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= 004857
(727 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 = 398 bits (1023), Expect = e-111, Method: Compositional matrix adjust.
Identities = 194/338 (57%), Positives = 255/338 (75%), Gaps = 2/338 (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 QMSQHKYASNVVEKCLEYGDTAERELLIEEILGQSE-ENDNLLVMMKDQYANYVVQKILE 685
+SQHK+ASNVVEKC+ + AER LLI+E+ Q++ + L MMKDQYANYVVQK+++
Sbjct: 246 ALSQHKFASNVVEKCVTHASRAERALLIDEVCCQNDGPHSALYTMMKDQYANYVVQKMID 305
Query: 686 KCNEKLRETLISRIRVHCDALKKYTYGKHIVARFEQLY 723
R+ ++ +IR H L+KYTYGKHI+A+ E+ Y
Sbjct: 306 MAEPAQRKIIMHKIRPHITTLRKYTYGKHILAKLEKYY 343
>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 = 393 bits (1009), Expect = e-109, Method: Compositional matrix adjust.
Identities = 194/340 (57%), Positives = 255/340 (75%), Gaps = 4/340 (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 IVQMSQHKYASNVVEKCLEYGDTAERELLIEEILGQSE-ENDNLLVMMKDQYANYVVQKI 683
++ +SQHK+ASNVVEKC+ + AER LLI+E+ Q++ + L MMKDQYANYVVQK+
Sbjct: 244 VLALSQHKFASNVVEKCVTHASRAERALLIDEVCCQNDGPHSALYTMMKDQYANYVVQKM 303
Query: 684 LEKCNEKLRETLISRIRVHCDALKKYTYGKHIVARFEQLY 723
++ R+ ++ +IR H L+KYTYGKHI+A+ E+ Y
Sbjct: 304 IDMAEPAQRKIIMHKIRPHITTLRKYTYGKHILAKLEKYY 343
>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 = 376 bits (965), Expect = e-104, Method: Compositional matrix adjust.
Identities = 184/338 (54%), Positives = 250/338 (73%), Gaps = 2/338 (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 QMSQHKYASNVVEKCLEYGDTAERELLIEEILGQSE-ENDNLLVMMKDQYANYVVQKILE 685
+SQHK+ASNVVEKC+ + ER +LI+E+ ++ + L MMKDQYANYVVQK+++
Sbjct: 244 VLSQHKFASNVVEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMID 303
Query: 686 KCNEKLRETLISRIRVHCDALKKYTYGKHIVARFEQLY 723
R+ ++ +IR H L+KYTYGKHI+A+ E+ Y
Sbjct: 304 VAEPGQRKIVMHKIRPHIATLRKYTYGKHILAKLEKYY 341
Score = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 41/183 (22%), Positives = 73/183 (39%), Gaps = 30/183 (16%)
Query: 567 RVLEHCSDEQQGQCIVDEILESAFALAQDQYGNYVTQHVLERGKSYERTQILSKLAGKIV 626
R+LE + + + EI +QDQ+G+ Q LER ER + +++
Sbjct: 4 RLLEDFRNNRYPNLQLREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAY 63
Query: 627 QMSQHKYASNVVEKCLEYGDTAERELLIEEILGQ-------------------------- 660
Q+ + + V++K E+G ++ L E I G
Sbjct: 64 QLMVDVFGNYVIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQ 123
Query: 661 ----SEENDNLLVMMKDQYANYVVQKILEKCNEKLRETLISRIRVHCDALKKYTYGKHIV 716
E + ++L +KDQ N+VVQK +E + + +I + AL + YG ++
Sbjct: 124 NEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVI 183
Query: 717 ARF 719
R
Sbjct: 184 QRI 186
>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 = 375 bits (964), Expect = e-104, Method: Compositional matrix adjust.
