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= 005600
(688 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 342 bits (877), Expect = 4e-94, Method: Compositional matrix adjust.
Identities = 166/283 (58%), Positives = 216/283 (76%), Gaps = 1/283 (0%)
Query: 387 FLEELKSSNAQKFELSDIAGRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPHASK 446
LE+ +++ +L D+ G IVEFS DQHGSRFIQQKLE + E+ VF E+L A +
Sbjct: 7 LLEDFRNNRFPNLQLRDLIGHIVEFSQDQHGSRFIQQKLERATPAERQIVFNEILQAAYQ 66
Query: 447 LMTDVFGNYVIQKFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQKS 506
LMTDVFGNYVIQKFFE GS DQ+ LA ++ G VLPL+LQMYGCRVIQKALE I Q+S
Sbjct: 67 LMTDVFGNYVIQKFFEFGSLDQKLALATRIRGHVLPLALQMYGCRVIQKALESISSDQQS 126
Query: 507 QLVLELDGHVMRCVRDQNGNHVIQKCIECVPAEKIEFIISAFRGQVATLSTHPYGCRVIQ 566
++V ELDGHV++CV+DQNGNHV+QKCIECV + ++FII AF+GQV LSTHPYGCRVIQ
Sbjct: 127 EMVKELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFVLSTHPYGCRVIQ 186
Query: 567 RVLEHCSDEQQGQCIVDEILESAFALAQDQYGNYVTQHVLERGKSYERTQILSKLAGKIV 626
R+LEHC+ EQ I++E+ + L QDQYGNYV QHVLE G+ ++++I+S++ GK++
Sbjct: 187 RILEHCTAEQTLP-ILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGKVL 245
Query: 627 QMSQHKYASNVVEKCLEYGDTAERELLIEEILGQSEENDNLLY 669
+SQHK+ASNVVEKC+ + AER LLI+E+ Q++ + LY
Sbjct: 246 ALSQHKFASNVVEKCVTHASRAERALLIDEVCCQNDGPHSALY 288
>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 = 337 bits (865), Expect = 1e-92, Method: Compositional matrix adjust.
Identities = 166/285 (58%), Positives = 216/285 (75%), Gaps = 3/285 (1%)
Query: 387 FLEELKSSNAQKFELSDIAGRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPHASK 446
LE+ +++ +L D+ G IVEFS DQHGSRFIQQKLE + E+ VF E+L A +
Sbjct: 5 LLEDFRNNRFPNLQLRDLIGHIVEFSQDQHGSRFIQQKLERATPAERQMVFNEILQAAYQ 64
Query: 447 LMTDVFGNYVIQKFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQK- 505
LMTDVFGNYVIQKFFE GS DQ+ LA ++ G VLPL+LQMYGCRVIQKALE I Q+
Sbjct: 65 LMTDVFGNYVIQKFFEFGSLDQKLALATRIRGHVLPLALQMYGCRVIQKALESISSDQQV 124
Query: 506 -SQLVLELDGHVMRCVRDQNGNHVIQKCIECVPAEKIEFIISAFRGQVATLSTHPYGCRV 564
S++V ELDGHV++CV+DQNGNHV+QKCIECV + ++FII AF+GQV LSTHPYGCRV
Sbjct: 125 ISEMVKELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFVLSTHPYGCRV 184
Query: 565 IQRVLEHCSDEQQGQCIVDEILESAFALAQDQYGNYVTQHVLERGKSYERTQILSKLAGK 624
IQR+LEHC+ EQ I++E+ + L QDQYGNYV QHVLE G+ ++++I+S++ GK
Sbjct: 185 IQRILEHCTAEQTLP-ILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGK 243
Query: 625 IVQMSQHKYASNVVEKCLEYGDTAERELLIEEILGQSEENDNLLY 669
++ +SQHK+ASNVVEKC+ + AER LLI+E+ Q++ + LY
Sbjct: 244 VLALSQHKFASNVVEKCVTHASRAERALLIDEVCCQNDGPHSALY 288
>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 = 332 bits (851), Expect = 4e-91, Method: Compositional matrix adjust.
Identities = 164/283 (57%), Positives = 209/283 (73%), Gaps = 4/283 (1%)
Query: 387 FLEELKSSNAQKFELSDIAGRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPHASK 446
LE+ ++ +L D+A IVEFS DQHGSRFIQQKLE +A EK VF E+L A
Sbjct: 7 LLEDFRNQRYPNLQLRDLANHIVEFSQDQHGSRFIQQKLERATAAEKQMVFSEILAAAYS 66
Query: 447 LMTDVFGNYVIQKFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQKS 506
LMTDVFGNYVIQKFFE G+P+Q+ L ++ G VL L+LQMYGCRVIQKALE I Q+
Sbjct: 67 LMTDVFGNYVIQKFFEFGTPEQKNTLGMQVKGHVLQLALQMYGCRVIQKALESISPEQQQ 126
Query: 507 QLVLELDGHVMRCVRDQNGNHVIQKCIECVPAEKIEFIISAFRGQVATLSTHPYGCRVIQ 566
++V ELDGHV++CV+DQNGNHV+QKCIECV ++FII+AF+GQV +LSTHPYGCRVIQ
Sbjct: 127 EIVHELDGHVLKCVKDQNGNHVVQKCIECVDPVALQFIINAFKGQVYSLSTHPYGCRVIQ 186
Query: 567 RVLEHCSDEQQGQCIVDEILESAFALAQDQYGNYVTQHVLERGKSYERTQILSKLAGKIV 626
R+LEHC+ EQ I+DE+ E L QDQYGNYV QHVLE GK +++ +++ + GK++
Sbjct: 187 RILEHCTAEQTTP-ILDELHEHTEQLIQDQYGNYVIQHVLEHGKQEDKSILINSVRGKVL 245
