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= 002096
(967 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 = 349 bits (895), Expect = 5e-96, Method: Compositional matrix adjust.
Identities = 161/273 (58%), Positives = 213/273 (78%), Gaps = 1/273 (0%)
Query: 681 SSLLDEFKSNKTKCFELSEIAGHVVEFSADQYGSRFIQQKLETATTEEKNMVFQEIMPQA 740
S LL++F++N+ +L ++ GH+VEFS DQ+GSRFIQQKLE AT E+ +VF EI+ A
Sbjct: 5 SRLLEDFRNNRFPNLQLRDLIGHIVEFSQDQHGSRFIQQKLERATPAERQIVFNEILQAA 64
Query: 741 LSLMTDVFGNYVIQKFFEHGTASQVRELADQLTGHVLTLSLQMYGCRVIQKAIEVVELDQ 800
LMTDVFGNYVIQKFFE G+ Q LA ++ GHVL L+LQMYGCRVIQKA+E + DQ
Sbjct: 65 YQLMTDVFGNYVIQKFFEFGSLDQKLALATRIRGHVLPLALQMYGCRVIQKALESISSDQ 124
Query: 801 QTQMVKELDGHIMRCVRDQNGNHVIQKCIECVPEDAIQFIVLTFYDQVVTLSTHPYGCRV 860
Q++MVKELDGH+++CV+DQNGNHV+QKCIECV ++QFI+ F QV LSTHPYGCRV
Sbjct: 125 QSEMVKELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFVLSTHPYGCRV 184
Query: 861 IQRVLEHCHDEKTQSIMMDEILQSVCMLAQDQYGNYVVQHVLEHGKPHERSAIIKKLTGQ 920
IQR+LEHC E+T I ++E+ Q L QDQYGNYV+QHVLEHG+P ++S I+ ++ G+
Sbjct: 185 IQRILEHCTAEQTLPI-LEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGK 243
Query: 921 IVQMSQQKFASNVIEKCLSFGTPAERQALVNEM 953
++ +SQ KFASNV+EKC++ + AER L++E+
Sbjct: 244 VLALSQHKFASNVVEKCVTHASRAERALLIDEV 276
Score = 72.8 bits (177), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 47/177 (26%), Positives = 82/177 (46%), Gaps = 7/177 (3%)
Query: 695 FELSEIAGHVVEFSADQYGSRFIQQKLETATTEEKNMVFQEIMPQALSLMTDVFGNYVIQ 754
F + G V S YG R IQ+ LE T E+ + +E+ L+ D +GNYVIQ
Sbjct: 163 FIIDAFKGQVFVLSTHPYGCRVIQRILEHCTAEQTLPILEELHQHTEQLVQDQYGNYVIQ 222
Query: 755 KFFEHGTASQVRELADQLTGHVLTLSLQMYGCRVIQKAIEVVELDQQTQMVKEL----DG 810
EHG ++ ++ G VL LS + V++K + ++ ++ E+ DG
Sbjct: 223 HVLEHGRPEDKSKIVSEIRGKVLALSQHKFASNVVEKCVTHASRAERALLIDEVCCQNDG 282
Query: 811 ---HIMRCVRDQNGNHVIQKCIECVPEDAIQFIVLTFYDQVVTLSTHPYGCRVIQRV 864
+ ++DQ N+V+QK I+ + I+ + TL + YG ++ ++
Sbjct: 283 PHSALYTMMKDQYANYVVQKMIDMAEPAQRKIIMHKIRPHITTLRKYTYGKHILAKL 339
Score = 56.2 bits (134), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 33/110 (30%), Positives = 59/110 (53%), Gaps = 1/110 (0%)
Query: 848 VVTLSTHPYGCRVIQRVLEHCHDEKTQSIMMDEILQSVCMLAQDQYGNYVVQHVLEHGKP 907
+V S +G R IQ+ LE + Q I+ +EILQ+ L D +GNYV+Q E G
Sbjct: 28 IVEFSQDQHGSRFIQQKLERATPAERQ-IVFNEILQAAYQLMTDVFGNYVIQKFFEFGSL 86
Query: 908 HERSAIIKKLTGQIVQMSQQKFASNVIEKCLSFGTPAERQALVNEMLGSI 957
++ A+ ++ G ++ ++ Q + VI+K L + ++ +V E+ G +
Sbjct: 87 DQKLALATRIRGHVLPLALQMYGCRVIQKALESISSDQQSEMVKELDGHV 136
Score = 45.1 bits (105), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/95 (24%), Positives = 48/95 (50%)
Query: 863 RVLEHCHDEKTQSIMMDEILQSVCMLAQDQYGNYVVQHVLEHGKPHERSAIIKKLTGQIV 922
R+LE + + ++ + +++ + +QDQ+G+ +Q LE P ER + ++
Sbjct: 6 RLLEDFRNNRFPNLQLRDLIGHIVEFSQDQHGSRFIQQKLERATPAERQIVFNEILQAAY 65
Query: 923 QMSQQKFASNVIEKCLSFGTPAERQALVNEMLGSI 957
Q+ F + VI+K FG+ ++ AL + G +
Sbjct: 66 QLMTDVFGNYVIQKFFEFGSLDQKLALATRIRGHV 100
>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 = 345 bits (885), Expect = 7e-95, Method: Compositional matrix adjust.
Identities = 162/275 (58%), Positives = 213/275 (77%), Gaps = 3/275 (1%)
Query: 681 SSLLDEFKSNKTKCFELSEIAGHVVEFSADQYGSRFIQQKLETATTEEKNMVFQEIMPQA 740
S LL++F++N+ +L ++ GH+VEFS DQ+GSRFIQQKLE AT E+ MVF EI+ A
Sbjct: 3 SRLLEDFRNNRFPNLQLRDLIGHIVEFSQDQHGSRFIQQKLERATPAERQMVFNEILQAA 62
Query: 741 LSLMTDVFGNYVIQKFFEHGTASQVRELADQLTGHVLTLSLQMYGCRVIQKAIEVVELDQ 800
LMTDVFGNYVIQKFFE G+ Q LA ++ GHVL L+LQMYGCRVIQKA+E + DQ
Sbjct: 63 YQLMTDVFGNYVIQKFFEFGSLDQKLALATRIRGHVLPLALQMYGCRVIQKALESISSDQ 122
Query: 801 Q--TQMVKELDGHIMRCVRDQNGNHVIQKCIECVPEDAIQFIVLTFYDQVVTLSTHPYGC 858
Q ++MVKELDGH+++CV+DQNGNHV+QKCIECV ++QFI+ F QV LSTHPYGC
Sbjct: 123 QVISEMVKELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFVLSTHPYGC 182
Query: 859 RVIQRVLEHCHDEKTQSIMMDEILQSVCMLAQDQYGNYVVQHVLEHGKPHERSAIIKKLT 918
RVIQR+LEHC E+T I ++E+ Q L QDQYGNYV+QHVLEHG+P ++S I+ ++
Sbjct: 183 RVIQRILEHCTAEQTLPI-LEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIR 241
Query: 919 GQIVQMSQQKFASNVIEKCLSFGTPAERQALVNEM 953
G+++ +SQ KFASNV+EKC++ + AER L++E+
Sbjct: 242 GKVLALSQHKFASNVVEKCVTHASRAERALLIDEV 276
Score = 72.0 bits (175), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 47/177 (26%), Positives = 82/177 (46%), Gaps = 7/177 (3%)
Query: 695 FELSEIAGHVVEFSADQYGSRFIQQKLETATTEEKNMVFQEIMPQALSLMTDVFGNYVIQ 754
F + G V S YG R IQ+ LE T E+ + +E+ L+ D +GNYVIQ
Sbjct: 163 FIIDAFKGQVFVLSTHPYGCRVIQRILEHCTAEQTLPILEELHQHTEQLVQDQYGNYVIQ 222
Query: 755 KFFEHGTASQVRELADQLTGHVLTLSLQMYGCRVIQKAIEVVELDQQTQMVKEL----DG 810
EHG ++ ++ G VL LS + V++K + ++ ++ E+ DG
Sbjct: 223 HVLEHGRPEDKSKIVSEIRGKVLALSQHKFASNVVEKCVTHASRAERALLIDEVCCQNDG 282
Query: 811 ---HIMRCVRDQNGNHVIQKCIECVPEDAIQFIVLTFYDQVVTLSTHPYGCRVIQRV 864
+ ++DQ N+V+QK I+ + I+ + TL + YG ++ ++
Sbjct: 283 PHSALYTMMKDQYANYVVQKMIDMAEPAQRKIIMHKIRPHITTLRKYTYGKHILAKL 339
Score = 44.7 bits (104), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/95 (24%), Positives = 48/95 (50%)
Query: 863 RVLEHCHDEKTQSIMMDEILQSVCMLAQDQYGNYVVQHVLEHGKPHERSAIIKKLTGQIV 922
R+LE + + ++ + +++ + +QDQ+G+ +Q LE P ER + ++
Sbjct: 4 RLLEDFRNNRFPNLQLRDLIGHIVEFSQDQHGSRFIQQKLERATPAERQMVFNEILQAAY 63
Query: 923 QMSQQKFASNVIEKCLSFGTPAERQALVNEMLGSI 957
Q+ F + VI+K FG+ ++ AL + G +
Sbjct: 64 QLMTDVFGNYVIQKFFEFGSLDQKLALATRIRGHV 98
>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 = 344 bits (882), Expect = 2e-94, Method: Compositional matrix adjust.
