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= 002587
(904 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 = 287 bits (735), Expect = 2e-77, Method: Compositional matrix adjust.
Identities = 135/219 (61%), Positives = 170/219 (77%), Gaps = 1/219 (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 IQRVLEHCHDEKTQSIMMDEILQSVCMLAQDQYGNYVVQ 899
IQR+LEHC E+T I ++E+ Q L QDQYGNYV+Q
Sbjct: 185 IQRILEHCTAEQTLPI-LEELHQHTEQLVQDQYGNYVIQ 222
Score = 108 bits (271), Expect = 9e-24, Method: Compositional matrix adjust.
Identities = 71/222 (31%), Positives = 119/222 (53%), Gaps = 10/222 (4%)
Query: 686 EFKSNKTKCFELSEIAGHVVEFSADQYGSRFIQQKLETATTEEKNMVFQEIMPQALSLMT 745
EF S K + I GHV+ + YG R IQ+ LE+ ++++++ + +E+ L +
Sbjct: 82 EFGSLDQKLALATRIRGHVLPLALQMYGCRVIQKALESISSDQQSEMVKELDGHVLKCVK 141
Query: 746 DVFGNYVIQKFFEHGTASQVRELADQLTGHVLTLSLQMYGCRVIQKAIEVVELDQQTQMV 805
D GN+V+QK E ++ + D G V LS YGCRVIQ+ +E +Q ++
Sbjct: 142 DQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFVLSTHPYGCRVIQRILEHCTAEQTLPIL 201
Query: 806 KELDGHIMRCVRDQNGNHVIQKCIEC-VPEDAIQFIVLTFYDQVVTLSTHPYGCRVIQRV 864
+EL H + V+DQ GN+VIQ +E PED + IV +V+ LS H + V+++
Sbjct: 202 EELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSK-IVSEIRGKVLALSQHKFASNVVEKC 260
Query: 865 LEHCHDEKTQSIMMDEIL-------QSVCMLAQDQYGNYVVQ 899
+ H +++++DE+ ++ + +DQY NYVVQ
Sbjct: 261 VTHA-SRAERALLIDEVCCQNDGPHSALYTMMKDQYANYVVQ 301
Score = 72.4 bits (176), 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 = 37.0 bits (84), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 22/55 (40%), Positives = 31/55 (56%), Gaps = 1/55 (1%)
Query: 848 VVTLSTHPYGCRVIQRVLEHCHDEKTQSIMMDEILQSVCMLAQDQYGNYVVQVCF 902
+V S +G R IQ+ LE + Q I+ +EILQ+ L D +GNYV+Q F
Sbjct: 28 IVEFSQDQHGSRFIQQKLERATPAERQ-IVFNEILQAAYQLMTDVFGNYVIQKFF 81
>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 = 285 bits (729), Expect = 7e-77, Method: Compositional matrix adjust.
Identities = 137/222 (61%), Positives = 169/222 (76%), Gaps = 1/222 (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 CRVIQRVLEHCHDEKTQSIMMDEILQSVCMLAQDQYGNYVVQ 899
CRVIQR+LEHC E+T I +DE+ + L QDQYGNYV+Q
Sbjct: 182 CRVIQRILEHCTAEQTTPI-LDELHEHTEQLIQDQYGNYVIQ 222
Score = 70.5 bits (171), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 43/140 (30%), Positives = 68/140 (48%), Gaps = 4/140 (2%)
Query: 695 FELSEIAGHVVEFSADQYGSRFIQQKLETATTEEKNMVFQEIMPQALSLMTDVFGNYVIQ 754
F ++ G V S YG R IQ+ LE T E+ + E+ L+ D +GNYVIQ
Sbjct: 163 FIINAFKGQVYSLSTHPYGCRVIQRILEHCTAEQTTPILDELHEHTEQLIQDQYGNYVIQ 222
Query: 755 KFFEHGTASQVRELADQLTGHVLTLSLQMYGCRVIQKAIEVVELDQQTQMVKEL----DG 810
EHG L + + G VL LS + V++K + ++T ++ E+ D
Sbjct: 223 HVLEHGKQEDKSILINSVRGKVLVLSQHKFASNVVEKCVTHATRGERTGLIDEVCTFNDN 282
Query: 811 HIMRCVRDQNGNHVIQKCIE 830
+ ++DQ N+V+QK I+
Sbjct: 283 ALHVMMKDQYANYVVQKMID 302
Score = 31.6 bits (70), Expect = 1.8, 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
Score = 31.6 bits (70), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 846 DQVVTLSTHPYGCRVIQRVLEHCHDEKTQSIMMDEILQSVCMLAQDQYGNYVVQVCF 902
+ +V S +G R IQ+ LE + Q ++ EIL + L D +GNYV+Q F
Sbjct: 26 NHIVEFSQDQHGSRFIQQKLERATAAEKQ-MVFSEILAAAYSLMTDVFGNYVIQKFF 81
>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 = 285 bits (728), Expect = 1e-76, Method: Compositional matrix adjust.
