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= 047627
(422 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 98.2 bits (243), Expect = 8e-21, Method: Compositional matrix adjust.
Identities = 80/330 (24%), Positives = 158/330 (47%), Gaps = 16/330 (4%)
Query: 100 ILLLAQDEQGSQYLQEKLTSGDSRFLDKVFNVVSEFTFQIICNQYARFVFGKFIETCNED 159
I+ +QD+ GS+++Q+KL VFN + + +Q++ + + +V KF E + D
Sbjct: 26 IVEFSQDQHGSRFIQQKLERATPAERQMVFNEILQAAYQLMTDVFGNYVIQKFFEFGSLD 85
Query: 160 QLLRITLQITSQDQLFVQASVDKFGSSSIRKLMKAVANRPPLLDLVMKALKRLFRLLMMT 219
Q L + +I + ++ +G I+K ++++++ ++ ++K L +
Sbjct: 86 QKLALATRIRGH---VLPLALQMYGCRVIQKALESISSDQQVISEMVKELDGHVLKCVKD 142
Query: 220 KPGSSVVLQCLEQIYHHNNKNDFIYQAALEHCLYLACHEQGCINMNNFIDEMKGPRRKQI 279
+ G+ VV +C+E + FI A L+ H GC + ++ + I
Sbjct: 143 QNGNHVVQKCIECV--QPQSLQFIIDAFKGQVFVLSTHPYGCRVIQRILEHCTAEQTLPI 200
Query: 280 LYLISVNAASLSRNFSGNYVVQHVLELEDPYLIETICFSLRGHYIDLSLTKCGSFVVQNC 339
L + + L ++ GNYV+QHVLE P I +RG + LS K S VV+ C
Sbjct: 201 LEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGKVLALSQHKFASNVVEKC 260
Query: 340 LKY--RITVNYIVEEFLLNSD----QIFRVACDKYGNYVIQTALIETMRPNSLHLHQRLV 393
+ + R +++E +D ++ + D+Y NYV+Q +I+ P + ++
Sbjct: 261 VTHASRAERALLIDEVCCQNDGPHSALYTMMKDQYANYVVQK-MIDMAEPAQRKI---IM 316
Query: 394 TKLQQNLDSLR-FGYGKHVYNFIKDCDLQN 422
K++ ++ +LR + YGKH+ ++ L+N
Sbjct: 317 HKIRPHITTLRKYTYGKHILAKLEKYYLKN 346
>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 = 95.9 bits (237), Expect = 4e-20, Method: Compositional matrix adjust.
Identities = 79/296 (26%), Positives = 149/296 (50%), Gaps = 13/296 (4%)
Query: 103 LAQDEQGSQYLQEKLTSGDSRFLDKVFNVVSEFTFQIICNQYARFVFGKFIETCNEDQLL 162
L +D+ G ++LQ++L S+ D +F ++T +++ + + ++ K +E +Q
Sbjct: 40 LCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVTTEQ-- 97
Query: 163 RITLQITSQDQLFVQASVDKFGSSSIRKLMKAVANRPPLLDLVMKALKRLFRLLMMTKPG 222
RI L S FV+ S++ G+ +++KL++ + +V+ +L+ L G
Sbjct: 98 RIVLTKISSPH-FVEISLNPHGTRALQKLIECIKTDEEA-QIVVDSLRPYTVQLSKDLNG 155
Query: 223 SSVVLQCLEQIYHHNNKNDFIYQAALEHCLYLACHEQGCINMNNFIDEMKGPRRKQILYL 282
+ V+ +CL+++ N + FI+ A + C+ +A H GC + +D + +
Sbjct: 156 NHVIQKCLQRLKPENFQ--FIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCDNLCDK 213
Query: 283 ISVNAASLSRNFSGNYVVQHVLELE---DPY-LIETICFSLRGHYIDLSLTKCGSFVVQN 338
+ L+ + GNYVVQ+++ E + Y I L+ I+LS+ K GS V++
Sbjct: 214 LLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVIEK 273
Query: 339 CLKYRITVNYIVEEFLLNSDQ--IFRVACDKYGNYVIQTALIETMRPNSLHLHQRL 392
LK I ++ E L N + I + D YGNYV+QTAL + + N +L++RL
Sbjct: 274 ILKTAIVSEPMILEILNNGGETGIQSLLNDSYGNYVLQTALDISHKQND-YLYKRL 328
Score = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 44/220 (20%), Positives = 99/220 (45%), Gaps = 10/220 (4%)
Query: 181 DKFGSSSIRKLMKAVANRPPLLDLVMKALKRLFRLLMMTKPGSSVVLQCLEQIYHHNNKN 240
D+ G ++K + + ++ D + + K LM G+ ++ + LE++ +
Sbjct: 43 DQHGCRFLQKQLDILGSKAA--DAIFEETKDYTVELMTDSFGNYLIQKLLEEVT--TEQR 98
Query: 241 DFIYQAALEHCLYLACHEQGCINMNNFIDEMKGPRRKQILY-LISVNAASLSRNFSGNYV 299
+ + + H + ++ + G + I+ +K QI+ + LS++ +GN+V
Sbjct: 99 IVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYTVQLSKDLNGNHV 158
Query: 300 VQHVLELEDPYLIETICFSLRGHYIDLSLTKCGSFVVQNCLKYRIT--VNYIVEEFLLNS 357
+Q L+ P + I ++ ID++ + G V+Q CL + T + + ++ L
Sbjct: 159 IQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCDNLCDKLLALV 218
Query: 358 DQIFRVACDKYGNYVIQTALIETMRPNSLHLHQRLVTKLQ 397
D ++ D +GNYV+Q + + N ++V L+
Sbjct: 219 D---KLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLK 255
>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 = 95.5 bits (236), Expect = 5e-20, Method: Compositional matrix adjust.
