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= psy10683
(429 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 = 225 bits (573), Expect = 4e-59, Method: Compositional matrix adjust.
Identities = 113/266 (42%), Positives = 164/266 (61%), Gaps = 14/266 (5%)
Query: 173 PFYIKGGEMRDYQVRGLNWMISLYENGINGILADEMGLGKTLQTISLLGYMKHYRNIAGP 232
P +IKGGE+RD+Q+ G+NWM L+ G NGILADEMGLGKT+QT++ + ++ R GP
Sbjct: 229 PPFIKGGELRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWLIFARRQNGP 288
Query: 233 HIVIVPKSTLLNWMNEFKKWCPTLRAICLIGDQDARNAMIRDVMM----------PGEWD 282
HI++VP ST+ W++ F+KW P L IC +G+Q +R+ IR+ +++
Sbjct: 289 HIIVVPLSTMPAWLDTFEKWAPDLNCICYMGNQKSRDT-IREYEFYTNPRAKGKKTMKFN 347
Query: 283 VCITSYEMCIRERGVFKKFNWRYLVIDEAHRIKNEKSKLSEIVREFKTTNRLLLTGTPLQ 342
V +T+YE +++R W+++ +DEAHR+KN +S L E + FK NR+L+TGTPLQ
Sbjct: 348 VLLTTYEYILKDRAELGSIKWQFMAVDEAHRLKNAESSLYESLNSFKVANRMLITGTPLQ 407
Query: 343 NNLHELWALLNFLLPXXXXXXXXXXXWFNTEEFMGDHSIIERLHSVLKPFLLRRLKSEVE 402
NN+ EL AL+NFL+P EE I LH ++PF+LRRLK +VE
Sbjct: 408 NNIKELAALVNFLMPGRFTIDQEIDFENQDEE---QEEYIHDLHRRIQPFILRRLKKDVE 464
Query: 403 KRLKPKKELKVYVGLSKMQREWYTKV 428
K L K E + V LS +Q E+Y +
Sbjct: 465 KSLPSKTERILRVELSDVQTEYYKNI 490
Score = 72.8 bits (177), Expect = 4e-13, Method: Compositional matrix adjust.
Identities = 30/49 (61%), Positives = 40/49 (81%)
Query: 28 PFYIKGGEMRDYQVRGLNWMISLYENGINGILADEMGLGKTLQTISLLG 76
P +IKGGE+RD+Q+ G+NWM L+ G NGILADEMGLGKT+QT++ +
Sbjct: 229 PPFIKGGELRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFIS 277
>pdb|1Z6A|A Chain A, Sulfolobus Solfataricus Swi2SNF2 ATPASE CORE DOMAIN
Length = 500
Score = 152 bits (384), Expect = 4e-37, Method: Compositional matrix adjust.
Identities = 91/255 (35%), Positives = 138/255 (54%), Gaps = 13/255 (5%)
Query: 173 PFYIKGGEMRDYQVRGLNWMISLYENGINGILADEMGLGKTLQTISLLGYMKHYRNIAGP 232
P+ IK +R YQ++G +WM + + G LAD+MGLGKTLQTI++ K N P
Sbjct: 31 PYNIKAN-LRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAVFSDAKK-ENELTP 88
Query: 233 HIVIVPKSTLLNWMNEFKKWCPTLRAICLIGDQDARNAMIRDVMMPGEWDVCITSYEMCI 292
+VI P S L NW E K+ P LR D R + ++D+ +T+Y + +
Sbjct: 89 SLVICPLSVLKNWEEELSKFAPHLRFAVFHED--------RSKIKLEDYDIILTTYAVLL 140
Query: 293 RERGVFKKFNWRYLVIDEAHRIKNEKSKLSEIVREFKTTNRLLLTGTPLQNNLHELWALL 352
R+ + K+ W+Y+VIDEA IKN ++K+ + V+E K+ R+ LTGTP++N + +LW+++
Sbjct: 141 RDTRL-KEVEWKYIVIDEAQNIKNPQTKIFKAVKELKSKYRIALTGTPIENKVDDLWSIM 199
Query: 353 NFLLPXXXXXXXXXXXWFNTEEFMGDHSIIERLHSVLKPFLLRRLKSE--VEKRLKPKKE 410
FL P F T GD+ E L +++ PF+LRR K + + L K E
Sbjct: 200 TFLNPGLLGSYSEFKSKFATPIKKGDNMAKEELKAIISPFILRRTKYDKAIINDLPDKIE 259
Query: 411 LKVYVGLSKMQREWY 425
VY L+ Q Y
Sbjct: 260 TNVYCNLTPEQAAMY 274
Score = 49.3 bits (116), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 23/49 (46%), Positives = 33/49 (67%), Gaps = 1/49 (2%)
Query: 28 PFYIKGGEMRDYQVRGLNWMISLYENGINGILADEMGLGKTLQTISLLG 76
P+ IK +R YQ++G +WM + + G LAD+MGLGKTLQTI++
Sbjct: 31 PYNIKAN-LRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAVFS 78
>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 = 145 bits (367), Expect = 3e-35, Method: Compositional matrix adjust.
