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= psy1604
(693 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 311 bits (796), Expect = 1e-84, Method: Compositional matrix adjust.
Identities = 157/258 (60%), Positives = 188/258 (72%), Gaps = 10/258 (3%)
Query: 400 KGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMPDVA 459
+GC++++AT GRL D +DR I+ RFVVLDEADRMLDMGF D++ +M H TM
Sbjct: 178 RGCHVVIATPGRLLDFVDRTFITFEDTRFVVLDEADRMLDMGFSEDMRRIMTHVTM--RP 235
Query: 460 NRQTLMFSATFPETIQ-------KNYIFIAVGIIGGASTDVVQTILEVPXXXXXXXXXXX 512
QTLMFSATFPE IQ KNY+F+A+GI+GGA +DV QTI EV
Sbjct: 236 EHQTLMFSATFPEEIQRMAGEFLKNYVFVAIGIVGGACSDVKQTIYEV-NKYAKRSKLIE 294
Query: 513 XXXXDEDGVIVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIHDFKTKKMKVL 572
DG IVFV T R ADF+A +L E E TTSIHG RLQSQREQA+ DFK MKVL
Sbjct: 295 ILSEQADGTIVFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKVL 354
Query: 573 VATAVASRGLDIKGIRHVINYDLPQEIDEYVHRIGRTGRVGNKGRATSFYDPDQDGAIAK 632
+AT+VASRGLDIK I+HVINYD+P +ID+YVHRIGRTGRVGN GRATSF+DP++D AIA
Sbjct: 355 IATSVASRGLDIKNIKHVINYDMPSKIDDYVHRIGRTGRVGNNGRATSFFDPEKDRAIAA 414
Query: 633 DLVRILEQAGQPVPEFLK 650
DLV+ILE +GQ VP+FL+
Sbjct: 415 DLVKILEGSGQTVPDFLR 432
Score = 264 bits (674), Expect = 2e-70, Method: Compositional matrix adjust.
Identities = 134/252 (53%), Positives = 171/252 (67%), Gaps = 5/252 (1%)
Query: 154 LYIPKDVDQSEDNLFSSGIQTGINFSGWENVEVKVSGDNPPRPIESFESAGLREILVKNL 213
YIP + +FSSGI +GI+FS + N+ VKV+G + P+PI+ F SA LR+I++ N+
Sbjct: 12 FYIPPEPSNDAIEIFSSGIASGIHFSKYNNIPVKVTGSDVPQPIQHFTSADLRDIIIDNV 71
Query: 214 KKSNYTKPTPIQKYAIPAGLEGRDLMGCAQTGSGKTAAFLIPIMHHLLESPGELVTGYCA 273
KS Y PTPIQK +IP GRDLM CAQTGSGKTAAFL+PI+ LLE P EL G
Sbjct: 72 NKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILSKLLEDPHELELG--- 128
Query: 274 QPEVIICAPTRELVMQIHEVACKYAYSSVLKICLHYGGASSMHFNRQLEKGCNILVATMG 333
+P+V+I +PTREL +QI A K+A+ S LKI + YGG S H N + +GC++++AT G
Sbjct: 129 RPQVVIVSPTRELAIQIFNEARKFAFESYLKIGIVYGGTSFRHQNECITRGCHVVIATPG 188
Query: 334 RLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMPDVANRQTLMFSATF 393
RL D +DR I+ RFVVLDEADRMLDMGF D++ +M H TM QTLMFSATF
Sbjct: 189 RLLDFVDRTFITFEDTRFVVLDEADRMLDMGFSEDMRRIMTHVTM--RPEHQTLMFSATF 246
Query: 394 PETIQKKGCNIL 405
PE IQ+ L
Sbjct: 247 PEEIQRMAGEFL 258
>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x
Length = 417
Score = 236 bits (601), Expect = 4e-62, Method: Compositional matrix adjust.
Identities = 123/260 (47%), Positives = 173/260 (66%), Gaps = 9/260 (3%)
Query: 399 KKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMPDV 458
++GC++LVAT GRL D+++RG+I L +++VLDEADRMLDMGF I+ +++ TMP
Sbjct: 149 ERGCHLLVATPGRLVDMMERGKIGLDFCKYLVLDEADRMLDMGFEPQIRRIVEQDTMPPK 208
Query: 459 ANRQTLMFSATFPETIQ-------KNYIFIAVGIIGGASTDVVQTILEVPXXXXXXXXXX 511
R T+MFSATFP+ IQ YIF+AVG +G S ++ Q ++ V
Sbjct: 209 GVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGRVGSTSENITQKVVWVEESDKRSFLLD 268
Query: 512 XXXXXDEDGV-IVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIHDFKTKKMK 570
+D + +VFV T + AD + +L A TSIHG R Q RE+A+H F++ K
Sbjct: 269 LLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSP 328
Query: 571 VLVATAVASRGLDIKGIRHVINYDLPQEIDEYVHRIGRTGRVGNKGRATSFYDPDQDGAI 630
+LVATAVA+RGLDI ++HVIN+DLP +I+EYVHRIGRTGRVGN G ATSF++ +++ I
Sbjct: 329 ILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFN-ERNINI 387
Query: 631 AKDLVRILEQAGQPVPEFLK 650
KDL+ +L +A Q VP +L+
Sbjct: 388 TKDLLDLLVEAKQEVPSWLE 407
Score = 211 bits (536), Expect = 1e-54, Method: Compositional matrix adjust.
Identities = 108/223 (48%), Positives = 150/223 (67%), Gaps = 10/223 (4%)
Query: 186 VKVSGDNPPRPIESFESAGLREILVKNLKKSNYTKPTPIQKYAIPAGLEGRDLMGCAQTG 245
V+ +G+N P IESF + EI++ N++ + YT+PTP+QK+AIP E RDLM CAQTG
Sbjct: 3 VEATGNNCPPHIESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTG 62
Query: 246 SGKTAAFLIPIMHHLL-ESPGELVTGYCAQ---------PEVIICAPTRELVMQIHEVAC 295
SGKTAAFL+PI+ + + PGE + P ++ APTREL +QI+E A
Sbjct: 63 SGKTAAFLLPILSQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEAR 122
Query: 296 KYAYSSVLKICLHYGGASSMHFNRQLEKGCNILVATMGRLKDILDRGRISLASVRFVVLD 355
K++Y S ++ C+ YGGA R LE+GC++LVAT GRL D+++RG+I L +++VLD
Sbjct: 123 KFSYRSRVRPCVVYGGADIGQQIRDLERGCHLLVATPGRLVDMMERGKIGLDFCKYLVLD 182
Query: 356 EADRMLDMGFLGDIQHVMQHSTMPDVANRQTLMFSATFPETIQ 398
EADRMLDMGF I+ +++ TMP R T+MFSATFP+ IQ
Sbjct: 183 EADRMLDMGFEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQ 225
>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 = 211 bits (538), Expect = 8e-55, Method: Compositional matrix adjust.
Identities = 111/242 (45%), Positives = 161/242 (66%), Gaps = 7/242 (2%)
Query: 178 FSGWENVEVKVSGDN--PPRPIESFESAGLREILVKNLKKSNYTKPTPIQKYAIPAGLEG 235
F ++++ V V+G + IE+F+ L + N+ ++Y +PTPIQK AIPA LE
Sbjct: 1 FDKYDSIPVSVTGPDYSATNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEH 60
Query: 236 RDLMGCAQTGSGKTAAFLIPIMHHLL-ESPGELVTGYCAQPEVIICAPTRELVMQIHEVA 294
RD+M CAQTGSGKTAAFLIPI++HL+ + + A P+ +I APTREL +QI +
Sbjct: 61 RDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSES 120
Query: 295 CKYAYSSVLKICLHYGGASSMHFNRQLEKGCNILVATMGRLKDILDRGRISLASVRFVVL 354
K++ ++ L+ C+ YGGA + R+++ GC++LVAT GRL D +++ +ISL +++VL
Sbjct: 121 QKFSLNTPLRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYIVL 180
Query: 355 DEADRMLDMGFLGDIQHVMQHSTMPDVANRQTLMFSATFPETIQKKGC----NILVATMG 410
DEADRMLDMGF I+ +++ S MP NRQTLMFSATFP+ IQK N + T+G
Sbjct: 181 DEADRMLDMGFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTVG 240
Query: 411 RL 412
R+
Sbjct: 241 RV 242
Score = 112 bits (280), Expect = 7e-25, Method: Compositional matrix adjust.
Identities = 55/104 (52%), Positives = 72/104 (69%), Gaps = 7/104 (6%)
Query: 401 GCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMPDVAN 460
GC++LVAT GRL D +++ +ISL +++VLDEADRMLDMGF I+ +++ S MP N
Sbjct: 150 GCHLLVATPGRLVDFIEKNKISLEFCKYIVLDEADRMLDMGFEPQIRKIIEESNMPSGIN 209
Query: 461 RQTLMFSATFPETIQK-------NYIFIAVGIIGGASTDVVQTI 497
RQTLMFSATFP+ IQK NYIF+ VG +G S + Q I
Sbjct: 210 RQTLMFSATFPKEIQKLAADFLYNYIFMTVGRVGSTSDSIKQEI 253
>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 = 155 bits (393), Expect = 5e-38, Method: Compositional matrix adjust.
Identities = 89/215 (41%), Positives = 128/215 (59%), Gaps = 7/215 (3%)
Query: 185 EVKVSGDNPPRPIESFESAGLREILVKNLKKSNYTKPTPIQKYAIPAGLEGRDLMGCAQT 244
E+ V G N P+P+ +F A ++ + + N+T+PT IQ P L G D++G AQT
Sbjct: 16 EITVRGHNCPKPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQT 75
Query: 245 GSGKTAAFLIPIMHHLLESPGELVTGYCAQPEVIICAPTRELVMQIHEVACKYAYSSVLK 304
GSGKT ++L+P + H+ P L G P ++ APTREL Q+ +VA +Y + LK
Sbjct: 76 GSGKTLSYLLPAIVHINHQPF-LERG--DGPICLVLAPTRELAQQVQQVAAEYCRACRLK 132
Query: 305 ICLHYGGASSMHFNRQLEKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMG 364
YGGA R LE+G I +AT GRL D L+ G+ +L ++VLDEADRMLDMG
Sbjct: 133 STCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLECGKTNLRRTTYLVLDEADRMLDMG 192
Query: 365 FLGDIQHVMQHSTMPDVANRQTLMFSATFPETIQK 399
F I+ ++ PD RQTLM+SAT+P+ +++
Sbjct: 193 FEPQIRKIVDQ-IRPD---RQTLMWSATWPKEVRQ 223
Score = 72.8 bits (177), Expect = 6e-13, Method: Compositional matrix adjust.
Identities = 41/95 (43%), Positives = 60/95 (63%), Gaps = 11/95 (11%)
Query: 399 KKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMPDV 458
++G I +AT GRL D L+ G+ +L ++VLDEADRMLDMGF I+ ++ PD
Sbjct: 150 ERGVEICIATPGRLIDFLECGKTNLRRTTYLVLDEADRMLDMGFEPQIRKIVDQ-IRPD- 207
Query: 459 ANRQTLMFSATFPETIQ-------KNYIFIAVGII 486
RQTLM+SAT+P+ ++ K+YI I +G +
Sbjct: 208 --RQTLMWSATWPKEVRQLAEDFLKDYIHINIGAL 240
>pdb|4A4D|A Chain A, Crystal Structure Of The N-Terminal Domain Of The Human
Dead-Box Rna Helicase Ddx5 (P68)
Length = 253
Score = 155 bits (393), Expect = 5e-38, Method: Compositional matrix adjust.
Identities = 90/221 (40%), Positives = 130/221 (58%), Gaps = 7/221 (3%)
Query: 185 EVKVSGDNPPRPIESFESAGLREILVKNLKKSNYTKPTPIQKYAIPAGLEGRDLMGCAQT 244
E+ V G N P+P+ +F A ++ + + N+T+PT IQ P L G D++G AQT
Sbjct: 30 EITVRGHNCPKPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQT 89
Query: 245 GSGKTAAFLIPIMHHLLESPGELVTGYCAQPEVIICAPTRELVMQIHEVACKYAYSSVLK 304
GSGKT ++L+P + H+ P L G P ++ APTREL Q+ +VA +Y + LK
Sbjct: 90 GSGKTLSYLLPAIVHINHQPF-LERG--DGPICLVLAPTRELAQQVQQVAAEYCRACRLK 146
Query: 305 ICLHYGGASSMHFNRQLEKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMG 364
YGGA R LE+G I +AT GRL D L+ G+ +L ++VLDEADRMLDMG
Sbjct: 147 STCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLECGKTNLRRTTYLVLDEADRMLDMG 206
Query: 365 FLGDIQHVMQHSTMPDVANRQTLMFSATFPETIQKKGCNIL 405
F I+ ++ PD RQTLM+SAT+P+ +++ + L
Sbjct: 207 FEPQIRKIVDQ-IRPD---RQTLMWSATWPKEVRQLAEDFL 243
Score = 73.2 bits (178), Expect = 5e-13, Method: Compositional matrix adjust.
Identities = 41/93 (44%), Positives = 59/93 (63%), Gaps = 11/93 (11%)
Query: 399 KKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMPDV 458
++G I +AT GRL D L+ G+ +L ++VLDEADRMLDMGF I+ ++ PD
Sbjct: 164 ERGVEICIATPGRLIDFLECGKTNLRRTTYLVLDEADRMLDMGFEPQIRKIVDQ-IRPD- 221
Query: 459 ANRQTLMFSATFPETIQ-------KNYIFIAVG 484
RQTLM+SAT+P+ ++ K+YI I +G
Sbjct: 222 --RQTLMWSATWPKEVRQLAEDFLKDYIHINIG 252
>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 = 147 bits (371), Expect = 2e-35, Method: Compositional matrix adjust.
Identities = 86/238 (36%), Positives = 130/238 (54%), Gaps = 16/238 (6%)
Query: 390 SATFPETIQKKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHV 449
A +P+ K NI+V T GR+ D ++RG ++L +V++ +LDEAD L+ GF+ D++ +
Sbjct: 112 KAIYPQIKALKNANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEXLNXGFIKDVEKI 171
Query: 450 MQHSTMPDVANRQTLMFSATFPETIQK-------NYIFIAVGIIGGASTDVVQTILEVPX 502
+ +++ L+FSAT P I +Y FI I + ++ Q+ +EV
Sbjct: 172 LNACN----KDKRILLFSATXPREILNLAKKYXGDYSFIKAKI----NANIEQSYVEVNE 223
Query: 503 XXXXXXXXXXXXXXDEDGVIVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIH 562
+ G +VF T R+ +A L + +IHG QSQRE+ I
Sbjct: 224 NERFEALCRLLKNKEFYG-LVFCKTKRDTKELASXLRDIGFKAGAIHGDLSQSQREKVIR 282
Query: 563 DFKTKKMKVLVATAVASRGLDIKGIRHVINYDLPQEIDEYVHRIGRTGRVGNKGRATS 620
FK KK+++L+AT V SRG+D+ + VINY LPQ + Y HRIGRTGR G KG+A S
Sbjct: 283 LFKQKKIRILIATDVXSRGIDVNDLNCVINYHLPQNPESYXHRIGRTGRAGKKGKAIS 340
Score = 109 bits (273), Expect = 4e-24, Method: Compositional matrix adjust.
Identities = 67/200 (33%), Positives = 109/200 (54%), Gaps = 15/200 (7%)
Query: 199 SFESAGLREILVKNLKKSNYTKPTPIQKYAIPAGLEGR-DLMGCAQTGSGKTAAFLIPIM 257
+F L + ++ ++ + KPT IQ IP L +++ A+TGSGKTA+F IP++
Sbjct: 7 NFNELNLSDNILNAIRNKGFEKPTDIQXKVIPLFLNDEYNIVAQARTGSGKTASFAIPLI 66
Query: 258 HHLLESPGELVTGYCAQPEVIICAPTRELVMQIHEVACKYAYSSVLKICLHYGGASSMHF 317
+ E+ G E II PTREL +Q+ + + LKI YGG +
Sbjct: 67 ELVNENNG---------IEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQ 117
Query: 318 NRQLEKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHST 377
+ L K NI+V T GR+ D ++RG ++L +V++ +LDEAD L+ GF+ D++ ++
Sbjct: 118 IKAL-KNANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEXLNXGFIKDVEKILNACN 176
Query: 378 MPDVANRQTLMFSATFPETI 397
+++ L+FSAT P I
Sbjct: 177 ----KDKRILLFSATXPREI 192
>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 = 143 bits (360), Expect = 3e-34, Method: Compositional matrix adjust.
Identities = 75/165 (45%), Positives = 106/165 (64%), Gaps = 2/165 (1%)
Query: 487 GGASTDVVQTILEVPXXXXXXXXXXXXXXXDEDGV-IVFVSTIRNADFIACYLCETEIAT 545
G S ++ Q ++ V +D + +VFV T + AD + +L A
Sbjct: 14 GSTSENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYAC 73
Query: 546 TSIHGSRLQSQREQAIHDFKTKKMKVLVATAVASRGLDIKGIRHVINYDLPQEIDEYVHR 605
TSIHG R Q RE+A+H F++ K +LVATAVA+RGLDI ++HVIN+DLP +I+EYVHR
Sbjct: 74 TSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHR 133
Query: 606 IGRTGRVGNKGRATSFYDPDQDGAIAKDLVRILEQAGQPVPEFLK 650
IGRTGRVGN G ATSF++ +++ I KDL+ +L +A Q VP +L+
Sbjct: 134 IGRTGRVGNLGLATSFFN-ERNINITKDLLDLLVEAKQEVPSWLE 177
>pdb|3BER|A Chain A, Human Dead-Box Rna-Helicase Ddx47, Conserved Domain I In
Complex With Amp
Length = 249
Score = 134 bits (336), Expect = 2e-31, Method: Compositional matrix adjust.
Identities = 83/238 (34%), Positives = 137/238 (57%), Gaps = 19/238 (7%)
Query: 169 SSGIQTGINFSGWENVEVKVSGDNPPRPI------ESFESAGLREILVKNLKKSNYTKPT 222
SSG+ G ++++E S +PI ++F+ G+ ++L + + +TKPT
Sbjct: 8 SSGVDLGTENLYFQSMEEHDSPTEASQPIVEEEETKTFKDLGVTDVLCEACDQLGWTKPT 67
Query: 223 PIQKYAIPAGLEGRDLMGCAQTGSGKTAAFLIPIMHHLLESPGELVTGYCAQPEVIICAP 282
IQ AIP L+GRD++G A+TGSGKT AF +PI++ LLE+P L ++ P
Sbjct: 68 KIQIEAIPLALQGRDIIGLAETGSGKTGAFALPILNALLETPQRLF--------ALVLTP 119
Query: 283 TRELVMQIHEVACKYAYSSVLKICLHYGGASSMHFNRQLEKGCNILVATMGRLKDILDRG 342
TREL QI E S ++ + GG SM + L K +I++AT GRL D L+
Sbjct: 120 TRELAFQISEQFEALGSSIGVQSAVIVGGIDSMSQSLALAKKPHIIIATPGRLIDHLENT 179
Query: 343 R-ISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMPDVANRQTLMFSATFPETIQK 399
+ +L +++++V+DEADR+L+M F ++ +++ +P +R+T +FSAT + +QK
Sbjct: 180 KGFNLRALKYLVMDEADRILNMDFETEVDKILK--VIP--RDRKTFLFSATMTKKVQK 233
Score = 52.0 bits (123), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 28/78 (35%), Positives = 53/78 (67%), Gaps = 5/78 (6%)
Query: 400 KGCNILVATMGRLKDILDRGR-ISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMPDV 458
K +I++AT GRL D L+ + +L +++++V+DEADR+L+M F ++ +++ +P
Sbjct: 160 KKPHIIIATPGRLIDHLENTKGFNLRALKYLVMDEADRILNMDFETEVDKILK--VIP-- 215
Query: 459 ANRQTLMFSATFPETIQK 476
+R+T +FSAT + +QK
Sbjct: 216 RDRKTFLFSATMTKKVQK 233
>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 = 129 bits (323), Expect = 6e-30, Method: Compositional matrix adjust.