Identities = 79/296 (26%), Positives = 149/296 (50%), Gaps = 13/296 (4%)
Query: 103 LAQDEQGSQYLQEKLTSGDSRFLDKVFNVVSEFTFQIICNQYARFVFGKFIETCNEDQLL 162
L +D+ G ++LQ++L S+ D +F ++T +++ + + ++ K +E +Q
Sbjct: 18 LCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVTTEQ-- 75
Query: 163 RITLQITSQDQLFVQASVDKFGSSSIRKLMKAVANRPPLLDLVMKALKRLFRLLMMTKPG 222
RI L S FV+ S++ G+ +++KL++ + +V+ +L+ L G
Sbjct: 76 RIVLTKISSPH-FVEISLNPHGTRALQKLIECIKTDEEA-QIVVDSLRPYTVQLSKDLNG 133
Query: 223 SSVVLQCLEQIYHHNNKNDFIYQAALEHCLYLACHEQGCINMNNFIDEMKGPRRKQILYL 282
+ V+ +CL+++ N + FI+ A + C+ +A H GC + +D + +
Sbjct: 134 NHVIQKCLQRLKPENFQ--FIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCDNLCDK 191
Query: 283 ISVNAASLSRNFSGNYVVQHVLELE---DPY-LIETICFSLRGHYIDLSLTKCGSFVVQN 338
+ L+ + GNYVVQ+++ E + Y I L+ I+LS+ K GS V++
Sbjct: 192 LLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVIEK 251
Query: 339 CLKYRITVNYIVEEFLLNSDQ--IFRVACDKYGNYVIQTALIETMRPNSLHLHQRL 392
LK I ++ E L N + I + D YGNYV+QTAL + + N +L++RL
Sbjct: 252 ILKTAIVSEPMILEILNNGGETGIQSLLNDSYGNYVLQTALDISHKQND-YLYKRL 306
Score = 42.7 bits (99), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 44/220 (20%), Positives = 99/220 (45%), Gaps = 10/220 (4%)
Query: 181 DKFGSSSIRKLMKAVANRPPLLDLVMKALKRLFRLLMMTKPGSSVVLQCLEQIYHHNNKN 240
D+ G ++K + + ++ D + + K LM G+ ++ + LE++ +
Sbjct: 21 DQHGCRFLQKQLDILGSKAA--DAIFEETKDYTVELMTDSFGNYLIQKLLEEVT--TEQR 76
Query: 241 DFIYQAALEHCLYLACHEQGCINMNNFIDEMKGPRRKQILY-LISVNAASLSRNFSGNYV 299
+ + + H + ++ + G + I+ +K QI+ + LS++ +GN+V
Sbjct: 77 IVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYTVQLSKDLNGNHV 136
Query: 300 VQHVLELEDPYLIETICFSLRGHYIDLSLTKCGSFVVQNCLKYRIT--VNYIVEEFLLNS 357
+Q L+ P + I ++ ID++ + G V+Q CL + T + + ++ L
Sbjct: 137 IQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCDNLCDKLLALV 196
Query: 358 DQIFRVACDKYGNYVIQTALIETMRPNSLHLHQRLVTKLQ 397
D ++ D +GNYV+Q + + N ++V L+
Sbjct: 197 D---KLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLK 233
>pdb|3BWT|A Chain A, Crystal Structure Of The Rna Binding Domain Of Puf4 From
Saccharomyces Cerevisiae
Length = 333
Score = 95.5 bits (236), Expect = 5e-20, Method: Compositional matrix adjust.
