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= psy7790
(367 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 181 bits (458), Expect = 7e-46, Method: Compositional matrix adjust.
Identities = 85/102 (83%), Positives = 98/102 (96%)
Query: 254 SMNVVQEVEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGVEAVAIHG 313
S++V+QEVEYVK+EAK+VYLLECLQKT PPVLIFAEKK DVDAIHEYLLLKGVEAVAIHG
Sbjct: 27 SLDVIQEVEYVKEEAKMVYLLECLQKTPPPVLIFAEKKADVDAIHEYLLLKGVEAVAIHG 86
Query: 314 GKDQEERTRSVESFRKGQKDVMVATDVASKGLDFEEIKHVIN 355
GKDQEERT+++E+FR+G+KDV+VATDVASKGLDF I+HVIN
Sbjct: 87 GKDQEERTKAIEAFREGKKDVLVATDVASKGLDFPAIQHVIN 128
>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x
Length = 417
Score = 110 bits (275), Expect = 1e-24, Method: Compositional matrix adjust.
Identities = 57/145 (39%), Positives = 89/145 (61%), Gaps = 4/145 (2%)
Query: 213 RGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGKIMPSMNVVQEVEYVKQEAKIVY 272
+G R T++FSAT PK+IQ AR L + I + VGR G S N+ Q+V +V++ K +
Sbjct: 208 KGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGRVGST--SENITQKVVWVEESDKRSF 265
Query: 273 LLECLQKT--EPPVLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEERTRSVESFRKG 330
LL+ L T + L+F E K+ D++ ++L +G +IHG + Q +R ++ FR G
Sbjct: 266 LLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSG 325
Query: 331 QKDVMVATDVASKGLDFEEIKHVIN 355
+ ++VAT VA++GLD +KHVIN
Sbjct: 326 KSPILVATAVAARGLDISNVKHVIN 350
Score = 30.4 bits (67), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 23/41 (56%)
Query: 158 GDDVPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIP 198
G++ PP SF +++ E ++ +E +PTP+Q IP
Sbjct: 7 GNNCPPHIESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIP 47
>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 = 93.6 bits (231), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 56/160 (35%), Positives = 87/160 (54%), Gaps = 4/160 (2%)
Query: 200 ALSEDVRTIFSF--FRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGKIMPSMNV 257
SED+R I + R + QTL+FSAT P++IQ A L + + +G G +V
Sbjct: 219 GFSEDMRRIMTHVTMRPEHQTLMFSATFPEEIQRMAGEFLKNYVFVAIGIVGG--ACSDV 276
Query: 258 VQEVEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQ 317
Q + V + AK L+E L + ++F E K+ D + +L K +IHG + Q
Sbjct: 277 KQTIYEVNKYAKRSKLIEILSEQADGTIVFVETKRGADFLASFLSEKEFPTTSIHGDRLQ 336
Query: 318 EERTRSVESFRKGQKDVMVATDVASKGLDFEEIKHVINTE 357
+R +++ F+ G V++AT VAS+GLD + IKHVIN +
Sbjct: 337 SQREQALRDFKNGSMKVLIATSVASRGLDIKNIKHVINYD 376
Score = 30.8 bits (68), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 23/48 (47%)
Query: 151 NLRILVEGDDVPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIP 198
N+ + V G DVP F L + ++ + G K PTPIQ IP
Sbjct: 41 NIPVKVTGSDVPQPIQHFTSADLRDIIIDNVNKSGYKIPTPIQKCSIP 88
>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 = 79.7 bits (195), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 38/105 (36%), Positives = 64/105 (60%), Gaps = 2/105 (1%)
Query: 253 PSMNVVQEVEYVKQEAKIVYLLECLQKT--EPPVLIFAEKKQDVDAIHEYLLLKGVEAVA 310
S N+ Q+V +V++ K +LL+ L T + L+F E K+ D++ ++L +G +
Sbjct: 16 TSENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTS 75
Query: 311 IHGGKDQEERTRSVESFRKGQKDVMVATDVASKGLDFEEIKHVIN 355
IHG + Q +R ++ FR G+ ++VAT VA++GLD +KHVIN
Sbjct: 76 IHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVIN 120
>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56
Length = 391
Score = 70.5 bits (171), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 48/162 (29%), Positives = 88/162 (54%), Gaps = 10/162 (6%)
Query: 201 LSEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGKIMPSMNVVQE 260
+ DV+ IF ++Q ++FSAT+ K+I+ R + P+ I V K+ +++ +Q+
Sbjct: 170 MRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKL--TLHGLQQ 227
Query: 261 VEYVK-----QEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGK 315
YVK + K+ LL+ L+ + V+IF + Q A+ + L+ + A+AIH G
Sbjct: 228 Y-YVKLKDNEKNRKLFDLLDVLEFNQ--VVIFVKSVQRCIALAQLLVEQNFPAIAIHRGM 284
Query: 316 DQEERTRSVESFRKGQKDVMVATDVASKGLDFEEIKHVINTE 357
QEER + F+ Q+ ++VAT++ +G+D E + N +
Sbjct: 285 PQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYD 326
>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp
Length = 386
Score = 70.5 bits (171), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 48/162 (29%), Positives = 88/162 (54%), Gaps = 10/162 (6%)
Query: 201 LSEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGKIMPSMNVVQE 260
+ DV+ IF ++Q ++FSAT+ K+I+ R + P+ I V K+ +++ +Q+
Sbjct: 170 MRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKL--TLHGLQQ 227
Query: 261 VEYVK-----QEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGK 315
YVK + K+ LL+ L+ + V+IF + Q A+ + L+ + A+AIH G
Sbjct: 228 Y-YVKLKDNEKNRKLFDLLDVLEFNQ--VVIFVKSVQRCIALAQLLVEQNFPAIAIHRGM 284
Query: 316 DQEERTRSVESFRKGQKDVMVATDVASKGLDFEEIKHVINTE 357
QEER + F+ Q+ ++VAT++ +G+D E + N +
Sbjct: 285 PQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYD 326
>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56
Length = 390
Score = 70.5 bits (171), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 48/162 (29%), Positives = 88/162 (54%), Gaps = 10/162 (6%)
Query: 201 LSEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGKIMPSMNVVQE 260
+ DV+ IF ++Q ++FSAT+ K+I+ R + P+ I V K+ +++ +Q+
Sbjct: 169 MRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKL--TLHGLQQ 226
Query: 261 VEYVK-----QEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGK 315
YVK + K+ LL+ L+ + V+IF + Q A+ + L+ + A+AIH G
Sbjct: 227 Y-YVKLKDNEKNRKLFDLLDVLEFNQ--VVIFVKSVQRCIALAQLLVEQNFPAIAIHRGM 283
Query: 316 DQEERTRSVESFRKGQKDVMVATDVASKGLDFEEIKHVINTE 357
QEER + F+ Q+ ++VAT++ +G+D E + N +
Sbjct: 284 PQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYD 325
>pdb|1HV8|A Chain A, Crystal Structure Of A Dead Box Protein From The
Hyperthermophile Methanococcus Jannaschii
pdb|1HV8|B Chain B, Crystal Structure Of A Dead Box Protein From The
Hyperthermophile Methanococcus Jannaschii
Length = 367
Score = 65.9 bits (159), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 46/155 (29%), Positives = 76/155 (49%), Gaps = 10/155 (6%)
Query: 203 EDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGKIMPSMNVVQEVE 262
+DV I + ++ LLFSAT P++I N A+ G I +N E
Sbjct: 166 KDVEKILNACNKDKRILLFSATXPREILNLAKKY--------XGDYSFIKAKINANIEQS 217
Query: 263 YVK--QEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEER 320
YV+ + + L L+ E L+F + K+D + L G +A AIHG Q +R
Sbjct: 218 YVEVNENERFEALCRLLKNKEFYGLVFCKTKRDTKELASXLRDIGFKAGAIHGDLSQSQR 277
Query: 321 TRSVESFRKGQKDVMVATDVASKGLDFEEIKHVIN 355
+ + F++ + +++ATDV S+G+D ++ VIN
Sbjct: 278 EKVIRLFKQKKIRILIATDVXSRGIDVNDLNCVIN 312
Score = 33.5 bits (75), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 16/56 (28%), Positives = 31/56 (55%)
Query: 167 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSEDVRTIFSFFRGQRQTLLFS 222
+F + L ++++ A+ KG +KPT IQ + IP L+++ + G +T F+
Sbjct: 7 NFNELNLSDNILNAIRNKGFEKPTDIQXKVIPLFLNDEYNIVAQARTGSGKTASFA 62
>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a
pdb|3EIQ|D Chain D, Crystal Structure Of Pdcd4-eif4a
Length = 414
Score = 62.8 bits (151), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 56/239 (23%), Positives = 98/239 (41%), Gaps = 29/239 (12%)
Query: 128 KTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALEAKGIK 187
K AP I+ P +V D++ R R L P F L + E L R +
Sbjct: 154 KLQMEAPHIIVGTPGRVFDMLNR--RYLS-----PKYIKMFVLDEADEMLSRGFK----- 201
Query: 188 KPTPIQVQGIPAALSEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGR 247
+ + IF Q +L SATMP + + + PI I V +
Sbjct: 202 ---------------DQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKK 246
Query: 248 AGKIMPSMNVVQEVEYVKQEAKIVYLLECLQK-TEPPVLIFAEKKQDVDAIHEYLLLKGV 306
+ + + ++E K+ L + + T +IF ++ VD + E + +
Sbjct: 247 EELTLEGIRQFY-INVEREEWKLDTLCDLYETLTITQAVIFINTRRKVDWLTEKMHARDF 305
Query: 307 EAVAIHGGKDQEERTRSVESFRKGQKDVMVATDVASKGLDFEEIKHVINTEAKIKKREH 365
A+HG DQ+ER + FR G V++ TD+ ++G+D +++ VIN + + +
Sbjct: 306 TVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENY 364
Score = 32.7 bits (73), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 35/65 (53%), Gaps = 3/65 (4%)
Query: 167 SFRLMKLPESLVRALEAKGIKKPTPIQVQGI-PAALSEDVRTIFSFFRGQRQTLLFSATM 225
SF M L ESL+R + A G +KP+ IQ + I P DV I G +T F+ ++
Sbjct: 41 SFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDV--IAQAQSGTGKTATFAISI 98
Query: 226 PKKIQ 230
++I+
Sbjct: 99 LQQIE 103
>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p
