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= 035754
(335 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 = 100 bits (249), Expect = 1e-21, Method: Compositional matrix adjust.
Identities = 81/289 (28%), Positives = 141/289 (48%), Gaps = 11/289 (3%)
Query: 14 LFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNES 73
+ SL +DQ G ++LQ+ L S+ D +F +T ELM+ +G ++ K +E
Sbjct: 15 IHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVTTE 74
Query: 74 QLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMMT 133
Q +++ KI+ F+ S++ G+ +++KLI+ + V+ +L+ L
Sbjct: 75 Q-RIVLTKISSPH--FVEISLNPHGTRALQKLIECIKTDEEAQI-VVDSLRPYTVQLSKD 130
Query: 134 KPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILH 193
G+ VI +CL+ FI+ A + C+ +A H GC L +D+ + +
Sbjct: 131 LNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCDNLCD 190
Query: 194 LISVNAASLSRHRSGNYVVQHVLSLEDPF----LIDAICFALRGHYVDLSLTKCGSFVVQ 249
+ L+ GNYVVQ++++ E I L+ ++LS+ K GS V++
Sbjct: 191 KLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVIE 250
Query: 250 KCLKYQNAVHYIIEELLNSD---QILQVANDKYGNYVIQTALAETMRQD 295
K LK +I E+LN+ I + ND YGNYV+QTAL + +Q+
Sbjct: 251 KILKTAIVSEPMILEILNNGGETGIQSLLNDSYGNYVLQTALDISHKQN 299
Score = 53.5 bits (127), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 50/204 (24%), Positives = 94/204 (46%), Gaps = 19/204 (9%)
Query: 130 LMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRK 189
LM G+ +I + LE + + + + H + ++ + G L I+ +K
Sbjct: 54 LMTDSFGNYLIQKLLEEVTTEQRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEA 113
Query: 190 QIL-HLISVNAASLSRHRSGNYVVQHVLSLEDP----FLIDAICFALRGHYVDLSLTKCG 244
QI+ + LS+ +GN+V+Q L P F+ DAI + +D++ + G
Sbjct: 114 QIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSC----IDIATHRHG 169
Query: 245 SFVVQKCLKYQNAVHYIIEELLN-SDQILQVAN----DKYGNYVIQTALAETMRQDRLSV 299
V+Q+CL H E+ N D++L + + D +GNYV+Q + + +++
Sbjct: 170 CCVLQRCLD-----HGTTEQCDNLCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDY 224
Query: 300 HQRLVTKLQQHLAALRVMKYGSNV 323
++V L+ L + K+GSNV
Sbjct: 225 THKIVHLLKPRAIELSIHKFGSNV 248
>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 = 100 bits (249), Expect = 1e-21, Method: Compositional matrix adjust.
Identities = 81/289 (28%), Positives = 141/289 (48%), Gaps = 11/289 (3%)
Query: 14 LFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNES 73
+ SL +DQ G ++LQ+ L S+ D +F +T ELM+ +G ++ K +E
Sbjct: 15 IHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVTTE 74
Query: 74 QLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMMT 133
Q +++ KI+ F+ S++ G+ +++KLI+ + V+ +L+ L
Sbjct: 75 Q-RIVLTKISSPH--FVEISLNPHGTRALQKLIECIKTDEEAQI-VVDSLRPYTVQLSKD 130
Query: 134 KPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILH 193
G+ VI +CL+ FI+ A + C+ +A H GC L +D+ + +
Sbjct: 131 LNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCDNLCD 190
Query: 194 LISVNAASLSRHRSGNYVVQHVLSLEDPF----LIDAICFALRGHYVDLSLTKCGSFVVQ 249
+ L+ GNYVVQ++++ E I L+ ++LS+ K GS V++
Sbjct: 191 KLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVIE 250
Query: 250 KCLKYQNAVHYIIEELLNSD---QILQVANDKYGNYVIQTALAETMRQD 295
K LK +I E+LN+ I + ND YGNYV+QTAL + +Q+
Sbjct: 251 KILKTAIVSEPMILEILNNGGETGIQSLLNDSYGNYVLQTALDISHKQN 299
Score = 53.5 bits (127), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 50/204 (24%), Positives = 94/204 (46%), Gaps = 19/204 (9%)
Query: 130 LMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRK 189
LM G+ +I + LE + + + + H + ++ + G L I+ +K
Sbjct: 54 LMTDSFGNYLIQKLLEEVTTEQRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEA 113
Query: 190 QIL-HLISVNAASLSRHRSGNYVVQHVLSLEDP----FLIDAICFALRGHYVDLSLTKCG 244
QI+ + LS+ +GN+V+Q L P F+ DAI + +D++ + G
Sbjct: 114 QIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSC----IDIATHRHG 169
Query: 245 SFVVQKCLKYQNAVHYIIEELLN-SDQILQVAN----DKYGNYVIQTALAETMRQDRLSV 299
V+Q+CL H E+ N D++L + + D +GNYV+Q + + +++
Sbjct: 170 CCVLQRCLD-----HGTTEQCDNLCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDY 224
Query: 300 HQRLVTKLQQHLAALRVMKYGSNV 323
++V L+ L + K+GSNV
Sbjct: 225 THKIVHLLKPRAIELSIHKFGSNV 248
>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 = 100 bits (248), Expect = 1e-21, Method: Compositional matrix adjust.