Identities = 184/338 (54%), Positives = 250/338 (73%), Gaps = 2/338 (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 QMSQHKYASNVVEKCLEYGDTAERELLIEEILGQSE-ENDNLLVMMKDQYANYVVQKILE 685
+SQHK+ASNVVEKC+ + ER +LI+E+ ++ + L MMKDQYANYVVQK+++
Sbjct: 244 VLSQHKFASNVVEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMID 303
Query: 686 KCNEKLRETLISRIRVHCDALKKYTYGKHIVARFEQLY 723
R+ ++ +IR H L+KYTYGKHI+A+ E+ Y
Sbjct: 304 VAEPGQRKIVMHKIRPHIATLRKYTYGKHILAKLEKYY 341
Score = 43.5 bits (101), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 41/183 (22%), Positives = 73/183 (39%), Gaps = 30/183 (16%)
Query: 567 RVLEHCSDEQQGQCIVDEILESAFALAQDQYGNYVTQHVLERGKSYERTQILSKLAGKIV 626
R+LE + + + EI +QDQ+G+ Q LER ER + +++
Sbjct: 4 RLLEDFRNNRYPNLQLREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAY 63
Query: 627 QMSQHKYASNVVEKCLEYGDTAERELLIEEILGQ-------------------------- 660
Q+ + + V++K E+G ++ L E I G
Sbjct: 64 QLMVDVFGNYVIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQ 123
Query: 661 ----SEENDNLLVMMKDQYANYVVQKILEKCNEKLRETLISRIRVHCDALKKYTYGKHIV 716
E + ++L +KDQ N+VVQK +E + + +I + AL + YG ++
Sbjct: 124 NEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVI 183
Query: 717 ARF 719
R
Sbjct: 184 QRI 186
>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 = 372 bits (955), Expect = e-103, Method: Compositional matrix adjust.
Identities = 182/338 (53%), Positives = 250/338 (73%), Gaps = 2/338 (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 QMSQHKYASNVVEKCLEYGDTAERELLIEEILGQSE-ENDNLLVMMKDQYANYVVQKILE 685
+SQHK+ASNVVEKC+ + ER +LI+E+ ++ + L MMKDQYANYVVQK+++
Sbjct: 245 VLSQHKFASNVVEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMID 304
Query: 686 KCNEKLRETLISRIRVHCDALKKYTYGKHIVARFEQLY 723
R+ ++ +IR H L+KYTYGKHI+A+ E+ Y
Sbjct: 305 VAEPGQRKIVMHKIRPHIATLRKYTYGKHILAKLEKYY 342
Score = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 41/183 (22%), Positives = 73/183 (39%), Gaps = 30/183 (16%)
Query: 567 RVLEHCSDEQQGQCIVDEILESAFALAQDQYGNYVTQHVLERGKSYERTQILSKLAGKIV 626
R+LE + + + EI +QDQ+G+ Q LER ER + +++
Sbjct: 5 RLLEDFRNNRYPNLQLREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAY 64
Query: 627 QMSQHKYASNVVEKCLEYGDTAERELLIEEILGQ-------------------------- 660
Q+ + + V++K E+G ++ L E I G
Sbjct: 65 QLMVDVFGNYVIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQ 124
Query: 661 ----SEENDNLLVMMKDQYANYVVQKILEKCNEKLRETLISRIRVHCDALKKYTYGKHIV 716
E + ++L +KDQ N+VVQK +E + + +I + AL + YG ++
Sbjct: 125 NEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVI 184
Query: 717 ARF 719
R
Sbjct: 185 QRI 187
>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 = 361 bits (926), Expect = e-100, Method: Compositional matrix adjust.
