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= 010762
(502 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3
Length = 395
Score = 321 bits (822), Expect = 6e-88, Method: Compositional matrix adjust.
Identities = 171/394 (43%), Positives = 262/394 (66%), Gaps = 15/394 (3%)
Query: 99 ATTFEDLNLSPELLKGLYVEMKFQKPSKIQAISLPMILTPPYRNLIAQARNGSGKTTCFV 158
A +F++L L+PELLKG+Y MKFQKPSKIQ +LP++L P RN+IAQ+++G+GKT F
Sbjct: 4 AKSFDELGLAPELLKGIYA-MKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFS 62
Query: 159 LGMLSRVDPNLKAPQALCICPTRELAIQNLEVLRKMGKHTGITSECAVPTDSTNYVPISK 218
L ML+RV+P +PQA+C+ P+RELA Q LEV+++MGK T ITS+ VP DS K
Sbjct: 63 LTMLTRVNPEDASPQAICLAPSRELARQTLEVVQEMGKFTKITSQLIVP-DS-----FEK 116
Query: 219 RPPVTAQVVIGTPGTIKKWMSAKKLGFSRLKILVYDEADHMLDEAGFRDDSLRIMKDIER 278
+ AQV++GTPGT+ M K + ++KI V DEAD+MLD+ G D +R+ + + +
Sbjct: 117 NKQINAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRFLPK 176
Query: 279 SSGHCQVLLFSATFNETVKNFVTRIVKDYNQLFVKKEELSLESVKQYKVYCPDELAKVMV 338
+ Q++LFSATF + V+ + +IV + N L ++ E++++++KQ + C +E K V
Sbjct: 177 DT---QLVLFSATFADAVRQYAKKIVPNANTLELQTNEVNVDAIKQLYMDCKNEADKFDV 233
Query: 339 IRDRIFELGEKMGQTIIFVRTKNSASALHKALKDFGYEVTTIMGATIQEERDKIVKEFKD 398
+ + ++ L +G +IIFV TK +A+ L+ LK G+EV+ + G +ERD+++ +F++
Sbjct: 234 LTE-LYGL-MTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFRE 291
Query: 399 GLTQVLISTDVLARGFDQQQVNLIVNYDPPVKHGKHLEPDCEVYLHRIGRAGRFGRKGVV 458
G ++VLI+T+VLARG D V+++VNYD P +P Y+HRIGR GRFGRKGV
Sbjct: 292 GRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADP--ATYIHRIGRTGRFGRKGVA 349
Query: 459 FNLLMDGDDMIIMEKIERYF-DIKVTEVRNSDED 491
+ + D + I+ I++YF DI++T V D D
Sbjct: 350 ISFVHDKNSFNILSAIQKYFGDIEMTRVPTDDWD 383
>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 = 321 bits (822), Expect = 7e-88, Method: Compositional matrix adjust.
Identities = 173/396 (43%), Positives = 260/396 (65%), Gaps = 19/396 (4%)
Query: 99 ATTFEDLNLSPELLKGLYVEMKFQKPSKIQAISLPMILTPPYRNLIAQARNGSGKTTCFV 158
A +F++L L+PELLKG+Y MKFQKPSKIQ +LP++L P RN+IAQ+++G+GKT F
Sbjct: 4 AKSFDELGLAPELLKGIYA-MKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFS 62
Query: 159 LGMLSRVDPNLKAPQALCICPTRELAIQNLEVLRKMGKHTGITSECAVPTDSTNYVPISK 218
L ML+RV+P +PQA+C+ P+RELA Q LEV+++MGK T ITS+ VP DS K
Sbjct: 63 LTMLTRVNPEDASPQAICLAPSRELARQTLEVVQEMGKFTKITSQLIVP-DS-----FEK 116
Query: 219 RPPVTAQVVIGTPGTIKKWMSAKKLGFSRLKILVYDEADHMLDEAGFRDDSLRIMKDIER 278
+ AQV++GTPGT+ M K + ++KI V DEAD+MLD+ G D +R+ + + +
Sbjct: 117 NKQINAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRFLPK 176
Query: 279 SSGHCQVLLFSATFNETVKNFVTRIVKDYNQLFVKKEELSLESVKQYKVYCPDELAKVMV 338
+ Q++LFSATF + V+ + +IV + N L ++ E++++++KQ + C +E K
Sbjct: 177 DT---QLVLFSATFADAVRQYAKKIVPNANTLELQTNEVNVDAIKQLYMDCKNEADKF-- 231
Query: 339 IRDRIFELGEKM--GQTIIFVRTKNSASALHKALKDFGYEVTTIMGATIQEERDKIVKEF 396
D + EL M G +IIFV TK +A+ L+ LK G+EV+ + G +ERD+++ +F
Sbjct: 232 --DVLTELYGVMTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDF 289
Query: 397 KDGLTQVLISTDVLARGFDQQQVNLIVNYDPPVKHGKHLEPDCEVYLHRIGRAGRFGRKG 456
++G ++VLI+T+VLARG D V+++VNYD P +P Y+HRIGR GRFGRKG
Sbjct: 290 REGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADP--ATYIHRIGRTGRFGRKG 347
Query: 457 VVFNLLMDGDDMIIMEKIERYF-DIKVTEVRNSDED 491
V + + D + I+ I++YF DI++T V D D
Sbjct: 348 VAISFVHDKNSFNILSAIQKYFGDIEMTRVPTDDWD 383
>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 = 294 bits (753), Expect = 7e-80, Method: Compositional matrix adjust.
Identities = 159/403 (39%), Positives = 251/403 (62%), Gaps = 19/403 (4%)
Query: 93 DTPYTSATTFEDLNLSPELLKGLYVEMKFQKPSKIQAISLPMILTPPYRNLIAQARNGSG 152
++P S +FE+L L P+LL+G+Y M F +PSKIQ +LP++L P +NLIAQ+++G+G
Sbjct: 85 NSPLYSVKSFEELRLKPQLLQGVYA-MGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTG 143
Query: 153 KTTCFVLGMLSRVDPNLKAPQALCICPTRELAIQNLEVLRKMGK-HTGITSECAVPTDST 211
KT FVL MLS+V+P K PQ LC+ PT ELA+Q +V+ +MGK + + AV +
Sbjct: 144 KTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNK- 202
Query: 212 NYVPISKRPPVTAQVVIGTPGTIKKWMSAKKLGF---SRLKILVYDEADHMLDEAGFRDD 268
+ + ++ Q+VIGTPGT+ W S KL F ++K+ V DEAD M+ G +D
Sbjct: 203 ----LERGQKISEQIVIGTPGTVLDWCS--KLKFIDPKKIKVFVLDEADVMIATQGHQDQ 256
Query: 269 SLRIMKDIERSSGHCQVLLFSATFNETVKNFVTRIVKDYNQLFVKKEELSLESVKQYKVY 328
S+RI + + R +CQ+LLFSATF ++V F ++V D N + +K+EE +L+++KQY V
Sbjct: 257 SIRIQRMLPR---NCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVL 313
Query: 329 CPDELAKVMVIRDRIFELGEKMGQTIIFVRTKNSASALHKALKDFGYEVTTIMGATIQEE 388
C K + + + + Q +IF T+ +AS L L G++V + G + E+
Sbjct: 314 CSSRDEKFQALCNLYGAI--TIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQ 371
Query: 389 RDKIVKEFKDGLTQVLISTDVLARGFDQQQVNLIVNYDPPVKHGKHLEPDCEVYLHRIGR 448
R +++ F++G +VL++T+V ARG D +QV++++N+D PV K PD E YLHRIGR
Sbjct: 372 RAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPV--DKDGNPDNETYLHRIGR 429
Query: 449 AGRFGRKGVVFNLLMDGDDMIIMEKIERYFDIKVTEVRNSDED 491
GRFG++G+ N++ M I+ +I+ +F+ K+ + D D
Sbjct: 430 TGRFGKRGLAVNMVDSKHSMNILNRIQEHFNKKIERLDTDDLD 472
>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 = 293 bits (750), Expect = 2e-79, Method: Compositional matrix adjust.
Identities = 159/403 (39%), Positives = 251/403 (62%), Gaps = 19/403 (4%)
Query: 93 DTPYTSATTFEDLNLSPELLKGLYVEMKFQKPSKIQAISLPMILTPPYRNLIAQARNGSG 152
++P S +FE+L L P+LL+G+Y M F +PSKIQ +LP++L P +NLIAQ+++G+G
Sbjct: 55 NSPLYSVKSFEELRLKPQLLQGVYA-MGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTG 113
Query: 153 KTTCFVLGMLSRVDPNLKAPQALCICPTRELAIQNLEVLRKMGK-HTGITSECAVPTDST 211
KT FVL MLS+V+P K PQ LC+ PT ELA+Q +V+ +MGK + + AV +
Sbjct: 114 KTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNK- 172
Query: 212 NYVPISKRPPVTAQVVIGTPGTIKKWMSAKKLGF---SRLKILVYDEADHMLDEAGFRDD 268
+ + ++ Q+VIGTPGT+ W S KL F ++K+ V DEAD M+ G +D
Sbjct: 173 ----LERGQKISEQIVIGTPGTVLDWCS--KLKFIDPKKIKVFVLDEADVMIATQGHQDQ 226
Query: 269 SLRIMKDIERSSGHCQVLLFSATFNETVKNFVTRIVKDYNQLFVKKEELSLESVKQYKVY 328
S+RI + + R +CQ+LLFSATF ++V F ++V D N + +K+EE +L+++KQY V
Sbjct: 227 SIRIQRMLPR---NCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVL 283
Query: 329 CPDELAKVMVIRDRIFELGEKMGQTIIFVRTKNSASALHKALKDFGYEVTTIMGATIQEE 388
C K + + + + Q +IF T+ +AS L L G++V + G + E+
Sbjct: 284 CSSRDEKFQALCNLYGAI--TIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQ 341
Query: 389 RDKIVKEFKDGLTQVLISTDVLARGFDQQQVNLIVNYDPPVKHGKHLEPDCEVYLHRIGR 448
R +++ F++G +VL++T+V ARG D +QV++++N+D PV K PD E YLHRIGR
Sbjct: 342 RAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVD--KDGNPDNETYLHRIGR 399
Query: 449 AGRFGRKGVVFNLLMDGDDMIIMEKIERYFDIKVTEVRNSDED 491
GRFG++G+ N++ M I+ +I+ +F+ K+ + D D
Sbjct: 400 TGRFGKRGLAVNMVDSKHSMNILNRIQEHFNKKIERLDTDDLD 442
>pdb|3G0H|A Chain A, Human Dead-box Rna Helicase Ddx19, In Complex With An
Atp-analogue And Rna
Length = 424
Score = 293 bits (749), Expect = 2e-79, Method: Compositional matrix adjust.
Identities = 159/403 (39%), Positives = 251/403 (62%), Gaps = 19/403 (4%)
Query: 93 DTPYTSATTFEDLNLSPELLKGLYVEMKFQKPSKIQAISLPMILTPPYRNLIAQARNGSG 152
++P S +FE+L L P+LL+G+Y M F +PSKIQ +LP++L P +NLIAQ+++G+G
Sbjct: 34 NSPLYSVKSFEELRLKPQLLQGVYA-MGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTG 92
Query: 153 KTTCFVLGMLSRVDPNLKAPQALCICPTRELAIQNLEVLRKMGK-HTGITSECAVPTDST 211
KT FVL MLS+V+P K PQ LC+ PT ELA+Q +V+ +MGK + + AV +
Sbjct: 93 KTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNK- 151
Query: 212 NYVPISKRPPVTAQVVIGTPGTIKKWMSAKKLGF---SRLKILVYDEADHMLDEAGFRDD 268
+ + ++ Q+VIGTPGT+ W S KL F ++K+ V DEAD M+ G +D
Sbjct: 152 ----LERGQKISEQIVIGTPGTVLDWCS--KLKFIDPKKIKVFVLDEADVMIATQGHQDQ 205
Query: 269 SLRIMKDIERSSGHCQVLLFSATFNETVKNFVTRIVKDYNQLFVKKEELSLESVKQYKVY 328
S+RI + + R +CQ+LLFSATF ++V F ++V D N + +K+EE +L+++KQY V
Sbjct: 206 SIRIQRMLPR---NCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVL 262
Query: 329 CPDELAKVMVIRDRIFELGEKMGQTIIFVRTKNSASALHKALKDFGYEVTTIMGATIQEE 388
C K + + + + Q +IF T+ +AS L L G++V + G + E+
Sbjct: 263 CSSRDEKFQALCNLYGAI--TIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQ 320
Query: 389 RDKIVKEFKDGLTQVLISTDVLARGFDQQQVNLIVNYDPPVKHGKHLEPDCEVYLHRIGR 448
R +++ F++G +VL++T+V ARG D +QV++++N+D PV K PD E YLHRIGR
Sbjct: 321 RAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPV--DKDGNPDNETYLHRIGR 378
Query: 449 AGRFGRKGVVFNLLMDGDDMIIMEKIERYFDIKVTEVRNSDED 491
GRFG++G+ N++ M I+ +I+ +F+ K+ + D D
Sbjct: 379 TGRFGKRGLAVNMVDSKHSMNILNRIQEHFNKKIERLDTDDLD 421
>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 = 293 bits (749), Expect = 2e-79, Method: Compositional matrix adjust.
Identities = 159/403 (39%), Positives = 251/403 (62%), Gaps = 19/403 (4%)
Query: 93 DTPYTSATTFEDLNLSPELLKGLYVEMKFQKPSKIQAISLPMILTPPYRNLIAQARNGSG 152
++P S +FE+L L P+LL+G+Y M F +PSKIQ +LP++L P +NLIAQ+++G+G
Sbjct: 18 NSPLYSVKSFEELRLKPQLLQGVYA-MGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTG 76
Query: 153 KTTCFVLGMLSRVDPNLKAPQALCICPTRELAIQNLEVLRKMGK-HTGITSECAVPTDST 211
KT FVL MLS+V+P K PQ LC+ PT ELA+Q +V+ +MGK + + AV +
Sbjct: 77 KTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNK- 135
Query: 212 NYVPISKRPPVTAQVVIGTPGTIKKWMSAKKLGF---SRLKILVYDEADHMLDEAGFRDD 268
+ + ++ Q+VIGTPGT+ W S KL F ++K+ V DEAD M+ G +D
Sbjct: 136 ----LERGQKISEQIVIGTPGTVLDWCS--KLKFIDPKKIKVFVLDEADVMIATQGHQDQ 189
Query: 269 SLRIMKDIERSSGHCQVLLFSATFNETVKNFVTRIVKDYNQLFVKKEELSLESVKQYKVY 328
S+RI + + R +CQ+LLFSATF ++V F ++V D N + +K+EE +L+++KQY V
Sbjct: 190 SIRIQRMLPR---NCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVL 246
Query: 329 CPDELAKVMVIRDRIFELGEKMGQTIIFVRTKNSASALHKALKDFGYEVTTIMGATIQEE 388
C K + + + + Q +IF T+ +AS L L G++V + G + E+
Sbjct: 247 CSSRDEKFQALCNLYGAI--TIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQ 304
Query: 389 RDKIVKEFKDGLTQVLISTDVLARGFDQQQVNLIVNYDPPVKHGKHLEPDCEVYLHRIGR 448
R +++ F++G +VL++T+V ARG D +QV++++N+D PV K PD E YLHRIGR
Sbjct: 305 RAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVD--KDGNPDNETYLHRIGR 362
Query: 449 AGRFGRKGVVFNLLMDGDDMIIMEKIERYFDIKVTEVRNSDED 491
GRFG++G+ N++ M I+ +I+ +F+ K+ + D D
Sbjct: 363 TGRFGKRGLAVNMVDSKHSMNILNRIQEHFNKKIERLDTDDLD 405
>pdb|3FHO|A Chain A, Structure Of S. Pombe Dbp5
pdb|3FHO|B Chain B, Structure Of S. Pombe Dbp5
Length = 508
Score = 273 bits (697), Expect = 2e-73, Method: Compositional matrix adjust.
Identities = 151/375 (40%), Positives = 229/375 (61%), Gaps = 14/375 (3%)
Query: 126 KIQAISLPMILTPPYRNLIAQARNGSGKTTCFVLGMLSRVDPNLKAPQALCICPTRELAI 185
KIQ +LP++L+ P RN+I Q+++G+GKT F L MLSRVD ++ PQA+C+ P+RELA
Sbjct: 144 KIQEKALPLLLSNPPRNMIGQSQSGTGKTAAFALTMLSRVDASVPKPQAICLAPSRELAR 203
Query: 186 QNLEVLRKMGKHTGITSECAVPTDSTNYVPISKRPPVTAQVVIGTPGTIKKWMSAKKLGF 245
Q ++V+ +MGK+T + + + DS + K + AQ+VIGTPGT+ M ++L
Sbjct: 204 QIMDVVTEMGKYTEVKTAFGI-KDS-----VPKGAKIDAQIVIGTPGTVMDLMKRRQLDA 257
Query: 246 SRLKILVYDEADHMLDEAGFRDDSLRIMKDIERSSGHCQVLLFSATFNETVKNFVTRIVK 305
+K+ V DEAD+MLD+ G D S+RI + R++ Q++LFSATF+E V+ + R
Sbjct: 258 RDIKVFVLDEADNMLDQQGLGDQSMRIKHLLPRNT---QIVLFSATFSERVEKYAERFAP 314
Query: 306 DYNQLFVKKEELSLESVKQYKVYCPDELAKVMVIRDRIFELGEKMGQTIIFVRTKNSASA 365
+ N++ +K EELS+E +KQ + C E K V+ + L +GQ+IIF + K++A
Sbjct: 315 NANEIRLKTEELSVEGIKQLYMDCQSEEHKYNVLVELYGLL--TIGQSIIFCKKKDTAEE 372
Query: 366 LHKALKDFGYEVTTIMGATIQEERDKIVKEFKDGLTQVLISTDVLARGFDQQQVNLIVNY 425
+ + + G+ V + G +RD I+ F+ G ++VL++T+V+ARG D QVNL+VNY
Sbjct: 373 IARRMTADGHTVACLTGNLEGAQRDAIMDSFRVGTSKVLVTTNVIARGIDVSQVNLVVNY 432
Query: 426 DPPVKHGKHLEPDCEVYLHRIGRAGRFGRKGVVFNLLMDGDDMIIMEKIERYFDIKVTEV 485
D P+ PD + YLHRIGR GRFGR GV N + D M I+ YF +T V
Sbjct: 433 DMPLDQAGR--PDPQTYLHRIGRTGRFGRVGVSINFVHDKKSWEEMNAIQEYFQRPITRV 490
Query: 486 RNSD-EDFKAALKAA 499
D E+ + +K A
Sbjct: 491 PTDDYEELEKVVKNA 505
>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p
Length = 400
Score = 225 bits (573), Expect = 5e-59, Method: Compositional matrix adjust.
