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= 008180
(575 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 = 244 bits (624), Expect = 7e-65, Method: Compositional matrix adjust.
Identities = 116/180 (64%), Positives = 141/180 (78%)
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
Score = 93.2 bits (230), Expect = 3e-19, Method: Compositional matrix adjust.
Identities = 51/175 (29%), Positives = 95/175 (54%), Gaps = 7/175 (4%)
Query: 398 KFELSDIAGRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPHASKLMTDVFGNYVI 457
+F + G++ S +G R IQ+ LEHC+AE+ + + +E+ H +L+ D +GNYVI
Sbjct: 162 QFIIDAFKGQVFVLSTHPYGCRVIQRILEHCTAEQTLPILEELHQHTEQLVQDQYGNYVI 221
Query: 458 QKFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQKSQLVLEL----D 513
Q EHG P+ + ++ ++ G+VL LS + V++K + +++ L+ E+ D
Sbjct: 222 QHVLEHGRPEDKSKIVSEIRGKVLALSQHKFASNVVEKCVTHASRAERALLIDEVCCQND 281
Query: 514 G---HVMRCVRDQNGNHVIQKCIECVPAEKIEFIISAFRGQVATLSTHPYGCRVI 565
G + ++DQ N+V+QK I+ + + I+ R + TL + YG ++
Sbjct: 282 GPHSALYTMMKDQYANYVVQKMIDMAEPAQRKIIMHKIRPHITTLRKYTYGKHIL 336
Score = 48.5 bits (114), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 28/102 (27%), Positives = 51/102 (50%), Gaps = 7/102 (6%)
Query: 401 LSDIAGRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVL-----PHAS--KLMTDVFG 453
+S+I G+++ S + S +++ + H S E+ + EV PH++ +M D +
Sbjct: 237 VSEIRGKVLALSQHKFASNVVEKCVTHASRAERALLIDEVCCQNDGPHSALYTMMKDQYA 296
Query: 454 NYVIQKFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQK 495
NYV+QK + P QRK + K+ + L YG ++ K
Sbjct: 297 NYVVQKMIDMAEPAQRKIIMHKIRPHITTLRKYTYGKHILAK 338
>pdb|3H3D|X Chain X, Drosophila Pumilio Rna Binding Domain (Puf Domain)
pdb|3H3D|Y Chain Y, Drosophila Pumilio Rna Binding Domain (Puf Domain)
Length = 323
Score = 241 bits (614), Expect = 1e-63, Method: Compositional matrix adjust.
Identities = 114/180 (63%), Positives = 139/180 (77%)
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
Score = 84.3 bits (207), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 50/166 (30%), Positives = 89/166 (53%), Gaps = 8/166 (4%)
Query: 396 AQKFELSDIAGRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPHASKLMTDVFGNY 455
A +F ++ G++ S +G R IQ+ LEHC+AE+ + E+ H +L+ D +GNY
Sbjct: 160 ALQFIINAFKGQVYSLSTHPYGCRVIQRILEHCTAEQTTPILDELHEHTEQLIQDQYGNY 219
Query: 456 VIQKFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQKSQLVLELDG- 514
VIQ EHG + + L + G+VL LS + V++K + +++ L+ E+
Sbjct: 220 VIQHVLEHGKQEDKSILINSVRGKVLVLSQHKFASNVVEKCVTHATRGERTGLIDEVCTF 279
Query: 515 -----HVMRCVRDQNGNHVIQKCIECVPAEKIEFIISAFRGQVATL 555
HVM ++DQ N+V+QK I+ +++ +++ R +A L
Sbjct: 280 NDNALHVM--MKDQYANYVVQKMIDVSEPTQLKKLMTKIRKNMAAL 323
>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 = 239 bits (611), Expect = 2e-63, Method: Compositional matrix adjust.