Identities = 183/321 (57%), Positives = 235/321 (73%), Gaps = 5/321 (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 QMSQHKYASNVVEKCLEYGDTAERELLIEEILGQSEENDNLL-VMMKDQYANYVVQKILE 685
+SQHK+ASNVVEKC+ + ER LI+E+ NDN L VMMKDQYANYVVQK+++
Sbjct: 246 VLSQHKFASNVVEKCVTHATRGERTGLIDEV---CTFNDNALHVMMKDQYANYVVQKMID 302
Query: 686 KCNEKLRETLISRIRVHCDAL 706
+ L+++IR + AL
Sbjct: 303 VSEPTQLKKLMTKIRKNMAAL 323
Score = 100 bits (250), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 70/243 (28%), Positives = 120/243 (49%), Gaps = 7/243 (2%)
Query: 476 LVGQVLPLSLQMYGCRVIQKALEVIELHQKSQLVLELDGHVMRCVRDQNGNHVIQKCIEC 535
L ++ S +G R IQ+ LE +K + E+ + D GN+VIQK E
Sbjct: 24 LANHIVEFSQDQHGSRFIQQKLERATAAEKQMVFSEILAAAYSLMTDVFGNYVIQKFFEF 83
Query: 536 VPAEKIEFIISAFRGQVATLSTHPYGCRVIQRVLEHCSDEQQGQCIVDEILESAFALAQD 595
E+ + +G V L+ YGCRVIQ+ LE S EQQ Q IV E+ +D
Sbjct: 84 GTPEQKNTLGMQVKGHVLQLALQMYGCRVIQKALESISPEQQ-QEIVHELDGHVLKCVKD 142
Query: 596 QYGNYVTQHVLERGKSYERTQILSKLAGKIVQMSQHKYASNVVEKCLEYGDTAERELLIE 655
Q GN+V Q +E I++ G++ +S H Y V+++ LE+ + +++
Sbjct: 143 QNGNHVVQKCIECVDPVALQFIINAFKGQVYSLSTHPYGCRVIQRILEHCTAEQTTPILD 202
Query: 656 EILGQSEENDNLLVMMKDQYANYVVQKILEKCNEKLRETLISRIRVHCDALKKYTYGKHI 715
E+ +E+ +++DQY NYV+Q +LE ++ + LI+ +R L ++ + ++
Sbjct: 203 ELHEHTEQ------LIQDQYGNYVIQHVLEHGKQEDKSILINSVRGKVLVLSQHKFASNV 256
Query: 716 VAR 718
V +
Sbjct: 257 VEK 259
Score = 40.4 bits (93), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 31/152 (20%), Positives = 69/152 (45%), Gaps = 6/152 (3%)
Query: 567 RVLEHCSDEQQGQCIVDEILESAFALAQDQYGNYVTQHVLERGKSYERTQILSKLAGKIV 626
R+LE +++ + ++ +QDQ+G+ Q LER + E+ + S++
Sbjct: 6 RLLEDFRNQRYPNLQLRDLANHIVEFSQDQHGSRFIQQKLERATAAEKQMVFSEILAAAY 65
Query: 627 QMSQHKYASNVVEKCLEYGDTAERELLIEEILGQSEENDNLLVMMKDQYANYVVQKILEK 686
+ + + V++K E+G ++ L ++ G ++L + Y V+QK LE
Sbjct: 66 SLMTDVFGNYVIQKFFEFGTPEQKNTLGMQVKG------HVLQLALQMYGCRVIQKALES 119
Query: 687 CNEKLRETLISRIRVHCDALKKYTYGKHIVAR 718
+ + ++ ++ + H K G H+V +
Sbjct: 120 ISPEQQQEIVHELDGHVLKCVKDQNGNHVVQK 151
>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 = 282 bits (721), Expect = 6e-76, Method: Compositional matrix adjust.
Identities = 153/336 (45%), Positives = 220/336 (65%), Gaps = 15/336 (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 SNVVEKCLEYGDTAERELLIEEILGQS-------EENDNLLVMMKDQYANYVVQKILEKC 687
SNVVEK + YG +++L+I +IL + E++ +++M+KDQ+ANYV+QK++
Sbjct: 265 SNVVEKSILYGSKNQKDLIISKILPRDKNHALNLEDDSPMILMIKDQFANYVIQKLVNVS 324
Query: 688 NEKLRETLISRIRVHCDALKKY-TYGKHIVARFEQL 722
+ ++ ++ IR + D L K + G +A E+L
Sbjct: 325 EGEGKKLIVIAIRAYLDKLNKSNSLGNRHLASVEKL 360
>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 = 172 bits (437), Expect = 4e-43, Method: Compositional matrix adjust.
