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= psy12466
(680 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1Z3I|X Chain X, Structure Of The Swi2SNF2 CHROMATIN REMODELING DOMAIN OF
EUKARYOTIC Rad54
Length = 644
Score = 249 bits (636), Expect = 3e-66, Method: Compositional matrix adjust.
Identities = 140/334 (41%), Positives = 203/334 (60%), Gaps = 17/334 (5%)
Query: 362 VDVTVDGFLSRVLKPHQRQGVSFLYERVCDLASLDLEGAILADEMGLGKTLQCIALIWTL 421
V V VD LS+VL+PHQR+GV FL++ V + G I+ADEMGLGKTLQCI LIWTL
Sbjct: 44 VHVVVDPVLSKVLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLIWTL 103
Query: 422 LRQGPYGMPVIRKVLIVTPSSLTSNWNDEFKKWLGLTRMCPYHVNQKNKAE------DYV 475
L+Q P P I KV++V+PSSL NW +E KWLG R+ P ++ +K E +++
Sbjct: 104 LKQSPDCKPEIDKVIVVSPSSLVRNWYNEVGKWLG-GRVQPVAIDGGSKDEIDSKLVNFI 162
Query: 476 YSRV----SPVLIISYEMLIRAYQTIVDTEFDLLICDEGHRLKNGKSKLYELMTGLNIRK 531
+ +P+LIISYE + + + L+ICDEGHRLKN ++ Y + +N ++
Sbjct: 163 SQQGMRIPTPILIISYETFRLHAEVLHKGKVGLVICDEGHRLKNSDNQTYLALNSMNAQR 222
Query: 532 RILLSGTPLQNDLQEFFYLNDFANPGVLGSLREFRKNFEEPILESRSPNSTEAQKSLGEL 591
R+L+SGTP+QNDL E+F L F N G+LG+ +EF+K FE PIL+ R ++++ ++ GE
Sbjct: 223 RVLISGTPIQNDLLEYFSLVHFVNSGILGTAQEFKKRFEIPILKGRDADASDKDRAAGEQ 282
Query: 592 RSSQLAKRTAGFILRRTSDVQASLLNSKRETLLVCRATPLQQSLY------LRCVEYWDA 645
+ +L ++RRTSD+ + L K E ++ C TPLQ+ LY + VE
Sbjct: 283 KLQELISIVNRCLIRRTSDILSKYLPVKIEQVVCCNLTPLQKELYKLFLKQAKPVESLQT 342
Query: 646 RASRDSHLSVTHALRKICNHPGLVQQPDMMEEEG 679
S LS +L+K+CNHP L+ + + EEG
Sbjct: 343 GKISVSSLSSITSLKKLCNHPALIYEKCLTGEEG 376
Score = 50.4 bits (119), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 32/93 (34%), Positives = 51/93 (54%), Gaps = 11/93 (11%)
Query: 192 ILRVLIVTPSSLTSNWNDEFKKWLGLTRMCPYHVNQKNKAE------DYVYSRV----SP 241
I +V++V+PSSL NW +E KWLG R+ P ++ +K E +++ + +P
Sbjct: 114 IDKVIVVSPSSLVRNWYNEVGKWLG-GRVQPVAIDGGSKDEIDSKLVNFISQQGMRIPTP 172
Query: 242 VLIISYEMLIRAYQTIVDTEFDLLICDEKSLLK 274
+LIISYE + + + L+ICDE LK
Sbjct: 173 ILIISYETFRLHAEVLHKGKVGLVICDEGHRLK 205
>pdb|1Z6A|A Chain A, Sulfolobus Solfataricus Swi2SNF2 ATPASE CORE DOMAIN
Length = 500
Score = 120 bits (302), Expect = 2e-27, Method: Compositional matrix adjust.
