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= 006165
(658 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 49.7 bits (117), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 58/250 (23%), Positives = 104/250 (41%), Gaps = 31/250 (12%)
Query: 132 LQKMKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEELQPHFLSLADNTYAVHLVKKM 191
L+++ G I E + SR +Q ++ + AER VF E+ L + + ++++K
Sbjct: 19 LREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKF 78
Query: 192 LDNASKKQLAGFISALHGHVASLLRHMVGSVVVEHAYQLGNATQKQELLVELYSTELQLF 251
+ S +Q + GHV SL M G V++ A + + Q+ E++ EL L+
Sbjct: 79 FEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQNEMVRELDGHVLKCV 138
Query: 252 KN----------LVSIKESRLVDVISKLGLQKASVLRH--MASVIQPILEKGIIDHSI-- 297
K+ + ++ L +I Q ++ H VIQ ILE + D ++
Sbjct: 139 KDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPDQTLPI 198
Query: 298 ---IHR-------------VLMEYLSMADKSSAADIIQQLSGPLLVRMIHTRDGSKIGML 341
+H+ V+ L + I+ ++ G +LV H + S +
Sbjct: 199 LEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLSQH-KFASNVVEK 257
Query: 342 CVKHGSAKER 351
CV H S ER
Sbjct: 258 CVTHASRTER 267
Score = 43.1 bits (100), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 27/106 (25%), Positives = 57/106 (53%), Gaps = 11/106 (10%)
Query: 122 ETRSKLISEALQKMKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEEL-----QPH-- 174
E +SK+++E ++G + ++ +S V++ CV + S+ ER + +E+ PH
Sbjct: 229 EDKSKIVAE----IRGNVLVLSQHKFASNVVEKCVTHASRTERAVLIDEVCTMNDGPHSA 284
Query: 175 FLSLADNTYAVHLVKKMLDNASKKQLAGFISALHGHVASLLRHMVG 220
++ + YA ++V+KM+D A Q + + H+A+L ++ G
Sbjct: 285 LYTMMKDQYANYVVQKMIDVAEPGQRKIVMHKIRPHIATLRKYTYG 330
Score = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/122 (17%), Positives = 56/122 (45%)
Query: 129 SEALQKMKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEELQPHFLSLADNTYAVHLV 188
+E ++++ G + + + V+Q C++ + + + +L+ + Y ++
Sbjct: 124 NEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVI 183
Query: 189 KKMLDNASKKQLAGFISALHGHVASLLRHMVGSVVVEHAYQLGNATQKQELLVELYSTEL 248
+++L++ Q + LH H L++ G+ V++H + G K +++ E+ L
Sbjct: 184 QRILEHCLPDQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVL 243
Query: 249 QL 250
L
Sbjct: 244 VL 245
Score = 39.7 bits (91), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 24/109 (22%), Positives = 54/109 (49%)
Query: 135 MKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEELQPHFLSLADNTYAVHLVKKMLDN 194
KG++ ++ RV+Q +++C + + EEL H L + Y ++++ +L++
Sbjct: 166 FKGQVFALSTHPYGCRVIQRILEHCLPDQTLPILEELHQHTEQLVQDQYGNYVIQHVLEH 225
Query: 195 ASKKQLAGFISALHGHVASLLRHMVGSVVVEHAYQLGNATQKQELLVEL 243
+ + ++ + G+V L +H S VVE + T++ L+ E+
Sbjct: 226 GRPEDKSKIVAEIRGNVLVLSQHKFASNVVEKCVTHASRTERAVLIDEV 274
>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 = 49.7 bits (117), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 58/250 (23%), Positives = 104/250 (41%), Gaps = 31/250 (12%)
