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= 039292
(520 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 = 149 bits (377), Expect = 3e-36, Method: Compositional matrix adjust.
Identities = 103/314 (32%), Positives = 160/314 (50%), Gaps = 32/314 (10%)
Query: 168 LKPYQLVGVNFLLLLYRKGIAGAILADEMGLGKTIQAITYLMLLKHLNNDPGPHLIVCPA 227
L+ +QL G+N++ L+ KG G ILADEMGLGKT+Q + ++ L GPH+IV P
Sbjct: 237 LRDFQLTGINWMAFLWSKGDNG-ILADEMGLGKTVQTVAFISWLIFARRQNGPHIIVVPL 295
Query: 228 SVLENWERELKKWCPSFSVLQYHGAGRT-----AYSRELSSLAKAGLPPPFNVLLVCYSL 282
S + W +KW P + + Y G ++ Y + AK FNVLL Y
Sbjct: 296 STMPAWLDTFEKWAPDLNCICYMGNQKSRDTIREYEFYTNPRAKGKKTMKFNVLLTTYEY 355
Query: 283 FERHSVQQKDDRKILKRWRWSCVLMDEAHALKDKNSYRWKNLMSVARNANQRLMLTGTPL 342
+ DR L +W + +DEAH LK+ S +++L S + AN R+++TGTPL
Sbjct: 356 ILK-------DRAELGSIKWQFMAVDEAHRLKNAESSLYESLNSF-KVAN-RMLITGTPL 406
Query: 343 QNDLHELWSLLEFMMPDLFAT-EDVDLKKLLNGEDRDLIGRMKSILGPFILRRLKSDVMQ 401
QN++ EL +L+ F+MP F +++D + + E + I + + PFILRRLK DV +
Sbjct: 407 QNNIKELAALVNFLMPGRFTIDQEIDFEN-QDEEQEEYIHDLHRRIQPFILRRLKKDVEK 465
Query: 402 QLVPKIQWVEYVTMERPQEDAYR-VAIEEYRAVSRARIAKLSDADLATIVGVLPQRQISN 460
L K + + V + Q + Y+ + + Y A++ AK L I+
Sbjct: 466 SLPSKTERILRVELSDVQTEYYKNILTKNYSALTAG--AKGGHFSLLNIMN--------- 514
Query: 461 YFVQFRKIANHPLL 474
+ +K +NHP L
Sbjct: 515 ---ELKKASNHPYL 525
>pdb|1Z6A|A Chain A, Sulfolobus Solfataricus Swi2SNF2 ATPASE CORE DOMAIN
Length = 500
Score = 127 bits (318), Expect = 2e-29, Method: Compositional matrix adjust.
Identities = 93/340 (27%), Positives = 162/340 (47%), Gaps = 43/340 (12%)
Query: 160 EDSDFQPVLKPYQLVGVNFLLLLYRKGIAGAILADEMGLGKTIQAITYLMLLKHLNNDPG 219
E + + L+PYQ+ G +++ + + G G LAD+MGLGKT+Q I K N+
Sbjct: 30 EPYNIKANLRPYQIKGFSWMRFMNKLGF-GICLADDMGLGKTLQTIAVFSDAKK-ENELT 87
Query: 220 PHLIVCPASVLENWERELKKWCPSFSVLQYHGAGRTAYSRELSSLAKAGLPPPFNVLLVC 279
P L++CP SVL+NWE EL K+ P +H R+ E ++++L
Sbjct: 88 PSLVICPLSVLKNWEEELSKFAPHLRFAVFH-EDRSKIKLE-----------DYDIILTT 135
Query: 280 YSLFERHSVQQKDDRKILKRWRWSCVLMDEAHALKDKNSYRWKNLMSVARNANQRLMLTG 339
Y++ R D R LK W +++DEA +K+ + +K + + + R+ LTG
Sbjct: 136 YAVLLR------DTR--LKEVEWKYIVIDEAQNIKNPQTKIFKAVKEL--KSKYRIALTG 185
Query: 340 TPLQNDLHELWSLLEFMMPDLFATEDVDLKKL---LNGEDRDLIGRMKSILGPFILRRLK 396
TP++N + +LWS++ F+ P L + K + D +K+I+ PFILRR K
Sbjct: 186 TPIENKVDDLWSIMTFLNPGLLGSYSEFKSKFATPIKKGDNMAKEELKAIISPFILRRTK 245
Query: 397 SD--VMQQLVPKIQWVEYVTMERPQEDAYRVAIEEYRAVSRARIAKLSDADLATIVGVLP 454
D ++ L KI+ Y + Q Y+ +E ++ ++ G+
Sbjct: 246 YDKAIINDLPDKIETNVYCNLTPEQAAMYKAEVENLF------------NNIDSVTGIKR 293
Query: 455 QRQISNYFVQFRKIANHPLLVRRIYSDDDVVRFAKKLHPM 494
+ I + ++ ++I +HP L++ + V R K + M
Sbjct: 294 KGMILSTLLKLKQIVDHPALLKG--GEQSVRRSGKMIRTM 331
>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 = 122 bits (305), Expect = 7e-28, Method: Compositional matrix adjust.
