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= 009214
(540 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 50.1 bits (118), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 58/250 (23%), Positives = 104/250 (41%), Gaps = 31/250 (12%)
Query: 14 LQKMKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEELQPHFLSLADNTYAVHLVKKM 73
L+++ G I E + SR +Q ++ + AER VF E+ L + + ++++K
Sbjct: 19 LREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKF 78
Query: 74 LDNASKKQLAGFISALHGHVASLLRHMVGSVVVEHAYQLGNATQKQELLVELYSTELQLF 133
+ S +Q + GHV SL M G V++ A + + Q+ E++ EL L+
Sbjct: 79 FEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQNEMVRELDGHVLKCV 138
Query: 134 KN----------LVSIKESRLVDVISKLGLQKASVLRHM--ASVIQPILEKGIIDHSI-- 179
K+ + ++ L +I Q ++ H VIQ ILE + D ++
Sbjct: 139 KDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPDQTLPI 198
Query: 180 ---IHR-------------VLMEYLSMADKSSAADIIQQLSGPLLVRMIHTRDGSKIGML 223
+H+ V+ L + I+ ++ G +LV H + S +
Sbjct: 199 LEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLSQH-KFASNVVEK 257
Query: 224 CVKHGSAKER 233
CV H S ER
Sbjct: 258 CVTHASRTER 267
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/115 (16%), Positives = 54/115 (46%)
Query: 11 SEALQKMKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEELQPHFLSLADNTYAVHLV 70
+E ++++ G + + + V+Q C++ + + + +L+ + Y ++
Sbjct: 124 NEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVI 183
Query: 71 KKMLDNASKKQLAGFISALHGHVASLLRHMVGSVVVEHAYQLGNATQKQELLVEL 125
+++L++ Q + LH H L++ G+ V++H + G K +++ E+
Sbjct: 184 QRILEHCLPDQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEI 238
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/99 (24%), Positives = 53/99 (53%), Gaps = 7/99 (7%)
Query: 11 SEALQKMKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEEL-----QPH--FLSLADN 63
S+ + +++G + ++ +S V++ CV + S+ ER + +E+ PH ++ +
Sbjct: 232 SKIVAEIRGNVLVLSQHKFASNVVEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKD 291
Query: 64 TYAVHLVKKMLDNASKKQLAGFISALHGHVASLLRHMVG 102
YA ++V+KM+D A Q + + H+A+L ++ G
Sbjct: 292 QYANYVVQKMIDVAEPGQRKIVMHKIRPHIATLRKYTYG 330
Score = 40.0 bits (92), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 24/109 (22%), Positives = 54/109 (49%)
Query: 17 MKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEELQPHFLSLADNTYAVHLVKKMLDN 76
KG++ ++ RV+Q +++C + + EEL H L + Y ++++ +L++
Sbjct: 166 FKGQVFALSTHPYGCRVIQRILEHCLPDQTLPILEELHQHTEQLVQDQYGNYVIQHVLEH 225
Query: 77 ASKKQLAGFISALHGHVASLLRHMVGSVVVEHAYQLGNATQKQELLVEL 125
+ + ++ + G+V L +H S VVE + T++ L+ E+
Sbjct: 226 GRPEDKSKIVAEIRGNVLVLSQHKFASNVVEKCVTHASRTERAVLIDEV 274
>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 = 50.1 bits (118), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 58/250 (23%), Positives = 104/250 (41%), Gaps = 31/250 (12%)
