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= psy18035
(104 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3FE2|A Chain A, Human Dead-Box Rna Helicase Ddx5 (P68), Conserved Domain I
In Complex With Adp
pdb|3FE2|B Chain B, Human Dead-Box Rna Helicase Ddx5 (P68), Conserved Domain I
In Complex With Adp
Length = 242
Score = 59.7 bits (143), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 28/81 (34%), Positives = 43/81 (53%)
Query: 14 IVQQTFKFVKELGKFTKLQSTCLLGGDSMDNQFARLHASPDIVVATPGRFLHIVVEMELK 73
+ QQ + E + +L+STC+ GG Q L +I +ATPGR + + +
Sbjct: 114 LAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLECGKTN 173
Query: 74 LSSIQYVVFDEADRLFEMGFD 94
L Y+V DEADR+ +MGF+
Sbjct: 174 LRRTTYLVLDEADRMLDMGFE 194
>pdb|4A4D|A Chain A, Crystal Structure Of The N-Terminal Domain Of The Human
Dead-Box Rna Helicase Ddx5 (P68)
Length = 253
Score = 59.3 bits (142), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 28/81 (34%), Positives = 43/81 (53%)
Query: 14 IVQQTFKFVKELGKFTKLQSTCLLGGDSMDNQFARLHASPDIVVATPGRFLHIVVEMELK 73
+ QQ + E + +L+STC+ GG Q L +I +ATPGR + + +
Sbjct: 128 LAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLECGKTN 187
Query: 74 LSSIQYVVFDEADRLFEMGFD 94
L Y+V DEADR+ +MGF+
Sbjct: 188 LRRTTYLVLDEADRMLDMGFE 208
>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna
Helicase From Sulfolobus Tokodaii
Length = 337
Score = 57.0 bits (136), Expect = 3e-09, Method: Composition-based stats.
Identities = 29/80 (36%), Positives = 47/80 (58%), Gaps = 1/80 (1%)
Query: 14 IVQQTFKFVKELGKFTKLQSTCLLGGDSMDNQFARLHASPDIVVATPGRFLHIVVEMELK 73
+ +Q ++++G++ + + GG Q R+ + DIVVATPGR L + + +
Sbjct: 68 LTRQVASHIRDIGRYMDTKVAEVYGGMPYKAQINRVR-NADIVVATPGRLLDLWSKGVID 126
Query: 74 LSSIQYVVFDEADRLFEMGF 93
LSS + V+ DEAD +FEMGF
Sbjct: 127 LSSFEIVIIDEADLMFEMGF 146
>pdb|3IUY|A Chain A, Crystal Structure Of Ddx53 Dead-Box Domain
pdb|3IUY|B Chain B, Crystal Structure Of Ddx53 Dead-Box Domain
Length = 228
Score = 56.2 bits (134), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 24/67 (35%), Positives = 40/67 (59%)
Query: 28 FTKLQSTCLLGGDSMDNQFARLHASPDIVVATPGRFLHIVVEMELKLSSIQYVVFDEADR 87
+ L+S C+ GG + + Q + DI++ATPGR + + + L SI Y+V DEAD+
Sbjct: 119 YKGLKSICIYGGRNRNGQIEDISKGVDIIIATPGRLNDLQMNNSVNLRSITYLVIDEADK 178
Query: 88 LFEMGFD 94
+ +M F+
Sbjct: 179 MLDMEFE 185
>pdb|3BER|A Chain A, Human Dead-Box Rna-Helicase Ddx47, Conserved Domain I In
Complex With Amp
Length = 249
Score = 55.5 bits (132), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 30/74 (40%), Positives = 43/74 (58%), Gaps = 3/74 (4%)
Query: 25 LGKFTKLQSTCLLGG-DSMDNQFARLHASPDIVVATPGRFL-HIVVEMELKLSSIQYVVF 82
LG +QS ++GG DSM A L P I++ATPGR + H+ L +++Y+V
Sbjct: 134 LGSSIGVQSAVIVGGIDSMSQSLA-LAKKPHIIIATPGRLIDHLENTKGFNLRALKYLVM 192
Query: 83 DEADRLFEMGFDVE 96
DEADR+ M F+ E
Sbjct: 193 DEADRILNMDFETE 206
>pdb|1WRB|A Chain A, Crystal Structure Of The N-Terminal Reca-Like Domain Of
Djvlgb, A Pranarian Vasa-Like Rna Helicase
pdb|1WRB|B Chain B, Crystal Structure Of The N-Terminal Reca-Like Domain Of
Djvlgb, A Pranarian Vasa-Like Rna Helicase
Length = 253