Identities = 144/395 (36%), Positives = 213/395 (53%), Gaps = 22/395 (5%)
Query: 91 TGDTPYTSATTFEDLNLSPELLKGLYVEMKFQKPSKIQAISLPMILTPPYRNLIAQARNG 150
T D T TFED L ELL G++ E F+KPS IQ ++P+ +T R+++A+A+NG
Sbjct: 12 TDDVLNTKGNTFEDFYLKRELLMGIF-EAGFEKPSPIQEEAIPVAITG--RDILARAKNG 68
Query: 151 SGKTTCFVLGMLSRVDPNLKAPQALCICPTRELAIQNLEVLRKMGKHTGITSECAVPTDS 210
+GKT FV+ L +V P L QAL + PTRELA+Q +V+R +GKH GI+ C V T
Sbjct: 69 TGKTAAFVIPTLEKVKPKLNKIQALIMVPTRELALQTSQVVRTLGKHCGIS--CMVTTGG 126
Query: 211 TNYVPISKRPPVTAQVVIGTPGTIKKWMSAKKLGFSRLKILVYDEADHMLDEAGFRDDSL 270
TN R T +++GTPG + S K S + + DEAD ML RD
Sbjct: 127 TNLRDDILRLNETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLS----RDFKT 182
Query: 271 RIMKDIERSSGHCQVLLFSATFNETVKNFVTRIVKDYNQLFVKKEELSLESVKQYKVYCP 330
I + + Q LLFSATF TVK F+ + + ++ + EEL+L+ + QY +
Sbjct: 183 IIEQILSFLPPTHQSLLFSATFPLTVKEFMVKHLHKPYEINL-MEELTLKGITQYYAFV- 240
Query: 331 DELAKVMVIRDRIFELGEKMGQTIIFVRTKNSASALHKALKDFGYEVTTIMGATIQEERD 390
+E K+ + +L ++ Q IIF + N L K + D GY Q+ER+
Sbjct: 241 EERQKLHCLNTLFSKL--QINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERN 298
Query: 391 KIVKEFKDGLTQVLISTDVLARGFDQQQVNLIVNYDPPVKHGKHLEPDCEVYLHRIGRAG 450
K+ EF+ G + L+ +D+L RG D Q VN+++N+D P E YLHRIGR+G
Sbjct: 299 KVFHEFRQGKVRTLVCSDLLTRGIDIQAVNVVINFDFP--------KTAETYLHRIGRSG 350
Query: 451 RFGRKGVVFNLLMDGDDMIIMEKIERYFDIKVTEV 485
RFG G+ NL+ + +D + KIE+ ++ +
Sbjct: 351 RFGHLGLAINLI-NWNDRFNLYKIEQELGTEIAAI 384
>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 = 220 bits (560), Expect = 1e-57, Method: Compositional matrix adjust.
Identities = 135/385 (35%), Positives = 222/385 (57%), Gaps = 20/385 (5%)
Query: 101 TFEDLNLSPELLKGLYVEMKFQKPSKIQAISLPMILTPPYRNLIAQARNGSGKTTCFVLG 160
TF+ + L +LL+G+Y F+KPS IQ ++ I+ R++IAQ+++G+GKT F +
Sbjct: 39 TFDTMGLREDLLRGIYA-YGFEKPSAIQQRAIKQIIKG--RDVIAQSQSGTGKTATFSIS 95
Query: 161 MLSRVDPNLKAPQALCICPTRELAIQNLEVLRKMGKHTGITSECAVPTDSTNYVPISKRP 220
+L +D ++ QAL + PTRELA+Q + L +G + + +C TN ++
Sbjct: 96 VLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNV--QCHACIGGTNVGEDIRKL 153
Query: 221 PVTAQVVIGTPGTIKKWMSAKKLGFSRLKILVYDEADHMLDEAGFRDDSLRIMKDIERSS 280
VV GTPG + + + L +K+LV DEAD ML++ GF++ + + + ++
Sbjct: 154 DYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNK-GFKEQIYDVYRYLPPAT 212
Query: 281 GHCQVLLFSATFNETVKNFVTRIVKDYNQLFVKKEELSLESVKQYKVYCPDELAKVMVIR 340
QV+L SAT + + + D ++ VK++EL+LE +KQ+ V E K +
Sbjct: 213 ---QVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLC 269
Query: 341 DRIFELGEKMGQTIIFVRTKNSASALHKALKDFGYEVTTIMGATIQEERDKIVKEFKDGL 400
D L + Q +IF TK L + +++ + V+++ G Q+ER+ I+KEF+ G
Sbjct: 270 DLYDTL--TITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGA 327
Query: 401 TQVLISTDVLARGFDQQQVNLIVNYDPPVKHGKHLEPDCEVYLHRIGRAGRFGRKGVVFN 460
++VLISTDV ARG D QV+LI+NYD P + E+Y+HRIGR+GR+GRKGV N
Sbjct: 328 SRVLISTDVWARGLDVPQVSLIINYDLP--------NNRELYIHRIGRSGRYGRKGVAIN 379
Query: 461 LLMDGDDMIIMEKIERYFDIKVTEV 485
+ + DD+ I+ IE+Y+ ++ E+
Sbjct: 380 FVKN-DDIRILRDIEQYYSTQIDEM 403
>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 = 220 bits (560), Expect = 1e-57, Method: Compositional matrix adjust.
Identities = 135/385 (35%), Positives = 222/385 (57%), Gaps = 20/385 (5%)
Query: 101 TFEDLNLSPELLKGLYVEMKFQKPSKIQAISLPMILTPPYRNLIAQARNGSGKTTCFVLG 160
TF+ + L +LL+G+Y F+KPS IQ ++ I+ R++IAQ+++G+GKT F +
Sbjct: 38 TFDTMGLREDLLRGIYA-YGFEKPSAIQQRAIKQIIKG--RDVIAQSQSGTGKTATFSIS 94
Query: 161 MLSRVDPNLKAPQALCICPTRELAIQNLEVLRKMGKHTGITSECAVPTDSTNYVPISKRP 220
+L +D ++ QAL + PTRELA+Q + L +G + + +C TN ++
Sbjct: 95 VLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNV--QCHACIGGTNVGEDIRKL 152
Query: 221 PVTAQVVIGTPGTIKKWMSAKKLGFSRLKILVYDEADHMLDEAGFRDDSLRIMKDIERSS 280
VV GTPG + + + L +K+LV DEAD ML++ GF++ + + + ++
Sbjct: 153 DYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNK-GFKEQIYDVYRYLPPAT 211
Query: 281 GHCQVLLFSATFNETVKNFVTRIVKDYNQLFVKKEELSLESVKQYKVYCPDELAKVMVIR 340
QV+L SAT + + + D ++ VK++EL+LE +KQ+ V E K +
Sbjct: 212 ---QVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLC 268
Query: 341 DRIFELGEKMGQTIIFVRTKNSASALHKALKDFGYEVTTIMGATIQEERDKIVKEFKDGL 400
D L + Q +IF TK L + +++ + V+++ G Q+ER+ I+KEF+ G
Sbjct: 269 DLYDTL--TITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGA 326
Query: 401 TQVLISTDVLARGFDQQQVNLIVNYDPPVKHGKHLEPDCEVYLHRIGRAGRFGRKGVVFN 460
++VLISTDV ARG D QV+LI+NYD P + E+Y+HRIGR+GR+GRKGV N
Sbjct: 327 SRVLISTDVWARGLDVPQVSLIINYDLP--------NNRELYIHRIGRSGRYGRKGVAIN 378
Query: 461 LLMDGDDMIIMEKIERYFDIKVTEV 485
+ + DD+ I+ IE+Y+ ++ E+
Sbjct: 379 FVKN-DDIRILRDIEQYYSTQIDEM 402
>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 = 220 bits (560), Expect = 2e-57, Method: Compositional matrix adjust.
Identities = 135/385 (35%), Positives = 222/385 (57%), Gaps = 20/385 (5%)
Query: 101 TFEDLNLSPELLKGLYVEMKFQKPSKIQAISLPMILTPPYRNLIAQARNGSGKTTCFVLG 160
TF+ + L +LL+G+Y F+KPS IQ ++ I+ R++IAQ+++G+GKT F +
Sbjct: 39 TFDTMGLREDLLRGIYA-YGFEKPSAIQQRAIKQIIKG--RDVIAQSQSGTGKTATFSIS 95
Query: 161 MLSRVDPNLKAPQALCICPTRELAIQNLEVLRKMGKHTGITSECAVPTDSTNYVPISKRP 220
+L +D ++ QAL + PTRELA+Q + L +G + + +C TN ++
Sbjct: 96 VLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNV--QCHACIGGTNVGEDIRKL 153
Query: 221 PVTAQVVIGTPGTIKKWMSAKKLGFSRLKILVYDEADHMLDEAGFRDDSLRIMKDIERSS 280
VV GTPG + + + L +K+LV DEAD ML++ GF++ + + + ++
Sbjct: 154 DYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNK-GFKEQIYDVYRYLPPAT 212
Query: 281 GHCQVLLFSATFNETVKNFVTRIVKDYNQLFVKKEELSLESVKQYKVYCPDELAKVMVIR 340
QV+L SAT + + + D ++ VK++EL+LE +KQ+ V E K +
Sbjct: 213 ---QVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLC 269
Query: 341 DRIFELGEKMGQTIIFVRTKNSASALHKALKDFGYEVTTIMGATIQEERDKIVKEFKDGL 400
D L + Q +IF TK L + +++ + V+++ G Q+ER+ I+KEF+ G
Sbjct: 270 DLYDTL--TITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGA 327
Query: 401 TQVLISTDVLARGFDQQQVNLIVNYDPPVKHGKHLEPDCEVYLHRIGRAGRFGRKGVVFN 460
++VLISTDV ARG D QV+LI+NYD P + E+Y+HRIGR+GR+GRKGV N
Sbjct: 328 SRVLISTDVWARGLDVPQVSLIINYDLP--------NNRELYIHRIGRSGRYGRKGVAIN 379
Query: 461 LLMDGDDMIIMEKIERYFDIKVTEV 485
+ + DD+ I+ IE+Y+ ++ E+
Sbjct: 380 FVKN-DDIRILRDIEQYYSTQIDEM 403
>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 = 219 bits (557), Expect = 3e-57, Method: Compositional matrix adjust.
Identities = 135/385 (35%), Positives = 221/385 (57%), Gaps = 20/385 (5%)
Query: 101 TFEDLNLSPELLKGLYVEMKFQKPSKIQAISLPMILTPPYRNLIAQARNGSGKTTCFVLG 160
TF+ + L +LL+G+Y F+KPS IQ ++ I+ R++IAQ+++G+GKT F +
Sbjct: 17 TFDTMGLREDLLRGIYA-YGFEKPSAIQQRAIKQIIKG--RDVIAQSQSGTGKTATFSIS 73
Query: 161 MLSRVDPNLKAPQALCICPTRELAIQNLEVLRKMGKHTGITSECAVPTDSTNYVPISKRP 220
+L +D ++ QAL + PTRELA+Q + L +G + + +C TN ++
Sbjct: 74 VLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNV--QCHACIGGTNVGEDIRKL 131
Query: 221 PVTAQVVIGTPGTIKKWMSAKKLGFSRLKILVYDEADHMLDEAGFRDDSLRIMKDIERSS 280
VV GTPG + + + L +K+LV DEAD ML++ GF++ + + + ++
Sbjct: 132 DYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNK-GFKEQIYDVYRYLPPAT 190
Query: 281 GHCQVLLFSATFNETVKNFVTRIVKDYNQLFVKKEELSLESVKQYKVYCPDELAKVMVIR 340
QV+L SAT + + + D ++ VK++EL+LE +KQ+ V E K +
Sbjct: 191 ---QVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLC 247
Query: 341 DRIFELGEKMGQTIIFVRTKNSASALHKALKDFGYEVTTIMGATIQEERDKIVKEFKDGL 400
D L + Q +IF TK L + +++ + V+++ G Q+ER+ I+KEF+ G
Sbjct: 248 DLYDTL--TITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGA 305
Query: 401 TQVLISTDVLARGFDQQQVNLIVNYDPPVKHGKHLEPDCEVYLHRIGRAGRFGRKGVVFN 460
++VLISTDV ARG D QV+LI+NYD P E+Y+HRIGR+GR+GRKGV N
Sbjct: 306 SRVLISTDVWARGLDVPQVSLIINYDLPNNR--------ELYIHRIGRSGRYGRKGVAIN 357
Query: 461 LLMDGDDMIIMEKIERYFDIKVTEV 485
+ + DD+ I+ IE+Y+ ++ E+
Sbjct: 358 FVKN-DDIRILRDIEQYYSTQIDEM 381
>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 218 bits (555), Expect = 7e-57, Method: Compositional matrix adjust.
Identities = 135/385 (35%), Positives = 222/385 (57%), Gaps = 20/385 (5%)
Query: 101 TFEDLNLSPELLKGLYVEMKFQKPSKIQAISLPMILTPPYRNLIAQARNGSGKTTCFVLG 160
TF+ + L +LL+G+Y F+KPS IQ ++ I+ R++IAQ+++G+GKT F +
Sbjct: 2 TFDTMGLREDLLRGIYA-YGFEKPSAIQQRAIKQIIKG--RDVIAQSQSGTGKTATFSVS 58
Query: 161 MLSRVDPNLKAPQALCICPTRELAIQNLEVLRKMGKHTGITSECAVPTDSTNYVPISKRP 220
+L +D ++ QAL + PTRELA+Q + L +G + + S + TN ++
Sbjct: 59 VLQCLDIQVRETQALILAPTRELAVQVQKGLLALGDYMNVQSHACI--GGTNVGEDIRKL 116
Query: 221 PVTAQVVIGTPGTIKKWMSAKKLGFSRLKILVYDEADHMLDEAGFRDDSLRIMKDIERSS 280
VV GTPG + + + L +K+LV DEAD ML++ GF++ + + + ++
Sbjct: 117 DYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNK-GFKEQIYDVYRYLPPAT 175
Query: 281 GHCQVLLFSATFNETVKNFVTRIVKDYNQLFVKKEELSLESVKQYKVYCPDELAKVMVIR 340
QV+L SAT V + + D ++ VK++EL+LE +KQ+ V E K +
Sbjct: 176 ---QVVLISATLPHEVLEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLC 232
Query: 341 DRIFELGEKMGQTIIFVRTKNSASALHKALKDFGYEVTTIMGATIQEERDKIVKEFKDGL 400
D L + Q +IF TK L + +++ + V+++ G Q+ER+ I+KEF+ G
Sbjct: 233 DLYDTL--TITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGA 290
Query: 401 TQVLISTDVLARGFDQQQVNLIVNYDPPVKHGKHLEPDCEVYLHRIGRAGRFGRKGVVFN 460
++VLISTDV ARG D QV+LI+NYD P + E+Y+HRIGR+GR+GRKGV N
Sbjct: 291 SRVLISTDVWARGLDVPQVSLIINYDLP--------NNRELYIHRIGRSGRYGRKGVAVN 342
Query: 461 LLMDGDDMIIMEKIERYFDIKVTEV 485
+ + DD+ ++ IE+Y+ ++ E+
Sbjct: 343 FVKN-DDIRVLRDIEQYYSTQIDEM 366
>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 218 bits (554), Expect = 8e-57, Method: Compositional matrix adjust.
Identities = 134/385 (34%), Positives = 221/385 (57%), Gaps = 20/385 (5%)
Query: 101 TFEDLNLSPELLKGLYVEMKFQKPSKIQAISLPMILTPPYRNLIAQARNGSGKTTCFVLG 160
TF+ + L +LL+G+Y F+KPS IQ ++ I+ R++IAQ+++G+GKT F +
Sbjct: 2 TFDTMGLREDLLRGIYA-YGFEKPSAIQQRAIKQIIKG--RDVIAQSQSGTGKTATFSVS 58
Query: 161 MLSRVDPNLKAPQALCICPTRELAIQNLEVLRKMGKHTGITSECAVPTDSTNYVPISKRP 220
+L +D ++ QAL + PTRELA+Q + L +G + + +C TN ++
Sbjct: 59 VLQCLDIQVRETQALILAPTRELAVQVQKGLLALGDYMNV--QCHACIGGTNVGEDIRKL 116
Query: 221 PVTAQVVIGTPGTIKKWMSAKKLGFSRLKILVYDEADHMLDEAGFRDDSLRIMKDIERSS 280
VV GTPG + + + L +K+LV DEAD ML++ GF++ + + + ++
Sbjct: 117 DYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNK-GFKEQIYDVYRYLPPAT 175
Query: 281 GHCQVLLFSATFNETVKNFVTRIVKDYNQLFVKKEELSLESVKQYKVYCPDELAKVMVIR 340
QV+L SAT + + + D ++ VK++EL+LE +KQ+ V E K +
Sbjct: 176 ---QVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLC 232
Query: 341 DRIFELGEKMGQTIIFVRTKNSASALHKALKDFGYEVTTIMGATIQEERDKIVKEFKDGL 400
D L + Q +IF TK L + +++ + V+++ G Q+ER+ I+KEF+ G
Sbjct: 233 DLYDTL--TITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGA 290
Query: 401 TQVLISTDVLARGFDQQQVNLIVNYDPPVKHGKHLEPDCEVYLHRIGRAGRFGRKGVVFN 460
++VLISTDV ARG D QV+LI+NYD P E+Y+HRIGR+GR+GRKGV N
Sbjct: 291 SRVLISTDVWARGLDVPQVSLIINYDLPNNR--------ELYIHRIGRSGRYGRKGVAVN 342
Query: 461 LLMDGDDMIIMEKIERYFDIKVTEV 485
+ + DD+ ++ IE+Y+ ++ E+
Sbjct: 343 FVKN-DDIRVLRDIEQYYSTQIDEM 366
>pdb|2KBE|A Chain A, Solution Structure Of Amino-Terminal Domain Of Dbp5p
Length = 226
Score = 201 bits (511), Expect = 9e-52, Method: Compositional matrix adjust.
