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= 004880
(725 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 = 350 bits (898), Expect = 2e-96, Method: Compositional matrix adjust.
Identities = 193/499 (38%), Positives = 288/499 (57%), Gaps = 37/499 (7%)
Query: 150 LLTGGKLKSYQLKGVKWLISLWQNGLNGILADQMGLGKTIQTIAFLAHLK-GNGLHGPYL 208
+ GG+L+ +QL G+ W+ LW G NGILAD+MGLGKT+QT+AF++ L +GP++
Sbjct: 231 FIKGGELRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWLIFARRQNGPHI 290
Query: 209 VIAPLSTLSNWVNEISRFVPSVSAIIYHGSKKERDEIRRKHM---PRAIGPK---FPIVV 262
++ PLST+ W++ ++ P ++ I Y G++K RD IR PRA G K F +++
Sbjct: 291 IVVPLSTMPAWLDTFEKWAPDLNCICYMGNQKSRDTIREYEFYTNPRAKGKKTMKFNVLL 350
Query: 263 TSYEVALSDARKYLRHYNWKYLVVDEGHRLKNPKCKLLKELKYIPIGNKLLLTGTPLQNN 322
T+YE L D R L W+++ VDE HRLKN + L + L + N++L+TGTPLQNN
Sbjct: 351 TTYEYILKD-RAELGSIKWQFMAVDEAHRLKNAESSLYESLNSFKVANRMLITGTPLQNN 409
Query: 323 LAELWSLLHFILPDIFSSLEEFQSWFDLSGKCNSEVMKEELEEKRRGQMVAKLHAILRPF 382
+ EL +L++F++P F+ + + + E EE EE + LH ++PF
Sbjct: 410 IKELAALVNFLMPGRFT----------IDQEIDFENQDEEQEE-----YIHDLHRRIQPF 454
Query: 383 LLRRMKSDVEQMLPRKKEIILYATMTEHQRNFQDHLINKTLENHLREKVFSAGRGMKGKL 442
+LRR+K DVE+ LP K E IL +++ Q + +++ K + + +G L
Sbjct: 455 ILRRLKKDVEKSLPSKTERILRVELSDVQTEYYKNILTKNYS-----ALTAGAKGGHFSL 509
Query: 443 NNLMVQLRKNCNHPDLLESA-------FSDSCFYPP--VEQIVEQCGKXXXXXXXXXXXX 493
N+M +L+K NHP L ++A F D + ++ GK
Sbjct: 510 LNIMNELKKASNHPYLFDNAEERVLQKFGDGKMTRENVLRGLIMSSGKMVLLDQLLTRLK 569
Query: 494 XXNHKVLVFSQWTKILDIMEYYFNEKGYEVCRIDGSVRLDERKRQIQDFNDVNSSYRIFL 553
H+VL+FSQ ++LDI+ Y + KG R+DG+V +R+ I FN +S+ +FL
Sbjct: 570 KDGHRVLIFSQMVRMLDILGDYLSIKGINFQRLDGTVPSAQRRISIDHFNSPDSNDFVFL 629
Query: 554 LSTRAGGLGINLTAADTCILYDSDWNPQMDLQAMDRCHRIGQTKPVHVYRLATAQSVEGR 613
LSTRAGGLGINL ADT +++DSDWNPQ DLQAM R HRIGQ V VYRL + +VE
Sbjct: 630 LSTRAGGLGINLMTADTVVIFDSDWNPQADLQAMARAHRIGQKNHVMVYRLVSKDTVEEE 689
Query: 614 ILKRAFSKLKLEHVVIGKG 632
+L+RA K+ LE+ +I G
Sbjct: 690 VLERARKKMILEYAIISLG 708
>pdb|1Z6A|A Chain A, Sulfolobus Solfataricus Swi2SNF2 ATPASE CORE DOMAIN
Length = 500
Score = 240 bits (613), Expect = 2e-63, Method: Compositional matrix adjust.