Identities = 158/273 (57%), Positives = 211/273 (77%), Gaps = 1/273 (0%)
Query: 681 SSLLDEFKSNKTKCFELSEIAGHVVEFSADQYGSRFIQQKLETATTEEKNMVFQEIMPQA 740
S LL++F++N+ +L EIAGH++EFS DQ+GSRFIQ KLE AT E+ +VF EI+ A
Sbjct: 3 SRLLEDFRNNRYPNLQLREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAA 62
Query: 741 LSLMTDVFGNYVIQKFFEHGTASQVRELADQLTGHVLTLSLQMYGCRVIQKAIEVVELDQ 800
LM DVFGNYVIQKFFE G+ Q LA+++ GHVL+L+LQMYGCRVIQKA+E + DQ
Sbjct: 63 YQLMVDVFGNYVIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQ 122
Query: 801 QTQMVKELDGHIMRCVRDQNGNHVIQKCIECVPEDAIQFIVLTFYDQVVTLSTHPYGCRV 860
Q +MV+ELDGH+++CV+DQNGNHV+QKCIECV ++QFI+ F QV LSTHPYGCRV
Sbjct: 123 QNEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRV 182
Query: 861 IQRVLEHCHDEKTQSIMMDEILQSVCMLAQDQYGNYVVQHVLEHGKPHERSAIIKKLTGQ 920
IQR+LEHC ++T I ++E+ Q L QDQYGNYV+QHVLEHG+P ++S I+ ++ G
Sbjct: 183 IQRILEHCLPDQTLPI-LEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGN 241
Query: 921 IVQMSQQKFASNVIEKCLSFGTPAERQALVNEM 953
++ +SQ KFASNV+EKC++ + ER L++E+
Sbjct: 242 VLVLSQHKFASNVVEKCVTHASRTERAVLIDEV 274
Score = 68.6 bits (166), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 44/177 (24%), Positives = 82/177 (46%), Gaps = 7/177 (3%)
Query: 695 FELSEIAGHVVEFSADQYGSRFIQQKLETATTEEKNMVFQEIMPQALSLMTDVFGNYVIQ 754
F + G V S YG R IQ+ LE ++ + +E+ L+ D +GNYVIQ
Sbjct: 161 FIIDAFKGQVFALSTHPYGCRVIQRILEHCLPDQTLPILEELHQHTEQLVQDQYGNYVIQ 220
Query: 755 KFFEHGTASQVRELADQLTGHVLTLSLQMYGCRVIQKAIEVVELDQQTQMVKEL----DG 810
EHG ++ ++ G+VL LS + V++K + ++ ++ E+ DG
Sbjct: 221 HVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNVVEKCVTHASRTERAVLIDEVCTMNDG 280
Query: 811 ---HIMRCVRDQNGNHVIQKCIECVPEDAIQFIVLTFYDQVVTLSTHPYGCRVIQRV 864
+ ++DQ N+V+QK I+ + ++ + TL + YG ++ ++
Sbjct: 281 PHSALYTMMKDQYANYVVQKMIDVAEPGQRKIVMHKIRPHIATLRKYTYGKHILAKL 337
Score = 56.6 bits (135), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 32/110 (29%), Positives = 59/110 (53%), Gaps = 1/110 (0%)
Query: 848 VVTLSTHPYGCRVIQRVLEHCHDEKTQSIMMDEILQSVCMLAQDQYGNYVVQHVLEHGKP 907
++ S +G R IQ LE + Q ++ +EILQ+ L D +GNYV+Q E G
Sbjct: 26 IMEFSQDQHGSRFIQLKLERATPAERQ-LVFNEILQAAYQLMVDVFGNYVIQKFFEFGSL 84
Query: 908 HERSAIIKKLTGQIVQMSQQKFASNVIEKCLSFGTPAERQALVNEMLGSI 957
++ A+ +++ G ++ ++ Q + VI+K L F ++ +V E+ G +
Sbjct: 85 EQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQNEMVRELDGHV 134
Score = 44.3 bits (103), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 25/95 (26%), Positives = 47/95 (49%)
Query: 863 RVLEHCHDEKTQSIMMDEILQSVCMLAQDQYGNYVVQHVLEHGKPHERSAIIKKLTGQIV 922
R+LE + + ++ + EI + +QDQ+G+ +Q LE P ER + ++
Sbjct: 4 RLLEDFRNNRYPNLQLREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAY 63
Query: 923 QMSQQKFASNVIEKCLSFGTPAERQALVNEMLGSI 957
Q+ F + VI+K FG+ ++ AL + G +
Sbjct: 64 QLMVDVFGNYVIQKFFEFGSLEQKLALAERIRGHV 98
>pdb|3BSB|A Chain A, Crystal Structure Of Human Pumilio1 In Complex With
Cyclinb Reverse Rna
pdb|3BSB|B Chain B, Crystal Structure Of Human Pumilio1 In Complex With
Cyclinb Reverse Rna
pdb|3BSX|A Chain A, Crystal Structure Of Human Pumilio 1 In Complex With Puf5
Rna
pdb|3BSX|B Chain B, Crystal Structure Of Human Pumilio 1 In Complex With Puf5
Rna
Length = 343
Score = 343 bits (881), Expect = 2e-94, Method: Compositional matrix adjust.
Identities = 158/273 (57%), Positives = 211/273 (77%), Gaps = 1/273 (0%)
Query: 681 SSLLDEFKSNKTKCFELSEIAGHVVEFSADQYGSRFIQQKLETATTEEKNMVFQEIMPQA 740
S LL++F++N+ +L EIAGH++EFS DQ+GSRFIQ KLE AT E+ +VF EI+ A
Sbjct: 3 SRLLEDFRNNRYPNLQLREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAA 62
Query: 741 LSLMTDVFGNYVIQKFFEHGTASQVRELADQLTGHVLTLSLQMYGCRVIQKAIEVVELDQ 800
LM DVFGNYVIQKFFE G+ Q LA+++ GHVL+L+LQMYGCRVIQKA+E + DQ
Sbjct: 63 YQLMVDVFGNYVIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQ 122
Query: 801 QTQMVKELDGHIMRCVRDQNGNHVIQKCIECVPEDAIQFIVLTFYDQVVTLSTHPYGCRV 860
Q +MV+ELDGH+++CV+DQNGNHV+QKCIECV ++QFI+ F QV LSTHPYGCRV
Sbjct: 123 QNEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRV 182
Query: 861 IQRVLEHCHDEKTQSIMMDEILQSVCMLAQDQYGNYVVQHVLEHGKPHERSAIIKKLTGQ 920
IQR+LEHC ++T I ++E+ Q L QDQYGNYV+QHVLEHG+P ++S I+ ++ G
Sbjct: 183 IQRILEHCLPDQTLPI-LEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGN 241
Query: 921 IVQMSQQKFASNVIEKCLSFGTPAERQALVNEM 953
++ +SQ KFASNV+EKC++ + ER L++E+
Sbjct: 242 VLVLSQHKFASNVVEKCVTHASRTERAVLIDEV 274
Score = 67.8 bits (164), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 44/177 (24%), Positives = 82/177 (46%), Gaps = 7/177 (3%)
Query: 695 FELSEIAGHVVEFSADQYGSRFIQQKLETATTEEKNMVFQEIMPQALSLMTDVFGNYVIQ 754
F + G V S YG R IQ+ LE ++ + +E+ L+ D +GNYVIQ
Sbjct: 161 FIIDAFKGQVFALSTHPYGCRVIQRILEHCLPDQTLPILEELHQHTEQLVQDQYGNYVIQ 220
Query: 755 KFFEHGTASQVRELADQLTGHVLTLSLQMYGCRVIQKAIEVVELDQQTQMVKEL----DG 810
EHG ++ ++ G+VL LS + V++K + ++ ++ E+ DG
Sbjct: 221 HVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNVVEKCVTHASRTERAVLIDEVCTMNDG 280
Query: 811 ---HIMRCVRDQNGNHVIQKCIECVPEDAIQFIVLTFYDQVVTLSTHPYGCRVIQRV 864
+ ++DQ N+V+QK I+ + ++ + TL + YG ++ ++
Sbjct: 281 PHSALYTMMKDQYANYVVQKMIDVAEPGQRKIVMHKIRPHIATLRKYTYGKHILAKL 337
Score = 56.2 bits (134), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 32/110 (29%), Positives = 59/110 (53%), Gaps = 1/110 (0%)
Query: 848 VVTLSTHPYGCRVIQRVLEHCHDEKTQSIMMDEILQSVCMLAQDQYGNYVVQHVLEHGKP 907
++ S +G R IQ LE + Q ++ +EILQ+ L D +GNYV+Q E G
Sbjct: 26 IMEFSQDQHGSRFIQLKLERATPAERQ-LVFNEILQAAYQLMVDVFGNYVIQKFFEFGSL 84
Query: 908 HERSAIIKKLTGQIVQMSQQKFASNVIEKCLSFGTPAERQALVNEMLGSI 957
++ A+ +++ G ++ ++ Q + VI+K L F ++ +V E+ G +
Sbjct: 85 EQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQNEMVRELDGHV 134
Score = 43.9 bits (102), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 25/95 (26%), Positives = 47/95 (49%)
Query: 863 RVLEHCHDEKTQSIMMDEILQSVCMLAQDQYGNYVVQHVLEHGKPHERSAIIKKLTGQIV 922
R+LE + + ++ + EI + +QDQ+G+ +Q LE P ER + ++
Sbjct: 4 RLLEDFRNNRYPNLQLREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAY 63
Query: 923 QMSQQKFASNVIEKCLSFGTPAERQALVNEMLGSI 957
Q+ F + VI+K FG+ ++ AL + G +
Sbjct: 64 QLMVDVFGNYVIQKFFEFGSLEQKLALAERIRGHV 98
>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 = 342 bits (878), Expect = 4e-94, Method: Compositional matrix adjust.