Identities = 81/219 (36%), Positives = 125/219 (57%), Gaps = 12/219 (5%)
Query: 194 PRPIESFESAGLR-EILVKNLKKSNYTKPTPIQKYAIPAGLEGRDLMGCAQTGSGKTAAF 252
P+P F+ A + L+K++ + KPTPIQ A P L+G DL+ AQTG+GKT ++
Sbjct: 15 PKPTCRFKDAFQQYPDLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSY 74
Query: 253 LIPIMHHLLESP--GELVTGYCAQPEVIICAPTRELVMQIHEVACKYAYSSVLKICLHYG 310
L+P HL P E G P +++ PTREL + + KY+Y + IC+ YG
Sbjct: 75 LMPGFIHLDSQPISREQRNG----PGMLVLTPTRELALHVEAECSKYSYKGLKSICI-YG 129
Query: 311 GASSMHFNRQLEKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQ 370
G + + KG +I++AT GRL D+ ++L S+ ++V+DEAD+MLDM F I+
Sbjct: 130 GRNRNGQIEDISKGVDIIIATPGRLNDLQMNNSVNLRSITYLVIDEADKMLDMEFEPQIR 189
Query: 371 HVMQHSTMPDVANRQTLMFSATFPETIQKKGCNILVATM 409
++ PD RQT+M SAT+P+T+++ + L M
Sbjct: 190 KIL-LDVRPD---RQTVMTSATWPDTVRQLALSYLKDPM 224
Score = 64.3 bits (155), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 33/77 (42%), Positives = 53/77 (68%), Gaps = 4/77 (5%)
Query: 400 KGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMPDVA 459
KG +I++AT GRL D+ ++L S+ ++V+DEAD+MLDM F I+ ++ PD
Sbjct: 142 KGVDIIIATPGRLNDLQMNNSVNLRSITYLVIDEADKMLDMEFEPQIRKIL-LDVRPD-- 198
Query: 460 NRQTLMFSATFPETIQK 476
RQT+M SAT+P+T+++
Sbjct: 199 -RQTVMTSATWPDTVRQ 214
>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna
Helicase From Sulfolobus Tokodaii
Length = 337
Score = 124 bits (310), Expect = 3e-28, Method: Compositional matrix adjust.
Identities = 88/230 (38%), Positives = 124/230 (53%), Gaps = 22/230 (9%)
Query: 400 KGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMPDVA 459
+ +I+VAT GRL D+ +G I L+S V++DEAD M +MGF+ DI+ ++ ++
Sbjct: 104 RNADIVVATPGRLLDLWSKGVIDLSSFEIVIIDEADLMFEMGFIDDIKIILAQTS----- 158
Query: 460 NRQ-TLMFSATFPETIQK-------NYIFIAVGIIGGASTDVVQTILEVPXXXXXXXXXX 511
NR+ T +FSAT PE I+K NY I IG A+ + + V
Sbjct: 159 NRKITGLFSATIPEEIRKVVKDFITNYEEIE-ACIGLANVE--HKFVHVKDDWRSKVQAL 215
Query: 512 XXXXXDEDGVIVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIHDFKTKKMKV 571
+ GVIVFV T RN L + I + G QS R + I F+ + +
Sbjct: 216 RENK--DKGVIVFVRT-RNRVAKLVRLFDNAI---ELRGDLPQSVRNRNIDAFREGEYDM 269
Query: 572 LVATAVASRGLDIKGIRHVINYDLPQEIDEYVHRIGRTGRVGNKGRATSF 621
L+ T VASRGLDI + VIN+D PQ++ Y+HRIGRTGR+G KG A +F
Sbjct: 270 LITTDVASRGLDIPLVEKVINFDAPQDLRTYIHRIGRTGRMGRKGEAITF 319
Score = 103 bits (256), Expect = 5e-22, Method: Compositional matrix adjust.
Identities = 72/205 (35%), Positives = 109/205 (53%), Gaps = 34/205 (16%)
Query: 198 ESFESAGLREILVKNLKKSNYTKPTPIQKYAIPAGLEGRDLMGCAQTGSGKTAAFLIPIM 257
E E A +RE+ KN T +Q IP L+G++++ A+TGSGKTAA+ IPI+
Sbjct: 3 EKIEQA-IREMGFKNF--------TEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPIL 53
Query: 258 HHLLESPGELVTGYCAQPEVIICAPTRELVMQIHEVACKYAYSSVLKICLHYGGASSMHF 317
++S ++ PTREL Q+ K+ YGG M +
Sbjct: 54 ELGMKS--------------LVVTPTRELTRQVASHIRDIGRYMDTKVAEVYGG---MPY 96
Query: 318 NRQLEK--GCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQH 375
Q+ + +I+VAT GRL D+ +G I L+S V++DEAD M +MGF+ DI+ ++
Sbjct: 97 KAQINRVRNADIVVATPGRLLDLWSKGVIDLSSFEIVIIDEADLMFEMGFIDDIKIILAQ 156
Query: 376 STMPDVANRQ-TLMFSATFPETIQK 399
++ NR+ T +FSAT PE I+K
Sbjct: 157 TS-----NRKITGLFSATIPEEIRK 176
>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 = 122 bits (305), Expect = 8e-28, Method: Composition-based stats.
Identities = 76/195 (38%), Positives = 108/195 (55%), Gaps = 11/195 (5%)
Query: 200 FESAGLREILVKNLKKSNYTKPTPIQKYAIPAGLEGRDLMGCAQTGSGKTAAFLIPIMHH 259
F+ L+ +++ L T PTPIQ A+P LEG+DL+G A+TG+GKT AF +PI
Sbjct: 3 FKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAER 62
Query: 260 LLESPGELVTGYCAQPEVIICAPTRELVMQIHEVACKYAYSSVLKICLHYGGASSMHFNR 319
L S +P ++ PTREL +Q+ A + LK+ YGG
Sbjct: 63 LAPSQER-----GRKPRALVLTPTRELALQVASELT--AVAPHLKVVAVYGGTGYGKQKE 115
Query: 320 QLEKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMP 379
L +G + +VAT GR D L +G + L+ V VLDEAD ML MGF +++ ++ +T P
Sbjct: 116 ALLRGADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSMGFEEEVEALLS-ATPP 174
Query: 380 DVANRQTLMFSATFP 394
+RQTL+FSAT P
Sbjct: 175 ---SRQTLLFSATLP 186
Score = 60.5 bits (145), Expect = 3e-09, Method: Composition-based stats.
Identities = 38/91 (41%), Positives = 53/91 (58%), Gaps = 11/91 (12%)
Query: 400 KGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMPDVA 459
+G + +VAT GR D L +G + L+ V VLDEAD ML MGF +++ ++ +T P
Sbjct: 119 RGADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSMGFEEEVEALLS-ATPP--- 174
Query: 460 NRQTLMFSATFP-------ETIQKNYIFIAV 483
+RQTL+FSAT P E KN + I V
Sbjct: 175 SRQTLLFSATLPSWAKRLAERYMKNPVLINV 205
>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 = 120 bits (302), Expect = 2e-27, Method: Composition-based stats.
Identities = 75/195 (38%), Positives = 108/195 (55%), Gaps = 11/195 (5%)
Query: 200 FESAGLREILVKNLKKSNYTKPTPIQKYAIPAGLEGRDLMGCAQTGSGKTAAFLIPIMHH 259
F+ L+ +++ L T PTPI+ A+P LEG+DL+G A+TG+GKT AF +PI
Sbjct: 3 FKDFPLKPEILEALHGRGLTTPTPIEAAALPLALEGKDLIGQARTGTGKTLAFALPIAER 62
Query: 260 LLESPGELVTGYCAQPEVIICAPTRELVMQIHEVACKYAYSSVLKICLHYGGASSMHFNR 319
L S +P ++ PTREL +Q+ A + LK+ YGG
Sbjct: 63 LAPSQER-----GRKPRALVLTPTRELALQVASELT--AVAPHLKVVAVYGGTGYGKQKE 115
Query: 320 QLEKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMP 379
L +G + +VAT GR D L +G + L+ V VLDEAD ML MGF +++ ++ +T P
Sbjct: 116 ALLRGADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSMGFEEEVEALLS-ATPP 174
Query: 380 DVANRQTLMFSATFP 394
+RQTL+FSAT P
Sbjct: 175 ---SRQTLLFSATLP 186
Score = 60.5 bits (145), Expect = 3e-09, Method: Composition-based stats.
Identities = 38/91 (41%), Positives = 53/91 (58%), Gaps = 11/91 (12%)
Query: 400 KGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMPDVA 459
+G + +VAT GR D L +G + L+ V VLDEAD ML MGF +++ ++ +T P
Sbjct: 119 RGADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSMGFEEEVEALLS-ATPP--- 174
Query: 460 NRQTLMFSATFP-------ETIQKNYIFIAV 483
+RQTL+FSAT P E KN + I V
Sbjct: 175 SRQTLLFSATLPSWAKRLAERYMKNPVLINV 205
>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 = 116 bits (291), Expect = 4e-26, Method: Compositional matrix adjust.
Identities = 67/165 (40%), Positives = 91/165 (55%), Gaps = 1/165 (0%)
Query: 486 IGGASTDVVQTILEVPXXXXXXXXXXXXXXXDEDGVIVFVSTIRNADFIACYLCETEIAT 545
+G AS DV+Q + E V++F + D I YL +
Sbjct: 23 MGAASLDVIQEV-EYVKEEAKMVYLLECLQKTPPPVLIFAEKKADVDAIHEYLLLKGVEA 81
Query: 546 TSIHGSRLQSQREQAIHDFKTKKMKVLVATAVASRGLDIKGIRHVINYDLPQEIDEYVHR 605
+IHG + Q +R +AI F+ K VLVAT VAS+GLD I+HVINYD+P+EI+ YVHR
Sbjct: 82 VAIHGGKDQEERTKAIEAFREGKKDVLVATDVASKGLDFPAIQHVINYDMPEEIENYVHR 141
Query: 606 IGRTGRVGNKGRATSFYDPDQDGAIAKDLVRILEQAGQPVPEFLK 650
IGRTG GN G AT+F + D ++ DL +L +A Q VP L+
Sbjct: 142 IGRTGCSGNTGIATTFINKACDESVLMDLKALLLEAKQKVPPVLQ 186
>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 = 111 bits (277), Expect = 1e-24, Method: Compositional matrix adjust.
Identities = 64/210 (30%), Positives = 116/210 (55%), Gaps = 29/210 (13%)
Query: 199 SFESAGLREILVKNLKKSNYTKPTPIQKYAIPAGLEGRDLMGCAQTGSGKTAAFLIPIMH 258
FE L+ L+ + + + KP+PIQ+ +IP L GRD++ A+ G+GK+ A+LIP++
Sbjct: 4 EFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLE 63
Query: 259 HLLESPGELVTGYCAQPEVIICAPTRELVMQIHEVACKYAYSSVLKICLHYGGASSMHFN 318
L + + ++ PTREL +Q+ ++ +++ H GGA M
Sbjct: 64 RLDLKKDNI--------QAMVIVPTRELALQVSQIC--------IQVSKHMGGAKVMATT 107
Query: 319 ---------RQLEKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDI 369
+L+ ++++AT GR+ D++ +G + V+ +VLDEAD++L F+ +
Sbjct: 108 GGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIM 167
Query: 370 QHVMQHSTMPDVANRQTLMFSATFPETIQK 399
+ ++ T+P NRQ L++SATFP ++QK
Sbjct: 168 EDII--LTLP--KNRQILLYSATFPLSVQK 193
Score = 57.0 bits (136), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 28/75 (37%), Positives = 51/75 (68%), Gaps = 4/75 (5%)
Query: 402 CNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMPDVANR 461
++++AT GR+ D++ +G + V+ +VLDEAD++L F+ ++ ++ T+P NR
Sbjct: 123 VHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIMEDII--LTLP--KNR 178
Query: 462 QTLMFSATFPETIQK 476
Q L++SATFP ++QK
Sbjct: 179 QILLYSATFPLSVQK 193
>pdb|2PL3|A Chain A, Human Dead-Box Rna Helicase Ddx10, Dead Domain In Complex
With Adp
Length = 236
Score = 108 bits (270), Expect = 1e-23, Method: Compositional matrix adjust.
Identities = 76/225 (33%), Positives = 117/225 (52%), Gaps = 21/225 (9%)
Query: 186 VKVSGDNPPRPIESFESAGLREIL-----------VKNLKKSNYTKPTPIQKYAIPAGLE 234
++V ++ R ++++E + EI +K L+++ Y T IQK I L+
Sbjct: 2 MQVERESISRLMQNYEKINVNEITRFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQ 61
Query: 235 GRDLMGCAQTGSGKTAAFLIPIMHHLLESPGELVTGYCAQPEVIICAPTRELVMQIHEVA 294
G+D++G A+TGSGKT AFL+P++ L G V+I +PTREL Q EV
Sbjct: 62 GKDVLGAAKTGSGKTLAFLVPVLEALYRLQWTSTDGLG----VLIISPTRELAYQTFEVL 117
Query: 295 CKYAYSSVLKICLHYGGASSMHFNRQLEKGCNILVATMGRLKDILDRG-RISLASVRFVV 353
K + L GG H ++ NILV T GRL +D ++ +V
Sbjct: 118 RKVGKNHDFSAGLIIGGKDLKHEAERI-NNINILVCTPGRLLQHMDETVSFHATDLQMLV 176
Query: 354 LDEADRMLDMGFLGDIQHVMQHSTMPDVANRQTLMFSATFPETIQ 398
LDEADR+LDMGF + V+++ +P RQTL+FSAT ++++
Sbjct: 177 LDEADRILDMGFADTMNAVIEN--LP--KKRQTLLFSATQTKSVK 217
Score = 50.1 bits (118), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 31/76 (40%), Positives = 46/76 (60%), Gaps = 5/76 (6%)
Query: 401 GCNILVATMGRLKDILDRG-RISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMPDVA 459
NILV T GRL +D ++ +VLDEADR+LDMGF + V+++ +P
Sbjct: 146 NINILVCTPGRLLQHMDETVSFHATDLQMLVLDEADRILDMGFADTMNAVIEN--LP--K 201
Query: 460 NRQTLMFSATFPETIQ 475
RQTL+FSAT ++++
Sbjct: 202 KRQTLLFSATQTKSVK 217
>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 = 108 bits (269), Expect = 1e-23, Method: Compositional matrix adjust.
Identities = 71/250 (28%), Positives = 122/250 (48%), Gaps = 29/250 (11%)
Query: 401 GCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMPDVAN 460
G +++ T GR+ D++ R + +++ +VLDEAD ML+ GF I V ++ +P
Sbjct: 156 GQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRY--LPPAT- 212
Query: 461 RQTLMFSATFPETIQKNYIFIAVGIIGGASTDVVQTILEVPXXXXXXXXXXXXXXXDED- 519
Q ++ SAT P I + + TD ++ +++ E+
Sbjct: 213 -QVVLISATLPHEI--------LEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEW 263
Query: 520 ---------------GVIVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIHDF 564
++F +T R D++ + E +S+HG Q +RE + +F
Sbjct: 264 KFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEF 323
Query: 565 KTKKMKVLVATAVASRGLDIKGIRHVINYDLPQEIDEYVHRIGRTGRVGNKGRATSFYDP 624
++ +VL++T V +RGLD+ + +INYDLP + Y+HRIGR+GR G KG A +F
Sbjct: 324 RSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKN 383
Query: 625 DQDGAIAKDL 634
D D I +D+
Sbjct: 384 D-DIRILRDI 392
Score = 99.8 bits (247), Expect = 5e-21, Method: Compositional matrix adjust.
Identities = 68/217 (31%), Positives = 115/217 (52%), Gaps = 18/217 (8%)
Query: 183 NVEVKVSGDNPPRPIESFESAGLREILVKNLKKSNYTKPTPIQKYAIPAGLEGRDLMGCA 242
VE + S + P +F++ GLRE L++ + + KP+ IQ+ AI ++GRD++ +
Sbjct: 25 KVEFETSEEVDVTP--TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQS 82
Query: 243 QTGSGKTAAFLIPIMHHLLESPGELVTGYCAQPEVIICAPTRELVMQIHEVACKYAYSSV 302
Q+G+GKTA F I ++ L + + +I APTREL +QI + A
Sbjct: 83 QSGTGKTATFSISVLQCL--------DIQVRETQALILAPTRELAVQIQKGLL--ALGDY 132
Query: 303 LKICLH--YGGASSMHFNRQLEKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRM 360
+ + H GG + R+L+ G +++ T GR+ D++ R + +++ +VLDEAD M
Sbjct: 133 MNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEM 192
Query: 361 LDMGFLGDIQHVMQHSTMPDVANRQTLMFSATFPETI 397
L+ GF I V ++ +P Q ++ SAT P I
Sbjct: 193 LNKGFKEQIYDVYRY--LPPAT--QVVLISATLPHEI 225
>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 = 108 bits (269), Expect = 1e-23, Method: Compositional matrix adjust.
Identities = 71/250 (28%), Positives = 122/250 (48%), Gaps = 29/250 (11%)
Query: 401 GCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMPDVAN 460
G +++ T GR+ D++ R + +++ +VLDEAD ML+ GF I V ++ +P
Sbjct: 156 GQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRY--LPPAT- 212
Query: 461 RQTLMFSATFPETIQKNYIFIAVGIIGGASTDVVQTILEVPXXXXXXXXXXXXXXXDED- 519
Q ++ SAT P I + + TD ++ +++ E+
Sbjct: 213 -QVVLISATLPHEI--------LEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEW 263
Query: 520 ---------------GVIVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIHDF 564
++F +T R D++ + E +S+HG Q +RE + +F
Sbjct: 264 KFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEF 323
Query: 565 KTKKMKVLVATAVASRGLDIKGIRHVINYDLPQEIDEYVHRIGRTGRVGNKGRATSFYDP 624
++ +VL++T V +RGLD+ + +INYDLP + Y+HRIGR+GR G KG A +F
Sbjct: 324 RSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKN 383
Query: 625 DQDGAIAKDL 634
D D I +D+
Sbjct: 384 D-DIRILRDI 392
Score = 99.8 bits (247), Expect = 5e-21, Method: Compositional matrix adjust.
Identities = 68/217 (31%), Positives = 115/217 (52%), Gaps = 18/217 (8%)
Query: 183 NVEVKVSGDNPPRPIESFESAGLREILVKNLKKSNYTKPTPIQKYAIPAGLEGRDLMGCA 242
VE + S + P +F++ GLRE L++ + + KP+ IQ+ AI ++GRD++ +
Sbjct: 25 KVEFETSEEVDVTP--TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQS 82
Query: 243 QTGSGKTAAFLIPIMHHLLESPGELVTGYCAQPEVIICAPTRELVMQIHEVACKYAYSSV 302
Q+G+GKTA F I ++ L + + +I APTREL +QI + A
Sbjct: 83 QSGTGKTATFSISVLQCL--------DIQVRETQALILAPTRELAVQIQKGLL--ALGDY 132
Query: 303 LKICLH--YGGASSMHFNRQLEKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRM 360
+ + H GG + R+L+ G +++ T GR+ D++ R + +++ +VLDEAD M
Sbjct: 133 MNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEM 192
Query: 361 LDMGFLGDIQHVMQHSTMPDVANRQTLMFSATFPETI 397
L+ GF I V ++ +P Q ++ SAT P I
Sbjct: 193 LNKGFKEQIYDVYRY--LPPAT--QVVLISATLPHEI 225
>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 = 108 bits (269), Expect = 1e-23, Method: Compositional matrix adjust.
