVIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGC---RVIQKALEFIPSDQQNEMV 127
Query: 110 ISAAYRRFKDMMFSKEASSVIIKCLETLDEQKNEVLYLAAMNHFRELATHVRGCVSLNNF 169
K + + + V+ KC+E + Q + + A L+TH GC +
Sbjct: 128 RELDGHVLK-CVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRI 186
Query: 170 INEMRGPRRGGLLDLISSHAEFLSKDPSGNYVVQHVLGLGDLKYSEKICSLLKGKFEELS 229
+ + +L+ + H E L +D GNYV+QHVL G + KI + ++G LS
Sbjct: 187 LEHCLPDQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLS 246
Query: 230 LLRCGSHLVEKY----------------------QRPSIFTPCQHKYGNFVIQQALRVTK 267
+ S++VEK +++T + +Y N+V+Q+ + V +
Sbjct: 247 QHKFASNVVEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMIDVAE 306
Score = 33.9 bits (76), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 55/240 (22%), Positives = 89/240 (37%), Gaps = 59/240 (24%)
Query: 41 IVLLGKTEGGSLFLQKMLSGKDSTITYKIFEAVYKYPFDLMTDGYGCHLARSMQKLIKLL 100
I+ + + GS F+Q L +F + + + LM D +G ++ +QK +
Sbjct: 26 IMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYV---IQKFFEF- 81
Query: 101 VGSPCISLVISAAYR-RFKDMMFSKEASSVIIKCLETL-DEQKNEVLYLAAMNHFRELAT 158
GS L ++ R + VI K LE + +Q+NE++ REL
Sbjct: 82 -GSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQNEMV--------RELDG 132
Query: 159 HVRGCVSLNNFINEMRGPRRGGLLDLISSHAEFLSKDPSGNYVVQHVLGLGDLKYSEKIC 218
HV CV KD +GN+VVQ + + + I
Sbjct: 133 HVLKCV-----------------------------KDQNGNHVVQKCIECVQPQSLQFII 163
Query: 219 SLLKGKFEELSLLRCGSHLVEK---YQRPSIFTP------------CQHKYGNFVIQQAL 263
KG+ LS G ++++ + P P Q +YGN+VIQ L
Sbjct: 164 DAFKGQVFALSTHPYGCRVIQRILEHCLPDQTLPILEELHQHTEQLVQDQYGNYVIQHVL 223
>pdb|3BSB|A Chain A, Crystal Structure Of Human Pumilio1 In Complex With
Cyclinb Reverse Rna
pdb|3BSB|B Chain B, Crystal Structure Of Human Pumilio1 In Complex With
Cyclinb Reverse Rna
pdb|3BSX|A Chain A, Crystal Structure Of Human Pumilio 1 In Complex With Puf5
Rna
pdb|3BSX|B Chain B, Crystal Structure Of Human Pumilio 1 In Complex With Puf5
Rna
Length = 343
Score = 55.1 bits (131), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 53/240 (22%), Positives = 97/240 (40%), Gaps = 26/240 (10%)
Query: 50 GSLFLQKMLSGKDSTITYKIFEAVYKYPFDLMTDGYGCHLARSMQKLIKLLVGSPCISLV 109
G+ +QK + E + + L YGC R +QK ++ + +V
Sbjct: 71 GNYVIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGC---RVIQKALEFIPSDQQNEMV 127
Query: 110 ISAAYRRFKDMMFSKEASSVIIKCLETLDEQKNEVLYLAAMNHFRELATHVRGCVSLNNF 169
K + + + V+ KC+E + Q + + A L+TH GC +
Sbjct: 128 RELDGHVLK-CVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRI 186
Query: 170 INEMRGPRRGGLLDLISSHAEFLSKDPSGNYVVQHVLGLGDLKYSEKICSLLKGKFEELS 229
