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= 048735
(579 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 = 159 bits (401), Expect = 5e-39, Method: Compositional matrix adjust.
Identities = 111/326 (34%), Positives = 178/326 (54%), Gaps = 19/326 (5%)
Query: 214 STNASSRYNNFYARARHHHHRTSYSSIEELRGRIILVAKDEQGCRFLQKKVDERNPIDIE 273
++NA++ + R R + + +++ G I + KD+ GCRFLQK++D +
Sbjct: 4 TSNATNSNSAEKQRKIEESSRFADAVLDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAAD 63
Query: 274 MILSEVIDDLHELMRHQSANHLIQKLIGVLNEEQMTKLILSVVSSQQRLLRICDDLSGSR 333
I E D ELM N+LIQKL+ + EQ +++L+ +SS + I + G+R
Sbjct: 64 AIFEETKDYTVELMTDSFGNYLIQKLLEEVTTEQ--RIVLTKISSPH-FVEISLNPHGTR 120
Query: 334 VMQKLLDAGEYPTRQQLTQEQQSLLVSALKNITVSLSKSPHGNHVIKRCLQKFPPDYTKD 393
+QKL++ + T E+ ++V +L+ TV LSK +GNHVI++CLQ+ P+ +
Sbjct: 121 ALQKLIECIK-------TDEEAQIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLKPENFQF 173
Query: 394 LLEEIAENCLDLATDRSGCCLLQYCIPLAQEEQKARLIADVVANAYVLSEHSYGNYVVQY 453
+ + I+++C+D+AT R GCC+LQ C+ EQ L ++A L+ +GNYVVQY
Sbjct: 174 IFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCDNLCDKLLALVDKLTLDPFGNYVVQY 233
Query: 454 ILGLKIPQ----VTADVVAQLAGRYFALSLGKCSSNVVQKCLLESGEEQSTGIINEIIRH 509
I+ + + T +V L R LS+ K SNV++K L S +I EI+ +
Sbjct: 234 IITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVIEKIL--KTAIVSEPMILEILNN 291
Query: 510 ---PEIVQLILDPYGNYVIQTAWDVS 532
I L+ D YGNYV+QTA D+S
Sbjct: 292 GGETGIQSLLNDSYGNYVLQTALDIS 317
>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 = 157 bits (396), Expect = 2e-38, Method: Compositional matrix adjust.
Identities = 108/306 (35%), Positives = 170/306 (55%), Gaps = 19/306 (6%)
Query: 234 RTSYSSIEELRGRIILVAKDEQGCRFLQKKVDERNPIDIEMILSEVIDDLHELMRHQSAN 293
R + + +++ G I + KD+ GCRFLQK++D + I E D ELM N
Sbjct: 2 RFADAVLDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGN 61
Query: 294 HLIQKLIGVLNEEQMTKLILSVVSSQQRLLRICDDLSGSRVMQKLLDAGEYPTRQQLTQE 353
+LIQKL+ + EQ +++L+ +SS + I + G+R +QKL++ + T E
Sbjct: 62 YLIQKLLEEVTTEQ--RIVLTKISSPH-FVEISLNPHGTRALQKLIECIK-------TDE 111
Query: 354 QQSLLVSALKNITVSLSKSPHGNHVIKRCLQKFPPDYTKDLLEEIAENCLDLATDRSGCC 413
+ ++V +L+ TV LSK +GNHVI++CLQ+ P+ + + + I+++C+D+AT R GCC
Sbjct: 112 EAQIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCC 171
Query: 414 LLQYCIPLAQEEQKARLIADVVANAYVLSEHSYGNYVVQYILGLKIPQ----VTADVVAQ 469
+LQ C+ EQ L ++A L+ +GNYVVQYI+ + + T +V
Sbjct: 172 VLQRCLDHGTTEQCDNLCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHL 231
Query: 470 LAGRYFALSLGKCSSNVVQKCLLESGEEQSTGIINEIIRH---PEIVQLILDPYGNYVIQ 526
L R LS+ K SNV++K L S +I EI+ + I L+ D YGNYV+Q
Sbjct: 232 LKPRAIELSIHKFGSNVIEKIL--KTAIVSEPMILEILNNGGETGIQSLLNDSYGNYVLQ 289
Query: 527 TAWDVS 532
TA D+S
Sbjct: 290 TALDIS 295
Score = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 41/168 (24%), Positives = 79/168 (47%), Gaps = 18/168 (10%)
Query: 405 LATDRSGCCLLQYCIPLAQEEQKARLIADVVANAYVLSEHSYGNYVVQYILGLKIPQVTA 464
L D+ GC LQ + + + + + L S+GNY++Q +L +VT
Sbjct: 18 LCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLL----EEVTT 73
Query: 465 D---VVAQLAGRYFA-LSLGKCSSNVVQKCLLESGEEQSTGIINEIIRHPEIVQLILDPY 520
+ V+ +++ +F +SL + +QK + ++ I+ + +R P VQL D
Sbjct: 74 EQRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLR-PYTVQLSKDLN 132
Query: 521 GNYVIQTAWDVSQGRRIR----QTLYDLVVDNSPFLQSHMYGKNVLAK 564
GN+VIQ +R++ Q ++D + D+ + +H +G VL +
Sbjct: 133 GNHVIQKCL-----QRLKPENFQFIFDAISDSCIDIATHRHGCCVLQR 175
>pdb|3BWT|A Chain A, Crystal Structure Of The Rna Binding Domain Of Puf4 From
Saccharomyces Cerevisiae
Length = 333
Score = 157 bits (396), Expect = 2e-38, Method: Compositional matrix adjust.
