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= 042165
(983 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 = 400 bits (1028), Expect = e-111, Method: Compositional matrix adjust.
Identities = 188/336 (55%), Positives = 254/336 (75%), Gaps = 4/336 (1%)
Query: 639 NFLEELKSGKGRRFELSDITGHIVEFSADQHGSRFIQQKLENCSVDEKASVFKEILPHAS 698
LE+ ++ + +L D+ GHIVEFS DQHGSRFIQQKLE + E+ VF EIL A
Sbjct: 6 RLLEDFRNNRFPNLQLRDLIGHIVEFSQDQHGSRFIQQKLERATPAERQIVFNEILQAAY 65
Query: 699 KLMTDVFGNYVIQKFFEYGSPAQRKELANQLVGQILPLSMQMYGCRVIQKALETIEIEQK 758
+LMTDVFGNYVIQKFFE+GS Q+ LA ++ G +LPL++QMYGCRVIQKALE+I +Q+
Sbjct: 66 QLMTDVFGNYVIQKFFEFGSLDQKLALATRIRGHVLPLALQMYGCRVIQKALESISSDQQ 125
Query: 759 AQLVRELDGQVMRCVRDQNGNHVIQKCIECIPPEKIGFIISAFCGQVAALSMHPYGCRVI 818
+++V+ELDG V++CV+DQNGNHV+QKCIEC+ P+ + FII AF GQV LS HPYGCRVI
Sbjct: 126 SEMVKELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFVLSTHPYGCRVI 185
Query: 819 QRVLEHCADKHQCQFIVDEILDNVCALAQDQYGNYVTQHVLQRGKPLERSKIIRKLSGHI 878
QR+LEHC + Q I++E+ + L QDQYGNYV QHVL+ G+P ++SKI+ ++ G +
Sbjct: 186 QRILEHCTAE-QTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGKV 244
Query: 879 VQLSQHKFASNVIEKCLAYGGPAERELIIEEILGHNE---ETLLTMMKDQFANYVVQKIF 935
+ LSQHKFASNV+EKC+ + AER L+I+E+ N+ L TMMKDQ+ANYVVQK+
Sbjct: 245 LALSQHKFASNVVEKCVTHASRAERALLIDEVCCQNDGPHSALYTMMKDQYANYVVQKMI 304
Query: 936 ELSSESQQAMMLSRIRTHAHVLKKYTYGKHIVARFE 971
+++ +Q+ +++ +IR H L+KYTYGKHI+A+ E
Sbjct: 305 DMAEPAQRKIIMHKIRPHITTLRKYTYGKHILAKLE 340
>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 = 395 bits (1015), Expect = e-110, Method: Compositional matrix adjust.
Identities = 188/338 (55%), Positives = 254/338 (75%), Gaps = 6/338 (1%)
Query: 639 NFLEELKSGKGRRFELSDITGHIVEFSADQHGSRFIQQKLENCSVDEKASVFKEILPHAS 698
LE+ ++ + +L D+ GHIVEFS DQHGSRFIQQKLE + E+ VF EIL A
Sbjct: 4 RLLEDFRNNRFPNLQLRDLIGHIVEFSQDQHGSRFIQQKLERATPAERQMVFNEILQAAY 63
Query: 699 KLMTDVFGNYVIQKFFEYGSPAQRKELANQLVGQILPLSMQMYGCRVIQKALETIEIEQK 758
+LMTDVFGNYVIQKFFE+GS Q+ LA ++ G +LPL++QMYGCRVIQKALE+I +Q+
Sbjct: 64 QLMTDVFGNYVIQKFFEFGSLDQKLALATRIRGHVLPLALQMYGCRVIQKALESISSDQQ 123
Query: 759 --AQLVRELDGQVMRCVRDQNGNHVIQKCIECIPPEKIGFIISAFCGQVAALSMHPYGCR 816
+++V+ELDG V++CV+DQNGNHV+QKCIEC+ P+ + FII AF GQV LS HPYGCR
Sbjct: 124 VISEMVKELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFVLSTHPYGCR 183
Query: 817 VIQRVLEHCADKHQCQFIVDEILDNVCALAQDQYGNYVTQHVLQRGKPLERSKIIRKLSG 876
VIQR+LEHC + Q I++E+ + L QDQYGNYV QHVL+ G+P ++SKI+ ++ G
Sbjct: 184 VIQRILEHCTAE-QTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRG 242
Query: 877 HIVQLSQHKFASNVIEKCLAYGGPAERELIIEEILGHNE---ETLLTMMKDQFANYVVQK 933
++ LSQHKFASNV+EKC+ + AER L+I+E+ N+ L TMMKDQ+ANYVVQK
Sbjct: 243 KVLALSQHKFASNVVEKCVTHASRAERALLIDEVCCQNDGPHSALYTMMKDQYANYVVQK 302
Query: 934 IFELSSESQQAMMLSRIRTHAHVLKKYTYGKHIVARFE 971
+ +++ +Q+ +++ +IR H L+KYTYGKHI+A+ E
Sbjct: 303 MIDMAEPAQRKIIMHKIRPHITTLRKYTYGKHILAKLE 340
>pdb|1IB2|A Chain A, Crystal Structure Of A Pumilio-Homology Domain
pdb|1M8Z|A Chain A, Crystal Structure Of A Pumilio-Homology Domain
pdb|1M8W|A Chain A, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Nre1-19 Rna
pdb|1M8W|B Chain B, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Nre1-19 Rna
pdb|1M8X|A Chain A, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Nre1-14 Rna
pdb|1M8X|B Chain B, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Nre1-14 Rna
pdb|1M8Y|A Chain A, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Nre2-10 Rna
pdb|1M8Y|B Chain B, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Nre2-10 Rna
pdb|3Q0L|A Chain A, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With P38alpha Nrea
pdb|3Q0L|B Chain B, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With P38alpha Nrea
pdb|3Q0M|A Chain A, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With P38alpha Nreb
pdb|3Q0M|B Chain B, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With P38alpha Nreb
pdb|3Q0N|A Chain A, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Erk2 Nre
pdb|3Q0N|B Chain B, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Erk2 Nre
pdb|3Q0O|A Chain A, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Erk2 Nre
pdb|3Q0O|B Chain B, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Erk2 Nre
pdb|3Q0P|A Chain A, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Hunchback Nre
pdb|3Q0P|B Chain B, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Hunchback Nre
Length = 349
Score = 384 bits (985), Expect = e-106, Method: Compositional matrix adjust.