Identities = 101/290 (34%), Positives = 166/290 (57%), Gaps = 9/290 (3%)
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 NVVEKCLEYGDTAERELLIEEILGQSEENDNLLVMMKDQYANYVVQKILE 685
NV+EK L+ +E +L EIL E + ++ D Y NYV+Q L+
Sbjct: 247 NVIEKILKTAIVSEPMIL--EILNNGGET-GIQSLLNDSYGNYVLQTALD 293
Score = 98.2 bits (243), Expect = 1e-20, Method: Compositional matrix adjust.
Identities = 56/219 (25%), Positives = 113/219 (51%), Gaps = 6/219 (2%)
Query: 472 LAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQKSQLVLELDGHVMRCVRDQNGNHVIQK 531
+ ++ +G + L +GCR +QK L+++ + E + + + D GN++IQK
Sbjct: 7 VLDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQK 66
Query: 532 CIECVPAEKIEFIISAFRGQVATLSTHPYGCRVIQRVLEHCSDEQQGQCIVDEILESAFA 591
+E V E+ + +S +P+GCR +Q+++E +++ Q +VD +
Sbjct: 67 LLEEVTTEQRIVLTKISSPHFVEISLNPHGCRALQKLIECIKTDEEAQIVVDSLRPYTVQ 126
Query: 592 LAQDQYGNYVTQHVLERGKSYERTQILSKLAGKIVQMSQHKYASNVVEKCLEYGDTAERE 651
L++D GN+V Q L+R K I ++ + ++ H++ V+++CL++G T + +
Sbjct: 127 LSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCRVLQRCLDHGTTEQCD 186
Query: 652 LLIEEILGQSEENDNLLVMMKDQYANYVVQKILEKCNEK 690
L +++L ++ + D + NYVVQ I+ K EK
Sbjct: 187 NLCDKLLALVDK------LTLDPFGNYVVQYIITKEAEK 219
Score = 58.2 bits (139), 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 = 55/245 (22%), Positives = 100/245 (40%), 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 RVLEHCSDEQQGQCIVDEILESAF-----ALAQDQYGNYVTQHVLERGKSYERTQILSKL 621
++L+ + ++ EIL + +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 = 166 bits (421), Expect = 4e-41, Method: Compositional matrix adjust.
Identities = 99/290 (34%), Positives = 164/290 (56%), Gaps = 9/290 (3%)
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 NVVEKCLEYGDTAERELLIEEILGQSEENDNLLVMMKDQYANYVVQKILE 685
NV+EK L+ +E +L EIL E + ++ D Y NYV+Q L+
Sbjct: 269 NVIEKILKTAIVSEPMIL--EILNNGGET-GIQSLLNDSYGNYVLQTALD 315
Score = 94.4 bits (233), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 55/219 (25%), Positives = 112/219 (51%), Gaps = 6/219 (2%)
Query: 472 LAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQKSQLVLELDGHVMRCVRDQNGNHVIQK 531
+ ++ +G + L +GCR +QK L+++ + E + + + D GN++IQK
Sbjct: 29 VLDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQK 88
Query: 532 CIECVPAEKIEFIISAFRGQVATLSTHPYGCRVIQRVLEHCSDEQQGQCIVDEILESAFA 591
+E V E+ + +S +P+G R +Q+++E +++ Q +VD +
Sbjct: 89 LLEEVTTEQRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYTVQ 148
Query: 592 LAQDQYGNYVTQHVLERGKSYERTQILSKLAGKIVQMSQHKYASNVVEKCLEYGDTAERE 651
L++D GN+V Q L+R K I ++ + ++ H++ V+++CL++G T + +
Sbjct: 149 LSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCD 208
Query: 652 LLIEEILGQSEENDNLLVMMKDQYANYVVQKILEKCNEK 690
L +++L ++ + D + NYVVQ I+ K EK
Sbjct: 209 NLCDKLLALVDK------LTLDPFGNYVVQYIITKEAEK 241
>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 = 165 bits (418), Expect = 7e-41, Method: Compositional matrix adjust.
Identities = 99/290 (34%), Positives = 164/290 (56%), Gaps = 9/290 (3%)
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 NVVEKCLEYGDTAERELLIEEILGQSEENDNLLVMMKDQYANYVVQKILE 685
NV+EK L+ +E +L EIL E + ++ D Y NYV+Q L+
Sbjct: 247 NVIEKILKTAIVSEPMIL--EILNNGGET-GIQSLLNDSYGNYVLQTALD 293
Score = 93.6 bits (231), Expect = 3e-19, Method: Compositional matrix adjust.
