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= 029806
(187 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a
pdb|3EIQ|D Chain D, Crystal Structure Of Pdcd4-eif4a
Length = 414
Score = 56.6 bits (135), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 38/144 (26%), Positives = 71/144 (49%), Gaps = 33/144 (22%)
Query: 23 RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS 82
R FY+ V+R ++K++TL +L + + ++ ++R ++D + + + D + S
Sbjct: 255 RQFYINVEREEWKLDTLCDLYETLTITQ-----AVIFINTRRKVDWLTEKM-HARDFTVS 308
Query: 83 SLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLS 142
++H D+ + ER +I+ EFR SG S +++ TD LL+
Sbjct: 309 AMHGDMDQKERDVIMREFR-------------SG----------SSRVLITTD----LLA 341
Query: 143 SGESAISARVLINYELPTKKETYI 166
G ++INY+LPT +E YI
Sbjct: 342 RGIDVQQVSLVINYDLPTNRENYI 365
>pdb|2ZU6|A Chain A, Crystal Structure Of The Eif4a-Pdcd4 Complex
pdb|2ZU6|C Chain C, Crystal Structure Of The Eif4a-Pdcd4 Complex
pdb|2ZU6|D Chain D, Crystal Structure Of The Eif4a-Pdcd4 Complex
pdb|2ZU6|F Chain F, Crystal Structure Of The Eif4a-Pdcd4 Complex
Length = 388
Score = 55.8 bits (133), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 38/144 (26%), Positives = 71/144 (49%), Gaps = 33/144 (22%)
Query: 23 RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS 82
R FY+ V+R ++K++TL +L + + ++ ++R ++D + + + D + S
Sbjct: 229 RQFYINVEREEWKLDTLCDLYETLTITQ-----AVIFINTRRKVDWLTEKM-HARDFTVS 282
Query: 83 SLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLS 142
++H D+ + ER +I+ EFR SG S +++ TD LL+
Sbjct: 283 AMHGDMDQKERDVIMREFR-------------SG----------SSRVLITTD----LLA 315
Query: 143 SGESAISARVLINYELPTKKETYI 166
G ++INY+LPT +E YI
Sbjct: 316 RGIDVQQVSLVINYDLPTNRENYI 339
>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 54.7 bits (130), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 36/147 (24%), Positives = 71/147 (48%), Gaps = 33/147 (22%)
Query: 23 RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS 82
+ F+VAV+R ++K +TL +L + + ++ C+++ ++D + + A+ + S
Sbjct: 215 KQFFVAVEREEWKFDTLCDLYDTLTITQ-----AVIFCNTKRKVDWLTEKMRE-ANFTVS 268
Query: 83 SLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLS 142
S+H D+ + ER I++EFR A S +++ TD + +
Sbjct: 269 SMHGDMPQKERESIMKEFRSGA-----------------------SRVLISTD----VWA 301
Query: 143 SGESAISARVLINYELPTKKETYIRRM 169
G ++INY+LP +E YI R+
Sbjct: 302 RGLDVPQVSLIINYDLPNNRELYIHRI 328
>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 54.7 bits (130), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 36/147 (24%), Positives = 71/147 (48%), Gaps = 33/147 (22%)
Query: 23 RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS 82
+ F+VAV+R ++K +TL +L + + ++ C+++ ++D + + A+ + S
Sbjct: 215 KQFFVAVEREEWKFDTLCDLYDTLTITQ-----AVIFCNTKRKVDWLTEKMRE-ANFTVS 268
Query: 83 SLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLS 142
S+H D+ + ER I++EFR A S +++ TD + +
Sbjct: 269 SMHGDMPQKERESIMKEFRSGA-----------------------SRVLISTD----VWA 301
Query: 143 SGESAISARVLINYELPTKKETYIRRM 169
G ++INY+LP +E YI R+
Sbjct: 302 RGLDVPQVSLIINYDLPNNRELYIHRI 328
>pdb|2J0Q|A Chain A, The Crystal Structure Of The Exon Junction Complex At 3.2
A Resolution
pdb|2J0Q|B Chain B, The Crystal Structure Of The Exon Junction Complex At 3.2
A Resolution
