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= psy10448
(1001 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 = 405 bits (1041), Expect = e-113, Method: Compositional matrix adjust.
Identities = 254/716 (35%), Positives = 366/716 (51%), Gaps = 146/716 (20%)
Query: 138 EWLIANRVINSK--TLRDGSTI--YLVKWRDLPYDKATWEDENEDIPGLKESIEFYNXXX 193
E+ + R+I+S+ +L DG++ YLVKWR L YD+ATWE+ + + E ++ +
Sbjct: 144 EFHVPERIIDSQRASLEDGTSQLQYLVKWRRLNYDEATWENATDIVKLAPEQVKHF---- 199
Query: 194 XXXXXXXXXXELQEDEDGASGSKPRRYTPPPEKPTTDLRKKYEK---QPPFLDDTGMQLH 250
Q E+ + P T R ++EK QPPF+ G +L
Sbjct: 200 ------------QNRENS-------KILPQYSSNYTSQRPRFEKLSVQPPFI--KGGELR 238
Query: 251 AYQLEGINWLRYSWGQNIDTILADEMGLGKTIQTITFLYSLFKEGHCKGPFLVSAPLSTI 310
+QL GINW+ + W + + ILADEMGLGKT+QT+ F+ L GP ++ PLST+
Sbjct: 239 DFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWLIFARRQNGPHIIVVPLSTM 298
Query: 311 INWEREFETWAPDFYVVTYVGDKDCRIVLRDHDISWEDTANRGGKPCRIRSSTVKFHVLL 370
W FE WAPD + Y+G++ R +R+++ + + +G K T+KF+VLL
Sbjct: 299 PAWLDTFEKWAPDLNCICYMGNQKSRDTIREYEF-YTNPRAKGKK-------TMKFNVLL 350
Query: 371 TSYELITNDVALLGSIEWAVLVVDEAHRLKSNQSKFFKFLSGYSIQNKLLLTGTPXXXXX 430
T+YE I D A LGSI+W + VDEAHRLK+ +S ++ L+ + + N++L+TGTP
Sbjct: 351 TTYEYILKDRAELGSIKWQFMAVDEAHRLKNAESSLYESLNSFKVANRMLITGTPLQNNI 410
Query: 431 XXXXXXXXXXTPEKFNDLTSFQAEFADISKEEQVKRLHDLLGPHMLRRLKADVLKNMPSK 490
P +F E D +EE + LH + P +LRRLK DV K++PSK
Sbjct: 411 KELAALVNFLMPGRFTIDQEIDFENQDEEQEEYIHDLHRRIQPFILRRLKKDVEKSLPSK 470
Query: 491 SEFIVRVELSPMQKKYYKYILTRNFEALNPKGGGQQVSLLNIMMDLKKCCNHPYLFPAAA 550
+E I+RVELS +Q +YYK ILT+N+ AL G SLLNIM +LKK NHPYLF A
Sbjct: 471 TERILRVELSDVQTEYYKNILTKNYSALTAGAKGGHFSLLNIMNELKKASNHPYLFDNAE 530
Query: 551 EEAPVQGG------QYEIQALTRAAGXXXXXXXXXXXXXEDGHRYGIKPEWLIANRVINS 604
E + G + ++ L ++G +DGHR I
Sbjct: 531 ERVLQKFGDGKMTRENVLRGLIMSSGKMVLLDQLLTRLKKDGHRVLI------------- 577
Query: 605 KTLRDGSTIYLVKWRDLPYDKATWEDENEDIPGLKESIEFYNMTKMLDILEDYLDGEGYK 664
F M +MLDIL DYL +G
Sbjct: 578 ---------------------------------------FSQMVRMLDILGDYLSIKGIN 598
Query: 665 YERIDGNITGSMRQESIDRFNAPGASQFVFLLSTRSGGLGINLATADTVIIYDSDWNPHN 724
++R+DG + + R+ SID FN+P ++ FVFLLSTR+GGLGINL TADTV+I+DSDWNP
Sbjct: 599 FQRLDGTVPSAQRRISIDHFNSPDSNDFVFLLSTRAGGLGINLMTADTVVIFDSDWNPQA 658
Query: 725 DIQAFSRAHRIGQQNKYINLATADTVIIYDSDWNPHNDIQAFSRAHRIGQQNKVMIYRFV 784
D+QA +RAHRIGQ +N VM+YR V
Sbjct: 659 DLQAMARAHRIGQ-------------------------------------KNHVMVYRLV 681
Query: 785 TRNSVEERVTQVAKRKMMLTHLVVRPGM--GGKQANFTKQ------ELDDILRFGT 832
++++VEE V + A++KM+L + ++ G+ G K +TK+ EL IL+FG
Sbjct: 682 SKDTVEEEVLERARKKMILEYAIISLGVTDGNK---YTKKNEPNAGELSAILKFGA 734
>pdb|1Z6A|A Chain A, Sulfolobus Solfataricus Swi2SNF2 ATPASE CORE DOMAIN
Length = 500
Score = 155 bits (391), Expect = 1e-37, Method: Compositional matrix adjust.