Length = 400
Score = 62.8 bits (151), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 44/160 (27%), Positives = 73/160 (45%), Gaps = 8/160 (5%)
Query: 201 LSEDVRTI----FSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGKIMPSMN 256
LS D +TI SF Q+LLFSAT P ++ F L KP IN+ +
Sbjct: 176 LSRDFKTIIEQILSFLPPTHQSLLFSATFPLTVKEFMVKHLHKPYEINLMEE---LTLKG 232
Query: 257 VVQEVEYVKQEAKIVYLLECLQKTE-PPVLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGK 315
+ Q +V++ K+ L K + +IF V+ + + + G H
Sbjct: 233 ITQYYAFVEERQKLHCLNTLFSKLQINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARM 292
Query: 316 DQEERTRSVESFRKGQKDVMVATDVASKGLDFEEIKHVIN 355
Q+ER + FR+G+ +V +D+ ++G+D + + VIN
Sbjct: 293 KQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQAVNVVIN 332
>pdb|2ZU6|A Chain A, Crystal Structure Of The Eif4a-Pdcd4 Complex
pdb|2ZU6|C Chain C, Crystal Structure Of The Eif4a-Pdcd4 Complex
pdb|2ZU6|D Chain D, Crystal Structure Of The Eif4a-Pdcd4 Complex
pdb|2ZU6|F Chain F, Crystal Structure Of The Eif4a-Pdcd4 Complex
Length = 388
Score = 62.4 bits (150), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 56/239 (23%), Positives = 98/239 (41%), Gaps = 29/239 (12%)
Query: 128 KTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALEAKGIK 187
K AP I+ P +V D++ R R L P F L + E L R +
Sbjct: 128 KLQMEAPHIIVGTPGRVFDMLNR--RYLS-----PKYIKMFVLDEADEMLSRGFK----- 175
Query: 188 KPTPIQVQGIPAALSEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGR 247
+ + IF Q +L SATMP + + + PI I V +
Sbjct: 176 ---------------DQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKK 220
Query: 248 AGKIMPSMNVVQEVEYVKQEAKIVYLLECLQK-TEPPVLIFAEKKQDVDAIHEYLLLKGV 306
+ + + ++E K+ L + + T +IF ++ VD + E + +
Sbjct: 221 EELTLEGIRQFY-INVEREEWKLDTLCDLYETLTITQAVIFINTRRKVDWLTEKMHARDF 279
Query: 307 EAVAIHGGKDQEERTRSVESFRKGQKDVMVATDVASKGLDFEEIKHVINTEAKIKKREH 365
A+HG DQ+ER + FR G V++ TD+ ++G+D +++ VIN + + +
Sbjct: 280 TVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENY 338
Score = 32.7 bits (73), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 35/65 (53%), Gaps = 3/65 (4%)
Query: 167 SFRLMKLPESLVRALEAKGIKKPTPIQVQGI-PAALSEDVRTIFSFFRGQRQTLLFSATM 225
SF M L ESL+R + A G +KP+ IQ + I P DV I G +T F+ ++
Sbjct: 15 SFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDV--IAQAQSGTGKTATFAISI 72
Query: 226 PKKIQ 230
++I+
Sbjct: 73 LQQIE 77
>pdb|2HJV|A Chain A, Structure Of The Second Domain (Residues 207-368) Of The
Bacillus Subtilis Yxin Protein
pdb|2HJV|B Chain B, Structure Of The Second Domain (Residues 207-368) Of The
Bacillus Subtilis Yxin Protein
Length = 163
Score = 60.8 bits (146), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 37/115 (32%), Positives = 61/115 (53%), Gaps = 1/115 (0%)
Query: 252 MPSMNVVQEVEYVKQEAKIVYLLECLQKTEP-PVLIFAEKKQDVDAIHEYLLLKGVEAVA 310
+ + N+ V V++E K L + L P +IF K+ V+ + + L G
Sbjct: 5 LTTRNIEHAVIQVREENKFSLLKDVLMTENPDSCIIFCRTKEHVNQLTDELDDLGYPCDK 64
Query: 311 IHGGKDQEERTRSVESFRKGQKDVMVATDVASKGLDFEEIKHVINTEAKIKKREH 365
IHGG QE+R + F++G+ +VATDVA++G+D E I VIN + ++K +
Sbjct: 65 IHGGMIQEDRFDVMNEFKRGEYRYLVATDVAARGIDIENISLVINYDLPLEKESY 119
>pdb|2J0Q|A Chain A, The Crystal Structure Of The Exon Junction Complex At 3.2
A Resolution
pdb|2J0Q|B Chain B, The Crystal Structure Of The Exon Junction Complex At 3.2
A Resolution
pdb|2J0S|A Chain A, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 410
Score = 58.2 bits (139), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 43/159 (27%), Positives = 74/159 (46%), Gaps = 6/159 (3%)
Query: 200 ALSEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGKIMPSMN--- 256
E + ++ + Q +L SAT+P +I + PI I V R + +
Sbjct: 195 GFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFF 254
Query: 257 VVQEVEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKD 316
V E E K + + L + L T+ +IF K+ VD + E + ++HG
Sbjct: 255 VAVEREEWKFDT-LCDLYDTLTITQA--VIFCNTKRKVDWLTEKMREANFTVSSMHGDMP 311
Query: 317 QEERTRSVESFRKGQKDVMVATDVASKGLDFEEIKHVIN 355
Q+ER ++ FR G V+++TDV ++GLD ++ +IN
Sbjct: 312 QKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIIN 350
>pdb|2HXY|A Chain A, Crystal Structure Of Human Apo-Eif4aiii
pdb|2HXY|B Chain B, Crystal Structure Of Human Apo-Eif4aiii
pdb|2HXY|C Chain C, Crystal Structure Of Human Apo-Eif4aiii
pdb|2HXY|D Chain D, Crystal Structure Of Human Apo-Eif4aiii
Length = 391
Score = 58.2 bits (139), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 43/161 (26%), Positives = 75/161 (46%), Gaps = 6/161 (3%)
Query: 200 ALSEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGKIMPSMN--- 256
E + ++ + Q +L SAT+P +I + PI I V R + +
Sbjct: 174 GFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFF 233
Query: 257 VVQEVEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKD 316
V E E K + + L + L T+ +IF K+ VD + E + ++HG
Sbjct: 234 VAVEREEWKFDT-LCDLYDTLTITQA--VIFCNTKRKVDWLTEKMREANFTVSSMHGDMP 290
Query: 317 QEERTRSVESFRKGQKDVMVATDVASKGLDFEEIKHVINTE 357
Q+ER ++ FR G V+++TDV ++GLD ++ +IN +
Sbjct: 291 QKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYD 331
>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 58.2 bits (139), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 43/161 (26%), Positives = 75/161 (46%), Gaps = 6/161 (3%)
Query: 200 ALSEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGKIMPSMN--- 256
E + ++ + Q +L SAT+P +I + PI I V R + +
Sbjct: 159 GFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFF 218
Query: 257 VVQEVEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKD 316
V E E K + + L + L T+ +IF K+ VD + E + ++HG
Sbjct: 219 VAVEREEWKFDT-LCDLYDTLTITQA--VIFCNTKRKVDWLTEKMREANFTVSSMHGDMP 275
Query: 317 QEERTRSVESFRKGQKDVMVATDVASKGLDFEEIKHVINTE 357
Q+ER ++ FR G V+++TDV ++GLD ++ +IN +
Sbjct: 276 QKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYD 316
>pdb|2XB2|A Chain A, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
pdb|2XB2|X Chain X, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
Length = 411
Score = 58.2 bits (139), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 43/159 (27%), Positives = 74/159 (46%), Gaps = 6/159 (3%)
Query: 200 ALSEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGKIMPSMN--- 256
E + ++ + Q +L SAT+P +I + PI I V R + +
Sbjct: 196 GFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFF 255
Query: 257 VVQEVEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKD 316
V E E K + + L + L T+ +IF K+ VD + E + ++HG
Sbjct: 256 VAVEREEWKFDT-LCDLYDTLTITQA--VIFCNTKRKVDWLTEKMREANFTVSSMHGDMP 312
Query: 317 QEERTRSVESFRKGQKDVMVATDVASKGLDFEEIKHVIN 355
Q+ER ++ FR G V+++TDV ++GLD ++ +IN
Sbjct: 313 QKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIIN 351
>pdb|2HYI|C Chain C, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2HYI|I Chain I, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|3EX7|C Chain C, The Crystal Structure Of Ejc In Its Transition State
pdb|3EX7|H Chain H, The Crystal Structure Of Ejc In Its Transition State
Length = 413
Score = 58.2 bits (139), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 43/159 (27%), Positives = 74/159 (46%), Gaps = 6/159 (3%)
Query: 200 ALSEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGKIMPSMN--- 256
E + ++ + Q +L SAT+P +I + PI I V R + +
Sbjct: 196 GFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFF 255
Query: 257 VVQEVEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKD 316
V E E K + + L + L T+ +IF K+ VD + E + ++HG
Sbjct: 256 VAVEREEWKFDT-LCDLYDTLTITQA--VIFCNTKRKVDWLTEKMREANFTVSSMHGDMP 312
Query: 317 QEERTRSVESFRKGQKDVMVATDVASKGLDFEEIKHVIN 355
Q+ER ++ FR G V+++TDV ++GLD ++ +IN
Sbjct: 313 QKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIIN 351
>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 57.8 bits (138), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 42/161 (26%), Positives = 75/161 (46%), Gaps = 6/161 (3%)
Query: 200 ALSEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGKIMPSMN--- 256
E + ++ + Q +L SAT+P ++ + PI I V R + +
Sbjct: 159 GFKEQIYDVYRYLPPATQVVLISATLPHEVLEMTNKFMTDPIRILVKRDELTLEGIKQFF 218
Query: 257 VVQEVEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKD 316
V E E K + + L + L T+ +IF K+ VD + E + ++HG
Sbjct: 219 VAVEREEWKFDT-LCDLYDTLTITQA--VIFCNTKRKVDWLTEKMREANFTVSSMHGDMP 275
Query: 317 QEERTRSVESFRKGQKDVMVATDVASKGLDFEEIKHVINTE 357
Q+ER ++ FR G V+++TDV ++GLD ++ +IN +
Sbjct: 276 QKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYD 316
