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= psy16353
(132 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3KX2|B Chain B, Crystal Structure Of Prp43p In Complex With Adp
pdb|3KX2|A Chain A, Crystal Structure Of Prp43p In Complex With Adp
Length = 767
Score = 63.5 bits (153), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 39/99 (39%), Positives = 55/99 (55%), Gaps = 7/99 (7%)
Query: 39 LHSSIPKEQQDLVFTRFP------PGVRKIVLSTNIAESSITVPDVKYVVDFCLTKVLTV 92
L+ S+P QQ +F P PG RK+V+STNIAE+S+T+ + YVVD +K
Sbjct: 344 LYGSLPPHQQQRIFEPAPESHNGRPG-RKVVISTNIAETSLTIDGIVYVVDPGFSKQKVY 402
Query: 93 AEGSNYSSLQLEWASESSCQQRAGRVGRVSEGRVYYMVT 131
SL + S++S QQRAGR GR G+ + + T
Sbjct: 403 NPRIRVESLLVSPISKASAQQRAGRAGRTRPGKCFRLYT 441
>pdb|2XAU|A Chain A, Crystal Structure Of The Prp43p Deah-Box Rna Helicase In
Complex With Adp
pdb|2XAU|B Chain B, Crystal Structure Of The Prp43p Deah-Box Rna Helicase In
Complex With Adp
Length = 773
Score = 63.5 bits (153), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 39/99 (39%), Positives = 55/99 (55%), Gaps = 7/99 (7%)
Query: 39 LHSSIPKEQQDLVFTRFP------PGVRKIVLSTNIAESSITVPDVKYVVDFCLTKVLTV 92
L+ S+P QQ +F P PG RK+V+STNIAE+S+T+ + YVVD +K
Sbjct: 344 LYGSLPPHQQQRIFEPAPESHNGRPG-RKVVISTNIAETSLTIDGIVYVVDPGFSKQKVY 402
Query: 93 AEGSNYSSLQLEWASESSCQQRAGRVGRVSEGRVYYMVT 131
SL + S++S QQRAGR GR G+ + + T
Sbjct: 403 NPRIRVESLLVSPISKASAQQRAGRAGRTRPGKCFRLYT 441
>pdb|2KBF|A Chain A, Solution Structure Of Carboxyl-Terminal Domain Of Dbp5p
Length = 187
Score = 39.3 bits (90), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 42/86 (48%), Gaps = 12/86 (13%)
Query: 35 KIVVLHSSIPKEQQDLVFTRFPPGVRKIVLSTNIAESSITVPDVKYVVDFCLTKVLTVAE 94
++ +LH + +++D + F G K++++TN+ I +P V VV++ L T+A
Sbjct: 61 EVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLP---TLAN 117
Query: 95 GSNYSSLQLEWASESSCQQRAGRVGR 120
G A ++ R GR GR
Sbjct: 118 GQ---------ADPATYIHRIGRTGR 134
>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3
Length = 395
Score = 38.9 bits (89), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 42/86 (48%), Gaps = 12/86 (13%)
Query: 35 KIVVLHSSIPKEQQDLVFTRFPPGVRKIVLSTNIAESSITVPDVKYVVDFCLTKVLTVAE 94
++ +LH + +++D + F G K++++TN+ I +P V VV++ L T+A
Sbjct: 269 EVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLP---TLAN 325
Query: 95 GSNYSSLQLEWASESSCQQRAGRVGR 120
G A ++ R GR GR
Sbjct: 326 GQ---------ADPATYIHRIGRTGR 342
>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 = 38.9 bits (89), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 42/86 (48%), Gaps = 12/86 (13%)
Query: 35 KIVVLHSSIPKEQQDLVFTRFPPGVRKIVLSTNIAESSITVPDVKYVVDFCLTKVLTVAE 94
++ +LH + +++D + F G K++++TN+ I +P V VV++ L T+A
Sbjct: 269 EVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLP---TLAN 325
Query: 95 GSNYSSLQLEWASESSCQQRAGRVGR 120
G A ++ R GR GR
Sbjct: 326 GQ---------ADPATYIHRIGRTGR 342
>pdb|3GFP|A Chain A, Structure Of The C-Terminal Domain Of The Dead-Box Protein
Dbp5
Length = 189