Identities = 55/219 (25%), Positives = 112/219 (51%), Gaps = 6/219 (2%)
Query: 472 LAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQKSQLVLELDGHVMRCVRDQNGNHVIQK 531
+ ++ +G + L +GCR +QK L+++ + E + + + D GN++IQK
Sbjct: 7 VLDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQK 66
Query: 532 CIECVPAEKIEFIISAFRGQVATLSTHPYGCRVIQRVLEHCSDEQQGQCIVDEILESAFA 591
+E V E+ + +S +P+G R +Q+++E +++ Q +VD +
Sbjct: 67 LLEEVTTEQRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYTVQ 126
Query: 592 LAQDQYGNYVTQHVLERGKSYERTQILSKLAGKIVQMSQHKYASNVVEKCLEYGDTAERE 651
L++D GN+V Q L+R K I ++ + ++ H++ V+++CL++G T + +
Sbjct: 127 LSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCD 186
Query: 652 LLIEEILGQSEENDNLLVMMKDQYANYVVQKILEKCNEK 690
L +++L ++ + D + NYVVQ I+ K EK
Sbjct: 187 NLCDKLLALVDK------LTLDPFGNYVVQYIITKEAEK 219
Score = 50.1 bits (118), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 55/245 (22%), Positives = 100/245 (40%), 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 RVLEHCSDEQQGQCIVDEILESAF-----ALAQDQYGNYVTQHVLERGKSYERTQILSKL 621
++L+ + ++ EIL + +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 = 165 bits (418), Expect = 8e-41, Method: Compositional matrix adjust.
Identities = 99/290 (34%), Positives = 164/290 (56%), Gaps = 9/290 (3%)
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 NVVEKCLEYGDTAERELLIEEILGQSEENDNLLVMMKDQYANYVVQKILE 685
NV+EK L+ +E +L EIL E + ++ D Y NYV+Q L+
Sbjct: 247 NVIEKILKTAIVSEPMIL--EILNNGGET-GIQSLLNDSYGNYVLQTALD 293
Score = 93.6 bits (231), Expect = 4e-19, Method: Compositional matrix adjust.
Identities = 55/219 (25%), Positives = 112/219 (51%), Gaps = 6/219 (2%)
Query: 472 LAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQKSQLVLELDGHVMRCVRDQNGNHVIQK 531
+ ++ +G + L +GCR +QK L+++ + E + + + D GN++IQK
Sbjct: 7 VLDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQK 66
Query: 532 CIECVPAEKIEFIISAFRGQVATLSTHPYGCRVIQRVLEHCSDEQQGQCIVDEILESAFA 591
+E V E+ + +S +P+G R +Q+++E +++ Q +VD +
Sbjct: 67 LLEEVTTEQRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYTVQ 126
Query: 592 LAQDQYGNYVTQHVLERGKSYERTQILSKLAGKIVQMSQHKYASNVVEKCLEYGDTAERE 651
L++D GN+V Q L+R K I ++ + ++ H++ V+++CL++G T + +
Sbjct: 127 LSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCD 186
Query: 652 LLIEEILGQSEENDNLLVMMKDQYANYVVQKILEKCNEK 690
L +++L ++ + D + NYVVQ I+ K EK
Sbjct: 187 NLCDKLLALVDK------LTLDPFGNYVVQYIITKEAEK 219
Score = 50.1 bits (118), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 55/245 (22%), Positives = 100/245 (40%), 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 RVLEHCSDEQQGQCIVDEILESAF-----ALAQDQYGNYVTQHVLERGKSYERTQILSKL 621
++L+ + ++ EIL + +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 = 127 bits (318), Expect = 3e-29, Method: Compositional matrix adjust.