Score = 55.1 bits (131), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 29/89 (32%), Positives = 48/89 (53%), Gaps = 3/89 (3%)
Query: 9 LISFPIVQQTFKFVKELGKF---TKLQSTCLLGGDSMDNQFARLHASPDIVVATPGRFLH 65
LI P + + + E KF T L+S + GG +Q + ++VATPGR +
Sbjct: 104 LILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVD 163
Query: 66 IVVEMELKLSSIQYVVFDEADRLFEMGFD 94
+ + ++ L +Y+V DEADR+ +MGF+
Sbjct: 164 FIEKNKISLEFCKYIVLDEADRMLDMGFE 192
>pdb|2PL3|A Chain A, Human Dead-Box Rna Helicase Ddx10, Dead Domain In Complex
With Adp
Length = 236
Score = 52.8 bits (125), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 49/78 (62%), Gaps = 2/78 (2%)
Query: 17 QTFKFVKELGKFTKLQSTCLLGGDSMDNQFARLHASPDIVVATPGRFL-HIVVEMELKLS 75
QTF+ ++++GK + ++GG + ++ R++ + +I+V TPGR L H+ + +
Sbjct: 112 QTFEVLRKVGKNHDFSAGLIIGGKDLKHEAERIN-NINILVCTPGRLLQHMDETVSFHAT 170
Query: 76 SIQYVVFDEADRLFEMGF 93
+Q +V DEADR+ +MGF
Sbjct: 171 DLQMLVLDEADRILDMGF 188
>pdb|1Q0U|A Chain A, Crystal Structure Of The Bstdead N-Terminal Domain
pdb|1Q0U|B Chain B, Crystal Structure Of The Bstdead N-Terminal Domain
Length = 219
Score = 52.8 bits (125), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 32/103 (31%), Positives = 48/103 (46%), Gaps = 9/103 (8%)
Query: 4 ANINYLISFP-------IVQQTFKFVKELGKFTKLQSTCLLGGDSMDNQFARLHASPDIV 56
A + +I+ P I +T K K K + + CL+GG +L+ P IV
Sbjct: 71 AEVQAVITAPTRELATQIYHETLKITKFCPKDRXIVARCLIGGTDKQKALEKLNVQPHIV 130
Query: 57 VATPGRFLHIVVEMELKLSSIQYVVFDEADRLFEMGF--DVEQ 97
+ TPGR + E L + + +V DEAD + GF DV+Q
Sbjct: 131 IGTPGRINDFIREQALDVHTAHILVVDEADLXLDXGFITDVDQ 173
>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x
Length = 417
Score = 50.1 bits (118), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 26/89 (29%), Positives = 48/89 (53%), Gaps = 3/89 (3%)
Query: 9 LISFPIVQQTFKFVKELGKFT---KLQSTCLLGGDSMDNQFARLHASPDIVVATPGRFLH 65
L+ P + + +E KF+ +++ + GG + Q L ++VATPGR +
Sbjct: 105 LVLAPTRELAVQIYEEARKFSYRSRVRPCVVYGGADIGQQIRDLERGCHLLVATPGRLVD 164
Query: 66 IVVEMELKLSSIQYVVFDEADRLFEMGFD 94
++ ++ L +Y+V DEADR+ +MGF+
Sbjct: 165 MMERGKIGLDFCKYLVLDEADRMLDMGFE 193
>pdb|3BOR|A Chain A, Crystal Structure Of The Deadc Domain Of Human Translation
Initiation Factor 4a-2
Length = 237
Score = 49.3 bits (116), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 27/81 (33%), Positives = 40/81 (49%), Gaps = 1/81 (1%)
Query: 14 IVQQTFKFVKELGKFTKLQSTCLLGGDSMDNQFARLHA-SPDIVVATPGRFLHIVVEMEL 72
+ QQ K + LG + +GG ++ N+ +L A +P IVV TPGR ++ L
Sbjct: 110 LAQQIQKVILALGDYMGATCHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYL 169
Query: 73 KLSSIQYVVFDEADRLFEMGF 93
I+ V DEAD + GF
Sbjct: 170 SPKWIKMFVLDEADEMLSRGF 190
>pdb|3LY5|A Chain A, Ddx18 Dead-Domain
pdb|3LY5|B Chain B, Ddx18 Dead-Domain
Length = 262
Score = 48.5 bits (114), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 28/84 (33%), Positives = 45/84 (53%), Gaps = 1/84 (1%)
Query: 14 IVQQTFKFVKELGKFTKLQSTCLLGGDSMDNQFARLHASPDIVVATPGRFL-HIVVEMEL 72
+ QTF +KEL ++GG + + +L +I+VATPGR L H+
Sbjct: 138 LAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQKLGNGINIIVATPGRLLDHMQNTPGF 197
Query: 73 KLSSIQYVVFDEADRLFEMGFDVE 96
++Q +V DEADR+ ++GF+ E
Sbjct: 198 MYKNLQCLVIDEADRILDVGFEEE 221