>pdb|3I32|A Chain A, Dimeric Structure Of A Hera Helicase Fragment Including
The C-Terminal Reca Domain, The Dimerization Domain, And
The Rna Binding Domain
Length = 300
Score = 57.4 bits (137), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 28/71 (39%), Positives = 45/71 (63%)
Query: 285 LIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEERTRSVESFRKGQKDVMVATDVASKG 344
++F K + + I + LL G A A+HG Q ER R + +FR+G+ V+VATDVA++G
Sbjct: 32 MVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGERERVMGAFRQGEVRVLVATDVAARG 91
Query: 345 LDFEEIKHVIN 355
LD ++ V++
Sbjct: 92 LDIPQVDLVVH 102
>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna
Helicase From Sulfolobus Tokodaii
Length = 337
Score = 56.6 bits (135), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 45/158 (28%), Positives = 81/158 (51%), Gaps = 14/158 (8%)
Query: 203 EDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGKIMPSMNVVQEVE 262
+D++ I + ++ T LFSAT+P++I+ +VK N + NV +
Sbjct: 148 DDIKIILAQTSNRKITGLFSATIPEEIRK-----VVKDFITNYEEIEACIGLANVEHKFV 202
Query: 263 YVKQE--AKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEER 320
+VK + +K+ L E K V++F + V + A+ + G Q R
Sbjct: 203 HVKDDWRSKVQALRENKDK---GVIVFVRTRNRVAKLVRLF----DNAIELRGDLPQSVR 255
Query: 321 TRSVESFRKGQKDVMVATDVASKGLDFEEIKHVINTEA 358
R++++FR+G+ D+++ TDVAS+GLD ++ VIN +A
Sbjct: 256 NRNIDAFREGEYDMLITTDVASRGLDIPLVEKVINFDA 293
>pdb|3EAQ|A Chain A, Novel Dimerization Motif In The Dead Box Rna Helicase Hera
Form 2, Complete Dimer, Symmetric
pdb|3EAQ|B Chain B, Novel Dimerization Motif In The Dead Box Rna Helicase Hera
Form 2, Complete Dimer, Symmetric
pdb|3EAR|A Chain A, Novel Dimerization Motif In The Dead Box Rna Helicase
Hera: Form 1, Partial Dimer
pdb|3EAR|B Chain B, Novel Dimerization Motif In The Dead Box Rna Helicase
Hera: Form 1, Partial Dimer
pdb|3EAS|A Chain A, Novel Dimerization Motif In The Dead Box Rna Helicase
Hera: Form 1, Complete Dimer, Asymmetric
pdb|3EAS|B Chain B, Novel Dimerization Motif In The Dead Box Rna Helicase
Hera: Form 1, Complete Dimer, Asymmetric
Length = 212
Score = 56.2 bits (134), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 28/71 (39%), Positives = 45/71 (63%)
Query: 285 LIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEERTRSVESFRKGQKDVMVATDVASKG 344
++F K + + I + LL G A A+HG Q ER R + +FR+G+ V+VATDVA++G
Sbjct: 35 MVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEVRVLVATDVAARG 94
Query: 345 LDFEEIKHVIN 355
LD ++ V++
Sbjct: 95 LDIPQVDLVVH 105
>pdb|2VSO|A Chain A, Crystal Structure Of A Translation Initiation Complex
pdb|2VSO|B Chain B, Crystal Structure Of A Translation Initiation Complex
pdb|2VSX|A Chain A, Crystal Structure Of A Translation Initiation Complex
pdb|2VSX|B Chain B, Crystal Structure Of A Translation Initiation Complex
Length = 395
Score = 53.1 bits (126), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 40/174 (22%), Positives = 75/174 (43%), Gaps = 10/174 (5%)
Query: 197 IPAALSEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGKIMPSMN 256
+ + E + IF+ Q +L SATMP + + P+ I V + + +
Sbjct: 176 LSSGFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKDELTLEGIK 235
Query: 257 VVQEVEYVKQEAKIVYLLECLQKTEPPV-----LIFAEKKQDVDAIHEYLLLKGVEAVAI 311
YV E + Y ECL + +IF ++ V+ + L AI
Sbjct: 236 QF----YVNVEEE-EYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAI 290
Query: 312 HGGKDQEERTRSVESFRKGQKDVMVATDVASKGLDFEEIKHVINTEAKIKKREH 365
+ Q+ER ++ FR G ++++TD+ ++G+D +++ VIN + K +
Sbjct: 291 YSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENY 344
>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3
Length = 395
Score = 52.0 bits (123), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 41/162 (25%), Positives = 74/162 (45%), Gaps = 30/162 (18%)
Query: 211 FFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGKIMPSMNVVQ------EVEYV 264
F Q +LFSAT ++ +A+ KI+P+ N ++ V+ +
Sbjct: 173 FLPKDTQLVLFSATFADAVRQYAK---------------KIVPNANTLELQTNEVNVDAI 217
Query: 265 KQ-------EAKIVYLLECLQK--TEPPVLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGK 315
KQ EA +L L T +IF K+ + ++ L +G E +HG
Sbjct: 218 KQLYMDCKNEADKFDVLTELYGLMTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDL 277
Query: 316 DQEERTRSVESFRKGQKDVMVATDVASKGLDFEEIKHVINTE 357
+ER R ++ FR+G+ V++ T+V ++G+D + V+N +
Sbjct: 278 QTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYD 319
>pdb|3PEW|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3
pdb|3RRM|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Nup159, Gle1 H337r, Ip6
And Adp
pdb|3RRN|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Gle1 H337r And Ip6
Length = 395
Score = 52.0 bits (123), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 41/162 (25%), Positives = 74/162 (45%), Gaps = 30/162 (18%)
Query: 211 FFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGKIMPSMNVVQ------EVEYV 264
F Q +LFSAT ++ +A+ KI+P+ N ++ V+ +
Sbjct: 173 FLPKDTQLVLFSATFADAVRQYAK---------------KIVPNANTLELQTNEVNVDAI 217
Query: 265 KQ-------EAKIVYLLECLQK--TEPPVLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGK 315
KQ EA +L L T +IF K+ + ++ L +G E +HG
Sbjct: 218 KQLYMDCKNEADKFDVLTELYGVMTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDL 277
Query: 316 DQEERTRSVESFRKGQKDVMVATDVASKGLDFEEIKHVINTE 357
+ER R ++ FR+G+ V++ T+V ++G+D + V+N +
Sbjct: 278 QTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYD 319
>pdb|3G0H|A Chain A, Human Dead-box Rna Helicase Ddx19, In Complex With An
Atp-analogue And Rna
Length = 424
Score = 51.2 bits (121), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 38/147 (25%), Positives = 69/147 (46%), Gaps = 2/147 (1%)
Query: 217 QTLLFSATMPKKIQNFARSALVKPITINVGRAGKIMPSMNVVQEVEYVKQEAKIVYLLEC 276
Q LLFSAT + FA+ + P I + R + + ++ V ++ K L
Sbjct: 218 QMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYY-VLCSSRDEKFQALCNL 276
Query: 277 LQK-TEPPVLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEERTRSVESFRKGQKDVM 335
T +IF ++ + L +G + + G E+R +E FR+G++ V+
Sbjct: 277 YGAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVL 336
Query: 336 VATDVASKGLDFEEIKHVINTEAKIKK 362
V T+V ++G+D E++ VIN + + K
Sbjct: 337 VTTNVCARGIDVEQVSVVINFDLPVDK 363
>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 = 51.2 bits (121), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 38/147 (25%), Positives = 69/147 (46%), Gaps = 2/147 (1%)
Query: 217 QTLLFSATMPKKIQNFARSALVKPITINVGRAGKIMPSMNVVQEVEYVKQEAKIVYLLEC 276
Q LLFSAT + FA+ + P I + R + + ++ V ++ K L
Sbjct: 269 QMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYY-VLCSSRDEKFQALCNL 327
Query: 277 LQK-TEPPVLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEERTRSVESFRKGQKDVM 335
T +IF ++ + L +G + + G E+R +E FR+G++ V+
Sbjct: 328 YGAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVL 387
Query: 336 VATDVASKGLDFEEIKHVINTEAKIKK 362
V T+V ++G+D E++ VIN + + K
Sbjct: 388 VTTNVCARGIDVEQVSVVINFDLPVDK 414
>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 = 51.2 bits (121), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 38/147 (25%), Positives = 69/147 (46%), Gaps = 2/147 (1%)
Query: 217 QTLLFSATMPKKIQNFARSALVKPITINVGRAGKIMPSMNVVQEVEYVKQEAKIVYLLEC 276
Q LLFSAT + FA+ + P I + R + + ++ V ++ K L
Sbjct: 202 QMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYY-VLCSSRDEKFQALCNL 260
Query: 277 LQK-TEPPVLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEERTRSVESFRKGQKDVM 335
T +IF ++ + L +G + + G E+R +E FR+G++ V+
Sbjct: 261 YGAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVL 320
Query: 336 VATDVASKGLDFEEIKHVINTEAKIKK 362
V T+V ++G+D E++ VIN + + K
Sbjct: 321 VTTNVCARGIDVEQVSVVINFDLPVDK 347
>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 = 51.2 bits (121), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 38/147 (25%), Positives = 69/147 (46%), Gaps = 2/147 (1%)
Query: 217 QTLLFSATMPKKIQNFARSALVKPITINVGRAGKIMPSMNVVQEVEYVKQEAKIVYLLEC 276
Q LLFSAT + FA+ + P I + R + + ++ V ++ K L
Sbjct: 239 QMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYY-VLCSSRDEKFQALCNL 297
Query: 277 LQK-TEPPVLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEERTRSVESFRKGQKDVM 335
T +IF ++ + L +G + + G E+R +E FR+G++ V+
Sbjct: 298 YGAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVL 357
Query: 336 VATDVASKGLDFEEIKHVINTEAKIKK 362
V T+V ++G+D E++ VIN + + K
Sbjct: 358 VTTNVCARGIDVEQVSVVINFDLPVDK 384
>pdb|1T5I|A Chain A, Crystal Structure Of The C-Terminal Domain Of Uap56
Length = 172