Identities = 184/335 (54%), Positives = 248/335 (74%), Gaps = 4/335 (1%)
Query: 640 FLEELKSGKGRRFELSDITGHIVEFSADQHGSRFIQQKLENCSVDEKASVFKEILPHASK 699
LE+ ++ + +L +I GHI+EFS DQHGSRFIQ KLE + E+ VF EIL A +
Sbjct: 5 LLEDFRNNRYPNLQLREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQ 64
Query: 700 LMTDVFGNYVIQKFFEYGSPAQRKELANQLVGQILPLSMQMYGCRVIQKALETIEIEQKA 759
LM DVFGNYVIQKFFE+GS Q+ LA ++ G +L L++QMYGCRVIQKALE I +Q+
Sbjct: 65 LMVDVFGNYVIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQN 124
Query: 760 QLVRELDGQVMRCVRDQNGNHVIQKCIECIPPEKIGFIISAFCGQVAALSMHPYGCRVIQ 819
++VRELDG V++CV+DQNGNHV+QKCIEC+ P+ + FII AF GQV ALS HPYGCRVIQ
Sbjct: 125 EMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQ 184
Query: 820 RVLEHCADKHQCQFIVDEILDNVCALAQDQYGNYVTQHVLQRGKPLERSKIIRKLSGHIV 879
R+LEHC Q I++E+ + L QDQYGNYV QHVL+ G+P ++SKI+ ++ G+++
Sbjct: 185 RILEHCLPD-QTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVL 243
Query: 880 QLSQHKFASNVIEKCLAYGGPAERELIIEEILGHNE---ETLLTMMKDQFANYVVQKIFE 936
LSQHKFASNV+EKC+ + ER ++I+E+ N+ L TMMKDQ+ANYVVQK+ +
Sbjct: 244 VLSQHKFASNVVEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMID 303
Query: 937 LSSESQQAMMLSRIRTHAHVLKKYTYGKHIVARFE 971
++ Q+ +++ +IR H L+KYTYGKHI+A+ E
Sbjct: 304 VAEPGQRKIVMHKIRPHIATLRKYTYGKHILAKLE 338
>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 = 383 bits (984), Expect = e-106, Method: Compositional matrix adjust.
Identities = 184/336 (54%), Positives = 248/336 (73%), Gaps = 4/336 (1%)
Query: 639 NFLEELKSGKGRRFELSDITGHIVEFSADQHGSRFIQQKLENCSVDEKASVFKEILPHAS 698
LE+ ++ + +L +I GHI+EFS DQHGSRFIQ KLE + E+ VF EIL A
Sbjct: 4 RLLEDFRNNRYPNLQLREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAY 63
Query: 699 KLMTDVFGNYVIQKFFEYGSPAQRKELANQLVGQILPLSMQMYGCRVIQKALETIEIEQK 758
+LM DVFGNYVIQKFFE+GS Q+ LA ++ G +L L++QMYGCRVIQKALE I +Q+
Sbjct: 64 QLMVDVFGNYVIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQ 123
Query: 759 AQLVRELDGQVMRCVRDQNGNHVIQKCIECIPPEKIGFIISAFCGQVAALSMHPYGCRVI 818
++VRELDG V++CV+DQNGNHV+QKCIEC+ P+ + FII AF GQV ALS HPYGCRVI
Sbjct: 124 NEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVI 183
Query: 819 QRVLEHCADKHQCQFIVDEILDNVCALAQDQYGNYVTQHVLQRGKPLERSKIIRKLSGHI 878
QR+LEHC Q I++E+ + L QDQYGNYV QHVL+ G+P ++SKI+ ++ G++
Sbjct: 184 QRILEHCLPD-QTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNV 242
Query: 879 VQLSQHKFASNVIEKCLAYGGPAERELIIEEILGHNE---ETLLTMMKDQFANYVVQKIF 935
+ LSQHKFASNV+EKC+ + ER ++I+E+ N+ L TMMKDQ+ANYVVQK+
Sbjct: 243 LVLSQHKFASNVVEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMI 302
Query: 936 ELSSESQQAMMLSRIRTHAHVLKKYTYGKHIVARFE 971
+++ Q+ +++ +IR H L+KYTYGKHI+A+ E
Sbjct: 303 DVAEPGQRKIVMHKIRPHIATLRKYTYGKHILAKLE 338
>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 = 380 bits (975), Expect = e-105, Method: Compositional matrix adjust.
Identities = 182/336 (54%), Positives = 248/336 (73%), Gaps = 4/336 (1%)
Query: 639 NFLEELKSGKGRRFELSDITGHIVEFSADQHGSRFIQQKLENCSVDEKASVFKEILPHAS 698
LE+ ++ + +L +I GHI+EFS DQHGSRFIQ KLE + E+ VF EIL A
Sbjct: 5 RLLEDFRNNRYPNLQLREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAY 64
Query: 699 KLMTDVFGNYVIQKFFEYGSPAQRKELANQLVGQILPLSMQMYGCRVIQKALETIEIEQK 758
+LM DVFGNYVIQKFFE+GS Q+ LA ++ G +L L++QMYGCRVIQKALE I +Q+
Sbjct: 65 QLMVDVFGNYVIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQ 124
Query: 759 AQLVRELDGQVMRCVRDQNGNHVIQKCIECIPPEKIGFIISAFCGQVAALSMHPYGCRVI 818
++VRELDG V++CV+DQNGNHV+QKCIEC+ P+ + FII AF GQV ALS HPYGCRVI
Sbjct: 125 NEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVI 184
Query: 819 QRVLEHCADKHQCQFIVDEILDNVCALAQDQYGNYVTQHVLQRGKPLERSKIIRKLSGHI 878
QR+LEHC Q I++E+ + L QDQYG+YV +HVL+ G+P ++SKI+ ++ G++
Sbjct: 185 QRILEHCLPD-QTLPILEELHQHTEQLVQDQYGSYVIRHVLEHGRPEDKSKIVAEIRGNV 243
Query: 879 VQLSQHKFASNVIEKCLAYGGPAERELIIEEILGHNE---ETLLTMMKDQFANYVVQKIF 935
+ LSQHKFASNV+EKC+ + ER ++I+E+ N+ L TMMKDQ+ANYVVQK+
Sbjct: 244 LVLSQHKFASNVVEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMI 303
Query: 936 ELSSESQQAMMLSRIRTHAHVLKKYTYGKHIVARFE 971
+++ Q+ +++ +IR H L+KYTYGKHI+A+ E
Sbjct: 304 DVAEPGQRKIVMHKIRPHIATLRKYTYGKHILAKLE 339
>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 = 364 bits (934), Expect = e-100, Method: Compositional matrix adjust.
Identities = 174/312 (55%), Positives = 229/312 (73%), Gaps = 1/312 (0%)
Query: 640 FLEELKSGKGRRFELSDITGHIVEFSADQHGSRFIQQKLENCSVDEKASVFKEILPHASK 699
LE+ ++ + +L D+ HIVEFS DQHGSRFIQQKLE + EK VF EIL A
Sbjct: 7 LLEDFRNQRYPNLQLRDLANHIVEFSQDQHGSRFIQQKLERATAAEKQMVFSEILAAAYS 66
Query: 700 LMTDVFGNYVIQKFFEYGSPAQRKELANQLVGQILPLSMQMYGCRVIQKALETIEIEQKA 759
LMTDVFGNYVIQKFFE+G+P Q+ L Q+ G +L L++QMYGCRVIQKALE+I EQ+
Sbjct: 67 LMTDVFGNYVIQKFFEFGTPEQKNTLGMQVKGHVLQLALQMYGCRVIQKALESISPEQQQ 126
Query: 760 QLVRELDGQVMRCVRDQNGNHVIQKCIECIPPEKIGFIISAFCGQVAALSMHPYGCRVIQ 819
++V ELDG V++CV+DQNGNHV+QKCIEC+ P + FII+AF GQV +LS HPYGCRVIQ
Sbjct: 127 EIVHELDGHVLKCVKDQNGNHVVQKCIECVDPVALQFIINAFKGQVYSLSTHPYGCRVIQ 186
Query: 820 RVLEHCADKHQCQFIVDEILDNVCALAQDQYGNYVTQHVLQRGKPLERSKIIRKLSGHIV 879
R+LEHC + Q I+DE+ ++ L QDQYGNYV QHVL+ GK ++S +I + G ++
Sbjct: 187 RILEHCTAE-QTTPILDELHEHTEQLIQDQYGNYVIQHVLEHGKQEDKSILINSVRGKVL 245
Query: 880 QLSQHKFASNVIEKCLAYGGPAERELIIEEILGHNEETLLTMMKDQFANYVVQKIFELSS 939
LSQHKFASNV+EKC+ + ER +I+E+ N+ L MMKDQ+ANYVVQK+ ++S
Sbjct: 246 VLSQHKFASNVVEKCVTHATRGERTGLIDEVCTFNDNALHVMMKDQYANYVVQKMIDVSE 305
Query: 940 ESQQAMMLSRIR 951
+Q ++++IR
Sbjct: 306 PTQLKKLMTKIR 317
Score = 110 bits (276), Expect = 3e-24, Method: Compositional matrix adjust.