Identities = 154/462 (33%), Positives = 238/462 (51%), Gaps = 43/462 (9%)
Query: 156 LKSYQLKGVKWLISLWQNGLNGILADQMGLGKTIQTIAFLAHLKGNGLHGPYLVIAPLST 215
L+ YQ+KG W+ + + G LAD MGLGKT+QTIA + K P LVI PLS
Sbjct: 38 LRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAVFSDAKKENELTPSLVICPLSV 97
Query: 216 LSNWVNEISRFVPSVSAIIYHGSKKERDEIRRKHMPRAIGPKFPIVVTSYEVALSDARKY 275
L NW E+S+F P + ++H ++R +I+ + + I++T+Y V L D R
Sbjct: 98 LKNWEEELSKFAPHLRFAVFH---EDRSKIKLED--------YDIILTTYAVLLRDTR-- 144
Query: 276 LRHYNWKYLVVDEGHRLKNPKCKLLKELKYIPIGNKLLLTGTPLQNNLAELWSLLHFILP 335
L+ WKY+V+DE +KNP+ K+ K +K + ++ LTGTP++N + +LWS++ F+ P
Sbjct: 145 LKEVEWKYIVIDEAQNIKNPQTKIFKAVKELKSKYRIALTGTPIENKVDDLWSIMTFLNP 204
Query: 336 DIFSSLEEFQSWFDLSGKCNSEVMKEELEEKRRGQMVAKLHAILRPFLLRRMKSD--VEQ 393
+ S EF+S F K + KEEL+ AI+ PF+LRR K D +
Sbjct: 205 GLLGSYSEFKSKFATPIKKGDNMAKEELK------------AIISPFILRRTKYDKAIIN 252
Query: 394 MLPRKKEIILYATMTEHQRNFQDHLINKTLENHLREKVFSAGRGMKGKLNNLMVQLRKNC 453
LP K E +Y +T Q + +EN G KG + + +++L++
Sbjct: 253 DLPDKIETNVYCNLTPEQA----AMYKAEVENLFNNIDSVTGIKRKGMILSTLLKLKQIV 308
Query: 454 NHPDLLESAFSDSCFYPPVEQIVEQCGKXXXXXXXXXXXXXXNHKVLVFSQWTKILDIME 513
+HP LL+ EQ V + GK K+ +F+Q+ + I+
Sbjct: 309 DHPALLKGG----------EQSVRRSGKMIRTMEIIEEALDEGDKIAIFTQFVDMGKIIR 358
Query: 514 YYF-NEKGYEVCRIDGSVRLDERKRQIQDFNDVNSSYRIFLLSTRAGGLGINLTAADTCI 572
E EV + G + ER I F + N S + +LS +AGG GINLT+A+ I
Sbjct: 359 NIIEKELNTEVPFLYGELSKKERDDIISKFQN-NPSVKFIVLSVKAGGFGINLTSANRVI 417
Query: 573 LYDSDWNPQMDLQAMDRCHRIGQTKPVHVYRLATAQSVEGRI 614
+D WNP ++ QA DR +RIGQT+ V V++L + ++E +I
Sbjct: 418 HFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVGTLEEKI 459
>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 = 233 bits (593), Expect = 4e-61, Method: Compositional matrix adjust.
Identities = 157/465 (33%), Positives = 236/465 (50%), Gaps = 49/465 (10%)
Query: 156 LKSYQLKGVKWLISLWQNGLNGILADQMGLGKTIQTIAFLAHLKGNGLHGPYLVIAPLST 215
L+ YQ+KG W + G LAD GLGKT+QTIA + K P LVI PLS
Sbjct: 38 LRPYQIKGFSWXRFXNKLGFGICLADDXGLGKTLQTIAVFSDAKKENELTPSLVICPLSV 97
Query: 216 LSNWVNEISRFVPSVSAIIYHGSKKERDEIRRKHMPRAIGPKFPIVVTSYEVALSDARKY 275
L NW E+S+F P + ++H ++R +I+ + + I++T+Y V L D R
Sbjct: 98 LKNWEEELSKFAPHLRFAVFH---EDRSKIKLED--------YDIILTTYAVLLRDTR-- 144
Query: 276 LRHYNWKYLVVDEGHRLKNPKCKLLKELKYIPIGNKLLLTGTPLQNNLAELWSLLHFILP 335
L+ WKY+V+DE +KNP+ K+ K +K + ++ LTGTP++N + +LWS+ F+ P
Sbjct: 145 LKEVEWKYIVIDEAQNIKNPQTKIFKAVKELKSKYRIALTGTPIENKVDDLWSIXTFLNP 204