Identities = 163/276 (59%), Positives = 209/276 (75%), Gaps = 1/276 (0%)
Query: 678 SFASSLLDEFKSNKTKCFELSEIAGHVVEFSADQYGSRFIQQKLETATTEEKNMVFQEIM 737
S S LL++F++ + +L ++A H+VEFS DQ+GSRFIQQKLE AT EK MVF EI+
Sbjct: 2 SHMSRLLEDFRNQRYPNLQLRDLANHIVEFSQDQHGSRFIQQKLERATAAEKQMVFSEIL 61
Query: 738 PQALSLMTDVFGNYVIQKFFEHGTASQVRELADQLTGHVLTLSLQMYGCRVIQKAIEVVE 797
A SLMTDVFGNYVIQKFFE GT Q L Q+ GHVL L+LQMYGCRVIQKA+E +
Sbjct: 62 AAAYSLMTDVFGNYVIQKFFEFGTPEQKNTLGMQVKGHVLQLALQMYGCRVIQKALESIS 121
Query: 798 LDQQTQMVKELDGHIMRCVRDQNGNHVIQKCIECVPEDAIQFIVLTFYDQVVTLSTHPYG 857
+QQ ++V ELDGH+++CV+DQNGNHV+QKCIECV A+QFI+ F QV +LSTHPYG
Sbjct: 122 PEQQQEIVHELDGHVLKCVKDQNGNHVVQKCIECVDPVALQFIINAFKGQVYSLSTHPYG 181
Query: 858 CRVIQRVLEHCHDEKTQSIMMDEILQSVCMLAQDQYGNYVVQHVLEHGKPHERSAIIKKL 917
CRVIQR+LEHC E+T I +DE+ + L QDQYGNYV+QHVLEHGK ++S +I +
Sbjct: 182 CRVIQRILEHCTAEQTTPI-LDELHEHTEQLIQDQYGNYVIQHVLEHGKQEDKSILINSV 240
Query: 918 TGQIVQMSQQKFASNVIEKCLSFGTPAERQALVNEM 953
G+++ +SQ KFASNV+EKC++ T ER L++E+
Sbjct: 241 RGKVLVLSQHKFASNVVEKCVTHATRGERTGLIDEV 276
Score = 61.6 bits (148), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 34/112 (30%), Positives = 63/112 (56%), Gaps = 1/112 (0%)
Query: 846 DQVVTLSTHPYGCRVIQRVLEHCHDEKTQSIMMDEILQSVCMLAQDQYGNYVVQHVLEHG 905
+ +V S +G R IQ+ LE + Q ++ EIL + L D +GNYV+Q E G
Sbjct: 26 NHIVEFSQDQHGSRFIQQKLERATAAEKQ-MVFSEILAAAYSLMTDVFGNYVIQKFFEFG 84
Query: 906 KPHERSAIIKKLTGQIVQMSQQKFASNVIEKCLSFGTPAERQALVNEMLGSI 957
P +++ + ++ G ++Q++ Q + VI+K L +P ++Q +V+E+ G +
Sbjct: 85 TPEQKNTLGMQVKGHVLQLALQMYGCRVIQKALESISPEQQQEIVHELDGHV 136
Score = 56.6 bits (135), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 39/153 (25%), Positives = 75/153 (49%), Gaps = 1/153 (0%)
Query: 805 VKELDGHIMRCVRDQNGNHVIQKCIECVPEDAIQFIVLTFYDQVVTLSTHPYGCRVIQRV 864
+++L HI+ +DQ+G+ IQ+ +E Q + +L T +G VIQ+
Sbjct: 21 LRDLANHIVEFSQDQHGSRFIQQKLERATAAEKQMVFSEILAAAYSLMTDVFGNYVIQKF 80
Query: 865 LEHCHDEKTQSIMMDEILQSVCMLAQDQYGNYVVQHVLEHGKPHERSAIIKKLTGQIVQM 924
E E+ ++ M ++ V LA YG V+Q LE P ++ I+ +L G +++
Sbjct: 81 FEFGTPEQKNTLGM-QVKGHVLQLALQMYGCRVIQKALESISPEQQQEIVHELDGHVLKC 139
Query: 925 SQQKFASNVIEKCLSFGTPAERQALVNEMLGSI 957
+ + ++V++KC+ P Q ++N G +
Sbjct: 140 VKDQNGNHVVQKCIECVDPVALQFIINAFKGQV 172
Score = 40.8 bits (94), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/95 (22%), Positives = 47/95 (49%)
Query: 863 RVLEHCHDEKTQSIMMDEILQSVCMLAQDQYGNYVVQHVLEHGKPHERSAIIKKLTGQIV 922
R+LE +++ ++ + ++ + +QDQ+G+ +Q LE E+ + ++
Sbjct: 6 RLLEDFRNQRYPNLQLRDLANHIVEFSQDQHGSRFIQQKLERATAAEKQMVFSEILAAAY 65
Query: 923 QMSQQKFASNVIEKCLSFGTPAERQALVNEMLGSI 957
+ F + VI+K FGTP ++ L ++ G +
Sbjct: 66 SLMTDVFGNYVIQKFFEFGTPEQKNTLGMQVKGHV 100
Score = 31.6 bits (70), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 19/80 (23%), Positives = 42/80 (52%), Gaps = 4/80 (5%)
Query: 697 LSEIAGHVVEFSADQYGSRFIQQKLETATTEEKNMVFQEIMP---QALS-LMTDVFGNYV 752
++ + G V+ S ++ S +++ + AT E+ + E+ AL +M D + NYV
Sbjct: 237 INSVRGKVLVLSQHKFASNVVEKCVTHATRGERTGLIDEVCTFNDNALHVMMKDQYANYV 296
Query: 753 IQKFFEHGTASQVRELADQL 772
+QK + +Q+++L ++
Sbjct: 297 VQKMIDVSEPTQLKKLMTKI 316
>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 = 340 bits (872), Expect = 2e-93, Method: Compositional matrix adjust.
Identities = 156/273 (57%), Positives = 211/273 (77%), Gaps = 1/273 (0%)
Query: 681 SSLLDEFKSNKTKCFELSEIAGHVVEFSADQYGSRFIQQKLETATTEEKNMVFQEIMPQA 740
S LL++F++N+ +L EIAGH++EFS DQ+GSRFIQ KLE AT E+ +VF EI+ A
Sbjct: 4 SRLLEDFRNNRYPNLQLREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAA 63
Query: 741 LSLMTDVFGNYVIQKFFEHGTASQVRELADQLTGHVLTLSLQMYGCRVIQKAIEVVELDQ 800
LM DVFGNYVIQKFFE G+ Q LA+++ GHVL+L+LQMYGCRVIQKA+E + DQ
Sbjct: 64 YQLMVDVFGNYVIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQ 123
Query: 801 QTQMVKELDGHIMRCVRDQNGNHVIQKCIECVPEDAIQFIVLTFYDQVVTLSTHPYGCRV 860
Q +MV+ELDGH+++CV+DQNGNHV+QKCIECV ++QFI+ F QV LSTHPYGCRV
Sbjct: 124 QNEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRV 183
Query: 861 IQRVLEHCHDEKTQSIMMDEILQSVCMLAQDQYGNYVVQHVLEHGKPHERSAIIKKLTGQ 920
IQR+LEHC ++T I ++E+ Q L QDQYG+YV++HVLEHG+P ++S I+ ++ G
Sbjct: 184 IQRILEHCLPDQTLPI-LEELHQHTEQLVQDQYGSYVIRHVLEHGRPEDKSKIVAEIRGN 242
Query: 921 IVQMSQQKFASNVIEKCLSFGTPAERQALVNEM 953
++ +SQ KFASNV+EKC++ + ER L++E+
Sbjct: 243 VLVLSQHKFASNVVEKCVTHASRTERAVLIDEV 275
Score = 64.7 bits (156), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 42/177 (23%), Positives = 82/177 (46%), Gaps = 7/177 (3%)
Query: 695 FELSEIAGHVVEFSADQYGSRFIQQKLETATTEEKNMVFQEIMPQALSLMTDVFGNYVIQ 754
F + G V S YG R IQ+ LE ++ + +E+ L+ D +G+YVI+
Sbjct: 162 FIIDAFKGQVFALSTHPYGCRVIQRILEHCLPDQTLPILEELHQHTEQLVQDQYGSYVIR 221
Query: 755 KFFEHGTASQVRELADQLTGHVLTLSLQMYGCRVIQKAIEVVELDQQTQMVKEL----DG 810
EHG ++ ++ G+VL LS + V++K + ++ ++ E+ DG
Sbjct: 222 HVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNVVEKCVTHASRTERAVLIDEVCTMNDG 281
Query: 811 ---HIMRCVRDQNGNHVIQKCIECVPEDAIQFIVLTFYDQVVTLSTHPYGCRVIQRV 864
+ ++DQ N+V+QK I+ + ++ + TL + YG ++ ++
Sbjct: 282 PHSALYTMMKDQYANYVVQKMIDVAEPGQRKIVMHKIRPHIATLRKYTYGKHILAKL 338
Score = 56.6 bits (135), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 32/110 (29%), Positives = 59/110 (53%), Gaps = 1/110 (0%)
Query: 848 VVTLSTHPYGCRVIQRVLEHCHDEKTQSIMMDEILQSVCMLAQDQYGNYVVQHVLEHGKP 907
++ S +G R IQ LE + Q ++ +EILQ+ L D +GNYV+Q E G
Sbjct: 27 IMEFSQDQHGSRFIQLKLERATPAERQ-LVFNEILQAAYQLMVDVFGNYVIQKFFEFGSL 85
Query: 908 HERSAIIKKLTGQIVQMSQQKFASNVIEKCLSFGTPAERQALVNEMLGSI 957
++ A+ +++ G ++ ++ Q + VI+K L F ++ +V E+ G +
Sbjct: 86 EQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQNEMVRELDGHV 135
Score = 44.3 bits (103), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 25/95 (26%), Positives = 47/95 (49%)
Query: 863 RVLEHCHDEKTQSIMMDEILQSVCMLAQDQYGNYVVQHVLEHGKPHERSAIIKKLTGQIV 922
R+LE + + ++ + EI + +QDQ+G+ +Q LE P ER + ++
Sbjct: 5 RLLEDFRNNRYPNLQLREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAY 64
Query: 923 QMSQQKFASNVIEKCLSFGTPAERQALVNEMLGSI 957
Q+ F + VI+K FG+ ++ AL + G +
Sbjct: 65 QLMVDVFGNYVIQKFFEFGSLEQKLALAERIRGHV 99
>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 = 241 bits (614), Expect = 2e-63, Method: Compositional matrix adjust.
