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= 000101
(2239 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 = 323 bits (829), Expect = 5e-88, Method: Compositional matrix adjust.
Identities = 188/493 (38%), Positives = 277/493 (56%), Gaps = 69/493 (13%)
Query: 987 ERVMRQPSMLRAGTLRDYQIVGLQWMLSLYNNKLNGILADEMGLGKTVQVMALIAYLMEF 1046
E++ QP ++ G LRD+Q+ G+ WM L++ NGILADEMGLGKTVQ +A I++L+
Sbjct: 223 EKLSVQPPFIKGGELRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWLIFA 282
Query: 1047 KGNYGPHLIIVPNAVLVNWKSELHKWLPSVSCIYYVGAKDQRSR-------LFSQVAA-- 1097
+ GPH+I+VP + + W KW P ++CI Y+G +Q+SR ++ A
Sbjct: 283 RRQNGPHIIVVPLSTMPAWLDTFEKWAPDLNCICYMG--NQKSRDTIREYEFYTNPRAKG 340
Query: 1098 ---LKFNVLVTTYEFIMYDRSKLSKVDWKYIIIDEAQRMKDRESVLARDLDRYRCQRRLL 1154
+KFNVL+TTYE+I+ DR++L + W+++ +DEA R+K+ ES L L+ ++ R+L
Sbjct: 341 KKTMKFNVLLTTYEYILKDRAELGSIKWQFMAVDEAHRLKNAESSLYESLNSFKVANRML 400
Query: 1155 LTGTPLQNDXXXXXXXXXXXXPEVFDNRKAFHDWFSQPFQKEGPTHNADDDWLETEKKVI 1214
+TGTPLQN+ P F +E N D++ E
Sbjct: 401 ITGTPLQNNIKELAALVNFLMPGRF------------TIDQEIDFENQDEEQEE------ 442
Query: 1215 IIHRLHQILEPFMLRRRVEDVEGSLPPKVSIVLRCRMSAIQSAIYDWIKATGTLRVDPED 1274
IH LH+ ++PF+LRR +DVE SLP K +LR +S +Q+ Y
Sbjct: 443 YIHDLHRRIQPFILRRLKKDVEKSLPSKTERILRVELSDVQTEYY--------------- 487
Query: 1275 EKRRVQKNPIYQAKV------YKTLNNRCMELRKTCNHPLLNYPYFSDLSKDF------- 1321
K + KN Y A + +L N EL+K NHP L + + F
Sbjct: 488 -KNILTKN--YSALTAGAKGGHFSLLNIMNELKKASNHPYLFDNAEERVLQKFGDGKMTR 544
Query: 1322 ------LVKSCGKLWILDRILIKLQRTGHRVLLFSTMTKLLDILEEYLQWRQLVYRRIDG 1375
L+ S GK+ +LD++L +L++ GHRVL+FS M ++LDIL +YL + + ++R+DG
Sbjct: 545 ENVLRGLIMSSGKMVLLDQLLTRLKKDGHRVLIFSQMVRMLDILGDYLSIKGINFQRLDG 604
Query: 1376 TTSLEDRESAIVDFNSHDSDCFIFLLSIRAAGRGLNLQSADTVIIYDPDPNPKNEEQAVA 1435
T R +I FNS DS+ F+FLLS RA G G+NL +ADTV+I+D D NP+ + QA+A
Sbjct: 605 TVPSAQRRISIDHFNSPDSNDFVFLLSTRAGGLGINLMTADTVVIFDSDWNPQADLQAMA 664
Query: 1436 RAHRIGQKREVKV 1448
RAHRIGQK V V
Sbjct: 665 RAHRIGQKNHVMV 677
>pdb|1Z3I|X Chain X, Structure Of The Swi2SNF2 CHROMATIN REMODELING DOMAIN OF
EUKARYOTIC Rad54
Length = 644
Score = 176 bits (446), Expect = 1e-43, Method: Compositional matrix adjust.