Identities = 116/182 (63%), Positives = 141/182 (77%), Gaps = 2/182 (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 IQ 566
IQ
Sbjct: 185 IQ 186
Score = 94.0 bits (232), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 62/173 (35%), Positives = 93/173 (53%), Gaps = 3/173 (1%)
Query: 397 QKFEL-SDIAGRIVEFSVDQHGSRFIQQKLEHCSAEEKV--SVFKEVLPHASKLMTDVFG 453
QK L + I G ++ ++ +G R IQ+ LE S++++V + KE+ H K + D G
Sbjct: 86 QKLALATRIRGHVLPLALQMYGCRVIQKALESISSDQQVISEMVKELDGHVLKCVKDQNG 145
Query: 454 NYVIQKFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQKSQLVLELD 513
N+V+QK E P + + + GQV LS YGCRVIQ+ LE Q ++ EL
Sbjct: 146 NHVVQKCIECVQPQSLQFIIDAFKGQVFVLSTHPYGCRVIQRILEHCTAEQTLPILEELH 205
Query: 514 GHVMRCVRDQNGNHVIQKCIECVPAEKIEFIISAFRGQVATLSTHPYGCRVIQ 566
H + V+DQ GN+VIQ +E E I+S RG+V LS H + V++
Sbjct: 206 QHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGKVLALSQHKFASNVVE 258
Score = 93.2 bits (230), Expect = 4e-19, Method: Compositional matrix adjust.
Identities = 51/175 (29%), Positives = 95/175 (54%), Gaps = 7/175 (4%)
Query: 398 KFELSDIAGRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPHASKLMTDVFGNYVI 457
+F + G++ S +G R IQ+ LEHC+AE+ + + +E+ H +L+ D +GNYVI
Sbjct: 162 QFIIDAFKGQVFVLSTHPYGCRVIQRILEHCTAEQTLPILEELHQHTEQLVQDQYGNYVI 221
Query: 458 QKFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQKSQLVLEL----D 513
Q EHG P+ + ++ ++ G+VL LS + V++K + +++ L+ E+ D
Sbjct: 222 QHVLEHGRPEDKSKIVSEIRGKVLALSQHKFASNVVEKCVTHASRAERALLIDEVCCQND 281
Query: 514 G---HVMRCVRDQNGNHVIQKCIECVPAEKIEFIISAFRGQVATLSTHPYGCRVI 565
G + ++DQ N+V+QK I+ + + I+ R + TL + YG ++
Sbjct: 282 GPHSALYTMMKDQYANYVVQKMIDMAEPAQRKIIMHKIRPHITTLRKYTYGKHIL 336
Score = 48.1 bits (113), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 28/102 (27%), Positives = 51/102 (50%), Gaps = 7/102 (6%)
Query: 401 LSDIAGRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVL-----PHAS--KLMTDVFG 453
+S+I G+++ S + S +++ + H S E+ + EV PH++ +M D +
Sbjct: 237 VSEIRGKVLALSQHKFASNVVEKCVTHASRAERALLIDEVCCQNDGPHSALYTMMKDQYA 296
Query: 454 NYVIQKFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQK 495
NYV+QK + P QRK + K+ + L YG ++ K
Sbjct: 297 NYVVQKMIDMAEPAQRKIIMHKIRPHITTLRKYTYGKHILAK 338
>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 = 236 bits (601), Expect = 4e-62, Method: Compositional matrix adjust.