Query: 14 LQKMKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEELQPHFLSLADNTYAVHLVKKM 73
L+++ G I E + SR +Q ++ + AER VF E+ L + + ++++K
Sbjct: 19 LREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKF 78
Query: 74 LDNASKKQLAGFISALHGHVASLLRHMVGSVVVEHAYQLGNATQKQELLVELYSTELQLF 133
+ S +Q + GHV SL M G V++ A + + Q+ E++ EL L+
Sbjct: 79 FEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQNEMVRELDGHVLKCV 138
Query: 134 KN----------LVSIKESRLVDVISKLGLQKASVLRHM--ASVIQPILEKGIIDHSI-- 179
K+ + ++ L +I Q ++ H VIQ ILE + D ++
Sbjct: 139 KDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPDQTLPI 198
Query: 180 ---IHR-------------VLMEYLSMADKSSAADIIQQLSGPLLVRMIHTRDGSKIGML 223
+H+ V+ L + I+ ++ G +LV H + S +
Sbjct: 199 LEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLSQH-KFASNVVEK 257
Query: 224 CVKHGSAKER 233
CV H S ER
Sbjct: 258 CVTHASRTER 267
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/99 (24%), Positives = 53/99 (53%), Gaps = 7/99 (7%)
Query: 11 SEALQKMKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEEL-----QPH--FLSLADN 63
S+ + +++G + ++ +S V++ CV + S+ ER + +E+ PH ++ +
Sbjct: 232 SKIVAEIRGNVLVLSQHKFASNVVEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKD 291
Query: 64 TYAVHLVKKMLDNASKKQLAGFISALHGHVASLLRHMVG 102
YA ++V+KM+D A Q + + H+A+L ++ G
Sbjct: 292 QYANYVVQKMIDVAEPGQRKIVMHKIRPHIATLRKYTYG 330
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/115 (16%), Positives = 54/115 (46%)
Query: 11 SEALQKMKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEELQPHFLSLADNTYAVHLV 70
+E ++++ G + + + V+Q C++ + + + +L+ + Y ++
Sbjct: 124 NEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVI 183
Query: 71 KKMLDNASKKQLAGFISALHGHVASLLRHMVGSVVVEHAYQLGNATQKQELLVEL 125
+++L++ Q + LH H L++ G+ V++H + G K +++ E+
Sbjct: 184 QRILEHCLPDQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEI 238
Score = 40.0 bits (92), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 24/109 (22%), Positives = 54/109 (49%)
Query: 17 MKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEELQPHFLSLADNTYAVHLVKKMLDN 76
KG++ ++ RV+Q +++C + + EEL H L + Y ++++ +L++
Sbjct: 166 FKGQVFALSTHPYGCRVIQRILEHCLPDQTLPILEELHQHTEQLVQDQYGNYVIQHVLEH 225
Query: 77 ASKKQLAGFISALHGHVASLLRHMVGSVVVEHAYQLGNATQKQELLVEL 125
+ + ++ + 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 = 49.7 bits (117), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 61/253 (24%), Positives = 105/253 (41%), Gaps = 37/253 (14%)
Query: 14 LQKMKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEELQPHFLSLADNTYAVHLVKKM 73
L+++ G I E + SR +Q ++ + AER VF E+ L + + ++++K
Sbjct: 20 LREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKF 79
Query: 74 LDNASKKQLAGFISALHGHVASLLRHMVGSVVVEHAYQLGNATQKQELLVELYSTELQLF 133