Identities = 81/289 (28%), Positives = 141/289 (48%), Gaps = 11/289 (3%)
Query: 14 LFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNES 73
+ SL +DQ G ++LQ+ L S+ D +F +T ELM+ +G ++ K +E
Sbjct: 37 IHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVTTE 96
Query: 74 QLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMMT 133
Q +++ KI+ F+ S++ G+ +++KLI+ + V+ +L+ L
Sbjct: 97 Q-RIVLTKISSPH--FVEISLNPHGTRALQKLIECIKTDEEAQI-VVDSLRPYTVQLSKD 152
Query: 134 KPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILH 193
G+ VI +CL+ FI+ A + C+ +A H GC L +D+ + +
Sbjct: 153 LNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCDNLCD 212
Query: 194 LISVNAASLSRHRSGNYVVQHVLSLEDPF----LIDAICFALRGHYVDLSLTKCGSFVVQ 249
+ L+ GNYVVQ++++ E I L+ ++LS+ K GS V++
Sbjct: 213 KLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVIE 272
Query: 250 KCLKYQNAVHYIIEELLNSD---QILQVANDKYGNYVIQTALAETMRQD 295
K LK +I E+LN+ I + ND YGNYV+QTAL + +Q+
Sbjct: 273 KILKTAIVSEPMILEILNNGGETGIQSLLNDSYGNYVLQTALDISHKQN 321
Score = 53.5 bits (127), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 50/204 (24%), Positives = 94/204 (46%), Gaps = 19/204 (9%)
Query: 130 LMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRK 189
LM G+ +I + LE + + + + H + ++ + G L I+ +K
Sbjct: 76 LMTDSFGNYLIQKLLEEVTTEQRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEA 135
Query: 190 QIL-HLISVNAASLSRHRSGNYVVQHVLSLEDP----FLIDAICFALRGHYVDLSLTKCG 244
QI+ + LS+ +GN+V+Q L P F+ DAI + +D++ + G
Sbjct: 136 QIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSC----IDIATHRHG 191
Query: 245 SFVVQKCLKYQNAVHYIIEELLN-SDQILQVAN----DKYGNYVIQTALAETMRQDRLSV 299
V+Q+CL H E+ N D++L + + D +GNYV+Q + + +++
Sbjct: 192 CCVLQRCLD-----HGTTEQCDNLCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDY 246
Query: 300 HQRLVTKLQQHLAALRVMKYGSNV 323
++V L+ L + K+GSNV
Sbjct: 247 THKIVHLLKPRAIELSIHKFGSNV 270
>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 = 98.6 bits (244), Expect = 4e-21, Method: Compositional matrix adjust.