Score = 50.4 bits (119), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 28/89 (31%), Positives = 50/89 (56%), Gaps = 2/89 (2%)
Query: 269 KIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEERTRSVESFR 328
K+ LL+ L+ + V+IF + Q A+ + L+ + A+AIH G QEER + F+
Sbjct: 21 KLFDLLDVLEFNQ--VVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFK 78
Query: 329 KGQKDVMVATDVASKGLDFEEIKHVINTE 357
Q+ ++VAT++ +G+D E + N +
Sbjct: 79 DFQRRILVATNLFGRGMDIERVNIAFNYD 107
>pdb|2YJT|D Chain D, Crystal Structure Of E. Coli Dead-Box Protein Srmb Bound
To Regulator Of Ribonuclease Activity A (Rraa)
Length = 170
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/90 (28%), Positives = 50/90 (55%), Gaps = 1/90 (1%)
Query: 267 EAKIVYLLECLQKTEPP-VLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEERTRSVE 325
E K L+ L++ E ++F K++ V + +L G+ + G Q +R +++
Sbjct: 15 EHKTALLVHLLKQPEATRSIVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIK 74
Query: 326 SFRKGQKDVMVATDVASKGLDFEEIKHVIN 355
+G+ +V+VATDVA++G+D ++ HV N
Sbjct: 75 RLTEGRVNVLVATDVAARGIDIPDVSHVFN 104
>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a
pdb|1FUU|B Chain B, Yeast Initiation Factor 4a
Length = 394
Score = 48.5 bits (114), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 39/174 (22%), Positives = 72/174 (41%), Gaps = 10/174 (5%)
Query: 197 IPAALSEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGKIMPSMN 256
+ + E + IF+ Q +L SAT P + P+ I V + + +
Sbjct: 175 LSSGFKEQIYQIFTLLPPTTQVVLLSATXPNDVLEVTTKFXRNPVRILVKKDELTLEGIK 234
Query: 257 VVQEVEYVKQEAKIVYLLECLQKTEPPV-----LIFAEKKQDVDAIHEYLLLKGVEAVAI 311
YV E + Y ECL + +IF ++ V+ + L AI
Sbjct: 235 QF----YVNVEEE-EYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAI 289
Query: 312 HGGKDQEERTRSVESFRKGQKDVMVATDVASKGLDFEEIKHVINTEAKIKKREH 365
+ Q+ER + FR G ++++TD+ ++G+D +++ VIN + K +
Sbjct: 290 YSDLPQQERDTIXKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENY 343
>pdb|2KBF|A Chain A, Solution Structure Of Carboxyl-Terminal Domain Of Dbp5p
Length = 187
Score = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 42/73 (57%)
Query: 285 LIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEERTRSVESFRKGQKDVMVATDVASKG 344
+IF K+ + ++ L +G E +HG +ER R ++ FR+G+ V++ T+V ++G
Sbjct: 39 IIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARG 98
Query: 345 LDFEEIKHVINTE 357
+D + V+N +
Sbjct: 99 IDIPTVSMVVNYD 111
>pdb|3GFP|A Chain A, Structure Of The C-Terminal Domain Of The Dead-Box Protein
Dbp5
Length = 189
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 42/73 (57%)
Query: 285 LIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEERTRSVESFRKGQKDVMVATDVASKG 344
+IF K+ + ++ L +G E +HG +ER R ++ FR+G+ V++ T+V ++G
Sbjct: 41 IIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARG 100
Query: 345 LDFEEIKHVINTE 357
+D + V+N +
Sbjct: 101 IDIPTVSXVVNYD 113
>pdb|3PEU|A Chain A, S. Cerevisiae Dbp5 L327v C-Terminal Domain Bound To Gle1
H337r And Ip6
pdb|3PEV|A Chain A, S. Cerevisiae Dbp5 L327v C-Terminal Domain Bound To Gle1
And Ip6
Length = 188
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 42/73 (57%)
Query: 285 LIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEERTRSVESFRKGQKDVMVATDVASKG 344
+IF K+ + ++ L +G E +HG +ER R ++ FR+G+ V++ T+V ++G
Sbjct: 40 IIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARG 99
Query: 345 LDFEEIKHVINTE 357
+D + V+N +
Sbjct: 100 IDIPTVSXVVNYD 112
>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And
Amp-Pnp
Length = 579
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 38/157 (24%), Positives = 70/157 (44%), Gaps = 26/157 (16%)
Query: 217 QTLLFSATMPKKIQNFARSALVKPITINVGRAGKIMP----------------SMNVVQE 260
+TLLFSAT+ K+Q A + + K + + K P + ++
Sbjct: 215 KTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEKFANSIFAA 274
Query: 261 VEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYL---LLKGVEAVAIHGGKDQ 317
VE++K++ K + + +IFA + + L K + + HG Q
Sbjct: 275 VEHIKKQIK-------ERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQ 327
Query: 318 EERTRSVESFRKGQKDVMVATDVASKGLDFEEIKHVI 354
+RT V+ F+K + ++V TDV ++G+DF + V+
Sbjct: 328 NKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVL 364
>pdb|3I5X|A Chain A, Structure Of Mss116p Bound To Ssrna And Amp-Pnp
pdb|3I5Y|A Chain A, Structure Of Mss116p Bound To Ssrna Containing A Single
5-Bru And Amp- Pnp
pdb|3I61|A Chain A, Structure Of Mss116p Bound To Ssrna And Adp-beryllium
Fluoride
pdb|3I62|A Chain A, Structure Of Mss116p Bound To Ssrna And Adp-aluminum
Fluoride
Length = 563
Score = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 38/157 (24%), Positives = 70/157 (44%), Gaps = 26/157 (16%)
Query: 217 QTLLFSATMPKKIQNFARSALVKPITINVGRAGKIMP----------------SMNVVQE 260
+TLLFSAT+ K+Q A + + K + + K P + ++
Sbjct: 266 KTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEKFANSIFAA 325
Query: 261 VEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYL---LLKGVEAVAIHGGKDQ 317
VE++K++ K + + +IFA + + L K + + HG Q
Sbjct: 326 VEHIKKQIK-------ERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQ 378
Query: 318 EERTRSVESFRKGQKDVMVATDVASKGLDFEEIKHVI 354
+RT V+ F+K + ++V TDV ++G+DF + V+
Sbjct: 379 NKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVL 415
>pdb|3SQX|A Chain A, Structure Of Mss116p (Nte And C-Tail Double Deletion)
Bound To Ssrna And Amp-Pnp
Length = 512
Score = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 38/157 (24%), Positives = 70/157 (44%), Gaps = 26/157 (16%)
Query: 217 QTLLFSATMPKKIQNFARSALVKPITINVGRAGKIMP----------------SMNVVQE 260
+TLLFSAT+ K+Q A + + K + + K P + ++
Sbjct: 215 KTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEKFANSIFAA 274
Query: 261 VEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYL---LLKGVEAVAIHGGKDQ 317
VE++K++ K + + +IFA + + L K + + HG Q
Sbjct: 275 VEHIKKQIK-------ERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQ 327
Query: 318 EERTRSVESFRKGQKDVMVATDVASKGLDFEEIKHVI 354
+RT V+ F+K + ++V TDV ++G+DF + V+
Sbjct: 328 NKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVL 364
>pdb|2WAX|A Chain A, Structure Of The Human Ddx6 C-Terminal Domain In Complex
With An Edc3-Fdf Peptide
pdb|2WAX|C Chain C, Structure Of The Human Ddx6 C-Terminal Domain In Complex
With An Edc3-Fdf Peptide
pdb|2WAY|A Chain A, Structure Of The Human Ddx6 C-Terminal Domain In Complex
With An Edc3-Fdf Peptide
pdb|2WAY|C Chain C, Structure Of The Human Ddx6 C-Terminal Domain In Complex
With An Edc3-Fdf Peptide
Length = 193
Score = 45.1 bits (105), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 28/100 (28%), Positives = 44/100 (44%), Gaps = 1/100 (1%)
Query: 257 VVQEVEYVKQEAKIVYLLECLQKTE-PPVLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGK 315
V Q YV + K+ L + + +IF Q V+ + + + G IH
Sbjct: 19 VTQYYAYVTERQKVHCLNTLFSRLQINQSIIFCNSSQRVELLAKKISQLGYSCFYIHAKM 78
Query: 316 DQEERTRSVESFRKGQKDVMVATDVASKGLDFEEIKHVIN 355
QE R R FR G +V TD+ ++G+D + + VIN
Sbjct: 79 RQEHRNRVFHDFRNGLCRNLVCTDLFTRGIDIQAVNVVIN 118
>pdb|3FHO|A Chain A, Structure Of S. Pombe Dbp5
pdb|3FHO|B Chain B, Structure Of S. Pombe Dbp5
Length = 508
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 38/154 (24%), Positives = 67/154 (43%), Gaps = 30/154 (19%)
Query: 217 QTLLFSATMPKKIQNFARSALVKPITINVGRAGKIMPSMNVVQ------EVEYVKQ---- 266
Q +LFSAT ++++ +A + P+ N ++ VE +KQ
Sbjct: 293 QIVLFSATFSERVEKYAE---------------RFAPNANEIRLKTEELSVEGIKQLYMD 337
Query: 267 ----EAKIVYLLECLQK-TEPPVLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEERT 321
E K L+E T +IF +KK + I + G + G + +R
Sbjct: 338 CQSEEHKYNVLVELYGLLTIGQSIIFCKKKDTAEEIARRMTADGHTVACLTGNLEGAQRD 397
Query: 322 RSVESFRKGQKDVMVATDVASKGLDFEEIKHVIN 355
++SFR G V+V T+V ++G+D ++ V+N
Sbjct: 398 AIMDSFRVGTSKVLVTTNVIARGIDVSQVNLVVN 431
>pdb|1FUK|A Chain A, Crystal Structure Of The Carboxy Terminal Domain Of Yeast
Eif4a
Length = 165
Score = 42.0 bits (97), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 24/99 (24%), Positives = 47/99 (47%), Gaps = 5/99 (5%)
Query: 272 YLLECLQKTEPPV-----LIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEERTRSVES 326
Y ECL + +IF ++ V+ + L AI+ Q+ER ++
Sbjct: 16 YKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKE 75
Query: 327 FRKGQKDVMVATDVASKGLDFEEIKHVINTEAKIKKREH 365
FR G ++++TD+ ++G+D +++ VIN + K +
Sbjct: 76 FRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENY 114
>pdb|2RB4|A Chain A, Crystal Structure Of The Helicase Domain Of Human Ddx25
Rna Helicase