+ S +Q + GHV SL M G V++ A + + Q+ E++ EL L+
Sbjct: 80 FEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQNEMVRELDGHVLKCV 139
Query: 134 KN----------LVSIKESRLVDVISKLGLQKASVLRHM--ASVIQPILEKGIIDH---- 177
K+ + ++ L +I Q ++ H VIQ ILE + D
Sbjct: 140 KDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPDQTLPI 199
Query: 178 -----------------SIIHRVLMEYLSMADKSSAADIIQQLSGPLLVRMIHTRDGSKI 220
S + R ++E+ DKS I+ ++ G +LV H + S +
Sbjct: 200 LEELHQHTEQLVQDQYGSYVIRHVLEHGRPEDKSK---IVAEIRGNVLVLSQH-KFASNV 255
Query: 221 GMLCVKHGSAKER 233
CV H S ER
Sbjct: 256 VEKCVTHASRTER 268
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/115 (17%), Positives = 53/115 (46%)
Query: 11 SEALQKMKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEELQPHFLSLADNTYAVHLV 70
+E ++++ G + + + V+Q C++ + + + +L+ + Y ++
Sbjct: 125 NEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVI 184
Query: 71 KKMLDNASKKQLAGFISALHGHVASLLRHMVGSVVVEHAYQLGNATQKQELLVEL 125
+++L++ Q + LH H L++ GS V+ H + G K +++ E+
Sbjct: 185 QRILEHCLPDQTLPILEELHQHTEQLVQDQYGSYVIRHVLEHGRPEDKSKIVAEI 239
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/99 (24%), Positives = 53/99 (53%), Gaps = 7/99 (7%)
Query: 11 SEALQKMKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEEL-----QPH--FLSLADN 63
S+ + +++G + ++ +S V++ CV + S+ ER + +E+ PH ++ +
Sbjct: 233 SKIVAEIRGNVLVLSQHKFASNVVEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKD 292
Query: 64 TYAVHLVKKMLDNASKKQLAGFISALHGHVASLLRHMVG 102
YA ++V+KM+D A Q + + H+A+L ++ G
Sbjct: 293 QYANYVVQKMIDVAEPGQRKIVMHKIRPHIATLRKYTYG 331
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/109 (22%), Positives = 54/109 (49%)
Query: 17 MKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEELQPHFLSLADNTYAVHLVKKMLDN 76
KG++ ++ RV+Q +++C + + EEL H L + Y ++++ +L++
Sbjct: 167 FKGQVFALSTHPYGCRVIQRILEHCLPDQTLPILEELHQHTEQLVQDQYGSYVIRHVLEH 226
Query: 77 ASKKQLAGFISALHGHVASLLRHMVGSVVVEHAYQLGNATQKQELLVEL 125
+ + ++ + G+V L +H S VVE + T++ L+ E+
Sbjct: 227 GRPEDKSKIVAEIRGNVLVLSQHKFASNVVEKCVTHASRTERAVLIDEV 275
>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 = 45.8 bits (107), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 25/110 (22%), Positives = 56/110 (50%)
Query: 16 KMKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEELQPHFLSLADNTYAVHLVKKMLD 75
+ KG + +++ + RV+Q ++Y +R + EL L + + H+++K ++
Sbjct: 100 QFKGNMKQLSLQMYACRVIQKALEYIDSNQRIELVLELSDSVLQMIKDQNGNHVIQKAIE 159
Query: 76 NASKKQLAGFISALHGHVASLLRHMVGSVVVEHAYQLGNATQKQELLVEL 125
++L +S+L GH+ L H G V++ + G++ ++ +L EL
Sbjct: 160 TIPIEKLPFILSSLTGHIYHLSTHSYGCRVIQRLLEFGSSEDQESILNEL 209
>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 = 45.4 bits (106), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 30/118 (25%), Positives = 56/118 (47%)