Identities = 108/306 (35%), Positives = 170/306 (55%), Gaps = 19/306 (6%)
Query: 234 RTSYSSIEELRGRIILVAKDEQGCRFLQKKVDERNPIDIEMILSEVIDDLHELMRHQSAN 293
R + + +++ G I + KD+ GCRFLQK++D + I E D ELM N
Sbjct: 2 RFADAVLDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGN 61
Query: 294 HLIQKLIGVLNEEQMTKLILSVVSSQQRLLRICDDLSGSRVMQKLLDAGEYPTRQQLTQE 353
+LIQKL+ + EQ +++L+ +SS + I + G+R +QKL++ + T E
Sbjct: 62 YLIQKLLEEVTTEQ--RIVLTKISSPH-FVEISLNPHGTRALQKLIECIK-------TDE 111
Query: 354 QQSLLVSALKNITVSLSKSPHGNHVIKRCLQKFPPDYTKDLLEEIAENCLDLATDRSGCC 413
+ ++V +L+ TV LSK +GNHVI++CLQ+ P+ + + + I+++C+D+AT R GCC
Sbjct: 112 EAQIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCC 171
Query: 414 LLQYCIPLAQEEQKARLIADVVANAYVLSEHSYGNYVVQYILGLKIPQ----VTADVVAQ 469
+LQ C+ EQ L ++A L+ +GNYVVQYI+ + + T +V
Sbjct: 172 VLQRCLDHGTTEQCDNLCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHL 231
Query: 470 LAGRYFALSLGKCSSNVVQKCLLESGEEQSTGIINEIIRH---PEIVQLILDPYGNYVIQ 526
L R LS+ K SNV++K L S +I EI+ + I L+ D YGNYV+Q
Sbjct: 232 LKPRAIELSIHKFGSNVIEKIL--KTAIVSEPMILEILNNGGETGIQSLLNDSYGNYVLQ 289
Query: 527 TAWDVS 532
TA D+S
Sbjct: 290 TALDIS 295
Score = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 41/168 (24%), Positives = 79/168 (47%), Gaps = 18/168 (10%)
Query: 405 LATDRSGCCLLQYCIPLAQEEQKARLIADVVANAYVLSEHSYGNYVVQYILGLKIPQVTA 464
L D+ GC LQ + + + + + L S+GNY++Q +L +VT
Sbjct: 18 LCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLL----EEVTT 73
Query: 465 D---VVAQLAGRYFA-LSLGKCSSNVVQKCLLESGEEQSTGIINEIIRHPEIVQLILDPY 520
+ V+ +++ +F +SL + +QK + ++ I+ + +R P VQL D
Sbjct: 74 EQRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLR-PYTVQLSKDLN 132
Query: 521 GNYVIQTAWDVSQGRRIR----QTLYDLVVDNSPFLQSHMYGKNVLAK 564
GN+VIQ +R++ Q ++D + D+ + +H +G VL +
Sbjct: 133 GNHVIQKCL-----QRLKPENFQFIFDAISDSCIDIATHRHGCCVLQR 175
>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 = 150 bits (380), Expect = 1e-36, Method: Compositional matrix adjust.
Identities = 107/306 (34%), Positives = 168/306 (54%), Gaps = 19/306 (6%)
Query: 234 RTSYSSIEELRGRIILVAKDEQGCRFLQKKVDERNPIDIEMILSEVIDDLHELMRHQSAN 293
R + + +++ G I + KD+ GCRFLQK++D + I E D ELM N
Sbjct: 2 RFADAVLDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGN 61
Query: 294 HLIQKLIGVLNEEQMTKLILSVVSSQQRLLRICDDLSGSRVMQKLLDAGEYPTRQQLTQE 353
+LIQKL+ + EQ +++L+ +SS + I + G R +QKL++ + T E
Sbjct: 62 YLIQKLLEEVTTEQ--RIVLTKISSPH-FVEISLNPHGCRALQKLIECIK-------TDE 111
Query: 354 QQSLLVSALKNITVSLSKSPHGNHVIKRCLQKFPPDYTKDLLEEIAENCLDLATDRSGCC 413
+ ++V +L+ TV LSK +GNHVI++CLQ+ P+ + + + I+++C+D+AT R GC
Sbjct: 112 EAQIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCR 171
Query: 414 LLQYCIPLAQEEQKARLIADVVANAYVLSEHSYGNYVVQYILGLKIPQ----VTADVVAQ 469
+LQ C+ EQ L ++A L+ +GNYVVQYI+ + + T +V
Sbjct: 172 VLQRCLDHGTTEQCDNLCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHL 231
Query: 470 LAGRYFALSLGKCSSNVVQKCLLESGEEQSTGIINEIIRH---PEIVQLILDPYGNYVIQ 526
L R LS+ K SNV++K L S +I EI+ + I L+ D YGNYV+Q
Sbjct: 232 LKPRAIELSIHKFGSNVIEKIL--KTAIVSEPMILEILNNGGETGIQSLLNDSYGNYVLQ 289
Query: 527 TAWDVS 532
TA D+S
Sbjct: 290 TALDIS 295
Score = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 41/168 (24%), Positives = 78/168 (46%), Gaps = 18/168 (10%)
Query: 405 LATDRSGCCLLQYCIPLAQEEQKARLIADVVANAYVLSEHSYGNYVVQYILGLKIPQVTA 464
L D+ GC LQ + + + + + L S+GNY++Q +L +VT
Sbjct: 18 LCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLL----EEVTT 73
Query: 465 D---VVAQLAGRYFA-LSLGKCSSNVVQKCLLESGEEQSTGIINEIIRHPEIVQLILDPY 520
+ V+ +++ +F +SL +QK + ++ I+ + +R P VQL D
Sbjct: 74 EQRIVLTKISSPHFVEISLNPHGCRALQKLIECIKTDEEAQIVVDSLR-PYTVQLSKDLN 132
Query: 521 GNYVIQTAWDVSQGRRIR----QTLYDLVVDNSPFLQSHMYGKNVLAK 564
GN+VIQ +R++ Q ++D + D+ + +H +G VL +
Sbjct: 133 GNHVIQKCL-----QRLKPENFQFIFDAISDSCIDIATHRHGCRVLQR 175
>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 = 134 bits (337), Expect = 1e-31, Method: Compositional matrix adjust.