Identities = 133/219 (60%), Positives = 170/219 (77%), Gaps = 1/219 (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 IQRVLEHCHDEKTQSIMMDEILQSVCMLAQDQYGNYVVQ 899
IQR+LEHC ++T I ++E+ Q L QDQYGNYV+Q
Sbjct: 183 IQRILEHCLPDQTLPI-LEELHQHTEQLVQDQYGNYVIQ 220
Score = 110 bits (274), Expect = 5e-24, Method: Compositional matrix adjust.
Identities = 73/222 (32%), Positives = 116/222 (52%), Gaps = 10/222 (4%)
Query: 686 EFKSNKTKCFELSEIAGHVVEFSADQYGSRFIQQKLETATTEEKNMVFQEIMPQALSLMT 745
EF S + K I GHV+ + YG R IQ+ LE ++++N + +E+ L +
Sbjct: 80 EFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQNEMVRELDGHVLKCVK 139
Query: 746 DVFGNYVIQKFFEHGTASQVRELADQLTGHVLTLSLQMYGCRVIQKAIEVVELDQQTQMV 805
D GN+V+QK E ++ + D G V LS YGCRVIQ+ +E DQ ++
Sbjct: 140 DQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPDQTLPIL 199
Query: 806 KELDGHIMRCVRDQNGNHVIQKCIEC-VPEDAIQFIVLTFYDQVVTLSTHPYGCRVIQRV 864
+EL H + V+DQ GN+VIQ +E PED + IV V+ LS H + V+++
Sbjct: 200 EELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSK-IVAEIRGNVLVLSQHKFASNVVEKC 258
Query: 865 LEHCHDEKTQSIMMDEILQ-------SVCMLAQDQYGNYVVQ 899
+ H +++++DE+ ++ + +DQY NYVVQ
Sbjct: 259 VTHA-SRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQ 299
Score = 68.2 bits (165), 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 = 32.7 bits (73), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 30/55 (54%), Gaps = 1/55 (1%)
Query: 848 VVTLSTHPYGCRVIQRVLEHCHDEKTQSIMMDEILQSVCMLAQDQYGNYVVQVCF 902
++ S +G R IQ LE + Q ++ +EILQ+ L D +GNYV+Q F
Sbjct: 26 IMEFSQDQHGSRFIQLKLERATPAERQ-LVFNEILQAAYQLMVDVFGNYVIQKFF 79
>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 = 284 bits (727), Expect = 1e-76, Method: Compositional matrix adjust.
Identities = 133/219 (60%), Positives = 170/219 (77%), Gaps = 1/219 (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 IQRVLEHCHDEKTQSIMMDEILQSVCMLAQDQYGNYVVQ 899
IQR+LEHC ++T I ++E+ Q L QDQYGNYV+Q
Sbjct: 183 IQRILEHCLPDQTLPI-LEELHQHTEQLVQDQYGNYVIQ 220
Score = 109 bits (272), Expect = 8e-24, Method: Compositional matrix adjust.
