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= 001912
(997 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1Z6A|A Chain A, Sulfolobus Solfataricus Swi2SNF2 ATPASE CORE DOMAIN
Length = 500
Score = 70.9 bits (172), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 50/181 (27%), Positives = 91/181 (50%), Gaps = 18/181 (9%)
Query: 203 PFQLEG---VRFGLRRGGRCLIADEMGLGKTLQAIAIAACFISAGSI---LVVCPAILRL 256
P+Q++G +RF + G +AD+MGLGKTLQ IA+ + + LV+CP +
Sbjct: 40 PYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAVFSDAKKENELTPSLVICPLSVLK 99
Query: 257 SWAEELERWLPFCLPADIHLVFGHRNNPVHLTRFPRVVVISYTMLHRLRKSMIEQDWALL 316
+W EEL ++ P A VF + + L + +++ +Y +L R + + E +W +
Sbjct: 100 NWEEELSKFAPHLRFA----VFHEDRSKIKLEDYD-IILTTYAVLLRDTR-LKEVEWKYI 153
Query: 317 IVDESHHVRCSKRTSEPEEXXXXXXXXXXXXRIVLLSGTPSLSRPYDIFHQINMLWPGLL 376
++DE+ +++ P+ + L+GTP ++ D++ + L PGLL
Sbjct: 154 VIDEAQNIK------NPQTKIFKAVKELKSKYRIALTGTPIENKVDDLWSIMTFLNPGLL 207
Query: 377 G 377
G
Sbjct: 208 G 208
Score = 34.7 bits (78), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 21/84 (25%), Positives = 38/84 (45%)
Query: 562 GNTLPRDRQSAVHSFQLSNEVKXXXXXXXXXXXXLDFSSAQNVVFLELPQSPSLMLQAED 621
G ++R + FQ + VK ++ +SA V+ + +P++ QA D
Sbjct: 374 GELSKKERDDIISKFQNNPSVKFIVLSVKAGGFGINLTSANRVIHFDRWWNPAVEDQATD 433
Query: 622 RAHRRGQTSAVNIYIFCAKDTTDE 645
R +R GQT V ++ + T +E
Sbjct: 434 RVYRIGQTRNVIVHKLISVGTLEE 457
>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 = 67.8 bits (164), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 49/181 (27%), Positives = 88/181 (48%), Gaps = 18/181 (9%)
Query: 203 PFQLEGV---RFGLRRGGRCLIADEMGLGKTLQAIAIAACFISAGSI---LVVCPAILRL 256
P+Q++G RF + G +AD+ GLGKTLQ IA+ + + LV+CP +
Sbjct: 40 PYQIKGFSWXRFXNKLGFGICLADDXGLGKTLQTIAVFSDAKKENELTPSLVICPLSVLK 99
Query: 257 SWAEELERWLPFCLPADIHLVFGHRNNPVHLTRFPRVVVISYTMLHRLRKSMIEQDWALL 316
+W EEL ++ P A VF + + L + +++ +Y +L R + + E +W +
Sbjct: 100 NWEEELSKFAPHLRFA----VFHEDRSKIKLEDYD-IILTTYAVLLRDTR-LKEVEWKYI 153
Query: 317 IVDESHHVRCSKRTSEPEEXXXXXXXXXXXXRIVLLSGTPSLSRPYDIFHQINMLWPGLL 376
++DE+ +++ P+ + L+GTP ++ D++ L PGLL
Sbjct: 154 VIDEAQNIK------NPQTKIFKAVKELKSKYRIALTGTPIENKVDDLWSIXTFLNPGLL 207
Query: 377 G 377
G
Sbjct: 208 G 208
Score = 34.7 bits (78), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 21/84 (25%), Positives = 38/84 (45%)
Query: 562 GNTLPRDRQSAVHSFQLSNEVKXXXXXXXXXXXXLDFSSAQNVVFLELPQSPSLMLQAED 621
G ++R + FQ + VK ++ +SA V+ + +P++ QA D
Sbjct: 374 GELSKKERDDIISKFQNNPSVKFIVLSVKAGGFGINLTSANRVIHFDRWWNPAVEDQATD 433
Query: 622 RAHRRGQTSAVNIYIFCAKDTTDE 645
R +R GQT V ++ + T +E
Sbjct: 434 RVYRIGQTRNVIVHKLISVGTLEE 457
>pdb|1Z3I|X Chain X, Structure Of The Swi2SNF2 CHROMATIN REMODELING DOMAIN OF
EUKARYOTIC Rad54
Length = 644
Score = 61.6 bits (148), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 62/240 (25%), Positives = 97/240 (40%), Gaps = 63/240 (26%)
