RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy10684
(288 letters)
>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double
chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces
cerevisiae}
Length = 800
Score = 312 bits (802), Expect = e-101
Identities = 97/214 (45%), Positives = 120/214 (56%), Gaps = 31/214 (14%)
Query: 2 VLMKDIDVVNGAGKLEKMRLQNILMQLRKCSNHPYLFDGAEP------GPPYTTDEH--- 52
+L K+ + K L NI+ +L+K SNHPYLFD AE G T E+
Sbjct: 490 ILTKNYSALTAGAKGGHFSLLNIMNELKKASNHPYLFDNAEERVLQKFGDGKMTRENVLR 549
Query: 53 -LVFNSGKMVVLDKLLPKLKAQESRVLIFSQMTRMLDILEDYCYWRGFKYCRLDGQTAHE 111
L+ +SGKMV+LD+LL +LK RVLIFSQM RMLDIL DY +G + RLDG
Sbjct: 550 GLIMSSGKMVLLDQLLTRLKKDGHRVLIFSQMVRMLDILGDYLSIKGINFQRLDGTVPSA 609
Query: 112 DRQRQINDFNMEGSDIFIFMLSTRAGGLGINLATADVVVLYDSDWNPQMDLQAMVR---- 167
R+ I+ FN S+ F+F+LSTRAGGLGINL TAD VV++DSDWNPQ DLQAM R
Sbjct: 610 QRRISIDHFNSPDSNDFVFLLSTRAGGLGINLMTADTVVIFDSDWNPQADLQAMARAHRI 669
Query: 168 -----------------EAKILRRGSIKKALEAK 184
E ++L R K LE
Sbjct: 670 GQKNHVMVYRLVSKDTVEEEVLERARKKMILEYA 703
Score = 144 bits (366), Expect = 3e-39
Identities = 41/71 (57%), Positives = 49/71 (69%)
Query: 213 RYLYCRLDGQTAHEDRQRQINDFNMEGSDIFIFMLSTRAGGLGINLATADVVVLYDSDWN 272
+ RLDG R+ I+ FN S+ F+F+LSTRAGGLGINL TAD VV++DSDWN
Sbjct: 596 GINFQRLDGTVPSAQRRISIDHFNSPDSNDFVFLLSTRAGGLGINLMTADTVVIFDSDWN 655
Query: 273 PQMDLQAMVRT 283
PQ DLQAM R
Sbjct: 656 PQADLQAMARA 666
>1z3i_X Similar to RAD54-like; recombination ATPase helicase,
recombination-DNA binding COM; 3.00A {Danio rerio} SCOP:
c.37.1.19 c.37.1.19
Length = 644
Score = 289 bits (741), Expect = 9e-94
Identities = 74/218 (33%), Positives = 104/218 (47%), Gaps = 35/218 (16%)
Query: 2 VLMKDIDVVNGAGKLEKMRLQNILMQLRKCSNHPYL-----------FDGAEPGPP--YT 48
L + V + + + + L+K NHP L FDGA P Y+
Sbjct: 330 FLKQAKPVESLQTGKISVSSLSSITSLKKLCNHPALIYEKCLTGEEGFDGALDLFPQNYS 389
Query: 49 TDEHLVFNSGKMVVLDKLLPKLKAQES-RVLIFSQMTRMLDILEDYCYWRGFKYCRLDGQ 107
T SGKM+VLD +L + S +V++ S T+ LD+ E C R + Y RLDG
Sbjct: 390 TKAVEPQLSGKMLVLDYILAMTRTTTSDKVVLVSNYTQTLDLFEKLCRNRRYLYVRLDGT 449
Query: 108 TAHEDRQRQINDFNMEGSDIFIFMLSTRAGGLGINLATADVVVLYDSDWNPQMDLQAMVR 167
+ + R + + FN S FIFMLS++AGG G+NL A+ +V++D DWNP D QAM R
Sbjct: 450 MSIKKRAKIVERFNNPSSPEFIFMLSSKAGGCGLNLIGANRLVMFDPDWNPANDEQAMAR 509
Query: 168 ---------------------EAKILRRGSIKKALEAK 184
E KIL+R + KKAL +
Sbjct: 510 VWRDGQKKTCYIYRLLSTGTIEEKILQRQAHKKALSSC 547
Score = 145 bits (369), Expect = 7e-40
Identities = 36/70 (51%), Positives = 47/70 (67%)
Query: 213 RYLYCRLDGQTAHEDRQRQINDFNMEGSDIFIFMLSTRAGGLGINLATADVVVLYDSDWN 272
RYLY RLDG + + R + + FN S FIFMLS++AGG G+NL A+ +V++D DWN
Sbjct: 440 RYLYVRLDGTMSIKKRAKIVERFNNPSSPEFIFMLSSKAGGCGLNLIGANRLVMFDPDWN 499
Query: 273 PQMDLQAMVR 282
P D QAM R
Sbjct: 500 PANDEQAMAR 509
>3hgt_A HDA1 complex subunit 3; RECA-like domain, SWI2/SNF2 helical domain,
chromatin regulator, coiled coil, nucleus, repressor,
transcription; 2.20A {Saccharomyces cerevisiae} PDB:
3hgq_A
Length = 328
Score = 193 bits (491), Expect = 4e-60
Identities = 32/177 (18%), Positives = 65/177 (36%), Gaps = 11/177 (6%)
Query: 3 LMKDIDVVNGAGKLEKMRLQNILMQLRKCSNHPYLF-DGAEPGPPYTTD--EHLVFNSGK 59