Query: 132 LQKMKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEELQPHFLSLADNTYAVHLVKKM 191
L+++ G I E + SR +Q ++ + AER VF E+ L + + ++++K
Sbjct: 19 LREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKF 78
Query: 192 LDNASKKQLAGFISALHGHVASLLRHMVGSVVVEHAYQLGNATQKQELLVELYSTELQLF 251
+ S +Q + GHV SL M G V++ A + + Q+ E++ EL L+
Sbjct: 79 FEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQNEMVRELDGHVLKCV 138
Query: 252 KN----------LVSIKESRLVDVISKLGLQKASVLRH--MASVIQPILEKGIIDHSI-- 297
K+ + ++ L +I Q ++ H VIQ ILE + D ++
Sbjct: 139 KDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPDQTLPI 198
Query: 298 ---IHR-------------VLMEYLSMADKSSAADIIQQLSGPLLVRMIHTRDGSKIGML 341
+H+ V+ L + I+ ++ G +LV H + S +
Sbjct: 199 LEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLSQH-KFASNVVEK 257
Query: 342 CVKHGSAKER 351
CV H S ER
Sbjct: 258 CVTHASRTER 267
Score = 43.1 bits (100), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 27/106 (25%), Positives = 57/106 (53%), Gaps = 11/106 (10%)
Query: 122 ETRSKLISEALQKMKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEEL-----QPH-- 174
E +SK+++E ++G + ++ +S V++ CV + S+ ER + +E+ PH
Sbjct: 229 EDKSKIVAE----IRGNVLVLSQHKFASNVVEKCVTHASRTERAVLIDEVCTMNDGPHSA 284
Query: 175 FLSLADNTYAVHLVKKMLDNASKKQLAGFISALHGHVASLLRHMVG 220
++ + YA ++V+KM+D A Q + + H+A+L ++ G
Sbjct: 285 LYTMMKDQYANYVVQKMIDVAEPGQRKIVMHKIRPHIATLRKYTYG 330
Score = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/122 (17%), Positives = 56/122 (45%)
Query: 129 SEALQKMKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEELQPHFLSLADNTYAVHLV 188
+E ++++ G + + + V+Q C++ + + + +L+ + Y ++
Sbjct: 124 NEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVI 183
Query: 189 KKMLDNASKKQLAGFISALHGHVASLLRHMVGSVVVEHAYQLGNATQKQELLVELYSTEL 248
+++L++ Q + LH H L++ G+ V++H + G K +++ E+ L
Sbjct: 184 QRILEHCLPDQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVL 243
Query: 249 QL 250
L
Sbjct: 244 VL 245
Score = 39.7 bits (91), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 24/109 (22%), Positives = 54/109 (49%)
Query: 135 MKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEELQPHFLSLADNTYAVHLVKKMLDN 194
KG++ ++ RV+Q +++C + + EEL H L + Y ++++ +L++
Sbjct: 166 FKGQVFALSTHPYGCRVIQRILEHCLPDQTLPILEELHQHTEQLVQDQYGNYVIQHVLEH 225
Query: 195 ASKKQLAGFISALHGHVASLLRHMVGSVVVEHAYQLGNATQKQELLVEL 243
+ + ++ + G+V L +H S VVE + T++ L+ E+
Sbjct: 226 GRPEDKSKIVAEIRGNVLVLSQHKFASNVVEKCVTHASRTERAVLIDEV 274
>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 = 49.3 bits (116), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 58/250 (23%), Positives = 104/250 (41%), Gaps = 31/250 (12%)
Query: 132 LQKMKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEELQPHFLSLADNTYAVHLVKKM 191
L+++ G I E + SR +Q ++ + AER VF E+ L + + ++++K
Sbjct: 20 LREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKF 79