Identities = 81/289 (28%), Positives = 140/289 (48%), Gaps = 11/289 (3%)
Query: 14 LFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNES 73
+ SL +DQ G ++LQ+ L S+ D +F +T ELM+ +G ++ K +E
Sbjct: 15 IHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVTTE 74
Query: 74 QLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMMT 133
Q +++ KI+ F+ S++ G +++KLI+ + V+ +L+ L
Sbjct: 75 Q-RIVLTKISSPH--FVEISLNPHGCRALQKLIECIKTDEEAQI-VVDSLRPYTVQLSKD 130
Query: 134 KPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILH 193
G+ VI +CL+ FI+ A + C+ +A H GC L +D+ + +
Sbjct: 131 LNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCRVLQRCLDHGTTEQCDNLCD 190
Query: 194 LISVNAASLSRHRSGNYVVQHVLSLEDPF----LIDAICFALRGHYVDLSLTKCGSFVVQ 249
+ L+ GNYVVQ++++ E I L+ ++LS+ K GS V++
Sbjct: 191 KLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVIE 250
Query: 250 KCLKYQNAVHYIIEELLNSD---QILQVANDKYGNYVIQTALAETMRQD 295
K LK +I E+LN+ I + ND YGNYV+QTAL + +Q+
Sbjct: 251 KILKTAIVSEPMILEILNNGGETGIQSLLNDSYGNYVLQTALDISHKQN 299
Score = 57.4 bits (137), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 51/204 (25%), Positives = 95/204 (46%), Gaps = 19/204 (9%)
Query: 130 LMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRK 189
LM G+ +I + LE + + + + H + ++ + GC L I+ +K
Sbjct: 54 LMTDSFGNYLIQKLLEEVTTEQRIVLTKISSPHFVEISLNPHGCRALQKLIECIKTDEEA 113
Query: 190 QIL-HLISVNAASLSRHRSGNYVVQHVLSLEDP----FLIDAICFALRGHYVDLSLTKCG 244
QI+ + LS+ +GN+V+Q L P F+ DAI + +D++ + G
Sbjct: 114 QIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSC----IDIATHRHG 169
Query: 245 SFVVQKCLKYQNAVHYIIEELLN-SDQILQVAN----DKYGNYVIQTALAETMRQDRLSV 299
V+Q+CL H E+ N D++L + + D +GNYV+Q + + +++
Sbjct: 170 CRVLQRCLD-----HGTTEQCDNLCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDY 224
Query: 300 HQRLVTKLQQHLAALRVMKYGSNV 323
++V L+ L + K+GSNV
Sbjct: 225 THKIVHLLKPRAIELSIHKFGSNV 248
>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 = 82.8 bits (203), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 72/319 (22%), Positives = 140/319 (43%), Gaps = 18/319 (5%)
Query: 14 LFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNES 73
+ +QDQ GS+++Q+ L +F + ++LM+ +G +V KF E +
Sbjct: 26 IVEFSQDQHGSRFIQQKLERATPAERQMVFNEILQAAYQLMTDVFGNYVIQKFFEFGSLD 85
Query: 74 QLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMMT 133
Q + +I L ++ +G ++K ++ ++ ++ ++ L +
Sbjct: 86 QKLALATRIRGH---VLPLALQMYGCRVIQKALESISSDQQVISEMVKELDGHVLKCVKD 142
Query: 134 KPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILH 193
+ G+ V+ +C+E FI A L+ H GC + +++ + IL
Sbjct: 143 QNGNHVVQKCIECVQPQSLQFIIDAFKGQVFVLSTHPYGCRVIQRILEHCTAEQTLPILE 202
Query: 194 LISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKCLK 253
+ + L + + GNYV+QHVL P I +RG + LS K S VV+KC+
Sbjct: 203 ELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGKVLALSQHKFASNVVEKCVT 262
Query: 254 YQNAVHY--IIEELLNSDQ-----ILQVANDKYGNYVIQTALAETMRQDRLSVHQR--LV 304
+ + +I+E+ + + + D+Y NYV+Q + D QR ++
Sbjct: 263 HASRAERALLIDEVCCQNDGPHSALYTMMKDQYANYVVQKMI------DMAEPAQRKIIM 316
Query: 305 TKLQQHLAALRVMKYGSNV 323
K++ H+ LR YG ++
Sbjct: 317 HKIRPHITTLRKYTYGKHI 335
Score = 37.4 bits (85), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 51/253 (20%), Positives = 100/253 (39%), Gaps = 20/253 (7%)
Query: 14 LFSLAQDQEGSQYLQENLSS--GDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCN 71
+ LA G + +Q+ L S D +++ ++ + G + + Q G V K IE
Sbjct: 98 VLPLALQMYGCRVIQKALESISSDQQVISEMVKELDGHVLKCVKDQNGNHVVQKCIECVQ 157
Query: 72 ESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIK---VVAHLPPLLYHVMSALKRLFK 128
L II F+ Q+F+L S +G ++++++ LP ++ L + +
Sbjct: 158 PQSLQFII--DAFKGQVFVL-STHPYGCRVIQRILEHCTAEQTLP-----ILEELHQHTE 209
Query: 129 FLMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRR 188
L+ + G+ VI LE I L L+ H+ + + + + R
Sbjct: 210 QLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGKVLALSQHKFASNVVEKCVTHASRAER 269
Query: 189 KQILHLISVNAA-------SLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLT 241
