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= 048245
(309 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3BWT|A Chain A, Crystal Structure Of The Rna Binding Domain Of Puf4 From
Saccharomyces Cerevisiae
Length = 333
Score = 94.0 bits (232), Expect = 9e-20, Method: Compositional matrix adjust.
Identities = 76/282 (26%), Positives = 136/282 (48%), Gaps = 11/282 (3%)
Query: 1 EEGSQYLQEKLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIIL 60
+ G ++LQ++L S+ D +F +T ELM+ +G ++ K +E Q +++
Sbjct: 22 QHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVTTEQ-RIVLT 80
Query: 61 KITFQDQLFLLASVDKFGSSSVKKLIKVVAQSPPLLYHVMSALKRLFKFLMMTKPGSSVI 120
KI+ F+ S++ G+ +++KLI+ + V+ +L+ L G+ VI
Sbjct: 81 KISSPH--FVEISLNPHGTRALQKLIECIKTDEEAQI-VVDSLRPYTVQLSKDLNGNHVI 137
Query: 121 LKCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHLISVNAA 180
KCL+ FI+ A + C+ +A H GC L +D+ + + +
Sbjct: 138 QKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCDNLCDKLLALVD 197
Query: 181 SLSRHRSGNYVVQHVLNLEDP----FLIDAICFALRGHYVDLSLTKCGSFVVQKFLKYQN 236
L+ GNYVVQ+++ E I L+ ++LS+ K GS V++K LK
Sbjct: 198 KLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVIEKILKTAI 257
Query: 237 AVHYIVEELLNS---DQILQVASDKYGNYVIQTALVETMRQD 275
++ E+LN+ I + +D YGNYV+QTAL + +Q+
Sbjct: 258 VSEPMILEILNNGGETGIQSLLNDSYGNYVLQTALDISHKQN 299
Score = 48.9 bits (115), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 49/203 (24%), Positives = 91/203 (44%), Gaps = 19/203 (9%)
Query: 110 LMMTKPGSSVILKCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRK 169
LM G+ +I K LE + + + + H + ++ + G L I+ +K
Sbjct: 54 LMTDSFGNYLIQKLLEEVTTEQRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEA 113
Query: 170 QIL-HLISVNAASLSRHRSGNYVVQHVLNLEDP----FLIDAICFALRGHYVDLSLTKCG 224
QI+ + LS+ +GN+V+Q L P F+ DAI + +D++ + G
Sbjct: 114 QIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSC----IDIATHRHG 169
Query: 225 SFVVQKFLKYQNAVHYIVEELLN-SDQILQVAS----DKYGNYVIQTALVETMRQDRLSV 279
V+Q+ L H E+ N D++L + D +GNYV+Q + + +++
Sbjct: 170 CCVLQRCLD-----HGTTEQCDNLCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDY 224
Query: 280 HQRLVTKLQQHLAALRVMKYGSN 302
++V L+ L + K+GSN
Sbjct: 225 THKIVHLLKPRAIELSIHKFGSN 247
Score = 30.4 bits (67), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 22/96 (22%), Positives = 47/96 (48%), Gaps = 1/96 (1%)
Query: 181 SLSRHRSGNYVVQHVLNLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKFLKYQNAVHY 240
SL + + G +Q L++ DAI + + V+L G++++QK L+
Sbjct: 17 SLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVTTEQR 76
Query: 241 IVEELLNSDQILQVASDKYGNYVIQTALVETMRQDR 276
IV ++S ++++ + +G +Q L+E ++ D
Sbjct: 77 IVLTKISSPHFVEISLNPHGTRALQ-KLIECIKTDE 111
>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 = 93.6 bits (231), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 76/282 (26%), Positives = 136/282 (48%), Gaps = 11/282 (3%)
Query: 1 EEGSQYLQEKLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIIL 60
+ G ++LQ++L S+ D +F +T ELM+ +G ++ K +E Q +++
Sbjct: 22 QHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVTTEQ-RIVLT 80
Query: 61 KITFQDQLFLLASVDKFGSSSVKKLIKVVAQSPPLLYHVMSALKRLFKFLMMTKPGSSVI 120
KI+ F+ S++ G+ +++KLI+ + V+ +L+ L G+ VI
Sbjct: 81 KISSPH--FVEISLNPHGTRALQKLIECIKTDEEAQI-VVDSLRPYTVQLSKDLNGNHVI 137
Query: 121 LKCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHLISVNAA 180
KCL+ FI+ A + C+ +A H GC L +D+ + + +
Sbjct: 138 QKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCDNLCDKLLALVD 197
Query: 181 SLSRHRSGNYVVQHVLNLEDP----FLIDAICFALRGHYVDLSLTKCGSFVVQKFLKYQN 236
L+ GNYVVQ+++ E I L+ ++LS+ K GS V++K LK
Sbjct: 198 KLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVIEKILKTAI 257
Query: 237 AVHYIVEELLNS---DQILQVASDKYGNYVIQTALVETMRQD 275
++ E+LN+ I + +D YGNYV+QTAL + +Q+
Sbjct: 258 VSEPMILEILNNGGETGIQSLLNDSYGNYVLQTALDISHKQN 299