Identities = 80/274 (29%), Positives = 138/274 (50%), Gaps = 17/274 (6%)
Query: 696 HASKLMTDVFGNYVIQKFFEYGSPAQRKELANQLVGQILPLSMQMYGCRVIQKALETIEI 755
H S+L+ D F N Q++ Q ++LAN +V S +G R IQ+ LE
Sbjct: 3 HMSRLLED-FRN---QRY----PNLQLRDLANHIV----EFSQDQHGSRFIQQKLERATA 50
Query: 756 EQKAQLVRELDGQVMRCVRDQNGNHVIQKCIECIPPEKIGFIISAFCGQVAALSMHPYGC 815
+K + E+ + D GN+VIQK E PE+ + G V L++ YGC
Sbjct: 51 AEKQMVFSEILAAAYSLMTDVFGNYVIQKFFEFGTPEQKNTLGMQVKGHVLQLALQMYGC 110
Query: 816 RVIQRVLEHCADKHQCQFIVDEILDNVCALAQDQYGNYVTQHVLQRGKPLERSKIIRKLS 875
RVIQ+ LE + + Q Q IV E+ +V +DQ GN+V Q ++ P+ II
Sbjct: 111 RVIQKALESISPEQQ-QEIVHELDGHVLKCVKDQNGNHVVQKCIECVDPVALQFIINAFK 169
Query: 876 GHIVQLSQHKFASNVIEKCLAYGGPAERELIIEEILGHNEETLLTMMKDQFANYVVQKIF 935
G + LS H + VI++ L + + I++E+ H E+ +++DQ+ NYV+Q +
Sbjct: 170 GQVYSLSTHPYGCRVIQRILEHCTAEQTTPILDELHEHTEQ----LIQDQYGNYVIQHVL 225
Query: 936 ELSSESQQAMMLSRIRTHAHVLKKYTYGKHIVAR 969
E + ++++++ +R VL ++ + ++V +
Sbjct: 226 EHGKQEDKSILINSVRGKVLVLSQHKFASNVVEK 259
>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 = 286 bits (732), Expect = 3e-77, Method: Compositional matrix adjust.
Identities = 150/321 (46%), Positives = 209/321 (65%), Gaps = 16/321 (4%)
Query: 654 LSDITGHIVEFSADQHGSRFIQQKLENCSVDEKASVFKEILPHASKLMTDVFGNYVIQKF 713
L DI GH +EF DQHGSRFIQ++L EK +F EI A +L DVFGNYVIQKF
Sbjct: 26 LKDIFGHSLEFCKDQHGSRFIQRELATSPASEKEVIFNEIRDDAIELSNDVFGNYVIQKF 85
Query: 714 FEYGSPAQRKELANQLVGQILPLSMQMYGCRVIQKALETIEIEQKAQLVRELDGQVMRCV 773
FE+GS Q+ L +Q G + LS+QMY CRVIQKALE I+ Q+ +LV EL V++ +
Sbjct: 86 FEFGSKIQKNTLVDQFKGNMKQLSLQMYACRVIQKALEYIDSNQRIELVLELSDSVLQMI 145
Query: 774 RDQNGNHVIQKCIECIPPEKIGFIISAFCGQVAALSMHPYGCRVIQRVLEHCADKHQCQF 833
+DQNGNHVIQK IE IP EK+ FI+S+ G + LS H YGCRVIQR+LE + + Q +
Sbjct: 146 KDQNGNHVIQKAIETIPIEKLPFILSSLTGHIYHLSTHSYGCRVIQRLLEFGSSEDQ-ES 204
Query: 834 IVDEILDNVCALAQDQYGNYVTQHVLQRGKPLERS------KIIRKLSGHIVQLSQHKFA 887
I++E+ D + L QDQYGNYV Q+VLQ+ + + +II ++ ++V+ S+HKFA
Sbjct: 205 ILNELKDFIPYLIQDQYGNYVIQYVLQQDQFTNKEMVDIKQEIIETVANNVVEYSKHKFA 264
Query: 888 SNVIEKCLAYGGPAERELIIEEIL---------GHNEETLLTMMKDQFANYVVQKIFELS 938
SNV+EK + YG +++LII +IL ++ ++ M+KDQFANYV+QK+ +S
Sbjct: 265 SNVVEKSILYGSKNQKDLIISKILPRDKNHALNLEDDSPMILMIKDQFANYVIQKLVNVS 324
Query: 939 SESQQAMMLSRIRTHAHVLKK 959
+ +++ IR + L K
Sbjct: 325 EGEGKKLIVIAIRAYLDKLNK 345
Score = 79.0 bits (193), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 52/176 (29%), Positives = 88/176 (50%), Gaps = 21/176 (11%)
Query: 822 LEHCADKHQCQFI---------------VDEILDNVCALAQDQYGNYVTQHVLQRGKPLE 866
LE C D+H +FI +EI D+ L+ D +GNYV Q + G ++
Sbjct: 34 LEFCKDQHGSRFIQRELATSPASEKEVIFNEIRDDAIELSNDVFGNYVIQKFFEFGSKIQ 93
Query: 867 RSKIIRKLSGHIVQLSQHKFASNVIEKCLAYGGPAER-ELIIEEILGHNEETLLTMMKDQ 925
++ ++ + G++ QLS +A VI+K L Y +R EL++E +++L M+KDQ
Sbjct: 94 KNTLVDQFKGNMKQLSLQMYACRVIQKALEYIDSNQRIELVLEL-----SDSVLQMIKDQ 148
Query: 926 FANYVVQKIFELSSESQQAMMLSRIRTHAHVLKKYTYGKHIVARFEMLIGEENQTS 981
N+V+QK E + +LS + H + L ++YG ++ R E+Q S
Sbjct: 149 NGNHVIQKAIETIPIEKLPFILSSLTGHIYHLSTHSYGCRVIQRLLEFGSSEDQES 204
>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 = 175 bits (444), Expect = 1e-43, Method: Compositional matrix adjust.
