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= 000684
(1352 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 = 623 bits (1606), Expect = e-178, Method: Compositional matrix adjust.
Identities = 330/701 (47%), Positives = 465/701 (66%), Gaps = 26/701 (3%)
Query: 9 PDWNEM----EFLIKWKGQSHLHCQWKSFAELQNLSGFKKVLNYAKK-VVED--VRFRKM 61
PD N EFLIKW +SHLH W+++ + + G K++ NY K+ ++ED VR
Sbjct: 63 PDLNNCKENYEFLIKWTDESHLHNTWETYESIGQVRGLKRLDNYCKQFIIEDQQVRLDPY 122
Query: 62 VSREEIELNDVSKEMDLDIIKQNSQVERIIADRISKDSSGNVTQEYLVKWKGLSYAEATW 121
V+ E+IE+ D+ +E LD ++ ERII + + G +YLVKW+ L+Y EATW
Sbjct: 123 VTAEDIEIMDMERERRLDEFEEFHVPERIIDSQRASLEDGTSQLQYLVKWRRLNYDEATW 182
Query: 122 EK-DEIIDFAQDAIDEYKAREAA--MAEQGKMVDLQRKKGKASLRKLDEQPEWLRGGKLR 178
E +I+ A + + ++ RE + + + QR + KL QP +++GG+LR
Sbjct: 183 ENATDIVKLAPEQVKHFQNRENSKILPQYSSNYTSQRPR----FEKLSVQPPFIKGGELR 238
Query: 179 DYQLEGLNFLVNSWRNDTNVILADEMGLGKTVQSVSMLGFLQNAQQIPGPFLVVVPLSTL 238
D+QL G+N++ W N ILADEMGLGKTVQ+V+ + +L A++ GP ++VVPLST+
Sbjct: 239 DFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWLIFARRQNGPHIIVVPLSTM 298
Query: 239 SNWAKEFRKWLPTMNVIVYVGTRASREVCQQYEFYND--KKVGRPIKFNTLLTTYEVVLK 296
W F KW P +N I Y+G + SR+ ++YEFY + K + +KFN LLTTYE +LK
Sbjct: 299 PAWLDTFEKWAPDLNCICYMGNQKSRDTIREYEFYTNPRAKGKKTMKFNVLLTTYEYILK 358
Query: 297 DKAVLSKIKWNYLMVDEAHRLKNSEAQLYTTLSEFSTKNKLLITGTPLQNSVEELWALLH 356
D+A L IKW ++ VDEAHRLKN+E+ LY +L+ F N++LITGTPLQN+++EL AL++
Sbjct: 359 DRAELGSIKWQFMAVDEAHRLKNAESSLYESLNSFKVANRMLITGTPLQNNIKELAALVN 418
Query: 357 FLDHDKFKSKDDFIQNYKNLSSFNENELANLHMELRPHILRRIIKDVEKSLPPKIERILR 416
FL +F + +++N E + +LH ++P ILRR+ KDVEKSLP K ERILR
Sbjct: 419 FLMPGRFTIDQEI--DFENQDEEQEEYIHDLHRRIQPFILRRLKKDVEKSLPSKTERILR 476
Query: 417 VEMSPLQKQYYKWILERNFHDLNKGVRGNQVSLLNIVVELKKCCNHPFLFESADHGY--- 473
VE+S +Q +YYK IL +N+ L G +G SLLNI+ ELKK NHP+LF++A+
Sbjct: 477 VELSDVQTEYYKNILTKNYSALTAGAKGGHFSLLNIMNELKKASNHPYLFDNAEERVLQK 536
Query: 474 GGDTSINDTSKLERIILSSGKLVILDKLLVRLHETKHRVLIFSQMVRMLDILAEYMSYKG 533
GD + + L +I+SSGK+V+LD+LL RL + HRVLIFSQMVRMLDIL +Y+S KG
Sbjct: 537 FGDGKMTRENVLRGLIMSSGKMVLLDQLLTRLKKDGHRVLIFSQMVRMLDILGDYLSIKG 596
Query: 534 FQFQRLDGSTKAELRHQAMDHFNAPGSEDFCFLLSTRAGGLGINLATADTVIIFDSDWNP 593
FQRLDG+ + R ++DHFN+P S DF FLLSTRAGGLGINL TADTV+IFDSDWNP
Sbjct: 597 INFQRLDGTVPSAQRRISIDHFNSPDSNDFVFLLSTRAGGLGINLMTADTVVIFDSDWNP 656
Query: 594 QNDLQAMSRAHRIGQQEVVNIYRFVTSKSVEEDILERAKKKMVLDHLVIQKLNAEGS-WR 652
Q DLQAM+RAHRIGQ+ V +YR V+ +VEE++LERA+KKM+L++ +I +G+ +
Sbjct: 657 QADLQAMARAHRIGQKNHVMVYRLVSKDTVEEEVLERARKKMILEYAIISLGVTDGNKYT 716
Query: 653 RKKQRKGNELSAILRFGAEELFKEDRNDEESKKRLLGMDID 693
+K + ELSAIL+FGA +F N +K+L +++D
Sbjct: 717 KKNEPNAGELSAILKFGAGNMFTATDN----QKKLEDLNLD 753
>pdb|1Z3I|X Chain X, Structure Of The Swi2SNF2 CHROMATIN REMODELING DOMAIN OF
EUKARYOTIC Rad54
Length = 644
Score = 229 bits (585), Expect = 6e-60, Method: Compositional matrix adjust.
