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= 003928
(786 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 39.7 bits (91), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 25/88 (28%), Positives = 44/88 (50%), Gaps = 6/88 (6%)
Query: 504 IIGSLILQAVFRFPSEFIQPYVTSITSMEAD-HVLEAAKDAAGARVIEAYLSSKVSAKQK 562
+ G+ ++Q F F + P + M+ HVL+ A G RVI+ L S +S +Q+
Sbjct: 71 VFGNYVIQKFFEFGT----PEQKNTLGMQVKGHVLQLALQMYGCRVIQKALES-ISPEQQ 125
Query: 563 HRVVLKLKGHFGELSVHPSGSFTVERCF 590
+V +L GH + +G+ V++C
Sbjct: 126 QEIVHELDGHVLKCVKDQNGNHVVQKCI 153
Score = 34.3 bits (77), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 41/176 (23%), Positives = 72/176 (40%), Gaps = 19/176 (10%)
Query: 459 EALAAAVS-STNVSPRCIVPGILFLESYFSCEDKSNWNWPKGIKIQIIGSLILQAVFRFP 517
E LAAA S T+V ++ F E F ++ N + +Q+ G ++ A+ +
Sbjct: 59 EILAAAYSLMTDVFGNYVIQK--FFE--FGTPEQKNT-----LGMQVKGHVLQLALQMYG 109
Query: 518 SEFIQPYVTSITSMEAD--------HVLEAAKDAAGARVIEAYLSSKVSAKQKHRVVLKL 569
IQ + SI+ + HVL+ KD G V++ + V ++
Sbjct: 110 CRVIQKALESISPEQQQEIVHELDGHVLKCVKDQNGNHVVQKCIEC-VDPVALQFIINAF 168
Query: 570 KGHFGELSVHPSGSFTVERCFTASSLSLRETIASELSAVRNELSKTKQGPHLIRKL 625
KG LS HP G ++R + I EL +L + + G ++I+ +
Sbjct: 169 KGQVYSLSTHPYGCRVIQRILEHCTAEQTTPILDELHEHTEQLIQDQYGNYVIQHV 224
Score = 33.9 bits (76), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 33/145 (22%), Positives = 70/145 (48%), Gaps = 11/145 (7%)
Query: 489 EDKSNWNWPKGIKIQIIGSLILQ-AVFRFPSEFIQPYVTSITSMEAD----HVLEAA--- 540
ED N +P ++++ + + I++ + + S FIQ + T+ E +L AA
Sbjct: 9 EDFRNQRYP-NLQLRDLANHIVEFSQDQHGSRFIQQKLERATAAEKQMVFSEILAAAYSL 67
Query: 541 -KDAAGARVIEAYLSSKVSAKQKHRVVLKLKGHFGELSVHPSGSFTVERCFTASSLSLRE 599
D G VI+ + + +QK+ + +++KGH +L++ G +++ + S ++
Sbjct: 68 MTDVFGNYVIQKFFEFG-TPEQKNTLGMQVKGHVLQLALQMYGCRVIQKALESISPEQQQ 126
Query: 600 TIASELSAVRNELSKTKQGPHLIRK 624
I EL + K + G H+++K
Sbjct: 127 EIVHELDGHVLKCVKDQNGNHVVQK 151
>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 = 37.0 bits (84), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 28/102 (27%), Positives = 49/102 (48%), Gaps = 2/102 (1%)
Query: 533 ADHVLEAAKDAAGARVIEAYLSSKVSAKQKHRVVLKLKGHFGELSVHPSGSFTVERCFTA 592
+D VL+ KD G VI+ + + + ++ ++ L GH LS H G ++R
Sbjct: 138 SDSVLQMIKDQNGNHVIQKAIET-IPIEKLPFILSSLTGHIYHLSTHSYGCRVIQRLLEF 196
Query: 593 SSLSLRETIASELSAVRNELSKTKQGPHLIRK-LDIDGFTAR 633
S +E+I +EL L + + G ++I+ L D FT +
Sbjct: 197 GSSEDQESILNELKDFIPYLIQDQYGNYVIQYVLQQDQFTNK 238
Score = 32.7 bits (73), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 24/93 (25%), Positives = 45/93 (48%), Gaps = 5/93 (5%)
Query: 534 DHVLEAAKDAAGARVIEAYL--SSKVSAKQKHRVVLKLKGHFGELSVHPSGSFTVERCFT 591
D +E + D G VI+ + SK+ QK+ +V + KG+ +LS+ +++
Sbjct: 67 DDAIELSNDVFGNYVIQKFFEFGSKI---QKNTLVDQFKGNMKQLSLQMYACRVIQKALE 123