Score = 48.9 bits (115), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 49/203 (24%), Positives = 91/203 (44%), Gaps = 19/203 (9%)
Query: 110 LMMTKPGSSVILKCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRK 169
LM G+ +I K LE + + + + H + ++ + G L I+ +K
Sbjct: 54 LMTDSFGNYLIQKLLEEVTTEQRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEA 113
Query: 170 QIL-HLISVNAASLSRHRSGNYVVQHVLNLEDP----FLIDAICFALRGHYVDLSLTKCG 224
QI+ + LS+ +GN+V+Q L P F+ DAI + +D++ + G
Sbjct: 114 QIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSC----IDIATHRHG 169
Query: 225 SFVVQKFLKYQNAVHYIVEELLN-SDQILQVAS----DKYGNYVIQTALVETMRQDRLSV 279
V+Q+ L H E+ N D++L + D +GNYV+Q + + +++
Sbjct: 170 CCVLQRCLD-----HGTTEQCDNLCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDY 224
Query: 280 HQRLVTKLQQHLAALRVMKYGSN 302
++V L+ L + K+GSN
Sbjct: 225 THKIVHLLKPRAIELSIHKFGSN 247
Score = 30.4 bits (67), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 22/96 (22%), Positives = 47/96 (48%), Gaps = 1/96 (1%)
Query: 181 SLSRHRSGNYVVQHVLNLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKFLKYQNAVHY 240
SL + + G +Q L++ DAI + + V+L G++++QK L+
Sbjct: 17 SLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVTTEQR 76
Query: 241 IVEELLNSDQILQVASDKYGNYVIQTALVETMRQDR 276
IV ++S ++++ + +G +Q L+E ++ D
Sbjct: 77 IVLTKISSPHFVEISLNPHGTRALQ-KLIECIKTDE 111
>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 = 93.6 bits (231), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 76/282 (26%), Positives = 136/282 (48%), Gaps = 11/282 (3%)
Query: 1 EEGSQYLQEKLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIIL 60
+ G ++LQ++L S+ D +F +T ELM+ +G ++ K +E Q +++
Sbjct: 44 QHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVTTEQ-RIVLT 102
Query: 61 KITFQDQLFLLASVDKFGSSSVKKLIKVVAQSPPLLYHVMSALKRLFKFLMMTKPGSSVI 120
KI+ F+ S++ G+ +++KLI+ + V+ +L+ L G+ VI
Sbjct: 103 KISSPH--FVEISLNPHGTRALQKLIECIKTDEEAQI-VVDSLRPYTVQLSKDLNGNHVI 159
Query: 121 LKCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHLISVNAA 180
KCL+ FI+ A + C+ +A H GC L +D+ + + +
Sbjct: 160 QKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCDNLCDKLLALVD 219
Query: 181 SLSRHRSGNYVVQHVLNLEDP----FLIDAICFALRGHYVDLSLTKCGSFVVQKFLKYQN 236
L+ GNYVVQ+++ E I L+ ++LS+ K GS V++K LK
Sbjct: 220 KLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVIEKILKTAI 279
Query: 237 AVHYIVEELLNS---DQILQVASDKYGNYVIQTALVETMRQD 275
++ E+LN+ I + +D YGNYV+QTAL + +Q+
Sbjct: 280 VSEPMILEILNNGGETGIQSLLNDSYGNYVLQTALDISHKQN 321
Score = 48.9 bits (115), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 49/203 (24%), Positives = 91/203 (44%), Gaps = 19/203 (9%)
Query: 110 LMMTKPGSSVILKCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRK 169
LM G+ +I K LE + + + + H + ++ + G L I+ +K
Sbjct: 76 LMTDSFGNYLIQKLLEEVTTEQRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEA 135
Query: 170 QIL-HLISVNAASLSRHRSGNYVVQHVLNLEDP----FLIDAICFALRGHYVDLSLTKCG 224
QI+ + LS+ +GN+V+Q L P F+ DAI + +D++ + G
Sbjct: 136 QIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSC----IDIATHRHG 191
Query: 225 SFVVQKFLKYQNAVHYIVEELLN-SDQILQVAS----DKYGNYVIQTALVETMRQDRLSV 279
V+Q+ L H E+ N D++L + D +GNYV+Q + + +++
Sbjct: 192 CCVLQRCLD-----HGTTEQCDNLCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDY 246
Query: 280 HQRLVTKLQQHLAALRVMKYGSN 302
++V L+ L + K+GSN
Sbjct: 247 THKIVHLLKPRAIELSIHKFGSN 269
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 22/96 (22%), Positives = 47/96 (48%), Gaps = 1/96 (1%)
Query: 181 SLSRHRSGNYVVQHVLNLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKFLKYQNAVHY 240
SL + + G +Q L++ DAI + + V+L G++++QK L+
Sbjct: 39 SLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVTTEQR 98
Query: 241 IVEELLNSDQILQVASDKYGNYVIQTALVETMRQDR 276
IV ++S ++++ + +G +Q L+E ++ D
Sbjct: 99 IVLTKISSPHFVEISLNPHGTRALQ-KLIECIKTDE 133
>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 = 92.0 bits (227), Expect = 4e-19, Method: Compositional matrix adjust.
