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= 038006
(808 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 = 214 bits (546), Expect = 1e-55, Method: Compositional matrix adjust.
Identities = 136/322 (42%), Positives = 183/322 (56%), Gaps = 18/322 (5%)
Query: 492 GYIYSMAKDQNGCRFLQRVFDEGTFLDLQIIFDEVIDHIVELMMEQFGNYLVQKLLNVCT 551
G I+S+ KDQ+GCRFLQ+ D IF+E D+ VELM + FGNYL+QKLL T
Sbjct: 35 GSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVT 94
Query: 552 EEQMTRILLMVTEEPGQLVRVCLNTYGTRVVQKLIETLKTRQQVSLVKAALKPGFLDLIK 611
EQ RI+L P V + LN +GTR +QKLIE +KT ++ +V +L+P + L K
Sbjct: 95 TEQ--RIVLTKISSP-HFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYTVQLSK 151
Query: 612 DLNGNHVLQRCLQCLSNEDNEVYLFFDAAAKFCVDIATHQHGCCVLQRCIAHSIGRHRDK 671
DLNGNHV+Q+CLQ L E+ + FDA + C+DIATH+HGCCVLQRC+ H D
Sbjct: 152 DLNGNHVIQKCLQRLKPENFQ--FIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCDN 209
Query: 672 LITEISKNGRHLAQDPFGNYVVQYII----ELKIPSVSANLLSQFKGHYVHLSTQKFSSH 727
L ++ L DPFGNYVVQYII E + ++ K + LS KF S+
Sbjct: 210 LCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSN 269
Query: 728 VVEKCLKHFGESRSQIVHELLS---VPHFEQLLQDPFANYVIQCALSVTKGP---LHASL 781
V+EK LK S I+ E+L+ + LL D + NYV+Q AL ++ L+ L
Sbjct: 270 VIEKILKTAIVSEPMIL-EILNNGGETGIQSLLNDSYGNYVLQTALDISHKQNDYLYKRL 328
Query: 782 IE--AARRHTNLRTSPYCKRIF 801
E A +R +P+ KRI
Sbjct: 329 SEIVAPLLVGPIRNTPHGKRII 350
Score = 40.8 bits (94), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 49/218 (22%), Positives = 94/218 (43%), Gaps = 51/218 (23%)
Query: 490 VRGYIYSMAKDQNGCRFLQRVFDEGTFLDLQIIFDEVIDHIVELMMEQFGNYLVQKLLNV 549
+R Y ++KD NG +Q+ + Q IFD + D +++ + G ++Q+ L+
Sbjct: 142 LRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDH 201
Query: 550 CTEEQMTRI---LLMVTEEPGQLVRVCLNTYGTRVVQKLIETLKTRQQVSLVKAALKPGF 606
T EQ + LL + + ++ L+ +G VVQ +I K A K +
Sbjct: 202 GTTEQCDNLCDKLLALVD------KLTLDPFGNYVVQYII-----------TKEAEKNKY 244
Query: 607 LDLIKDLNGNHVLQRCLQCLSNEDNEVYLFFDAAAKFCVDIATHQHGCCVLQRCIAHSIG 666
+ H + V+L A ++++ H+ G V+++ + +I
Sbjct: 245 -------DYTHKI-------------VHLLKPRA----IELSIHKFGSNVIEKILKTAIV 280
Query: 667 RHRDKLITEISKNG-----RHLAQDPFGNYVVQYIIEL 699
+ +I EI NG + L D +GNYV+Q +++
Sbjct: 281 --SEPMILEILNNGGETGIQSLLNDSYGNYVLQTALDI 316
>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 = 213 bits (542), Expect = 3e-55, Method: Compositional matrix adjust.
Identities = 136/322 (42%), Positives = 183/322 (56%), Gaps = 18/322 (5%)
Query: 492 GYIYSMAKDQNGCRFLQRVFDEGTFLDLQIIFDEVIDHIVELMMEQFGNYLVQKLLNVCT 551
G I+S+ KDQ+GCRFLQ+ D IF+E D+ VELM + FGNYL+QKLL T
Sbjct: 13 GSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVT 72
Query: 552 EEQMTRILLMVTEEPGQLVRVCLNTYGTRVVQKLIETLKTRQQVSLVKAALKPGFLDLIK 611
EQ RI+L P V + LN +GTR +QKLIE +KT ++ +V +L+P + L K
Sbjct: 73 TEQ--RIVLTKISSP-HFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYTVQLSK 129
Query: 612 DLNGNHVLQRCLQCLSNEDNEVYLFFDAAAKFCVDIATHQHGCCVLQRCIAHSIGRHRDK 671
DLNGNHV+Q+CLQ L E+ + FDA + C+DIATH+HGCCVLQRC+ H D
Sbjct: 130 DLNGNHVIQKCLQRLKPENFQ--FIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCDN 187
Query: 672 LITEISKNGRHLAQDPFGNYVVQYII----ELKIPSVSANLLSQFKGHYVHLSTQKFSSH 727
L ++ L DPFGNYVVQYII E + ++ K + LS KF S+
Sbjct: 188 LCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSN 247
Query: 728 VVEKCLKHFGESRSQIVHELLS---VPHFEQLLQDPFANYVIQCALSVTKGP---LHASL 781
V+EK LK S I+ E+L+ + LL D + NYV+Q AL ++ L+ L
Sbjct: 248 VIEKILKTAIVSEPMIL-EILNNGGETGIQSLLNDSYGNYVLQTALDISHKQNDYLYKRL 306
Query: 782 --IEAARRHTNLRTSPYCKRIF 801
I A +R +P+ KRI
Sbjct: 307 SEIVAPLLVGPIRNTPHGKRII 328
Score = 39.7 bits (91), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 49/218 (22%), Positives = 94/218 (43%), Gaps = 51/218 (23%)
Query: 490 VRGYIYSMAKDQNGCRFLQRVFDEGTFLDLQIIFDEVIDHIVELMMEQFGNYLVQKLLNV 549
+R Y ++KD NG +Q+ + Q IFD + D +++ + G ++Q+ L+
Sbjct: 120 LRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDH 179
Query: 550 CTEEQMTRI---LLMVTEEPGQLVRVCLNTYGTRVVQKLIETLKTRQQVSLVKAALKPGF 606
T EQ + LL + + ++ L+ +G VVQ +I K A K +
Sbjct: 180 GTTEQCDNLCDKLLALVD------KLTLDPFGNYVVQYII-----------TKEAEKNKY 222
Query: 607 LDLIKDLNGNHVLQRCLQCLSNEDNEVYLFFDAAAKFCVDIATHQHGCCVLQRCIAHSIG 666
+ H + V+L A ++++ H+ G V+++ + +I
Sbjct: 223 -------DYTHKI-------------VHLLKPRA----IELSIHKFGSNVIEKILKTAIV 258
Query: 667 RHRDKLITEISKNG-----RHLAQDPFGNYVVQYIIEL 699
+ +I EI NG + L D +GNYV+Q +++
Sbjct: 259 --SEPMILEILNNGGETGIQSLLNDSYGNYVLQTALDI 294
>pdb|3BWT|A Chain A, Crystal Structure Of The Rna Binding Domain Of Puf4 From
Saccharomyces Cerevisiae
Length = 333
Score = 213 bits (541), Expect = 4e-55, Method: Compositional matrix adjust.