Identities = 112/180 (62%), Positives = 140/180 (77%)
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
Score = 91.7 bits (226), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 59/174 (33%), Positives = 92/174 (52%), Gaps = 1/174 (0%)
Query: 394 SNAQKFELSD-IAGRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPHASKLMTDVF 452
S QK L++ I G ++ ++ +G R IQ+ LE ++++ + +E+ H K + D
Sbjct: 83 SLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQNEMVRELDGHVLKCVKDQN 142
Query: 453 GNYVIQKFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQKSQLVLEL 512
GN+V+QK E P + + + GQV LS YGCRVIQ+ LE Q ++ EL
Sbjct: 143 GNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPDQTLPILEEL 202
Query: 513 DGHVMRCVRDQNGNHVIQKCIECVPAEKIEFIISAFRGQVATLSTHPYGCRVIQ 566
H + V+DQ GN+VIQ +E E I++ RG V LS H + V++
Sbjct: 203 HQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNVVE 256
Score = 87.4 bits (215), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 49/175 (28%), Positives = 93/175 (53%), Gaps = 7/175 (4%)
Query: 398 KFELSDIAGRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPHASKLMTDVFGNYVI 457
+F + G++ S +G R IQ+ LEHC ++ + + +E+ H +L+ D +GNYVI
Sbjct: 160 QFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPDQTLPILEELHQHTEQLVQDQYGNYVI 219
Query: 458 QKFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQKSQLVLEL----D 513
Q EHG P+ + ++ ++ G VL LS + V++K + +++ L+ E+ D
Sbjct: 220 QHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNVVEKCVTHASRTERAVLIDEVCTMND 279
Query: 514 G---HVMRCVRDQNGNHVIQKCIECVPAEKIEFIISAFRGQVATLSTHPYGCRVI 565
G + ++DQ N+V+QK I+ + + ++ R +ATL + YG ++
Sbjct: 280 GPHSALYTMMKDQYANYVVQKMIDVAEPGQRKIVMHKIRPHIATLRKYTYGKHIL 334
Score = 44.7 bits (104), 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
>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 = 235 bits (600), Expect = 4e-62, Method: Compositional matrix adjust.
Identities = 112/180 (62%), Positives = 140/180 (77%)
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
Score = 91.3 bits (225), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 59/174 (33%), Positives = 92/174 (52%), Gaps = 1/174 (0%)
Query: 394 SNAQKFELSD-IAGRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPHASKLMTDVF 452
S QK L++ I G ++ ++ +G R IQ+ LE ++++ + +E+ H K + D
Sbjct: 83 SLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQNEMVRELDGHVLKCVKDQN 142
Query: 453 GNYVIQKFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQKSQLVLEL 512
GN+V+QK E P + + + GQV LS YGCRVIQ+ LE Q ++ EL
Sbjct: 143 GNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPDQTLPILEEL 202
Query: 513 DGHVMRCVRDQNGNHVIQKCIECVPAEKIEFIISAFRGQVATLSTHPYGCRVIQ 566
H + V+DQ GN+VIQ +E E I++ RG V LS H + V++
Sbjct: 203 HQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNVVE 256
Score = 87.0 bits (214), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 49/175 (28%), Positives = 93/175 (53%), Gaps = 7/175 (4%)
Query: 398 KFELSDIAGRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPHASKLMTDVFGNYVI 457
+F + G++ S +G R IQ+ LEHC ++ + + +E+ H +L+ D +GNYVI
Sbjct: 160 QFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPDQTLPILEELHQHTEQLVQDQYGNYVI 219
Query: 458 QKFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQKSQLVLEL----D 513
Q EHG P+ + ++ ++ G VL LS + V++K + +++ L+ E+ D
Sbjct: 220 QHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNVVEKCVTHASRTERAVLIDEVCTMND 279
Query: 514 G---HVMRCVRDQNGNHVIQKCIECVPAEKIEFIISAFRGQVATLSTHPYGCRVI 565
G + ++DQ N+V+QK I+ + + ++ R +ATL + YG ++
Sbjct: 280 GPHSALYTMMKDQYANYVVQKMIDVAEPGQRKIVMHKIRPHIATLRKYTYGKHIL 334
Score = 44.7 bits (104), 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
>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 = 235 bits (600), Expect = 4e-62, Method: Compositional matrix adjust.
