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= 044036
(875 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 = 228 bits (580), Expect = 1e-59, Method: Compositional matrix adjust.
Identities = 187/594 (31%), Positives = 278/594 (46%), Gaps = 109/594 (18%)
Query: 127 IQVPASINCRLLEHQREGVKFLYKLYKNKHGGILGDDMGLGKTIQTIAFLA-AVFGKDES 185
+Q P L + Q G+ ++ L+ GIL D+MGLGKT+QT+AF++ +F + ++
Sbjct: 227 VQPPFIKGGELRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWLIFARRQN 286
Query: 186 SDSTILKDNKVDKKGYVLIICPSSVIQNWEIEFSRWS-TFNVSIYHG--PNRDMILE--- 239
G +I+ P S + W F +W+ N Y G +RD I E
Sbjct: 287 --------------GPHIIVVPLSTMPAWLDTFEKWAPDLNCICYMGNQKSRDTIREYEF 332
Query: 240 -------KLEACGVEVLITSFDSYRIHGSILSEVNWEIVIVDEAHRLKNEKSKLYMACLE 292
+ VL+T+++ + L + W+ + VDEAHRLKN +S LY +
Sbjct: 333 YTNPRAKGKKTMKFNVLLTTYEYILKDRAELGSIKWQFMAVDEAHRLKNAESSLYESLNS 392
Query: 293 LKTRNRIGLTGTIMQNKIMELYNLFDWVAPGSLGTREHFREFYDEPLKHGQRLTAPERFI 352
K NR+ +TGT +QN I EL L +++ PG R D+ + + E +I
Sbjct: 393 FKVANRMLITGTPLQNNIKELAALVNFLMPG--------RFTIDQEIDFENQDEEQEEYI 444
Query: 353 RIADERKQHLVAVLRKYLLRRTKEETIGHLMMGKEDNVVFCTMSDLQKRAYRRLLQLPEI 412
R ++ ++LRR K++ + + K + ++ +SD+Q Y+ +L
Sbjct: 445 HDLHRR-------IQPFILRRLKKD-VEKSLPSKTERILRVELSDVQTEYYKNIL----- 491
Query: 413 QCLINKDLPCSCGSPLTQVECCKRLDNLDGCDSCPFCLVLPCLVKLQQISNHLELIKPNP 472
S LT G F L L + +L++ SNH P
Sbjct: 492 ---------TKNYSALTA-----------GAKGGHFSL-LNIMNELKKASNH-----PYL 525
Query: 473 RDEPDKQRKDAELASAVFGPDIDLVGGNAQNESFIGLSDVKSCGKMRALEKLMYSWASKG 532
D + E FG G + GL + S GKM L++L+ G
Sbjct: 526 FDNAE------ERVLQKFGD-----GKMTRENVLRGL--IMSSGKMVLLDQLLTRLKKDG 572
Query: 533 DKILLFSYSVRMLDILEKFLIRKGYSFSRLDGSTPSNLRQSLVDDFNSSPSKQ-VFLIST 591
++L+FS VRMLDIL +L KG +F RLDG+ PS R+ +D FNS S VFL+ST
Sbjct: 573 HRVLIFSQMVRMLDILGDYLSIKGINFQRLDGTVPSAQRRISIDHFNSPDSNDFVFLLST 632
Query: 592 RAGGLGLNLVSANRVVIFDPNWNPAQDLQAQDRSFRFGQKRHVIVFRLLSAGSLEELVYT 651
RAGGLG+NL++A+ VVIFD +WNP DLQA R+ R GQK HV+V+RL+S ++EE V
Sbjct: 633 RAGGLGINLMTADTVVIFDSDWNPQADLQAMARAHRIGQKNHVMVYRLVSKDTVEEEVLE 692
Query: 652 RQVYKQQLSNIAVSGKLEKRYFEGVQDCKEFQ-------GEL-----FGICNLF 693
R K L +S GV D ++ GEL FG N+F
Sbjct: 693 RARKKMILEYAIISL--------GVTDGNKYTKKNEPNAGELSAILKFGAGNMF 738
>pdb|1Z6A|A Chain A, Sulfolobus Solfataricus Swi2SNF2 ATPASE CORE DOMAIN
Length = 500
Score = 218 bits (555), Expect = 1e-56, Method: Compositional matrix adjust.