Identities = 105/291 (36%), Positives = 162/291 (55%), Gaps = 9/291 (3%)
Query: 654 LSDITGHIVEFSADQHGSRFIQQKLENCSVDEKASVFKEILPHASKLMTDVFGNYVIQKF 713
L G I DQHG RF+Q++L+ ++F+E + +LMTD FGNY+IQK
Sbjct: 8 LDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKL 67
Query: 714 FEYGSPAQRKELANQLVGQILPLSMQMYGCRVIQKALETIEIEQKAQLVRE-LDGQVMRC 772
E + QR L + +S+ +GCR +QK +E I+ +++AQ+V + L ++
Sbjct: 68 LEEVTTEQRIVLTKISSPHFVEISLNPHGCRALQKLIECIKTDEEAQIVVDSLRPYTVQL 127
Query: 773 VRDQNGNHVIQKCIECIPPEKIGFIISAFCGQVAALSMHPYGCRVIQRVLEHCADKHQCQ 832
+D NGNHVIQKC++ + PE FI A ++ H +GCRV+QR L+H QC
Sbjct: 128 SKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCRVLQRCLDH-GTTEQCD 186
Query: 833 FIVDEILDNVCALAQDQYGNYVTQHVL----QRGKPLERSKIIRKLSGHIVQLSQHKFAS 888
+ D++L V L D +GNYV Q+++ ++ K KI+ L ++LS HKF S
Sbjct: 187 NLCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGS 246
Query: 889 NVIEKCLAYGGPAERELIIEEILGHNEET-LLTMMKDQFANYVVQKIFELS 938
NVIEK L +E +I EIL + ET + +++ D + NYV+Q ++S
Sbjct: 247 NVIEKILKTAIVSEP--MILEILNNGGETGIQSLLNDSYGNYVLQTALDIS 295
Score = 97.1 bits (240), Expect = 4e-20, Method: Compositional matrix adjust.
Identities = 62/234 (26%), Positives = 114/234 (48%), Gaps = 7/234 (2%)
Query: 725 LANQLVGQILPLSMQMYGCRVIQKALETIEIEQKAQLVRELDGQVMRCVRDQNGNHVIQK 784
+ +Q +G I L +GCR +QK L+ + + + E + + D GN++IQK
Sbjct: 7 VLDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQK 66
Query: 785 CIECIPPEKIGFIISAFCGQVAALSMHPYGCRVIQRVLEHCADKHQCQFIVDEILDNVCA 844
+E + E+ + +S++P+GCR +Q+++E + Q +VD +
Sbjct: 67 LLEEVTTEQRIVLTKISSPHFVEISLNPHGCRALQKLIECIKTDEEAQIVVDSLRPYTVQ 126
Query: 845 LAQDQYGNYVTQHVLQRGKPLERSKIIRKLSGHIVQLSQHKFASNVIEKCLAYGGPAERE 904
L++D GN+V Q LQR KP I +S + ++ H+ V+++CL +G + +
Sbjct: 127 LSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCRVLQRCLDHGTTEQCD 186
Query: 905 LIIEEILGHNEETLLTMMKDQFANYVVQKIFELSSESQQAMMLSRIRTHAHVLK 958
+ +++L ++ L D F NYVVQ I +E + +I H+LK
Sbjct: 187 NLCDKLLALVDKLTL----DPFGNYVVQYIITKEAEKNKYDYTHKI---VHLLK 233
Score = 50.1 bits (118), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 33/146 (22%), Positives = 74/146 (50%), Gaps = 11/146 (7%)
Query: 651 RFELSDITGHIVEFSADQHGSRFIQQKLENCSVDEKASVFKEILPHASKLMTDVFGNYVI 710
+F I+ ++ + +HG R +Q+ L++ + ++ ++ ++L KL D FGNYV+
Sbjct: 150 QFIFDAISDSCIDIATHRHGCRVLQRCLDHGTTEQCDNLCDKLLALVDKLTLDPFGNYVV 209
Query: 711 QKFFEYGSPAQRKELANQLVGQILP----LSMQMYGCRVIQKALETIEIEQKAQLVREL- 765
Q + + + +++V + P LS+ +G VI+K L+T + + ++ E+
Sbjct: 210 QYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVIEKILKTAIVSEP--MILEIL 267
Query: 766 ----DGQVMRCVRDQNGNHVIQKCIE 787
+ + + D GN+V+Q ++
Sbjct: 268 NNGGETGIQSLLNDSYGNYVLQTALD 293
Score = 47.8 bits (112), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 49/225 (21%), Positives = 96/225 (42%), Gaps = 40/225 (17%)
Query: 640 FLEELKSGKGRRFELSDITGHIVEFSADQHGSRFIQQKLENCSVDEKASVFKEILPHASK 699
+E +K+ + + + + + V+ S D +G+ IQ+ L+ + +F I
Sbjct: 103 LIECIKTDEEAQIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCID 162
Query: 700 LMTDVFGNYVIQKFFEYGSPAQRKELANQLVGQILPLSMQMYGCRVIQKALETIEIEQKA 759
+ T G V+Q+ ++G+ Q L ++L+ + L++ +G V+Q I ++A
Sbjct: 163 IATHRHGCRVLQRCLDHGTTEQCDNLCDKLLALVDKLTLDPFGNYVVQYI-----ITKEA 217
Query: 760 QLVRELDGQVMRCVRDQNGNHVIQKCIECIPPEKIGFIISAFCGQVAALSMHPYGCRVIQ 819
+ +N K + + P I LS+H +G VI+
Sbjct: 218 E---------------KNKYDYTHKIVHLLKPRAI------------ELSIHKFGSNVIE 250
Query: 820 RVLEHCADKHQCQFIVDEILDN-----VCALAQDQYGNYVTQHVL 859
++L+ + ++ EIL+N + +L D YGNYV Q L
Sbjct: 251 KILKTAIVS---EPMILEILNNGGETGIQSLLNDSYGNYVLQTAL 292
>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 = 169 bits (429), Expect = 5e-42, Method: Compositional matrix adjust.
Identities = 103/291 (35%), Positives = 160/291 (54%), Gaps = 9/291 (3%)
Query: 654 LSDITGHIVEFSADQHGSRFIQQKLENCSVDEKASVFKEILPHASKLMTDVFGNYVIQKF 713
L G I DQHG RF+Q++L+ ++F+E + +LMTD FGNY+IQK
Sbjct: 30 LDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKL 89
Query: 714 FEYGSPAQRKELANQLVGQILPLSMQMYGCRVIQKALETIEIEQKAQLVRE-LDGQVMRC 772
E + QR L + +S+ +G R +QK +E I+ +++AQ+V + L ++
Sbjct: 90 LEEVTTEQRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYTVQL 149
Query: 773 VRDQNGNHVIQKCIECIPPEKIGFIISAFCGQVAALSMHPYGCRVIQRVLEHCADKHQCQ 832
+D NGNHVIQKC++ + PE FI A ++ H +GC V+QR L+H QC
Sbjct: 150 SKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDH-GTTEQCD 208
Query: 833 FIVDEILDNVCALAQDQYGNYVTQHVL----QRGKPLERSKIIRKLSGHIVQLSQHKFAS 888
+ D++L V L D +GNYV Q+++ ++ K KI+ L ++LS HKF S
Sbjct: 209 NLCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGS 268
Query: 889 NVIEKCLAYGGPAERELIIEEILGHNEET-LLTMMKDQFANYVVQKIFELS 938
NVIEK L +E +I EIL + ET + +++ D + NYV+Q ++S
Sbjct: 269 NVIEKILKTAIVSEP--MILEILNNGGETGIQSLLNDSYGNYVLQTALDIS 317
Score = 94.4 bits (233), Expect = 3e-19, Method: Compositional matrix adjust.
