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= psy10684
(288 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3MWY|W Chain W, Crystal Structure Of The Chromodomain-atpase Portion Of
The Yeast Chd1 Chromatin Remodeler
Length = 800
Score = 172 bits (436), Expect = 2e-43, Method: Compositional matrix adjust.
Identities = 100/231 (43%), Positives = 134/231 (58%), Gaps = 20/231 (8%)
Query: 2 VLMKDIDVVNGAGKLEKMRLQNILMQLRKCSNHPYLFDGAEP------GPPYTTDEH--- 52
+L K+ + K L NI+ +L+K SNHPYLFD AE G T E+
Sbjct: 490 ILTKNYSALTAGAKGGHFSLLNIMNELKKASNHPYLFDNAEERVLQKFGDGKMTRENVLR 549
Query: 53 -LVFNSGKMVVLDKLLPKLKAQESRVLIFSQMTRMLDILEDYCYWRGFKYCRLDGQTAHE 111
L+ +SGKMV+LD+LL +LK RVLIFSQM RMLDIL DY +G + RLDG
Sbjct: 550 GLIMSSGKMVLLDQLLTRLKKDGHRVLIFSQMVRMLDILGDYLSIKGINFQRLDGTVPSA 609
Query: 112 DRQRQINDFNMEGSDIFIFMLSTRAGGLGINLATADVVVLYDSDWNPQMDLQAMVREAKI 171
R+ I+ FN S+ F+F+LSTRAGGLGINL TAD VV++DSDWNPQ DLQAM R +I
Sbjct: 610 QRRISIDHFNSPDSNDFVFLLSTRAGGLGINLMTADTVVIFDSDWNPQADLQAMARAHRI 669
Query: 172 LRRGSI-------KKALEAKM---SRYRAPFHQLRIAYGANKGKNYTEEED 212
++ + K +E ++ +R + I+ G G YT++ +
Sbjct: 670 GQKNHVMVYRLVSKDTVEEEVLERARKKMILEYAIISLGVTDGNKYTKKNE 720
Score = 89.0 bits (219), Expect = 3e-18, Method: Compositional matrix adjust.
Identities = 41/67 (61%), Positives = 49/67 (73%)
Query: 216 YCRLDGQTAHEDRQRQINDFNMEGSDIFIFMLSTRAGGLGINLATADVVVLYDSDWNPQM 275
+ RLDG R+ I+ FN S+ F+F+LSTRAGGLGINL TAD VV++DSDWNPQ
Sbjct: 599 FQRLDGTVPSAQRRISIDHFNSPDSNDFVFLLSTRAGGLGINLMTADTVVIFDSDWNPQA 658
Query: 276 DLQAMVR 282
DLQAM R
Sbjct: 659 DLQAMAR 665
>pdb|1Z3I|X Chain X, Structure Of The Swi2SNF2 CHROMATIN REMODELING DOMAIN OF
EUKARYOTIC Rad54
Length = 644
Score = 103 bits (256), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 81/232 (34%), Positives = 114/232 (49%), Gaps = 45/232 (19%)
Query: 29 RKCSNHPYL-----------FDGAEPGPP--YTTDEHLVFNSGKMVVLDKLLPKLKAQES 75
+K NHP L FDGA P Y+T SGKM+VLD +L + S
Sbjct: 357 KKLCNHPALIYEKCLTGEEGFDGALDLFPQNYSTKAVEPQLSGKMLVLDYILAMTRTTTS 416
Query: 76 -RVLIFSQMTRMLDILEDYCYWRGFKYCRLDGQTAHEDRQRQINDFNMEGSDIFIFMLST 134
+V++ S T+ LD+ E C R + Y RLDG + + R + + FN S FIFMLS+
Sbjct: 417 DKVVLVSNYTQTLDLFEKLCRNRRYLYVRLDGTMSIKKRAKIVERFNNPSSPEFIFMLSS 476
Query: 135 RAGGLGINLATADVVVLYDSDWNPQMDLQAMVR---------------------EAKILR 173
+AGG G+NL A+ +V++D DWNP D QAM R E KIL+
Sbjct: 477 KAGGCGLNLIGANRLVMFDPDWNPANDEQAMARVWRDGQKKTCYIYRLLSTGTIEEKILQ 536
Query: 174 RGSIKKAL-------EAKMSRYRAPFHQLRIAYGANKGKNYTEEEDRYLYCR 218
R + KKAL E + R+ + +LR + N+ K ++ DR+ CR
Sbjct: 537 RQAHKKALSSCVVDEEQDVERHFS-LGELRELFSLNE-KTLSDTHDRF-RCR 585
Score = 78.6 bits (192), Expect = 4e-15, Method: Compositional matrix adjust.