Query: 627 QMSQHKYASNVVEKCLEYGDTAERELLIEEILGQSEENDNLLY 669
+SQHK+ASNVVEKC+ + ER LI+E+ NDN L+
Sbjct: 246 VLSQHKFASNVVEKCVTHATRGERTGLIDEV---CTFNDNALH 285
Score = 84.7 bits (208), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 48/164 (29%), Positives = 88/164 (53%), Gaps = 4/164 (2%)
Query: 396 AQKFELSDIAGRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPHASKLMTDVFGNY 455
A +F ++ G++ S +G R IQ+ LEHC+AE+ + E+ H +L+ D +GNY
Sbjct: 160 ALQFIINAFKGQVYSLSTHPYGCRVIQRILEHCTAEQTTPILDELHEHTEQLIQDQYGNY 219
Query: 456 VIQKFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQKSQLVLEL--- 512
VIQ EHG + + L + G+VL LS + V++K + +++ L+ E+
Sbjct: 220 VIQHVLEHGKQEDKSILINSVRGKVLVLSQHKFASNVVEKCVTHATRGERTGLIDEVCTF 279
Query: 513 -DGHVMRCVRDQNGNHVIQKCIECVPAEKIEFIISAFRGQVATL 555
D + ++DQ N+V+QK I+ +++ +++ R +A L
Sbjct: 280 NDNALHVMMKDQYANYVVQKMIDVSEPTQLKKLMTKIRKNMAAL 323
Score = 32.0 bits (71), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 19/93 (20%), Positives = 44/93 (47%)
Query: 567 RVLEHCSDEQQGQCIVDEILESAFALAQDQYGNYVTQHVLERGKSYERTQILSKLAGKIV 626
R+LE +++ + ++ +QDQ+G+ Q LER + E+ + S++
Sbjct: 6 RLLEDFRNQRYPNLQLRDLANHIVEFSQDQHGSRFIQQKLERATAAEKQMVFSEILAAAY 65
Query: 627 QMSQHKYASNVVEKCLEYGDTAERELLIEEILG 659
+ + + V++K E+G ++ L ++ G
Sbjct: 66 SLMTDVFGNYVIQKFFEFGTPEQKNTLGMQVKG 98
>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 = 322 bits (824), Expect = 6e-88, Method: Compositional matrix adjust.
Identities = 156/283 (55%), Positives = 211/283 (74%), Gaps = 1/283 (0%)
Query: 387 FLEELKSSNAQKFELSDIAGRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPHASK 446
LE+ +++ +L +IAG I+EFS DQHGSRFIQ KLE + E+ VF E+L A +
Sbjct: 5 LLEDFRNNRYPNLQLREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQ 64
Query: 447 LMTDVFGNYVIQKFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQKS 506
LM DVFGNYVIQKFFE GS +Q+ LAE++ G VL L+LQMYGCRVIQKALE I Q++
Sbjct: 65 LMVDVFGNYVIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQN 124
Query: 507 QLVLELDGHVMRCVRDQNGNHVIQKCIECVPAEKIEFIISAFRGQVATLSTHPYGCRVIQ 566
++V ELDGHV++CV+DQNGNHV+QKCIECV + ++FII AF+GQV LSTHPYGCRVIQ
Sbjct: 125 EMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQ 184
Query: 567 RVLEHCSDEQQGQCIVDEILESAFALAQDQYGNYVTQHVLERGKSYERTQILSKLAGKIV 626
R+LEHC +Q I++E+ + L QDQYGNYV QHVLE G+ ++++I++++ G ++
Sbjct: 185 RILEHCLPDQTLP-ILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVL 243
Query: 627 QMSQHKYASNVVEKCLEYGDTAERELLIEEILGQSEENDNLLY 669
+SQHK+ASNVVEKC+ + ER +LI+E+ ++ + LY
Sbjct: 244 VLSQHKFASNVVEKCVTHASRTERAVLIDEVCTMNDGPHSALY 286
Score = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 27/102 (26%), Positives = 50/102 (49%), Gaps = 7/102 (6%)
Query: 401 LSDIAGRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVL-----PHAS--KLMTDVFG 453
+++I G ++ S + S +++ + H S E+ + EV PH++ +M D +
Sbjct: 235 VAEIRGNVLVLSQHKFASNVVEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYA 294
Query: 454 NYVIQKFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQK 495
NYV+QK + P QRK + K+ + L YG ++ K
Sbjct: 295 NYVVQKMIDVAEPGQRKIVMHKIRPHIATLRKYTYGKHILAK 336
Score = 35.8 bits (81), Expect = 0.077, Method: Compositional matrix adjust.
Identities = 24/93 (25%), Positives = 43/93 (46%)
Query: 567 RVLEHCSDEQQGQCIVDEILESAFALAQDQYGNYVTQHVLERGKSYERTQILSKLAGKIV 626
R+LE + + + EI +QDQ+G+ Q LER ER + +++
Sbjct: 4 RLLEDFRNNRYPNLQLREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAY 63
Query: 627 QMSQHKYASNVVEKCLEYGDTAERELLIEEILG 659
Q+ + + V++K E+G ++ L E I G
Sbjct: 64 QLMVDVFGNYVIQKFFEFGSLEQKLALAERIRG 96
>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 = 321 bits (823), Expect = 8e-88, Method: Compositional matrix adjust.
