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= psy14604
(209 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 = 99.8 bits (247), Expect = 9e-22, Method: Compositional matrix adjust.
Identities = 49/118 (41%), Positives = 72/118 (61%), Gaps = 5/118 (4%)
Query: 85 TDLRKKYEK---QPPFLDDTGMQLHAYQLEGINWLRYSWGQNIDTILADEMGLGKTIQTI 141
T R ++EK QPPF+ G +L +QL GINW+ + W + + ILADEMGLGKT+QT+
Sbjct: 216 TSQRPRFEKLSVQPPFI--KGGELRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTV 273
Query: 142 TFLYSLFKEGHCKGPFLVSAPLSTIINWEREFETWAPDFYVVTYVGDKDCRIVLRDHD 199
F+ L GP ++ PLST+ W FE WAPD + Y+G++ R +R+++
Sbjct: 274 AFISWLIFARRQNGPHIIVVPLSTMPAWLDTFEKWAPDLNCICYMGNQKSRDTIREYE 331
>pdb|1Z6A|A Chain A, Sulfolobus Solfataricus Swi2SNF2 ATPASE CORE DOMAIN
Length = 500
Score = 68.6 bits (166), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 38/97 (39%), Positives = 51/97 (52%), Gaps = 2/97 (2%)
Query: 104 QLHAYQLEGINWLRYSWGQNIDTILADEMGLGKTIQTITFLYSLFKEGHCKGPFLVSAPL 163
L YQ++G +W+R+ LAD+MGLGKT+QTI KE P LV PL
Sbjct: 37 NLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAVFSDAKKENELT-PSLVICPL 95
Query: 164 STIINWEREFETWAPDFYVVTYVGDKDCRIVLRDHDI 200
S + NWE E +AP + D+ +I L D+DI
Sbjct: 96 SVLKNWEEELSKFAPHLRFAVFHEDR-SKIKLEDYDI 131
>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 = 65.1 bits (157), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 39/112 (34%), Positives = 55/112 (49%), Gaps = 4/112 (3%)
Query: 89 KKYEKQPPFLDDTGMQLHAYQLEGINWLRYSWGQNIDTILADEMGLGKTIQTITFLYSLF 148
K ++ P+ + L YQ++G +W R+ LAD+ GLGKT+QTI
Sbjct: 24 KSFQLLEPY--NIKANLRPYQIKGFSWXRFXNKLGFGICLADDXGLGKTLQTIAVFSDAK 81
Query: 149 KEGHCKGPFLVSAPLSTIINWEREFETWAPDFYVVTYVGDKDCRIVLRDHDI 200
KE P LV PLS + NWE E +AP + D+ +I L D+DI
Sbjct: 82 KENELT-PSLVICPLSVLKNWEEELSKFAPHLRFAVFHEDR-SKIKLEDYDI 131
>pdb|1Z3I|X Chain X, Structure Of The Swi2SNF2 CHROMATIN REMODELING DOMAIN OF
EUKARYOTIC Rad54
Length = 644
Score = 50.8 bits (120), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 39/116 (33%), Positives = 55/116 (47%), Gaps = 18/116 (15%)
Query: 76 YTPPPEKPTTDLRKKYEKQP------PFLDDTGMQLHAYQLEGINWL-RYSWGQNID--- 125
Y PP ++ EK P P L L +Q EG+ +L G+ I+
Sbjct: 24 YEPPAISAHDLIKADKEKLPVHVVVDPVLSKV---LRPHQREGVKFLWDCVTGRRIENSY 80
Query: 126 -TILADEMGLGKTIQTITFLYSLFKEG-HCK---GPFLVSAPLSTIINWEREFETW 176
I+ADEMGLGKT+Q IT +++L K+ CK +V +P S + NW E W
Sbjct: 81 GCIMADEMGLGKTLQCITLIWTLLKQSPDCKPEIDKVIVVSPSSLVRNWYNEVGKW 136
>pdb|2WJV|A Chain A, Crystal Structure Of The Complex Between Human Nonsense
Mediated Decay Factors Upf1 And Upf2
pdb|2WJV|B Chain B, Crystal Structure Of The Complex Between Human Nonsense
Mediated Decay Factors Upf1 And Upf2
pdb|2WJY|A Chain A, Crystal Structure Of The Complex Between Human Nonsense
Mediated Decay Factors Upf1 And Upf2 Orthorhombic Form
Length = 800