Identities = 136/322 (42%), Positives = 183/322 (56%), Gaps = 18/322 (5%)
Query: 492 GYIYSMAKDQNGCRFLQRVFDEGTFLDLQIIFDEVIDHIVELMMEQFGNYLVQKLLNVCT 551
G I+S+ KDQ+GCRFLQ+ D IF+E D+ VELM + FGNYL+QKLL T
Sbjct: 13 GSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVT 72
Query: 552 EEQMTRILLMVTEEPGQLVRVCLNTYGTRVVQKLIETLKTRQQVSLVKAALKPGFLDLIK 611
EQ RI+L P V + LN +GTR +QKLIE +KT ++ +V +L+P + L K
Sbjct: 73 TEQ--RIVLTKISSP-HFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYTVQLSK 129
Query: 612 DLNGNHVLQRCLQCLSNEDNEVYLFFDAAAKFCVDIATHQHGCCVLQRCIAHSIGRHRDK 671
DLNGNHV+Q+CLQ L E+ + FDA + C+DIATH+HGCCVLQRC+ H D
Sbjct: 130 DLNGNHVIQKCLQRLKPENFQ--FIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCDN 187
Query: 672 LITEISKNGRHLAQDPFGNYVVQYII----ELKIPSVSANLLSQFKGHYVHLSTQKFSSH 727
L ++ L DPFGNYVVQYII E + ++ K + LS KF S+
Sbjct: 188 LCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSN 247
Query: 728 VVEKCLKHFGESRSQIVHELLS---VPHFEQLLQDPFANYVIQCALSVTKGP---LHASL 781
V+EK LK S I+ E+L+ + LL D + NYV+Q AL ++ L+ L
Sbjct: 248 VIEKILKTAIVSEPMIL-EILNNGGETGIQSLLNDSYGNYVLQTALDISHKQNDYLYKRL 306
Query: 782 --IEAARRHTNLRTSPYCKRIF 801
I A +R +P+ KRI
Sbjct: 307 SEIVAPLLVGPIRNTPHGKRII 328
Score = 39.7 bits (91), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 49/218 (22%), Positives = 94/218 (43%), Gaps = 51/218 (23%)
Query: 490 VRGYIYSMAKDQNGCRFLQRVFDEGTFLDLQIIFDEVIDHIVELMMEQFGNYLVQKLLNV 549
+R Y ++KD NG +Q+ + Q IFD + D +++ + G ++Q+ L+
Sbjct: 120 LRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDH 179
Query: 550 CTEEQMTRI---LLMVTEEPGQLVRVCLNTYGTRVVQKLIETLKTRQQVSLVKAALKPGF 606
T EQ + LL + + ++ L+ +G VVQ +I K A K +
Sbjct: 180 GTTEQCDNLCDKLLALVD------KLTLDPFGNYVVQYII-----------TKEAEKNKY 222
Query: 607 LDLIKDLNGNHVLQRCLQCLSNEDNEVYLFFDAAAKFCVDIATHQHGCCVLQRCIAHSIG 666
+ H + V+L A ++++ H+ G V+++ + +I
Sbjct: 223 -------DYTHKI-------------VHLLKPRA----IELSIHKFGSNVIEKILKTAIV 258
Query: 667 RHRDKLITEISKNG-----RHLAQDPFGNYVVQYIIEL 699
+ +I EI NG + L D +GNYV+Q +++
Sbjct: 259 --SEPMILEILNNGGETGIQSLLNDSYGNYVLQTALDI 294
>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 = 205 bits (522), Expect = 7e-53, Method: Compositional matrix adjust.
Identities = 134/322 (41%), Positives = 181/322 (56%), Gaps = 18/322 (5%)
Query: 492 GYIYSMAKDQNGCRFLQRVFDEGTFLDLQIIFDEVIDHIVELMMEQFGNYLVQKLLNVCT 551
G I+S+ KDQ+GCRFLQ+ D IF+E D+ VELM + FGNYL+QKLL T
Sbjct: 13 GSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVT 72
Query: 552 EEQMTRILLMVTEEPGQLVRVCLNTYGTRVVQKLIETLKTRQQVSLVKAALKPGFLDLIK 611
EQ RI+L P V + LN +G R +QKLIE +KT ++ +V +L+P + L K
Sbjct: 73 TEQ--RIVLTKISSP-HFVEISLNPHGCRALQKLIECIKTDEEAQIVVDSLRPYTVQLSK 129
Query: 612 DLNGNHVLQRCLQCLSNEDNEVYLFFDAAAKFCVDIATHQHGCCVLQRCIAHSIGRHRDK 671
DLNGNHV+Q+CLQ L E+ + FDA + C+DIATH+HGC VLQRC+ H D
Sbjct: 130 DLNGNHVIQKCLQRLKPENFQ--FIFDAISDSCIDIATHRHGCRVLQRCLDHGTTEQCDN 187
Query: 672 LITEISKNGRHLAQDPFGNYVVQYII----ELKIPSVSANLLSQFKGHYVHLSTQKFSSH 727
L ++ L DPFGNYVVQYII E + ++ K + LS KF S+
Sbjct: 188 LCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSN 247
Query: 728 VVEKCLKHFGESRSQIVHELLS---VPHFEQLLQDPFANYVIQCALSVTKGP---LHASL 781
V+EK LK S I+ E+L+ + LL D + NYV+Q AL ++ L+ L
Sbjct: 248 VIEKILKTAIVSEPMIL-EILNNGGETGIQSLLNDSYGNYVLQTALDISHKQNDYLYKRL 306
Query: 782 --IEAARRHTNLRTSPYCKRIF 801
I A +R +P+ KRI
Sbjct: 307 SEIVAPLLVGPIRNTPHGKRII 328
Score = 41.2 bits (95), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 39/187 (20%), Positives = 79/187 (42%), Gaps = 45/187 (24%)
Query: 490 VRGYIYSMAKDQN------------------------------------GCRFLQRVFDE 513
+R Y ++KD N GCR LQR D
Sbjct: 120 LRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCRVLQRCLDH 179
Query: 514 GTFLDLQIIFDEVIDHIVELMMEQFGNYLVQKLLNVCTEEQ----MTRILLMVTEEPGQL 569
GT + D+++ + +L ++ FGNY+VQ ++ E+ +I+ ++
Sbjct: 180 GTTEQCDNLCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRA--- 236
Query: 570 VRVCLNTYGTRVVQKLIETLKTRQQVSL--VKAALKPGFLDLIKDLNGNHVLQRCLQCLS 627
+ + ++ +G+ V++K+++T + + L + + G L+ D GN+VLQ L
Sbjct: 237 IELSIHKFGSNVIEKILKTAIVSEPMILEILNNGGETGIQSLLNDSYGNYVLQTALDISH 296
Query: 628 NEDNEVY 634
+++ +Y
Sbjct: 297 KQNDYLY 303
>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 = 178 bits (451), Expect = 1e-44, Method: Compositional matrix adjust.