Identities = 76/282 (26%), Positives = 135/282 (47%), Gaps = 11/282 (3%)
Query: 1 EEGSQYLQEKLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIIL 60
+ G ++LQ++L S+ D +F +T ELM+ +G ++ K +E Q +++
Sbjct: 22 QHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVTTEQ-RIVLT 80
Query: 61 KITFQDQLFLLASVDKFGSSSVKKLIKVVAQSPPLLYHVMSALKRLFKFLMMTKPGSSVI 120
KI+ F+ S++ G +++KLI+ + V+ +L+ L G+ VI
Sbjct: 81 KISSPH--FVEISLNPHGCRALQKLIECIKTDEEAQI-VVDSLRPYTVQLSKDLNGNHVI 137
Query: 121 LKCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHLISVNAA 180
KCL+ FI+ A + C+ +A H GC L +D+ + + +
Sbjct: 138 QKCLQRLKPENFQFIFDAISDSCIDIATHRHGCRVLQRCLDHGTTEQCDNLCDKLLALVD 197
Query: 181 SLSRHRSGNYVVQHVLNLEDP----FLIDAICFALRGHYVDLSLTKCGSFVVQKFLKYQN 236
L+ GNYVVQ+++ E I L+ ++LS+ K GS V++K LK
Sbjct: 198 KLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVIEKILKTAI 257
Query: 237 AVHYIVEELLNS---DQILQVASDKYGNYVIQTALVETMRQD 275
++ E+LN+ I + +D YGNYV+QTAL + +Q+
Sbjct: 258 VSEPMILEILNNGGETGIQSLLNDSYGNYVLQTALDISHKQN 299
Score = 52.8 bits (125), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 50/203 (24%), Positives = 92/203 (45%), Gaps = 19/203 (9%)
Query: 110 LMMTKPGSSVILKCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRK 169
LM G+ +I K LE + + + + H + ++ + GC L I+ +K
Sbjct: 54 LMTDSFGNYLIQKLLEEVTTEQRIVLTKISSPHFVEISLNPHGCRALQKLIECIKTDEEA 113
Query: 170 QIL-HLISVNAASLSRHRSGNYVVQHVLNLEDP----FLIDAICFALRGHYVDLSLTKCG 224
QI+ + LS+ +GN+V+Q L P F+ DAI + +D++ + G
Sbjct: 114 QIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSC----IDIATHRHG 169
Query: 225 SFVVQKFLKYQNAVHYIVEELLN-SDQILQVAS----DKYGNYVIQTALVETMRQDRLSV 279
V+Q+ L H E+ N D++L + D +GNYV+Q + + +++
Sbjct: 170 CRVLQRCLD-----HGTTEQCDNLCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDY 224
Query: 280 HQRLVTKLQQHLAALRVMKYGSN 302
++V L+ L + K+GSN
Sbjct: 225 THKIVHLLKPRAIELSIHKFGSN 247
Score = 29.3 bits (64), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 22/96 (22%), Positives = 47/96 (48%), Gaps = 1/96 (1%)
Query: 181 SLSRHRSGNYVVQHVLNLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKFLKYQNAVHY 240
SL + + G +Q L++ DAI + + V+L G++++QK L+
Sbjct: 17 SLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVTTEQR 76
Query: 241 IVEELLNSDQILQVASDKYGNYVIQTALVETMRQDR 276
IV ++S ++++ + +G +Q L+E ++ D
Sbjct: 77 IVLTKISSPHFVEISLNPHGCRALQ-KLIECIKTDE 111
>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 = 75.1 bits (183), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 69/311 (22%), Positives = 135/311 (43%), Gaps = 18/311 (5%)
Query: 1 EEGSQYLQEKLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIIL 60
+ GS+++Q+KL +F + ++LM+ +G +V KF E + Q +
Sbjct: 33 QHGSRFIQQKLERATPAERQMVFNEILQAAYQLMTDVFGNYVIQKFFEFGSLDQKLALAT 92
Query: 61 KITFQDQLFLLASVDKFGSSSVKKLIKVVAQSPPLLYHVMSALKRLFKFLMMTKPGSSVI 120
+I L ++ +G ++K ++ ++ ++ ++ L + + G+ V+
Sbjct: 93 RIRGH---VLPLALQMYGCRVIQKALESISSDQQVISEMVKELDGHVLKCVKDQNGNHVV 149
Query: 121 LKCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHLISVNAA 180
KC+E FI A L+ H GC + +++ + IL + +
Sbjct: 150 QKCIECVQPQSLQFIIDAFKGQVFVLSTHPYGCRVIQRILEHCTAEQTLPILEELHQHTE 209
Query: 181 SLSRHRSGNYVVQHVLNLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKFLKYQNAVH- 239
L + + GNYV+QHVL P I +RG + LS K S VV+K + + +
Sbjct: 210 QLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGKVLALSQHKFASNVVEKCVTHASRAER 269
Query: 240 -YIVEELLNSDQ-----ILQVASDKYGNYVIQTALVETMRQDRLSVHQR--LVTKLQQHL 291
+++E+ + + + D+Y NYV+Q + D QR ++ K++ H+
Sbjct: 270 ALLIDEVCCQNDGPHSALYTMMKDQYANYVVQKMI------DMAEPAQRKIIMHKIRPHI 323
Query: 292 AALRVMKYGSN 302
LR YG +
Sbjct: 324 TTLRKYTYGKH 334
Score = 40.8 bits (94), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 50/243 (20%), Positives = 99/243 (40%), Gaps = 18/243 (7%)
Query: 3 GSQYLQEKLSS--GDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIIL 60
G + +Q+ L S D +++ ++ + G + + Q G V K IE L II
Sbjct: 107 GCRVIQKALESISSDQQVISEMVKELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFII- 165
Query: 61 KITFQDQLFLLASVDKFGSSSVKKLIK--VVAQSPPLLYHVMSALKRLFKFLMMTKPGSS 118
F+ Q+F+L S +G ++++++ Q+ P+L L + + L+ + G+
Sbjct: 166 -DAFKGQVFVL-STHPYGCRVIQRILEHCTAEQTLPIL----EELHQHTEQLVQDQYGNY 219
Query: 119 VILKCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHLISVN 178
VI LE I L L+ H+ + + + + R ++ +
Sbjct: 220 VIQHVLEHGRPEDKSKIVSEIRGKVLALSQHKFASNVVEKCVTHASRAERALLIDEVCCQ 279
Query: 179 AA-------SLSRHRSGNYVVQHVLNLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKF 231
++ + + NYVVQ ++++ +P I +R H L G ++ K
Sbjct: 280 NDGPHSALYTMMKDQYANYVVQKMIDMAEPAQRKIIMHKIRPHITTLRKYTYGKHILAKL 339
Query: 232 LKY 234
KY
Sbjct: 340 EKY 342
>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 = 70.9 bits (172), Expect = 9e-13, Method: Compositional matrix adjust.