Identities = 71/250 (28%), Positives = 122/250 (48%), Gaps = 29/250 (11%)
Query: 401 GCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMPDVAN 460
G +++ T GR+ D++ R + +++ +VLDEAD ML+ GF I V ++ +P
Sbjct: 155 GQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRY--LPPAT- 211
Query: 461 RQTLMFSATFPETIQKNYIFIAVGIIGGASTDVVQTILEVPXXXXXXXXXXXXXXXDED- 519
Q ++ SAT P I + + TD ++ +++ E+
Sbjct: 212 -QVVLISATLPHEI--------LEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEW 262
Query: 520 ---------------GVIVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIHDF 564
++F +T R D++ + E +S+HG Q +RE + +F
Sbjct: 263 KFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEF 322
Query: 565 KTKKMKVLVATAVASRGLDIKGIRHVINYDLPQEIDEYVHRIGRTGRVGNKGRATSFYDP 624
++ +VL++T V +RGLD+ + +INYDLP + Y+HRIGR+GR G KG A +F
Sbjct: 323 RSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKN 382
Query: 625 DQDGAIAKDL 634
D D I +D+
Sbjct: 383 D-DIRILRDI 391
Score = 99.8 bits (247), Expect = 5e-21, Method: Compositional matrix adjust.
Identities = 68/217 (31%), Positives = 115/217 (52%), Gaps = 18/217 (8%)
Query: 183 NVEVKVSGDNPPRPIESFESAGLREILVKNLKKSNYTKPTPIQKYAIPAGLEGRDLMGCA 242
VE + S + P +F++ GLRE L++ + + KP+ IQ+ AI ++GRD++ +
Sbjct: 24 KVEFETSEEVDVTP--TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQS 81
Query: 243 QTGSGKTAAFLIPIMHHLLESPGELVTGYCAQPEVIICAPTRELVMQIHEVACKYAYSSV 302
Q+G+GKTA F I ++ L + + +I APTREL +QI + A
Sbjct: 82 QSGTGKTATFSISVLQCL--------DIQVRETQALILAPTRELAVQIQKGLL--ALGDY 131
Query: 303 LKICLH--YGGASSMHFNRQLEKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRM 360
+ + H GG + R+L+ G +++ T GR+ D++ R + +++ +VLDEAD M
Sbjct: 132 MNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEM 191
Query: 361 LDMGFLGDIQHVMQHSTMPDVANRQTLMFSATFPETI 397
L+ GF I V ++ +P Q ++ SAT P I
Sbjct: 192 LNKGFKEQIYDVYRY--LPPAT--QVVLISATLPHEI 224
>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 = 107 bits (268), Expect = 2e-23, Method: Compositional matrix adjust.
Identities = 71/250 (28%), Positives = 122/250 (48%), Gaps = 29/250 (11%)
Query: 401 GCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMPDVAN 460
G +++ T GR+ D++ R + +++ +VLDEAD ML+ GF I V ++ +P
Sbjct: 134 GQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRY--LPPAT- 190
Query: 461 RQTLMFSATFPETIQKNYIFIAVGIIGGASTDVVQTILEVPXXXXXXXXXXXXXXXDED- 519
Q ++ SAT P I + + TD ++ +++ E+
Sbjct: 191 -QVVLISATLPHEI--------LEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEW 241
Query: 520 ---------------GVIVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIHDF 564
++F +T R D++ + E +S+HG Q +RE + +F
Sbjct: 242 KFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEF 301
Query: 565 KTKKMKVLVATAVASRGLDIKGIRHVINYDLPQEIDEYVHRIGRTGRVGNKGRATSFYDP 624
++ +VL++T V +RGLD+ + +INYDLP + Y+HRIGR+GR G KG A +F
Sbjct: 302 RSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKN 361
Query: 625 DQDGAIAKDL 634
D D I +D+
Sbjct: 362 D-DIRILRDI 370
Score = 99.4 bits (246), Expect = 6e-21, Method: Compositional matrix adjust.
Identities = 64/201 (31%), Positives = 109/201 (54%), Gaps = 16/201 (7%)
Query: 199 SFESAGLREILVKNLKKSNYTKPTPIQKYAIPAGLEGRDLMGCAQTGSGKTAAFLIPIMH 258
+F++ GLRE L++ + + KP+ IQ+ AI ++GRD++ +Q+G+GKTA F I ++
Sbjct: 17 TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQ 76
Query: 259 HLLESPGELVTGYCAQPEVIICAPTRELVMQIHEVACKYAYSSVLKICLH--YGGASSMH 316
L + + +I APTREL +QI + A + + H GG +
Sbjct: 77 CL--------DIQVRETQALILAPTRELAVQIQKGLL--ALGDYMNVQCHACIGGTNVGE 126
Query: 317 FNRQLEKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHS 376
R+L+ G +++ T GR+ D++ R + +++ +VLDEAD ML+ GF I V ++
Sbjct: 127 DIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRY- 185
Query: 377 TMPDVANRQTLMFSATFPETI 397
+P Q ++ SAT P I
Sbjct: 186 -LPPAT--QVVLISATLPHEI 203
>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 107 bits (268), Expect = 2e-23, Method: Compositional matrix adjust.
Identities = 70/250 (28%), Positives = 122/250 (48%), Gaps = 29/250 (11%)
Query: 401 GCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMPDVAN 460
G +++ T GR+ D++ R + +++ +VLDEAD ML+ GF I V ++ +P
Sbjct: 119 GQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRY--LPPAT- 175
Query: 461 RQTLMFSATFPETIQKNYIFIAVGIIGGASTDVVQTILEVPXXXXXXXXXXXXXXXDEDG 520
Q ++ SAT P I + + TD ++ +++ E+
Sbjct: 176 -QVVLISATLPHEI--------LEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEW 226
Query: 521 ----------------VIVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIHDF 564
++F +T R D++ + E +S+HG Q +RE + +F
Sbjct: 227 KFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEF 286
Query: 565 KTKKMKVLVATAVASRGLDIKGIRHVINYDLPQEIDEYVHRIGRTGRVGNKGRATSFYDP 624
++ +VL++T V +RGLD+ + +INYDLP + Y+HRIGR+GR G KG A +F
Sbjct: 287 RSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAVNFVKN 346
Query: 625 DQDGAIAKDL 634
D D + +D+
Sbjct: 347 D-DIRVLRDI 355
Score = 98.2 bits (243), Expect = 1e-20, Method: Compositional matrix adjust.
Identities = 62/201 (30%), Positives = 109/201 (54%), Gaps = 16/201 (7%)
Query: 199 SFESAGLREILVKNLKKSNYTKPTPIQKYAIPAGLEGRDLMGCAQTGSGKTAAFLIPIMH 258
+F++ GLRE L++ + + KP+ IQ+ AI ++GRD++ +Q+G+GKTA F + ++
Sbjct: 2 TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSVSVLQ 61
Query: 259 HLLESPGELVTGYCAQPEVIICAPTRELVMQIHEVACKYAYSSVLKICLH--YGGASSMH 316
L + + +I APTREL +Q+ + A + + H GG +
Sbjct: 62 CL--------DIQVRETQALILAPTRELAVQVQKGLL--ALGDYMNVQCHACIGGTNVGE 111
Query: 317 FNRQLEKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHS 376
R+L+ G +++ T GR+ D++ R + +++ +VLDEAD ML+ GF I V ++
Sbjct: 112 DIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRY- 170
Query: 377 TMPDVANRQTLMFSATFPETI 397
+P Q ++ SAT P I
Sbjct: 171 -LPPAT--QVVLISATLPHEI 188
>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3
Length = 395
Score = 107 bits (267), Expect = 2e-23, Method: Compositional matrix adjust.
Identities = 80/250 (32%), Positives = 123/250 (49%), Gaps = 30/250 (12%)
Query: 394 PETIQKK---GCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVM 450
P++ +K ++V T G + D++ R + L ++ VLDEAD MLD LGD Q +
Sbjct: 111 PDSFEKNKQINAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGD-QCIR 169
Query: 451 QHSTMPDVANRQTLMFSATFPETIQKNYIFIAVGIIGGASTDVVQTILEVPXXXXXXXXX 510
+P + Q ++FSATF + +++ A I+ A+T +QT EV
Sbjct: 170 VKRFLP--KDTQLVLFSATFADAVRQ----YAKKIVPNANTLELQTN-EVNVDAIKQLYM 222
Query: 511 XXXXXXDEDGV-------------IVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQR 557
D+ V I+FV+T + A+ + L + +HG +R
Sbjct: 223 DCKNEADKFDVLTELYGLMTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQER 282
Query: 558 EQAIHDFKTKKMKVLVATAVASRGLDIKGIRHVINYDLPQEID------EYVHRIGRTGR 611
++ I DF+ + KVL+ T V +RG+DI + V+NYDLP + Y+HRIGRTGR
Sbjct: 283 DRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGR 342
Query: 612 VGNKGRATSF 621
G KG A SF
Sbjct: 343 FGRKGVAISF 352
Score = 92.0 bits (227), Expect = 9e-19, Method: Compositional matrix adjust.
Identities = 66/210 (31%), Positives = 110/210 (52%), Gaps = 17/210 (8%)
Query: 198 ESFESAGLREILVKNLKKSNYTKPTPIQKYAIPAGLEG--RDLMGCAQTGSGKTAAFLIP 255
+SF+ GL L+K + + KP+ IQ+ A+P L R+++ +Q+G+GKTAAF +
Sbjct: 5 KSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLT 64
Query: 256 IMHHLLESPGELVTGYCAQPEVIICAPTRELVMQIHEVACKYAYSSVLKICLHYGGASSM 315
++ + +P + A P+ I AP+REL Q EV + + KI S
Sbjct: 65 MLTRV--NPED------ASPQAICLAPSRELARQTLEVVQEMGKFT--KITSQLIVPDSF 114
Query: 316 HFNRQLEKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQH 375
N+Q+ ++V T G + D++ R + L ++ VLDEAD MLD LGD Q +
Sbjct: 115 EKNKQI--NAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGD-QCIRVK 171
Query: 376 STMPDVANRQTLMFSATFPETIQKKGCNIL 405
+P + Q ++FSATF + +++ I+
Sbjct: 172 RFLP--KDTQLVLFSATFADAVRQYAKKIV 199
>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 = 107 bits (267), Expect = 2e-23, Method: Compositional matrix adjust.
Identities = 80/250 (32%), Positives = 123/250 (49%), Gaps = 30/250 (12%)
Query: 394 PETIQKK---GCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVM 450
P++ +K ++V T G + D++ R + L ++ VLDEAD MLD LGD Q +
Sbjct: 111 PDSFEKNKQINAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGD-QCIR 169
Query: 451 QHSTMPDVANRQTLMFSATFPETIQKNYIFIAVGIIGGASTDVVQTILEVPXXXXXXXXX 510
+P + Q ++FSATF + +++ A I+ A+T +QT EV
Sbjct: 170 VKRFLP--KDTQLVLFSATFADAVRQ----YAKKIVPNANTLELQTN-EVNVDAIKQLYM 222
Query: 511 XXXXXXDEDGV-------------IVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQR 557
D+ V I+FV+T + A+ + L + +HG +R
Sbjct: 223 DCKNEADKFDVLTELYGVMTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQER 282
Query: 558 EQAIHDFKTKKMKVLVATAVASRGLDIKGIRHVINYDLPQEID------EYVHRIGRTGR 611
++ I DF+ + KVL+ T V +RG+DI + V+NYDLP + Y+HRIGRTGR
Sbjct: 283 DRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGR 342
Query: 612 VGNKGRATSF 621
G KG A SF
Sbjct: 343 FGRKGVAISF 352
Score = 92.0 bits (227), Expect = 9e-19, Method: Compositional matrix adjust.
Identities = 66/210 (31%), Positives = 110/210 (52%), Gaps = 17/210 (8%)
Query: 198 ESFESAGLREILVKNLKKSNYTKPTPIQKYAIPAGLEG--RDLMGCAQTGSGKTAAFLIP 255
+SF+ GL L+K + + KP+ IQ+ A+P L R+++ +Q+G+GKTAAF +
Sbjct: 5 KSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLT 64
Query: 256 IMHHLLESPGELVTGYCAQPEVIICAPTRELVMQIHEVACKYAYSSVLKICLHYGGASSM 315
++ + +P + A P+ I AP+REL Q EV + + KI S
Sbjct: 65 MLTRV--NPED------ASPQAICLAPSRELARQTLEVVQEMGKFT--KITSQLIVPDSF 114
Query: 316 HFNRQLEKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQH 375
N+Q+ ++V T G + D++ R + L ++ VLDEAD MLD LGD Q +
Sbjct: 115 EKNKQI--NAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGD-QCIRVK 171
Query: 376 STMPDVANRQTLMFSATFPETIQKKGCNIL 405
+P + Q ++FSATF + +++ I+
Sbjct: 172 RFLP--KDTQLVLFSATFADAVRQYAKKIV 199
>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 107 bits (267), Expect = 2e-23, Method: Compositional matrix adjust.
Identities = 71/242 (29%), Positives = 124/242 (51%), Gaps = 13/242 (5%)
Query: 401 GCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMPDVAN 460
G +++ T GR+ D++ R + +++ +VLDEAD ML+ GF I V ++ +P
Sbjct: 119 GQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRY--LPPAT- 175
Query: 461 RQTLMFSATFP-ETIQKNYIFIA--VGIIGGASTDVVQTILEVPXXXXXXXXXXXXXXXD 517
Q ++ SAT P E ++ F+ + I+ ++ I +
Sbjct: 176 -QVVLISATLPHEVLEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDL 234
Query: 518 EDGV-----IVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIHDFKTKKMKVL 572
D + ++F +T R D++ + E +S+HG Q +RE + +F++ +VL
Sbjct: 235 YDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVL 294
Query: 573 VATAVASRGLDIKGIRHVINYDLPQEIDEYVHRIGRTGRVGNKGRATSFYDPDQDGAIAK 632
++T V +RGLD+ + +INYDLP + Y+HRIGR+GR G KG A +F D D + +
Sbjct: 295 ISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAVNFVKND-DIRVLR 353
Query: 633 DL 634
D+
Sbjct: 354 DI 355
Score = 97.4 bits (241), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 61/201 (30%), Positives = 109/201 (54%), Gaps = 16/201 (7%)
Query: 199 SFESAGLREILVKNLKKSNYTKPTPIQKYAIPAGLEGRDLMGCAQTGSGKTAAFLIPIMH 258
+F++ GLRE L++ + + KP+ IQ+ AI ++GRD++ +Q+G+GKTA F + ++
Sbjct: 2 TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSVSVLQ 61
Query: 259 HLLESPGELVTGYCAQPEVIICAPTRELVMQIHEVACKYAYSSVLKICLH--YGGASSMH 316
L + + +I APTREL +Q+ + A + + H GG +
Sbjct: 62 CL--------DIQVRETQALILAPTRELAVQVQKGLL--ALGDYMNVQSHACIGGTNVGE 111
Query: 317 FNRQLEKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHS 376
R+L+ G +++ T GR+ D++ R + +++ +VLDEAD ML+ GF I V ++
Sbjct: 112 DIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRY- 170
Query: 377 TMPDVANRQTLMFSATFPETI 397
+P Q ++ SAT P +
Sbjct: 171 -LPPAT--QVVLISATLPHEV 188
>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p
Length = 400
Score = 107 bits (267), Expect = 2e-23, Method: Compositional matrix adjust.
Identities = 66/201 (32%), Positives = 108/201 (53%), Gaps = 12/201 (5%)
Query: 199 SFESAGLREILVKNLKKSNYTKPTPIQKYAIPAGLEGRDLMGCAQTGSGKTAAFLIPIMH 258
+FE L+ L+ + ++ + KP+PIQ+ AIP + GRD++ A+ G+GKTAAF+IP +
Sbjct: 22 TFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTL- 80
Query: 259 HLLESPGELVTGYCAQPEVIICAPTRELVMQIHEVACKYAYSSVLKICLHYGGASSMHFN 318
E V + + +I PTREL +Q +V + + GG +
Sbjct: 81 -------EKVKPKLNKIQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDI 133
Query: 319 RQLEKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTM 378
+L + +ILV T GR+ D+ R L+ ++DEAD+ML F I+ ++ S +
Sbjct: 134 LRLNETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSRDFKTIIEQIL--SFL 191
Query: 379 PDVANRQTLMFSATFPETIQK 399
P Q+L+FSATFP T+++
Sbjct: 192 P--PTHQSLLFSATFPLTVKE 210
Score = 99.4 bits (246), Expect = 7e-21, Method: Compositional matrix adjust.
Identities = 61/227 (26%), Positives = 112/227 (49%), Gaps = 10/227 (4%)
Query: 403 NILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMPDVANRQ 462
+ILV T GR+ D+ R L+ ++DEAD+ML F I+ ++ S +P Q
Sbjct: 141 HILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSRDFKTIIEQIL--SFLP--PTHQ 196
Query: 463 TLMFSATFPETIQKNYIF-----IAVGIIGGASTD-VVQTILEVPXXXXXXXXXXXXXXX 516
+L+FSATFP T+++ + + ++ + + Q V
Sbjct: 197 SLLFSATFPLTVKEFMVKHLHKPYEINLMEELTLKGITQYYAFVEERQKLHCLNTLFSKL 256
Query: 517 DEDGVIVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIHDFKTKKMKVLVATA 576
+ I+F ++ + +A + + + H Q +R + H+F+ K++ LV +
Sbjct: 257 QINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSD 316
Query: 577 VASRGLDIKGIRHVINYDLPQEIDEYVHRIGRTGRVGNKGRATSFYD 623
+ +RG+DI+ + VIN+D P+ + Y+HRIGR+GR G+ G A + +
Sbjct: 317 LLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLIN 363
>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56
Length = 390
Score = 106 bits (265), Expect = 4e-23, Method: Compositional matrix adjust.
Identities = 68/250 (27%), Positives = 122/250 (48%), Gaps = 14/250 (5%)
Query: 395 ETIQKKGC-NILVATMGRLKDILDRGRISLASVRFVVLDEADRMLD-MGFLGDIQHVMQH 452
E + KK C +I+V T GR+ + ++L ++ +LDEAD+ML+ + D+Q + +
Sbjct: 120 EEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDEADKMLEQLDMRRDVQEIFRM 179
Query: 453 STMPDVANRQTLMFSATFPETIQ---KNYIFIAVGIIGGASTDVV-----QTILEVPXXX 504
+ +Q +MFSAT + I+ + ++ + I T + Q +++
Sbjct: 180 TP----HEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNE 235
Query: 505 XXXXXXXXXXXXDEDGVIVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIHDF 564
+ + V++FV +++ +A L E +IH Q +R F
Sbjct: 236 KNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQF 295
Query: 565 KTKKMKVLVATAVASRGLDIKGIRHVINYDLPQEIDEYVHRIGRTGRVGNKGRATSFYDP 624
K + ++LVAT + RG+DI+ + NYD+P++ D Y+HR+ R GR G KG A +F
Sbjct: 296 KDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSD 355
Query: 625 DQDGAIAKDL 634
+ D I D+
Sbjct: 356 ENDAKILNDV 365
Score = 85.1 bits (209), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 60/208 (28%), Positives = 107/208 (51%), Gaps = 15/208 (7%)
Query: 194 PRPIESFESAGLREILVKNLKKSNYTKPTPIQKYAIPAGLEGRDLMGCAQTGSGKTAAFL 253
P + F L+ L++ + + P+ +Q IP + G D++ A++G GKTA F+
Sbjct: 3 PGHMSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFV 62
Query: 254 IPIMHHLLESPGELVTGYCAQPEVIICAPTRELVMQIHEVACKYA-YSSVLKICLHYGGA 312
+ + L E VTG Q V++ TREL QI + +++ Y +K+ + +GG
Sbjct: 63 LATLQQL-----EPVTG---QVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGL 114
Query: 313 SSMHFNRQLEKGC-NILVATMGRLKDILDRGRISLASVRFVVLDEADRMLD-MGFLGDIQ 370
S L+K C +I+V T GR+ + ++L ++ +LDEAD+ML+ + D+Q
Sbjct: 115 SIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDEADKMLEQLDMRRDVQ 174
Query: 371 HVMQHSTMPDVANRQTLMFSATFPETIQ 398
+ + + +Q +MFSAT + I+
Sbjct: 175 EIFRMTP----HEKQVMMFSATLSKEIR 198
>pdb|3DKP|A Chain A, Human Dead-Box Rna-Helicase Ddx52, Conserved Domain I In
Complex With Adp
Length = 245
Score = 105 bits (263), Expect = 6e-23, Method: Compositional matrix adjust.