Identities = 61/234 (26%), Positives = 113/234 (48%), Gaps = 7/234 (2%)
Query: 725 LANQLVGQILPLSMQMYGCRVIQKALETIEIEQKAQLVRELDGQVMRCVRDQNGNHVIQK 784
+ +Q +G I L +GCR +QK L+ + + + E + + D GN++IQK
Sbjct: 29 VLDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQK 88
Query: 785 CIECIPPEKIGFIISAFCGQVAALSMHPYGCRVIQRVLEHCADKHQCQFIVDEILDNVCA 844
+E + E+ + +S++P+G R +Q+++E + Q +VD +
Sbjct: 89 LLEEVTTEQRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYTVQ 148
Query: 845 LAQDQYGNYVTQHVLQRGKPLERSKIIRKLSGHIVQLSQHKFASNVIEKCLAYGGPAERE 904
L++D GN+V Q LQR KP I +S + ++ H+ V+++CL +G + +
Sbjct: 149 LSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCD 208
Query: 905 LIIEEILGHNEETLLTMMKDQFANYVVQKIFELSSESQQAMMLSRIRTHAHVLK 958
+ +++L ++ L D F NYVVQ I +E + +I H+LK
Sbjct: 209 NLCDKLLALVDKLTL----DPFGNYVVQYIITKEAEKNKYDYTHKI---VHLLK 255
Score = 48.5 bits (114), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 50/225 (22%), Positives = 95/225 (42%), Gaps = 40/225 (17%)
Query: 640 FLEELKSGKGRRFELSDITGHIVEFSADQHGSRFIQQKLENCSVDEKASVFKEILPHASK 699
+E +K+ + + + + + V+ S D +G+ IQ+ L+ + +F I
Sbjct: 125 LIECIKTDEEAQIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCID 184
Query: 700 LMTDVFGNYVIQKFFEYGSPAQRKELANQLVGQILPLSMQMYGCRVIQKALETIEIEQKA 759
+ T G V+Q+ ++G+ Q L ++L+ + L++ +G V+Q + T E E
Sbjct: 185 IATHRHGCCVLQRCLDHGTTEQCDNLCDKLLALVDKLTLDPFGNYVVQYII-TKEAE--- 240
Query: 760 QLVRELDGQVMRCVRDQNGNHVIQKCIECIPPEKIGFIISAFCGQVAALSMHPYGCRVIQ 819
+N K + + P I LS+H +G VI+
Sbjct: 241 ----------------KNKYDYTHKIVHLLKPRAI------------ELSIHKFGSNVIE 272
Query: 820 RVLEHCADKHQCQFIVDEILDN-----VCALAQDQYGNYVTQHVL 859
++L+ + ++ EIL+N + +L D YGNYV Q L
Sbjct: 273 KILKTAIVS---EPMILEILNNGGETGIQSLLNDSYGNYVLQTAL 314
>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 = 168 bits (425), Expect = 2e-41, Method: Compositional matrix adjust.
Identities = 103/291 (35%), Positives = 160/291 (54%), Gaps = 9/291 (3%)
Query: 654 LSDITGHIVEFSADQHGSRFIQQKLENCSVDEKASVFKEILPHASKLMTDVFGNYVIQKF 713
L G I DQHG RF+Q++L+ ++F+E + +LMTD FGNY+IQK
Sbjct: 8 LDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKL 67
Query: 714 FEYGSPAQRKELANQLVGQILPLSMQMYGCRVIQKALETIEIEQKAQLVRE-LDGQVMRC 772
E + QR L + +S+ +G R +QK +E I+ +++AQ+V + L ++
Sbjct: 68 LEEVTTEQRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYTVQL 127
Query: 773 VRDQNGNHVIQKCIECIPPEKIGFIISAFCGQVAALSMHPYGCRVIQRVLEHCADKHQCQ 832
+D NGNHVIQKC++ + PE FI A ++ H +GC V+QR L+H QC
Sbjct: 128 SKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDH-GTTEQCD 186
Query: 833 FIVDEILDNVCALAQDQYGNYVTQHVL----QRGKPLERSKIIRKLSGHIVQLSQHKFAS 888
+ D++L V L D +GNYV Q+++ ++ K KI+ L ++LS HKF S
Sbjct: 187 NLCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGS 246
Query: 889 NVIEKCLAYGGPAERELIIEEILGHNEET-LLTMMKDQFANYVVQKIFELS 938
NVIEK L +E +I EIL + ET + +++ D + NYV+Q ++S
Sbjct: 247 NVIEKILKTAIVSEP--MILEILNNGGETGIQSLLNDSYGNYVLQTALDIS 295
Score = 92.8 bits (229), Expect = 9e-19, Method: Compositional matrix adjust.
Identities = 61/234 (26%), Positives = 113/234 (48%), Gaps = 7/234 (2%)
Query: 725 LANQLVGQILPLSMQMYGCRVIQKALETIEIEQKAQLVRELDGQVMRCVRDQNGNHVIQK 784
+ +Q +G I L +GCR +QK L+ + + + E + + D GN++IQK
Sbjct: 7 VLDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQK 66
Query: 785 CIECIPPEKIGFIISAFCGQVAALSMHPYGCRVIQRVLEHCADKHQCQFIVDEILDNVCA 844
+E + E+ + +S++P+G R +Q+++E + Q +VD +
Sbjct: 67 LLEEVTTEQRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYTVQ 126
Query: 845 LAQDQYGNYVTQHVLQRGKPLERSKIIRKLSGHIVQLSQHKFASNVIEKCLAYGGPAERE 904
L++D GN+V Q LQR KP I +S + ++ H+ V+++CL +G + +
Sbjct: 127 LSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCD 186
Query: 905 LIIEEILGHNEETLLTMMKDQFANYVVQKIFELSSESQQAMMLSRIRTHAHVLK 958
+ +++L ++ L D F NYVVQ I +E + +I H+LK
Sbjct: 187 NLCDKLLALVDKLTL----DPFGNYVVQYIITKEAEKNKYDYTHKI---VHLLK 233
Score = 47.8 bits (112), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 49/225 (21%), Positives = 96/225 (42%), Gaps = 40/225 (17%)
Query: 640 FLEELKSGKGRRFELSDITGHIVEFSADQHGSRFIQQKLENCSVDEKASVFKEILPHASK 699
+E +K+ + + + + + V+ S D +G+ IQ+ L+ + +F I
Sbjct: 103 LIECIKTDEEAQIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCID 162
Query: 700 LMTDVFGNYVIQKFFEYGSPAQRKELANQLVGQILPLSMQMYGCRVIQKALETIEIEQKA 759
+ T G V+Q+ ++G+ Q L ++L+ + L++ +G V+Q I ++A
Sbjct: 163 IATHRHGCCVLQRCLDHGTTEQCDNLCDKLLALVDKLTLDPFGNYVVQYI-----ITKEA 217
Query: 760 QLVRELDGQVMRCVRDQNGNHVIQKCIECIPPEKIGFIISAFCGQVAALSMHPYGCRVIQ 819
+ +N K + + P I LS+H +G VI+
Sbjct: 218 E---------------KNKYDYTHKIVHLLKPRAI------------ELSIHKFGSNVIE 250
Query: 820 RVLEHCADKHQCQFIVDEILDN-----VCALAQDQYGNYVTQHVL 859
++L+ + ++ EIL+N + +L D YGNYV Q L
Sbjct: 251 KILKTAIVS---EPMILEILNNGGETGIQSLLNDSYGNYVLQTAL 292
>pdb|3BWT|A Chain A, Crystal Structure Of The Rna Binding Domain Of Puf4 From
Saccharomyces Cerevisiae
Length = 333
Score = 167 bits (424), Expect = 2e-41, Method: Compositional matrix adjust.
