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= 005980
(666 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 = 132 bits (332), Expect = 6e-31, Method: Compositional matrix adjust.
Identities = 145/518 (27%), Positives = 226/518 (43%), Gaps = 68/518 (13%)
Query: 140 ENLHPLVQRAIASASAAPDLREKYDQIPAHIESKLLPFQRDGVR---FALQHGGRILLAD 196
EN L Q + S P + Q P +L FQ G+ F G +LAD
Sbjct: 203 ENSKILPQYSSNYTSQRPRFEKLSVQPPFIKGGELRDFQLTGINWMAFLWSKGDNGILAD 262
Query: 197 EMGLGKTIQAIAVATCF----RDVWPVLILTPSSLRLHWAAMIQQWLNIPPSEIVVVLSQ 252
EMGLGKT+Q +A + R P +I+ P S W ++W P + +
Sbjct: 263 EMGLGKTVQTVAFISWLIFARRQNGPHIIVVPLSTMPAWLDTFEKW--APDLNCICYM-- 318
Query: 253 LGGSNRSGFTIVSSNTKRNIPLDGL----FNII--SYDVVLKLQNILMSSNFKIVIADES 306
G+ +S TI N G FN++ +Y+ +LK + L S ++ + DE+
Sbjct: 319 --GNQKSRDTIREYEFYTNPRAKGKKTMKFNVLLTTYEYILKDRAELGSIKWQFMAVDEA 376
Query: 307 HFLKNAQAKRTAATLPIIKKAQYALLLSGTPALSRPIELFKQLEALYPDVYKNVHE--YG 364
H LKNA++ +L K A +L++GTP + EL + L P + E +
Sbjct: 377 HRLKNAESS-LYESLNSFKVAN-RMLITGTPLQNNIKELAALVNFLMPGRFTIDQEIDFE 434
Query: 365 NRYCKGGVFGIYQGASNHEELHNLMKAT--VMIRRLKKDVLAQLPVKRRQ---------- 412
N Q E +H+L + ++RRLKKDV LP K +
Sbjct: 435 N-----------QDEEQEEYIHDLHRRIQPFILRRLKKDVEKSLPSKTERILRVELSDVQ 483
Query: 413 -QVFLDVAEKDMRQIYA-----LFRELEVVKGKIKACK-------SEEEV----QSLKFT 455
+ + ++ K+ + A F L ++ KA +EE V K T
Sbjct: 484 TEYYKNILTKNYSALTAGAKGGHFSLLNIMNELKKASNHPYLFDNAEERVLQKFGDGKMT 543
Query: 456 EKNLINKIYTDSAEAKIPAVLDYLETVIEA-GCKFLIFAHHQPMLDAIHQLFLKKKVHCI 514
+N++ + S + +LD L T ++ G + LIF+ MLD + K ++
Sbjct: 544 RENVLRGLIMSSGKM---VLLDQLLTRLKKDGHRVLIFSQMVRMLDILGDYLSIKGINFQ 600
Query: 515 RIDGGTPPASRQALVTEFQEKDDVKAA-VLSMKAGGVGLTLTAASTVIFAELSWTPGDLI 573
R+DG P A R+ + F D +LS +AGG+G+ L A TV+ + W P +
Sbjct: 601 RLDGTVPSAQRRISIDHFNSPDSNDFVFLLSTRAGGLGINLMTADTVVIFDSDWNPQADL 660
Query: 574 QAEDRAHRIGQVSSVNVYYLLANDTVDDIVWDVVRSKL 611
QA RAHRIGQ + V VY L++ DTV++ V + R K+
Sbjct: 661 QAMARAHRIGQKNHVMVYRLVSKDTVEEEVLERARKKM 698
>pdb|1Z6A|A Chain A, Sulfolobus Solfataricus Swi2SNF2 ATPASE CORE DOMAIN
Length = 500
Score = 118 bits (296), Expect = 1e-26, Method: Compositional matrix adjust.