Identities = 132/504 (26%), Positives = 216/504 (42%), Gaps = 106/504 (21%)
Query: 249 LHAYQLEGINWLRYSWGQNIDTILADEMGLGKTIQTITFLYSLFKEGHCKGPFLVSAPLS 308
L YQ++G +W+R+ LAD+MGLGKT+QTI KE P LV PLS
Sbjct: 38 LRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAVFSDAKKENELT-PSLVICPLS 96
Query: 309 TIINWEREFETWAPDFYVVTYVGDKDCRIVLRDHDISWEDTANRGGKPCRIRSSTVKFHV 368
+ NWE E +AP + D+ +I L D+DI
Sbjct: 97 VLKNWEEELSKFAPHLRFAVFHEDR-SKIKLEDYDI------------------------ 131
Query: 369 LLTSYELITNDVALLGSIEWAVLVVDEAHRLKSNQSKFFKFLSGYSIQNKLLLTGTPXXX 428
+LT+Y ++ D L +EW +V+DEA +K+ Q+K FK + + ++ LTGTP
Sbjct: 132 ILTTYAVLLRDTRL-KEVEWKYIVIDEAQNIKNPQTKIFKAVKELKSKYRIALTGTPIEN 190
Query: 429 XXXXXXXXXXXXTPEKFNDLTSFQAEFA-------DISKEEQVKRLHDLLGPHMLRRLKA 481
P + F+++FA +++KEE L ++ P +LRR K
Sbjct: 191 KVDDLWSIMTFLNPGLLGSYSEFKSKFATPIKKGDNMAKEE----LKAIISPFILRRTKY 246
Query: 482 D--VLKNMPSKSEFIVRVELSPMQKKYYKYILTRNFEALNPKGGGQQVSL-LNIMMDLKK 538
D ++ ++P K E V L+P Q YK + F ++ G ++ + L+ ++ LK+
Sbjct: 247 DKAIINDLPDKIETNVYCNLTPEQAAMYKAEVENLFNNIDSVTGIKRKGMILSTLLKLKQ 306
Query: 539 CCNHPYLFPAAAEEAPVQGGQYEIQALTRAAGXXXXXXXXXXXXXEDGHRYGIKPEWLIA 598
+HP L ++GG+ + R +G ++G + I +++
Sbjct: 307 IVDHPAL---------LKGGEQSV----RRSGKMIRTMEIIEEALDEGDKIAIFTQFVDM 353
Query: 599 NRVINSKTLRDGSTIYLVKWRDLPYDKATWEDENEDIPGLKESIEFYNMTKMLDILEDYL 658
++I + ++ N ++P +L
Sbjct: 354 GKIIRN---------------------IIEKELNTEVP--------------------FL 372
Query: 659 DGEGYKYERIDGNITGSMRQESIDRFNAPGASQFVFLLSTRSGGLGINLATADTVIIYDS 718
GE K ER D I +F + +F+ +LS ++GG GINL +A+ VI +D
Sbjct: 373 YGELSKKERDD----------IISKFQNNPSVKFI-VLSVKAGGFGINLTSANRVIHFDR 421
Query: 719 DWNPHNDIQAFSRAHRIGQQNKYI 742
WNP + QA R +RIGQ I
Sbjct: 422 WWNPAVEDQATDRVYRIGQTRNVI 445
>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 = 149 bits (377), Expect = 6e-36, Method: Compositional matrix adjust.
Identities = 134/504 (26%), Positives = 216/504 (42%), Gaps = 106/504 (21%)
Query: 249 LHAYQLEGINWLRYSWGQNIDTILADEMGLGKTIQTITFLYSLFKEGHCKGPFLVSAPLS 308
L YQ++G +W R+ LAD+ GLGKT+QTI KE P LV PLS
Sbjct: 38 LRPYQIKGFSWXRFXNKLGFGICLADDXGLGKTLQTIAVFSDAKKENELT-PSLVICPLS 96
Query: 309 TIINWEREFETWAPDFYVVTYVGDKDCRIVLRDHDISWEDTANRGGKPCRIRSSTVKFHV 368
+ NWE E +AP + D+ +I L D+DI
Sbjct: 97 VLKNWEEELSKFAPHLRFAVFHEDR-SKIKLEDYDI------------------------ 131
Query: 369 LLTSYELITNDVALLGSIEWAVLVVDEAHRLKSNQSKFFKFLSGYSIQNKLLLTGTPXXX 428
+LT+Y ++ D L +EW +V+DEA +K+ Q+K FK + + ++ LTGTP
Sbjct: 132 ILTTYAVLLRDTRL-KEVEWKYIVIDEAQNIKNPQTKIFKAVKELKSKYRIALTGTPIEN 190
Query: 429 XXXXXXXXXXXXTPEKFNDLTSFQAEFA-------DISKEEQVKRLHDLLGPHMLRRLKA 481
P + F+++FA + +KEE L ++ P +LRR K
Sbjct: 191 KVDDLWSIXTFLNPGLLGSYSEFKSKFATPIKKGDNXAKEE----LKAIISPFILRRTKY 246
Query: 482 D--VLKNMPSKSEFIVRVELSPMQKKYYKYILTRNFEALNPKGG-GQQVSLLNIMMDLKK 538
D ++ ++P K E V L+P Q YK + F ++ G ++ +L+ ++ LK+
Sbjct: 247 DKAIINDLPDKIETNVYCNLTPEQAAXYKAEVENLFNNIDSVTGIKRKGXILSTLLKLKQ 306
Query: 539 CCNHPYLFPAAAEEAPVQGGQYEIQALTRAAGXXXXXXXXXXXXXEDGHRYGIKPEWLIA 598
+HP L ++GG+ + R +G ++G + I +++
Sbjct: 307 IVDHPAL---------LKGGEQSV----RRSGKXIRTXEIIEEALDEGDKIAIFTQFVDX 353
Query: 599 NRVINSKTLRDGSTIYLVKWRDLPYDKATWEDENEDIPGLKESIEFYNMTKMLDILEDYL 658
++I + ++ N ++P +L
Sbjct: 354 GKIIRN---------------------IIEKELNTEVP--------------------FL 372
Query: 659 DGEGYKYERIDGNITGSMRQESIDRFNAPGASQFVFLLSTRSGGLGINLATADTVIIYDS 718
GE K ER D I +F + +F+ +LS ++GG GINL +A+ VI +D
Sbjct: 373 YGELSKKERDD----------IISKFQNNPSVKFI-VLSVKAGGFGINLTSANRVIHFDR 421
Query: 719 DWNPHNDIQAFSRAHRIGQQNKYI 742
WNP + QA R +RIGQ I
Sbjct: 422 WWNPAVEDQATDRVYRIGQTRNVI 445
>pdb|1Z3I|X Chain X, Structure Of The Swi2SNF2 CHROMATIN REMODELING DOMAIN OF
EUKARYOTIC Rad54
Length = 644
Score = 93.2 bits (230), Expect = 7e-19, Method: Compositional matrix adjust.