Identities = 76/225 (33%), Positives = 117/225 (52%), Gaps = 20/225 (8%)
Query: 185 EVKVSGDNPPRPIESFESA----GLREILVKNLKKSNYTKPTPIQKYAIPAGLEGRDLMG 240
++ V G + P PI +F+ + L++N+ + + PTPIQ AIP L GR+L+
Sbjct: 12 KIHVQGTDLPDPIATFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLA 71
Query: 241 CAQTGSGKTAAFLIPIMHHLLESPGELVTGYCAQPEVIICAPTRELVMQIHEVACKYAYS 300
A TGSGKT AF IPI+ L + + G+ A +I +PTREL QIH K +
Sbjct: 72 SAPTGSGKTLAFSIPILMQLKQPANK---GFRA----LIISPTRELASQIHRELIKISEG 124
Query: 301 SVLKI-CLHYGGASSMHFNRQLEKGCNILVATMGRLKDIL--DRGRISLASVRFVVLDEA 357
+ +I +H ++ F + K +ILV T RL +L D I LASV ++V+DE+
Sbjct: 125 TGFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPPGIDLASVEWLVVDES 184
Query: 358 DRMLD---MGFLGDIQHVMQHSTMPDVANRQTLMFSATFPETIQK 399
D++ + GF + + T V + MFSATF +++
Sbjct: 185 DKLFEDGKTGFRDQLASIFLACTSHKV---RRAMFSATFAYDVEQ 226
Score = 35.4 bits (80), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 31/97 (31%), Positives = 49/97 (50%), Gaps = 15/97 (15%)
Query: 400 KGCNILVATMGRLKDIL--DRGRISLASVRFVVLDEADRMLD---MGFLGDIQHVMQHST 454
K +ILV T RL +L D I LASV ++V+DE+D++ + GF + + T
Sbjct: 148 KKFDILVTTPNRLIYLLKQDPPGIDLASVEWLVVDESDKLFEDGKTGFRDQLASIFLACT 207
Query: 455 MPDVANRQTLMFSATFPETIQK-------NYIFIAVG 484
V + MFSATF +++ N I +++G
Sbjct: 208 SHKV---RRAMFSATFAYDVEQWCKLNLDNVISVSIG 241
>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp
Length = 386
Score = 105 bits (261), Expect = 1e-22, Method: Compositional matrix adjust.
Identities = 67/250 (26%), Positives = 121/250 (48%), Gaps = 14/250 (5%)
Query: 395 ETIQKKGC-NILVATMGRLKDILDRGRISLASVRFVVLDEADRMLD-MGFLGDIQHVMQH 452
E + KK C +I+V T GR+ + ++L ++ +LDE D+ML+ + D+Q + +
Sbjct: 121 EEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRM 180
Query: 453 STMPDVANRQTLMFSATFPETIQ---KNYIFIAVGIIGGASTDVV-----QTILEVPXXX 504
+ +Q +MFSAT + I+ + ++ + I T + Q +++
Sbjct: 181 TP----HEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNE 236
Query: 505 XXXXXXXXXXXXDEDGVIVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIHDF 564
+ + V++FV +++ +A L E +IH Q +R F
Sbjct: 237 KNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQF 296
Query: 565 KTKKMKVLVATAVASRGLDIKGIRHVINYDLPQEIDEYVHRIGRTGRVGNKGRATSFYDP 624
K + ++LVAT + RG+DI+ + NYD+P++ D Y+HR+ R GR G KG A +F
Sbjct: 297 KDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSD 356
Query: 625 DQDGAIAKDL 634
+ D I D+
Sbjct: 357 ENDAKILNDV 366
Score = 84.0 bits (206), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 60/205 (29%), Positives = 106/205 (51%), Gaps = 20/205 (9%)
Query: 202 SAGLREILVK-----NLKKSNYTKPTPIQKYAIPAGLEGRDLMGCAQTGSGKTAAFLIPI 256
S+G R+ L+K + + P+ +Q IP + G D++ A++G GKTA F++
Sbjct: 7 SSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLAT 66
Query: 257 MHHLLESPGELVTGYCAQPEVIICAPTRELVMQIHEVACKYA-YSSVLKICLHYGGASSM 315
+ L E VTG Q V++ TREL QI + +++ Y +K+ + +GG S
Sbjct: 67 LQQL-----EPVTG---QVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIK 118
Query: 316 HFNRQLEKGC-NILVATMGRLKDILDRGRISLASVRFVVLDEADRMLD-MGFLGDIQHVM 373
L+K C +I+V T GR+ + ++L ++ +LDE D+ML+ + D+Q +
Sbjct: 119 KDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIF 178
Query: 374 QHSTMPDVANRQTLMFSATFPETIQ 398
+ + +Q +MFSAT + I+
Sbjct: 179 RMTP----HEKQVMMFSATLSKEIR 199
>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56
Length = 391
Score = 104 bits (260), Expect = 1e-22, Method: Compositional matrix adjust.
Identities = 67/250 (26%), Positives = 121/250 (48%), Gaps = 14/250 (5%)
Query: 395 ETIQKKGC-NILVATMGRLKDILDRGRISLASVRFVVLDEADRMLD-MGFLGDIQHVMQH 452
E + KK C +I+V T GR+ + ++L ++ +LDE D+ML+ + D+Q + +
Sbjct: 121 EEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRM 180
Query: 453 STMPDVANRQTLMFSATFPETIQ---KNYIFIAVGIIGGASTDVV-----QTILEVPXXX 504
+ +Q +MFSAT + I+ + ++ + I T + Q +++
Sbjct: 181 TP----HEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNE 236
Query: 505 XXXXXXXXXXXXDEDGVIVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIHDF 564
+ + V++FV +++ +A L E +IH Q +R F
Sbjct: 237 KNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQF 296
Query: 565 KTKKMKVLVATAVASRGLDIKGIRHVINYDLPQEIDEYVHRIGRTGRVGNKGRATSFYDP 624
K + ++LVAT + RG+DI+ + NYD+P++ D Y+HR+ R GR G KG A +F
Sbjct: 297 KDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSD 356
Query: 625 DQDGAIAKDL 634
+ D I D+
Sbjct: 357 ENDAKILNDV 366
Score = 84.0 bits (206), Expect = 3e-16, Method: Compositional matrix adjust.
Identities = 60/205 (29%), Positives = 106/205 (51%), Gaps = 20/205 (9%)
Query: 202 SAGLREILVK-----NLKKSNYTKPTPIQKYAIPAGLEGRDLMGCAQTGSGKTAAFLIPI 256
S+G R+ L+K + + P+ +Q IP + G D++ A++G GKTA F++
Sbjct: 7 SSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLAT 66
Query: 257 MHHLLESPGELVTGYCAQPEVIICAPTRELVMQIHEVACKYA-YSSVLKICLHYGGASSM 315
+ L E VTG Q V++ TREL QI + +++ Y +K+ + +GG S
Sbjct: 67 LQQL-----EPVTG---QVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIK 118
Query: 316 HFNRQLEKGC-NILVATMGRLKDILDRGRISLASVRFVVLDEADRMLD-MGFLGDIQHVM 373
L+K C +I+V T GR+ + ++L ++ +LDE D+ML+ + D+Q +
Sbjct: 119 KDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIF 178
Query: 374 QHSTMPDVANRQTLMFSATFPETIQ 398
+ + +Q +MFSAT + I+
Sbjct: 179 RMTP----HEKQVMMFSATLSKEIR 199
>pdb|3LY5|A Chain A, Ddx18 Dead-Domain
pdb|3LY5|B Chain B, Ddx18 Dead-Domain
Length = 262
Score = 102 bits (255), Expect = 5e-22, Method: Compositional matrix adjust.
Identities = 72/193 (37%), Positives = 108/193 (55%), Gaps = 17/193 (8%)
Query: 205 LREILVKNLKKSNYTKPTPIQKYAIPAGLEGRDLMGCAQTGSGKTAAFLIPIMHHLLESP 264
+ E +K +K+ +T T IQ +I LEGRDL+ A+TGSGKT AFLIP +
Sbjct: 61 VNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAV------- 113
Query: 265 GELVTGYCAQPE----VIICAPTRELVMQIHEVACKYAYSSVLKICLHYGGASSMHFNRQ 320
EL+ P V+I +PTREL MQ V + V L GG++ ++
Sbjct: 114 -ELIVKLRFMPRNGTGVLILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQK 172
Query: 321 LEKGCNILVATMGRLKD-ILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMP 379
L G NI+VAT GRL D + + +++ +V+DEADR+LD+GF +++ +++ +P
Sbjct: 173 LGNGINIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEADRILDVGFEEELKQIIK--LLP 230
Query: 380 DVANRQTLMFSAT 392
RQT++FSAT
Sbjct: 231 --TRRQTMLFSAT 241
Score = 48.1 bits (113), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 39/121 (32%), Positives = 65/121 (53%), Gaps = 11/121 (9%)
Query: 352 VVLDEADRMLDMGFLGDIQHVMQHSTMPDVANRQTLMFSATFPETIQK--KGCNILVATM 409
V++ R L M G ++ +M H V +M + QK G NI+VAT
Sbjct: 129 VLILSPTRELAMQTFGVLKELMTHH----VHTYGLIMGGSNRSAEAQKLGNGINIIVATP 184
Query: 410 GRLKD-ILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMPDVANRQTLMFSA 468
GRL D + + +++ +V+DEADR+LD+GF +++ +++ +P RQT++FSA
Sbjct: 185 GRLLDHMQNTPGFMYKNLQCLVIDEADRILDVGFEEELKQIIK--LLP--TRRQTMLFSA 240
Query: 469 T 469
T
Sbjct: 241 T 241
>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And
Amp-Pnp
Length = 579
Score = 102 bits (253), Expect = 9e-22, Method: Compositional matrix adjust.
Identities = 74/211 (35%), Positives = 113/211 (53%), Gaps = 19/211 (9%)
Query: 222 TPIQKYAIPAGL--EGRDLMGCAQTGSGKTAAFLIPIMHHLLESPGELVTGYCAQPEVII 279
TP+Q+ I L E D++ A+TG+GKT AFLIPI HL+ + + + Y + +I
Sbjct: 45 TPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINT--KFDSQYMVK--AVI 100
Query: 280 CAPTRELVMQIH-EVACKYAYSSVLK--ICLHYGGASSMH--FNRQLEKGCNILVATMGR 334
APTR+L +QI EV + + LK C+ G + N+ + NI++AT GR
Sbjct: 101 VAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGR 160
Query: 335 LKDILDRGRISLASVRFV---VLDEADRMLDMGFLGDIQH---VMQHSTMPDVANRQTLM 388
L D+L+ + S RFV VLDEADR+L++GF D++ ++ N +TL+
Sbjct: 161 LIDVLE--KYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILNEKNSKSADNIKTLL 218
Query: 389 FSATFPETIQKKGCNILVATMGRLKDILDRG 419
FSAT + +QK NI+ D +D+
Sbjct: 219 FSATLDDKVQKLANNIMNKKECLFLDTVDKN 249
Score = 95.9 bits (237), Expect = 6e-20, Method: Compositional matrix adjust.
Identities = 80/277 (28%), Positives = 125/277 (45%), Gaps = 49/277 (17%)
Query: 403 NILVATMGRLKDILDRGRISLASVRFV---VLDEADRMLDMGFLGDIQHV---MQHSTMP 456
NI++AT GRL D+L++ S RFV VLDEADR+L++GF D++ + +
Sbjct: 152 NIVIATPGRLIDVLEK--YSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILNEKNSK 209
Query: 457 DVANRQTLMFSATFPETIQKNYIFIAVGIIGG---------------ASTDVVQTIL--- 498
N +TL+FSAT + +QK +A I+ A + Q+++
Sbjct: 210 SADNIKTLLFSATLDDKVQK----LANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISE 265
Query: 499 EVPXXXXXXXXXXXXXXXDEDG---VIVFVSTIRNADFIACYLCETE----IATTSIHGS 551
+ + D I+F T++ F+ C + + E + HG
Sbjct: 266 KFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFL-CSILKNEFKKDLPILEFHGK 324
Query: 552 RLQSQREQAIHDFKTKKMKVLVATAVASRGLDIKGIRHVINYDLPQEIDEYVHRIGRTGR 611
Q++R + FK + +LV T V +RG+D + V+ +P E+ Y+HRIGRT R
Sbjct: 325 ITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTAR 384
Query: 612 VGNKGRATSFYDPDQDGAIAKD---LVRILEQAGQPV 645
G +G + F I KD VR LE A V
Sbjct: 385 SGKEGSSVLF--------ICKDELPFVRELEDAKNIV 413
>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 = 101 bits (251), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 74/211 (35%), Positives = 113/211 (53%), Gaps = 19/211 (9%)
Query: 222 TPIQKYAIPAGL--EGRDLMGCAQTGSGKTAAFLIPIMHHLLESPGELVTGYCAQPEVII 279
TP+Q+ I L E D++ A+TG+GKT AFLIPI HL+ + + + Y + +I
Sbjct: 96 TPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFD--SQYMVK--AVI 151
Query: 280 CAPTRELVMQIH-EVACKYAYSSVLK--ICLHYGGASSMH--FNRQLEKGCNILVATMGR 334
APTR+L +QI EV + + LK C+ G + N+ + NI++AT GR
Sbjct: 152 VAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGR 211
Query: 335 LKDILDRGRISLASVRFV---VLDEADRMLDMGFLGDIQH---VMQHSTMPDVANRQTLM 388
L D+L+ + S RFV VLDEADR+L++GF D++ ++ N +TL+
Sbjct: 212 LIDVLE--KYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILNEKNSKSADNIKTLL 269
Query: 389 FSATFPETIQKKGCNILVATMGRLKDILDRG 419
FSAT + +QK NI+ D +D+
Sbjct: 270 FSATLDDKVQKLANNIMNKKECLFLDTVDKN 300
Score = 95.5 bits (236), Expect = 9e-20, Method: Compositional matrix adjust.
Identities = 80/277 (28%), Positives = 125/277 (45%), Gaps = 49/277 (17%)
Query: 403 NILVATMGRLKDILDRGRISLASVRFV---VLDEADRMLDMGFLGDIQHV---MQHSTMP 456
NI++AT GRL D+L++ S RFV VLDEADR+L++GF D++ + +
Sbjct: 203 NIVIATPGRLIDVLEK--YSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILNEKNSK 260
Query: 457 DVANRQTLMFSATFPETIQKNYIFIAVGIIGG---------------ASTDVVQTIL--- 498
N +TL+FSAT + +QK +A I+ A + Q+++
Sbjct: 261 SADNIKTLLFSATLDDKVQK----LANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISE 316
Query: 499 EVPXXXXXXXXXXXXXXXDEDG---VIVFVSTIRNADFIACYLCETE----IATTSIHGS 551
+ + D I+F T++ F+ C + + E + HG
Sbjct: 317 KFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFL-CSILKNEFKKDLPILEFHGK 375
Query: 552 RLQSQREQAIHDFKTKKMKVLVATAVASRGLDIKGIRHVINYDLPQEIDEYVHRIGRTGR 611
Q++R + FK + +LV T V +RG+D + V+ +P E+ Y+HRIGRT R
Sbjct: 376 ITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTAR 435
Query: 612 VGNKGRATSFYDPDQDGAIAKD---LVRILEQAGQPV 645
G +G + F I KD VR LE A V
Sbjct: 436 SGKEGSSVLF--------ICKDELPFVRELEDAKNIV 464
>pdb|3SQX|A Chain A, Structure Of Mss116p (Nte And C-Tail Double Deletion)
Bound To Ssrna And Amp-Pnp
Length = 512
Score = 100 bits (250), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 74/211 (35%), Positives = 113/211 (53%), Gaps = 19/211 (9%)
Query: 222 TPIQKYAIPAGL--EGRDLMGCAQTGSGKTAAFLIPIMHHLLESPGELVTGYCAQPEVII 279
TP+Q+ I L E D++ A+TG+GKT AFLIPI HL+ + + + Y + +I
Sbjct: 45 TPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFD--SQYMVK--AVI 100
Query: 280 CAPTRELVMQIH-EVACKYAYSSVLK--ICLHYGGASSMH--FNRQLEKGCNILVATMGR 334
APTR+L +QI EV + + LK C+ G + N+ + NI++AT GR
Sbjct: 101 VAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGR 160
Query: 335 LKDILDRGRISLASVRFV---VLDEADRMLDMGFLGDIQH---VMQHSTMPDVANRQTLM 388
L D+L+ + S RFV VLDEADR+L++GF D++ ++ N +TL+
Sbjct: 161 LIDVLE--KYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILNEKNSKSADNIKTLL 218
Query: 389 FSATFPETIQKKGCNILVATMGRLKDILDRG 419
FSAT + +QK NI+ D +D+
Sbjct: 219 FSATLDDKVQKLANNIMNKKECLFLDTVDKN 249
Score = 95.1 bits (235), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 80/277 (28%), Positives = 125/277 (45%), Gaps = 49/277 (17%)
Query: 403 NILVATMGRLKDILDRGRISLASVRFV---VLDEADRMLDMGFLGDIQHV---MQHSTMP 456
NI++AT GRL D+L++ S RFV VLDEADR+L++GF D++ + +
Sbjct: 152 NIVIATPGRLIDVLEK--YSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILNEKNSK 209
Query: 457 DVANRQTLMFSATFPETIQKNYIFIAVGIIGG---------------ASTDVVQTIL--- 498
N +TL+FSAT + +QK +A I+ A + Q+++
Sbjct: 210 SADNIKTLLFSATLDDKVQK----LANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISE 265
Query: 499 EVPXXXXXXXXXXXXXXXDEDG---VIVFVSTIRNADFIACYLCETE----IATTSIHGS 551
+ + D I+F T++ F+ C + + E + HG
Sbjct: 266 KFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFL-CSILKNEFKKDLPILEFHGK 324
Query: 552 RLQSQREQAIHDFKTKKMKVLVATAVASRGLDIKGIRHVINYDLPQEIDEYVHRIGRTGR 611
Q++R + FK + +LV T V +RG+D + V+ +P E+ Y+HRIGRT R
Sbjct: 325 ITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTAR 384
Query: 612 VGNKGRATSFYDPDQDGAIAKD---LVRILEQAGQPV 645
G +G + F I KD VR LE A V
Sbjct: 385 SGKEGSSVLF--------ICKDELPFVRELEDAKNIV 413
>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 = 97.8 bits (242), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 64/198 (32%), Positives = 110/198 (55%), Gaps = 15/198 (7%)
Query: 200 FESAGLREILVKNLKKSNYTKPTPIQKYAIPAGLEGRDLMGCAQTGSGKTAAF-LIPIMH 258
FES L +++ L+ + + +P+P+Q AIP G G DL+ A++G+GKT F I +
Sbjct: 26 FESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDS 85
Query: 259 HLLESPGELVTGYCAQPEVIICAPTRELVMQIHEVACKYAYSSVLKICLHYGGASSMHFN 318
+LE+ +++I APTRE+ +QIH V C + G + + +
Sbjct: 86 LVLEN---------LSTQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQD 136
Query: 319 RQLEKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMG-FLGDIQHVMQHST 377
+ K C+I V + GR+K +++ ++ S+R +LDEAD++L+ G F I + +S+
Sbjct: 137 KTRLKKCHIAVGSPGRIKQLIELDYLNPGSIRLFILDEADKLLEEGSFQEQINWI--YSS 194
Query: 378 MPDVANRQTLMFSATFPE 395
+P A++Q L SAT+PE
Sbjct: 195 LP--ASKQMLAVSATYPE 210
Score = 51.2 bits (121), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 28/74 (37%), Positives = 48/74 (64%), Gaps = 5/74 (6%)
Query: 400 KGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMG-FLGDIQHVMQHSTMPDV 458
K C+I V + GR+K +++ ++ S+R +LDEAD++L+ G F I + +S++P
Sbjct: 141 KKCHIAVGSPGRIKQLIELDYLNPGSIRLFILDEADKLLEEGSFQEQINWI--YSSLP-- 196
Query: 459 ANRQTLMFSATFPE 472
A++Q L SAT+PE
Sbjct: 197 ASKQMLAVSATYPE 210
>pdb|1Q0U|A Chain A, Crystal Structure Of The Bstdead N-Terminal Domain
pdb|1Q0U|B Chain B, Crystal Structure Of The Bstdead N-Terminal Domain
Length = 219
Score = 95.9 bits (237), Expect = 7e-20, Method: Composition-based stats.