Score = 32.0 bits (71), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 35/68 (51%), Gaps = 9/68 (13%)
Query: 108 YQLEGINWLRYSWGQNIDTILADEM-------GLGKTIQTITFLYSLFKEGHCKGPFLVS 160
+ +G+ L +S + T+L + G GKT+ + T +Y L ++G+ GP LV
Sbjct: 349 FTAQGLPDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGN--GPVLVC 406
Query: 161 APLSTIIN 168
AP + ++
Sbjct: 407 APSNIAVD 414
>pdb|2GJK|A Chain A, Structural And Functional Insights Into The Human Upf1
Helicase Core
pdb|2GK6|A Chain A, Structural And Functional Insights Into The Human Upf1
Helicase Core
pdb|2GK6|B Chain B, Structural And Functional Insights Into The Human Upf1
Helicase Core
pdb|2GK7|A Chain A, Structural And Functional Insights Into The Human Upf1
Helicase Core
Length = 624
Score = 31.6 bits (70), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 9/72 (12%)
Query: 108 YQLEGINWLRYSWGQNIDTILADEM-------GLGKTIQTITFLYSLFKEGHCKGPFLVS 160
+ +G+ L +S + T+L + G GKT+ + T +Y L ++G+ GP LV
Sbjct: 173 FTAQGLPDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGN--GPVLVC 230
Query: 161 APLSTIINWERE 172
AP + ++ E
Sbjct: 231 APSNIAVDQLTE 242
>pdb|2XZO|A Chain A, Upf1 Helicase - Rna Complex
pdb|2XZP|A Chain A, Upf1 Helicase
Length = 623
Score = 31.6 bits (70), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 9/72 (12%)
Query: 108 YQLEGINWLRYSWGQNIDTILADEM-------GLGKTIQTITFLYSLFKEGHCKGPFLVS 160
+ +G+ L +S + T+L + G GKT+ + T +Y L ++G+ GP LV
Sbjct: 172 FTAQGLPDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGN--GPVLVC 229
Query: 161 APLSTIINWERE 172
AP + ++ E
Sbjct: 230 APSNIAVDQLTE 241
>pdb|4A15|A Chain A, Crystal Structure Of An Xpd Dna Complex
Length = 620
Score = 29.3 bits (64), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 24/52 (46%)
Query: 108 YQLEGINWLRYSWGQNIDTILADEMGLGKTIQTITFLYSLFKEGHCKGPFLV 159
YQ+E I++LR S ++ L G GKTI + E K +LV
Sbjct: 7 YQVEAIDFLRSSLQKSYGVALESPTGSGKTIMALKSALQYSSERKLKVLYLV 58
>pdb|2VTY|A Chain A, Vaccinia Virus Anti-Apoptotic F1l Is A Novel Bcl-2-Like
Domain Swapped Dimer
Length = 182
Score = 28.1 bits (61), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 2/39 (5%)
Query: 118 YSWGQNIDTILADEMGLGKTIQTITFLYSLFKEGHCKGP 156
Y ++TI+ D GLG + TI+F+ L + C P
Sbjct: 119 YDINNEVNTIMLDNKGLGVRLATISFITELGRR--CMNP 155
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
0.318 0.138 0.441
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,694,187
Number of Sequences: 62578
Number of extensions: 229641
Number of successful extensions: 580
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 573
Number of HSP's gapped (non-prelim): 9
length of query: 209
length of database: 14,973,337
effective HSP length: 94
effective length of query: 115
effective length of database: 9,091,005
effective search space: 1045465575
effective search space used: 1045465575
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: 49 (23.5 bits)