Identities = 98/370 (26%), Positives = 155/370 (41%), Gaps = 70/370 (18%)
Query: 220 YTPPPEKPTTDLRKKYEKQP------PFLDDTGMQLHAYQLEGINWLRYSW----GQNID 269
Y PP ++ EK P P L L +Q EG+ +L W G+ I+
Sbjct: 24 YEPPAISAHDLIKADKEKLPVHVVVDPVLSKV---LRPHQREGVKFL---WDCVTGRRIE 77
Query: 270 ----TILADEMGLGKTIQTITFLYSLFKEG-HCK---GPFLVSAPLSTIINWEREFETWA 321
I+ADEMGLGKT+Q IT +++L K+ CK +V +P S + NW E W
Sbjct: 78 NSYGCIMADEMGLGKTLQCITLIWTLLKQSPDCKPEIDKVIVVSPSSLVRNWYNEVGKW- 136
Query: 322 PDFYVVTYVGDKDCRIVLRDHDISWEDTANRGGKPCRIRSSTVKF----------HVLLT 371
+G + + A GG I S V F +L+
Sbjct: 137 --------LGGR------------VQPVAIDGGSKDEIDSKLVNFISQQGMRIPTPILII 176
Query: 372 SYELITNDVALLGSIEWAVLVVDEAHRLKSNQSKFFKFLSGYSIQNKLLLTGTPXXXXXX 431
SYE +L + +++ DE HRLK++ ++ + L+ + Q ++L++GTP
Sbjct: 177 SYETFRLHAEVLHKGKVGLVICDEGHRLKNSDNQTYLALNSMNAQRRVLISGTPIQNDLL 236
Query: 432 XXXXXXXXXTPEKFNDLTSFQAEF---------ADISK------EEQVKRLHDLLGPHML 476
F+ F AD S E++++ L ++ ++
Sbjct: 237 EYFSLVHFVNSGILGTAQEFKKRFEIPILKGRDADASDKDRAAGEQKLQELISIVNRCLI 296
Query: 477 RRLKADVLKNMPSKSEFIVRVELSPMQKKYYKYILTRNFEALNPKGGGQQVSLLNIMMDL 536
RR + K +P K E +V L+P+QK+ YK L + + + G VS L+ + L
Sbjct: 297 RRTSDILSKYLPVKIEQVVCCNLTPLQKELYKLFLKQAKPVESLQTGKISVSSLSSITSL 356
Query: 537 KKCCNHPYLF 546
KK CNHP L
Sbjct: 357 KKLCNHPALI 366
Score = 92.4 bits (228), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 49/163 (30%), Positives = 79/163 (48%), Gaps = 37/163 (22%)
Query: 646 NMTKMLDILEDYLDGEGYKYERIDGNITGSMRQESIDRFNAPGASQFVFLLSTRSGGLGI 705
N T+ LD+ E Y Y R+DG ++ R + ++RFN P + +F+F+LS+++GG G+
Sbjct: 424 NYTQTLDLFEKLCRNRRYLYVRLDGTMSIKKRAKIVERFNNPSSPEFIFMLSSKAGGCGL 483
Query: 706 NLATADTVIIYDSDWNPHNDIQAFSRAHRIGQQNKYINLATADTVIIYDSDWNPHNDIQA 765
NL A+ ++++D DWNP ND QA +R W
Sbjct: 484 NLIGANRLVMFDPDWNPANDEQAMARV------------------------W-------- 511
Query: 766 FSRAHRIGQQNKVMIYRFVTRNSVEERVTQVAKRKMMLTHLVV 808
R GQ+ IYR ++ ++EE++ Q K L+ VV
Sbjct: 512 -----RDGQKKTCYIYRLLSTGTIEEKILQRQAHKKALSSCVV 549
>pdb|2EE1|A Chain A, Solution Structures Of The Chromo Domain Of Human
Chromodomain Helicase-Dna-Binding Protein 4
Length = 64
Score = 57.8 bits (138), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 22/44 (50%), Positives = 33/44 (75%)
Query: 136 KPEWLIANRVINSKTLRDGSTIYLVKWRDLPYDKATWEDENEDI 179
KPEW++ +R++N + G YL+KWRDLPYD+A+WE E+ +I
Sbjct: 8 KPEWMMIHRILNHSVDKKGHVHYLIKWRDLPYDQASWESEDVEI 51
Score = 57.8 bits (138), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 22/44 (50%), Positives = 33/44 (75%)
Query: 592 KPEWLIANRVINSKTLRDGSTIYLVKWRDLPYDKATWEDENEDI 635
KPEW++ +R++N + G YL+KWRDLPYD+A+WE E+ +I
Sbjct: 8 KPEWMMIHRILNHSVDKKGHVHYLIKWRDLPYDQASWESEDVEI 51
>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 = 56.6 bits (135), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 59/258 (22%), Positives = 103/258 (39%), Gaps = 66/258 (25%)
Query: 486 NMPSKSEFIVRVELSPMQKKYYKYILTRNFEALNPKGGGQQVSL-LNIMMDLKKCCNHPY 544
++P K E V L+P Q YK + F ++ G ++ + L+ ++ LK+ +HP
Sbjct: 24 DLPDKIETNVYCNLTPEQAAMYKAEVENLFNNIDSVTGIKRKGMILSTLLKLKQIVDHPA 83
Query: 545 LFPAAAEEAPVQGGQYEIQALTRAAGXXXXXXXXXXXXXEDGHRYGIKPEWLIANRVINS 604
L +GG+ + R +G ++G + I +++ ++I +
Sbjct: 84 LL---------KGGEQSV----RRSGKMIRTMEIIEEALDEGDKIAIFTQFVDMGKIIRN 130
Query: 605 KTLRDGSTIYLVKWRDLPYDKATWEDENEDIPGLKESIEFYNMTKMLDILEDYLDGEGYK 664
++ N ++P +L GE K
Sbjct: 131 ---------------------IIEKELNTEVP--------------------FLYGELSK 149
Query: 665 YERIDGNITGSMRQESIDRFNAPGASQFVFLLSTRSGGLGINLATADTVIIYDSDWNPHN 724
ER D I +F + +F+ +LS ++GG GINL +A+ VI +D WNP
Sbjct: 150 KERDD----------IISKFQNNPSVKFI-VLSVKAGGFGINLTSANRVIHFDRWWNPAV 198
Query: 725 DIQAFSRAHRIGQQNKYI 742
+ QA R +RIGQ I
Sbjct: 199 EDQATDRVYRIGQTRNVI 216
>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x
Length = 417
Score = 41.2 bits (95), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 32/109 (29%), Positives = 55/109 (50%), Gaps = 9/109 (8%)