pdb|2RB4|B Chain B, Crystal Structure Of The Helicase Domain Of Human Ddx25
Rna Helicase
Length = 175
Score = 41.6 bits (96), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 18/80 (22%), Positives = 46/80 (57%)
Query: 285 LIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEERTRSVESFRKGQKDVMVATDVASKG 344
+IF + +++ + ++ G + + G E+R ++ FR G++ V++ T+V ++G
Sbjct: 38 IIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNVCARG 97
Query: 345 LDFEEIKHVINTEAKIKKRE 364
+D +++ V+N + +K+ E
Sbjct: 98 IDVKQVTIVVNFDLPVKQGE 117
>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 = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/34 (55%), Positives = 22/34 (64%)
Query: 216 RQTLLFSATMPKKIQNFARSALVKPITINVGRAG 249
RQTL+FSAT PK+IQ A L I + VGR G
Sbjct: 210 RQTLMFSATFPKEIQKLAADFLYNYIFMTVGRVG 243
>pdb|4DB2|A Chain A, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex
pdb|4DB2|B Chain B, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex
Length = 257
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 30/51 (58%)
Query: 304 KGVEAVAIHGGKDQEERTRSVESFRKGQKDVMVATDVASKGLDFEEIKHVI 354
K + + HG Q +RT V+ F+K + ++V TDV ++G+DF + V+
Sbjct: 59 KDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVL 109
>pdb|4DB4|A Chain A, Mss116p Dead-Box Helicase Domain 2 Bound To A Chimaeric
Rna-Dna Duplex
pdb|4DB4|B Chain B, Mss116p Dead-Box Helicase Domain 2 Bound To A Chimaeric
Rna-Dna Duplex
Length = 256
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 30/51 (58%)
Query: 304 KGVEAVAIHGGKDQEERTRSVESFRKGQKDVMVATDVASKGLDFEEIKHVI 354
K + + HG Q +RT V+ F+K + ++V TDV ++G+DF + V+
Sbjct: 59 KDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVL 109
>pdb|4DB2|C Chain C, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex
pdb|4DB2|D Chain D, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex
Length = 257
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 30/51 (58%)
Query: 304 KGVEAVAIHGGKDQEERTRSVESFRKGQKDVMVATDVASKGLDFEEIKHVI 354
K + + HG Q +RT V+ F+K + ++V TDV ++G+DF + V+
Sbjct: 59 KDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVL 109
>pdb|3DKP|A Chain A, Human Dead-Box Rna-Helicase Ddx52, Conserved Domain I In
Complex With Adp
Length = 245
Score = 37.4 bits (85), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 41/81 (50%), Gaps = 5/81 (6%)
Query: 146 DIIRRNLRILVEGDDVPPACCSFRLM----KLPESLVRALEAKGIKKPTPIQVQGIPAAL 201
+ +R +I V+G D+P +F+ + K+ L++ + G + PTPIQ+Q IP L
Sbjct: 5 NFLRNKHKIHVQGTDLPDPIATFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVML 64
Query: 202 SEDVRTIFSFFRGQRQTLLFS 222
+ S G +TL FS
Sbjct: 65 -HGRELLASAPTGSGKTLAFS 84
>pdb|3MWJ|A Chain A, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Apo Form
pdb|3MWJ|B Chain B, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Apo Form
pdb|3MWK|A Chain A, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Complex
With 8-Oxo- Amp
pdb|3MWK|B Chain B, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Complex
With 8-Oxo- Amp
pdb|3MWL|A Chain A, Q28e Mutant Of Hera N-Terminal Reca-Like Domain In Complex
With 8- Oxoadenosine
pdb|3MWL|B Chain B, Q28e Mutant Of Hera N-Terminal Reca-Like Domain In Complex
With 8- Oxoadenosine
pdb|3NBF|A Chain A, Q28e Mutant Of Hera Helicase N-Terminal Domain Bound To
8-Oxo-Adp
pdb|3NBF|B Chain B, Q28e Mutant Of Hera Helicase N-Terminal Domain Bound To
8-Oxo-Adp
pdb|3NBF|C Chain C, Q28e Mutant Of Hera Helicase N-Terminal Domain Bound To
8-Oxo-Adp
pdb|3NBF|D Chain D, Q28e Mutant Of Hera Helicase N-Terminal Domain Bound To
8-Oxo-Adp
pdb|3NEJ|A Chain A, Q28e Mutant Of Hera Rna Helicase N-Terminal Domain -
Perfectly Twinned Hexagonal Form
pdb|3NEJ|B Chain B, Q28e Mutant Of Hera Rna Helicase N-Terminal Domain -
Perfectly Twinned Hexagonal Form
Length = 207
Score = 37.0 bits (84), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 18/43 (41%), Positives = 24/43 (55%)
Query: 203 EDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINV 245
E+V + S RQTLLFSAT+P + A + P+ INV
Sbjct: 163 EEVEALLSATPPSRQTLLFSATLPSWAKRLAERYMKNPVLINV 205
Score = 28.9 bits (63), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 1/62 (1%)
Query: 168 FRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSEDVRTIFSFFRGQRQTLLFSATMPK 227
F+ L ++ AL +G+ PTPI+ +P AL E I G +TL F+ + +
Sbjct: 3 FKDFPLKPEILEALHGRGLTTPTPIEAAALPLAL-EGKDLIGQARTGTGKTLAFALPIAE 61
Query: 228 KI 229
++
Sbjct: 62 RL 63
>pdb|2GXQ|A Chain A, Hera N-Terminal Domain In Complex With Amp, Crystal Form 1
pdb|2GXS|A Chain A, Hera N-Terminal Domain In Complex With Amp, Crystal Form 2
pdb|2GXS|B Chain B, Hera N-Terminal Domain In Complex With Amp, Crystal Form 2
pdb|2GXU|A Chain A, Hera N-Terminal Domain In Complex With Orthophosphate,
Crystal Form 1
Length = 207
Score = 36.6 bits (83), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 18/43 (41%), Positives = 24/43 (55%)
Query: 203 EDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINV 245
E+V + S RQTLLFSAT+P + A + P+ INV
Sbjct: 163 EEVEALLSATPPSRQTLLFSATLPSWAKRLAERYMKNPVLINV 205
Score = 30.4 bits (67), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 31/62 (50%), Gaps = 1/62 (1%)
Query: 168 FRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSEDVRTIFSFFRGQRQTLLFSATMPK 227
F+ L ++ AL +G+ PTPIQ +P AL E I G +TL F+ + +
Sbjct: 3 FKDFPLKPEILEALHGRGLTTPTPIQAAALPLAL-EGKDLIGQARTGTGKTLAFALPIAE 61
Query: 228 KI 229
++
Sbjct: 62 RL 63
>pdb|4A4D|A Chain A, Crystal Structure Of The N-Terminal Domain Of The Human
Dead-Box Rna Helicase Ddx5 (P68)
Length = 253
Score = 36.2 bits (82), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 18/42 (42%), Positives = 25/42 (59%)
Query: 205 VRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVG 246
+R I R RQTL++SAT PK+++ A L I IN+G
Sbjct: 211 IRKIVDQIRPDRQTLMWSATWPKEVRQLAEDFLKDYIHINIG 252
Score = 35.8 bits (81), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 27/54 (50%)
Query: 149 RRNLRILVEGDDVPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALS 202
RR+ I V G + P +F P +++ + + +PT IQ QG P ALS
Sbjct: 26 RRSKEITVRGHNCPKPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALS 79
>pdb|3FE2|A Chain A, Human Dead-Box Rna Helicase Ddx5 (P68), Conserved Domain I
In Complex With Adp
pdb|3FE2|B Chain B, Human Dead-Box Rna Helicase Ddx5 (P68), Conserved Domain I
In Complex With Adp
Length = 242
Score = 36.2 bits (82), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 18/42 (42%), Positives = 25/42 (59%)
Query: 205 VRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVG 246
+R I R RQTL++SAT PK+++ A L I IN+G
Sbjct: 197 IRKIVDQIRPDRQTLMWSATWPKEVRQLAEDFLKDYIHINIG 238
Score = 35.8 bits (81), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 27/54 (50%)
Query: 149 RRNLRILVEGDDVPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALS 202
RR+ I V G + P +F P +++ + + +PT IQ QG P ALS
Sbjct: 12 RRSKEITVRGHNCPKPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALS 65
>pdb|3BER|A Chain A, Human Dead-Box Rna-Helicase Ddx47, Conserved Domain I In
Complex With Amp
Length = 249
Score = 35.4 bits (80), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 16/30 (53%), Positives = 20/30 (66%)
Query: 216 RQTLLFSATMPKKIQNFARSALVKPITINV 245
R+T LFSATM KK+Q R+AL P+ V
Sbjct: 218 RKTFLFSATMTKKVQKLQRAALKNPVKCAV 247
>pdb|1WP9|A Chain A, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
pdb|1WP9|B Chain B, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
pdb|1WP9|C Chain C, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
pdb|1WP9|D Chain D, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
pdb|1WP9|E Chain E, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
pdb|1WP9|F Chain F, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
Length = 494
Score = 35.0 bits (79), Expect = 0.068, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 42/88 (47%), Gaps = 8/88 (9%)
Query: 278 QKTEPPVLIFAEKKQDVDAIHEYLLLKGVEAVAIHG--------GKDQEERTRSVESFRK 329
+K +++F ++ I L+ G++A G G Q E+ ++ F +
Sbjct: 358 RKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFAR 417
Query: 330 GQKDVMVATDVASKGLDFEEIKHVINTE 357
G+ +V+VAT V +GLD E+ V+ E
Sbjct: 418 GEFNVLVATSVGEEGLDVPEVDLVVFYE 445
>pdb|1VEC|A Chain A, Crystal Structure Of The N-Terminal Domain Of RckP54, A
Human Dead-Box Protein
pdb|1VEC|B Chain B, Crystal Structure Of The N-Terminal Domain Of RckP54, A
Human Dead-Box Protein
Length = 206
Score = 35.0 bits (79), Expect = 0.075, Method: Compositional matrix adjust.