Identities = 119/264 (45%), Positives = 176/264 (66%), Gaps = 7/264 (2%)
Query: 697 LSEIAGHVVEFSADQYGSRFIQQKLETATTEEKNMVFQEIMPQALSLMTDVFGNYVIQKF 756
L +I GH +EF DQ+GSRFIQ++L T+ EK ++F EI A+ L DVFGNYVIQKF
Sbjct: 26 LKDIFGHSLEFCKDQHGSRFIQRELATSPASEKEVIFNEIRDDAIELSNDVFGNYVIQKF 85
Query: 757 FEHGTASQVRELADQLTGHVLTLSLQMYGCRVIQKAIEVVELDQQTQMVKELDGHIMRCV 816
FE G+ Q L DQ G++ LSLQMY CRVIQKA+E ++ +Q+ ++V EL +++ +
Sbjct: 86 FEFGSKIQKNTLVDQFKGNMKQLSLQMYACRVIQKALEYIDSNQRIELVLELSDSVLQMI 145
Query: 817 RDQNGNHVIQKCIECVPEDAIQFIVLTFYDQVVTLSTHPYGCRVIQRVLEHCHDEKTQSI 876
+DQNGNHVIQK IE +P + + FI+ + + LSTH YGCRVIQR+LE E +SI
Sbjct: 146 KDQNGNHVIQKAIETIPIEKLPFILSSLTGHIYHLSTHSYGCRVIQRLLEFGSSEDQESI 205
Query: 877 MMDEILQSVCMLAQDQYGNYVVQHVLEHGKPHERSA------IIKKLTGQIVQMSQQKFA 930
++E+ + L QDQYGNYV+Q+VL+ + + II+ + +V+ S+ KFA
Sbjct: 206 -LNELKDFIPYLIQDQYGNYVIQYVLQQDQFTNKEMVDIKQEIIETVANNVVEYSKHKFA 264
Query: 931 SNVIEKCLSFGTPAERQALVNEML 954
SNV+EK + +G+ ++ +++++L
Sbjct: 265 SNVVEKSILYGSKNQKDLIISKIL 288
Score = 88.6 bits (218), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 68/239 (28%), Positives = 115/239 (48%), Gaps = 26/239 (10%)
Query: 686 EFKSNKTKCFELSEIAGHVVEFSADQYGSRFIQQKLETATTEEKNMVFQEIMPQALSLMT 745
EF S K + + G++ + S Y R IQ+ LE + ++ + E+ L ++
Sbjct: 87 EFGSKIQKNTLVDQFKGNMKQLSLQMYACRVIQKALEYIDSNQRIELVLELSDSVLQMIK 146
Query: 746 DVFGNYVIQKFFEHGTASQVRELADQLTGHVLTLSLQMYGCRVIQKAIEVVELDQQTQMV 805
D GN+VIQK E ++ + LTGH+ LS YGCRVIQ+ +E + Q ++
Sbjct: 147 DQNGNHVIQKAIETIPIEKLPFILSSLTGHIYHLSTHSYGCRVIQRLLEFGSSEDQESIL 206
Query: 806 KELDGHIMRCVRDQNGNHVIQKCI--------ECVPEDAIQFIVLTFYDQVVTLSTHPYG 857
EL I ++DQ GN+VIQ + E V D Q I+ T + VV S H +
Sbjct: 207 NELKDFIPYLIQDQYGNYVIQYVLQQDQFTNKEMV--DIKQEIIETVANNVVEYSKHKFA 264
Query: 858 CRVIQRVLEHCHDEKTQS-IMMDEIL-------------QSVCMLAQDQYGNYVVQHVL 902
V+++ + + K Q +++ +IL + ++ +DQ+ NYV+Q ++
Sbjct: 265 SNVVEKSI--LYGSKNQKDLIISKILPRDKNHALNLEDDSPMILMIKDQFANYVIQKLV 321
Score = 59.3 bits (142), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 42/167 (25%), Positives = 78/167 (46%), Gaps = 19/167 (11%)
Query: 695 FELSEIAGHVVEFSADQYGSRFIQQKLETATTEEKNMVFQEIMPQALSLMTDVFGNYVIQ 754
F LS + GH+ S YG R IQ+ LE ++E++ + E+ L+ D +GNYVIQ
Sbjct: 168 FILSSLTGHIYHLSTHSYGCRVIQRLLEFGSSEDQESILNELKDFIPYLIQDQYGNYVIQ 227
Query: 755 ------KFFEHGTASQVRELADQLTGHVLTLSLQMYGCRVIQKAI-------------EV 795
+F +E+ + + +V+ S + V++K+I ++
Sbjct: 228 YVLQQDQFTNKEMVDIKQEIIETVANNVVEYSKHKFASNVVEKSILYGSKNQKDLIISKI 287
Query: 796 VELDQQTQMVKELDGHIMRCVRDQNGNHVIQKCIECVPEDAIQFIVL 842
+ D+ + E D ++ ++DQ N+VIQK + + + IV+
Sbjct: 288 LPRDKNHALNLEDDSPMILMIKDQFANYVIQKLVNVSEGEGKKLIVI 334
Score = 54.7 bits (130), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 31/102 (30%), Positives = 53/102 (51%), Gaps = 1/102 (0%)
Query: 856 YGCRVIQRVLEHCHDEKTQSIMMDEILQSVCMLAQDQYGNYVVQHVLEHGKPHERSAIIK 915
+G R IQR L + ++ +EI L+ D +GNYV+Q E G +++ ++
Sbjct: 41 HGSRFIQRELA-TSPASEKEVIFNEIRDDAIELSNDVFGNYVIQKFFEFGSKIQKNTLVD 99
Query: 916 KLTGQIVQMSQQKFASNVIEKCLSFGTPAERQALVNEMLGSI 957
+ G + Q+S Q +A VI+K L + +R LV E+ S+
Sbjct: 100 QFKGNMKQLSLQMYACRVIQKALEYIDSNQRIELVLELSDSV 141
Score = 38.1 bits (87), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 17/72 (23%), Positives = 38/72 (52%)
Query: 888 LAQDQYGNYVVQHVLEHGKPHERSAIIKKLTGQIVQMSQQKFASNVIEKCLSFGTPAERQ 947
+DQ+G+ +Q L E+ I ++ +++S F + VI+K FG+ ++
Sbjct: 36 FCKDQHGSRFIQRELATSPASEKEVIFNEIRDDAIELSNDVFGNYVIQKFFEFGSKIQKN 95
Query: 948 ALVNEMLGSIEE 959
LV++ G++++
Sbjct: 96 TLVDQFKGNMKQ 107
>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 = 163 bits (412), Expect = 5e-40, Method: Compositional matrix adjust.