Query: 641 SIEFYNMTKMLDILEDYLDGEGYKYERIDGNITGSMRQESIDRFNAPGASQFVFLLSTRS 700
++ F K D LED+L EGY I G+ + R+E++ +F + G S L++T
Sbjct: 279 TLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRS-GKSP--ILVATAV 335
Query: 701 GGLGINLATADTVIIYDSDWNPHNDIQAFSRAHRIGQQNKYINLATADT 749
G++++ VI +D +DI+ + HRIG+ + NL A +
Sbjct: 336 AARGLDISNVKHVINFDLP----SDIEEY--VHRIGRTGRVGNLGLATS 378
>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 = 40.4 bits (93), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 28/107 (26%), Positives = 48/107 (44%), Gaps = 3/107 (2%)
Query: 641 SIEFYNMTKMLDILEDYLDGEGYKYERIDGNITGSMRQESIDRFNAPGASQFVFLLSTRS 700
I F + ++ L D LD GY ++I G G ++++ D N ++ +L++T
Sbjct: 38 CIIFCRTKEHVNQLTDELDDLGYPCDKIHG---GMIQEDRFDVMNEFKRGEYRYLVATDV 94
Query: 701 GGLGINLATADTVIIYDSDWNPHNDIQAFSRAHRIGQQNKYINLATA 747
GI++ VI YD + + R R G + K I+ TA
Sbjct: 95 AARGIDIENISLVINYDLPLEKESYVHRTGRTGRAGNKGKAISFVTA 141
>pdb|2DY8|A Chain A, Solution Structure Of The Second Chromodomain Of Yeast
Chd1
Length = 69
Score = 39.7 bits (91), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 39/65 (60%), Gaps = 4/65 (6%)
Query: 594 EWLIANRVINSK--TLRDGSTI--YLVKWRDLPYDKATWEDENEDIPGLKESIEFYNMTK 649
E+ + R+I+S+ +L DG++ YLVKWR L YD+ATWE+ + + E ++ + +
Sbjct: 5 EFHVPERIIDSQRASLEDGTSQLQYLVKWRRLNYDEATWENATDIVKLAPEQVKHFQNRE 64
Query: 650 MLDIL 654
IL
Sbjct: 65 NSKIL 69
Score = 39.3 bits (90), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 36/56 (64%), Gaps = 4/56 (7%)
Query: 138 EWLIANRVINSK--TLRDGSTI--YLVKWRDLPYDKATWEDENEDIPGLKESIEFY 189
E+ + R+I+S+ +L DG++ YLVKWR L YD+ATWE+ + + E ++ +
Sbjct: 5 EFHVPERIIDSQRASLEDGTSQLQYLVKWRRLNYDEATWENATDIVKLAPEQVKHF 60
>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 = 39.3 bits (90), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 30/107 (28%), Positives = 53/107 (49%), Gaps = 9/107 (8%)
Query: 641 SIEFYNMTKMLDILEDYLDGEGYKYERIDGNITGSMRQESIDRFNAPGASQFVFLLSTRS 700
++ F K D LED+L EGY I G+ + R+E++ +F + + L++T
Sbjct: 49 TLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSP---ILVATAV 105
Query: 701 GGLGINLATADTVIIYDSDWNPHNDIQAFSRAHRIGQQNKYINLATA 747
G++++ VI +D +DI+ + HRIG+ + NL A
Sbjct: 106 AARGLDISNVKHVINFDLP----SDIEEY--VHRIGRTGRVGNLGLA 146
>pdb|2H1E|A Chain A, Tandem Chromodomains Of Budding Yeast Chd1
pdb|2H1E|B Chain B, Tandem Chromodomains Of Budding Yeast Chd1
Length = 177
Score = 39.3 bits (90), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 36/56 (64%), Gaps = 4/56 (7%)
Query: 138 EWLIANRVINSK--TLRDGSTI--YLVKWRDLPYDKATWEDENEDIPGLKESIEFY 189
E+ + R+I+S+ +L DG++ YLVKWR L YD+ATWE+ + + E ++ +
Sbjct: 119 EFHVPERIIDSQRASLEDGTSQLQYLVKWRRLNYDEATWENATDIVKLAPEQVKHF 174
Score = 39.3 bits (90), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 36/56 (64%), Gaps = 4/56 (7%)
Query: 594 EWLIANRVINSK--TLRDGSTI--YLVKWRDLPYDKATWEDENEDIPGLKESIEFY 645
E+ + R+I+S+ +L DG++ YLVKWR L YD+ATWE+ + + E ++ +
Sbjct: 119 EFHVPERIIDSQRASLEDGTSQLQYLVKWRRLNYDEATWENATDIVKLAPEQVKHF 174
>pdb|3FHO|A Chain A, Structure Of S. Pombe Dbp5
pdb|3FHO|B Chain B, Structure Of S. Pombe Dbp5
Length = 508
Score = 37.7 bits (86), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 27/129 (20%), Positives = 55/129 (42%), Gaps = 3/129 (2%)
Query: 638 LKESIEFYNMTKMLDILEDYLDGEGYKYERIDGNITGSMRQESIDRFNAPGASQFVFLLS 697
+ +SI F + + + +G+ + GN+ G+ R +D F G S+ L++
Sbjct: 357 IGQSIIFCKKKDTAEEIARRMTADGHTVACLTGNLEGAQRDAIMDSFRV-GTSK--VLVT 413
Query: 698 TRSGGLGINLATADTVIIYDSDWNPHNDIQAFSRAHRIGQQNKYINLATADTVIIYDSDW 757
T GI+++ + V+ YD + + HRIG+ ++ + + + W
Sbjct: 414 TNVIARGIDVSQVNLVVNYDMPLDQAGRPDPQTYLHRIGRTGRFGRVGVSINFVHDKKSW 473
Query: 758 NPHNDIQAF 766
N IQ +
Sbjct: 474 EEMNAIQEY 482
>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 = 36.6 bits (83), Expect = 0.076, Method: Compositional matrix adjust.