++ + ++ + + NYVVQ ++ + +P I +R H L
Sbjct: 270 ALLIDEVCCQNDGPHSALYTMMKDQYANYVVQKMIDMAEPAQRKIIMHKIRPHITTLRKY 329
Query: 242 KCGSFVVQKCLKY 254
G ++ K KY
Sbjct: 330 TYGKHILAKLEKY 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 = 80.5 bits (197), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 75/325 (23%), Positives = 141/325 (43%), Gaps = 32/325 (9%)
Query: 14 LFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNES 73
+ +QDQ GS+++Q+ L +F + ++LM+ +G +V KF E +
Sbjct: 28 IVEFSQDQHGSRFIQQKLERATPAERQIVFNEILQAAYQLMTDVFGNYVIQKFFEFGSLD 87
Query: 74 QLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAH------LPPLLYHVMSALKRLF 127
Q + +I L ++ +G ++K ++ ++ + L HV+ +K
Sbjct: 88 QKLALATRIRGH---VLPLALQMYGCRVIQKALESISSDQQSEMVKELDGHVLKCVK--- 141
Query: 128 KFLMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSR 187
+ G+ V+ +C+E FI A L+ H GC + +++ +
Sbjct: 142 -----DQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFVLSTHPYGCRVIQRILEHCTAEQ 196
Query: 188 RKQILHLISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFV 247
IL + + L + + GNYV+QHVL P I +RG + LS K S V
Sbjct: 197 TLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGKVLALSQHKFASNV 256
Query: 248 VQKCLKYQNAVHY--IIEELLNSDQ-----ILQVANDKYGNYVIQTALAETMRQDRLSVH 300
V+KC+ + + +I+E+ + + + D+Y NYV+Q + D
Sbjct: 257 VEKCVTHASRAERALLIDEVCCQNDGPHSALYTMMKDQYANYVVQKMI------DMAEPA 310
Query: 301 QR--LVTKLQQHLAALRVMKYGSNV 323
QR ++ K++ H+ LR YG ++
Sbjct: 311 QRKIIMHKIRPHITTLRKYTYGKHI 335
>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 = 76.3 bits (186), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 77/325 (23%), Positives = 142/325 (43%), Gaps = 32/325 (9%)
Query: 14 LFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNES 73
+ +QDQ GS+++Q L +F + ++LM +G +V KF E +
Sbjct: 26 IMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKFFEFGSLE 85
Query: 74 QLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAH------LPPLLYHVMSALKRLF 127
Q + +I L ++ +G ++K ++ + + L HV+ +K
Sbjct: 86 QKLALAERIRGH---VLSLALQMYGCRVIQKALEFIPSDQQNEMVRELDGHVLKCVK--- 139
Query: 128 KFLMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSR 187
+ G+ V+ +C+E FI A L+ H GC + +++ +
Sbjct: 140 -----DQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPDQ 194
Query: 188 RKQILHLISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFV 247
IL + + L + + GNYV+QHVL P I +RG+ + LS K S V
Sbjct: 195 TLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNV 254
Query: 248 VQKCLKYQNAVH--YIIEELLNSDQ-----ILQVANDKYGNYVIQTAL--AETMRQDRLS 298
V+KC+ + + +I+E+ + + + D+Y NYV+Q + AE Q ++
Sbjct: 255 VEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMIDVAEPG-QRKIV 313
Query: 299 VHQRLVTKLQQHLAALRVMKYGSNV 323
+H K++ H+A LR YG ++
Sbjct: 314 MH-----KIRPHIATLRKYTYGKHI 333
Score = 38.5 bits (88), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 53/260 (20%), Positives = 104/260 (40%), Gaps = 12/260 (4%)
Query: 2 QTIAFEHCTNHDLFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRF 61
Q +A + SLA G + +Q+ L S +++ + G + + Q G
Sbjct: 86 QKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQNEMVRELDGHVLKCVKDQNGNH 145
Query: 62 VFGKFIESCNESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMS 121
V K IE L II F+ Q+F L S +G ++++++ LP ++
Sbjct: 146 VVQKCIECVQPQSLQFII--DAFKGQVFAL-STHPYGCRVIQRILEHC--LPDQTLPILE 200
Query: 122 ALKRLFKFLMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFID 181
L + + L+ + G+ VI LE I + L L+ H+ + +
Sbjct: 201 ELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNVVEKCVT 260
Query: 182 NMKGSRRKQIL-HLISVNAA------SLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGH 234
+ + R ++ + ++N ++ + + NYVVQ ++ + +P + +R H
Sbjct: 261 HASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMIDVAEPGQRKIVMHKIRPH 320
Query: 235 YVDLSLTKCGSFVVQKCLKY 254
L G ++ K KY
Sbjct: 321 IATLRKYTYGKHILAKLEKY 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 = 76.3 bits (186), Expect = 3e-14, Method: Compositional matrix adjust.