Identities = 155/540 (28%), Positives = 267/540 (49%), Gaps = 102/540 (18%)
Query: 130 PASINCRLLEHQREGVKFLYKLYKNKHGGILGDDMGLGKTIQTIAFLAAVFGKDESSDST 189
P +I L +Q +G ++ + K G L DDMGLGKT+QTIA + ++E + S
Sbjct: 31 PYNIKANLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAVFSDAKKENELTPS- 89
Query: 190 ILKDNKVDKKGYVLIICPSSVIQNWEIEFSRWST-FNVSIYHGPNRDMILEKLEACGVEV 248
L+ICP SV++NWE E S+++ +++H + LE + +
Sbjct: 90 -------------LVICPLSVLKNWEEELSKFAPHLRFAVFHEDRSKIKLEDYD-----I 131
Query: 249 LITSFDSYRIHGSILSEVNWEIVIVDEAHRLKNEKSKLYMACLELKTRNRIGLTGTIMQN 308
++T++ + + + L EV W+ +++DEA +KN ++K++ A ELK++ RI LTGT ++N
Sbjct: 132 ILTTY-AVLLRDTRLKEVEWKYIVIDEAQNIKNPQTKIFKAVKELKSKYRIALTGTPIEN 190
Query: 309 KIMELYNLFDWVAPGSLGTREHFREFYDEPLKHGQRLTAPERFIRIADERKQHLVAVLRK 368
K+ +L+++ ++ PG LG+ F+ + P+K G + K+ L A++
Sbjct: 191 KVDDLWSIMTFLNPGLLGSYSEFKSKFATPIKKGDNMA------------KEELKAIISP 238
Query: 369 YLLRRTK-EETIGHLMMGKEDNVVFCTMSDLQKRAYRRLLQLPEIQCLINKDLPCSCGSP 427
++LRRTK ++ I + + K + V+C ++ Q Y+ E++ L N
Sbjct: 239 FILRRTKYDKAIINDLPDKIETNVYCNLTPEQAAMYK-----AEVENLFN---------- 283
Query: 428 LTQVECCKRLDNLDGCDSCPFCLVLPCLVKLQQISNHLELIKPNPRDEPDKQRKDAELAS 487
+D++ G ++L L+KL+QI +H L+K
Sbjct: 284 --------NIDSVTGIKRK--GMILSTLLKLKQIVDHPALLK------------------ 315
Query: 488 AVFGPDIDLVGGNAQNESFIGLSDVKSCGKMRALEKLMYSWASKGDKILLFSYSVRMLDI 547
GG V+ GKM +++ +GDKI +F+ V M I
Sbjct: 316 ----------GGE---------QSVRRSGKMIRTMEIIEEALDEGDKIAIFTQFVDMGKI 356
Query: 548 LEKFLIRK-GYSFSRLDGSTPSNLRQSLVDDFNSSPSKQVFLISTRAGGLGLNLVSANRV 606
+ + ++ L G R ++ F ++PS + ++S +AGG G+NL SANRV
Sbjct: 357 IRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVKAGGFGINLTSANRV 416
Query: 607 VIFDPNWNPAQDLQAQDRSFRFGQKRHVIVFRLLSAGSLEE-----LVYTRQVYKQQLSN 661
+ FD WNPA + QA DR +R GQ R+VIV +L+S G+LEE L + R ++K +S+
Sbjct: 417 IHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVGTLEEKIDQLLAFKRSLFKDIISS 476
>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 = 208 bits (529), Expect = 1e-53, Method: Compositional matrix adjust.