Identities = 160/498 (32%), Positives = 259/498 (52%), Gaps = 36/498 (7%)
Query: 177 LRDYQLEGLNFL---VNSWR--NDTNVILADEMGLGKTVQSVSMLGFLQNAQQIPGP--- 228
LR +Q EG+ FL V R N I+ADEMGLGKT+Q ++++ L P
Sbjct: 56 LRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLIWTLLKQSPDCKPEID 115
Query: 229 -FLVVVPLSTLSNWAKEFRKWLPTMNVIVYVGTRASREVCQQYEFYNDKKVGRPIKFNTL 287
+VV P S + NW E KWL V + + E+ + + ++ G I L
Sbjct: 116 KVIVVSPSSLVRNWYNEVGKWLGGRVQPVAIDGGSKDEIDSKLVNFISQQ-GMRIPTPIL 174
Query: 288 LTTYEVVLKDKAVLSKIKWNYLMVDEAHRLKNSEAQLYTTLSEFSTKNKLLITGTPLQNS 347
+ +YE VL K K ++ DE HRLKNS+ Q Y L+ + + ++LI+GTP+QN
Sbjct: 175 IISYETFRLHAEVLHKGKVGLVICDEGHRLKNSDNQTYLALNSMNAQRRVLISGTPIQND 234
Query: 348 VEELWALLHFLDHDKFKSKDDFIQNYK-------------NLSSFNENELANLHMELRPH 394
+ E ++L+HF++ + +F + ++ + E +L L +
Sbjct: 235 LLEYFSLVHFVNSGILGTAQEFKKRFEIPILKGRDADASDKDRAAGEQKLQELISIVNRC 294
Query: 395 ILRRIIKDVEKSLPPKIERILRVEMSPLQKQYYKWILE--RNFHDLNKGVRGNQVSLLNI 452
++RR + K LP KIE+++ ++PLQK+ YK L+ + L G VS L+
Sbjct: 295 LIRRTSDILSKYLPVKIEQVVCCNLTPLQKELYKLFLKQAKPVESLQTG--KISVSSLSS 352
Query: 453 VVELKKCCNHPFLFE----SADHGYGGDTSI---NDTSKLERIILSSGKLVILDKLLVRL 505
+ LKK CNHP L + + G+ G + N ++K LS GK+++LD +L
Sbjct: 353 ITSLKKLCNHPALIYEKCLTGEEGFDGALDLFPQNYSTKAVEPQLS-GKMLVLDYILAMT 411
Query: 506 HETKH-RVLIFSQMVRMLDILAEYMSYKGFQFQRLDGSTKAELRHQAMDHFNAPGSEDFC 564
T +V++ S + LD+ + + + + RLDG+ + R + ++ FN P S +F
Sbjct: 412 RTTTSDKVVLVSNYTQTLDLFEKLCRNRRYLYVRLDGTMSIKKRAKIVERFNNPSSPEFI 471
Query: 565 FLLSTRAGGLGINLATADTVIIFDSDWNPQNDLQAMSRAHRIGQQEVVNIYRFVTSKSVE 624
F+LS++AGG G+NL A+ +++FD DWNP ND QAM+R R GQ++ IYR +++ ++E
Sbjct: 472 FMLSSKAGGCGLNLIGANRLVMFDPDWNPANDEQAMARVWRDGQKKTCYIYRLLSTGTIE 531
Query: 625 EDILERAKKKMVLDHLVI 642
E IL+R K L V+
Sbjct: 532 EKILQRQAHKKALSSCVV 549
>pdb|1Z6A|A Chain A, Sulfolobus Solfataricus Swi2SNF2 ATPASE CORE DOMAIN
Length = 500
Score = 193 bits (491), Expect = 5e-49, Method: Compositional matrix adjust.
Identities = 135/462 (29%), Positives = 243/462 (52%), Gaps = 51/462 (11%)
Query: 177 LRDYQLEGLNFLVNSWRNDTNVILADEMGLGKTVQSVSMLGFLQNAQQIPGPFLVVVPLS 236
LR YQ++G +++ + + LAD+MGLGKT+Q++++ + ++ P LV+ PLS
Sbjct: 38 LRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAVFSDAKKENELT-PSLVICPLS 96
Query: 237 TLSNWAKEFRKWLPTMNVIVYVGTRASREVCQQYEFYNDKKVGRPIKFNTLLTTYEVVLK 296
L NW +E K+ P + V F+ D+ + ++ +LTTY V+L+
Sbjct: 97 VLKNWEEELSKFAPHLRFAV---------------FHEDRSKIKLEDYDIILTTYAVLLR 141
Query: 297 DKAVLSKIKWNYLMVDEAHRLKNSEAQLYTTLSEFSTKNKLLITGTPLQNSVEELWALLH 356
D L +++W Y+++DEA +KN + +++ + E +K ++ +TGTP++N V++LW+++
Sbjct: 142 DTR-LKEVEWKYIVIDEAQNIKNPQTKIFKAVKELKSKYRIALTGTPIENKVDDLWSIMT 200
Query: 357 FLD------HDKFKSKDDFIQNYKNLSSFNENELANLHMELRPHILRRIIKD--VEKSLP 408
FL+ + +FKSK F K + + EL + + P ILRR D + LP
Sbjct: 201 FLNPGLLGSYSEFKSK--FATPIKKGDNMAKEELKAI---ISPFILRRTKYDKAIINDLP 255
Query: 409 PKIERILRVEMSPLQKQYYKWILERNFHDLNK--GVRGNQVSLLNIVVELKKCCNHPFLF 466
KIE + ++P Q YK +E F++++ G++ + +L+ +++LK+ +HP L
Sbjct: 256 DKIETNVYCNLTPEQAAMYKAEVENLFNNIDSVTGIKRKGM-ILSTLLKLKQIVDHPALL 314
Query: 467 ESADHGYGGDTSINDTSKLERIILSSGKLVILDKLLVRLHETKHRVLIFSQMVRMLDILA 526
+ GG+ S+ SGK++ +++ + ++ IF+Q V M I+
Sbjct: 315 K------GGEQSVR----------RSGKMIRTMEIIEEALDEGDKIAIFTQFVDMGKIIR 358
Query: 527 EYMSYK-GFQFQRLDGSTKAELRHQAMDHFNAPGSEDFCFLLSTRAGGLGINLATADTVI 585
+ + + L G + R + F S F +LS +AGG GINL +A+ VI
Sbjct: 359 NIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFI-VLSVKAGGFGINLTSANRVI 417
Query: 586 IFDSDWNPQNDLQAMSRAHRIGQQEVVNIYRFVTSKSVEEDI 627
FD WNP + QA R +RIGQ V +++ ++ ++EE I
Sbjct: 418 HFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVGTLEEKI 459
>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 = 186 bits (471), Expect = 1e-46, Method: Compositional matrix adjust.
Identities = 133/462 (28%), Positives = 238/462 (51%), Gaps = 51/462 (11%)
Query: 177 LRDYQLEGLNFLVNSWRNDTNVILADEMGLGKTVQSVSMLGFLQNAQQIPGPFLVVVPLS 236
LR YQ++G ++ + + LAD+ GLGKT+Q++++ + ++ P LV+ PLS
Sbjct: 38 LRPYQIKGFSWXRFXNKLGFGICLADDXGLGKTLQTIAVFSDAKKENELT-PSLVICPLS 96
Query: 237 TLSNWAKEFRKWLPTMNVIVYVGTRASREVCQQYEFYNDKKVGRPIKFNTLLTTYEVVLK 296
L NW +E K+ P + V F+ D+ + ++ +LTTY V+L+
Sbjct: 97 VLKNWEEELSKFAPHLRFAV---------------FHEDRSKIKLEDYDIILTTYAVLLR 141
Query: 297 DKAVLSKIKWNYLMVDEAHRLKNSEAQLYTTLSEFSTKNKLLITGTPLQNSVEELWALLH 356
D L +++W Y+++DEA +KN + +++ + E +K ++ +TGTP++N V++LW++
Sbjct: 142 DTR-LKEVEWKYIVIDEAQNIKNPQTKIFKAVKELKSKYRIALTGTPIENKVDDLWSIXT 200
Query: 357 FLD------HDKFKSKDDFIQNYKNLSSFNENELANLHMELRPHILRRIIKD--VEKSLP 408
FL+ + +FKSK F K + + EL + + P ILRR D + LP
Sbjct: 201 FLNPGLLGSYSEFKSK--FATPIKKGDNXAKEELKAI---ISPFILRRTKYDKAIINDLP 255
Query: 409 PKIERILRVEMSPLQKQYYKWILERNFHDLNK--GVRGNQVSLLNIVVELKKCCNHPFLF 466
KIE + ++P Q YK +E F++++ G++ + +L+ +++LK+ +HP L
Sbjct: 256 DKIETNVYCNLTPEQAAXYKAEVENLFNNIDSVTGIK-RKGXILSTLLKLKQIVDHPALL 314
Query: 467 ESADHGYGGDTSINDTSKLERIILSSGKLVILDKLLVRLHETKHRVLIFSQMVRMLDILA 526
+ GG+ S+ SGK + +++ + ++ IF+Q V I+
Sbjct: 315 K------GGEQSVR----------RSGKXIRTXEIIEEALDEGDKIAIFTQFVDXGKIIR 358
Query: 527 EYMSYK-GFQFQRLDGSTKAELRHQAMDHFNAPGSEDFCFLLSTRAGGLGINLATADTVI 585
+ + + L G + R + F S F +LS +AGG GINL +A+ VI
Sbjct: 359 NIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKF-IVLSVKAGGFGINLTSANRVI 417
Query: 586 IFDSDWNPQNDLQAMSRAHRIGQQEVVNIYRFVTSKSVEEDI 627
FD WNP + QA R +RIGQ V +++ ++ ++EE I
Sbjct: 418 HFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVGTLEEKI 459
>pdb|2B2U|A Chain A, Tandem Chromodomains Of Human Chd1 Complexed With Histone
H3 Tail Containing Trimethyllysine 4 And
Dimethylarginine 2
pdb|2B2U|B Chain B, Tandem Chromodomains Of Human Chd1 Complexed With Histone
H3 Tail Containing Trimethyllysine 4 And
Dimethylarginine 2
pdb|2B2V|A Chain A, Crystal Structure Analysis Of Human Chd1 Chromodomains 1
And 2 Bound To Histone H3 Resi 1-15 Mek4
pdb|2B2V|B Chain B, Crystal Structure Analysis Of Human Chd1 Chromodomains 1
And 2 Bound To Histone H3 Resi 1-15 Mek4
pdb|2B2W|A Chain A, Tandem Chromodomains Of Human Chd1 Complexed With Histone
H3 Tail Containing Trimethyllysine 4
pdb|2B2W|B Chain B, Tandem Chromodomains Of Human Chd1 Complexed With Histone
H3 Tail Containing Trimethyllysine 4
pdb|2B2Y|A Chain A, Tandem Chromodomains Of Human Chd1
pdb|2B2Y|B Chain B, Tandem Chromodomains Of Human Chd1
Length = 187
Score = 90.1 bits (222), Expect = 8e-18, Method: Compositional matrix adjust.