Query: 192 LDNASKKQLAGFISALHGHVASLLRHMVGSVVVEHAYQLGNATQKQELLVELYSTELQLF 251
+ S +Q + GHV SL M G V++ A + + Q+ E++ EL L+
Sbjct: 80 FEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQNEMVRELDGHVLKCV 139
Query: 252 KN----------LVSIKESRLVDVISKLGLQKASVLRH--MASVIQPILEKGIIDHSI-- 297
K+ + ++ L +I Q ++ H VIQ ILE + D ++
Sbjct: 140 KDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPDQTLPI 199
Query: 298 ---IHR-------------VLMEYLSMADKSSAADIIQQLSGPLLVRMIHTRDGSKIGML 341
+H+ V+ L + I+ ++ G +LV H + S +
Sbjct: 200 LEELHQHTEQLVQDQYGSYVIRHVLEHGRPEDKSKIVAEIRGNVLVLSQH-KFASNVVEK 258
Query: 342 CVKHGSAKER 351
CV H S ER
Sbjct: 259 CVTHASRTER 268
Score = 43.1 bits (100), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 27/106 (25%), Positives = 57/106 (53%), Gaps = 11/106 (10%)
Query: 122 ETRSKLISEALQKMKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEEL-----QPH-- 174
E +SK+++E ++G + ++ +S V++ CV + S+ ER + +E+ PH
Sbjct: 230 EDKSKIVAE----IRGNVLVLSQHKFASNVVEKCVTHASRTERAVLIDEVCTMNDGPHSA 285
Query: 175 FLSLADNTYAVHLVKKMLDNASKKQLAGFISALHGHVASLLRHMVG 220
++ + YA ++V+KM+D A Q + + H+A+L ++ G
Sbjct: 286 LYTMMKDQYANYVVQKMIDVAEPGQRKIVMHKIRPHIATLRKYTYG 331
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/122 (18%), Positives = 55/122 (45%)
Query: 129 SEALQKMKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEELQPHFLSLADNTYAVHLV 188
+E ++++ G + + + V+Q C++ + + + +L+ + Y ++
Sbjct: 125 NEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVI 184
Query: 189 KKMLDNASKKQLAGFISALHGHVASLLRHMVGSVVVEHAYQLGNATQKQELLVELYSTEL 248
+++L++ Q + LH H L++ GS V+ H + G K +++ E+ L
Sbjct: 185 QRILEHCLPDQTLPILEELHQHTEQLVQDQYGSYVIRHVLEHGRPEDKSKIVAEIRGNVL 244
Query: 249 QL 250
L
Sbjct: 245 VL 246
Score = 40.4 bits (93), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 24/109 (22%), Positives = 54/109 (49%)
Query: 135 MKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEELQPHFLSLADNTYAVHLVKKMLDN 194
KG++ ++ RV+Q +++C + + EEL H L + Y ++++ +L++
Sbjct: 167 FKGQVFALSTHPYGCRVIQRILEHCLPDQTLPILEELHQHTEQLVQDQYGSYVIRHVLEH 226
Query: 195 ASKKQLAGFISALHGHVASLLRHMVGSVVVEHAYQLGNATQKQELLVEL 243
+ + ++ + G+V L +H S VVE + T++ L+ E+
Sbjct: 227 GRPEDKSKIVAEIRGNVLVLSQHKFASNVVEKCVTHASRTERAVLIDEV 275
>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 = 47.0 bits (110), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 29/106 (27%), Positives = 58/106 (54%), Gaps = 11/106 (10%)
Query: 122 ETRSKLISEALQKMKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEEL-----QPH-- 174
E +SK++SE ++GK+ ++ +S V++ CV + S+AER + +E+ PH
Sbjct: 231 EDKSKIVSE----IRGKVLALSQHKFASNVVEKCVTHASRAERALLIDEVCCQNDGPHSA 286
Query: 175 FLSLADNTYAVHLVKKMLDNASKKQLAGFISALHGHVASLLRHMVG 220
++ + YA ++V+KM+D A Q + + H+ +L ++ G
Sbjct: 287 LYTMMKDQYANYVVQKMIDMAEPAQRKIIMHKIRPHITTLRKYTYG 332
Score = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 31/122 (25%), Positives = 58/122 (47%)
