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= 001197
(1125 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 = 435 bits (1119), Expect = e-122, Method: Compositional matrix adjust.
Identities = 233/540 (43%), Positives = 340/540 (62%), Gaps = 37/540 (6%)
Query: 394 EKVTEQPTLLQGGELRAYQLEGLQWMLSLFNNNLNGILADEMGLGKTIQTIALIAYLLEN 453
EK++ QP ++GGELR +QL G+ WM L++ NGILADEMGLGKT+QT+A I++L+
Sbjct: 223 EKLSVQPPFIKGGELRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWLIFA 282
Query: 454 KGVTGPHVIVAPKAVLPNWINEFSTWAPSIAAVVYDGRPDERKAMRE-EFFSE---RGR- 508
+ GPH+IV P + +P W++ F WAP + + Y G R +RE EF++ +G+
Sbjct: 283 RRQNGPHIIVVPLSTMPAWLDTFEKWAPDLNCICYMGNQKSRDTIREYEFYTNPRAKGKK 342
Query: 509 ---FNVLITHYDLIMRDRQYLKKVQWIYMIVDEGHRLKNHECALAKTISGYQIQRRLLLT 565
FNVL+T Y+ I++DR L ++W +M VDE HRLKN E +L ++++ +++ R+L+T
Sbjct: 343 TMKFNVLLTTYEYILKDRAELGSIKWQFMAVDEAHRLKNAESSLYESLNSFKVANRMLIT 402
Query: 566 GTPIQNSLQELWSLLNFLLPTIFNSVENFEEWFNAPFKDRGQVALTDEEQLLIIRRLHHV 625
GTP+QN+++EL +L+NFL+P F + + F+++ DEEQ I LH
Sbjct: 403 GTPLQNNIKELAALVNFLMPGRFTIDQEID------FENQ------DEEQEEYIHDLHRR 450
Query: 626 IRPFILRRKKDEVEKYLPGKSQVILKCDMSAWQKVYYQQVTDVGRVGLDTGT-GKSKSLQ 684
I+PFILRR K +VEK LP K++ IL+ ++S Q YY+ + L G G SL
Sbjct: 451 IQPFILRRLKKDVEKSLPSKTERILRVELSDVQTEYYKNILTKNYSALTAGAKGGHFSLL 510
Query: 685 NLSMQLRKCCNHPYLF----------VGEYNMWRKE---EIIRASGKFELLDRLLPKLRK 731
N+ +L+K NHPYLF G+ M R+ +I +SGK LLD+LL +L+K
Sbjct: 511 NIMNELKKASNHPYLFDNAEERVLQKFGDGKMTRENVLRGLIMSSGKMVLLDQLLTRLKK 570
Query: 732 SGHRVLLFSQMTRLMDILEIYLKLNDFKFLRLDGSTKTEERGTLLKQFNAPDSPYFMFLL 791
GHRVL+FSQM R++DIL YL + F RLDG+ + +R + FN+PDS F+FLL
Sbjct: 571 DGHRVLIFSQMVRMLDILGDYLSIKGINFQRLDGTVPSAQRRISIDHFNSPDSNDFVFLL 630
Query: 792 STRAGGLGLNLQTADTVIIFDSDWNPQMDQQAEDRAHRIGQKKEVRVFVLVSVGSIEEVI 851
STRAGGLG+NL TADTV+IFDSDWNPQ D QA RAHRIGQK V V+ LVS ++EE +
Sbjct: 631 STRAGGLGINLMTADTVVIFDSDWNPQADLQAMARAHRIGQKNHVMVYRLVSKDTVEEEV 690
Query: 852 LERAKQKMGIDAKVIQAGLFN---TTSTAQDRREMLKEIMRRGTSSLGTDVPSEREINRL 908
LERA++KM ++ +I G+ + T + L I++ G ++ T +++++ L
Sbjct: 691 LERARKKMILEYAIISLGVTDGNKYTKKNEPNAGELSAILKFGAGNMFTATDNQKKLEDL 750
>pdb|1Z3I|X Chain X, Structure Of The Swi2SNF2 CHROMATIN REMODELING DOMAIN OF
EUKARYOTIC Rad54
Length = 644
Score = 246 bits (627), Expect = 7e-65, Method: Compositional matrix adjust.