Identities = 156/542 (28%), Positives = 266/542 (49%), Gaps = 106/542 (19%)
Query: 130 PASINCRLLEHQREGVKFLYKLYKNKHG-GI-LGDDMGLGKTIQTIAFLAAVFGKDESSD 187
P +I L +Q +G F + + NK G GI L DD GLGKT+QTIA + ++E +
Sbjct: 31 PYNIKANLRPYQIKG--FSWXRFXNKLGFGICLADDXGLGKTLQTIAVFSDAKKENELTP 88
Query: 188 STILKDNKVDKKGYVLIICPSSVIQNWEIEFSRWST-FNVSIYHGPNRDMILEKLEACGV 246
S L+ICP SV++NWE E S+++ +++H + LE +
Sbjct: 89 S--------------LVICPLSVLKNWEEELSKFAPHLRFAVFHEDRSKIKLEDYD---- 130
Query: 247 EVLITSFDSYRIHGSILSEVNWEIVIVDEAHRLKNEKSKLYMACLELKTRNRIGLTGTIM 306
+++T++ + + + L EV W+ +++DEA +KN ++K++ A ELK++ RI LTGT +
Sbjct: 131 -IILTTY-AVLLRDTRLKEVEWKYIVIDEAQNIKNPQTKIFKAVKELKSKYRIALTGTPI 188
Query: 307 QNKIMELYNLFDWVAPGSLGTREHFREFYDEPLKHGQRLTAPERFIRIADERKQHLVAVL 366
+NK+ +L+++ ++ PG LG+ F+ + P+K G + K+ L A++
Sbjct: 189 ENKVDDLWSIXTFLNPGLLGSYSEFKSKFATPIKKGD------------NXAKEELKAII 236
Query: 367 RKYLLRRTK-EETIGHLMMGKEDNVVFCTMSDLQKRAYRRLLQLPEIQCLINKDLPCSCG 425
++LRRTK ++ I + + K + V+C ++ Q Y+ E++ L N
Sbjct: 237 SPFILRRTKYDKAIINDLPDKIETNVYCNLTPEQAAXYK-----AEVENLFN-------- 283
Query: 426 SPLTQVECCKRLDNLDGCDSCPFCLVLPCLVKLQQISNHLELIKPNPRDEPDKQRKDAEL 485
+D++ G +L L+KL+QI +H L+K
Sbjct: 284 ----------NIDSVTGIKRK--GXILSTLLKLKQIVDHPALLK---------------- 315
Query: 486 ASAVFGPDIDLVGGNAQNESFIGLSDVKSCGKMRALEKLMYSWASKGDKILLFSYSVRML 545
GG V+ GK +++ +GDKI +F+ V
Sbjct: 316 ------------GGE---------QSVRRSGKXIRTXEIIEEALDEGDKIAIFTQFVDXG 354
Query: 546 DILEKFLIRK-GYSFSRLDGSTPSNLRQSLVDDFNSSPSKQVFLISTRAGGLGLNLVSAN 604
I+ + ++ L G R ++ F ++PS + ++S +AGG G+NL SAN
Sbjct: 355 KIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVKAGGFGINLTSAN 414
Query: 605 RVVIFDPNWNPAQDLQAQDRSFRFGQKRHVIVFRLLSAGSLEE-----LVYTRQVYKQQL 659
RV+ FD WNPA + QA DR +R GQ R+VIV +L+S G+LEE L + R ++K +
Sbjct: 415 RVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVGTLEEKIDQLLAFKRSLFKDII 474
Query: 660 SN 661
S+
Sbjct: 475 SS 476
>pdb|1Z3I|X Chain X, Structure Of The Swi2SNF2 CHROMATIN REMODELING DOMAIN OF
EUKARYOTIC Rad54
Length = 644
Score = 144 bits (364), Expect = 2e-34, Method: Compositional matrix adjust.
Identities = 86/287 (29%), Positives = 154/287 (53%), Gaps = 25/287 (8%)
Query: 137 LLEHQREGVKFLY-----KLYKNKHGGILGDDMGLGKTIQTIAFLAAVFGKDESSDSTIL 191
L HQREGVKFL+ + +N +G I+ D+MGLGKT+Q I + + + I
Sbjct: 56 LRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLIWTLLKQSPDCKPEID 115
Query: 192 KDNKVDKKGYVLIICPSSVIQNWEIEFSRWSTFNVS--IYHGPNRDMILEKL-------- 241
K V+++ PSS+++NW E +W V G ++D I KL
Sbjct: 116 K---------VIVVSPSSLVRNWYNEVGKWLGGRVQPVAIDGGSKDEIDSKLVNFISQQG 166
Query: 242 EACGVEVLITSFDSYRIHGSILSEVNWEIVIVDEAHRLKNEKSKLYMACLELKTRNRIGL 301
+LI S++++R+H +L + +VI DE HRLKN ++ Y+A + + R+ +
Sbjct: 167 MRIPTPILIISYETFRLHAEVLHKGKVGLVICDEGHRLKNSDNQTYLALNSMNAQRRVLI 226
Query: 302 TGTIMQNKIMELYNLFDWVAPGSLGTREHFREFYDEPLKHGQRLTAPERFIRIADERKQH 361
+GT +QN ++E ++L +V G LGT + F++ ++ P+ G+ A ++ +++ Q
Sbjct: 227 SGTPIQNDLLEYFSLVHFVNSGILGTAQEFKKRFEIPILKGRDADASDKDRAAGEQKLQE 286
Query: 362 LVAVLRKYLLRRTKEETIGHLMMGKEDNVVFCTMSDLQKRAYRRLLQ 408
L++++ + L+RRT + + + K + VV C ++ LQK Y+ L+
Sbjct: 287 LISIVNRCLIRRT-SDILSKYLPVKIEQVVCCNLTPLQKELYKLFLK 332
Score = 127 bits (318), Expect = 4e-29, Method: Compositional matrix adjust.