>pdb|3MWJ|A Chain A, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Apo Form
pdb|3MWJ|B Chain B, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Apo Form
pdb|3MWK|A Chain A, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Complex
With 8-Oxo- Amp
pdb|3MWK|B Chain B, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Complex
With 8-Oxo- Amp
pdb|3MWL|A Chain A, Q28e Mutant Of Hera N-Terminal Reca-Like Domain In Complex
With 8- Oxoadenosine
pdb|3MWL|B Chain B, Q28e Mutant Of Hera N-Terminal Reca-Like Domain In Complex
With 8- Oxoadenosine
pdb|3NBF|A Chain A, Q28e Mutant Of Hera Helicase N-Terminal Domain Bound To
8-Oxo-Adp
pdb|3NBF|B Chain B, Q28e Mutant Of Hera Helicase N-Terminal Domain Bound To
8-Oxo-Adp
pdb|3NBF|C Chain C, Q28e Mutant Of Hera Helicase N-Terminal Domain Bound To
8-Oxo-Adp
pdb|3NBF|D Chain D, Q28e Mutant Of Hera Helicase N-Terminal Domain Bound To
8-Oxo-Adp
pdb|3NEJ|A Chain A, Q28e Mutant Of Hera Rna Helicase N-Terminal Domain -
Perfectly Twinned Hexagonal Form
pdb|3NEJ|B Chain B, Q28e Mutant Of Hera Rna Helicase N-Terminal Domain -
Perfectly Twinned Hexagonal Form
Length = 207
Score = 48.5 bits (114), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 30/92 (32%), Positives = 43/92 (46%), Gaps = 1/92 (1%)
Query: 9 LISFPIVQQTFKFVKELGKFTK-LQSTCLLGGDSMDNQFARLHASPDIVVATPGRFLHIV 67
L+ P + + EL L+ + GG Q L D VVATPGR L +
Sbjct: 76 LVLTPTRELALQVASELTAVAPHLKVVAVYGGTGYGKQKEALLRGADAVVATPGRALDYL 135
Query: 68 VEMELKLSSIQYVVFDEADRLFEMGFDVEQQS 99
+ L LS ++ V DEAD + MGF+ E ++
Sbjct: 136 RQGVLDLSRVEVAVLDEADEMLSMGFEEEVEA 167
>pdb|2GXQ|A Chain A, Hera N-Terminal Domain In Complex With Amp, Crystal Form 1
pdb|2GXS|A Chain A, Hera N-Terminal Domain In Complex With Amp, Crystal Form 2
pdb|2GXS|B Chain B, Hera N-Terminal Domain In Complex With Amp, Crystal Form 2
pdb|2GXU|A Chain A, Hera N-Terminal Domain In Complex With Orthophosphate,
Crystal Form 1
Length = 207
Score = 48.5 bits (114), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 30/92 (32%), Positives = 43/92 (46%), Gaps = 1/92 (1%)
Query: 9 LISFPIVQQTFKFVKELGKFTK-LQSTCLLGGDSMDNQFARLHASPDIVVATPGRFLHIV 67
L+ P + + EL L+ + GG Q L D VVATPGR L +
Sbjct: 76 LVLTPTRELALQVASELTAVAPHLKVVAVYGGTGYGKQKEALLRGADAVVATPGRALDYL 135
Query: 68 VEMELKLSSIQYVVFDEADRLFEMGFDVEQQS 99
+ L LS ++ V DEAD + MGF+ E ++
Sbjct: 136 RQGVLDLSRVEVAVLDEADEMLSMGFEEEVEA 167
>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 48.5 bits (114), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 38/77 (49%)
Query: 17 QTFKFVKELGKFTKLQSTCLLGGDSMDNQFARLHASPDIVVATPGRFLHIVVEMELKLSS 76
Q K + LG + +QS +GG ++ +L +V TPGR ++ L+ +
Sbjct: 84 QVQKGLLALGDYMNVQSHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRA 143
Query: 77 IQYVVFDEADRLFEMGF 93
I+ +V DEAD + GF
Sbjct: 144 IKMLVLDEADEMLNKGF 160
>pdb|1VEC|A Chain A, Crystal Structure Of The N-Terminal Domain Of RckP54, A
Human Dead-Box Protein
pdb|1VEC|B Chain B, Crystal Structure Of The N-Terminal Domain Of RckP54, A
Human Dead-Box Protein
Length = 206
Score = 47.0 bits (110), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 24/84 (28%), Positives = 44/84 (52%), Gaps = 3/84 (3%)
