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= psy14708
(513 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 = 129 bits (324), Expect = 4e-30, Method: Compositional matrix adjust.
Identities = 74/210 (35%), Positives = 112/210 (53%), Gaps = 5/210 (2%)
Query: 298 SRNMLQEYELFFRNDKNQFIKEKDLYKFHVLITTFEIIISDCLELKDFNWRLCIIDEAHR 357
SR+ ++EYE + N K K KF+VL+TT+E I+ D EL W+ +DEAHR
Sbjct: 323 SRDTIREYEFY----TNPRAKGKKTMKFNVLLTTYEYILKDRAELGSIKWQFMAVDEAHR 378
Query: 358 LKNRNCKXXXXXXXXXXXXXXXXSGTPLQNNVNELFSLLNFLEPQQFSNNEAFMSEFGQL 417
LKN +GTPLQNN+ EL +L+NFL P +F+ ++ E
Sbjct: 379 LKNAESSLYESLNSFKVANRMLITGTPLQNNIKELAALVNFLMPGRFTIDQEIDFENQDE 438
Query: 418 KTESEVNXXXXXXXXXXXXXXXEDVEKSIAPKEETVVEVELTNIQKKYYRGILERNFSFL 477
+ E ++ +DVEKS+ K E ++ VEL+++Q +YY+ IL +N+S L
Sbjct: 439 EQEEYIHDLHRRIQPFILRRLKKDVEKSLPSKTERILRVELSDVQTEYYKNILTKNYSAL 498
Query: 478 SKGTTSANVPNLMNTMMELRKCCIHPYLLN 507
+ G + +L+N M EL+K HPYL +
Sbjct: 499 TAGAKGGHF-SLLNIMNELKKASNHPYLFD 527
Score = 80.9 bits (198), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 44/112 (39%), Positives = 59/112 (52%), Gaps = 19/112 (16%)
Query: 18 KLEKSPVYKNDNTLRAYQLEGLNWLMFSWFNGRNCILADEMGLGKTIQSLTRNCILADEM 77
KL P + LR +QL G+NW+ F W G N ILADEMGLGKT+Q
Sbjct: 224 KLSVQPPFIKGGELRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQ------------ 271
Query: 78 GLGKTIQSLTFVDAVFKTGIRGPFLVIAPLSTIPNWQREFEAWT-DLNVIVY 128
T+ ++++ +F GP +++ PLST+P W FE W DLN I Y
Sbjct: 272 ----TVAFISWL--IFARRQNGPHIIVVPLSTMPAWLDTFEKWAPDLNCICY 317
Score = 43.5 bits (101), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 19/43 (44%), Positives = 25/43 (58%), Gaps = 1/43 (2%)
Query: 154 VFKTGIRGPFLVIAPLSTIPNWQREFEAWT-DLNVIVYHGRRK 195
+F GP +++ PLST+P W FE W DLN I Y G +K
Sbjct: 280 IFARRQNGPHIIVVPLSTMPAWLDTFEKWAPDLNCICYMGNQK 322
>pdb|1Z6A|A Chain A, Sulfolobus Solfataricus Swi2SNF2 ATPASE CORE DOMAIN
Length = 500
Score = 68.6 bits (166), Expect = 7e-12, Method: Compositional matrix adjust.