Identities = 79/296 (26%), Positives = 149/296 (50%), Gaps = 13/296 (4%)
Query: 103 LAQDEQGSQYLQEKLTSGDSRFLDKVFNVVSEFTFQIICNQYARFVFGKFIETCNEDQLL 162
L +D+ G ++LQ++L S+ D +F ++T +++ + + ++ K +E +Q
Sbjct: 18 LCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVTTEQ-- 75
Query: 163 RITLQITSQDQLFVQASVDKFGSSSIRKLMKAVANRPPLLDLVMKALKRLFRLLMMTKPG 222
RI L S FV+ S++ G+ +++KL++ + +V+ +L+ L G
Sbjct: 76 RIVLTKISSPH-FVEISLNPHGTRALQKLIECIKTDEEA-QIVVDSLRPYTVQLSKDLNG 133
Query: 223 SSVVLQCLEQIYHHNNKNDFIYQAALEHCLYLACHEQGCINMNNFIDEMKGPRRKQILYL 282
+ V+ +CL+++ N + FI+ A + C+ +A H GC + +D + +
Sbjct: 134 NHVIQKCLQRLKPENFQ--FIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCDNLCDK 191
Query: 283 ISVNAASLSRNFSGNYVVQHVLELE---DPY-LIETICFSLRGHYIDLSLTKCGSFVVQN 338
+ L+ + GNYVVQ+++ E + Y I L+ I+LS+ K GS V++
Sbjct: 192 LLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVIEK 251
Query: 339 CLKYRITVNYIVEEFLLNSDQ--IFRVACDKYGNYVIQTALIETMRPNSLHLHQRL 392
LK I ++ E L N + I + D YGNYV+QTAL + + N +L++RL
Sbjct: 252 ILKTAIVSEPMILEILNNGGETGIQSLLNDSYGNYVLQTALDISHKQND-YLYKRL 306
Score = 42.7 bits (99), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 44/220 (20%), Positives = 99/220 (45%), Gaps = 10/220 (4%)
Query: 181 DKFGSSSIRKLMKAVANRPPLLDLVMKALKRLFRLLMMTKPGSSVVLQCLEQIYHHNNKN 240
D+ G ++K + + ++ D + + K LM G+ ++ + LE++ +
Sbjct: 21 DQHGCRFLQKQLDILGSKAA--DAIFEETKDYTVELMTDSFGNYLIQKLLEEVT--TEQR 76
Query: 241 DFIYQAALEHCLYLACHEQGCINMNNFIDEMKGPRRKQILY-LISVNAASLSRNFSGNYV 299
+ + + H + ++ + G + I+ +K QI+ + LS++ +GN+V
Sbjct: 77 IVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYTVQLSKDLNGNHV 136
Query: 300 VQHVLELEDPYLIETICFSLRGHYIDLSLTKCGSFVVQNCLKYRIT--VNYIVEEFLLNS 357
+Q L+ P + I ++ ID++ + G V+Q CL + T + + ++ L
Sbjct: 137 IQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCDNLCDKLLALV 196
Query: 358 DQIFRVACDKYGNYVIQTALIETMRPNSLHLHQRLVTKLQ 397
D ++ D +GNYV+Q + + N ++V L+
Sbjct: 197 D---KLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLK 233
>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 = 94.0 bits (232), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 79/296 (26%), Positives = 148/296 (50%), Gaps = 13/296 (4%)
Query: 103 LAQDEQGSQYLQEKLTSGDSRFLDKVFNVVSEFTFQIICNQYARFVFGKFIETCNEDQLL 162
L +D+ G ++LQ++L S+ D +F ++T +++ + + ++ K +E +Q
Sbjct: 18 LCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVTTEQ-- 75
Query: 163 RITLQITSQDQLFVQASVDKFGSSSIRKLMKAVANRPPLLDLVMKALKRLFRLLMMTKPG 222
RI L S FV+ S++ G +++KL++ + +V+ +L+ L G
Sbjct: 76 RIVLTKISSPH-FVEISLNPHGCRALQKLIECIKTDEEA-QIVVDSLRPYTVQLSKDLNG 133
Query: 223 SSVVLQCLEQIYHHNNKNDFIYQAALEHCLYLACHEQGCINMNNFIDEMKGPRRKQILYL 282
+ V+ +CL+++ N + FI+ A + C+ +A H GC + +D + +
Sbjct: 134 NHVIQKCLQRLKPENFQ--FIFDAISDSCIDIATHRHGCRVLQRCLDHGTTEQCDNLCDK 191