Identities = 88/322 (27%), Positives = 152/322 (47%), Gaps = 41/322 (12%)
Query: 160 EDSDFQPVLKPYQLVGVNFLLLLYRKGIAGAILADEMGLGKTIQAITYLMLLKHLNNDPG 219
E + + L+PYQ+ G ++ + G G LAD+ GLGKT+Q I K N+
Sbjct: 30 EPYNIKANLRPYQIKGFSWXRFXNKLGF-GICLADDXGLGKTLQTIAVFSDAKK-ENELT 87
Query: 220 PHLIVCPASVLENWERELKKWCPSFSVLQYHGAGRTAYSRELSSLAKAGLPPPFNVLLVC 279
P L++CP SVL+NWE EL K+ P +H R+ E ++++L
Sbjct: 88 PSLVICPLSVLKNWEEELSKFAPHLRFAVFH-EDRSKIKLE-----------DYDIILTT 135
Query: 280 YSLFERHSVQQKDDRKILKRWRWSCVLMDEAHALKDKNSYRWKNLMSVARNANQRLMLTG 339
Y++ R D R LK W +++DEA +K+ + +K + + + R+ LTG
Sbjct: 136 YAVLLR------DTR--LKEVEWKYIVIDEAQNIKNPQTKIFKAVKEL--KSKYRIALTG 185
Query: 340 TPLQNDLHELWSLLEFMMPDLFATEDVDLKKL---LNGEDRDLIGRMKSILGPFILRRLK 396
TP++N + +LWS+ F+ P L + K + D +K+I+ PFILRR K
Sbjct: 186 TPIENKVDDLWSIXTFLNPGLLGSYSEFKSKFATPIKKGDNXAKEELKAIISPFILRRTK 245
Query: 397 SD--VMQQLVPKIQWVEYVTMERPQEDAYRVAIEEYRAVSRARIAKLSDADLATIVGVLP 454
D ++ L KI+ Y + Q Y+ +E ++ ++ G+
Sbjct: 246 YDKAIINDLPDKIETNVYCNLTPEQAAXYKAEVENLF------------NNIDSVTGIKR 293
Query: 455 QRQISNYFVQFRKIANHPLLVR 476
+ I + ++ ++I +HP L++
Sbjct: 294 KGXILSTLLKLKQIVDHPALLK 315
>pdb|1Z3I|X Chain X, Structure Of The Swi2SNF2 CHROMATIN REMODELING DOMAIN OF
EUKARYOTIC Rad54
Length = 644
Score = 112 bits (279), Expect = 6e-25, Method: Compositional matrix adjust.