Identities = 94/272 (34%), Positives = 151/272 (55%), Gaps = 19/272 (6%)
Query: 679 FASSLLDEFKSNKTKCFELSEIAGHVVEFSADQYGSRFIQQKLETATTEEKNMVFQEIMP 738
FA ++LD++ G + DQ+G RF+Q++L+ ++ + +F+E
Sbjct: 3 FADAVLDQY-------------IGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKD 49
Query: 739 QALSLMTDVFGNYVIQKFFEHGTASQVRELADQLTGHVLTLSLQMYGCRVIQKAIEVVEL 798
+ LMTD FGNY+IQK E T Q L + H + +SL +GCR +QK IE ++
Sbjct: 50 YTVELMTDSFGNYLIQKLLEEVTTEQRIVLTKISSPHFVEISLNPHGCRALQKLIECIKT 109
Query: 799 DQQTQMVKE-LDGHIMRCVRDQNGNHVIQKCIECVPEDAIQFIVLTFYDQVVTLSTHPYG 857
D++ Q+V + L + ++ +D NGNHVIQKC++ + + QFI D + ++TH +G
Sbjct: 110 DEEAQIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHG 169
Query: 858 CRVIQRVLEHCHDEKTQSIMMDEILQSVCMLAQDQYGNYVVQHVL----EHGKPHERSAI 913
CRV+QR L+H E+ + + D++L V L D +GNYVVQ+++ E K I
Sbjct: 170 CRVLQRCLDHGTTEQCDN-LCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKI 228
Query: 914 IKKLTGQIVQMSQQKFASNVIEKCLSFGTPAE 945
+ L + +++S KF SNVIEK L +E
Sbjct: 229 VHLLKPRAIELSIHKFGSNVIEKILKTAIVSE 260
Score = 84.7 bits (208), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 50/192 (26%), Positives = 100/192 (52%), Gaps = 4/192 (2%)
Query: 770 DQLTGHVLTLSLQMYGCRVIQKAIEVVELDQQTQMVKELDGHIMRCVRDQNGNHVIQKCI 829
DQ G + +L +GCR +QK ++++ + +E + + + D GN++IQK +
Sbjct: 9 DQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLL 68
Query: 830 ECVPEDAIQFIVLTFYD--QVVTLSTHPYGCRVIQRVLEHCHDEKTQSIMMDEILQSVCM 887
E V + Q IVLT V +S +P+GCR +Q+++E ++ I++D +
Sbjct: 69 EEVTTE--QRIVLTKISSPHFVEISLNPHGCRALQKLIECIKTDEEAQIVVDSLRPYTVQ 126
Query: 888 LAQDQYGNYVVQHVLEHGKPHERSAIIKKLTGQIVQMSQQKFASNVIEKCLSFGTPAERQ 947
L++D GN+V+Q L+ KP I ++ + ++ + V+++CL GT +
Sbjct: 127 LSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCRVLQRCLDHGTTEQCD 186
Query: 948 ALVNEMLGSIEE 959
L +++L +++
Sbjct: 187 NLCDKLLALVDK 198
Score = 78.6 bits (192), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 65/233 (27%), Positives = 112/233 (48%), Gaps = 21/233 (9%)
Query: 703 HVVEFSADQYGSRFIQQKLETATT-EEKNMVFQEIMPQALSLMTDVFGNYVIQKFFEHGT 761
H VE S + +G R +Q+ +E T EE +V + P + L D+ GN+VIQK +
Sbjct: 86 HFVEISLNPHGCRALQKLIECIKTDEEAQIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLK 145
Query: 762 ASQVRELADQLTGHVLTLSLQMYGCRVIQKAIEVVELDQQTQMVKELDGHIMRCVRDQNG 821
+ + D ++ + ++ +GCRV+Q+ ++ +Q + +L + + D G
Sbjct: 146 PENFQFIFDAISDSCIDIATHRHGCRVLQRCLDHGTTEQCDNLCDKLLALVDKLTLDPFG 205
Query: 822 NHVIQKCIECVPE----DAIQFIVLTFYDQVVTLSTHPYGCRVIQRVLEHCHDEKTQSI- 876
N+V+Q I E D IV + + LS H +G VI+++L KT +
Sbjct: 206 NYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVIEKIL------KTAIVS 259
Query: 877 --MMDEILQS-----VCMLAQDQYGNYVVQHVLEHGKPHERSAIIKKLTGQIV 922
M+ EIL + + L D YGNYV+Q L+ H+++ + K +IV
Sbjct: 260 EPMILEILNNGGETGIQSLLNDSYGNYVLQTALD--ISHKQNDYLYKRLSEIV 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 = 157 bits (397), Expect = 3e-38, Method: Compositional matrix adjust.
Identities = 95/284 (33%), Positives = 155/284 (54%), Gaps = 21/284 (7%)
Query: 669 SEAGGSLDES--FASSLLDEFKSNKTKCFELSEIAGHVVEFSADQYGSRFIQQKLETATT 726
+E ++ES FA ++LD++ G + DQ+G RF+Q++L+ +
Sbjct: 13 AEKQRKIEESSRFADAVLDQY-------------IGSIHSLCKDQHGCRFLQKQLDILGS 59
Query: 727 EEKNMVFQEIMPQALSLMTDVFGNYVIQKFFEHGTASQVRELADQLTGHVLTLSLQMYGC 786
+ + +F+E + LMTD FGNY+IQK E T Q L + H + +SL +G
Sbjct: 60 KAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVTTEQRIVLTKISSPHFVEISLNPHGT 119
Query: 787 RVIQKAIEVVELDQQTQMVKE-LDGHIMRCVRDQNGNHVIQKCIECVPEDAIQFIVLTFY 845
R +QK IE ++ D++ Q+V + L + ++ +D NGNHVIQKC++ + + QFI
Sbjct: 120 RALQKLIECIKTDEEAQIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAIS 179
Query: 846 DQVVTLSTHPYGCRVIQRVLEHCHDEKTQSIMMDEILQSVCMLAQDQYGNYVVQHVL--- 902
D + ++TH +GC V+QR L+H E+ + + D++L V L D +GNYVVQ+++
Sbjct: 180 DSCIDIATHRHGCCVLQRCLDHGTTEQCDN-LCDKLLALVDKLTLDPFGNYVVQYIITKE 238
Query: 903 -EHGKPHERSAIIKKLTGQIVQMSQQKFASNVIEKCLSFGTPAE 945
E K I+ L + +++S KF SNVIEK L +E
Sbjct: 239 AEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVIEKILKTAIVSE 282
Score = 81.3 bits (199), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 49/192 (25%), Positives = 99/192 (51%), Gaps = 4/192 (2%)
Query: 770 DQLTGHVLTLSLQMYGCRVIQKAIEVVELDQQTQMVKELDGHIMRCVRDQNGNHVIQKCI 829
DQ G + +L +GCR +QK ++++ + +E + + + D GN++IQK +
Sbjct: 31 DQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLL 90
Query: 830 ECVPEDAIQFIVLTFYD--QVVTLSTHPYGCRVIQRVLEHCHDEKTQSIMMDEILQSVCM 887
E V + Q IVLT V +S +P+G R +Q+++E ++ I++D +
Sbjct: 91 EEVTTE--QRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYTVQ 148
Query: 888 LAQDQYGNYVVQHVLEHGKPHERSAIIKKLTGQIVQMSQQKFASNVIEKCLSFGTPAERQ 947
L++D GN+V+Q L+ KP I ++ + ++ + V+++CL GT +
Sbjct: 149 LSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCD 208
Query: 948 ALVNEMLGSIEE 959
L +++L +++
Sbjct: 209 NLCDKLLALVDK 220
Score = 77.0 bits (188), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 64/233 (27%), Positives = 112/233 (48%), Gaps = 21/233 (9%)
Query: 703 HVVEFSADQYGSRFIQQKLETATT-EEKNMVFQEIMPQALSLMTDVFGNYVIQKFFEHGT 761
H VE S + +G+R +Q+ +E T EE +V + P + L D+ GN+VIQK +
Sbjct: 108 HFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLK 167
Query: 762 ASQVRELADQLTGHVLTLSLQMYGCRVIQKAIEVVELDQQTQMVKELDGHIMRCVRDQNG 821
+ + D ++ + ++ +GC V+Q+ ++ +Q + +L + + D G
Sbjct: 168 PENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCDNLCDKLLALVDKLTLDPFG 227
Query: 822 NHVIQKCIECVPE----DAIQFIVLTFYDQVVTLSTHPYGCRVIQRVLEHCHDEKTQSI- 876
N+V+Q I E D IV + + LS H +G VI+++L KT +
Sbjct: 228 NYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVIEKIL------KTAIVS 281
Query: 877 --MMDEILQS-----VCMLAQDQYGNYVVQHVLEHGKPHERSAIIKKLTGQIV 922
M+ EIL + + L D YGNYV+Q L+ H+++ + K +IV
Sbjct: 282 EPMILEILNNGGETGIQSLLNDSYGNYVLQTALD--ISHKQNDYLYKRLSEIV 332
>pdb|3BX2|A Chain A, Puf4 Rna Binding Domain Bound To Ho Endonuclease Rna 3'
Utr Recognition Sequence
pdb|3BX2|B Chain B, Puf4 Rna Binding Domain Bound To Ho Endonuclease Rna 3'
Utr Recognition Sequence
Length = 335
Score = 155 bits (391), Expect = 1e-37, Method: Compositional matrix adjust.