Query: 283 ISVNAASLSRNFSGNYVVQHVLELE---DPY-LIETICFSLRGHYIDLSLTKCGSFVVQN 338
+ L+ + GNYVVQ+++ E + Y I L+ I+LS+ K GS V++
Sbjct: 192 LLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVIEK 251
Query: 339 CLKYRITVNYIVEEFLLNSDQ--IFRVACDKYGNYVIQTALIETMRPNSLHLHQRL 392
LK I ++ E L N + I + D YGNYV+QTAL + + N +L++RL
Sbjct: 252 ILKTAIVSEPMILEILNNGGETGIQSLLNDSYGNYVLQTALDISHKQND-YLYKRL 306
Score = 46.6 bits (109), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 45/220 (20%), Positives = 100/220 (45%), Gaps = 10/220 (4%)
Query: 181 DKFGSSSIRKLMKAVANRPPLLDLVMKALKRLFRLLMMTKPGSSVVLQCLEQIYHHNNKN 240
D+ G ++K + + ++ D + + K LM G+ ++ + LE++ +
Sbjct: 21 DQHGCRFLQKQLDILGSKAA--DAIFEETKDYTVELMTDSFGNYLIQKLLEEVT--TEQR 76
Query: 241 DFIYQAALEHCLYLACHEQGCINMNNFIDEMKGPRRKQILY-LISVNAASLSRNFSGNYV 299
+ + + H + ++ + GC + I+ +K QI+ + LS++ +GN+V
Sbjct: 77 IVLTKISSPHFVEISLNPHGCRALQKLIECIKTDEEAQIVVDSLRPYTVQLSKDLNGNHV 136
Query: 300 VQHVLELEDPYLIETICFSLRGHYIDLSLTKCGSFVVQNCLKYRIT--VNYIVEEFLLNS 357
+Q L+ P + I ++ ID++ + G V+Q CL + T + + ++ L
Sbjct: 137 IQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCRVLQRCLDHGTTEQCDNLCDKLLALV 196
Query: 358 DQIFRVACDKYGNYVIQTALIETMRPNSLHLHQRLVTKLQ 397
D ++ D +GNYV+Q + + N ++V L+
Sbjct: 197 D---KLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLK 233
>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 = 91.7 bits (226), Expect = 7e-19, Method: Compositional matrix adjust.
Identities = 80/330 (24%), Positives = 156/330 (47%), Gaps = 18/330 (5%)
Query: 100 ILLLAQDEQGSQYLQEKLTSGDSRFLDKVFNVVSEFTFQIICNQYARFVFGKFIETCNED 159
I+ +QD+ GS+++Q+KL VFN + + +Q++ + + +V KF E + D
Sbjct: 28 IVEFSQDQHGSRFIQQKLERATPAERQIVFNEILQAAYQLMTDVFGNYVIQKFFEFGSLD 87
Query: 160 QLLRITLQITSQDQLFVQASVDKFGSSSIRKLMKAVANRPPLLDLVMKALKRLFRLLMMT 219
Q L + +I + ++ +G I+K ++++++ ++K L +
Sbjct: 88 QKLALATRIRGH---VLPLALQMYGCRVIQKALESISSDQQ--SEMVKELDGHVLKCVKD 142
Query: 220 KPGSSVVLQCLEQIYHHNNKNDFIYQAALEHCLYLACHEQGCINMNNFIDEMKGPRRKQI 279
+ G+ VV +C+E + FI A L+ H GC + ++ + I
Sbjct: 143 QNGNHVVQKCIECV--QPQSLQFIIDAFKGQVFVLSTHPYGCRVIQRILEHCTAEQTLPI 200
Query: 280 LYLISVNAASLSRNFSGNYVVQHVLELEDPYLIETICFSLRGHYIDLSLTKCGSFVVQNC 339
L + + L ++ GNYV+QHVLE P I +RG + LS K S VV+ C
Sbjct: 201 LEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGKVLALSQHKFASNVVEKC 260
Query: 340 LKY--RITVNYIVEEFLLNSD----QIFRVACDKYGNYVIQTALIETMRPNSLHLHQRLV 393
+ + R +++E +D ++ + D+Y NYV+Q +I+ P + ++
Sbjct: 261 VTHASRAERALLIDEVCCQNDGPHSALYTMMKDQYANYVVQK-MIDMAEPAQRKI---IM 316
Query: 394 TKLQQNLDSLR-FGYGKHVYNFIKDCDLQN 422
K++ ++ +LR + YGKH+ ++ L+N
Sbjct: 317 HKIRPHITTLRKYTYGKHILAKLEKYYLKN 346
>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 = 82.4 bits (202), Expect = 4e-16, Method: Compositional matrix adjust.