Identities = 156/283 (55%), Positives = 211/283 (74%), Gaps = 1/283 (0%)
Query: 387 FLEELKSSNAQKFELSDIAGRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPHASK 446
LE+ +++ +L +IAG I+EFS DQHGSRFIQ KLE + E+ VF E+L A +
Sbjct: 5 LLEDFRNNRYPNLQLREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQ 64
Query: 447 LMTDVFGNYVIQKFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQKS 506
LM DVFGNYVIQKFFE GS +Q+ LAE++ G VL L+LQMYGCRVIQKALE I Q++
Sbjct: 65 LMVDVFGNYVIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQN 124
Query: 507 QLVLELDGHVMRCVRDQNGNHVIQKCIECVPAEKIEFIISAFRGQVATLSTHPYGCRVIQ 566
++V ELDGHV++CV+DQNGNHV+QKCIECV + ++FII AF+GQV LSTHPYGCRVIQ
Sbjct: 125 EMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQ 184
Query: 567 RVLEHCSDEQQGQCIVDEILESAFALAQDQYGNYVTQHVLERGKSYERTQILSKLAGKIV 626
R+LEHC +Q I++E+ + L QDQYGNYV QHVLE G+ ++++I++++ G ++
Sbjct: 185 RILEHCLPDQTLP-ILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVL 243
Query: 627 QMSQHKYASNVVEKCLEYGDTAERELLIEEILGQSEENDNLLY 669
+SQHK+ASNVVEKC+ + ER +LI+E+ ++ + LY
Sbjct: 244 VLSQHKFASNVVEKCVTHASRTERAVLIDEVCTMNDGPHSALY 286
Score = 45.4 bits (106), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 27/102 (26%), Positives = 50/102 (49%), Gaps = 7/102 (6%)
Query: 401 LSDIAGRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVL-----PHAS--KLMTDVFG 453
+++I G ++ S + S +++ + H S E+ + EV PH++ +M D +
Sbjct: 235 VAEIRGNVLVLSQHKFASNVVEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYA 294
Query: 454 NYVIQKFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQK 495
NYV+QK + P QRK + K+ + L YG ++ K
Sbjct: 295 NYVVQKMIDVAEPGQRKIVMHKIRPHIATLRKYTYGKHILAK 336
Score = 36.2 bits (82), Expect = 0.071, Method: Compositional matrix adjust.
Identities = 24/93 (25%), Positives = 43/93 (46%)
Query: 567 RVLEHCSDEQQGQCIVDEILESAFALAQDQYGNYVTQHVLERGKSYERTQILSKLAGKIV 626
R+LE + + + EI +QDQ+G+ Q LER ER + +++
Sbjct: 4 RLLEDFRNNRYPNLQLREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAY 63
Query: 627 QMSQHKYASNVVEKCLEYGDTAERELLIEEILG 659
Q+ + + V++K E+G ++ L E I G
Sbjct: 64 QLMVDVFGNYVIQKFFEFGSLEQKLALAERIRG 96
>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 = 318 bits (814), Expect = 9e-87, Method: Compositional matrix adjust.
Identities = 154/283 (54%), Positives = 211/283 (74%), Gaps = 1/283 (0%)
Query: 387 FLEELKSSNAQKFELSDIAGRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPHASK 446
LE+ +++ +L +IAG I+EFS DQHGSRFIQ KLE + E+ VF E+L A +
Sbjct: 6 LLEDFRNNRYPNLQLREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQ 65
Query: 447 LMTDVFGNYVIQKFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQKS 506
LM DVFGNYVIQKFFE GS +Q+ LAE++ G VL L+LQMYGCRVIQKALE I Q++
Sbjct: 66 LMVDVFGNYVIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQN 125
Query: 507 QLVLELDGHVMRCVRDQNGNHVIQKCIECVPAEKIEFIISAFRGQVATLSTHPYGCRVIQ 566
++V ELDGHV++CV+DQNGNHV+QKCIECV + ++FII AF+GQV LSTHPYGCRVIQ
Sbjct: 126 EMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQ 185
Query: 567 RVLEHCSDEQQGQCIVDEILESAFALAQDQYGNYVTQHVLERGKSYERTQILSKLAGKIV 626
R+LEHC +Q I++E+ + L QDQYG+YV +HVLE G+ ++++I++++ G ++
Sbjct: 186 RILEHCLPDQTLP-ILEELHQHTEQLVQDQYGSYVIRHVLEHGRPEDKSKIVAEIRGNVL 244
Query: 627 QMSQHKYASNVVEKCLEYGDTAERELLIEEILGQSEENDNLLY 669
+SQHK+ASNVVEKC+ + ER +LI+E+ ++ + LY
Sbjct: 245 VLSQHKFASNVVEKCVTHASRTERAVLIDEVCTMNDGPHSALY 287
Score = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 27/102 (26%), Positives = 50/102 (49%), Gaps = 7/102 (6%)
Query: 401 LSDIAGRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVL-----PHAS--KLMTDVFG 453
+++I G ++ S + S +++ + H S E+ + EV PH++ +M D +
Sbjct: 236 VAEIRGNVLVLSQHKFASNVVEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYA 295
Query: 454 NYVIQKFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQK 495
NYV+QK + P QRK + K+ + L YG ++ K
Sbjct: 296 NYVVQKMIDVAEPGQRKIVMHKIRPHIATLRKYTYGKHILAK 337
Score = 36.2 bits (82), Expect = 0.067, Method: Compositional matrix adjust.
Identities = 24/93 (25%), Positives = 43/93 (46%)
Query: 567 RVLEHCSDEQQGQCIVDEILESAFALAQDQYGNYVTQHVLERGKSYERTQILSKLAGKIV 626
R+LE + + + EI +QDQ+G+ Q LER ER + +++
Sbjct: 5 RLLEDFRNNRYPNLQLREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAY 64
Query: 627 QMSQHKYASNVVEKCLEYGDTAERELLIEEILG 659
Q+ + + V++K E+G ++ L E I G
Sbjct: 65 QLMVDVFGNYVIQKFFEFGSLEQKLALAERIRG 97
>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 = 256 bits (653), Expect = 4e-68, Method: Compositional matrix adjust.