Identities = 84/331 (25%), Positives = 175/331 (52%), Gaps = 17/331 (5%)
Query: 240 IEELRGRIILVAKDEQGCRFLQKKVDERNPIDIEMILSEVIDDLHELMRHQSANHLIQKL 299
+ +L G I+ ++D+ G RF+Q+K++ P + +++ +E++ ++LM N++IQK
Sbjct: 21 LRDLIGHIVEFSQDQHGSRFIQQKLERATPAERQIVFNEILQAAYQLMTDVFGNYVIQKF 80
Query: 300 IGVLNEEQMTKLILSVVSSQQRLLRICDDLSGSRVMQKLLDAGEYPTRQQLTQEQQSLLV 359
+ +Q L + + +L + + G RV+QK L++ ++ +QQS +V
Sbjct: 81 FEFGSLDQKLALATRI---RGHVLPLALQMYGCRVIQKALES--------ISSDQQSEMV 129
Query: 360 SALKNITVSLSKSPHGNHVIKRCLQKFPPDYTKDLLEEIAENCLDLATDRSGCCLLQYCI 419
L + K +GNHV+++C++ P + +++ L+T GC ++Q +
Sbjct: 130 KELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFVLSTHPYGCRVIQRIL 189
Query: 420 PLAQEEQKARLIADVVANAYVLSEHSYGNYVVQYILGLKIPQVTADVVAQLAGRYFALSL 479
EQ ++ ++ + L + YGNYV+Q++L P+ + +V+++ G+ ALS
Sbjct: 190 EHCTAEQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGKVLALSQ 249
Query: 480 GKCSSNVVQKCLLESGEEQSTGIINEIIR-----HPEIVQLILDPYGNYVIQTAWDVSQG 534
K +SNVV+KC+ + + +I+E+ H + ++ D Y NYV+Q D+++
Sbjct: 250 HKFASNVVEKCVTHASRAERALLIDEVCCQNDGPHSALYTMMKDQYANYVVQKMIDMAEP 309
Query: 535 RRIRQTLYDLVVDNSPFLQSHMYGKNVLAKV 565
+ R+ + + + L+ + YGK++LAK+
Sbjct: 310 AQ-RKIIMHKIRPHITTLRKYTYGKHILAKL 339
>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 = 131 bits (330), Expect = 1e-30, Method: Compositional matrix adjust.
Identities = 85/331 (25%), Positives = 174/331 (52%), Gaps = 15/331 (4%)
Query: 240 IEELRGRIILVAKDEQGCRFLQKKVDERNPIDIEMILSEVIDDLHELMRHQSANHLIQKL 299
+ +L G I+ ++D+ G RF+Q+K++ P + +M+ +E++ ++LM N++IQK
Sbjct: 19 LRDLIGHIVEFSQDQHGSRFIQQKLERATPAERQMVFNEILQAAYQLMTDVFGNYVIQKF 78
Query: 300 IGVLNEEQMTKLILSVVSSQQRLLRICDDLSGSRVMQKLLDAGEYPTRQQLTQEQQSLLV 359
+ +Q L + + +L + + G RV+QK L++ + QQ+ E +V
Sbjct: 79 FEFGSLDQKLALATRI---RGHVLPLALQMYGCRVIQKALES--ISSDQQVISE----MV 129
Query: 360 SALKNITVSLSKSPHGNHVIKRCLQKFPPDYTKDLLEEIAENCLDLATDRSGCCLLQYCI 419
L + K +GNHV+++C++ P + +++ L+T GC ++Q +
Sbjct: 130 KELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFVLSTHPYGCRVIQRIL 189
Query: 420 PLAQEEQKARLIADVVANAYVLSEHSYGNYVVQYILGLKIPQVTADVVAQLAGRYFALSL 479
EQ ++ ++ + L + YGNYV+Q++L P+ + +V+++ G+ ALS
Sbjct: 190 EHCTAEQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGKVLALSQ 249
Query: 480 GKCSSNVVQKCLLESGEEQSTGIINEIIR-----HPEIVQLILDPYGNYVIQTAWDVSQG 534
K +SNVV+KC+ + + +I+E+ H + ++ D Y NYV+Q D+++
Sbjct: 250 HKFASNVVEKCVTHASRAERALLIDEVCCQNDGPHSALYTMMKDQYANYVVQKMIDMAEP 309
Query: 535 RRIRQTLYDLVVDNSPFLQSHMYGKNVLAKV 565
+ R+ + + + L+ + YGK++LAK+
Sbjct: 310 AQ-RKIIMHKIRPHITTLRKYTYGKHILAKL 339
>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 = 129 bits (323), Expect = 6e-30, Method: Compositional matrix adjust.