Identities = 40/87 (45%), Positives = 52/87 (59%), Gaps = 9/87 (10%)
Query: 206 NYTEEED---------RYLYCRLDGQTAHEDRQRQINDFNMEGSDIFIFMLSTRAGGLGI 256
NYT+ D RYLY RLDG + + R + + FN S FIFMLS++AGG G+
Sbjct: 424 NYTQTLDLFEKLCRNRRYLYVRLDGTMSIKKRAKIVERFNNPSSPEFIFMLSSKAGGCGL 483
Query: 257 NLATADVVVLYDSDWNPQMDLQAMVRT 283
NL A+ +V++D DWNP D QAM R
Sbjct: 484 NLIGANRLVMFDPDWNPANDEQAMARV 510
>pdb|1OFC|X Chain X, Nucleosome Recognition Module Of Iswi Atpase
Length = 304
Score = 84.7 bits (208), Expect = 5e-17, Method: Compositional matrix adjust.
Identities = 47/84 (55%), Positives = 56/84 (66%), Gaps = 9/84 (10%)
Query: 145 TADVVVLYDSD-WNPQMDLQAMVR--------EAKILRRGSIKKALEAKMSRYRAPFHQL 195
T + V+ Y++ W +LQ + R E KI RR SIKKAL+ KMSRYRAPFHQL
Sbjct: 144 TPEEVIEYNAVFWERCTELQDIERIMGQIERGEGKIQRRLSIKKALDQKMSRYRAPFHQL 203
Query: 196 RIAYGANKGKNYTEEEDRYLYCRL 219
R+ YG NKGKNYTE EDR+L C L
Sbjct: 204 RLQYGNNKGKNYTEIEDRFLVCML 227
>pdb|1Z6A|A Chain A, Sulfolobus Solfataricus Swi2SNF2 ATPASE CORE DOMAIN
Length = 500
Score = 64.7 bits (156), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 50/170 (29%), Positives = 85/170 (50%), Gaps = 13/170 (7%)
Query: 3 LMKDIDVVNGAGKLEKMRLQNILMQLRKCSNHPYLFDGAEPGPPYTTDEHLVFNSGKMVV 62
L +ID V G + K + + L++L++ +HP L G E V SGKM+
Sbjct: 281 LFNNIDSVTGIKR--KGMILSTLLKLKQIVDHPALLKGGEQS---------VRRSGKMIR 329
Query: 63 LDKLLPKLKAQESRVLIFSQMTRMLDILEDYCYWR-GFKYCRLDGQTAHEDRQRQINDFN 121
+++ + + ++ IF+Q M I+ + + L G+ + ++R I+ F
Sbjct: 330 TMEIIEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQ 389
Query: 122 MEGSDIFIFMLSTRAGGLGINLATADVVVLYDSDWNPQMDLQAMVREAKI 171
S FI +LS +AGG GINL +A+ V+ +D WNP ++ QA R +I
Sbjct: 390 NNPSVKFI-VLSVKAGGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRI 438
Score = 48.1 bits (113), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 29/79 (36%), Positives = 44/79 (55%), Gaps = 1/79 (1%)
Query: 205 KNYTEEEDRYLYCRLDGQTAHEDRQRQINDFNMEGSDIFIFMLSTRAGGLGINLATADVV 264
+N E+E L G+ + ++R I+ F S FI +LS +AGG GINL +A+ V
Sbjct: 358 RNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFI-VLSVKAGGFGINLTSANRV 416
Query: 265 VLYDSDWNPQMDLQAMVRT 283
+ +D WNP ++ QA R
Sbjct: 417 IHFDRWWNPAVEDQATDRV 435
>pdb|1Z5Z|A Chain A, Sulfolobus Solfataricus Swi2SNF2 ATPASE C-Terminal Domain
pdb|1Z5Z|B Chain B, Sulfolobus Solfataricus Swi2SNF2 ATPASE C-Terminal Domain
Length = 271
Score = 64.7 bits (156), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 50/170 (29%), Positives = 85/170 (50%), Gaps = 13/170 (7%)
Query: 3 LMKDIDVVNGAGKLEKMRLQNILMQLRKCSNHPYLFDGAEPGPPYTTDEHLVFNSGKMVV 62