Identities = 140/301 (46%), Positives = 197/301 (65%), Gaps = 15/301 (4%)
Query: 401 LSDIAGRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPHASKLMTDVFGNYVIQKF 460
L DI G +EF DQHGSRFIQ++L A EK +F E+ A +L DVFGNYVIQKF
Sbjct: 26 LKDIFGHSLEFCKDQHGSRFIQRELATSPASEKEVIFNEIRDDAIELSNDVFGNYVIQKF 85
Query: 461 FEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQKSQLVLELDGHVMRCV 520
FE GS Q+ L ++ G + LSLQMY CRVIQKALE I+ +Q+ +LVLEL V++ +
Sbjct: 86 FEFGSKIQKNTLVDQFKGNMKQLSLQMYACRVIQKALEYIDSNQRIELVLELSDSVLQMI 145
Query: 521 RDQNGNHVIQKCIECVPAEKIEFIISAFRGQVATLSTHPYGCRVIQRVLEHCSDEQQGQC 580
+DQNGNHVIQK IE +P EK+ FI+S+ G + LSTH YGCRVIQR+LE S E Q +
Sbjct: 146 KDQNGNHVIQKAIETIPIEKLPFILSSLTGHIYHLSTHSYGCRVIQRLLEFGSSEDQ-ES 204
Query: 581 IVDEILESAFALAQDQYGNYVTQHVLERGKSYERT------QILSKLAGKIVQMSQHKYA 634
I++E+ + L QDQYGNYV Q+VL++ + + +I+ +A +V+ S+HK+A
Sbjct: 205 ILNELKDFIPYLIQDQYGNYVIQYVLQQDQFTNKEMVDIKQEIIETVANNVVEYSKHKFA 264
Query: 635 SNVVEKCLEYGDTAERELLIEEILGQSE------ENDN--LLYYKSRLAGSMLICLTSWT 686
SNVVEK + YG +++L+I +IL + + E+D+ +L K + A ++ L + +
Sbjct: 265 SNVVEKSILYGSKNQKDLIISKILPRDKNHALNLEDDSPMILMIKDQFANYVIQKLVNVS 324
Query: 687 E 687
E
Sbjct: 325 E 325
Score = 67.4 bits (163), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 49/177 (27%), Positives = 83/177 (46%), Gaps = 19/177 (10%)
Query: 399 FELSDIAGRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPHASKLMTDVFGNYVIQ 458
F LS + G I S +G R IQ+ LE S+E++ S+ E+ L+ D +GNYVIQ
Sbjct: 168 FILSSLTGHIYHLSTHSYGCRVIQRLLEFGSSEDQESILNELKDFIPYLIQDQYGNYVIQ 227
Query: 459 ------KFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQKSQLV--- 509
+F D ++E+ E + V+ S + V++K++ +QK ++
Sbjct: 228 YVLQQDQFTNKEMVDIKQEIIETVANNVVEYSKHKFASNVVEKSILYGSKNQKDLIISKI 287
Query: 510 ----------LELDGHVMRCVRDQNGNHVIQKCIECVPAEKIEFIISAFRGQVATLS 556
LE D ++ ++DQ N+VIQK + E + I+ A R + L+
Sbjct: 288 LPRDKNHALNLEDDSPMILMIKDQFANYVIQKLVNVSEGEGKKLIVIAIRAYLDKLN 344
>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 = 162 bits (410), Expect = 5e-40, Method: Compositional matrix adjust.
Identities = 94/269 (34%), Positives = 154/269 (57%), Gaps = 8/269 (2%)
Query: 401 LSDIAGRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPHASKLMTDVFGNYVIQKF 460
L G I DQHG RF+Q++L+ ++ ++F+E + +LMTD FGNY+IQK
Sbjct: 8 LDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKL 67
Query: 461 FEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQKSQLVLE-LDGHVMRC 519
E + +QR L + + +SL +GCR +QK +E I+ +++Q+V++ L + ++
Sbjct: 68 LEEVTTEQRIVLTKISSPHFVEISLNPHGCRALQKLIECIKTDEEAQIVVDSLRPYTVQL 127
Query: 520 VRDQNGNHVIQKCIECVPAEKIEFIISAFRGQVATLSTHPYGCRVIQRVLEHCSDEQQGQ 579
+D NGNHVIQKC++ + E +FI A ++TH +GCRV+QR L+H + EQ
Sbjct: 128 SKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCRVLQRCLDHGTTEQCDN 187
Query: 580 CIVDEILESAFALAQDQYGNYVTQHVL----ERGKSYERTQILSKLAGKIVQMSQHKYAS 635
+ D++L L D +GNYV Q+++ E+ K +I+ L + +++S HK+ S
Sbjct: 188 -LCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGS 246
Query: 636 NVVEKCLEYGDTAERELLIEEILGQSEEN 664
NV+EK L+ +E +L EIL E
Sbjct: 247 NVIEKILKTAIVSEPMIL--EILNNGGET 273
Score = 57.8 bits (138), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 48/192 (25%), Positives = 93/192 (48%), Gaps = 18/192 (9%)
Query: 388 LEELKSSNAQKFELSDIAGRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPHASKL 447
L+ LK N Q F I+ ++ + +HG R +Q+ L+H + E+ ++ ++L KL
Sbjct: 141 LQRLKPENFQ-FIFDAISDSCIDIATHRHGCRVLQRCLDHGTTEQCDNLCDKLLALVDKL 199
Query: 448 MTDVFGNYVIQKFFEHGSPDQRKELAEKLVGQVLP----LSLQMYGCRVIQKALEVIELH 503
D FGNYV+Q + + + K+V + P LS+ +G VI+K L+ +
Sbjct: 200 TLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVIEKILKTAIVS 259
Query: 504 QKSQLVLEL-----DGHVMRCVRDQNGNHVIQKCIECVPAEKIEFIISAFRGQVATL--- 555
+ ++LE+ + + + D GN+V+Q ++ + ++ +++ VA L
Sbjct: 260 EP--MILEILNNGGETGIQSLLNDSYGNYVLQTALD-ISHKQNDYLYKRLSEIVAPLLVG 316
Query: 556 --STHPYGCRVI 565
P+G R+I
Sbjct: 317 PIRNTPHGKRII 328
Score = 50.1 bits (118), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 56/245 (22%), Positives = 101/245 (41%), Gaps = 42/245 (17%)
Query: 387 FLEELKSSNAQKFELSDIAGRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPHASK 446
+E +K+ + + + V+ S D +G+ IQ+ L+ E +F +
Sbjct: 103 LIECIKTDEEAQIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCID 162
Query: 447 LMTDVFGNYVIQKFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQKS 506
+ T G V+Q+ +HG+ +Q L +KL+ V L+L +G V+Q
Sbjct: 163 IATHRHGCRVLQRCLDHGTTEQCDNLCDKLLALVDKLTLDPFGNYVVQ------------ 210
Query: 507 QLVLELDGHVMRCVRDQNGNHVIQKCIECVPAEKIEFIISAFRGQVATLSTHPYGCRVIQ 566
++I K E + I+ + + LS H +G VI+
Sbjct: 211 --------------------YIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVIE 250
Query: 567 RVLEHCSDEQQGQCIVDEIL----ESAF-ALAQDQYGNYVTQHVLERGKSYERTQILSKL 621
++L+ + ++ EIL E+ +L D YGNYV Q L+ S+++ L K
Sbjct: 251 KILKTAIVSEP---MILEILNNGGETGIQSLLNDSYGNYVLQTALD--ISHKQNDYLYKR 305
Query: 622 AGKIV 626
+IV
Sbjct: 306 LSEIV 310
>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 = 155 bits (393), Expect = 6e-38, Method: Compositional matrix adjust.