Identities = 16/29 (55%), Positives = 18/29 (62%)
Query: 216 RQTLLFSATMPKKIQNFARSALVKPITIN 244
RQ LL+SAT P +Q F S L KP IN
Sbjct: 178 RQILLYSATFPLSVQKFMNSHLEKPYEIN 206
>pdb|4GL2|A Chain A, Structural Basis For Dsrna Duplex Backbone Recognition By
Mda5
pdb|4GL2|B Chain B, Structural Basis For Dsrna Duplex Backbone Recognition By
Mda5
Length = 699
Score = 34.3 bits (77), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 23/84 (27%), Positives = 41/84 (48%), Gaps = 14/84 (16%)
Query: 285 LIFAEKKQDVDAIHEYLLLK------GVEAVAIHGG--------KDQEERTRSVESFRKG 330
+IF + +Q A+ +++ GV+A + G Q E+ + FR G
Sbjct: 404 IIFTKTRQSAYALSQWITENEKFAEVGVKAHHLIGAGHSSEFKPMTQNEQKEVISKFRTG 463
Query: 331 QKDVMVATDVASKGLDFEEIKHVI 354
+ ++++AT VA +GLD +E VI
Sbjct: 464 KINLLIATTVAEEGLDIKECNIVI 487
>pdb|3P4X|A Chain A, Helicase Domain Of Reverse Gyrase From Thermotoga Maritima
pdb|3P4X|B Chain B, Helicase Domain Of Reverse Gyrase From Thermotoga Maritima
Length = 413
Score = 33.9 bits (76), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 22/87 (25%), Positives = 46/87 (52%), Gaps = 10/87 (11%)
Query: 273 LLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEERTRSVESFRKGQK 332
L+E L+ +LIFA+ +++ ++EYL + + G+ E ++ E F+ G+
Sbjct: 243 LVELLEIFRDGILIFAQTEEEGKELYEYL-----KRFKFNVGETWSEFEKNFEDFKVGKI 297
Query: 333 DVMVATDVA----SKGLDF-EEIKHVI 354
++++ ++G+D E IK+VI
Sbjct: 298 NILIGVQAYYGKLTRGVDLPERIKYVI 324
>pdb|3OIY|A Chain A, Helicase Domain Of Reverse Gyrase From Thermotoga Maritima
pdb|3OIY|B Chain B, Helicase Domain Of Reverse Gyrase From Thermotoga Maritima
Length = 414
Score = 33.9 bits (76), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 22/87 (25%), Positives = 46/87 (52%), Gaps = 10/87 (11%)
Query: 273 LLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEERTRSVESFRKGQK 332
L+E L+ +LIFA+ +++ ++EYL + + G+ E ++ E F+ G+
Sbjct: 244 LVELLEIFRDGILIFAQTEEEGKELYEYL-----KRFKFNVGETWSEFEKNFEDFKVGKI 298
Query: 333 DVMVATDVA----SKGLDF-EEIKHVI 354
++++ ++G+D E IK+VI
Sbjct: 299 NILIGVQAYYGKLTRGVDLPERIKYVI 325
>pdb|3P4Y|A Chain A, Helicase Domain Of Reverse Gyrase From Thermotoga Maritima
- P2 Form
Length = 415
Score = 33.9 bits (76), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 22/87 (25%), Positives = 46/87 (52%), Gaps = 10/87 (11%)
Query: 273 LLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEERTRSVESFRKGQK 332
L+E L+ +LIFA+ +++ ++EYL + + G+ E ++ E F+ G+
Sbjct: 245 LVELLEIFRDGILIFAQTEEEGKELYEYL-----KRFKFNVGETWSEFEKNFEDFKVGKI 299
Query: 333 DVMVATDVA----SKGLDF-EEIKHVI 354
++++ ++G+D E IK+VI
Sbjct: 300 NILIGVQAYYGKLTRGVDLPERIKYVI 326
>pdb|3LY5|A Chain A, Ddx18 Dead-Domain
pdb|3LY5|B Chain B, Ddx18 Dead-Domain
Length = 262
Score = 33.5 bits (75), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 25/40 (62%)
Query: 200 ALSEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVK 239
E+++ I +RQT+LFSAT +K+++ AR +L K
Sbjct: 217 GFEEELKQIIKLLPTRRQTMLFSATQTRKVEDLARISLKK 256
>pdb|4I1S|A Chain A, Melanoma Differentiation Associated Protein-5 Helicase
Domain Complex With Inhibitor Non-structural Protein V
Length = 243
Score = 33.1 bits (74), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 26/98 (26%), Positives = 46/98 (46%), Gaps = 16/98 (16%)
Query: 273 LLECLQKTEPPV--LIFAEKKQDVDAIHEYLLLK------GVEAVAIHGG--------KD 316
+ E +TE +IF + +Q A+ +++ GV+A + G
Sbjct: 140 IXEHFTRTEESARGIIFTKTRQSAYALSQWITDNKKFAEVGVKAHHLIGAGHSSEFKPXT 199
Query: 317 QEERTRSVESFRKGQKDVMVATDVASKGLDFEEIKHVI 354
Q E+ + FR G+ ++++AT VA +GLD +E VI
Sbjct: 200 QNEQREVISKFRTGKINLLIATTVAEEGLDIKECNIVI 237
>pdb|2VA8|A Chain A, Dna Repair Helicase Hel308
pdb|2VA8|B Chain B, Dna Repair Helicase Hel308
Length = 715
Score = 33.1 bits (74), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 37/72 (51%), Gaps = 1/72 (1%)
Query: 171 MKLPESLVRALEAKGIKKPTPIQVQGIPAALSEDVRTIFSFFRGQRQTLLFS-ATMPKKI 229
+KLP +++ ++ +GIKK P Q + + L E R + + G +TL+ + +
Sbjct: 13 LKLPSNVIEIIKKRGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGIISFLL 72
Query: 230 QNFARSALVKPI 241
+N ++ V P+
Sbjct: 73 KNGGKAIYVTPL 84
>pdb|4DDT|A Chain A, Thermotoga Maritima Reverse Gyrase, C2 Form 2
pdb|4DDU|A Chain A, Thermotoga Maritima Reverse Gyrase, C2 Form 1
pdb|4DDV|A Chain A, Thermotoga Maritima Reverse Gyrase, Triclinic Form
pdb|4DDV|B Chain B, Thermotoga Maritima Reverse Gyrase, Triclinic Form
pdb|4DDW|A Chain A, Thermotoga Maritima Reverse Gyrase, C-centered
Orthorhombic Form
pdb|4DDX|A Chain A, Thermotoga Maritima Reverse Gyrase, Primitive Monoclinic
Form
pdb|4DDX|B Chain B, Thermotoga Maritima Reverse Gyrase, Primitive Monoclinic
Form
Length = 1104
Score = 32.7 bits (73), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 22/87 (25%), Positives = 46/87 (52%), Gaps = 10/87 (11%)
Query: 273 LLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEERTRSVESFRKGQK 332
L+E L+ +LIFA+ +++ ++EYL + + G+ E ++ E F+ G+
Sbjct: 301 LVELLEIFRDGILIFAQTEEEGKELYEYL-----KRFKFNVGETWSEFEKNFEDFKVGKI 355
Query: 333 DVMVATDVA----SKGLDF-EEIKHVI 354
++++ ++G+D E IK+VI
Sbjct: 356 NILIGVQAYYGKLTRGVDLPERIKYVI 382
>pdb|1GM5|A Chain A, Structure Of Recg Bound To Three-Way Dna Junction
Length = 780
Score = 32.7 bits (73), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 23/36 (63%)
Query: 311 IHGGKDQEERTRSVESFRKGQKDVMVATDVASKGLD 346
+HG QEE+ R + F +G+ D++V+T V G+D
Sbjct: 619 MHGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVGID 654
>pdb|1OYW|A Chain A, Structure Of The Recq Catalytic Core
Length = 523
Score = 32.3 bits (72), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 17/71 (23%), Positives = 33/71 (46%)
Query: 285 LIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEERTRSVESFRKGQKDVMVATDVASKG 344
+I+ + V+ L KG+ A A H G + R E F++ ++VAT G
Sbjct: 240 IIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGXG 299
Query: 345 LDFEEIKHVIN 355
++ ++ V++
Sbjct: 300 INKPNVRFVVH 310
>pdb|1OYY|A Chain A, Structure Of The Recq Catalytic Core Bound To Atp-Gamma-S
Length = 523
Score = 32.0 bits (71), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 17/71 (23%), Positives = 33/71 (46%)
Query: 285 LIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEERTRSVESFRKGQKDVMVATDVASKG 344
+I+ + V+ L KG+ A A H G + R E F++ ++VAT G
Sbjct: 240 IIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMG 299
Query: 345 LDFEEIKHVIN 355
++ ++ V++
Sbjct: 300 INKPNVRFVVH 310
>pdb|2PL3|A Chain A, Human Dead-Box Rna Helicase Ddx10, Dead Domain In Complex
With Adp
Length = 236
Score = 32.0 bits (71), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 14/26 (53%), Positives = 19/26 (73%)
Query: 215 QRQTLLFSATMPKKIQNFARSALVKP 240
+RQTLLFSAT K +++ AR +L P
Sbjct: 202 KRQTLLFSATQTKSVKDLARLSLKNP 227
>pdb|1T5L|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb Point
Mutant Y96a Revealing A Novel Fold For Domain 2
pdb|1T5L|B Chain B, Crystal Structure Of The Dna Repair Protein Uvrb Point
Mutant Y96a Revealing A Novel Fold For Domain 2
Length = 658
Score = 32.0 bits (71), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 18/70 (25%), Positives = 33/70 (47%)
Query: 284 VLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEERTRSVESFRKGQKDVMVATDVASK 343
L+ K+ + + +YL G++ +H ER + R G+ DV+V ++ +
Sbjct: 448 TLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLRE 507
Query: 344 GLDFEEIKHV 353
GLD E+ V
Sbjct: 508 GLDIPEVSLV 517
>pdb|1D9X|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb
Length = 658
Score = 31.6 bits (70), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 18/70 (25%), Positives = 33/70 (47%)