Identities = 63/151 (41%), Positives = 98/151 (64%), Gaps = 2/151 (1%)
Query: 516 GKMRALEKLM-YSWASKGDKILLFSYSVRMLDILEKFLIRKGYSFSRLDGSTPSNLRQSL 574
GKM L+ ++ + + DK++L S + LD+ EK + Y + RLDG+ R +
Sbjct: 399 GKMLVLDYILAMTRTTTSDKVVLVSNYTQTLDLFEKLCRNRRYLYVRLDGTMSIKKRAKI 458
Query: 575 VDDFNSSPSKQ-VFLISTRAGGLGLNLVSANRVVIFDPNWNPAQDLQAQDRSFRFGQKRH 633
V+ FN+ S + +F++S++AGG GLNL+ ANR+V+FDP+WNPA D QA R +R GQK+
Sbjct: 459 VERFNNPSSPEFIFMLSSKAGGCGLNLIGANRLVMFDPDWNPANDEQAMARVWRDGQKKT 518
Query: 634 VIVFRLLSAGSLEELVYTRQVYKQQLSNIAV 664
++RLLS G++EE + RQ +K+ LS+ V
Sbjct: 519 CYIYRLLSTGTIEEKILQRQAHKKALSSCVV 549
>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 = 102 bits (255), Expect = 6e-22, Method: Compositional matrix adjust.
Identities = 58/160 (36%), Positives = 90/160 (56%), Gaps = 6/160 (3%)
Query: 508 GLSDVKSCGKMRALEKLMYSWASKGDKILLFSYSVRMLDILEKFLIRK-GYSFSRLDGST 566
G V+ GKM +++ +GDKI +F+ V M I+ + ++ L G
Sbjct: 88 GEQSVRRSGKMIRTMEIIEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGEL 147
Query: 567 PSNLRQSLVDDFNSSPSKQVFLISTRAGGLGLNLVSANRVVIFDPNWNPAQDLQAQDRSF 626
R ++ F ++PS + ++S +AGG G+NL SANRV+ FD WNPA + QA DR +
Sbjct: 148 SKKERDDIISKFQNNPSVKFIVLSVKAGGFGINLTSANRVIHFDRWWNPAVEDQATDRVY 207
Query: 627 RFGQKRHVIVFRLLSAGSLEE-----LVYTRQVYKQQLSN 661
R GQ R+VIV +L+S G+LEE L + R ++K +S+
Sbjct: 208 RIGQTRNVIVHKLISVGTLEEKIDQLLAFKRSLFKDIISS 247
>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3
Length = 395
Score = 40.4 bits (93), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 33/119 (27%), Positives = 55/119 (46%), Gaps = 9/119 (7%)
Query: 525 MYSWASKGDKILLFSYSVRMLDILEKFLIRKGYSFSRLDGSTPSNLRQSLVDDFNSSPSK 584
+Y + G I+ F + + ++L L +G+ S L G + R L+DDF SK
Sbjct: 237 LYGLMTIGSSII-FVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSK 295
Query: 585 QVFLISTRAGGLGLNLVSANRVVIFD------PNWNPAQDLQAQDRSFRFGQKRHVIVF 637
LI+T G+++ + + VV +D +PA + R+ RFG+K I F
Sbjct: 296 --VLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISF 352
>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 = 40.0 bits (92), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 33/119 (27%), Positives = 55/119 (46%), Gaps = 9/119 (7%)
Query: 525 MYSWASKGDKILLFSYSVRMLDILEKFLIRKGYSFSRLDGSTPSNLRQSLVDDFNSSPSK 584
+Y + G I+ F + + ++L L +G+ S L G + R L+DDF SK
Sbjct: 237 LYGVMTIGSSII-FVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSK 295
Query: 585 QVFLISTRAGGLGLNLVSANRVVIFD------PNWNPAQDLQAQDRSFRFGQKRHVIVF 637
LI+T G+++ + + VV +D +PA + R+ RFG+K I F
Sbjct: 296 --VLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISF 352
>pdb|2KBF|A Chain A, Solution Structure Of Carboxyl-Terminal Domain Of Dbp5p
Length = 187
Score = 40.0 bits (92), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 33/119 (27%), Positives = 55/119 (46%), Gaps = 9/119 (7%)
Query: 525 MYSWASKGDKILLFSYSVRMLDILEKFLIRKGYSFSRLDGSTPSNLRQSLVDDFNSSPSK 584
+Y + G I+ F + + ++L L +G+ S L G + R L+DDF SK
Sbjct: 29 LYGLMTIGSSII-FVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSK 87
Query: 585 QVFLISTRAGGLGLNLVSANRVVIFD------PNWNPAQDLQAQDRSFRFGQKRHVIVF 637