+++ + + + ++ + + + HPYL D P T D HL NSGK
Sbjct: 51 ILRYFETSHYKEDVILESMKTMCLNGSLVATHPYLLIDHYMPKSLITRDVPAHLAENSGK 110
Query: 60 MVVLDKLLPKLKAQESRVLIFSQMTRMLDILEDYCYWRGFKYCRLDGQTAHEDRQRQIND 119
VL L+ ++ E+ I + R +D+LE R DG +
Sbjct: 111 FSVLRDLINLVQEYETETAIVCRPGRTMDLLEALLLGNKVHIKRYDGHSIKSAAAANDFS 170
Query: 120 --FNMEGSDIFIFMLSTRAGGLGINLATADVVVLYDSDWNPQM-DLQAMVREAKILR 173
++ S+ F D+++ D+ + D+Q +++ + +
Sbjct: 171 CTVHLFSSEGINFTKYPIKSKAR-----FDMLICLDTTVDTSQKDIQYLLQYKRERK 222
Score = 66.9 bits (163), Expect = 7e-13
Identities = 9/73 (12%), Positives = 23/73 (31%), Gaps = 8/73 (10%)
Query: 213 RYLYCRLDGQTAHEDRQRQIND--FNMEGSDIFIFMLSTRAGGLGINLATADVVVLYDSD 270
+ R DG + ++ S+ F D+++ D+
Sbjct: 149 KVHIKRYDGHSIKSAAAANDFSCTVHLFSSEGINFTKYPIKSKAR-----FDMLICLDTT 203
Query: 271 WNPQM-DLQAMVR 282
+ D+Q +++
Sbjct: 204 VDTSQKDIQYLLQ 216
>1z5z_A Helicase of the SNF2/RAD54 family; hydrolase, recombination,
hydrolase-recombination complex; 2.00A {Sulfolobus
solfataricus} SCOP: c.37.1.19
Length = 271
Score = 123 bits (312), Expect = 4e-34
Identities = 38/141 (26%), Positives = 69/141 (48%), Gaps = 11/141 (7%)
Query: 25 LMQLRKCSNHPYLFDGAEPGPPYTTDEHLVFNSGKMVVLDKLLPKLKAQESRVLIFSQMT 84
L++L++ +HP L G E SGKM+ +++ + + ++ IF+Q
Sbjct: 72 LLKLKQIVDHPALLKGGEQSVR---------RSGKMIRTMEIIEEALDEGDKIAIFTQFV 122
Query: 85 RMLDILEDYCYWR-GFKYCRLDGQTAHEDRQRQINDFNMEGSDIFIFMLSTRAGGLGINL 143
M I+ + + L G+ + ++R I+ F + +LS +AGG GINL
Sbjct: 123 DMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQ-NNPSVKFIVLSVKAGGFGINL 181
Query: 144 ATADVVVLYDSDWNPQMDLQA 164
+A+ V+ +D WNP ++ QA
Sbjct: 182 TSANRVIHFDRWWNPAVEDQA 202
Score = 71.9 bits (177), Expect = 8e-15
Identities = 25/75 (33%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 205 KNYTEEEDRYLYCRLDGQTAHEDRQRQINDFNMEGSDIFIFMLSTRAGGLGINLATADVV 264
+N E+E L G+ + ++R I+ F + +LS +AGG GINL +A+ V
Sbjct: 129 RNIIEKELNTEVPFLYGELSKKERDDIISKFQ-NNPSVKFIVLSVKAGGFGINLTSANRV 187
Query: 265 VLYDSDWNPQMDLQA 279
+ +D WNP ++ QA
Sbjct: 188 IHFDRWWNPAVEDQA 202
>1z63_A Helicase of the SNF2/RAD54 hamily; protein-DNA complex,
hydrolase/DNA complex complex; 3.00A {Sulfolobus
solfataricus} SCOP: c.37.1.19 c.37.1.19 PDB: 1z6a_A
Length = 500
Score = 126 bits (318), Expect = 3e-33
Identities = 38/141 (26%), Positives = 69/141 (48%), Gaps = 11/141 (7%)
Query: 25 LMQLRKCSNHPYLFDGAEPGPPYTTDEHLVFNSGKMVVLDKLLPKLKAQESRVLIFSQMT 84
L++L++ +HP L G E SGKM+ +++ + + ++ IF+Q
Sbjct: 301 LLKLKQIVDHPALLKGGEQSVR---------RSGKMIRTMEIIEEALDEGDKIAIFTQFV 351
Query: 85 RMLDILEDYCYWR-GFKYCRLDGQTAHEDRQRQINDFNMEGSDIFIFMLSTRAGGLGINL 143
M I+ + + L G+ + ++R I+ F + +LS +AGG GINL
Sbjct: 352 DMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQ-NNPSVKFIVLSVKAGGFGINL 410
Query: 144 ATADVVVLYDSDWNPQMDLQA 164
+A+ V+ +D WNP ++ QA
Sbjct: 411 TSANRVIHFDRWWNPAVEDQA 431
Score = 72.2 bits (178), Expect = 2e-14
Identities = 25/75 (33%), Positives = 40/75 (53%), Gaps = 1/75 (1%)
Query: 209 EEEDRYLYCRLDGQTAHEDRQRQINDFNMEGSDIFIFMLSTRAGGLGINLATADVVVLYD 268
E+E L G+ + ++R I+ F + +LS +AGG GINL +A+ V+ +D
Sbjct: 362 EKELNTEVPFLYGELSKKERDDIISKFQ-NNPSVKFIVLSVKAGGFGINLTSANRVIHFD 420