pdb|2J0S|A Chain A, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 410
Score = 54.7 bits (130), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 36/147 (24%), Positives = 71/147 (48%), Gaps = 33/147 (22%)
Query: 23 RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS 82
+ F+VAV+R ++K +TL +L + + ++ C+++ ++D + + A+ + S
Sbjct: 251 KQFFVAVEREEWKFDTLCDLYDTLTITQ-----AVIFCNTKRKVDWLTEKMRE-ANFTVS 304
Query: 83 SLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLS 142
S+H D+ + ER I++EFR A S +++ TD + +
Sbjct: 305 SMHGDMPQKERESIMKEFRSGA-----------------------SRVLISTD----VWA 337
Query: 143 SGESAISARVLINYELPTKKETYIRRM 169
G ++INY+LP +E YI R+
Sbjct: 338 RGLDVPQVSLIINYDLPNNRELYIHRI 364
>pdb|2XB2|A Chain A, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
pdb|2XB2|X Chain X, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
Length = 411
Score = 54.7 bits (130), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 36/147 (24%), Positives = 71/147 (48%), Gaps = 33/147 (22%)
Query: 23 RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS 82
+ F+VAV+R ++K +TL +L + + ++ C+++ ++D + + A+ + S
Sbjct: 252 KQFFVAVEREEWKFDTLCDLYDTLTITQ-----AVIFCNTKRKVDWLTEKMRE-ANFTVS 305
Query: 83 SLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLS 142
S+H D+ + ER I++EFR A S +++ TD + +
Sbjct: 306 SMHGDMPQKERESIMKEFRSGA-----------------------SRVLISTD----VWA 338
Query: 143 SGESAISARVLINYELPTKKETYIRRM 169
G ++INY+LP +E YI R+
Sbjct: 339 RGLDVPQVSLIINYDLPNNRELYIHRI 365
>pdb|2HXY|A Chain A, Crystal Structure Of Human Apo-Eif4aiii
pdb|2HXY|B Chain B, Crystal Structure Of Human Apo-Eif4aiii
pdb|2HXY|C Chain C, Crystal Structure Of Human Apo-Eif4aiii
pdb|2HXY|D Chain D, Crystal Structure Of Human Apo-Eif4aiii
Length = 391
Score = 54.7 bits (130), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 36/147 (24%), Positives = 71/147 (48%), Gaps = 33/147 (22%)
Query: 23 RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS 82
+ F+VAV+R ++K +TL +L + + ++ C+++ ++D + + A+ + S
Sbjct: 230 KQFFVAVEREEWKFDTLCDLYDTLTITQ-----AVIFCNTKRKVDWLTEKMRE-ANFTVS 283
Query: 83 SLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLS 142
S+H D+ + ER I++EFR A S +++ TD + +
Sbjct: 284 SMHGDMPQKERESIMKEFRSGA-----------------------SRVLISTD----VWA 316
Query: 143 SGESAISARVLINYELPTKKETYIRRM 169
G ++INY+LP +E YI R+
Sbjct: 317 RGLDVPQVSLIINYDLPNNRELYIHRI 343
>pdb|2HYI|C Chain C, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2HYI|I Chain I, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|3EX7|C Chain C, The Crystal Structure Of Ejc In Its Transition State
pdb|3EX7|H Chain H, The Crystal Structure Of Ejc In Its Transition State
Length = 413
Score = 54.3 bits (129), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 36/147 (24%), Positives = 71/147 (48%), Gaps = 33/147 (22%)
Query: 23 RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS 82
+ F+VAV+R ++K +TL +L + + ++ C+++ ++D + + A+ + S
Sbjct: 252 KQFFVAVEREEWKFDTLCDLYDTLTITQ-----AVIFCNTKRKVDWLTEKMRE-ANFTVS 305
Query: 83 SLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLS 142
S+H D+ + ER I++EFR A S +++ TD + +
Sbjct: 306 SMHGDMPQKERESIMKEFRSGA-----------------------SRVLISTD----VWA 338
Query: 143 SGESAISARVLINYELPTKKETYIRRM 169
G ++INY+LP +E YI R+
Sbjct: 339 RGLDVPQVSLIINYDLPNNRELYIHRI 365