Query: 10 ISFPIVQQTFKFVKELGKFTKLQSTCLLGGDSMDNQFARLHASPDIVVATPGRFLHIVVE 69
++ + Q + K +G + +T GG ++ + RL + +V+ATPGR L ++ +
Sbjct: 83 LALQVSQICIQVSKHMGGAKVMATT---GGTNLRDDIMRLDDTVHVVIATPGRILDLIKK 139
Query: 70 MELKLSSIQYVVFDEADRLFEMGF 93
K+ +Q +V DEAD+L F
Sbjct: 140 GVAKVDHVQMIVLDEADKLLSQDF 163
>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p
Length = 400
Score = 46.6 bits (109), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 28/91 (30%), Positives = 42/91 (46%), Gaps = 3/91 (3%)
Query: 6 INYLISFP---IVQQTFKFVKELGKFTKLQSTCLLGGDSMDNQFARLHASPDIVVATPGR 62
I LI P + QT + V+ LGK + GG ++ + RL+ + I+V TPGR
Sbjct: 90 IQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLNETVHILVGTPGR 149
Query: 63 FLHIVVEMELKLSSIQYVVFDEADRLFEMGF 93
L + LS + DEAD++ F
Sbjct: 150 VLDLASRKVADLSDCSLFIMDEADKMLSRDF 180
>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 46.6 bits (109), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 37/77 (48%)
Query: 17 QTFKFVKELGKFTKLQSTCLLGGDSMDNQFARLHASPDIVVATPGRFLHIVVEMELKLSS 76
Q K + LG + +Q +GG ++ +L +V TPGR ++ L+ +
Sbjct: 84 QVQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRA 143
Query: 77 IQYVVFDEADRLFEMGF 93
I+ +V DEAD + GF
Sbjct: 144 IKMLVLDEADEMLNKGF 160
>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 = 46.2 bits (108), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 34/69 (49%)
Query: 25 LGKFTKLQSTCLLGGDSMDNQFARLHASPDIVVATPGRFLHIVVEMELKLSSIQYVVFDE 84
LG + +Q +GG ++ +L +V TPGR ++ L+ +I+ +V DE
Sbjct: 128 LGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDE 187
Query: 85 ADRLFEMGF 93
AD + GF
Sbjct: 188 ADEMLNKGF 196
>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 = 46.2 bits (108), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 34/69 (49%)
Query: 25 LGKFTKLQSTCLLGGDSMDNQFARLHASPDIVVATPGRFLHIVVEMELKLSSIQYVVFDE 84
LG + +Q +GG ++ +L +V TPGR ++ L+ +I+ +V DE
Sbjct: 129 LGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDE 188
Query: 85 ADRLFEMGF 93
AD + GF
Sbjct: 189 ADEMLNKGF 197
>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 = 46.2 bits (108), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 34/69 (49%)
Query: 25 LGKFTKLQSTCLLGGDSMDNQFARLHASPDIVVATPGRFLHIVVEMELKLSSIQYVVFDE 84
LG + +Q +GG ++ +L +V TPGR ++ L+ +I+ +V DE
Sbjct: 107 LGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDE 166
Query: 85 ADRLFEMGF 93
AD + GF
Sbjct: 167 ADEMLNKGF 175
>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 = 46.2 bits (108), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 34/69 (49%)
Query: 25 LGKFTKLQSTCLLGGDSMDNQFARLHASPDIVVATPGRFLHIVVEMELKLSSIQYVVFDE 84
LG + +Q +GG ++ +L +V TPGR ++ L+ +I+ +V DE
Sbjct: 129 LGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDE 188
Query: 85 ADRLFEMGF 93
AD + GF
Sbjct: 189 ADEMLNKGF 197
>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 = 45.8 bits (107), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 39/77 (50%)
Query: 17 QTFKFVKELGKFTKLQSTCLLGGDSMDNQFARLHASPDIVVATPGRFLHIVVEMELKLSS 76
Q F ++ + L+ + GG S +Q + +V+ATPGR L V +
Sbjct: 144 QIFNEARKFAFESYLKIGIVYGGTSFRHQNECITRGCHVVIATPGRLLDFVDRTFITFED 203
Query: 77 IQYVVFDEADRLFEMGF 93
