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= 001037
(1179 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 = 249 bits (635), Expect = 8e-66, Method: Compositional matrix adjust.
Identities = 151/416 (36%), Positives = 220/416 (52%), Gaps = 64/416 (15%)
Query: 1 MSMWQSELHKWLPSVSCIYYVGAKDQRSRLFSQEV---------AALKFNVLVTTYEFIM 51
M W KW P ++CI Y+G + R + E +KFNVL+TTYE+I+
Sbjct: 298 MPAWLDTFEKWAPDLNCICYMGNQKSRDTIREYEFYTNPRAKGKKTMKFNVLLTTYEYIL 357
Query: 52 YDRSKLSKVDWKYIIIDEAQRMKDRESVLARDLDRYRCQRRLLLTGTPLQNDXXXXXXXX 111
DR++L + W+++ +DEA R+K+ ES L L+ ++ R+L+TGTPLQN+
Sbjct: 358 KDRAELGSIKWQFMAVDEAHRLKNAESSLYESLNSFKVANRMLITGTPLQNNIKELAALV 417
Query: 112 XXXXPEVFDNRKAFHDWFSQPFQKEGPTHNADDDWLETEKKVIIIHRLHQILEPFMLRRR 171
P F +E N D++ E IH LH+ ++PF+LRR
Sbjct: 418 NFLMPGRF------------TIDQEIDFENQDEEQEE------YIHDLHRRIQPFILRRL 459
Query: 172 VEDVEGSLPPKVSIVLRCRMSAIQSAIYDWIKATGTLRVDPEDEKRRVQKNPIYQAKV-- 229
+DVE SLP K +LR +S +Q+ Y K + KN Y A
Sbjct: 460 KKDVEKSLPSKTERILRVELSDVQTEYY----------------KNILTKN--YSALTAG 501
Query: 230 ----YKTLNNRCMELRKTCNHPLLNYPYFSDLSKDF-------------LVKSCGKLWIL 272
+ +L N EL+K NHP L + + F L+ S GK+ +L
Sbjct: 502 AKGGHFSLLNIMNELKKASNHPYLFDNAEERVLQKFGDGKMTRENVLRGLIMSSGKMVLL 561
Query: 273 DRILIKLQRTGHRVLLFSTMTKLLDILEEYLQWRQLVYRRIDGTTSLEDRESAIVDFNSH 332
D++L +L++ GHRVL+FS M ++LDIL +YL + + ++R+DGT R +I FNS
Sbjct: 562 DQLLTRLKKDGHRVLIFSQMVRMLDILGDYLSIKGINFQRLDGTVPSAQRRISIDHFNSP 621
Query: 333 DSDCFIFLLSIRAAGRGLNLQSADTVIIYDPDPNPKNEEQAVARAHRIGQKREVKV 388
DS+ F+FLLS RA G G+NL +ADTV+I+D D NP+ + QA+ARAHRIGQK V V
Sbjct: 622 DSNDFVFLLSTRAGGLGINLMTADTVVIFDSDWNPQADLQAMARAHRIGQKNHVMV 677
>pdb|1Z3I|X Chain X, Structure Of The Swi2SNF2 CHROMATIN REMODELING DOMAIN OF
EUKARYOTIC Rad54
Length = 644
Score = 150 bits (379), Expect = 4e-36, Method: Compositional matrix adjust.