Identities = 55/140 (39%), Positives = 81/140 (57%), Gaps = 5/140 (3%)
Query: 5 FDSEPDWNEMEFLIKWKGQSHLHCQWKSFAEL--QNLSGFKKVLNYAKKVVEDVRFRKMV 62
F+ + E+++LIKWKG SH+H W++ L QN+ G KK+ NY KK E R+ K
Sbjct: 49 FEKNKEPGEIQYLIKWKGWSHIHNTWETEETLKQQNVRGMKKLDNYKKKDQETKRWLKNA 108
Query: 63 SREEIELNDVSKEMDLDIIKQNSQVERIIADRISKDSSGNVTQEYLVKWKGLSYAEATWE 122
S E++E + +E+ D+ KQ V RIIA K ++G +Y KW+GL Y+E +WE
Sbjct: 109 SPEDVEYYNCQQELTDDLHKQYQIVGRIIAHSNQKSAAG--YPDYYCKWQGLPYSECSWE 166
Query: 123 KDEIIDFA-QDAIDEYKARE 141
+I Q IDEY +R+
Sbjct: 167 DGALISKKFQACIDEYFSRK 186
>pdb|2B2T|A Chain A, Tandem Chromodomains Of Human Chd1 Complexed With Histone
H3 Tail Containing Trimethyllysine 4 And
Phosphothreonine 3
pdb|2B2T|B Chain B, Tandem Chromodomains Of Human Chd1 Complexed With Histone
H3 Tail Containing Trimethyllysine 4 And
Phosphothreonine 3
Length = 187
Score = 88.6 bits (218), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 55/139 (39%), Positives = 80/139 (57%), Gaps = 5/139 (3%)
Query: 5 FDSEPDWNEMEFLIKWKGQSHLHCQWKSFAEL--QNLSGFKKVLNYAKKVVEDVRFRKMV 62
F+ + E+++LIKWKG SH+H W++ L QN+ G KK+ NY KK E R+ K
Sbjct: 49 FEKNKEPGEIQYLIKWKGWSHIHNTWETEETLKQQNVRGXKKLDNYKKKDQETKRWLKNA 108
Query: 63 SREEIELNDVSKEMDLDIIKQNSQVERIIADRISKDSSGNVTQEYLVKWKGLSYAEATWE 122
S E++E + +E+ D+ KQ V RIIA K ++G +Y KW+GL Y+E +WE
Sbjct: 109 SPEDVEYYNCQQELTDDLHKQYQIVGRIIAHSNQKSAAG--YPDYYCKWQGLPYSECSWE 166
Query: 123 KDEIIDFA-QDAIDEYKAR 140
+I Q IDEY +R
Sbjct: 167 DGALISKKFQAXIDEYFSR 185
>pdb|2H1E|A Chain A, Tandem Chromodomains Of Budding Yeast Chd1
pdb|2H1E|B Chain B, Tandem Chromodomains Of Budding Yeast Chd1
Length = 177
Score = 84.7 bits (208), Expect = 3e-16, Method: Compositional matrix adjust.
Identities = 50/140 (35%), Positives = 80/140 (57%), Gaps = 8/140 (5%)
Query: 9 PDWNEM----EFLIKWKGQSHLHCQWKSFAELQNLSGFKKVLNYAKK-VVED--VRFRKM 61
PD N EFLIKW +SHLH W+++ + + G K++ NY K+ ++ED VR
Sbjct: 38 PDLNNCKENYEFLIKWTDESHLHNTWETYESIGQVRGLKRLDNYCKQFIIEDQQVRLDPY 97
Query: 62 VSREEIELNDVSKEMDLDIIKQNSQVERIIADRISKDSSGNVTQEYLVKWKGLSYAEATW 121
V+ E+IE+ D+ +E LD ++ ERII + + G +YLVKW+ L+Y EATW
Sbjct: 98 VTAEDIEIMDMERERRLDEFEEFHVPERIIDSQRASLEDGTSQLQYLVKWRRLNYDEATW 157
Query: 122 EK-DEIIDFAQDAIDEYKAR 140
E +I+ A + + ++ +
Sbjct: 158 ENATDIVKLAPEQVKHFQKK 177
>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 = 83.6 bits (205), Expect = 7e-16, Method: Compositional matrix adjust.