Query: 269 SDWNPQMDLQAMVRT 283
WNP ++ QA R
Sbjct: 421 RWWNPAVEDQATDRV 435
>3dmq_A RNA polymerase-associated protein RAPA; SWF2/SNF2, transcription
factor, RNA polymerase recycling, activator,
ATP-binding, DNA-binding; 3.20A {Escherichia coli K12}
Length = 968
Score = 97.1 bits (241), Expect = 8e-23
Identities = 24/112 (21%), Positives = 42/112 (37%), Gaps = 4/112 (3%)
Query: 57 SGKMVVLDKLLPKLKAQESRVLIFSQMTRMLDILEDYCYWR-GFKYCRLDGQTAHEDRQR 115
++ L L ++Q +VL+ LE R G + + +R R
Sbjct: 488 DPRVEWLMGYLTSHRSQ--KVLVICAKAATALQLEQVLREREGIRAAVFHEGMSIIERDR 545
Query: 116 QINDFNMEGSDIFIFMLSTRAGGLGINLATADVVVLYDSDWNPQMDLQAMVR 167
F E + +L + G G N A +V++D +NP + Q + R
Sbjct: 546 AAAWFAEEDTGAQ-VLLCSEIGSEGRNFQFASHMVMFDLPFNPDLLEQRIGR 596
Score = 68.6 bits (167), Expect = 4e-13
Identities = 15/67 (22%), Positives = 26/67 (38%), Gaps = 1/67 (1%)
Query: 216 YCRLDGQTAHEDRQRQINDFNMEGSDIFIFMLSTRAGGLGINLATADVVVLYDSDWNPQM 275
+ +R R F E + +L + G G N A +V++D +NP +
Sbjct: 531 AAVFHEGMSIIERDRAAAWFAEEDTGAQ-VLLCSEIGSEGRNFQFASHMVMFDLPFNPDL 589
Query: 276 DLQAMVR 282
Q + R
Sbjct: 590 LEQRIGR 596
>1ofc_X ISWI protein; nuclear protein, chromatin remodeling factor, ATPase,
SANT domain, nucleosome recognition; HET: GLC G4D; 1.9A
{Drosophila melanogaster} SCOP: a.4.1.3 a.4.1.13
a.187.1.1 PDB: 2nog_A
Length = 304
Score = 74.3 bits (182), Expect = 2e-15
Identities = 40/53 (75%), Positives = 43/53 (81%)
Query: 168 EAKILRRGSIKKALEAKMSRYRAPFHQLRIAYGANKGKNYTEEEDRYLYCRLD 220
E KI RR SIKKAL+ KMSRYRAPFHQLR+ YG NKGKNYTE EDR+L C L
Sbjct: 176 EGKIQRRLSIKKALDQKMSRYRAPFHQLRLQYGNNKGKNYTEIEDRFLVCMLH 228
>2y9y_A Imitation switch protein 1 (DEL_ATPase); transcription, nuclear
protein complex, chromatin remodeling nucleosome
remodeling; 3.25A {Saccharomyces cerevisiae} PDB: 2y9z_A
Length = 374
Score = 65.2 bits (158), Expect = 3e-12
Identities = 20/55 (36%), Positives = 32/55 (58%), Gaps = 2/55 (3%)
Query: 168 EAKILRRGSIKKALEAKMSRYRAPFHQLRIAY--GANKGKNYTEEEDRYLYCRLD 220
E KI R ++AL K+S Y+ PF L++ + +N + Y+EEEDR++ L
Sbjct: 190 EEKIKRVKMQQEALRRKLSEYKNPFFDLKLKHPPSSNNKRTYSEEEDRFILLMLF 244
>1wp9_A ATP-dependent RNA helicase, putative; ATPase, DNA replication, DNA
repair, DNA recombina hydrolase; 2.90A {Pyrococcus
furiosus} SCOP: c.37.1.19 c.37.1.19
Length = 494
Score = 50.2 bits (119), Expect = 3e-07
Identities = 21/121 (17%), Positives = 51/121 (42%), Gaps = 13/121 (10%)
Query: 59 KMVVLDKLLPKL--KAQESRVLIFSQMTRMLDILEDYCYWRGFKYCRLDGQTA------- 109
KM L +++ + + Q S++++F+ + + G K R GQ +
Sbjct: 344 KMDKLKEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGL 403
Query: 110 -HEDRQRQINDFNMEGSDIFIFMLSTRAGGLGINLATADVVVLYDSDWNPQMDLQAMVRE 168
+++ +++F ++ + +T G G+++ D+VV Y+ + +Q R
Sbjct: 404 SQREQKLILDEFARGEFNVLV---ATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRT 460
Query: 169 A 169
Sbjct: 461 G 461
Score = 39.4 bits (91), Expect = 0.001
Identities = 11/59 (18%), Positives = 28/59 (47%), Gaps = 3/59 (5%)
Query: 225 HEDRQRQINDFNMEGSDIFIFMLSTRAGGLGINLATADVVVLYDSDWNPQMDLQAMVRT 283
+++ +++F ++ + +T G G+++ D+VV Y+ + +Q RT
Sbjct: 405 QREQKLILDEFARGEFNVLV---ATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRT 460