Identities = 88/307 (28%), Positives = 152/307 (49%), Gaps = 39/307 (12%)
Query: 374 LKPHQRQGVSFLYERVCDLASLDLEGAILADEMGLGKTLQCIALIWTLLRQGPYGMPVIR 433
L+P+Q +G S++ R + G LAD+MGLGKTLQ IA+ ++ +
Sbjct: 38 LRPYQIKGFSWM--RFMNKLGF---GICLADDMGLGKTLQTIAVFSDAKKENE-----LT 87
Query: 434 KVLIVTPSSLTSNWNDEFKKWLGLTRMCPYHVNQ-KNKAEDYVYSRVSPVLIISYEMLIR 492
L++ P S+ NW +E K+ R +H ++ K K EDY +++ +Y +L+R
Sbjct: 88 PSLVICPLSVLKNWEEELSKFAPHLRFAVFHEDRSKIKLEDY------DIILTTYAVLLR 141
Query: 493 AYQTIVDTEFDLLICDEGHRLKNGKSKLYELMTGLNIRKRILLSGTPLQNDLQEFFYLND 552
+ + + E+ ++ DE +KN ++K+++ + L + RI L+GTP++N + + + +
Sbjct: 142 DTR-LKEVEWKYIVIDEAQNIKNPQTKIFKAVKELKSKYRIALTGTPIENKVDDLWSIMT 200
Query: 553 FANPGVLGSLREFRKNFEEPILESRSPNSTEAQKSLGELRSSQLAKRTAGFILRRTSDVQ 612
F NPG+LGS EF+ F PI K + +L + FILRRT +
Sbjct: 201 FLNPGLLGSYSEFKSKFATPI------------KKGDNMAKEELKAIISPFILRRTKYDK 248
Query: 613 ASL--LNSKRETLLVCRATPLQQSLY-------LRCVEYWDARASRDSHLSVTHALRKIC 663
A + L K ET + C TP Q ++Y ++ + LS L++I
Sbjct: 249 AIINDLPDKIETNVYCNLTPEQAAMYKAEVENLFNNIDSVTGIKRKGMILSTLLKLKQIV 308
Query: 664 NHPGLVQ 670
+HP L++
Sbjct: 309 DHPALLK 315
>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 = 116 bits (290), Expect = 5e-26, Method: Compositional matrix adjust.
Identities = 88/307 (28%), Positives = 150/307 (48%), Gaps = 39/307 (12%)
Query: 374 LKPHQRQGVSFLYERVCDLASLDLEGAILADEMGLGKTLQCIALIWTLLRQGPYGMPVIR 433
L+P+Q +G F + R + G LAD+ GLGKTLQ IA+ ++ +
Sbjct: 38 LRPYQIKG--FSWXRFXNKLGF---GICLADDXGLGKTLQTIAVFSDAKKENE-----LT 87
Query: 434 KVLIVTPSSLTSNWNDEFKKWLGLTRMCPYHVNQ-KNKAEDYVYSRVSPVLIISYEMLIR 492
L++ P S+ NW +E K+ R +H ++ K K EDY +++ +Y +L+R
Sbjct: 88 PSLVICPLSVLKNWEEELSKFAPHLRFAVFHEDRSKIKLEDY------DIILTTYAVLLR 141
Query: 493 AYQTIVDTEFDLLICDEGHRLKNGKSKLYELMTGLNIRKRILLSGTPLQNDLQEFFYLND 552
+ + + E+ ++ DE +KN ++K+++ + L + RI L+GTP++N + + + +
Sbjct: 142 DTR-LKEVEWKYIVIDEAQNIKNPQTKIFKAVKELKSKYRIALTGTPIENKVDDLWSIXT 200
Query: 553 FANPGVLGSLREFRKNFEEPILESRSPNSTEAQKSLGELRSSQLAKRTAGFILRRTSDVQ 612
F NPG+LGS EF+ F PI A++ L + S FILRRT +
Sbjct: 201 FLNPGLLGSYSEFKSKFATPI----KKGDNXAKEELKAIISP--------FILRRTKYDK 248
Query: 613 ASL--LNSKRETLLVCRATPLQQSLY-------LRCVEYWDARASRDSHLSVTHALRKIC 663
A + L K ET + C TP Q + Y ++ + LS L++I
Sbjct: 249 AIINDLPDKIETNVYCNLTPEQAAXYKAEVENLFNNIDSVTGIKRKGXILSTLLKLKQIV 308
Query: 664 NHPGLVQ 670
+HP L++
Sbjct: 309 DHPALLK 315
>pdb|3MWY|W Chain W, Crystal Structure Of The Chromodomain-atpase Portion Of
The Yeast Chd1 Chromatin Remodeler
Length = 800
Score = 113 bits (283), Expect = 3e-25, Method: Compositional matrix adjust.