Identities = 76/325 (23%), Positives = 139/325 (42%), Gaps = 32/325 (9%)
Query: 14 LFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNES 73
+ +QDQ GS+++Q L +F + ++LM +G +V KF E +
Sbjct: 26 IMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKFFEFGSLE 85
Query: 74 QLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAH------LPPLLYHVMSALKRLF 127
Q + +I L ++ +G ++K ++ + + L HV+ +K
Sbjct: 86 QKLALAERIRGH---VLSLALQMYGCRVIQKALEFIPSDQQNEMVRELDGHVLKCVK--- 139
Query: 128 KFLMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSR 187
+ G+ V+ +C+E FI A L+ H GC + +++ +
Sbjct: 140 -----DQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPDQ 194
Query: 188 RKQILHLISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFV 247
IL + + L + + GNYV+QHVL P I +RG+ + LS K S V
Sbjct: 195 TLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNV 254
Query: 248 VQKCLKYQNAVH--YIIEELLNSDQ-----ILQVANDKYGNYVIQTALAETMRQDRLSVH 300
V+KC+ + + +I+E+ + + + D+Y NYV+Q + D
Sbjct: 255 VEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMI------DVAEPG 308
Query: 301 QRLVT--KLQQHLAALRVMKYGSNV 323
QR + K++ H+A LR YG ++
Sbjct: 309 QRKIVMHKIRPHIATLRKYTYGKHI 333
Score = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 53/260 (20%), Positives = 104/260 (40%), Gaps = 12/260 (4%)
Query: 2 QTIAFEHCTNHDLFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRF 61
Q +A + SLA G + +Q+ L S +++ + G + + Q G
Sbjct: 86 QKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQNEMVRELDGHVLKCVKDQNGNH 145
Query: 62 VFGKFIESCNESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMS 121
V K IE L II F+ Q+F L S +G ++++++ LP ++
Sbjct: 146 VVQKCIECVQPQSLQFII--DAFKGQVFAL-STHPYGCRVIQRILEHC--LPDQTLPILE 200
Query: 122 ALKRLFKFLMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFID 181
L + + L+ + G+ VI LE I + L L+ H+ + +
Sbjct: 201 ELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNVVEKCVT 260
Query: 182 NMKGSRRKQIL-HLISVNAA------SLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGH 234
+ + R ++ + ++N ++ + + NYVVQ ++ + +P + +R H
Sbjct: 261 HASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMIDVAEPGQRKIVMHKIRPH 320
Query: 235 YVDLSLTKCGSFVVQKCLKY 254
L G ++ K KY
Sbjct: 321 IATLRKYTYGKHILAKLEKY 340
>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 = 75.1 bits (183), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 75/313 (23%), Positives = 147/313 (46%), Gaps = 22/313 (7%)
Query: 10 TNHDLFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIES 69
NH + +QDQ GS+++Q+ L + +F + + LM+ +G +V KF E
Sbjct: 25 ANH-IVEFSQDQHGSRFIQQKLERATAAEKQMVFSEILAAAYSLMTDVFGNYVIQKFFEF 83
Query: 70 CNESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKF 129
Q + +++ L ++ +G ++K ++ ++ P ++ L
Sbjct: 84 GTPEQKNTLGMQVKGH---VLQLALQMYGCRVIQKALESIS--PEQQQEIVHELDGHVLK 138
Query: 130 LMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRK 189
+ + G+ V+ +C+E FI A L+ H GC + +++ +
Sbjct: 139 CVKDQNGNHVVQKCIECVDPVALQFIINAFKGQVYSLSTHPYGCRVIQRILEHCTAEQTT 198
Query: 190 QILHLISVNAASLSRHRSGNYVVQHVLS---LEDP-FLIDAICFALRGHYVDLSLTKCGS 245
IL + + L + + GNYV+QHVL ED LI+++ RG + LS K S
Sbjct: 199 PILDELHEHTEQLIQDQYGNYVIQHVLEHGKQEDKSILINSV----RGKVLVLSQHKFAS 254
Query: 246 FVVQKCLKY--QNAVHYIIEEL--LNSDQILQVANDKYGNYVIQTALAETMRQDRLSVHQ 301