Identities = 121/442 (27%), Positives = 200/442 (45%), Gaps = 41/442 (9%)
Query: 4 WQSELHKWLPSVSCIYYV--GAKDQ----RSRLFSQEVAALKFNVLVTTYEFIMYDRSKL 57
W +E+ KWL + G+KD+ SQ+ + +L+ +YE L
Sbjct: 129 WYNEVGKWLGGRVQPVAIDGGSKDEIDSKLVNFISQQGMRIPTPILIISYETFRLHAEVL 188
Query: 58 SKVDWKYIIIDEAQRMKDRESVLARDLDRYRCQRRLLLTGTPLQNDXXXXXXXXXXXXPE 117
K +I DE R+K+ ++ L+ QRR+L++GTP+QND
Sbjct: 189 HKGKVGLVICDEGHRLKNSDNQTYLALNSMNAQRRVLISGTPIQNDLLEYFSLVHFVNSG 248
Query: 118 VFDNRKAFHDWFSQPFQKEGPTHNADDDWLETEKKVIIIHRLHQILEPFMLRRRVEDVEG 177
+ + F F P K +D D E+K + L I+ ++RR + +
Sbjct: 249 ILGTAQEFKKRFEIPILKGRDADASDKDRAAGEQK---LQELISIVNRCLIRRTSDILSK 305
Query: 178 SLPPKVSIVLRCRMSAIQSAIYDWIKATGTLRVDPEDEKRRVQKNPIYQAKVYKTLNNRC 237
LP K+ V+ C ++ +Q +Y K+ + K+ + +
Sbjct: 306 YLPVKIEQVVCCNLTPLQKELYKLFL------------KQAKPVESLQTGKISVSSLSSI 353
Query: 238 MELRKTCNHPLLNYP-----------YFSDLSKDFLVKSC-----GKLWILDRIL-IKLQ 280
L+K CNHP L Y +++ K+ GK+ +LD IL +
Sbjct: 354 TSLKKLCNHPALIYEKCLTGEEGFDGALDLFPQNYSTKAVEPQLSGKMLVLDYILAMTRT 413
Query: 281 RTGHRVLLFSTMTKLLDILEEYLQWRQLVYRRIDGTTSLEDRESAIVDFNSHDSDCFIFL 340
T +V+L S T+ LD+ E+ + R+ +Y R+DGT S++ R + FN+ S FIF+
Sbjct: 414 TTSDKVVLVSNYTQTLDLFEKLCRNRRYLYVRLDGTMSIKKRAKIVERFNNPSSPEFIFM 473
Query: 341 LSIRAAGRGLNLQSADTVIIYDPDPNPKNEEQAVARAHRIGQKREV---KVIYMEAVVDK 397
LS +A G GLNL A+ ++++DPD NP N+EQA+AR R GQK+ +++ + +K
Sbjct: 474 LSSKAGGCGLNLIGANRLVMFDPDWNPANDEQAMARVWRDGQKKTCYIYRLLSTGTIEEK 533
Query: 398 ISSHQKEDELRSGGTVDLEDDL 419
I Q + S VD E D+
Sbjct: 534 ILQRQAHKKALSSCVVDEEQDV 555
>pdb|1Z6A|A Chain A, Sulfolobus Solfataricus Swi2SNF2 ATPASE CORE DOMAIN
Length = 500
Score = 117 bits (292), Expect = 4e-26, Method: Compositional matrix adjust.
Identities = 110/435 (25%), Positives = 206/435 (47%), Gaps = 66/435 (15%)
Query: 4 WQSELHKWLPSVSCIYYVGAKDQRSRLFSQEVAALK---FNVLVTTYEFIMYDRSKLSKV 60
W+ EL K+ P + R +F ++ + +K +++++TTY ++ D ++L +V
Sbjct: 101 WEEELSKFAPHL-----------RFAVFHEDRSKIKLEDYDIILTTYAVLLRD-TRLKEV 148
Query: 61 DWKYIIIDEAQRMKDRESVLARDLDRYRCQRRLLLTGTPLQNDXXXXXXXXXXXXPEVFD 120
+WKYI+IDEAQ +K+ ++ + + + + + R+ LTGTP++N P +
Sbjct: 149 EWKYIVIDEAQNIKNPQTKIFKAVKELKSKYRIALTGTPIENKVDDLWSIMTFLNPGLLG 208
Query: 121 NRKAFHDWFSQPFQKEGPTHNADDDWLETEKKVIIIHRLHQILEPFMLRRRVED--VEGS 178
+ F F+ P +K D+ + E K II PF+LRR D +
Sbjct: 209 SYSEFKSKFATPIKK-------GDNMAKEELKAII--------SPFILRRTKYDKAIIND 253
Query: 179 LPPKVSIVLRCRMSAIQSAIYDWIKATGTLRVDPEDEKRRVQKNPIYQAKVYKTLNNRCM 238
LP K+ + C ++ Q+A+Y KA + D +++ + + TL +
Sbjct: 254 LPDKIETNVYCNLTPEQAAMY---KAEVENLFNNIDSVTGIKR----KGMILSTL----L 302
Query: 239 ELRKTCNHPLLNYPYFSDLSKDFLVKSCGKLWILDRILIKLQRTGHRVLLFSTMTKLLDI 298
+L++ +HP L + V+ GK+ I+ + G ++ +F+ + I
Sbjct: 303 KLKQIVDHPALLK------GGEQSVRRSGKMIRTMEIIEEALDEGDKIAIFTQFVDMGKI 356
Query: 299 LEEYLQWRQLVYRRID-------GTTSLEDRESAIVDFNSHDSDCFIFLLSIRAAGRGLN 351
+ R ++ + ++ G S ++R+ I F ++ S FI +LS++A G G+N
Sbjct: 357 I------RNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFI-VLSVKAGGFGIN 409
Query: 352 LQSADTVIIYDPDPNPKNEEQAVARAHRIGQKREVKVIYMEAVVDKISSHQKEDELRSGG 411
L SA+ VI +D NP E+QA R +RIGQ R V V ++ + +K D+L +
Sbjct: 410 LTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIV---HKLISVGTLEEKIDQLLAFK 466
Query: 412 TVDLEDDLAGKDRYI 426
+D ++ D +I
Sbjct: 467 RSLFKDIISSGDSWI 481
>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 = 114 bits (284), Expect = 4e-25, Method: Compositional matrix adjust.