L +ID V G + K + + L++L++ +HP L G E V SGKM+
Sbjct: 52 LFNNIDSVTGIKR--KGMILSTLLKLKQIVDHPALLKGGEQS---------VRRSGKMIR 100
Query: 63 LDKLLPKLKAQESRVLIFSQMTRMLDILEDYCYWR-GFKYCRLDGQTAHEDRQRQINDFN 121
+++ + + ++ IF+Q M I+ + + L G+ + ++R I+ F
Sbjct: 101 TMEIIEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQ 160
Query: 122 MEGSDIFIFMLSTRAGGLGINLATADVVVLYDSDWNPQMDLQAMVREAKI 171
S FI +LS +AGG GINL +A+ V+ +D WNP ++ QA R +I
Sbjct: 161 NNPSVKFI-VLSVKAGGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRI 209
Score = 47.4 bits (111), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 29/79 (36%), Positives = 44/79 (55%), Gaps = 1/79 (1%)
Query: 205 KNYTEEEDRYLYCRLDGQTAHEDRQRQINDFNMEGSDIFIFMLSTRAGGLGINLATADVV 264
+N E+E L G+ + ++R I+ F S FI +LS +AGG GINL +A+ V
Sbjct: 129 RNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFI-VLSVKAGGFGINLTSANRV 187
Query: 265 VLYDSDWNPQMDLQAMVRT 283
+ +D WNP ++ QA R
Sbjct: 188 IHFDRWWNPAVEDQATDRV 206
>pdb|1Z63|A Chain A, Sulfolobus Solfataricus Swi2SNF2 ATPASE CORE IN COMPLEX
With Dsdna
pdb|1Z63|B Chain B, Sulfolobus Solfataricus Swi2SNF2 ATPASE CORE IN COMPLEX
With Dsdna
Length = 500
Score = 61.6 bits (148), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 48/170 (28%), Positives = 83/170 (48%), Gaps = 13/170 (7%)
Query: 3 LMKDIDVVNGAGKLEKMRLQNILMQLRKCSNHPYLFDGAEPGPPYTTDEHLVFNSGKMVV 62
L +ID V G + K + + L++L++ +HP L G E V SGK +
Sbjct: 281 LFNNIDSVTGIKR--KGXILSTLLKLKQIVDHPALLKGGEQS---------VRRSGKXIR 329
Query: 63 LDKLLPKLKAQESRVLIFSQMTRMLDILEDYCYWR-GFKYCRLDGQTAHEDRQRQINDFN 121
+++ + + ++ IF+Q I+ + + L G+ + ++R I+ F
Sbjct: 330 TXEIIEEALDEGDKIAIFTQFVDXGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQ 389
Query: 122 MEGSDIFIFMLSTRAGGLGINLATADVVVLYDSDWNPQMDLQAMVREAKI 171
S FI +LS +AGG GINL +A+ V+ +D WNP ++ QA R +I
Sbjct: 390 NNPSVKFI-VLSVKAGGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRI 438
Score = 48.1 bits (113), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 29/79 (36%), Positives = 44/79 (55%), Gaps = 1/79 (1%)
Query: 205 KNYTEEEDRYLYCRLDGQTAHEDRQRQINDFNMEGSDIFIFMLSTRAGGLGINLATADVV 264
+N E+E L G+ + ++R I+ F S FI +LS +AGG GINL +A+ V
Sbjct: 358 RNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFI-VLSVKAGGFGINLTSANRV 416
Query: 265 VLYDSDWNPQMDLQAMVRT 283
+ +D WNP ++ QA R
Sbjct: 417 IHFDRWWNPAVEDQATDRV 435
>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x
Length = 417
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 19/82 (23%), Positives = 39/82 (47%), Gaps = 3/82 (3%)
Query: 72 AQESRVLIFSQMTRMLDILEDYCYWRGFKYCRLDGQTAHEDRQRQINDFNMEGSDIFIFM 131