Identities = 76/319 (23%), Positives = 150/319 (47%), Gaps = 18/319 (5%)
Query: 100 ILLLAQDEQGSQYLQEKLTSGDSRFLDKVFNVVSEFTFQIICNQYARFVFGKFIETCNED 159
I+ +QD+ GS+++Q KL VFN + + +Q++ + + +V KF E + +
Sbjct: 26 IMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKFFEFGSLE 85
Query: 160 QLLRITLQITSQDQLFVQASVDKFGSSSIRKLMKAVANRPPLLDLVMKALKRLFRLLMMT 219
Q L + +I + ++ +G I+K ++ + + + +++ L +
Sbjct: 86 QKLALAERIRGH---VLSLALQMYGCRVIQKALEFIPSDQQ--NEMVRELDGHVLKCVKD 140
Query: 220 KPGSSVVLQCLEQIYHHNNKNDFIYQAALEHCLYLACHEQGCINMNNFIDEMKGPRRKQI 279
+ G+ VV +C+E + FI A L+ H GC + ++ + I
Sbjct: 141 QNGNHVVQKCIECV--QPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPDQTLPI 198
Query: 280 LYLISVNAASLSRNFSGNYVVQHVLELEDPYLIETICFSLRGHYIDLSLTKCGSFVVQNC 339
L + + L ++ GNYV+QHVLE P I +RG+ + LS K S VV+ C
Sbjct: 199 LEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNVVEKC 258
Query: 340 LKY--RITVNYIVEEFLLNSD----QIFRVACDKYGNYVIQTALIETMRPNSLHLHQRLV 393
+ + R +++E +D ++ + D+Y NYV+Q +I+ P + ++
Sbjct: 259 VTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQK-MIDVAEPGQRKI---VM 314
Query: 394 TKLQQNLDSLR-FGYGKHV 411
K++ ++ +LR + YGKH+
Sbjct: 315 HKIRPHIATLRKYTYGKHI 333
>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 = 82.4 bits (202), Expect = 5e-16, Method: Compositional matrix adjust.
Identities = 76/319 (23%), Positives = 150/319 (47%), Gaps = 18/319 (5%)
Query: 100 ILLLAQDEQGSQYLQEKLTSGDSRFLDKVFNVVSEFTFQIICNQYARFVFGKFIETCNED 159
I+ +QD+ GS+++Q KL VFN + + +Q++ + + +V KF E + +
Sbjct: 26 IMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKFFEFGSLE 85
Query: 160 QLLRITLQITSQDQLFVQASVDKFGSSSIRKLMKAVANRPPLLDLVMKALKRLFRLLMMT 219
Q L + +I + ++ +G I+K ++ + + + +++ L +
Sbjct: 86 QKLALAERIRGH---VLSLALQMYGCRVIQKALEFIPSDQQ--NEMVRELDGHVLKCVKD 140
Query: 220 KPGSSVVLQCLEQIYHHNNKNDFIYQAALEHCLYLACHEQGCINMNNFIDEMKGPRRKQI 279
+ G+ VV +C+E + FI A L+ H GC + ++ + I
Sbjct: 141 QNGNHVVQKCIECV--QPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPDQTLPI 198
Query: 280 LYLISVNAASLSRNFSGNYVVQHVLELEDPYLIETICFSLRGHYIDLSLTKCGSFVVQNC 339
L + + L ++ GNYV+QHVLE P I +RG+ + LS K S VV+ C
Sbjct: 199 LEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNVVEKC 258
Query: 340 LKY--RITVNYIVEEFLLNSD----QIFRVACDKYGNYVIQTALIETMRPNSLHLHQRLV 393
+ + R +++E +D ++ + D+Y NYV+Q +I+ P + ++
Sbjct: 259 VTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQK-MIDVAEPGQRKI---VM 314
Query: 394 TKLQQNLDSLR-FGYGKHV 411
K++ ++ +LR + YGKH+
Sbjct: 315 HKIRPHIATLRKYTYGKHI 333
>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 = 81.6 bits (200), Expect = 8e-16, Method: Compositional matrix adjust.