Identities = 72/317 (22%), Positives = 135/317 (42%), Gaps = 32/317 (10%)
Query: 1 EEGSQYLQEKLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIIL 60
+ GS+++Q+KL +F + ++LM+ +G +V KF E + Q +
Sbjct: 35 QHGSRFIQQKLERATPAERQIVFNEILQAAYQLMTDVFGNYVIQKFFEFGSLDQKLALAT 94
Query: 61 KITFQDQLFLLASVDKFGSSSVKKLIKVVAQS------PPLLYHVMSALKRLFKFLMMTK 114
+I L ++ +G ++K ++ ++ L HV+ +K +
Sbjct: 95 RIRGH---VLPLALQMYGCRVIQKALESISSDQQSEMVKELDGHVLKCVK--------DQ 143
Query: 115 PGSSVILKCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHL 174
G+ V+ KC+E FI A L+ H GC + +++ + IL
Sbjct: 144 NGNHVVQKCIECVQPQSLQFIIDAFKGQVFVLSTHPYGCRVIQRILEHCTAEQTLPILEE 203
Query: 175 ISVNAASLSRHRSGNYVVQHVLNLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKFLKY 234
+ + L + + GNYV+QHVL P I +RG + LS K S VV+K + +
Sbjct: 204 LHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGKVLALSQHKFASNVVEKCVTH 263
Query: 235 QNAVH--YIVEELLNSDQ-----ILQVASDKYGNYVIQTALVETMRQDRLSVHQR--LVT 285
+ +++E+ + + + D+Y NYV+Q + D QR ++
Sbjct: 264 ASRAERALLIDEVCCQNDGPHSALYTMMKDQYANYVVQKMI------DMAEPAQRKIIMH 317
Query: 286 KLQQHLAALRVMKYGSN 302
K++ H+ LR YG +
Sbjct: 318 KIRPHITTLRKYTYGKH 334
Score = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 50/241 (20%), Positives = 96/241 (39%), Gaps = 16/241 (6%)
Query: 3 GSQYLQEKLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIILKI 62
G + +Q+ L S S ++ + G + + Q G V K IE L II
Sbjct: 109 GCRVIQKALESISSDQQSEMVKELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFII--D 166
Query: 63 TFQDQLFLLASVDKFGSSSVKKLIK--VVAQSPPLLYHVMSALKRLFKFLMMTKPGSSVI 120
F+ Q+F+L S +G ++++++ Q+ P+L L + + L+ + G+ VI
Sbjct: 167 AFKGQVFVL-STHPYGCRVIQRILEHCTAEQTLPIL----EELHQHTEQLVQDQYGNYVI 221
Query: 121 LKCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHLISVNAA 180
LE I L L+ H+ + + + + R ++ +
Sbjct: 222 QHVLEHGRPEDKSKIVSEIRGKVLALSQHKFASNVVEKCVTHASRAERALLIDEVCCQND 281
Query: 181 -------SLSRHRSGNYVVQHVLNLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKFLK 233
++ + + NYVVQ ++++ +P I +R H L G ++ K K
Sbjct: 282 GPHSALYTMMKDQYANYVVQKMIDMAEPAQRKIIMHKIRPHITTLRKYTYGKHILAKLEK 341
Query: 234 Y 234
Y
Sbjct: 342 Y 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 = 68.9 bits (167), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 71/302 (23%), Positives = 141/302 (46%), Gaps = 21/302 (6%)
Query: 1 EEGSQYLQEKLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIIL 60
+ GS+++Q+KL + +F + + LM+ +G +V KF E Q + +
Sbjct: 35 QHGSRFIQQKLERATAAEKQMVFSEILAAAYSLMTDVFGNYVIQKFFEFGTPEQKNTLGM 94
Query: 61 KITFQDQLFLLASVDKFGSSSVKKLIKVVAQSPPLLYHVMSALKRLFKFLMMTKPGSSVI 120
++ L ++ +G ++K ++ + SP ++ L + + G+ V+
Sbjct: 95 QVKGH---VLQLALQMYGCRVIQKALESI--SPEQQQEIVHELDGHVLKCVKDQNGNHVV 149
Query: 121 LKCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHLISVNAA 180
KC+E FI A L+ H GC + +++ + IL + +
Sbjct: 150 QKCIECVDPVALQFIINAFKGQVYSLSTHPYGCRVIQRILEHCTAEQTTPILDELHEHTE 209
Query: 181 SLSRHRSGNYVVQHVLN---LED-PFLIDAICFALRGHYVDLSLTKCGSFVVQKFLKYQN 236
L + + GNYV+QHVL ED LI+++ RG + LS K S VV+K + +
Sbjct: 210 QLIQDQYGNYVIQHVLEHGKQEDKSILINSV----RGKVLVLSQHKFASNVVEKCVTHAT 265
Query: 237 AVHY--IVEEL--LNSDQILQVASDKYGNYVIQTALVETMRQDRLSVHQRLVTKLQQHLA 292
+++E+ N + + + D+Y NYV+Q +++ +L ++L+TK+++++A
Sbjct: 266 RGERTGLIDEVCTFNDNALHVMMKDQYANYVVQ-KMIDVSEPTQL---KKLMTKIRKNMA 321
Query: 293 AL 294
AL
Sbjct: 322 AL 323