LI+T G+++ + + VV +D +PA + R+ RFG+K I F
Sbjct: 88 --VLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISF 144
>pdb|3GFP|A Chain A, Structure Of The C-Terminal Domain Of The Dead-Box Protein
Dbp5
Length = 189
Score = 39.7 bits (91), Expect = 0.008, Method: Composition-based stats.
Identities = 34/119 (28%), Positives = 56/119 (47%), Gaps = 9/119 (7%)
Query: 525 MYSWASKGDKILLFSYSVRMLDILEKFLIRKGYSFSRLDGSTPSNLRQSLVDDFNSSPSK 584
+Y + G I+ F + + ++L L +G+ S L G + R L+DDF SK
Sbjct: 31 LYGLXTIGSSII-FVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSK 89
Query: 585 QVFLISTRAGGLGLNLVSANRVVIFD-PNW-----NPAQDLQAQDRSFRFGQKRHVIVF 637
LI+T G+++ + + VV +D P +PA + R+ RFG+K I F
Sbjct: 90 --VLITTNVLARGIDIPTVSXVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISF 146
>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 = 39.3 bits (90), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 27/102 (26%), Positives = 50/102 (49%), Gaps = 2/102 (1%)
Query: 536 LLFSYSVRMLDILEKFLIRKGYSFSRLDGSTPSNLRQSLVDDFNSSPSKQVFLISTRAGG 595
++F + R +D L + + ++ S + G P R+S++ +F S S+ LIST
Sbjct: 281 VIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASR--VLISTDVWA 338
Query: 596 LGLNLVSANRVVIFDPNWNPAQDLQAQDRSFRFGQKRHVIVF 637
GL++ + ++ +D N + RS R+G+K I F
Sbjct: 339 RGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINF 380
>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 = 39.3 bits (90), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 27/102 (26%), Positives = 50/102 (49%), Gaps = 2/102 (1%)
Query: 536 LLFSYSVRMLDILEKFLIRKGYSFSRLDGSTPSNLRQSLVDDFNSSPSKQVFLISTRAGG 595
++F + R +D L + + ++ S + G P R+S++ +F S S+ LIST
Sbjct: 281 VIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASR--VLISTDVWA 338
Query: 596 LGLNLVSANRVVIFDPNWNPAQDLQAQDRSFRFGQKRHVIVF 637
GL++ + ++ +D N + RS R+G+K I F
Sbjct: 339 RGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINF 380
>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 = 39.3 bits (90), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 27/102 (26%), Positives = 50/102 (49%), Gaps = 2/102 (1%)
Query: 536 LLFSYSVRMLDILEKFLIRKGYSFSRLDGSTPSNLRQSLVDDFNSSPSKQVFLISTRAGG 595
++F + R +D L + + ++ S + G P R+S++ +F S S+ LIST
Sbjct: 280 VIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASR--VLISTDVWA 337
Query: 596 LGLNLVSANRVVIFDPNWNPAQDLQAQDRSFRFGQKRHVIVF 637
GL++ + ++ +D N + RS R+G+K I F
Sbjct: 338 RGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINF 379
>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 = 38.9 bits (89), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 27/102 (26%), Positives = 50/102 (49%), Gaps = 2/102 (1%)
Query: 536 LLFSYSVRMLDILEKFLIRKGYSFSRLDGSTPSNLRQSLVDDFNSSPSKQVFLISTRAGG 595
++F + R +D L + + ++ S + G P R+S++ +F S S+ LIST
Sbjct: 259 VIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASR--VLISTDVWA 316
Query: 596 LGLNLVSANRVVIFDPNWNPAQDLQAQDRSFRFGQKRHVIVF 637
GL++ + ++ +D N + RS R+G+K I F
Sbjct: 317 RGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINF 358
>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 = 0.012, Method: Composition-based stats.