Identities = 102/322 (31%), Positives = 180/322 (55%), Gaps = 13/322 (4%)
Query: 489 DVRGYIYSMAKDQNGCRFLQRVFDEGTFLDLQIIFDEVIDHIVELMMEQFGNYLVQKLLN 548
D+ G+I ++DQ+G RF+Q+ + T + QI+F+E++ +LM + FGNY++QK
Sbjct: 23 DLIGHIVEFSQDQHGSRFIQQKLERATPAERQIVFNEILQAAYQLMTDVFGNYVIQKFFE 82
Query: 549 VCTEEQMTRILLMVTEEPGQLVRVCLNTYGTRVVQKLIETLKTRQQVSLVKAALKPGFLD 608
+ +Q L + T G ++ + L YG RV+QK +E++ + QQ +VK L L
Sbjct: 83 FGSLDQK---LALATRIRGHVLPLALQMYGCRVIQKALESISSDQQSEMVKE-LDGHVLK 138
Query: 609 LIKDLNGNHVLQRCLQCLSNEDNEVYLFFDAAAKFCVDIATHQHGCCVLQRCIAHSIGRH 668
+KD NGNHV+Q+C++C+ + + DA ++TH +GC V+QR + H
Sbjct: 139 CVKDQNGNHVVQKCIECV--QPQSLQFIIDAFKGQVFVLSTHPYGCRVIQRILEHCTAEQ 196
Query: 669 RDKLITEISKNGRHLAQDPFGNYVVQYIIELKIPSVSANLLSQFKGHYVHLSTQKFSSHV 728
++ E+ ++ L QD +GNYV+Q+++E P + ++S+ +G + LS KF+S+V
Sbjct: 197 TLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGKVLALSQHKFASNV 256
Query: 729 VEKCLKHFGES-RSQIVHELLSV---PH--FEQLLQDPFANYVIQCALSVTKGPLHASLI 782
VEKC+ H + R+ ++ E+ PH +++D +ANYV+Q + + + ++
Sbjct: 257 VEKCVTHASRAERALLIDEVCCQNDGPHSALYTMMKDQYANYVVQKMIDMAEPAQRKIIM 316
Query: 783 EAARRH-TNLRTSPYCKRIFSR 803
R H T LR Y K I ++
Sbjct: 317 HKIRPHITTLRKYTYGKHILAK 338
Score = 84.7 bits (208), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 60/254 (23%), Positives = 128/254 (50%), Gaps = 13/254 (5%)
Query: 490 VRGYIYSMAKDQNGCRFLQRVFDEGTFLDLQIIFDEVIDHIVELMMEQFGNYLVQKLLNV 549
+RG++ +A GCR +Q+ + + + E+ H+++ + +Q GN++VQK +
Sbjct: 96 IRGHVLPLALQMYGCRVIQKALESISSDQQSEMVKELDGHVLKCVKDQNGNHVVQKCIE- 154
Query: 550 CTEEQMTRILLMVTEEPGQLVRVCLNTYGTRVVQKLIETLKTRQQVSLVKAALKPGFLDL 609
C + Q + ++ + GQ+ + + YG RV+Q+++E Q + +++ L L
Sbjct: 155 CVQPQSLQFIIDAFK--GQVFVLSTHPYGCRVIQRILEHCTAEQTLPILEE-LHQHTEQL 211
Query: 610 IKDLNGNHVLQRCLQCLSNEDNEVYLFFDAAAKFCVDIATHQHGCCVLQRCIAHSIGRHR 669
++D GN+V+Q L+ ED + + K + ++ H+ V+++C+ H+ R
Sbjct: 212 VQDQYGNYVIQHVLEHGRPEDKS-KIVSEIRGKV-LALSQHKFASNVVEKCVTHASRAER 269
Query: 670 DKLITEI--SKNGRH-----LAQDPFGNYVVQYIIELKIPSVSANLLSQFKGHYVHLSTQ 722
LI E+ +G H + +D + NYVVQ +I++ P+ ++ + + H L
Sbjct: 270 ALLIDEVCCQNDGPHSALYTMMKDQYANYVVQKMIDMAEPAQRKIIMHKIRPHITTLRKY 329
Query: 723 KFSSHVVEKCLKHF 736
+ H++ K K++
Sbjct: 330 TYGKHILAKLEKYY 343
>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 = 174 bits (441), Expect = 2e-43, Method: Compositional matrix adjust.
Identities = 101/323 (31%), Positives = 180/323 (55%), Gaps = 13/323 (4%)
Query: 489 DVRGYIYSMAKDQNGCRFLQRVFDEGTFLDLQIIFDEVIDHIVELMMEQFGNYLVQKLLN 548
D+ G+I ++DQ+G RF+Q+ + T + Q++F+E++ +LM + FGNY++QK
Sbjct: 21 DLIGHIVEFSQDQHGSRFIQQKLERATPAERQMVFNEILQAAYQLMTDVFGNYVIQKFFE 80
Query: 549 VCTEEQMTRILLMVTEEPGQLVRVCLNTYGTRVVQKLIETLKTRQQV-SLVKAALKPGFL 607
+ +Q L + T G ++ + L YG RV+QK +E++ + QQV S + L L
Sbjct: 81 FGSLDQK---LALATRIRGHVLPLALQMYGCRVIQKALESISSDQQVISEMVKELDGHVL 137
Query: 608 DLIKDLNGNHVLQRCLQCLSNEDNEVYLFFDAAAKFCVDIATHQHGCCVLQRCIAHSIGR 667
+KD NGNHV+Q+C++C+ + + DA ++TH +GC V+QR + H
Sbjct: 138 KCVKDQNGNHVVQKCIECV--QPQSLQFIIDAFKGQVFVLSTHPYGCRVIQRILEHCTAE 195
Query: 668 HRDKLITEISKNGRHLAQDPFGNYVVQYIIELKIPSVSANLLSQFKGHYVHLSTQKFSSH 727
++ E+ ++ L QD +GNYV+Q+++E P + ++S+ +G + LS KF+S+
Sbjct: 196 QTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGKVLALSQHKFASN 255
Query: 728 VVEKCLKHFGES-RSQIVHELLSV---PH--FEQLLQDPFANYVIQCALSVTKGPLHASL 781
VVEKC+ H + R+ ++ E+ PH +++D +ANYV+Q + + + +
Sbjct: 256 VVEKCVTHASRAERALLIDEVCCQNDGPHSALYTMMKDQYANYVVQKMIDMAEPAQRKII 315
Query: 782 IEAARRH-TNLRTSPYCKRIFSR 803
+ R H T LR Y K I ++
Sbjct: 316 MHKIRPHITTLRKYTYGKHILAK 338
Score = 85.5 bits (210), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 64/257 (24%), Positives = 131/257 (50%), Gaps = 17/257 (6%)
Query: 490 VRGYIYSMAKDQNGCRFLQRVFDEGTFLDLQIIFDEVID---HIVELMMEQFGNYLVQKL 546
+RG++ +A GCR +Q+ E D Q+I + V + H+++ + +Q GN++VQK
Sbjct: 94 IRGHVLPLALQMYGCRVIQKAL-ESISSDQQVISEMVKELDGHVLKCVKDQNGNHVVQKC 152
Query: 547 LNVCTEEQMTRILLMVTEEPGQLVRVCLNTYGTRVVQKLIETLKTRQQVSLVKAALKPGF 606
+ C + Q + ++ + GQ+ + + YG RV+Q+++E Q + +++ L
Sbjct: 153 IE-CVQPQSLQFIIDAFK--GQVFVLSTHPYGCRVIQRILEHCTAEQTLPILEE-LHQHT 208
Query: 607 LDLIKDLNGNHVLQRCLQCLSNEDNEVYLFFDAAAKFCVDIATHQHGCCVLQRCIAHSIG 666
L++D GN+V+Q L+ ED + + K + ++ H+ V+++C+ H+
Sbjct: 209 EQLVQDQYGNYVIQHVLEHGRPEDKS-KIVSEIRGK-VLALSQHKFASNVVEKCVTHASR 266
Query: 667 RHRDKLITEI--SKNGRH-----LAQDPFGNYVVQYIIELKIPSVSANLLSQFKGHYVHL 719
R LI E+ +G H + +D + NYVVQ +I++ P+ ++ + + H L
Sbjct: 267 AERALLIDEVCCQNDGPHSALYTMMKDQYANYVVQKMIDMAEPAQRKIIMHKIRPHITTL 326
Query: 720 STQKFSSHVVEKCLKHF 736
+ H++ K K++
Sbjct: 327 RKYTYGKHILAKLEKYY 343
>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 = 172 bits (436), Expect = 6e-43, Method: Compositional matrix adjust.