Identities = 92/268 (34%), Positives = 152/268 (56%), Gaps = 8/268 (2%)
Query: 401 LSDIAGRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPHASKLMTDVFGNYVIQKF 460
L G I DQHG RF+Q++L+ ++ ++F+E + +LMTD FGNY+IQK
Sbjct: 30 LDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKL 89
Query: 461 FEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQKSQLVLE-LDGHVMRC 519
E + +QR L + + +SL +G R +QK +E I+ +++Q+V++ L + ++
Sbjct: 90 LEEVTTEQRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYTVQL 149
Query: 520 VRDQNGNHVIQKCIECVPAEKIEFIISAFRGQVATLSTHPYGCRVIQRVLEHCSDEQQGQ 579
+D NGNHVIQKC++ + E +FI A ++TH +GC V+QR L+H + EQ
Sbjct: 150 SKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCDN 209
Query: 580 CIVDEILESAFALAQDQYGNYVTQHVL----ERGKSYERTQILSKLAGKIVQMSQHKYAS 635
+ D++L L D +GNYV Q+++ E+ K +I+ L + +++S HK+ S
Sbjct: 210 -LCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGS 268
Query: 636 NVVEKCLEYGDTAERELLIEEILGQSEE 663
NV+EK L+ +E +L EIL E
Sbjct: 269 NVIEKILKTAIVSEPMIL--EILNNGGE 294
>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 = 155 bits (391), Expect = 9e-38, Method: Compositional matrix adjust.
Identities = 92/269 (34%), Positives = 152/269 (56%), Gaps = 8/269 (2%)
Query: 401 LSDIAGRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPHASKLMTDVFGNYVIQKF 460
L G I DQHG RF+Q++L+ ++ ++F+E + +LMTD FGNY+IQK
Sbjct: 8 LDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKL 67
Query: 461 FEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQKSQLVLE-LDGHVMRC 519
E + +QR L + + +SL +G R +QK +E I+ +++Q+V++ L + ++
Sbjct: 68 LEEVTTEQRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYTVQL 127
Query: 520 VRDQNGNHVIQKCIECVPAEKIEFIISAFRGQVATLSTHPYGCRVIQRVLEHCSDEQQGQ 579
+D NGNHVIQKC++ + E +FI A ++TH +GC V+QR L+H + EQ
Sbjct: 128 SKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCDN 187
Query: 580 CIVDEILESAFALAQDQYGNYVTQHVL----ERGKSYERTQILSKLAGKIVQMSQHKYAS 635
+ D++L L D +GNYV Q+++ E+ K +I+ L + +++S HK+ S
Sbjct: 188 -LCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGS 246
Query: 636 NVVEKCLEYGDTAERELLIEEILGQSEEN 664
NV+EK L+ +E +L EIL E
Sbjct: 247 NVIEKILKTAIVSEPMIL--EILNNGGET 273
Score = 50.1 bits (118), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 56/245 (22%), Positives = 101/245 (41%), Gaps = 42/245 (17%)
Query: 387 FLEELKSSNAQKFELSDIAGRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPHASK 446
+E +K+ + + + V+ S D +G+ IQ+ L+ E +F +
Sbjct: 103 LIECIKTDEEAQIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCID 162
Query: 447 LMTDVFGNYVIQKFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQKS 506
+ T G V+Q+ +HG+ +Q L +KL+ V L+L +G V+Q
Sbjct: 163 IATHRHGCCVLQRCLDHGTTEQCDNLCDKLLALVDKLTLDPFGNYVVQ------------ 210
Query: 507 QLVLELDGHVMRCVRDQNGNHVIQKCIECVPAEKIEFIISAFRGQVATLSTHPYGCRVIQ 566
++I K E + I+ + + LS H +G VI+
Sbjct: 211 --------------------YIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVIE 250
Query: 567 RVLEHCSDEQQGQCIVDEIL----ESAF-ALAQDQYGNYVTQHVLERGKSYERTQILSKL 621
++L+ + ++ EIL E+ +L D YGNYV Q L+ S+++ L K
Sbjct: 251 KILKTAIVSEP---MILEILNNGGETGIQSLLNDSYGNYVLQTALD--ISHKQNDYLYKR 305
Query: 622 AGKIV 626
+IV
Sbjct: 306 LSEIV 310
>pdb|3BWT|A Chain A, Crystal Structure Of The Rna Binding Domain Of Puf4 From
Saccharomyces Cerevisiae
Length = 333
Score = 155 bits (391), Expect = 1e-37, Method: Compositional matrix adjust.