Score = 61.6 bits (148), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 62/234 (26%), Positives = 113/234 (48%), Gaps = 14/234 (5%)
Query: 73 SVDKFGSSSVK-KLIKVVAQSPPLLYHVMSALKRLFKFLMMTKPGSSVILKCLEPSYNHK 131
S D+ GS ++ KL + A +++ S + LM G+ VI K E +
Sbjct: 32 SQDQHGSRFIQQKLERATAAEKQMVF---SEILAAAYSLMTDVFGNYVIQKFFEFGTPEQ 88
Query: 132 NDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHLISVNAASLSRHRSGNYV 191
+ + H L LA GC + ++++ ++++I+H + + + ++GN+V
Sbjct: 89 KNTLGMQVKGHVLQLALQMYGCRVIQKALESISPEQQQEIVHELDGHVLKCVKDQNGNHV 148
Query: 192 VQHVLNLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKFLKYQNAVHY--IVEEL-LNS 248
VQ + DP + I A +G LS G V+Q+ L++ A I++EL ++
Sbjct: 149 VQKCIECVDPVALQFIINAFKGQVYSLSTHPYGCRVIQRILEHCTAEQTTPILDELHEHT 208
Query: 249 DQILQVASDKYGNYVIQTALVETMRQDRLSVHQRLVTKLQQHLAALRVMKYGSN 302
+Q++Q D+YGNYVIQ L E +Q+ S+ L+ ++ + L K+ SN
Sbjct: 209 EQLIQ---DQYGNYVIQHVL-EHGKQEDKSI---LINSVRGKVLVLSQHKFASN 255
>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 = 67.8 bits (164), Expect = 7e-12, Method: Compositional matrix adjust.
Identities = 73/316 (23%), Positives = 135/316 (42%), Gaps = 30/316 (9%)
Query: 1 EEGSQYLQEKLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIIL 60
+ GS+++Q KL +F + ++LM +G +V KF E + Q +
Sbjct: 33 QHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKFFEFGSLEQKLALAE 92
Query: 61 KITFQDQLFLLASVDKFGSSSVKKLIKVVAQSP------PLLYHVMSALKRLFKFLMMTK 114
+I L ++ +G ++K ++ + L HV+ +K +
Sbjct: 93 RIRGH---VLSLALQMYGCRVIQKALEFIPSDQQNEMVRELDGHVLKCVK--------DQ 141
Query: 115 PGSSVILKCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHL 174
G+ V+ KC+E FI A L+ H GC + +++ + IL
Sbjct: 142 NGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPDQTLPILEE 201
Query: 175 ISVNAASLSRHRSGNYVVQHVLNLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKFLKY 234
+ + L + + GNYV+QHVL P I +RG+ + LS K S VV+K + +
Sbjct: 202 LHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNVVEKCVTH 261
Query: 235 QNAVH--YIVEELLNSDQ-----ILQVASDKYGNYVIQTAL-VETMRQDRLSVHQRLVTK 286
+ +++E+ + + + D+Y NYV+Q + V Q ++ +H K
Sbjct: 262 ASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMIDVAEPGQRKIVMH-----K 316
Query: 287 LQQHLAALRVMKYGSN 302
++ H+A LR YG +
Sbjct: 317 IRPHIATLRKYTYGKH 332
Score = 35.4 bits (80), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 49/241 (20%), Positives = 100/241 (41%), Gaps = 16/241 (6%)
Query: 3 GSQYLQEKLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIILKI 62
G + +Q+ L S +++ + G + + Q G V K IE L II
Sbjct: 107 GCRVIQKALEFIPSDQQNEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFII--D 164
Query: 63 TFQDQLFLLASVDKFGSSSVKKLIK--VVAQSPPLLYHVMSALKRLFKFLMMTKPGSSVI 120
F+ Q+F L S +G ++++++ + Q+ P+L L + + L+ + G+ VI
Sbjct: 165 AFKGQVFAL-STHPYGCRVIQRILEHCLPDQTLPIL----EELHQHTEQLVQDQYGNYVI 219
Query: 121 LKCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQIL-HLISVNA 179
LE I + L L+ H+ + + + + R ++ + ++N
Sbjct: 220 QHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNVVEKCVTHASRTERAVLIDEVCTMND 279
Query: 180 A------SLSRHRSGNYVVQHVLNLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKFLK 233
++ + + NYVVQ ++++ +P + +R H L G ++ K K
Sbjct: 280 GPHSALYTMMKDQYANYVVQKMIDVAEPGQRKIVMHKIRPHIATLRKYTYGKHILAKLEK 339
Query: 234 Y 234
Y
Sbjct: 340 Y 340
>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 = 67.8 bits (164), Expect = 8e-12, Method: Compositional matrix adjust.