Identities = 33/131 (25%), Positives = 55/131 (41%), Gaps = 6/131 (4%)
Query: 638 LKESIEFYNMTKMLDILEDYLDGEGYKYERIDGNITGSMRQESIDRFNAPGASQFVFLLS 697
+ SI F K ++L L EG++ + G++ R ID F G S+ L++
Sbjct: 243 IGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFRE-GRSKV--LIT 299
Query: 698 TRSGGLGINLATADTVIIYDSDWNPHNDIQAFSRAHRIGQQNKYINLATADTVIIYDSDW 757
T GI++ T V+ YD + + HRIG+ ++ A I + D
Sbjct: 300 TNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVA---ISFVHDK 356
Query: 758 NPHNDIQAFSR 768
N N + A +
Sbjct: 357 NSFNILSAIQK 367
>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3
Length = 395
Score = 36.6 bits (83), Expect = 0.079, Method: Compositional matrix adjust.
Identities = 33/131 (25%), Positives = 55/131 (41%), Gaps = 6/131 (4%)
Query: 638 LKESIEFYNMTKMLDILEDYLDGEGYKYERIDGNITGSMRQESIDRFNAPGASQFVFLLS 697
+ SI F K ++L L EG++ + G++ R ID F G S+ L++
Sbjct: 243 IGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFRE-GRSKV--LIT 299
Query: 698 TRSGGLGINLATADTVIIYDSDWNPHNDIQAFSRAHRIGQQNKYINLATADTVIIYDSDW 757
T GI++ T V+ YD + + HRIG+ ++ A I + D
Sbjct: 300 TNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVA---ISFVHDK 356
Query: 758 NPHNDIQAFSR 768
N N + A +
Sbjct: 357 NSFNILSAIQK 367
>pdb|2EPB|A Chain A, Solution Structure Of Chromo Domain 2 In Chromodomain-
Helicase-Dna-Binding Protein 6
Length = 68
Score = 36.2 bits (82), Expect = 0.097, Method: Composition-based stats.
Identities = 19/54 (35%), Positives = 32/54 (59%), Gaps = 6/54 (11%)
Query: 137 PEWLIANRVINSKTLRDGST-----IYLVKWRDLPYDKATWE-DENEDIPGLKE 184
P+++ +R++ +D T YLVKW LPY+++TWE +E+ D +KE
Sbjct: 9 PDYVEVDRILEVAHTKDAETGEEVTHYLVKWCSLPYEESTWELEEDVDPAKVKE 62
Score = 36.2 bits (82), Expect = 0.097, Method: Composition-based stats.