Identities = 61/204 (29%), Positives = 98/204 (48%), Gaps = 18/204 (8%)
Query: 200 FESAGLREILVKNLKKSNYTKPTPIQKYAIPAGLEGRDLMGCAQTGSGKTAAFLIPIMHH 259
F + +++ +K + KPT IQ+ IP L G +G +QTG+GKT A+L+PI
Sbjct: 6 FTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESXVGQSQTGTGKTHAYLLPIXEK 65
Query: 260 LLESPGELVTGYCAQPEVIICAPTRELVMQIHEVACKYAY-----SSVLKICLHYGGASS 314
+ E+ + +I APTREL QI+ K ++ CL GG
Sbjct: 66 IKPERAEV--------QAVITAPTRELATQIYHETLKITKFCPKDRXIVARCL-IGGTDK 116
Query: 315 MHFNRQLEKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQ 374
+L +I++ T GR+ D + + + + +V+DEAD LD GF+ D+ +
Sbjct: 117 QKALEKLNVQPHIVIGTPGRINDFIREQALDVHTAHILVVDEADLXLDXGFITDVDQIAA 176
Query: 375 HSTMPDVANRQTLMFSATFPETIQ 398
+ Q L+FSAT PE ++
Sbjct: 177 RXP----KDLQXLVFSATIPEKLK 196
Score = 47.0 bits (110), Expect = 4e-05, Method: Composition-based stats.
Identities = 23/73 (31%), Positives = 40/73 (54%), Gaps = 4/73 (5%)
Query: 403 NILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMPDVANRQ 462
+I++ T GR+ D + + + + +V+DEAD LD GF+ D+ + + Q
Sbjct: 128 HIVIGTPGRINDFIREQALDVHTAHILVVDEADLXLDXGFITDVDQIAARXP----KDLQ 183
Query: 463 TLMFSATFPETIQ 475
L+FSAT PE ++
Sbjct: 184 XLVFSATIPEKLK 196
>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a
pdb|3EIQ|D Chain D, Crystal Structure Of Pdcd4-eif4a
Length = 414
Score = 95.5 bits (236), Expect = 9e-20, Method: Compositional matrix adjust.
Identities = 66/204 (32%), Positives = 106/204 (51%), Gaps = 17/204 (8%)
Query: 197 IESFESAGLREILVKNLKKSNYTKPTPIQKYAIPAGLEGRDLMGCAQTGSGKTAAFLIPI 256
++SF+ L E L++ + + KP+ IQ+ AI ++G D++ AQ+G+GKTA F I I
Sbjct: 39 VDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISI 98
Query: 257 MHHLLESPGELVTGYCAQPEVIICAPTRELVMQIHEVACKYAYSSVLKICLH--YGGASS 314
+ + EL + ++ APTREL QI +V A + H GG +
Sbjct: 99 LQQI-----EL---DLKATQALVLAPTRELAQQIQKVVM--ALGDYMGASCHACIGGTNV 148
Query: 315 MHFNRQLE-KGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVM 373
++L+ + +I+V T GR+ D+L+R +S ++ VLDEAD ML GF I +
Sbjct: 149 RAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIF 208
Query: 374 QHSTMPDVANRQTLMFSATFPETI 397
Q +N Q ++ SAT P +
Sbjct: 209 QKLN----SNTQVVLLSATMPSDV 228
Score = 87.0 bits (214), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 57/220 (25%), Positives = 109/220 (49%), Gaps = 12/220 (5%)
Query: 395 ETIQKKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHST 454
+ +Q + +I+V T GR+ D+L+R +S ++ VLDEAD ML GF I + Q
Sbjct: 153 QKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLN 212
Query: 455 MPDVANRQTLMFSATFPE---TIQKNYIFIAVGIIGGASTDVVQTILEVPXXXXXXXXXX 511
+N Q ++ SAT P + K ++ + I+ ++ I +
Sbjct: 213 ----SNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKL 268
Query: 512 XXXXXDEDGV-----IVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIHDFKT 566
+ + ++F++T R D++ + + +++HG Q +R+ + +F++
Sbjct: 269 DTLCDLYETLTITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRS 328
Query: 567 KKMKVLVATAVASRGLDIKGIRHVINYDLPQEIDEYVHRI 606
+VL+ T + +RG+D++ + VINYDLP + Y+HRI
Sbjct: 329 GSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHRI 368
>pdb|1QVA|A Chain A, Yeast Initiation Factor 4a N-Terminal Domain
Length = 223
Score = 95.1 bits (235), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 64/218 (29%), Positives = 105/218 (48%), Gaps = 13/218 (5%)
Query: 180 GWENVEVKVSGDNPPRPIESFESAGLREILVKNLKKSNYTKPTPIQKYAIPAGLEGRDLM 239
G ++E N + + F+ L E L++ + + +P+ IQ+ AI +EG D++
Sbjct: 3 GITDIEESQIQTNYQKVVYKFDDMELDEQLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVL 62
Query: 240 GCAQTGSGKTAAFLIPIMHHLLESPGELVTGYCAQPEVIICAPTRELVMQIHEVACKYAY 299
AQ+G+GKT F I + + S P+ ++ APTREL +QI +V A+
Sbjct: 63 AQAQSGTGKTGTFSIAALQRIDTS--------VKAPQALMLAPTRELALQIQKVVMALAF 114
Query: 300 SSVLKICLHYGGASSMHFNRQLEKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADR 359
+K+ GG S + L + I+V T GR+ D + R R ++ +LDEAD
Sbjct: 115 HMDIKVHACIGGTSFVEDAEGL-RDAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADE 173
Query: 360 MLDMGFLGDIQHVMQHSTMPDVANRQTLMFSATFPETI 397
ML GF I + + +P Q ++ SAT P +
Sbjct: 174 MLSSGFKEQIYQIF--TLLP--PTTQVVLLSATMPNDV 207
Score = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 37/75 (49%), Gaps = 4/75 (5%)
Query: 400 KGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMPDVA 459
+ I+V T GR+ D + R R ++ +LDEAD ML GF I + + +P
Sbjct: 137 RDAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIF--TLLP--P 192
Query: 460 NRQTLMFSATFPETI 474
Q ++ SAT P +
Sbjct: 193 TTQVVLLSATMPNDV 207
>pdb|3BOR|A Chain A, Crystal Structure Of The Deadc Domain Of Human Translation
Initiation Factor 4a-2
Length = 237
Score = 94.7 bits (234), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 70/221 (31%), Positives = 113/221 (51%), Gaps = 19/221 (8%)
Query: 179 SGWENVEVK--VSGDNPPRPIESFESAGLREILVKNLKKSNYTKPTPIQKYAIPAGLEGR 236
SG EN+ + V N +++F+ L+E L++ + + KP+ IQ+ AI ++G
Sbjct: 9 SGRENLYFQGGVIESNWNEIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGY 68
Query: 237 DLMGCAQTGSGKTAAFLIPIMHHLLESPGELVTGYCAQPEVIICAPTRELVMQIHEVACK 296
D++ AQ+G+GKTA F I I+ L E + ++ APTREL QI +V
Sbjct: 69 DVIAQAQSGTGKTATFAISILQQLEIEFKE--------TQALVLAPTRELAQQIQKVIL- 119
Query: 297 YAYSSVLKICLH--YGGASSMHFNRQLE-KGCNILVATMGRLKDILDRGRISLASVRFVV 353
A + H GG + + ++L+ + +I+V T GR+ D+L+R +S ++ V
Sbjct: 120 -ALGDYMGATCHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFV 178
Query: 354 LDEADRMLDMGFLGDIQHVMQHSTMPDVANRQTLMFSATFP 394
LDEAD ML GF I + Q + Q ++ SAT P
Sbjct: 179 LDEADEMLSRGFKDQIYEIFQKLN----TSIQVVLLSATMP 215
Score = 47.8 bits (112), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 42/77 (54%), Gaps = 4/77 (5%)
Query: 395 ETIQKKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHST 454
+ +Q + +I+V T GR+ D+L+R +S ++ VLDEAD ML GF I + Q
Sbjct: 143 QKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSRGFKDQIYEIFQKLN 202
Query: 455 MPDVANRQTLMFSATFP 471
+ Q ++ SAT P
Sbjct: 203 ----TSIQVVLLSATMP 215
>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 = 94.7 bits (234), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 64/218 (29%), Positives = 105/218 (48%), Gaps = 13/218 (5%)
Query: 180 GWENVEVKVSGDNPPRPIESFESAGLREILVKNLKKSNYTKPTPIQKYAIPAGLEGRDLM 239
G ++E N + + F+ L E L++ + + +P+ IQ+ AI +EG D++
Sbjct: 4 GITDIEESQIQTNYDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVL 63
Query: 240 GCAQTGSGKTAAFLIPIMHHLLESPGELVTGYCAQPEVIICAPTRELVMQIHEVACKYAY 299
AQ+G+GKT F I + + S P+ ++ APTREL +QI +V A+
Sbjct: 64 AQAQSGTGKTGTFSIAALQRIDTS--------VKAPQALMLAPTRELALQIQKVVMALAF 115
Query: 300 SSVLKICLHYGGASSMHFNRQLEKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADR 359
+K+ GG S + L + I+V T GR+ D + R R ++ +LDEAD
Sbjct: 116 HMDIKVHACIGGTSFVEDAEGL-RDAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADE 174
Query: 360 MLDMGFLGDIQHVMQHSTMPDVANRQTLMFSATFPETI 397
ML GF I + + +P Q ++ SAT P +
Sbjct: 175 MLSSGFKEQIYQIF--TLLP--PTTQVVLLSATMPNDV 208
Score = 72.4 bits (176), Expect = 8e-13, Method: Compositional matrix adjust.
Identities = 63/239 (26%), Positives = 114/239 (47%), Gaps = 12/239 (5%)
Query: 400 KGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMPDVA 459
+ I+V T GR+ D + R R ++ +LDEAD ML GF I + + +P
Sbjct: 138 RDAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIF--TLLP--P 193
Query: 460 NRQTLMFSATFPETIQK---NYIFIAVGIIGGASTDVVQTILEVPXXXXXXXXXXXXXXX 516
Q ++ SAT P + + ++ V I+ ++ I +
Sbjct: 194 TTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKDELTLEGIKQFYVNVEEEEYKYECLTD 253
Query: 517 DEDGV-----IVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIHDFKTKKMKV 571
D + ++F +T R + + L + ++I+ Q +R+ + +F++ ++
Sbjct: 254 LYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRI 313
Query: 572 LVATAVASRGLDIKGIRHVINYDLPQEIDEYVHRIGRTGRVGNKGRATSFYDPDQDGAI 630
L++T + +RG+D++ + VINYDLP + Y+HRIGR GR G KG A +F + GA+
Sbjct: 314 LISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAM 372
>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 = 94.4 bits (233), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 66/204 (32%), Positives = 106/204 (51%), Gaps = 17/204 (8%)
Query: 197 IESFESAGLREILVKNLKKSNYTKPTPIQKYAIPAGLEGRDLMGCAQTGSGKTAAFLIPI 256
++SF+ L E L++ + + KP+ IQ+ AI ++G D++ AQ+G+GKTA F I I
Sbjct: 13 VDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISI 72
Query: 257 MHHLLESPGELVTGYCAQPEVIICAPTRELVMQIHEVACKYAYSSVLKICLH--YGGASS 314
+ + EL + ++ APTREL QI +V A + H GG +
Sbjct: 73 LQQI-----EL---DLKATQALVLAPTRELAQQIQKVVM--ALGDYMGASCHACIGGTNV 122
Query: 315 MHFNRQLE-KGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVM 373
++L+ + +I+V T GR+ D+L+R +S ++ VLDEAD ML GF I +
Sbjct: 123 RAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIF 182
Query: 374 QHSTMPDVANRQTLMFSATFPETI 397
Q +N Q ++ SAT P +
Sbjct: 183 QKLN----SNTQVVLLSATMPSDV 202
Score = 85.5 bits (210), Expect = 8e-17, Method: Compositional matrix adjust.
Identities = 57/220 (25%), Positives = 109/220 (49%), Gaps = 12/220 (5%)
Query: 395 ETIQKKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHST 454
+ +Q + +I+V T GR+ D+L+R +S ++ VLDEAD ML GF I + Q
Sbjct: 127 QKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLN 186
Query: 455 MPDVANRQTLMFSATFPE---TIQKNYIFIAVGIIGGASTDVVQTILEVPXXXXXXXXXX 511
+N Q ++ SAT P + K ++ + I+ ++ I +
Sbjct: 187 ----SNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKL 242
Query: 512 XXXXXDEDGV-----IVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIHDFKT 566
+ + ++F++T R D++ + + +++HG Q +R+ + +F++
Sbjct: 243 DTLCDLYETLTITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRS 302
Query: 567 KKMKVLVATAVASRGLDIKGIRHVINYDLPQEIDEYVHRI 606
+VL+ T + +RG+D++ + VINYDLP + Y+HRI
Sbjct: 303 GSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHRI 342
>pdb|1QDE|A Chain A, Crystal Structure Of The Atpase Domain Of Translation
Initiation Factor 4a From Saccharomyces Cerevisiae-The
Prototype Of The Dead Box Protein Family
Length = 224
Score = 94.0 bits (232), Expect = 3e-19, Method: Compositional matrix adjust.
Identities = 62/206 (30%), Positives = 101/206 (49%), Gaps = 13/206 (6%)
Query: 192 NPPRPIESFESAGLREILVKNLKKSNYTKPTPIQKYAIPAGLEGRDLMGCAQTGSGKTAA 251
N + + F+ L E L++ + + +P+ IQ+ AI +EG D++ AQ+G+GKT
Sbjct: 8 NYDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGT 67
Query: 252 FLIPIMHHLLESPGELVTGYCAQPEVIICAPTRELVMQIHEVACKYAYSSVLKICLHYGG 311
F I + + S P+ ++ APTREL +QI +V A+ +K+ GG
Sbjct: 68 FSIAALQRIDTS--------VKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGG 119
Query: 312 ASSMHFNRQLEKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQH 371
S + L + I+V T GR+ D + R R ++ +LDEAD ML GF I
Sbjct: 120 TSFVEDAEGL-RDAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQ 178
Query: 372 VMQHSTMPDVANRQTLMFSATFPETI 397
+ + +P Q ++ SAT P +
Sbjct: 179 IF--TLLP--PTTQVVLLSATMPNDV 200
Score = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 37/75 (49%), Gaps = 4/75 (5%)
Query: 400 KGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMPDVA 459
+ I+V T GR+ D + R R ++ +LDEAD ML GF I + + +P
Sbjct: 130 RDAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIF--TLLP--P 185
Query: 460 NRQTLMFSATFPETI 474
Q ++ SAT P +
Sbjct: 186 TTQVVLLSATMPNDV 200
>pdb|2KBE|A Chain A, Solution Structure Of Amino-Terminal Domain Of Dbp5p
Length = 226
Score = 92.8 bits (229), Expect = 6e-19, Method: Compositional matrix adjust.