Identities = 103/218 (47%), Positives = 150/218 (68%), Gaps = 10/218 (4%)
Query: 93 DTPYTSATTFEDLNLSPELLKGLYVEMKFQKPSKIQAISLPMILTPPYRNLIAQARNGSG 152
++P SA +F++L L+PELLKG+Y MKFQKPSKIQ +LP++L P RN+IAQ+++G+G
Sbjct: 15 NSPLYSAKSFDELGLAPELLKGIYA-MKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTG 73
Query: 153 KTTCFVLGMLSRVDPNLKAPQALCICPTRELAIQNLEVLRKMGKHTGITSECAVPTDSTN 212
KT F L ML+RV+P +PQA+C+ P+RELA Q LEV+++MGK T ITS+ VP DS
Sbjct: 74 KTAAFSLTMLTRVNPEDASPQAICLAPSRELARQTLEVVQEMGKFTKITSQLIVP-DS-- 130
Query: 213 YVPISKRPPVTAQVVIGTPGTIKKWMSAKKLGFSRLKILVYDEADHMLDEAGFRDDSLRI 272
K + AQV++GTPGT+ M K + ++KI V DEAD+MLD+ G D +R+
Sbjct: 131 ---FEKNKQINAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIRV 187
Query: 273 MKDIERSSGHCQVLLFSATFNETVKNFVTRIVKDYNQL 310
+ + + + Q++LFSATF + V+ + +IV + N L
Sbjct: 188 KRFLPKDT---QLVLFSATFADAVRQYAKKIVPNANTL 222
>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a
pdb|3EIQ|D Chain D, Crystal Structure Of Pdcd4-eif4a
Length = 414
Score = 197 bits (500), Expect = 2e-50, Method: Compositional matrix adjust.
Identities = 140/389 (35%), Positives = 225/389 (57%), Gaps = 27/389 (6%)
Query: 101 TFEDLNLSPELLKGLYVEMKFQKPSKIQAIS-LPMILTPPYRNLIAQARNGSGKTTCFVL 159
+F+D+NLS LL+G+Y F+KPS IQ + LP I ++IAQA++G+GKT F +
Sbjct: 41 SFDDMNLSESLLRGIYA-YGFEKPSAIQQRAILPCI---KGYDVIAQAQSGTGKTATFAI 96
Query: 160 GMLSRVDPNLKAPQALCICPTRELAIQNLEVLRKMGKHTGITSECAVPTDSTNY-VPISK 218
+L +++ +LKA QAL + PTRELA Q +V+ +G + G + C TN + K
Sbjct: 97 SILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMG--ASCHACIGGTNVRAEVQK 154
Query: 219 RPPVTAQVVIGTPGTIKKWMSAKKLGFSRLKILVYDEADHMLDEAGFRDDSLRIMKDIER 278
+++GTPG + ++ + L +K+ V DEAD ML GF+D +I ++
Sbjct: 155 LQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSR-GFKD---QIYDIFQK 210
Query: 279 SSGHCQVLLFSATFNETVKNFVTRIVKDYNQLFVKKEELSLESVKQYKVYCPDELAKVMV 338
+ + QV+L SAT V + ++D ++ VKKEEL+LE ++Q+ + E K+
Sbjct: 211 LNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKL-- 268
Query: 339 IRDRIFELGEKMG--QTIIFVRTKNSASALHKALKDFGYEVTTIMGATIQEERDKIVKEF 396
D + +L E + Q +IF+ T+ L + + + V+ + G Q+ERD I++EF
Sbjct: 269 --DTLCDLYETLTITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREF 326
Query: 397 KDGLTQVLISTDVLARGFDQQQVNLIVNYDPPVKHGKHLEPDCEVYLHRIGRAGRFGRKG 456
+ G ++VLI+TD+LARG D QQV+L++NYD P E Y+HRIGR GRFGRKG
Sbjct: 327 RSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNR--------ENYIHRIGRGGRFGRKG 378
Query: 457 VVFNLLMDGDDMIIMEKIERYFDIKVTEV 485
V N++ + +D + IE +++ + E+
Sbjct: 379 VAINMVTE-EDKRTLRDIETFYNTSIEEM 406
>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 = 196 bits (499), Expect = 2e-50, Method: Compositional matrix adjust.
Identities = 141/389 (36%), Positives = 226/389 (58%), Gaps = 27/389 (6%)
Query: 101 TFEDLNLSPELLKGLYVEMKFQKPSKIQAIS-LPMILTPPYRNLIAQARNGSGKTTCFVL 159
+F+D+NLS LL+G+Y F+KPS IQ + LP I Y ++IAQA++G+GKT F +
Sbjct: 15 SFDDMNLSESLLRGIYA-YGFEKPSAIQQRAILPCI--KGY-DVIAQAQSGTGKTATFAI 70
Query: 160 GMLSRVDPNLKAPQALCICPTRELAIQNLEVLRKMGKHTGITSECAVPTDSTNY-VPISK 218
+L +++ +LKA QAL + PTRELA Q +V+ +G + G + C TN + K
Sbjct: 71 SILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMG--ASCHACIGGTNVRAEVQK 128
Query: 219 RPPVTAQVVIGTPGTIKKWMSAKKLGFSRLKILVYDEADHMLDEAGFRDDSLRIMKDIER 278
+++GTPG + ++ + L +K+ V DEAD ML GF+D +I ++
Sbjct: 129 LQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSR-GFKD---QIYDIFQK 184
Query: 279 SSGHCQVLLFSATFNETVKNFVTRIVKDYNQLFVKKEELSLESVKQYKVYCPDELAKVMV 338
+ + QV+L SAT V + ++D ++ VKKEEL+LE ++Q+ + E K+
Sbjct: 185 LNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKL-- 242
Query: 339 IRDRIFELGEKMG--QTIIFVRTKNSASALHKALKDFGYEVTTIMGATIQEERDKIVKEF 396
D + +L E + Q +IF+ T+ L + + + V+ + G Q+ERD I++EF
Sbjct: 243 --DTLCDLYETLTITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREF 300
Query: 397 KDGLTQVLISTDVLARGFDQQQVNLIVNYDPPVKHGKHLEPDCEVYLHRIGRAGRFGRKG 456
+ G ++VLI+TD+LARG D QQV+L++NYD P E Y+HRIGR GRFGRKG
Sbjct: 301 RSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNR--------ENYIHRIGRGGRFGRKG 352
Query: 457 VVFNLLMDGDDMIIMEKIERYFDIKVTEV 485
V N++ + +D + IE +++ + E+
Sbjct: 353 VAINMVTE-EDKRTLRDIETFYNTSIEEM 380
>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 = 192 bits (487), Expect = 5e-49, Method: Compositional matrix adjust.
Identities = 134/384 (34%), Positives = 225/384 (58%), Gaps = 21/384 (5%)
Query: 102 FEDLNLSPELLKGLYVEMKFQKPSKIQAISLPMILTPPYRNLIAQARNGSGKTTCFVLGM 161
F+D+ L LL+G++ F++PS IQ ++ I+ +++AQA++G+GKT F +
Sbjct: 24 FDDMELDENLLRGVF-GYGFEEPSAIQQRAIMPIIEG--HDVLAQAQSGTGKTGTFSIAA 80
Query: 162 LSRVDPNLKAPQALCICPTRELAIQNLEVLRKMGKHTGITSECAVPTDSTNYVPISKRPP 221
L R+D ++KAPQAL + PTRELA+Q +V+ + H I + T++V ++
Sbjct: 81 LQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACI--GGTSFVEDAEGLR 138
Query: 222 VTAQVVIGTPGTIKKWMSAKKLGFSRLKILVYDEADHMLDEAGFRDDSLRIMKDIERSSG 281
AQ+V+GTPG + + ++ ++K+ + DEAD ML +GF++ +I + ++
Sbjct: 139 -DAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLS-SGFKEQIYQIFTLLPPTT- 195
Query: 282 HCQVLLFSATFNETVKNFVTRIVKDYNQLFVKKEELSLESVKQYKVYCPDELAKVMVIRD 341
QV+L SAT V T+ +++ ++ VKK+EL+LE +KQ+ V +E K + D
Sbjct: 196 --QVVLLSATMPNDVLEVTTKFMRNPVRILVKKDELTLEGIKQFYVNVEEEEYKYECLTD 253
Query: 342 RIFELGEKMGQTIIFVRTKNSASALHKALKDFGYEVTTIMGATIQEERDKIVKEFKDGLT 401
+ + Q +IF T+ L L++ + V+ I Q+ERD I+KEF+ G +
Sbjct: 254 LYDSIS--VTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSS 311
Query: 402 QVLISTDVLARGFDQQQVNLIVNYDPPVKHGKHLEPDCEVYLHRIGRAGRFGRKGVVFNL 461
++LISTD+LARG D QQV+L++NYD P E Y+HRIGR GRFGRKGV N
Sbjct: 312 RILISTDLLARGIDVQQVSLVINYDLPANK--------ENYIHRIGRGGRFGRKGVAINF 363
Query: 462 LMDGDDMIIMEKIERYFDIKVTEV 485
+ + +D+ M ++E+++ ++ E+
Sbjct: 364 VTN-EDVGAMRELEKFYSTQIEEL 386
>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a
pdb|1FUU|B Chain B, Yeast Initiation Factor 4a
Length = 394
Score = 184 bits (466), Expect = 1e-46, Method: Compositional matrix adjust.
Identities = 132/384 (34%), Positives = 219/384 (57%), Gaps = 21/384 (5%)
Query: 102 FEDLNLSPELLKGLYVEMKFQKPSKIQAISLPMILTPPYRNLIAQARNGSGKTTCFVLGM 161
F+D L LL+G++ F++PS IQ ++ I+ +++AQA++G+GKT F +
Sbjct: 23 FDDXELDENLLRGVF-GYGFEEPSAIQQRAIXPIIEG--HDVLAQAQSGTGKTGTFSIAA 79
Query: 162 LSRVDPNLKAPQALCICPTRELAIQNLEVLRKMGKHTGITSECAVPTDSTNYVPISKRPP 221
L R+D ++KAPQAL + PTRELA+Q +V+ + H I + T++V ++
Sbjct: 80 LQRIDTSVKAPQALXLAPTRELALQIQKVVXALAFHXDIKVHACI--GGTSFVEDAEGLR 137
Query: 222 VTAQVVIGTPGTIKKWMSAKKLGFSRLKILVYDEADHMLDEAGFRDDSLRIMKDIERSSG 281
AQ+V+GTPG + + ++ ++K + DEAD L +GF++ +I + ++
Sbjct: 138 -DAQIVVGTPGRVFDNIQRRRFRTDKIKXFILDEADEXLS-SGFKEQIYQIFTLLPPTT- 194
Query: 282 HCQVLLFSATFNETVKNFVTRIVKDYNQLFVKKEELSLESVKQYKVYCPDELAKVMVIRD 341
QV+L SAT V T+ ++ ++ VKK+EL+LE +KQ+ V +E K + D
Sbjct: 195 --QVVLLSATXPNDVLEVTTKFXRNPVRILVKKDELTLEGIKQFYVNVEEEEYKYECLTD 252
Query: 342 RIFELGEKMGQTIIFVRTKNSASALHKALKDFGYEVTTIMGATIQEERDKIVKEFKDGLT 401
+ + Q +IF T+ L L++ + V+ I Q+ERD I KEF+ G +
Sbjct: 253 LYDSIS--VTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIXKEFRSGSS 310
Query: 402 QVLISTDVLARGFDQQQVNLIVNYDPPVKHGKHLEPDCEVYLHRIGRAGRFGRKGVVFNL 461
++LISTD+LARG D QQV+L++NYD P E Y+HRIGR GRFGRKGV N
Sbjct: 311 RILISTDLLARGIDVQQVSLVINYDLPANK--------ENYIHRIGRGGRFGRKGVAINF 362
Query: 462 LMDGDDMIIMEKIERYFDIKVTEV 485
+ + +D+ ++E+++ ++ E+
Sbjct: 363 VTN-EDVGAXRELEKFYSTQIEEL 385
>pdb|3FHC|B Chain B, Crystal Structure Of Human Dbp5 In Complex With Nup214
Length = 235
Score = 179 bits (453), Expect = 4e-45, Method: Compositional matrix adjust.
Identities = 99/228 (43%), Positives = 148/228 (64%), Gaps = 15/228 (6%)
Query: 93 DTPYTSATTFEDLNLSPELLKGLYVEMKFQKPSKIQAISLPMILTPPYRNLIAQARNGSG 152
++P S +FE+L L P+LL+G+Y M F +PSKIQ +LP++L P +NLIAQ+++G+G
Sbjct: 18 NSPLYSVKSFEELRLKPQLLQGVYA-MGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTG 76
Query: 153 KTTCFVLGMLSRVDPNLKAPQALCICPTRELAIQNLEVLRKMGK-HTGITSECAVPTDST 211
KT FVL MLS+V+P K PQ LC+ PT ELA+Q +V+ +MGK + + AV +
Sbjct: 77 KTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNK- 135
Query: 212 NYVPISKRPPVTAQVVIGTPGTIKKWMSAKKLGF---SRLKILVYDEADHMLDEAGFRDD 268
+ + ++ Q+VIGTPGT+ W S KL F ++K+ V DEAD M+ G +D
Sbjct: 136 ----LERGQKISEQIVIGTPGTVLDWCS--KLKFIDPKKIKVFVLDEADVMIATQGHQDQ 189
Query: 269 SLRIMKDIERSSGHCQVLLFSATFNETVKNFVTRIVKDYNQLFVKKEE 316
S+RI + + R +CQ+LLFSATF ++V F ++V D N + +K+EE
Sbjct: 190 SIRIQRMLPR---NCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREE 234
>pdb|3FMO|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex
With The Dead- Box Helicase Ddx19
Length = 300
Score = 178 bits (451), Expect = 8e-45, Method: Compositional matrix adjust.
Identities = 98/227 (43%), Positives = 147/227 (64%), Gaps = 15/227 (6%)
Query: 93 DTPYTSATTFEDLNLSPELLKGLYVEMKFQKPSKIQAISLPMILTPPYRNLIAQARNGSG 152
++P S +FE+L L P+LL+G+Y M F +PSKIQ +LP++L P +NLIAQ+++G+G
Sbjct: 85 NSPLYSVKSFEELRLKPQLLQGVYA-MGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTG 143
Query: 153 KTTCFVLGMLSRVDPNLKAPQALCICPTRELAIQNLEVLRKMGK-HTGITSECAVPTDST 211
KT FVL MLS+V+P K PQ LC+ PT ELA+Q +V+ +MGK + + AV +
Sbjct: 144 KTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNK- 202
Query: 212 NYVPISKRPPVTAQVVIGTPGTIKKWMSAKKLGF---SRLKILVYDEADHMLDEAGFRDD 268
+ + ++ Q+VIGTPGT+ W S KL F ++K+ V DEAD M+ G +D
Sbjct: 203 ----LERGQKISEQIVIGTPGTVLDWCS--KLKFIDPKKIKVFVLDEADVMIATQGHQDQ 256
Query: 269 SLRIMKDIERSSGHCQVLLFSATFNETVKNFVTRIVKDYNQLFVKKE 315
S+RI + + R +CQ+LLFSATF ++V F ++V D N + +K+E
Sbjct: 257 SIRIQRMLPR---NCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKRE 300
>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp
Length = 386
Score = 175 bits (443), Expect = 6e-44, Method: Compositional matrix adjust.
Identities = 118/399 (29%), Positives = 203/399 (50%), Gaps = 30/399 (7%)
Query: 94 TPYTSATTFEDLNLSPELLKGLYVEMKFQKPSKIQAISLPMILTPPYRNLIAQARNGSGK 153
+P ++ F D L PELL+ + V+ F+ PS++Q +P + +++ QA++G GK
Sbjct: 2 SPGHMSSGFRDFLLKPELLRAI-VDCGFEHPSEVQHECIPQAILG--MDVLCQAKSGMGK 58
Query: 154 TTCFVLGMLSRVDPNLKAPQALCICPTRELAIQ---NLEVLRKMGKHTGITSECAVPTDS 210
T FVL L +++P L +C TRELA Q E K + + +
Sbjct: 59 TAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIK 118
Query: 211 TNYVPISKRPPVTAQVVIGTPGTIKKWMSAKKLGFSRLKILVYDEADHMLDEAGFRDDSL 270
+ + K P +V+GTPG I K L +K + DE D ML++ R D
Sbjct: 119 KDEEVLKKNCP---HIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRD-- 173
Query: 271 RIMKDIERSSGH-CQVLLFSATFNETVKNFVTRIVKDYNQLFVKKE-ELSLESVKQYKVY 328
+++I R + H QV++FSAT ++ ++ + ++D ++FV E +L+L ++QY V
Sbjct: 174 --VQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVK 231
Query: 329 CPDELAKVMVIRDRIFELGE--KMGQTIIFVRTKNSASALHKALKDFGYEVTTIMGATIQ 386
D ++F+L + + Q +IFV++ AL + L + + I Q
Sbjct: 232 LKDNEKN-----RKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQ 286
Query: 387 EERDKIVKEFKDGLTQVLISTDVLARGFDQQQVNLIVNYDPPVKHGKHLEPDCEVYLHRI 446
EER ++FKD ++L++T++ RG D ++VN+ NYD P D + YLHR+
Sbjct: 287 EERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMP--------EDSDTYLHRV 338
Query: 447 GRAGRFGRKGVVFNLLMDGDDMIIMEKIERYFDIKVTEV 485
RAGRFG KG+ + D +D I+ ++ F++ ++E+
Sbjct: 339 ARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISEL 377
>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56
Length = 391
Score = 174 bits (442), Expect = 7e-44, Method: Compositional matrix adjust.
Identities = 118/399 (29%), Positives = 203/399 (50%), Gaps = 30/399 (7%)
Query: 94 TPYTSATTFEDLNLSPELLKGLYVEMKFQKPSKIQAISLPMILTPPYRNLIAQARNGSGK 153
+P ++ F D L PELL+ + V+ F+ PS++Q +P + +++ QA++G GK
Sbjct: 2 SPGHMSSGFRDFLLKPELLRAI-VDCGFEHPSEVQHECIPQAILG--MDVLCQAKSGMGK 58
Query: 154 TTCFVLGMLSRVDPNLKAPQALCICPTRELAIQ---NLEVLRKMGKHTGITSECAVPTDS 210
T FVL L +++P L +C TRELA Q E K + + +
Sbjct: 59 TAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIK 118
Query: 211 TNYVPISKRPPVTAQVVIGTPGTIKKWMSAKKLGFSRLKILVYDEADHMLDEAGFRDDSL 270
+ + K P +V+GTPG I K L +K + DE D ML++ R D
Sbjct: 119 KDEEVLKKNCP---HIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRD-- 173
Query: 271 RIMKDIERSSGH-CQVLLFSATFNETVKNFVTRIVKDYNQLFVKKE-ELSLESVKQYKVY 328
+++I R + H QV++FSAT ++ ++ + ++D ++FV E +L+L ++QY V
Sbjct: 174 --VQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVK 231
Query: 329 CPDELAKVMVIRDRIFELGE--KMGQTIIFVRTKNSASALHKALKDFGYEVTTIMGATIQ 386
D ++F+L + + Q +IFV++ AL + L + + I Q
Sbjct: 232 LKDNEKN-----RKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQ 286
Query: 387 EERDKIVKEFKDGLTQVLISTDVLARGFDQQQVNLIVNYDPPVKHGKHLEPDCEVYLHRI 446
EER ++FKD ++L++T++ RG D ++VN+ NYD P D + YLHR+
Sbjct: 287 EERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMP--------EDSDTYLHRV 338
Query: 447 GRAGRFGRKGVVFNLLMDGDDMIIMEKIERYFDIKVTEV 485
RAGRFG KG+ + D +D I+ ++ F++ ++E+
Sbjct: 339 ARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISEL 377
>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56
Length = 390
Score = 174 bits (442), Expect = 8e-44, Method: Compositional matrix adjust.