Identities = 103/291 (35%), Positives = 160/291 (54%), Gaps = 9/291 (3%)
Query: 654 LSDITGHIVEFSADQHGSRFIQQKLENCSVDEKASVFKEILPHASKLMTDVFGNYVIQKF 713
L G I DQHG RF+Q++L+ ++F+E + +LMTD FGNY+IQK
Sbjct: 8 LDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKL 67
Query: 714 FEYGSPAQRKELANQLVGQILPLSMQMYGCRVIQKALETIEIEQKAQLVRE-LDGQVMRC 772
E + QR L + +S+ +G R +QK +E I+ +++AQ+V + L ++
Sbjct: 68 LEEVTTEQRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYTVQL 127
Query: 773 VRDQNGNHVIQKCIECIPPEKIGFIISAFCGQVAALSMHPYGCRVIQRVLEHCADKHQCQ 832
+D NGNHVIQKC++ + PE FI A ++ H +GC V+QR L+H QC
Sbjct: 128 SKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDH-GTTEQCD 186
Query: 833 FIVDEILDNVCALAQDQYGNYVTQHVL----QRGKPLERSKIIRKLSGHIVQLSQHKFAS 888
+ D++L V L D +GNYV Q+++ ++ K KI+ L ++LS HKF S
Sbjct: 187 NLCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGS 246
Query: 889 NVIEKCLAYGGPAERELIIEEILGHNEET-LLTMMKDQFANYVVQKIFELS 938
NVIEK L +E +I EIL + ET + +++ D + NYV+Q ++S
Sbjct: 247 NVIEKILKTAIVSEP--MILEILNNGGETGIQSLLNDSYGNYVLQTALDIS 295
Score = 92.4 bits (228), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 61/234 (26%), Positives = 113/234 (48%), Gaps = 7/234 (2%)
Query: 725 LANQLVGQILPLSMQMYGCRVIQKALETIEIEQKAQLVRELDGQVMRCVRDQNGNHVIQK 784
+ +Q +G I L +GCR +QK L+ + + + E + + D GN++IQK
Sbjct: 7 VLDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQK 66
Query: 785 CIECIPPEKIGFIISAFCGQVAALSMHPYGCRVIQRVLEHCADKHQCQFIVDEILDNVCA 844
+E + E+ + +S++P+G R +Q+++E + Q +VD +
Sbjct: 67 LLEEVTTEQRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYTVQ 126
Query: 845 LAQDQYGNYVTQHVLQRGKPLERSKIIRKLSGHIVQLSQHKFASNVIEKCLAYGGPAERE 904
L++D GN+V Q LQR KP I +S + ++ H+ V+++CL +G + +
Sbjct: 127 LSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCD 186
Query: 905 LIIEEILGHNEETLLTMMKDQFANYVVQKIFELSSESQQAMMLSRIRTHAHVLK 958
+ +++L ++ L D F NYVVQ I +E + +I H+LK
Sbjct: 187 NLCDKLLALVDKLTL----DPFGNYVVQYIITKEAEKNKYDYTHKI---VHLLK 233
Score = 47.8 bits (112), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 49/225 (21%), Positives = 96/225 (42%), Gaps = 40/225 (17%)
Query: 640 FLEELKSGKGRRFELSDITGHIVEFSADQHGSRFIQQKLENCSVDEKASVFKEILPHASK 699
+E +K+ + + + + + V+ S D +G+ IQ+ L+ + +F I
Sbjct: 103 LIECIKTDEEAQIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCID 162
Query: 700 LMTDVFGNYVIQKFFEYGSPAQRKELANQLVGQILPLSMQMYGCRVIQKALETIEIEQKA 759
+ T G V+Q+ ++G+ Q L ++L+ + L++ +G V+Q I ++A
Sbjct: 163 IATHRHGCCVLQRCLDHGTTEQCDNLCDKLLALVDKLTLDPFGNYVVQYI-----ITKEA 217
Query: 760 QLVRELDGQVMRCVRDQNGNHVIQKCIECIPPEKIGFIISAFCGQVAALSMHPYGCRVIQ 819
+ +N K + + P I LS+H +G VI+
Sbjct: 218 E---------------KNKYDYTHKIVHLLKPRAI------------ELSIHKFGSNVIE 250
Query: 820 RVLEHCADKHQCQFIVDEILDN-----VCALAQDQYGNYVTQHVL 859
++L+ + ++ EIL+N + +L D YGNYV Q L
Sbjct: 251 KILKTAIVS---EPMILEILNNGGETGIQSLLNDSYGNYVLQTAL 292
>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 = 124 bits (312), Expect = 2e-28, Method: Compositional matrix adjust.
Identities = 89/332 (26%), Positives = 169/332 (50%), Gaps = 41/332 (12%)
Query: 651 RFELSDI--TGHIVEFSADQHGSRFIQQKLE-NCSVDEKASVFKEILPHAS---KLMTDV 704
R LS++ +G +++F+ D+ G +F+++ ++ + + +K +F++++ KL T++
Sbjct: 20 RLSLSEVLDSGDLMKFAVDKTGCQFLEKAVKGSLTSYQKFQLFEQVIGRKDDFLKLSTNI 79
Query: 705 FGNYVIQKFF-------EYGSPAQRKELANQLVGQILPLSMQMYGCRVIQKALETIEIEQ 757
FGNY++Q + G ++++L N + Q+ + + + CRVIQ +L+ +++
Sbjct: 80 FGNYLVQSVIGISLATNDDGYTKRQEKLKNFISSQMTDMCLDKFACRVIQSSLQNMDLSL 139
Query: 758 KAQLVREL--DGQVMRCVRDQNGNHVIQKCIECIPPEKIGFIISAFCG--QVAALSMHPY 813
+LV+ L D +++ DQN NHVIQK + IP + FI+ + + Y
Sbjct: 140 ACKLVQALPRDARLIAICVDQNANHVIQKVVAVIPLKNWEFIVDFVATPEHLRQICSDKY 199
Query: 814 GCRVIQRVLEHC-AD--------------KHQCQFIVDEILDNVCALAQDQYGNYVTQHV 858
GCRV+Q ++E AD + Q ++ + + LA ++Y NY+ QH+
Sbjct: 200 GCRVVQTIIEKLTADSMNVDLTSAAQNLRERALQRLMTSVTNRCQELATNEYANYIIQHI 259
Query: 859 LQRGK-PLERSKIIRK-LSGHIVQLSQHKFASNVIEKCLAYGGPAERELIIEEIL----- 911
+ + R II K L +++ LSQ KFAS+V+EK + +++EI
Sbjct: 260 VSNDDLAVYRECIIEKCLMRNLLSLSQEKFASHVVEKAFLHAPLELLAEMMDEIFDGYIP 319
Query: 912 --GHNEETLLTMMKDQFANYVVQKIFELSSES 941
++ L MM QF NYVVQ + + ++
Sbjct: 320 HPDTGKDALDIMMFHQFGNYVVQCMLTICCDA 351
>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 = 124 bits (312), Expect = 2e-28, Method: Compositional matrix adjust.