Identities = 98/322 (30%), Positives = 181/322 (56%), Gaps = 13/322 (4%)
Query: 489 DVRGYIYSMAKDQNGCRFLQRVFDEGTFLDLQIIFDEVIDHIVELMMEQFGNYLVQKLLN 548
++ G+I ++DQ+G RF+Q + T + Q++F+E++ +LM++ FGNY++QK
Sbjct: 21 EIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKFFE 80
Query: 549 VCTEEQMTRILLMVTEEPGQLVRVCLNTYGTRVVQKLIETLKTRQQVSLVKAALKPGFLD 608
+ EQ L + G ++ + L YG RV+QK +E + + QQ +V+ L L
Sbjct: 81 FGSLEQK---LALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQNEMVRE-LDGHVLK 136
Query: 609 LIKDLNGNHVLQRCLQCLSNEDNEVYLFFDAAAKFCVDIATHQHGCCVLQRCIAHSIGRH 668
+KD NGNHV+Q+C++C+ + + DA ++TH +GC V+QR + H +
Sbjct: 137 CVKDQNGNHVVQKCIECV--QPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPDQ 194
Query: 669 RDKLITEISKNGRHLAQDPFGNYVVQYIIELKIPSVSANLLSQFKGHYVHLSTQKFSSHV 728
++ E+ ++ L QD +GNYV+Q+++E P + ++++ +G+ + LS KF+S+V
Sbjct: 195 TLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNV 254
Query: 729 VEKCLKHFGES-RSQIVHELLSV---PH--FEQLLQDPFANYVIQCALSVTKGPLHASLI 782
VEKC+ H + R+ ++ E+ ++ PH +++D +ANYV+Q + V + ++
Sbjct: 255 VEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMIDVAEPGQRKIVM 314
Query: 783 EAARRH-TNLRTSPYCKRIFSR 803
R H LR Y K I ++
Sbjct: 315 HKIRPHIATLRKYTYGKHILAK 336
Score = 80.5 bits (197), Expect = 4e-15, Method: Compositional matrix adjust.
Identities = 61/254 (24%), Positives = 126/254 (49%), Gaps = 13/254 (5%)
Query: 490 VRGYIYSMAKDQNGCRFLQRVFDEGTFLDLQIIFDEVIDHIVELMMEQFGNYLVQKLLNV 549
+RG++ S+A GCR +Q+ + + E+ H+++ + +Q GN++VQK +
Sbjct: 94 IRGHVLSLALQMYGCRVIQKALEFIPSDQQNEMVRELDGHVLKCVKDQNGNHVVQKCIE- 152
Query: 550 CTEEQMTRILLMVTEEPGQLVRVCLNTYGTRVVQKLIETLKTRQQVSLVKAALKPGFLDL 609
C + Q + ++ + GQ+ + + YG RV+Q+++E Q + +++ L L
Sbjct: 153 CVQPQSLQFIIDAFK--GQVFALSTHPYGCRVIQRILEHCLPDQTLPILEE-LHQHTEQL 209
Query: 610 IKDLNGNHVLQRCLQCLSNEDNEVYLFFDAAAKFCVDIATHQHGCCVLQRCIAHSIGRHR 669
++D GN+V+Q L+ ED + + V ++ H+ V+++C+ H+ R
Sbjct: 210 VQDQYGNYVIQHVLEHGRPEDKS-KIVAEIRGNVLV-LSQHKFASNVVEKCVTHASRTER 267
Query: 670 DKLITEISK--NGRH-----LAQDPFGNYVVQYIIELKIPSVSANLLSQFKGHYVHLSTQ 722
LI E+ +G H + +D + NYVVQ +I++ P ++ + + H L
Sbjct: 268 AVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMIDVAEPGQRKIVMHKIRPHIATLRKY 327
Query: 723 KFSSHVVEKCLKHF 736
+ H++ K K++
Sbjct: 328 TYGKHILAKLEKYY 341
>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 = 172 bits (435), Expect = 9e-43, Method: Compositional matrix adjust.
Identities = 98/322 (30%), Positives = 181/322 (56%), Gaps = 13/322 (4%)
Query: 489 DVRGYIYSMAKDQNGCRFLQRVFDEGTFLDLQIIFDEVIDHIVELMMEQFGNYLVQKLLN 548
++ G+I ++DQ+G RF+Q + T + Q++F+E++ +LM++ FGNY++QK
Sbjct: 21 EIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKFFE 80
Query: 549 VCTEEQMTRILLMVTEEPGQLVRVCLNTYGTRVVQKLIETLKTRQQVSLVKAALKPGFLD 608
+ EQ L + G ++ + L YG RV+QK +E + + QQ +V+ L L
Sbjct: 81 FGSLEQK---LALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQNEMVRE-LDGHVLK 136
Query: 609 LIKDLNGNHVLQRCLQCLSNEDNEVYLFFDAAAKFCVDIATHQHGCCVLQRCIAHSIGRH 668
+KD NGNHV+Q+C++C+ + + DA ++TH +GC V+QR + H +
Sbjct: 137 CVKDQNGNHVVQKCIECV--QPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPDQ 194
Query: 669 RDKLITEISKNGRHLAQDPFGNYVVQYIIELKIPSVSANLLSQFKGHYVHLSTQKFSSHV 728
++ E+ ++ L QD +GNYV+Q+++E P + ++++ +G+ + LS KF+S+V
Sbjct: 195 TLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNV 254
Query: 729 VEKCLKHFGES-RSQIVHELLSV---PH--FEQLLQDPFANYVIQCALSVTKGPLHASLI 782
VEKC+ H + R+ ++ E+ ++ PH +++D +ANYV+Q + V + ++
Sbjct: 255 VEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMIDVAEPGQRKIVM 314
Query: 783 EAARRH-TNLRTSPYCKRIFSR 803
R H LR Y K I ++
Sbjct: 315 HKIRPHIATLRKYTYGKHILAK 336
Score = 80.1 bits (196), Expect = 5e-15, Method: Compositional matrix adjust.