Identities = 52/205 (25%), Positives = 94/205 (45%), Gaps = 10/205 (4%)
Query: 309 FRNDKNQFIKEKDLYKFHVLITTFEIIISDCLELKDFNWRLCIIDEAHRLKNRNCKXXXX 368
F D+++ IK +D + +++TT+ +++ D LK+ W+ +IDEA +KN K
Sbjct: 117 FHEDRSK-IKLED---YDIILTTYAVLLRDT-RLKEVEWKYIVIDEAQNIKNPQTKIFKA 171
Query: 369 XXXXXXXXXXXXSGTPLQNNVNELFSLLNFLEPQQFSNNEAFMSEFGQ-LKTESEVNXXX 427
+GTP++N V++L+S++ FL P + F S+F +K +
Sbjct: 172 VKELKSKYRIALTGTPIENKVDDLWSIMTFLNPGLLGSYSEFKSKFATPIKKGDNMAKEE 231
Query: 428 XXXXXXXXXXXXEDVEKSI----APKEETVVEVELTNIQKKYYRGILERNFSFLSKGTTS 483
+K+I K ET V LT Q Y+ +E F+ + T
Sbjct: 232 LKAIISPFILRRTKYDKAIINDLPDKIETNVYCNLTPEQAAMYKAEVENLFNNIDSVTGI 291
Query: 484 ANVPNLMNTMMELRKCCIHPYLLNG 508
+++T+++L++ HP LL G
Sbjct: 292 KRKGMILSTLLKLKQIVDHPALLKG 316
Score = 54.7 bits (130), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 34/106 (32%), Positives = 49/106 (46%), Gaps = 20/106 (18%)
Query: 25 YKNDNTLRAYQLEGLNWLMFSWFNGRNCILADEMGLGKTIQSLTRNCILADEMGLGKTIQ 84
Y LR YQ++G +W+ F +++G G LAD+MGLGKT+Q
Sbjct: 32 YNIKANLRPYQIKGFSWMRF----------MNKLGFG---------ICLADDMGLGKTLQ 72
Query: 85 SLTFVDAVFKTGIRGPFLVIAPLSTIPNWQREFEAWT-DLNVIVYH 129
++ K P LVI PLS + NW+ E + L V+H
Sbjct: 73 TIAVFSDAKKENELTPSLVICPLSVLKNWEEELSKFAPHLRFAVFH 118
Score = 32.7 bits (73), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 1/51 (1%)
Query: 162 PFLVIAPLSTIPNWQREFEAWT-DLNVIVYHGRRKKLSRRDKERLRLKYVA 211
P LVI PLS + NW+ E + L V+H R K+ D + + Y
Sbjct: 88 PSLVICPLSVLKNWEEELSKFAPHLRFAVFHEDRSKIKLEDYDIILTTYAV 138
>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 = 67.0 bits (162), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 48/192 (25%), Positives = 84/192 (43%), Gaps = 6/192 (3%)
Query: 322 LYKFHVLITTFEIIISDCLELKDFNWRLCIIDEAHRLKNRNCKXXXXXXXXXXXXXXXXS 381
L + +++TT+ +++ D LK+ W+ +IDEA +KN K +
Sbjct: 126 LEDYDIILTTYAVLLRDT-RLKEVEWKYIVIDEAQNIKNPQTKIFKAVKELKSKYRIALT 184
Query: 382 GTPLQNNVNELFSLLNFLEPQQFSNNEAFMSEFGQ-LKTESEVNXXXXXXXXXXXXXXXE 440
GTP++N V++L+S+ FL P + F S+F +K
Sbjct: 185 GTPIENKVDDLWSIXTFLNPGLLGSYSEFKSKFATPIKKGDNXAKEELKAIISPFILRRT 244
Query: 441 DVEKSI----APKEETVVEVELTNIQKKYYRGILERNFSFLSKGTTSANVPNLMNTMMEL 496
+K+I K ET V LT Q Y+ +E F+ + T +++T+++L
Sbjct: 245 KYDKAIINDLPDKIETNVYCNLTPEQAAXYKAEVENLFNNIDSVTGIKRKGXILSTLLKL 304
Query: 497 RKCCIHPYLLNG 508
++ HP LL G
Sbjct: 305 KQIVDHPALLKG 316
Score = 51.2 bits (121), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 33/106 (31%), Positives = 47/106 (44%), Gaps = 20/106 (18%)
Query: 25 YKNDNTLRAYQLEGLNWLMFSWFNGRNCILADEMGLGKTIQSLTRNCILADEMGLGKTIQ 84
Y LR YQ++G +W F +++G G LAD+ GLGKT+Q
Sbjct: 32 YNIKANLRPYQIKGFSWXRF----------XNKLGFG---------ICLADDXGLGKTLQ 72
Query: 85 SLTFVDAVFKTGIRGPFLVIAPLSTIPNWQREFEAWT-DLNVIVYH 129
++ K P LVI PLS + NW+ E + L V+H
Sbjct: 73 TIAVFSDAKKENELTPSLVICPLSVLKNWEEELSKFAPHLRFAVFH 118
Score = 32.3 bits (72), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 1/51 (1%)