Identities = 118/393 (30%), Positives = 201/393 (51%), Gaps = 30/393 (7%)
Query: 100 TTFEDLNLSPELLKGLYVEMKFQKPSKIQAISLPMILTPPYRNLIAQARNGSGKTTCFVL 159
+ F D L PELL+ + V+ F+ PS++Q +P + +++ QA++G GKT FVL
Sbjct: 7 SGFRDFLLKPELLRAI-VDCGFEHPSEVQHECIPQAILG--MDVLCQAKSGMGKTAVFVL 63
Query: 160 GMLSRVDPNLKAPQALCICPTRELAIQ---NLEVLRKMGKHTGITSECAVPTDSTNYVPI 216
L +++P L +C TRELA Q E K + + + + +
Sbjct: 64 ATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVL 123
Query: 217 SKRPPVTAQVVIGTPGTIKKWMSAKKLGFSRLKILVYDEADHMLDEAGFRDDSLRIMKDI 276
K P +V+GTPG I K L +K + DEAD ML++ R D +++I
Sbjct: 124 KKNCP---HIVVGTPGRILALARNKSLNLKHIKHFILDEADKMLEQLDMRRD----VQEI 176
Query: 277 ERSSGH-CQVLLFSATFNETVKNFVTRIVKDYNQLFVKKE-ELSLESVKQYKVYCPDELA 334
R + H QV++FSAT ++ ++ + ++D ++FV E +L+L ++QY V D
Sbjct: 177 FRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEK 236
Query: 335 KVMVIRDRIFELGE--KMGQTIIFVRTKNSASALHKALKDFGYEVTTIMGATIQEERDKI 392
++F+L + + Q +IFV++ AL + L + + I QEER
Sbjct: 237 N-----RKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSR 291
Query: 393 VKEFKDGLTQVLISTDVLARGFDQQQVNLIVNYDPPVKHGKHLEPDCEVYLHRIGRAGRF 452
++FKD ++L++T++ RG D ++VN+ NYD P D + YLHR+ RAGRF
Sbjct: 292 YQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMP--------EDSDTYLHRVARAGRF 343
Query: 453 GRKGVVFNLLMDGDDMIIMEKIERYFDIKVTEV 485
G KG+ + D +D I+ ++ F++ ++E+
Sbjct: 344 GTKGLAITFVSDENDAKILNDVQDRFEVNISEL 376
>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 = 169 bits (427), Expect = 5e-42, Method: Compositional matrix adjust.
Identities = 117/342 (34%), Positives = 184/342 (53%), Gaps = 25/342 (7%)
Query: 121 FQKPSKIQAISLPMILTPPYRNLIAQARNGSGKTTCFVLGMLSRV--DPN---LKAPQAL 175
++ P+ IQ S+P+I + R+L+A A+ GSGKT F+L +LS++ DP+ L PQ +
Sbjct: 76 YKIPTPIQKCSIPVISSG--RDLMACAQTGSGKTAAFLLPILSKLLEDPHELELGRPQVV 133
Query: 176 CICPTRELAIQNLEVLRKMGKHTGITSECAVPTDSTNYVPISKRPPVTAQVVIGTPGTIK 235
+ PTRELAIQ RK + + + + T++ ++ VVI TPG +
Sbjct: 134 IVSPTRELAIQIFNEARKFAFESYL--KIGIVYGGTSFRHQNECITRGCHVVIATPGRLL 191
Query: 236 KWMSAKKLGFSRLKILVYDEADHMLDEAGFRDDSLRIMKDIERSSGHCQVLLFSATFNET 295
++ + F + +V DEAD MLD GF +D RIM + H Q L+FSATF E
Sbjct: 192 DFVDRTFITFEDTRFVVLDEADRMLD-MGFSEDMRRIMTHVTMRPEH-QTLMFSATFPEE 249
Query: 296 VKNFVTRIVKDYNQLFVKKEELSLESVKQYKVYCPDELAKVMVIRDRIFE-LGEKMGQTI 354
++ +K+Y + + + VKQ +Y ++ AK R ++ E L E+ TI
Sbjct: 250 IQRMAGEFLKNYVFVAIGIVGGACSDVKQ-TIYEVNKYAK----RSKLIEILSEQADGTI 304
Query: 355 IFVRTKNSASALHKALKDFGYEVTTIMGATIQEERDKIVKEFKDGLTQVLISTDVLARGF 414
+FV TK A L L + + T+I G +Q +R++ +++FK+G +VLI+T V +RG
Sbjct: 305 VFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATSVASRGL 364
Query: 415 DQQQVNLIVNYDPPVKHGKHLEPDCEVYLHRIGRAGRFGRKG 456
D + + ++NYD P K + Y+HRIGR GR G G
Sbjct: 365 DIKNIKHVINYDMPSK--------IDDYVHRIGRTGRVGNNG 398
>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 = 160 bits (406), Expect = 1e-39, Method: Compositional matrix adjust.
Identities = 116/371 (31%), Positives = 181/371 (48%), Gaps = 44/371 (11%)
Query: 101 TFEDLNLSPELLKGLYVEMKFQKPSKIQAISLPMILTPPYRNLIAQARNGSGKTTCFVLG 160
F +LNLS +L + F+KP+ IQ +P+ L Y N++AQAR GSGKT F +
Sbjct: 7 NFNELNLSDNILNAIR-NKGFEKPTDIQXKVIPLFLNDEY-NIVAQARTGSGKTASFAIP 64
Query: 161 MLSRVDPNLKAPQALCICPTRELAIQNLEVLRKMGKHTGITSECAVPTDSTNYVPISKRP 220
++ V+ N +A+ + PTRELAIQ + + + + + + Y I +
Sbjct: 65 LIELVNEN-NGIEAIILTPTRELAIQVADEIESLKGNKNLKI-AKIYGGKAIYPQI--KA 120
Query: 221 PVTAQVVIGTPGTIKKWMSAKKLGFSRLKILVYDEADHMLDEAGFRDDSLRIMKDIERSS 280
A +V+GTPG I ++ L +K + DEAD L+ GF +KD+E+
Sbjct: 121 LKNANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEXLN-XGF-------IKDVEKIL 172
Query: 281 GHC----QVLLFSATFNETVKNFVTRIVKDYNQLFVKKEELSLESVKQYKVYCPDELAKV 336
C ++LLFSAT + N + DY+ F+K K+ E + V
Sbjct: 173 NACNKDKRILLFSATXPREILNLAKKYXGDYS--FIKA-----------KINANIEQSYV 219
Query: 337 MVIRDRIFE-----LGEKMGQTIIFVRTKNSASALHKALKDFGYEVTTIMGATIQEERDK 391
V + FE L K ++F +TK L L+D G++ I G Q +R+K
Sbjct: 220 EVNENERFEALCRLLKNKEFYGLVFCKTKRDTKELASXLRDIGFKAGAIHGDLSQSQREK 279
Query: 392 IVKEFKDGLTQVLISTDVLARGFDQQQVNLIVNYDPPVKHGKHLEPDCEVYLHRIGRAGR 451
+++ FK ++LI+TDV +RG D +N ++NY HL + E Y HRIGR GR
Sbjct: 280 VIRLFKQKKIRILIATDVXSRGIDVNDLNCVINY--------HLPQNPESYXHRIGRTGR 331
Query: 452 FGRKGVVFNLL 462
G+KG +++
Sbjct: 332 AGKKGKAISII 342
>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x
Length = 417
Score = 149 bits (375), Expect = 5e-36, Method: Compositional matrix adjust.
Identities = 120/389 (30%), Positives = 190/389 (48%), Gaps = 39/389 (10%)
Query: 90 TTGDTPYTSATTFEDLNLSPELLKGLYVEMKFQKPSKIQAISLPMILTPPYRNLIAQARN 149
TG+ +F D+ + E++ G ++ +P+ +Q ++P+I R+L+A A+
Sbjct: 5 ATGNNCPPHIESFSDVEMG-EIIMGNIELTRYTRPTPVQKHAIPII--KEKRDLMACAQT 61
Query: 150 GSGKTTCFVLGMLSRVDPN-----LKA-------------PQALCICPTRELAIQNLEVL 191
GSGKT F+L +LS++ + L+A P +L + PTRELA+Q E
Sbjct: 62 GSGKTAAFLLPILSQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEA 121
Query: 192 RKMGKHTGITSECAV--PTDSTNYVPISKRPPVTAQVVIGTPGTIKKWMSAKKLGFSRLK 249
RK + + C V D + +R +++ TPG + M K+G K
Sbjct: 122 RKFSYRSRVRP-CVVYGGADIGQQIRDLER---GCHLLVATPGRLVDMMERGKIGLDFCK 177
Query: 250 ILVYDEADHMLDEAGFRDDSLRIM-KDIERSSGHCQVLLFSATFNETVKNFVTRIVKDYN 308
LV DEAD MLD GF RI+ +D G ++FSATF + ++ + +Y
Sbjct: 178 YLVLDEADRMLD-MGFEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYI 236
Query: 309 QLFVKKEELSLESVKQYKVYCPDELAKVMVIRDRIFELGEKMGQTIIFVRTKNSASALHK 368
L V + + E++ Q KV +E K + D + G K T++FV TK A +L
Sbjct: 237 FLAVGRVGSTSENITQ-KVVWVEESDKRSFLLDLLNATG-KDSLTLVFVETKKGADSLED 294
Query: 369 ALKDFGYEVTTIMGATIQEERDKIVKEFKDGLTQVLISTDVLARGFDQQQVNLIVNYDPP 428
L GY T+I G Q +R++ + +F+ G + +L++T V ARG D V ++N+D P
Sbjct: 295 FLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLP 354
Query: 429 VKHGKHLEPDCEVYLHRIGRAGRFGRKGV 457
D E Y+HRIGR GR G G+
Sbjct: 355 --------SDIEEYVHRIGRTGRVGNLGL 375
>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna
Helicase From Sulfolobus Tokodaii
Length = 337
Score = 131 bits (329), Expect = 9e-31, Method: Compositional matrix adjust.
Identities = 99/348 (28%), Positives = 175/348 (50%), Gaps = 37/348 (10%)
Query: 118 EMKFQKPSKIQAISLPMILTPPYRNLIAQARNGSGKTTCFVLGMLSRVDPNLKAPQALCI 177
EM F+ +++Q+ ++P++L +N++ +A+ GSGKT + + +L ++L +
Sbjct: 11 EMGFKNFTEVQSKTIPLMLQG--KNVVVRAKTGSGKTAAYAIPILEL------GMKSLVV 62
Query: 178 CPTRELAIQNLEVLRKMGKHTGITSECAVPTDSTNYVPISKRPPVTAQVVIGTPGTIKKW 237
PTREL Q +R +G++ + ++ A Y R A +V+ TPG +
Sbjct: 63 TPTRELTRQVASHIRDIGRY--MDTKVAEVYGGMPYKAQINRVR-NADIVVATPGRLLDL 119
Query: 238 MSAKKLGFSRLKILVYDEADHMLDEAGFRDDSLRIMKDIERSSGHCQVLLFSATFNETVK 297
S + S +I++ DEAD M E GF DD ++I+ + ++S LFSAT E ++
Sbjct: 120 WSKGVIDLSSFEIVIIDEADLMF-EMGFIDD-IKII--LAQTSNRKITGLFSATIPEEIR 175
Query: 298 NFVTRIVKDYNQLFVKKEELSLESVKQYKVYCPDEL-AKVMVIRDRIFELGEKMGQTIIF 356
V + +Y ++ + + L +V+ V+ D+ +KV +R+ K I+F
Sbjct: 176 KVVKDFITNYEEI---EACIGLANVEHKFVHVKDDWRSKVQALRE------NKDKGVIVF 226
Query: 357 VRTKNSASALHKALKDFGYEVTTIMGATIQEERDKIVKEFKDGLTQVLISTDVLARGFDQ 416
VRT+N + L + + + G Q R++ + F++G +LI+TDV +RG D
Sbjct: 227 VRTRNRVAKLVRLFDN----AIELRGDLPQSVRNRNIDAFREGEYDMLITTDVASRGLDI 282
Query: 417 QQVNLIVNYDPPVKHGKHLEPDCEVYLHRIGRAGRFGRKGVVFNLLMD 464
V ++N+D P D Y+HRIGR GR GRKG +++
Sbjct: 283 PLVEKVINFDAP--------QDLRTYIHRIGRTGRMGRKGEAITFILN 322
>pdb|2KBF|A Chain A, Solution Structure Of Carboxyl-Terminal Domain Of Dbp5p
Length = 187
Score = 128 bits (322), Expect = 6e-30, Method: Compositional matrix adjust.
Identities = 70/177 (39%), Positives = 114/177 (64%), Gaps = 5/177 (2%)
Query: 316 ELSLESVKQYKVYCPDELAKVMVIRDRIFELGEKMGQTIIFVRTKNSASALHKALKDFGY 375
E++++++KQ + C +E K V+ + ++ L +G +IIFV TK +A+ L+ LK G+
Sbjct: 3 EVNVDAIKQLYMDCKNEADKFDVLTE-LYGL-MTIGSSIIFVATKKTANVLYGKLKSEGH 60
Query: 376 EVTTIMGATIQEERDKIVKEFKDGLTQVLISTDVLARGFDQQQVNLIVNYDPPVKHGKHL 435
EV+ + G +ERD+++ +F++G ++VLI+T+VLARG D V+++VNYD P
Sbjct: 61 EVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQA 120
Query: 436 EPDCEVYLHRIGRAGRFGRKGVVFNLLMDGDDMIIMEKIERYF-DIKVTEVRNSDED 491
+P Y+HRIGR GRFGRKGV + + D + I+ I++YF DI++T V D D
Sbjct: 121 DP--ATYIHRIGRTGRFGRKGVAISFVHDKNSFNILSAIQKYFGDIEMTRVPTDDWD 175
>pdb|3GFP|A Chain A, Structure Of The C-Terminal Domain Of The Dead-Box Protein
Dbp5
Length = 189
Score = 127 bits (318), Expect = 2e-29, Method: Compositional matrix adjust.
Identities = 70/177 (39%), Positives = 111/177 (62%), Gaps = 5/177 (2%)
Query: 316 ELSLESVKQYKVYCPDELAKVMVIRDRIFELGEKMGQTIIFVRTKNSASALHKALKDFGY 375
E++++++KQ C +E K V+ + ++ L +G +IIFV TK +A+ L+ LK G+
Sbjct: 5 EVNVDAIKQLYXDCKNEADKFDVLTE-LYGL-XTIGSSIIFVATKKTANVLYGKLKSEGH 62
Query: 376 EVTTIMGATIQEERDKIVKEFKDGLTQVLISTDVLARGFDQQQVNLIVNYDPPVKHGKHL 435
EV+ + G +ERD+++ +F++G ++VLI+T+VLARG D V+ +VNYD P
Sbjct: 63 EVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSXVVNYDLPTLANGQA 122
Query: 436 EPDCEVYLHRIGRAGRFGRKGVVFNLLMDGDDMIIMEKIERYF-DIKVTEVRNSDED 491
+P Y+HRIGR GRFGRKGV + + D + I+ I++YF DI+ T V D D
Sbjct: 123 DP--ATYIHRIGRTGRFGRKGVAISFVHDKNSFNILSAIQKYFGDIEXTRVPTDDWD 177
>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 = 126 bits (317), Expect = 2e-29, Method: Compositional matrix adjust.
Identities = 67/175 (38%), Positives = 109/175 (62%), Gaps = 5/175 (2%)
Query: 317 LSLESVKQYKVYCPDELAKVMVIRDRIFELGEKMGQTIIFVRTKNSASALHKALKDFGYE 376
L+L +++QY V C K + + + +GQ IIF +T+ +A L + G++
Sbjct: 3 LTLNNIRQYYVLCEHRKDKYQALCNIYGSI--TIGQAIIFCQTRRNAKWLTVEMIQDGHQ 60
Query: 377 VTTIMGATIQEERDKIVKEFKDGLTQVLISTDVLARGFDQQQVNLIVNYDPPVKHGKHLE 436
V+ + G E+R I++ F+DG +VLI+T+V ARG D +QV ++VN+D PVK G+ E
Sbjct: 61 VSLLSGELTVEQRASIIQRFRDGKEKVLITTNVCARGIDVKQVTIVVNFDLPVKQGE--E 118
Query: 437 PDCEVYLHRIGRAGRFGRKGVVFNLLMDGDDMIIMEKIERYFDIKVTEVRNSDED 491
PD E YLHRIGR GRFG+KG+ FN++ + D++ + KI+ +F+ + ++ D D
Sbjct: 119 PDYETYLHRIGRTGRFGKKGLAFNMI-EVDELPSLMKIQDHFNSSIKQLNAEDMD 172
>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 = 125 bits (314), Expect = 5e-29, Method: Compositional matrix adjust.
Identities = 69/177 (38%), Positives = 111/177 (62%), Gaps = 5/177 (2%)
Query: 316 ELSLESVKQYKVYCPDELAKVMVIRDRIFELGEKMGQTIIFVRTKNSASALHKALKDFGY 375
E++++++KQ C +E K V+ + ++ + +G +IIFV TK +A+ L+ LK G+
Sbjct: 4 EVNVDAIKQLYXDCKNEADKFDVLTE-LYGV-XTIGSSIIFVATKKTANVLYGKLKSEGH 61
Query: 376 EVTTIMGATIQEERDKIVKEFKDGLTQVLISTDVLARGFDQQQVNLIVNYDPPVKHGKHL 435
EV+ + G +ERD+++ +F++G ++VLI+T+VLARG D V+ +VNYD P
Sbjct: 62 EVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSXVVNYDLPTLANGQA 121
Query: 436 EPDCEVYLHRIGRAGRFGRKGVVFNLLMDGDDMIIMEKIERYF-DIKVTEVRNSDED 491
+P Y+HRIGR GRFGRKGV + + D + I+ I++YF DI+ T V D D
Sbjct: 122 DP--ATYIHRIGRTGRFGRKGVAISFVHDKNSFNILSAIQKYFGDIEXTRVPTDDWD 176
>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 = 116 bits (291), Expect = 3e-26, Method: Compositional matrix adjust.