Identities = 112/180 (62%), Positives = 140/180 (77%)
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
Score = 87.4 bits (215), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 57/174 (32%), Positives = 92/174 (52%), Gaps = 1/174 (0%)
Query: 394 SNAQKFELSD-IAGRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPHASKLMTDVF 452
S QK L++ I G ++ ++ +G R IQ+ LE ++++ + +E+ H K + D
Sbjct: 84 SLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQNEMVRELDGHVLKCVKDQN 143
Query: 453 GNYVIQKFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQKSQLVLEL 512
GN+V+QK E P + + + GQV LS YGCRVIQ+ LE Q ++ EL
Sbjct: 144 GNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPDQTLPILEEL 203
Query: 513 DGHVMRCVRDQNGNHVIQKCIECVPAEKIEFIISAFRGQVATLSTHPYGCRVIQ 566
H + V+DQ G++VI+ +E E I++ RG V LS H + V++
Sbjct: 204 HQHTEQLVQDQYGSYVIRHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNVVE 257
Score = 83.6 bits (205), Expect = 3e-16, Method: Compositional matrix adjust.
Identities = 47/175 (26%), Positives = 93/175 (53%), Gaps = 7/175 (4%)
Query: 398 KFELSDIAGRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPHASKLMTDVFGNYVI 457
+F + G++ S +G R IQ+ LEHC ++ + + +E+ H +L+ D +G+YVI
Sbjct: 161 QFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPDQTLPILEELHQHTEQLVQDQYGSYVI 220
Query: 458 QKFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQKSQLVLEL----D 513
+ EHG P+ + ++ ++ G VL LS + V++K + +++ L+ E+ D
Sbjct: 221 RHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNVVEKCVTHASRTERAVLIDEVCTMND 280
Query: 514 G---HVMRCVRDQNGNHVIQKCIECVPAEKIEFIISAFRGQVATLSTHPYGCRVI 565
G + ++DQ N+V+QK I+ + + ++ R +ATL + YG ++
Sbjct: 281 GPHSALYTMMKDQYANYVVQKMIDVAEPGQRKIVMHKIRPHIATLRKYTYGKHIL 335
Score = 44.7 bits (104), 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
>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 = 191 bits (485), Expect = 9e-49, Method: Compositional matrix adjust.
Identities = 94/166 (56%), Positives = 117/166 (70%)
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 RDQNGNHVIQKCIECVPAEKIEFIISAFRGQVATLSTHPYGCRVIQ 566
+DQNGNHVIQK IE +P EK+ FI+S+ G + LSTH YGCRVIQ
Sbjct: 146 KDQNGNHVIQKAIETIPIEKLPFILSSLTGHIYHLSTHSYGCRVIQ 191
Score = 66.6 bits (161), 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 = 119 bits (297), Expect = 6e-27, Method: Compositional matrix adjust.
Identities = 61/167 (36%), Positives = 100/167 (59%), Gaps = 1/167 (0%)
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 VRDQNGNHVIQKCIECVPAEKIEFIISAFRGQVATLSTHPYGCRVIQ 566
+D NGNHVIQKC++ + E +FI A ++TH +GCRV+Q
Sbjct: 128 SKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCRVLQ 174
Score = 67.0 bits (162), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 52/187 (27%), Positives = 94/187 (50%), Gaps = 10/187 (5%)
Query: 387 FLEELKSSNAQKFELSDIAG-RIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVL-PHA 444
LEE+ + Q+ L+ I+ VE S++ HG R +Q+ +E +E+ + + L P+
Sbjct: 67 LLEEV--TTEQRIVLTKISSPHFVEISLNPHGCRALQKLIECIKTDEEAQIVVDSLRPYT 124
Query: 445 SKLMTDVFGNYVIQKFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQ 504
+L D+ GN+VIQK + P+ + + + + + ++ +GCRV+Q+ L+ Q
Sbjct: 125 VQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCRVLQRCLDHGTTEQ 184
Query: 505 KSQLVLELDGHVMRCVRDQNGNHVIQKCIECVPAEKIEF-----IISAFRGQVATLSTHP 559
L +L V + D GN+V+Q I AEK ++ I+ + + LS H
Sbjct: 185 CDNLCDKLLALVDKLTLDPFGNYVVQYIIT-KEAEKNKYDYTHKIVHLLKPRAIELSIHK 243
Query: 560 YGCRVIQ 566
+G VI+
Sbjct: 244 FGSNVIE 250
Score = 56.6 bits (135), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 41/156 (26%), Positives = 78/156 (50%), Gaps = 12/156 (7%)
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-----DGHVMRCVRDQNGNHVIQKCIE 534
+ ++LE+ + + + D GN+V+Q ++
Sbjct: 260 EP--MILEILNNGGETGIQSLLNDSYGNYVLQTALD 293
>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 = 112 bits (281), Expect = 5e-25, Method: Compositional matrix adjust.