Identities = 89/255 (34%), Positives = 134/255 (52%), Gaps = 13/255 (5%)
Query: 173 PFYIKGGEMRDYQVRGLNWMISLYENGINGILADEMGLGKTLQTISLLGYMKHYRNIAGP 232
P+ IK +R YQ++G +W + G LAD+ GLGKTLQTI++ K N P
Sbjct: 31 PYNIKAN-LRPYQIKGFSWXRFXNKLGFGICLADDXGLGKTLQTIAVFSDAKK-ENELTP 88
Query: 233 HIVIVPKSTLLNWMNEFKKWCPTLRAICLIGDQDARNAMIRDVMMPGEWDVCITSYEMCI 292
+VI P S L NW E K+ P LR D R + ++D+ +T+Y + +
Sbjct: 89 SLVICPLSVLKNWEEELSKFAPHLRFAVFHED--------RSKIKLEDYDIILTTYAVLL 140
Query: 293 RERGVFKKFNWRYLVIDEAHRIKNEKSKLSEIVREFKTTNRLLLTGTPLQNNLHELWALL 352
R+ + K+ W+Y+VIDEA IKN ++K+ + V+E K+ R+ LTGTP++N + +LW++
Sbjct: 141 RDTRL-KEVEWKYIVIDEAQNIKNPQTKIFKAVKELKSKYRIALTGTPIENKVDDLWSIX 199
Query: 353 NFLLPXXXXXXXXXXXWFNTEEFMGDHSIIERLHSVLKPFLLRRLKSE--VEKRLKPKKE 410
FL P F T GD+ E L +++ PF+LRR K + + L K E
Sbjct: 200 TFLNPGLLGSYSEFKSKFATPIKKGDNXAKEELKAIISPFILRRTKYDKAIINDLPDKIE 259
Query: 411 LKVYVGLSKMQREWY 425
VY L+ Q Y
Sbjct: 260 TNVYCNLTPEQAAXY 274
Score = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/49 (42%), Positives = 30/49 (61%), Gaps = 1/49 (2%)
Query: 28 PFYIKGGEMRDYQVRGLNWMISLYENGINGILADEMGLGKTLQTISLLG 76
P+ IK +R YQ++G +W + G LAD+ GLGKTLQTI++
Sbjct: 31 PYNIKAN-LRPYQIKGFSWXRFXNKLGFGICLADDXGLGKTLQTIAVFS 78
>pdb|1Z3I|X Chain X, Structure Of The Swi2SNF2 CHROMATIN REMODELING DOMAIN OF
EUKARYOTIC Rad54
Length = 644
Score = 82.8 bits (203), Expect = 3e-16, Method: Compositional matrix adjust.