Identities = 64/224 (28%), Positives = 113/224 (50%), Gaps = 21/224 (9%)
Query: 407 LPPKIERILRVEMSPLQKQYYKWILERNFHDLNK--GVRGNQVSLLNIVVELKKCCNHPF 464
LP KIE + ++P Q YK +E F++++ G++ + +L+ +++LK+ +HP
Sbjct: 25 LPDKIETNVYCNLTPEQAAMYKAEVENLFNNIDSVTGIKRKGM-ILSTLLKLKQIVDHPA 83
Query: 465 LFESADHGYGGDTSINDTSKLERIILSSGKLVILDKLLVRLHETKHRVLIFSQMVRMLDI 524
L + GG+ S+ SGK++ +++ + ++ IF+Q V M I
Sbjct: 84 LLK------GGEQSVR----------RSGKMIRTMEIIEEALDEGDKIAIFTQFVDMGKI 127
Query: 525 LAEYMSYK-GFQFQRLDGSTKAELRHQAMDHFNAPGSEDFCFLLSTRAGGLGINLATADT 583
+ + + + L G + R + F S F +LS +AGG GINL +A+
Sbjct: 128 IRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKF-IVLSVKAGGFGINLTSANR 186
Query: 584 VIIFDSDWNPQNDLQAMSRAHRIGQQEVVNIYRFVTSKSVEEDI 627
VI FD WNP + QA R +RIGQ V +++ ++ ++EE I
Sbjct: 187 VIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVGTLEEKI 230
>pdb|4B4C|A Chain A, Crystal Structure Of The Dna-Binding Domain Of Human Chd1
Length = 211
Score = 72.4 bits (176), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 58/197 (29%), Positives = 98/197 (49%), Gaps = 20/197 (10%)
Query: 817 NLSKRDATRFYRAVMKFGNQ-SQISLIARDAGGAVATAPQEVVVELFDILIDGCREAVEV 875
S + RF ++ KFG ++ IARDA + + + L +++ +GC +A++
Sbjct: 9 GFSDAEIRRFIKSYKKFGGPLERLDAIARDA--ELVDKSETDLRRLGELVHNGCIKALKD 66
Query: 876 GSPDP----------KGPPLLDFFGVSVKANDLINRVEELQLLAKRISRYEDPIKQFRVL 925
S KGP GV V A +I+ EEL L K I + KQ+ +
Sbjct: 67 SSSGTERTGGRLGKVKGP-TFRISGVQVNAKLVISHEEELIPLHKSIPSDPEERKQYTIP 125
Query: 926 SYLKPSNWSKGCGWNQFDDARLLLGIHYHGFGNWENIRLDERLGLTKKIAPVELQHHETF 985
+ K +++ W + DD+ LL+GI+ +G+G+WE I++D L LT KI P +
Sbjct: 126 CHTKAAHFD--IDWGKEDDSNLLIGIYEYGYGSWEMIKMDPDLSLTHKILPDDPDKK--- 180
Query: 986 LPRAPNLKERANALLEM 1002
P+A L+ RA+ L+++
Sbjct: 181 -PQAKQLQTRADYLIKL 196
>pdb|2XB0|X Chain X, Dna-Binding Domain From Saccharomyces Cerevisiae
Chromatin- Remodelling Protein Chd1
Length = 270
Score = 62.0 bits (149), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 58/206 (28%), Positives = 94/206 (45%), Gaps = 50/206 (24%)
Query: 816 GNLSKRDATRFYRAVMKFGNQSQISLIARDAGGAVATAPQEVVVELFDILIDGCREAV-- 873
G++ + + Y+A++KFGN +I L A G + E E +D +++ ++ V
Sbjct: 4 GSIGESEVRALYKAILKFGNLKEI-LDELIADGTLPVKSFEKYGETYDEMMEAAKDCVHE 62
Query: 874 --------------------------EVGSPD-PKGPPL--------------LDFFGV- 891
E+ + + PK PL +F GV
Sbjct: 63 EEKNRKEILEKLEKHATAYRAKLKSGEIKAENQPKDNPLTRLSLKKREKKAVLFNFKGVK 122
Query: 892 SVKANDLINRVEELQLLAKRI-SRY-EDPIKQFRVLSYLKP-SNWSKGCGWNQFDDARLL 948
S+ A L++RVE+L+ L I S Y +DP+K + KP NWS W + +D +LL
Sbjct: 123 SLNAESLLSRVEDLKYLKNLINSNYKDDPLKFSLGNNTPKPVQNWS--SNWTKEEDEKLL 180
Query: 949 LGIHYHGFGNWENIRLDERLGLTKKI 974
+G+ +G+G+W IR D LG+T KI
Sbjct: 181 IGVFKYGYGSWTQIRDDPFLGITDKI 206
>pdb|3TED|A Chain A, Crystal Structure Of The Chd1 Dna-Binding Domain In
Complex With A Dna Duplex
Length = 271
Score = 60.1 bits (144), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 57/196 (29%), Positives = 89/196 (45%), Gaps = 50/196 (25%)
Query: 826 FYRAVMKFGNQSQISLIARDAGGAVATAPQEVVVELFDILIDGCREAV------------ 873
Y+A++KFGN +I L A G + E E +D +++ ++ V
Sbjct: 15 LYKAILKFGNLKEI-LDELIADGTLPVKSFEKYGETYDEMMEAAKDCVHEEEKNRKEILE 73
Query: 874 ----------------EVGSPD-PKGPPL--------------LDFFGV-SVKANDLINR 901
E+ + + PK PL +F GV S+ A L++R
Sbjct: 74 KLEKHATAYRAKLKSGEIKAENQPKDNPLTRLSLKKREKKAVLFNFKGVKSLNAESLLSR 133
Query: 902 VEELQLLAKRI-SRY-EDPIKQFRVLSYLKP-SNWSKGCGWNQFDDARLLLGIHYHGFGN 958
VE+L+ L I S Y +DP+K + KP NWS W + +D +LL+G+ +G+G+
Sbjct: 134 VEDLKYLKNLINSNYKDDPLKFSLGNNTPKPVQNWS--SNWTKEEDEKLLIGVFKYGYGS 191
Query: 959 WENIRLDERLGLTKKI 974
W IR D LG+T KI
Sbjct: 192 WTQIRDDPFLGITDKI 207
>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 = 56.2 bits (134), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 54/198 (27%), Positives = 95/198 (47%), Gaps = 32/198 (16%)
Query: 193 RNDTNVILADEMGLGKTVQSVSMLGFLQNAQQIPGP---FLVVVPLSTLSNWAKE-FRKW 248
R+ V+LADE+GLGKT+++ G + + Q + G L++VP + W E R++
Sbjct: 168 RHAPRVLLADEVGLGKTIEA----GXILHQQLLSGAAERVLIIVPETLQHQWLVEXLRRF 223
Query: 249 LPTMNVIVYVGTRASREVCQQYEFYNDKKVGRPIKFNT---LLTTYEVVLKDKAVLSKI- 304
+ ++ R + Q++ YN F+T ++ + + + K L +
Sbjct: 224 --NLRFALFDDERYAE---AQHDAYN--------PFDTEQLVICSLDFARRSKQRLEHLC 270
Query: 305 --KWNYLMVDEAHRLKNSE---AQLYTTLSEFS--TKNKLLITGTPLQNSVEELWALLHF 357
+W+ L+VDEAH L SE ++ Y + + + LL+T TP Q E +A L
Sbjct: 271 EAEWDLLVVDEAHHLVWSEDAPSREYQAIEQLAEHVPGVLLLTATPEQLGXESHFARLRL 330
Query: 358 LDHDKFKSKDDFIQNYKN 375
LD ++F F++ KN
Sbjct: 331 LDPNRFHDFAQFVEEQKN 348
>pdb|2B2U|C Chain C, Tandem Chromodomains Of Human Chd1 Complexed With Histone
H3 Tail Containing Trimethyllysine 4 And
Dimethylarginine 2
pdb|2B2V|C Chain C, Crystal Structure Analysis Of Human Chd1 Chromodomains 1
And 2 Bound To Histone H3 Resi 1-15 Mek4
pdb|2B2W|C Chain C, Tandem Chromodomains Of Human Chd1 Complexed With Histone
H3 Tail Containing Trimethyllysine 4
pdb|2B2Y|C Chain C, Tandem Chromodomains Of Human Chd1
Length = 115
Score = 52.0 bits (123), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 28/66 (42%), Positives = 41/66 (62%), Gaps = 2/66 (3%)