Identities = 126/483 (26%), Positives = 220/483 (45%), Gaps = 65/483 (13%)
Query: 145 LVQRAIASASAAPDLREKYDQIPAHIESKLLPFQRDG---VRFALQHGGRILLADEMGLG 201
LV R AS + L E P +I++ L P+Q G +RF + G I LAD+MGLG
Sbjct: 14 LVPRGSHMASKSFQLLE-----PYNIKANLRPYQIKGFSWMRFMNKLGFGICLADDMGLG 68
Query: 202 KTIQAIAV---ATCFRDVWPVLILTPSSLRLHWAAMIQQWLNIPPSEIVVVLSQLGGSNR 258
KT+Q IAV A ++ P L++ P S+ +W + ++ P V + +R
Sbjct: 69 KTLQTIAVFSDAKKENELTPSLVICPLSVLKNWEEELSKF---APHLRFAVFHE----DR 121
Query: 259 SGFTIVSSNTKRNIPLDGLFNIISYDVVLKLQNILMSSN------FKIVIADESHFLKNA 312
S I L+ YD++L +L+ +K ++ DE+ +KN
Sbjct: 122 S-----------KIKLE------DYDIILTTYAVLLRDTRLKEVEWKYIVIDEAQNIKNP 164
Query: 313 QAKRTAATLPIIKKAQYALLLSGTPALSRPIELFKQLEALYPDVYKNVHEYGNRYCKGGV 372
Q K A + K++Y + L+GTP ++ +L+ + L P + + E+ +++
Sbjct: 165 QTKIFKAVKEL--KSKYRIALTGTPIENKVDDLWSIMTFLNPGLLGSYSEFKSKFATP-- 220
Query: 373 FGIYQGASNHEELHNLMKATVMIRRLKKD--VLAQLPVKRRQQVFLDVAEKDMR----QI 426
I +G + +E + + ++RR K D ++ LP K V+ ++ + ++
Sbjct: 221 --IKKGDNMAKEELKAIISPFILRRTKYDKAIINDLPDKIETNVYCNLTPEQAAMYKAEV 278
Query: 427 YALFRELEVVKGKIKACKSEEEVQSLKFTEKNLIN-----KIYTDSAE--AKIPAVLDYL 479
LF ++ V G K + + S K +++ K S K+ ++ +
Sbjct: 279 ENLFNNIDSVTG----IKRKGMILSTLLKLKQIVDHPALLKGGEQSVRRSGKMIRTMEII 334
Query: 480 ETVIEAGCKFLIFAHHQPMLDAIHQLFLKK-KVHCIRIDGGTPPASRQALVTEFQEKDDV 538
E ++ G K IF M I + K+ + G R ++++FQ V
Sbjct: 335 EEALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSV 394
Query: 539 KAAVLSMKAGGVGLTLTAASTVIFAELSWTPGDLIQAEDRAHRIGQVSSVNVYYLLANDT 598
K VLS+KAGG G+ LT+A+ VI + W P QA DR +RIGQ +V V+ L++ T
Sbjct: 395 KFIVLSVKAGGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVGT 454
Query: 599 VDD 601
+++
Sbjct: 455 LEE 457
>pdb|1Z3I|X Chain X, Structure Of The Swi2SNF2 CHROMATIN REMODELING DOMAIN OF
EUKARYOTIC Rad54
Length = 644
Score = 113 bits (283), Expect = 3e-25, Method: Compositional matrix adjust.
Identities = 131/516 (25%), Positives = 223/516 (43%), Gaps = 78/516 (15%)
Query: 153 ASAAPDL-REKYDQIPAHIE-----SKLL-PFQRDGVRFALQ--HGGRI------LLADE 197
A +A DL + +++P H+ SK+L P QR+GV+F G RI ++ADE
Sbjct: 28 AISAHDLIKADKEKLPVHVVVDPVLSKVLRPHQREGVKFLWDCVTGRRIENSYGCIMADE 87
Query: 198 MGLGKTIQAIAV--------ATCFRDVWPVLILTPSSLRLHWAAMIQQWLNIPPSEIVVV 249
MGLGKT+Q I + C ++ V++++PSSL +W + +WL + V
Sbjct: 88 MGLGKTLQCITLIWTLLKQSPDCKPEIDKVIVVSPSSLVRNWYNEVGKWLG---GRVQPV 144
Query: 250 LSQLGGSNRSGFTIVSSNTKRNIPLDGLFNIISYDVVLKLQNILMSSNFKIVIADESHFL 309
G + +V+ +++ + + IISY+ +L +VI DE H L
Sbjct: 145 AIDGGSKDEIDSKLVNFISQQGMRIPTPILIISYETFRLHAEVLHKGKVGLVICDEGHRL 204
Query: 310 KNAQAKRTAATLPIIKKAQYALLLSGTPALSRPIELFKQLEALYPDVYKNVHEYGNRYCK 369
KN+ + A + AQ +L+SGTP + +E F + + + E+ R+
Sbjct: 205 KNSDNQTYLALNSM--NAQRRVLISGTPIQNDLLEYFSLVHFVNSGILGTAQEFKKRF-- 260
Query: 370 GGVFGIYQG----------ASNHEELHNLMKAT--VMIRRLKKDVLAQ-LPVKRRQQVFL 416
I +G A+ ++L L+ +IRR D+L++ LPVK Q V
Sbjct: 261 --EIPILKGRDADASDKDRAAGEQKLQELISIVNRCLIRR-TSDILSKYLPVKIEQVVCC 317