Identities = 34/119 (28%), Positives = 56/119 (47%), Gaps = 9/119 (7%)
Query: 525 MYSWASKGDKILLFSYSVRMLDILEKFLIRKGYSFSRLDGSTPSNLRQSLVDDFNSSPSK 584
+Y + G I+ F + + ++L L +G+ S L G + R L+DDF SK
Sbjct: 30 LYGVXTIGSSII-FVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSK 88
Query: 585 QVFLISTRAGGLGLNLVSANRVVIFD-PNW-----NPAQDLQAQDRSFRFGQKRHVIVF 637
LI+T G+++ + + VV +D P +PA + R+ RFG+K I F
Sbjct: 89 --VLITTNVLARGIDIPTVSXVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISF 145
>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 38.5 bits (88), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 26/102 (25%), Positives = 50/102 (49%), Gaps = 2/102 (1%)
Query: 536 LLFSYSVRMLDILEKFLIRKGYSFSRLDGSTPSNLRQSLVDDFNSSPSKQVFLISTRAGG 595
++F + R +D L + + ++ S + G P R+S++ +F S S+ LIST
Sbjct: 244 VIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASR--VLISTDVWA 301
Query: 596 LGLNLVSANRVVIFDPNWNPAQDLQAQDRSFRFGQKRHVIVF 637
GL++ + ++ +D N + RS R+G+K + F
Sbjct: 302 RGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAVNF 343
>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 38.1 bits (87), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 26/102 (25%), Positives = 50/102 (49%), Gaps = 2/102 (1%)
Query: 536 LLFSYSVRMLDILEKFLIRKGYSFSRLDGSTPSNLRQSLVDDFNSSPSKQVFLISTRAGG 595
++F + R +D L + + ++ S + G P R+S++ +F S S+ LIST
Sbjct: 244 VIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASR--VLISTDVWA 301
Query: 596 LGLNLVSANRVVIFDPNWNPAQDLQAQDRSFRFGQKRHVIVF 637
GL++ + ++ +D N + RS R+G+K + F
Sbjct: 302 RGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAVNF 343
>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 = 37.7 bits (86), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 51/206 (24%), Positives = 78/206 (37%), Gaps = 56/206 (27%)
Query: 159 ILGDDMGLGKTIQTIAFLAAVFGKDESSDSTILKDNKVDKKG-YVLIICPSSVIQNWEIE 217
+L D++GLGKTI+ IL + VLII P ++ W +E
Sbjct: 174 LLADEVGLGKTIEA---------------GXILHQQLLSGAAERVLIIVPETLQHQWLVE 218
Query: 218 ----FS-RWSTFNVSIYHGPNRDMI----LEKLEACGVEVLITSFDSYRIHGSILSEVNW 268
F+ R++ F+ Y D E+L C ++ S R+ L E W
Sbjct: 219 XLRRFNLRFALFDDERYAEAQHDAYNPFDTEQLVICSLDFARRS--KQRLEH--LCEAEW 274
Query: 269 EIVIVDEAHRL---KNEKSKLYMACLELKTRNRIGLTGTIMQNKIMELYNLFDWVAPGSL 325
++++VDEAH L ++ S+ Y A +L + G ++ P L
Sbjct: 275 DLLVVDEAHHLVWSEDAPSREYQAIEQLAEH----VPGVLLLT-----------ATPEQL 319
Query: 326 GTREHFREFYDEPLKHGQRLTAPERF 351
G HF RL P RF
Sbjct: 320 GXESHFARL---------RLLDPNRF 336
>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x
Length = 417
Score = 36.6 bits (83), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 38/171 (22%), Positives = 71/171 (41%), Gaps = 22/171 (12%)