Score = 38.9 bits (89), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 42/86 (48%), Gaps = 12/86 (13%)
Query: 35 KIVVLHSSIPKEQQDLVFTRFPPGVRKIVLSTNIAESSITVPDVKYVVDFCLTKVLTVAE 94
++ +LH + +++D + F G K++++TN+ I +P V VV++ L T+A
Sbjct: 63 EVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSXVVNYDLP---TLAN 119
Query: 95 GSNYSSLQLEWASESSCQQRAGRVGR 120
G A ++ R GR GR
Sbjct: 120 GQ---------ADPATYIHRIGRTGR 136
>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 = 38.9 bits (89), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 42/86 (48%), Gaps = 12/86 (13%)
Query: 35 KIVVLHSSIPKEQQDLVFTRFPPGVRKIVLSTNIAESSITVPDVKYVVDFCLTKVLTVAE 94
++ +LH + +++D + F G K++++TN+ I +P V VV++ L T+A
Sbjct: 62 EVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSXVVNYDLP---TLAN 118
Query: 95 GSNYSSLQLEWASESSCQQRAGRVGR 120
G A ++ R GR GR
Sbjct: 119 GQ---------ADPATYIHRIGRTGR 135
>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 = 35.0 bits (79), Expect = 0.011, Method: Composition-based stats.
Identities = 11/56 (19%), Positives = 32/56 (57%)
Query: 31 EVQWKIVVLHSSIPKEQQDLVFTRFPPGVRKIVLSTNIAESSITVPDVKYVVDFCL 86
E + + +H +P+++++ + F G ++++ST++ + VP V ++++ L
Sbjct: 299 EANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDL 354
>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 = 35.0 bits (79), Expect = 0.011, Method: Composition-based stats.
Identities = 11/56 (19%), Positives = 32/56 (57%)
Query: 31 EVQWKIVVLHSSIPKEQQDLVFTRFPPGVRKIVLSTNIAESSITVPDVKYVVDFCL 86
E + + +H +P+++++ + F G ++++ST++ + VP V ++++ L
Sbjct: 298 EANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDL 353
>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 = 35.0 bits (79), Expect = 0.011, Method: Composition-based stats.
Identities = 11/56 (19%), Positives = 32/56 (57%)
Query: 31 EVQWKIVVLHSSIPKEQQDLVFTRFPPGVRKIVLSTNIAESSITVPDVKYVVDFCL 86
E + + +H +P+++++ + F G ++++ST++ + VP V ++++ L
Sbjct: 299 EANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDL 354
>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 34.7 bits (78), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 11/56 (19%), Positives = 32/56 (57%)
Query: 31 EVQWKIVVLHSSIPKEQQDLVFTRFPPGVRKIVLSTNIAESSITVPDVKYVVDFCL 86
E + + +H +P+++++ + F G ++++ST++ + VP V ++++ L
Sbjct: 262 EANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDL 317
>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 34.7 bits (78), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 11/56 (19%), Positives = 32/56 (57%)
Query: 31 EVQWKIVVLHSSIPKEQQDLVFTRFPPGVRKIVLSTNIAESSITVPDVKYVVDFCL 86
E + + +H +P+++++ + F G ++++ST++ + VP V ++++ L
Sbjct: 262 EANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDL 317
>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 = 34.7 bits (78), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 11/56 (19%), Positives = 32/56 (57%)
Query: 31 EVQWKIVVLHSSIPKEQQDLVFTRFPPGVRKIVLSTNIAESSITVPDVKYVVDFCL 86
E + + +H +P+++++ + F G ++++ST++ + VP V ++++ L
Sbjct: 277 EANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDL 332