Query: 185 VVDEMIGKLPKSLLDVILPFQLEGVRF--------GLRRGGRCLIADEMGLGKTLQAIAI 236
VVD ++ K V+ P Q EGV+F + C++ADEMGLGKTLQ I +
Sbjct: 47 VVDPVLSK-------VLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITL 99
Query: 237 A--------ACFISAGSILVVCPAILRLSWAEELERWLPFCLPADIHLVFGHRNNPVHL- 287
C ++VV P+ L +W E+ +WL G R PV +
Sbjct: 100 IWTLLKQSPDCKPEIDKVIVVSPSSLVRNWYNEVGKWL------------GGRVQPVAID 147
Query: 288 -------------------TRFPR-VVVISYTMLHRLRKSMIEQDWALLIVDESHHVRCS 327
R P +++ISY + + + L+I DE H ++ S
Sbjct: 148 GGSKDEIDSKLVNFISQQGMRIPTPILIISYETFRLHAEVLHKGKVGLVICDEGHRLKNS 207
Query: 328 KRTSEPEEXXXXXXXXXXXXRIVLLSGTPSLSRPYDIFHQINMLWPGLLGKAKYDFAKTY 387
+ R VL+SGTP + + F ++ + G+LG A+ +F K +
Sbjct: 208 ------DNQTYLALNSMNAQRRVLISGTPIQNDLLEYFSLVHFVNSGILGTAQ-EFKKRF 260
Score = 32.7 bits (73), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 27/121 (22%), Positives = 49/121 (40%), Gaps = 1/121 (0%)
Query: 530 SNKMIIFAHHLKVLDGVQEFISEKGIGFVRIDGNTLPRDRQSAVHSF-QLSNEVKXXXXX 588
S+K+++ +++ + LD ++ + +VR+DG + R V F S+
Sbjct: 416 SDKVVLVSNYTQTLDLFEKLCRNRRYLYVRLDGTMSIKKRAKIVERFNNPSSPEFIFMLS 475
Query: 589 XXXXXXXLDFSSAQNVVFLELPQSPSLMLQAEDRAHRRGQTSAVNIYIFCAKDTTDESHW 648
L+ A +V + +P+ QA R R GQ IY + T +E
Sbjct: 476 SKAGGCGLNLIGANRLVMFDPDWNPANDEQAMARVWRDGQKKTCYIYRLLSTGTIEEKIL 535
Query: 649 Q 649
Q
Sbjct: 536 Q 536
>pdb|3MWY|W Chain W, Crystal Structure Of The Chromodomain-atpase Portion Of
The Yeast Chd1 Chromatin Remodeler
Length = 800
Score = 59.7 bits (143), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 49/191 (25%), Positives = 78/191 (40%), Gaps = 27/191 (14%)
Query: 204 FQLEGVR---FGLRRGGRCLIADEMGLGKTLQAIAIAACFISA----GSILVVCPAILRL 256
FQL G+ F +G ++ADEMGLGKT+Q +A + I A G ++V P
Sbjct: 240 FQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWLIFARRQNGPHIIVVPLSTMP 299
Query: 257 SWAEELERWLP----FCLPA-----DIHLVFGHRNNP----VHLTRFPRVVVISYTMLHR 303
+W + E+W P C D + NP +F V++ +Y + +
Sbjct: 300 AWLDTFEKWAPDLNCICYMGNQKSRDTIREYEFYTNPRAKGKKTMKF-NVLLTTYEYILK 358
Query: 304 LRKSMIEQDWALLIVDESHHVRCSKRTSEPEEXXXXXXXXXXXXRIVLLSGTPSLSRPYD 363
R + W + VDE+H R E +L++GTP + +
Sbjct: 359 DRAELGSIKWQFMAVDEAH------RLKNAESSLYESLNSFKVANRMLITGTPLQNNIKE 412
Query: 364 IFHQINMLWPG 374
+ +N L PG
Sbjct: 413 LAALVNFLMPG 423
Score = 57.0 bits (136), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 35/118 (29%), Positives = 61/118 (51%), Gaps = 3/118 (2%)
Query: 530 SNKMIIFAHHLKVLDGVQEFISEKGIGFVRIDGNTLPRDRQSAVHSFQL--SNEVKXXXX 587
++++IF+ +++LD + +++S KGI F R+DG R+ ++ F SN+
Sbjct: 572 GHRVLIFSQMVRMLDILGDYLSIKGINFQRLDGTVPSAQRRISIDHFNSPDSNDF-VFLL 630
Query: 588 XXXXXXXXLDFSSAQNVVFLELPQSPSLMLQAEDRAHRRGQTSAVNIYIFCAKDTTDE 645
++ +A VV + +P LQA RAHR GQ + V +Y +KDT +E
Sbjct: 631 STRAGGLGINLMTADTVVIFDSDWNPQADLQAMARAHRIGQKNHVMVYRLVSKDTVEE 688
>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 = 58.5 bits (140), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 59/207 (28%), Positives = 93/207 (44%), Gaps = 25/207 (12%)