Identities = 159/494 (32%), Positives = 259/494 (52%), Gaps = 35/494 (7%)
Query: 408 LRAYQLEGLQWMLSLFN-----NNLNGILADEMGLGKTIQTIALIAYLLENKGVTGPHV- 461
LR +Q EG++++ N+ I+ADEMGLGKT+Q I LI LL+ P +
Sbjct: 56 LRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLIWTLLKQSPDCKPEID 115
Query: 462 ---IVAPKAVLPNWINEFSTW-APSIAAVVYDG-RPDERKAMREEFFSERGR---FNVLI 513
+V+P +++ NW NE W + V DG DE + F S++G +LI
Sbjct: 116 KVIVVSPSSLVRNWYNEVGKWLGGRVQPVAIDGGSKDEIDSKLVNFISQQGMRIPTPILI 175
Query: 514 THYDLIMRDRQYLKKVQWIYMIVDEGHRLKNHECALAKTISGYQIQRRLLLTGTPIQNSL 573
Y+ + L K + +I DEGHRLKN + ++ QRR+L++GTPIQN L
Sbjct: 176 ISYETFRLHAEVLHKGKVGLVICDEGHRLKNSDNQTYLALNSMNAQRRVLISGTPIQNDL 235
Query: 574 QELWSLLNFLLPTIFNSVENFEEWFNAPFKDRGQVALTDEEQLL---IIRRLHHVIRPFI 630
E +SL++F+ I + + F++ F P +D+++ ++ L ++ +
Sbjct: 236 LEYFSLVHFVNSGILGTAQEFKKRFEIPILKGRDADASDKDRAAGEQKLQELISIVNRCL 295
Query: 631 LRRKKDEVEKYLPGKSQVILKCDMSAWQKVYYQQVTDVGRVGLDTGTGKSKSLQNLSMQL 690
+RR D + KYLP K + ++ C+++ QK Y+ + TGK S+
Sbjct: 296 IRRTSDILSKYLPVKIEQVVCCNLTPLQKELYKLFLKQAKPVESLQTGKISVSSLSSITS 355
Query: 691 -RKCCNHPYL-----------FVGEYNMWRKEEIIRA-----SGKFELLDRLLPKLRKS- 732
+K CNHP L F G +++ + +A SGK +LD +L R +
Sbjct: 356 LKKLCNHPALIYEKCLTGEEGFDGALDLFPQNYSTKAVEPQLSGKMLVLDYILAMTRTTT 415
Query: 733 GHRVLLFSQMTRLMDILEIYLKLNDFKFLRLDGSTKTEERGTLLKQFNAPDSPYFMFLLS 792
+V+L S T+ +D+ E + + ++RLDG+ ++R ++++FN P SP F+F+LS
Sbjct: 416 SDKVVLVSNYTQTLDLFEKLCRNRRYLYVRLDGTMSIKKRAKIVERFNNPSSPEFIFMLS 475
Query: 793 TRAGGLGLNLQTADTVIIFDSDWNPQMDQQAEDRAHRIGQKKEVRVFVLVSVGSIEEVIL 852
++AGG GLNL A+ +++FD DWNP D+QA R R GQKK ++ L+S G+IEE IL
Sbjct: 476 SKAGGCGLNLIGANRLVMFDPDWNPANDEQAMARVWRDGQKKTCYIYRLLSTGTIEEKIL 535
Query: 853 ERAKQKMGIDAKVI 866
+R K + + V+
Sbjct: 536 QRQAHKKALSSCVV 549
>pdb|1Z6A|A Chain A, Sulfolobus Solfataricus Swi2SNF2 ATPASE CORE DOMAIN
Length = 500
Score = 224 bits (572), Expect = 1e-58, Method: Compositional matrix adjust.