Identities = 74/307 (24%), Positives = 144/307 (46%), Gaps = 14/307 (4%)
Query: 100 ILLLAQDEQGSQYLQEKLTSGDSRFLDKVFNVVSEFTFQIICNQYARFVFGKFIETCNED 159
I+ +QD+ GS+++Q+KL + VF+ + + ++ + + +V KF E +
Sbjct: 28 IVEFSQDQHGSRFIQQKLERATAAEKQMVFSEILAAAYSLMTDVFGNYVIQKFFEFGTPE 87
Query: 160 QLLRITLQITSQDQLFVQASVDKFGSSSIRKLMKAVANRPPLLDLVMKALKRLFRLLMMT 219
Q + +Q+ +Q ++ +G I+K +++++ P ++ L +
Sbjct: 88 QKNTLGMQVKGH---VLQLALQMYGCRVIQKALESIS--PEQQQEIVHELDGHVLKCVKD 142
Query: 220 KPGSSVVLQCLEQIYHHNNKNDFIYQAALEHCLYLACHEQGCINMNNFIDEMKGPRRKQI 279
+ G+ VV +C+E + FI A L+ H GC + ++ + I
Sbjct: 143 QNGNHVVQKCIECV--DPVALQFIINAFKGQVYSLSTHPYGCRVIQRILEHCTAEQTTPI 200
Query: 280 LYLISVNAASLSRNFSGNYVVQHVLELEDPYLIETICFSLRGHYIDLSLTKCGSFVVQNC 339
L + + L ++ GNYV+QHVLE + S+RG + LS K S VV+ C
Sbjct: 201 LDELHEHTEQLIQDQYGNYVIQHVLEHGKQEDKSILINSVRGKVLVLSQHKFASNVVEKC 260
Query: 340 LKY--RITVNYIVEEFLLNSDQIFRVAC-DKYGNYVIQTALIETMRPNSLHLHQRLVTKL 396
+ + R +++E +D V D+Y NYV+Q +I+ P L ++L+TK+
Sbjct: 261 VTHATRGERTGLIDEVCTFNDNALHVMMKDQYANYVVQK-MIDVSEPTQL---KKLMTKI 316
Query: 397 QQNLDSL 403
++N+ +L
Sbjct: 317 RKNMAAL 323
Score = 53.1 bits (126), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 56/215 (26%), Positives = 100/215 (46%), Gaps = 11/215 (5%)
Query: 166 LQITSQDQLFVQASVDKFGSSSIR-KLMKAVANRPPLLDLVMKALKRLFRLLMMTKPGSS 224
LQ+ V+ S D+ GS I+ KL +A A ++ + L + L MT +
Sbjct: 19 LQLRDLANHIVEFSQDQHGSRFIQQKLERATAAEKQMV--FSEILAAAYSL--MTDVFGN 74
Query: 225 VVLQCLEQIYHHNNKNDFIYQAALEHCLYLACHEQGCINMNNFIDEMKGPRRKQILYLIS 284
V+Q + KN Q H L LA GC + ++ + ++++I++ +
Sbjct: 75 YVIQKFFEFGTPEQKNTLGMQVK-GHVLQLALQMYGCRVIQKALESISPEQQQEIVHELD 133
Query: 285 VNAASLSRNFSGNYVVQHVLELEDPYLIETICFSLRGHYIDLSLTKCGSFVVQNCLKYRI 344
+ ++ +GN+VVQ +E DP ++ I + +G LS G V+Q L++
Sbjct: 134 GHVLKCVKDQNGNHVVQKCIECVDPVALQFIINAFKGQVYSLSTHPYGCRVIQRILEHCT 193
Query: 345 T--VNYIVEEFLLNSDQIFRVACDKYGNYVIQTAL 377
I++E +++Q+ + D+YGNYVIQ L
Sbjct: 194 AEQTTPILDELHEHTEQLIQ---DQYGNYVIQHVL 225
>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 = 78.6 bits (192), Expect = 5e-15, Method: Compositional matrix adjust.
Identities = 74/319 (23%), Positives = 150/319 (47%), Gaps = 18/319 (5%)
Query: 100 ILLLAQDEQGSQYLQEKLTSGDSRFLDKVFNVVSEFTFQIICNQYARFVFGKFIETCNED 159
I+ +QD+ GS+++Q KL VFN + + +Q++ + + +V KF E + +
Sbjct: 27 IMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKFFEFGSLE 86
Query: 160 QLLRITLQITSQDQLFVQASVDKFGSSSIRKLMKAVANRPPLLDLVMKALKRLFRLLMMT 219
Q L + +I + ++ +G I+K ++ + + + +++ L +
Sbjct: 87 QKLALAERIRGH---VLSLALQMYGCRVIQKALEFIPSDQQ--NEMVRELDGHVLKCVKD 141
Query: 220 KPGSSVVLQCLEQIYHHNNKNDFIYQAALEHCLYLACHEQGCINMNNFIDEMKGPRRKQI 279
+ G+ VV +C+E + FI A L+ H GC + ++ + I
Sbjct: 142 QNGNHVVQKCIECV--QPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPDQTLPI 199
Query: 280 LYLISVNAASLSRNFSGNYVVQHVLELEDPYLIETICFSLRGHYIDLSLTKCGSFVVQNC 339
L + + L ++ G+YV++HVLE P I +RG+ + LS K S VV+ C
Sbjct: 200 LEELHQHTEQLVQDQYGSYVIRHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNVVEKC 259