Identities = 67/223 (30%), Positives = 113/223 (50%), Gaps = 17/223 (7%)
Query: 185 EVKVSGDNPPRPIESFESAGLREILVKNLKKSNYTKPTPIQKYAIPAGLEG--RDLMGCA 242
+++ ++P +SF+ GL L+K + + KP+ IQ+ A+P L R+++ +
Sbjct: 9 DIQADPNSPLYSAKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQS 68
Query: 243 QTGSGKTAAFLIPIMHHLLESPGELVTGYCAQPEVIICAPTRELVMQIHEVACKYAYSSV 302
Q+G+GKTAAF + ++ V A P+ I AP+REL Q EV + +
Sbjct: 69 QSGTGKTAAFSLTMLTR--------VNPEDASPQAICLAPSRELARQTLEVVQEMGKFT- 119
Query: 303 LKICLHYGGASSMHFNRQLEKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLD 362
KI S N+Q+ ++V T G + D++ R + L ++ VLDEAD MLD
Sbjct: 120 -KITSQLIVPDSFEKNKQI--NAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLD 176
Query: 363 MGFLGDIQHVMQHSTMPDVANRQTLMFSATFPETIQKKGCNIL 405
LGD Q + +P + Q ++FSATF + +++ I+
Sbjct: 177 QQGLGD-QCIRVKRFLPK--DTQLVLFSATFADAVRQYAKKIV 216
Score = 48.9 bits (115), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 34/106 (32%), Positives = 57/106 (53%), Gaps = 10/106 (9%)
Query: 394 PETIQKK---GCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVM 450
P++ +K ++V T G + D++ R + L ++ VLDEAD MLD LGD Q +
Sbjct: 128 PDSFEKNKQINAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGD-QCIR 186
Query: 451 QHSTMPDVANRQTLMFSATFPETIQKNYIFIAVGIIGGASTDVVQT 496
+P + Q ++FSATF + +++ A I+ A+T +QT
Sbjct: 187 VKRFLPK--DTQLVLFSATFADAVRQ----YAKKIVPNANTLELQT 226
>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a
pdb|1FUU|B Chain B, Yeast Initiation Factor 4a
Length = 394
Score = 91.7 bits (226), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 63/218 (28%), Positives = 103/218 (47%), Gaps = 13/218 (5%)
Query: 180 GWENVEVKVSGDNPPRPIESFESAGLREILVKNLKKSNYTKPTPIQKYAIPAGLEGRDLM 239
G ++E N + + F+ L E L++ + + +P+ IQ+ AI +EG D++
Sbjct: 3 GITDIEESQIQTNYDKVVYKFDDXELDENLLRGVFGYGFEEPSAIQQRAIXPIIEGHDVL 62
Query: 240 GCAQTGSGKTAAFLIPIMHHLLESPGELVTGYCAQPEVIICAPTRELVMQIHEVACKYAY 299
AQ+G+GKT F I + + S P+ + APTREL +QI +V A+
Sbjct: 63 AQAQSGTGKTGTFSIAALQRIDTS--------VKAPQALXLAPTRELALQIQKVVXALAF 114
Query: 300 SSVLKICLHYGGASSMHFNRQLEKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADR 359
+K+ GG S + L + I+V T GR+ D + R R ++ +LDEAD
Sbjct: 115 HXDIKVHACIGGTSFVEDAEGL-RDAQIVVGTPGRVFDNIQRRRFRTDKIKXFILDEADE 173
Query: 360 MLDMGFLGDIQHVMQHSTMPDVANRQTLMFSATFPETI 397
L GF I + + +P Q ++ SAT P +
Sbjct: 174 XLSSGFKEQIYQIF--TLLP--PTTQVVLLSATXPNDV 207
Score = 66.6 bits (161), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 51/215 (23%), Positives = 97/215 (45%), Gaps = 12/215 (5%)
Query: 400 KGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMPDVA 459
+ I+V T GR+ D + R R ++ +LDEAD L GF I + + +P
Sbjct: 137 RDAQIVVGTPGRVFDNIQRRRFRTDKIKXFILDEADEXLSSGFKEQIYQIF--TLLP--P 192
Query: 460 NRQTLMFSATFPETIQK---NYIFIAVGIIGGASTDVVQTILEVPXXXXXXXXXXXXXXX 516
Q ++ SAT P + + + V I+ ++ I +
Sbjct: 193 TTQVVLLSATXPNDVLEVTTKFXRNPVRILVKKDELTLEGIKQFYVNVEEEEYKYECLTD 252
Query: 517 DEDGV-----IVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIHDFKTKKMKV 571
D + ++F +T R + + L + ++I+ Q +R+ +F++ ++
Sbjct: 253 LYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIXKEFRSGSSRI 312
Query: 572 LVATAVASRGLDIKGIRHVINYDLPQEIDEYVHRI 606
L++T + +RG+D++ + VINYDLP + Y+HRI
Sbjct: 313 LISTDLLARGIDVQQVSLVINYDLPANKENYIHRI 347
>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 = 91.3 bits (225), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 47/103 (45%), Positives = 63/103 (61%)
Query: 519 DGVIVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIHDFKTKKMKVLVATAVA 578
D I+F T + + + L + IHG +Q R +++FK + + LVAT VA
Sbjct: 36 DSCIIFCRTKEHVNQLTDELDDLGYPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVATDVA 95
Query: 579 SRGLDIKGIRHVINYDLPQEIDEYVHRIGRTGRVGNKGRATSF 621
+RG+DI+ I VINYDLP E + YVHR GRTGR GNKG+A SF
Sbjct: 96 ARGIDIENISLVINYDLPLEKESYVHRTGRTGRAGNKGKAISF 138
>pdb|2G9N|A Chain A, Structure Of The Dead Domain Of Human Eukaryotic
Initiation Factor 4a, Eif4a
pdb|2G9N|B Chain B, Structure Of The Dead Domain Of Human Eukaryotic
Initiation Factor 4a, Eif4a
Length = 221
Score = 87.0 bits (214), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 64/204 (31%), Positives = 100/204 (49%), Gaps = 17/204 (8%)
Query: 197 IESFESAGLREILVKNLKKSNYTKPTPIQKYAIPAGLEGRDLMGCAQTGSGKTAAFLIPI 256
++SF+ L E L++ + + P+ IQ+ AI + G D++ AQ+G+G TA F I I
Sbjct: 14 VDSFDDMNLSESLLRGIYAYGFEXPSAIQQRAILPCIXGYDVIAQAQSGTGXTATFAISI 73
Query: 257 MHHLLESPGELVTGYCAQPEVIICAPTRELVMQIHEVACKYAYSSVLKICLH--YGGASS 314
+ + EL + ++ APTREL QI V A + H GG +
Sbjct: 74 LQQI-----EL---DLXATQALVLAPTRELAQQIQXVVM--ALGDYMGASCHACIGGTNV 123
Query: 315 MHFNRQLE-KGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVM 373
+ L+ + +I+V T GR+ D+L+R +S + VLDEAD ML GF I +
Sbjct: 124 RAEVQXLQMEAPHIIVGTPGRVFDMLNRRYLSPXYIXMFVLDEADEMLSRGFXDQIYDIF 183
Query: 374 QHSTMPDVANRQTLMFSATFPETI 397
Q +N Q ++ SAT P +
Sbjct: 184 QXLN----SNTQVVLLSATMPSDV 203
Score = 50.4 bits (119), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 28/80 (35%), Positives = 43/80 (53%), Gaps = 4/80 (5%)
Query: 395 ETIQKKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHST 454
+ +Q + +I+V T GR+ D+L+R +S + VLDEAD ML GF I + Q
Sbjct: 128 QXLQMEAPHIIVGTPGRVFDMLNRRYLSPXYIXMFVLDEADEMLSRGFXDQIYDIFQXLN 187
Query: 455 MPDVANRQTLMFSATFPETI 474
+N Q ++ SAT P +
Sbjct: 188 ----SNTQVVLLSATMPSDV 203
>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 = 85.5 bits (210), Expect = 1e-16, Method: Composition-based stats.
Identities = 43/102 (42%), Positives = 59/102 (57%)
Query: 522 IVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIHDFKTKKMKVLVATAVASRG 581
IVFV +A +L E I + G +Q +R +AI ++ VLVAT VA+RG
Sbjct: 34 IVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGRVNVLVATDVAARG 93
Query: 582 LDIKGIRHVINYDLPQEIDEYVHRIGRTGRVGNKGRATSFYD 623
+DI + HV N+D+P+ D Y+HRIGRT R G KG A S +
Sbjct: 94 IDIPDVSHVFNFDMPRSGDTYLHRIGRTARAGRKGTAISLVE 135
>pdb|3FHO|A Chain A, Structure Of S. Pombe Dbp5
pdb|3FHO|B Chain B, Structure Of S. Pombe Dbp5
Length = 508
Score = 84.7 bits (208), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 69/239 (28%), Positives = 110/239 (46%), Gaps = 21/239 (8%)
Query: 399 KKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMPDV 458
K I++ T G + D++ R ++ ++ VLDEAD MLD LGD ++H +P
Sbjct: 233 KIDAQIVIGTPGTVMDLMKRRQLDARDIKVFVLDEADNMLDQQGLGDQSMRIKH-LLP-- 289
Query: 459 ANRQTLMFSATFPETIQK-------NYIFIAVGIIGGASTDVVQTILEVPXXXXXXXXXX 511
N Q ++FSATF E ++K N I + + + Q ++
Sbjct: 290 RNTQIVLFSATFSERVEKYAERFAPNANEIRLKTEELSVEGIKQLYMDCQSEEHKYNVLV 349
Query: 512 XXXXXDEDG-VIVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIHDFKTKKMK 570
G I+F A+ IA + + G+ +QR+ + F+ K
Sbjct: 350 ELYGLLTIGQSIIFCKKKDTAEEIARRMTADGHTVACLTGNLEGAQRDAIMDSFRVGTSK 409
Query: 571 VLVATAVASRGLDIKGIRHVINYDLPQEIDE--------YVHRIGRTGRVGNKGRATSF 621
VLV T V +RG+D+ + V+NYD+P +D+ Y+HRIGRTGR G G + +F
Sbjct: 410 VLVTTNVIARGIDVSQVNLVVNYDMP--LDQAGRPDPQTYLHRIGRTGRFGRVGVSINF 466
Score = 84.7 bits (208), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 57/178 (32%), Positives = 96/178 (53%), Gaps = 17/178 (9%)
Query: 224 IQKYAIPAGLEG--RDLMGCAQTGSGKTAAFLIPIMHHLLESPGELVTGYCAQPEVIICA 281
IQ+ A+P L R+++G +Q+G+GKTAAF + ++ V +P+ I A
Sbjct: 145 IQEKALPLLLSNPPRNMIGQSQSGTGKTAAFALTMLSR--------VDASVPKPQAICLA 196
Query: 282 PTRELVMQIHEVACKYAYSSVLKICLHYGGASSMHFNRQLEKGCNILVATMGRLKDILDR 341
P+REL QI +V + + +K +G S+ +++ I++ T G + D++ R
Sbjct: 197 PSRELARQIMDVVTEMGKYTEVKTA--FGIKDSVPKGAKID--AQIVIGTPGTVMDLMKR 252
Query: 342 GRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMPDVANRQTLMFSATFPETIQK 399
++ ++ VLDEAD MLD LGD ++H +P N Q ++FSATF E ++K
Sbjct: 253 RQLDARDIKVFVLDEADNMLDQQGLGDQSMRIKH-LLP--RNTQIVLFSATFSERVEK 307
>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 = 84.7 bits (208), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 61/208 (29%), Positives = 107/208 (51%), Gaps = 20/208 (9%)
Query: 199 SFESAGLREILVK-----NLKKSNYTKPTPIQKYAIPAGLEGRDLMGCAQTGSGKTAAFL 253
S S+G R+ L+K + + P+ +Q IP + G D++ A++G GKTA F+
Sbjct: 10 SIHSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFV 69
Query: 254 IPIMHHLLESPGELVTGYCAQPEVIICAPTRELVMQIHEVACKYA-YSSVLKICLHYGGA 312
+ + L E VTG Q V++ TREL QI + +++ Y +K+ + +GG
Sbjct: 70 LATLQQL-----EPVTG---QVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGL 121
Query: 313 SSMHFNRQLEKGC-NILVATMGRLKDILDRGRISLASVRFVVLDEADRMLD-MGFLGDIQ 370
S L+K C +I+V T GR+ + ++L ++ +LDE D+ML+ + D+Q
Sbjct: 122 SIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQ 181
Query: 371 HVMQHSTMPDVANRQTLMFSATFPETIQ 398
+ + + +Q +MFSAT + I+
Sbjct: 182 EIFRMTP----HEKQVMMFSATLSKEIR 205
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 46/83 (55%), Gaps = 6/83 (7%)
Query: 395 ETIQKKGC-NILVATMGRLKDILDRGRISLASVRFVVLDEADRMLD-MGFLGDIQHVMQH 452
E + KK C +I+V T GR+ + ++L ++ +LDE D+ML+ + D+Q + +
Sbjct: 127 EEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRM 186
Query: 453 STMPDVANRQTLMFSATFPETIQ 475
+ +Q +MFSAT + I+
Sbjct: 187 TP----HEKQVMMFSATLSKEIR 205
>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 = 82.0 bits (201), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 71/247 (28%), Positives = 109/247 (44%), Gaps = 30/247 (12%)
Query: 398 QKKGCNILVATMGRLKDILDRGR-ISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMP 456
QK I++ T G + D + + I ++ VLDEAD M+ D Q + +P
Sbjct: 140 QKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQD-QSIRIQRMLP 198
Query: 457 DVANRQTLMFSATFPETIQKNYIFIAVGIIGGASTDVVQTILEVPXXXXXXXXXXXXXXX 516
N Q L+FSATF +++ K A ++ +V++ E
Sbjct: 199 --RNCQMLLFSATFEDSVWK----FAQKVV--PDPNVIKLKREEETLDTIKQYYVLCSSR 250
Query: 517 DED--------------GVIVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIH 562
DE ++F T + A ++A L + + G + QR I
Sbjct: 251 DEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIE 310
Query: 563 DFKTKKMKVLVATAVASRGLDIKGIRHVINYDLPQEID------EYVHRIGRTGRVGNKG 616
F+ K KVLV T V +RG+D++ + VIN+DLP + D Y+HRIGRTGR G +G
Sbjct: 311 RFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRG 370
Query: 617 RATSFYD 623
A + D
Sbjct: 371 LAVNMVD 377
Score = 66.6 bits (161), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 67/248 (27%), Positives = 121/248 (48%), Gaps = 33/248 (13%)
Query: 185 EVKVSGDNPPRP---IESFESAGLREILVKNLKKSNYTKPTPIQKYAIPAGLEG--RDLM 239
+V+V +P P ++SFE L+ L++ + + +P+ IQ+ A+P L ++L+
Sbjct: 9 QVEVLQRDPNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLI 68
Query: 240 GCAQTGSGKTAAFLIPIMHHLLESPGELVTGYCAQPEVIICAPTRELVMQIHEVACKYA- 298
+Q+G+GKTAAF++ ++ + E Y P+ + +PT EL +Q +V +
Sbjct: 69 AQSQSGTGKTAAFVLAMLSQV-----EPANKY---PQCLCLSPTYELALQTGKVIEQMGK 120
Query: 299 YSSVLKICLHYGGASSMHFNRQLEKGC----NILVATMGRLKDILDRGR-ISLASVRFVV 353
+ LK+ G +LE+G I++ T G + D + + I ++ V
Sbjct: 121 FYPELKLAYAVRG-------NKLERGQKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFV 173
Query: 354 LDEADRMLDMGFLGDIQHVMQHSTMPDVANRQTLMFSATFPETIQKKGCNIL----VATM 409
LDEAD M+ D Q + +P N Q L+FSATF +++ K ++ V +
Sbjct: 174 LDEADVMIATQGHQD-QSIRIQRMLP--RNCQMLLFSATFEDSVWKFAQKVVPDPNVIKL 230
Query: 410 GRLKDILD 417
R ++ LD
Sbjct: 231 KREEETLD 238
>pdb|1T5I|A Chain A, Crystal Structure Of The C-Terminal Domain Of Uap56
Length = 172
Score = 82.0 bits (201), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 39/114 (34%), Positives = 62/114 (54%)
Query: 521 VIVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIHDFKTKKMKVLVATAVASR 580
V++FV +++ +A L E +IH Q +R FK + ++LVAT + R
Sbjct: 34 VVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGR 93
Query: 581 GLDIKGIRHVINYDLPQEIDEYVHRIGRTGRVGNKGRATSFYDPDQDGAIAKDL 634
G+DI+ + NYD+P++ D Y+HR+ R GR G KG A +F + D I D+
Sbjct: 94 GMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDV 147
>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 = 82.0 bits (201), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 71/247 (28%), Positives = 109/247 (44%), Gaps = 30/247 (12%)
Query: 398 QKKGCNILVATMGRLKDILDRGR-ISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMP 456
QK I++ T G + D + + I ++ VLDEAD M+ D Q + +P
Sbjct: 207 QKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQD-QSIRIQRMLP 265
Query: 457 DVANRQTLMFSATFPETIQKNYIFIAVGIIGGASTDVVQTILEVPXXXXXXXXXXXXXXX 516
N Q L+FSATF +++ K A ++ +V++ E
Sbjct: 266 --RNCQMLLFSATFEDSVWK----FAQKVV--PDPNVIKLKREEETLDTIKQYYVLCSSR 317
Query: 517 DED--------------GVIVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIH 562
DE ++F T + A ++A L + + G + QR I
Sbjct: 318 DEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIE 377
Query: 563 DFKTKKMKVLVATAVASRGLDIKGIRHVINYDLPQEID------EYVHRIGRTGRVGNKG 616
F+ K KVLV T V +RG+D++ + VIN+DLP + D Y+HRIGRTGR G +G
Sbjct: 378 RFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRG 437
Query: 617 RATSFYD 623
A + D
Sbjct: 438 LAVNMVD 444
Score = 67.0 bits (162), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 67/248 (27%), Positives = 121/248 (48%), Gaps = 33/248 (13%)
Query: 185 EVKVSGDNPPRP---IESFESAGLREILVKNLKKSNYTKPTPIQKYAIPAGLEG--RDLM 239
+V+V +P P ++SFE L+ L++ + + +P+ IQ+ A+P L ++L+
Sbjct: 76 QVEVLQRDPNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLI 135
Query: 240 GCAQTGSGKTAAFLIPIMHHLLESPGELVTGYCAQPEVIICAPTRELVMQIHEVACKYA- 298
+Q+G+GKTAAF++ ++ + E Y P+ + +PT EL +Q +V +
Sbjct: 136 AQSQSGTGKTAAFVLAMLSQV-----EPANKY---PQCLCLSPTYELALQTGKVIEQMGK 187
Query: 299 YSSVLKICLHYGGASSMHFNRQLEKGC----NILVATMGRLKDILDRGR-ISLASVRFVV 353
+ LK+ G +LE+G I++ T G + D + + I ++ V
Sbjct: 188 FYPELKLAYAVRG-------NKLERGQKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFV 240
Query: 354 LDEADRMLDMGFLGDIQHVMQHSTMPDVANRQTLMFSATFPETIQKKGCNIL----VATM 409
LDEAD M+ D Q + +P N Q L+FSATF +++ K ++ V +
Sbjct: 241 LDEADVMIATQGHQD-QSIRIQRMLP--RNCQMLLFSATFEDSVWKFAQKVVPDPNVIKL 297
Query: 410 GRLKDILD 417
R ++ LD
Sbjct: 298 KREEETLD 305
>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 = 82.0 bits (201), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 71/247 (28%), Positives = 109/247 (44%), Gaps = 30/247 (12%)
Query: 398 QKKGCNILVATMGRLKDILDRGR-ISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMP 456
QK I++ T G + D + + I ++ VLDEAD M+ D Q + +P
Sbjct: 177 QKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQD-QSIRIQRMLP 235
Query: 457 DVANRQTLMFSATFPETIQKNYIFIAVGIIGGASTDVVQTILEVPXXXXXXXXXXXXXXX 516
N Q L+FSATF +++ K A ++ +V++ E
Sbjct: 236 --RNCQMLLFSATFEDSVWK----FAQKVV--PDPNVIKLKREEETLDTIKQYYVLCSSR 287
Query: 517 DED--------------GVIVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIH 562
DE ++F T + A ++A L + + G + QR I
Sbjct: 288 DEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIE 347
Query: 563 DFKTKKMKVLVATAVASRGLDIKGIRHVINYDLPQEID------EYVHRIGRTGRVGNKG 616
F+ K KVLV T V +RG+D++ + VIN+DLP + D Y+HRIGRTGR G +G
Sbjct: 348 RFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRG 407
Query: 617 RATSFYD 623
A + D
Sbjct: 408 LAVNMVD 414
Score = 68.6 bits (166), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 73/277 (26%), Positives = 131/277 (47%), Gaps = 32/277 (11%)
Query: 154 LYIPKDVDQSEDNLFSSGIQTGINFSGWENVEVKVSGDNPP-RPIESFESAGLREILVKN 212
LY D++ +L + I++ + VEV N P ++SFE L+ L++
Sbjct: 18 LYFQSMEDRAAQSLLNKLIRSNL-VDNTNQVEVLQRDPNSPLYSVKSFEELRLKPQLLQG 76
Query: 213 LKKSNYTKPTPIQKYAIPAGLEG--RDLMGCAQTGSGKTAAFLIPIMHHLLESPGELVTG 270
+ + +P+ IQ+ A+P L ++L+ +Q+G+GKTAAF++ ++ + E
Sbjct: 77 VYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQV-----EPANK 131
Query: 271 YCAQPEVIICAPTRELVMQIHEVACKYA-YSSVLKICLHYGGASSMHFNRQLEKGC---- 325
Y P+ + +PT EL +Q +V + + LK+ G +LE+G
Sbjct: 132 Y---PQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRG-------NKLERGQKISE 181
Query: 326 NILVATMGRLKDILDRGR-ISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMPDVANR 384
I++ T G + D + + I ++ VLDEAD M+ D Q + +P N
Sbjct: 182 QIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQD-QSIRIQRMLP--RNC 238
Query: 385 QTLMFSATFPETIQKKGCNIL----VATMGRLKDILD 417
Q L+FSATF +++ K ++ V + R ++ LD
Sbjct: 239 QMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLD 275
>pdb|3G0H|A Chain A, Human Dead-box Rna Helicase Ddx19, In Complex With An
Atp-analogue And Rna
Length = 424
Score = 81.6 bits (200), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 71/247 (28%), Positives = 109/247 (44%), Gaps = 30/247 (12%)
Query: 398 QKKGCNILVATMGRLKDILDRGR-ISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMP 456
QK I++ T G + D + + I ++ VLDEAD M+ D Q + +P
Sbjct: 156 QKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQD-QSIRIQRMLP 214
Query: 457 DVANRQTLMFSATFPETIQKNYIFIAVGIIGGASTDVVQTILEVPXXXXXXXXXXXXXXX 516
N Q L+FSATF +++ K A ++ +V++ E
Sbjct: 215 --RNCQMLLFSATFEDSVWK----FAQKVV--PDPNVIKLKREEETLDTIKQYYVLCSSR 266
Query: 517 DED--------------GVIVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIH 562
DE ++F T + A ++A L + + G + QR I
Sbjct: 267 DEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIE 326
Query: 563 DFKTKKMKVLVATAVASRGLDIKGIRHVINYDLPQEID------EYVHRIGRTGRVGNKG 616
F+ K KVLV T V +RG+D++ + VIN+DLP + D Y+HRIGRTGR G +G
Sbjct: 327 RFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRG 386
Query: 617 RATSFYD 623
A + D
Sbjct: 387 LAVNMVD 393
Score = 67.0 bits (162), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 71/270 (26%), Positives = 129/270 (47%), Gaps = 32/270 (11%)
Query: 161 DQSEDNLFSSGIQTGINFSGWENVEVKVSGDNPP-RPIESFESAGLREILVKNLKKSNYT 219
D++ +L + I++ + VEV N P ++SFE L+ L++ + +
Sbjct: 4 DRAAQSLLNKLIRSNL-VDNTNQVEVLQRDPNSPLYSVKSFEELRLKPQLLQGVYAMGFN 62
Query: 220 KPTPIQKYAIPAGLEG--RDLMGCAQTGSGKTAAFLIPIMHHLLESPGELVTGYCAQPEV 277
+P+ IQ+ A+P L ++L+ +Q+G+GKTAAF++ ++ + E Y P+
Sbjct: 63 RPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQV-----EPANKY---PQC 114
Query: 278 IICAPTRELVMQIHEVACKYA-YSSVLKICLHYGGASSMHFNRQLEKGC----NILVATM 332
+ +PT EL +Q +V + + LK+ G +LE+G I++ T
Sbjct: 115 LCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRG-------NKLERGQKISEQIVIGTP 167
Query: 333 GRLKDILDRGR-ISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMPDVANRQTLMFSA 391
G + D + + I ++ VLDEAD M+ D Q + +P N Q L+FSA
Sbjct: 168 GTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQD-QSIRIQRMLP--RNCQMLLFSA 224
Query: 392 TFPETIQKKGCNIL----VATMGRLKDILD 417
TF +++ K ++ V + R ++ LD
Sbjct: 225 TFEDSVWKFAQKVVPDPNVIKLKREEETLD 254
>pdb|3GFP|A Chain A, Structure Of The C-Terminal Domain Of The Dead-Box Protein
Dbp5
Length = 189
Score = 79.7 bits (195), Expect = 4e-15, Method: Composition-based stats.