Query: 284 VLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEERTRSVESFRKGQKDVMVATDVASK 343
L+ K+ + + +YL G++ +H ER + R G+ DV+V ++ +
Sbjct: 448 TLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLRE 507
Query: 344 GLDFEEIKHV 353
GLD E+ V
Sbjct: 508 GLDIPEVSLV 517
>pdb|2FDC|A Chain A, Structural Basis Of Dna Damage Recognition And Processing
By Uvrb: Crystal Structure Of A UvrbDNA COMPLEX
pdb|2FDC|B Chain B, Structural Basis Of Dna Damage Recognition And Processing
By Uvrb: Crystal Structure Of A UvrbDNA COMPLEX
Length = 658
Score = 31.6 bits (70), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 18/70 (25%), Positives = 33/70 (47%)
Query: 284 VLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEERTRSVESFRKGQKDVMVATDVASK 343
L+ K+ + + +YL G++ +H ER + R G+ DV+V ++ +
Sbjct: 448 TLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLRE 507
Query: 344 GLDFEEIKHV 353
GLD E+ V
Sbjct: 508 GLDIPEVSLV 517
>pdb|1D9Z|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb In
Complex With Atp
Length = 657
Score = 31.6 bits (70), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 18/70 (25%), Positives = 33/70 (47%)
Query: 284 VLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEERTRSVESFRKGQKDVMVATDVASK 343
L+ K+ + + +YL G++ +H ER + R G+ DV+V ++ +
Sbjct: 447 TLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLRE 506
Query: 344 GLDFEEIKHV 353
GLD E+ V
Sbjct: 507 GLDIPEVSLV 516
>pdb|3UWX|B Chain B, Crystal Structure Of Uvra-Uvrb Complex
Length = 683
Score = 31.6 bits (70), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 18/70 (25%), Positives = 33/70 (47%)
Query: 284 VLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEERTRSVESFRKGQKDVMVATDVASK 343
L+ K+ + + +YL G++ +H ER + R G+ DV+V ++ +
Sbjct: 473 TLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLRE 532
Query: 344 GLDFEEIKHV 353
GLD E+ V
Sbjct: 533 GLDIPEVSLV 542
>pdb|1T6N|A Chain A, Crystal Structure Of The N-Terminal Domain Of Human Uap56
pdb|1T6N|B Chain B, Crystal Structure Of The N-Terminal Domain Of Human Uap56
Length = 220
Score = 31.2 bits (69), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 26/45 (57%)
Query: 201 LSEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINV 245
+ DV+ IF ++Q ++FSAT+ K+I+ R + P+ I V
Sbjct: 176 MRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFV 220
>pdb|1XPI|A Chain A, Crystal Structure Of The Catalytic Domain Of E. Coli
Pseudouridine Synthase Rluc
pdb|1XPI|B Chain B, Crystal Structure Of The Catalytic Domain Of E. Coli
Pseudouridine Synthase Rluc
Length = 231
Score = 31.2 bits (69), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 32/54 (59%)
Query: 254 SMNVVQEVEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGVE 307
S V++ + ++ EA+ + L+ L + VL+ A+K+ + ++HE L KG++
Sbjct: 32 SFGVIEGLRALRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQ 85
>pdb|1V9K|A Chain A, The Crystal Structure Of The Catalytic Domain Of
Pseudouridine Synthase Rluc From Escherichia Coli
pdb|1V9K|B Chain B, The Crystal Structure Of The Catalytic Domain Of
Pseudouridine Synthase Rluc From Escherichia Coli
Length = 228
Score = 30.4 bits (67), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 31/54 (57%)
Query: 254 SMNVVQEVEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGVE 307
S V++ + ++ EA+ + L+ L + VL+ A+K+ + ++HE L KG +
Sbjct: 29 SFGVIEGLRALRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGXQ 82
>pdb|3IUY|A Chain A, Crystal Structure Of Ddx53 Dead-Box Domain
pdb|3IUY|B Chain B, Crystal Structure Of Ddx53 Dead-Box Domain
Length = 228
Score = 30.4 bits (67), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 43/183 (23%), Positives = 74/183 (40%), Gaps = 51/183 (27%)
Query: 161 VPPACCSFR--LMKLPESLVRALEAKGIKKPTPIQVQGIPAALSEDVRTIFSFFRGQRQT 218
+P C F+ + P+ L++++ GI KPTPIQ Q P L + + I G +T
Sbjct: 14 IPKPTCRFKDAFQQYPD-LLKSIIRVGILKPTPIQSQAWPIIL-QGIDLIVVAQTGTGKT 71
Query: 219 LLFSATMPKKIQNFARSALVKPITINVGRAGKIMPSMNVVQEVEYVKQEAKIVYLLECLQ 278
L S MP I + S + +E Q
Sbjct: 72 L--SYLMPGFIH---------------------LDSQPISRE-----------------Q 91
Query: 279 KTEPPVLIFAEKKQ---DVDAIHEYLLLKGVEAVAIHGGKDQEERTRSVESFRKGQKDVM 335
+ P +L+ ++ V+A KG++++ I+GG++ R +E KG D++
Sbjct: 92 RNGPGMLVLTPTRELALHVEAECSKYSYKGLKSICIYGGRN---RNGQIEDISKG-VDII 147
Query: 336 VAT 338
+AT
Sbjct: 148 IAT 150
Score = 30.0 bits (66), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 22/41 (53%)
Query: 205 VRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINV 245
+R I R RQT++ SAT P ++ A S L P+ + V
Sbjct: 188 IRKILLDVRPDRQTVMTSATWPDTVRQLALSYLKDPMIVYV 228
>pdb|3V4R|A Chain A, Crystal Structure Of A Uvrb Dimer-Dna Complex
pdb|3V4R|B Chain B, Crystal Structure Of A Uvrb Dimer-Dna Complex
Length = 667
Score = 30.4 bits (67), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 34/70 (48%)
Query: 284 VLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEERTRSVESFRKGQKDVMVATDVASK 343
VL+ K+ + + +YL G++ +H ER + R G+ DV+V ++ +
Sbjct: 454 VLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLRE 513
Query: 344 GLDFEEIKHV 353
GLD E+ V
Sbjct: 514 GLDIPEVSLV 523
>pdb|2D7D|A Chain A, Structural Insights Into The Cryptic Dna Dependent Atp-Ase
Activity Of Uvrb
pdb|2NMV|A Chain A, Damage Detection By The Uvrabc Pathway: Crystal Structure
Of Uvrb Bound To Fluorescein-Adducted Dna
Length = 661
Score = 30.4 bits (67), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 34/70 (48%)
Query: 284 VLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEERTRSVESFRKGQKDVMVATDVASK 343
VL+ K+ + + +YL G++ +H ER + R G+ DV+V ++ +
Sbjct: 448 VLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLRE 507
Query: 344 GLDFEEIKHV 353
GLD E+ V
Sbjct: 508 GLDIPEVSLV 517
>pdb|3BOR|A Chain A, Crystal Structure Of The Deadc Domain Of Human Translation
Initiation Factor 4a-2
Length = 237
Score = 29.6 bits (65), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 17/40 (42%), Positives = 23/40 (57%), Gaps = 1/40 (2%)
Query: 167 SFRLMKLPESLVRALEAKGIKKPTPIQVQG-IPAALSEDV 205
+F M L ESL+R + A G +KP+ IQ + IP DV
Sbjct: 31 NFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDV 70
>pdb|3RC3|A Chain A, Human Mitochondrial Helicase Suv3
Length = 677
Score = 29.6 bits (65), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 20/83 (24%), Positives = 36/83 (43%), Gaps = 3/83 (3%)
Query: 274 LECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEERTRSVESFRKGQK- 332
LE L P I K D+ ++ + ++G+E+ I+G + + F
Sbjct: 313 LESLDNLRPGDCIVCFSKNDIYSVSRQIEIRGLESAVIYGSLPPGTKLAQAKKFNDPNDP 372
Query: 333 -DVMVATDVASKGLDFEEIKHVI 354
++VATD GL+ I+ +I
Sbjct: 373 CKILVATDAIGXGLNL-SIRRII 394
>pdb|3TBK|A Chain A, Mouse Rig-I Atpase Domain
Length = 555
Score = 29.6 bits (65), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 22/89 (24%), Positives = 40/89 (44%), Gaps = 13/89 (14%)
Query: 279 KTEPPVLIFAEKKQDVDAIHEYL------------LLKGVEAVAIHGGKDQEERTRSVES 326
K E ++F + + VDA+ +++ +L G G + +E+
Sbjct: 387 KPETKTILFVKTRALVDALKKWIEENPALSFLKPGILTGRGRTNRATGXTLPAQKCVLEA 446
Query: 327 FR-KGQKDVMVATDVASKGLDFEEIKHVI 354
FR G ++++AT VA +G+D E VI
Sbjct: 447 FRASGDNNILIATSVADEGIDIAECNLVI 475
>pdb|3RC8|A Chain A, Human Mitochondrial Helicase Suv3 In Complex With Short
Rna Fragment
Length = 677
Score = 29.6 bits (65), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 20/83 (24%), Positives = 36/83 (43%), Gaps = 3/83 (3%)
Query: 274 LECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEERTRSVESFRKGQK- 332
LE L P I K D+ ++ + ++G+E+ I+G + + F
Sbjct: 313 LESLDNLRPGDCIVCFSKNDIYSVSRQIEIRGLESAVIYGSLPPGTKLAQAKKFNDPNDP 372
Query: 333 -DVMVATDVASKGLDFEEIKHVI 354
++VATD GL+ I+ +I
Sbjct: 373 CKILVATDAIGMGLNL-SIRRII 394
>pdb|2ZJ2|A Chain A, Archaeal Dna Helicase Hjm Apo State In Form 1
pdb|2ZJ5|A Chain A, Archaeal Dna Helicase Hjm Complexed With Adp In Form 1
pdb|2ZJ8|A Chain A, Archaeal Dna Helicase Hjm Apo State In Form 2
pdb|2ZJA|A Chain A, Archaeal Dna Helicase Hjm Complexed With Amppcp In Form 2
Length = 720
Score = 29.3 bits (64), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 23/43 (53%)
Query: 312 HGGKDQEERTRSVESFRKGQKDVMVATDVASKGLDFEEIKHVI 354
H G ++ER E+FRKG +VAT S G++ + +I
Sbjct: 301 HAGLGRDERVLVEENFRKGIIKAVVATPTLSAGINTPAFRVII 343
>pdb|3MWY|W Chain W, Crystal Structure Of The Chromodomain-atpase Portion Of
The Yeast Chd1 Chromatin Remodeler
Length = 800
Score = 29.3 bits (64), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 30/55 (54%)
Query: 273 LLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEERTRSVESF 327
LL L+K VLIF++ + +D + +YL +KG+ + G +R S++ F
Sbjct: 564 LLTRLKKDGHRVLIFSQMVRMLDILGDYLSIKGINFQRLDGTVPSAQRRISIDHF 618
>pdb|2GHI|A Chain A, Crystal Structure Of Plasmodium Yoelii Multidrug
Resistance Protein 2
pdb|2GHI|B Chain B, Crystal Structure Of Plasmodium Yoelii Multidrug
Resistance Protein 2
pdb|2GHI|C Chain C, Crystal Structure Of Plasmodium Yoelii Multidrug
Resistance Protein 2
pdb|2GHI|D Chain D, Crystal Structure Of Plasmodium Yoelii Multidrug
Resistance Protein 2
Length = 260
Score = 28.5 bits (62), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 21/37 (56%), Gaps = 1/37 (2%)
Query: 271 VYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGVE 307
+ + CL K +P ++IF E +D+ EYL K VE
Sbjct: 164 IAIARCLLK-DPKIVIFDEATSSLDSKTEYLFQKAVE 199
>pdb|2V1X|A Chain A, Crystal Structure Of Human Recq-Like Dna Helicase
pdb|2V1X|B Chain B, Crystal Structure Of Human Recq-Like Dna Helicase
pdb|2WWY|A Chain A, Structure Of Human Recq-Like Helicase In Complex With A
Dna Substrate
pdb|2WWY|B Chain B, Structure Of Human Recq-Like Helicase In Complex With A
Dna Substrate
Length = 591
Score = 28.5 bits (62), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 17/71 (23%), Positives = 35/71 (49%)
Query: 285 LIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEERTRSVESFRKGQKDVMVATDVASKG 344
+I+ ++D + + L G+ A A H + E++T + + V+VAT G
Sbjct: 271 IIYCFSQKDSEQVTVSLQNLGIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATVAFGMG 330
Query: 345 LDFEEIKHVIN 355
+D +++ VI+
Sbjct: 331 IDKPDVRFVIH 341
>pdb|2FZL|A Chain A, Structure Of C-Terminal Domain Of Archaeoglobus Fulgidus
Xpb
Length = 219
Score = 28.1 bits (61), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 39/79 (49%), Gaps = 6/79 (7%)
Query: 269 KIVYLLECLQK-TEPPVLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEERTRSVESF 327
KI L E L++ + ++IF + V I + L+ AI +EER +E F
Sbjct: 101 KIRKLREILERHRKDKIIIFTRHNELVYRISKVFLIP-----AITHRTSREEREEILEGF 155
Query: 328 RKGQKDVMVATDVASKGLD 346
R G+ +V++ V +G+D
Sbjct: 156 RTGRFRAIVSSQVLDEGID 174
>pdb|2YHS|A Chain A, Structure Of The E. Coli Srp Receptor Ftsy
Length = 503
Score = 28.1 bits (61), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 13/55 (23%), Positives = 32/55 (58%), Gaps = 4/55 (7%)
Query: 23 KLIQLGRLAQERHEEKKKLVLSDDEDNNKDSTDEENDESKVWGRMSNISLLDQHS 77
K +G+LA++ ++ K ++L+ + + ++ +VWG+ +NI ++ QH+
Sbjct: 306 KTTTIGKLARQFEQQGKSVMLAAGDTFRAAAVEQ----LQVWGQRNNIPVIAQHT 356
>pdb|2OXC|A Chain A, Human Dead-Box Rna Helicase Ddx20, Dead Domain In Complex
With Adp
pdb|2OXC|B Chain B, Human Dead-Box Rna Helicase Ddx20, Dead Domain In Complex
With Adp
pdb|3B7G|A Chain A, Human Dead-Box Rna Helicase Ddx20, Conserved Domain I
(Dead) In Complex With Amppnp
(Adenosine-(Beta,Gamma)-Imidotriphosphate)
pdb|3B7G|B Chain B, Human Dead-Box Rna Helicase Ddx20, Conserved Domain I
(Dead) In Complex With Amppnp
(Adenosine-(Beta,Gamma)-Imidotriphosphate)
Length = 230
Score = 27.7 bits (60), Expect = 9.7, Method: Compositional matrix adjust.
Identities = 10/31 (32%), Positives = 19/31 (61%)
Query: 168 FRLMKLPESLVRALEAKGIKKPTPIQVQGIP 198
F + L ++ L A G ++P+P+Q++ IP
Sbjct: 26 FESLLLSRPVLEGLRAAGFERPSPVQLKAIP 56
>pdb|1XI4|A Chain A, Clathrin D6 Coat
pdb|1XI4|B Chain B, Clathrin D6 Coat
pdb|1XI4|C Chain C, Clathrin D6 Coat
pdb|1XI4|D Chain D, Clathrin D6 Coat
pdb|1XI4|E Chain E, Clathrin D6 Coat
pdb|1XI4|F Chain F, Clathrin D6 Coat
pdb|1XI4|G Chain G, Clathrin D6 Coat
pdb|1XI4|H Chain H, Clathrin D6 Coat
pdb|1XI4|I Chain I, Clathrin D6 Coat
pdb|1XI5|A Chain A, Clathrin D6 Coat With Auxilin J-Domain
pdb|1XI5|B Chain B, Clathrin D6 Coat With Auxilin J-Domain
pdb|1XI5|C Chain C, Clathrin D6 Coat With Auxilin J-Domain
pdb|1XI5|D Chain D, Clathrin D6 Coat With Auxilin J-Domain
pdb|1XI5|E Chain E, Clathrin D6 Coat With Auxilin J-Domain
pdb|1XI5|F Chain F, Clathrin D6 Coat With Auxilin J-Domain
pdb|1XI5|G Chain G, Clathrin D6 Coat With Auxilin J-Domain
pdb|1XI5|H Chain H, Clathrin D6 Coat With Auxilin J-Domain
pdb|1XI5|I Chain I, Clathrin D6 Coat With Auxilin J-Domain
pdb|3IYV|A Chain A, Clathrin D6 Coat As Full-Length Triskelions
pdb|3IYV|B Chain B, Clathrin D6 Coat As Full-Length Triskelions
pdb|3IYV|C Chain C, Clathrin D6 Coat As Full-Length Triskelions
pdb|3IYV|D Chain D, Clathrin D6 Coat As Full-Length Triskelions
pdb|3IYV|E Chain E, Clathrin D6 Coat As Full-Length Triskelions
pdb|3IYV|F Chain F, Clathrin D6 Coat As Full-Length Triskelions
pdb|3IYV|G Chain G, Clathrin D6 Coat As Full-Length Triskelions
pdb|3IYV|H Chain H, Clathrin D6 Coat As Full-Length Triskelions
pdb|3IYV|I Chain I, Clathrin D6 Coat As Full-Length Triskelions
Length = 1630
Score = 27.7 bits (60), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 57/249 (22%), Positives = 99/249 (39%), Gaps = 22/249 (8%)
Query: 115 AELAKGIQYNDPIKTSWRAPRCILSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLP 174
A A+G Y++ K + AP+ IL P D IRR + + P F ++ L
Sbjct: 370 ALFAQG-NYSEAAKVAANAPKGILRTP----DTIRRFQSVPAQPGQTSPLLQYFGIL-LD 423
Query: 175 ESLVRALEAKGIKKPTPIQ--VQGIPAALSED----VRTIFSFFRGQRQTLLFS----AT 224
+ + E+ + +P Q Q + L ED + + TL S A
Sbjct: 424 QGQLNKYESLELCRPVLQQGRKQLLEKWLKEDKLECSEELGDLVKSVDPTLALSVYLRAN 483
Query: 225 MPKK-IQNFARSALVKPITINVGRAGKIMPSMNVVQEVEYVKQEAKIVYLLECLQKTEPP 283
+P K IQ FA + V+ I + + G + +++ V + + + +Q EP
Sbjct: 484 VPNKVIQCFAETGQVQKIVLYAKKVGYTPDWIFLLRNVMRISPDQGQQFAQMLVQDEEP- 542
Query: 284 VLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEERTRSVESFRKGQKDVMVATDVASK 343
A+ Q VD EY L++ A + K+ +++ R + ++M A VA
Sbjct: 543 ---LADITQIVDVFMEYNLIQQCTAFLLDALKNNRPSEGPLQT-RLLEMNLMHAPQVADA 598
Query: 344 GLDFEEIKH 352
L + H
Sbjct: 599 ILGNQMFTH 607
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 0.132 0.369
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,172,001
Number of Sequences: 62578
Number of extensions: 336466
Number of successful extensions: 1365
Number of sequences better than 100.0: 93
Number of HSP's better than 100.0 without gapping: 77
Number of HSP's successfully gapped in prelim test: 16
Number of HSP's that attempted gapping in prelim test: 1242
Number of HSP's gapped (non-prelim): 117
length of query: 367
length of database: 14,973,337
effective HSP length: 100
effective length of query: 267
effective length of database: 8,715,537
effective search space: 2327048379
effective search space used: 2327048379
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: 52 (24.6 bits)