Identities = 92/269 (34%), Positives = 152/269 (56%), Gaps = 8/269 (2%)
Query: 401 LSDIAGRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPHASKLMTDVFGNYVIQKF 460
L G I DQHG RF+Q++L+ ++ ++F+E + +LMTD FGNY+IQK
Sbjct: 8 LDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKL 67
Query: 461 FEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQKSQLVLE-LDGHVMRC 519
E + +QR L + + +SL +G R +QK +E I+ +++Q+V++ L + ++
Sbjct: 68 LEEVTTEQRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYTVQL 127
Query: 520 VRDQNGNHVIQKCIECVPAEKIEFIISAFRGQVATLSTHPYGCRVIQRVLEHCSDEQQGQ 579
+D NGNHVIQKC++ + E +FI A ++TH +GC V+QR L+H + EQ
Sbjct: 128 SKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCDN 187
Query: 580 CIVDEILESAFALAQDQYGNYVTQHVL----ERGKSYERTQILSKLAGKIVQMSQHKYAS 635
+ D++L L D +GNYV Q+++ E+ K +I+ L + +++S HK+ S
Sbjct: 188 -LCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGS 246
Query: 636 NVVEKCLEYGDTAERELLIEEILGQSEEN 664
NV+EK L+ +E +L EIL E
Sbjct: 247 NVIEKILKTAIVSEPMIL--EILNNGGET 273
Score = 50.1 bits (118), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 56/245 (22%), Positives = 101/245 (41%), Gaps = 42/245 (17%)
Query: 387 FLEELKSSNAQKFELSDIAGRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPHASK 446
+E +K+ + + + V+ S D +G+ IQ+ L+ E +F +
Sbjct: 103 LIECIKTDEEAQIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCID 162
Query: 447 LMTDVFGNYVIQKFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQKS 506
+ T G V+Q+ +HG+ +Q L +KL+ V L+L +G V+Q
Sbjct: 163 IATHRHGCCVLQRCLDHGTTEQCDNLCDKLLALVDKLTLDPFGNYVVQ------------ 210
Query: 507 QLVLELDGHVMRCVRDQNGNHVIQKCIECVPAEKIEFIISAFRGQVATLSTHPYGCRVIQ 566
++I K E + I+ + + LS H +G VI+
Sbjct: 211 --------------------YIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVIE 250
Query: 567 RVLEHCSDEQQGQCIVDEIL----ESAF-ALAQDQYGNYVTQHVLERGKSYERTQILSKL 621
++L+ + ++ EIL E+ +L D YGNYV Q L+ S+++ L K
Sbjct: 251 KILKTAIVSEP---MILEILNNGGETGIQSLLNDSYGNYVLQTALD--ISHKQNDYLYKR 305
Query: 622 AGKIV 626
+IV
Sbjct: 306 LSEIV 310
>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 = 114 bits (286), Expect = 1e-25, Method: Compositional matrix adjust.
Identities = 81/292 (27%), Positives = 149/292 (51%), Gaps = 37/292 (12%)
Query: 398 KFELSDI--AGRIVEFSVDQHGSRFIQQKLE-HCSAEEKVSVFKEVLPHAS---KLMTDV 451
+ LS++ +G +++F+VD+ G +F+++ ++ ++ +K +F++V+ KL T++
Sbjct: 20 RLSLSEVLDSGDLMKFAVDKTGCQFLEKAVKGSLTSYQKFQLFEQVIGRKDDFLKLSTNI 79
Query: 452 FGNYVIQKFF-------EHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQ 504
FGNY++Q + G ++++L + Q+ + L + CRVIQ +L+ ++L
Sbjct: 80 FGNYLVQSVIGISLATNDDGYTKRQEKLKNFISSQMTDMCLDKFACRVIQSSLQNMDLSL 139
Query: 505 KSQLVLEL--DGHVMRCVRDQNGNHVIQKCIECVPAEKIEFIIS--AFRGQVATLSTHPY 560
+LV L D ++ DQN NHVIQK + +P + EFI+ A + + + Y
Sbjct: 140 ACKLVQALPRDARLIAICVDQNANHVIQKVVAVIPLKNWEFIVDFVATPEHLRQICSDKY 199
Query: 561 GCRVIQRVLEHCS---------------DEQQGQCIVDEILESAFALAQDQYGNYVTQHV 605
GCRV+Q ++E + E+ Q ++ + LA ++Y NY+ QH+
Sbjct: 200 GCRVVQTIIEKLTADSMNVDLTSAAQNLRERALQRLMTSVTNRCQELATNEYANYIIQHI 259
Query: 606 LERGK--SYERTQILSKLAGKIVQMSQHKYASNVVEKCLEYGDTAERELLIE 655
+ Y I L ++ +SQ K+AS+VVEK + A ELL E
Sbjct: 260 VSNDDLAVYRECIIEKCLMRNLLSLSQEKFASHVVEKAFLH---APLELLAE 308
>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 = 114 bits (285), Expect = 2e-25, Method: Compositional matrix adjust.