Query: 132 LQKMKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEELQPHFLSLADNTYAVHLVKKM 191
L+ + G I E + SR +Q ++ + AER VF E+ L + + ++++K
Sbjct: 21 LRDLIGHIVEFSQDQHGSRFIQQKLERATPAERQIVFNEILQAAYQLMTDVFGNYVIQKF 80
Query: 192 LDNASKKQLAGFISALHGHVASLLRHMVGSVVVEHAYQLGNATQKQELLVELYSTELQLF 251
+ S Q + + GHV L M G V++ A + ++ Q+ E++ EL L+
Sbjct: 81 FEFGSLDQKLALATRIRGHVLPLALQMYGCRVIQKALESISSDQQSEMVKELDGHVLKCV 140
Query: 252 KN 253
K+
Sbjct: 141 KD 142
Score = 42.7 bits (99), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 22/122 (18%), Positives = 57/122 (46%)
Query: 129 SEALQKMKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEELQPHFLSLADNTYAVHLV 188
SE ++++ G + + + V+Q C++ + + + L+ + Y ++
Sbjct: 126 SEMVKELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFVLSTHPYGCRVI 185
Query: 189 KKMLDNASKKQLAGFISALHGHVASLLRHMVGSVVVEHAYQLGNATQKQELLVELYSTEL 248
+++L++ + +Q + LH H L++ G+ V++H + G K +++ E+ L
Sbjct: 186 QRILEHCTAEQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGKVL 245
Query: 249 QL 250
L
Sbjct: 246 AL 247
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/91 (24%), Positives = 47/91 (51%)
Query: 135 MKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEELQPHFLSLADNTYAVHLVKKMLDN 194
KG++ ++ RV+Q +++C+ + + EEL H L + Y ++++ +L++
Sbjct: 168 FKGQVFVLSTHPYGCRVIQRILEHCTAEQTLPILEELHQHTEQLVQDQYGNYVIQHVLEH 227
Query: 195 ASKKQLAGFISALHGHVASLLRHMVGSVVVE 225
+ + +S + G V +L +H S VVE
Sbjct: 228 GRPEDKSKIVSEIRGKVLALSQHKFASNVVE 258
>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 = 47.0 bits (110), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 29/106 (27%), Positives = 58/106 (54%), Gaps = 11/106 (10%)
Query: 122 ETRSKLISEALQKMKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEEL-----QPH-- 174
E +SK++SE ++GK+ ++ +S V++ CV + S+AER + +E+ PH
Sbjct: 231 EDKSKIVSE----IRGKVLALSQHKFASNVVEKCVTHASRAERALLIDEVCCQNDGPHSA 286
Query: 175 FLSLADNTYAVHLVKKMLDNASKKQLAGFISALHGHVASLLRHMVG 220
++ + YA ++V+KM+D A Q + + H+ +L ++ G
Sbjct: 287 LYTMMKDQYANYVVQKMIDMAEPAQRKIIMHKIRPHITTLRKYTYG 332
Score = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/125 (18%), Positives = 60/125 (48%)
Query: 126 KLISEALQKMKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEELQPHFLSLADNTYAV 185
++ISE ++++ G + + + V+Q C++ + + + L+ + Y
Sbjct: 123 QVISEMVKELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFVLSTHPYGC 182
Query: 186 HLVKKMLDNASKKQLAGFISALHGHVASLLRHMVGSVVVEHAYQLGNATQKQELLVELYS 245
+++++L++ + +Q + LH H L++ G+ V++H + G K +++ E+
Sbjct: 183 RVIQRILEHCTAEQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRG 242
Query: 246 TELQL 250
L L
Sbjct: 243 KVLAL 247
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/91 (24%), Positives = 47/91 (51%)
Query: 135 MKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEELQPHFLSLADNTYAVHLVKKMLDN 194
KG++ ++ RV+Q +++C+ + + EEL H L + Y ++++ +L++
Sbjct: 168 FKGQVFVLSTHPYGCRVIQRILEHCTAEQTLPILEELHQHTEQLVQDQYGNYVIQHVLEH 227