Identities = 111/435 (25%), Positives = 204/435 (46%), Gaps = 66/435 (15%)
Query: 4 WQSELHKWLPSVSCIYYVGAKDQRSRLFSQEVAALK---FNVLVTTYEFIMYDRSKLSKV 60
W+ EL K+ P + R +F ++ + +K +++++TTY ++ D ++L +V
Sbjct: 101 WEEELSKFAPHL-----------RFAVFHEDRSKIKLEDYDIILTTYAVLLRD-TRLKEV 148
Query: 61 DWKYIIIDEAQRMKDRESVLARDLDRYRCQRRLLLTGTPLQNDXXXXXXXXXXXXPEVFD 120
+WKYI+IDEAQ +K+ ++ + + + + + R+ LTGTP++N P +
Sbjct: 149 EWKYIVIDEAQNIKNPQTKIFKAVKELKSKYRIALTGTPIENKVDDLWSIXTFLNPGLLG 208
Query: 121 NRKAFHDWFSQPFQKEGPTHNADDDWLETEKKVIIIHRLHQILEPFMLRRRVED--VEGS 178
+ F F+ P +K D+ + E K II PF+LRR D +
Sbjct: 209 SYSEFKSKFATPIKK-------GDNXAKEELKAII--------SPFILRRTKYDKAIIND 253
Query: 179 LPPKVSIVLRCRMSAIQSAIYDWIKATGTLRVDPEDEKRRVQKNPIYQAKVYKTLNNRCM 238
LP K+ + C ++ Q+A Y KA + D +++ + + TL +
Sbjct: 254 LPDKIETNVYCNLTPEQAAXY---KAEVENLFNNIDSVTGIKR----KGXILSTL----L 302
Query: 239 ELRKTCNHPLLNYPYFSDLSKDFLVKSCGKLWILDRILIKLQRTGHRVLLFSTMTKLLDI 298
+L++ +HP L + V+ GK I+ + G ++ +F+ I
Sbjct: 303 KLKQIVDHPALLK------GGEQSVRRSGKXIRTXEIIEEALDEGDKIAIFTQFVDXGKI 356
Query: 299 LEEYLQWRQLVYRRID-------GTTSLEDRESAIVDFNSHDSDCFIFLLSIRAAGRGLN 351
+ R ++ + ++ G S ++R+ I F ++ S FI +LS++A G G+N
Sbjct: 357 I------RNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFI-VLSVKAGGFGIN 409
Query: 352 LQSADTVIIYDPDPNPKNEEQAVARAHRIGQKREVKVIYMEAVVDKISSHQKEDELRSGG 411
L SA+ VI +D NP E+QA R +RIGQ R V V ++ + +K D+L +
Sbjct: 410 LTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIV---HKLISVGTLEEKIDQLLAFK 466
Query: 412 TVDLEDDLAGKDRYI 426
+D ++ D +I
Sbjct: 467 RSLFKDIISSGDSWI 481
>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 = 58.2 bits (139), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 55/217 (25%), Positives = 99/217 (45%), Gaps = 31/217 (14%)
Query: 179 LPPKVSIVLRCRMSAIQSAIYDWIKATGTLRVDPEDEKRRVQKNPIYQAKVYKTLNNRCM 238
LP K+ + C ++ Q+A+Y E E + + K + + +
Sbjct: 25 LPDKIETNVYCNLTPEQAAMYK-----------AEVENLFNNIDSVTGIKRKGMILSTLL 73
Query: 239 ELRKTCNHPLLNYPYFSDLSKDFLVKSCGKLWILDRILIKLQRTGHRVLLFSTMTKLLDI 298
+L++ +HP L + V+ GK+ I+ + G ++ +F+ + I
Sbjct: 74 KLKQIVDHPALLK------GGEQSVRRSGKMIRTMEIIEEALDEGDKIAIFTQFVDMGKI 127
Query: 299 LEEYLQWRQLVYRRID-------GTTSLEDRESAIVDFNSHDSDCFIFLLSIRAAGRGLN 351
+ R ++ + ++ G S ++R+ I F ++ S FI +LS++A G G+N
Sbjct: 128 I------RNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFI-VLSVKAGGFGIN 180
Query: 352 LQSADTVIIYDPDPNPKNEEQAVARAHRIGQKREVKV 388
L SA+ VI +D NP E+QA R +RIGQ R V V
Sbjct: 181 LTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIV 217
>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 = 39.3 bits (90), Expect = 0.014, Method: Composition-based stats.