Query: 8 RLISEALQKMKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEELQPHFLSLADNTYAV 67
R + L+ + G I E + SR +Q ++ + AER VF E+ L + +
Sbjct: 15 RFPNLQLRDLIGHIVEFSQDQHGSRFIQQKLERATPAERQIVFNEILQAAYQLMTDVFGN 74
Query: 68 HLVKKMLDNASKKQLAGFISALHGHVASLLRHMVGSVVVEHAYQLGNATQKQELLVEL 125
++++K + S Q + + GHV L M G V++ A + ++ Q+ E++ EL
Sbjct: 75 YVIQKFFEFGSLDQKLALATRIRGHVLPLALQMYGCRVIQKALESISSDQQSEMVKEL 132
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 25/99 (25%), Positives = 54/99 (54%), Gaps = 7/99 (7%)
Query: 11 SEALQKMKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEEL-----QPH--FLSLADN 63
S+ + +++GK+ ++ +S V++ CV + S+AER + +E+ PH ++ +
Sbjct: 234 SKIVSEIRGKVLALSQHKFASNVVEKCVTHASRAERALLIDEVCCQNDGPHSALYTMMKD 293
Query: 64 TYAVHLVKKMLDNASKKQLAGFISALHGHVASLLRHMVG 102
YA ++V+KM+D A Q + + H+ +L ++ G
Sbjct: 294 QYANYVVQKMIDMAEPAQRKIIMHKIRPHITTLRKYTYG 332
Score = 42.7 bits (99), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 22/122 (18%), Positives = 57/122 (46%)
Query: 11 SEALQKMKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEELQPHFLSLADNTYAVHLV 70
SE ++++ G + + + V+Q C++ + + + L+ + Y ++
Sbjct: 126 SEMVKELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFVLSTHPYGCRVI 185
Query: 71 KKMLDNASKKQLAGFISALHGHVASLLRHMVGSVVVEHAYQLGNATQKQELLVELYSTEL 130
+++L++ + +Q + LH H L++ G+ V++H + G K +++ E+ L
Sbjct: 186 QRILEHCTAEQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGKVL 245
Query: 131 QL 132
L
Sbjct: 246 AL 247
Score = 42.0 bits (97), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 22/91 (24%), Positives = 47/91 (51%)
Query: 17 MKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEELQPHFLSLADNTYAVHLVKKMLDN 76
KG++ ++ RV+Q +++C+ + + EEL H L + Y ++++ +L++
Sbjct: 168 FKGQVFVLSTHPYGCRVIQRILEHCTAEQTLPILEELHQHTEQLVQDQYGNYVIQHVLEH 227
Query: 77 ASKKQLAGFISALHGHVASLLRHMVGSVVVE 107
+ + +S + G V +L +H S VVE
Sbjct: 228 GRPEDKSKIVSEIRGKVLALSQHKFASNVVE 258
Score = 28.5 bits (62), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 11/44 (25%), Positives = 24/44 (54%)
Query: 30 SSRVLQTCVKYCSQAERDAVFEELQPHFLSLADNTYAVHLVKKM 73
++ V+Q + A+R + +++PH +L TY H++ K+
Sbjct: 296 ANYVVQKMIDMAEPAQRKIIMHKIRPHITTLRKYTYGKHILAKL 339
>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 = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/125 (18%), Positives = 60/125 (48%)
Query: 8 RLISEALQKMKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEELQPHFLSLADNTYAV 67
++ISE ++++ G + + + V+Q C++ + + + L+ + Y
Sbjct: 123 QVISEMVKELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFVLSTHPYGC 182
Query: 68 HLVKKMLDNASKKQLAGFISALHGHVASLLRHMVGSVVVEHAYQLGNATQKQELLVELYS 127
+++++L++ + +Q + LH H L++ G+ V++H + G K +++ E+