Identities = 61/254 (24%), Positives = 126/254 (49%), Gaps = 13/254 (5%)
Query: 490 VRGYIYSMAKDQNGCRFLQRVFDEGTFLDLQIIFDEVIDHIVELMMEQFGNYLVQKLLNV 549
+RG++ S+A GCR +Q+ + + E+ H+++ + +Q GN++VQK +
Sbjct: 94 IRGHVLSLALQMYGCRVIQKALEFIPSDQQNEMVRELDGHVLKCVKDQNGNHVVQKCIE- 152
Query: 550 CTEEQMTRILLMVTEEPGQLVRVCLNTYGTRVVQKLIETLKTRQQVSLVKAALKPGFLDL 609
C + Q + ++ + GQ+ + + YG RV+Q+++E Q + +++ L L
Sbjct: 153 CVQPQSLQFIIDAFK--GQVFALSTHPYGCRVIQRILEHCLPDQTLPILEE-LHQHTEQL 209
Query: 610 IKDLNGNHVLQRCLQCLSNEDNEVYLFFDAAAKFCVDIATHQHGCCVLQRCIAHSIGRHR 669
++D GN+V+Q L+ ED + + V ++ H+ V+++C+ H+ R
Sbjct: 210 VQDQYGNYVIQHVLEHGRPEDKS-KIVAEIRGNVLV-LSQHKFASNVVEKCVTHASRTER 267
Query: 670 DKLITEISK--NGRH-----LAQDPFGNYVVQYIIELKIPSVSANLLSQFKGHYVHLSTQ 722
LI E+ +G H + +D + NYVVQ +I++ P ++ + + H L
Sbjct: 268 AVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMIDVAEPGQRKIVMHKIRPHIATLRKY 327
Query: 723 KFSSHVVEKCLKHF 736
+ H++ K K++
Sbjct: 328 TYGKHILAKLEKYY 341
>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 = 169 bits (427), Expect = 8e-42, Method: Compositional matrix adjust.
Identities = 96/322 (29%), Positives = 181/322 (56%), Gaps = 13/322 (4%)
Query: 489 DVRGYIYSMAKDQNGCRFLQRVFDEGTFLDLQIIFDEVIDHIVELMMEQFGNYLVQKLLN 548
++ G+I ++DQ+G RF+Q + T + Q++F+E++ +LM++ FGNY++QK
Sbjct: 22 EIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKFFE 81
Query: 549 VCTEEQMTRILLMVTEEPGQLVRVCLNTYGTRVVQKLIETLKTRQQVSLVKAALKPGFLD 608
+ EQ L + G ++ + L YG RV+QK +E + + QQ +V+ L L
Sbjct: 82 FGSLEQK---LALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQNEMVRE-LDGHVLK 137
Query: 609 LIKDLNGNHVLQRCLQCLSNEDNEVYLFFDAAAKFCVDIATHQHGCCVLQRCIAHSIGRH 668
+KD NGNHV+Q+C++C+ + + DA ++TH +GC V+QR + H +
Sbjct: 138 CVKDQNGNHVVQKCIECV--QPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPDQ 195
Query: 669 RDKLITEISKNGRHLAQDPFGNYVVQYIIELKIPSVSANLLSQFKGHYVHLSTQKFSSHV 728
++ E+ ++ L QD +G+YV+++++E P + ++++ +G+ + LS KF+S+V
Sbjct: 196 TLPILEELHQHTEQLVQDQYGSYVIRHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNV 255
Query: 729 VEKCLKHFGES-RSQIVHELLSV---PH--FEQLLQDPFANYVIQCALSVTKGPLHASLI 782
VEKC+ H + R+ ++ E+ ++ PH +++D +ANYV+Q + V + ++
Sbjct: 256 VEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMIDVAEPGQRKIVM 315
Query: 783 EAARRH-TNLRTSPYCKRIFSR 803
R H LR Y K I ++
Sbjct: 316 HKIRPHIATLRKYTYGKHILAK 337
Score = 76.6 bits (187), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 59/254 (23%), Positives = 126/254 (49%), Gaps = 13/254 (5%)
Query: 490 VRGYIYSMAKDQNGCRFLQRVFDEGTFLDLQIIFDEVIDHIVELMMEQFGNYLVQKLLNV 549
+RG++ S+A GCR +Q+ + + E+ H+++ + +Q GN++VQK +
Sbjct: 95 IRGHVLSLALQMYGCRVIQKALEFIPSDQQNEMVRELDGHVLKCVKDQNGNHVVQKCIE- 153
Query: 550 CTEEQMTRILLMVTEEPGQLVRVCLNTYGTRVVQKLIETLKTRQQVSLVKAALKPGFLDL 609
C + Q + ++ + GQ+ + + YG RV+Q+++E Q + +++ L L
Sbjct: 154 CVQPQSLQFIIDAFK--GQVFALSTHPYGCRVIQRILEHCLPDQTLPILEE-LHQHTEQL 210
Query: 610 IKDLNGNHVLQRCLQCLSNEDNEVYLFFDAAAKFCVDIATHQHGCCVLQRCIAHSIGRHR 669
++D G++V++ L+ ED + + V ++ H+ V+++C+ H+ R
Sbjct: 211 VQDQYGSYVIRHVLEHGRPEDKS-KIVAEIRGNVLV-LSQHKFASNVVEKCVTHASRTER 268
Query: 670 DKLITEISK--NGRH-----LAQDPFGNYVVQYIIELKIPSVSANLLSQFKGHYVHLSTQ 722
LI E+ +G H + +D + NYVVQ +I++ P ++ + + H L
Sbjct: 269 AVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMIDVAEPGQRKIVMHKIRPHIATLRKY 328
Query: 723 KFSSHVVEKCLKHF 736
+ H++ K K++
Sbjct: 329 TYGKHILAKLEKYY 342
>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 = 158 bits (400), Expect = 1e-38, Method: Compositional matrix adjust.
Identities = 95/303 (31%), Positives = 166/303 (54%), Gaps = 11/303 (3%)
Query: 489 DVRGYIYSMAKDQNGCRFLQRVFDEGTFLDLQIIFDEVIDHIVELMMEQFGNYLVQKLLN 548
D+ +I ++DQ+G RF+Q+ + T + Q++F E++ LM + FGNY++QK
Sbjct: 23 DLANHIVEFSQDQHGSRFIQQKLERATAAEKQMVFSEILAAAYSLMTDVFGNYVIQKFFE 82
Query: 549 VCTEEQMTRILLMVTEEPGQLVRVCLNTYGTRVVQKLIETLKTRQQVSLVKAALKPGFLD 608
T EQ + + V G ++++ L YG RV+QK +E++ QQ +V L L
Sbjct: 83 FGTPEQKNTLGMQV---KGHVLQLALQMYGCRVIQKALESISPEQQQEIVHE-LDGHVLK 138
Query: 609 LIKDLNGNHVLQRCLQCLSNEDNEVYLFFDAAAKFCV-DIATHQHGCCVLQRCIAHSIGR 667
+KD NGNHV+Q+C++C+ D F A K V ++TH +GC V+QR + H
Sbjct: 139 CVKDQNGNHVVQKCIECV---DPVALQFIINAFKGQVYSLSTHPYGCRVIQRILEHCTAE 195
Query: 668 HRDKLITEISKNGRHLAQDPFGNYVVQYIIELKIPSVSANLLSQFKGHYVHLSTQKFSSH 727
++ E+ ++ L QD +GNYV+Q+++E + L++ +G + LS KF+S+
Sbjct: 196 QTTPILDELHEHTEQLIQDQYGNYVIQHVLEHGKQEDKSILINSVRGKVLVLSQHKFASN 255
Query: 728 VVEKCLKHFGE-SRSQIVHELLSVPH--FEQLLQDPFANYVIQCALSVTKGPLHASLIEA 784
VVEKC+ H R+ ++ E+ + +++D +ANYV+Q + V++ L+
Sbjct: 256 VVEKCVTHATRGERTGLIDEVCTFNDNALHVMMKDQYANYVVQKMIDVSEPTQLKKLMTK 315
Query: 785 ARR 787
R+
Sbjct: 316 IRK 318
>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 = 136 bits (342), Expect = 5e-32, Method: Compositional matrix adjust.