Identities = 96/342 (28%), Positives = 171/342 (50%), Gaps = 51/342 (14%)
Query: 161 DSDFQPVLKPYQLVGVNFL--LLLYRK--GIAGAILADEMGLGKTIQAITYLMLLKHLNN 216
D VL+P+Q GV FL + R+ G I+ADEMGLGKT+Q IT + L +
Sbjct: 49 DPVLSKVLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLIWTLLKQSP 108
Query: 217 DPGPHL----IVCPASVLENWERELKKWCPSF--SVLQYHGAGRTAYSRELSSLAKAGLP 270
D P + +V P+S++ NW E+ KW V G+ S+ ++ +++ G+
Sbjct: 109 DCKPEIDKVIVVSPSSLVRNWYNEVGKWLGGRVQPVAIDGGSKDEIDSKLVNFISQQGMR 168
Query: 271 PPFNVLLVCYSLFERHSVQQKDDRKILKRWRWSCVLMDEAHALKDKNSYRWKNLMSVARN 330
P +L++ Y F H+ ++L + + V+ DE H LK+ ++ + L S+ N
Sbjct: 169 IPTPILIISYETFRLHA-------EVLHKGKVGLVICDEGHRLKNSDNQTYLALNSM--N 219
Query: 331 ANQRLMLTGTPLQNDLHELWSLLEFMMPDLFATEDVDLKK-----LLNGEDRDL------ 379
A +R++++GTP+QNDL E +SL+ F+ + T + KK +L G D D
Sbjct: 220 AQRRVLISGTPIQNDLLEYFSLVHFVNSGILGTAQ-EFKKRFEIPILKGRDADASDKDRA 278
Query: 380 -----IGRMKSILGPFILRRLKSDVMQQLVP-KIQWVEYVTMERPQEDAYRVAIEEYRAV 433
+ + SI+ ++RR SD++ + +P KI+ V + Q++ Y++ +++ + V
Sbjct: 279 AGEQKLQELISIVNRCLIRR-TSDILSKYLPVKIEQVVCCNLTPLQKELYKLFLKQAKPV 337
Query: 434 SRARIAKLSDADLATIVGVLPQRQISNYFVQFRKIANHPLLV 475
+ K+S + L++I +K+ NHP L+
Sbjct: 338 ESLQTGKISVSSLSSI-------------TSLKKLCNHPALI 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 = 53.9 bits (128), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 56/203 (27%), Positives = 95/203 (46%), Gaps = 29/203 (14%)
Query: 168 LKPYQLVGVNFLLLLYRKGIAGAILADEMGLGKTIQAITYLMLLKHLNNDPGPHLIVCPA 227
L P+QL N + R+ +LADE+GLGKTI+A ++ + L+ LI+ P
Sbjct: 154 LIPHQL---NIAHDVGRRHAPRVLLADEVGLGKTIEA-GXILHQQLLSGAAERVLIIVPE 209
Query: 228 SVLENWERE-LKKWCPSFSVL---QYHGAGRTAYSRELSSLAKAGLPPPFNV--LLVCYS 281
++ W E L+++ F++ +Y A AY+ PF+ L++C
Sbjct: 210 TLQHQWLVEXLRRFNLRFALFDDERYAEAQHDAYN-------------PFDTEQLVICSL 256
Query: 282 LFERHSVQQKDDRKILKRWRWSCVLMDEAHAL---KDKNSYRWKNLMSVARNANQRLMLT 338
F R S Q+ + L W +++DEAH L +D S ++ + +A + L+LT
Sbjct: 257 DFARRSKQRLEH---LCEAEWDLLVVDEAHHLVWSEDAPSREYQAIEQLAEHVPGVLLLT 313
Query: 339 GTPLQNDLHELWSLLEFMMPDLF 361
TP Q ++ L + P+ F
Sbjct: 314 ATPEQLGXESHFARLRLLDPNRF 336
>pdb|3BJC|A Chain A, Crystal Structure Of The Pde5a Catalytic Domain In Complex
With A Novel Inhibitor
Length = 878
Score = 31.2 bits (69), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 21/40 (52%)
Query: 231 ENWERELKKWCPSFSVLQYHGAGRTAYSRELSSLAKAGLP 270
E ER + K + VL YH + +REL SLA A +P
Sbjct: 513 EAVERAMAKQMVTLEVLSYHASAAEEETRELQSLAAAVVP 552
>pdb|3TJZ|B Chain B, Crystal Structure Of Arf1 Bound To The GammaZETA-Cop Core
Complex
pdb|3TJZ|E Chain E, Crystal Structure Of Arf1 Bound To The GammaZETA-Cop Core
Complex
Length = 355
Score = 31.2 bits (69), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 46/183 (25%), Positives = 75/183 (40%), Gaps = 34/183 (18%)
Query: 121 LKRELYGTTTSAACDRYAEVEASSVRIVTQSDIDDACGDEDSDFQPVLKPYQLVGVNFLL 180
L+R Y T +C A V IVT S D G EDS P ++ + + +L
Sbjct: 84 LRRMCYLTIKEMSCI------AEDVIIVTSSLTKDMTGKEDSYRGPAVRALCQITDSTML 137
Query: 181 LLYRKGIAGAILADEMGLGKTIQAITYLMLLKHLNNDPGPHLIVCPASVLENWERELKKW 240