Query: 5 FDSEPDWNEMEFLIKWKGQSHLHCQWKSFAEL--QNLSGFKKVLNYAKKVVEDVRFRKMV 62
F+ + E+++LIKWKG SH+H W++ L QN+ G KK+ NY KK E R+ K
Sbjct: 49 FEKNKEPGEIQYLIKWKGWSHIHNTWETEETLKQQNVRGMKKLDNYKKKDQETKRWLKNA 108
Query: 63 SREEIE 68
S E++E
Sbjct: 109 SPEDVE 114
Score = 30.4 bits (67), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 11/22 (50%), Positives = 16/22 (72%)
Query: 106 EYLVKWKGLSYAEATWEKDEII 127
+YL+KWKG S+ TWE +E +
Sbjct: 59 QYLIKWKGWSHIHNTWETEETL 80
>pdb|2B2T|C Chain C, Tandem Chromodomains Of Human Chd1 Complexed With Histone
H3 Tail Containing Trimethyllysine 4 And
Phosphothreonine 3
Length = 115
Score = 51.2 bits (121), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 28/67 (41%), Positives = 41/67 (61%), Gaps = 2/67 (2%)
Query: 5 FDSEPDWNEMEFLIKWKGQSHLHCQWKSFAEL--QNLSGFKKVLNYAKKVVEDVRFRKMV 62
F+ + E+++LIKWKG SH+H W++ L QN+ G KK+ NY KK E R+ K
Sbjct: 49 FEKNKEPGEIQYLIKWKGWSHIHNTWETEETLKQQNVRGXKKLDNYKKKDQETKRWLKNA 108
Query: 63 SREEIEL 69
S E++E
Sbjct: 109 SPEDVEY 115
Score = 30.4 bits (67), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 11/22 (50%), Positives = 16/22 (72%)
Query: 106 EYLVKWKGLSYAEATWEKDEII 127
+YL+KWKG S+ TWE +E +
Sbjct: 59 QYLIKWKGWSHIHNTWETEETL 80
>pdb|2DY7|A Chain A, Solution Structure Of The First Chromodomain Of Yeast
Chd1
Length = 81
Score = 43.5 bits (101), Expect = 9e-04, Method: Composition-based stats.
Identities = 19/49 (38%), Positives = 29/49 (59%), Gaps = 4/49 (8%)
Query: 9 PDWNE----MEFLIKWKGQSHLHCQWKSFAELQNLSGFKKVLNYAKKVV 53
PD N EFLIKW +SHLH W+++ + + G K++ NY K+ +
Sbjct: 31 PDLNNCKENYEFLIKWTDESHLHNTWETYESIGQVRGLKRLDNYCKQFI 79
>pdb|2DY8|A Chain A, Solution Structure Of The Second Chromodomain Of Yeast
Chd1
Length = 69
Score = 40.0 bits (92), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 21/55 (38%), Positives = 32/55 (58%), Gaps = 1/55 (1%)
Query: 88 ERIIADRISKDSSGNVTQEYLVKWKGLSYAEATWEK-DEIIDFAQDAIDEYKARE 141
ERII + + G +YLVKW+ L+Y EATWE +I+ A + + ++ RE
Sbjct: 10 ERIIDSQRASLEDGTSQLQYLVKWRRLNYDEATWENATDIVKLAPEQVKHFQNRE 64
>pdb|2EPB|A Chain A, Solution Structure Of Chromo Domain 2 In Chromodomain-
Helicase-Dna-Binding Protein 6
Length = 68
Score = 38.5 bits (88), Expect = 0.027, Method: Composition-based stats.
Identities = 20/47 (42%), Positives = 30/47 (63%), Gaps = 1/47 (2%)
Query: 86 QVERIIADRISKDS-SGNVTQEYLVKWKGLSYAEATWEKDEIIDFAQ 131
+V+RI+ +KD+ +G YLVKW L Y E+TWE +E +D A+
Sbjct: 13 EVDRILEVAHTKDAETGEEVTHYLVKWCSLPYEESTWELEEDVDPAK 59
>pdb|3FMP|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex
With The Dead- Box Helicase Ddx19
pdb|3FMP|D Chain D, Crystal Structure Of The Nucleoporin Nup214 In Complex
With The Dead- Box Helicase Ddx19
Length = 479
Score = 37.7 bits (86), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 31/105 (29%), Positives = 45/105 (42%), Gaps = 11/105 (10%)
Query: 508 TKHRVLIFSQMVRMLDILAEYMSYKGFQFQRLDGSTKAELRHQAMDHFNAPGSEDFCFLL 567
T + +IF + LA +S +G Q L G E R ++ F G E L+
Sbjct: 332 TIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFRE-GKEKV--LV 388
Query: 568 STRAGGLGINLATADTVIIF----DSDWNPQNDLQAMSRAHRIGQ 608
+T GI++ VI F D D NP N+ + HRIG+
Sbjct: 389 TTNVCARGIDVEQVSVVINFDLPVDKDGNPDNE----TYLHRIGR 429
>pdb|3FHT|A Chain A, Crystal Structure Of Human Dbp5 In Complex With Amppnp And
Rna
pdb|3FHT|B Chain B, Crystal Structure Of Human Dbp5 In Complex With Amppnp And
Rna
Length = 412
Score = 37.4 bits (85), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 31/105 (29%), Positives = 45/105 (42%), Gaps = 11/105 (10%)
Query: 508 TKHRVLIFSQMVRMLDILAEYMSYKGFQFQRLDGSTKAELRHQAMDHFNAPGSEDFCFLL 567
T + +IF + LA +S +G Q L G E R ++ F G E L+
Sbjct: 265 TIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFRE-GKEKV--LV 321
Query: 568 STRAGGLGINLATADTVIIF----DSDWNPQNDLQAMSRAHRIGQ 608
+T GI++ VI F D D NP N+ + HRIG+
Sbjct: 322 TTNVCARGIDVEQVSVVINFDLPVDKDGNPDNE----TYLHRIGR 362
>pdb|3G0H|A Chain A, Human Dead-box Rna Helicase Ddx19, In Complex With An
Atp-analogue And Rna
Length = 424
Score = 37.4 bits (85), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 31/105 (29%), Positives = 45/105 (42%), Gaps = 11/105 (10%)
Query: 508 TKHRVLIFSQMVRMLDILAEYMSYKGFQFQRLDGSTKAELRHQAMDHFNAPGSEDFCFLL 567
T + +IF + LA +S +G Q L G E R ++ F G E L+
Sbjct: 281 TIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFRE-GKEKV--LV 337
Query: 568 STRAGGLGINLATADTVIIF----DSDWNPQNDLQAMSRAHRIGQ 608
+T GI++ VI F D D NP N+ + HRIG+
Sbjct: 338 TTNVCARGIDVEQVSVVINFDLPVDKDGNPDNE----TYLHRIGR 378
>pdb|4HAE|A Chain A, Crystal Structure Of The Cdyl2-Chromodomain
Length = 81
Score = 37.4 bits (85), Expect = 0.061, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 29/54 (53%), Gaps = 4/54 (7%)
Query: 86 QVERIIADRISKDSSGNVTQEYLVKWKGLSYAEATWEKDEIIDFAQDAIDEYKA 139
+VERI+ R +K EYL++WKG E TWE + + ++ IDE+
Sbjct: 25 EVERIVDKRKNKKGK----WEYLIRWKGYGSTEDTWEPEHHLLHCEEFIDEFNG 74
>pdb|3EWS|A Chain A, Human Dead-Box Rna-Helicase Ddx19 In Complex With Adp
pdb|3EWS|B Chain B, Human Dead-Box Rna-Helicase Ddx19 In Complex With Adp
Length = 445
Score = 37.4 bits (85), Expect = 0.065, Method: Compositional matrix adjust.