Identities = 59/167 (35%), Positives = 98/167 (58%), Gaps = 1/167 (0%)
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 VRDQNGNHVIQKCIECVPAEKIEFIISAFRGQVATLSTHPYGCRVIQ 566
+D NGNHVIQKC++ + E +FI A ++TH +GC V+Q
Sbjct: 150 SKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQ 196
Score = 65.5 bits (158), Expect = 9e-11, Method: Compositional matrix adjust.
Identities = 51/187 (27%), Positives = 94/187 (50%), Gaps = 10/187 (5%)
Query: 387 FLEELKSSNAQKFELSDIAG-RIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVL-PHA 444
LEE+ + Q+ L+ I+ VE S++ HG+R +Q+ +E +E+ + + L P+
Sbjct: 89 LLEEV--TTEQRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYT 146
Query: 445 SKLMTDVFGNYVIQKFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQ 504
+L D+ GN+VIQK + P+ + + + + + ++ +GC V+Q+ L+ Q
Sbjct: 147 VQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQ 206
Query: 505 KSQLVLELDGHVMRCVRDQNGNHVIQKCIECVPAEKIEF-----IISAFRGQVATLSTHP 559
L +L V + D GN+V+Q I AEK ++ I+ + + LS H
Sbjct: 207 CDNLCDKLLALVDKLTLDPFGNYVVQYIIT-KEAEKNKYDYTHKIVHLLKPRAIELSIHK 265
Query: 560 YGCRVIQ 566
+G VI+
Sbjct: 266 FGSNVIE 272
Score = 54.3 bits (129), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 47/192 (24%), Positives = 92/192 (47%), Gaps = 18/192 (9%)
Query: 388 LEELKSSNAQKFELSDIAGRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPHASKL 447
L+ LK N Q F I+ ++ + +HG +Q+ L+H + E+ ++ ++L KL
Sbjct: 163 LQRLKPENFQ-FIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCDNLCDKLLALVDKL 221
Query: 448 MTDVFGNYVIQKFFEHGSPDQRKELAEKLVGQVLP----LSLQMYGCRVIQKALEVIELH 503
D FGNYV+Q + + + K+V + P LS+ +G VI+K L+ +
Sbjct: 222 TLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVIEKILKTAIVS 281
Query: 504 QKSQLVLEL-----DGHVMRCVRDQNGNHVIQKCIECVPAEKIEFIISAFRGQVATL--- 555
+ ++LE+ + + + D GN+V+Q ++ + ++ +++ VA L
Sbjct: 282 EP--MILEILNNGGETGIQSLLNDSYGNYVLQTALD-ISHKQNDYLYKRLSEIVAPLLVG 338
Query: 556 --STHPYGCRVI 565
P+G R+I
Sbjct: 339 PIRNTPHGKRII 350
>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 = 111 bits (277), Expect = 1e-24, Method: Compositional matrix adjust.