Identities = 144/519 (27%), Positives = 243/519 (46%), Gaps = 57/519 (10%)
Query: 1000 TLRDYQIVGLQWMLSLYN-----NKLNGILADEMGLGKTVQVMALIAYLMEFKGNYGPHL 1054
LR +Q G++++ N I+ADEMGLGKT+Q + LI L++ + P +
Sbjct: 55 VLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLIWTLLKQSPDCKPEI 114
Query: 1055 ----IIVPNAVLVNWKSELHKWLPSVSCIYYV--GAKDQ-RSRLFSQVAA----LKFNVL 1103
++ P++++ NW +E+ KWL + G+KD+ S+L + ++ + +L
Sbjct: 115 DKVIVVSPSSLVRNWYNEVGKWLGGRVQPVAIDGGSKDEIDSKLVNFISQQGMRIPTPIL 174
Query: 1104 VTTYEFIMYDRSKLSKVDWKYIIIDEAQRMKDRESVLARDLDRYRCQRRLLLTGTPLQND 1163
+ +YE L K +I DE R+K+ ++ L+ QRR+L++GTP+QND
Sbjct: 175 IISYETFRLHAEVLHKGKVGLVICDEGHRLKNSDNQTYLALNSMNAQRRVLISGTPIQND 234
Query: 1164 XXXXXXXXXXXXPEVFDNRKAFHDWFSQPFQKEGPTHNADDDWLETEKKVIIIHRLHQIL 1223
+ + F F P K +D D E+K + L I+
Sbjct: 235 LLEYFSLVHFVNSGILGTAQEFKKRFEIPILKGRDADASDKDRAAGEQK---LQELISIV 291
Query: 1224 EPFMLRRRVEDVEGSLPPKVSIVLRCRMSAIQSAIYDWIKATGTLRVDPEDEKRRVQKNP 1283
++RR + + LP K+ V+ C ++ +Q +Y Q P
Sbjct: 292 NRCLIRRTSDILSKYLPVKIEQVVCCNLTPLQKELYKLFLK---------------QAKP 336
Query: 1284 I---YQAKVYKTLNNRCMELRKTCNHPLLNYP-----------YFSDLSKDFLVKSC--- 1326
+ K+ + + L+K CNHP L Y +++ K+
Sbjct: 337 VESLQTGKISVSSLSSITSLKKLCNHPALIYEKCLTGEEGFDGALDLFPQNYSTKAVEPQ 396
Query: 1327 --GKLWILDRIL-IKLQRTGHRVLLFSTMTKLLDILEEYLQWRQLVYRRIDGTTSLEDRE 1383
GK+ +LD IL + T +V+L S T+ LD+ E+ + R+ +Y R+DGT S++ R
Sbjct: 397 LSGKMLVLDYILAMTRTTTSDKVVLVSNYTQTLDLFEKLCRNRRYLYVRLDGTMSIKKRA 456
Query: 1384 SAIVDFNSHDSDCFIFLLSIRAAGRGLNLQSADTVIIYDPDPNPKNEEQAVARAHRIGQK 1443
+ FN+ S FIF+LS +A G GLNL A+ ++++DPD NP N+EQA+AR R GQK
Sbjct: 457 KIVERFNNPSSPEFIFMLSSKAGGCGLNLIGANRLVMFDPDWNPANDEQAMARVWRDGQK 516
Query: 1444 REV---KVIYMEAVVDKISSHQKEDELRSGGTVDLEDDL 1479
+ +++ + +KI Q + S VD E D+
Sbjct: 517 KTCYIYRLLSTGTIEEKILQRQAHKKALSSCVVDEEQDV 555
>pdb|1Z6A|A Chain A, Sulfolobus Solfataricus Swi2SNF2 ATPASE CORE DOMAIN
Length = 500
Score = 159 bits (401), Expect = 2e-38, Method: Compositional matrix adjust.