Identities = 32/103 (31%), Positives = 46/103 (44%), Gaps = 6/103 (5%)
Query: 279 LQRTGHRVLLFSTMTKLLDILEEYLQWRQLVYRRIDGTTSLEDRESAIVDFNSHDSDCFI 338
LQ+T VL+F+ +D + EYL + + I G E+R AI F D
Sbjct: 50 LQKTPPPVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDV-- 107
Query: 339 FLLSIRAAGRGLNLQSADTVIIYDPDPNPKNEEQAVARAHRIG 381
L++ A +GL+ + VI YD P+ E V R R G
Sbjct: 108 -LVATDVASKGLDFPAIQHVINYD---MPEEIENYVHRIGRTG 146
>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x
Length = 417
Score = 38.1 bits (87), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 31/96 (32%), Positives = 44/96 (45%), Gaps = 6/96 (6%)
Query: 287 LLFSTMTKLLDILEEYLQWRQLVYRRIDGTTSLEDRESAIVDFNSHDSDCFIFLLSIRAA 346
L+F K D LE++L I G S DRE A+ F S S L++ A
Sbjct: 280 LVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSP---ILVATAVA 336
Query: 347 GRGLNLQSADTVIIYDPDPNPKNEEQAVARAHRIGQ 382
RGL++ + VI +D P + E+ V R R G+
Sbjct: 337 ARGLDISNVKHVINFDL---PSDIEEYVHRIGRTGR 369
>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 = 36.6 bits (83), Expect = 0.079, Method: Compositional matrix adjust.
Identities = 31/96 (32%), Positives = 44/96 (45%), Gaps = 6/96 (6%)
Query: 287 LLFSTMTKLLDILEEYLQWRQLVYRRIDGTTSLEDRESAIVDFNSHDSDCFIFLLSIRAA 346
L+F K D LE++L I G S DRE A+ F S S L++ A
Sbjct: 50 LVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPI---LVATAVA 106
Query: 347 GRGLNLQSADTVIIYDPDPNPKNEEQAVARAHRIGQ 382
RGL++ + VI +D P + E+ V R R G+
Sbjct: 107 ARGLDISNVKHVINFDL---PSDIEEYVHRIGRTGR 139
>pdb|2WP1|A Chain A, Structure Of Brdt Bromodomain 2 Bound To An Acetylated
Histone H3 Peptide
pdb|2WP1|B Chain B, Structure Of Brdt Bromodomain 2 Bound To An Acetylated
Histone H3 Peptide
Length = 126
Score = 36.6 bits (83), Expect = 0.087, Method: Composition-based stats.
Identities = 18/55 (32%), Positives = 28/55 (50%)
Query: 923 NILDLRKIDQRVDRLEYNGVMELVSDVQFMLKGAMQFYGFSHEVRSEARKVHDLF 977
N +DL I ++D EY E +DV+ M ++ HEV + AR + D+F
Sbjct: 58 NPMDLGTIKGKMDNQEYKDAYEFAADVRLMFMNCYKYNPPDHEVVAMARTLQDVF 112
>pdb|2I8N|A Chain A, Solution Structure Of The Second Bromodomain Of Brd4
Length = 114
Score = 35.8 bits (81), Expect = 0.16, Method: Composition-based stats.