Identities = 92/272 (33%), Positives = 149/272 (54%), Gaps = 19/272 (6%)
Query: 679 FASSLLDEFKSNKTKCFELSEIAGHVVEFSADQYGSRFIQQKLETATTEEKNMVFQEIMP 738
FA ++LD++ G + DQ+G RF+Q++L+ ++ + +F+E
Sbjct: 3 FADAVLDQY-------------IGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKD 49
Query: 739 QALSLMTDVFGNYVIQKFFEHGTASQVRELADQLTGHVLTLSLQMYGCRVIQKAIEVVEL 798
+ LMTD FGNY+IQK E T Q L + H + +SL +G R +QK IE ++
Sbjct: 50 YTVELMTDSFGNYLIQKLLEEVTTEQRIVLTKISSPHFVEISLNPHGTRALQKLIECIKT 109
Query: 799 DQQTQMVKE-LDGHIMRCVRDQNGNHVIQKCIECVPEDAIQFIVLTFYDQVVTLSTHPYG 857
D++ Q+V + L + ++ +D NGNHVIQKC++ + + QFI D + ++TH +G
Sbjct: 110 DEEAQIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHG 169
Query: 858 CRVIQRVLEHCHDEKTQSIMMDEILQSVCMLAQDQYGNYVVQHVL----EHGKPHERSAI 913
C V+QR L+H E+ + + D++L V L D +GNYVVQ+++ E K I
Sbjct: 170 CCVLQRCLDHGTTEQCDN-LCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKI 228
Query: 914 IKKLTGQIVQMSQQKFASNVIEKCLSFGTPAE 945
+ L + +++S KF SNVIEK L +E
Sbjct: 229 VHLLKPRAIELSIHKFGSNVIEKILKTAIVSE 260
Score = 79.7 bits (195), Expect = 7e-15, Method: Compositional matrix adjust.
Identities = 49/192 (25%), Positives = 99/192 (51%), Gaps = 4/192 (2%)
Query: 770 DQLTGHVLTLSLQMYGCRVIQKAIEVVELDQQTQMVKELDGHIMRCVRDQNGNHVIQKCI 829
DQ G + +L +GCR +QK ++++ + +E + + + D GN++IQK +
Sbjct: 9 DQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLL 68
Query: 830 ECVPEDAIQFIVLTFYD--QVVTLSTHPYGCRVIQRVLEHCHDEKTQSIMMDEILQSVCM 887
E V + Q IVLT V +S +P+G R +Q+++E ++ I++D +
Sbjct: 69 EEVTTE--QRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYTVQ 126
Query: 888 LAQDQYGNYVVQHVLEHGKPHERSAIIKKLTGQIVQMSQQKFASNVIEKCLSFGTPAERQ 947
L++D GN+V+Q L+ KP I ++ + ++ + V+++CL GT +
Sbjct: 127 LSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCD 186
Query: 948 ALVNEMLGSIEE 959
L +++L +++
Sbjct: 187 NLCDKLLALVDK 198
Score = 75.5 bits (184), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 64/233 (27%), Positives = 112/233 (48%), Gaps = 21/233 (9%)
Query: 703 HVVEFSADQYGSRFIQQKLETATT-EEKNMVFQEIMPQALSLMTDVFGNYVIQKFFEHGT 761
H VE S + +G+R +Q+ +E T EE +V + P + L D+ GN+VIQK +
Sbjct: 86 HFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLK 145
Query: 762 ASQVRELADQLTGHVLTLSLQMYGCRVIQKAIEVVELDQQTQMVKELDGHIMRCVRDQNG 821
+ + D ++ + ++ +GC V+Q+ ++ +Q + +L + + D G
Sbjct: 146 PENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCDNLCDKLLALVDKLTLDPFG 205
Query: 822 NHVIQKCIECVPE----DAIQFIVLTFYDQVVTLSTHPYGCRVIQRVLEHCHDEKTQSI- 876
N+V+Q I E D IV + + LS H +G VI+++L KT +
Sbjct: 206 NYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVIEKIL------KTAIVS 259
Query: 877 --MMDEILQS-----VCMLAQDQYGNYVVQHVLEHGKPHERSAIIKKLTGQIV 922
M+ EIL + + L D YGNYV+Q L+ H+++ + K +IV
Sbjct: 260 EPMILEILNNGGETGIQSLLNDSYGNYVLQTALD--ISHKQNDYLYKRLSEIV 310
>pdb|3BWT|A Chain A, Crystal Structure Of The Rna Binding Domain Of Puf4 From
Saccharomyces Cerevisiae
Length = 333
Score = 155 bits (391), Expect = 1e-37, Method: Compositional matrix adjust.
Identities = 92/272 (33%), Positives = 149/272 (54%), Gaps = 19/272 (6%)
Query: 679 FASSLLDEFKSNKTKCFELSEIAGHVVEFSADQYGSRFIQQKLETATTEEKNMVFQEIMP 738
FA ++LD++ G + DQ+G RF+Q++L+ ++ + +F+E
Sbjct: 3 FADAVLDQY-------------IGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKD 49
Query: 739 QALSLMTDVFGNYVIQKFFEHGTASQVRELADQLTGHVLTLSLQMYGCRVIQKAIEVVEL 798
+ LMTD FGNY+IQK E T Q L + H + +SL +G R +QK IE ++
Sbjct: 50 YTVELMTDSFGNYLIQKLLEEVTTEQRIVLTKISSPHFVEISLNPHGTRALQKLIECIKT 109
Query: 799 DQQTQMVKE-LDGHIMRCVRDQNGNHVIQKCIECVPEDAIQFIVLTFYDQVVTLSTHPYG 857
D++ Q+V + L + ++ +D NGNHVIQKC++ + + QFI D + ++TH +G
Sbjct: 110 DEEAQIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHG 169
Query: 858 CRVIQRVLEHCHDEKTQSIMMDEILQSVCMLAQDQYGNYVVQHVL----EHGKPHERSAI 913
C V+QR L+H E+ + + D++L V L D +GNYVVQ+++ E K I
Sbjct: 170 CCVLQRCLDHGTTEQCDN-LCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKI 228
Query: 914 IKKLTGQIVQMSQQKFASNVIEKCLSFGTPAE 945
+ L + +++S KF SNVIEK L +E
Sbjct: 229 VHLLKPRAIELSIHKFGSNVIEKILKTAIVSE 260
Score = 79.7 bits (195), Expect = 8e-15, Method: Compositional matrix adjust.
Identities = 49/194 (25%), Positives = 100/194 (51%), Gaps = 4/194 (2%)
Query: 768 LADQLTGHVLTLSLQMYGCRVIQKAIEVVELDQQTQMVKELDGHIMRCVRDQNGNHVIQK 827
+ DQ G + +L +GCR +QK ++++ + +E + + + D GN++IQK
Sbjct: 7 VLDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQK 66
Query: 828 CIECVPEDAIQFIVLTFYD--QVVTLSTHPYGCRVIQRVLEHCHDEKTQSIMMDEILQSV 885
+E V + Q IVLT V +S +P+G R +Q+++E ++ I++D +
Sbjct: 67 LLEEVTTE--QRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYT 124
Query: 886 CMLAQDQYGNYVVQHVLEHGKPHERSAIIKKLTGQIVQMSQQKFASNVIEKCLSFGTPAE 945
L++D GN+V+Q L+ KP I ++ + ++ + V+++CL GT +
Sbjct: 125 VQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQ 184
Query: 946 RQALVNEMLGSIEE 959
L +++L +++
Sbjct: 185 CDNLCDKLLALVDK 198
Score = 75.5 bits (184), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 64/233 (27%), Positives = 112/233 (48%), Gaps = 21/233 (9%)
Query: 703 HVVEFSADQYGSRFIQQKLETATT-EEKNMVFQEIMPQALSLMTDVFGNYVIQKFFEHGT 761
H VE S + +G+R +Q+ +E T EE +V + P + L D+ GN+VIQK +
Sbjct: 86 HFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLK 145
Query: 762 ASQVRELADQLTGHVLTLSLQMYGCRVIQKAIEVVELDQQTQMVKELDGHIMRCVRDQNG 821
+ + D ++ + ++ +GC V+Q+ ++ +Q + +L + + D G
Sbjct: 146 PENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCDNLCDKLLALVDKLTLDPFG 205
Query: 822 NHVIQKCIECVPE----DAIQFIVLTFYDQVVTLSTHPYGCRVIQRVLEHCHDEKTQSI- 876
N+V+Q I E D IV + + LS H +G VI+++L KT +
Sbjct: 206 NYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVIEKIL------KTAIVS 259
Query: 877 --MMDEILQS-----VCMLAQDQYGNYVVQHVLEHGKPHERSAIIKKLTGQIV 922
M+ EIL + + L D YGNYV+Q L+ H+++ + K +IV
Sbjct: 260 EPMILEILNNGGETGIQSLLNDSYGNYVLQTALD--ISHKQNDYLYKRLSEIV 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 = 115 bits (289), Expect = 9e-26, Method: Compositional matrix adjust.