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 43.5 bits (102), Expect = 7e-05
Identities = 42/248 (16%), Positives = 67/248 (27%), Gaps = 92/248 (37%)
Query: 82 QMTRMLDILEDYCYWRGFKYCRLDGQTAHEDRQRQINDFNM---EGSDIFIFMLSTRAGG 138
+ ML I ++ Q +N N G + I
Sbjct: 334 VPSPMLSI-------SNLTQEQV---------QDYVNKTNSHLPAGKQVEI--------S 369
Query: 139 LGINLATADVVVLYDSDWNPQMDLQAMVREAKILRRGSIKKALE---AKMS--------R 187
L +N A VV P L + LR+ L+ S R
Sbjct: 370 L-VNGAKNLVVS------GPPQSLYGLNLT---LRKAKAPSGLDQSRIPFSERKLKFSNR 419
Query: 188 Y---RAPFH-------------------------QLRIA-YGANKGKNYTEEED----RY 214
+ +PFH ++I Y G + R
Sbjct: 420 FLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERI 479
Query: 215 LYC----RLDGQTAHEDRQRQINDFNMEGSDIFIFMLSTR-AGGLGINLATADVVVLYDS 269
+ C + +T + + I DF G + +L+ R G G+ + A +
Sbjct: 480 VDCIIRLPVKWETTTQFKATHILDFG-PGGASGLGVLTHRNKDGTGVRVIVAGTL----- 533
Query: 270 DWNPQMDL 277
D NP D
Sbjct: 534 DINPDDDY 541
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 42.1 bits (98), Expect = 1e-04
Identities = 32/204 (15%), Positives = 58/204 (28%), Gaps = 48/204 (23%)
Query: 19 MRLQNILMQLRKCSNHPYLFDGAEPGPPYTTDEHLVFNSGKMVVLDKLLPKLKAQESRVL 78
LQ +L Q+ N D + ++A+ R+L
Sbjct: 200 EMLQKLLYQIDP--NWTSRSDHSSN-IKLRIHS------------------IQAELRRLL 238
Query: 79 IFSQMTRMLDILEDYCY---WRGFKY-CRL----------DGQTAHEDRQRQINDFNM-- 122
L +L + W F C++ D +A ++ +M
Sbjct: 239 KSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTL 298
Query: 123 ---EGSDIFIFMLSTRAGGL-----GINLATADVVVLYDSDWNPQMDLQAMVREAKILRR 174
E + + L R L N ++ D D V K+
Sbjct: 299 TPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTT- 357
Query: 175 GSIKKALEA-KMSRYRAPFHQLRI 197
I+ +L + + YR F +L +
Sbjct: 358 -IIESSLNVLEPAEYRKMFDRLSV 380
Score = 37.5 bits (86), Expect = 0.005
Identities = 38/224 (16%), Positives = 67/224 (29%), Gaps = 63/224 (28%)
Query: 17 EKMRLQNILMQLRKCSNHPYLF-DGAEPGPPYTTDEHLVFNSGK-----MVVLDKLLPKL 70
++L+ L++LR + DG G SGK V L +
Sbjct: 136 PYLKLRQALLELRP---AKNVLIDGV-LG------------SGKTWVALDVCLSYKV--Q 177
Query: 71 KAQESRV--LIFSQMTR---MLDILEDYCYWRGFKYC-RLDGQTAHEDRQRQINDFNMEG 124
+ ++ L +L++L+ Y + R D + + R I+ E
Sbjct: 178 CKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLR---IHSIQAEL 234
Query: 125 SDIFIFMLSTRAGGLGINLATADVVVLYDSDWNPQMDLQAMVREAKIL---RRGSIKKAL 181
+ ++VL + N + A KIL R + L
Sbjct: 235 RRLLKSKPYENC-----------LLVL-LNVQNAK-AWNAFNLSCKILLTTRFKQVTDFL 281
Query: 182 EAKMSRYRAPFHQLRIAYGANKGKNYTEEED-----RYLYCRLD 220
A + + + H T +E +YL CR
Sbjct: 282 SAATTTHISLDHHS---------MTLTPDEVKSLLLKYLDCRPQ 316
>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics,
structural genomic consortium, SGC, hydrolase; 2.60A
{Homo sapiens}
Length = 191
Score = 39.1 bits (92), Expect = 5e-04
Identities = 15/57 (26%), Positives = 26/57 (45%)
Query: 64 DKLLPKLKAQESRVLIFSQMTRMLDILEDYCYWRGFKYCRLDGQTAHEDRQRQINDF 120
LL L+ VLIF++ +D + +Y +G + + G E+R + I F
Sbjct: 44 VYLLECLQKTPPPVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAF 100
>2jgn_A DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosphorylation,
nucleotide-binding, hydrolase, RNA-binding, ATP-binding,