Query: 195 ASKKQLAGFISALHGHVASLLRHMVGSVVVE 225
+ + +S + G V +L +H S VVE
Sbjct: 228 GRPEDKSKIVSEIRGKVLALSQHKFASNVVE 258
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 28/112 (25%), Positives = 53/112 (47%), Gaps = 2/112 (1%)
Query: 132 LQKMKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEELQPHFLSLADNTYAVHLVKKM 191
L+ + G I E + SR +Q ++ + AER VF E+ L + + ++++K
Sbjct: 19 LRDLIGHIVEFSQDQHGSRFIQQKLERATPAERQMVFNEILQAAYQLMTDVFGNYVIQKF 78
Query: 192 LDNASKKQLAGFISALHGHVASLLRHMVGSVVVEHAYQLGNATQKQELLVEL 243
+ S Q + + GHV L M G V++ A L + + Q+++ E+
Sbjct: 79 FEFGSLDQKLALATRIRGHVLPLALQMYGCRVIQKA--LESISSDQQVISEM 128
>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 = 46.2 bits (108), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 25/110 (22%), Positives = 56/110 (50%)
Query: 134 KMKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEELQPHFLSLADNTYAVHLVKKMLD 193
+ KG + +++ + RV+Q ++Y +R + EL L + + H+++K ++
Sbjct: 100 QFKGNMKQLSLQMYACRVIQKALEYIDSNQRIELVLELSDSVLQMIKDQNGNHVIQKAIE 159
Query: 194 NASKKQLAGFISALHGHVASLLRHMVGSVVVEHAYQLGNATQKQELLVEL 243
++L +S+L GH+ L H G V++ + G++ ++ +L EL
Sbjct: 160 TIPIEKLPFILSSLTGHIYHLSTHSYGCRVIQRLLEFGSSEDQESILNEL 209
>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 = 42.7 bits (99), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 31/120 (25%), Positives = 55/120 (45%)
Query: 134 KMKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEELQPHFLSLADNTYAVHLVKKMLD 193
++KG + ++A RV+Q ++ S ++ + EL H L + H+V+K ++
Sbjct: 95 QVKGHVLQLALQMYGCRVIQKALESISPEQQQEIVHELDGHVLKCVKDQNGNHVVQKCIE 154
Query: 194 NASKKQLAGFISALHGHVASLLRHMVGSVVVEHAYQLGNATQKQELLVELYSTELQLFKN 253
L I+A G V SL H G V++ + A Q +L EL+ QL ++
Sbjct: 155 CVDPVALQFIINAFKGQVYSLSTHPYGCRVIQRILEHCTAEQTTPILDELHEHTEQLIQD 214
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 59/250 (23%), Positives = 101/250 (40%), Gaps = 31/250 (12%)
Query: 132 LQKMKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEELQPHFLSLADNTYAVHLVKKM 191
L+ + I E + SR +Q ++ + AE+ VF E+ SL + + ++++K
Sbjct: 21 LRDLANHIVEFSQDQHGSRFIQQKLERATAAEKQMVFSEILAAAYSLMTDVFGNYVIQKF 80
Query: 192 LDNASKKQLAGFISALHGHVASLLRHMVGSVVVEHAYQLGNATQKQELLVELYSTELQLF 251
+ + +Q + GHV L M G V++ A + + Q+QE++ EL L+
Sbjct: 81 FEFGTPEQKNTLGMQVKGHVLQLALQMYGCRVIQKALESISPEQQQEIVHELDGHVLKCV 140
Query: 252 K----NLVSIKESRLVD------VISKLGLQKASVLRH--MASVIQPILE---------- 289
K N V K VD +I+ Q S+ H VIQ ILE
Sbjct: 141 KDQNGNHVVQKCIECVDPVALQFIINAFKGQVYSLSTHPYGCRVIQRILEHCTAEQTTPI 200
Query: 290 --------KGIIDHSIIHRVLMEYLSMADKSSAADIIQQLSGPLLVRMIHTRDGSKIGML 341
+ +I + V+ L + + +I + G +LV H + S +
Sbjct: 201 LDELHEHTEQLIQDQYGNYVIQHVLEHGKQEDKSILINSVRGKVLVLSQH-KFASNVVEK 259
Query: 342 CVKHGSAKER 351
CV H + ER
Sbjct: 260 CVTHATRGER 269
Score = 40.0 bits (92), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/111 (18%), Positives = 50/111 (45%)