Query: 340 LKY--RITVNYIVEEFLLNSD----QIFRVACDKYGNYVIQTALIETMRPNSLHLHQRLV 393
+ + R +++E +D ++ + D+Y NYV+Q +I+ P + ++
Sbjct: 260 VTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQK-MIDVAEPGQRKI---VM 315
Query: 394 TKLQQNLDSLR-FGYGKHV 411
K++ ++ +LR + YGKH+
Sbjct: 316 HKIRPHIATLRKYTYGKHI 334
Score = 35.4 bits (80), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 49/255 (19%), Positives = 97/255 (38%), Gaps = 36/255 (14%)
Query: 88 QANPFQHCANSGILLLAQDEQGSQYLQEKLTSGDSRFLDKVFNVVSEFTFQIICNQYARF 147
Q N + +L +D+ G+ +Q+ + + L + + F + + Y
Sbjct: 123 QQNEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCR 182
Query: 148 VFGKFIETCNEDQLLRITLQITSQDQLFVQASVDKFGSSSIRKLMKAVANRPPLLDLVMK 207
V + +E C DQ L I ++ + VQ D++GS IR +++ RP ++
Sbjct: 183 VIQRILEHCLPDQTLPILEELHQHTEQLVQ---DQYGSYVIRHVLEH--GRPEDKSKIVA 237
Query: 208 ALKRLFRLLMMTKPGSSVVLQCLEQIYHHNNKNDFIYQAALEHCLYLACHEQGCINMNNF 267
++ +L K S+VV E C+ A + + ++
Sbjct: 238 EIRGNVLVLSQHKFASNVV----------------------EKCVTHASRTERAVLIDEV 275
Query: 268 IDEMKGPRRKQILYLISVNAASLSRNFSGNYVVQHVLELEDPYLIETICFSLRGHYIDLS 327
GP LY ++ ++ NYVVQ ++++ +P + + +R H L
Sbjct: 276 CTMNDGPH--SALY-------TMMKDQYANYVVQKMIDVAEPGQRKIVMHKIRPHIATLR 326
Query: 328 LTKCGSFVVQNCLKY 342
G ++ KY
Sbjct: 327 KYTYGKHILAKLEKY 341
>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 = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 35/99 (35%), Positives = 50/99 (50%), Gaps = 2/99 (2%)
Query: 283 ISVNAASLSRNFSGNYVVQHVLELEDPYLIETICFSLRGHYIDLSLTKCGSFVVQNCLKY 342
I +A LS + GNYV+Q E T+ +G+ LSL V+Q L+Y
Sbjct: 65 IRDDAIELSNDVFGNYVIQKFFEFGSKIQKNTLVDQFKGNMKQLSLQMYACRVIQKALEY 124
Query: 343 RITVNYIVEEFLLNSDQIFRVACDKYGNYVIQTALIETM 381
I N +E L SD + ++ D+ GN+VIQ A IET+
Sbjct: 125 -IDSNQRIELVLELSDSVLQMIKDQNGNHVIQKA-IETI 161
Score = 42.7 bits (99), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 59/289 (20%), Positives = 132/289 (45%), Gaps = 27/289 (9%)
Query: 105 QDEQGSQYLQEKLTSGDSRFLDKVFNVVSEFTFQIICNQYARFVFGKFIETCNEDQLLRI 164
+D+ GS+++Q +L + + + +FN + + ++ + + +V KF E ++ Q +
Sbjct: 38 KDQHGSRFIQRELATSPASEKEVIFNEIRDDAIELSNDVFGNYVIQKFFEFGSKIQKNTL 97
Query: 165 TLQITSQDQLFVQASVDKFGSSSIRKLMKAVANRPPLLDLVMKALKRLFRLLMMTKPGSS 224
Q Q S+ + I+K ++ + + + +LV++ + +++ + G+
Sbjct: 98 VDQFKGN---MKQLSLQMYACRVIQKALEYIDSNQRI-ELVLELSDSVLQMIK-DQNGNH 152
Query: 225 VVLQCLEQIYHHNNKNDFIYQAALEHCLYLACHEQGCINMNNFIDEMKGPRRKQILYLIS 284
V+ + +E I K FI + H +L+ H GC + ++ ++ IL +
Sbjct: 153 VIQKAIETI--PIEKLPFILSSLTGHIYHLSTHSYGCRVIQRLLEFGSSEDQESILNELK 210
Query: 285 VNAASLSRNFSGNYVVQHVLELEDPY-------LIETICFSLRGHYIDLSLTKCGSFVVQ 337
L ++ GNYV+Q+VL+ +D + + + I ++ + ++ S K S VV+
Sbjct: 211 DFIPYLIQDQYGNYVIQYVLQ-QDQFTNKEMVDIKQEIIETVANNVVEYSKHKFASNVVE 269
Query: 338 NCLKY--RITVNYIVEEFL---------LNSDQ-IFRVACDKYGNYVIQ 374
+ Y + + I+ + L L D + + D++ NYVIQ
Sbjct: 270 KSILYGSKNQKDLIISKILPRDKNHALNLEDDSPMILMIKDQFANYVIQ 318
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 39/157 (24%), Positives = 74/157 (47%), Gaps = 11/157 (7%)