Identities = 143/508 (28%), Positives = 253/508 (49%), Gaps = 65/508 (12%)
Query: 990 MRQPSMLRAGTLRDYQIVGLQWMLSLYNNKLN-GI-LADEMGLGKTVQVMALIAYLMEFK 1047
+ +P ++A LR YQI G WM + NKL GI LAD+MGLGKT+Q +A+ + + +
Sbjct: 28 LLEPYNIKAN-LRPYQIKGFSWMR--FMNKLGFGICLADDMGLGKTLQTIAVFSDAKK-E 83
Query: 1048 GNYGPHLIIVPNAVLVNWKSELHKWLPSVSCIYYVGAKDQRSRLFSQVAALKFNVLVTTY 1107
P L+I P +VL NW+ EL K+ P + + V +D+ S++ +++++TTY
Sbjct: 84 NELTPSLVICPLSVLKNWEEELSKFAPHLR--FAVFHEDR-----SKIKLEDYDIILTTY 136
Query: 1108 EFIMYDRSKLSKVDWKYIIIDEAQRMKDRESVLARDLDRYRCQRRLLLTGTPLQNDXXXX 1167
++ D ++L +V+WKYI+IDEAQ +K+ ++ + + + + + R+ LTGTP++N
Sbjct: 137 AVLLRD-TRLKEVEWKYIVIDEAQNIKNPQTKIFKAVKELKSKYRIALTGTPIENKVDDL 195
Query: 1168 XXXXXXXXPEVFDNRKAFHDWFSQPFQKEGPTHNADDDWLETEKKVIIIHRLHQILEPFM 1227
P + + F F+ P +K D+ + E K II PF+
Sbjct: 196 WSIMTFLNPGLLGSYSEFKSKFATPIKK-------GDNMAKEELKAII--------SPFI 240
Query: 1228 LRRRVED--VEGSLPPKVSIVLRCRMSAIQSAIYDWIKATGTLRVDPEDEKRRVQKNPIY 1285
LRR D + LP K+ + C ++ Q+A+Y KA + D +++
Sbjct: 241 LRRTKYDKAIINDLPDKIETNVYCNLTPEQAAMY---KAEVENLFNNIDSVTGIKR---- 293
Query: 1286 QAKVYKTLNNRCMELRKTCNHPLLNYPYFSDLSKDFLVKSCGKLWILDRILIKLQRTGHR 1345
+ + TL ++L++ +HP L + V+ GK+ I+ + G +
Sbjct: 294 KGMILSTL----LKLKQIVDHPALLK------GGEQSVRRSGKMIRTMEIIEEALDEGDK 343
Query: 1346 VLLFSTMTKLLDILEEYLQWRQLVYRRID-------GTTSLEDRESAIVDFNSHDSDCFI 1398
+ +F+ + I+ R ++ + ++ G S ++R+ I F ++ S FI
Sbjct: 344 IAIFTQFVDMGKII------RNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFI 397
Query: 1399 FLLSIRAAGRGLNLQSADTVIIYDPDPNPKNEEQAVARAHRIGQKREVKVIYMEAVVDKI 1458
+LS++A G G+NL SA+ VI +D NP E+QA R +RIGQ R V V ++
Sbjct: 398 -VLSVKAGGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIV---HKLISVG 453
Query: 1459 SSHQKEDELRSGGTVDLEDDLAGKDRYI 1486
+ +K D+L + +D ++ D +I
Sbjct: 454 TLEEKIDQLLAFKRSLFKDIISSGDSWI 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 = 152 bits (383), Expect = 3e-36, Method: Compositional matrix adjust.
Identities = 142/508 (27%), Positives = 249/508 (49%), Gaps = 65/508 (12%)
Query: 990 MRQPSMLRAGTLRDYQIVGLQWMLSLYNNKLN-GI-LADEMGLGKTVQVMALIAYLMEFK 1047
+ +P ++A LR YQI G W + NKL GI LAD+ GLGKT+Q +A+ + + +
Sbjct: 28 LLEPYNIKAN-LRPYQIKGFSW--XRFXNKLGFGICLADDXGLGKTLQTIAVFSDAKK-E 83
Query: 1048 GNYGPHLIIVPNAVLVNWKSELHKWLPSVSCIYYVGAKDQRSRLFSQVAALKFNVLVTTY 1107
P L+I P +VL NW+ EL K+ P + + V +D+ S++ +++++TTY
Sbjct: 84 NELTPSLVICPLSVLKNWEEELSKFAPHLR--FAVFHEDR-----SKIKLEDYDIILTTY 136
Query: 1108 EFIMYDRSKLSKVDWKYIIIDEAQRMKDRESVLARDLDRYRCQRRLLLTGTPLQNDXXXX 1167
++ D ++L +V+WKYI+IDEAQ +K+ ++ + + + + + R+ LTGTP++N
Sbjct: 137 AVLLRD-TRLKEVEWKYIVIDEAQNIKNPQTKIFKAVKELKSKYRIALTGTPIENKVDDL 195
Query: 1168 XXXXXXXXPEVFDNRKAFHDWFSQPFQKEGPTHNADDDWLETEKKVIIIHRLHQILEPFM 1227
P + + F F+ P +K D+ + E K II PF+
Sbjct: 196 WSIXTFLNPGLLGSYSEFKSKFATPIKK-------GDNXAKEELKAII--------SPFI 240