+ + +L+ + H E L +D GNYV+QHVL G + KI + ++G LS
Sbjct: 187 LEHCLPDQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLS 246
Query: 230 LLRCGSHLVEKY----------------------QRPSIFTPCQHKYGNFVIQQALRVTK 267
+ S++VEK +++T + +Y N+V+Q+ + V +
Sbjct: 247 QHKFASNVVEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMIDVAE 306
Score = 33.5 bits (75), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 55/240 (22%), Positives = 89/240 (37%), Gaps = 59/240 (24%)
Query: 41 IVLLGKTEGGSLFLQKMLSGKDSTITYKIFEAVYKYPFDLMTDGYGCHLARSMQKLIKLL 100
I+ + + GS F+Q L +F + + + LM D +G ++ +QK +
Sbjct: 26 IMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYV---IQKFFEF- 81
Query: 101 VGSPCISLVISAAYR-RFKDMMFSKEASSVIIKCLETL-DEQKNEVLYLAAMNHFRELAT 158
GS L ++ R + VI K LE + +Q+NE++ REL
Sbjct: 82 -GSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQNEMV--------RELDG 132
Query: 159 HVRGCVSLNNFINEMRGPRRGGLLDLISSHAEFLSKDPSGNYVVQHVLGLGDLKYSEKIC 218
HV CV KD +GN+VVQ + + + I
Sbjct: 133 HVLKCV-----------------------------KDQNGNHVVQKCIECVQPQSLQFII 163
Query: 219 SLLKGKFEELSLLRCGSHLVEK---YQRPSIFTP------------CQHKYGNFVIQQAL 263
KG+ LS G ++++ + P P Q +YGN+VIQ L
Sbjct: 164 DAFKGQVFALSTHPYGCRVIQRILEHCLPDQTLPILEELHQHTEQLVQDQYGNYVIQHVL 223
>pdb|2YJY|A Chain A, A Specific And Modular Binding Code For Cytosine
Recognition In Puf Domains
pdb|2YJY|B Chain B, A Specific And Modular Binding Code For Cytosine
Recognition In Puf Domains
Length = 350
Score = 51.2 bits (121), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 51/240 (21%), Positives = 97/240 (40%), Gaps = 26/240 (10%)
Query: 50 GSLFLQKMLSGKDSTITYKIFEAVYKYPFDLMTDGYGCHLARSMQKLIKLLVGSPCISLV 109
G+ +QK + E + + L YGC R +QK ++ + +V
Sbjct: 72 GNYVIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGC---RVIQKALEFIPSDQQNEMV 128
Query: 110 ISAAYRRFKDMMFSKEASSVIIKCLETLDEQKNEVLYLAAMNHFRELATHVRGCVSLNNF 169
K + + + V+ KC+E + Q + + A L+TH GC +
Sbjct: 129 RELDGHVLK-CVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRI 187
Query: 170 INEMRGPRRGGLLDLISSHAEFLSKDPSGNYVVQHVLGLGDLKYSEKICSLLKGKFEELS 229
+ + +L+ + H E L +D G+YV++HVL G + KI + ++G LS
Sbjct: 188 LEHCLPDQTLPILEELHQHTEQLVQDQYGSYVIRHVLEHGRPEDKSKIVAEIRGNVLVLS 247
Query: 230 LLRCGSHLVEKY----------------------QRPSIFTPCQHKYGNFVIQQALRVTK 267
+ S++VEK +++T + +Y N+V+Q+ + V +
Sbjct: 248 QHKFASNVVEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMIDVAE 307
Score = 29.6 bits (65), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 53/240 (22%), Positives = 89/240 (37%), Gaps = 59/240 (24%)
Query: 41 IVLLGKTEGGSLFLQKMLSGKDSTITYKIFEAVYKYPFDLMTDGYGCHLARSMQKLIKLL 100