Query: 592 ASSLSLRETIASELSAVRNELSKTKQGPHLIRK 624
+ R + ELS ++ K + G H+I+K
Sbjct: 124 YIDSNQRIELVLELSDSVLQMIKDQNGNHVIQK 156
Score = 30.0 bits (66), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 22/90 (24%), Positives = 42/90 (46%), Gaps = 1/90 (1%)
Query: 535 HVLEAAKDAAGARVIEAYLSSKVSAKQKHRVVLKLKGHFGELSVHPSGSFTVERCFTASS 594
H LE KD G+R I+ L++ A +K + +++ ELS G++ +++ F S
Sbjct: 32 HSLEFCKDQHGSRFIQRELATS-PASEKEVIFNEIRDDAIELSNDVFGNYVIQKFFEFGS 90
Query: 595 LSLRETIASELSAVRNELSKTKQGPHLIRK 624
+ T+ + +LS +I+K
Sbjct: 91 KIQKNTLVDQFKGNMKQLSLQMYACRVIQK 120
>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 = 33.5 bits (75), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 35/141 (24%), Positives = 60/141 (42%), Gaps = 12/141 (8%)
Query: 503 QIIGSLILQAVFRFPSEFIQPYVTSITS-------MEAD-HVLEAAKDAAGARVIEAYLS 554
+I G ++ A+ + IQ + SI+S E D HVL+ KD G V++ +
Sbjct: 95 RIRGHVLPLALQMYGCRVIQKALESISSDQQSEMVKELDGHVLKCVKDQNGNHVVQKCIE 154
Query: 555 SKVSAKQKHRVVLKLKGHFGELSVHPSGSFTVERCFTASSLSLRETIASELSAVRNELSK 614
V + ++ KG LS HP G ++R + I EL +L +
Sbjct: 155 C-VQPQSLQFIIDAFKGQVFVLSTHPYGCRVIQRILEHCTAEQTLPILEELHQHTEQLVQ 213
Query: 615 TKQGPHLIRKLDIDGFTARPD 635
+ G ++I+ + G RP+
Sbjct: 214 DQYGNYVIQHVLEHG---RPE 231
Score = 31.6 bits (70), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 42/81 (51%), Gaps = 4/81 (4%)
Query: 354 VLNLMKETAYSHLMEVILE-VAPQSLYDEMFTKVFRNSLFDLSSHHCANFVVQALVSHAR 412
VL +K+ +H+++ +E V PQSL + F+ +F LS+H V+Q ++ H
Sbjct: 136 VLKCVKDQNGNHVVQKCIECVQPQSL--QFIIDAFKGQVFVLSTHPYGCRVIQRILEHC- 192
Query: 413 DQDQMALIWEELGGKFRELLE 433
+Q I EEL +L++
Sbjct: 193 TAEQTLPILEELHQHTEQLVQ 213
Score = 30.4 bits (67), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 38/86 (44%), Gaps = 8/86 (9%)
Query: 535 HVLEAAKDAAGARVIEAYLSSKVSAKQKHRVVLKLKGHFGELSVHPSGSFTVERCFTASS 594
H + +D G VI+ L + K ++V +++G LS H S VE+C T +S
Sbjct: 207 HTEQLVQDQYGNYVIQHVLEHG-RPEDKSKIVSEIRGKVLALSQHKFASNVVEKCVTHAS 265
Query: 595 LSLRETIASELSAVRNELSKTKQGPH 620
+ R + E+ + GPH
Sbjct: 266 RAERALLIDEVCCQND-------GPH 284
>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 = 33.1 bits (74), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 25/101 (24%), Positives = 43/101 (42%), Gaps = 4/101 (3%)
Query: 535 HVLEAAKDAAGARVIEAYLSSKVSAKQKHRVVLKLKGHFGELSVHPSGSFTVERCFTASS 594
HVL+ KD G V++ + V + ++ KG LS HP G ++R +
Sbjct: 135 HVLKCVKDQNGNHVVQKCIEC-VQPQSLQFIIDAFKGQVFVLSTHPYGCRVIQRILEHCT 193
Query: 595 LSLRETIASELSAVRNELSKTKQGPHLIRKLDIDGFTARPD 635
I EL +L + + G ++I+ + G RP+
Sbjct: 194 AEQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHG---RPE 231
Score = 31.2 bits (69), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 42/81 (51%), Gaps = 4/81 (4%)
Query: 354 VLNLMKETAYSHLMEVILE-VAPQSLYDEMFTKVFRNSLFDLSSHHCANFVVQALVSHAR 412