Query: 417 DVAEKDMRQIYALFRELEVVKGKIKACKSEEEVQSLKFTEKNLINK---IY--------- 464
++ +++Y LF + ++ K S + K L N IY
Sbjct: 318 NLTPL-QKELYKLFLKQAKPVESLQTGKISVSSLSSITSLKKLCNHPALIYEKCLTGEEG 376
Query: 465 -------------TDSAEAKIPA---VLDYL--ETVIEAGCKFLIFAHHQPMLDAIHQLF 506
T + E ++ VLDY+ T K ++ +++ LD +L
Sbjct: 377 FDGALDLFPQNYSTKAVEPQLSGKMLVLDYILAMTRTTTSDKVVLVSNYTQTLDLFEKLC 436
Query: 507 LKKKVHCIRIDGGTPPASRQALVTEFQEKDDVKAA-VLSMKAGGVGLTLTAASTVIFAEL 565
++ +R+DG R +V F + +LS KAGG GL L A+ ++ +
Sbjct: 437 RNRRYLYVRLDGTMSIKKRAKIVERFNNPSSPEFIFMLSSKAGGCGLNLIGANRLVMFDP 496
Query: 566 SWTPGDLIQAEDRAHRIGQVSSVNVYYLLANDTVDD 601
W P + QA R R GQ + +Y LL+ T+++
Sbjct: 497 DWNPANDEQAMARVWRDGQKKTCYIYRLLSTGTIEE 532
>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 = 110 bits (276), Expect = 2e-24, Method: Compositional matrix adjust.
Identities = 125/477 (26%), Positives = 212/477 (44%), Gaps = 53/477 (11%)
Query: 145 LVQRAIASASAAPDLREKYDQIPAHIESKLLPFQRDGV---RFALQHGGRILLADEMGLG 201
LV R AS + L E P +I++ L P+Q G RF + G I LAD+ GLG
Sbjct: 14 LVPRGSHMASKSFQLLE-----PYNIKANLRPYQIKGFSWXRFXNKLGFGICLADDXGLG 68
Query: 202 KTIQAIAV---ATCFRDVWPVLILTPSSLRLHWAAMIQQWLNIPPSEIVVVLSQLGGSNR 258
KT+Q IAV A ++ P L++ P S+ +W + ++ P V + +R
Sbjct: 69 KTLQTIAVFSDAKKENELTPSLVICPLSVLKNWEEELSKF---APHLRFAVFHE----DR 121
Query: 259 SGFTIVSSNTKRNIPLDGLFNIISYDVVLKLQNILMSSNFKIVIADESHFLKNAQAKRTA 318
S I L+ I++ VL L +K ++ DE+ +KN Q K
Sbjct: 122 S-----------KIKLEDYDIILTTYAVLLRDTRLKEVEWKYIVIDEAQNIKNPQTKIFK 170
Query: 319 ATLPIIKKAQYALLLSGTPALSRPIELFKQLEALYPDVYKNVHEYGNRYCKGGVFGIYQG 378
A + K++Y + L+GTP ++ +L+ L P + + E+ +++ I +G
Sbjct: 171 AVKEL--KSKYRIALTGTPIENKVDDLWSIXTFLNPGLLGSYSEFKSKFATP----IKKG 224
Query: 379 ASNHEELHNLMKATVMIRRLKKD--VLAQLPVKRRQQVFLDV----AEKDMRQIYALFRE 432
+ +E + + ++RR K D ++ LP K V+ ++ A ++ LF
Sbjct: 225 DNXAKEELKAIISPFILRRTKYDKAIINDLPDKIETNVYCNLTPEQAAXYKAEVENLFNN 284
Query: 433 LEVVKGKIKACKSEEEVQSLKFTEKNLIN-----KIYTDSAE--AKIPAVLDYLETVIEA 485
++ V G K + + S K +++ K S K + +E ++
Sbjct: 285 IDSVTG----IKRKGXILSTLLKLKQIVDHPALLKGGEQSVRRSGKXIRTXEIIEEALDE 340
Query: 486 GCKFLIFAHHQPMLDAIHQLFLKK-KVHCIRIDGGTPPASRQALVTEFQEKDDVKAAVLS 544
G K IF I + K+ + G R ++++FQ VK VLS
Sbjct: 341 GDKIAIFTQFVDXGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLS 400
Query: 545 MKAGGVGLTLTAASTVIFAELSWTPGDLIQAEDRAHRIGQVSSVNVYYLLANDTVDD 601
+KAGG G+ LT+A+ VI + W P QA DR +RIGQ +V V+ L++ T+++
Sbjct: 401 VKAGGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVGTLEE 457
>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 = 68.6 bits (166), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 42/133 (31%), Positives = 68/133 (51%), Gaps = 1/133 (0%)
Query: 470 AKIPAVLDYLETVIEAGCKFLIFAHHQPMLDAIHQLFLKK-KVHCIRIDGGTPPASRQAL 528
K+ ++ +E ++ G K IF M I + K+ + G R +
Sbjct: 96 GKMIRTMEIIEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDI 155
Query: 529 VTEFQEKDDVKAAVLSMKAGGVGLTLTAASTVIFAELSWTPGDLIQAEDRAHRIGQVSSV 588