Identities = 73/222 (32%), Positives = 116/222 (52%), Gaps = 10/222 (4%)
Query: 686 EFKSNKTKCFELSEIAGHVVEFSADQYGSRFIQQKLETATTEEKNMVFQEIMPQALSLMT 745
EF S + K I GHV+ + YG R IQ+ LE ++++N + +E+ L +
Sbjct: 80 EFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQNEMVRELDGHVLKCVK 139
Query: 746 DVFGNYVIQKFFEHGTASQVRELADQLTGHVLTLSLQMYGCRVIQKAIEVVELDQQTQMV 805
D GN+V+QK E ++ + D G V LS YGCRVIQ+ +E DQ ++
Sbjct: 140 DQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPDQTLPIL 199
Query: 806 KELDGHIMRCVRDQNGNHVIQKCIEC-VPEDAIQFIVLTFYDQVVTLSTHPYGCRVIQRV 864
+EL H + V+DQ GN+VIQ +E PED + IV V+ LS H + V+++
Sbjct: 200 EELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSK-IVAEIRGNVLVLSQHKFASNVVEKC 258
Query: 865 LEHCHDEKTQSIMMDEILQ-------SVCMLAQDQYGNYVVQ 899
+ H +++++DE+ ++ + +DQY NYVVQ
Sbjct: 259 VTHA-SRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQ 299
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 = 32.3 bits (72), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 30/55 (54%), Gaps = 1/55 (1%)
Query: 848 VVTLSTHPYGCRVIQRVLEHCHDEKTQSIMMDEILQSVCMLAQDQYGNYVVQVCF 902
++ S +G R IQ LE + Q ++ +EILQ+ L D +GNYV+Q F
Sbjct: 26 IMEFSQDQHGSRFIQLKLERATPAERQ-LVFNEILQAAYQLMVDVFGNYVIQKFF 79
>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 = 283 bits (725), Expect = 2e-76, Method: Compositional matrix adjust.
Identities = 136/221 (61%), Positives = 170/221 (76%), Gaps = 3/221 (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 RVIQRVLEHCHDEKTQSIMMDEILQSVCMLAQDQYGNYVVQ 899
RVIQR+LEHC E+T I ++E+ Q L QDQYGNYV+Q
Sbjct: 183 RVIQRILEHCTAEQTLPI-LEELHQHTEQLVQDQYGNYVIQ 222
Score = 103 bits (258), Expect = 3e-22, Method: Compositional matrix adjust.
Identities = 71/224 (31%), Positives = 119/224 (53%), Gaps = 12/224 (5%)
Query: 686 EFKSNKTKCFELSEIAGHVVEFSADQYGSRFIQQKLETATTEEKNM--VFQEIMPQALSL 743
EF S K + I GHV+ + YG R IQ+ LE+ +++++ + + +E+ L
Sbjct: 80 EFGSLDQKLALATRIRGHVLPLALQMYGCRVIQKALESISSDQQVISEMVKELDGHVLKC 139
Query: 744 MTDVFGNYVIQKFFEHGTASQVRELADQLTGHVLTLSLQMYGCRVIQKAIEVVELDQQTQ 803
+ D GN+V+QK E ++ + D G V LS YGCRVIQ+ +E +Q
Sbjct: 140 VKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFVLSTHPYGCRVIQRILEHCTAEQTLP 199
Query: 804 MVKELDGHIMRCVRDQNGNHVIQKCIEC-VPEDAIQFIVLTFYDQVVTLSTHPYGCRVIQ 862
+++EL H + V+DQ GN+VIQ +E PED + IV +V+ LS H + V++
Sbjct: 200 ILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSK-IVSEIRGKVLALSQHKFASNVVE 258
Query: 863 RVLEHCHDEKTQSIMMDEIL-------QSVCMLAQDQYGNYVVQ 899
+ + H +++++DE+ ++ + +DQY NYVVQ
Sbjct: 259 KCVTHA-SRAERALLIDEVCCQNDGPHSALYTMMKDQYANYVVQ 301
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 = 58.2 bits (139), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 43/132 (32%), Positives = 65/132 (49%), Gaps = 1/132 (0%)
Query: 772 LTGHVLTLSLQMYGCRVIQKAIEVVELDQQTQMVKELDGHIMRCVRDQNGNHVIQKCIEC 831
L GH++ S +G R IQ+ +E ++ + E+ + + D GN+VIQK E
Sbjct: 22 LIGHIVEFSQDQHGSRFIQQKLERATPAERQMVFNEILQAAYQLMTDVFGNYVIQKFFEF 81
Query: 832 VPEDAIQFIVLTFYDQVVTLSTHPYGCRVIQRVLEHCH-DEKTQSIMMDEILQSVCMLAQ 890
D + V+ L+ YGCRVIQ+ LE D++ S M+ E+ V +
Sbjct: 82 GSLDQKLALATRIRGHVLPLALQMYGCRVIQKALESISSDQQVISEMVKELDGHVLKCVK 141
Query: 891 DQYGNYVVQVCF 902
DQ GN+VVQ C
Sbjct: 142 DQNGNHVVQKCI 153
>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 = 281 bits (718), Expect = 1e-75, Method: Compositional matrix adjust.