Identities = 88/320 (27%), Positives = 167/320 (52%), Gaps = 24/320 (7%)
Query: 489 DVRGYIYSMAKDQNGCRFLQRVFDEGTFLDLQIIFDEVIDHIVELMMEQFGNYLVQKLLN 548
D+ G+ KDQ+G RF+QR + ++IF+E+ D +EL + FGNY++QK
Sbjct: 28 DIFGHSLEFCKDQHGSRFIQRELATSPASEKEVIFNEIRDDAIELSNDVFGNYVIQKFFE 87
Query: 549 VCTEEQMTRILLMVTEEPGQLVRVCLNTYGTRVVQKLIETLKTRQQVSLVKAALKPGFLD 608
++ Q +V + G + ++ L Y RV+QK +E + + Q++ LV L L
Sbjct: 88 FGSKIQKNT---LVDQFKGNMKQLSLQMYACRVIQKALEYIDSNQRIELV-LELSDSVLQ 143
Query: 609 LIKDLNGNHVLQRCLQCLSNEDNEVYLFFDAAAKFCVDIATHQHGCCVLQRCIAHSIGRH 668
+IKD NGNHV+Q+ ++ + E ++ + ++TH +GC V+QR +
Sbjct: 144 MIKDQNGNHVIQKAIETIPIE--KLPFILSSLTGHIYHLSTHSYGCRVIQRLLEFGSSED 201
Query: 669 RDKLITEISKNGRHLAQDPFGNYVVQYIIEL------KIPSVSANLLSQFKGHYVHLSTQ 722
++ ++ E+ +L QD +GNYV+QY+++ ++ + ++ + V S
Sbjct: 202 QESILNELKDFIPYLIQDQYGNYVIQYVLQQDQFTNKEMVDIKQEIIETVANNVVEYSKH 261
Query: 723 KFSSHVVEKCLKHFGESRSQ-IVHELLS-----VPHFEQ------LLQDPFANYVIQCAL 770
KF+S+VVEK + + +++ I+ ++L + E +++D FANYVIQ +
Sbjct: 262 KFASNVVEKSILYGSKNQKDLIISKILPRDKNHALNLEDDSPMILMIKDQFANYVIQKLV 321
Query: 771 SVTKGPLHASLIEAARRHTN 790
+V++G ++ A R + +
Sbjct: 322 NVSEGEGKKLIVIAIRAYLD 341
Score = 68.2 bits (165), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 53/172 (30%), Positives = 81/172 (47%), Gaps = 12/172 (6%)
Query: 636 FFDAAAKFCVDIATHQHGCCVLQRCIAHSIGRHRDKLITEISKNGRHLAQDPFGNYVVQY 695
F + +FC D QHG +QR +A S ++ + EI + L+ D FGNYV+Q
Sbjct: 29 IFGHSLEFCKD----QHGSRFIQRELATSPASEKEVIFNEIRDDAIELSNDVFGNYVIQK 84
Query: 696 IIELKIPSVSANLLSQFKGHYVHLSTQKFSSHVVEKCLKHF-GESRSQIVHELLSVPHFE 754
E L+ QFKG+ LS Q ++ V++K L++ R ++V EL
Sbjct: 85 FFEFGSKIQKNTLVDQFKGNMKQLSLQMYACRVIQKALEYIDSNQRIELVLEL--SDSVL 142
Query: 755 QLLQDPFANYVIQCALS---VTKGPLHASLIEAARRHTNLRTSPYCKRIFSR 803
Q+++D N+VIQ A+ + K P S + H L T Y R+ R
Sbjct: 143 QMIKDQNGNHVIQKAIETIPIEKLPFILSSLTGHIYH--LSTHSYGCRVIQR 192
Score = 52.0 bits (123), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 39/152 (25%), Positives = 77/152 (50%), Gaps = 17/152 (11%)
Query: 488 ADVRGYIYSMAKDQNGCRFLQRVFDEGTFLDLQIIFDEVIDHIVELMMEQFGNYLVQKLL 547
+ + G+IY ++ GCR +QR+ + G+ D + I +E+ D I L+ +Q+GNY++Q +L
Sbjct: 171 SSLTGHIYHLSTHSYGCRVIQRLLEFGSSEDQESILNELKDFIPYLIQDQYGNYVIQYVL 230
Query: 548 --NVCTEEQMTRILLMVTEE-PGQLVRVCLNTYGTRVVQKLIETLKTRQQVSLVKAALKP 604
+ T ++M I + E +V + + + VV+K I ++ Q L+ + + P
Sbjct: 231 QQDQFTNKEMVDIKQEIIETVANNVVEYSKHKFASNVVEKSI-LYGSKNQKDLIISKILP 289
Query: 605 -------------GFLDLIKDLNGNHVLQRCL 623
+ +IKD N+V+Q+ +
Sbjct: 290 RDKNHALNLEDDSPMILMIKDQFANYVIQKLV 321
>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 = 95.1 bits (235), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 80/325 (24%), Positives = 154/325 (47%), Gaps = 51/325 (15%)
Query: 492 GYIYSMAKDQNGCRFLQRVFDEGTFLDLQI--IFDEVI---DHIVELMMEQFGNYLVQKL 546
G + A D+ GC+FL++ +G+ Q +F++VI D ++L FGNYLVQ +
Sbjct: 30 GDLMKFAVDKTGCQFLEKAV-KGSLTSYQKFQLFEQVIGRKDDFLKLSTNIFGNYLVQSV 88
Query: 547 LNVCT----------EEQMTRILLMVTEEPGQLVRVCLNTYGTRVVQKLIETLKTRQQVS 596
+ + +E++ + Q+ +CL+ + RV+Q ++ +
Sbjct: 89 IGISLATNDDGYTKRQEKLKNFI------SSQMTDMCLDKFACRVIQSSLQNMDLSLACK 142
Query: 597 LVKAALKPG-FLDLIKDLNGNHVLQRCLQCLSNEDNEVYLFFDAAAKFCVDIATHQHGCC 655
LV+A + + + D N NHV+Q+ + + ++ E + F A + I + ++GC
Sbjct: 143 LVQALPRDARLIAICVDQNANHVIQKVVAVIPLKNWEFIVDFVATPEHLRQICSDKYGCR 202
Query: 656 VLQRCI----AHSIG------------RHRDKLITEISKNGRHLAQDPFGNYVVQYIIEL 699
V+Q I A S+ R +L+T ++ + LA + + NY++Q+I+
Sbjct: 203 VVQTIIEKLTADSMNVDLTSAAQNLRERALQRLMTSVTNRCQELATNEYANYIIQHIVSN 262
Query: 700 KIPSVSANLLSQ--FKGHYVHLSTQKFSSHVVEKCLKHFG-ESRSQIVHELLS--VPH-- 752
+V + + + + LS +KF+SHVVEK H E ++++ E+ +PH
Sbjct: 263 DDLAVYRECIIEKCLMRNLLSLSQEKFASHVVEKAFLHAPLELLAEMMDEIFDGYIPHPD 322
Query: 753 -----FEQLLQDPFANYVIQCALSV 772
+ ++ F NYV+QC L++
Sbjct: 323 TGKDALDIMMFHQFGNYVVQCMLTI 347
Score = 37.0 bits (84), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 49/215 (22%), Positives = 93/215 (43%), Gaps = 28/215 (13%)
Query: 530 IVELMMEQFGNYLVQKLLNVCTEEQMTRILLMVTEEPGQLVRVCLNTYGTRVVQKLIETL 589