++S L+F + + D LED+ Y G+ + G + DR+ ++ F S I +
Sbjct: 274 GKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILV-- 331
Query: 132 LSTRAGGLGINLATADVVVLYD 153
+T G++++ V+ +D
Sbjct: 332 -ATAVAARGLDISNVKHVINFD 352
>pdb|2Y9Z|A Chain A, Chromatin Remodeling Factor Isw1a(Del_atpase) In Dna
Complex
Length = 374
Score = 38.1 bits (87), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 31/50 (62%), Gaps = 2/50 (4%)
Query: 168 EAKILRRGSIKKALEAKMSRYRAPFHQLRIAY--GANKGKNYTEEEDRYL 215
E KI R ++AL K+S Y+ PF L++ + +N + Y+EEEDR++
Sbjct: 190 EEKIKRVKMQQEALRRKLSEYKNPFFDLKLKHPPSSNNKRTYSEEEDRFI 239
>pdb|2Y9Y|A Chain A, Chromatin Remodeling Factor Isw1a(Del_atpase)
Length = 374
Score = 38.1 bits (87), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 31/50 (62%), Gaps = 2/50 (4%)
Query: 168 EAKILRRGSIKKALEAKMSRYRAPFHQLRIAY--GANKGKNYTEEEDRYL 215
E KI R ++AL K+S Y+ PF L++ + +N + Y+EEEDR++
Sbjct: 190 EEKIKRVKMQQEALRRKLSEYKNPFFDLKLKHPPSSNNKRTYSEEEDRFI 239
>pdb|2JGN|A Chain A, Ddx3 Helicase Domain
pdb|2JGN|B Chain B, Ddx3 Helicase Domain
pdb|2JGN|C Chain C, Ddx3 Helicase Domain
Length = 185
Score = 37.7 bits (86), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 19/82 (23%), Positives = 39/82 (47%), Gaps = 3/82 (3%)
Query: 72 AQESRVLIFSQMTRMLDILEDYCYWRGFKYCRLDGQTAHEDRQRQINDFNMEGSDIFIFM 131
++S L+F + + D LED+ Y G+ + G + DR+ ++ F S I +
Sbjct: 44 GKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILV-- 101
Query: 132 LSTRAGGLGINLATADVVVLYD 153
+T G++++ V+ +D
Sbjct: 102 -ATAVAARGLDISNVKHVINFD 122
>pdb|3HGT|A Chain A, Structural And Functional Studies Of The Yeast Class Ii
Hda1 Hdac Complex
pdb|3HGT|B Chain B, Structural And Functional Studies Of The Yeast Class Ii
Hda1 Hdac Complex
Length = 328
Score = 36.6 bits (83), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 32/113 (28%), Positives = 49/113 (43%), Gaps = 8/113 (7%)
Query: 32 SNHPYLF-DGAEPGPPYTTD--EHLVFNSGKMVVLDKLLPKLKAQESRVLIFSQMTRMLD 88
+ HPYL D P T D HL NSGK VL L+ ++ E+ I + R +D
Sbjct: 80 ATHPYLLIDHYMPKSLITRDVPAHLAENSGKFSVLRDLINLVQEYETETAIVCRPGRTMD 139
Query: 89 ILEDYCYWRGFKYCRLDGQT-----AHEDRQRQINDFNMEGSDIFIFMLSTRA 136
+LE R DG + A D ++ F+ EG + + + ++A
Sbjct: 140 LLEALLLGNKVHIKRYDGHSIKSAAAANDFSCTVHLFSSEGINFTKYPIKSKA 192
>pdb|3HGQ|A Chain A, Structural And Functional Studies Of The Yeast Class Ii
Hda1 Hdac Complex
pdb|3HGQ|B Chain B, Structural And Functional Studies Of The Yeast Class Ii
Hda1 Hdac Complex
pdb|3HGQ|C Chain C, Structural And Functional Studies Of The Yeast Class Ii
Hda1 Hdac Complex
pdb|3HGQ|D Chain D, Structural And Functional Studies Of The Yeast Class Ii