Identities = 131/219 (59%), Positives = 170/219 (77%), Gaps = 1/219 (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 IQRVLEHCHDEKTQSIMMDEILQSVCMLAQDQYGNYVVQ 899
IQR+LEHC ++T I ++E+ Q L QDQYG+YV++
Sbjct: 184 IQRILEHCLPDQTLPI-LEELHQHTEQLVQDQYGSYVIR 221
Score = 106 bits (264), Expect = 7e-23, Method: Compositional matrix adjust.
Identities = 71/222 (31%), Positives = 116/222 (52%), Gaps = 10/222 (4%)
Query: 686 EFKSNKTKCFELSEIAGHVVEFSADQYGSRFIQQKLETATTEEKNMVFQEIMPQALSLMT 745
EF S + K I GHV+ + YG R IQ+ LE ++++N + +E+ L +
Sbjct: 81 EFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQNEMVRELDGHVLKCVK 140
Query: 746 DVFGNYVIQKFFEHGTASQVRELADQLTGHVLTLSLQMYGCRVIQKAIEVVELDQQTQMV 805
D GN+V+QK E ++ + D G V LS YGCRVIQ+ +E DQ ++
Sbjct: 141 DQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPDQTLPIL 200
Query: 806 KELDGHIMRCVRDQNGNHVIQKCIEC-VPEDAIQFIVLTFYDQVVTLSTHPYGCRVIQRV 864
+EL H + V+DQ G++VI+ +E PED + IV V+ LS H + V+++
Sbjct: 201 EELHQHTEQLVQDQYGSYVIRHVLEHGRPEDKSK-IVAEIRGNVLVLSQHKFASNVVEKC 259
Query: 865 LEHCHDEKTQSIMMDEILQ-------SVCMLAQDQYGNYVVQ 899
+ H +++++DE+ ++ + +DQY NYVVQ
Sbjct: 260 VTHA-SRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQ 300
Score = 64.3 bits (155), 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 = 32.7 bits (73), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 30/55 (54%), Gaps = 1/55 (1%)
Query: 848 VVTLSTHPYGCRVIQRVLEHCHDEKTQSIMMDEILQSVCMLAQDQYGNYVVQVCF 902
++ S +G R IQ LE + Q ++ +EILQ+ L D +GNYV+Q F
Sbjct: 27 IMEFSQDQHGSRFIQLKLERATPAERQ-LVFNEILQAAYQLMVDVFGNYVIQKFF 80
>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 = 211 bits (537), Expect = 1e-54, Method: Compositional matrix adjust.
Identities = 103/203 (50%), Positives = 140/203 (68%), Gaps = 1/203 (0%)
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 MMDEILQSVCMLAQDQYGNYVVQ 899
++E+ + L QDQYGNYV+Q
Sbjct: 206 -LNELKDFIPYLIQDQYGNYVIQ 227
Score = 88.2 bits (217), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 68/236 (28%), Positives = 113/236 (47%), Gaps = 26/236 (11%)
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-------------QSVCMLAQDQYGNYVVQ 899
V+++ + + K Q +++ +IL + ++ +DQ+ NYV+Q
Sbjct: 265 SNVVEKSI--LYGSKNQKDLIISKILPRDKNHALNLEDDSPMILMIKDQFANYVIQ 318
Score = 58.9 bits (141), 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
>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 = 144 bits (362), Expect = 3e-34, Method: Compositional matrix adjust.
Identities = 79/222 (35%), Positives = 127/222 (57%), Gaps = 15/222 (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 CRVIQRVLEHCHDEKTQSIMMDEILQSVCMLAQDQYGNYVVQ 899
CRV+QR L+H E+ + + D++L V L D +GNYVVQ
Sbjct: 170 CRVLQRCLDHGTTEQCDN-LCDKLLALVDKLTLDPFGNYVVQ 210
Score = 77.0 bits (188), Expect = 4e-14, Method: Compositional matrix adjust.