++ + ++Q N+++QK++ V + I+ V P L ++C + YG RVVQ +IE L
Sbjct: 153 LIAICVDQNANHVIQKVVAVIPLKNWEFIVDFVAT-PEHLRQICSDKYGCRVVQTIIEKL 211
Query: 590 KT-RQQVSLVKAA----------LKPGFLDLIKDLNGNHVLQRCLQ-CLSNEDNEVY--- 634
V L AA L + ++L N +Q +SN+D VY
Sbjct: 212 TADSMNVDLTSAAQNLRERALQRLMTSVTNRCQELATNEYANYIIQHIVSNDDLAVYREC 271
Query: 635 LFFDAAAKFCVDIATHQHGCCVLQRCIAHSIGRHRDKLITEI-------SKNGRH----L 683
+ + + ++ + V+++ H+ +++ EI G+ +
Sbjct: 272 IIEKCLMRNLLSLSQEKFASHVVEKAFLHAPLELLAEMMDEIFDGYIPHPDTGKDALDIM 331
Query: 684 AQDPFGNYVVQYIIELKIPSVSANLLSQFKGHYVH 718
FGNYVVQ ++ + +VS ++ +G Y H
Sbjct: 332 MFHQFGNYVVQCMLTICCDAVSGRRQTK-EGGYDH 365
Score = 30.8 bits (68), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 16/70 (22%), Positives = 33/70 (47%), Gaps = 11/70 (15%)
Query: 494 IYSMAKDQNGCRFLQRVFDEGTFLDLQIIFDEVIDHIVE-----------LMMEQFGNYL 542
+ S+++++ +++ F L + DE+ D + +M QFGNY+
Sbjct: 281 LLSLSQEKFASHVVEKAFLHAPLELLAEMMDEIFDGYIPHPDTGKDALDIMMFHQFGNYV 340
Query: 543 VQKLLNVCTE 552
VQ +L +C +
Sbjct: 341 VQCMLTICCD 350
>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 = 95.1 bits (235), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 80/325 (24%), Positives = 154/325 (47%), Gaps = 51/325 (15%)
Query: 492 GYIYSMAKDQNGCRFLQRVFDEGTFLDLQI--IFDEVI---DHIVELMMEQFGNYLVQKL 546
G + A D+ GC+FL++ +G+ Q +F++VI D ++L FGNYLVQ +
Sbjct: 29 GDLMKFAVDKTGCQFLEKAV-KGSLTSYQKFQLFEQVIGRKDDFLKLSTNIFGNYLVQSV 87
Query: 547 LNVCT----------EEQMTRILLMVTEEPGQLVRVCLNTYGTRVVQKLIETLKTRQQVS 596
+ + +E++ + Q+ +CL+ + RV+Q ++ +
Sbjct: 88 IGISLATNDDGYTKRQEKLKNFI------SSQMTDMCLDKFACRVIQSSLQNMDLSLACK 141
Query: 597 LVKAALKPG-FLDLIKDLNGNHVLQRCLQCLSNEDNEVYLFFDAAAKFCVDIATHQHGCC 655
LV+A + + + D N NHV+Q+ + + ++ E + F A + I + ++GC
Sbjct: 142 LVQALPRDARLIAICVDQNANHVIQKVVAVIPLKNWEFIVDFVATPEHLRQICSDKYGCR 201
Query: 656 VLQRCI----AHSIG------------RHRDKLITEISKNGRHLAQDPFGNYVVQYIIEL 699
V+Q I A S+ R +L+T ++ + LA + + NY++Q+I+
Sbjct: 202 VVQTIIEKLTADSMNVDLTSAAQNLRERALQRLMTSVTNRCQELATNEYANYIIQHIVSN 261
Query: 700 KIPSVSANLLSQ--FKGHYVHLSTQKFSSHVVEKCLKHFG-ESRSQIVHELLS--VPH-- 752
+V + + + + LS +KF+SHVVEK H E ++++ E+ +PH
Sbjct: 262 DDLAVYRECIIEKCLMRNLLSLSQEKFASHVVEKAFLHAPLELLAEMMDEIFDGYIPHPD 321
Query: 753 -----FEQLLQDPFANYVIQCALSV 772
+ ++ F NYV+QC L++
Sbjct: 322 TGKDALDIMMFHQFGNYVVQCMLTI 346
Score = 37.0 bits (84), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 46/202 (22%), Positives = 87/202 (43%), Gaps = 27/202 (13%)
Query: 530 IVELMMEQFGNYLVQKLLNVCTEEQMTRILLMVTEEPGQLVRVCLNTYGTRVVQKLIETL 589
++ + ++Q N+++QK++ V + I+ V P L ++C + YG RVVQ +IE L
Sbjct: 152 LIAICVDQNANHVIQKVVAVIPLKNWEFIVDFVAT-PEHLRQICSDKYGCRVVQTIIEKL 210
Query: 590 KT-RQQVSLVKAA----------LKPGFLDLIKDLNGNHVLQRCLQ-CLSNEDNEVY--- 634
V L AA L + ++L N +Q +SN+D VY
Sbjct: 211 TADSMNVDLTSAAQNLRERALQRLMTSVTNRCQELATNEYANYIIQHIVSNDDLAVYREC 270
Query: 635 LFFDAAAKFCVDIATHQHGCCVLQRCIAHSIGRHRDKLITEI-------SKNGRH----L 683
+ + + ++ + V+++ H+ +++ EI G+ +
Sbjct: 271 IIEKCLMRNLLSLSQEKFASHVVEKAFLHAPLELLAEMMDEIFDGYIPHPDTGKDALDIM 330
Query: 684 AQDPFGNYVVQYIIELKIPSVS 705
FGNYVVQ ++ + +VS
Sbjct: 331 MFHQFGNYVVQCMLTICCDAVS 352
Score = 30.8 bits (68), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 16/70 (22%), Positives = 33/70 (47%), Gaps = 11/70 (15%)
Query: 494 IYSMAKDQNGCRFLQRVFDEGTFLDLQIIFDEVIDHIVE-----------LMMEQFGNYL 542
+ S+++++ +++ F L + DE+ D + +M QFGNY+
Sbjct: 280 LLSLSQEKFASHVVEKAFLHAPLELLAEMMDEIFDGYIPHPDTGKDALDIMMFHQFGNYV 339
Query: 543 VQKLLNVCTE 552
VQ +L +C +
Sbjct: 340 VQCMLTICCD 349
>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 = 92.0 bits (227), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 79/325 (24%), Positives = 153/325 (47%), Gaps = 51/325 (15%)
Query: 492 GYIYSMAKDQNGCRFLQRVFDEGTFLDLQI--IFDEVI---DHIVELMMEQFGNYLVQKL 546
G + A D+ GC+FL++ +G+ Q +F++VI D ++L FGNYLVQ +
Sbjct: 30 GDLMKFAVDKTGCQFLEKAV-KGSLTSYQKFQLFEQVIGRKDDFLKLSTNIFGNYLVQSV 88
Query: 547 LNVCT----------EEQMTRILLMVTEEPGQLVRVCLNTYGTRVVQKLIETLKTRQQVS 596