DNA-binding, nuclear protein; 1.91A {Homo sapiens}
Length = 185
Score = 36.4 bits (85), Expect = 0.004
Identities = 17/62 (27%), Positives = 29/62 (46%), Gaps = 1/62 (1%)
Query: 59 KMVVLDKLLPKLKAQESRVLIFSQMTRMLDILEDYCYWRGFKYCRLDGQTAHEDRQRQIN 118
K L LL ++S L+F + + D LED+ Y G+ + G + DR+ ++
Sbjct: 32 KRSFLLDLLNAT-GKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALH 90
Query: 119 DF 120
F
Sbjct: 91 QF 92
>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant
helicase, T4-bacteriophage, recombination, hydrolase;
2.70A {Enterobacteria phage T4}
Length = 510
Score = 37.6 bits (86), Expect = 0.004
Identities = 26/148 (17%), Positives = 47/148 (31%), Gaps = 6/148 (4%)
Query: 33 NHPYLFDGAEPGPPYTTD-EHLVFNSGKMVVLDKLLPKLKAQESRVLIFSQMTRMLDILE 91
+P F G Y + + + S + + KL KL ++ + + +
Sbjct: 305 RYPDEFTTKLKGKTYQEEIKIITGLSKRNKWIAKLAIKLAQKDENAFVMFKHVSHGKAIF 364
Query: 92 DYCYWRGFKYCRLDGQTAHEDRQRQINDFNMEGSDIFIFMLSTRAGGLGINLATADVVVL 151
D K + G+ E R I + GI++ VVL
Sbjct: 365 DLIKNEYDKVYYVSGEVDTETRNIMKTLAENGKGIIIVASYGV--FSTGISVKNLHHVVL 422
Query: 152 YDSDWNPQMDLQAMVREAKILRRGSIKK 179
+ + LQ + R +LR+ K
Sbjct: 423 AHGVKSKIIVLQTIGR---VLRKHGSKT 447
>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate
immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*
Length = 696
Score = 37.3 bits (85), Expect = 0.005
Identities = 32/208 (15%), Positives = 68/208 (32%), Gaps = 46/208 (22%)
Query: 55 FNSGKMVVLDKLLPK--LKAQESRVLIFSQMTRM----LDILEDYCYWRGFKYCRLDGQT 108
+ K+ L +L + E+ ++F + + + +E K L G+
Sbjct: 377 NENPKLEDLCFILQEEYHLNPETITILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRG 436
Query: 109 A--------HEDRQRQINDFNMEGSDIFIFMLSTRAGGLGINLATADVVVLYDSDWNPQM 160
++ ++ F G +++T GI++A ++V+LY+ N
Sbjct: 437 KTNQNTGMTLPAQKCILDAFKASGD--HNILIATSVADEGIDIAQCNLVILYEYVGNVIK 494
Query: 161 DLQA-------------MVREAKILRRGSIKKALEAKMSR-----------------YRA 190
+Q + A ++ + I E M+
Sbjct: 495 MIQTRGRGRARGSKCFLLTSNAGVIEKEQINMYKEKMMNDSILRLQTWDEAVFREKILHI 554
Query: 191 PFHQLRIAYGANKGKNYTEEEDRYLYCR 218
H+ I K K ++E++ L CR
Sbjct: 555 QTHEKFIRDSQEKPKPVPDKENKKLLCR 582
Score = 34.2 bits (77), Expect = 0.052
Identities = 12/58 (20%), Positives = 26/58 (44%), Gaps = 2/58 (3%)
Query: 225 HEDRQRQINDFNMEGSDIFIFMLSTRAGGLGINLATADVVVLYDSDWNPQMDLQAMVR 282
++ ++ F G +++T GI++A ++V+LY+ N +Q R
Sbjct: 446 LPAQKCILDAFKASGD--HNILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRGR 501
>2fwr_A DNA repair protein RAD25; DNA unwinding, XPB, DNA binding protein;
HET: DNA; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.19
c.37.1.19 PDB: 2fzl_A*
Length = 472
Score = 36.7 bits (85), Expect = 0.006
Identities = 18/96 (18%), Positives = 45/96 (46%), Gaps = 10/96 (10%)
Query: 56 NSGKMVVLDKLLPKLKAQESRVLIFSQMTRMLDILEDYCYWRGFKYCRLDGQTAHEDRQR 115
+ K+ L ++L + + + +++IF++ ++ + F + +T+ E+R+
Sbjct: 333 SKNKIRKLREILERHR--KDKIIIFTRHNELVYRISKV-----FLIPAITHRTSREEREE 385
Query: 116 QINDFNMEGSDIFIFMLSTRAGGLGINLATADVVVL 151
+ F G I S++ GI++ A+V V+
Sbjct: 386 ILEGFR-TGRFRAIV--SSQVLDEGIDVPDANVGVI 418
Score = 27.9 bits (62), Expect = 5.1
Identities = 12/46 (26%), Positives = 23/46 (50%), Gaps = 3/46 (6%)