Query: 260 GCINMNNFIDEMKGPRRKQILYLISVNAASLSRNFSGNYVVQHVLELEDPYLIETICFSL 319
C + ++ + +R +++ +S + + ++ +GN+V+Q +E + I SL
Sbjct: 114 ACRVIQKALEYIDSNQRIELVLELSDSVLQMIKDQNGNHVIQKAIETIPIEKLPFILSSL 173
Query: 320 RGHYIDLSLTKCGSFVVQNCLKYRITVNYIVEEFLLN--SDQIFRVACDKYGNYVIQTAL 377
GH LS G V+Q L++ + + +E +LN D I + D+YGNYVIQ L
Sbjct: 174 TGHIYHLSTHSYGCRVIQRLLEFGSSED---QESILNELKDFIPYLIQDQYGNYVIQYVL 230
Query: 378 IETMRPNS--LHLHQRLVTKLQQNLDSLRFGYGKHVY 412
+ N + + Q ++ + N+ Y KH +
Sbjct: 231 QQDQFTNKEMVDIKQEIIETVANNV----VEYSKHKF 263
>pdb|3EUH|A Chain A, Crystal Structure Of The Muke-Mukf Complex
pdb|3EUH|B Chain B, Crystal Structure Of The Muke-Mukf Complex
Length = 440
Score = 32.3 bits (72), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 22/47 (46%), Gaps = 10/47 (21%)
Query: 380 TMRPNSLHLHQRLVTKLQQNLD----------SLRFGYGKHVYNFIK 416
TM + LH RLV LQ LD L GY +HV+ FI+
Sbjct: 240 TMTHDDLHFVDRLVFDLQSKLDRIISWGQQSIDLWIGYDRHVHKFIR 286
>pdb|3RPU|A Chain A, Crystal Structure Of The Muke-Mukf Complex
pdb|3RPU|B Chain B, Crystal Structure Of The Muke-Mukf Complex
pdb|3RPU|X Chain X, Crystal Structure Of The Muke-Mukf Complex
Length = 460
Score = 32.3 bits (72), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 22/47 (46%), Gaps = 10/47 (21%)
Query: 380 TMRPNSLHLHQRLVTKLQQNLD----------SLRFGYGKHVYNFIK 416
TM + LH RLV LQ LD L GY +HV+ FI+
Sbjct: 260 TMTHDDLHFVDRLVFDLQSKLDRIISWGQQSIDLWIGYDRHVHKFIR 306
>pdb|2R62|A Chain A, Crystal Structure Of Helicobacter Pylori Atp Dependent
Protease, Ftsh
pdb|2R62|B Chain B, Crystal Structure Of Helicobacter Pylori Atp Dependent
Protease, Ftsh
pdb|2R65|A Chain A, Crystal Structure Of Helicobacter Pylori Atp Dependent
Protease, Ftsh Adp Complex
pdb|2R65|B Chain B, Crystal Structure Of Helicobacter Pylori Atp Dependent
Protease, Ftsh Adp Complex
pdb|2R65|C Chain C, Crystal Structure Of Helicobacter Pylori Atp Dependent
Protease, Ftsh Adp Complex
pdb|2R65|D Chain D, Crystal Structure Of Helicobacter Pylori Atp Dependent
Protease, Ftsh Adp Complex
pdb|2R65|E Chain E, Crystal Structure Of Helicobacter Pylori Atp Dependent
Protease, Ftsh Adp Complex
Length = 268
Score = 30.0 bits (66), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 24/44 (54%)
Query: 178 ASVDKFGSSSIRKLMKAVANRPPLLDLVMKALKRLFRLLMMTKP 221
A +D FGS + ++ A NRP +LD + R R +++ KP
Sbjct: 140 AEMDGFGSENAPVIVLAATNRPEILDPALMRPGRFDRQVLVDKP 183
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 0.136 0.401
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,940,705
Number of Sequences: 62578
Number of extensions: 466182
Number of successful extensions: 1160
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1060
Number of HSP's gapped (non-prelim): 27
length of query: 422
length of database: 14,973,337
effective HSP length: 101
effective length of query: 321
effective length of database: 8,652,959
effective search space: 2777599839
effective search space used: 2777599839
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: 53 (25.0 bits)