Identities = 73/219 (33%), Positives = 129/219 (58%), Gaps = 10/219 (4%)
Query: 102 FEDLNLSPELLKGLYVEMKFQKPSKIQAISLPMILTPPYRNLIAQARNGSGKTTCFVLGM 161
F+D+ L LL+G++ F++PS IQ ++ I+ +++AQA++G+GKT F +
Sbjct: 16 FDDMELDENLLRGVF-GYGFEEPSAIQQRAIMPIIEG--HDVLAQAQSGTGKTGTFSIAA 72
Query: 162 LSRVDPNLKAPQALCICPTRELAIQNLEVLRKMGKHTGITSECAVPTDSTNYVPISKRPP 221
L R+D ++KAPQAL + PTRELA+Q +V+ + H I + T++V ++
Sbjct: 73 LQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACI--GGTSFVEDAEGLR 130
Query: 222 VTAQVVIGTPGTIKKWMSAKKLGFSRLKILVYDEADHMLDEAGFRDDSLRIMKDIERSSG 281
AQ+V+GTPG + + ++ ++K+ + DEAD ML +GF++ +I + ++
Sbjct: 131 -DAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEML-SSGFKEQIYQIFTLLPPTT- 187
Query: 282 HCQVLLFSATFNETVKNFVTRIVKDYNQLFVKKEELSLE 320
QV+L SAT V T+ +++ ++ VKK+EL+LE
Sbjct: 188 --QVVLLSATMPNDVLEVTTKFMRNPVRILVKKDELTLE 224
>pdb|3BOR|A Chain A, Crystal Structure Of The Deadc Domain Of Human Translation
Initiation Factor 4a-2
Length = 237
Score = 110 bits (276), Expect = 1e-24, Method: Compositional matrix adjust.
Identities = 76/217 (35%), Positives = 117/217 (53%), Gaps = 12/217 (5%)
Query: 101 TFEDLNLSPELLKGLYVEMKFQKPSKIQAISL-PMILTPPYRNLIAQARNGSGKTTCFVL 159
F+D+NL LL+G+Y F+KPS IQ ++ P I ++IAQA++G+GKT F +
Sbjct: 31 NFDDMNLKESLLRGIYA-YGFEKPSAIQQRAIIPCI---KGYDVIAQAQSGTGKTATFAI 86
Query: 160 GMLSRVDPNLKAPQALCICPTRELAIQNLEVLRKMGKHTGITSE-CAVPTDSTNYVPISK 218
+L +++ K QAL + PTRELA Q +V+ +G + G T C T+ N + K
Sbjct: 87 SILQQLEIEFKETQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRN--EMQK 144
Query: 219 RPPVTAQVVIGTPGTIKKWMSAKKLGFSRLKILVYDEADHMLDEAGFRDDSLRIMKDIER 278
+V+GTPG + ++ + L +K+ V DEAD ML GF+D I + +
Sbjct: 145 LQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSR-GFKDQIYEIFQKLNT 203
Query: 279 SSGHCQVLLFSATFNETVKNFVTRIVKDYNQLFVKKE 315
S QV+L SAT V + ++D ++ VKKE
Sbjct: 204 S---IQVVLLSATMPTDVLEVTKKFMRDPIRILVKKE 237
>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 = 110 bits (276), Expect = 2e-24, Method: Compositional matrix adjust.
Identities = 73/201 (36%), Positives = 117/201 (58%), Gaps = 10/201 (4%)
Query: 102 FEDLNLSPELLKGLYVEMKFQKPSKIQAISLPMILTPPYRNLIAQARNGSGKTTCFVLGM 161
FED L ELL G++ EM ++KPS IQ S+P+ L+ R+++A+A+NG+GK+ +++ +
Sbjct: 5 FEDYCLKRELLMGIF-EMGWEKPSPIQEESIPIALSG--RDILARAKNGTGKSGAYLIPL 61
Query: 162 LSRVDPNLKAPQALCICPTRELAIQNLEVLRKMGKHTGITSECAVPTDSTNYVPISKRPP 221
L R+D QA+ I PTRELA+Q ++ ++ KH G ++ T TN R
Sbjct: 62 LERLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMG-GAKVMATTGGTNLRDDIMRLD 120
Query: 222 VTAQVVIGTPGTIKKWMSAKKLGFSRLKILVYDEADHMLDEAGFRDDSLRIMKDIERS-S 280
T VVI TPG I + ++++V DEAD +L + D ++IM+DI +
Sbjct: 121 DTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQ-----DFVQIMEDIILTLP 175
Query: 281 GHCQVLLFSATFNETVKNFVT 301
+ Q+LL+SATF +V+ F+
Sbjct: 176 KNRQILLYSATFPLSVQKFMN 196
>pdb|1QVA|A Chain A, Yeast Initiation Factor 4a N-Terminal Domain
Length = 223
Score = 105 bits (263), Expect = 4e-23, Method: Compositional matrix adjust.
Identities = 67/211 (31%), Positives = 122/211 (57%), Gaps = 10/211 (4%)
Query: 102 FEDLNLSPELLKGLYVEMKFQKPSKIQAISLPMILTPPYRNLIAQARNGSGKTTCFVLGM 161
F+D+ L +LL+G++ F++PS IQ ++ I+ +++AQA++G+GKT F +
Sbjct: 23 FDDMELDEQLLRGVF-GYGFEEPSAIQQRAIMPIIEG--HDVLAQAQSGTGKTGTFSIAA 79
Query: 162 LSRVDPNLKAPQALCICPTRELAIQNLEVLRKMGKHTGITSECAVPTDSTNYVPISKRPP 221
L R+D ++KAPQAL + PTRELA+Q +V+ + H I + T++V ++
Sbjct: 80 LQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACI--GGTSFVEDAEGLR 137
Query: 222 VTAQVVIGTPGTIKKWMSAKKLGFSRLKILVYDEADHMLDEAGFRDDSLRIMKDIERSSG 281
AQ+V+GTPG + + ++ ++K+ + DEAD ML +GF++ +I + ++
Sbjct: 138 -DAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLS-SGFKEQIYQIFTLLPPTT- 194
Query: 282 HCQVLLFSATFNETVKNFVTRIVKDYNQLFV 312
QV+L SAT V T+ +++ ++ V
Sbjct: 195 --QVVLLSATMPNDVLEVTTKFMRNPVRILV 223
>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And
Amp-Pnp
Length = 579
Score = 102 bits (254), Expect = 5e-22, Method: Compositional matrix adjust.
Identities = 110/378 (29%), Positives = 178/378 (47%), Gaps = 44/378 (11%)
Query: 107 LSPELLKGLYVEMKFQKPSKIQAISLPMILTPPYRNLIAQARNGSGKTTCFVLGML---- 162
L E+ K + M+F + +Q ++ IL+ ++IA+A+ G+GKT F++ +
Sbjct: 28 LDKEIHKAI-TRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLI 86
Query: 163 -SRVDPNLKAPQALCICPTRELAIQ-NLEVLRKMGKHTGITS-ECAVPTDSTNY-VPISK 218
++ D +A+ + PTR+LA+Q EV + + G+ C T++ ++K
Sbjct: 87 NTKFDSQYMV-KAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNK 145
Query: 219 RPPVTAQVVIGTPG----TIKKWMSAKKLGFSRLKILVYDEADHMLDEAGFRDDSLRIMK 274
+ +VI TPG ++K+ S K F K+L DEAD +L E GFRDD L +
Sbjct: 146 MNKLRPNIVIATPGRLIDVLEKY-SNKFFRFVDYKVL--DEADRLL-EIGFRDD-LETIS 200
Query: 275 DI-----ERSSGHCQVLLFSATFNETVKNFVTRIVKDYNQLFV----KKEELSLESVKQY 325
I +S+ + + LLFSAT ++ V+ I+ LF+ K E + E + Q
Sbjct: 201 GILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQS 260
Query: 326 KV----YCPDELAKVMVIRDRIFELGEKMGQTIIFVRTKNSASALHKALKD-FGYE--VT 378
V + A V I+ +I E + IIF T S L LK+ F + +
Sbjct: 261 VVISEKFANSIFAAVEHIKKQIKERDSNY-KAIIFAPTVKFTSFLCSILKNEFKKDLPIL 319
Query: 379 TIMGATIQEERDKIVKEFKDGLTQVLISTDVLARGFDQQQVNLIVNYDPPVKHGKHLEPD 438
G Q +R +VK FK + +L+ TDV ARG D V+ ++ P +
Sbjct: 320 EFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELAN----- 374
Query: 439 CEVYLHRIGRAGRFGRKG 456
Y+HRIGR R G++G
Sbjct: 375 ---YIHRIGRTARSGKEG 389
>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 = 102 bits (253), Expect = 7e-22, Method: Compositional matrix adjust.
Identities = 110/378 (29%), Positives = 178/378 (47%), Gaps = 44/378 (11%)
Query: 107 LSPELLKGLYVEMKFQKPSKIQAISLPMILTPPYRNLIAQARNGSGKTTCFVLGML---- 162
L E+ K + M+F + +Q ++ IL+ ++IA+A+ G+GKT F++ +
Sbjct: 79 LDKEIHKAI-TRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLI 137
Query: 163 -SRVDPNLKAPQALCICPTRELAIQ-NLEVLRKMGKHTGITS-ECAVPTDSTNY-VPISK 218
++ D +A+ + PTR+LA+Q EV + + G+ C T++ ++K
Sbjct: 138 NTKFDSQYMV-KAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNK 196
Query: 219 RPPVTAQVVIGTPG----TIKKWMSAKKLGFSRLKILVYDEADHMLDEAGFRDDSLRIMK 274
+ +VI TPG ++K+ S K F K+L DEAD +L E GFRDD L +
Sbjct: 197 MNKLRPNIVIATPGRLIDVLEKY-SNKFFRFVDYKVL--DEADRLL-EIGFRDD-LETIS 251
Query: 275 DI-----ERSSGHCQVLLFSATFNETVKNFVTRIVKDYNQLFV----KKEELSLESVKQY 325
I +S+ + + LLFSAT ++ V+ I+ LF+ K E + E + Q
Sbjct: 252 GILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQS 311
Query: 326 KV----YCPDELAKVMVIRDRIFELGEKMGQTIIFVRTKNSASALHKALKD-FGYE--VT 378
V + A V I+ +I E + IIF T S L LK+ F + +
Sbjct: 312 VVISEKFANSIFAAVEHIKKQIKERDSNY-KAIIFAPTVKFTSFLCSILKNEFKKDLPIL 370
Query: 379 TIMGATIQEERDKIVKEFKDGLTQVLISTDVLARGFDQQQVNLIVNYDPPVKHGKHLEPD 438
G Q +R +VK FK + +L+ TDV ARG D V+ ++ P +
Sbjct: 371 EFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELAN----- 425
Query: 439 CEVYLHRIGRAGRFGRKG 456
Y+HRIGR R G++G
Sbjct: 426 ---YIHRIGRTARSGKEG 440
>pdb|3SQX|A Chain A, Structure Of Mss116p (Nte And C-Tail Double Deletion)
Bound To Ssrna And Amp-Pnp
Length = 512
Score = 101 bits (252), Expect = 8e-22, Method: Compositional matrix adjust.
Identities = 110/378 (29%), Positives = 178/378 (47%), Gaps = 44/378 (11%)
Query: 107 LSPELLKGLYVEMKFQKPSKIQAISLPMILTPPYRNLIAQARNGSGKTTCFVLGML---- 162
L E+ K + M+F + +Q ++ IL+ ++IA+A+ G+GKT F++ +
Sbjct: 28 LDKEIHKAI-TRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLI 86
Query: 163 -SRVDPNLKAPQALCICPTRELAIQ-NLEVLRKMGKHTGITS-ECAVPTDSTNY-VPISK 218
++ D +A+ + PTR+LA+Q EV + + G+ C T++ ++K
Sbjct: 87 NTKFDSQYMV-KAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNK 145
Query: 219 RPPVTAQVVIGTPG----TIKKWMSAKKLGFSRLKILVYDEADHMLDEAGFRDDSLRIMK 274
+ +VI TPG ++K+ S K F K+L DEAD +L E GFRDD L +
Sbjct: 146 MNKLRPNIVIATPGRLIDVLEKY-SNKFFRFVDYKVL--DEADRLL-EIGFRDD-LETIS 200
Query: 275 DI-----ERSSGHCQVLLFSATFNETVKNFVTRIVKDYNQLFV----KKEELSLESVKQY 325
I +S+ + + LLFSAT ++ V+ I+ LF+ K E + E + Q
Sbjct: 201 GILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQS 260
Query: 326 KV----YCPDELAKVMVIRDRIFELGEKMGQTIIFVRTKNSASALHKALKD-FGYE--VT 378
V + A V I+ +I E + IIF T S L LK+ F + +
Sbjct: 261 VVISEKFANSIFAAVEHIKKQIKERDSNY-KAIIFAPTVKFTSFLCSILKNEFKKDLPIL 319
Query: 379 TIMGATIQEERDKIVKEFKDGLTQVLISTDVLARGFDQQQVNLIVNYDPPVKHGKHLEPD 438
G Q +R +VK FK + +L+ TDV ARG D V+ ++ P +
Sbjct: 320 EFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELAN----- 374
Query: 439 CEVYLHRIGRAGRFGRKG 456
Y+HRIGR R G++G
Sbjct: 375 ---YIHRIGRTARSGKEG 389
>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 = 100 bits (248), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 69/208 (33%), Positives = 110/208 (52%), Gaps = 12/208 (5%)
Query: 101 TFEDLNLSPELLKGLYVEMKFQKPSKIQAIS-LPMILTPPYRNLIAQARNGSGKTTCFVL 159
+F+D+NLS LL+G+Y F+ PS IQ + LP I ++IAQA++G+G T F +
Sbjct: 16 SFDDMNLSESLLRGIYA-YGFEXPSAIQQRAILPCIXG---YDVIAQAQSGTGXTATFAI 71
Query: 160 GMLSRVDPNLKAPQALCICPTRELAIQNLEVLRKMGKHTGITSECAVPTDSTNYVPISKR 219
+L +++ +L A QAL + PTRELA Q V+ +G + G + C TN +
Sbjct: 72 SILQQIELDLXATQALVLAPTRELAQQIQXVVMALGDYMG--ASCHACIGGTNVRAEVQX 129
Query: 220 PPVTA-QVVIGTPGTIKKWMSAKKLGFSRLKILVYDEADHMLDEAGFRDDSLRIMKDIER 278
+ A +++GTPG + ++ + L + + V DEAD ML GF D I + +
Sbjct: 130 LQMEAPHIIVGTPGRVFDMLNRRYLSPXYIXMFVLDEADEMLSR-GFXDQIYDIFQXLNS 188
Query: 279 SSGHCQVLLFSATFNETVKNFVTRIVKD 306
++ QV+L SAT V ++D
Sbjct: 189 NT---QVVLLSATMPSDVLEVTXXFMRD 213
>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 = 99.8 bits (247), Expect = 3e-21, Method: Compositional matrix adjust.
Identities = 58/161 (36%), Positives = 84/161 (52%), Gaps = 12/161 (7%)
Query: 315 EELSLESVKQYKVYCPDELAKVMVIRDRIFELGEKMGQTIIFVRTKNSASALHKALKDFG 374
EEL+L+ V QY Y E KV + L ++ Q+IIF + L K + G
Sbjct: 12 EELTLKGVTQYYAYVT-ERQKVHCLNTLFSRL--QINQSIIFCNSSQRVELLAKKISQLG 68
Query: 375 YEVTTIMGATIQEERDKIVKEFKDGLTQVLISTDVLARGFDQQQVNLIVNYDPPVKHGKH 434
Y I QE R+++ +F++GL + L+ TD+ RG D Q VN+++N+D P
Sbjct: 69 YSCFYIHAKMRQEHRNRVFHDFRNGLCRNLVCTDLFTRGIDIQAVNVVINFDFP------ 122
Query: 435 LEPDCEVYLHRIGRAGRFGRKGVVFNLLMDGDDMIIMEKIE 475
E YLHRIGR+GRFG G+ NL+ DD ++ IE
Sbjct: 123 --KLAETYLHRIGRSGRFGHLGLAINLIT-YDDRFNLKSIE 160
>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 = 95.5 bits (236), Expect = 5e-20, Method: Compositional matrix adjust.