Identities = 81/292 (27%), Positives = 149/292 (51%), Gaps = 37/292 (12%)
Query: 398 KFELSDI--AGRIVEFSVDQHGSRFIQQKLE-HCSAEEKVSVFKEVLPHAS---KLMTDV 451
+ LS++ +G +++F+VD+ G +F+++ ++ ++ +K +F++V+ KL T++
Sbjct: 19 RLSLSEVLDSGDLMKFAVDKTGCQFLEKAVKGSLTSYQKFQLFEQVIGRKDDFLKLSTNI 78
Query: 452 FGNYVIQKFF-------EHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQ 504
FGNY++Q + G ++++L + Q+ + L + CRVIQ +L+ ++L
Sbjct: 79 FGNYLVQSVIGISLATNDDGYTKRQEKLKNFISSQMTDMCLDKFACRVIQSSLQNMDLSL 138
Query: 505 KSQLVLEL--DGHVMRCVRDQNGNHVIQKCIECVPAEKIEFIIS--AFRGQVATLSTHPY 560
+LV L D ++ DQN NHVIQK + +P + EFI+ A + + + Y
Sbjct: 139 ACKLVQALPRDARLIAICVDQNANHVIQKVVAVIPLKNWEFIVDFVATPEHLRQICSDKY 198
Query: 561 GCRVIQRVLEHCS---------------DEQQGQCIVDEILESAFALAQDQYGNYVTQHV 605
GCRV+Q ++E + E+ Q ++ + LA ++Y NY+ QH+
Sbjct: 199 GCRVVQTIIEKLTADSMNVDLTSAAQNLRERALQRLMTSVTNRCQELATNEYANYIIQHI 258
Query: 606 LERGK--SYERTQILSKLAGKIVQMSQHKYASNVVEKCLEYGDTAERELLIE 655
+ Y I L ++ +SQ K+AS+VVEK + A ELL E
Sbjct: 259 VSNDDLAVYRECIIEKCLMRNLLSLSQEKFASHVVEKAFLH---APLELLAE 307
>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 = 111 bits (278), Expect = 1e-24, Method: Compositional matrix adjust.
Identities = 80/292 (27%), Positives = 148/292 (50%), Gaps = 37/292 (12%)
Query: 398 KFELSDI--AGRIVEFSVDQHGSRFIQQKLE-HCSAEEKVSVFKEVLPHAS---KLMTDV 451
+ LS++ +G +++F+VD+ G +F+++ ++ ++ +K +F++V+ KL T++
Sbjct: 20 RLSLSEVLDSGDLMKFAVDKTGCQFLEKAVKGSLTSYQKFQLFEQVIGRKDDFLKLSTNI 79
Query: 452 FGNYVIQKFF-------EHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQ 504
FGNY++Q + G ++++L + Q+ + L + C VIQ +L+ ++L
Sbjct: 80 FGNYLVQSVIGISLATNDDGYTKRQEKLKNFISSQMTDMCLDKFACYVIQSSLQNMDLSL 139
Query: 505 KSQLVLEL--DGHVMRCVRDQNGNHVIQKCIECVPAEKIEFIIS--AFRGQVATLSTHPY 560
+LV L D ++ DQN NHVIQK + +P + EFI+ A + + + Y
Sbjct: 140 ACKLVQALPRDARLIAICVDQNANHVIQKVVAVIPLKNWEFIVDFVATPEHLRQICSDKY 199
Query: 561 GCRVIQRVLEHCS---------------DEQQGQCIVDEILESAFALAQDQYGNYVTQHV 605
GCRV+Q ++E + E+ Q ++ + LA ++Y NY+ QH+
Sbjct: 200 GCRVVQTIIEKLTADSMNVDLTSAAQNLRERALQRLMTSVTNRCQELATNEYANYIIQHI 259
Query: 606 LERGK--SYERTQILSKLAGKIVQMSQHKYASNVVEKCLEYGDTAERELLIE 655
+ Y I L ++ +SQ K+AS+VVEK + A ELL E
Sbjct: 260 VSNDDLAVYRECIIEKCLMRNLLSLSQEKFASHVVEKAFLH---APLELLAE 308
>pdb|3V71|A Chain A, Crystal Structure Of Puf-6 In Complex With 5be13 Rna
Length = 382
Score = 98.2 bits (243), Expect = 1e-20, Method: Compositional matrix adjust.
Identities = 67/275 (24%), Positives = 136/275 (49%), Gaps = 21/275 (7%)
Query: 406 GRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPHASKLMTDVF----GNYVIQKFF 461
G++++F++D G +F++ S ++ E ++ L + GN+++QK
Sbjct: 20 GQLIDFAIDPSGVKFLEANYPLDSEDQIRKAVFEKFTESTTLFVGLCHSRNGNFIVQKLV 79
Query: 462 EHGSPDQRKELAEKLV-GQVLPLSLQMYGCRVIQKALEVIELHQKSQLVLELDGHVMRCV 520
E +P +++EL +++ G +L + + CRV+Q AL+ + QL+ EL + +
Sbjct: 80 ELATPAEQRELLRQMIDGGLLAMCKDKFACRVVQLALQKFDHSNVFQLIQELSTFDLAAM 139
Query: 521 -RDQNGNHVIQKCIECVPAEKIEFIISAFRG--QVATLSTHPYGCRVIQRVLEHCSDEQQ 577
DQ HVIQ+ ++ +P + F + + + YGCR++Q+V++ ++ +
Sbjct: 140 CTDQISIHVIQRVVKQLPVDMWTFFVHFLSSGDSLMAVCQDKYGCRLVQQVIDRLAENPK 199
Query: 578 GQC----------IVDEILESAFALAQDQYGNYVTQHVLERG---KSYERTQILSKLAGK 624
C ++ I+ + + L+ +++ NYV Q+V++ + Y T I L
Sbjct: 200 LPCFKFRIQLLHSLMTCIVRNCYRLSSNEFANYVIQYVIKSSGIMEMYRDTIIDKCLLRN 259
Query: 625 IVQMSQHKYASNVVEKCLEYGDTAERELLIEEILG 659
++ MSQ KYAS+V+E + A ++EEI
Sbjct: 260 LLSMSQDKYASHVIEGAFLFAPPALLHEMMEEIFS 294
>pdb|1GQ2|A Chain A, Malic Enzyme From Pigeon Liver
pdb|1GQ2|B Chain B, Malic Enzyme From Pigeon Liver
pdb|1GQ2|C Chain C, Malic Enzyme From Pigeon Liver
pdb|1GQ2|D Chain D, Malic Enzyme From Pigeon Liver
pdb|1GQ2|E Chain E, Malic Enzyme From Pigeon Liver
pdb|1GQ2|F Chain F, Malic Enzyme From Pigeon Liver
pdb|1GQ2|G Chain G, Malic Enzyme From Pigeon Liver
pdb|1GQ2|H Chain H, Malic Enzyme From Pigeon Liver
pdb|1GQ2|I Chain I, Malic Enzyme From Pigeon Liver
pdb|1GQ2|J Chain J, Malic Enzyme From Pigeon Liver