Identities = 83/299 (27%), Positives = 155/299 (51%), Gaps = 46/299 (15%)
Query: 697 LSEI--AGHVVEFSADQYGSRFIQQKLE-TATTEEKNMVFQEIMPQA---LSLMTDVFGN 750
LSE+ +G +++F+ D+ G +F+++ ++ + T+ +K +F++++ + L L T++FGN
Sbjct: 23 LSEVLDSGDLMKFAVDKTGCQFLEKAVKGSLTSYQKFQLFEQVIGRKDDFLKLSTNIFGN 82
Query: 751 YVIQKFF-------EHGTASQVRELADQLTGHVLTLSLQMYGCRVIQKAIEVVELDQQTQ 803
Y++Q + G + +L + ++ + + L + CRVIQ +++ ++L +
Sbjct: 83 YLVQSVIGISLATNDDGYTKRQEKLKNFISSQMTDMCLDKFACRVIQSSLQNMDLSLACK 142
Query: 804 MVKEL--DGHIMRCVRDQNGNHVIQKCIECVPEDAIQFIVLTFYDQVVT------LSTHP 855
+V+ L D ++ DQN NHVIQK + +P +FIV D V T + +
Sbjct: 143 LVQALPRDARLIAICVDQNANHVIQKVVAVIPLKNWEFIV----DFVATPEHLRQICSDK 198
Query: 856 YGCRVIQRVLEHCH---------------DEKTQSIMMDEILQSVCMLAQDQYGNYVVQH 900
YGCRV+Q ++E E+ +M + LA ++Y NY++QH
Sbjct: 199 YGCRVVQTIIEKLTADSMNVDLTSAAQNLRERALQRLMTSVTNRCQELATNEYANYIIQH 258
Query: 901 VLEHGK-PHERSAIIKK-LTGQIVQMSQQKFASNVIEKCLSFGTPAERQALVNEMLGSI 957
++ + R II+K L ++ +SQ+KFAS+V+EK P E L+ EM+ I
Sbjct: 259 IVSNDDLAVYRECIIEKCLMRNLLSLSQEKFASHVVEKAF-LHAPLE---LLAEMMDEI 313
Score = 42.4 bits (98), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 54/243 (22%), Positives = 95/243 (39%), Gaps = 48/243 (19%)
Query: 700 IAGHVVEFSADQYGSRFIQQKLETATTEEKNMVFQEIMPQA--LSLMTDVFGNYVIQKFF 757
I+ + + D++ R IQ L+ + Q + A +++ D N+VIQK
Sbjct: 111 ISSQMTDMCLDKFACRVIQSSLQNMDLSLACKLVQALPRDARLIAICVDQNANHVIQKVV 170
Query: 758 EHGTASQVRELADQLTG--HVLTLSLQMYGCRVIQKAIEV-------VELDQQTQMVKE- 807
+ D + H+ + YGCRV+Q IE V+L Q ++E
Sbjct: 171 AVIPLKNWEFIVDFVATPEHLRQICSDKYGCRVVQTIIEKLTADSMNVDLTSAAQNLRER 230
Query: 808 -----LDGHIMRC---VRDQNGNHVIQKCI---------ECVPEDAIQFIVLTFYDQVVT 850
+ RC ++ N++IQ + EC+ E + +++
Sbjct: 231 ALQRLMTSVTNRCQELATNEYANYIIQHIVSNDDLAVYRECIIEKCLM-------RNLLS 283
Query: 851 LSTHPYGCRVIQRVLEHCHDEKTQSIMMDEILQ-----------SVCMLAQDQYGNYVVQ 899
LS + V+++ H E MMDEI ++ ++ Q+GNYVVQ
Sbjct: 284 LSQEKFASHVVEKAFLHAPLELLAE-MMDEIFDGYIPHPDTGKDALDIMMFHQFGNYVVQ 342
Query: 900 HVL 902
+L
Sbjct: 343 CML 345
>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 = 115 bits (288), Expect = 1e-25, Method: Compositional matrix adjust.
Identities = 83/299 (27%), Positives = 155/299 (51%), Gaps = 46/299 (15%)
Query: 697 LSEI--AGHVVEFSADQYGSRFIQQKLE-TATTEEKNMVFQEIMPQA---LSLMTDVFGN 750
LSE+ +G +++F+ D+ G +F+++ ++ + T+ +K +F++++ + L L T++FGN
Sbjct: 22 LSEVLDSGDLMKFAVDKTGCQFLEKAVKGSLTSYQKFQLFEQVIGRKDDFLKLSTNIFGN 81
Query: 751 YVIQKFF-------EHGTASQVRELADQLTGHVLTLSLQMYGCRVIQKAIEVVELDQQTQ 803
Y++Q + G + +L + ++ + + L + CRVIQ +++ ++L +
Sbjct: 82 YLVQSVIGISLATNDDGYTKRQEKLKNFISSQMTDMCLDKFACRVIQSSLQNMDLSLACK 141
Query: 804 MVKEL--DGHIMRCVRDQNGNHVIQKCIECVPEDAIQFIVLTFYDQVVT------LSTHP 855
+V+ L D ++ DQN NHVIQK + +P +FIV D V T + +
Sbjct: 142 LVQALPRDARLIAICVDQNANHVIQKVVAVIPLKNWEFIV----DFVATPEHLRQICSDK 197
Query: 856 YGCRVIQRVLEHCH---------------DEKTQSIMMDEILQSVCMLAQDQYGNYVVQH 900
YGCRV+Q ++E E+ +M + LA ++Y NY++QH
Sbjct: 198 YGCRVVQTIIEKLTADSMNVDLTSAAQNLRERALQRLMTSVTNRCQELATNEYANYIIQH 257
Query: 901 VLEHGK-PHERSAIIKK-LTGQIVQMSQQKFASNVIEKCLSFGTPAERQALVNEMLGSI 957
++ + R II+K L ++ +SQ+KFAS+V+EK P E L+ EM+ I
Sbjct: 258 IVSNDDLAVYRECIIEKCLMRNLLSLSQEKFASHVVEKAF-LHAPLE---LLAEMMDEI 312
Score = 42.0 bits (97), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 54/243 (22%), Positives = 95/243 (39%), Gaps = 48/243 (19%)
Query: 700 IAGHVVEFSADQYGSRFIQQKLETATTEEKNMVFQEIMPQA--LSLMTDVFGNYVIQKFF 757
I+ + + D++ R IQ L+ + Q + A +++ D N+VIQK
Sbjct: 110 ISSQMTDMCLDKFACRVIQSSLQNMDLSLACKLVQALPRDARLIAICVDQNANHVIQKVV 169
Query: 758 EHGTASQVRELADQLTG--HVLTLSLQMYGCRVIQKAIEV-------VELDQQTQMVKE- 807
+ D + H+ + YGCRV+Q IE V+L Q ++E
Sbjct: 170 AVIPLKNWEFIVDFVATPEHLRQICSDKYGCRVVQTIIEKLTADSMNVDLTSAAQNLRER 229
Query: 808 -----LDGHIMRC---VRDQNGNHVIQKCI---------ECVPEDAIQFIVLTFYDQVVT 850
+ RC ++ N++IQ + EC+ E + +++
Sbjct: 230 ALQRLMTSVTNRCQELATNEYANYIIQHIVSNDDLAVYRECIIEKCLM-------RNLLS 282
Query: 851 LSTHPYGCRVIQRVLEHCHDEKTQSIMMDEILQ-----------SVCMLAQDQYGNYVVQ 899
LS + V+++ H E MMDEI ++ ++ Q+GNYVVQ
Sbjct: 283 LSQEKFASHVVEKAFLHAPLELLAE-MMDEIFDGYIPHPDTGKDALDIMMFHQFGNYVVQ 341
Query: 900 HVL 902
+L
Sbjct: 342 CML 344
>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 = 112 bits (281), Expect = 8e-25, Method: Compositional matrix adjust.