Identities = 151/471 (32%), Positives = 252/471 (53%), Gaps = 36/471 (7%)
Query: 406 GELRAYQLEGLQWMLSLFNNNLNGILADEMGLGKTIQTIALIAYLLENKGVTGPHVIVAP 465
LR YQ++G WM + LAD+MGLGKT+QTIA+ + + +T P +++ P
Sbjct: 36 ANLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAVFSDAKKENELT-PSLVICP 94
Query: 466 KAVLPNWINEFSTWAPSIAAVVYDGRPDERKAMREEFFSERGRFNVLITHYDLIMRDRQY 525
+VL NW E S +AP + V+ ++R ++ E +++++T Y +++RD +
Sbjct: 95 LSVLKNWEEELSKFAPHLRFAVFH---EDRSKIKLE------DYDIILTTYAVLLRDTR- 144
Query: 526 LKKVQWIYMIVDEGHRLKNHECALAKTISGYQIQRRLLLTGTPIQNSLQELWSLLNFLLP 585
LK+V+W Y+++DE +KN + + K + + + R+ LTGTPI+N + +LWS++ FL P
Sbjct: 145 LKEVEWKYIVIDEAQNIKNPQTKIFKAVKELKSKYRIALTGTPIENKVDDLWSIMTFLNP 204
Query: 586 TIFNSVENFEEWFNAPFKDRGQVALTDEEQLLIIRRLHHVIRPFILRRKKDE--VEKYLP 643
+ S F+ F P K +A EE L +I PFILRR K + + LP
Sbjct: 205 GLLGSYSEFKSKFATPIKKGDNMA--KEE-------LKAIISPFILRRTKYDKAIINDLP 255
Query: 644 GKSQVILKCDMSAWQKVYYQQVTDVGRVGLDTGTGKSKSLQNLS--MQLRKCCNHPYLFV 701
K + + C+++ Q Y+ + +D+ TG + LS ++L++ +HP L
Sbjct: 256 DKIETNVYCNLTPEQAAMYKAEVENLFNNIDSVTGIKRKGMILSTLLKLKQIVDHPALLK 315
Query: 702 GEYNMWRKEEIIRASGKFELLDRLLPKLRKSGHRVLLFSQMTRLMDILE--IYLKLN-DF 758
G E+ +R SGK ++ + G ++ +F+Q + I+ I +LN +
Sbjct: 316 G------GEQSVRRSGKMIRTMEIIEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEV 369
Query: 759 KFLRLDGSTKTEERGTLLKQFNAPDSPYFMFLLSTRAGGLGLNLQTADTVIIFDSDWNPQ 818
FL G +ER ++ +F S F+ +LS +AGG G+NL +A+ VI FD WNP
Sbjct: 370 PFLY--GELSKKERDDIISKFQNNPSVKFI-VLSVKAGGFGINLTSANRVIHFDRWWNPA 426
Query: 819 MDQQAEDRAHRIGQKKEVRVFVLVSVGSIEEVILERAKQKMGIDAKVIQAG 869
++ QA DR +RIGQ + V V L+SVG++EE I + K + +I +G
Sbjct: 427 VEDQATDRVYRIGQTRNVIVHKLISVGTLEEKIDQLLAFKRSLFKDIISSG 477
>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 = 217 bits (553), Expect = 3e-56, Method: Compositional matrix adjust.
Identities = 153/473 (32%), Positives = 252/473 (53%), Gaps = 40/473 (8%)
Query: 406 GELRAYQLEGLQWMLSLFNNNLN-GI-LADEMGLGKTIQTIALIAYLLENKGVTGPHVIV 463
LR YQ++G W F N L GI LAD+ GLGKT+QTIA+ + + +T P +++
Sbjct: 36 ANLRPYQIKGFSW--XRFXNKLGFGICLADDXGLGKTLQTIAVFSDAKKENELT-PSLVI 92
Query: 464 APKAVLPNWINEFSTWAPSIAAVVYDGRPDERKAMREEFFSERGRFNVLITHYDLIMRDR 523
P +VL NW E S +AP + V+ ++R ++ E +++++T Y +++RD
Sbjct: 93 CPLSVLKNWEEELSKFAPHLRFAVFH---EDRSKIKLE------DYDIILTTYAVLLRDT 143
Query: 524 QYLKKVQWIYMIVDEGHRLKNHECALAKTISGYQIQRRLLLTGTPIQNSLQELWSLLNFL 583
+ LK+V+W Y+++DE +KN + + K + + + R+ LTGTPI+N + +LWS+ FL
Sbjct: 144 R-LKEVEWKYIVIDEAQNIKNPQTKIFKAVKELKSKYRIALTGTPIENKVDDLWSIXTFL 202
Query: 584 LPTIFNSVENFEEWFNAPFKDRGQVALTDEEQLLIIRRLHHVIRPFILRRKKDE--VEKY 641
P + S F+ F P K +G +E L +I PFILRR K + +
Sbjct: 203 NPGLLGSYSEFKSKFATPIK-KGDNXAKEE--------LKAIISPFILRRTKYDKAIIND 253
Query: 642 LPGKSQVILKCDMSAWQKVYYQQVTDVGRVGLDTGTGKSKSLQNLS--MQLRKCCNHPYL 699
LP K + + C+++ Q Y+ + +D+ TG + LS ++L++ +HP L