++VV DEADR+ +MGF
Sbjct: 204 TRFVVLDEADRMLDMGF 220
>pdb|3I5X|A Chain A, Structure Of Mss116p Bound To Ssrna And Amp-Pnp
pdb|3I5Y|A Chain A, Structure Of Mss116p Bound To Ssrna Containing A Single
5-Bru And Amp- Pnp
pdb|3I61|A Chain A, Structure Of Mss116p Bound To Ssrna And Adp-beryllium
Fluoride
pdb|3I62|A Chain A, Structure Of Mss116p Bound To Ssrna And Adp-aluminum
Fluoride
Length = 563
Score = 44.7 bits (104), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 36/68 (52%), Gaps = 2/68 (2%)
Query: 28 FTKLQSTCLLGGDSMDNQFARLHA-SPDIVVATPGRFLHIVVEMELKLSS-IQYVVFDEA 85
K L+GG +++ P+IV+ATPGR + ++ + K + Y V DEA
Sbjct: 176 LKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEA 235
Query: 86 DRLFEMGF 93
DRL E+GF
Sbjct: 236 DRLLEIGF 243
>pdb|3SQX|A Chain A, Structure Of Mss116p (Nte And C-Tail Double Deletion)
Bound To Ssrna And Amp-Pnp
Length = 512
Score = 44.7 bits (104), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 36/68 (52%), Gaps = 2/68 (2%)
Query: 28 FTKLQSTCLLGGDSMDNQFARLHA-SPDIVVATPGRFLHIVVEMELKLSS-IQYVVFDEA 85
K L+GG +++ P+IV+ATPGR + ++ + K + Y V DEA
Sbjct: 125 LKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEA 184
Query: 86 DRLFEMGF 93
DRL E+GF
Sbjct: 185 DRLLEIGF 192
>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 = 44.7 bits (104), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 43/80 (53%), Gaps = 4/80 (5%)
Query: 11 SFPIVQQTFKFVKELGKFTKLQSTCLLGGDSMDNQFARLHASPDIVVATPGRFLHIVVEM 70
S + +QT + V+E+GKFTK+ S ++ N+ + ++V TPG L ++
Sbjct: 84 SRELARQTLEVVQEMGKFTKITSQLIVPDSFEKNK----QINAQVIVGTPGTVLDLMRRK 139
Query: 71 ELKLSSIQYVVFDEADRLFE 90
++L I+ V DEAD + +
Sbjct: 140 LMQLQKIKIFVLDEADNMLD 159
>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3
Length = 395
Score = 44.7 bits (104), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 43/80 (53%), Gaps = 4/80 (5%)
Query: 11 SFPIVQQTFKFVKELGKFTKLQSTCLLGGDSMDNQFARLHASPDIVVATPGRFLHIVVEM 70
S + +QT + V+E+GKFTK+ S ++ N+ + ++V TPG L ++
Sbjct: 84 SRELARQTLEVVQEMGKFTKITSQLIVPDSFEKNK----QINAQVIVGTPGTVLDLMRRK 139
Query: 71 ELKLSSIQYVVFDEADRLFE 90
++L I+ V DEAD + +
Sbjct: 140 LMQLQKIKIFVLDEADNMLD 159
>pdb|2KBE|A Chain A, Solution Structure Of Amino-Terminal Domain Of Dbp5p
Length = 226
Score = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 42/77 (54%), Gaps = 4/77 (5%)
Query: 14 IVQQTFKFVKELGKFTKLQSTCLLGGDSMDNQFARLHASPDIVVATPGRFLHIVVEMELK 73
+ +QT + V+E+GKFTK+ S ++ N+ + ++V TPG L ++ ++
Sbjct: 104 LARQTLEVVQEMGKFTKITSQLIVPDSFEKNK----QINAQVIVGTPGTVLDLMRRKLMQ 159
Query: 74 LSSIQYVVFDEADRLFE 90
L I+ V DEAD + +
Sbjct: 160 LQKIKIFVLDEADNMLD 176
>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a
pdb|3EIQ|D Chain D, Crystal Structure Of Pdcd4-eif4a
Length = 414
Score = 43.9 bits (102), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 38/81 (46%), Gaps = 1/81 (1%)
Query: 14 IVQQTFKFVKELGKFTKLQSTCLLGGDSMDNQFARLH-ASPDIVVATPGRFLHIVVEMEL 72
+ QQ K V LG + +GG ++ + +L +P I+V TPGR ++ L
Sbjct: 120 LAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYL 179
Query: 73 KLSSIQYVVFDEADRLFEMGF 93
I+ V DEAD + GF
Sbjct: 180 SPKYIKMFVLDEADEMLSRGF 200
>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56