Identities = 86/335 (25%), Positives = 173/335 (51%), Gaps = 25/335 (7%)
Query: 240 IEELRGRIILVAKDEQGCRFLQKKVDERNPIDIEMILSEVIDDLHELMRHQSANHLIQKL 299
+ E+ G I+ ++D+ G RF+Q K++ P + +++ +E++ ++LM N++IQK
Sbjct: 19 LREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKF 78
Query: 300 IGVLNEEQMTKLILSVVSSQQRLLRICDDLSGSRVMQKLLDAGEYPTRQQLTQEQQSLLV 359
+ EQ L + + +L + + G RV+QK L+ + +QQ+ +V
Sbjct: 79 FEFGSLEQKLALAERI---RGHVLSLALQMYGCRVIQKALEF--------IPSDQQNEMV 127
Query: 360 SALKNITVSLSKSPHGNHVIKRCLQKFPPDYTKDLLEEIAENCLDLATDRSGCCLLQ--- 416
L + K +GNHV+++C++ P + +++ L+T GC ++Q
Sbjct: 128 RELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRIL 187
Query: 417 -YCIPLAQEEQKARLIADVVANAYVLSEHSYGNYVVQYILGLKIPQVTADVVAQLAGRYF 475
+C+P +Q ++ ++ + L + YGNYV+Q++L P+ + +VA++ G
Sbjct: 188 EHCLP----DQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVL 243
Query: 476 ALSLGKCSSNVVQKCLLESGEEQSTGIINEIIR-----HPEIVQLILDPYGNYVIQTAWD 530
LS K +SNVV+KC+ + + +I+E+ H + ++ D Y NYV+Q D
Sbjct: 244 VLSQHKFASNVVEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMID 303
Query: 531 VSQGRRIRQTLYDLVVDNSPFLQSHMYGKNVLAKV 565
V++ + R+ + + + L+ + YGK++LAK+
Sbjct: 304 VAEPGQ-RKIVMHKIRPHIATLRKYTYGKHILAKL 337
>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 = 129 bits (323), Expect = 6e-30, Method: Compositional matrix adjust.
Identities = 86/335 (25%), Positives = 173/335 (51%), Gaps = 25/335 (7%)
Query: 240 IEELRGRIILVAKDEQGCRFLQKKVDERNPIDIEMILSEVIDDLHELMRHQSANHLIQKL 299
+ E+ G I+ ++D+ G RF+Q K++ P + +++ +E++ ++LM N++IQK
Sbjct: 19 LREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKF 78
Query: 300 IGVLNEEQMTKLILSVVSSQQRLLRICDDLSGSRVMQKLLDAGEYPTRQQLTQEQQSLLV 359
+ EQ L + + +L + + G RV+QK L+ + +QQ+ +V
Sbjct: 79 FEFGSLEQKLALAERI---RGHVLSLALQMYGCRVIQKALEF--------IPSDQQNEMV 127
Query: 360 SALKNITVSLSKSPHGNHVIKRCLQKFPPDYTKDLLEEIAENCLDLATDRSGCCLLQ--- 416
L + K +GNHV+++C++ P + +++ L+T GC ++Q
Sbjct: 128 RELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRIL 187
Query: 417 -YCIPLAQEEQKARLIADVVANAYVLSEHSYGNYVVQYILGLKIPQVTADVVAQLAGRYF 475
+C+P +Q ++ ++ + L + YGNYV+Q++L P+ + +VA++ G
Sbjct: 188 EHCLP----DQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVL 243
Query: 476 ALSLGKCSSNVVQKCLLESGEEQSTGIINEIIR-----HPEIVQLILDPYGNYVIQTAWD 530
LS K +SNVV+KC+ + + +I+E+ H + ++ D Y NYV+Q D
Sbjct: 244 VLSQHKFASNVVEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMID 303
Query: 531 VSQGRRIRQTLYDLVVDNSPFLQSHMYGKNVLAKV 565
V++ + R+ + + + L+ + YGK++LAK+
Sbjct: 304 VAEPGQ-RKIVMHKIRPHIATLRKYTYGKHILAKL 337
>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 = 125 bits (313), Expect = 8e-29, Method: Compositional matrix adjust.