I+ + + GS F+Q L +F + + + LM D +G ++ +QK +
Sbjct: 27 IMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYV---IQKFFEF- 82
Query: 101 VGSPCISLVISAAYR-RFKDMMFSKEASSVIIKCLETL-DEQKNEVLYLAAMNHFRELAT 158
GS L ++ R + VI K LE + +Q+NE++ REL
Sbjct: 83 -GSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQNEMV--------RELDG 133
Query: 159 HVRGCVSLNNFINEMRGPRRGGLLDLISSHAEFLSKDPSGNYVVQHVLGLGDLKYSEKIC 218
HV CV KD +GN+VVQ + + + I
Sbjct: 134 HVLKCV-----------------------------KDQNGNHVVQKCIECVQPQSLQFII 164
Query: 219 SLLKGKFEELSLLRCGSHLVEK---YQRPSIFTP------------CQHKYGNFVIQQAL 263
KG+ LS G ++++ + P P Q +YG++VI+ L
Sbjct: 165 DAFKGQVFALSTHPYGCRVIQRILEHCLPDQTLPILEELHQHTEQLVQDQYGSYVIRHVL 224
Score = 28.1 bits (61), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 38/221 (17%), Positives = 87/221 (39%), Gaps = 11/221 (4%)
Query: 30 KNALLAQPDYDIVLLGKTEGGSLFLQKMLSGKDSTITYKIFEAVYKYPFDLMTDGYGCHL 89
+N ++ + D ++ K + G+ +QK + I +A F L T YGC
Sbjct: 124 QNEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGC-- 181
Query: 90 ARSMQKLIKLLVGSPCISLVISAAYRRFKDMMFSKEASSVIIKCLETLDEQKNEVLYLAA 149
R +Q++++ + + ++ ++ + ++ + S VI LE + +
Sbjct: 182 -RVIQRILEHCLPDQTLP-ILEELHQHTEQLVQDQYGSYVIRHVLEHGRPEDKSKIVAEI 239
Query: 150 MNHFRELATHVRGCVSLNNFINEMRGPRRGGLLDLISS-----HAEF--LSKDPSGNYVV 202
+ L+ H + + R L+D + + H+ + KD NYVV
Sbjct: 240 RGNVLVLSQHKFASNVVEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVV 299
Query: 203 QHVLGLGDLKYSEKICSLLKGKFEELSLLRCGSHLVEKYQR 243
Q ++ + + + + ++ L G H++ K ++
Sbjct: 300 QKMIDVAEPGQRKIVMHKIRPHIATLRKYTYGKHILAKLEK 340
>pdb|3K49|A Chain A, Puf3 Rna Binding Domain Bound To Cox17 Rna 3' Utr
Recognition Sequence Site B
pdb|3K49|C Chain C, Puf3 Rna Binding Domain Bound To Cox17 Rna 3' Utr
Recognition Sequence Site B
pdb|3K49|E Chain E, Puf3 Rna Binding Domain Bound To Cox17 Rna 3' Utr
Recognition Sequence Site B
pdb|3K4E|A Chain A, Puf3 Rna Binding Domain Bound To Cox17 Rna 3' Utr
Recognition Sequence Site A
pdb|3K4E|C Chain C, Puf3 Rna Binding Domain Bound To Cox17 Rna 3' Utr
Recognition Sequence Site A
pdb|3K4E|E Chain E, Puf3 Rna Binding Domain Bound To Cox17 Rna 3' Utr
Recognition Sequence Site A
Length = 369
Score = 44.7 bits (104), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 40/164 (24%), Positives = 75/164 (45%), Gaps = 14/164 (8%)
Query: 85 YGCHLARSMQKLIKLLVGSPCISLVISAAYRRFKDMMFSKEASSVIIKCLETLDEQKNEV 144
Y C R +QK ++ + + I LV+ + + M+ + + VI K +ET+ +K
Sbjct: 113 YAC---RVIQKALEYIDSNQRIELVLELSDSVLQ-MIKDQNGNHVIQKAIETIPIEKLPF 168