Length = 390
Score = 43.9 bits (102), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 29/88 (32%), Positives = 44/88 (50%), Gaps = 8/88 (9%)
Query: 18 TFKFVKELGKFTK----LQSTCLLGGDSMDNQFARLHAS-PDIVVATPGRFLHIVVEMEL 72
F+ KE +F+K ++ GG S+ L + P IVV TPGR L + L
Sbjct: 88 AFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSL 147
Query: 73 KLSSIQYVVFDEADRLFE---MGFDVEQ 97
L I++ + DEAD++ E M DV++
Sbjct: 148 NLKHIKHFILDEADKMLEQLDMRRDVQE 175
>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 = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 38/81 (46%), Gaps = 1/81 (1%)
Query: 14 IVQQTFKFVKELGKFTKLQSTCLLGGDSMDNQFARLH-ASPDIVVATPGRFLHIVVEMEL 72
+ QQ K V LG + +GG ++ + +L +P I+V TPGR ++ L
Sbjct: 94 LAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYL 153
Query: 73 KLSSIQYVVFDEADRLFEMGF 93
I+ V DEAD + GF
Sbjct: 154 SPKYIKMFVLDEADEMLSRGF 174
>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And
Amp-Pnp
Length = 579
Score = 43.5 bits (101), Expect = 3e-05, Method: Composition-based stats.
Identities = 24/66 (36%), Positives = 36/66 (54%), Gaps = 2/66 (3%)
Query: 30 KLQSTCLLGGDSMDNQFARLHA-SPDIVVATPGRFLHIVVEMELKLSS-IQYVVFDEADR 87
K L+GG +++ P+IV+ATPGR + ++ + K + Y V DEADR
Sbjct: 127 KYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADR 186
Query: 88 LFEMGF 93
L E+GF
Sbjct: 187 LLEIGF 192
>pdb|1T6N|A Chain A, Crystal Structure Of The N-Terminal Domain Of Human Uap56
pdb|1T6N|B Chain B, Crystal Structure Of The N-Terminal Domain Of Human Uap56
Length = 220
Score = 42.0 bits (97), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 29/102 (28%), Positives = 48/102 (47%), Gaps = 8/102 (7%)
Query: 4 ANINYLISFPIVQQTFKFVKELGKFTK----LQSTCLLGGDSMDNQFARLHAS-PDIVVA 58
++ L+ + F+ KE +F+K ++ GG S+ L + P IVV
Sbjct: 81 GQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVG 140
Query: 59 TPGRFLHIVVEMELKLSSIQYVVFDEADRLFE---MGFDVEQ 97
TPGR L + L L I++ + DE D++ E M DV++
Sbjct: 141 TPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQE 182
>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp
Length = 386
Score = 42.0 bits (97), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 28/88 (31%), Positives = 43/88 (48%), Gaps = 8/88 (9%)
Query: 18 TFKFVKELGKFTK----LQSTCLLGGDSMDNQFARLHAS-PDIVVATPGRFLHIVVEMEL 72
F+ KE +F+K ++ GG S+ L + P IVV TPGR L + L
Sbjct: 89 AFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSL 148
Query: 73 KLSSIQYVVFDEADRLFE---MGFDVEQ 97
L I++ + DE D++ E M DV++
Sbjct: 149 NLKHIKHFILDECDKMLEQLDMRRDVQE 176
>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56
Length = 391
Score = 42.0 bits (97), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 28/88 (31%), Positives = 43/88 (48%), Gaps = 8/88 (9%)
Query: 18 TFKFVKELGKFTK----LQSTCLLGGDSMDNQFARLHAS-PDIVVATPGRFLHIVVEMEL 72
F+ KE +F+K ++ GG S+ L + P IVV TPGR L + L
Sbjct: 89 AFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSL 148
Query: 73 KLSSIQYVVFDEADRLFE---MGFDVEQ 97
L I++ + DE D++ E M DV++
Sbjct: 149 NLKHIKHFILDECDKMLEQLDMRRDVQE 176
>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 = 42.0 bits (97), Expect = 1e-04, Method: Composition-based stats.