Query: 221 GQTAHEDRQRQINDFNMEGSDIFIFMLSTRAGGLGINLATADVVVL 266
+T+ E+R+ + F G I S++ GI++ A+V V+
Sbjct: 376 HRTSREEREEILEGFR-TGRFRAIV--SSQVLDEGIDVPDANVGVI 418
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 35.3 bits (80), Expect = 0.008
Identities = 11/40 (27%), Positives = 16/40 (40%), Gaps = 14/40 (35%)
Query: 174 RGSIKKALEAKMSRY---RAPFHQLRIAYGANKGKNYTEE 210
+ ++KK L+A + Y AP L I T E
Sbjct: 19 KQALKK-LQASLKLYADDSAP--ALAI--------KATME 47
Score = 27.6 bits (60), Expect = 2.9
Identities = 6/18 (33%), Positives = 10/18 (55%), Gaps = 1/18 (5%)
Query: 151 LYDSDWNPQMDLQAMVRE 168
LY D P + ++A + E
Sbjct: 31 LYADDSAPALAIKATM-E 47
Score = 27.6 bits (60), Expect = 2.9
Identities = 5/16 (31%), Positives = 9/16 (56%)
Query: 266 LYDSDWNPQMDLQAMV 281
LY D P + ++A +
Sbjct: 31 LYADDSAPALAIKATM 46
>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex,
ATPase, riken structural genomics/proteomics initiative,
RSGI; HET: ANP; 2.20A {Drosophila melanogaster}
Length = 434
Score = 35.6 bits (83), Expect = 0.014
Identities = 13/57 (22%), Positives = 23/57 (40%)
Query: 64 DKLLPKLKAQESRVLIFSQMTRMLDILEDYCYWRGFKYCRLDGQTAHEDRQRQINDF 120
KL+ L Q ++F + R D L + + F + G R++ + DF
Sbjct: 290 SKLIEILSEQADGTIVFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQALRDF 346
>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling,
archaea, isomeras; 2.35A {Thermotoga maritima} PDB:
3p4y_A 3p4x_A*
Length = 414
Score = 35.1 bits (81), Expect = 0.019
Identities = 12/69 (17%), Positives = 22/69 (31%), Gaps = 11/69 (15%)
Query: 52 HLVFNSGKMVVLDKLLPKLKAQESRVLIFSQMTRMLDILEDYCYWRGFKYCRLDGQTAHE 111
+ K+V L ++ +LIF+Q L +Y F
Sbjct: 236 ISSRSKEKLVELLEIF------RDGILIFAQTEEEGKELYEYLKRFKFN-----VGETWS 284
Query: 112 DRQRQINDF 120
+ ++ DF
Sbjct: 285 EFEKNFEDF 293
>4a2q_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2
RNA helicase, ATP and dsRNA binding antiviral signalling
pathway; 3.40A {Anas platyrhynchos}
Length = 797
Score = 35.3 bits (80), Expect = 0.025
Identities = 20/139 (14%), Positives = 51/139 (36%), Gaps = 27/139 (19%)
Query: 74 ESRVLIFSQM----TRMLDILEDYCYWRGFKYCRLDGQTA--------HEDRQRQINDFN 121
++R L+F++ + + +E+ K L G+ ++ ++ F
Sbjct: 631 QTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFK 690
Query: 122 MEGSDIFIFMLSTRAGGLGINLATADVVVLYDSDWNPQMDLQA-------------MVRE 168
S +++T GI++ ++VVLY+ N +Q + +
Sbjct: 691 T--SKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGRGRAAGSKCILVTSK 748
Query: 169 AKILRRGSIKKALEAKMSR 187
+++ + E M++
Sbjct: 749 TEVVENEKCNRYKEEMMNK 767
Score = 30.7 bits (68), Expect = 0.63
Identities = 12/58 (20%), Positives = 25/58 (43%), Gaps = 2/58 (3%)
Query: 225 HEDRQRQINDFNMEGSDIFIFMLSTRAGGLGINLATADVVVLYDSDWNPQMDLQAMVR 282
++ ++ F S +++T GI++ ++VVLY+ N +Q R
Sbjct: 679 LPSQKGVLDAFKT--SKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR 734
>4a2w_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2
RNA helicase, ATP and dsRNA binding antiviral signalling
pathway; 3.70A {Anas platyrhynchos}
Length = 936
Score = 34.2 bits (77), Expect = 0.050
Identities = 20/140 (14%), Positives = 51/140 (36%), Gaps = 27/140 (19%)