Query: 201 ILPFQLEGVR-FGLRRGGRCLIADEMGLGKTLQAIAIAACFISAGS---ILVVCPAILRL 256
++P QL G R R L+ADE+GLGKT++A I + +G+ +L++ P L+
Sbjct: 154 LIPHQLNIAHDVGRRHAPRVLLADEVGLGKTIEAGXILHQQLLSGAAERVLIIVPETLQH 213
Query: 257 SW-AEELERW-LPFCLPADIHLVFGHRN--NPVHLTRFPRVVVISYTMLHRLRKS---MI 309
W E L R+ L F L D + NP ++V+ S R ++ +
Sbjct: 214 QWLVEXLRRFNLRFALFDDERYAEAQHDAYNPFDTE---QLVICSLDFARRSKQRLEHLC 270
Query: 310 EQDWALLIVDESHHVRCSKRTSEPEEXXXXXXXXXXXXRIVLLSGTPSLSRPYDIFHQIN 369
E +W LL+VDE+HH+ S+ + E ++LL+ TP F ++
Sbjct: 271 EAEWDLLVVDEAHHLVWSE-DAPSREYQAIEQLAEHVPGVLLLTATPEQLGXESHFARLR 329
Query: 370 MLWPGLLGKAKYDFA------KTYCDV 390
+L P +DFA K YC V
Sbjct: 330 LLDPNRF----HDFAQFVEEQKNYCPV 352
>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 = 38.9 bits (89), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 25/98 (25%), Positives = 45/98 (45%), Gaps = 8/98 (8%)
Query: 533 MIIFAHHLKVLDGVQEFISEKGIGFVRIDGNTLPRDRQSAVHSFQLSNEVKXXXXXXXXX 592
++IFA +D + E++ KG+ V I G +R A+ +F+ K
Sbjct: 57 VLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGK--KDVLVATDVA 114
Query: 593 XXXLDFSSAQNVVFLELPQSPSLMLQAEDRAHRRGQTS 630
LDF + Q+V+ ++P+ + E+ HR G+T
Sbjct: 115 SKGLDFPAIQHVINYDMPE------EIENYVHRIGRTG 146
>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x
Length = 417
Score = 37.7 bits (86), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 25/110 (22%), Positives = 47/110 (42%), Gaps = 8/110 (7%)
Query: 524 IDVNPRSNKMIIFAHHLKVLDGVQEFISEKGIGFVRIDGNTLPRDRQSAVHSFQLSNEVK 583
++ + + ++F K D +++F+ +G I G+ RDR+ A+H F+
Sbjct: 270 LNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGK--S 327
Query: 584 XXXXXXXXXXXXLDFSSAQNVVFLELPQSPSLMLQAEDRAHRRGQTSAVN 633
LD S+ ++V+ +LP E+ HR G+T V
Sbjct: 328 PILVATAVAARGLDISNVKHVINFDLPSD------IEEYVHRIGRTGRVG 371
>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 = 37.0 bits (84), Expect = 0.054, Method: Compositional matrix adjust.
Identities = 25/109 (22%), Positives = 47/109 (43%), Gaps = 8/109 (7%)
Query: 524 IDVNPRSNKMIIFAHHLKVLDGVQEFISEKGIGFVRIDGNTLPRDRQSAVHSFQLSNEVK 583
++ + + ++F K D +++F+ +G I G+ RDR+ A+H F+
Sbjct: 40 LNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGK--S 97
Query: 584 XXXXXXXXXXXXLDFSSAQNVVFLELPQSPSLMLQAEDRAHRRGQTSAV 632
LD S+ ++V+ +LP E+ HR G+T V
Sbjct: 98 PILVATAVAARGLDISNVKHVINFDLPS------DIEEYVHRIGRTGRV 140
>pdb|1WP9|A Chain A, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
pdb|1WP9|B Chain B, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
pdb|1WP9|C Chain C, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
pdb|1WP9|D Chain D, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
pdb|1WP9|E Chain E, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
pdb|1WP9|F Chain F, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
Length = 494
Score = 36.2 bits (82), Expect = 0.091, Method: Compositional matrix adjust.