+ + +E++ + Q+ +CL+ + V+Q ++ +
Sbjct: 89 IGISLATNDDGYTKRQEKLKNFI------SSQMTDMCLDKFACYVIQSSLQNMDLSLACK 142
Query: 597 LVKAALKPG-FLDLIKDLNGNHVLQRCLQCLSNEDNEVYLFFDAAAKFCVDIATHQHGCC 655
LV+A + + + D N NHV+Q+ + + ++ E + F A + I + ++GC
Sbjct: 143 LVQALPRDARLIAICVDQNANHVIQKVVAVIPLKNWEFIVDFVATPEHLRQICSDKYGCR 202
Query: 656 VLQRCI----AHSIG------------RHRDKLITEISKNGRHLAQDPFGNYVVQYIIEL 699
V+Q I A S+ R +L+T ++ + LA + + NY++Q+I+
Sbjct: 203 VVQTIIEKLTADSMNVDLTSAAQNLRERALQRLMTSVTNRCQELATNEYANYIIQHIVSN 262
Query: 700 KIPSVSANLLSQ--FKGHYVHLSTQKFSSHVVEKCLKHFG-ESRSQIVHELLS--VPH-- 752
+V + + + + LS +KF+SHVVEK H E ++++ E+ +PH
Sbjct: 263 DDLAVYRECIIEKCLMRNLLSLSQEKFASHVVEKAFLHAPLELLAEMMDEIFDGYIPHPD 322
Query: 753 -----FEQLLQDPFANYVIQCALSV 772
+ ++ F NYV+QC L++
Sbjct: 323 TGKDALDIMMFHQFGNYVVQCMLTI 347
Score = 37.0 bits (84), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 46/202 (22%), Positives = 87/202 (43%), Gaps = 27/202 (13%)
Query: 530 IVELMMEQFGNYLVQKLLNVCTEEQMTRILLMVTEEPGQLVRVCLNTYGTRVVQKLIETL 589
++ + ++Q N+++QK++ V + I+ V P L ++C + YG RVVQ +IE L
Sbjct: 153 LIAICVDQNANHVIQKVVAVIPLKNWEFIVDFVAT-PEHLRQICSDKYGCRVVQTIIEKL 211
Query: 590 KT-RQQVSLVKAA----------LKPGFLDLIKDLNGNHVLQRCLQ-CLSNEDNEVY--- 634
V L AA L + ++L N +Q +SN+D VY
Sbjct: 212 TADSMNVDLTSAAQNLRERALQRLMTSVTNRCQELATNEYANYIIQHIVSNDDLAVYREC 271
Query: 635 LFFDAAAKFCVDIATHQHGCCVLQRCIAHSIGRHRDKLITEI-------SKNGRH----L 683
+ + + ++ + V+++ H+ +++ EI G+ +
Sbjct: 272 IIEKCLMRNLLSLSQEKFASHVVEKAFLHAPLELLAEMMDEIFDGYIPHPDTGKDALDIM 331
Query: 684 AQDPFGNYVVQYIIELKIPSVS 705
FGNYVVQ ++ + +VS
Sbjct: 332 MFHQFGNYVVQCMLTICCDAVS 353
Score = 30.8 bits (68), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 16/70 (22%), Positives = 33/70 (47%), Gaps = 11/70 (15%)
Query: 494 IYSMAKDQNGCRFLQRVFDEGTFLDLQIIFDEVIDHIVE-----------LMMEQFGNYL 542
+ S+++++ +++ F L + DE+ D + +M QFGNY+
Sbjct: 281 LLSLSQEKFASHVVEKAFLHAPLELLAEMMDEIFDGYIPHPDTGKDALDIMMFHQFGNYV 340
Query: 543 VQKLLNVCTE 552
VQ +L +C +
Sbjct: 341 VQCMLTICCD 350
>pdb|3V71|A Chain A, Crystal Structure Of Puf-6 In Complex With 5be13 Rna
Length = 382
Score = 45.1 bits (105), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 58/285 (20%), Positives = 109/285 (38%), Gaps = 79/285 (27%)
Query: 563 TEEPGQLVRVCLNTYGTRVVQKLIETLKTRQQVSLVKAALKPGFLDLIKDLNG------- 615
TE V +C + G +VQKL+E +Q L++ + G L + KD
Sbjct: 56 TESTTLFVGLCHSRNGNFIVQKLVELATPAEQRELLRQMIDGGLLAMCKDKFACRVVQLA 115
Query: 616 ------------------------------NHVLQRCLQCLSNEDNEVYLFFDAAAKFCV 645
HV+QR ++ L + ++ F ++ +
Sbjct: 116 LQKFDHSNVFQLIQELSTFDLAAMCTDQISIHVIQRVVKQLPVDMWTFFVHFLSSGDSLM 175
Query: 646 DIATHQHGCCVLQRCIAHSIGRHR-----------DKLITEISKNGRHLAQDPFGNYVVQ 694
+ ++GC ++Q+ I + L+T I +N L+ + F NYV+Q
Sbjct: 176 AVCQDKYGCRLVQQVIDRLAENPKLPCFKFRIQLLHSLMTCIVRNCYRLSSNEFANYVIQ 235
Query: 695 YIIELKIPSVSANLLSQFKGHYV---------HLSTQKFSSHVVEKCLKHFGESRSQIVH 745
Y+I+ S+ ++ ++ + +S K++SHV+E F + ++H
Sbjct: 236 YVIK------SSGIMEMYRDTIIDKCLLRNLLSMSQDKYASHVIEGA---FLFAPPALLH 286
Query: 746 ELLS------VPHFEQ-------LLQDPFANYVIQCALSVTKGPL 777
E++ V E LL + NYV+Q +S+ L
Sbjct: 287 EMMEEIFSGYVKDVESNRDALDILLFHQYGNYVVQQMISICTAAL 331
Score = 29.6 bits (65), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 9/19 (47%), Positives = 17/19 (89%)
Query: 533 LMMEQFGNYLVQKLLNVCT 551
L+ Q+GNY+VQ+++++CT
Sbjct: 310 LLFHQYGNYVVQQMISICT 328
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
0.320 0.136 0.402
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 22,709,771
Number of Sequences: 62578
Number of extensions: 931081
Number of successful extensions: 2465
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 2172
Number of HSP's gapped (non-prelim): 41
length of query: 808
length of database: 14,973,337
effective HSP length: 107
effective length of query: 701
effective length of database: 8,277,491
effective search space: 5802521191
effective search space used: 5802521191
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.8 bits)