Identities = 16/53 (30%), Positives = 28/53 (52%)
Query: 925 LDLRKIDQRVDRLEYNGVMELVSDVQFMLKGAMQFYGFSHEVRSEARKVHDLF 977
+D+ I +++ EY E +DV+ M ++ HEV + ARK+ D+F
Sbjct: 47 MDMSTIKSKLEAREYRDAQEFGADVRLMFSNCYKYNPPDHEVVAMARKLQDVF 99
>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 = 35.4 bits (80), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 45/167 (26%), Positives = 73/167 (43%), Gaps = 20/167 (11%)
Query: 290 STMTKLLDILEEYLQWRQLVYRRIDGTTSLEDRESAIVDFNSHDSDCFIFLLSIRAAGRG 349
+T +L +L E R V+ +G + +E R+ A F D+ + L S G
Sbjct: 514 ATALQLEQVLREREGIRAAVFH--EGXSIIE-RDRAAAWFAEEDTGAQVLLCS-EIGSEG 569
Query: 350 LNLQSADTVIIYDPDPNPKNEEQAVARAHRIGQKREVK--VIYMEAVVDKISS---HQKE 404
N Q A + +D NP EQ + R RIGQ +++ V Y+E + H+
Sbjct: 570 RNFQFASHXVXFDLPFNPDLLEQRIGRLDRIGQAHDIQIHVPYLEKTAQSVLVRWYHEGL 629
Query: 405 DELR----SGGTV------DLEDDLAGKDRYIGSIEGLIRNNIQQYK 441
D +G T+ DL + LA D+ G + LI+N +Q++
Sbjct: 630 DAFEHTCPTGRTIYDSVYNDLINYLASPDQTEG-FDDLIKNCREQHE 675
>pdb|2LSP|B Chain B, Solution Structures Of Brd4 Second Bromodomain With
Nf-Kb-K310ac Peptide
Length = 128
Score = 35.4 bits (80), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 28/53 (52%)
Query: 925 LDLRKIDQRVDRLEYNGVMELVSDVQFMLKGAMQFYGFSHEVRSEARKVHDLF 977
+D+ I +++ EY E +DV+ M ++ HEV + ARK+ D+F
Sbjct: 66 MDMSTIKSKLEAREYRDAQEFGADVRLMFSNCYKYNPPDHEVVAMARKLQDVF 118
>pdb|3JVL|A Chain A, Crystal Structure Of Bromodomain 2 Of Mouse Brd4
pdb|3JVM|A Chain A, Crystal Structure Of Bromodomain 2 Of Mouse Brd4
Length = 120
Score = 35.4 bits (80), Expect = 0.19, Method: Composition-based stats.
Identities = 16/53 (30%), Positives = 28/53 (52%)
Query: 925 LDLRKIDQRVDRLEYNGVMELVSDVQFMLKGAMQFYGFSHEVRSEARKVHDLF 977
+D+ I +++ EY E +DV+ M ++ HEV + ARK+ D+F
Sbjct: 55 MDMSTIKSKLESREYRDAQEFGADVRLMFSNCYKYNPPDHEVVAMARKLQDVF 107
>pdb|2OUO|A Chain A, Crystal Structure Of The Bromo Domain 2 In Human
Bromodomain Containing Protein 4 (Brd4)
pdb|2YEM|A Chain A, Crystal Structure Of The Second Bromodomain Of Human Brd4
With The Inhibitor Gw841819x
pdb|2YEM|B Chain B, Crystal Structure Of The Second Bromodomain Of Human Brd4
With The Inhibitor Gw841819x
Length = 130
Score = 35.4 bits (80), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 28/53 (52%)
Query: 925 LDLRKIDQRVDRLEYNGVMELVSDVQFMLKGAMQFYGFSHEVRSEARKVHDLF 977
+D+ I +++ EY E +DV+ M ++ HEV + ARK+ D+F
Sbjct: 68 MDMSTIKSKLEAREYRDAQEFGADVRLMFSNCYKYNPPDHEVVAMARKLQDVF 120
>pdb|2OO1|A Chain A, Crystal Structure Of The Bromo Domain 2 Of Human
Bromodomain Containing Protein 3 (Brd3)
pdb|2OO1|B Chain B, Crystal Structure Of The Bromo Domain 2 Of Human
Bromodomain Containing Protein 3 (Brd3)
pdb|2OO1|C Chain C, Crystal Structure Of The Bromo Domain 2 Of Human
Bromodomain Containing Protein 3 (Brd3)
pdb|2OO1|D Chain D, Crystal Structure Of The Bromo Domain 2 Of Human
Bromodomain Containing Protein 3 (Brd3)
pdb|3S92|A Chain A, Crystal Structure Of The Second Bromodomain Of Human Brd3
In Complex With The Inhibitor Jq1
Length = 113
Score = 34.7 bits (78), Expect = 0.33, Method: Composition-based stats.