>pdb|2VSO|A Chain A, Crystal Structure Of A Translation Initiation Complex
pdb|2VSO|B Chain B, Crystal Structure Of A Translation Initiation Complex
pdb|2VSX|A Chain A, Crystal Structure Of A Translation Initiation Complex
pdb|2VSX|B Chain B, Crystal Structure Of A Translation Initiation Complex
Length = 395
Score = 52.0 bits (123), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 38/144 (26%), Positives = 69/144 (47%), Gaps = 33/144 (22%)
Query: 23 RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS 82
+ FYV V+ ++K E L +L + + ++ C++R +++ + + + N + S
Sbjct: 235 KQFYVNVEEEEYKYECLTDLYDSISVTQ-----AVIFCNTRRKVEELTTKLRN-DKFTVS 288
Query: 83 SLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLS 142
+++SDL + ER I++EFR SG S +++ TD LL+
Sbjct: 289 AIYSDLPQQERDTIMKEFR-------------SG----------SSRILISTD----LLA 321
Query: 143 SGESAISARVLINYELPTKKETYI 166
G ++INY+LP KE YI
Sbjct: 322 RGIDVQQVSLVINYDLPANKENYI 345
>pdb|1FUK|A Chain A, Crystal Structure Of The Carboxy Terminal Domain Of Yeast
Eif4a
Length = 165
Score = 51.6 bits (122), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 38/144 (26%), Positives = 69/144 (47%), Gaps = 33/144 (22%)
Query: 23 RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS 82
+ FYV V+ ++K E L +L + + ++ C++R +++ + + + N + S
Sbjct: 5 KQFYVNVEEEEYKYECLTDLYDSISVTQ-----AVIFCNTRRKVEELTTKLRN-DKFTVS 58
Query: 83 SLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLS 142
+++SDL + ER I++EFR SG S +++ TD LL+
Sbjct: 59 AIYSDLPQQERDTIMKEFR-------------SG----------SSRILISTD----LLA 91
Query: 143 SGESAISARVLINYELPTKKETYI 166
G ++INY+LP KE YI
Sbjct: 92 RGIDVQQVSLVINYDLPANKENYI 115
>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a
pdb|1FUU|B Chain B, Yeast Initiation Factor 4a
Length = 394
Score = 50.8 bits (120), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 38/144 (26%), Positives = 68/144 (47%), Gaps = 33/144 (22%)
Query: 23 RHFYVAVDRLQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFS 82
+ FYV V+ ++K E L +L + + ++ C++R +++ + + + N + S
Sbjct: 234 KQFYVNVEEEEYKYECLTDLYDSISVTQ-----AVIFCNTRRKVEELTTKLRN-DKFTVS 287
Query: 83 SLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLS 142
+++SDL + ER I +EFR SG S +++ TD LL+
Sbjct: 288 AIYSDLPQQERDTIXKEFR-------------SG----------SSRILISTD----LLA 320
Query: 143 SGESAISARVLINYELPTKKETYI 166
G ++INY+LP KE YI
Sbjct: 321 RGIDVQQVSLVINYDLPANKENYI 344
>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p
Length = 400
Score = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 27/113 (23%), Positives = 48/113 (42%), Gaps = 28/113 (24%)
Query: 57 IVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSG 116
I+ C+S + ++ + +++L + S H+ + + ER + EFR
Sbjct: 262 IIFCNSTNRVELLAKKITDLGYSCYYS-HARMKQQERNKVFHEFRQ-------------- 306
Query: 117 DESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRM 169
GK V T C LL+ G + V+IN++ P ETY+ R+
Sbjct: 307 -----GK--------VRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRI 346
>pdb|1HV8|A Chain A, Crystal Structure Of A Dead Box Protein From The
Hyperthermophile Methanococcus Jannaschii
pdb|1HV8|B Chain B, Crystal Structure Of A Dead Box Protein From The
Hyperthermophile Methanococcus Jannaschii
Length = 367
Score = 33.5 bits (75), Expect = 0.078, Method: Compositional matrix adjust.