Hda1 Hdac Complex
Length = 328
Score = 35.8 bits (81), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 32/113 (28%), Positives = 48/113 (42%), Gaps = 8/113 (7%)
Query: 32 SNHPYLF-DGAEPGPPYTTD--EHLVFNSGKMVVLDKLLPKLKAQESRVLIFSQMTRMLD 88
+ HPYL D P T D HL NSGK VL L+ ++ E+ I + R D
Sbjct: 80 ATHPYLLIDHYXPKSLITRDVPAHLAENSGKFSVLRDLINLVQEYETETAIVCRPGRTXD 139
Query: 89 ILEDYCYWRGFKYCRLDGQT-----AHEDRQRQINDFNMEGSDIFIFMLSTRA 136
+LE R DG + A D ++ F+ EG + + + ++A
Sbjct: 140 LLEALLLGNKVHIKRYDGHSIKSAAAANDFSCTVHLFSSEGINFTKYPIKSKA 192
>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 = 33.9 bits (76), Expect = 0.094, Method: Compositional matrix adjust.
Identities = 21/88 (23%), Positives = 38/88 (43%), Gaps = 3/88 (3%)
Query: 66 LLPKLKAQESRVLIFSQMTRMLDILEDYCYWRGFKYCRLDGQTAHEDRQRQINDFNMEGS 125
LL L+ VLIF++ +D + +Y +G + + G E+R + I F
Sbjct: 46 LLECLQKTPPPVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKK 105
Query: 126 DIFIFMLSTRAGGLGINLATADVVVLYD 153
D+ + +T G++ V+ YD
Sbjct: 106 DVLV---ATDVASKGLDFPAIQHVINYD 130
>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 = 31.2 bits (69), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 34/76 (44%), Gaps = 3/76 (3%)
Query: 78 LIFSQMTRMLDILEDYCYWRGFKYCRLDGQTAHEDRQRQINDFNMEGSDIFIFMLSTRAG 137
+IF + ++L G + L G ++R R I+DF S + I +T
Sbjct: 247 IIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLI---TTNVL 303
Query: 138 GLGINLATADVVVLYD 153
GI++ T +VV YD
Sbjct: 304 ARGIDIPTVSMVVNYD 319
>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3
Length = 395
Score = 31.2 bits (69), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 34/76 (44%), Gaps = 3/76 (3%)
Query: 78 LIFSQMTRMLDILEDYCYWRGFKYCRLDGQTAHEDRQRQINDFNMEGSDIFIFMLSTRAG 137
+IF + ++L G + L G ++R R I+DF S + I +T
Sbjct: 247 IIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLI---TTNVL 303
Query: 138 GLGINLATADVVVLYD 153
GI++ T +VV YD
Sbjct: 304 ARGIDIPTVSMVVNYD 319
>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 30.4 bits (67), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 20/101 (19%), Positives = 44/101 (43%), Gaps = 3/101 (2%)
Query: 75 SRVLIFSQMTRMLDILEDYCYWRGFKYCRLDGQTAHEDRQRQINDFNMEGSDIFIFMLST 134
++ +IF R +D L + F + G ++R+ + +F S + I ST
Sbjct: 241 TQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLI---ST 297
Query: 135 RAGGLGINLATADVVVLYDSDWNPQMDLQAMVREAKILRRG 175
G+++ +++ YD N ++ + + R + R+G
Sbjct: 298 DVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKG 338
>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 = 1.1, Method: Compositional matrix adjust.