Query: 145 LYLAAMNHFRELATHVRGCVSLNNFINEMRGPRRGGLLDLISSHAEFLSKDPSGNYVVQH 204
+ + H L+TH GC + + + +L+ + +L +D GNYV+Q+
Sbjct: 169 ILSSLTGHIYHLSTHSYGCRVIQRLLEFGSSEDQESILNELKDFIPYLIQDQYGNYVIQY 228
Query: 205 VLG--------LGDLKYSEKICSLLKGKFEELSLLRCGSHLVEK 240
VL + D+K ++I + E S + S++VEK
Sbjct: 229 VLQQDQFTNKEMVDIK--QEIIETVANNVVEYSKHKFASNVVEK 270
Score = 30.4 bits (67), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 36/88 (40%), Gaps = 15/88 (17%)
Query: 192 LSKDPSGNYVVQHVLGLGDLKYSEKICSLLKGKFEELSLLRCGSHLVEKY-------QR- 243
LS D GNYV+Q G + KG ++LSL +++K QR
Sbjct: 72 LSNDVFGNYVIQKFFEFGSKIQKNTLVDQFKGNMKQLSLQMYACRVIQKALEYIDSNQRI 131
Query: 244 -------PSIFTPCQHKYGNFVIQQALR 264
S+ + + GN VIQ+A+
Sbjct: 132 ELVLELSDSVLQMIKDQNGNHVIQKAIE 159
Score = 30.0 bits (66), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 35/159 (22%), Positives = 69/159 (43%), Gaps = 16/159 (10%)
Query: 152 HFRELATHVRGCVSLNNFINEMRGPRRGGLLDLISSHAEFLSKDPSGNYVVQHVLGLGDL 211
+ ++L+ + C + + + +R L+ +S + KD +GN+V+Q + +
Sbjct: 104 NMKQLSLQMYACRVIQKALEYIDSNQRIELVLELSDSVLQMIKDQNGNHVIQKAIETIPI 163
Query: 212 KYSEKICSLLKGKFEELSLLRCGSHLVEKY-------QRPSI------FTP--CQHKYGN 256
+ I S L G LS G ++++ + SI F P Q +YGN
Sbjct: 164 EKLPFILSSLTGHIYHLSTHSYGCRVIQRLLEFGSSEDQESILNELKDFIPYLIQDQYGN 223
Query: 257 FVIQQALRVTKGFQMTERNIIQELGQSSFIQGIVPFNFH 295
+VIQ L+ + +I QE+ + + +V ++ H
Sbjct: 224 YVIQYVLQQDQFTNKEMVDIKQEIIE-TVANNVVEYSKH 261
>pdb|3QGB|A Chain A, Crystal Structure Of Fbf-2 R288y Mutant In Complex With
Gld-1 Fbea
pdb|3QGC|A Chain A, Crystal Structure Of Fbf-2 R288y Mutant In Complex With
Gld-1 Fbea A7u Mutant
Length = 413
Score = 37.4 bits (85), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 40/182 (21%), Positives = 76/182 (41%), Gaps = 22/182 (12%)
Query: 79 DLMTDGYGCHLARSMQKLIKLLVGSPCISLVISAAYRRFKDMMFSKEASSVIIKCLETLD 138
D+ D + C++ +S + + L + + + A R + + A+ VI K + +
Sbjct: 117 DMCLDKFACYVIQSSLQNMDLSLACKLVQALPRDA--RLIAICVDQNANHVIQKVVAVIP 174
Query: 139 EQKNE--VLYLAAMNHFRELATHVRGC----------------VSLNNFINEMRGPRRGG 180
+ E V ++A H R++ + GC V L + +R
Sbjct: 175 LKNWEFIVDFVATPEHLRQICSDKYGCRVVQTIIEKLTADSMNVDLTSAAQNLRERALQR 234
Query: 181 LLDLISSHAEFLSKDPSGNYVVQHVLGLGDLK-YSEKICS-LLKGKFEELSLLRCGSHLV 238
L+ +++ + L+ + NY++QH++ DL Y E I L LS + SH+V
Sbjct: 235 LMTSVTNRCQELATNEYANYIIQHIVSNDDLAVYRECIIEKCLMRNLLSLSQEKFASHVV 294
Query: 239 EK 240
EK
Sbjct: 295 EK 296
>pdb|3QG9|A Chain A, Crystal Structure Of Fbf-2GLD-1 Fbea A7u Mutant Complex
pdb|3V6Y|A Chain A, Crystal Structure Of Fbf-2 In Complex With A Mutant Gld-1
Fbea13 Rna
pdb|3V74|A Chain A, Crystal Structure Of Fbf-2 In Complex With Gld-1 Fbea13
