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= 000096
(2260 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 = 177 bits (450), Expect = 5e-44, Method: Compositional matrix adjust.
Identities = 96/206 (46%), Positives = 124/206 (60%), Gaps = 6/206 (2%)
Query: 18 SVHNSVMELRNICNHPYLSQLHAEEV------DTLIPKHYLPPIVRLCGKLEMLDRLLPK 71
S+ N + EL+ NHPYL E V + ++ L ++ GK+ +LD+LL +
Sbjct: 508 SLLNIMNELKKASNHPYLFDNAEERVLQKFGDGKMTRENVLRGLIMSSGKMVLLDQLLTR 567
Query: 72 LKATDHRVLFFSTMTRLLDVMEDYLTFKQYRYLRLDGHTSGGDRGALIDKFNQQDSPFFI 131
LK HRVL FS M R+LD++ DYL+ K + RLDG R ID FN DS F+
Sbjct: 568 LKKDGHRVLIFSQMVRMLDILGDYLSIKGINFQRLDGTVPSAQRRISIDHFNSPDSNDFV 627
Query: 132 FLLSIRAGGVGVNLQAADTVIIFDTDWNPQVDLQAQARAHRIGQKRDVLVLRFETVQTVE 191
FLLS RAGG+G+NL ADTV+IFD+DWNPQ DLQA ARAHRIGQK V+V R + TVE
Sbjct: 628 FLLSTRAGGLGINLMTADTVVIFDSDWNPQADLQAMARAHRIGQKNHVMVYRLVSKDTVE 687
Query: 192 EQVRASAEHKLGVANQSITAGFFDNN 217
E+V A K+ + I+ G D N
Sbjct: 688 EEVLERARKKMILEYAIISLGVTDGN 713
>pdb|1Z3I|X Chain X, Structure Of The Swi2SNF2 CHROMATIN REMODELING DOMAIN OF
EUKARYOTIC Rad54
Length = 644
Score = 120 bits (302), Expect = 7e-27, Method: Composition-based stats.
Identities = 70/190 (36%), Positives = 106/190 (55%), Gaps = 10/190 (5%)
Query: 27 RNICNHP---YLSQLHAEE----VDTLIPKHYLPPIV--RLCGKLEMLDRLLPKLKAT-D 76
+ +CNHP Y L EE L P++Y V +L GK+ +LD +L + T
Sbjct: 357 KKLCNHPALIYEKCLTGEEGFDGALDLFPQNYSTKAVEPQLSGKMLVLDYILAMTRTTTS 416
Query: 77 HRVLFFSTMTRLLDVMEDYLTFKQYRYLRLDGHTSGGDRGALIDKFNQQDSPFFIFLLSI 136
+V+ S T+ LD+ E ++Y Y+RLDG S R ++++FN SP FIF+LS
Sbjct: 417 DKVVLVSNYTQTLDLFEKLCRNRRYLYVRLDGTMSIKKRAKIVERFNNPSSPEFIFMLSS 476
Query: 137 RAGGVGVNLQAADTVIIFDTDWNPQVDLQAQARAHRIGQKRDVLVLRFETVQTVEEQVRA 196
+AGG G+NL A+ +++FD DWNP D QA AR R GQK+ + R + T+EE++
Sbjct: 477 KAGGCGLNLIGANRLVMFDPDWNPANDEQAMARVWRDGQKKTCYIYRLLSTGTIEEKILQ 536
Query: 197 SAEHKLGVAN 206
HK +++
Sbjct: 537 RQAHKKALSS 546
>pdb|1Z6A|A Chain A, Sulfolobus Solfataricus Swi2SNF2 ATPASE CORE DOMAIN
Length = 500
Score = 77.8 bits (190), Expect = 6e-14, Method: Composition-based stats.
Identities = 48/124 (38%), Positives = 72/124 (58%), Gaps = 2/124 (1%)
Query: 106 LDGHTSGGDRGALIDKFNQQDSPFFIFLLSIRAGGVGVNLQAADTVIIFDTDWNPQVDLQ 165
L G S +R +I KF S FI +LS++AGG G+NL +A+ VI FD WNP V+ Q
Sbjct: 372 LYGELSKKERDDIISKFQNNPSVKFI-VLSVKAGGFGINLTSANRVIHFDRWWNPAVEDQ 430
Query: 166 AQARAHRIGQKRDVLVLRFETVQTVEEQVRASAEHKLGVANQSITAG-FFDNNTSAEDRR 224
A R +RIGQ R+V+V + +V T+EE++ K + I++G + S E+ R
Sbjct: 431 ATDRVYRIGQTRNVIVHKLISVGTLEEKIDQLLAFKRSLFKDIISSGDSWITELSTEELR 490
Query: 225 EYLE 228
+ +E
Sbjct: 491 KVIE 494
>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 = 77.4 bits (189), Expect = 8e-14, Method: Composition-based stats.