Identities = 20/103 (19%), Positives = 39/103 (37%), Gaps = 3/103 (2%)
Query: 51 EHLVFNSGKMVVLDKLLPKLKAQESRVLIFSQMTRMLDILEDYCYWRGFKYCRLDGQTAH 110
+ ++ K KL+ L Q ++F + R D L + + F + G
Sbjct: 277 KQTIYEVNKYAKRSKLIEILSEQADGTIVFVETKRGADFLASFLSEKEFPTTSIHGDRLQ 336
Query: 111 EDRQRQINDFNMEGSDIFIFMLSTRAGGLGINLATADVVVLYD 153
R++ + DF + I +T G+++ V+ YD
Sbjct: 337 SQREQALRDFKNGSMKVLI---ATSVASRGLDIKNIKHVINYD 376
>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 30.4 bits (67), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 20/101 (19%), Positives = 44/101 (43%), Gaps = 3/101 (2%)
Query: 75 SRVLIFSQMTRMLDILEDYCYWRGFKYCRLDGQTAHEDRQRQINDFNMEGSDIFIFMLST 134
++ +IF R +D L + F + G ++R+ + +F S + I ST
Sbjct: 241 TQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLI---ST 297
Query: 135 RAGGLGINLATADVVVLYDSDWNPQMDLQAMVREAKILRRG 175
G+++ +++ YD N ++ + + R + R+G
Sbjct: 298 DVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKG 338
>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 = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 20/101 (19%), Positives = 44/101 (43%), Gaps = 3/101 (2%)
Query: 75 SRVLIFSQMTRMLDILEDYCYWRGFKYCRLDGQTAHEDRQRQINDFNMEGSDIFIFMLST 134
++ +IF R +D L + F + G ++R+ + +F S + I ST
Sbjct: 256 TQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLI---ST 312
Query: 135 RAGGLGINLATADVVVLYDSDWNPQMDLQAMVREAKILRRG 175
G+++ +++ YD N ++ + + R + R+G
Sbjct: 313 DVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKG 353
>pdb|2KBF|A Chain A, Solution Structure Of Carboxyl-Terminal Domain Of Dbp5p
Length = 187
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 25/104 (24%), Positives = 43/104 (41%), Gaps = 9/104 (8%)
Query: 78 LIFSQMTRMLDILEDYCYWRGFKYCRLDGQTAHEDRQRQINDFNMEGSDIFIFMLSTRAG 137
+IF + ++L G + L G ++R R I+DF S + I +T
Sbjct: 39 IIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLI---TTNVL 95
Query: 138 GLGINLATADVVVLYD------SDWNPQMDLQAMVREAKILRRG 175
GI++ T +VV YD +P + + R + R+G
Sbjct: 96 ARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKG 139
>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 = 30.0 bits (66), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 20/101 (19%), Positives = 44/101 (43%), Gaps = 3/101 (2%)
Query: 75 SRVLIFSQMTRMLDILEDYCYWRGFKYCRLDGQTAHEDRQRQINDFNMEGSDIFIFMLST 134
++ +IF R +D L + F + G ++R+ + +F S + I ST
Sbjct: 278 TQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLI---ST 334
Query: 135 RAGGLGINLATADVVVLYDSDWNPQMDLQAMVREAKILRRG 175
G+++ +++ YD N ++ + + R + R+G
Sbjct: 335 DVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKG 375
>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 = 30.0 bits (66), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 20/101 (19%), Positives = 44/101 (43%), Gaps = 3/101 (2%)
Query: 75 SRVLIFSQMTRMLDILEDYCYWRGFKYCRLDGQTAHEDRQRQINDFNMEGSDIFIFMLST 134
++ +IF R +D L + F + G ++R+ + +F S + I ST
Sbjct: 278 TQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLI---ST 334
Query: 135 RAGGLGINLATADVVVLYDSDWNPQMDLQAMVREAKILRRG 175
G+++ +++ YD N ++ + + R + R+G
Sbjct: 335 DVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKG 375
>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 = 30.0 bits (66), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 20/101 (19%), Positives = 44/101 (43%), Gaps = 3/101 (2%)
Query: 75 SRVLIFSQMTRMLDILEDYCYWRGFKYCRLDGQTAHEDRQRQINDFNMEGSDIFIFMLST 134
++ +IF R +D L + F + G ++R+ + +F S + I ST