Identities = 60/210 (28%), Positives = 101/210 (48%), Gaps = 19/210 (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-----VCMLAQDQYGNYVVQ 899
M+ EIL + + L D YGNYV+Q
Sbjct: 260 EPMILEILNNGGETGIQSLLNDSYGNYVLQ 289
Score = 65.1 bits (157), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 40/137 (29%), Positives = 74/137 (54%), Gaps = 4/137 (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+GCR +Q+++E ++ I++D +
Sbjct: 67 LLEEVTTE--QRIVLTKISSPHFVEISLNPHGCRALQKLIECIKTDEEAQIVVDSLRPYT 124
Query: 886 CMLAQDQYGNYVVQVCF 902
L++D GN+V+Q C
Sbjct: 125 VQLSKDLNGNHVIQKCL 141
>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 = 138 bits (347), Expect = 2e-32, Method: Compositional matrix adjust.
Identities = 80/234 (34%), Positives = 131/234 (55%), Gaps = 17/234 (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 DQVVTLSTHPYGCRVIQRVLEHCHDEKTQSIMMDEILQSVCMLAQDQYGNYVVQ 899
D + ++TH +GC V+QR L+H E+ + + D++L V L D +GNYVVQ
Sbjct: 180 DSCIDIATHRHGCCVLQRCLDHGTTEQCDN-LCDKLLALVDKLTLDPFGNYVVQ 232
Score = 75.5 bits (184), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 59/210 (28%), Positives = 101/210 (48%), Gaps = 19/210 (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-----VCMLAQDQYGNYVVQ 899
M+ EIL + + L D YGNYV+Q
Sbjct: 282 EPMILEILNNGGETGIQSLLNDSYGNYVLQ 311
Score = 62.4 bits (150), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 39/137 (28%), Positives = 73/137 (53%), Gaps = 4/137 (2%)
Query: 768 LADQLTGHVLTLSLQMYGCRVIQKAIEVVELDQQTQMVKELDGHIMRCVRDQNGNHVIQK 827
+ DQ G + +L +GCR +QK ++++ + +E + + + D GN++IQK
Sbjct: 29 VLDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQK 88
Query: 828 CIECVPEDAIQFIVLTFYD--QVVTLSTHPYGCRVIQRVLEHCHDEKTQSIMMDEILQSV 885
+E V + Q IVLT V +S +P+G R +Q+++E ++ I++D +
Sbjct: 89 LLEEVTTE--QRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYT 146
Query: 886 CMLAQDQYGNYVVQVCF 902
L++D GN+V+Q C
Sbjct: 147 VQLSKDLNGNHVIQKCL 163
>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 = 135 bits (341), Expect = 8e-32, Method: Compositional matrix adjust.
Identities = 77/222 (34%), Positives = 125/222 (56%), Gaps = 15/222 (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 CRVIQRVLEHCHDEKTQSIMMDEILQSVCMLAQDQYGNYVVQ 899
C V+QR L+H E+ + + D++L V L D +GNYVVQ
Sbjct: 170 CCVLQRCLDHGTTEQCDN-LCDKLLALVDKLTLDPFGNYVVQ 210
Score = 74.3 bits (181), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 59/210 (28%), Positives = 101/210 (48%), Gaps = 19/210 (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-----VCMLAQDQYGNYVVQ 899
M+ EIL + + L D YGNYV+Q
Sbjct: 260 EPMILEILNNGGETGIQSLLNDSYGNYVLQ 289
Score = 60.5 bits (145), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 39/137 (28%), Positives = 73/137 (53%), Gaps = 4/137 (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 CMLAQDQYGNYVVQVCF 902
L++D GN+V+Q C
Sbjct: 125 VQLSKDLNGNHVIQKCL 141
>pdb|3BWT|A Chain A, Crystal Structure Of The Rna Binding Domain Of Puf4 From
Saccharomyces Cerevisiae
Length = 333
Score = 135 bits (341), Expect = 8e-32, Method: Compositional matrix adjust.