Identities = 16/53 (30%), Positives = 28/53 (52%)
Query: 925 LDLRKIDQRVDRLEYNGVMELVSDVQFMLKGAMQFYGFSHEVRSEARKVHDLF 977
+DL + +++D EY +DV+ M ++ HEV + ARK+ D+F
Sbjct: 53 MDLSTVKRKMDGREYPDAQGFAADVRLMFSNCYKYNPPDHEVVAMARKLQDVF 105
>pdb|2E7N|A Chain A, Solution Structure Of The Second Bromodomain From Human
Bromodomain-Containing Protein 3
Length = 117
Score = 34.7 bits (78), Expect = 0.35, Method: Composition-based stats.
Identities = 16/53 (30%), Positives = 28/53 (52%)
Query: 925 LDLRKIDQRVDRLEYNGVMELVSDVQFMLKGAMQFYGFSHEVRSEARKVHDLF 977
+DL + +++D EY +DV+ M ++ HEV + ARK+ D+F
Sbjct: 58 MDLSTVKRKMDGREYPDAQGFAADVRLMFSNCYKYNPPDHEVVAMARKLQDVF 110
>pdb|3ONI|A Chain A, Crystal Structure Of The Second Bromodomain Of Human Brd2
In Complex With The Inhibitor Jq1
Length = 114
Score = 34.3 bits (77), Expect = 0.39, Method: Composition-based stats.
Identities = 14/53 (26%), Positives = 29/53 (54%)
Query: 925 LDLRKIDQRVDRLEYNGVMELVSDVQFMLKGAMQFYGFSHEVRSEARKVHDLF 977
+DL + ++++ +Y E +DV+ M ++ H+V + ARK+ D+F
Sbjct: 53 MDLSTVKRKMENRDYRDAQEFAADVRLMFSNCYKYNPPDHDVVAMARKLQDVF 105
>pdb|2DVV|A Chain A, Crystal Structure Of The Second Bromodomain Of The Human
Brd2 Protein
pdb|2E3K|A Chain A, Crystal Structure Of The Human Brd2 Second Bromodomain In
Complexed With The Acetylated Histone H4 Peptide
pdb|2E3K|B Chain B, Crystal Structure Of The Human Brd2 Second Bromodomain In
Complexed With The Acetylated Histone H4 Peptide
pdb|2E3K|C Chain C, Crystal Structure Of The Human Brd2 Second Bromodomain In
Complexed With The Acetylated Histone H4 Peptide
pdb|2E3K|D Chain D, Crystal Structure Of The Human Brd2 Second Bromodomain In
Complexed With The Acetylated Histone H4 Peptide
Length = 112
Score = 34.3 bits (77), Expect = 0.40, Method: Composition-based stats.
Identities = 14/53 (26%), Positives = 29/53 (54%)
Query: 925 LDLRKIDQRVDRLEYNGVMELVSDVQFMLKGAMQFYGFSHEVRSEARKVHDLF 977
+DL + ++++ +Y E +DV+ M ++ H+V + ARK+ D+F
Sbjct: 51 MDLSTVKRKMENRDYRDAQEFAADVRLMFSNCYKYNPPDHDVVAMARKLQDVF 103
>pdb|2G4A|A Chain A, Solution Structure Of A Bromodomain From Ring3 Protein
Length = 116
Score = 34.3 bits (77), Expect = 0.42, Method: Composition-based stats.