Sbjct: 277 TQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLI---ST 333
Query: 135 RAGGLGINLATADVVVLYDSDWNPQMDLQAMVREAKILRRG 175
G+++ +++ YD N ++ + + R + R+G
Sbjct: 334 DVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKG 374
>pdb|3GFP|A Chain A, Structure Of The C-Terminal Domain Of The Dead-Box Protein
Dbp5
Length = 189
Score = 30.0 bits (66), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 25/104 (24%), Positives = 42/104 (40%), Gaps = 9/104 (8%)
Query: 78 LIFSQMTRMLDILEDYCYWRGFKYCRLDGQTAHEDRQRQINDFNMEGSDIFIFMLSTRAG 137
+IF + ++L G + L G ++R R I+DF S + I +T
Sbjct: 41 IIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLI---TTNVL 97
Query: 138 GLGINLATADVVVLYD------SDWNPQMDLQAMVREAKILRRG 175
GI++ T VV YD +P + + R + R+G
Sbjct: 98 ARGIDIPTVSXVVNYDLPTLANGQADPATYIHRIGRTGRFGRKG 141
>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 = 30.0 bits (66), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 25/104 (24%), Positives = 42/104 (40%), Gaps = 9/104 (8%)
Query: 78 LIFSQMTRMLDILEDYCYWRGFKYCRLDGQTAHEDRQRQINDFNMEGSDIFIFMLSTRAG 137
+IF + ++L G + L G ++R R I+DF S + I +T
Sbjct: 40 IIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLI---TTNVL 96
Query: 138 GLGINLATADVVVLYD------SDWNPQMDLQAMVREAKILRRG 175
GI++ T VV YD +P + + R + R+G
Sbjct: 97 ARGIDIPTVSXVVNYDLPTLANGQADPATYIHRIGRTGRFGRKG 140
>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 = 30.0 bits (66), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 21/90 (23%), Positives = 40/90 (44%), Gaps = 9/90 (10%)
Query: 71 KAQESRVLIFSQMTRMLDILEDYCYWRGFKYCRLDGQTAHED-------RQRQINDFNME 123
+ Q S++++F+ + + G K R GQ + E+ Q+ I D
Sbjct: 358 RKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFAR 417
Query: 124 GSDIFIFMLSTRAGGLGINLATADVVVLYD 153
G F +++T G G+++ D+VV Y+
Sbjct: 418 GE--FNVLVATSVGEEGLDVPEVDLVVFYE 445
>pdb|3IO3|A Chain A, Get3 With Adp From D. Hansenii In Closed Form
Length = 348
Score = 28.5 bits (62), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 39/79 (49%), Gaps = 3/79 (3%)
Query: 191 PFHQLRIAYGANKGKNYTEEED-RYLYC-RLDGQTAHEDRQRQINDFNMEGSDIFIFMLS 248
P H L A+ GK+ + E L C +D + A D Q+Q + +N + +D M+S
Sbjct: 58 PAHNLSDAFCQKFGKDARKVEGLPNLSCMEIDPEAAMSDLQQQASQYNNDPNDPLKSMMS 117
Query: 249 TRAGGL-GINLATADVVVL 266
G + GI+ A + + VL
Sbjct: 118 DMTGSIPGIDEALSFMEVL 136
>pdb|2KIN|A Chain A, Kinesin (Monomeric) From Rattus Norvegicus
pdb|3KIN|A Chain A, Kinesin (Dimeric) From Rattus Norvegicus
pdb|3KIN|C Chain C, Kinesin (Dimeric) From Rattus Norvegicus
Length = 238
Score = 27.3 bits (59), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 5/51 (9%)
Query: 45 PPYTTDEHLVFNSGKMVVLDKLLPKLKAQESRVLIFSQMTRML--DILEDY 93
P + +E +V GK V D++LP QE +++ + + D+LE Y
Sbjct: 30 PKFKGEETVVIGQGKPYVFDRVLPPNTTQEQ---VYNACAKQIVKDVLEGY 77
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
0.323 0.138 0.412
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,327,797
Number of Sequences: 62578
Number of extensions: 330108
Number of successful extensions: 843
Number of sequences better than 100.0: 31
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 17
Number of HSP's that attempted gapping in prelim test: 813
Number of HSP's gapped (non-prelim): 40
length of query: 288
length of database: 14,973,337
effective HSP length: 98
effective length of query: 190
effective length of database: 8,840,693
effective search space: 1679731670
effective search space used: 1679731670
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 51 (24.3 bits)