Query: 73 QESRVLIFSQM----TRMLDILEDYCYWRGFKYCRLDGQTA--------HEDRQRQINDF 120
++R L+F++ + + +E+ K L G+ ++ ++ F
Sbjct: 630 PQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAF 689
Query: 121 NMEGSDIFIFMLSTRAGGLGINLATADVVVLYDSDWNPQMDLQA-------------MVR 167
S +++T GI++ ++VVLY+ N +Q +
Sbjct: 690 KT--SKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGRGRAAGSKCILVTS 747
Query: 168 EAKILRRGSIKKALEAKMSR 187
+ +++ + E M++
Sbjct: 748 KTEVVENEKCNRYKEEMMNK 767
Score = 29.5 bits (65), Expect = 1.7
Identities = 12/58 (20%), Positives = 25/58 (43%), Gaps = 2/58 (3%)
Query: 225 HEDRQRQINDFNMEGSDIFIFMLSTRAGGLGINLATADVVVLYDSDWNPQMDLQAMVR 282
++ ++ F S +++T GI++ ++VVLY+ N +Q R
Sbjct: 679 LPSQKGVLDAFKT--SKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR 734
>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC,
structural GE consortium, hydrolase; HET: AMP; 2.20A
{Homo sapiens}
Length = 417
Score = 32.9 bits (76), Expect = 0.11
Identities = 17/62 (27%), Positives = 29/62 (46%), Gaps = 1/62 (1%)
Query: 59 KMVVLDKLLPKLKAQESRVLIFSQMTRMLDILEDYCYWRGFKYCRLDGQTAHEDRQRQIN 118
K L LL ++S L+F + + D LED+ Y G+ + G + DR+ ++
Sbjct: 262 KRSFLLDLLNAT-GKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALH 320
Query: 119 DF 120
F
Sbjct: 321 QF 322
>4a2p_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2
RNA helicase, ATP and dsRNA binding antiviral signalling
pathway; 3.00A {Anas platyrhynchos} PDB: 4a36_A*
Length = 556
Score = 31.1 bits (69), Expect = 0.44
Identities = 20/142 (14%), Positives = 51/142 (35%), Gaps = 27/142 (19%)
Query: 71 KAQESRVLIFSQM----TRMLDILEDYCYWRGFKYCRLDGQTAHEDR--------QRQIN 118
++R L+F++ + + +E+ K L G+ + + ++
Sbjct: 387 YNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLD 446
Query: 119 DFNMEGSDIFIFMLSTRAGGLGINLATADVVVLYDSDWNPQMDLQA-------------M 165
F S +++T GI++ ++VVLY+ N +Q +
Sbjct: 447 AFKT--SKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGRGRAAGSKCILV 504
Query: 166 VREAKILRRGSIKKALEAKMSR 187
+ +++ + E M++
Sbjct: 505 TSKTEVVENEKCNRYKEEMMNK 526
>1mp9_A Tata-binding protein; transcription regulation, DNA-binding
protein, transcription factor, DNA binding protein;
2.00A {Sulfolobus acidocaldarius} SCOP: d.129.1.1
d.129.1.1
Length = 198
Score = 29.2 bits (65), Expect = 1.0
Identities = 16/51 (31%), Positives = 20/51 (39%), Gaps = 8/51 (15%)
Query: 18 KMRLQNILMQLRKCSNHPYLFDGAEPGPPYTTDEH----LVFNSGKMVVLD 64
+ L L P F PG Y DE L+F+SGKMV+
Sbjct: 118 IVNLDKAAFLLENNMYEPEQF----PGLIYRMDEPRVVLLIFSSGKMVITG 164
>1ais_A TBP, protein (tata-binding protein); hyperthermophIle, ribosome
binding, complex (ribosome binding/ DNA); HET: DNA 5IU;
2.10A {Pyrococcus woesei} SCOP: d.129.1.1 d.129.1.1 PDB:
1d3u_A* 1pcz_A
Length = 182
Score = 28.4 bits (63), Expect = 2.0
Identities = 15/50 (30%), Positives = 21/50 (42%), Gaps = 8/50 (16%)
Query: 18 KMRLQNILMQLRKCSNHPYLFDGAEPGPPYTTDEH----LVFNSGKMVVL 63
+ L + + L C P F PG Y E L+F+SGK+V
Sbjct: 114 EFNLDVVALTLPNCEYEPEQF----PGVIYRVKEPKSVILLFSSGKIVCS 159
>2kkh_A Putative heavy metal transporter; zinc transport, metal binding,
metal selectivity, ferredoxin fold, ATP-binding,
hydrolase; NMR {Arabidopsis thaliana}
Length = 95