VL +K+ +H+++ +E V PQSL + F+ +F LS+H V+Q ++ H
Sbjct: 136 VLKCVKDQNGNHVVQKCIECVQPQSL--QFIIDAFKGQVFVLSTHPYGCRVIQRILEHC- 192
Query: 413 DQDQMALIWEELGGKFRELLE 433
+Q I EEL +L++
Sbjct: 193 TAEQTLPILEELHQHTEQLVQ 213
Score = 30.4 bits (67), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 38/86 (44%), Gaps = 8/86 (9%)
Query: 535 HVLEAAKDAAGARVIEAYLSSKVSAKQKHRVVLKLKGHFGELSVHPSGSFTVERCFTASS 594
H + +D G VI+ L + K ++V +++G LS H S VE+C T +S
Sbjct: 207 HTEQLVQDQYGNYVIQHVLEHG-RPEDKSKIVSEIRGKVLALSQHKFASNVVEKCVTHAS 265
Query: 595 LSLRETIASELSAVRNELSKTKQGPH 620
+ R + E+ + GPH
Sbjct: 266 RAERALLIDEVCCQND-------GPH 284
Score = 29.6 bits (65), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 25/88 (28%), Positives = 41/88 (46%), Gaps = 4/88 (4%)
Query: 504 IIGSLILQAVFRFPSEFIQPYVTSITSMEADHVLEAAKDAAGARVIEAYLSSKVSAKQK- 562
+ G+ ++Q F F S + + T + HVL A G RVI+ L S S +Q
Sbjct: 69 VFGNYVIQKFFEFGS--LDQKLALATRIRG-HVLPLALQMYGCRVIQKALESISSDQQVI 125
Query: 563 HRVVLKLKGHFGELSVHPSGSFTVERCF 590
+V +L GH + +G+ V++C
Sbjct: 126 SEMVKELDGHVLKCVKDQNGNHVVQKCI 153
>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 = 33.1 bits (74), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 40/86 (46%), Gaps = 8/86 (9%)
Query: 535 HVLEAAKDAAGARVIEAYLSSKVSAKQKHRVVLKLKGHFGELSVHPSGSFTVERCFTASS 594
H + +D G VI+ L + K ++V +++G+ LS H S VE+C T +S
Sbjct: 205 HTEQLVQDQYGNYVIQHVLEHG-RPEDKSKIVAEIRGNVLVLSQHKFASNVVEKCVTHAS 263
Query: 595 LSLRETIASELSAVRNELSKTKQGPH 620
+ R + E+ + + GPH
Sbjct: 264 RTERAVLIDEVCTMND-------GPH 282
Score = 32.7 bits (73), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 42/81 (51%), Gaps = 4/81 (4%)
Query: 354 VLNLMKETAYSHLMEVILE-VAPQSLYDEMFTKVFRNSLFDLSSHHCANFVVQALVSHAR 412
VL +K+ +H+++ +E V PQSL + F+ +F LS+H V+Q ++ H
Sbjct: 134 VLKCVKDQNGNHVVQKCIECVQPQSL--QFIIDAFKGQVFALSTHPYGCRVIQRILEHCL 191
Query: 413 DQDQMALIWEELGGKFRELLE 433
DQ I EEL +L++
Sbjct: 192 P-DQTLPILEELHQHTEQLVQ 211
Score = 30.8 bits (68), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 22/91 (24%), Positives = 42/91 (46%), Gaps = 4/91 (4%)
Query: 500 IKIQIIGSLILQAVFRFPSEFIQPYVTSITSMEADHVLEAAKDAAGARVIEAYLSSKVSA 559
+ + + G+ ++Q F F S ++ HVL A G RVI+ L + +
Sbjct: 65 LMVDVFGNYVIQKFFEFGS---LEQKLALAERIRGHVLSLALQMYGCRVIQKALEF-IPS 120
Query: 560 KQKHRVVLKLKGHFGELSVHPSGSFTVERCF 590
Q++ +V +L GH + +G+ V++C
Sbjct: 121 DQQNEMVRELDGHVLKCVKDQNGNHVVQKCI 151
>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 = 33.1 bits (74), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 40/86 (46%), Gaps = 8/86 (9%)
Query: 535 HVLEAAKDAAGARVIEAYLSSKVSAKQKHRVVLKLKGHFGELSVHPSGSFTVERCFTASS 594
H + +D G VI+ L + K ++V +++G+ LS H S VE+C T +S
Sbjct: 205 HTEQLVQDQYGNYVIQHVLEHG-RPEDKSKIVAEIRGNVLVLSQHKFASNVVEKCVTHAS 263
Query: 595 LSLRETIASELSAVRNELSKTKQGPH 620