Rna
Length = 413
Score = 36.6 bits (83), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 40/182 (21%), Positives = 75/182 (41%), Gaps = 22/182 (12%)
Query: 79 DLMTDGYGCHLARSMQKLIKLLVGSPCISLVISAAYRRFKDMMFSKEASSVIIKCLETLD 138
D+ D + C + +S + + L + + + A R + + A+ VI K + +
Sbjct: 117 DMCLDKFACRVIQSSLQNMDLSLACKLVQALPRDA--RLIAICVDQNANHVIQKVVAVIP 174
Query: 139 EQKNE--VLYLAAMNHFRELATHVRGC----------------VSLNNFINEMRGPRRGG 180
+ E V ++A H R++ + GC V L + +R
Sbjct: 175 LKNWEFIVDFVATPEHLRQICSDKYGCRVVQTIIEKLTADSMNVDLTSAAQNLRERALQR 234
Query: 181 LLDLISSHAEFLSKDPSGNYVVQHVLGLGDLK-YSEKICS-LLKGKFEELSLLRCGSHLV 238
L+ +++ + L+ + NY++QH++ DL Y E I L LS + SH+V
Sbjct: 235 LMTSVTNRCQELATNEYANYIIQHIVSNDDLAVYRECIIEKCLMRNLLSLSQEKFASHVV 294
Query: 239 EK 240
EK
Sbjct: 295 EK 296
>pdb|3K5Q|A Chain A, Crystal Structure Of Fbf-2FBE COMPLEX
pdb|3K5Y|A Chain A, Crystal Structure Of Fbf-2GLD-1 Fbea Complex
pdb|3K5Z|A Chain A, Crystal Structure Of Fbf-2GLD-1 Fbea G4a Mutant Complex
pdb|3K61|A Chain A, Crystal Structure Of Fbf-2FOG-1 Fbea Complex
pdb|3K62|A Chain A, Crystal Structure Of Fbf-2GLD-1 Fbeb Complex
pdb|3K64|A Chain A, Crystal Structure Of Fbf-2FEM-3 Pme Complex
Length = 412
Score = 36.6 bits (83), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 40/182 (21%), Positives = 75/182 (41%), Gaps = 22/182 (12%)
Query: 79 DLMTDGYGCHLARSMQKLIKLLVGSPCISLVISAAYRRFKDMMFSKEASSVIIKCLETLD 138
D+ D + C + +S + + L + + + A R + + A+ VI K + +
Sbjct: 116 DMCLDKFACRVIQSSLQNMDLSLACKLVQALPRDA--RLIAICVDQNANHVIQKVVAVIP 173
Query: 139 EQKNE--VLYLAAMNHFRELATHVRGC----------------VSLNNFINEMRGPRRGG 180
+ E V ++A H R++ + GC V L + +R
Sbjct: 174 LKNWEFIVDFVATPEHLRQICSDKYGCRVVQTIIEKLTADSMNVDLTSAAQNLRERALQR 233
Query: 181 LLDLISSHAEFLSKDPSGNYVVQHVLGLGDLK-YSEKICS-LLKGKFEELSLLRCGSHLV 238
L+ +++ + L+ + NY++QH++ DL Y E I L LS + SH+V
Sbjct: 234 LMTSVTNRCQELATNEYANYIIQHIVSNDDLAVYRECIIEKCLMRNLLSLSQEKFASHVV 293
Query: 239 EK 240
EK
Sbjct: 294 EK 295
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
0.322 0.139 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,867,770
Number of Sequences: 62578
Number of extensions: 361963
Number of successful extensions: 1004
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 921
Number of HSP's gapped (non-prelim): 46
length of query: 304
length of database: 14,973,337
effective HSP length: 98
effective length of query: 206
effective length of database: 8,840,693
effective search space: 1821182758
effective search space used: 1821182758
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (24.3 bits)