Identities = 69/208 (33%), Positives = 102/208 (49%), Gaps = 14/208 (6%)
Query: 102 FEDLNLSPELLKGLYVEMKFQKPSKIQAISLPMILTPPYRNLIAQARNGSGKTTCFVLGM 161
F+D L PE+L+ L+ P+ IQA +LP+ L ++LI QAR G+GKT F L +
Sbjct: 3 FKDFPLKPEILEALHGR-GLTTPTPIQAAALPLALE--GKDLIGQARTGTGKTLAFALPI 59
Query: 162 LSRVDPNL---KAPQALCICPTRELAIQNLEVLRKMGKHTGITSECAVPTDSTNYVPISK 218
R+ P+ + P+AL + PTRELA+Q L + H + + T Y +
Sbjct: 60 AERLAPSQERGRKPRALVLTPTRELALQVASELTAVAPHLKVVAVYG----GTGYGKQKE 115
Query: 219 RPPVTAQVVIGTPGTIKKWMSAKKLGFSRLKILVYDEADHMLDEAGFRDDSLRIMKDIER 278
A V+ TPG ++ L SR+++ V DEAD ML GF ++ ++
Sbjct: 116 ALLRGADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLS-MGFEEEVEALLSATPP 174
Query: 279 SSGHCQVLLFSATFNETVKNFVTRIVKD 306
S Q LLFSAT K R +K+
Sbjct: 175 SR---QTLLFSATLPSWAKRLAERYMKN 199
>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 = 94.4 bits (233), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 68/208 (32%), Positives = 102/208 (49%), Gaps = 14/208 (6%)
Query: 102 FEDLNLSPELLKGLYVEMKFQKPSKIQAISLPMILTPPYRNLIAQARNGSGKTTCFVLGM 161
F+D L PE+L+ L+ P+ I+A +LP+ L ++LI QAR G+GKT F L +
Sbjct: 3 FKDFPLKPEILEALHGR-GLTTPTPIEAAALPLALE--GKDLIGQARTGTGKTLAFALPI 59
Query: 162 LSRVDPNL---KAPQALCICPTRELAIQNLEVLRKMGKHTGITSECAVPTDSTNYVPISK 218
R+ P+ + P+AL + PTRELA+Q L + H + + T Y +
Sbjct: 60 AERLAPSQERGRKPRALVLTPTRELALQVASELTAVAPHLKVVAVYG----GTGYGKQKE 115
Query: 219 RPPVTAQVVIGTPGTIKKWMSAKKLGFSRLKILVYDEADHMLDEAGFRDDSLRIMKDIER 278
A V+ TPG ++ L SR+++ V DEAD ML GF ++ ++
Sbjct: 116 ALLRGADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLS-MGFEEEVEALLSATPP 174
Query: 279 SSGHCQVLLFSATFNETVKNFVTRIVKD 306
S Q LLFSAT K R +K+
Sbjct: 175 SR---QTLLFSATLPSWAKRLAERYMKN 199
>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 = 94.0 bits (232), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 77/254 (30%), Positives = 132/254 (51%), Gaps = 22/254 (8%)
Query: 85 SIKTVTTGDTPYTSATT----FEDLNLSPELLKGLYVEMKFQKPSKIQAISLPMILTPPY 140
SI TG P SAT F++L L P + + + +Q+P+ IQ ++P IL +
Sbjct: 6 SIPVSVTG--PDYSATNVIENFDELKLDPTIRNNILLA-SYQRPTPIQKNAIPAILE--H 60
Query: 141 RNLIAQARNGSGKTTCFVLGMLSRV---DPNLK------APQALCICPTRELAIQNLEVL 191
R+++A A+ GSGKT F++ +++ + D N + P+ L + PTRELAIQ L
Sbjct: 61 RDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSES 120
Query: 192 RKMGKHTGITSECAVPTDSTNYVPISKRPPVTAQVVIGTPGTIKKWMSAKKLGFSRLKIL 251
+K +T + S C V + + I + + +++ TPG + ++ K+ K +
Sbjct: 121 QKFSLNTPLRS-CVVYGGADTHSQI-REVQMGCHLLVATPGRLVDFIEKNKISLEFCKYI 178
Query: 252 VYDEADHMLDEAGFRDDSLRIMKDIERSSG-HCQVLLFSATFNETVKNFVTRIVKDYNQL 310
V DEAD MLD GF +I+++ SG + Q L+FSATF + ++ + +Y +
Sbjct: 179 VLDEADRMLD-MGFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFM 237
Query: 311 FVKKEELSLESVKQ 324
V + + +S+KQ
Sbjct: 238 TVGRVGSTSDSIKQ 251
>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 = 90.9 bits (224), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 65/225 (28%), Positives = 110/225 (48%), Gaps = 14/225 (6%)
Query: 92 GDTPYTSATTFEDLNLSPELLKGLYVEMKFQKPSKIQAISLPMILTPPYRNLIAQARNGS 151
G ++ F D L PELL+ + V+ F+ PS++Q +P + +++ QA++G
Sbjct: 6 GSYVSIHSSGFRDFLLKPELLRAI-VDCGFEHPSEVQHECIPQAILG--MDVLCQAKSGM 62
Query: 152 GKTTCFVLGMLSRVDPNLKAPQALCICPTRELAIQ---NLEVLRKMGKHTGITSECAVPT 208
GKT FVL L +++P L +C TRELA Q E K + + +
Sbjct: 63 GKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLS 122
Query: 209 DSTNYVPISKRPPVTAQVVIGTPGTIKKWMSAKKLGFSRLKILVYDEADHMLDEAGFRDD 268
+ + K P +V+GTPG I K L +K + DE D ML++ R D
Sbjct: 123 IKKDEEVLKKNCP---HIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRD 179
Query: 269 SLRIMKDIERSSGH-CQVLLFSATFNETVKNFVTRIVKDYNQLFV 312
+++I R + H QV++FSAT ++ ++ + ++D ++FV
Sbjct: 180 ----VQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFV 220
>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 = 90.9 bits (224), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 76/230 (33%), Positives = 118/230 (51%), Gaps = 16/230 (6%)
Query: 81 AEDSSIKTVTTGDTPYTSATTFEDLNLSPELLKGLYVEMKFQKPSKIQAISLPMILTPPY 140
A+D S TGD FE L LS +L+GL F++PS +Q ++P L
Sbjct: 5 AQDLSSPRTRTGDVLLAEPADFESLLLSRPVLEGLRAA-GFERPSPVQLKAIP--LGRCG 61
Query: 141 RNLIAQARNGSGKTTCF-VLGMLSRVDPNLKAPQALCICPTRELAIQNLEVLRKMG-KHT 198
+LI QA++G+GKT F + + S V NL Q L + PTRE+A+Q V+ +G K
Sbjct: 62 LDLIVQAKSGTGKTCVFSTIALDSLVLENLST-QILILAPTREIAVQIHSVITAIGIKME 120
Query: 199 GITSECAVPTDSTNYVPIS--KRPPVTAQVVIGTPGTIKKWMSAKKLGFSRLKILVYDEA 256
G+ EC V T P+S K + +G+PG IK+ + L +++ + DEA
Sbjct: 121 GL--ECHVFIGGT---PLSQDKTRLKKCHIAVGSPGRIKQLIELDYLNPGSIRLFILDEA 175
Query: 257 DHMLDEAGFRDDSLRIMKDIERSSGHCQVLLFSATFNETVKNFVTRIVKD 306
D +L+E F++ I + S Q+L SAT+ E + N +T+ ++D
Sbjct: 176 DKLLEEGSFQEQINWIYSSLPASK---QMLAVSATYPEFLANALTKYMRD 222
>pdb|1T5I|A Chain A, Crystal Structure Of The C-Terminal Domain Of Uap56
Length = 172
Score = 89.0 bits (219), Expect = 6e-18, Method: Compositional matrix adjust.
Identities = 52/170 (30%), Positives = 89/170 (52%), Gaps = 15/170 (8%)
Query: 318 SLESVKQYKVYCPDELAKVMVIRDRIFELGE--KMGQTIIFVRTKNSASALHKALKDFGY 375
SL ++QY V D ++F+L + + Q +IFV++ AL + L + +
Sbjct: 2 SLHGLQQYYVKLKDNEKN-----RKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNF 56
Query: 376 EVTTIMGATIQEERDKIVKEFKDGLTQVLISTDVLARGFDQQQVNLIVNYDPPVKHGKHL 435
I QEER ++FKD ++L++T++ RG D ++VN+ NYD P
Sbjct: 57 PAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMP------- 109
Query: 436 EPDCEVYLHRIGRAGRFGRKGVVFNLLMDGDDMIIMEKIERYFDIKVTEV 485
D + YLHR+ RAGRFG KG+ + D +D I+ ++ F++ ++E+
Sbjct: 110 -EDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISEL 158
>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 = 88.2 bits (217), Expect = 9e-18, Method: Compositional matrix adjust.
Identities = 48/132 (36%), Positives = 72/132 (54%), Gaps = 9/132 (6%)
Query: 354 IIFVRTKNSASALHKALKDFGYEVTTIMGATIQEERDKIVKEFKDGLTQVLISTDVLARG 413
IIF RTK + L L D GY I G IQE+R ++ EFK G + L++TDV ARG
Sbjct: 39 IIFCRTKEHVNQLTDELDDLGYPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVATDVAARG 98
Query: 414 FDQQQVNLIVNYDPPVKHGKHLEPDCEVYLHRIGRAGRFGRKGVVFNLLMDGDDMIIMEK 473
D + ++L++NYD P++ E Y+HR GR GR G KG + + + + +
Sbjct: 99 IDIENISLVINYDLPLEK--------ESYVHRTGRTGRAGNKGKAISFVTAFEKRFLAD- 149
Query: 474 IERYFDIKVTEV 485
IE Y ++ ++
Sbjct: 150 IEEYIGFEIQKI 161
>pdb|1FUK|A Chain A, Crystal Structure Of The Carboxy Terminal Domain Of Yeast
Eif4a
Length = 165
Score = 84.7 bits (208), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 63/167 (37%), Positives = 98/167 (58%), Gaps = 11/167 (6%)
Query: 319 LESVKQYKVYCPDELAKVMVIRDRIFELGEKMGQTIIFVRTKNSASALHKALKDFGYEVT 378
LE +KQ+ V +E K + D + + Q +IF T+ L L++ + V+
Sbjct: 1 LEGIKQFYVNVEEEEYKYECLTDLYDSIS--VTQAVIFCNTRRKVEELTTKLRNDKFTVS 58
Query: 379 TIMGATIQEERDKIVKEFKDGLTQVLISTDVLARGFDQQQVNLIVNYDPPVKHGKHLEPD 438
I Q+ERD I+KEF+ G +++LISTD+LARG D QQV+L++NYD P
Sbjct: 59 AIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANK------- 111
Query: 439 CEVYLHRIGRAGRFGRKGVVFNLLMDGDDMIIMEKIERYFDIKVTEV 485
E Y+HRIGR GRFGRKGV N + + +D+ M ++E+++ ++ E+
Sbjct: 112 -ENYIHRIGRGGRFGRKGVAINFVTN-EDVGAMRELEKFYSTQIEEL 156
>pdb|3BER|A Chain A, Human Dead-Box Rna-Helicase Ddx47, Conserved Domain I In
Complex With Amp
Length = 249
Score = 83.2 bits (204), Expect = 3e-16, Method: Compositional matrix adjust.
Identities = 71/212 (33%), Positives = 109/212 (51%), Gaps = 20/212 (9%)
Query: 101 TFEDLNLSPELLKGLYVEMKFQKPSKIQAISLPMILTPPYRNLIAQARNGSGKTTCFVLG 160
TF+DL ++ L + ++ + KP+KIQ ++P+ L R++I A GSGKT F L
Sbjct: 44 TFKDLGVTDVLCEACD-QLGWTKPTKIQIEAIPLALQG--RDIIGLAETGSGKTGAFALP 100
Query: 161 MLSRVDPNLKAPQ---ALCICPTRELAIQNLEVLRKMGKHTGITSECAV-PTDS-TNYVP 215
+L+ + L+ PQ AL + PTRELA Q E +G G+ S V DS + +
Sbjct: 101 ILNAL---LETPQRLFALVLTPTRELAFQISEQFEALGSSIGVQSAVIVGGIDSMSQSLA 157
Query: 216 ISKRPPVTAQVVIGTPG-TIKKWMSAKKLGFSRLKILVYDEADHMLDEAGFRDDSLRIMK 274
++K+P ++I TPG I + K LK LV DEAD +L+ F + +I+K
Sbjct: 158 LAKKP----HIIIATPGRLIDHLENTKGFNLRALKYLVMDEADRILN-MDFETEVDKILK 212
Query: 275 DIERSSGHCQVLLFSATFNETVKNFVTRIVKD 306
I R + LFSAT + V+ +K+
Sbjct: 213 VIPRDR---KTFLFSATMTKKVQKLQRAALKN 241
>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 = 82.0 bits (201), Expect = 6e-16, Method: Compositional matrix adjust.
Identities = 63/209 (30%), Positives = 101/209 (48%), Gaps = 13/209 (6%)
Query: 98 SATTFEDLNLSPELLKGLYVEMKFQKPSKIQAISLPMILTPPYRNLIAQARNGSGKTTCF 157
+ T F P +++ + ++F KP++IQ +P L + + Q++ G+GKT +
Sbjct: 2 AETQFTRFPFQPFIIEAIKT-LRFYKPTEIQERIIPGALR--GESXVGQSQTGTGKTHAY 58
Query: 158 VLGMLSRVDPNLKAPQALCICPTRELAIQ----NLEVLRKMGKHTGITSECAVPTDSTNY 213
+L + ++ P QA+ PTRELA Q L++ + K I + C + T+
Sbjct: 59 LLPIXEKIKPERAEVQAVITAPTRELATQIYHETLKITKFCPKDRXIVARCLI--GGTDK 116
Query: 214 VPISKRPPVTAQVVIGTPGTIKKWMSAKKLGFSRLKILVYDEADHMLDEAGFRDDSLRIM 273
++ V +VIGTPG I ++ + L ILV DEAD LD GF D +I
Sbjct: 117 QKALEKLNVQPHIVIGTPGRINDFIREQALDVHTAHILVVDEADLXLD-XGFITDVDQIA 175
Query: 274 KDIERSSGHCQVLLFSATFNETVKNFVTR 302
R Q L+FSAT E +K F+ +
Sbjct: 176 A---RXPKDLQXLVFSATIPEKLKPFLKK 201
>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 = 80.5 bits (197), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 42/128 (32%), Positives = 69/128 (53%), Gaps = 9/128 (7%)
Query: 352 QTIIFVRTKNSASALHKALKDFGYEVTTIMGATIQEERDKIVKEFKDGLTQVLISTDVLA 411
++I+FVR + L L++ G + G +Q +R++ +K +G VL++TDV A
Sbjct: 32 RSIVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGRVNVLVATDVAA 91
Query: 412 RGFDQQQVNLIVNYDPPVKHGKHLEPDCEVYLHRIGRAGRFGRKGVVFNLLMDGDDMIIM 471
RG D V+ + N+D P + YLHRIGR R GRKG + L++ D +++
Sbjct: 92 RGIDIPDVSHVFNFDMP--------RSGDTYLHRIGRTARAGRKGTAIS-LVEAHDHLLL 142
Query: 472 EKIERYFD 479
K+ RY +
Sbjct: 143 GKVGRYIE 150
>pdb|2JGN|A Chain A, Ddx3 Helicase Domain
pdb|2JGN|B Chain B, Ddx3 Helicase Domain
pdb|2JGN|C Chain C, Ddx3 Helicase Domain
Length = 185
Score = 79.3 bits (194), Expect = 5e-15, Method: Compositional matrix adjust.
Identities = 40/105 (38%), Positives = 59/105 (56%), Gaps = 8/105 (7%)
Query: 353 TIIFVRTKNSASALHKALKDFGYEVTTIMGATIQEERDKIVKEFKDGLTQVLISTDVLAR 412
T++FV TK A +L L GY T+I G Q +R++ + +F+ G + +L++T V AR
Sbjct: 49 TLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAAR 108
Query: 413 GFDQQQVNLIVNYDPPVKHGKHLEPDCEVYLHRIGRAGRFGRKGV 457
G D V ++N+D P D E Y+HRIGR GR G G+
Sbjct: 109 GLDISNVKHVINFDLP--------SDIEEYVHRIGRTGRVGNLGL 145
>pdb|2PL3|A Chain A, Human Dead-Box Rna Helicase Ddx10, Dead Domain In Complex
With Adp
Length = 236
Score = 77.0 bits (188), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 68/222 (30%), Positives = 116/222 (52%), Gaps = 17/222 (7%)
Query: 100 TTFEDLNLSPELLKGLYVEMKFQKPSKIQAISLPMILTPPYRNLIAQARNGSGKTTCF-- 157
T F D LS + LKGL E +++ ++IQ ++ + L ++++ A+ GSGKT F
Sbjct: 25 TRFSDFPLSKKTLKGLQ-EAQYRLVTEIQKQTIGLALQG--KDVLGAAKTGSGKTLAFLV 81
Query: 158 -VLGMLSRVD-PNLKAPQALCICPTRELAIQNLEVLRKMGKHTGITSECAVPTDSTNYVP 215
VL L R+ + L I PTRELA Q EVLRK+GK+ ++ + +
Sbjct: 82 PVLEALYRLQWTSTDGLGVLIISPTRELAYQTFEVLRKVGKNHDFSAGLIIGGKDLKH-- 139
Query: 216 ISKRPPVTAQVVIGTPGTIKKWMSAKKLGF--SRLKILVYDEADHMLDEAGFRDDSLRIM 273
+++ TPG + + M + + F + L++LV DEAD +LD GF D ++
Sbjct: 140 -EAERINNINILVCTPGRLLQHMD-ETVSFHATDLQMLVLDEADRILD-MGFADTMNAVI 196
Query: 274 KDIERSSGHCQVLLFSATFNETVKNFVTRIVKDYNQLFVKKE 315
+++ + Q LLFSAT ++VK+ +K+ ++V ++
Sbjct: 197 ENLPKKR---QTLLFSATQTKSVKDLARLSLKNPEYVWVHEK 235
>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 = 73.6 bits (179), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 61/207 (29%), Positives = 96/207 (46%), Gaps = 23/207 (11%)
Query: 121 FQKPSKIQAISLPMILTPPYRNLIAQARNGSGKTTCFVLGMLSRVD--PNLK---APQAL 175
F +P+ IQA P+ L+ +++ A+ GSGKT ++L + ++ P L+ P L
Sbjct: 49 FTEPTAIQAQGWPVALSG--LDMVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDGPICL 106
Query: 176 CICPTRELAIQNLEVLRKMGKHTGITSECAVPTDSTNYVPISKRPPVT-----AQVVIGT 230
+ PTRELA Q +V + + + S C Y K P + ++ I T
Sbjct: 107 VLAPTRELAQQVQQVAAEYCRACRLKSTCI-------YGGAPKGPQIRDLERGVEICIAT 159
Query: 231 PGTIKKWMSAKKLGFSRLKILVYDEADHMLDEAGFRDDSLRIMKDIERSSGHCQVLLFSA 290
PG + ++ K R LV DEAD MLD GF +I+ I Q L++SA
Sbjct: 160 PGRLIDFLECGKTNLRRTTYLVLDEADRMLD-MGFEPQIRKIVDQIRPDR---QTLMWSA 215
Query: 291 TFNETVKNFVTRIVKDYNQLFVKKEEL 317
T+ + V+ +KDY + + EL
Sbjct: 216 TWPKEVRQLAEDFLKDYIHINIGALEL 242
>pdb|3LY5|A Chain A, Ddx18 Dead-Domain
pdb|3LY5|B Chain B, Ddx18 Dead-Domain
Length = 262
Score = 73.6 bits (179), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 76/267 (28%), Positives = 125/267 (46%), Gaps = 22/267 (8%)
Query: 57 STAELDVEGLTIDESKKVNKFLDEAEDSSIKTVTTGDTPYTSATTFEDL-NLSPELLKGL 115
S +L E L V K ++ ++S + ++ G T T+F L NL E
Sbjct: 9 SGVDLGTENLYFQSMNNVEKPDNDEDESEVPSLPLGLTGAFEDTSFASLCNLVNENTLKA 68
Query: 116 YVEMKFQKPSKIQAISLPMILTPPYRNLIAQARNGSGKTTCFVLGMLSRVDPNLKAPQ-- 173
EM F ++IQ S+ +L R+L+A A+ GSGKT F++ + + P+
Sbjct: 69 IKEMGFTNMTEIQHKSIRPLLEG--RDLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNG 126
Query: 174 --ALCICPTRELAIQNLEVLRKMGKHTGITSECAVPTDSTNYVPISKRPPVTAQVVIGTP 231
L + PTRELA+Q VL+++ H + +N +++ +++ TP
Sbjct: 127 TGVLILSPTRELAMQTFGVLKELMTHH--VHTYGLIMGGSNRSAEAQKLGNGINIIVATP 184
Query: 232 GTIKKWM-SAKKLGFSRLKILVYDEADHMLDEAGFRDDSLRIMKDIERSSGHCQVLLFSA 290
G + M + + L+ LV DEAD +LD GF ++ +I+K + Q +LFSA
Sbjct: 185 GRLLDHMQNTPGFMYKNLQCLVIDEADRILD-VGFEEELKQIIKLLPTRR---QTMLFSA 240
Query: 291 TFNETVKNFVTRIVKDYNQLFVKKEEL 317
T TR V+D ++ +KKE L
Sbjct: 241 T--------QTRKVEDLARISLKKEPL 259
>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 = 73.2 bits (178), Expect = 4e-13, Method: Compositional matrix adjust.