Identities = 19/54 (35%), Positives = 32/54 (59%), Gaps = 6/54 (11%)
Query: 593 PEWLIANRVINSKTLRDGST-----IYLVKWRDLPYDKATWE-DENEDIPGLKE 640
P+++ +R++ +D T YLVKW LPY+++TWE +E+ D +KE
Sbjct: 9 PDYVEVDRILEVAHTKDAETGEEVTHYLVKWCSLPYEESTWELEEDVDPAKVKE 62
>pdb|3DMQ|A Chain A, Crystal Structure Of Rapa, A Swi2SNF2 PROTEIN THAT
Recycles Rna Polymerase During Transcription
pdb|3DMQ|B Chain B, Crystal Structure Of Rapa, A Swi2SNF2 PROTEIN THAT
Recycles Rna Polymerase During Transcription
Length = 968
Score = 36.2 bits (82), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 46/193 (23%), Positives = 74/193 (38%), Gaps = 28/193 (14%)
Query: 270 TILADEMGLGKTIQTITFLYSLFKEGHCKGPFLVSAPLSTIINWEREFETWAPDFYVVTY 329
+LADE+GLGKTI+ L+ G + L+ P + W +V
Sbjct: 173 VLLADEVGLGKTIEAGXILHQQLLSGAAE-RVLIIVPETLQHQW------------LVEX 219
Query: 330 VGDKDCRIVLRDHDISWEDTANRGGKPCRIRSSTVKFHVLLTSYELITND---VALLGSI 386
+ + R L D D + + + P +++ S + + L
Sbjct: 220 LRRFNLRFALFD-DERYAEAQHDAYNPFDTE------QLVICSLDFARRSKQRLEHLCEA 272
Query: 387 EWAVLVVDEAHRL---KSNQSKFFKFLSGYS--IQNKLLLTGTPXXXXXXXXXXXXXXXT 441
EW +LVVDEAH L + S+ ++ + + + LLLT TP
Sbjct: 273 EWDLLVVDEAHHLVWSEDAPSREYQAIEQLAEHVPGVLLLTATPEQLGXESHFARLRLLD 332
Query: 442 PEKFNDLTSFQAE 454
P +F+D F E
Sbjct: 333 PNRFHDFAQFVEE 345
>pdb|3GFP|A Chain A, Structure Of The C-Terminal Domain Of The Dead-Box Protein
Dbp5
Length = 189
Score = 34.3 bits (77), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 33/131 (25%), Positives = 55/131 (41%), Gaps = 6/131 (4%)
Query: 638 LKESIEFYNMTKMLDILEDYLDGEGYKYERIDGNITGSMRQESIDRFNAPGASQFVFLLS 697
+ SI F K ++L L EG++ + G++ R ID F G S+ L++
Sbjct: 37 IGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFR-EGRSKV--LIT 93
Query: 698 TRSGGLGINLATADTVIIYDSDWNPHNDIQAFSRAHRIGQQNKYINLATADTVIIYDSDW 757
T GI++ T V+ YD + + HRIG+ ++ A I + D
Sbjct: 94 TNVLARGIDIPTVSXVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVA---ISFVHDK 150
Query: 758 NPHNDIQAFSR 768
N N + A +
Sbjct: 151 NSFNILSAIQK 161
>pdb|2KBF|A Chain A, Solution Structure Of Carboxyl-Terminal Domain Of Dbp5p
Length = 187
Score = 34.3 bits (77), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 33/131 (25%), Positives = 55/131 (41%), Gaps = 6/131 (4%)
Query: 638 LKESIEFYNMTKMLDILEDYLDGEGYKYERIDGNITGSMRQESIDRFNAPGASQFVFLLS 697
+ SI F K ++L L EG++ + G++ R ID F G S+ L++
Sbjct: 35 IGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFR-EGRSKV--LIT 91
Query: 698 TRSGGLGINLATADTVIIYDSDWNPHNDIQAFSRAHRIGQQNKYINLATADTVIIYDSDW 757
T GI++ T V+ YD + + HRIG+ ++ A I + D
Sbjct: 92 TNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVA---ISFVHDK 148
Query: 758 NPHNDIQAFSR 768
N N + A +
Sbjct: 149 NSFNILSAIQK 159
>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 = 34.3 bits (77), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 33/134 (24%), Positives = 56/134 (41%), Gaps = 6/134 (4%)
Query: 635 IPGLKESIEFYNMTKMLDILEDYLDGEGYKYERIDGNITGSMRQESIDRFNAPGASQFVF 694
+ + SI F K ++L L EG++ + G++ R ID F G S+
Sbjct: 33 VXTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFR-EGRSKV-- 89
Query: 695 LLSTRSGGLGINLATADTVIIYDSDWNPHNDIQAFSRAHRIGQQNKYINLATADTVIIYD 754
L++T GI++ T V+ YD + + HRIG+ ++ A I +
Sbjct: 90 LITTNVLARGIDIPTVSXVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVA---ISFV 146
Query: 755 SDWNPHNDIQAFSR 768
D N N + A +
Sbjct: 147 HDKNSFNILSAIQK 160
>pdb|2K1B|A Chain A, Solution Nmr Structure Of The Chromo Domain Of The
Chromobox Protein Homolog 7
Length = 73
Score = 33.1 bits (74), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 19/37 (51%)
Query: 140 LIANRVINSKTLRDGSTIYLVKWRDLPYDKATWEDEN 176
+ A I K +R G YLVKW+ P +TWE E
Sbjct: 21 VFAVESIRKKRVRKGKVEYLVKWKGWPPKYSTWEPEE 57
Score = 33.1 bits (74), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 19/37 (51%)
Query: 596 LIANRVINSKTLRDGSTIYLVKWRDLPYDKATWEDEN 632
+ A I K +R G YLVKW+ P +TWE E
Sbjct: 21 VFAVESIRKKRVRKGKVEYLVKWKGWPPKYSTWEPEE 57
>pdb|2KVM|A Chain A, Solution Structure Of The Cbx7 Chromodomain In Complex
With A H3k27me2 Peptide
Length = 74
Score = 32.7 bits (73), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 19/37 (51%)
Query: 140 LIANRVINSKTLRDGSTIYLVKWRDLPYDKATWEDEN 176
+ A I K +R G YLVKW+ P +TWE E
Sbjct: 13 VFAVESIRKKRVRKGKVEYLVKWKGWPPKYSTWEPEE 49
Score = 32.7 bits (73), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 19/37 (51%)
Query: 596 LIANRVINSKTLRDGSTIYLVKWRDLPYDKATWEDEN 632
+ A I K +R G YLVKW+ P +TWE E
Sbjct: 13 VFAVESIRKKRVRKGKVEYLVKWKGWPPKYSTWEPEE 49
>pdb|2L12|A Chain A, Solution Nmr Structure Of The Chromobox Protein 7 With
H3k9me3
pdb|2L1B|A Chain A, Solution Nmr Structure Of The Chromobox Protein Cbx7 With
H3k27me3
Length = 56
Score = 32.7 bits (73), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 19/37 (51%)
Query: 140 LIANRVINSKTLRDGSTIYLVKWRDLPYDKATWEDEN 176
+ A I K +R G YLVKW+ P +TWE E
Sbjct: 4 VFAVESIRKKRVRKGKVEYLVKWKGWPPKYSTWEPEE 40
Score = 32.7 bits (73), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 19/37 (51%)
Query: 596 LIANRVINSKTLRDGSTIYLVKWRDLPYDKATWEDEN 632
+ A I K +R G YLVKW+ P +TWE E
Sbjct: 4 VFAVESIRKKRVRKGKVEYLVKWKGWPPKYSTWEPEE 40
>pdb|2D9U|A Chain A, Solution Structure Of The Chromo Domain Of Chromobox
Homolog 2 From Human
Length = 74
Score = 32.3 bits (72), Expect = 1.5, Method: Composition-based stats.