VV+KC+ + + +I+E+ N + + + D+Y NYV+Q + + +L +
Sbjct: 255 NVVEKCVTHATRGERTGLIDEVCTFNDNALHVMMKDQYANYVVQ-KMIDVSEPTQL---K 310
Query: 302 RLVTKLQQHLAAL 314
+L+TK+++++AAL
Sbjct: 311 KLMTKIRKNMAAL 323
Score = 61.6 bits (148), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 53/197 (26%), Positives = 98/197 (49%), Gaps = 10/197 (5%)
Query: 130 LMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRK 189
LM G+ VI + E + + + H L LA GC + ++++ +++
Sbjct: 67 LMTDVFGNYVIQKFFEFGTPEQKNTLGMQVKGHVLQLALQMYGCRVIQKALESISPEQQQ 126
Query: 190 QILHLISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQ 249
+I+H + + + ++GN+VVQ + DP + I A +G LS G V+Q
Sbjct: 127 EIVHELDGHVLKCVKDQNGNHVVQKCIECVDPVALQFIINAFKGQVYSLSTHPYGCRVIQ 186
Query: 250 KCLKYQNAVHY--IIEEL-LNSDQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLVTK 306
+ L++ A I++EL +++Q++Q D+YGNYVIQ L ++D+ S+ L+
Sbjct: 187 RILEHCTAEQTTPILDELHEHTEQLIQ---DQYGNYVIQHVLEHGKQEDK-SI---LINS 239
Query: 307 LQQHLAALRVMKYGSNV 323
++ + L K+ SNV
Sbjct: 240 VRGKVLVLSQHKFASNV 256
>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 = 72.4 bits (176), Expect = 4e-13, Method: Compositional matrix adjust.
Identities = 74/325 (22%), Positives = 139/325 (42%), Gaps = 32/325 (9%)
Query: 14 LFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNES 73
+ +QDQ GS+++Q L +F + ++LM +G +V KF E +
Sbjct: 27 IMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKFFEFGSLE 86
Query: 74 QLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAH------LPPLLYHVMSALKRLF 127
Q + +I L ++ +G ++K ++ + + L HV+ +K
Sbjct: 87 QKLALAERIRGH---VLSLALQMYGCRVIQKALEFIPSDQQNEMVRELDGHVLKCVK--- 140
Query: 128 KFLMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSR 187
+ G+ V+ +C+E FI A L+ H GC + +++ +
Sbjct: 141 -----DQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPDQ 195
Query: 188 RKQILHLISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCGSFV 247
IL + + L + + G+YV++HVL P I +RG+ + LS K S V
Sbjct: 196 TLPILEELHQHTEQLVQDQYGSYVIRHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNV 255
Query: 248 VQKCLKYQNAVH--YIIEELLNSDQ-----ILQVANDKYGNYVIQTALAETMRQDRLSVH 300
V+KC+ + + +I+E+ + + + D+Y NYV+Q + D
Sbjct: 256 VEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMI------DVAEPG 309
Query: 301 QRLVT--KLQQHLAALRVMKYGSNV 323
QR + K++ H+A LR YG ++
Sbjct: 310 QRKIVMHKIRPHIATLRKYTYGKHI 334
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 54/260 (20%), Positives = 104/260 (40%), Gaps = 12/260 (4%)
Query: 2 QTIAFEHCTNHDLFSLAQDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRF 61
Q +A + SLA G + +Q+ L S +++ + G + + Q G
Sbjct: 87 QKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQNEMVRELDGHVLKCVKDQNGNH 146
Query: 62 VFGKFIESCNESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAHLPPLLYHVMS 121
V K IE L II F+ Q+F L S +G ++++++ LP ++
Sbjct: 147 VVQKCIECVQPQSLQFII--DAFKGQVFAL-STHPYGCRVIQRILEHC--LPDQTLPILE 201
Query: 122 ALKRLFKFLMMTKPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFID 181
L + + L+ + GS VI LE I + L L+ H+ + +
Sbjct: 202 ELHQHTEQLVQDQYGSYVIRHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNVVEKCVT 261
Query: 182 NMKGSRRKQIL-HLISVNAA------SLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGH 234
+ + R ++ + ++N ++ + + NYVVQ ++ + +P + +R H