Identities = 94/299 (31%), Positives = 137/299 (45%), Gaps = 47/299 (15%)
Query: 398 EGAILADEMGLGKTLQCIALI-WTLL---RQGPYGMPVIRKVLIVTPSSLTSNWNDEFKK 453
+ ILADEMGLGKT+Q +A I W + + GP+ +IV P S W D F+K
Sbjct: 256 DNGILADEMGLGKTVQTVAFISWLIFARRQNGPH--------IIVVPLSTMPAWLDTFEK 307
Query: 454 WLGLTRMCPYHVNQKNK-----AEDYVYSRVSP-------VLIISYEMLIRAYQTIVDTE 501
W Y NQK++ E Y R VL+ +YE +++ + +
Sbjct: 308 WAPDLNCICYMGNQKSRDTIREYEFYTNPRAKGKKTMKFNVLLTTYEYILKDRAELGSIK 367
Query: 502 FDLLICDEGHRLKNGKSKLYELMTGLNIRKRILLSGTPLQNDLQEFFYLNDFANPGVLGS 561
+ + DE HRLKN +S LYE + + R+L++GTPLQN+++E L +F PG
Sbjct: 368 WQFMAVDEAHRLKNAESSLYESLNSFKVANRMLITGTPLQNNIKELAALVNFLMPGRFTI 427
Query: 562 LREFRKNFEEPILESRSPNSTEAQKSLGELRSSQLAKRTAGFILRR-TSDVQASLLNSKR 620
+E +FE N E Q E L +R FILRR DV+ S L SK
Sbjct: 428 DQEI--DFE---------NQDEEQ----EEYIHDLHRRIQPFILRRLKKDVEKS-LPSKT 471
Query: 621 ETLLVCRATPLQQSLYLRCVE------YWDARASRDSHLSVTHALRKICNHPGLVQQPD 673
E +L + +Q Y + A+ S L++ + L+K NHP L +
Sbjct: 472 ERILRVELSDVQTEYYKNILTKNYSALTAGAKGGHFSLLNIMNELKKASNHPYLFDNAE 530
Score = 30.0 bits (66), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 24/91 (26%), Positives = 37/91 (40%), Gaps = 12/91 (13%)
Query: 196 LIVTPSSLTSNWNDEFKKWLGLTRMCPYHVNQKNK-----AEDYVYSRVSP-------VL 243
+IV P S W D F+KW Y NQK++ E Y R VL
Sbjct: 290 IIVVPLSTMPAWLDTFEKWAPDLNCICYMGNQKSRDTIREYEFYTNPRAKGKKTMKFNVL 349
Query: 244 IISYEMLIRAYQTIVDTEFDLLICDEKSLLK 274
+ +YE +++ + ++ + DE LK
Sbjct: 350 LTTYEYILKDRAELGSIKWQFMAVDEAHRLK 380
>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 = 51.2 bits (121), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 47/182 (25%), Positives = 84/182 (46%), Gaps = 19/182 (10%)
Query: 401 ILADEMGLGKTLQCIALIWTLLRQGPYGMPVIRKVLIVTPSSLTSNWNDEFKKWLGLTRM 460
+LADE+GLGKT++ ++ L G +VLI+ P +L W E + L R
Sbjct: 174 LLADEVGLGKTIEAGXILHQQLLSG-----AAERVLIIVPETLQHQWLVEXLRRFNL-RF 227
Query: 461 CPYHVNQKNKAEDYVYS--RVSPVLIISYEMLIRAYQT---IVDTEFDLLICDEGHRL-- 513
+ + +A+ Y+ ++I S + R+ Q + + E+DLL+ DE H L
Sbjct: 228 ALFDDERYAEAQHDAYNPFDTEQLVICSLDFARRSKQRLEHLCEAEWDLLVVDEAHHLVW 287
Query: 514 -KNGKSKLYELMTGL--NIRKRILLSGTPLQNDLQEFFYLNDFANPGVLGSLREF---RK 567
++ S+ Y+ + L ++ +LL+ TP Q + F +P +F +K
Sbjct: 288 SEDAPSREYQAIEQLAEHVPGVLLLTATPEQLGXESHFARLRLLDPNRFHDFAQFVEEQK 347
Query: 568 NF 569
N+
Sbjct: 348 NY 349
>pdb|2I4K|A Chain A, Solution Structure Of The Px Domain Of Sorting Nexin 1
Length = 128
Score = 31.6 bits (70), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 30/99 (30%), Positives = 45/99 (45%), Gaps = 11/99 (11%)
Query: 250 LIRAYQTIVDTEF-DLLICDEKSLLKPPSGNSPGNDSGIPSLPRKSDSGIGSLPCKRPLE 308
L R+ Q V F D L EK S N +P P KS G+ + + +
Sbjct: 34 LFRSKQFAVKRRFSDFLGLYEKL-----SEKHSQNGFIVPPPPEKSLIGMTKVKVGKE-D 87