Identities = 89/332 (26%), Positives = 169/332 (50%), Gaps = 41/332 (12%)
Query: 651 RFELSDI--TGHIVEFSADQHGSRFIQQKLE-NCSVDEKASVFKEILPHAS---KLMTDV 704
R LS++ +G +++F+ D+ G +F+++ ++ + + +K +F++++ KL T++
Sbjct: 19 RLSLSEVLDSGDLMKFAVDKTGCQFLEKAVKGSLTSYQKFQLFEQVIGRKDDFLKLSTNI 78
Query: 705 FGNYVIQKFF-------EYGSPAQRKELANQLVGQILPLSMQMYGCRVIQKALETIEIEQ 757
FGNY++Q + G ++++L N + Q+ + + + CRVIQ +L+ +++
Sbjct: 79 FGNYLVQSVIGISLATNDDGYTKRQEKLKNFISSQMTDMCLDKFACRVIQSSLQNMDLSL 138
Query: 758 KAQLVREL--DGQVMRCVRDQNGNHVIQKCIECIPPEKIGFIISAFCG--QVAALSMHPY 813
+LV+ L D +++ DQN NHVIQK + IP + FI+ + + Y
Sbjct: 139 ACKLVQALPRDARLIAICVDQNANHVIQKVVAVIPLKNWEFIVDFVATPEHLRQICSDKY 198
Query: 814 GCRVIQRVLEHC-AD--------------KHQCQFIVDEILDNVCALAQDQYGNYVTQHV 858
GCRV+Q ++E AD + Q ++ + + LA ++Y NY+ QH+
Sbjct: 199 GCRVVQTIIEKLTADSMNVDLTSAAQNLRERALQRLMTSVTNRCQELATNEYANYIIQHI 258
Query: 859 LQRGK-PLERSKIIRK-LSGHIVQLSQHKFASNVIEKCLAYGGPAERELIIEEIL----- 911
+ + R II K L +++ LSQ KFAS+V+EK + +++EI
Sbjct: 259 VSNDDLAVYRECIIEKCLMRNLLSLSQEKFASHVVEKAFLHAPLELLAEMMDEIFDGYIP 318
Query: 912 --GHNEETLLTMMKDQFANYVVQKIFELSSES 941
++ L MM QF NYVVQ + + ++
Sbjct: 319 HPDTGKDALDIMMFHQFGNYVVQCMLTICCDA 350
>pdb|3V71|A Chain A, Crystal Structure Of Puf-6 In Complex With 5be13 Rna
Length = 382
Score = 122 bits (306), Expect = 9e-28, Method: Compositional matrix adjust.
Identities = 94/358 (26%), Positives = 175/358 (48%), Gaps = 47/358 (13%)
Query: 657 ITGHIVEFSADQHGSRFIQQKLENCSVDEKASVFKEILPHASKLMTDVF----GNYVIQK 712
+ G +++F+ D G +F++ S D+ E ++ L + GN+++QK
Sbjct: 18 LNGQLIDFAIDPSGVKFLEANYPLDSEDQIRKAVFEKFTESTTLFVGLCHSRNGNFIVQK 77
Query: 713 FFEYGSPAQRKELANQLV-GQILPLSMQMYGCRVIQKALETIEIEQKAQLVRELDG-QVM 770
E +PA+++EL Q++ G +L + + CRV+Q AL+ + QL++EL +
Sbjct: 78 LVELATPAEQRELLRQMIDGGLLAMCKDKFACRVVQLALQKFDHSNVFQLIQELSTFDLA 137
Query: 771 RCVRDQNGNHVIQKCIECIPPEKIGFIISAFCG--QVAALSMHPYGCRVIQRVLEHCAD- 827
DQ HVIQ+ ++ +P + F + + A+ YGCR++Q+V++ A+
Sbjct: 138 AMCTDQISIHVIQRVVKQLPVDMWTFFVHFLSSGDSLMAVCQDKYGCRLVQQVIDRLAEN 197
Query: 828 ------KHQCQF---IVDEILDNVCALAQDQYGNYVTQHVLQRGKPLE--RSKIIRK-LS 875
K + Q ++ I+ N L+ +++ NYV Q+V++ +E R II K L
Sbjct: 198 PKLPCFKFRIQLLHSLMTCIVRNCYRLSSNEFANYVIQYVIKSSGIMEMYRDTIIDKCLL 257
Query: 876 GHIVQLSQHKFASNVIEKCLAYGGPAERELIIEEILG-------HNEETLLTMMKDQFAN 928
+++ +SQ K+AS+VIE + PA ++EEI N + L ++ Q+ N
Sbjct: 258 RNLLSMSQDKYASHVIEGAFLFAPPALLHEMMEEIFSGYVKDVESNRDALDILLFHQYGN 317
Query: 929 YVVQKIFELSS---------ESQQAMML----------SRIRTHAHVLKKYTYGKHIV 967
YVVQ++ + + E A++L R+ HA L++++ GK I+
Sbjct: 318 YVVQQMISICTAALIGKEERELPPAILLLYSGWYEKMKQRVLQHASRLERFSSGKKII 375
>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 = 121 bits (304), Expect = 2e-27, Method: Compositional matrix adjust.
Identities = 88/332 (26%), Positives = 168/332 (50%), Gaps = 41/332 (12%)
Query: 651 RFELSDI--TGHIVEFSADQHGSRFIQQKLE-NCSVDEKASVFKEILPHAS---KLMTDV 704
R LS++ +G +++F+ D+ G +F+++ ++ + + +K +F++++ KL T++
Sbjct: 20 RLSLSEVLDSGDLMKFAVDKTGCQFLEKAVKGSLTSYQKFQLFEQVIGRKDDFLKLSTNI 79
Query: 705 FGNYVIQKFF-------EYGSPAQRKELANQLVGQILPLSMQMYGCRVIQKALETIEIEQ 757
FGNY++Q + G ++++L N + Q+ + + + C VIQ +L+ +++
Sbjct: 80 FGNYLVQSVIGISLATNDDGYTKRQEKLKNFISSQMTDMCLDKFACYVIQSSLQNMDLSL 139
Query: 758 KAQLVREL--DGQVMRCVRDQNGNHVIQKCIECIPPEKIGFIISAFCG--QVAALSMHPY 813
+LV+ L D +++ DQN NHVIQK + IP + FI+ + + Y
Sbjct: 140 ACKLVQALPRDARLIAICVDQNANHVIQKVVAVIPLKNWEFIVDFVATPEHLRQICSDKY 199
Query: 814 GCRVIQRVLEHC-AD--------------KHQCQFIVDEILDNVCALAQDQYGNYVTQHV 858
GCRV+Q ++E AD + Q ++ + + LA ++Y NY+ QH+
Sbjct: 200 GCRVVQTIIEKLTADSMNVDLTSAAQNLRERALQRLMTSVTNRCQELATNEYANYIIQHI 259
Query: 859 LQRGK-PLERSKIIRK-LSGHIVQLSQHKFASNVIEKCLAYGGPAERELIIEEIL----- 911
+ + R II K L +++ LSQ KFAS+V+EK + +++EI
Sbjct: 260 VSNDDLAVYRECIIEKCLMRNLLSLSQEKFASHVVEKAFLHAPLELLAEMMDEIFDGYIP 319
Query: 912 --GHNEETLLTMMKDQFANYVVQKIFELSSES 941
++ L MM QF NYVVQ + + ++
Sbjct: 320 HPDTGKDALDIMMFHQFGNYVVQCMLTICCDA 351
>pdb|1O5L|A Chain A, Crystal Structure Of Transcriptional Regulator (Tm1171)
From Thermotoga Maritima At 2.30 A Resolution
Length = 213
Score = 33.9 bits (76), Expect = 0.43, Method: Composition-based stats.