Query: 130 EALQKMKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEELQPHFLSLADNTYAVHLVK 189
E + ++ G + + + V+Q C++ + + SL+ + Y +++
Sbjct: 127 EIVHELDGHVLKCVKDQNGNHVVQKCIECVDPVALQFIINAFKGQVYSLSTHPYGCRVIQ 186
Query: 190 KMLDNASKKQLAGFISALHGHVASLLRHMVGSVVVEHAYQLGNATQKQELL 240
++L++ + +Q + LH H L++ G+ V++H + G K L+
Sbjct: 187 RILEHCTAEQTTPILDELHEHTEQLIQDQYGNYVIQHVLEHGKQEDKSILI 237
>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 = 35.4 bits (80), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 21/85 (24%), Positives = 40/85 (47%), Gaps = 2/85 (2%)
Query: 115 RQRNIAKETRSKLISEALQKMKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEELQPH 174
+QR I E S+ L + G I + R LQ + DA+FEE + +
Sbjct: 15 KQRKI--EESSRFADAVLDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDY 72
Query: 175 FLSLADNTYAVHLVKKMLDNASKKQ 199
+ L +++ +L++K+L+ + +Q
Sbjct: 73 TVELMTDSFGNYLIQKLLEEVTTEQ 97
>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 = 33.1 bits (74), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 17/75 (22%), Positives = 35/75 (46%)
Query: 125 SKLISEALQKMKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEELQPHFLSLADNTYA 184
S+ L + G I + R LQ + DA+FEE + + + L +++
Sbjct: 1 SRFADAVLDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFG 60
Query: 185 VHLVKKMLDNASKKQ 199
+L++K+L+ + +Q
Sbjct: 61 NYLIQKLLEEVTTEQ 75
>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 = 33.1 bits (74), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 17/75 (22%), Positives = 35/75 (46%)
Query: 125 SKLISEALQKMKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEELQPHFLSLADNTYA 184
S+ L + G I + R LQ + DA+FEE + + + L +++
Sbjct: 1 SRFADAVLDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFG 60
Query: 185 VHLVKKMLDNASKKQ 199
+L++K+L+ + +Q
Sbjct: 61 NYLIQKLLEEVTTEQ 75
>pdb|3BWT|A Chain A, Crystal Structure Of The Rna Binding Domain Of Puf4 From
Saccharomyces Cerevisiae
Length = 333
Score = 32.7 bits (73), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 17/75 (22%), Positives = 35/75 (46%)
Query: 125 SKLISEALQKMKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEELQPHFLSLADNTYA 184
S+ L + G I + R LQ + DA+FEE + + + L +++
Sbjct: 1 SRFADAVLDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFG 60
Query: 185 VHLVKKMLDNASKKQ 199
+L++K+L+ + +Q
Sbjct: 61 NYLIQKLLEEVTTEQ 75
>pdb|1O5K|A Chain A, Crystal Structure Of Dihydrodipicolinate Synthase (Tm1521)
From Thermotoga Maritima At 1.80 A Resolution
pdb|1O5K|B Chain B, Crystal Structure Of Dihydrodipicolinate Synthase (Tm1521)
From Thermotoga Maritima At 1.80 A Resolution
Length = 306
Score = 30.8 bits (68), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 27/46 (58%), Gaps = 2/46 (4%)
Query: 119 IAKETRSKLISEALQKMKGKIPEIAGSHVSSRVLQTCVKYCSQAER 164
+ ++ R KL+S L+ + GKIP I G+ +S + +K QAE+
Sbjct: 62 VNEDEREKLVSRTLEIVDGKIPVIVGAGTNST--EKTLKLVKQAEK 105
>pdb|3PB2|A Chain A, Characterisation Of The First Monomeric