+ + AI+ D++ + ++ L LLK C V++ W E ++
Sbjct: 138 QAIERYMKQAIV-DKVPSVSSSALVSSLHLLK------------CSFDVVKRWVNEAQEA 184
Query: 241 CPSFSVL-QYHGAG---------RTAYSRELSSLAKAGLPPPFNVLLVCYSLFERHSVQQ 290
S +++ QYH G R A S+ +S + GL PF Y + R + +Q
Sbjct: 185 ASSDNIMVQYHALGLLYHVRKNDRLAVSKMISKFTRHGLKSPF-----AYCMMIRVASRQ 239
Query: 291 KDD 293
+D
Sbjct: 240 LED 242
>pdb|3P0T|A Chain A, Crystal Structure Of An Hit-Like Protein From
Mycobacterium Paratuberculosis
pdb|3P0T|B Chain B, Crystal Structure Of An Hit-Like Protein From
Mycobacterium Paratuberculosis
Length = 138
Score = 30.0 bits (66), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 21/51 (41%), Positives = 26/51 (50%), Gaps = 4/51 (7%)
Query: 465 FRKIANHPLLVRRIYSDDDVVRFAKKLHPMGAFGFECTLERVIEELKNYSD 515
F KI N L R +Y DDDVV F + PM G + R EE+ N+ D
Sbjct: 9 FTKIINRELPGRFVYEDDDVVAFL-TIEPMTQ-GHTLVVPR--EEIDNWQD 55
>pdb|3I5X|A Chain A, Structure Of Mss116p Bound To Ssrna And Amp-Pnp
pdb|3I5Y|A Chain A, Structure Of Mss116p Bound To Ssrna Containing A Single
5-Bru And Amp- Pnp
pdb|3I61|A Chain A, Structure Of Mss116p Bound To Ssrna And Adp-beryllium
Fluoride
pdb|3I62|A Chain A, Structure Of Mss116p Bound To Ssrna And Adp-aluminum
Fluoride
Length = 563
Score = 30.0 bits (66), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 41/86 (47%), Gaps = 11/86 (12%)
Query: 308 DEAHALKDKNSYRWKNLMSVARNANQR-----LMLTGTPLQNDLHELWSLLEFMMPDLFA 362
DE H DK ++ L+ V + N + +L L ++H+ + +EF P L
Sbjct: 44 DEVHF--DKTTF--SKLIHVPKEDNSKEVTLDSLLEEGVLDKEIHKAITRMEF--PGLTP 97
Query: 363 TEDVDLKKLLNGEDRDLIGRMKSILG 388
+ +K +L+ ED D+I R K+ G
Sbjct: 98 VQQKTIKPILSSEDHDVIARAKTGTG 123
>pdb|3SQX|A Chain A, Structure Of Mss116p (Nte And C-Tail Double Deletion)
Bound To Ssrna And Amp-Pnp
Length = 512
Score = 29.3 bits (64), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 26/47 (55%), Gaps = 2/47 (4%)
Query: 342 LQNDLHELWSLLEFMMPDLFATEDVDLKKLLNGEDRDLIGRMKSILG 388
L ++H+ + +EF P L + +K +L+ ED D+I R K+ G
Sbjct: 28 LDKEIHKAITRMEF--PGLTPVQQKTIKPILSSEDHDVIARAKTGTG 72
>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And
Amp-Pnp
Length = 579
Score = 29.3 bits (64), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 26/47 (55%), Gaps = 2/47 (4%)
Query: 342 LQNDLHELWSLLEFMMPDLFATEDVDLKKLLNGEDRDLIGRMKSILG 388
L ++H+ + +EF P L + +K +L+ ED D+I R K+ G
Sbjct: 28 LDKEIHKAITRMEF--PGLTPVQQKTIKPILSSEDHDVIARAKTGTG 72
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
0.320 0.136 0.404
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,157,460
Number of Sequences: 62578
Number of extensions: 545362
Number of successful extensions: 1194
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: 1171
Number of HSP's gapped (non-prelim): 11
length of query: 520
length of database: 14,973,337
effective HSP length: 103
effective length of query: 417
effective length of database: 8,527,803
effective search space: 3556093851
effective search space used: 3556093851
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (25.4 bits)