Score = 27.4 bits (61), Expect = 2.0
Identities = 7/44 (15%), Positives = 16/44 (36%), Gaps = 4/44 (9%)
Query: 141 INLATADVVVLYDSDWNPQMDLQAMVR----EAKILRRGSIKKA 180
+ + + V+V++DS + + EA + G
Sbjct: 49 VIVPSRTVIVVHDSLLISPFQIAKALNEARLEANVRVNGETSFK 92
>2z8u_A Tata-box-binding protein; transcription, DNA-binding protein,
transcription factor, transcription regulation; 1.90A
{Methanococcus jannaschii}
Length = 188
Score = 28.4 bits (63), Expect = 2.3
Identities = 17/80 (21%), Positives = 32/80 (40%), Gaps = 16/80 (20%)
Query: 18 KMRLQNILMQLRKCSNHPYLFDGAEPGPPYTTDEH----LVFNSGKMVVLDKLLPKLKAQ 73
+ L +I + + P F PG Y D+ L+F SGK+V+
Sbjct: 118 EPNLDDIALMVEGTEYEPEQF----PGLVYRLDDPKVVVLIFGSGKVVITGL-------- 165
Query: 74 ESRVLIFSQMTRMLDILEDY 93
+S + ++LD +++
Sbjct: 166 KSEEDAKRALKKILDTIKEV 185
>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET:
ANP; 2.14A {Mus musculus}
Length = 555
Score = 28.3 bits (62), Expect = 2.9
Identities = 22/127 (17%), Positives = 48/127 (37%), Gaps = 16/127 (12%)
Query: 55 FNSGKMVVLDKLLPK--LKAQESRVLIFSQMTRMLDILEDYCYW----RGFKYCRLDGQT 108
+ K+ L +L + E++ ++F + ++D L+ + K L G+
Sbjct: 368 NENPKLRDLYLVLQEEYHLKPETKTILFVKTRALVDALKKWIEENPALSFLKPGILTGRG 427
Query: 109 AHEDR--------QRQINDFNMEGSDIFIFMLSTRAGGLGINLATADVVVLYDSDWNPQM 160
+ + F G +++T GI++A ++V+LY+ N
Sbjct: 428 RTNRATGMTLPAQKCVLEAFRASGD--NNILIATSVADEGIDIAECNLVILYEYVGNVIK 485
Query: 161 DLQAMVR 167
+Q R
Sbjct: 486 MIQTRGR 492
Score = 27.2 bits (59), Expect = 7.7
Identities = 12/54 (22%), Positives = 24/54 (44%), Gaps = 2/54 (3%)
Query: 229 QRQINDFNMEGSDIFIFMLSTRAGGLGINLATADVVVLYDSDWNPQMDLQAMVR 282
+ + F G +++T GI++A ++V+LY+ N +Q R
Sbjct: 441 KCVLEAFRASGD--NNILIATSVADEGIDIAECNLVILYEYVGNVIKMIQTRGR 492
>1ois_A DNA topoisomerase I; DNA-binding protein; HET: DNA; 1.90A
{Saccharomyces cerevisiae} SCOP: e.15.1.1
Length = 223
Score = 27.2 bits (60), Expect = 5.3
Identities = 12/35 (34%), Positives = 20/35 (57%), Gaps = 6/35 (17%)
Query: 209 EEEDRYLYCRLDGQTAHEDRQRQINDFNMEGSDIF 243
+ E+ Y +C LDG R+ Q+ +F +E D+F
Sbjct: 125 KFEEDYKFCELDG------RREQVGNFKVEPPDLF 153
>2pzm_A Putative nucleotide sugar epimerase/ dehydratase; rossman fold,
protein-NAD complex, protein-nucleotide comple binding
protein; HET: NAD UDP; 2.00A {Bordetella bronchiseptica}
PDB: 2pzl_A* 2pzk_A*
Length = 330
Score = 27.5 bits (62), Expect = 5.8
Identities = 6/35 (17%), Positives = 14/35 (40%), Gaps = 8/35 (22%)
Query: 262 DVVVLY-DSD-------WNPQMDLQAMVRTVIAYF 288
DV + D W ++D + + +A++
Sbjct: 279 DVPSVVLDPSKTETEFGWKAKVDFKDTITGQLAWY 313
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.323 0.138 0.412
Gapped
Lambda K H
0.267 0.0620 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,562,805
Number of extensions: 272669
Number of successful extensions: 691
Number of sequences better than 10.0: 1
Number of HSP's gapped: 672
Number of HSP's successfully gapped: 55
Length of query: 288
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 195
Effective length of database: 4,105,140
Effective search space: 800502300
Effective search space used: 800502300
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 57 (26.0 bits)