Sbjct: 254 LPDKIETNVYCNLTPEQAAXYKAEVENLFNNIDSVTGIKRKGXILSTLLKLKQIVDHPAL 313
Query: 700 FVGEYNMWRKEEIIRASGKFELLDRLLPKLRKSGHRVLLFSQMTRLMDILE--IYLKLN- 756
G E+ +R SGK ++ + G ++ +F+Q I+ I +LN
Sbjct: 314 LKG------GEQSVRRSGKXIRTXEIIEEALDEGDKIAIFTQFVDXGKIIRNIIEKELNT 367
Query: 757 DFKFLRLDGSTKTEERGTLLKQFNAPDSPYFMFLLSTRAGGLGLNLQTADTVIIFDSDWN 816
+ FL G +ER ++ +F S F+ +LS +AGG G+NL +A+ VI FD WN
Sbjct: 368 EVPFLY--GELSKKERDDIISKFQNNPSVKFI-VLSVKAGGFGINLTSANRVIHFDRWWN 424
Query: 817 PQMDQQAEDRAHRIGQKKEVRVFVLVSVGSIEEVILERAKQKMGIDAKVIQAG 869
P ++ QA DR +RIGQ + V V L+SVG++EE I + K + +I +G
Sbjct: 425 PAVEDQATDRVYRIGQTRNVIVHKLISVGTLEEKIDQLLAFKRSLFKDIISSG 477
>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 = 97.4 bits (241), Expect = 4e-20, Method: Compositional matrix adjust.
Identities = 72/233 (30%), Positives = 121/233 (51%), Gaps = 14/233 (6%)
Query: 642 LPGKSQVILKCDMSAWQKVYYQQVTDVGRVGLDTGTGKSKSLQNLS--MQLRKCCNHPYL 699
LP K + + C+++ Q Y+ + +D+ TG + LS ++L++ +HP L
Sbjct: 25 LPDKIETNVYCNLTPEQAAMYKAEVENLFNNIDSVTGIKRKGMILSTLLKLKQIVDHPAL 84
Query: 700 FVGEYNMWRKEEIIRASGKFELLDRLLPKLRKSGHRVLLFSQMTRLMDILE--IYLKLN- 756
G E+ +R SGK ++ + G ++ +F+Q + I+ I +LN
Sbjct: 85 LKG------GEQSVRRSGKMIRTMEIIEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNT 138
Query: 757 DFKFLRLDGSTKTEERGTLLKQFNAPDSPYFMFLLSTRAGGLGLNLQTADTVIIFDSDWN 816
+ FL G +ER ++ +F S F+ +LS +AGG G+NL +A+ VI FD WN
Sbjct: 139 EVPFLY--GELSKKERDDIISKFQNNPSVKFI-VLSVKAGGFGINLTSANRVIHFDRWWN 195
Query: 817 PQMDQQAEDRAHRIGQKKEVRVFVLVSVGSIEEVILERAKQKMGIDAKVIQAG 869
P ++ QA DR +RIGQ + V V L+SVG++EE I + K + +I +G
Sbjct: 196 PAVEDQATDRVYRIGQTRNVIVHKLISVGTLEEKIDQLLAFKRSLFKDIISSG 248
>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 = 47.8 bits (112), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 50/181 (27%), Positives = 83/181 (45%), Gaps = 24/181 (13%)
Query: 430 ILADEMGLGKTIQTIALIAYLLENKGVTGPHVIVAPKAVLPNWINEFSTWAPSIAAVVYD 489
+LADE+GLGKTI+ ++ L + G +I+ P+ + W+ E ++ ++D
Sbjct: 174 LLADEVGLGKTIEAGXILHQQLLS-GAAERVLIIVPETLQHQWLVE-XLRRFNLRFALFD 231
Query: 490 GRPDERKA-MREEFFSERGRFNVLITHYDLIMRDRQ---YLKKVQWIYMIVDEGHRLKNH 545
DER A + + ++ ++I D R +Q +L + +W ++VDE H L
Sbjct: 232 ---DERYAEAQHDAYNPFDTEQLVICSLDFARRSKQRLEHLCEAEWDLLVVDEAHHLVWS 288
Query: 546 ECA----------LAKTISGYQIQRRLLLTGTPIQNSLQELWSLLNFLLPTIFNSVENFE 595
E A LA+ + G LLLT TP Q + ++ L L P F+ F
Sbjct: 289 EDAPSREYQAIEQLAEHVPGV-----LLLTATPEQLGXESHFARLRLLDPNRFHDFAQFV 343
Query: 596 E 596
E
Sbjct: 344 E 344
Score = 36.2 bits (82), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 27/51 (52%)
Query: 790 LLSTRAGGLGLNLQTADTVIIFDSDWNPQMDQQAEDRAHRIGQKKEVRVFV 840
LL + G G N Q A + FD +NP + +Q R RIGQ ++++ V
Sbjct: 560 LLCSEIGSEGRNFQFASHXVXFDLPFNPDLLEQRIGRLDRIGQAHDIQIHV 610
>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 = 36.6 bits (83), Expect = 0.085, Method: Composition-based stats.