Identities = 73/316 (23%), Positives = 135/316 (42%), Gaps = 30/316 (9%)
Query: 1 EEGSQYLQEKLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIIL 60
+ GS+++Q KL +F + ++LM +G +V KF E + Q +
Sbjct: 33 QHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKFFEFGSLEQKLALAE 92
Query: 61 KITFQDQLFLLASVDKFGSSSVKKLIKVVAQSP------PLLYHVMSALKRLFKFLMMTK 114
+I L ++ +G ++K ++ + L HV+ +K +
Sbjct: 93 RIRGH---VLSLALQMYGCRVIQKALEFIPSDQQNEMVRELDGHVLKCVK--------DQ 141
Query: 115 PGSSVILKCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHL 174
G+ V+ KC+E FI A L+ H GC + +++ + IL
Sbjct: 142 NGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPDQTLPILEE 201
Query: 175 ISVNAASLSRHRSGNYVVQHVLNLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKFLKY 234
+ + L + + GNYV+QHVL P I +RG+ + LS K S VV+K + +
Sbjct: 202 LHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNVVEKCVTH 261
Query: 235 QNAVH--YIVEELLNSDQ-----ILQVASDKYGNYVIQTAL-VETMRQDRLSVHQRLVTK 286
+ +++E+ + + + D+Y NYV+Q + V Q ++ +H K
Sbjct: 262 ASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMIDVAEPGQRKIVMH-----K 316
Query: 287 LQQHLAALRVMKYGSN 302
++ H+A LR YG +
Sbjct: 317 IRPHIATLRKYTYGKH 332
Score = 35.4 bits (80), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 49/241 (20%), Positives = 100/241 (41%), Gaps = 16/241 (6%)
Query: 3 GSQYLQEKLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIILKI 62
G + +Q+ L S +++ + G + + Q G V K IE L II
Sbjct: 107 GCRVIQKALEFIPSDQQNEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFII--D 164
Query: 63 TFQDQLFLLASVDKFGSSSVKKLIK--VVAQSPPLLYHVMSALKRLFKFLMMTKPGSSVI 120
F+ Q+F L S +G ++++++ + Q+ P+L L + + L+ + G+ VI
Sbjct: 165 AFKGQVFAL-STHPYGCRVIQRILEHCLPDQTLPIL----EELHQHTEQLVQDQYGNYVI 219
Query: 121 LKCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQIL-HLISVNA 179
LE I + L L+ H+ + + + + R ++ + ++N
Sbjct: 220 QHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNVVEKCVTHASRTERAVLIDEVCTMND 279
Query: 180 A------SLSRHRSGNYVVQHVLNLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKFLK 233
++ + + NYVVQ ++++ +P + +R H L G ++ K K
Sbjct: 280 GPHSALYTMMKDQYANYVVQKMIDVAEPGQRKIVMHKIRPHIATLRKYTYGKHILAKLEK 339
Query: 234 Y 234
Y
Sbjct: 340 Y 340
>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 = 63.9 bits (154), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 71/316 (22%), Positives = 135/316 (42%), Gaps = 30/316 (9%)
Query: 1 EEGSQYLQEKLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIIL 60
+ GS+++Q KL +F + ++LM +G +V KF E + Q +
Sbjct: 34 QHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKFFEFGSLEQKLALAE 93
Query: 61 KITFQDQLFLLASVDKFGSSSVKKLIKVVAQSP------PLLYHVMSALKRLFKFLMMTK 114
+I L ++ +G ++K ++ + L HV+ +K +
Sbjct: 94 RIRGH---VLSLALQMYGCRVIQKALEFIPSDQQNEMVRELDGHVLKCVK--------DQ 142
Query: 115 PGSSVILKCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHL 174
G+ V+ KC+E FI A L+ H GC + +++ + IL
Sbjct: 143 NGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPDQTLPILEE 202
Query: 175 ISVNAASLSRHRSGNYVVQHVLNLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKFLKY 234
+ + L + + G+YV++HVL P I +RG+ + LS K S VV+K + +
Sbjct: 203 LHQHTEQLVQDQYGSYVIRHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNVVEKCVTH 262
Query: 235 QNAVH--YIVEELLNSDQ-----ILQVASDKYGNYVIQTAL-VETMRQDRLSVHQRLVTK 286
+ +++E+ + + + D+Y NYV+Q + V Q ++ +H K
Sbjct: 263 ASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMIDVAEPGQRKIVMH-----K 317
Query: 287 LQQHLAALRVMKYGSN 302
++ H+A LR YG +
Sbjct: 318 IRPHIATLRKYTYGKH 333
Score = 37.0 bits (84), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 50/241 (20%), Positives = 100/241 (41%), Gaps = 16/241 (6%)
Query: 3 GSQYLQEKLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIILKI 62
G + +Q+ L S +++ + G + + Q G V K IE L II
Sbjct: 108 GCRVIQKALEFIPSDQQNEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFII--D 165
Query: 63 TFQDQLFLLASVDKFGSSSVKKLIK--VVAQSPPLLYHVMSALKRLFKFLMMTKPGSSVI 120
F+ Q+F L S +G ++++++ + Q+ P+L L + + L+ + GS VI
Sbjct: 166 AFKGQVFAL-STHPYGCRVIQRILEHCLPDQTLPIL----EELHQHTEQLVQDQYGSYVI 220