Query: 476 PDKQRKDAELASAVFGPDIDLVGGNAQNES-FIGLSDVKSCGKMRALEKLMYSWASKGDK 534
P K + + SA F +I ++ + +E F+ + V S + +K++ W + DK
Sbjct: 206 PPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGRVGSTSE-NITQKVV--WVEESDK 262
Query: 535 ----------------ILLFSYSVRMLDILEKFLIRKGYSFSRLDGSTPSNLRQSLVDDF 578
L+F + + D LE FL +GY+ + + G R+ + F
Sbjct: 263 RSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQF 322
Query: 579 NSSPSKQVFLISTRAGGLGLNLVSANRVVIFDPNWNPAQDLQAQDRSFRFG 629
S K L++T GL++ + V+ FD + + + R+ R G
Sbjct: 323 RS--GKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVG 371
>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 = 35.0 bits (79), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 36/75 (48%), Gaps = 2/75 (2%)
Query: 536 LLFSYSVRMLDILEKFLIRKGYSFSRLDGSTPSNLRQSLVDDFNSSPSKQVFLISTRAGG 595
L+F + + D LE FL +GY+ + + G R+ + F S S L++T
Sbjct: 50 LVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSP--ILVATAVAA 107
Query: 596 LGLNLVSANRVVIFD 610
GL++ + V+ FD
Sbjct: 108 RGLDISNVKHVINFD 122
>pdb|3RC8|A Chain A, Human Mitochondrial Helicase Suv3 In Complex With Short
Rna Fragment
Length = 677
Score = 31.6 bits (70), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 40/156 (25%), Positives = 68/156 (43%), Gaps = 34/156 (21%)
Query: 532 GDKILLFS----YSV-RMLDILEKFLIRKGYSFSRLDGSTPSNLRQSLVDDFNSSPSKQV 586
GD I+ FS YSV R ++I +G + + GS P + + FN
Sbjct: 322 GDCIVCFSKNDIYSVSRQIEI-------RGLESAVIYGSLPPGTKLAQAKKFNDPNDPCK 374
Query: 587 FLISTRAGGLGLNLVSANRVVIFD---PNWN-----------PAQDLQAQDRSFRFGQKR 632
L++T A G+GLNL S R++ + P+ N +Q LQ R+ RF +
Sbjct: 375 ILVATDAIGMGLNL-SIRRIIFYSLIKPSINEKGERELEPITTSQALQIAGRAGRFSSR- 432
Query: 633 HVIVFRLLSAGSL--EELVYTRQVYKQQLSNIAVSG 666
F+ ++ E+L +++ K+ + I +G
Sbjct: 433 ----FKEGEVTTMNHEDLSLLKEILKRPVDPIRAAG 464
>pdb|3E20|C Chain C, Crystal Structure Of S.Pombe Erf1ERF3 COMPLEX
pdb|3E20|B Chain B, Crystal Structure Of S.Pombe Erf1ERF3 COMPLEX
pdb|3E20|H Chain H, Crystal Structure Of S.Pombe Erf1ERF3 COMPLEX
pdb|3E20|K Chain K, Crystal Structure Of S.Pombe Erf1ERF3 COMPLEX
Length = 441
Score = 30.8 bits (68), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 31/120 (25%), Positives = 50/120 (41%), Gaps = 14/120 (11%)
Query: 310 IMELYNLFDWVAPGSLGTREHFREF-YDEPLKHGQRLTAPERFIRIADERKQHLVAVLRK 368
+M+ + V GS RE + F D P KHG+ + RF R+ DE++ + V
Sbjct: 155 VMDGHQTLYGVVSGS--AREVLQRFTVDLPKKHGRGGQSALRFARLRDEKRHNYV----- 207
Query: 369 YLLRRTKEETIGHLMMGKEDNV---VFCTMSDLQKRAYRRLLQLPEIQCLINKDLPCSCG 425
R+ E + H + + NV V +D + + L +Q I K + S G
Sbjct: 208 ---RKVAEGAVQHFITDDKPNVAGIVLAGSADFKTELGQSDLFDQRLQSRIIKTVDVSYG 264
>pdb|3RC3|A Chain A, Human Mitochondrial Helicase Suv3