Sbjct: 183 RVIQRILEHCTAEQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRG 242
Query: 128 TELQL 132
L L
Sbjct: 243 KVLAL 247
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 25/99 (25%), Positives = 54/99 (54%), Gaps = 7/99 (7%)
Query: 11 SEALQKMKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEEL-----QPH--FLSLADN 63
S+ + +++GK+ ++ +S V++ CV + S+AER + +E+ PH ++ +
Sbjct: 234 SKIVSEIRGKVLALSQHKFASNVVEKCVTHASRAERALLIDEVCCQNDGPHSALYTMMKD 293
Query: 64 TYAVHLVKKMLDNASKKQLAGFISALHGHVASLLRHMVG 102
YA ++V+KM+D A Q + + H+ +L ++ G
Sbjct: 294 QYANYVVQKMIDMAEPAQRKIIMHKIRPHITTLRKYTYG 332
Score = 42.0 bits (97), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 22/91 (24%), Positives = 47/91 (51%)
Query: 17 MKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEELQPHFLSLADNTYAVHLVKKMLDN 76
KG++ ++ RV+Q +++C+ + + EEL H L + Y ++++ +L++
Sbjct: 168 FKGQVFVLSTHPYGCRVIQRILEHCTAEQTLPILEELHQHTEQLVQDQYGNYVIQHVLEH 227
Query: 77 ASKKQLAGFISALHGHVASLLRHMVGSVVVE 107
+ + +S + G V +L +H S VVE
Sbjct: 228 GRPEDKSKIVSEIRGKVLALSQHKFASNVVE 258
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 29/118 (24%), Positives = 55/118 (46%), Gaps = 2/118 (1%)
Query: 8 RLISEALQKMKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEELQPHFLSLADNTYAV 67
R + L+ + G I E + SR +Q ++ + AER VF E+ L + +
Sbjct: 13 RFPNLQLRDLIGHIVEFSQDQHGSRFIQQKLERATPAERQMVFNEILQAAYQLMTDVFGN 72
Query: 68 HLVKKMLDNASKKQLAGFISALHGHVASLLRHMVGSVVVEHAYQLGNATQKQELLVEL 125
++++K + S Q + + GHV L M G V++ A L + + Q+++ E+
Sbjct: 73 YVIQKFFEFGSLDQKLALATRIRGHVLPLALQMYGCRVIQKA--LESISSDQQVISEM 128
Score = 28.5 bits (62), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 11/44 (25%), Positives = 24/44 (54%)
Query: 30 SSRVLQTCVKYCSQAERDAVFEELQPHFLSLADNTYAVHLVKKM 73
++ V+Q + A+R + +++PH +L TY H++ K+
Sbjct: 296 ANYVVQKMIDMAEPAQRKIIMHKIRPHITTLRKYTYGKHILAKL 339
>pdb|3H3D|X Chain X, Drosophila Pumilio Rna Binding Domain (Puf Domain)
pdb|3H3D|Y Chain Y, Drosophila Pumilio Rna Binding Domain (Puf Domain)
Length = 323
Score = 43.1 bits (100), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 31/120 (25%), Positives = 55/120 (45%)
Query: 16 KMKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEELQPHFLSLADNTYAVHLVKKMLD 75
++KG + ++A RV+Q ++ S ++ + EL H L + H+V+K ++
Sbjct: 95 QVKGHVLQLALQMYGCRVIQKALESISPEQQQEIVHELDGHVLKCVKDQNGNHVVQKCIE 154
Query: 76 NASKKQLAGFISALHGHVASLLRHMVGSVVVEHAYQLGNATQKQELLVELYSTELQLFKN 135
L I+A G V SL H G V++ + A Q +L EL+ QL ++
Sbjct: 155 CVDPVALQFIINAFKGQVYSLSTHPYGCRVIQRILEHCTAEQTTPILDELHEHTEQLIQD 214
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 59/250 (23%), Positives = 101/250 (40%), Gaps = 31/250 (12%)
Query: 14 LQKMKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEELQPHFLSLADNTYAVHLVKKM 73
L+ + I E + SR +Q ++ + AE+ VF E+ SL + + ++++K