Identities = 18/42 (42%), Positives = 20/42 (47%)
Query: 134 GIKPEWLIANRVINSKTLRDGSTIYLVKWRDLPYDKATWEDE 175
G E + A I SK LR G YLVKWR +WE E
Sbjct: 4 GSSGEQVFAAECILSKRLRKGKLEYLVKWRGWSSKHNSWEPE 45
Score = 32.3 bits (72), Expect = 1.5, Method: Composition-based stats.
Identities = 18/42 (42%), Positives = 20/42 (47%)
Query: 590 GIKPEWLIANRVINSKTLRDGSTIYLVKWRDLPYDKATWEDE 631
G E + A I SK LR G YLVKWR +WE E
Sbjct: 4 GSSGEQVFAAECILSKRLRKGKLEYLVKWRGWSSKHNSWEPE 45
>pdb|2GJK|A Chain A, Structural And Functional Insights Into The Human Upf1
Helicase Core
pdb|2GK6|A Chain A, Structural And Functional Insights Into The Human Upf1
Helicase Core
pdb|2GK6|B Chain B, Structural And Functional Insights Into The Human Upf1
Helicase Core
pdb|2GK7|A Chain A, Structural And Functional Insights Into The Human Upf1
Helicase Core
Length = 624
Score = 32.0 bits (71), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 35/68 (51%), Gaps = 9/68 (13%)
Query: 252 YQLEGINWLRYSWGQNIDTILADEM-------GLGKTIQTITFLYSLFKEGHCKGPFLVS 304
+ +G+ L +S + T+L + G GKT+ + T +Y L ++G+ GP LV
Sbjct: 173 FTAQGLPDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGN--GPVLVC 230
Query: 305 APLSTIIN 312
AP + ++
Sbjct: 231 APSNIAVD 238
>pdb|2XZO|A Chain A, Upf1 Helicase - Rna Complex
pdb|2XZP|A Chain A, Upf1 Helicase
Length = 623
Score = 32.0 bits (71), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 35/68 (51%), Gaps = 9/68 (13%)
Query: 252 YQLEGINWLRYSWGQNIDTILADEM-------GLGKTIQTITFLYSLFKEGHCKGPFLVS 304
+ +G+ L +S + T+L + G GKT+ + T +Y L ++G+ GP LV
Sbjct: 172 FTAQGLPDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGN--GPVLVC 229
Query: 305 APLSTIIN 312
AP + ++
Sbjct: 230 APSNIAVD 237
>pdb|2WJV|A Chain A, Crystal Structure Of The Complex Between Human Nonsense
Mediated Decay Factors Upf1 And Upf2
pdb|2WJV|B Chain B, Crystal Structure Of The Complex Between Human Nonsense
Mediated Decay Factors Upf1 And Upf2
pdb|2WJY|A Chain A, Crystal Structure Of The Complex Between Human Nonsense
Mediated Decay Factors Upf1 And Upf2 Orthorhombic Form
Length = 800
Score = 32.0 bits (71), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 35/68 (51%), Gaps = 9/68 (13%)
Query: 252 YQLEGINWLRYSWGQNIDTILADEM-------GLGKTIQTITFLYSLFKEGHCKGPFLVS 304
+ +G+ L +S + T+L + G GKT+ + T +Y L ++G+ GP LV
Sbjct: 349 FTAQGLPDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGN--GPVLVC 406
Query: 305 APLSTIIN 312
AP + ++
Sbjct: 407 APSNIAVD 414
>pdb|3H91|A Chain A, Crystal Structure Of The Complex Of Human Chromobox
Homolog 2 (Cbx2) And H3k27 Peptide
pdb|3H91|B Chain B, Crystal Structure Of The Complex Of Human Chromobox
Homolog 2 (Cbx2) And H3k27 Peptide
Length = 54
Score = 31.6 bits (70), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 18/36 (50%)
Query: 140 LIANRVINSKTLRDGSTIYLVKWRDLPYDKATWEDE 175
+ A I SK LR G YLVKWR +WE E
Sbjct: 3 VFAAECILSKRLRKGKLEYLVKWRGWSSKHNSWEPE 38
Score = 31.6 bits (70), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 18/36 (50%)
Query: 596 LIANRVINSKTLRDGSTIYLVKWRDLPYDKATWEDE 631
+ A I SK LR G YLVKWR +WE E
Sbjct: 3 VFAAECILSKRLRKGKLEYLVKWRGWSSKHNSWEPE 38
>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 = 31.6 bits (70), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 27/119 (22%), Positives = 52/119 (43%), Gaps = 3/119 (2%)
Query: 634 DIPGLKESIEFYNMTKMLDILEDYLDGEGYKYERIDGNITGSMRQESIDRFNAPGASQFV 693
D + +++ F N + +D L + + + + G++ R+ + F + GAS+
Sbjct: 251 DTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRS-GASRV- 308
Query: 694 FLLSTRSGGLGINLATADTVIIYDSDWNPHNDIQAFSRAHRIGQQNKYINLATADTVII 752
L+ST G+++ +I YD N I R+ R G++ IN D + I
Sbjct: 309 -LISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRI 366
>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 = 31.2 bits (69), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 27/119 (22%), Positives = 52/119 (43%), Gaps = 3/119 (2%)
Query: 634 DIPGLKESIEFYNMTKMLDILEDYLDGEGYKYERIDGNITGSMRQESIDRFNAPGASQFV 693
D + +++ F N + +D L + + + + G++ R+ + F + GAS+
Sbjct: 272 DTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRS-GASRV- 329
Query: 694 FLLSTRSGGLGINLATADTVIIYDSDWNPHNDIQAFSRAHRIGQQNKYINLATADTVII 752
L+ST G+++ +I YD N I R+ R G++ IN D + I
Sbjct: 330 -LISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRI 387