Identities = 84/335 (25%), Positives = 173/335 (51%), Gaps = 25/335 (7%)
Query: 240 IEELRGRIILVAKDEQGCRFLQKKVDERNPIDIEMILSEVIDDLHELMRHQSANHLIQKL 299
+ E+ G I+ ++D+ G RF+Q K++ P + +++ +E++ ++LM N++IQK
Sbjct: 20 LREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKF 79
Query: 300 IGVLNEEQMTKLILSVVSSQQRLLRICDDLSGSRVMQKLLDAGEYPTRQQLTQEQQSLLV 359
+ EQ L + + +L + + G RV+QK L+ + +QQ+ +V
Sbjct: 80 FEFGSLEQKLALAERI---RGHVLSLALQMYGCRVIQKALEF--------IPSDQQNEMV 128
Query: 360 SALKNITVSLSKSPHGNHVIKRCLQKFPPDYTKDLLEEIAENCLDLATDRSGCCLLQ--- 416
L + K +GNHV+++C++ P + +++ L+T GC ++Q
Sbjct: 129 RELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRIL 188
Query: 417 -YCIPLAQEEQKARLIADVVANAYVLSEHSYGNYVVQYILGLKIPQVTADVVAQLAGRYF 475
+C+P +Q ++ ++ + L + YG+YV++++L P+ + +VA++ G
Sbjct: 189 EHCLP----DQTLPILEELHQHTEQLVQDQYGSYVIRHVLEHGRPEDKSKIVAEIRGNVL 244
Query: 476 ALSLGKCSSNVVQKCLLESGEEQSTGIINEIIR-----HPEIVQLILDPYGNYVIQTAWD 530
LS K +SNVV+KC+ + + +I+E+ H + ++ D Y NYV+Q D
Sbjct: 245 VLSQHKFASNVVEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMID 304
Query: 531 VSQGRRIRQTLYDLVVDNSPFLQSHMYGKNVLAKV 565
V++ + R+ + + + L+ + YGK++LAK+
Sbjct: 305 VAEPGQ-RKIVMHKIRPHIATLRKYTYGKHILAKL 338
>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 = 119 bits (299), Expect = 4e-27, Method: Compositional matrix adjust.
Identities = 78/304 (25%), Positives = 156/304 (51%), Gaps = 13/304 (4%)
Query: 240 IEELRGRIILVAKDEQGCRFLQKKVDERNPIDIEMILSEVIDDLHELMRHQSANHLIQKL 299
+ +L I+ ++D+ G RF+Q+K++ + +M+ SE++ + LM N++IQK
Sbjct: 21 LRDLANHIVEFSQDQHGSRFIQQKLERATAAEKQMVFSEILAAAYSLMTDVFGNYVIQKF 80
Query: 300 IGVLNEEQMTKLILSVVSSQQRLLRICDDLSGSRVMQKLLDAGEYPTRQQLTQEQQSLLV 359
EQ L + V + +L++ + G RV+QK L++ ++ EQQ +V
Sbjct: 81 FEFGTPEQKNTLGMQV---KGHVLQLALQMYGCRVIQKALES--------ISPEQQQEIV 129
Query: 360 SALKNITVSLSKSPHGNHVIKRCLQKFPPDYTKDLLEEIAENCLDLATDRSGCCLLQYCI 419
L + K +GNHV+++C++ P + ++ L+T GC ++Q +
Sbjct: 130 HELDGHVLKCVKDQNGNHVVQKCIECVDPVALQFIINAFKGQVYSLSTHPYGCRVIQRIL 189
Query: 420 PLAQEEQKARLIADVVANAYVLSEHSYGNYVVQYILGLKIPQVTADVVAQLAGRYFALSL 479
EQ ++ ++ + L + YGNYV+Q++L + + ++ + G+ LS
Sbjct: 190 EHCTAEQTTPILDELHEHTEQLIQDQYGNYVIQHVLEHGKQEDKSILINSVRGKVLVLSQ 249
Query: 480 GKCSSNVVQKCLLESGEEQSTGIINEIIRHPE--IVQLILDPYGNYVIQTAWDVSQGRRI 537
K +SNVV+KC+ + + TG+I+E+ + + ++ D Y NYV+Q DVS+ ++
Sbjct: 250 HKFASNVVEKCVTHATRGERTGLIDEVCTFNDNALHVMMKDQYANYVVQKMIDVSEPTQL 309
Query: 538 RQTL 541
++ +
Sbjct: 310 KKLM 313
Score = 58.2 bits (139), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 62/246 (25%), Positives = 94/246 (38%), Gaps = 39/246 (15%)
Query: 362 LKNITVSLSKSPHGNHVIKRCLQKFPPDYTKDLLEEIAENCLDLATDRSGCCLLQYCIPL 421
L N V S+ HG+ I++ L++ + + EI L TD G ++Q
Sbjct: 24 LANHIVEFSQDQHGSRFIQQKLERATAAEKQMVFSEILAAAYSLMTDVFGNYVIQKFFEF 83
Query: 422 AQEEQKARLIADVVANAYVLSEHSYGNYVVQYILGLKIPQVTADVVAQLAGRYFALSLGK 481
EQK L V + L+ YG V+Q L P+ ++V +L G +
Sbjct: 84 GTPEQKNTLGMQVKGHVLQLALQMYGCRVIQKALESISPEQQQEIVHELDGHVLKCVKDQ 143
Query: 482 CSSNVVQKC------------------------------------LLESGEEQSTGIINE 505
++VVQKC L EQ+T I++E
Sbjct: 144 NGNHVVQKCIECVDPVALQFIINAFKGQVYSLSTHPYGCRVIQRILEHCTAEQTTPILDE 203
Query: 506 IIRHPEIVQLILDPYGNYVIQTAWDVSQGRRIRQTLYDLVVDNSPFLQSHMYGKNVLAKV 565
+ H E QLI D YGNYVIQ + + + + L + V L H + NV+ K
Sbjct: 204 LHEHTE--QLIQDQYGNYVIQHVLEHGK-QEDKSILINSVRGKVLVLSQHKFASNVVEKC 260
Query: 566 RGNKNR 571
+ R
Sbjct: 261 VTHATR 266
Score = 33.9 bits (76), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 24/102 (23%), Positives = 52/102 (50%), Gaps = 6/102 (5%)
Query: 220 RYNNFYARARHHHHRTSYSSI--EELRGRIILVAKDEQGCRFLQKKVDERNPIDIEMILS 277
+Y N+ + H + SI +RG+++++++ + ++K V + ++
Sbjct: 215 QYGNYVIQHVLEHGKQEDKSILINSVRGKVLVLSQHKFASNVVEKCVTHATRGERTGLID 274
Query: 278 EVI----DDLHELMRHQSANHLIQKLIGVLNEEQMTKLILSV 315
EV + LH +M+ Q AN+++QK+I V Q+ KL+ +
Sbjct: 275 EVCTFNDNALHVMMKDQYANYVVQKMIDVSEPTQLKKLMTKI 316
>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 = 96.7 bits (239), Expect = 3e-20, Method: Compositional matrix adjust.