Sbjct: 21 LRDLANHIVEFSQDQHGSRFIQQKLERATAAEKQMVFSEILAAAYSLMTDVFGNYVIQKF 80
Query: 74 LDNASKKQLAGFISALHGHVASLLRHMVGSVVVEHAYQLGNATQKQELLVELYSTELQLF 133
+ + +Q + GHV L M G V++ A + + Q+QE++ EL L+
Sbjct: 81 FEFGTPEQKNTLGMQVKGHVLQLALQMYGCRVIQKALESISPEQQQEIVHELDGHVLKCV 140
Query: 134 K----NLVSIKESRLVD------VISKLGLQKASVLRHM--ASVIQPILE---------- 171
K N V K VD +I+ Q S+ H VIQ ILE
Sbjct: 141 KDQNGNHVVQKCIECVDPVALQFIINAFKGQVYSLSTHPYGCRVIQRILEHCTAEQTTPI 200
Query: 172 --------KGIIDHSIIHRVLMEYLSMADKSSAADIIQQLSGPLLVRMIHTRDGSKIGML 223
+ +I + V+ L + + +I + G +LV H + S +
Sbjct: 201 LDELHEHTEQLIQDQYGNYVIQHVLEHGKQEDKSILINSVRGKVLVLSQH-KFASNVVEK 259
Query: 224 CVKHGSAKER 233
CV H + ER
Sbjct: 260 CVTHATRGER 269
Score = 40.0 bits (92), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/111 (18%), Positives = 50/111 (45%)
Query: 12 EALQKMKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEELQPHFLSLADNTYAVHLVK 71
E + ++ G + + + V+Q C++ + + SL+ + Y +++
Sbjct: 127 EIVHELDGHVLKCVKDQNGNHVVQKCIECVDPVALQFIINAFKGQVYSLSTHPYGCRVIQ 186
Query: 72 KMLDNASKKQLAGFISALHGHVASLLRHMVGSVVVEHAYQLGNATQKQELL 122
++L++ + +Q + LH H L++ G+ V++H + G K L+
Sbjct: 187 RILEHCTAEQTTPILDELHEHTEQLIQDQYGNYVIQHVLEHGKQEDKSILI 237
>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 = 32.7 bits (73), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 17/74 (22%), Positives = 34/74 (45%)
Query: 8 RLISEALQKMKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEELQPHFLSLADNTYAV 67
R L + G I + R LQ + DA+FEE + + + L +++
Sbjct: 2 RFADAVLDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGN 61
Query: 68 HLVKKMLDNASKKQ 81
+L++K+L+ + +Q
Sbjct: 62 YLIQKLLEEVTTEQ 75
Score = 28.5 bits (62), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 25/129 (19%), Positives = 51/129 (39%), Gaps = 13/129 (10%)
Query: 4 FLLIRLISEALQKMKGKIPEIAGSHV--------SSRVLQT---CVKYCSQAERDAVFEE 52
+L+ +L+ E + + + +I+ H +R LQ C+K + E V +
Sbjct: 62 YLIQKLLEEVTTEQRIVLTKISSPHFVEISLNPHGTRALQKLIECIK--TDEEAQIVVDS 119
Query: 53 LQPHFLSLADNTYAVHLVKKMLDNASKKQLAGFISALHGHVASLLRHMVGSVVVEHAYQL 112
L+P+ + L+ + H+++K L + A+ + H G V++
Sbjct: 120 LRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDH 179
Query: 113 GNATQKQEL 121
G Q L
Sbjct: 180 GTTEQCDNL 188
>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 = 32.7 bits (73), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 17/74 (22%), Positives = 34/74 (45%)
Query: 8 RLISEALQKMKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEELQPHFLSLADNTYAV 67
R L + G I + R LQ + DA+FEE + + + L +++
Sbjct: 2 RFADAVLDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGN 61
Query: 68 HLVKKMLDNASKKQ 81
+L++K+L+ + +Q
Sbjct: 62 YLIQKLLEEVTTEQ 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 = 0.53, Method: Compositional matrix adjust.