+++FQ VK VLS+KAGG G+ LT+A+ VI + W P QA DR +RIGQ +V
Sbjct: 156 ISKFQNNPSVKFIVLSVKAGGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNV 215
Query: 589 NVYYLLANDTVDD 601
V+ L++ T+++
Sbjct: 216 IVHKLISVGTLEE 228
>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 = 40.0 bits (92), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 38/139 (27%), Positives = 61/139 (43%), Gaps = 13/139 (9%)
Query: 450 QSLKFTEKNLINKIYTDSAEAKIPAVLDYLETVIEAGCKFLIFAHHQPMLDAIHQLFLKK 509
QS+ ++I ++ EAK+ +L+ L+ LIFA + +DAIH+ L K
Sbjct: 21 QSMGAASLDVIQEVEYVKEEAKMVYLLECLQKTPPP---VLIFAEKKADVDAIHEYLLLK 77
Query: 510 KVHCIRIDGGTPPASRQALVTEFQE-KDDVKAAVLSMKAGGVGLTLTAASTVIFAELSWT 568
V + I GG R + F+E K DV +++ GL A VI ++
Sbjct: 78 GVEAVAIHGGKDQEERTKAIEAFREGKKDV---LVATDVASKGLDFPAIQHVINYDMPE- 133
Query: 569 PGDLIQAEDRAHRIGQVSS 587
+ E+ HRIG+
Sbjct: 134 -----EIENYVHRIGRTGC 147
>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 = 36.6 bits (83), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 43/194 (22%), Positives = 79/194 (40%), Gaps = 23/194 (11%)
Query: 187 QHGGRILLADEMGLGKTIQAIAV---ATCFRDVWPVLILTPSSLRLHWAAMIQQWLNIPP 243
+H R+LLADE+GLGKTI+A + VLI+ P +L+ W + N+
Sbjct: 168 RHAPRVLLADEVGLGKTIEAGXILHQQLLSGAAERVLIIVPETLQHQWLVEXLRRFNL-- 225
Query: 244 SEIVVVLSQLGGSNRSGFTIVSSNTKRNIPLDGLFNIISYDVVLKLQNI---LMSSNFKI 300
+ + + + + L I S D + + L + + +
Sbjct: 226 --------RFALFDDERYAEAQHDAYNPFDTEQLV-ICSLDFARRSKQRLEHLCEAEWDL 276
Query: 301 VIADESHFL---KNAQAKRTAATLPIIKKAQYALLLSGTPALSRPIELFKQLEALYPDVY 357
++ DE+H L ++A ++ A + + LLL+ TP F +L L P+ +
Sbjct: 277 LVVDEAHHLVWSEDAPSREYQAIEQLAEHVPGVLLLTATPEQLGXESHFARLRLLDPNRF 336
Query: 358 KNVHEY---GNRYC 368
+ ++ YC
Sbjct: 337 HDFAQFVEEQKNYC 350
>pdb|3BS8|A Chain A, Crystal Structure Of Glutamate 1-Semialdehyde
Aminotransferase Complexed With
Pyridoxamine-5'-Phosphate From Bacillus Subtilis
Length = 438
Score = 32.0 bits (71), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 25/67 (37%), Positives = 33/67 (49%), Gaps = 8/67 (11%)
Query: 330 ALLLSGTP-ALSRPIELFKQLEALYPDVYKNVHEYGNRYCKGGVFGIYQGASNHEELHNL 388
A LSG P A++ +E KQL PD YKN + G+R + GI + A H H
Sbjct: 306 AGTLSGNPLAMTAGLETLKQLT---PDSYKNFIKKGDRLEE----GISKAAEAHGIPHTF 358
Query: 389 MKATVMI 395
+A MI
Sbjct: 359 NRAGSMI 365
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 0.134 0.385
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,538,992
Number of Sequences: 62578
Number of extensions: 735565
Number of successful extensions: 1902
Number of sequences better than 100.0: 22
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 1880
Number of HSP's gapped (non-prelim): 23
length of query: 666
length of database: 14,973,337
effective HSP length: 105
effective length of query: 561
effective length of database: 8,402,647
effective search space: 4713884967
effective search space used: 4713884967
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)