Identities = 40/121 (33%), Positives = 62/121 (51%), Gaps = 9/121 (7%)
Query: 353 TIIFVRTKNSASALHKALKDFGYEVTTIMGATIQEERDKIVKEFKDGLTQVLISTDVLAR 412
+IF K A+H+ L G E I G QEER K ++ F++G VL++TDV ++
Sbjct: 57 VLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVASK 116
Query: 413 GFDQQQVNLIVNYDPPVKHGKHLEPDCEVYLHRIGRAGRFGRKGVVFNLLMDG-DDMIIM 471
G D + ++NYD P + E Y+HRIGR G G G+ + D+ ++M
Sbjct: 117 GLDFPAIQHVINYDMP--------EEIENYVHRIGRTGCSGNTGIATTFINKACDESVLM 168
Query: 472 E 472
+
Sbjct: 169 D 169
>pdb|4A4D|A Chain A, Crystal Structure Of The N-Terminal Domain Of The Human
Dead-Box Rna Helicase Ddx5 (P68)
Length = 253
Score = 72.4 bits (176), Expect = 5e-13, Method: Compositional matrix adjust.
Identities = 59/197 (29%), Positives = 92/197 (46%), Gaps = 23/197 (11%)
Query: 121 FQKPSKIQAISLPMILTPPYRNLIAQARNGSGKTTCFVLGMLSRVD--PNLK---APQAL 175
F +P+ IQA P+ L+ +++ A+ GSGKT ++L + ++ P L+ P L
Sbjct: 63 FTEPTAIQAQGWPVALSG--LDMVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDGPICL 120
Query: 176 CICPTRELAIQNLEVLRKMGKHTGITSECAVPTDSTNYVPISKRPPVT-----AQVVIGT 230
+ PTRELA Q +V + + + S C Y K P + ++ I T
Sbjct: 121 VLAPTRELAQQVQQVAAEYCRACRLKSTCI-------YGGAPKGPQIRDLERGVEICIAT 173
Query: 231 PGTIKKWMSAKKLGFSRLKILVYDEADHMLDEAGFRDDSLRIMKDIERSSGHCQVLLFSA 290
PG + ++ K R LV DEAD MLD GF +I+ I Q L++SA
Sbjct: 174 PGRLIDFLECGKTNLRRTTYLVLDEADRMLD-MGFEPQIRKIVDQIRPDR---QTLMWSA 229
Query: 291 TFNETVKNFVTRIVKDY 307
T+ + V+ +KDY
Sbjct: 230 TWPKEVRQLAEDFLKDY 246
>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 = 62.8 bits (151), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 60/212 (28%), Positives = 98/212 (46%), Gaps = 20/212 (9%)
Query: 109 PELLKGLYVEMKFQKPSKIQAISLPMILTPPYRNLIAQARNGSGKTTCFVLGMLSRVDPN 168
P+LLK + + + KP+ IQ+ + P+IL +LI A+ G+GKT +++ +D
Sbjct: 29 PDLLKSI-IRVGILKPTPIQSQAWPIILQG--IDLIVVAQTGTGKTLSYLMPGFIHLDSQ 85
Query: 169 ------LKAPQALCICPTRELAIQNLEVLRKMGKHTGITSECAVPTDSTN--YVPISKRP 220
P L + PTRELA+ ++E + G+ S C + N ISK
Sbjct: 86 PISREQRNGPGMLVLTPTRELAL-HVEAECSKYSYKGLKSICIYGGRNRNGQIEDISK-- 142
Query: 221 PVTAQVVIGTPGTIKKWMSAKKLGFSRLKILVYDEADHMLDEAGFRDDSLRIMKDIERSS 280
++I TPG + + + LV DEAD MLD F +I+ D+
Sbjct: 143 --GVDIIIATPGRLNDLQMNNSVNLRSITYLVIDEADKMLDME-FEPQIRKILLDVRPDR 199
Query: 281 GHCQVLLFSATFNETVKNFVTRIVKDYNQLFV 312
Q ++ SAT+ +TV+ +KD ++V
Sbjct: 200 ---QTVMTSATWPDTVRQLALSYLKDPMIVYV 228
>pdb|3DKP|A Chain A, Human Dead-Box Rna-Helicase Ddx52, Conserved Domain I In
Complex With Adp
Length = 245
Score = 62.4 bits (150), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 63/213 (29%), Positives = 107/213 (50%), Gaps = 23/213 (10%)
Query: 100 TTFEDLN----LSPELLKGLYVEMKFQKPSKIQAISLPMILTPPYRNLIAQARNGSGKTT 155
TF+ L+ ++ LL+ + ++ FQ P+ IQ ++P++L R L+A A GSGKT
Sbjct: 25 ATFQQLDQEYKINSRLLQNI-LDAGFQMPTPIQMQAIPVMLHG--RELLASAPTGSGKTL 81
Query: 156 CFVLGMLSRV-DPNLKAPQALCICPTRELAIQNLEVLRKMGKHTG----ITSECAVPTDS 210
F + +L ++ P K +AL I PTRELA Q L K+ + TG + + AV +
Sbjct: 82 AFSIPILMQLKQPANKGFRALIISPTRELASQIHRELIKISEGTGFRIHMIHKAAVA--A 139
Query: 211 TNYVPISKRPPVTAQVVIGTPGTIKKWMSAKKLG--FSRLKILVYDEADHMLDEA--GFR 266
+ P S + +++ TP + + G + ++ LV DE+D + ++ GFR
Sbjct: 140 KKFGPKSSK---KFDILVTTPNRLIYLLKQDPPGIDLASVEWLVVDESDKLFEDGKTGFR 196
Query: 267 DDSLRIMKDIERSSGHCQVLLFSATFNETVKNF 299
D I + +S + +FSATF V+ +
Sbjct: 197 DQLASIF--LACTSHKVRRAMFSATFAYDVEQW 227
>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 = 61.2 bits (147), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 45/77 (58%)
Query: 352 QTIIFVRTKNSASALHKALKDFGYEVTTIMGATIQEERDKIVKEFKDGLTQVLISTDVLA 411
+ ++F RTK + + L G+ + G Q ER++++ F+ G +VL++TDV A
Sbjct: 30 RAMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGERERVMGAFRQGEVRVLVATDVAA 89
Query: 412 RGFDQQQVNLIVNYDPP 428
RG D QV+L+V+Y P
Sbjct: 90 RGLDIPQVDLVVHYRMP 106
>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 = 60.1 bits (144), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 45/77 (58%)
Query: 352 QTIIFVRTKNSASALHKALKDFGYEVTTIMGATIQEERDKIVKEFKDGLTQVLISTDVLA 411
+ ++F RTK + + L G+ + G Q ER++++ F+ G +VL++TDV A
Sbjct: 33 RAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEVRVLVATDVAA 92
Query: 412 RGFDQQQVNLIVNYDPP 428
RG D QV+L+V+Y P
Sbjct: 93 RGLDIPQVDLVVHYRLP 109
>pdb|1GM5|A Chain A, Structure Of Recg Bound To Three-Way Dna Junction
Length = 780
Score = 49.3 bits (116), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 94/412 (22%), Positives = 168/412 (40%), Gaps = 70/412 (16%)
Query: 107 LSPELLKGLYVEMKFQKPSKIQAISLPMILTPPYRNLIAQARNGSGKTTCFVLGMLSRVD 166
L+ E +K L ++ + Q I MI P L+ Q GSGKT L +L +
Sbjct: 357 LAEEFIKSLPFKLTNAQKRAHQEIRNDMISEKPMNRLL-QGDVGSGKTVVAQLAILDNYE 415
Query: 167 PNLKAPQALCICPTRELAIQN----LEVLRKMGKHTGITSECAVPTDSTNYVPISKRPPV 222
Q + PT LAIQ+ +E K H + P++ + +
Sbjct: 416 AGF---QTAFMVPTSILAIQHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQI 472
Query: 223 TAQVVIGTPGTIKKWMSAKKLGFSRLKILVYDEA--------DHMLDEAGFRDDSLRIMK 274
VVIGT I++ + F L +++ DE + ++++ D +
Sbjct: 473 --DVVIGTHALIQE-----DVHFKNLGLVIIDEQHRFGVKQREALMNKGKMVDTLVMSAT 525
Query: 275 DIERSSGHCQVLLFSATFNETVKNFVTRIVKDYNQLFVKKEELSLESVKQYKVYCPDELA 334
I RS L F + TV + + K+ + V + ++ +VY E
Sbjct: 526 PIPRSMA----LAFYGDLDVTVIDEMPPGRKEVQTMLVPMDRVN-------EVY---EFV 571
Query: 335 KVMVIRDRIFELGEKMGQTIIFVRTKNSASALH--KALKDFGY---------EVTTIMGA 383
+ V+R GQ I + L+ A++ + Y ++ + G
Sbjct: 572 RQEVMRG---------GQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGR 622
Query: 384 TIQEERDKIVKEFKDGLTQVLISTDVLARGFDQQQVNLIVNYDPPVKHGKHLEPDCEVYL 443
QEE+D+++ EF +G +L+ST V+ G D + N++V +P E L
Sbjct: 623 LSQEEKDRVMLEFAEGRYDILVSTTVIEVGIDVPRANVMVIENP--------ERFGLAQL 674
Query: 444 HRI-GRAGRFGRKGVVFNLLMD-GDDMIIMEKIERYFDIKVTEVRNSDEDFK 493
H++ GR GR G++ F ++ D G++ ME++ R+F + + ++ D K
Sbjct: 675 HQLRGRVGRGGQEAYCFLVVGDVGEEA--MERL-RFFTLNTDGFKIAEYDLK 723
>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 = 48.5 bits (114), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 35/108 (32%), Positives = 51/108 (47%), Gaps = 11/108 (10%)
Query: 352 QTIIFVRTKNSASALHKALKD-FGYE--VTTIMGATIQEERDKIVKEFKDGLTQVLISTD 408
+ IIF T S L LK+ F + + G Q +R +VK FK + +L+ TD
Sbjct: 35 KAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTD 94
Query: 409 VLARGFDQQQVNLIVNYDPPVKHGKHLEPDCEVYLHRIGRAGRFGRKG 456
V ARG D V+ ++ P + Y+HRIGR R G++G
Sbjct: 95 VGARGMDFPNVHEVLQIGVPSELAN--------YIHRIGRTARSGKEG 134
>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 = 48.5 bits (114), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 35/108 (32%), Positives = 51/108 (47%), Gaps = 11/108 (10%)
Query: 352 QTIIFVRTKNSASALHKALKD-FGYE--VTTIMGATIQEERDKIVKEFKDGLTQVLISTD 408
+ IIF T S L LK+ F + + G Q +R +VK FK + +L+ TD
Sbjct: 35 KAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTD 94
Query: 409 VLARGFDQQQVNLIVNYDPPVKHGKHLEPDCEVYLHRIGRAGRFGRKG 456
V ARG D V+ ++ P + Y+HRIGR R G++G
Sbjct: 95 VGARGMDFPNVHEVLQIGVPSELAN--------YIHRIGRTARSGKEG 134
>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 = 48.5 bits (114), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 35/108 (32%), Positives = 51/108 (47%), Gaps = 11/108 (10%)
Query: 352 QTIIFVRTKNSASALHKALK-DFGYE--VTTIMGATIQEERDKIVKEFKDGLTQVLISTD 408
+ IIF T S L LK +F + + G Q +R +VK FK + +L+ TD
Sbjct: 35 KAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTD 94
Query: 409 VLARGFDQQQVNLIVNYDPPVKHGKHLEPDCEVYLHRIGRAGRFGRKG 456
V ARG D V+ ++ P + Y+HRIGR R G++G
Sbjct: 95 VGARGMDFPNVHEVLQIGVPSELAN--------YIHRIGRTARSGKEG 134
>pdb|4I1S|A Chain A, Melanoma Differentiation Associated Protein-5 Helicase
Domain Complex With Inhibitor Non-structural Protein V
Length = 243
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 32/130 (24%), Positives = 65/130 (50%), Gaps = 15/130 (11%)
Query: 310 LFVKKEELSLESVKQYKVYCPDELAKVMVIRDRIFELGEKMGQTIIFVRTKNSASAL--- 366
LF++ +++ L+ + + Y ++L K+ F E+ + IIF +T+ SA AL
Sbjct: 111 LFLRNKKI-LKKLAENPEYENEKLTKLRNTIXEHFTRTEESARGIIFTKTRQSAYALSQW 169
Query: 367 ---HKALKDFGYEVTTIMGA--------TIQEERDKIVKEFKDGLTQVLISTDVLARGFD 415
+K + G + ++GA Q E+ +++ +F+ G +LI+T V G D
Sbjct: 170 ITDNKKFAEVGVKAHHLIGAGHSSEFKPXTQNEQREVISKFRTGKINLLIATTVAEEGLD 229
Query: 416 QQQVNLIVNY 425
++ N+++ Y
Sbjct: 230 IKECNIVIRY 239
>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 = 42.4 bits (98), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 29/111 (26%), Positives = 55/111 (49%), Gaps = 17/111 (15%)
Query: 332 ELAKVMVIRDRIFEL---GEKMGQTIIFVRTKNSASAL------HKALKDFGYEVTTIMG 382
E K+ +R+ I E E+ + IIF +T+ SA AL ++ + G + ++G
Sbjct: 379 ENEKLTKLRNTIMEQYTRTEESARGIIFTKTRQSAYALSQWITENEKFAEVGVKAHHLIG 438
Query: 383 A--------TIQEERDKIVKEFKDGLTQVLISTDVLARGFDQQQVNLIVNY 425
A Q E+ +++ +F+ G +LI+T V G D ++ N+++ Y
Sbjct: 439 AGHSSEFKPMTQNEQKEVISKFRTGKINLLIATTVAEEGLDIKECNIVIRY 489
>pdb|4F91|B Chain B, Brr2 Helicase Region
Length = 1724
Score = 38.1 bits (87), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 82/374 (21%), Positives = 143/374 (38%), Gaps = 77/374 (20%)
Query: 142 NLIAQARNGSGKTTCFVLGMLSRVDP--------NLKAPQALCICPTRELAIQNLEVLRK 193
NL+ A G+GKT ++ ML + N+ + + I P R L + + K
Sbjct: 97 NLLLCAPTGAGKTNVALMCMLREIGKHINMDGTINVDDFKIIYIAPMRSLVQEMVGSFGK 156
Query: 194 MGKHTGITSECAVPTDSTNYVPISKRPPVTAQVVIGTPGTIKKWMSAKKLGFSR-----L 248
GIT + T + K Q+++ TP +KW + G R +
Sbjct: 157 RLATYGITV-----AELTGDHQLCKEEISATQIIVCTP---EKWDIITRKGGERTYTQLV 208
Query: 249 KILVYDEADHMLDEAGFRDDSL--RIMKDIERSSGHCQVLLFSATF--NETVKNFVTRIV 304
++++ DE + D+ G ++L R +++IE + +++ SAT E V F+ V
Sbjct: 209 RLIILDEIHLLHDDRGPVLEALVARAIRNIEMTQEDVRLIGLSATLPNYEDVATFLR--V 266
Query: 305 KDYNQLFVKKEELSLESVKQYKVYCPDELA----KVM--VIRDRIFELGEKMGQTIIFVR 358
LF ++Q V ++ A ++M ++ ++I E K Q ++FV
Sbjct: 267 DPAKGLFYFDNSFRPVPLEQTYVGITEKKAIKRFQIMNEIVYEKIMEHAGK-NQVLVFVH 325
Query: 359 TKNSASALHKALKDFGYEVTTI-------------------------------MGATIQE 387
++ +A++D E T+ G I
Sbjct: 326 SRKETGKTARAIRDMCLEKDTLGLFLREGSASTEVLRTEAEQCKNLELKDLLPYGFAIHH 385
Query: 388 ------ERDKIVKEFKDGLTQVLISTDVLARGFDQQQVNLIVN----YDPPVKHGKHLEP 437
+R + F D QVL+ST LA G + +I+ Y P + G+ E
Sbjct: 386 AGMTRVDRTLVEDLFADKHIQVLVSTATLAWGVNLPAHTVIIKGTQVYSP--EKGRWTEL 443
Query: 438 DCEVYLHRIGRAGR 451
L +GRAGR
Sbjct: 444 GALDILQMLGRAGR 457
>pdb|4F92|B Chain B, Brr2 Helicase Region S1087l
pdb|4F93|B Chain B, Brr2 Helicase Region S1087l, Mg-Atp
Length = 1724
Score = 38.1 bits (87), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 82/374 (21%), Positives = 143/374 (38%), Gaps = 77/374 (20%)
Query: 142 NLIAQARNGSGKTTCFVLGMLSRVDP--------NLKAPQALCICPTRELAIQNLEVLRK 193
NL+ A G+GKT ++ ML + N+ + + I P R L + + K
Sbjct: 97 NLLLCAPTGAGKTNVALMCMLREIGKHINMDGTINVDDFKIIYIAPMRSLVQEMVGSFGK 156
Query: 194 MGKHTGITSECAVPTDSTNYVPISKRPPVTAQVVIGTPGTIKKWMSAKKLGFSR-----L 248
GIT + T + K Q+++ TP +KW + G R +
Sbjct: 157 RLATYGITV-----AELTGDHQLCKEEISATQIIVCTP---EKWDIITRKGGERTYTQLV 208
Query: 249 KILVYDEADHMLDEAGFRDDSL--RIMKDIERSSGHCQVLLFSATF--NETVKNFVTRIV 304
++++ DE + D+ G ++L R +++IE + +++ SAT E V F+ V
Sbjct: 209 RLIILDEIHLLHDDRGPVLEALVARAIRNIEMTQEDVRLIGLSATLPNYEDVATFLR--V 266
Query: 305 KDYNQLFVKKEELSLESVKQYKVYCPDELA----KVM--VIRDRIFELGEKMGQTIIFVR 358
LF ++Q V ++ A ++M ++ ++I E K Q ++FV
Sbjct: 267 DPAKGLFYFDNSFRPVPLEQTYVGITEKKAIKRFQIMNEIVYEKIMEHAGK-NQVLVFVH 325
Query: 359 TKNSASALHKALKDFGYEVTTI-------------------------------MGATIQE 387
++ +A++D E T+ G I
Sbjct: 326 SRKETGKTARAIRDMCLEKDTLGLFLREGSASTEVLRTEAEQCKNLELKDLLPYGFAIHH 385
Query: 388 ------ERDKIVKEFKDGLTQVLISTDVLARGFDQQQVNLIVN----YDPPVKHGKHLEP 437
+R + F D QVL+ST LA G + +I+ Y P + G+ E
Sbjct: 386 AGMTRVDRTLVEDLFADKHIQVLVSTATLAWGVNLPAHTVIIKGTQVYSP--EKGRWTEL 443
Query: 438 DCEVYLHRIGRAGR 451
L +GRAGR
Sbjct: 444 GALDILQMLGRAGR 457
>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 = 37.7 bits (86), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 45/183 (24%), Positives = 78/183 (42%), Gaps = 36/183 (19%)
Query: 299 FVTRIVKDYNQLFVKKEELSLESVKQYKVYCPDELAKVMVIRDRIFELGEKMGQTIIFVR 358
F + +K L V+ +E+ L+ K D+L ++ IR+++ ++ + I+F