Query: 121 LKCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQIL-HLISVNA 179
LE I + L L+ H+ + + + + R ++ + ++N
Sbjct: 221 RHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNVVEKCVTHASRTERAVLIDEVCTMND 280
Query: 180 A------SLSRHRSGNYVVQHVLNLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKFLK 233
++ + + NYVVQ ++++ +P + +R H L G ++ K K
Sbjct: 281 GPHSALYTMMKDQYANYVVQKMIDVAEPGQRKIVMHKIRPHIATLRKYTYGKHILAKLEK 340
Query: 234 Y 234
Y
Sbjct: 341 Y 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 = 52.8 bits (125), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 67/290 (23%), Positives = 131/290 (45%), Gaps = 36/290 (12%)
Query: 1 EEGSQYLQEKLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIIL 60
+ GS+++Q +L++ + + +F + EL + +G +V KF E ++ Q
Sbjct: 40 QHGSRFIQRELATSPASEKEVIFNEIRDDAIELSNDVFGNYVIQKFFEFGSKIQ------ 93
Query: 61 KITFQDQL---FLLASVDKFGSSSVKKLIKVVA--QSPPLLYHVMSALKRLFKFLMMTKP 115
K T DQ S+ + ++K ++ + Q L+ + ++ ++ K +
Sbjct: 94 KNTLVDQFKGNMKQLSLQMYACRVIQKALEYIDSNQRIELVLELSDSVLQMIK----DQN 149
Query: 116 GSSVILKCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHLI 175
G+ VI K +E K FI + H +L+ H GC + ++ ++ IL+ +
Sbjct: 150 GNHVIQKAIETIPIEKLPFILSSLTGHIYHLSTHSYGCRVIQRLLEFGSSEDQESILNEL 209
Query: 176 SVNAASLSRHRSGNYVVQHVLNLEDPF----LID---AICFALRGHYVDLSLTKCGSFVV 228
L + + GNYV+Q+VL +D F ++D I + + V+ S K S VV
Sbjct: 210 KDFIPYLIQDQYGNYVIQYVLQ-QDQFTNKEMVDIKQEIIETVANNVVEYSKHKFASNVV 268
Query: 229 QKFLKY--QNAVHYIVEELLNSDQ-----------ILQVASDKYGNYVIQ 265
+K + Y +N I+ ++L D+ ++ + D++ NYVIQ
Sbjct: 269 EKSILYGSKNQKDLIISKILPRDKNHALNLEDDSPMILMIKDQFANYVIQ 318
Score = 51.6 bits (122), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 41/136 (30%), Positives = 66/136 (48%), Gaps = 4/136 (2%)
Query: 165 GSRRKQILHLISVNAASLSRHRSGNYVVQHVLNLEDPFLIDAICFALRGHYVDLSLTKCG 224
S ++ I + I +A LS GNYV+Q + + +G+ LSL
Sbjct: 55 ASEKEVIFNEIRDDAIELSNDVFGNYVIQKFFEFGSKIQKNTLVDQFKGNMKQLSLQMYA 114
Query: 225 SFVVQKFLKYQNAVHYIVEELLNSDQILQVASDKYGNYVIQTALVETMRQDRLSVHQRLV 284
V+QK L+Y ++ I L SD +LQ+ D+ GN+VIQ A +ET+ ++L ++
Sbjct: 115 CRVIQKALEYIDSNQRIELVLELSDSVLQMIKDQNGNHVIQKA-IETIPIEKLPF---IL 170
Query: 285 TKLQQHLAALRVMKYG 300
+ L H+ L YG
Sbjct: 171 SSLTGHIYHLSTHSYG 186
Score = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 35/155 (22%), Positives = 75/155 (48%), Gaps = 6/155 (3%)
Query: 152 GCINLNNFIDNMKGSRRKQILHLISVNAASLSRHRSGNYVVQHVLNLEDPFLIDAICFAL 211
C + ++ + ++R +++ +S + + + ++GN+V+Q + + I +L
Sbjct: 114 ACRVIQKALEYIDSNQRIELVLELSDSVLQMIKDQNGNHVIQKAIETIPIEKLPFILSSL 173
Query: 212 RGHYVDLSLTKCGSFVVQKFLKYQNAVHYIVEELLNS--DQILQVASDKYGNYVIQTALV 269
GH LS G V+Q+ L++ ++ E +LN D I + D+YGNYVIQ L
Sbjct: 174 TGHIYHLSTHSYGCRVIQRLLEFGSSEDQ--ESILNELKDFIPYLIQDQYGNYVIQYVLQ 231
Query: 270 ET--MRQDRLSVHQRLVTKLQQHLAALRVMKYGSN 302
+ ++ + + Q ++ + ++ K+ SN
Sbjct: 232 QDQFTNKEMVDIKQEIIETVANNVVEYSKHKFASN 266
>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 = 33.5 bits (75), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 34/148 (22%), Positives = 69/148 (46%), Gaps = 7/148 (4%)
Query: 161 DNMKGSRRKQILHLISVNAASLSRHRSGNYVVQHVLNLEDPFLIDAICFAL--RGHYVDL 218
D+ R++++ + IS + + YV+Q L D L + AL + +
Sbjct: 97 DDGYTKRQEKLKNFISSQMTDMCLDKFACYVIQSSLQNMDLSLACKLVQALPRDARLIAI 156
Query: 219 SLTKCGSFVVQKF---LKYQNAVHYIVEELLNSDQILQVASDKYGNYVIQTALVETMRQD 275
+ + + V+QK + +N +IV+ + + + Q+ SDKYG V+QT ++E + D
Sbjct: 157 CVDQNANHVIQKVVAVIPLKNW-EFIVDFVATPEHLRQICSDKYGCRVVQT-IIEKLTAD 214
Query: 276 RLSVHQRLVTKLQQHLAALRVMKYGSNK 303
++V + + A R+M +N+
Sbjct: 215 SMNVDLTSAAQNLRERALQRLMTSVTNR 242
>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 = 31.6 bits (70), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 35/65 (53%), Gaps = 1/65 (1%)
Query: 239 HYIVEELLNSDQILQVASDKYGNYVIQTALVETMRQDRLSVHQRLVTKLQQHLAALRVMK 298
+IV+ + + + Q+ SDKYG V+QT ++E + D ++V + + A R+M
Sbjct: 179 EFIVDFVATPEHLRQICSDKYGCRVVQT-IIEKLTADSMNVDLTSAAQNLRERALQRLMT 237
Query: 299 YGSNK 303
+N+
Sbjct: 238 SVTNR 242
>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 = 31.6 bits (70), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 35/65 (53%), Gaps = 1/65 (1%)