Identities = 29/108 (26%), Positives = 49/108 (45%), Gaps = 9/108 (8%)
Query: 725 LLPKLRKSGHRVLLFSQMTRLMDILEIYLKLNDFKFLRLDGSTKTEERGTLLKQFNAPDS 784
LL L+K+ VL+F++ +D + YL L + + + G EER ++ F
Sbjct: 46 LLECLQKTPPPVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKK 105
Query: 785 PYFMFLLSTRAGGLGLNLQTADTVIIFDSDWNPQMDQQAEDRAHRIGQ 832
L++T GL+ VI +D M ++ E+ HRIG+
Sbjct: 106 D---VLVATDVASKGLDFPAIQHVINYD------MPEEIENYVHRIGR 144
>pdb|1JCU|A Chain A, Solution Structure Of Mth1692 Protein From
Methanobacterium Thermoautotrophicum
Length = 208
Score = 30.0 bits (66), Expect = 6.7, Method: Composition-based stats.
Identities = 21/93 (22%), Positives = 46/93 (49%), Gaps = 3/93 (3%)
Query: 819 MDQQAEDRAHRIGQKKEVRVFVLVSVGSIEEVILERAKQKMGIDAKVIQAGLFNTTSTAQ 878
+D+ A R R+ + + V + V ++E+ R + G ++++ L +
Sbjct: 44 LDEDAVRRLFRVKGRSPHKP-VSICVSCVDEI--PRFSRPSGDAMELMERILPGPYTVVL 100
Query: 879 DRREMLKEIMRRGTSSLGTDVPSEREINRLAAR 911
+R E++ +++ G+S +G VP + R+AAR
Sbjct: 101 ERNELIPDVITGGSSRVGIRVPDDEICRRIAAR 133
>pdb|3HGT|A Chain A, Structural And Functional Studies Of The Yeast Class Ii
Hda1 Hdac Complex
pdb|3HGT|B Chain B, Structural And Functional Studies Of The Yeast Class Ii
Hda1 Hdac Complex
Length = 328
Score = 30.0 bits (66), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 25/93 (26%), Positives = 39/93 (41%), Gaps = 10/93 (10%)
Query: 681 KSLQNLSMQLRKCCNHPYLFVGEYNMWRKEEIIR--------ASGKFELLDRLLPKLRKS 732
+S++ + + HPYL + Y K I R SGKF +L L+ +++
Sbjct: 67 ESMKTMCLNGSLVATHPYLLIDHY--MPKSLITRDVPAHLAENSGKFSVLRDLINLVQEY 124
Query: 733 GHRVLLFSQMTRLMDILEIYLKLNDFKFLRLDG 765
+ + R MD+LE L N R DG
Sbjct: 125 ETETAIVCRPGRTMDLLEALLLGNKVHIKRYDG 157
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
0.317 0.133 0.386
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 29,945,500
Number of Sequences: 62578
Number of extensions: 1177174
Number of successful extensions: 2685
Number of sequences better than 100.0: 29
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 22
Number of HSP's that attempted gapping in prelim test: 2642
Number of HSP's gapped (non-prelim): 32
length of query: 1125
length of database: 14,973,337
effective HSP length: 109
effective length of query: 1016
effective length of database: 8,152,335
effective search space: 8282772360
effective search space used: 8282772360
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: 57 (26.6 bits)