Query: 1228 LRRRVED--VEGSLPPKVSIVLRCRMSAIQSAIYDWIKATGTLRVDPEDEKRRVQKNPIY 1285
LRR D + LP K+ + C ++ Q+A Y KA + D +++
Sbjct: 241 LRRTKYDKAIINDLPDKIETNVYCNLTPEQAAXY---KAEVENLFNNIDSVTGIKR---- 293
Query: 1286 QAKVYKTLNNRCMELRKTCNHPLLNYPYFSDLSKDFLVKSCGKLWILDRILIKLQRTGHR 1345
+ + TL ++L++ +HP L + V+ GK I+ + G +
Sbjct: 294 KGXILSTL----LKLKQIVDHPALLK------GGEQSVRRSGKXIRTXEIIEEALDEGDK 343
Query: 1346 VLLFSTMTKLLDILEEYLQWRQLVYRRID-------GTTSLEDRESAIVDFNSHDSDCFI 1398
+ +F+ I+ R ++ + ++ G S ++R+ I F ++ S FI
Sbjct: 344 IAIFTQFVDXGKII------RNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFI 397
Query: 1399 FLLSIRAAGRGLNLQSADTVIIYDPDPNPKNEEQAVARAHRIGQKREVKVIYMEAVVDKI 1458
+LS++A G G+NL SA+ VI +D NP E+QA R +RIGQ R V V ++
Sbjct: 398 -VLSVKAGGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIV---HKLISVG 453
Query: 1459 SSHQKEDELRSGGTVDLEDDLAGKDRYI 1486
+ +K D+L + +D ++ D +I
Sbjct: 454 TLEEKIDQLLAFKRSLFKDIISSGDSWI 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 = 57.4 bits (137), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 55/217 (25%), Positives = 99/217 (45%), Gaps = 31/217 (14%)
Query: 1239 LPPKVSIVLRCRMSAIQSAIYDWIKATGTLRVDPEDEKRRVQKNPIYQAKVYKTLNNRCM 1298
LP K+ + C ++ Q+A+Y E E + + K + + +
Sbjct: 25 LPDKIETNVYCNLTPEQAAMYK-----------AEVENLFNNIDSVTGIKRKGMILSTLL 73
Query: 1299 ELRKTCNHPLLNYPYFSDLSKDFLVKSCGKLWILDRILIKLQRTGHRVLLFSTMTKLLDI 1358
+L++ +HP L + V+ GK+ I+ + G ++ +F+ + I
Sbjct: 74 KLKQIVDHPALLK------GGEQSVRRSGKMIRTMEIIEEALDEGDKIAIFTQFVDMGKI 127
Query: 1359 LEEYLQWRQLVYRRID-------GTTSLEDRESAIVDFNSHDSDCFIFLLSIRAAGRGLN 1411
+ R ++ + ++ G S ++R+ I F ++ S FI +LS++A G G+N
Sbjct: 128 I------RNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFI-VLSVKAGGFGIN 180
Query: 1412 LQSADTVIIYDPDPNPKNEEQAVARAHRIGQKREVKV 1448
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 = 38.9 bits (89), Expect = 0.035, Method: Composition-based stats.
Identities = 32/103 (31%), Positives = 46/103 (44%), Gaps = 6/103 (5%)
Query: 1339 LQRTGHRVLLFSTMTKLLDILEEYLQWRQLVYRRIDGTTSLEDRESAIVDFNSHDSDCFI 1398
LQ+T VL+F+ +D + EYL + + I G E+R AI F D
Sbjct: 50 LQKTPPPVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDV-- 107
Query: 1399 FLLSIRAAGRGLNLQSADTVIIYDPDPNPKNEEQAVARAHRIG 1441
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 = 38.5 bits (88), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 31/96 (32%), Positives = 44/96 (45%), Gaps = 6/96 (6%)
Query: 1347 LLFSTMTKLLDILEEYLQWRQLVYRRIDGTTSLEDRESAIVDFNSHDSDCFIFLLSIRAA 1406
L+F K D LE++L I G S DRE A+ F S S L++ A
Sbjct: 280 LVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSP---ILVATAVA 336
Query: 1407 GRGLNLQSADTVIIYDPDPNPKNEEQAVARAHRIGQ 1442
RGL++ + VI +D P + E+ V R R G+
Sbjct: 337 ARGLDISNVKHVINFDL---PSDIEEYVHRIGRTGR 369
>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 = 0.16, Method: Composition-based stats.