Identities = 31/105 (29%), Positives = 45/105 (42%), Gaps = 11/105 (10%)
Query: 508 TKHRVLIFSQMVRMLDILAEYMSYKGFQFQRLDGSTKAELRHQAMDHFNAPGSEDFCFLL 567
T + +IF + LA +S +G Q L G E R ++ F G E L+
Sbjct: 302 TIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFRE-GKEKV--LV 358
Query: 568 STRAGGLGINLATADTVIIF----DSDWNPQNDLQAMSRAHRIGQ 608
+T GI++ VI F D D NP N+ + HRIG+
Sbjct: 359 TTNVCARGIDVEQVSVVINFDLPVDKDGNPDNE----TYLHRIGR 399
>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 = 37.0 bits (84), Expect = 0.079, Method: Composition-based stats.
Identities = 34/128 (26%), Positives = 57/128 (44%), Gaps = 6/128 (4%)
Query: 501 LLVRLHETKHRVLIFSQMVRMLDILAEYMSYKGFQFQRLDGSTKAELRHQAMDHFNAPGS 560
LL L +T VLIF++ +D + EY+ KG + + G E R +A++ F G
Sbjct: 46 LLECLQKTPPPVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFRE-GK 104
Query: 561 EDFCFLLSTRAGGLGINLATADTVIIFDSDWNPQNDLQAMSRAHRIGQQEVVNIYRFVTS 620
+D L++T G++ VI +D P+ + R R G I +
Sbjct: 105 KD--VLVATDVASKGLDFPAIQHVINYDM---PEEIENYVHRIGRTGCSGNTGIATTFIN 159
Query: 621 KSVEEDIL 628
K+ +E +L
Sbjct: 160 KACDESVL 167
>pdb|1KNA|A Chain A, Chromo Domain Of Hp1 Complexed With Histone H3 Tail
Containing Dimethyllysine 9.
pdb|1KNE|A Chain A, Chromo Domain Of Hp1 Complexed With Histone H3 Tail
Containing Trimethyllysine 9
pdb|1Q3L|A Chain A, Chromodomain Of Hp1 Complexed With Histone H3 Tail
Containing Monomethyllysine 9
Length = 69
Score = 36.2 bits (82), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 24/53 (45%), Positives = 31/53 (58%), Gaps = 6/53 (11%)
Query: 87 VERIIADRISKDSSGNVTQEYLVKWKGLSYAEATWEKDEIIDFAQDAIDEYKA 139
VE+II R+ K G V EY +KWKG E TWE + +D QD I +Y+A
Sbjct: 19 VEKIIDRRVRK---GMV--EYYLKWKGYPETENTWEPENNLD-CQDLIQQYEA 65
>pdb|2RSN|A Chain A, Solution Structure Of The Chromodomain Of Chp1 In Complex
With H3k9me3 Peptide
Length = 75
Score = 36.2 bits (82), Expect = 0.13, Method: Composition-based stats.
Identities = 19/51 (37%), Positives = 29/51 (56%), Gaps = 8/51 (15%)
Query: 75 EMDLDIIKQNSQVERIIADRISKDSSGNVTQEYLVKWKGLSYAEATWEKDE 125
E D D+ +VE I+ADR++K N EY +KW G + + TWE ++
Sbjct: 16 ETDADVY----EVEDILADRVNK----NGINEYYIKWAGYDWYDNTWEPEQ 58
>pdb|3G7L|A Chain A, Chromodomain Of Chp1 In Complex With Histone H3k9me3
Peptide
Length = 61
Score = 36.2 bits (82), Expect = 0.14, Method: Composition-based stats.
Identities = 19/51 (37%), Positives = 29/51 (56%), Gaps = 8/51 (15%)
Query: 75 EMDLDIIKQNSQVERIIADRISKDSSGNVTQEYLVKWKGLSYAEATWEKDE 125
E D D+ +VE I+ADR++K N EY +KW G + + TWE ++
Sbjct: 2 ETDADVY----EVEDILADRVNK----NGINEYYIKWAGYDWYDNTWEPEQ 44
>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x
Length = 417
Score = 36.2 bits (82), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 33/158 (20%), Positives = 70/158 (44%), Gaps = 5/158 (3%)
Query: 472 GYGGDTSINDTSKLERIILSSGKLVILDKLLVRLHETKHRVLIFSQMVRMLDILAEYMSY 531
G G TS N T K+ + S + +LD L+ L+F + + D L +++ +
Sbjct: 241 GRVGSTSENITQKVVWVEESDKRSFLLD--LLNATGKDSLTLVFVETKKGADSLEDFLYH 298
Query: 532 KGFQFQRLDGSTKAELRHQAMDHFNAPGSEDFCFLLSTRAGGLGINLATADTVIIFDSDW 591
+G+ + G R +A+ F + S L++T G++++ VI FD
Sbjct: 299 EGYACTSIHGDRSQRDREEALHQFRSGKSP---ILVATAVAARGLDISNVKHVINFDLPS 355
Query: 592 NPQNDLQAMSRAHRIGQQEVVNIYRFVTSKSVEEDILE 629
+ + + + R R+G + + + ++ +D+L+
Sbjct: 356 DIEEYVHRIGRTGRVGNLGLATSFFNERNINITKDLLD 393
>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 = 35.4 bits (80), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 30/135 (22%), Positives = 60/135 (44%), Gaps = 5/135 (3%)
Query: 473 YGGDTSINDTSKLERIILSSGKLVILDKLLVRLHETKHRVLIFSQMVRMLDILAEYMSYK 532
+ G TS N T K+ + S + +LD L+ L+F + + D L +++ ++
Sbjct: 12 FQGSTSENITQKVVWVEESDKRSFLLD--LLNATGKDSLTLVFVETKKGADSLEDFLYHE 69
Query: 533 GFQFQRLDGSTKAELRHQAMDHFNAPGSEDFCFLLSTRAGGLGINLATADTVIIFDSDWN 592
G+ + G R +A+ F + S L++T G++++ VI FD +
Sbjct: 70 GYACTSIHGDRSQRDREEALHQFRSGKSP---ILVATAVAARGLDISNVKHVINFDLPSD 126
Query: 593 PQNDLQAMSRAHRIG 607
+ + + R R+G
Sbjct: 127 IEEYVHRIGRTGRVG 141
>pdb|3F2U|A Chain A, Crystal Structure Of Human Chromobox Homolog 1 (Cbx1)
Length = 55
Score = 34.3 bits (77), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 22/51 (43%), Positives = 31/51 (60%), Gaps = 6/51 (11%)
Query: 87 VERIIADRISKDSSGNVTQEYLVKWKGLSYAEATWEKDEIIDFAQDAIDEY 137
VE+++ R+ K G V EYL+KWKG S + TWE +E +D D I E+
Sbjct: 5 VEKVLDRRVVK---GKV--EYLLKWKGFSDEDNTWEPEENLD-CPDLIAEF 49
>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 = 33.9 bits (76), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 29/126 (23%), Positives = 51/126 (40%), Gaps = 3/126 (2%)
Query: 482 TSKLERIILSSGKLVILDKLLVRLHETKHRVLIFSQMVRMLDILAEYMSYKGFQFQRLDG 541
S +++ I K KL+ L E ++F + R D LA ++S K F + G
Sbjct: 273 CSDVKQTIYEVNKYAKRSKLIEILSEQADGTIVFVETKRGADFLASFLSEKEFPTTSIHG 332
Query: 542 STKAELRHQAMDHFNAPGSEDFCFLLSTRAGGLGINLATADTVIIFDSDWNPQNDLQAMS 601