Query: 336 DIFSSLEEFQSWFDLSGKCNSEVMKEELEEKRRGQMVAKLHAILRPFLLRRMKSD--VEQ 393
+ S EF+S F K KEEL+ AI+ PF+LRR K D +
Sbjct: 205 GLLGSYSEFKSKFATPIKKGDNXAKEELK------------AIISPFILRRTKYDKAIIN 252
Query: 394 MLPRKKEIILYATMTEHQRNFQDHLINKTLENHLREKVFSAGRGMKGKLNNLMVQLRKNC 453
LP K E +Y +T Q +EN G KG + + +++L++
Sbjct: 253 DLPDKIETNVYCNLTPEQA----AXYKAEVENLFNNIDSVTGIKRKGXILSTLLKLKQIV 308
Query: 454 NHPDLLESAFSDSCFYPPVEQIVEQCGKXXXXXXXXXXXXXXNHKVLVFSQWTK----IL 509
+HP LL+ EQ V + GK K+ +F+Q+ I
Sbjct: 309 DHPALLKGG----------EQSVRRSGKXIRTXEIIEEALDEGDKIAIFTQFVDXGKIIR 358
Query: 510 DIMEYYFNEKGYEVCRIDGSVRLDERKRQIQDFNDVNSSYRIFLLSTRAGGLGINLTAAD 569
+I+E N EV + G + ER I F + N S + +LS +AGG GINLT+A+
Sbjct: 359 NIIEKELNT---EVPFLYGELSKKERDDIISKFQN-NPSVKFIVLSVKAGGFGINLTSAN 414
Query: 570 TCILYDSDWNPQMDLQAMDRCHRIGQTKPVHVYRLATAQSVEGRI 614
I +D WNP ++ QA DR +RIGQT+ V V++L + ++E +I
Sbjct: 415 RVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVGTLEEKI 459
>pdb|1Z3I|X Chain X, Structure Of The Swi2SNF2 CHROMATIN REMODELING DOMAIN OF
EUKARYOTIC Rad54
Length = 644
Score = 186 bits (471), Expect = 5e-47, Method: Compositional matrix adjust.
Identities = 148/510 (29%), Positives = 249/510 (48%), Gaps = 44/510 (8%)
Query: 156 LKSYQLKGVKWLISLW--------QNGLNGILADQMGLGKTIQTIAFL-AHLKGNGLHGP 206
L+ +Q +GVK+L W +N I+AD+MGLGKT+Q I + LK + P
Sbjct: 56 LRPHQREGVKFL---WDCVTGRRIENSYGCIMADEMGLGKTLQCITLIWTLLKQSPDCKP 112
Query: 207 ----YLVIAPLSTLSNWVNEISRFVPS-VSAIIYHGSKKERDEIRRKHM----PRAIGPK 257
+V++P S + NW NE+ +++ V + G K DEI K + + +
Sbjct: 113 EIDKVIVVSPSSLVRNWYNEVGKWLGGRVQPVAIDGGSK--DEIDSKLVNFISQQGMRIP 170
Query: 258 FPIVVTSYEVALSDARKYLRHYNWKYLVVDEGHRLKNPKCKLLKELKYIPIGNKLLLTGT 317
PI++ SYE A + L ++ DEGHRLKN + L + ++L++GT
Sbjct: 171 TPILIISYETFRLHA-EVLHKGKVGLVICDEGHRLKNSDNQTYLALNSMNAQRRVLISGT 229
Query: 318 PLQNNLAELWSLLHFILPDIFSSLEEFQSWFDLSGKCNSEVMKEELEEKRRGQMVAKLHA 377
P+QN+L E +SL+HF+ I + +EF+ F++ + + + Q + +L +
Sbjct: 230 PIQNDLLEYFSLVHFVNSGILGTAQEFKKRFEIPILKGRDADASDKDRAAGEQKLQELIS 289
Query: 378 ILRPFLLRRMKSDVEQMLPRKKEIILYATMTEHQRNFQDHLINKTLENHLREKVFSAGRG 437
I+ L+RR + + LP K E ++ +T Q+ + + + V S G
Sbjct: 290 IVNRCLIRRTSDILSKYLPVKIEQVVCCNLTPLQKELYKLFLKQA------KPVESLQTG 343
Query: 438 -MKGKLNNLMVQLRKNCNHPDLL-------ESAFSDSCFYPP---VEQIVEQ--CGKX-X 483
+ + + L+K CNHP L+ E F + P + VE GK
Sbjct: 344 KISVSSLSSITSLKKLCNHPALIYEKCLTGEEGFDGALDLFPQNYSTKAVEPQLSGKMLV 403
Query: 484 XXXXXXXXXXXXNHKVLVFSQWTKILDIMEYYFNEKGYEVCRIDGSVRLDERKRQIQDFN 543