Dihydrodipicolinate Synthase Variant Reveals
Evolutionary Insights
pdb|3PB2|B Chain B, Characterisation Of The First Monomeric
Dihydrodipicolinate Synthase Variant Reveals
Evolutionary Insights
pdb|3PB2|C Chain C, Characterisation Of The First Monomeric
Dihydrodipicolinate Synthase Variant Reveals
Evolutionary Insights
pdb|3PB2|D Chain D, Characterisation Of The First Monomeric
Dihydrodipicolinate Synthase Variant Reveals
Evolutionary Insights
pdb|3PB2|E Chain E, Characterisation Of The First Monomeric
Dihydrodipicolinate Synthase Variant Reveals
Evolutionary Insights
pdb|3PB2|F Chain F, Characterisation Of The First Monomeric
Dihydrodipicolinate Synthase Variant Reveals
Evolutionary Insights
Length = 300
Score = 30.8 bits (68), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 27/46 (58%), Gaps = 2/46 (4%)
Query: 119 IAKETRSKLISEALQKMKGKIPEIAGSHVSSRVLQTCVKYCSQAER 164
+ ++ R KL+S L+ + GKIP I G+ +S + +K QAE+
Sbjct: 56 VNEDEREKLVSRTLEIVDGKIPVIVGAGTNST--EKTLKLVKQAEK 99
>pdb|3PB0|A Chain A, Characterisation Of The First Monomeric
Dihydrodipicolinate Synthase Variant Reveals
Evolutionary Insights
pdb|3PB0|B Chain B, Characterisation Of The First Monomeric
Dihydrodipicolinate Synthase Variant Reveals
Evolutionary Insights
pdb|3PB0|C Chain C, Characterisation Of The First Monomeric
Dihydrodipicolinate Synthase Variant Reveals
Evolutionary Insights
pdb|3PB0|D Chain D, Characterisation Of The First Monomeric
Dihydrodipicolinate Synthase Variant Reveals
Evolutionary Insights
Length = 300
Score = 30.4 bits (67), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 27/46 (58%), Gaps = 2/46 (4%)
Query: 119 IAKETRSKLISEALQKMKGKIPEIAGSHVSSRVLQTCVKYCSQAER 164
+ ++ R KL+S L+ + GKIP I G+ +S + +K QAE+
Sbjct: 56 VNEDEREKLVSRTLEIVDGKIPVIVGAGTNST--EKTLKLVKQAEK 99
>pdb|1SXJ|B Chain B, Crystal Structure Of The Eukaryotic Clamp Loader
(Replication Factor C, Rfc) Bound To The Dna Sliding
Clamp (Proliferating Cell Nuclear Antigen, Pcna)
Length = 323
Score = 29.6 bits (65), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 12/45 (26%), Positives = 28/45 (62%)
Query: 241 VELYSTELQLFKNLVSIKESRLVDVISKLGLQKASVLRHMASVIQ 285
+++ +T ++ KNL +KES +++I ++GL +L + + +Q
Sbjct: 264 IDIVTTSFRVTKNLAQVKESVRLEMIKEIGLTHMRILEGVGTYLQ 308
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.315 0.130 0.359
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,871,852
Number of Sequences: 62578
Number of extensions: 547963
Number of successful extensions: 1516
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 1454
Number of HSP's gapped (non-prelim): 52
length of query: 658
length of database: 14,973,337
effective HSP length: 105
effective length of query: 553
effective length of database: 8,402,647
effective search space: 4646663791
effective search space used: 4646663791
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.8 bits)