Identities = 18/55 (32%), Positives = 28/55 (50%)
Query: 1983 NILDLRKIDQRVDRLEYNGVMELVSDVQFMLKGAMQFYGFSHEVRSEARKVHDLF 2037
N +DL I ++D EY E +DV+ M ++ HEV + AR + D+F
Sbjct: 58 NPMDLGTIKGKMDNQEYKDAYEFAADVRLMFMNCYKYNPPDHEVVAMARTLQDVF 112
>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 = 0.18, Method: Compositional matrix adjust.
Identities = 31/96 (32%), Positives = 44/96 (45%), Gaps = 6/96 (6%)
Query: 1347 LLFSTMTKLLDILEEYLQWRQLVYRRIDGTTSLEDRESAIVDFNSHDSDCFIFLLSIRAA 1406
L+F K D LE++L I G S DRE A+ F S S L++ A
Sbjct: 50 LVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPI---LVATAVA 106
Query: 1407 GRGLNLQSADTVIIYDPDPNPKNEEQAVARAHRIGQ 1442
RGL++ + VI +D P + E+ V R R G+
Sbjct: 107 ARGLDISNVKHVINFDL---PSDIEEYVHRIGRTGR 139
>pdb|2I8N|A Chain A, Solution Structure Of The Second Bromodomain Of Brd4
Length = 114
Score = 35.8 bits (81), Expect = 0.27, Method: Composition-based stats.
Identities = 16/53 (30%), Positives = 28/53 (52%)
Query: 1985 LDLRKIDQRVDRLEYNGVMELVSDVQFMLKGAMQFYGFSHEVRSEARKVHDLF 2037
+D+ I +++ EY E +DV+ M ++ HEV + ARK+ D+F
Sbjct: 47 MDMSTIKSKLEAREYRDAQEFGADVRLMFSNCYKYNPPDHEVVAMARKLQDVF 99
>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 = 35.8 bits (81), Expect = 0.32, Method: Composition-based stats.
Identities = 16/53 (30%), Positives = 28/53 (52%)
Query: 1985 LDLRKIDQRVDRLEYNGVMELVSDVQFMLKGAMQFYGFSHEVRSEARKVHDLF 2037
+D+ I +++ EY E +DV+ M ++ HEV + ARK+ D+F
Sbjct: 55 MDMSTIKSKLESREYRDAQEFGADVRLMFSNCYKYNPPDHEVVAMARKLQDVF 107
>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 = 35.8 bits (81), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 38/153 (24%), Positives = 66/153 (43%), Gaps = 22/153 (14%)
Query: 1023 ILADEMGLGKTVQVMALIAYLMEFKGNYGPHLIIVPNAVLVNWKSELHKWLPSVSCIYYV 1082
+LADE+GLGKT++ I + G LIIVP + W E + ++
Sbjct: 174 LLADEVGLGKTIEA-GXILHQQLLSGAAERVLIIVPETLQHQWLVEXLRRFNLRFALF-- 230
Query: 1083 GAKDQRSRLFSQVAALKFN---VLVTTYEFIMYDRSK---LSKVDWKYIIIDEAQRMKDR 1136
D+R A F+ +++ + +F + + L + +W +++DEA +
Sbjct: 231 --DDERYAEAQHDAYNPFDTEQLVICSLDFARRSKQRLEHLCEAEWDLLVVDEAHHLVWS 288
Query: 1137 ESVLARDLDRYRCQRR--------LLLTGTPLQ 1161
E +R+ Y+ + LLLT TP Q
Sbjct: 289 EDAPSRE---YQAIEQLAEHVPGVLLLTATPEQ 318
Score = 35.4 bits (80), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 45/167 (26%), Positives = 73/167 (43%), Gaps = 20/167 (11%)
Query: 1350 STMTKLLDILEEYLQWRQLVYRRIDGTTSLEDRESAIVDFNSHDSDCFIFLLSIRAAGRG 1409
+T +L +L E R V+ +G + +E R+ A F D+ + L S G
Sbjct: 514 ATALQLEQVLREREGIRAAVFH--EGXSIIE-RDRAAAWFAEEDTGAQVLLCS-EIGSEG 569
Query: 1410 LNLQSADTVIIYDPDPNPKNEEQAVARAHRIGQKREVK--VIYMEAVVDKI---SSHQKE 1464
N Q A + +D NP EQ + R RIGQ +++ V Y+E + H+
Sbjct: 570 RNFQFASHXVXFDLPFNPDLLEQRIGRLDRIGQAHDIQIHVPYLEKTAQSVLVRWYHEGL 629
Query: 1465 DELR----SGGTV------DLEDDLAGKDRYIGSIEGLIRNNIQQYK 1501
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 = 0.39, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 28/53 (52%)