Identities = 14/53 (26%), Positives = 29/53 (54%)
Query: 925 LDLRKIDQRVDRLEYNGVMELVSDVQFMLKGAMQFYGFSHEVRSEARKVHDLF 977
+DL + ++++ +Y E +DV+ M ++ H+V + ARK+ D+F
Sbjct: 47 MDLSTVKRKMENRDYRDAQEFAADVRLMFSNCYKYNPPDHDVVAMARKLQDVF 99
>pdb|3IU5|A Chain A, Crystal Structure Of The First Bromodomain Of Human
Poly-Bromodomain Containing Protein 1 (Pb1)
Length = 116
Score = 32.7 bits (73), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 24/97 (24%), Positives = 40/97 (41%), Gaps = 1/97 (1%)
Query: 882 CKNVISKLQRRIEKEGHQIVPLLTDLWKRIETSGYVSGAGNNILDLRKIDQRVDRLEYNG 941
C + + ++ +++G + L KR Y I DL KI Q++ EY+
Sbjct: 10 CHELYNTIRDYKDEQGRLLCELFIRAPKRRNQPDYYEVVSQPI-DLMKIQQKLKMEEYDD 68
Query: 942 VMELVSDVQFMLKGAMQFYGFSHEVRSEARKVHDLFF 978
V L +D Q + A +Y A K+ DL+
Sbjct: 69 VNLLTADFQLLFNNAKSYYKPDSPEYKAACKLWDLYL 105
>pdb|3LQH|A Chain A, Crystal Structure Of Mll1 Phd3-Bromo In The Free Form
pdb|3LQI|A Chain A, Crystal Structure Of Mll1 Phd3-Bromo Complexed With
H3(1-9)k4me2 Peptide
pdb|3LQI|B Chain B, Crystal Structure Of Mll1 Phd3-Bromo Complexed With
H3(1-9)k4me2 Peptide
pdb|3LQI|C Chain C, Crystal Structure Of Mll1 Phd3-Bromo Complexed With
H3(1-9)k4me2 Peptide
pdb|3LQJ|A Chain A, Crystal Structure Of Mll1 Phd3-Bromo Complexed With
H3(1-9)k4me3 Peptide
pdb|3LQJ|B Chain B, Crystal Structure Of Mll1 Phd3-Bromo Complexed With
H3(1-9)k4me3 Peptide
Length = 183
Score = 32.3 bits (72), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 21/92 (22%), Positives = 41/92 (44%)
Query: 903 LLTDLWKRIETSGYVSGAGNNILDLRKIDQRVDRLEYNGVMELVSDVQFMLKGAMQFYGF 962
+LT L TS + LDL + +++D+ Y V+E D+ +++ A+ G
Sbjct: 83 VLTALLNSRTTSHLLRYRQQQPLDLEGVKRKMDQGNYTSVLEFSDDIVKIIQAAINSDGG 142
Query: 963 SHEVRSEARKVHDLFFDLLKIAFPDTDFREAR 994
E++ V F ++ FP +++R
Sbjct: 143 QPEIKKANSMVKSFFIRQMERVFPWFSVKKSR 174
>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 = 32.0 bits (71), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 23/95 (24%), Positives = 40/95 (42%), Gaps = 3/95 (3%)
Query: 287 LLFSTMTKLLDILEEYLQWRQLVYRRIDGTTSLEDRESAIVDFNSHDSDCFIFLLSIRAA 346
++F + D L +L ++ I G RE A+ DF + L++ A
Sbjct: 304 IVFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKV---LIATSVA 360
Query: 347 GRGLNLQSADTVIIYDPDPNPKNEEQAVARAHRIG 381
RGL++++ VI YD + + R R+G
Sbjct: 361 SRGLDIKNIKHVINYDMPSKIDDYVHRIGRTGRVG 395
>pdb|2R9Z|A Chain A, Glutathione Amide Reductase From Chromatium Gracile
pdb|2R9Z|B Chain B, Glutathione Amide Reductase From Chromatium Gracile
pdb|2RAB|A Chain A, Structure Of Glutathione Amide Reductase From Chromatium
Gracile In Complex With Nad
pdb|2RAB|B Chain B, Structure Of Glutathione Amide Reductase From Chromatium
Gracile In Complex With Nad
Length = 463
Score = 31.2 bits (69), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 22/38 (57%)
Query: 409 SGGTVDLEDDLAGKDRYIGSIEGLIRNNIQQYKIDMAD 446
SGGT+D +AG+DRYIG+I +++ I D
Sbjct: 74 SGGTLDWPRLVAGRDRYIGAINSFWDGYVERLGITRVD 111
>pdb|1WRB|A Chain A, Crystal Structure Of The N-Terminal Reca-Like Domain Of
Djvlgb, A Pranarian Vasa-Like Rna Helicase
pdb|1WRB|B Chain B, Crystal Structure Of The N-Terminal Reca-Like Domain Of
Djvlgb, A Pranarian Vasa-Like Rna Helicase
Length = 253
Score = 31.2 bits (69), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 24/67 (35%), Positives = 38/67 (56%), Gaps = 10/67 (14%)
Query: 13 PSVSCIYYVGAKDQRSRLFSQEVAALKFNVLVTT----YEFIMYDRSKLSKVDWKYIIID 68
P SC+ Y GA D S++ ++ ++LV T +FI +++K+S KYI++D
Sbjct: 128 PLRSCVVYGGA-DTHSQIREVQMGC---HLLVATPGRLVDFI--EKNKISLEFCKYIVLD 181
Query: 69 EAQRMKD 75
EA RM D
Sbjct: 182 EADRMLD 188
>pdb|2DWW|A Chain A, Crystal Structure Of Bromodomain-Containing Protein 4
Length = 114
Score = 30.8 bits (68), Expect = 4.1, Method: Composition-based stats.