Identities = 42/106 (39%), Positives = 61/106 (57%), Gaps = 6/106 (5%)
Query: 522 IVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIHDFKTKKMKVLVATAVASRG 581
I+FV+T + A+ + L + +HG +R++ I DF+ + KVL+ T V +RG
Sbjct: 41 IIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARG 100
Query: 582 LDIKGIRHVINYDLPQEID------EYVHRIGRTGRVGNKGRATSF 621
+DI + V+NYDLP + Y+HRIGRTGR G KG A SF
Sbjct: 101 IDIPTVSXVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISF 146
>pdb|2KBF|A Chain A, Solution Structure Of Carboxyl-Terminal Domain Of Dbp5p
Length = 187
Score = 78.6 bits (192), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 42/106 (39%), Positives = 61/106 (57%), Gaps = 6/106 (5%)
Query: 522 IVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIHDFKTKKMKVLVATAVASRG 581
I+FV+T + A+ + L + +HG +R++ I DF+ + KVL+ T V +RG
Sbjct: 39 IIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARG 98
Query: 582 LDIKGIRHVINYDLPQEID------EYVHRIGRTGRVGNKGRATSF 621
+DI + V+NYDLP + Y+HRIGRTGR G KG A SF
Sbjct: 99 IDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISF 144
>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 = 78.6 bits (192), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 42/106 (39%), Positives = 61/106 (57%), Gaps = 6/106 (5%)
Query: 522 IVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIHDFKTKKMKVLVATAVASRG 581
I+FV+T + A+ + L + +HG +R++ I DF+ + KVL+ T V +RG
Sbjct: 40 IIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARG 99
Query: 582 LDIKGIRHVINYDLPQEID------EYVHRIGRTGRVGNKGRATSF 621
+DI + V+NYDLP + Y+HRIGRTGR G KG A SF
Sbjct: 100 IDIPTVSXVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISF 145
>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 = 75.1 bits (183), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 42/117 (35%), Positives = 64/117 (54%), Gaps = 6/117 (5%)
Query: 522 IVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIHDFKTKKMKVLVATAVASRG 581
I+F T RNA ++ + + + + G QR I F+ K KVL+ T V +RG
Sbjct: 38 IIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNVCARG 97
Query: 582 LDIKGIRHVINYDLPQEIDE------YVHRIGRTGRVGNKGRATSFYDPDQDGAIAK 632
+D+K + V+N+DLP + E Y+HRIGRTGR G KG A + + D+ ++ K
Sbjct: 98 IDVKQVTIVVNFDLPVKQGEEPDYETYLHRIGRTGRFGKKGLAFNMIEVDELPSLMK 154
>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 = 74.3 bits (181), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 41/128 (32%), Positives = 68/128 (53%), Gaps = 7/128 (5%)
Query: 522 IVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIHDFKTKKMKVLVATAVASRG 581
I+F ++ + + +A + + + IH Q R + HDF+ + LV T + +RG
Sbjct: 48 IIFCNSSQRVELLAKKISQLGYSCFYIHAKMRQEHRNRVFHDFRNGLCRNLVCTDLFTRG 107
Query: 582 LDIKGIRHVINYDLPQEIDEYVHRIGRTGRVGNKGRATSFYDPDQDGAIAKDLVRILEQA 641
+DI+ + VIN+D P+ + Y+HRIGR+GR G+ G A + D +L I EQ
Sbjct: 108 IDIQAVNVVINFDFPKLAETYLHRIGRSGRFGHLGLAINLITYDDRF----NLKSIEEQL 163
Query: 642 G---QPVP 646
G +P+P
Sbjct: 164 GTEIKPIP 171
>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 = 66.6 bits (161), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 34/109 (31%), Positives = 56/109 (51%), Gaps = 5/109 (4%)
Query: 522 IVFVSTIRNADFIACYLCETE----IATTSIHGSRLQSQREQAIHDFKTKKMKVLVATAV 577
I+F T++ F+ C + + E + HG Q++R + FK + +LV T V
Sbjct: 37 IIFAPTVKFTSFL-CSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDV 95
Query: 578 ASRGLDIKGIRHVINYDLPQEIDEYVHRIGRTGRVGNKGRATSFYDPDQ 626
+RG+D + V+ +P E+ Y+HRIGRT R G +G + F D+
Sbjct: 96 GARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDE 144
>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 = 66.6 bits (161), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 34/109 (31%), Positives = 56/109 (51%), Gaps = 5/109 (4%)
Query: 522 IVFVSTIRNADFIACYLCETE----IATTSIHGSRLQSQREQAIHDFKTKKMKVLVATAV 577
I+F T++ F+ C + + E + HG Q++R + FK + +LV T V
Sbjct: 37 IIFAPTVKFTSFL-CSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDV 95
Query: 578 ASRGLDIKGIRHVINYDLPQEIDEYVHRIGRTGRVGNKGRATSFYDPDQ 626
+RG+D + V+ +P E+ Y+HRIGRT R G +G + F D+
Sbjct: 96 GARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDE 144
>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 = 66.6 bits (161), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 34/109 (31%), Positives = 56/109 (51%), Gaps = 5/109 (4%)
Query: 522 IVFVSTIRNADFIACYLCETE----IATTSIHGSRLQSQREQAIHDFKTKKMKVLVATAV 577
I+F T++ F+ C + + E + HG Q++R + FK + +LV T V
Sbjct: 37 IIFAPTVKFTSFL-CSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDV 95
Query: 578 ASRGLDIKGIRHVINYDLPQEIDEYVHRIGRTGRVGNKGRATSFYDPDQ 626
+RG+D + V+ +P E+ Y+HRIGRT R G +G + F D+
Sbjct: 96 GARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDE 144
>pdb|3FMO|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex
With The Dead- Box Helicase Ddx19
Length = 300
Score = 66.2 bits (160), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 63/226 (27%), Positives = 112/226 (49%), Gaps = 29/226 (12%)
Query: 185 EVKVSGDNPPRP---IESFESAGLREILVKNLKKSNYTKPTPIQKYAIPAGLE--GRDLM 239
+V+V +P P ++SFE L+ L++ + + +P+ IQ+ A+P L ++L+
Sbjct: 76 QVEVLQRDPNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLI 135
Query: 240 GCAQTGSGKTAAFLIPIMHHLLESPGELVTGYCAQPEVIICAPTRELVMQIHEVACKYA- 298
+Q+G+GKTAAF++ ++ + E Y P+ + +PT EL +Q +V +
Sbjct: 136 AQSQSGTGKTAAFVLAMLSQV-----EPANKY---PQCLCLSPTYELALQTGKVIEQMGK 187
Query: 299 YSSVLKICLHYGGASSMHFNRQLEKGC----NILVATMGRLKDILDRGR-ISLASVRFVV 353
+ LK+ G +LE+G I++ T G + D + + I ++ V
Sbjct: 188 FYPELKLAYAVRG-------NKLERGQKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFV 240
Query: 354 LDEADRMLDMGFLGDIQHVMQHSTMPDVANRQTLMFSATFPETIQK 399
LDEAD M+ D Q + +P N Q L+FSATF +++ K
Sbjct: 241 LDEADVMIATQGHQD-QSIRIQRMLPR--NCQMLLFSATFEDSVWK 283
Score = 31.6 bits (70), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 40/80 (50%), Gaps = 4/80 (5%)
Query: 398 QKKGCNILVATMGRLKDILDRGR-ISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMP 456
QK I++ T G + D + + I ++ VLDEAD M+ D Q + +P
Sbjct: 207 QKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQD-QSIRIQRMLP 265
Query: 457 DVANRQTLMFSATFPETIQK 476
N Q L+FSATF +++ K
Sbjct: 266 R--NCQMLLFSATFEDSVWK 283
>pdb|3FHC|B Chain B, Crystal Structure Of Human Dbp5 In Complex With Nup214
Length = 235
Score = 65.9 bits (159), Expect = 8e-11, Method: Compositional matrix adjust.
Identities = 63/226 (27%), Positives = 112/226 (49%), Gaps = 29/226 (12%)
Query: 185 EVKVSGDNPPRP---IESFESAGLREILVKNLKKSNYTKPTPIQKYAIPAGL--EGRDLM 239
+V+V +P P ++SFE L+ L++ + + +P+ IQ+ A+P L ++L+
Sbjct: 9 QVEVLQRDPNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLI 68
Query: 240 GCAQTGSGKTAAFLIPIMHHLLESPGELVTGYCAQPEVIICAPTRELVMQIHEVACKYA- 298
+Q+G+GKTAAF++ ++ + E Y P+ + +PT EL +Q +V +
Sbjct: 69 AQSQSGTGKTAAFVLAMLSQV-----EPANKY---PQCLCLSPTYELALQTGKVIEQMGK 120
Query: 299 YSSVLKICLHYGGASSMHFNRQLEKGC----NILVATMGRLKDILDRGR-ISLASVRFVV 353
+ LK+ G +LE+G I++ T G + D + + I ++ V
Sbjct: 121 FYPELKLAYAVRG-------NKLERGQKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFV 173
Query: 354 LDEADRMLDMGFLGDIQHVMQHSTMPDVANRQTLMFSATFPETIQK 399
LDEAD M+ D Q + +P N Q L+FSATF +++ K
Sbjct: 174 LDEADVMIATQGHQD-QSIRIQRMLP--RNCQMLLFSATFEDSVWK 216
Score = 31.6 bits (70), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 40/80 (50%), Gaps = 4/80 (5%)
Query: 398 QKKGCNILVATMGRLKDILDRGR-ISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMP 456
QK I++ T G + D + + I ++ VLDEAD M+ D Q + +P
Sbjct: 140 QKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQD-QSIRIQRMLP 198
Query: 457 DVANRQTLMFSATFPETIQK 476
N Q L+FSATF +++ K
Sbjct: 199 --RNCQMLLFSATFEDSVWK 216
>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 = 58.5 bits (140), Expect = 1e-08, Method: Composition-based stats.
Identities = 47/132 (35%), Positives = 69/132 (52%), Gaps = 3/132 (2%)
Query: 519 DGVIVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIHDFKTKKMKVLVATAVA 578
D +VF T + IA L ++HG Q +RE+ + F+ +++VLVAT VA
Sbjct: 32 DRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEVRVLVATDVA 91
Query: 579 SRGLDIKGIRHVINYDLPQEIDEYVHRIGRTGRVGNKGRATSFYDPDQD---GAIAKDLV 635
+RGLDI + V++Y LP + Y HR GRTGR G GR Y P + A+ + +
Sbjct: 92 ARGLDIPQVDLVVHYRLPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRERRDVEALERAVG 151
Query: 636 RILEQAGQPVPE 647
R ++ P PE
Sbjct: 152 RRFKRVNPPTPE 163
>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 = 3e-08, Method: Compositional matrix adjust.
Identities = 46/132 (34%), Positives = 69/132 (52%), Gaps = 3/132 (2%)
Query: 519 DGVIVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIHDFKTKKMKVLVATAVA 578
D +VF T + IA L ++HG Q +RE+ + F+ +++VLVAT VA
Sbjct: 29 DRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGERERVMGAFRQGEVRVLVATDVA 88
Query: 579 SRGLDIKGIRHVINYDLPQEIDEYVHRIGRTGRVGNKGRATSFYDPDQD---GAIAKDLV 635
+RGLDI + V++Y +P + Y HR GRTGR G GR Y P + A+ + +
Sbjct: 89 ARGLDIPQVDLVVHYRMPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRERRDVEALERAVG 148
Query: 636 RILEQAGQPVPE 647
R ++ P PE
Sbjct: 149 RRFKRVNPPTPE 160
>pdb|1OYW|A Chain A, Structure Of The Recq Catalytic Core
Length = 523
Score = 55.5 bits (132), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 27/103 (26%), Positives = 49/103 (47%)
Query: 522 IVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIHDFKTKKMKVLVATAVASRG 581
I++ ++ + A L I+ + H + R F+ ++++VAT G
Sbjct: 240 IIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGXG 299
Query: 582 LDIKGIRHVINYDLPQEIDEYVHRIGRTGRVGNKGRATSFYDP 624
++ +R V+++D+P+ I+ Y GR GR G A FYDP
Sbjct: 300 INKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAXLFYDP 342
>pdb|1FUK|A Chain A, Crystal Structure Of The Carboxy Terminal Domain Of Yeast
Eif4a
Length = 165
Score = 55.5 bits (132), Expect = 9e-08, Method: Composition-based stats.