Identities = 17/74 (22%), Positives = 34/74 (45%)
Query: 8 RLISEALQKMKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEELQPHFLSLADNTYAV 67
R L + G I + R LQ + DA+FEE + + + L +++
Sbjct: 2 RFADAVLDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGN 61
Query: 68 HLVKKMLDNASKKQ 81
+L++K+L+ + +Q
Sbjct: 62 YLIQKLLEEVTTEQ 75
>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 = 32.7 bits (73), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 17/74 (22%), Positives = 34/74 (45%)
Query: 8 RLISEALQKMKGKIPEIAGSHVSSRVLQTCVKYCSQAERDAVFEELQPHFLSLADNTYAV 67
R L + G I + R LQ + DA+FEE + + + L +++
Sbjct: 24 RFADAVLDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGN 83
Query: 68 HLVKKMLDNASKKQ 81
+L++K+L+ + +Q
Sbjct: 84 YLIQKLLEEVTTEQ 97
>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 = 29.3 bits (64), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 12/45 (26%), Positives = 28/45 (62%)
Query: 123 VELYSTELQLFKNLVSIKESRLVDVISKLGLQKASVLRHMASVIQ 167
+++ +T ++ KNL +KES +++I ++GL +L + + +Q
Sbjct: 264 IDIVTTSFRVTKNLAQVKESVRLEMIKEIGLTHMRILEGVGTYLQ 308
>pdb|2R98|A Chain A, Crystal Structure Of N-Acetylglutamate Synthase (Selenomet
Substituted) From Neisseria Gonorrhoeae
Length = 456
Score = 28.9 bits (63), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 43/95 (45%), Gaps = 21/95 (22%)
Query: 92 HVASLLRHMVGSVVVE-----HAYQLGNATQKQELLVELYSTE---LQLFKN-LVSIKES 142
H AS R ++ S V H Q+ N LL EL++ + K VSI+++
Sbjct: 253 HAASETRRLISSAVAALEGGVHRVQILNGAADGSLLQELFTRNGIGTSIAKEAFVSIRQA 312
Query: 143 RLVDVISKLGLQKASVLRHMASVIQPILEKGIIDH 177
D+ H+A++I+P+ E+GI+ H
Sbjct: 313 HSGDIP------------HIAALIRPLEEQGILLH 335
>pdb|2R8V|A Chain A, Native Structure Of N-Acetylglutamate Synthase From
Neisseria Gonorrhoeae
pdb|3B8G|A Chain A, Crysta Structure Of N-Acetylglutamate Synthase From
Neisseria Gonorrhoeae Complexed With Coenzyme A And
N-Acetyl-Glutamate
pdb|3D2P|A Chain A, Crystal Structure Of N-acetylglutamate Synthase From
Neisseria Gonorrhoeae Complexed With Coenzyme A And
L-arginine
pdb|3D2P|B Chain B, Crystal Structure Of N-acetylglutamate Synthase From
Neisseria Gonorrhoeae Complexed With Coenzyme A And
L-arginine
pdb|3D2M|A Chain A, Crystal Structure Of N-Acetylglutamate Synthase From
Neisseria Gonorrhoeae Complexed With Coenzyme A And
L-Glutamate
pdb|4I49|A Chain A, Structure Of Ngnags Bound With Bisubstrate Analog Coa-Nag
Length = 456
Score = 28.9 bits (63), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 43/95 (45%), Gaps = 21/95 (22%)
Query: 92 HVASLLRHMVGSVVVE-----HAYQLGNATQKQELLVELYSTE---LQLFKN-LVSIKES 142
H AS R ++ S V H Q+ N LL EL++ + K VSI+++
Sbjct: 253 HAASETRRLISSAVAALEGGVHRVQILNGAADGSLLQELFTRNGIGTSIAKEAFVSIRQA 312
Query: 143 RLVDVISKLGLQKASVLRHMASVIQPILEKGIIDH 177
D+ H+A++I+P+ E+GI+ H
Sbjct: 313 HSGDIP------------HIAALIRPLEEQGILLH 335
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
0.318 0.133 0.368
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,930,133
Number of Sequences: 62578
Number of extensions: 447832
Number of successful extensions: 1266
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1204
Number of HSP's gapped (non-prelim): 51
length of query: 540
length of database: 14,973,337
effective HSP length: 104
effective length of query: 436
effective length of database: 8,465,225
effective search space: 3690838100
effective search space used: 3690838100
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)