+ KV++ S +T+ LD+ E + Y R+DG++ + +R + ++ FN
Sbjct: 404 LDYILAMTRTTTSDKVVLVSNYTQTLDLFEKLCRNRRYLYVRLDGTMSIKKRAKIVERFN 463
Query: 544 DVNSSYRIFLLSTRAGGLGINLTAADTCILYDSDWNPQMDLQAMDRCHRIGQTKPVHVYR 603
+ +S IF+LS++AGG G+NL A+ +++D DWNP D QAM R R GQ K ++YR
Sbjct: 464 NPSSPEFIFMLSSKAGGCGLNLIGANRLVMFDPDWNPANDEQAMARVWRDGQKKTCYIYR 523
Query: 604 LATAQSVEGRILKRAFSKLKLEHVVIGKGQ 633
L + ++E +IL+R K L V+ + Q
Sbjct: 524 LLSTGTIEEKILQRQAHKKALSSCVVDEEQ 553
>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 = 92.0 bits (227), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 69/229 (30%), Positives = 108/229 (47%), Gaps = 20/229 (8%)
Query: 387 MKSDVEQMLPRKKEIILYATMTEHQRNFQDHLINKTLENHLREKVFSAGRGMKGKLNNLM 446
M SD LP K E +Y +T Q + +EN G KG + + +
Sbjct: 21 MASD----LPDKIETNVYCNLTPEQA----AMYKAEVENLFNNIDSVTGIKRKGMILSTL 72
Query: 447 VQLRKNCNHPDLLESAFSDSCFYPPVEQIVEQCGKXXXXXXXXXXXXXXNHKVLVFSQWT 506
++L++ +HP LL+ EQ V + GK K+ +F+Q+
Sbjct: 73 LKLKQIVDHPALLKGG----------EQSVRRSGKMIRTMEIIEEALDEGDKIAIFTQFV 122
Query: 507 KILDIMEYYF-NEKGYEVCRIDGSVRLDERKRQIQDFNDVNSSYRIFLLSTRAGGLGINL 565
+ I+ E EV + G + ER I F + N S + +LS +AGG GINL
Sbjct: 123 DMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQN-NPSVKFIVLSVKAGGFGINL 181
Query: 566 TAADTCILYDSDWNPQMDLQAMDRCHRIGQTKPVHVYRLATAQSVEGRI 614
T+A+ I +D WNP ++ QA DR +RIGQT+ V V++L + ++E +I
Sbjct: 182 TSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVGTLEEKI 230
>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 = 42.7 bits (99), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 47/176 (26%), Positives = 72/176 (40%), Gaps = 16/176 (9%)
Query: 178 ILADQMGLGKTIQTIAFLAHLKGNGLHGPYLVIAPLSTLSNWVNEISRFVPSVSAIIYHG 237
+LAD++GLGKTI+ L +G L+I P + W+ E R A+
Sbjct: 174 LLADEVGLGKTIEAGXILHQQLLSGAAERVLIIVPETLQHQWLVEXLRRFNLRFALF--- 230
Query: 238 SKKERDEIRRKHMPRAIGP--KFPIVVTSYEVALSDARK--YLRHYNWKYLVVDEGHRLK 293
DE + A P +V+ S + A ++ +L W LVVDE H L
Sbjct: 231 ----DDERYAEAQHDAYNPFDTEQLVICSLDFARRSKQRLEHLCEAEWDLLVVDEAHHLV 286
Query: 294 NPKCKLLKELKYIP-----IGNKLLLTGTPLQNNLAELWSLLHFILPDIFSSLEEF 344
+ +E + I + LLLT TP Q ++ L + P+ F +F
Sbjct: 287 WSEDAPSREYQAIEQLAEHVPGVLLLTATPEQLGXESHFARLRLLDPNRFHDFAQF 342
Score = 35.4 bits (80), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 38/80 (47%), Gaps = 4/80 (5%)
Query: 534 ERKRQIQDFNDVNSSYRIFLLSTRAGGLGINLTAADTCILYDSDWNPQMDLQAMDRCHRI 593
ER R F + ++ ++ LL + G G N A + +D +NP + Q + R RI
Sbjct: 542 ERDRAAAWFAEEDTGAQV-LLCSEIGSEGRNFQFASHXVXFDLPFNPDLLEQRIGRLDRI 600