Query: 1985 LDLRKIDQRVDRLEYNGVMELVSDVQFMLKGAMQFYGFSHEVRSEARKVHDLF 2037
+D+ I +++ EY E +DV+ M ++ HEV + ARK+ D+F
Sbjct: 66 MDMSTIKSKLEAREYRDAQEFGADVRLMFSNCYKYNPPDHEVVAMARKLQDVF 118
>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 = 0.40, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 28/53 (52%)
Query: 1985 LDLRKIDQRVDRLEYNGVMELVSDVQFMLKGAMQFYGFSHEVRSEARKVHDLF 2037
+D+ I +++ EY E +DV+ M ++ HEV + ARK+ D+F
Sbjct: 68 MDMSTIKSKLEAREYRDAQEFGADVRLMFSNCYKYNPPDHEVVAMARKLQDVF 120
>pdb|2E7N|A Chain A, Solution Structure Of The Second Bromodomain From Human
Bromodomain-Containing Protein 3
Length = 117
Score = 35.0 bits (79), Expect = 0.52, Method: Composition-based stats.
Identities = 16/53 (30%), Positives = 28/53 (52%)
Query: 1985 LDLRKIDQRVDRLEYNGVMELVSDVQFMLKGAMQFYGFSHEVRSEARKVHDLF 2037
+DL + +++D EY +DV+ M ++ HEV + ARK+ D+F
Sbjct: 58 MDLSTVKRKMDGREYPDAQGFAADVRLMFSNCYKYNPPDHEVVAMARKLQDVF 110
>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 = 35.0 bits (79), Expect = 0.53, Method: Composition-based stats.
Identities = 16/53 (30%), Positives = 28/53 (52%)
Query: 1985 LDLRKIDQRVDRLEYNGVMELVSDVQFMLKGAMQFYGFSHEVRSEARKVHDLF 2037
+DL + +++D EY +DV+ M ++ HEV + ARK+ D+F
Sbjct: 53 MDLSTVKRKMDGREYPDAQGFAADVRLMFSNCYKYNPPDHEVVAMARKLQDVF 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 = 34.7 bits (78), Expect = 0.61, Method: Composition-based stats.
Identities = 14/53 (26%), Positives = 29/53 (54%)
Query: 1985 LDLRKIDQRVDRLEYNGVMELVSDVQFMLKGAMQFYGFSHEVRSEARKVHDLF 2037
+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 = 34.7 bits (78), Expect = 0.63, Method: Composition-based stats.
Identities = 14/53 (26%), Positives = 29/53 (54%)
Query: 1985 LDLRKIDQRVDRLEYNGVMELVSDVQFMLKGAMQFYGFSHEVRSEARKVHDLF 2037
+DL + ++++ +Y E +DV+ M ++ H+V + ARK+ D+F
Sbjct: 47 MDLSTVKRKMENRDYRDAQEFAADVRLMFSNCYKYNPPDHDVVAMARKLQDVF 99
>pdb|3ONI|A Chain A, Crystal Structure Of The Second Bromodomain Of Human Brd2 In
Complex With The Inhibitor Jq1
Length = 114
Score = 34.7 bits (78), Expect = 0.64, Method: Composition-based stats.
Identities = 14/53 (26%), Positives = 29/53 (54%)
Query: 1985 LDLRKIDQRVDRLEYNGVMELVSDVQFMLKGAMQFYGFSHEVRSEARKVHDLF 2037
+DL + ++++ +Y E +DV+ M ++ H+V + ARK+ D+F
Sbjct: 53 MDLSTVKRKMENRDYRDAQEFAADVRLMFSNCYKYNPPDHDVVAMARKLQDVF 105
>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 = 33.5 bits (75), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 33/97 (34%), Positives = 50/97 (51%), Gaps = 13/97 (13%)
Query: 1047 KGNYGPHLIIVPNAVL-VNWKSELHKW---LPSVSCIYYVGAKDQRSRLFSQVAALKFNV 1102
K Y LI+ P L + SE K+ P SC+ Y GA D S++ + + ++
Sbjct: 97 KTAYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGA-DTHSQI--REVQMGCHL 153
Query: 1103 LVTT----YEFIMYDRSKLSKVDWKYIIIDEAQRMKD 1135
LV T +FI +++K+S KYI++DEA RM D
Sbjct: 154 LVATPGRLVDFI--EKNKISLEFCKYIVLDEADRMLD 188
>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 = 2.6, Method: Compositional matrix adjust.