>pdb|2RB4|A Chain A, Crystal Structure Of The Helicase Domain Of Human Ddx25
Rna Helicase
pdb|2RB4|B Chain B, Crystal Structure Of The Helicase Domain Of Human Ddx25
Rna Helicase
Length = 175
Score = 33.5 bits (75), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 26/97 (26%), Positives = 43/97 (44%), Gaps = 13/97 (13%)
Query: 35 KIVVLHSSIPKEQQDLVFTRFPPGVRKIVLSTNIAESSITVPDVKYVVDFCLTKVLTVAE 94
++ +L + EQ+ + RF G K++++TN+ I V V VV+F L V +
Sbjct: 60 QVSLLSGELTVEQRASIIQRFRDGKEKVLITTNVCARGIDVKQVTIVVNF----DLPVKQ 115
Query: 95 GSNYSSLQLEWASESSCQQRAGRVGRVS-EGRVYYMV 130
G E + R GR GR +G + M+
Sbjct: 116 G--------EEPDYETYLHRIGRTGRFGKKGLAFNMI 144
>pdb|3EWS|A Chain A, Human Dead-Box Rna-Helicase Ddx19 In Complex With Adp
pdb|3EWS|B Chain B, Human Dead-Box Rna-Helicase Ddx19 In Complex With Adp
Length = 445
Score = 33.1 bits (74), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 28/52 (53%)
Query: 35 KIVVLHSSIPKEQQDLVFTRFPPGVRKIVLSTNIAESSITVPDVKYVVDFCL 86
++ +L + EQ+ V RF G K++++TN+ I V V V++F L
Sbjct: 329 QVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDL 380
>pdb|3G0H|A Chain A, Human Dead-box Rna Helicase Ddx19, In Complex With An
Atp-analogue And Rna
Length = 424
Score = 33.1 bits (74), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 28/52 (53%)
Query: 35 KIVVLHSSIPKEQQDLVFTRFPPGVRKIVLSTNIAESSITVPDVKYVVDFCL 86
++ +L + EQ+ V RF G K++++TN+ I V V V++F L
Sbjct: 308 QVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDL 359
>pdb|3FHT|A Chain A, Crystal Structure Of Human Dbp5 In Complex With Amppnp And
Rna
pdb|3FHT|B Chain B, Crystal Structure Of Human Dbp5 In Complex With Amppnp And
Rna
Length = 412
Score = 32.7 bits (73), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 28/52 (53%)
Query: 35 KIVVLHSSIPKEQQDLVFTRFPPGVRKIVLSTNIAESSITVPDVKYVVDFCL 86
++ +L + EQ+ V RF G K++++TN+ I V V V++F L
Sbjct: 292 QVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDL 343
>pdb|3FMP|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex
With The Dead- Box Helicase Ddx19
pdb|3FMP|D Chain D, Crystal Structure Of The Nucleoporin Nup214 In Complex
With The Dead- Box Helicase Ddx19
Length = 479
Score = 32.3 bits (72), Expect = 0.068, Method: Composition-based stats.
Identities = 16/52 (30%), Positives = 28/52 (53%)
Query: 35 KIVVLHSSIPKEQQDLVFTRFPPGVRKIVLSTNIAESSITVPDVKYVVDFCL 86
++ +L + EQ+ V RF G K++++TN+ I V V V++F L
Sbjct: 359 QVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDL 410
>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 = 29.6 bits (65), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 12/48 (25%), Positives = 27/48 (56%)
Query: 39 LHSSIPKEQQDLVFTRFPPGVRKIVLSTNIAESSITVPDVKYVVDFCL 86
LH + + +++ V F G +++++T++A + +P V VV + L
Sbjct: 61 LHGDLSQGERERVLGAFRQGEVRVLVATDVAARGLDIPQVDLVVHYRL 108
>pdb|3FHO|A Chain A, Structure Of S. Pombe Dbp5
pdb|3FHO|B Chain B, Structure Of S. Pombe Dbp5
Length = 508
Score = 29.3 bits (64), Expect = 0.61, Method: Composition-based stats.