Identities = 24/85 (28%), Positives = 51/85 (60%)
Query: 522 IVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIHDFKTKKMKVLVATAVASRG 581
++F +T R + + L + ++I+ Q +R+ + +F++ ++L++T + +RG
Sbjct: 34 VIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARG 93
Query: 582 LDIKGIRHVINYDLPQEIDEYVHRI 606
+D++ + VINYDLP + Y+HRI
Sbjct: 94 IDVQQVSLVINYDLPANKENYIHRI 118
>pdb|1OYY|A Chain A, Structure Of The Recq Catalytic Core Bound To Atp-Gamma-S
Length = 523
Score = 55.5 bits (132), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 27/103 (26%), Positives = 49/103 (47%)
Query: 522 IVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIHDFKTKKMKVLVATAVASRG 581
I++ ++ + A L I+ + H + R F+ ++++VAT G
Sbjct: 240 IIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMG 299
Query: 582 LDIKGIRHVINYDLPQEIDEYVHRIGRTGRVGNKGRATSFYDP 624
++ +R V+++D+P+ I+ Y GR GR G A FYDP
Sbjct: 300 INKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDP 342
>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 = 40.8 bits (94), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 27/88 (30%), Positives = 44/88 (50%), Gaps = 14/88 (15%)
Query: 522 IVFVSTIRNADFIACYLCETE-IATTSIHGSRL-------------QSQREQAIHDFKTK 567
I+F T ++A ++ ++ E E A + L Q+++++ I F+T
Sbjct: 404 IIFTKTRQSAYALSQWITENEKFAEVGVKAHHLIGAGHSSEFKPMTQNEQKEVISKFRTG 463
Query: 568 KMKVLVATAVASRGLDIKGIRHVINYDL 595
K+ +L+AT VA GLDIK VI Y L
Sbjct: 464 KINLLIATTVAEEGLDIKECNIVIRYGL 491
>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 = 39.7 bits (91), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 34/100 (34%), Positives = 47/100 (47%), Gaps = 10/100 (10%)
Query: 521 VIVFVSTIRNADFIACYLCETEIATTSIHGS------RLQSQREQAI--HDFKTKKMKVL 572
+IVF + A I L + I G R SQREQ + +F + VL
Sbjct: 364 IIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVL 423
Query: 573 VATAVASRGLDIKGIRHVINYD-LPQEIDEYVHRIGRTGR 611
VAT+V GLD+ + V+ Y+ +P I + R GRTGR
Sbjct: 424 VATSVGEEGLDVPEVDLVVFYEPVPSAIRS-IQRRGRTGR 462
Score = 36.6 bits (83), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 32/116 (27%), Positives = 54/116 (46%), Gaps = 11/116 (9%)
Query: 244 TGSGKTAAFLIPIMHHLLESPGELVTGYCAQPEVIICAPTRELVMQIHEVACKYAYSSVL 303
TG GKT ++ + L + G+ V++ APT+ LV+Q H + + ++
Sbjct: 32 TGLGKTLIAMMIAEYRLTKYGGK----------VLMLAPTKPLVLQ-HAESFRRLFNLPP 80
Query: 304 KICLHYGGASSMHFNRQLEKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADR 359
+ + G S + ++VAT +++ L GRISL V +V DEA R
Sbjct: 81 EKIVALTGEKSPEERSKAWARAKVIVATPQTIENDLLAGRISLEDVSLIVFDEAHR 136
Score = 29.3 bits (64), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 21/35 (60%)
Query: 402 CNILVATMGRLKDILDRGRISLASVRFVVLDEADR 436
++VAT +++ L GRISL V +V DEA R
Sbjct: 102 AKVIVATPQTIENDLLAGRISLEDVSLIVFDEAHR 136
>pdb|4I1S|A Chain A, Melanoma Differentiation Associated Protein-5 Helicase
Domain Complex With Inhibitor Non-structural Protein V
Length = 243
Score = 38.9 bits (89), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 19/42 (45%), Positives = 27/42 (64%)
Query: 554 QSQREQAIHDFKTKKMKVLVATAVASRGLDIKGIRHVINYDL 595
Q+++ + I F+T K+ +L+AT VA GLDIK VI Y L
Sbjct: 200 QNEQREVISKFRTGKINLLIATTVAEEGLDIKECNIVIRYGL 241
>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 = 37.4 bits (85), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 22/102 (21%), Positives = 50/102 (49%), Gaps = 2/102 (1%)
Query: 522 IVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIH-DFKTKKMKVLVATAVASR 580
I++ + ++++ + L I + H + L+ + + +H + +++V+VAT
Sbjct: 271 IIYCFSQKDSEQVTVSLQNLGIHAGAYHAN-LEPEDKTTVHRKWSANEIQVVVATVAFGM 329
Query: 581 GLDIKGIRHVINYDLPQEIDEYVHRIGRTGRVGNKGRATSFY 622
G+D +R VI++ + + ++ Y GR GR K +Y
Sbjct: 330 GIDKPDVRFVIHHSMSKSMENYYQESGRAGRDDMKADCILYY 371
>pdb|2VA8|A Chain A, Dna Repair Helicase Hel308
pdb|2VA8|B Chain B, Dna Repair Helicase Hel308
Length = 715
Score = 34.3 bits (77), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 51/206 (24%), Positives = 83/206 (40%), Gaps = 27/206 (13%)
Query: 196 PIESFESAGLREILVKNLKKSNYTKPTPIQKYAIPAGL-EGRDLMGCAQTGSGKTAAFLI 254
PIE + L +++ +KK K P Q A+ GL EG L+ + TGSGKT +
Sbjct: 9 PIEDLK---LPSNVIEIIKKRGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEM 65
Query: 255 PIMHHLLESPGELVTGYCAQPEVIICAPTRELVMQIHEVACKYAYSSVLKICLHYGGASS 314
I+ LL++ G + I P R L + + + K+ + G +
Sbjct: 66 GIISFLLKNGG----------KAIYVTPLRALTNEKYLTFKDWELIG-FKVAMTSGDYDT 114
Query: 315 MHFNRQLEKGCNILVATMGRLKDILDRGRISLASVRFVVLDEADRMLDMGFLGDIQH--V 372
+ K +I++ T +L + L V + VLDE + +L D + V
Sbjct: 115 ---DDAWLKNYDIIITTYEKLDSLWRHRPEWLNEVNYFVLDE------LHYLNDPERGPV 165
Query: 373 MQHSTMPDVANRQTLMFSATFPETIQ 398
++ T+ R L SAT Q
Sbjct: 166 VESVTIR-AKRRNLLALSATISNYKQ 190
>pdb|3TMI|A Chain A, Structural Basis For Rna Recognition And Activation Of
Rig-I
Length = 695
Score = 33.5 bits (75), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 37/139 (26%), Positives = 63/139 (45%), Gaps = 9/139 (6%)
Query: 220 KPTPIQ-KYAIPAGLEGRDLMGCAQTGSGKTAAFLIPIMHHLLESPGELVTGYCAQPEVI 278
KP Q + A+PA ++G++ + CA TG GKT L+ HHL + P + +V+
Sbjct: 12 KPRNYQLELALPA-MKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQG------QKGKVV 64
Query: 279 ICAPTRELVMQIHEVACKYAYSSVLKICLHYGGASSMHFNRQLEKGCNILVATMGRLKDI 338
A + Q V KY ++ G + Q+ + +I++ T L +
Sbjct: 65 FFANQIPVYEQQKSVFSKYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQILVNN 124
Query: 339 LDRGRI-SLASVRFVVLDE 356
L +G I SL+ ++ DE
Sbjct: 125 LKKGTIPSLSIFTLMIFDE 143
>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 = 33.5 bits (75), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 24/44 (54%)
Query: 570 KVLVATAVASRGLDIKGIRHVINYDLPQEIDEYVHRIGRTGRVG 613
+VL+ + + S G + + H + +DLP D RIGR R+G
Sbjct: 558 QVLLCSEIGSEGRNFQFASHXVXFDLPFNPDLLEQRIGRLDRIG 601
>pdb|2YKG|A Chain A, Structural Insights Into Rna Recognition By Rig-I
Length = 696
Score = 33.5 bits (75), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 37/139 (26%), Positives = 63/139 (45%), Gaps = 9/139 (6%)
Query: 220 KPTPIQ-KYAIPAGLEGRDLMGCAQTGSGKTAAFLIPIMHHLLESPGELVTGYCAQPEVI 278
KP Q + A+PA ++G++ + CA TG GKT L+ HHL + P + +V+
Sbjct: 13 KPRNYQLELALPA-MKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQG------QKGKVV 65
Query: 279 ICAPTRELVMQIHEVACKYAYSSVLKICLHYGGASSMHFNRQLEKGCNILVATMGRLKDI 338
A + Q V KY ++ G + Q+ + +I++ T L +
Sbjct: 66 FFANQIPVYEQNKSVFSKYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQILVNN 125
Query: 339 LDRGRI-SLASVRFVVLDE 356
L +G I SL+ ++ DE
Sbjct: 126 LKKGTIPSLSIFTLMIFDE 144
>pdb|4AY2|A Chain A, Capturing 5' Tri-Phosphorylated Rna Duplex By Rig-I
Length = 687
Score = 33.5 bits (75), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 37/139 (26%), Positives = 63/139 (45%), Gaps = 9/139 (6%)
Query: 220 KPTPIQ-KYAIPAGLEGRDLMGCAQTGSGKTAAFLIPIMHHLLESPGELVTGYCAQPEVI 278
KP Q + A+PA ++G++ + CA TG GKT L+ HHL + P + +V+
Sbjct: 4 KPRNYQLELALPA-MKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQG------QKGKVV 56
Query: 279 ICAPTRELVMQIHEVACKYAYSSVLKICLHYGGASSMHFNRQLEKGCNILVATMGRLKDI 338
A + Q V KY ++ G + Q+ + +I++ T L +
Sbjct: 57 FFANQIPVYEQNKSVFSKYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQILVNN 116
Query: 339 LDRGRI-SLASVRFVVLDE 356
L +G I SL+ ++ DE
Sbjct: 117 LKKGTIPSLSIFTLMIFDE 135
>pdb|2FZL|A Chain A, Structure Of C-Terminal Domain Of Archaeoglobus Fulgidus
Xpb
Length = 219
Score = 32.7 bits (73), Expect = 0.71, Method: Composition-based stats.
Identities = 15/70 (21%), Positives = 32/70 (45%)
Query: 554 QSQREQAIHDFKTKKMKVLVATAVASRGLDIKGIRHVINYDLPQEIDEYVHRIGRTGRVG 613
+ +RE+ + F+T + + +V++ V G+D+ + EY+ R+GR R
Sbjct: 145 REEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQRLGRILRPS 204
Query: 614 NKGRATSFYD 623
+ Y+
Sbjct: 205 KGKKEAVLYE 214
>pdb|3TBK|A Chain A, Mouse Rig-I Atpase Domain
Length = 555
Score = 32.0 bits (71), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 19/46 (41%), Positives = 27/46 (58%), Gaps = 2/46 (4%)
Query: 220 KPTPIQ-KYAIPAGLEGRDLMGCAQTGSGKTAAFLIPIMHHLLESP 264
KP Q + A+PA +G++ + CA TG GKT L+ HHL + P
Sbjct: 4 KPRNYQLELALPAK-KGKNTIICAPTGCGKTFVSLLICEHHLKKFP 48
>pdb|2EYQ|A Chain A, Crystal Structure Of Escherichia Coli Transcription-Repair
Coupling Factor
pdb|2EYQ|B Chain B, Crystal Structure Of Escherichia Coli Transcription-Repair
Coupling Factor
Length = 1151
Score = 32.0 bits (71), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 26/96 (27%), Positives = 47/96 (48%), Gaps = 13/96 (13%)
Query: 529 RNADFIACYLCETEIATTSIHGSRLQSQREQAIHDFKTKKMKVLVATAVASRGLDIKGIR 588
+ A+ +A + E IA HG + + E+ ++DF ++ VLV T + G+DI
Sbjct: 827 KAAERLAELVPEARIAIG--HGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTAN 884
Query: 589 HVI-----NYDLPQEIDEYVHRI-GRTGRVGNKGRA 618
+I ++ L Q +H++ GR GR ++ A
Sbjct: 885 TIIIERADHFGLAQ-----LHQLRGRVGRSHHQAYA 915
>pdb|3UWX|B Chain B, Crystal Structure Of Uvra-Uvrb Complex
Length = 683
Score = 30.8 bits (68), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 27/98 (27%), Positives = 39/98 (39%), Gaps = 5/98 (5%)
Query: 522 IVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIHDFKTKKMKVLVATAVASRG 581
+V T + A+ + YL E I +H +R + I D + K VLV + G
Sbjct: 474 LVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREG 533
Query: 582 LDIKGIRHVINYDLPQE-----IDEYVHRIGRTGRVGN 614
LDI + V D +E + IGR R N
Sbjct: 534 LDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNAN 571
>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 = 30.8 bits (68), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 29/108 (26%), Positives = 44/108 (40%), Gaps = 6/108 (5%)
Query: 521 VIVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIHDFKTKKMKVLVATAVASR 580
V+V T + ++ + YL E I +H +R + I D + K VLV +
Sbjct: 454 VLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLRE 513
Query: 581 GLDIKGIRHVINYDLPQE-----IDEYVHRIGRTGRVGNKGRATSFYD 623
GLDI + V D +E + IGR R +GR + D
Sbjct: 514 GLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAAR-NAEGRVIMYAD 560
>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 = 30.8 bits (68), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 29/108 (26%), Positives = 44/108 (40%), Gaps = 6/108 (5%)
Query: 521 VIVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIHDFKTKKMKVLVATAVASR 580
V+V T + ++ + YL E I +H +R + I D + K VLV +
Sbjct: 448 VLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLRE 507
Query: 581 GLDIKGIRHVINYDLPQE-----IDEYVHRIGRTGRVGNKGRATSFYD 623
GLDI + V D +E + IGR R +GR + D
Sbjct: 508 GLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAAR-NAEGRVIMYAD 554
>pdb|4A2Q|A Chain A, Structure Of Duck Rig-I Tandem Cards And Helicase Domain
pdb|4A2Q|B Chain B, Structure Of Duck Rig-I Tandem Cards And Helicase Domain
pdb|4A2Q|D Chain D, Structure Of Duck Rig-I Tandem Cards And Helicase Domain
pdb|4A2Q|E Chain E, Structure Of Duck Rig-I Tandem Cards And Helicase Domain
Length = 797
Score = 30.8 bits (68), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 35/67 (52%), Gaps = 2/67 (2%)
Query: 550 GSRLQSQREQAIHDFKTKK-MKVLVATAVASRGLDIKGIRHVINYDLPQEIDEYVHRIGR 608
G L SQ+ + FKT K ++L+AT+VA G+DI V+ Y+ + + + GR
Sbjct: 676 GMTLPSQK-GVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR 734
Query: 609 TGRVGNK 615
G+K
Sbjct: 735 GRAAGSK 741
Score = 30.0 bits (66), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 228 AIPAGLEGRDLMGCAQTGSGKTAAFLIPIMHHLLESPG 265
A PA + G++ + CA TGSGKT ++ HH P
Sbjct: 257 AQPA-INGKNALICAPTGSGKTFVSILICEHHFQNMPA 293
>pdb|1D9Z|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb In
Complex With Atp
Length = 657
Score = 30.8 bits (68), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 27/98 (27%), Positives = 39/98 (39%), Gaps = 5/98 (5%)
Query: 522 IVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIHDFKTKKMKVLVATAVASRG 581
+V T + A+ + YL E I +H +R + I D + K VLV + G
Sbjct: 448 LVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREG 507
Query: 582 LDIKGIRHVINYDLPQE-----IDEYVHRIGRTGRVGN 614
LDI + V D +E + IGR R N
Sbjct: 508 LDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNAN 545
>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 = 30.8 bits (68), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 27/98 (27%), Positives = 39/98 (39%), Gaps = 5/98 (5%)
Query: 522 IVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIHDFKTKKMKVLVATAVASRG 581
+V T + A+ + YL E I +H +R + I D + K VLV + G
Sbjct: 449 LVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREG 508
Query: 582 LDIKGIRHVINYDLPQE-----IDEYVHRIGRTGRVGN 614
LDI + V D +E + IGR R N
Sbjct: 509 LDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNAN 546
>pdb|1D9X|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb
Length = 658
Score = 30.8 bits (68), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 27/98 (27%), Positives = 39/98 (39%), Gaps = 5/98 (5%)
Query: 522 IVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIHDFKTKKMKVLVATAVASRG 581
+V T + A+ + YL E I +H +R + I D + K VLV + G
Sbjct: 449 LVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREG 508
Query: 582 LDIKGIRHVINYDLPQE-----IDEYVHRIGRTGRVGN 614
LDI + V D +E + IGR R N
Sbjct: 509 LDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNAN 546
>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 = 30.8 bits (68), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 27/98 (27%), Positives = 39/98 (39%), Gaps = 5/98 (5%)
Query: 522 IVFVSTIRNADFIACYLCETEIATTSIHGSRLQSQREQAIHDFKTKKMKVLVATAVASRG 581
+V T + A+ + YL E I +H +R + I D + K VLV + G
Sbjct: 449 LVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREG 508
Query: 582 LDIKGIRHVINYDLPQE-----IDEYVHRIGRTGRVGN 614
LDI + V D +E + IGR R N
Sbjct: 509 LDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNAN 546
>pdb|4A2W|A Chain A, Structure Of Full-Length Duck Rig-I
pdb|4A2W|B Chain B, Structure Of Full-Length Duck Rig-I
Length = 936
Score = 30.4 bits (67), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 35/67 (52%), Gaps = 2/67 (2%)
Query: 550 GSRLQSQREQAIHDFKTKK-MKVLVATAVASRGLDIKGIRHVINYDLPQEIDEYVHRIGR 608
G L SQ+ + FKT K ++L+AT+VA G+DI V+ Y+ + + + GR
Sbjct: 676 GMTLPSQK-GVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR 734
Query: 609 TGRVGNK 615
G+K
Sbjct: 735 GRAAGSK 741
Score = 30.0 bits (66), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 228 AIPAGLEGRDLMGCAQTGSGKTAAFLIPIMHHLLESPG 265
A PA + G++ + CA TGSGKT ++ HH P
Sbjct: 257 AQPA-INGKNALICAPTGSGKTFVSILICEHHFQNMPA 293
>pdb|2P6R|A Chain A, Crystal Structure Of Superfamily 2 Helicase Hel308 In
Complex With Unwound Dna
pdb|2P6U|A Chain A, Apo Structure Of The Hel308 Superfamily 2 Helicase
Length = 702
Score = 30.4 bits (67), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 33/80 (41%), Gaps = 7/80 (8%)
Query: 549 HGSRLQSQREQAIHDFKTKKMKVLVATAVASRGLDIKGIRHVIN-------YDLPQEIDE 601
H L QR F+ +KV+VAT + G+++ R ++ Y ++ E
Sbjct: 303 HAGLLNGQRRVVEDAFRRGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSE 362
Query: 602 YVHRIGRTGRVGNKGRATSF 621
Y GR GR G R +
Sbjct: 363 YKQMAGRAGRPGMDERGEAI 382
>pdb|4A2P|A Chain A, Structure Of Duck Rig-I Helicase Domain
pdb|4A36|A Chain A, Structure Of Duck Rig-I Helicase Domain Bound To 19-Mer
Dsrna And Atp Transition State Analogue
pdb|4A36|B Chain B, Structure Of Duck Rig-I Helicase Domain Bound To 19-Mer
Dsrna And Atp Transition State Analogue
Length = 556
Score = 30.4 bits (67), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 228 AIPAGLEGRDLMGCAQTGSGKTAAFLIPIMHHLLESPG 265
A PA + G++ + CA TGSGKT ++ HH P
Sbjct: 16 AQPA-INGKNALICAPTGSGKTFVSILICEHHFQNMPA 52
Score = 30.0 bits (66), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 29/53 (54%), Gaps = 1/53 (1%)
Query: 564 FKTKK-MKVLVATAVASRGLDIKGIRHVINYDLPQEIDEYVHRIGRTGRVGNK 615
FKT K ++L+AT+VA G+DI V+ Y+ + + + GR G+K
Sbjct: 448 FKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGRGRAAGSK 500
>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 = 30.0 bits (66), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 35/147 (23%), Positives = 61/147 (41%), Gaps = 17/147 (11%)
Query: 212 NLKKSNYTKPTPIQKYAIPAG-LEGRDLMGCAQTGSGKTAAFLIPIMHHLLESPGELVTG 270
LK+ P Q A+ +G LEG++ + T SGKT I ++H +L G+ V
Sbjct: 15 TLKERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRILTQGGKAVY- 73
Query: 271 YCAQPEVIICAPTRELVMQIHEVACKYAYSSVLKICLHYGGASSMHFNRQLEKG-CNILV 329
P + L + + + KI L A+ + ++ G +I++
Sbjct: 74 ---------IVPLKALAEEKFQ-----EFQDWEKIGLRVAMATGDYDSKDEWLGKYDIII 119
Query: 330 ATMGRLKDILDRGRISLASVRFVVLDE 356
AT + +L G + V+ +V DE
Sbjct: 120 ATAEKFDSLLRHGSSWIKDVKILVADE 146
>pdb|2FWR|A Chain A, Structure Of Archaeoglobus Fulgidis Xpb
pdb|2FWR|B Chain B, Structure Of Archaeoglobus Fulgidis Xpb
pdb|2FWR|C Chain C, Structure Of Archaeoglobus Fulgidis Xpb
pdb|2FWR|D Chain D, Structure Of Archaeoglobus Fulgidis Xpb
Length = 472
Score = 29.6 bits (65), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 15/70 (21%), Positives = 32/70 (45%)
Query: 554 QSQREQAIHDFKTKKMKVLVATAVASRGLDIKGIRHVINYDLPQEIDEYVHRIGRTGRVG 613
+ +RE+ + F+T + + +V++ V G+D+ + EY+ R+GR R
Sbjct: 380 REEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQRLGRILRPS 439
Query: 614 NKGRATSFYD 623
+ Y+
Sbjct: 440 KGKKEAVLYE 449
>pdb|3B6E|A Chain A, Crystal Structure Of Human Dech-Box Rna Helicase Mda5
(Melanoma Differentiation-Associated Protein 5),
Dech-Domain
Length = 216
Score = 29.6 bits (65), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 40/177 (22%), Positives = 71/177 (40%), Gaps = 30/177 (16%)
Query: 223 PIQKYAIPAGLEGRDLMGCAQTGSGKTAAFLIPIMHHLLESPGELVTGYCAQPEVIICAP 282
P Q LEG++++ C TGSGKT + HL + ++P +I
Sbjct: 36 PYQMEVAQPALEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKK------ASEPGKVIVLV 89
Query: 283 TRELVMQIHEVACKYAYSSVLKICLHYGGASSMHFNRQLE-------KGCNILVATMGRL 335
+ L++ E + + LK G S + QL+ K C+I+++T L
Sbjct: 90 NKVLLV---EQLFRKEFQPFLKKWYRVIGLSG---DTQLKISFPEVVKSCDIIISTAQIL 143
Query: 336 KDIL-------DRGRISLASVRFVVLDEADRMLDMGFLGDIQHVMQHSTMPDVANRQ 385
++ L D G + L+ +++DE +I M+H M + N +
Sbjct: 144 ENSLLNLENGEDAG-VQLSDFSLIIIDECHHTNKEAVYNNI---MRHYLMQKLKNNR 196
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
0.321 0.137 0.406
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,883,613
Number of Sequences: 62578
Number of extensions: 584281
Number of successful extensions: 1551
Number of sequences better than 100.0: 100
Number of HSP's better than 100.0 without gapping: 86
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 1214
Number of HSP's gapped (non-prelim): 200
length of query: 693
length of database: 14,973,337
effective HSP length: 106
effective length of query: 587
effective length of database: 8,340,069
effective search space: 4895620503
effective search space used: 4895620503
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 55 (25.8 bits)