Identities = 24/97 (24%), Positives = 40/97 (41%), Gaps = 1/97 (1%)
Query: 1942 CKNVISKLQRRIEKEGHQIVPLLTDLWKRIETSGYVSGAGNNILDLRKIDQRVDRLEYNG 2001
C + + ++ +++G + L KR Y I DL KI Q++ EY+
Sbjct: 10 CHELYNTIRDYKDEQGRLLCELFIRAPKRRNQPDYYEVVSQPI-DLMKIQQKLKMEEYDD 68
Query: 2002 VMELVSDVQFMLKGAMQFYGFSHEVRSEARKVHDLFF 2038
V L +D Q + A +Y A K+ DL+
Sbjct: 69 VNLLTADFQLLFNNAKSYYKPDSPEYKAACKLWDLYL 105
>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 = 3.8, Method: Compositional matrix adjust.
Identities = 23/95 (24%), Positives = 40/95 (42%), Gaps = 3/95 (3%)
Query: 1347 LLFSTMTKLLDILEEYLQWRQLVYRRIDGTTSLEDRESAIVDFNSHDSDCFIFLLSIRAA 1406
++F + D L +L ++ I G RE A+ DF + L++ A
Sbjct: 304 IVFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKV---LIATSVA 360
Query: 1407 GRGLNLQSADTVIIYDPDPNPKNEEQAVARAHRIG 1441
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 = 32.0 bits (71), Expect = 4.3, Method: Composition-based stats.
Identities = 15/38 (39%), Positives = 22/38 (57%)
Query: 1469 SGGTVDLEDDLAGKDRYIGSIEGLIRNNIQQYKIDMAD 1506
SGGT+D +AG+DRYIG+I +++ I D
Sbjct: 74 SGGTLDWPRLVAGRDRYIGAINSFWDGYVERLGITRVD 111
>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 = 32.0 bits (71), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 16/70 (22%), Positives = 34/70 (48%)
Query: 1985 LDLRKIDQRVDRLEYNGVMELVSDVQFMLKGAMQFYGFSHEVRSEARKVHDLFFDLLKIA 2044
LDL + +++D+ Y V+E D+ +++ A+ G E++ V F ++
Sbjct: 105 LDLEGVKRKMDQGNYTSVLEFSDDIVKIIQAAINSDGGQPEIKKANSMVKSFFIRQMERV 164
Query: 2045 FPDTDFREAR 2054
FP +++R
Sbjct: 165 FPWFSVKKSR 174
>pdb|2DWW|A Chain A, Crystal Structure Of Bromodomain-Containing Protein 4
Length = 114
Score = 31.2 bits (69), Expect = 6.3, Method: Composition-based stats.
Identities = 15/52 (28%), Positives = 25/52 (48%)
Query: 1986 DLRKIDQRVDRLEYNGVMELVSDVQFMLKGAMQFYGFSHEVRSEARKVHDLF 2037
D I +++ EY E +DV+ ++ HEV + ARK+ D+F
Sbjct: 54 DXSTIKSKLESREYRDAQEFGADVRLXFSNCYKYNPPDHEVVAXARKLQDVF 105
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
0.315 0.131 0.376
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 57,357,288
Number of Sequences: 62578
Number of extensions: 2182263
Number of successful extensions: 4907
Number of sequences better than 100.0: 38
Number of HSP's better than 100.0 without gapping: 20
Number of HSP's successfully gapped in prelim test: 18
Number of HSP's that attempted gapping in prelim test: 4865
Number of HSP's gapped (non-prelim): 43
length of query: 2239
length of database: 14,973,337
effective HSP length: 114
effective length of query: 2125
effective length of database: 7,839,445
effective search space: 16658820625
effective search space used: 16658820625
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: 59 (27.3 bits)