+ R + E+ + + GPH
Sbjct: 264 RTERAVLIDEVCTMND-------GPH 282
Score = 32.7 bits (73), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 42/81 (51%), Gaps = 4/81 (4%)
Query: 354 VLNLMKETAYSHLMEVILE-VAPQSLYDEMFTKVFRNSLFDLSSHHCANFVVQALVSHAR 412
VL +K+ +H+++ +E V PQSL + F+ +F LS+H V+Q ++ H
Sbjct: 134 VLKCVKDQNGNHVVQKCIECVQPQSL--QFIIDAFKGQVFALSTHPYGCRVIQRILEHCL 191
Query: 413 DQDQMALIWEELGGKFRELLE 433
DQ I EEL +L++
Sbjct: 192 P-DQTLPILEELHQHTEQLVQ 211
Score = 30.8 bits (68), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 22/91 (24%), Positives = 42/91 (46%), Gaps = 4/91 (4%)
Query: 500 IKIQIIGSLILQAVFRFPSEFIQPYVTSITSMEADHVLEAAKDAAGARVIEAYLSSKVSA 559
+ + + G+ ++Q F F S ++ HVL A G RVI+ L + +
Sbjct: 65 LMVDVFGNYVIQKFFEFGS---LEQKLALAERIRGHVLSLALQMYGCRVIQKALEF-IPS 120
Query: 560 KQKHRVVLKLKGHFGELSVHPSGSFTVERCF 590
Q++ +V +L GH + +G+ V++C
Sbjct: 121 DQQNEMVRELDGHVLKCVKDQNGNHVVQKCI 151
>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 = 32.7 bits (73), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 40/86 (46%), Gaps = 8/86 (9%)
Query: 535 HVLEAAKDAAGARVIEAYLSSKVSAKQKHRVVLKLKGHFGELSVHPSGSFTVERCFTASS 594
H + +D G+ VI L + K ++V +++G+ LS H S VE+C T +S
Sbjct: 206 HTEQLVQDQYGSYVIRHVLEHG-RPEDKSKIVAEIRGNVLVLSQHKFASNVVEKCVTHAS 264
Query: 595 LSLRETIASELSAVRNELSKTKQGPH 620
+ R + E+ + + GPH
Sbjct: 265 RTERAVLIDEVCTMND-------GPH 283
Score = 32.7 bits (73), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 42/81 (51%), Gaps = 4/81 (4%)
Query: 354 VLNLMKETAYSHLMEVILE-VAPQSLYDEMFTKVFRNSLFDLSSHHCANFVVQALVSHAR 412
VL +K+ +H+++ +E V PQSL + F+ +F LS+H V+Q ++ H
Sbjct: 135 VLKCVKDQNGNHVVQKCIECVQPQSL--QFIIDAFKGQVFALSTHPYGCRVIQRILEHCL 192
Query: 413 DQDQMALIWEELGGKFRELLE 433
DQ I EEL +L++
Sbjct: 193 P-DQTLPILEELHQHTEQLVQ 212
Score = 30.8 bits (68), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 22/91 (24%), Positives = 42/91 (46%), Gaps = 4/91 (4%)
Query: 500 IKIQIIGSLILQAVFRFPSEFIQPYVTSITSMEADHVLEAAKDAAGARVIEAYLSSKVSA 559
+ + + G+ ++Q F F S ++ HVL A G RVI+ L + +
Sbjct: 66 LMVDVFGNYVIQKFFEFGS---LEQKLALAERIRGHVLSLALQMYGCRVIQKALEF-IPS 121
Query: 560 KQKHRVVLKLKGHFGELSVHPSGSFTVERCF 590
Q++ +V +L GH + +G+ V++C
Sbjct: 122 DQQNEMVRELDGHVLKCVKDQNGNHVVQKCI 152
>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 = 32.3 bits (72), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 34/132 (25%), Positives = 60/132 (45%), Gaps = 12/132 (9%)
Query: 503 QIIGSLILQAVFRFPSEFIQPYVTSITSMEADHVLEAAKDAAGARVIEA---YLSSKV-- 557
Q IGS+ + F+Q + + S AD + E KD + ++ YL K+
Sbjct: 10 QYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLE 69
Query: 558 SAKQKHRVVL-KLKG-HFGELSVHPSGSFTVER---CFTASSLSLRETIASELSAVRNEL 612
+ R+VL K+ HF E+S++P G+ +++ C + + + L +L
Sbjct: 70 EVTTEQRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEA--QIVVDSLRPYTVQL 127