Identities = 15/52 (28%), Positives = 25/52 (48%)
Query: 926 DLRKIDQRVDRLEYNGVMELVSDVQFMLKGAMQFYGFSHEVRSEARKVHDLF 977
D I +++ EY E +DV+ ++ HEV + ARK+ D+F
Sbjct: 54 DXSTIKSKLESREYRDAQEFGADVRLXFSNCYKYNPPDHEVVAXARKLQDVF 105
>pdb|3P5P|A Chain A, Crystal Structure Of Taxadiene Synthase From Pacific Yew
(Taxus Brevifolia) In Complex With Mg2+ And
13-Aza-13,14-Dihydrocopalyl Diphosphate
pdb|3P5R|A Chain A, Crystal Structure Of Taxadiene Synthase From Pacific Yew
(Taxus Brevifolia) In Complex With Mg2+ And
2-Fluorogeranylgeranyl Diphosphate
pdb|3P5R|B Chain B, Crystal Structure Of Taxadiene Synthase From Pacific Yew
(Taxus Brevifolia) In Complex With Mg2+ And
2-Fluorogeranylgeranyl Diphosphate
Length = 764
Score = 30.4 bits (67), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 27/52 (51%), Gaps = 1/52 (1%)
Query: 290 STMTKLLDILEEYLQWRQLV-YRRIDGTTSLEDRESAIVDFNSHDSDCFIFL 340
+ M L+ LEE + W +++ ++ DG+ +A V N+ D CF FL
Sbjct: 176 ANMLNALEGLEEVIDWNKIMRFQSKDGSFLSSPASTACVLMNTGDEKCFTFL 227
>pdb|2OZG|A Chain A, Crystal Structure Of Gcn5-Related N-Acetyltransferase
(Yp_325469.1) From Anabaena Variabilis Atcc 29413 At
2.00 A Resolution
Length = 396
Score = 30.4 bits (67), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 37/83 (44%), Gaps = 14/83 (16%)
Query: 19 YYVGAKD--QRSRLFSQE----VAALKFNVLVTT--------YEFIMYDRSKLSKVDWKY 64
Y +G KD Q +F+QE + L+ VT + FI RS++ KV WK
Sbjct: 204 YLIGDKDKPQGYIIFTQERTRDGSILRIRDWVTLSNPAVQSFWTFIANHRSQIDKVTWKS 263
Query: 65 IIIDEAQRMKDRESVLARDLDRY 87
+ID + +S R DR+
Sbjct: 264 SVIDALTLLLPEQSATIRSQDRW 286
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
0.316 0.133 0.389
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 33,315,482
Number of Sequences: 62578
Number of extensions: 1328056
Number of successful extensions: 3077
Number of sequences better than 100.0: 40
Number of HSP's better than 100.0 without gapping: 24
Number of HSP's successfully gapped in prelim test: 16
Number of HSP's that attempted gapping in prelim test: 3039
Number of HSP's gapped (non-prelim): 44
length of query: 1179
length of database: 14,973,337
effective HSP length: 110
effective length of query: 1069
effective length of database: 8,089,757
effective search space: 8647950233
effective search space used: 8647950233
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: 57 (26.6 bits)