Identities = 59/167 (35%), Positives = 98/167 (58%), Gaps = 1/167 (0%)
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 VRDQNGNHVIQKCIECVPAEKIEFIISAFRGQVATLSTHPYGCRVIQ 566
+D NGNHVIQKC++ + E +FI A ++TH +GC V+Q
Sbjct: 128 SKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQ 174
Score = 64.3 bits (155), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 51/187 (27%), Positives = 94/187 (50%), Gaps = 10/187 (5%)
Query: 387 FLEELKSSNAQKFELSDIAG-RIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVL-PHA 444
LEE+ + Q+ L+ I+ VE S++ HG+R +Q+ +E +E+ + + L P+
Sbjct: 67 LLEEV--TTEQRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYT 124
Query: 445 SKLMTDVFGNYVIQKFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQ 504
+L D+ GN+VIQK + P+ + + + + + ++ +GC V+Q+ L+ Q
Sbjct: 125 VQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQ 184
Query: 505 KSQLVLELDGHVMRCVRDQNGNHVIQKCIECVPAEKIEF-----IISAFRGQVATLSTHP 559
L +L V + D GN+V+Q I AEK ++ I+ + + LS H
Sbjct: 185 CDNLCDKLLALVDKLTLDPFGNYVVQYIIT-KEAEKNKYDYTHKIVHLLKPRAIELSIHK 243
Query: 560 YGCRVIQ 566
+G VI+
Sbjct: 244 FGSNVIE 250
Score = 53.1 bits (126), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 40/156 (25%), Positives = 77/156 (49%), Gaps = 12/156 (7%)
Query: 388 LEELKSSNAQKFELSDIAGRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPHASKL 447
L+ LK N Q F I+ ++ + +HG +Q+ L+H + E+ ++ ++L KL
Sbjct: 141 LQRLKPENFQ-FIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCDNLCDKLLALVDKL 199
Query: 448 MTDVFGNYVIQKFFEHGSPDQRKELAEKLVGQVLP----LSLQMYGCRVIQKALEVIELH 503
D FGNYV+Q + + + K+V + P LS+ +G VI+K L+ +
Sbjct: 200 TLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVIEKILKTAIVS 259
Query: 504 QKSQLVLEL-----DGHVMRCVRDQNGNHVIQKCIE 534
+ ++LE+ + + + D GN+V+Q ++
Sbjct: 260 EP--MILEILNNGGETGIQSLLNDSYGNYVLQTALD 293
>pdb|3BWT|A Chain A, Crystal Structure Of The Rna Binding Domain Of Puf4 From
Saccharomyces Cerevisiae
Length = 333
Score = 111 bits (277), Expect = 1e-24, Method: Compositional matrix adjust.
Identities = 59/167 (35%), Positives = 98/167 (58%), Gaps = 1/167 (0%)
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 VRDQNGNHVIQKCIECVPAEKIEFIISAFRGQVATLSTHPYGCRVIQ 566
+D NGNHVIQKC++ + E +FI A ++TH +GC V+Q
Sbjct: 128 SKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQ 174
Score = 63.9 bits (154), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 51/187 (27%), Positives = 94/187 (50%), Gaps = 10/187 (5%)
Query: 387 FLEELKSSNAQKFELSDIAG-RIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVL-PHA 444
LEE+ + Q+ L+ I+ VE S++ HG+R +Q+ +E +E+ + + L P+
Sbjct: 67 LLEEV--TTEQRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYT 124
Query: 445 SKLMTDVFGNYVIQKFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQ 504
+L D+ GN+VIQK + P+ + + + + + ++ +GC V+Q+ L+ Q
Sbjct: 125 VQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQ 184
Query: 505 KSQLVLELDGHVMRCVRDQNGNHVIQKCIECVPAEKIEF-----IISAFRGQVATLSTHP 559
L +L V + D GN+V+Q I AEK ++ I+ + + LS H
Sbjct: 185 CDNLCDKLLALVDKLTLDPFGNYVVQYIIT-KEAEKNKYDYTHKIVHLLKPRAIELSIHK 243
Query: 560 YGCRVIQ 566
+G VI+
Sbjct: 244 FGSNVIE 250
Score = 53.1 bits (126), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 40/156 (25%), Positives = 77/156 (49%), Gaps = 12/156 (7%)
Query: 388 LEELKSSNAQKFELSDIAGRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPHASKL 447
L+ LK N Q F I+ ++ + +HG +Q+ L+H + E+ ++ ++L KL
Sbjct: 141 LQRLKPENFQ-FIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCDNLCDKLLALVDKL 199
Query: 448 MTDVFGNYVIQKFFEHGSPDQRKELAEKLVGQVLP----LSLQMYGCRVIQKALEVIELH 503
D FGNYV+Q + + + K+V + P LS+ +G VI+K L+ +
Sbjct: 200 TLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVIEKILKTAIVS 259
Query: 504 QKSQLVLEL-----DGHVMRCVRDQNGNHVIQKCIE 534
+ ++LE+ + + + D GN+V+Q ++
Sbjct: 260 EP--MILEILNNGGETGIQSLLNDSYGNYVLQTALD 293
>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 = 90.1 bits (222), Expect = 3e-18, Method: Compositional matrix adjust.