Query: 162 PFLVIAPLSTIPNWQREFEAWT-DLNVIVYHGRRKKLSRRDKERLRLKYVA 211
P LVI PLS + NW+ E + L V+H R K+ D + + Y
Sbjct: 88 PSLVICPLSVLKNWEEELSKFAPHLRFAVFHEDRSKIKLEDYDIILTTYAV 138
>pdb|1Z3I|X Chain X, Structure Of The Swi2SNF2 CHROMATIN REMODELING DOMAIN OF
EUKARYOTIC Rad54
Length = 644
Score = 50.1 bits (118), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 40/123 (32%), Positives = 60/123 (48%), Gaps = 25/123 (20%)
Query: 3 LIKKPKKKPPASDWVKLEKSPVYKNDNTLRAYQLEGLNWLMFSWFNGRNCILADEMGLGK 62
LIK K+K P V + PV LR +Q EG+ +L W +C+ G+
Sbjct: 34 LIKADKEKLP----VHVVVDPVLSK--VLRPHQREGVKFL---W----DCVT------GR 74
Query: 63 TIQSLTRNCILADEMGLGKTIQSLTFVDAVFKTGIR-----GPFLVIAPLSTIPNWQREF 117
I++ + CI+ADEMGLGKT+Q +T + + K +V++P S + NW E
Sbjct: 75 RIEN-SYGCIMADEMGLGKTLQCITLIWTLLKQSPDCKPEIDKVIVVSPSSLVRNWYNEV 133
Query: 118 EAW 120
W
Sbjct: 134 GKW 136
Score = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 48/195 (24%), Positives = 80/195 (41%), Gaps = 16/195 (8%)
Query: 327 VLITTFEIIISDCLELKDFNWRLCIIDEAHRLKNRNCKXXXXXXXXXXXXXXXXSGTPLQ 386
+LI ++E L L I DE HRLKN + + SGTP+Q
Sbjct: 173 ILIISYETFRLHAEVLHKGKVGLVICDEGHRLKNSDNQTYLALNSMNAQRRVLISGTPIQ 232
Query: 387 NNVNELFSLLNFLE------PQQF---------SNNEAFMSEFGQLKTESEVNXXXXXXX 431
N++ E FSL++F+ Q+F +A S+ + E ++
Sbjct: 233 NDLLEYFSLVHFVNSGILGTAQEFKKRFEIPILKGRDADASDKDRAAGEQKLQELISIVN 292
Query: 432 XXXXXXXXEDVEKSIAPKEETVVEVELTNIQKKYYRGILERNFSFLSKGTTSANVPNLMN 491
+ + K + K E VV LT +QK+ Y+ L++ S T + ++
Sbjct: 293 RCLIRRTSDILSKYLPVKIEQVVCCNLTPLQKELYKLFLKQAKPVESL-QTGKISVSSLS 351
Query: 492 TMMELRKCCIHPYLL 506
++ L+K C HP L+
Sbjct: 352 SITSLKKLCNHPALI 366
>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 = 32.0 bits (71), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 23/43 (53%)
Query: 71 CILADEMGLGKTIQSLTFVDAVFKTGIRGPFLVIAPLSTIPNW 113
+LADE+GLGKTI++ + +G L+I P + W
Sbjct: 173 VLLADEVGLGKTIEAGXILHQQLLSGAAERVLIIVPETLQHQW 215
>pdb|1GM5|A Chain A, Structure Of Recg Bound To Three-Way Dna Junction
Length = 780
Score = 30.4 bits (67), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 14/58 (24%), Positives = 32/58 (55%)
Query: 70 NCILADEMGLGKTIQSLTFVDAVFKTGIRGPFLVIAPLSTIPNWQREFEAWTDLNVIV 127
N +L ++G GKT+ + + ++ G + F+V + I +++R E+++ N+ V
Sbjct: 391 NRLLQGDVGSGKTVVAQLAILDNYEAGFQTAFMVPTSILAIQHYRRTVESFSKFNIHV 448
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
0.321 0.137 0.420
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,089,984
Number of Sequences: 62578
Number of extensions: 552736
Number of successful extensions: 1120
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 1088
Number of HSP's gapped (non-prelim): 20
length of query: 513
length of database: 14,973,337
effective HSP length: 103
effective length of query: 410
effective length of database: 8,527,803
effective search space: 3496399230
effective search space used: 3496399230
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (25.4 bits)