Identities = 82/299 (27%), Positives = 154/299 (51%), Gaps = 46/299 (15%)
Query: 697 LSEI--AGHVVEFSADQYGSRFIQQKLE-TATTEEKNMVFQEIMPQA---LSLMTDVFGN 750
LSE+ +G +++F+ D+ G +F+++ ++ + T+ +K +F++++ + L L T++FGN
Sbjct: 23 LSEVLDSGDLMKFAVDKTGCQFLEKAVKGSLTSYQKFQLFEQVIGRKDDFLKLSTNIFGN 82
Query: 751 YVIQKFF-------EHGTASQVRELADQLTGHVLTLSLQMYGCRVIQKAIEVVELDQQTQ 803
Y++Q + G + +L + ++ + + L + C VIQ +++ ++L +
Sbjct: 83 YLVQSVIGISLATNDDGYTKRQEKLKNFISSQMTDMCLDKFACYVIQSSLQNMDLSLACK 142
Query: 804 MVKEL--DGHIMRCVRDQNGNHVIQKCIECVPEDAIQFIVLTFYDQVVT------LSTHP 855
+V+ L D ++ DQN NHVIQK + +P +FIV D V T + +
Sbjct: 143 LVQALPRDARLIAICVDQNANHVIQKVVAVIPLKNWEFIV----DFVATPEHLRQICSDK 198
Query: 856 YGCRVIQRVLEHCH---------------DEKTQSIMMDEILQSVCMLAQDQYGNYVVQH 900
YGCRV+Q ++E E+ +M + LA ++Y NY++QH
Sbjct: 199 YGCRVVQTIIEKLTADSMNVDLTSAAQNLRERALQRLMTSVTNRCQELATNEYANYIIQH 258
Query: 901 VLEHGK-PHERSAIIKK-LTGQIVQMSQQKFASNVIEKCLSFGTPAERQALVNEMLGSI 957
++ + R II+K L ++ +SQ+KFAS+V+EK P E L+ EM+ I
Sbjct: 259 IVSNDDLAVYRECIIEKCLMRNLLSLSQEKFASHVVEKAF-LHAPLE---LLAEMMDEI 313
Score = 39.3 bits (90), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 53/243 (21%), Positives = 94/243 (38%), Gaps = 48/243 (19%)
Query: 700 IAGHVVEFSADQYGSRFIQQKLETATTEEKNMVFQEIMPQA--LSLMTDVFGNYVIQKFF 757
I+ + + D++ IQ L+ + Q + A +++ D N+VIQK
Sbjct: 111 ISSQMTDMCLDKFACYVIQSSLQNMDLSLACKLVQALPRDARLIAICVDQNANHVIQKVV 170
Query: 758 EHGTASQVRELADQLTG--HVLTLSLQMYGCRVIQKAIEV-------VELDQQTQMVKE- 807
+ D + H+ + YGCRV+Q IE V+L Q ++E
Sbjct: 171 AVIPLKNWEFIVDFVATPEHLRQICSDKYGCRVVQTIIEKLTADSMNVDLTSAAQNLRER 230
Query: 808 -----LDGHIMRC---VRDQNGNHVIQKCI---------ECVPEDAIQFIVLTFYDQVVT 850
+ RC ++ N++IQ + EC+ E + +++
Sbjct: 231 ALQRLMTSVTNRCQELATNEYANYIIQHIVSNDDLAVYRECIIEKCLM-------RNLLS 283
Query: 851 LSTHPYGCRVIQRVLEHCHDEKTQSIMMDEILQ-----------SVCMLAQDQYGNYVVQ 899
LS + V+++ H E MMDEI ++ ++ Q+GNYVVQ
Sbjct: 284 LSQEKFASHVVEKAFLHAPLELLAE-MMDEIFDGYIPHPDTGKDALDIMMFHQFGNYVVQ 342
Query: 900 HVL 902
+L
Sbjct: 343 CML 345
>pdb|3V71|A Chain A, Crystal Structure Of Puf-6 In Complex With 5be13 Rna
Length = 382
Score = 104 bits (260), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 77/277 (27%), Positives = 142/277 (51%), Gaps = 25/277 (9%)
Query: 702 GHVVEFSADQYGSRFIQQKLETATTEEKNMVFQEIMPQALSLMTDVF----GNYVIQKFF 757
G +++F+ D G +F++ + ++ E ++ +L + GN+++QK
Sbjct: 20 GQLIDFAIDPSGVKFLEANYPLDSEDQIRKAVFEKFTESTTLFVGLCHSRNGNFIVQKLV 79
Query: 758 EHGTASQVRELADQLT-GHVLTLSLQMYGCRVIQKAIEVVELDQQTQMVKELDGH-IMRC 815
E T ++ REL Q+ G +L + + CRV+Q A++ + Q+++EL +
Sbjct: 80 ELATPAEQRELLRQMIDGGLLAMCKDKFACRVVQLALQKFDHSNVFQLIQELSTFDLAAM 139
Query: 816 VRDQNGNHVIQKCIECVPEDAIQFIV--LTFYDQVVTLSTHPYGCRVIQRVLEH------ 867
DQ HVIQ+ ++ +P D F V L+ D ++ + YGCR++Q+V++
Sbjct: 140 CTDQISIHVIQRVVKQLPVDMWTFFVHFLSSGDSLMAVCQDKYGCRLVQQVIDRLAENPK 199
Query: 868 --CHDEKTQSI--MMDEILQSVCMLAQDQYGNYVVQHVLEHGKPHE--RSAIIKK-LTGQ 920
C + Q + +M I+++ L+ +++ NYV+Q+V++ E R II K L
Sbjct: 200 LPCFKFRIQLLHSLMTCIVRNCYRLSSNEFANYVIQYVIKSSGIMEMYRDTIIDKCLLRN 259
Query: 921 IVQMSQQKFASNVIEKCLSFGTPAERQALVNEMLGSI 957
++ MSQ K+AS+VIE F P AL++EM+ I
Sbjct: 260 LLSMSQDKYASHVIEGAFLFAPP----ALLHEMMEEI 292
Score = 34.3 bits (77), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 58/242 (23%), Positives = 97/242 (40%), Gaps = 51/242 (21%)
Query: 700 IAGHVVEFSADQYGSRFIQQKLETATTEEKNMVFQEIMPQALSLM-TDVFGNYVIQK--- 755
I G ++ D++ R +Q L+ + QE+ L+ M TD +VIQ+
Sbjct: 95 IDGGLLAMCKDKFACRVVQLALQKFDHSNVFQLIQELSTFDLAAMCTDQISIHVIQRVVK 154
Query: 756 --------FFEHGTASQVRELADQLTGHVLTLSLQMYGCRVIQKAIEVVE-------LDQ 800
FF H +S D L + + YGCR++Q+ I+ +
Sbjct: 155 QLPVDMWTFFVHFLSS-----GDSL----MAVCQDKYGCRLVQQVIDRLAENPKLPCFKF 205
Query: 801 QTQMVKELDGHIMR-CVR---DQNGNHVIQKCIEC-----VPEDAIQFIVLTFYDQVVTL 851
+ Q++ L I+R C R ++ N+VIQ I+ + D I I ++++
Sbjct: 206 RIQLLHSLMTCIVRNCYRLSSNEFANYVIQYVIKSSGIMEMYRDTI--IDKCLLRNLLSM 263
Query: 852 STHPYGCRVIQRVLEHCHDEKTQSIMMDEIL-----------QSVCMLAQDQYGNYVVQH 900
S Y VI+ MM+EI ++ +L QYGNYVVQ
Sbjct: 264 SQDKYASHVIEGAFLFAPPALLHE-MMEEIFSGYVKDVESNRDALDILLFHQYGNYVVQQ 322
Query: 901 VL 902
++
Sbjct: 323 MI 324
>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 = 30.8 bits (68), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 34/67 (50%), Gaps = 4/67 (5%)
Query: 711 QYGSRFIQQKLETATTEEKNMVFQEIMPQALSLMTDVFGNYV--IQKFFEHG--TASQVR 766
++ +R IQ+ LE T EE V Q + L T VFG V ++++ G T ++R
Sbjct: 71 EHSTRVIQELLEHGTCEEVKQVRCSERYQTMKLFTQVFGVGVKTANRWYQEGLRTLDELR 130
Query: 767 ELADQLT 773
E +LT
Sbjct: 131 EQPQRLT 137
>pdb|2CUN|A Chain A, Crystal Structure Of Phosphoglycerate Kinase From
Pyrococcus Horikoshii Ot3
pdb|2CUN|B Chain B, Crystal Structure Of Phosphoglycerate Kinase From
Pyrococcus Horikoshii Ot3
Length = 410
Score = 30.4 bits (67), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 30/95 (31%), Positives = 44/95 (46%), Gaps = 16/95 (16%)
Query: 725 TTEEKNMVFQEIMPQALSLMTDVFGNYVIQKFFEHGTASQVRELADQLTGHVLTL-SLQM 783
TTEE V E++ Q + + D+FG Y +K ++EL +G V L +L+
Sbjct: 68 TTEEHARVLSELLDQHVEYIEDIFGRYAREK---------IKELK---SGEVAILENLRF 115
Query: 784 YGCRVIQKAIEVVELDQQTQMVKELDGHIMRCVRD 818
V K IE E +T +VK+L I V D
Sbjct: 116 SAEEVKNKPIEECE---KTFLVKKLSKVIDYVVND 147
>pdb|2RGH|A Chain A, Structure Of Alpha-Glycerophosphate Oxidase From
Streptococcus Sp.: A Template For The Mitochondrial
Alpha- Glycerophosphate Dehydrogenase
Length = 571
Score = 30.0 bits (66), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 50/177 (28%), Positives = 70/177 (39%), Gaps = 21/177 (11%)
Query: 587 YLGALLSPQKSQYGVPYLNKSGSLNNNLYGNPAFGLG---MSYPG-GPLLPNSPVGSGSP 642
Y G P+ +Q V YL + N+ Y L S+ G PLL + GS S
Sbjct: 317 YQGDFTDPKVTQEDVDYLL---DVINHRYPEANITLADIEASWAGLRPLLIGNS-GSPST 372
Query: 643 VRHGDRNMRFPSGMRNLSGGVMGPWHSEAGGSLDESFASSLLDEFKSNKTKCFELSEIAG 702
+ G R P G+ LSGG + + A G+L LL E +TK EI
Sbjct: 373 ISRGSSLEREPDGLLTLSGGKITDYRKXAEGAL--RLIRQLLKEEYGIETK-----EIDS 425
Query: 703 HVVEFSADQYGSRFIQQKLETATTE-EKNMVFQEIMPQALSLMTDVFGNYVIQKFFE 758
+ S G F KLE TE K V + + + + D +G ++ FE
Sbjct: 426 KKYQIS----GGNFDPTKLEETVTELAKEGVAAGLEEEDATYIADFYGTNA-RRIFE 477
>pdb|3C38|A Chain A, Crystal Structure Of The Periplasmic Domain Of Vibrio
Cholerae Luxq
Length = 270
Score = 30.0 bits (66), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 38/78 (48%), Gaps = 3/78 (3%)
Query: 370 HMKQHPFLGRSESGHLLMHSASHSTKGSYPNMGKSGVGIDMNNASLMADGHKSALSSSNS 429
H+ Q P G+S H+LM +S G+ +G VGI +N+ + + +S +S N
Sbjct: 123 HLVQTPSEGKSV--HILMRRSSLIEAGTGQVVGYLYVGIVLNDNFALLENIRSGSNSENL 180
Query: 430 YLKGPCTPTLNG-GGNSP 446
L TP ++ GN P
Sbjct: 181 VLAVDTTPLVSTLKGNEP 198
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
0.314 0.130 0.370
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 24,763,890
Number of Sequences: 62578
Number of extensions: 958230
Number of successful extensions: 2003
Number of sequences better than 100.0: 22
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1742
Number of HSP's gapped (non-prelim): 77
length of query: 967
length of database: 14,973,337
effective HSP length: 108
effective length of query: 859
effective length of database: 8,214,913
effective search space: 7056610267
effective search space used: 7056610267
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 56 (26.2 bits)