Identities = 90/329 (27%), Positives = 164/329 (49%), Gaps = 39/329 (11%)
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--SYERTQILSKLAGKIVQMSQHKYASNVVEKCLEYGDTAERELLIEEILGQ--- 660
+ Y I L ++ +SQ K+AS+VVEK + +++EI
Sbjct: 260 VSNDDLAVYRECIIEKCLMRNLLSLSQEKFASHVVEKAFLHAPLELLAEMMDEIFDGYIP 319
Query: 661 --SEENDNLLVMMKDQYANYVVQKILEKC 687
D L +MM Q+ NYVVQ +L C
Sbjct: 320 HPDTGKDALDIMMFHQFGNYVVQCMLTIC 348
>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 = 127 bits (318), Expect = 3e-29, Method: Compositional matrix adjust.
Identities = 90/329 (27%), Positives = 164/329 (49%), Gaps = 39/329 (11%)
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--SYERTQILSKLAGKIVQMSQHKYASNVVEKCLEYGDTAERELLIEEILGQ--- 660
+ Y I L ++ +SQ K+AS+VVEK + +++EI
Sbjct: 259 VSNDDLAVYRECIIEKCLMRNLLSLSQEKFASHVVEKAFLHAPLELLAEMMDEIFDGYIP 318
Query: 661 --SEENDNLLVMMKDQYANYVVQKILEKC 687
D L +MM Q+ NYVVQ +L C
Sbjct: 319 HPDTGKDALDIMMFHQFGNYVVQCMLTIC 347
>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 = 124 bits (310), Expect = 3e-28, Method: Compositional matrix adjust.
Identities = 89/329 (27%), Positives = 163/329 (49%), Gaps = 39/329 (11%)
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--SYERTQILSKLAGKIVQMSQHKYASNVVEKCLEYGDTAERELLIEEILGQ--- 660
+ Y I L ++ +SQ K+AS+VVEK + +++EI
Sbjct: 260 VSNDDLAVYRECIIEKCLMRNLLSLSQEKFASHVVEKAFLHAPLELLAEMMDEIFDGYIP 319
Query: 661 --SEENDNLLVMMKDQYANYVVQKILEKC 687
D L +MM Q+ NYVVQ +L C
Sbjct: 320 HPDTGKDALDIMMFHQFGNYVVQCMLTIC 348
>pdb|3V71|A Chain A, Crystal Structure Of Puf-6 In Complex With 5be13 Rna
Length = 382
Score = 116 bits (291), Expect = 4e-26, Method: Compositional matrix adjust.
Identities = 87/356 (24%), Positives = 169/356 (47%), Gaps = 45/356 (12%)
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----QSEEN-DNLLVMMKDQYANYV 679
++ MSQ KYAS+V+E + A ++EEI E N D L +++ QY NYV
Sbjct: 260 LLSMSQDKYASHVIEGAFLFAPPALLHEMMEEIFSGYVKDVESNRDALDILLFHQYGNYV 319
Query: 680 VQKILEKCNEKL-------------------RETLISRIRVHCDALKKYTYGKHIV 716
VQ+++ C L E + R+ H L++++ GK I+
Sbjct: 320 VQQMISICTAALIGKEERELPPAILLLYSGWYEKMKQRVLQHASRLERFSSGKKII 375
>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 = 32.0 bits (71), Expect = 1.3, 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 = 30.0 bits (66), Expect = 4.3, 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 = 5.0, 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 = 5.0, 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 = 30.0 bits (66), Expect = 5.3, 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
>pdb|1O5L|A Chain A, Crystal Structure Of Transcriptional Regulator (Tm1171)
From Thermotoga Maritima At 2.30 A Resolution
Length = 213
Score = 29.6 bits (65), Expect = 6.3, Method: Composition-based stats.