Identities = 28/125 (22%), Positives = 48/125 (38%), Gaps = 33/125 (26%)
Query: 56 MIVCCSSRDELDAVCSAVSNLADISF--SSLHSDLAETERTLILEEFRHTAMKWNQKVTE 113
++ C + RD S L DI F ++H DL++++R ++ F+
Sbjct: 242 LVFCKTKRD----TKELASXLRDIGFKAGAIHGDLSQSQREKVIRLFK------------ 285
Query: 114 QSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCL 173
+ K +++ TD + S G +INY LP E+Y R+
Sbjct: 286 -----------QKKIRILIATD----VXSRGIDVNDLNCVINYHLPQNPESYXHRIGRTG 330
Query: 174 AAGTS 178
AG
Sbjct: 331 RAGKK 335
>pdb|2HJV|A Chain A, Structure Of The Second Domain (Residues 207-368) Of The
Bacillus Subtilis Yxin Protein
pdb|2HJV|B Chain B, Structure Of The Second Domain (Residues 207-368) Of The
Bacillus Subtilis Yxin Protein
Length = 163
Score = 32.7 bits (73), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 28/147 (19%), Positives = 58/147 (39%), Gaps = 29/147 (19%)
Query: 32 LQFKMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAET 91
+Q + E LL V+ P I+ C +++ ++ + + +L +H + +
Sbjct: 15 IQVREENKFSLLKDVLMTENPD-SCIIFCRTKEHVNQLTDELDDLG-YPCDKIHGGMIQE 72
Query: 92 ERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISAR 151
+R ++ EF+ ++ +V TD + G +
Sbjct: 73 DRFDVMNEFKRGEYRY-----------------------LVATDVA----ARGIDIENIS 105
Query: 152 VLINYELPTKKETYIRRMTTCLAAGTS 178
++INY+LP +KE+Y+ R AG
Sbjct: 106 LVINYDLPLEKESYVHRTGRTGRAGNK 132
>pdb|2P6N|A Chain A, Human Dead-box Rna Helicase Ddx41, Helicase Domain
pdb|2P6N|B Chain B, Human Dead-box Rna Helicase Ddx41, Helicase Domain
Length = 191
Score = 32.0 bits (71), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 26/124 (20%), Positives = 51/124 (41%), Gaps = 28/124 (22%)
Query: 55 PMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQ 114
P+++ + ++DA+ + L + ++H + ERT +E FR
Sbjct: 56 PVLIFAEKKADVDAIHEYLL-LKGVEAVAIHGGKDQEERTKAIEAFR------------- 101
Query: 115 SGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRMTTCLA 174
E K ++V TD S G + + +INY++P + E Y+ R+
Sbjct: 102 ----------EGKKDVLVATDVA----SKGLDFPAIQHVINYDMPEEIENYVHRIGRTGC 147
Query: 175 AGTS 178
+G +
Sbjct: 148 SGNT 151
>pdb|2WAX|A Chain A, Structure Of The Human Ddx6 C-Terminal Domain In Complex
With An Edc3-Fdf Peptide
pdb|2WAX|C Chain C, Structure Of The Human Ddx6 C-Terminal Domain In Complex
With An Edc3-Fdf Peptide
pdb|2WAY|A Chain A, Structure Of The Human Ddx6 C-Terminal Domain In Complex
With An Edc3-Fdf Peptide
pdb|2WAY|C Chain C, Structure Of The Human Ddx6 C-Terminal Domain In Complex
With An Edc3-Fdf Peptide
Length = 193
Score = 30.4 bits (67), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 21/113 (18%), Positives = 42/113 (37%), Gaps = 28/113 (24%)
Query: 57 IVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSG 116
I+ C+S ++ + +S L F +H+ + + R + +FR+ +
Sbjct: 48 IIFCNSSQRVELLAKKISQLGYSCFY-IHAKMRQEHRNRVFHDFRNGLCR---------- 96
Query: 117 DESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLINYELPTKKETYIRRM 169
C L + G + V+IN++ P ETY+ R+