Identities = 34/140 (24%), Positives = 71/140 (50%), Gaps = 17/140 (12%)
Query: 828 KHQCQFIVDEILDNVCALAQDQYGNYVTQHVLQRGKPLERSKI--IRKLSGHIVQLSQHK 885
KHQ D+ +++V L + G T+HV + GK LE +I ++ ++ + S+ +
Sbjct: 34 KHQ-----DDPIEDVLILLE---GTLKTEHVSENGKTLEIDEIKPVQIIASGFIFSSEPR 85
Query: 886 FASNVI--EKCLAYGGPAERELIIEEILGHNEETLLTMMKDQFANY--VVQKIFELSSES 941
F NV+ E P E + ++L + E LL +KD ++ V +K+F L++++
Sbjct: 86 FPVNVVAGENSKILSIPKE---VFLDLLMKDRELLLFFLKDVSEHFRVVSEKLFFLTTKT 142
Query: 942 QQAMMLSRIRTHAHVLKKYT 961
+ +++ + H + ++ T
Sbjct: 143 LREKLMNFLVRHMNEKRELT 162
>pdb|3D0R|A Chain A, Crystal Structure Of Calg3 From Micromonospora Echinospora
Determined In Space Group P2(1)
pdb|3D0R|B Chain B, Crystal Structure Of Calg3 From Micromonospora Echinospora
Determined In Space Group P2(1)
pdb|3OTI|A Chain A, Crystal Structure Of Calg3, Calicheamicin
Glycostyltransferase, Tdp And Calicheamicin T0 Bound
Form
pdb|3OTI|B Chain B, Crystal Structure Of Calg3, Calicheamicin
Glycostyltransferase, Tdp And Calicheamicin T0 Bound
Form
Length = 398
Score = 31.6 bits (70), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 28/93 (30%), Positives = 39/93 (41%), Gaps = 4/93 (4%)
Query: 192 VKVAGQNRNLVD--IKQEDFPRSSSPVYNQSHSFGYSDSSSLRDPSVISSNGVSTTTGAH 249
V++A NR LVD + D R VY Q + G + P+V + T G H
Sbjct: 109 VQIAAVNRPLVDGTMALVDDYRPDLVVYEQGATVGLLAADRAGVPAVQRNQSAWRTRGMH 168
Query: 250 NTGVSSKVDVSTAYNVSSSSHDWTATISSTPPT 282
+ S D+ + VS ATI S PP+
Sbjct: 169 RSIASFLTDLMDKHQVSLPEP--VATIESFPPS 199
>pdb|3DU5|A Chain A, Structure Of The Catalytic Subunit Of Telomerase, Tert
pdb|3DU5|B Chain B, Structure Of The Catalytic Subunit Of Telomerase, Tert
pdb|3DU6|A Chain A, Structure Of The Catalytic Subunit Of Telomerase, Tert
pdb|3DU6|B Chain B, Structure Of The Catalytic Subunit Of Telomerase, Tert
pdb|3KYL|A Chain A, Structure Of The Catalytic Subunit Of Telomerase Bound To
Its Rna Template And Telomeric Dna
Length = 596
Score = 31.2 bits (69), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 25/54 (46%), Gaps = 3/54 (5%)
Query: 812 PYGCRVIQRVLEHCADKHQCQFIVDEILDNVCALAQDQYGNYVTQHVLQRGKPL 865
P C++IQ + H D + FIVD I + A + Y H L +G PL
Sbjct: 262 PVLCKLIQSIPTHLLDSEKKNFIVDHISNQFVAFRRKIYK---WNHGLLQGDPL 312
>pdb|3D0Q|A Chain A, Crystal Structure Of Calg3 From Micromonospora Echinospora
Determined In Space Group I222
pdb|3D0Q|B Chain B, Crystal Structure Of Calg3 From Micromonospora Echinospora
Determined In Space Group I222
Length = 398
Score = 30.8 bits (68), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 28/94 (29%), Positives = 40/94 (42%), Gaps = 6/94 (6%)
Query: 192 VKVAGQNRNLVD---IKQEDFPRSSSPVYNQSHSFGYSDSSSLRDPSVISSNGVSTTTGA 248
V++A NR LVD +D+ R VY Q + G + P+V + T G
Sbjct: 109 VQIAAVNRPLVDGTXALVDDY-RPDLVVYEQGATVGLLAADRAGVPAVQRNQSAWRTRGX 167
Query: 249 HNTGVSSKVDVSTAYNVSSSSHDWTATISSTPPT 282
H + S D+ + VS ATI S PP+
Sbjct: 168 HRSIASFLTDLXDKHQVSLPEP--VATIESFPPS 199
>pdb|3LV4|A Chain A, Crystal Structure Of The Glycoside Hydrolase, Family 43
Yxia Protein From Bacillus Licheniformis. Northeast
Structural Genomics Consortium Target Bir14.
pdb|3LV4|B Chain B, Crystal Structure Of The Glycoside Hydrolase, Family 43
Yxia Protein From Bacillus Licheniformis. Northeast
Structural Genomics Consortium Target Bir14
Length = 456
Score = 30.4 bits (67), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 32/71 (45%), Gaps = 6/71 (8%)
Query: 230 SLRDPSVISSNGVSTTTGAHNTGVSSKVDVSTAYNVSSSSHDWTATISST----PPTEEV 285
++ DPS+I +NG G+H S D+ +SSS HD I + T E
Sbjct: 12 TVHDPSIIKANGTYYVFGSHLASAKS-TDLXNWTQISSSVHDGNPLIPNVYEELKETFEW 70
Query: 286 TSNDTDIWTKD 296
+DT +W D
Sbjct: 71 AESDT-LWAPD 80
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 0.131 0.384
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 27,740,369
Number of Sequences: 62578
Number of extensions: 1119225
Number of successful extensions: 2937
Number of sequences better than 100.0: 26
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 2600
Number of HSP's gapped (non-prelim): 56
length of query: 983
length of database: 14,973,337
effective HSP length: 108
effective length of query: 875
effective length of database: 8,214,913
effective search space: 7188048875
effective search space used: 7188048875
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: 56 (26.2 bits)