Identities = 54/187 (28%), Positives = 104/187 (55%), Gaps = 17/187 (9%)
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 GCRVIQP 567
GCRV+Q
Sbjct: 200 GCRVVQT 206
>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 = 90.1 bits (222), Expect = 3e-18, Method: Compositional matrix adjust.
Identities = 54/187 (28%), Positives = 104/187 (55%), Gaps = 17/187 (9%)
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 GCRVIQP 567
GCRV+Q
Sbjct: 199 GCRVVQT 205
>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 = 87.0 bits (214), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 53/187 (28%), Positives = 103/187 (55%), Gaps = 17/187 (9%)
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 GCRVIQP 567
GCRV+Q
Sbjct: 200 GCRVVQT 206
>pdb|3V71|A Chain A, Crystal Structure Of Puf-6 In Complex With 5be13 Rna
Length = 382
Score = 64.7 bits (156), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 41/169 (24%), Positives = 84/169 (49%), Gaps = 8/169 (4%)
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--QVATLSTHPYGCRVIQ 566
DQ HVIQ+ ++ +P + F + + + YGCR++Q
Sbjct: 140 CTDQISIHVIQRVVKQLPVDMWTFFVHFLSSGDSLMAVCQDKYGCRLVQ 188
Score = 30.8 bits (68), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 26/98 (26%), Positives = 43/98 (43%), Gaps = 14/98 (14%)
Query: 414 DQHGSRFIQQKLEHCSAEEKVSVFKEVLPHASKLMTDV-----------FGNYVIQKFFE 462
D++G R +QQ ++ + K+ FK + LMT + F NYVIQ +
Sbjct: 180 DKYGCRLVQQVIDRLAENPKLPCFKFRIQLLHSLMTCIVRNCYRLSSNEFANYVIQYVIK 239
Query: 463 HGSPDQ--RKELAEK-LVGQVLPLSLQMYGCRVIQKAL 497
+ R + +K L+ +L +S Y VI+ A
Sbjct: 240 SSGIMEMYRDTIIDKCLLRNLLSMSQDKYASHVIEGAF 277
>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 = 31.2 bits (69), Expect = 1.6, 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|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 = 31.2 bits (69), Expect = 1.8, 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|1U04|A Chain A, Crystal Structure Of Full Length Argonaute From Pyrococcus
Furiosus
Length = 771
Score = 30.4 bits (67), Expect = 2.7, 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 = 30.4 bits (67), Expect = 2.8, 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---ELENKI--RVRDDKG 340
Query: 526 NHV 528
N V
Sbjct: 341 NSV 343
>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 = 6.5, 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
>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 = 28.9 bits (63), Expect = 7.3, 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
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 0.389
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,265,824
Number of Sequences: 62578
Number of extensions: 646380
Number of successful extensions: 1223
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1063
Number of HSP's gapped (non-prelim): 69
length of query: 575
length of database: 14,973,337
effective HSP length: 104
effective length of query: 471
effective length of database: 8,465,225
effective search space: 3987120975
effective search space used: 3987120975
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: 54 (25.4 bits)