Identities = 48/124 (38%), Positives = 72/124 (58%), Gaps = 2/124 (1%)
Query: 106 LDGHTSGGDRGALIDKFNQQDSPFFIFLLSIRAGGVGVNLQAADTVIIFDTDWNPQVDLQ 165
L G S +R +I KF S FI +LS++AGG G+NL +A+ VI FD WNP V+ Q
Sbjct: 372 LYGELSKKERDDIISKFQNNPSVKFI-VLSVKAGGFGINLTSANRVIHFDRWWNPAVEDQ 430
Query: 166 AQARAHRIGQKRDVLVLRFETVQTVEEQVRASAEHKLGVANQSITAG-FFDNNTSAEDRR 224
A R +RIGQ R+V+V + +V T+EE++ K + I++G + S E+ R
Sbjct: 431 ATDRVYRIGQTRNVIVHKLISVGTLEEKIDQLLAFKRSLFKDIISSGDSWITELSTEELR 490
Query: 225 EYLE 228
+ +E
Sbjct: 491 KVIE 494
>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 = 77.0 bits (188), Expect = 1e-13, Method: Composition-based stats.
Identities = 48/124 (38%), Positives = 72/124 (58%), Gaps = 2/124 (1%)
Query: 106 LDGHTSGGDRGALIDKFNQQDSPFFIFLLSIRAGGVGVNLQAADTVIIFDTDWNPQVDLQ 165
L G S +R +I KF S FI +LS++AGG G+NL +A+ VI FD WNP V+ Q
Sbjct: 143 LYGELSKKERDDIISKFQNNPSVKFI-VLSVKAGGFGINLTSANRVIHFDRWWNPAVEDQ 201
Query: 166 AQARAHRIGQKRDVLVLRFETVQTVEEQVRASAEHKLGVANQSITAG-FFDNNTSAEDRR 224
A R +RIGQ R+V+V + +V T+EE++ K + I++G + S E+ R
Sbjct: 202 ATDRVYRIGQTRNVIVHKLISVGTLEEKIDQLLAFKRSLFKDIISSGDSWITELSTEELR 261
Query: 225 EYLE 228
+ +E
Sbjct: 262 KVIE 265
>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 = 32.7 bits (73), Expect = 2.5, Method: Composition-based stats.
Identities = 29/109 (26%), Positives = 45/109 (41%), Gaps = 5/109 (4%)
Query: 68 LLPKLKAT--DHRVLFFSTMTRLLDVMEDYLTFKQYRYLRLDGHTSGGDRGALIDKFNQQ 125
LL L AT D L F + D +ED+L + Y + G S DR + +F
Sbjct: 36 LLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSG 95
Query: 126 DSPFFIFLLSIRAGGVGVNLQAADTVIIFDTDWNPQVDLQAQARAHRIG 174
SP L++ G+++ VI FD + + + R R+G
Sbjct: 96 KSP---ILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVG 141
>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 = 4.3, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 23/49 (46%)
Query: 133 LLSIRAGGVGVNLQAADTVIIFDTDWNPQVDLQAQARAHRIGQKRDVLV 181
LL G G N Q A + FD +NP + Q R RIGQ D+ +
Sbjct: 560 LLCSEIGSEGRNFQFASHXVXFDLPFNPDLLEQRIGRLDRIGQAHDIQI 608
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
0.306 0.126 0.349
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 63,176,791
Number of Sequences: 62578
Number of extensions: 2598529
Number of successful extensions: 3529
Number of sequences better than 100.0: 25
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 3514
Number of HSP's gapped (non-prelim): 26
length of query: 2260
length of database: 14,973,337
effective HSP length: 114
effective length of query: 2146
effective length of database: 7,839,445
effective search space: 16823448970
effective search space used: 16823448970
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 43 (22.0 bits)
S2: 59 (27.3 bits)