Identities = 22/92 (23%), Positives = 37/92 (40%), Gaps = 16/92 (17%)
Query: 36 IVVLHSSIPKEQQDLVFTRFPPGVRKIVLSTNIAESSITVPDVKYVVDFCLTKVLTVAEG 95
+ L ++ Q+D + F G K++++TN+ I V V VV++
Sbjct: 384 VACLTGNLEGAQRDAIMDSFRVGTSKVLVTTNVIARGIDVSQVNLVVNY----------- 432
Query: 96 SNYSSLQLEWASESSCQQRAGRVGRVSE-GRV 126
+ L+ A Q R+GR GRV
Sbjct: 433 ----DMPLDQAGRPDPQTYLHRIGRTGRFGRV 460
>pdb|3I32|A Chain A, Dimeric Structure Of A Hera Helicase Fragment Including
The C-Terminal Reca Domain, The Dimerization Domain, And
The Rna Binding Domain
Length = 300
Score = 29.3 bits (64), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 11/49 (22%), Positives = 27/49 (55%)
Query: 38 VLHSSIPKEQQDLVFTRFPPGVRKIVLSTNIAESSITVPDVKYVVDFCL 86
LH + + +++ V F G +++++T++A + +P V VV + +
Sbjct: 57 ALHGDMSQGERERVMGAFRQGEVRVLVATDVAARGLDIPQVDLVVHYRM 105
>pdb|3V4R|A Chain A, Crystal Structure Of A Uvrb Dimer-Dna Complex
pdb|3V4R|B Chain B, Crystal Structure Of A Uvrb Dimer-Dna Complex
Length = 667
Score = 27.7 bits (60), Expect = 1.8, Method: Composition-based stats.
Identities = 23/96 (23%), Positives = 39/96 (40%), Gaps = 13/96 (13%)
Query: 31 EVQWKIVVLHSSIPKEQQDLVFTRFPPGVRKIVLSTNIAESSITVPDVKYVVDFCLTKVL 90
E+ K+ LHS I ++ + G +++ N+ + +P+V V
Sbjct: 473 EIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLV--------- 523
Query: 91 TVAEGSNYSSLQLEWASESSCQQRAGRVGRVSEGRV 126
+ + L+ SE S Q GR R +EGRV
Sbjct: 524 AILDADKEGFLR----SERSLIQTIGRAARNAEGRV 555
>pdb|2D7D|A Chain A, Structural Insights Into The Cryptic Dna Dependent Atp-Ase
Activity Of Uvrb
pdb|2NMV|A Chain A, Damage Detection By The Uvrabc Pathway: Crystal Structure
Of Uvrb Bound To Fluorescein-Adducted Dna
Length = 661
Score = 27.7 bits (60), Expect = 1.8, Method: Composition-based stats.
Identities = 23/96 (23%), Positives = 39/96 (40%), Gaps = 13/96 (13%)
Query: 31 EVQWKIVVLHSSIPKEQQDLVFTRFPPGVRKIVLSTNIAESSITVPDVKYVVDFCLTKVL 90
E+ K+ LHS I ++ + G +++ N+ + +P+V V
Sbjct: 467 EIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLV--------- 517
Query: 91 TVAEGSNYSSLQLEWASESSCQQRAGRVGRVSEGRV 126
+ + L+ SE S Q GR R +EGRV
Sbjct: 518 AILDADKEGFLR----SERSLIQTIGRAARNAEGRV 549
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 0.132 0.388
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,834,566
Number of Sequences: 62578
Number of extensions: 128919
Number of successful extensions: 330
Number of sequences better than 100.0: 29
Number of HSP's better than 100.0 without gapping: 23
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 305
Number of HSP's gapped (non-prelim): 29
length of query: 132
length of database: 14,973,337
effective HSP length: 88
effective length of query: 44
effective length of database: 9,466,473
effective search space: 416524812
effective search space used: 416524812
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 46 (22.3 bits)