Identities = 30/132 (22%), Positives = 64/132 (48%), Gaps = 10/132 (7%)
Query: 583 DEILESAFALAQDQYGNYVTQHVLERGKSYERTQI--LSKLAGKIVQMSQHKYASNVVEK 640
D+ +E L + G T+HV E GK+ E +I + +A + S+ ++ NVV
Sbjct: 37 DDPIEDVLILLE---GTLKTEHVSENGKTLEIDEIKPVQIIASGFIFSSEPRFPVNVVAG 93
Query: 641 CLEYGDTAERELLIEEILGQSEENDNLLVMMKD--QYANYVVQKILEKCNEKLRETLISR 698
+ +E+ ++ ++ ++ + LL +KD ++ V +K+ + LRE L++
Sbjct: 94 ENSKILSIPKEVFLDLLM---KDRELLLFFLKDVSEHFRVVSEKLFFLTTKTLREKLMNF 150
Query: 699 IRVHCDALKKYT 710
+ H + ++ T
Sbjct: 151 LVRHMNEKRELT 162
>pdb|3GTN|A Chain A, Crystal Structure Of Xync From Bacillus Subtilis 168
pdb|3GTN|B Chain B, Crystal Structure Of Xync From Bacillus Subtilis 168
pdb|3KL0|A Chain A, Crystal Structure Of The Glucuronoxylan Xylanohydrolase
Xync From Bacillus Subtilis
pdb|3KL0|B Chain B, Crystal Structure Of The Glucuronoxylan Xylanohydrolase
Xync From Bacillus Subtilis
pdb|3KL0|C Chain C, Crystal Structure Of The Glucuronoxylan Xylanohydrolase
Xync From Bacillus Subtilis
pdb|3KL0|D Chain D, Crystal Structure Of The Glucuronoxylan Xylanohydrolase
Xync From Bacillus Subtilis
pdb|3KL3|A Chain A, Crystal Structure Of Ligand Bound Xync
pdb|3KL3|B Chain B, Crystal Structure Of Ligand Bound Xync
pdb|3KL3|C Chain C, Crystal Structure Of Ligand Bound Xync
pdb|3KL3|D Chain D, Crystal Structure Of Ligand Bound Xync
pdb|3KL5|A Chain A, Structure Analysis Of A Xylanase From Glycosyl Hydrolase
Family Thirty: Carbohydrate Ligand Complexes Reveal This
Family Of Enzymes Unique Mechanism Of Substrate
Specificity And Recognition
pdb|3KL5|B Chain B, Structure Analysis Of A Xylanase From Glycosyl Hydrolase
Family Thirty: Carbohydrate Ligand Complexes Reveal This
Family Of Enzymes Unique Mechanism Of Substrate
Specificity And Recognition
pdb|3KL5|C Chain C, Structure Analysis Of A Xylanase From Glycosyl Hydrolase
Family Thirty: Carbohydrate Ligand Complexes Reveal This
Family Of Enzymes Unique Mechanism Of Substrate
Specificity And Recognition
pdb|3KL5|D Chain D, Structure Analysis Of A Xylanase From Glycosyl Hydrolase
Family Thirty: Carbohydrate Ligand Complexes Reveal This
Family Of Enzymes Unique Mechanism Of Substrate
Specificity And Recognition
Length = 401
Score = 29.3 bits (64), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 25/95 (26%), Positives = 44/95 (46%), Gaps = 4/95 (4%)
Query: 587 ESAFALAQDQYGNYVTQ-HVLERGKSYERTQILSKLA---GKIVQMSQHKYASNVVEKCL 642
E+AF Q+Q G + + HV E ++ + +K A G IV S S++VE
Sbjct: 37 ETAFGNGQNQLGFSILRIHVDENRNNWYKEVETAKSAVKHGAIVFASPWNPPSDMVETFN 96
Query: 643 EYGDTAERELLIEEILGQSEENDNLLVMMKDQYAN 677
GDT+ + L + ++ ++ + MK+ N
Sbjct: 97 RNGDTSAKRLKYNKYAAYAQHLNDFVTFMKNNGVN 131
>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 = 8.2, 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
0.316 0.132 0.384
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 20,484,816
Number of Sequences: 62578
Number of extensions: 823108
Number of successful extensions: 1967
Number of sequences better than 100.0: 29
Number of HSP's better than 100.0 without gapping: 21
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 1622
Number of HSP's gapped (non-prelim): 50
length of query: 727
length of database: 14,973,337
effective HSP length: 106
effective length of query: 621
effective length of database: 8,340,069
effective search space: 5179182849
effective search space used: 5179182849
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)