R QA+ F + L++T G+++ VI +D + + +
Sbjct: 333 DRLQSQREQALRDFK---NGSMKVLIATSVASRGLDIKNIKHVINYDMPSKIDDYVHRIG 389
Query: 602 RAHRIG 607
R R+G
Sbjct: 390 RTGRVG 395
>pdb|3FDT|A Chain A, Crystal Structure Of The Complex Of Human Chromobox
Homolog 5 (Cbx5) With H3k9(Me)3 Peptide
Length = 59
Score = 33.9 bits (76), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 33/60 (55%), Gaps = 6/60 (10%)
Query: 87 VERIIADRISKDSSGNVTQEYLVKWKGLSYAEATWEKDEIIDFAQDAIDEYKAREAAMAE 146
VE+++ R+ K G V EYL+KWKG S TWE ++ +D + I E+ + M E
Sbjct: 6 VEKVLDRRVVK---GQV--EYLLKWKGFSEEHNTWEPEKNLD-CPELISEFMKKYKKMKE 59
>pdb|2DNT|A Chain A, Solution Structure Of Rsgi Ruh-064, A Chromo Domain From
Human Cdna
Length = 78
Score = 33.1 bits (74), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 31/55 (56%), Gaps = 4/55 (7%)
Query: 86 QVERIIADRISKDSSGNVTQEYLVKWKGLSYAEATWEKDEIIDFAQDAIDEYKAR 140
+VERI+ R K+ G EYLV+WKG + TWE ++ + ++ I ++ R
Sbjct: 15 EVERIVDKR--KNKKGKT--EYLVRWKGYDSEDDTWEPEQHLVNCEEYIHDFNRR 65
>pdb|1AP0|A Chain A, Structure Of The Chromatin Binding (Chromo) Domain From
Mouse Modifier Protein 1, Nmr, 26 Structures
pdb|1GUW|A Chain A, Structure Of The Chromodomain From Mouse Hp1beta In
Complex With The Lysine 9-Methyl Histone H3 N-Terminal
Peptide, Nmr, 25 Structures
Length = 73
Score = 32.7 bits (73), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 18/44 (40%), Positives = 24/44 (54%), Gaps = 1/44 (2%)
Query: 106 EYLVKWKGLSYAEATWEKDEIIDFAQDAIDEYKAREAAMAEQGK 149
EYL+KWKG S + TWE +E +D D I E+ + E K
Sbjct: 30 EYLLKWKGFSDEDNTWEPEENLD-CPDLIAEFLQSQKTAHETDK 72
>pdb|3GV6|A Chain A, Crystal Structure Of Human Chromobox Homolog 6 (Cbx6) With
H3k9 Peptide
Length = 58
Score = 32.7 bits (73), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 26/56 (46%), Positives = 31/56 (55%), Gaps = 6/56 (10%)
Query: 87 VERIIADRISKDSSGNVTQEYLVKWKGLSYAEATWEKDE-IIDFAQDAIDEYKARE 141
E II RI K G + EYLVKWKG + +TWE +E I+D A E K RE
Sbjct: 6 AESIIKRRIRK---GRI--EYLVKWKGWAIKYSTWEPEENILDSRLIAAFEQKERE 56
>pdb|3TZD|A Chain A, Crystal Structure Of The Complex Of Human Chromobox
Homolog 3 (cbx3)
Length = 58
Score = 32.3 bits (72), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 27/42 (64%), Gaps = 5/42 (11%)
Query: 87 VERIIADRISKDSSGNVTQEYLVKWKGLSYAEATWEKDEIID 128
VE+++ R+ +G V EY +KWKG + A+ TWE +E +D
Sbjct: 9 VEKVLDRRVV---NGKV--EYFLKWKGFTDADNTWEPEENLD 45
>pdb|3DM1|A Chain A, Crystal Structure Of The Complex Of Human Chromobox
Homolog 3 (cbx3) With Peptide
pdb|3DM1|C Chain C, Crystal Structure Of The Complex Of Human Chromobox
Homolog 3 (cbx3) With Peptide
pdb|3DM1|E Chain E, Crystal Structure Of The Complex Of Human Chromobox
Homolog 3 (cbx3) With Peptide
pdb|3DM1|G Chain G, Crystal Structure Of The Complex Of Human Chromobox
Homolog 3 (cbx3) With Peptide
Length = 58
Score = 32.3 bits (72), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 27/42 (64%), Gaps = 5/42 (11%)
Query: 87 VERIIADRISKDSSGNVTQEYLVKWKGLSYAEATWEKDEIID 128
VE+++ R+ +G V EY +KWKG + A+ TWE +E +D
Sbjct: 4 VEKVLDRRVV---NGKV--EYFLKWKGFTDADNTWEPEENLD 40
>pdb|2L11|A Chain A, Solution Nmr Structure Of The Cbx3 In Complex With H3k9me3
Peptide
Length = 54
Score = 32.3 bits (72), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 25/42 (59%), Gaps = 5/42 (11%)
Query: 87 VERIIADRISKDSSGNVTQEYLVKWKGLSYAEATWEKDEIID 128
VE+++ R+ N EY +KWKG + A+ TWE +E +D
Sbjct: 5 VEKVLDRRVV-----NGKVEYFLKWKGFTDADNTWEPEENLD 41
>pdb|2KVM|A Chain A, Solution Structure Of The Cbx7 Chromodomain In Complex
With A H3k27me2 Peptide
Length = 74
Score = 31.6 bits (70), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 24/53 (45%), Positives = 29/53 (54%), Gaps = 6/53 (11%)
Query: 76 MDLDII-KQNSQVERIIADRISKDSSGNVTQEYLVKWKGLSYAEATWEKDEII 127
M+L I +Q VE I R+ K G V EYLVKWKG +TWE +E I
Sbjct: 4 MELSAIGEQVFAVESIRKKRVRK---GKV--EYLVKWKGWPPKYSTWEPEEHI 51
>pdb|3I90|A Chain A, Crystal Structure Of Human Chromobox Homolog 6 (Cbx6) With
H3k27 Peptide
pdb|3I90|B Chain B, Crystal Structure Of Human Chromobox Homolog 6 (Cbx6) With
H3k27 Peptide
Length = 51
Score = 31.2 bits (69), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 21/42 (50%), Positives = 26/42 (61%), Gaps = 6/42 (14%)
Query: 88 ERIIADRISKDSSGNVTQEYLVKWKGLSYAEATWEKDE-IID 128
E II RI K G + EYLVKWKG + +TWE +E I+D
Sbjct: 6 ESIIKRRIRK---GRI--EYLVKWKGWAIKYSTWEPEENILD 42
>pdb|2DNV|A Chain A, Solution Structure Of Rsgi Ruh-055, A Chromo Domain From
Mus Musculus Cdna
Length = 64
Score = 31.2 bits (69), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 14/22 (63%), Positives = 16/22 (72%)
Query: 106 EYLVKWKGLSYAEATWEKDEII 127
EYLVKWKG S +TWE +E I
Sbjct: 27 EYLVKWKGWSQKYSTWEPEENI 48
>pdb|1X3P|A Chain A, 3d Solution Structure Of The Chromo-3 Domain Of Cpsrp43
Length = 54
Score = 30.8 bits (68), Expect = 4.8, Method: Composition-based stats.