Identities = 24/64 (37%), Positives = 35/64 (54%), Gaps = 3/64 (4%)
Query: 36 LLGGDSMDNQFARLHASPDIVVATPGRFLHIVVEMELKLSSIQYVVFDEADRLFEMGF-- 93
+ GG ++ Q L + +IVV TPGR L + L L +++Y + DEAD GF
Sbjct: 108 IYGGKAIYPQIKALK-NANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEXLNXGFIK 166
Query: 94 DVEQ 97
DVE+
Sbjct: 167 DVEK 170
>pdb|2G9N|A Chain A, Structure Of The Dead Domain Of Human Eukaryotic
Initiation Factor 4a, Eif4a
pdb|2G9N|B Chain B, Structure Of The Dead Domain Of Human Eukaryotic
Initiation Factor 4a, Eif4a
Length = 221
Score = 39.7 bits (91), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 35/81 (43%), Gaps = 1/81 (1%)
Query: 14 IVQQTFKFVKELGKFTKLQSTCLLGGDSMDNQFARLH-ASPDIVVATPGRFLHIVVEMEL 72
+ QQ V LG + +GG ++ + L +P I+V TPGR ++ L
Sbjct: 95 LAQQIQXVVMALGDYMGASCHACIGGTNVRAEVQXLQMEAPHIIVGTPGRVFDMLNRRYL 154
Query: 73 KLSSIQYVVFDEADRLFEMGF 93
I V DEAD + GF
Sbjct: 155 SPXYIXMFVLDEADEMLSRGF 175
>pdb|3DKP|A Chain A, Human Dead-Box Rna-Helicase Ddx52, Conserved Domain I In
Complex With Adp
Length = 245
Score = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 30/41 (73%), Gaps = 2/41 (4%)
Query: 54 DIVVATPGRFLHIVVE--MELKLSSIQYVVFDEADRLFEMG 92
DI+V TP R ++++ + + L+S++++V DE+D+LFE G
Sbjct: 151 DILVTTPNRLIYLLKQDPPGIDLASVEWLVVDESDKLFEDG 191
>pdb|2OXC|A Chain A, Human Dead-Box Rna Helicase Ddx20, Dead Domain In Complex
With Adp
pdb|2OXC|B Chain B, Human Dead-Box Rna Helicase Ddx20, Dead Domain In Complex
With Adp
pdb|3B7G|A Chain A, Human Dead-Box Rna Helicase Ddx20, Conserved Domain I
(Dead) In Complex With Amppnp
(Adenosine-(Beta,Gamma)-Imidotriphosphate)
pdb|3B7G|B Chain B, Human Dead-Box Rna Helicase Ddx20, Conserved Domain I
(Dead) In Complex With Amppnp
(Adenosine-(Beta,Gamma)-Imidotriphosphate)
Length = 230
Score = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 26/85 (30%), Positives = 37/85 (43%), Gaps = 2/85 (2%)
Query: 14 IVQQTFKFVKELG-KFTKLQSTCLLGGDSMDNQFARLHASPDIVVATPGRFLHIVVEMEL 72
I Q + +G K L+ +GG + RL I V +PGR ++ L
Sbjct: 104 IAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRLKKC-HIAVGSPGRIKQLIELDYL 162
Query: 73 KLSSIQYVVFDEADRLFEMGFDVEQ 97
SI+ + DEAD+L E G EQ
Sbjct: 163 NPGSIRLFILDEADKLLEEGSFQEQ 187
>pdb|3FHO|A Chain A, Structure Of S. Pombe Dbp5
pdb|3FHO|B Chain B, Structure Of S. Pombe Dbp5
Length = 508
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 41/80 (51%), Gaps = 4/80 (5%)
Query: 11 SFPIVQQTFKFVKELGKFTKLQSTCLLGGDSMDNQFARLHASPDIVVATPGRFLHIVVEM 70
S + +Q V E+GK+T++++ G + A++ A IV+ TPG + ++
Sbjct: 198 SRELARQIMDVVTEMGKYTEVKTA--FGIKDSVPKGAKIDAQ--IVIGTPGTVMDLMKRR 253
Query: 71 ELKLSSIQYVVFDEADRLFE 90
+L I+ V DEAD + +
Sbjct: 254 QLDARDIKVFVLDEADNMLD 273
>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 = 32.3 bits (72), Expect = 0.076, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 19/39 (48%)
Query: 55 IVVATPGRFLHIVVEMELKLSSIQYVVFDEADRLFEMGF 93
IVV TPGR + + I+ + DEAD + GF
Sbjct: 142 IVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGF 180
>pdb|1QDE|A Chain A, Crystal Structure Of The Atpase Domain Of Translation
Initiation Factor 4a From Saccharomyces Cerevisiae-The
Prototype Of The Dead Box Protein Family
Length = 224