Query: 594 GQTKPVHV---YRLATAQSV 610
GQ + + Y TAQSV
Sbjct: 601 GQAHDIQIHVPYLEKTAQSV 620
>pdb|1TXG|A Chain A, Structure Of Glycerol-3-Phosphate Dehydrogenase From
Archaeoglobus Fulgidus
pdb|1TXG|B Chain B, Structure Of Glycerol-3-Phosphate Dehydrogenase From
Archaeoglobus Fulgidus
Length = 335
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 28/103 (27%), Positives = 50/103 (48%)
Query: 139 RVDKEQRELVSLLTGGKLKSYQLKGVKWLISLWQNGLNGILADQMGLGKTIQTIAFLAHL 198
R E EL+ +L G + ++ L G LI+ ++ G NG+L + +G G +I
Sbjct: 223 RAINEMAELIEILGGDRETAFGLSGFGDLIATFRGGRNGMLGELLGKGLSIDEAMEELER 282
Query: 199 KGNGLHGPYLVIAPLSTLSNWVNEISRFVPSVSAIIYHGSKKE 241
+G G+ Y LS+ +N ++ + S+ ++Y G K E
Sbjct: 283 RGVGVVEGYKTAEKAYRLSSKINADTKLLDSIYRVLYEGLKVE 325
>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3
Length = 395
Score = 37.0 bits (84), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 27/99 (27%), Positives = 45/99 (45%), Gaps = 7/99 (7%)
Query: 500 LVFSQWTKILDIMEYYFNEKGYEVCRIDGSVRLDERKRQIQDFNDVNSSYRIFLLSTRAG 559
++F K +++ +G+EV + G ++ ER R I DF + S L++T
Sbjct: 247 IIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSK---VLITTNVL 303
Query: 560 GLGINLTAADTCILYD--SDWNPQMDLQAMDRCHRIGQT 596
GI++ + YD + N Q D HRIG+T
Sbjct: 304 ARGIDIPTVSMVVNYDLPTLANGQAD--PATYIHRIGRT 340
>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 = 37.0 bits (84), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 27/99 (27%), Positives = 45/99 (45%), Gaps = 7/99 (7%)
Query: 500 LVFSQWTKILDIMEYYFNEKGYEVCRIDGSVRLDERKRQIQDFNDVNSSYRIFLLSTRAG 559
++F K +++ +G+EV + G ++ ER R I DF + S L++T
Sbjct: 247 IIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSK---VLITTNVL 303
Query: 560 GLGINLTAADTCILYD--SDWNPQMDLQAMDRCHRIGQT 596
GI++ + YD + N Q D HRIG+T
Sbjct: 304 ARGIDIPTVSMVVNYDLPTLANGQAD--PATYIHRIGRT 340
>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 = 36.6 bits (83), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 27/98 (27%), Positives = 44/98 (44%), Gaps = 9/98 (9%)
Query: 499 VLVFSQWTKILDIMEYYFNEKGYEVCRIDGSVRLDERKRQIQDFNDVNSSYRIFLLSTRA 558
VL+F++ +D + Y KG E I G +ER + I+ F + + L++T
Sbjct: 57 VLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFRE---GKKDVLVATDV 113
Query: 559 GGLGINLTAADTCILYDSDWNPQMDLQAMDRCHRIGQT 596
G++ A I YD M + + HRIG+T
Sbjct: 114 ASKGLDFPAIQHVINYD------MPEEIENYVHRIGRT 145
>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 = 35.4 bits (80), Expect = 0.11, Method: Composition-based stats.