Sbjct: 262 HASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMIDVAEPGQRKIVMHKIRPH 321
Query: 235 YVDLSLTKCGSFVVQKCLKY 254
L G ++ K KY
Sbjct: 322 IATLRKYTYGKHILAKLEKY 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 = 54.3 bits (129), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 68/292 (23%), Positives = 131/292 (44%), Gaps = 36/292 (12%)
Query: 19 QDQEGSQYLQENLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALI 78
+DQ GS+++Q L++ + + +F + EL + +G +V KF E ++ Q
Sbjct: 38 KDQHGSRFIQRELATSPASEKEVIFNEIRDDAIELSNDVFGNYVIQKFFEFGSKIQ---- 93
Query: 79 ILKITFQDQL---FLLASVDKFGSSSVKKLIKVVA--HLPPLLYHVMSALKRLFKFLMMT 133
K T DQ S+ + ++K ++ + L+ + ++ ++ K
Sbjct: 94 --KNTLVDQFKGNMKQLSLQMYACRVIQKALEYIDSNQRIELVLELSDSVLQMIK----D 147
Query: 134 KPGSSVILQCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILH 193
+ G+ VI + +E K FI + H +L+ H GC + ++ ++ IL+
Sbjct: 148 QNGNHVIQKAIETIPIEKLPFILSSLTGHIYHLSTHSYGCRVIQRLLEFGSSEDQESILN 207
Query: 194 LISVNAASLSRHRSGNYVVQHVLSLEDPF----LID---AICFALRGHYVDLSLTKCGSF 246
+ L + + GNYV+Q+VL +D F ++D I + + V+ S K S
Sbjct: 208 ELKDFIPYLIQDQYGNYVIQYVLQ-QDQFTNKEMVDIKQEIIETVANNVVEYSKHKFASN 266
Query: 247 VVQKCLKY--QNAVHYIIEELLNSDQ-----------ILQVANDKYGNYVIQ 285
VV+K + Y +N II ++L D+ ++ + D++ NYVIQ
Sbjct: 267 VVEKSILYGSKNQKDLIISKILPRDKNHALNLEDDSPMILMIKDQFANYVIQ 318
Score = 52.4 bits (124), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 42/139 (30%), Positives = 67/139 (48%), Gaps = 4/139 (2%)
Query: 185 GSRRKQILHLISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFALRGHYVDLSLTKCG 244
S ++ I + I +A LS GNYV+Q + + +G+ LSL
Sbjct: 55 ASEKEVIFNEIRDDAIELSNDVFGNYVIQKFFEFGSKIQKNTLVDQFKGNMKQLSLQMYA 114
Query: 245 SFVVQKCLKYQNAVHYIIEELLNSDQILQVANDKYGNYVIQTALAETMRQDRLSVHQRLV 304
V+QK L+Y ++ I L SD +LQ+ D+ GN+VIQ A+ ET+ ++L ++
Sbjct: 115 CRVIQKALEYIDSNQRIELVLELSDSVLQMIKDQNGNHVIQKAI-ETIPIEKLPF---IL 170
Query: 305 TKLQQHLAALRVMKYGSNV 323
+ L H+ L YG V
Sbjct: 171 SSLTGHIYHLSTHSYGCRV 189
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 36/160 (22%), Positives = 78/160 (48%), Gaps = 6/160 (3%)
Query: 172 GCINLNNFIDNMKGSRRKQILHLISVNAASLSRHRSGNYVVQHVLSLEDPFLIDAICFAL 231
C + ++ + ++R +++ +S + + + ++GN+V+Q + + I +L
Sbjct: 114 ACRVIQKALEYIDSNQRIELVLELSDSVLQMIKDQNGNHVIQKAIETIPIEKLPFILSSL 173
Query: 232 RGHYVDLSLTKCGSFVVQKCLKYQNAVHYIIEELLNS--DQILQVANDKYGNYVIQTALA 289
GH LS G V+Q+ L++ ++ E +LN D I + D+YGNYVIQ L
Sbjct: 174 TGHIYHLSTHSYGCRVIQRLLEFGSSEDQ--ESILNELKDFIPYLIQDQYGNYVIQYVLQ 231
Query: 290 ET--MRQDRLSVHQRLVTKLQQHLAALRVMKYGSNVYKWT 327
+ ++ + + Q ++ + ++ K+ SNV + +
Sbjct: 232 QDQFTNKEMVDIKQEIIETVANNVVEYSKHKFASNVVEKS 271
>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 = 29.6 bits (65), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 30/57 (52%), Gaps = 4/57 (7%)
Query: 259 HYIIEELLNSDQILQVANDKYGNYVIQTAL----AETMRQDRLSVHQRLVTKLQQHL 311
+I++ + + + Q+ +DKYG V+QT + A++M D S Q L + Q L
Sbjct: 179 EFIVDFVATPEHLRQICSDKYGCRVVQTIIEKLTADSMNVDLTSAAQNLRERALQRL 235
>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 = 29.6 bits (65), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 30/57 (52%), Gaps = 4/57 (7%)
Query: 259 HYIIEELLNSDQILQVANDKYGNYVIQTAL----AETMRQDRLSVHQRLVTKLQQHL 311
+I++ + + + Q+ +DKYG V+QT + A++M D S Q L + Q L
Sbjct: 178 EFIVDFVATPEHLRQICSDKYGCRVVQTIIEKLTADSMNVDLTSAAQNLRERALQRL 234