Query: 239 HYIVEELLNSDQILQVASDKYGNYVIQTALVETMRQDRLSVHQRLVTKLQQHLAALRVMK 298
+IV+ + + + Q+ SDKYG V+QT ++E + D ++V + + A R+M
Sbjct: 178 EFIVDFVATPEHLRQICSDKYGCRVVQT-IIEKLTADSMNVDLTSAAQNLRERALQRLMT 236
Query: 299 YGSNK 303
+N+
Sbjct: 237 SVTNR 241
>pdb|4A0C|A Chain A, Structure Of The Cand1-Cul4b-Rbx1 Complex
pdb|4A0C|B Chain B, Structure Of The Cand1-Cul4b-Rbx1 Complex
Length = 1253
Score = 30.8 bits (68), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 32/116 (27%), Positives = 56/116 (48%), Gaps = 11/116 (9%)
Query: 72 ASVDKFGSSSVKKLIKVVAQSPPLLYHVMSALKRLFKFLMMTKP---GSSVILKCLE-PS 127
+S+ K S + +LI +V +SP L +SA+ F+ L++T G +L+ L P
Sbjct: 748 SSLSKISGSILNELIGLV-RSPLLQGGALSAMLDFFQALVVTGTNNLGYMDLLRMLTGPV 806
Query: 128 YN------HKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHLISV 177
Y+ HK + A L AC ++G + FI ++K SR + L+++
Sbjct: 807 YSQSTALTHKQSYYSIAKCVAALTRACPKEGPAVVGQFIQDVKNSRSTDSIRLLAL 862
>pdb|1U6G|C Chain C, Crystal Structure Of The Cand1-Cul1-Roc1 Complex
Length = 1230
Score = 30.8 bits (68), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 32/116 (27%), Positives = 56/116 (48%), Gaps = 11/116 (9%)
Query: 72 ASVDKFGSSSVKKLIKVVAQSPPLLYHVMSALKRLFKFLMMTKP---GSSVILKCLE-PS 127
+S+ K S + +LI +V +SP L +SA+ F+ L++T G +L+ L P
Sbjct: 725 SSLSKISGSILNELIGLV-RSPLLQGGALSAMLDFFQALVVTGTNNLGYMDLLRMLTGPV 783
Query: 128 YN------HKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHLISV 177
Y+ HK + A L AC ++G + FI ++K SR + L+++
Sbjct: 784 YSQSTALTHKQSYYSIAKCVAALTRACPKEGPAVVGQFIQDVKNSRSTDSIRLLAL 839
>pdb|1AP2|B Chain B, Single Chain Fv Of C219
pdb|1AP2|D Chain D, Single Chain Fv Of C219
Length = 123
Score = 28.5 bits (62), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 10/25 (40%), Positives = 17/25 (68%)
Query: 112 MTKPGSSVILKCLEPSYNHKNDFIY 136
+ +PG+SV L C +N K+DF++
Sbjct: 11 LVRPGASVKLSCTASGFNIKDDFMH 35
>pdb|1MVU|B Chain B, Single Chain Fv Of C219 Heavy Chain V101l Mutant In
Complex With Synthetic Epitope Peptide
Length = 121
Score = 28.5 bits (62), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 10/25 (40%), Positives = 17/25 (68%)
Query: 112 MTKPGSSVILKCLEPSYNHKNDFIY 136
+ +PG+SV L C +N K+DF++
Sbjct: 11 LVRPGASVKLSCTASGFNIKDDFMH 35
>pdb|2AP2|B Chain B, Single Chain Fv Of C219 In Complex With Synthetic Epitope
Peptide
pdb|2AP2|D Chain D, Single Chain Fv Of C219 In Complex With Synthetic Epitope
Peptide
Length = 122
Score = 28.5 bits (62), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 10/25 (40%), Positives = 17/25 (68%)
Query: 112 MTKPGSSVILKCLEPSYNHKNDFIY 136
+ +PG+SV L C +N K+DF++
Sbjct: 11 LVRPGASVKLSCTASGFNIKDDFMH 35
>pdb|3V71|A Chain A, Crystal Structure Of Puf-6 In Complex With 5be13 Rna
Length = 382
Score = 27.3 bits (59), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 39/148 (26%), Positives = 65/148 (43%), Gaps = 26/148 (17%)
Query: 144 LYLACHEQ-GCINLNNFIDNMKGSR-------RKQILH----LISVNAASLSRHRSGNYV 191
L C ++ GC + ID + + R Q+LH I N LS + NYV
Sbjct: 174 LMAVCQDKYGCRLVQQVIDRLAENPKLPCFKFRIQLLHSLMTCIVRNCYRLSSNEFANYV 233
Query: 192 VQHVL---NLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQ-KFLKYQNAV-HYIVEELL 246
+Q+V+ + + + I L + + +S K S V++ FL A+ H ++EE+
Sbjct: 234 IQYVIKSSGIMEMYRDTIIDKCLLRNLLSMSQDKYASHVIEGAFLFAPPALLHEMMEEIF 293
Query: 247 ---------NSDQILQVASDKYGNYVIQ 265
N D + + +YGNYV+Q
Sbjct: 294 SGYVKDVESNRDALDILLFHQYGNYVVQ 321
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
0.324 0.137 0.394
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,179,117
Number of Sequences: 62578
Number of extensions: 303283
Number of successful extensions: 1102
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 973
Number of HSP's gapped (non-prelim): 53
length of query: 309
length of database: 14,973,337
effective HSP length: 99
effective length of query: 210
effective length of database: 8,778,115
effective search space: 1843404150
effective search space used: 1843404150
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 51 (24.3 bits)