Query: 613 SKTKQGPHLIRK 624
SK G H+I+K
Sbjct: 128 SKDLNGNHVIQK 139
>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 = 32.3 bits (72), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 34/132 (25%), Positives = 60/132 (45%), Gaps = 12/132 (9%)
Query: 503 QIIGSLILQAVFRFPSEFIQPYVTSITSMEADHVLEAAKDAAGARVIEA---YLSSKV-- 557
Q IGS+ + F+Q + + S AD + E KD + ++ YL K+
Sbjct: 32 QYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLE 91
Query: 558 SAKQKHRVVL-KLKG-HFGELSVHPSGSFTVER---CFTASSLSLRETIASELSAVRNEL 612
+ R+VL K+ HF E+S++P G+ +++ C + + + L +L
Sbjct: 92 EVTTEQRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEA--QIVVDSLRPYTVQL 149
Query: 613 SKTKQGPHLIRK 624
SK G H+I+K
Sbjct: 150 SKDLNGNHVIQK 161
>pdb|3BWT|A Chain A, Crystal Structure Of The Rna Binding Domain Of Puf4 From
Saccharomyces Cerevisiae
Length = 333
Score = 32.3 bits (72), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 34/132 (25%), Positives = 60/132 (45%), Gaps = 12/132 (9%)
Query: 503 QIIGSLILQAVFRFPSEFIQPYVTSITSMEADHVLEAAKDAAGARVIEA---YLSSKV-- 557
Q IGS+ + F+Q + + S AD + E KD + ++ YL K+
Sbjct: 10 QYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLE 69
Query: 558 SAKQKHRVVL-KLKG-HFGELSVHPSGSFTVER---CFTASSLSLRETIASELSAVRNEL 612
+ R+VL K+ HF E+S++P G+ +++ C + + + L +L
Sbjct: 70 EVTTEQRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEA--QIVVDSLRPYTVQL 127
Query: 613 SKTKQGPHLIRK 624
SK G H+I+K
Sbjct: 128 SKDLNGNHVIQK 139
>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 = 31.6 bits (70), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 34/132 (25%), Positives = 59/132 (44%), Gaps = 12/132 (9%)
Query: 503 QIIGSLILQAVFRFPSEFIQPYVTSITSMEADHVLEAAKDAAGARVIEA---YLSSKV-- 557
Q IGS+ + F+Q + + S AD + E KD + ++ YL K+
Sbjct: 10 QYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLE 69
Query: 558 SAKQKHRVVL-KLKG-HFGELSVHPSGSFTVER---CFTASSLSLRETIASELSAVRNEL 612
+ R+VL K+ HF E+S++P G +++ C + + + L +L
Sbjct: 70 EVTTEQRIVLTKISSPHFVEISLNPHGCRALQKLIECIKTDEEA--QIVVDSLRPYTVQL 127
Query: 613 SKTKQGPHLIRK 624
SK G H+I+K
Sbjct: 128 SKDLNGNHVIQK 139
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
0.317 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: 19,876,472
Number of Sequences: 62578
Number of extensions: 712026
Number of successful extensions: 2026
Number of sequences better than 100.0: 26
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 1967
Number of HSP's gapped (non-prelim): 75
length of query: 786
length of database: 14,973,337
effective HSP length: 107
effective length of query: 679
effective length of database: 8,277,491
effective search space: 5620416389
effective search space used: 5620416389
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: 55 (25.8 bits)