Identities = 17/41 (41%), Positives = 23/41 (56%), Gaps = 5/41 (12%)
Query: 88 ERIIADRISKDSSGNVTQEYLVKWKGLSYAEATWEKDEIID 128
E +I R+ D T EYLVKW +S +ATWE + +D
Sbjct: 4 ESVIGKRVGDDGK---TIEYLVKWTDMS--DATWEPQDNVD 39
>pdb|2K1B|A Chain A, Solution Nmr Structure Of The Chromo Domain Of The
Chromobox Protein Homolog 7
Length = 73
Score = 30.8 bits (68), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 19/45 (42%), Positives = 24/45 (53%), Gaps = 2/45 (4%)
Query: 83 QNSQVERIIADRISKDSSGNVTQEYLVKWKGLSYAEATWEKDEII 127
Q QV + + R + G V EYLVKWKG +TWE +E I
Sbjct: 17 QGEQVFAVESIRKKRVRKGKV--EYLVKWKGWPPKYSTWEPEEHI 59
>pdb|2EE1|A Chain A, Solution Structures Of The Chromo Domain Of Human
Chromodomain Helicase-Dna-Binding Protein 4
Length = 64
Score = 30.8 bits (68), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 25/40 (62%), Gaps = 4/40 (10%)
Query: 87 VERIIADRISKDSSGNVTQEYLVKWKGLSYAEATWEKDEI 126
+ RI+ + D G+V YL+KW+ L Y +A+WE +++
Sbjct: 14 IHRILNHSV--DKKGHV--HYLIKWRDLPYDQASWESEDV 49
>pdb|3I91|A Chain A, Crystal Structure Of Human Chromobox Homolog 8 (Cbx8) With
H3k9 Peptide
pdb|3I91|B Chain B, Crystal Structure Of Human Chromobox Homolog 8 (Cbx8) With
H3k9 Peptide
Length = 54
Score = 30.4 bits (67), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 15/24 (62%), Positives = 18/24 (75%), Gaps = 1/24 (4%)
Query: 106 EYLVKWKGLSYAEATWEKDE-IID 128
EYLVKWKG S +TWE +E I+D
Sbjct: 20 EYLVKWKGWSQKYSTWEPEENILD 43
>pdb|1YII|A Chain A, Crystal Structures Of Chicken Annexin V In Complex With
Ca2+
pdb|1YJ0|A Chain A, Crystal Structures Of Chicken Annexin V In Complex With
Zn2+
Length = 320
Score = 30.4 bits (67), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 35/75 (46%), Gaps = 10/75 (13%)
Query: 42 FKKVLNYAKKVV---EDVRFRKMVSREEIELNDVSKEMDLDIIKQNSQVERIIADRISKD 98
F + L Y+ K +D R MVSR EI+L D+ E + K Q+ I KD
Sbjct: 250 FAETLYYSMKGAGTDDDTLIRVMVSRSEIDLLDIRHEFRKNFAKSLYQM-------IQKD 302
Query: 99 SSGNVTQEYLVKWKG 113
+SG+ + L+ G
Sbjct: 303 TSGDYRKALLLLCGG 317
>pdb|1ALA|A Chain A, Structure Of Chicken Annexin V At 2.25-Angstroms
Resolution
Length = 321
Score = 30.4 bits (67), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 35/75 (46%), Gaps = 10/75 (13%)
Query: 42 FKKVLNYAKKVV---EDVRFRKMVSREEIELNDVSKEMDLDIIKQNSQVERIIADRISKD 98
F + L Y+ K +D R MVSR EI+L D+ E + K Q+ I KD
Sbjct: 251 FAETLYYSMKGAGTDDDTLIRVMVSRSEIDLLDIRHEFRKNFAKSLYQM-------IQKD 303
Query: 99 SSGNVTQEYLVKWKG 113
+SG+ + L+ G
Sbjct: 304 TSGDYRKALLLLCGG 318
>pdb|2P4W|A Chain A, Crystal Structure Of Heat Shock Regulator From Pyrococcus
Furiosus
pdb|2P4W|B Chain B, Crystal Structure Of Heat Shock Regulator From Pyrococcus
Furiosus
Length = 202
Score = 30.0 bits (66), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 24/90 (26%), Positives = 43/90 (47%), Gaps = 4/90 (4%)
Query: 330 EFSTKNKLLITGTPLQNSVEELWALLHFLDH---DKFKSKDDFIQNYKNLSSFNENELAN 386
E+ +L+ + P+ + EL LH L+ + + K + + + ++ EN +
Sbjct: 106 EYEQAKELIKSQEPINVKMRELAEFLHELNERIREIIEEKRELEEARILIETYIENTMRR 165
Query: 387 LHMELRPHILRRIIKDVEKSLPPKIERILR 416
L E R I+ I +D+EK LPP R L+
Sbjct: 166 LAEENR-QIIEEIFRDIEKILPPGYARSLK 194
>pdb|2K28|A Chain A, Solution Nmr Structure Of The Chromo Domain Of The
Chromobox Protein Homolog 4
Length = 60
Score = 30.0 bits (66), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 21/41 (51%), Positives = 23/41 (56%), Gaps = 5/41 (12%)
Query: 87 VERIIADRISKDSSGNVTQEYLVKWKGLSYAEATWEKDEII 127
VE I RI K G V EYLVKW+G S TWE +E I
Sbjct: 8 VESIEKKRIRK---GRV--EYLVKWRGWSPKYNTWEPEENI 43
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 0.134 0.394
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 39,798,217
Number of Sequences: 62578
Number of extensions: 1663204
Number of successful extensions: 4297
Number of sequences better than 100.0: 69
Number of HSP's better than 100.0 without gapping: 40
Number of HSP's successfully gapped in prelim test: 29
Number of HSP's that attempted gapping in prelim test: 4185
Number of HSP's gapped (non-prelim): 101
length of query: 1352
length of database: 14,973,337
effective HSP length: 111
effective length of query: 1241
effective length of database: 8,027,179
effective search space: 9961729139
effective search space used: 9961729139
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 58 (26.9 bits)