Sbjct: 97 -----------------NLVCTDLFTRGIDIQAVNVVINFDFPKLAETYLHRI 132
>pdb|2DB3|A Chain A, Structural Basis For Rna Unwinding By The Dead-Box Protein
Drosophila Vasa
pdb|2DB3|B Chain B, Structural Basis For Rna Unwinding By The Dead-Box Protein
Drosophila Vasa
pdb|2DB3|C Chain C, Structural Basis For Rna Unwinding By The Dead-Box Protein
Drosophila Vasa
pdb|2DB3|D Chain D, Structural Basis For Rna Unwinding By The Dead-Box Protein
Drosophila Vasa
Length = 434
Score = 30.4 bits (67), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 33/152 (21%), Positives = 61/152 (40%), Gaps = 39/152 (25%)
Query: 35 KMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERT 94
K L+E+L G IV ++ D + S +S + +S+H D +++R
Sbjct: 288 KRSKLIEILSEQADG------TIVFVETKRGADFLASFLSE-KEFPTTSIHGDRLQSQRE 340
Query: 95 LILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLI 154
L +F++ +MK +++ T S G + + +I
Sbjct: 341 QALRDFKNGSMK-----------------------VLIATSVA----SRGLDIKNIKHVI 373
Query: 155 NYELPTKKETYIRRMTTCLAAG-----TSFSD 181
NY++P+K + Y+ R+ G TSF D
Sbjct: 374 NYDMPSKIDDYVHRIGRTGRVGNNGRATSFFD 405
>pdb|3EAQ|A Chain A, Novel Dimerization Motif In The Dead Box Rna Helicase Hera
Form 2, Complete Dimer, Symmetric
pdb|3EAQ|B Chain B, Novel Dimerization Motif In The Dead Box Rna Helicase Hera
Form 2, Complete Dimer, Symmetric
pdb|3EAR|A Chain A, Novel Dimerization Motif In The Dead Box Rna Helicase
Hera: Form 1, Partial Dimer
pdb|3EAR|B Chain B, Novel Dimerization Motif In The Dead Box Rna Helicase
Hera: Form 1, Partial Dimer
pdb|3EAS|A Chain A, Novel Dimerization Motif In The Dead Box Rna Helicase
Hera: Form 1, Complete Dimer, Asymmetric
pdb|3EAS|B Chain B, Novel Dimerization Motif In The Dead Box Rna Helicase
Hera: Form 1, Complete Dimer, Asymmetric
Length = 212
Score = 28.9 bits (63), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 26/131 (19%), Positives = 52/131 (39%), Gaps = 33/131 (25%)
Query: 35 KMETLVELLHLVVAGRRPGLPMIVCCSSRDELDAVCSAVSNLADISFSSLHSDLAETERT 94
++E L +LL++ R +V ++ E + + + L + +LH DL++ ER
Sbjct: 18 RLEVLSDLLYVASPDR-----AMVFTRTKAETEEIAQGLLRLGHPA-QALHGDLSQGERE 71
Query: 95 LILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLLSSGESAISARVLI 154
+L FR ++ ++V TD + G +++
Sbjct: 72 RVLGAFRQGEVR-----------------------VLVATDVA----ARGLDIPQVDLVV 104
Query: 155 NYELPTKKETY 165
+Y LP + E Y
Sbjct: 105 HYRLPDRAEAY 115
>pdb|3PEW|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3
pdb|3RRM|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Nup159, Gle1 H337r, Ip6
And Adp
pdb|3RRN|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Gle1 H337r And Ip6
Length = 395
Score = 28.5 bits (62), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 23/94 (24%), Positives = 40/94 (42%), Gaps = 33/94 (35%)
Query: 82 SSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLL 141
S LH DL ER ++++FR E +S +++ T+ +L
Sbjct: 271 SILHGDLQTQERDRLIDDFR-----------------------EGRSKVLITTN----VL 303
Query: 142 SSGESAISARVLINYELPT------KKETYIRRM 169