>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 = 31.2 bits (69), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 27/119 (22%), Positives = 52/119 (43%), Gaps = 3/119 (2%)
Query: 634 DIPGLKESIEFYNMTKMLDILEDYLDGEGYKYERIDGNITGSMRQESIDRFNAPGASQFV 693
D + +++ F N + +D L + + + + G++ R+ + F + GAS+
Sbjct: 273 DTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRS-GASRV- 330
Query: 694 FLLSTRSGGLGINLATADTVIIYDSDWNPHNDIQAFSRAHRIGQQNKYINLATADTVII 752
L+ST G+++ +I YD N I R+ R G++ IN D + I
Sbjct: 331 -LISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRI 388
>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 = 31.2 bits (69), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 27/119 (22%), Positives = 52/119 (43%), Gaps = 3/119 (2%)
Query: 634 DIPGLKESIEFYNMTKMLDILEDYLDGEGYKYERIDGNITGSMRQESIDRFNAPGASQFV 693
D + +++ F N + +D L + + + + G++ R+ + F + GAS+
Sbjct: 273 DTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRS-GASRV- 330
Query: 694 FLLSTRSGGLGINLATADTVIIYDSDWNPHNDIQAFSRAHRIGQQNKYINLATADTVII 752
L+ST G+++ +I YD N I R+ R G++ IN D + I
Sbjct: 331 -LISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRI 388
>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 = 31.2 bits (69), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 39/83 (46%), Gaps = 3/83 (3%)
Query: 662 GYKYERIDGNITGSMRQESIDRFNAPGASQFVFLLSTRSGGLGINLATADTVIIYDSDWN 721
G+K I G+++ S R++ I F + L++T GI++ + VI Y N
Sbjct: 262 GFKAGAIHGDLSQSQREKVIRLFKQ---KKIRILIATDVXSRGIDVNDLNCVINYHLPQN 318
Query: 722 PHNDIQAFSRAHRIGQQNKYINL 744
P + R R G++ K I++
Sbjct: 319 PESYXHRIGRTGRAGKKGKAISI 341
>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 31.2 bits (69), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 25/117 (21%), Positives = 51/117 (43%), Gaps = 3/117 (2%)
Query: 634 DIPGLKESIEFYNMTKMLDILEDYLDGEGYKYERIDGNITGSMRQESIDRFNAPGASQFV 693
D + +++ F N + +D L + + + + G++ R+ + F + GAS+
Sbjct: 236 DTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRS-GASRV- 293
Query: 694 FLLSTRSGGLGINLATADTVIIYDSDWNPHNDIQAFSRAHRIGQQNKYINLATADTV 750
L+ST G+++ +I YD N I R+ R G++ +N D +
Sbjct: 294 -LISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAVNFVKNDDI 349
>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 30.8 bits (68), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 25/117 (21%), Positives = 51/117 (43%), Gaps = 3/117 (2%)
Query: 634 DIPGLKESIEFYNMTKMLDILEDYLDGEGYKYERIDGNITGSMRQESIDRFNAPGASQFV 693
D + +++ F N + +D L + + + + G++ R+ + F + GAS+
Sbjct: 236 DTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRS-GASRV- 293
Query: 694 FLLSTRSGGLGINLATADTVIIYDSDWNPHNDIQAFSRAHRIGQQNKYINLATADTV 750
L+ST G+++ +I YD N I R+ R G++ +N D +
Sbjct: 294 -LISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAVNFVKNDDI 349
>pdb|2K28|A Chain A, Solution Nmr Structure Of The Chromo Domain Of The
Chromobox Protein Homolog 4
Length = 60
Score = 29.6 bits (65), Expect = 10.0, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 24/51 (47%), Gaps = 1/51 (1%)
Query: 140 LIANRVINSKTLRDGSTIYLVKWRDLPYDKATWEDENEDIPGLKESIEFYN 190
+ A I K +R G YLVKWR TWE E E+I + I F N
Sbjct: 5 VFAVESIEKKRIRKGRVEYLVKWRGWSPKYNTWEPE-ENILDPRLLIAFQN 54
Score = 29.6 bits (65), Expect = 10.0, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 24/51 (47%), Gaps = 1/51 (1%)
Query: 596 LIANRVINSKTLRDGSTIYLVKWRDLPYDKATWEDENEDIPGLKESIEFYN 646
+ A I K +R G YLVKWR TWE E E+I + I F N
Sbjct: 5 VFAVESIEKKRIRKGRVEYLVKWRGWSPKYNTWEPE-ENILDPRLLIAFQN 54
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 0.136 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 27,616,445
Number of Sequences: 62578
Number of extensions: 1095087
Number of successful extensions: 2532
Number of sequences better than 100.0: 51
Number of HSP's better than 100.0 without gapping: 23
Number of HSP's successfully gapped in prelim test: 28
Number of HSP's that attempted gapping in prelim test: 2453
Number of HSP's gapped (non-prelim): 96
length of query: 1001
length of database: 14,973,337
effective HSP length: 108
effective length of query: 893
effective length of database: 8,214,913
effective search space: 7335917309
effective search space used: 7335917309
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: 56 (26.2 bits)