Identities = 77/222 (34%), Positives = 125/222 (56%), Gaps = 15/222 (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 CRVIQRVLEHCHDEKTQSIMMDEILQSVCMLAQDQYGNYVVQ 899
C V+QR L+H E+ + + D++L V L D +GNYVVQ
Sbjct: 170 CCVLQRCLDHGTTEQCDN-LCDKLLALVDKLTLDPFGNYVVQ 210
Score = 73.9 bits (180), Expect = 4e-13, Method: Compositional matrix adjust.
Identities = 59/210 (28%), Positives = 101/210 (48%), Gaps = 19/210 (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-----VCMLAQDQYGNYVVQ 899
M+ EIL + + L D YGNYV+Q
Sbjct: 260 EPMILEILNNGGETGIQSLLNDSYGNYVLQ 289
Score = 60.5 bits (145), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 39/137 (28%), Positives = 73/137 (53%), Gaps = 4/137 (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 CMLAQDQYGNYVVQVCF 902
L++D GN+V+Q C
Sbjct: 125 VQLSKDLNGNHVIQKCL 141
>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 = 93.2 bits (230), Expect = 7e-19, Method: Compositional matrix adjust.
Identities = 62/239 (25%), Positives = 122/239 (51%), Gaps = 40/239 (16%)
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---------------DEKTQSIMMDEILQSVCMLAQDQYGNYVVQ 899
YGCRV+Q ++E E+ +M + LA ++Y NY++Q
Sbjct: 199 YGCRVVQTIIEKLTADSMNVDLTSAAQNLRERALQRLMTSVTNRCQELATNEYANYIIQ 257
>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 = 92.8 bits (229), Expect = 8e-19, Method: Compositional matrix adjust.
Identities = 62/239 (25%), Positives = 122/239 (51%), Gaps = 40/239 (16%)
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---------------DEKTQSIMMDEILQSVCMLAQDQYGNYVVQ 899
YGCRV+Q ++E E+ +M + LA ++Y NY++Q
Sbjct: 198 YGCRVVQTIIEKLTADSMNVDLTSAAQNLRERALQRLMTSVTNRCQELATNEYANYIIQ 256
>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 = 90.1 bits (222), Expect = 5e-18, Method: Compositional matrix adjust.
Identities = 61/239 (25%), Positives = 121/239 (50%), Gaps = 40/239 (16%)
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---------------DEKTQSIMMDEILQSVCMLAQDQYGNYVVQ 899
YGCRV+Q ++E E+ +M + LA ++Y NY++Q
Sbjct: 199 YGCRVVQTIIEKLTADSMNVDLTSAAQNLRERALQRLMTSVTNRCQELATNEYANYIIQ 257
>pdb|3V71|A Chain A, Crystal Structure Of Puf-6 In Complex With 5be13 Rna
Length = 382
Score = 79.0 bits (193), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 54/216 (25%), Positives = 109/216 (50%), Gaps = 18/216 (8%)
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--MMDEILQSVCMLAQDQYGNYVVQ 899
C + Q + +M I+++ L+ +++ NYV+Q
Sbjct: 200 LPCFKFRIQLLHSLMTCIVRNCYRLSSNEFANYVIQ 235
Score = 33.1 bits (74), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 58/239 (24%), Positives = 95/239 (39%), Gaps = 51/239 (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-----------QSVCMLAQDQYGNYVVQ 899
S Y VI+ MM+EI ++ +L QYGNYVVQ
Sbjct: 264 SQDKYASHVIEGAFLFAPPALLHE-MMEEIFSGYVKDVESNRDALDILLFHQYGNYVVQ 321
>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 = 3.1, 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 = 30.8 bits (68), Expect = 3.7, 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 = 30.4 bits (67), Expect = 5.0, 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 = 30.4 bits (67), Expect = 5.2, 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 0.372
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 23,067,805
Number of Sequences: 62578
Number of extensions: 892858
Number of successful extensions: 1755
Number of sequences better than 100.0: 22
Number of HSP's better than 100.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1536
Number of HSP's gapped (non-prelim): 78
length of query: 904
length of database: 14,973,337
effective HSP length: 108
effective length of query: 796
effective length of database: 8,214,913
effective search space: 6539070748
effective search space used: 6539070748
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)