+ G + +++NY+LPT TYI R+
Sbjct: 304 ARGIDIPTVSMVVNYDLPTLANGQADPATYIHRI 337
>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3
Length = 395
Score = 28.5 bits (62), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 23/94 (24%), Positives = 40/94 (42%), Gaps = 33/94 (35%)
Query: 82 SSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLL 141
S LH DL ER ++++FR E +S +++ T+ +L
Sbjct: 271 SILHGDLQTQERDRLIDDFR-----------------------EGRSKVLITTN----VL 303
Query: 142 SSGESAISARVLINYELPT------KKETYIRRM 169
+ G + +++NY+LPT TYI R+
Sbjct: 304 ARGIDIPTVSMVVNYDLPTLANGQADPATYIHRI 337
>pdb|2KBF|A Chain A, Solution Structure Of Carboxyl-Terminal Domain Of Dbp5p
Length = 187
Score = 27.7 bits (60), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 23/94 (24%), Positives = 40/94 (42%), Gaps = 33/94 (35%)
Query: 82 SSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLL 141
S LH DL ER ++++FR E +S +++ T+ +L
Sbjct: 63 SILHGDLQTQERDRLIDDFR-----------------------EGRSKVLITTN----VL 95
Query: 142 SSGESAISARVLINYELPTKKE------TYIRRM 169
+ G + +++NY+LPT TYI R+
Sbjct: 96 ARGIDIPTVSMVVNYDLPTLANGQADPATYIHRI 129
>pdb|3GFP|A Chain A, Structure Of The C-Terminal Domain Of The Dead-Box Protein
Dbp5
Length = 189
Score = 27.3 bits (59), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 23/94 (24%), Positives = 39/94 (41%), Gaps = 33/94 (35%)
Query: 82 SSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLL 141
S LH DL ER ++++FR E +S +++ T+ +L
Sbjct: 65 SILHGDLQTQERDRLIDDFR-----------------------EGRSKVLITTN----VL 97
Query: 142 SSGESAISARVLINYELPTKKE------TYIRRM 169
+ G + ++NY+LPT TYI R+
Sbjct: 98 ARGIDIPTVSXVVNYDLPTLANGQADPATYIHRI 131
>pdb|3PEU|A Chain A, S. Cerevisiae Dbp5 L327v C-Terminal Domain Bound To Gle1
H337r And Ip6
pdb|3PEV|A Chain A, S. Cerevisiae Dbp5 L327v C-Terminal Domain Bound To Gle1
And Ip6
Length = 188
Score = 27.3 bits (59), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 23/94 (24%), Positives = 39/94 (41%), Gaps = 33/94 (35%)
Query: 82 SSLHSDLAETERTLILEEFRHTAMKWNQKVTEQSGDESETGKDEHKSHMIVVTDACLPLL 141
S LH DL ER ++++FR E +S +++ T+ +L
Sbjct: 64 SILHGDLQTQERDRLIDDFR-----------------------EGRSKVLITTN----VL 96
Query: 142 SSGESAISARVLINYELPTKKE------TYIRRM 169
+ G + ++NY+LPT TYI R+
Sbjct: 97 ARGIDIPTVSXVVNYDLPTLANGQADPATYIHRI 130
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
0.320 0.132 0.386
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,032,456
Number of Sequences: 62578
Number of extensions: 175937
Number of successful extensions: 450
Number of sequences better than 100.0: 25
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 416
Number of HSP's gapped (non-prelim): 25
length of query: 187
length of database: 14,973,337
effective HSP length: 93
effective length of query: 94
effective length of database: 9,153,583
effective search space: 860436802
effective search space used: 860436802
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 bits)