Identities = 78/312 (25%), Positives = 148/312 (47%), Gaps = 28/312 (8%)
Query: 240 IEELRGRIILVAKDEQGCRFLQKKVDERNPIDIEMILSEVIDDLHELMRHQSANHLIQKL 299
++++ G + KD+ G RF+Q+++ + E+I +E+ DD EL N++IQK
Sbjct: 26 LKDIFGHSLEFCKDQHGSRFIQRELATSPASEKEVIFNEIRDDAIELSNDVFGNYVIQKF 85
Query: 300 IGVLNEEQMTKLILSVVSSQQRLLRICDDLSGSRVMQKLLDAGEYPTRQQLTQEQQSLLV 359
++ Q L+ + ++L + RV+QK L EY Q + LV
Sbjct: 86 FEFGSKIQKNTLVDQFKGNMKQL---SLQMYACRVIQKAL---EYIDSNQRIE-----LV 134
Query: 360 SALKNITVSLSKSPHGNHVIKRCLQKFPPDYTKDLLEEIAENCLDLATDRSGCCLLQYCI 419
L + + + K +GNHVI++ ++ P + +L + + L+T GC ++Q +
Sbjct: 135 LELSDSVLQMIKDQNGNHVIQKAIETIPIEKLPFILSSLTGHIYHLSTHSYGCRVIQRLL 194
Query: 420 PLAQEEQKARLIADVVANAYVLSEHSYGNYVVQYIL------GLKIPQVTADVVAQLAGR 473
E + ++ ++ L + YGNYV+QY+L ++ + +++ +A
Sbjct: 195 EFGSSEDQESILNELKDFIPYLIQDQYGNYVIQYVLQQDQFTNKEMVDIKQEIIETVANN 254
Query: 474 YFALSLGKCSSNVVQKCLLESGEEQSTGIINEIIRHPE-----------IVQLILDPYGN 522
S K +SNVV+K +L + Q II++I+ + ++ +I D + N
Sbjct: 255 VVEYSKHKFASNVVEKSILYGSKNQKDLIISKILPRDKNHALNLEDDSPMILMIKDQFAN 314
Query: 523 YVIQTAWDVSQG 534
YVIQ +VS+G
Sbjct: 315 YVIQKLVNVSEG 326
>pdb|3V71|A Chain A, Crystal Structure Of Puf-6 In Complex With 5be13 Rna
Length = 382
Score = 72.0 bits (175), Expect = 8e-13, Method: Compositional matrix adjust.
Identities = 80/325 (24%), Positives = 149/325 (45%), Gaps = 48/325 (14%)
Query: 237 YSSIEE--LRGRIILVAKDEQGCRFLQKKVDERNPIDIE-MILSEVIDDLHE-------L 286
+ S+E+ L G++I A D G +FL+ P+D E I V + E L
Sbjct: 10 FISLEDVLLNGQLIDFAIDPSGVKFLEANY----PLDSEDQIRKAVFEKFTESTTLFVGL 65
Query: 287 MRHQSANHLIQKLIGVLNEEQMTKLILSVVSSQQRLLRICDDLSGSRVMQKLLDAGEYPT 346
++ N ++QKL+ + + +L+ ++ LL +C D RV+Q L ++
Sbjct: 66 CHSRNGNFIVQKLVELATPAEQRELLRQMIDGG--LLAMCKDKFACRVVQLALQKFDHSN 123
Query: 347 RQQLTQEQQSLLVSALKNITVSLSKSPHGNHVIKRCLQKFPPDYTKDLLEEIA--ENCLD 404
QL QE + ++A+ +S+ HVI+R +++ P D + ++ ++ +
Sbjct: 124 VFQLIQELSTFDLAAMCTDQISI-------HVIQRVVKQLPVDMWTFFVHFLSSGDSLMA 176
Query: 405 LATDRSGCCLLQYCIPLAQEEQKA-----------RLIADVVANAYVLSEHSYGNYVVQY 453
+ D+ GC L+Q I E K L+ +V N Y LS + + NYV+QY
Sbjct: 177 VCQDKYGCRLVQQVIDRLAENPKLPCFKFRIQLLHSLMTCIVRNCYRLSSNEFANYVIQY 236
Query: 454 IL-GLKIPQVTADVVAQ--LAGRYFALSLGKCSSNVVQKCLL--------ESGEEQSTGI 502
++ I ++ D + L ++S K +S+V++ L E EE +G
Sbjct: 237 VIKSSGIMEMYRDTIIDKCLLRNLLSMSQDKYASHVIEGAFLFAPPALLHEMMEEIFSGY 296
Query: 503 INEIIRHPEIVQLIL-DPYGNYVIQ 526
+ ++ + + + ++L YGNYV+Q