Identities = 76/272 (27%), Positives = 118/272 (43%), Gaps = 27/272 (9%)
Query: 181 MRDYQVRGLNWMISLY-----ENGINGILADEMGLGKTLQTISLLGYMKHYRNIAGPHI- 234
+R +Q G+ ++ EN I+ADEMGLGKTLQ I+L+ + P I
Sbjct: 56 LRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLIWTLLKQSPDCKPEID 115
Query: 235 ---VIVPKSTLLNWMNEFKKWCPTLRAICLI--GDQDARNAMIRDVM----MPGEWDVCI 285
V+ P S + NW NE KW I G +D ++ + + + M + I
Sbjct: 116 KVIVVSPSSLVRNWYNEVGKWLGGRVQPVAIDGGSKDEIDSKLVNFISQQGMRIPTPILI 175
Query: 286 TSYEMCIRERGVFKKFNWRYLVIDEAHRIKNEKSKLSEIVREFKTTNRLLLTGTPLQNNL 345
SYE V K ++ DE HR+KN ++ + R+L++GTP+QN+L
Sbjct: 176 ISYETFRLHAEVLHKGKVGLVICDEGHRLKNSDNQTYLALNSMNAQRRVLISGTPIQNDL 235
Query: 346 HELWALLNFLLPXXXXXXXXXXXWFNTEEFMG---DHSIIER---------LHSVLKPFL 393
E ++L++F+ F G D S +R L S++ L
Sbjct: 236 LEYFSLVHFVNSGILGTAQEFKKRFEIPILKGRDADASDKDRAAGEQKLQELISIVNRCL 295
Query: 394 LRRLKSEVEKRLKPKKELKVYVGLSKMQREWY 425
+RR + K L K E V L+ +Q+E Y
Sbjct: 296 IRRTSDILSKYLPVKIEQVVCCNLTPLQKELY 327
Score = 36.2 bits (82), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 19/45 (42%), Positives = 27/45 (60%), Gaps = 5/45 (11%)
Query: 36 MRDYQVRGLNWMISLY-----ENGINGILADEMGLGKTLQTISLL 75
+R +Q G+ ++ EN I+ADEMGLGKTLQ I+L+
Sbjct: 56 LRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLI 100
>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 = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 46/167 (27%), Positives = 76/167 (45%), Gaps = 19/167 (11%)
Query: 203 ILADEMGLGKTLQTISLLGYMKHYRNIAGPH---IVIVPKSTLLNWMNEFKKWCPTLRAI 259
+LADE+GLGKT++ G + H + ++G ++IVP++ W+ E + LR
Sbjct: 174 LLADEVGLGKTIEA----GXILHQQLLSGAAERVLIIVPETLQHQWLVEXLRRF-NLR-F 227
Query: 260 CLIGDQDARNAMIRDVMMPGEWD-VCITSYEMCIRERGVFKKF---NWRYLVIDEAHRI- 314
L D+ A D P + + + I S + R + + W LV+DEAH +
Sbjct: 228 ALFDDERYAEAQ-HDAYNPFDTEQLVICSLDFARRSKQRLEHLCEAEWDLLVVDEAHHLV 286
Query: 315 --KNEKSKLSEIVREFK--TTNRLLLTGTPLQNNLHELWALLNFLLP 357
++ S+ + + + LLLT TP Q +A L L P
Sbjct: 287 WSEDAPSREYQAIEQLAEHVPGVLLLTATPEQLGXESHFARLRLLDP 333
>pdb|1EI3|A Chain A, Crystal Structure Of Native Chicken Fibrinogen
pdb|1EI3|D Chain D, Crystal Structure Of Native Chicken Fibrinogen
Length = 491
Score = 31.6 bits (70), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 15/61 (24%), Positives = 31/61 (50%), Gaps = 10/61 (16%)
Query: 281 WDVCI-----TSYEMCIRERGVFKKFNWRYLVIDEAHRIKNEKSKLSEIVREFKTTNRLL 335
W +C+ T C R +G+ + Y + RI N + +L++ ++KT+NR++
Sbjct: 34 WPICVDDDWGTKCPSCCRMQGIIDDTDQNY-----SQRIDNIRQQLADSQNKYKTSNRVI 88
Query: 336 L 336
+
Sbjct: 89 V 89
>pdb|3ANW|B Chain B, A Protein Complex Essential Initiation Of Dna Replication
Length = 171
Score = 29.3 bits (64), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 26/41 (63%), Gaps = 1/41 (2%)
Query: 384 RLHSVLKPFLLRRLKSEVEKRLKPKKELKVYVGLSKMQREW 424
R + +LK +LR E+ RL P+ E ++Y+ +SK++ EW
Sbjct: 128 RFNKILKAVMLRPNSLELLSRLAPE-ERRIYLQMSKIRNEW 167
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 0.137 0.412
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,873,623
Number of Sequences: 62578
Number of extensions: 468909
Number of successful extensions: 1019
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: 1000
Number of HSP's gapped (non-prelim): 18
length of query: 429
length of database: 14,973,337
effective HSP length: 102
effective length of query: 327
effective length of database: 8,590,381
effective search space: 2809054587
effective search space used: 2809054587
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: 53 (25.0 bits)