Length = 677
Score = 30.4 bits (67), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 40/156 (25%), Positives = 68/156 (43%), Gaps = 34/156 (21%)
Query: 532 GDKILLFS----YSV-RMLDILEKFLIRKGYSFSRLDGSTPSNLRQSLVDDFNSSPSKQV 586
GD I+ FS YSV R ++I +G + + GS P + + FN
Sbjct: 322 GDCIVCFSKNDIYSVSRQIEI-------RGLESAVIYGSLPPGTKLAQAKKFNDPNDPCK 374
Query: 587 FLISTRAGGLGLNLVSANRVVIFD---PNWN-----------PAQDLQAQDRSFRFGQKR 632
L++T A G GLNL S R++ + P+ N +Q LQ R+ RF +
Sbjct: 375 ILVATDAIGXGLNL-SIRRIIFYSLIKPSINEKGERELEPITTSQALQIAGRAGRFSSR- 432
Query: 633 HVIVFR--LLSAGSLEELVYTRQVYKQQLSNIAVSG 666
F+ ++ + E+L +++ K+ + I +G
Sbjct: 433 ----FKEGEVTTXNHEDLSLLKEILKRPVDPIRAAG 464
>pdb|3VOR|A Chain A, Crystal Structure Analysis Of The Cofa
Length = 182
Score = 29.6 bits (65), Expect = 7.0, Method: Composition-based stats.
Identities = 31/105 (29%), Positives = 44/105 (41%), Gaps = 22/105 (20%)
Query: 120 KDGEYPIIQVPASINCRLLEHQREGVKF-----LYKLYKNK-HGGILGDDMGLGKTIQTI 173
+DG+YP Q P S+ ++ G+ L KL ++ GI GD +G+G I
Sbjct: 27 RDGKYPDYQAPLSLTADSIKTDSTGIAVAQLVQLGKLTPDEARNGISGDYIGIGGAIT-- 84
Query: 174 AFLAAVFGKDESSDSTILKDNKVDKKGYVLIICPSSVIQ---NWE 215
SS STI K ++ G C S + Q NWE
Sbjct: 85 -----------SSGSTINKGFAMELNGLSQEQCRSILGQVGDNWE 118
>pdb|3S0T|A Chain A, Crystal Structure Of The Cofa Type Iv Pilin Subunit From
Enterotoxigenic E. Coli
pdb|3S0T|B Chain B, Crystal Structure Of The Cofa Type Iv Pilin Subunit From
Enterotoxigenic E. Coli
Length = 184
Score = 29.6 bits (65), Expect = 7.0, Method: Composition-based stats.
Identities = 31/105 (29%), Positives = 44/105 (41%), Gaps = 22/105 (20%)
Query: 120 KDGEYPIIQVPASINCRLLEHQREGVKF-----LYKLYKNK-HGGILGDDMGLGKTIQTI 173
+DG+YP Q P S+ ++ G+ L KL ++ GI GD +G+G I
Sbjct: 29 RDGKYPDYQAPLSLTADSIKTDSTGIAVAQLVQLGKLTPDEARNGISGDYIGIGGAIT-- 86
Query: 174 AFLAAVFGKDESSDSTILKDNKVDKKGYVLIICPSSVIQ---NWE 215
SS STI K ++ G C S + Q NWE
Sbjct: 87 -----------SSGSTINKGFAMELNGLSQEQCRSILGQVGDNWE 120
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.320 0.137 0.406
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 24,707,982
Number of Sequences: 62578
Number of extensions: 1012549
Number of successful extensions: 2085
Number of sequences better than 100.0: 33
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 19
Number of HSP's that attempted gapping in prelim test: 2033
Number of HSP's gapped (non-prelim): 54
length of query: 875
length of database: 14,973,337
effective HSP length: 107
effective length of query: 768
effective length of database: 8,277,491
effective search space: 6357113088
effective search space used: 6357113088
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (26.2 bits)