Sbjct: 297 VKDVESNRDALDILLFHQYGNYVVQ 321
Score = 52.0 bits (123), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 57/234 (24%), Positives = 108/234 (46%), Gaps = 25/234 (10%)
Query: 245 GRIILVAKDEQGCRFLQ---KKVDERNPIDIEMILSEVIDDLHELMRHQSANHLIQKLIG 301
G ++ + KD+ CR +Q +K D N + LS DL + Q + H+IQ+++
Sbjct: 97 GGLLAMCKDKFACRVVQLALQKFDHSNVFQLIQELSTF--DLAAMCTDQISIHVIQRVVK 154
Query: 302 VLNEEQMTKLILSVVSSQQRLLRICDDLSGSRVMQKLLDA----GEYPTRQQLTQEQQSL 357
L + T + +SS L+ +C D G R++Q+++D + P + Q SL
Sbjct: 155 QLPVDMWT-FFVHFLSSGDSLMAVCQDKYGCRLVQQVIDRLAENPKLPCFKFRIQLLHSL 213
Query: 358 LVSALKNITVSLSKSPHGNHVIKRCLQK--FPPDYTKDLLEE-IAENCLDLATDRSGCCL 414
+ ++N LS + N+VI+ ++ Y ++++ + N L ++ D+ +
Sbjct: 214 MTCIVRN-CYRLSSNEFANYVIQYVIKSSGIMEMYRDTIIDKCLLRNLLSMSQDKYASHV 272
Query: 415 LQYCIPLA--------QEEQKARLIADVVAN---AYVLSEHSYGNYVVQYILGL 457
++ A EE + + DV +N +L H YGNYVVQ ++ +
Sbjct: 273 IEGAFLFAPPALLHEMMEEIFSGYVKDVESNRDALDILLFHQYGNYVVQQMISI 326
>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 = 65.9 bits (159), Expect = 7e-11, Method: Compositional matrix adjust.
Identities = 90/355 (25%), Positives = 157/355 (44%), Gaps = 56/355 (15%)
Query: 245 GRIILVAKDEQGCRFLQKKVD-ERNPIDIEMILSEVI---DDLHELMRHQSANHLIQKLI 300
G ++ A D+ GC+FL+K V + +VI DD +L + N+L+Q +I
Sbjct: 30 GDLMKFAVDKTGCQFLEKAVKGSLTSYQKFQLFEQVIGRKDDFLKLSTNIFGNYLVQSVI 89
Query: 301 GV---LNEEQMTKL---ILSVVSSQQRLLRICDDLSGSRVMQKLLDAGEYPTRQQLTQEQ 354
G+ N++ TK + + +SSQ + +C D RV+Q L Q +
Sbjct: 90 GISLATNDDGYTKRQEKLKNFISSQ--MTDMCLDKFACRVIQSSL--------QNMDLSL 139
Query: 355 QSLLVSALKNIT--VSLSKSPHGNHVIKRCLQKFPPDYTKDLLEEIA--ENCLDLATDRS 410
LV AL +++ + NHVI++ + P + +++ +A E+ + +D+
Sbjct: 140 ACKLVQALPRDARLIAICVDQNANHVIQKVVAVIPLKNWEFIVDFVATPEHLRQICSDKY 199
Query: 411 GCCLLQYCI-------------PLAQ---EEQKARLIADVVANAYVLSEHSYGNYVVQYI 454
GC ++Q I AQ E RL+ V L+ + Y NY++Q+I
Sbjct: 200 GCRVVQTIIEKLTADSMNVDLTSAAQNLRERALQRLMTSVTNRCQELATNEYANYIIQHI 259
Query: 455 LGLKIPQVTADVVAQ--LAGRYFALSLGKCSSNVVQKCLLESGEEQSTGIINEI----IR 508
+ V + + + L +LS K +S+VV+K L + E +++EI I
Sbjct: 260 VSNDDLAVYRECIIEKCLMRNLLSLSQEKFASHVVEKAFLHAPLELLAEMMDEIFDGYIP 319
Query: 509 HPEIVQLILD-----PYGNYVIQT----AWDVSQGRR-IRQTLYDLVVDNSPFLQ 553
HP+ + LD +GNYV+Q D GRR ++ YD + +L+
Sbjct: 320 HPDTGKDALDIMMFHQFGNYVVQCMLTICCDAVSGRRQTKEGGYDHAISFQDWLK 374
>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 = 65.5 bits (158), Expect = 7e-11, Method: Compositional matrix adjust.