Identities = 38/133 (28%), Positives = 60/133 (45%), Gaps = 10/133 (7%)
Query: 199 DVILPFQLEGVRFGLRRGGRCLIADEMGLGKTLQAIAIAACFIS--AGSILVVCPAI-LR 255
D+I P + V + + CLI GLGKTL A+ IA ++ G +L++ P L
Sbjct: 6 DLIQPRIYQEVIYAKCKETNCLIVLPTGLGKTLIAMMIAEYRLTKYGGKVLMLAPTKPLV 65
Query: 256 LSWAEELERWLPFCLPADIHLVFGHRNNPVHLT----RFPRVVVISYTMLHRLRKSMIE- 310
L AE R F LP + + +P + R +V T+ + L I
Sbjct: 66 LQHAESFRRL--FNLPPEKIVALTGEKSPEERSKAWARAKVIVATPQTIENDLLAGRISL 123
Query: 311 QDWALLIVDESHH 323
+D +L++ DE+H
Sbjct: 124 EDVSLIVFDEAHR 136
>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 = 34.7 bits (78), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 21/84 (25%), Positives = 38/84 (45%)
Query: 562 GNTLPRDRQSAVHSFQLSNEVKXXXXXXXXXXXXLDFSSAQNVVFLELPQSPSLMLQAED 621
G ++R + FQ + VK ++ +SA V+ + +P++ QA D
Sbjct: 145 GELSKKERDDIISKFQNNPSVKFIVLSVKAGGFGINLTSANRVIHFDRWWNPAVEDQATD 204
Query: 622 RAHRRGQTSAVNIYIFCAKDTTDE 645
R +R GQT V ++ + T +E
Sbjct: 205 RVYRIGQTRNVIVHKLISVGTLEE 228
>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 = 33.5 bits (75), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 36/151 (23%), Positives = 58/151 (38%), Gaps = 25/151 (16%)
Query: 483 SGACCRLGKISYQELGIAKLSGFREWLSIHPVIAESDGAADIDVNPRSNKMIIFAHHLKV 542
GAC + + Y+ AK S E LS ++DG I+F +
Sbjct: 270 GGACSDVKQTIYEVNKYAKRSKLIEILS-----EQADGT------------IVFVETKRG 312
Query: 543 LDGVQEFISEKGIGFVRIDGNTLPRDRQSAVHSFQLSNEVKXXXXXXXXXXXXLDFSSAQ 602
D + F+SEK I G+ L R+ A+ F+ N LD + +
Sbjct: 313 ADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFK--NGSMKVLIATSVASRGLDIKNIK 370
Query: 603 NVVFLELPQSPSLMLQAEDRAHRRGQTSAVN 633
+V+ ++P + +D HR G+T V
Sbjct: 371 HVINYDMPS------KIDDYVHRIGRTGRVG 395
>pdb|2VA8|A Chain A, Dna Repair Helicase Hel308
pdb|2VA8|B Chain B, Dna Repair Helicase Hel308
Length = 715
Score = 32.7 bits (73), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 33/70 (47%), Gaps = 10/70 (14%)
Query: 192 KLPKSLLDVIL--------PFQLEGVRFGLRRGGRCLIADEMGLGKTLQAIAIAACFI-- 241
KLP +++++I P Q E V+ GL G R L+ G GKTL A F+
Sbjct: 14 KLPSNVIEIIKKRGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGIISFLLK 73
Query: 242 SAGSILVVCP 251
+ G + V P
Sbjct: 74 NGGKAIYVTP 83
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 0.406
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 28,296,787
Number of Sequences: 62578
Number of extensions: 1164068
Number of successful extensions: 2163
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 2138
Number of HSP's gapped (non-prelim): 24
length of query: 997
length of database: 14,973,337
effective HSP length: 108
effective length of query: 889
effective length of database: 8,214,913
effective search space: 7303057657
effective search space used: 7303057657
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: 56 (26.2 bits)