Score = 32.0 bits (71), Expect = 0.079, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 19/39 (48%)
Query: 55 IVVATPGRFLHIVVEMELKLSSIQYVVFDEADRLFEMGF 93
IVV TPGR + + I+ + DEAD + GF
Sbjct: 134 IVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGF 172
>pdb|1QVA|A Chain A, Yeast Initiation Factor 4a N-Terminal Domain
Length = 223
Score = 32.0 bits (71), Expect = 0.079, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 19/39 (48%)
Query: 55 IVVATPGRFLHIVVEMELKLSSIQYVVFDEADRLFEMGF 93
IVV TPGR + + I+ + DEAD + GF
Sbjct: 141 IVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGF 179
>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a
pdb|1FUU|B Chain B, Yeast Initiation Factor 4a
Length = 394
Score = 31.6 bits (70), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 30/77 (38%), Gaps = 1/77 (1%)
Query: 17 QTFKFVKELGKFTKLQSTCLLGGDSMDNQFARLHASPDIVVATPGRFLHIVVEMELKLSS 76
Q K V L ++ +GG S L + IVV TPGR + +
Sbjct: 104 QIQKVVXALAFHXDIKVHACIGGTSFVEDAEGLRDA-QIVVGTPGRVFDNIQRRRFRTDK 162
Query: 77 IQYVVFDEADRLFEMGF 93
I+ + DEAD GF
Sbjct: 163 IKXFILDEADEXLSSGF 179
>pdb|1WP9|A Chain A, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
pdb|1WP9|B Chain B, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
pdb|1WP9|C Chain C, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
pdb|1WP9|D Chain D, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
pdb|1WP9|E Chain E, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
pdb|1WP9|F Chain F, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
Length = 494
Score = 28.9 bits (63), Expect = 0.76, Method: Composition-based stats.
Identities = 14/51 (27%), Positives = 26/51 (50%)
Query: 37 LGGDSMDNQFARLHASPDIVVATPGRFLHIVVEMELKLSSIQYVVFDEADR 87
L G+ + ++ A ++VATP + ++ + L + +VFDEA R
Sbjct: 86 LTGEKSPEERSKAWARAKVIVATPQTIENDLLAGRISLEDVSLIVFDEAHR 136
>pdb|2AKO|A Chain A, Crystal Structure Of Glutamate 5-Kinase From Campylobacter
Jejuni
pdb|2AKO|B Chain B, Crystal Structure Of Glutamate 5-Kinase From Campylobacter
Jejuni
pdb|2AKO|C Chain C, Crystal Structure Of Glutamate 5-Kinase From Campylobacter
Jejuni
pdb|2AKO|D Chain D, Crystal Structure Of Glutamate 5-Kinase From Campylobacter
Jejuni
Length = 251
Score = 28.1 bits (61), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 30/64 (46%), Gaps = 2/64 (3%)
Query: 25 LGKFTKLQSTCLLGGDSMDNQFARLHASPDIVVATPGRFLHIVVEMELKLSSIQYVVFDE 84
L KF KL LL G D++ A HA I L I+ E + ++I+ +VF +
Sbjct: 84 LAKFNKLGGQILLTGKDFDSRKATKHAKNAIDXXINLGILPIINEND--ATAIEEIVFGD 141
Query: 85 ADRL 88
D L
Sbjct: 142 NDSL 145
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
0.325 0.139 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,833,544
Number of Sequences: 62578
Number of extensions: 95612
Number of successful extensions: 349
Number of sequences better than 100.0: 45
Number of HSP's better than 100.0 without gapping: 44
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 297
Number of HSP's gapped (non-prelim): 45
length of query: 104
length of database: 14,973,337
effective HSP length: 69
effective length of query: 35
effective length of database: 10,655,455
effective search space: 372940925
effective search space used: 372940925
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 45 (21.9 bits)