pdb|1GQ2|K Chain K, Malic Enzyme From Pigeon Liver
pdb|1GQ2|L Chain L, Malic Enzyme From Pigeon Liver
pdb|1GQ2|M Chain M, Malic Enzyme From Pigeon Liver
pdb|1GQ2|N Chain N, Malic Enzyme From Pigeon Liver
pdb|1GQ2|O Chain O, Malic Enzyme From Pigeon Liver
pdb|1GQ2|P Chain P, Malic Enzyme From Pigeon Liver
Length = 555
Score = 31.6 bits (70), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 19/44 (43%), Positives = 22/44 (50%), Gaps = 6/44 (13%)
Query: 141 SGNPFYPSFQPSGAGVYPSQYNVGGYALNSALFPPFVAGYPSQG 184
SG+PF P PSG +YP Q N NS +FP G S G
Sbjct: 420 SGSPFDPVTLPSGQTLYPGQGN------NSYVFPGVALGVISCG 457
>pdb|2IHM|A Chain A, Polymerase Mu In Ternary Complex With Gapped 11mer Dna
Duplex And Bound Incoming Nucleotide
pdb|2IHM|B Chain B, Polymerase Mu In Ternary Complex With Gapped 11mer Dna
Duplex And Bound Incoming Nucleotide
Length = 360
Score = 30.4 bits (67), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 35/69 (50%), Gaps = 4/69 (5%)
Query: 415 QHGSRFIQQKLEHCSAEEKVSVFKEVLPHASKLMTDVFGNYV--IQKFFEHG--SPDQRK 470
+H +R IQ+ LEH + EE V KL T VFG V ++++ G + D+ +
Sbjct: 71 EHSTRVIQELLEHGTCEEVKQVRCSERYQTMKLFTQVFGVGVKTANRWYQEGLRTLDELR 130
Query: 471 ELAEKLVGQ 479
E ++L Q
Sbjct: 131 EQPQRLTQQ 139
>pdb|1U04|A Chain A, Crystal Structure Of Full Length Argonaute From Pyrococcus
Furiosus
Length = 771
Score = 30.0 bits (66), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 33/63 (52%), Gaps = 13/63 (20%)
Query: 466 PDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQKSQLVLELDGHVMRCVRDQNG 525
P++RKEL E ++ +V +I K+L IE+ + +Q EL+ + VRD G
Sbjct: 294 PEERKELLENILAEV--------DSDIIDKSLSEIEVEKIAQ---ELENKIR--VRDDKG 340
Query: 526 NHV 528
N V
Sbjct: 341 NSV 343
>pdb|1Z25|A Chain A, Structure Of P.Furiosus Argonaute With Bound Mn2+
pdb|1Z26|A Chain A, Structure Of Pyrococcus Furiosus Argonaute With Bound
Tungstate
Length = 771
Score = 30.0 bits (66), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 33/63 (52%), Gaps = 13/63 (20%)
Query: 466 PDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQKSQLVLELDGHVMRCVRDQNG 525
P++RKEL E ++ +V +I K+L IE+ + +Q EL+ + VRD G
Sbjct: 294 PEERKELLENILAEV--------DSDIIDKSLSEIEVEKIAQ---ELENKIR--VRDDKG 340
Query: 526 NHV 528
N V
Sbjct: 341 NSV 343
>pdb|2AW5|A Chain A, Crystal Structure Of A Human Malic Enzyme
pdb|2AW5|B Chain B, Crystal Structure Of A Human Malic Enzyme
pdb|2AW5|C Chain C, Crystal Structure Of A Human Malic Enzyme
Length = 575
Score = 29.6 bits (65), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 17/44 (38%), Positives = 22/44 (50%), Gaps = 6/44 (13%)
Query: 141 SGNPFYPSFQPSGAGVYPSQYNVGGYALNSALFPPFVAGYPSQG 184
SG+PF P P+G +YP Q N NS +FP G + G
Sbjct: 443 SGSPFDPVTLPNGQTLYPGQGN------NSYVFPGVALGVVACG 480
>pdb|1Z56|A Chain A, Co-Crystal Structure Of Lif1p-Lig4p
pdb|1Z56|B Chain B, Co-Crystal Structure Of Lif1p-Lig4p
Length = 246
Score = 29.3 bits (64), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 35/69 (50%), Gaps = 9/69 (13%)
Query: 346 GLRHE-MRLPQGLNRNTGIYS----GWQGQRTFEGQRTFEDSKKHSFLEELKSSNAQKFE 400
GLR E M + +G TGI+S G R F G+ E+SKK+ + E LK K
Sbjct: 47 GLRIEKMLVSEG----TGIFSKSSFGINDLRIFTGENIDEESKKYVWYELLKMLTGHKVY 102
Query: 401 LSDIAGRIV 409
++ + ++V
Sbjct: 103 IASLDEKVV 111
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
0.315 0.132 0.385
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,412,187
Number of Sequences: 62578
Number of extensions: 777111
Number of successful extensions: 1740
Number of sequences better than 100.0: 27
Number of HSP's better than 100.0 without gapping: 21
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1482
Number of HSP's gapped (non-prelim): 72
length of query: 688
length of database: 14,973,337
effective HSP length: 105
effective length of query: 583
effective length of database: 8,402,647
effective search space: 4898743201
effective search space used: 4898743201
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.8 bits)