Query: 309 ESTAETLQCNQINSHLSVTHALRKICNHPGLVQQPDVME 347
S+AE L+ + ++ L++I NHP ++Q PDV E
Sbjct: 88 SSSAEFLEKRRA----ALERYLQRIVNHPTMLQDPDVRE 122
>pdb|2YWG|A Chain A, Crystal Structure Of Gtp-Bound Lepa From Aquifex Aeolicus
Length = 600
Score = 31.2 bits (69), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 36/76 (47%), Gaps = 4/76 (5%)
Query: 382 VSFLYERVCDLASLDLEGAILADEMGLGKTLQCIALIWTLLRQGPYGMPVIRKVLIVTPS 441
V F YE LA+ EGA+L + G Q +A W + Q +PVI K+ + PS
Sbjct: 84 VDFSYEVSRALAAC--EGALLLIDASQGIEAQTVANFWKAVEQDLVIIPVINKIDL--PS 139
Query: 442 SLTSNWNDEFKKWLGL 457
+ + ++ LGL
Sbjct: 140 ADVDRVKKQIEEVLGL 155
>pdb|2YWE|A Chain A, Crystal Structure Of Lepa From Aquifex Aeolicus
pdb|2YWF|A Chain A, Crystal Structure Of Gmppnp-Bound Lepa From Aquifex
Aeolicus
pdb|2YWH|A Chain A, Crystal Structure Of Gdp-Bound Lepa From Aquifex Aeolicus
Length = 600
Score = 30.8 bits (68), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 36/76 (47%), Gaps = 4/76 (5%)
Query: 382 VSFLYERVCDLASLDLEGAILADEMGLGKTLQCIALIWTLLRQGPYGMPVIRKVLIVTPS 441
V F YE LA+ EGA+L + G Q +A W + Q +PVI K+ + PS
Sbjct: 84 VDFSYEVSRALAAC--EGALLLIDASQGIEAQTVANFWKAVEQDLVIIPVINKIDL--PS 139
Query: 442 SLTSNWNDEFKKWLGL 457
+ + ++ LGL
Sbjct: 140 ADVDRVKKQIEEVLGL 155
>pdb|2LCQ|A Chain A, Solution Structure Of The Endonuclease Nob1 From
P.Horikoshii
Length = 165
Score = 30.8 bits (68), Expect = 2.9, Method: Composition-based stats.
Identities = 15/63 (23%), Positives = 29/63 (46%)
Query: 231 AEDYVYSRVSPVLIISYEMLIRAYQTIVDTEFDLLICDEKSLLKPPSGNSPGNDSGIPSL 290
++DY ++ +L + + L R + ++ + + C K PP G P S + +
Sbjct: 102 SDDYNVQNIASLLGLRFRTLKRGIKKVIKWRYVCIGCGRKFSTLPPGGVCPDCGSKVKLI 161
Query: 291 PRK 293
PRK
Sbjct: 162 PRK 164
>pdb|1GUI|A Chain A, Cbm4 Structure And Function
Length = 155
Score = 30.0 bits (66), Expect = 4.6, Method: Composition-based stats.
Identities = 18/65 (27%), Positives = 29/65 (44%), Gaps = 13/65 (20%)
Query: 419 WTLLRQGPYGMPVIR-----------KVLIVTPSSLTSNWNDEFKKWLGLTRMCPYHVNQ 467
W + + G YG+ R + I P T W+ +F +W+GL R Y ++
Sbjct: 22 WFIWQAGDYGISGARVSDYGVRDGYAYITIADPG--TDTWHIQFNQWIGLYRGKTYTISF 79
Query: 468 KNKAE 472
K KA+
Sbjct: 80 KAKAD 84
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
0.316 0.133 0.391
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,996,166
Number of Sequences: 62578
Number of extensions: 823177
Number of successful extensions: 1988
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1969
Number of HSP's gapped (non-prelim): 17
length of query: 680
length of database: 14,973,337
effective HSP length: 105
effective length of query: 575
effective length of database: 8,402,647
effective search space: 4831522025
effective search space used: 4831522025
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.8 bits)