>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 = 28.1 bits (61), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 10/25 (40%), Positives = 17/25 (68%)
Query: 132 MTKPGSSVILQCLEPSYNHKNDFIY 156
+ +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 = 28.1 bits (61), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 10/25 (40%), Positives = 17/25 (68%)
Query: 132 MTKPGSSVILQCLEPSYNHKNDFIY 156
+ +PG+SV L C +N K+DF++
Sbjct: 11 LVRPGASVKLSCTASGFNIKDDFMH 35
>pdb|1AP2|B Chain B, Single Chain Fv Of C219
pdb|1AP2|D Chain D, Single Chain Fv Of C219
Length = 123
Score = 28.1 bits (61), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 10/25 (40%), Positives = 17/25 (68%)
Query: 132 MTKPGSSVILQCLEPSYNHKNDFIY 156
+ +PG+SV L C +N K+DF++
Sbjct: 11 LVRPGASVKLSCTASGFNIKDDFMH 35
>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 = 28.1 bits (61), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 31/116 (26%), Positives = 54/116 (46%), Gaps = 11/116 (9%)
Query: 92 ASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMMTKP---GSSVILQCLE-PS 147
+S+ K S + +LI +V P L +SA+ F+ L++T G +L+ L P
Sbjct: 748 SSLSKISGSILNELIGLVRS-PLLQGGALSAMLDFFQALVVTGTNNLGYMDLLRMLTGPV 806
Query: 148 YN------HKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHLISV 197
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 = 28.1 bits (61), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 31/116 (26%), Positives = 54/116 (46%), Gaps = 11/116 (9%)
Query: 92 ASVDKFGSSSVKKLIKVVAHLPPLLYHVMSALKRLFKFLMMTKP---GSSVILQCLE-PS 147
+S+ K S + +LI +V P L +SA+ F+ L++T G +L+ L P
Sbjct: 725 SSLSKISGSILNELIGLVRS-PLLQGGALSAMLDFFQALVVTGTNNLGYMDLLRMLTGPV 783
Query: 148 YN------HKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHLISV 197
Y+ HK + A L AC ++G + FI ++K SR + L+++
Sbjct: 784 YSQSTALTHKQSYYSIAKCVAALTRACPKEGPAVVGQFIQDVKNSRSTDSIRLLAL 839
>pdb|3V71|A Chain A, Crystal Structure Of Puf-6 In Complex With 5be13 Rna
Length = 382
Score = 27.7 bits (60), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 36/152 (23%), Positives = 65/152 (42%), Gaps = 26/152 (17%)
Query: 164 LYLACHEQ-GCINLNNFIDNMKGSR-------RKQILH----LISVNAASLSRHRSGNYV 211
L C ++ GC + ID + + R Q+LH I N LS + NYV
Sbjct: 174 LMAVCQDKYGCRLVQQVIDRLAENPKLPCFKFRIQLLHSLMTCIVRNCYRLSSNEFANYV 233
Query: 212 VQHVL---SLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKCLKYQNA--VHYIIEELL 266
+Q+V+ + + + I L + + +S K S V++ + +H ++EE+
Sbjct: 234 IQYVIKSSGIMEMYRDTIIDKCLLRNLLSMSQDKYASHVIEGAFLFAPPALLHEMMEEIF 293
Query: 267 ---------NSDQILQVANDKYGNYVIQTALA 289
N D + + +YGNYV+Q ++
Sbjct: 294 SGYVKDVESNRDALDILLFHQYGNYVVQQMIS 325
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
0.325 0.137 0.406
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,025,494
Number of Sequences: 62578
Number of extensions: 334926
Number of successful extensions: 1317
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1178
Number of HSP's gapped (non-prelim): 48
length of query: 335
length of database: 14,973,337
effective HSP length: 99
effective length of query: 236
effective length of database: 8,778,115
effective search space: 2071635140
effective search space used: 2071635140
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 52 (24.6 bits)