Identities = 90/355 (25%), Positives = 157/355 (44%), Gaps = 56/355 (15%)
Query: 245 GRIILVAKDEQGCRFLQKKVD-ERNPIDIEMILSEVI---DDLHELMRHQSANHLIQKLI 300
G ++ A D+ GC+FL+K V + +VI DD +L + N+L+Q +I
Sbjct: 29 GDLMKFAVDKTGCQFLEKAVKGSLTSYQKFQLFEQVIGRKDDFLKLSTNIFGNYLVQSVI 88
Query: 301 GV---LNEEQMTKL---ILSVVSSQQRLLRICDDLSGSRVMQKLLDAGEYPTRQQLTQEQ 354
G+ N++ TK + + +SSQ + +C D RV+Q L Q +
Sbjct: 89 GISLATNDDGYTKRQEKLKNFISSQ--MTDMCLDKFACRVIQSSL--------QNMDLSL 138
Query: 355 QSLLVSALKNIT--VSLSKSPHGNHVIKRCLQKFPPDYTKDLLEEIA--ENCLDLATDRS 410
LV AL +++ + NHVI++ + P + +++ +A E+ + +D+
Sbjct: 139 ACKLVQALPRDARLIAICVDQNANHVIQKVVAVIPLKNWEFIVDFVATPEHLRQICSDKY 198
Query: 411 GCCLLQYCI-------------PLAQ---EEQKARLIADVVANAYVLSEHSYGNYVVQYI 454
GC ++Q I AQ E RL+ V L+ + Y NY++Q+I
Sbjct: 199 GCRVVQTIIEKLTADSMNVDLTSAAQNLRERALQRLMTSVTNRCQELATNEYANYIIQHI 258
Query: 455 LGLKIPQVTADVVAQ--LAGRYFALSLGKCSSNVVQKCLLESGEEQSTGIINEI----IR 508
+ V + + + L +LS K +S+VV+K L + E +++EI I
Sbjct: 259 VSNDDLAVYRECIIEKCLMRNLLSLSQEKFASHVVEKAFLHAPLELLAEMMDEIFDGYIP 318
Query: 509 HPEIVQLILD-----PYGNYVIQT----AWDVSQGRR-IRQTLYDLVVDNSPFLQ 553
HP+ + LD +GNYV+Q D GRR ++ YD + +L+
Sbjct: 319 HPDTGKDALDIMMFHQFGNYVVQCMLTICCDAVSGRRQTKEGGYDHAISFQDWLK 373
>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 = 62.8 bits (151), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 89/355 (25%), Positives = 156/355 (43%), Gaps = 56/355 (15%)
Query: 245 GRIILVAKDEQGCRFLQKKVD-ERNPIDIEMILSEVI---DDLHELMRHQSANHLIQKLI 300
G ++ A D+ GC+FL+K V + +VI DD +L + N+L+Q +I
Sbjct: 30 GDLMKFAVDKTGCQFLEKAVKGSLTSYQKFQLFEQVIGRKDDFLKLSTNIFGNYLVQSVI 89
Query: 301 GV---LNEEQMTKL---ILSVVSSQQRLLRICDDLSGSRVMQKLLDAGEYPTRQQLTQEQ 354
G+ N++ TK + + +SSQ + +C D V+Q L Q +
Sbjct: 90 GISLATNDDGYTKRQEKLKNFISSQ--MTDMCLDKFACYVIQSSL--------QNMDLSL 139
Query: 355 QSLLVSALKNIT--VSLSKSPHGNHVIKRCLQKFPPDYTKDLLEEIA--ENCLDLATDRS 410
LV AL +++ + NHVI++ + P + +++ +A E+ + +D+
Sbjct: 140 ACKLVQALPRDARLIAICVDQNANHVIQKVVAVIPLKNWEFIVDFVATPEHLRQICSDKY 199
Query: 411 GCCLLQYCI-------------PLAQ---EEQKARLIADVVANAYVLSEHSYGNYVVQYI 454
GC ++Q I AQ E RL+ V L+ + Y NY++Q+I
Sbjct: 200 GCRVVQTIIEKLTADSMNVDLTSAAQNLRERALQRLMTSVTNRCQELATNEYANYIIQHI 259
Query: 455 LGLKIPQVTADVVAQ--LAGRYFALSLGKCSSNVVQKCLLESGEEQSTGIINEI----IR 508
+ V + + + L +LS K +S+VV+K L + E +++EI I
Sbjct: 260 VSNDDLAVYRECIIEKCLMRNLLSLSQEKFASHVVEKAFLHAPLELLAEMMDEIFDGYIP 319
Query: 509 HPEIVQLILD-----PYGNYVIQT----AWDVSQGRR-IRQTLYDLVVDNSPFLQ 553
HP+ + LD +GNYV+Q D GRR ++ YD + +L+
Sbjct: 320 HPDTGKDALDIMMFHQFGNYVVQCMLTICCDAVSGRRQTKEGGYDHAISFQDWLK 374
>pdb|4AEZ|A Chain A, Crystal Structure Of Mitotic Checkpoint Complex
pdb|4AEZ|D Chain D, Crystal Structure Of Mitotic Checkpoint Complex
pdb|4AEZ|G Chain G, Crystal Structure Of Mitotic Checkpoint Complex
Length = 401
Score = 32.0 bits (71), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 14/51 (27%), Positives = 25/51 (49%)
Query: 129 SFINSLPTSFPLENHETIDLQSGFDLQSGFEGLNIDGLGLPRPNNLTVQRN 179
+F+NS+ + P + E++ GFDL + +D +P +L Q N
Sbjct: 13 AFVNSISSDVPFDYSESVAEACGFDLNTRVLAFKLDAPEAKKPVDLRTQHN 63
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
0.318 0.133 0.393
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,740,171
Number of Sequences: 62578
Number of extensions: 693227
Number of successful extensions: 2818
Number of sequences better than 100.0: 26
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 2588
Number of HSP's gapped (non-prelim): 42
length of query: 579
length of database: 14,973,337
effective HSP length: 104
effective length of query: 475
effective length of database: 8,465,225
effective search space: 4020981875
effective search space used: 4020981875
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)