Identities = 27/99 (27%), Positives = 45/99 (45%), Gaps = 7/99 (7%)
Query: 500 LVFSQWTKILDIMEYYFNEKGYEVCRIDGSVRLDERKRQIQDFNDVNSSYRIFLLSTRAG 559
++F K +++ +G+EV + G ++ ER R I DF + S L++T
Sbjct: 40 IIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSK---VLITTNVL 96
Query: 560 GLGINLTAADTCILYD--SDWNPQMDLQAMDRCHRIGQT 596
GI++ + YD + N Q D HRIG+T
Sbjct: 97 ARGIDIPTVSXVVNYDLPTLANGQAD--PATYIHRIGRT 133
>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 = 35.4 bits (80), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 25/97 (25%), Positives = 46/97 (47%), Gaps = 9/97 (9%)
Query: 500 LVFSQWTKILDIMEYYFNEKGYEVCRIDGSVRLDERKRQIQDFNDVNSSYRIFLLSTRAG 559
+VF + + D + + +EK + I G +R++ ++DF N S ++ L++T
Sbjct: 304 IVFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFK--NGSMKV-LIATSVA 360
Query: 560 GLGINLTAADTCILYDSDWNPQMDLQAMDRCHRIGQT 596
G+++ I YD M + D HRIG+T
Sbjct: 361 SRGLDIKNIKHVINYD------MPSKIDDYVHRIGRT 391
>pdb|2KBF|A Chain A, Solution Structure Of Carboxyl-Terminal Domain Of Dbp5p
Length = 187
Score = 35.4 bits (80), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 27/99 (27%), Positives = 45/99 (45%), Gaps = 7/99 (7%)
Query: 500 LVFSQWTKILDIMEYYFNEKGYEVCRIDGSVRLDERKRQIQDFNDVNSSYRIFLLSTRAG 559
++F K +++ +G+EV + G ++ ER R I DF + S L++T
Sbjct: 39 IIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSK---VLITTNVL 95
Query: 560 GLGINLTAADTCILYD--SDWNPQMDLQAMDRCHRIGQT 596
GI++ + YD + N Q D HRIG+T
Sbjct: 96 ARGIDIPTVSMVVNYDLPTLANGQADPATY--IHRIGRT 132
>pdb|3GFP|A Chain A, Structure Of The C-Terminal Domain Of The Dead-Box Protein
Dbp5
Length = 189
Score = 35.4 bits (80), Expect = 0.12, Method: Composition-based stats.
Identities = 27/99 (27%), Positives = 45/99 (45%), Gaps = 7/99 (7%)
Query: 500 LVFSQWTKILDIMEYYFNEKGYEVCRIDGSVRLDERKRQIQDFNDVNSSYRIFLLSTRAG 559
++F K +++ +G+EV + G ++ ER R I DF + S L++T
Sbjct: 41 IIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSK---VLITTNVL 97
Query: 560 GLGINLTAADTCILYD--SDWNPQMDLQAMDRCHRIGQT 596
GI++ + YD + N Q D HRIG+T
Sbjct: 98 ARGIDIPTVSXVVNYDLPTLANGQAD--PATYIHRIGRT 134
>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x
Length = 417
Score = 32.3 bits (72), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 27/109 (24%), Positives = 46/109 (42%), Gaps = 9/109 (8%)
Query: 499 VLVFSQWTKILDIMEYYFNEKGYEVCRIDGSVRLDERKRQIQDFNDVNSSYRIFLLSTRA 558
LVF + K D +E + +GY I G +R+ + F S L++T
Sbjct: 279 TLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSP---ILVATAV 335
Query: 559 GGLGINLTAADTCILYDSDWNPQMDLQAMDRCHRIGQTKPVHVYRLATA 607
G++++ I +D + + + HRIG+T V LAT+
Sbjct: 336 AARGLDISNVKHVINFDLPSDIE------EYVHRIGRTGRVGNLGLATS 378
>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 = 32.0 bits (71), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 27/109 (24%), Positives = 45/109 (41%), Gaps = 9/109 (8%)
Query: 499 VLVFSQWTKILDIMEYYFNEKGYEVCRIDGSVRLDERKRQIQDFNDVNSSYRIFLLSTRA 558
LVF + K D +E + +GY I G +R+ + F S L++T
Sbjct: 49 TLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSP---ILVATAV 105
Query: 559 GGLGINLTAADTCILYDSDWNPQMDLQAMDRCHRIGQTKPVHVYRLATA 607
G++++ I +D + + HRIG+T V LAT+
Sbjct: 106 AARGLDISNVKHVINFD------LPSDIEEYVHRIGRTGRVGNLGLATS 148
>pdb|3RC8|A Chain A, Human Mitochondrial Helicase Suv3 In Complex With Short
Rna Fragment
Length = 677
Score = 31.2 bits (69), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 28/48 (58%), Gaps = 1/48 (2%)
Query: 519 KGYEVCRIDGSVRLDERKRQIQDFNDVNSSYRIFLLSTRAGGLGINLT 566
+G E I GS+ + Q + FND N +I L++T A G+G+NL+
Sbjct: 343 RGLESAVIYGSLPPGTKLAQAKKFNDPNDPCKI-LVATDAIGMGLNLS 389
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
0.319 0.135 0.397
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,871,904
Number of Sequences: 62578
Number of extensions: 718475
Number of successful extensions: 1596
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 1571
Number of HSP's gapped (non-prelim): 20
length of query: 725
length of database: 14,973,337
effective HSP length: 106
effective length of query: 619
effective length of database: 8,340,069
effective search space: 5162502711
effective search space used: 5162502711
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)