Sbjct: 320 FSDKRMKKAISLLVQAKEIGLDHPKM------DKLKEI--IREQLQR--KQNSKIIVFTN 369
Query: 359 TKNSASALHKALKDFGYEVTTIMGATIQE--------ERDKIVKEFKDGLTQVLISTDVL 410
+ +A + L G + +G +E E+ I+ EF G VL++T V
Sbjct: 370 YRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVATSVG 429
Query: 411 ARGFDQQQVNLIVNYDPPVKHGKHLEPDCEVYLHRIGRAGRFGRKGVVFNLLMDGDDMII 470
G D +V+L+V Y+P P + R GR GR M G +I+
Sbjct: 430 EEGLDVPEVDLVVFYEPV--------PSAIRSIQRRGRTGRH----------MPGRVIIL 471
Query: 471 MEK 473
M K
Sbjct: 472 MAK 474
Score = 34.7 bits (78), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 32/151 (21%), Positives = 67/151 (44%), Gaps = 19/151 (12%)
Query: 150 GSGKTTCFVLGMLSRVDPNLKAPQALCICPTRELAIQNLEVLRKM-----GKHTGITSEC 204
G GKT + M++ + L + PT+ L +Q+ E R++ K +T E
Sbjct: 33 GLGKT--LIAMMIAEYRLTKYGGKVLMLAPTKPLVLQHAESFRRLFNLPPEKIVALTGEK 90
Query: 205 AVPTDSTNYVPISKRPPVTAQVVIGTPGTIKKWMSAKKLGFSRLKILVYDEADHMLDEAG 264
+ S + A+V++ TP TI+ + A ++ + ++V+DEA +
Sbjct: 91 SPEERSKAWA--------RAKVIVATPQTIENDLLAGRISLEDVSLIVFDEAHRAVGNYA 142
Query: 265 FRDDSLRIMKDIERSSGHCQVLLFSATFNET 295
+ + I ++ +R + + V+ +A+ T
Sbjct: 143 Y----VFIAREYKRQAKNPLVIGLTASPGST 169
>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 = 36.2 bits (82), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 34/121 (28%), Positives = 58/121 (47%), Gaps = 7/121 (5%)
Query: 339 IRDRIFELGEKMGQTIIFVRTKNSASALHKALKDFGYEVTTIMGATIQEERDKIVKEFKD 398
IR+R+ E+ +T++ TK A L LK+ G +V + ER +I+++ +
Sbjct: 438 IRERV----ERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRL 493
Query: 399 GLTQVLISTDVLARGFDQQQVNLIVNYDPPVKHGKHLEPDCEVYLHRIGRAGRFGRKGVV 458
G VL+ ++L G D +V+L+ D K G L + + + IGRA R V+
Sbjct: 494 GKYDVLVGINLLREGLDIPEVSLVAILDAD-KEG-FLRSERSL-IQTIGRAARNANGHVI 550
Query: 459 F 459
Sbjct: 551 M 551
>pdb|1D9X|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb
Length = 658
Score = 36.2 bits (82), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 34/121 (28%), Positives = 58/121 (47%), Gaps = 7/121 (5%)
Query: 339 IRDRIFELGEKMGQTIIFVRTKNSASALHKALKDFGYEVTTIMGATIQEERDKIVKEFKD 398
IR+R+ E+ +T++ TK A L LK+ G +V + ER +I+++ +
Sbjct: 438 IRERV----ERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRL 493
Query: 399 GLTQVLISTDVLARGFDQQQVNLIVNYDPPVKHGKHLEPDCEVYLHRIGRAGRFGRKGVV 458
G VL+ ++L G D +V+L+ D K G L + + + IGRA R V+
Sbjct: 494 GKYDVLVGINLLREGLDIPEVSLVAILDAD-KEG-FLRSERSL-IQTIGRAARNANGHVI 550
Query: 459 F 459
Sbjct: 551 M 551
>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 = 36.2 bits (82), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 34/121 (28%), Positives = 58/121 (47%), Gaps = 7/121 (5%)
Query: 339 IRDRIFELGEKMGQTIIFVRTKNSASALHKALKDFGYEVTTIMGATIQEERDKIVKEFKD 398
IR+R+ E+ +T++ TK A L LK+ G +V + ER +I+++ +
Sbjct: 438 IRERV----ERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRL 493
Query: 399 GLTQVLISTDVLARGFDQQQVNLIVNYDPPVKHGKHLEPDCEVYLHRIGRAGRFGRKGVV 458
G VL+ ++L G D +V+L+ D K G L + + + IGRA R V+
Sbjct: 494 GKYDVLVGINLLREGLDIPEVSLVAILDAD-KEG-FLRSERSL-IQTIGRAARNANGHVI 550
Query: 459 F 459
Sbjct: 551 M 551
>pdb|1D9Z|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb In
Complex With Atp
Length = 657
Score = 36.2 bits (82), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 34/121 (28%), Positives = 58/121 (47%), Gaps = 7/121 (5%)
Query: 339 IRDRIFELGEKMGQTIIFVRTKNSASALHKALKDFGYEVTTIMGATIQEERDKIVKEFKD 398
IR+R+ E+ +T++ TK A L LK+ G +V + ER +I+++ +
Sbjct: 437 IRERV----ERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRL 492
Query: 399 GLTQVLISTDVLARGFDQQQVNLIVNYDPPVKHGKHLEPDCEVYLHRIGRAGRFGRKGVV 458
G VL+ ++L G D +V+L+ D K G L + + + IGRA R V+
Sbjct: 493 GKYDVLVGINLLREGLDIPEVSLVAILDAD-KEG-FLRSERSL-IQTIGRAARNANGHVI 549
Query: 459 F 459
Sbjct: 550 M 550
>pdb|3UWX|B Chain B, Crystal Structure Of Uvra-Uvrb Complex
Length = 683
Score = 35.8 bits (81), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 24/84 (28%), Positives = 42/84 (50%)
Query: 343 IFELGEKMGQTIIFVRTKNSASALHKALKDFGYEVTTIMGATIQEERDKIVKEFKDGLTQ 402
I E E+ +T++ TK A L LK+ G +V + ER +I+++ + G
Sbjct: 463 IHERVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYD 522
Query: 403 VLISTDVLARGFDQQQVNLIVNYD 426
VL+ ++L G D +V+L+ D
Sbjct: 523 VLVGINLLREGLDIPEVSLVAILD 546
>pdb|1GKU|B Chain B, Reverse Gyrase From Archaeoglobus Fulgidus
Length = 1054
Score = 34.7 bits (78), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 36/105 (34%), Positives = 48/105 (45%), Gaps = 13/105 (12%)
Query: 105 LNLSPE--LLKGLYVEMKFQK----PSKIQAISLPMILTPPYRNLIAQARNGSGKTTCFV 158
L L PE LLK +VE F+K P IQ + IL + A A G GKT+
Sbjct: 34 LCLFPEDFLLKE-FVEF-FRKCVGEPRAIQKMWAKRILRKE--SFAATAPTGVGKTS--- 86
Query: 159 LGMLSRVDPNLKAPQALCICPTRELAIQNLEVLRKMGKHTGITSE 203
G+ + LK + I PT L IQ E +RK + G+ +E
Sbjct: 87 FGLAMSLFLALKGKRCYVIFPTSLLVIQAAETIRKYAEKAGVGTE 131
>pdb|1GL9|B Chain B, Archaeoglobus Fulgidus Reverse Gyrase Complexed With Adpnp
pdb|1GL9|C Chain C, Archaeoglobus Fulgidus Reverse Gyrase Complexed With Adpnp
Length = 1054
Score = 34.3 bits (77), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 36/105 (34%), Positives = 48/105 (45%), Gaps = 13/105 (12%)
Query: 105 LNLSPE--LLKGLYVEMKFQK----PSKIQAISLPMILTPPYRNLIAQARNGSGKTTCFV 158
L L PE LLK +VE F+K P IQ + IL + A A G GKT+
Sbjct: 34 LCLFPEDFLLKE-FVEF-FRKCVGEPRAIQKMWAKRILRKE--SFAATAPTGVGKTS--- 86
Query: 159 LGMLSRVDPNLKAPQALCICPTRELAIQNLEVLRKMGKHTGITSE 203
G+ + LK + I PT L IQ E +RK + G+ +E
Sbjct: 87 FGLAMSLFLALKGKRCYVIFPTSLLVIQAAETIRKYAEKAGVGTE 131
>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 = 32.3 bits (72), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 34/143 (23%), Positives = 64/143 (44%), Gaps = 13/143 (9%)
Query: 348 EKMGQTIIFVRTKNSASALHKALKDFGYEVTTIMGATIQEERDKIVKEFKDGLTQVLIST 407
E+ + ++ TK + L LK+ G +V + ER +I+++ + G VL+
Sbjct: 449 ERNERVLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGI 508
Query: 408 DVLARGFDQQQVNLIVNYDPPVKHGKHLEPDCEVYLHRIGRAGRFGRKGVVFNLLMDGDD 467
++L G D +V+L+ D K G L + + + IGRA R +G
Sbjct: 509 NLLREGLDIPEVSLVAILDAD-KEG-FLRSERSL-IQTIGRAARNA----------EGRV 555
Query: 468 MIIMEKIERYFDIKVTEVRNSDE 490
++ +KI + +I + E + E
Sbjct: 556 IMYADKITKSMEIAINETKRRRE 578
>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 = 32.3 bits (72), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 34/143 (23%), Positives = 64/143 (44%), Gaps = 13/143 (9%)
Query: 348 EKMGQTIIFVRTKNSASALHKALKDFGYEVTTIMGATIQEERDKIVKEFKDGLTQVLIST 407
E+ + ++ TK + L LK+ G +V + ER +I+++ + G VL+
Sbjct: 443 ERNERVLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGI 502
Query: 408 DVLARGFDQQQVNLIVNYDPPVKHGKHLEPDCEVYLHRIGRAGRFGRKGVVFNLLMDGDD 467
++L G D +V+L+ D K G L + + + IGRA R +G
Sbjct: 503 NLLREGLDIPEVSLVAILDAD-KEG-FLRSERSL-IQTIGRAARNA----------EGRV 549
Query: 468 MIIMEKIERYFDIKVTEVRNSDE 490
++ +KI + +I + E + E
Sbjct: 550 IMYADKITKSMEIAINETKRRRE 572
>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 = 31.6 bits (70), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 28/114 (24%), Positives = 51/114 (44%), Gaps = 10/114 (8%)
Query: 352 QTIIFVRTKNSASALHKALKDFGYEVTTIMGATIQEERDKIVKEFKDGLTQVLISTDVLA 411
+ IIF R + K + + I T +EER++I++ F+ G + ++S+ VL
Sbjct: 351 KIIIFTRHNELVYRISKV-----FLIPAITHRTSREEREEILEGFRTGRFRAIVSSQVLD 405
Query: 412 RGFDQQQVNLIVNYDPPVKHGKHLEPDCEVYLHRIGRAGRFGRKGVVFNLLMDG 465
G D N+ V + G + L RI R + ++ V++ L+ G
Sbjct: 406 EGIDVPDANVGV-----IMSGSGSAREYIQRLGRILRPSKGKKEAVLYELISRG 454
>pdb|2FZL|A Chain A, Structure Of C-Terminal Domain Of Archaeoglobus Fulgidus
Xpb
Length = 219
Score = 30.4 bits (67), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 31/117 (26%), Positives = 53/117 (45%), Gaps = 16/117 (13%)
Query: 352 QTIIFVRTKNSASALHKALKDFGYEVTTIMGATIQEERDKIVKEFKDGLTQVLISTDVLA 411
+ IIF R + K + + I T +EER++I++ F+ G + ++S+ VL
Sbjct: 116 KIIIFTRHNELVYRISKV-----FLIPAITHRTSREEREEILEGFRTGRFRAIVSSQVLD 170
Query: 412 RGFDQQQVNLIVNYDPPVKHGKHLEPDCEVYLHRIGRAGR--FGRK-GVVFNLLMDG 465
G D N+ V + G Y+ R+GR R G+K V++ L+ G
Sbjct: 171 EGIDVPDANVGV-----IMSG---SGSAREYIQRLGRILRPSKGKKEAVLYELISRG 219
>pdb|2J59|M Chain M, Crystal Structure Of The Arf1:arhgap21-Arfbd Complex
pdb|2J59|N Chain N, Crystal Structure Of The Arf1:arhgap21-Arfbd Complex
pdb|2J59|O Chain O, Crystal Structure Of The Arf1:arhgap21-Arfbd Complex
pdb|2J59|P Chain P, Crystal Structure Of The Arf1:arhgap21-Arfbd Complex
pdb|2J59|Q Chain Q, Crystal Structure Of The Arf1:arhgap21-Arfbd Complex
pdb|2J59|R Chain R, Crystal Structure Of The Arf1:arhgap21-Arfbd Complex
Length = 168
Score = 30.0 bits (66), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 30/58 (51%), Gaps = 5/58 (8%)
Query: 260 LDEAGFRDDSLRIMKDIERSSGHCQVLLFSATFNETVKNFVTRIVKDYNQLFVKKEEL 317
L +A RDD L +K I+ SS L T ++ ++R +K+YN L K E+L
Sbjct: 90 LFQAEDRDDMLAWIKTIQESSN-----LNEEDTGVTNRDLISRRIKEYNNLMSKAEQL 142
>pdb|1KLN|A Chain A, Dna Polymerase I Klenow Fragment (E.C.2.7.7.7) MutantDNA
Complex
Length = 605
Score = 28.9 bits (63), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 29/119 (24%), Positives = 51/119 (42%), Gaps = 11/119 (9%)
Query: 55 DKSTAELDVEGLTIDESKKVNKFLDEAEDSSIKTVTTGDTPYTSATTFEDLNLSPELLKG 114
+K E+ E + +K++ L E + T G P TS E+L L L K
Sbjct: 244 EKKAHEIAGEEFNLSSTKQLQTILFEKQGIKPLKKTPGGAPSTSEEVLEELALDYPLPK- 302
Query: 115 LYVEMKFQKPSKIQAI---SLPMILTPPYRNLIAQARNGSGKTTCFVLGMLSRVDPNLK 170
V ++++ +K+++ LP+++ P + + S G LS DPNL+
Sbjct: 303 --VILEYRGLAKLKSTYTDKLPLMINPKTGRV-----HTSYHQAVTATGRLSSTDPNLQ 354
>pdb|1D8Y|A Chain A, Crystal Structure Of The Complex Of Dna Polymerase I
Klenow Fragment With Dna
Length = 605
Score = 28.9 bits (63), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 29/119 (24%), Positives = 51/119 (42%), Gaps = 11/119 (9%)
Query: 55 DKSTAELDVEGLTIDESKKVNKFLDEAEDSSIKTVTTGDTPYTSATTFEDLNLSPELLKG 114
+K E+ E + +K++ L E + T G P TS E+L L L K
Sbjct: 244 EKKAHEIAGEEFNLSSTKQLQTILFEKQGIKPLKKTPGGAPSTSEEVLEELALDYPLPK- 302
Query: 115 LYVEMKFQKPSKIQAI---SLPMILTPPYRNLIAQARNGSGKTTCFVLGMLSRVDPNLK 170
V ++++ +K+++ LP+++ P + + S G LS DPNL+
Sbjct: 303 --VILEYRGLAKLKSTYTDKLPLMINPKTGRV-----HTSYHQAVTATGRLSSTDPNLQ 354
>pdb|1KFS|A Chain A, Dna Polymerase I Klenow Fragment (e.c.2.7.7.7) Mutant/dna
Complex
pdb|1KRP|A Chain A, Dna Polymerase I Klenow Fragment (E.C.2.7.7.7) MutantDNA
Complex
pdb|1KSP|A Chain A, Dna Polymerase I Klenow Fragment (E.C.2.7.7.7) MutantDNA
Complex
pdb|2KFN|A Chain A, Klenow Fragment With Bridging-Sulfur Substrate And
Manganese
pdb|2KFZ|A Chain A, Klenow Fragment With Bridging-Sulfur Substrate And Zinc
Only
pdb|2KZM|A Chain A, Klenow Fragment With Normal Substrate And Zinc And
Manganese
pdb|2KZZ|A Chain A, Klenow Fragment With Normal Substrate And Zinc Only
pdb|1QSL|A Chain A, Klenow Fragment Complexed With Single-Stranded Substrate
And Europium (Iii) Ion
pdb|1D9D|A Chain A, Crystall Structure Of The Complex Of Dna Polymerase I
Klenow Fragment With Short Dna Fragment Carrying 2'-0-
Aminopropyl-Rna Modifications 5'-D(Tcg)-Ap(Auc)-3'
pdb|1D9F|A Chain A, Crystal Structure Of The Complex Of Dna Polymerase I
Klenow Fragment With Dna Tetramer Carrying
2'-O-(3-Aminopropyl)- Rna Modification
5'-D(Tt)-Ap(U)-D(T)-3'
Length = 605
Score = 28.9 bits (63), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 29/119 (24%), Positives = 51/119 (42%), Gaps = 11/119 (9%)
Query: 55 DKSTAELDVEGLTIDESKKVNKFLDEAEDSSIKTVTTGDTPYTSATTFEDLNLSPELLKG 114
+K E+ E + +K++ L E + T G P TS E+L L L K
Sbjct: 244 EKKAHEIAGEEFNLSSTKQLQTILFEKQGIKPLKKTPGGAPSTSEEVLEELALDYPLPK- 302
Query: 115 LYVEMKFQKPSKIQAI---SLPMILTPPYRNLIAQARNGSGKTTCFVLGMLSRVDPNLK 170
V ++++ +K+++ LP+++ P + + S G LS DPNL+
Sbjct: 303 --VILEYRGLAKLKSTYTDKLPLMINPKTGRV-----HTSYHQAVTATGRLSSTDPNLQ 354
>pdb|1DPI|A Chain A, Structure Of Large Fragment Of Escherichia Coli Dna
Polymerase I Complexed With DTMP
pdb|1KFD|A Chain A, Crystal Structures Of The Klenow Fragment Of Dna
Polymerase I Complexed With Deoxynucleoside Triphosphate
And Pyrophosphate
Length = 605
Score = 28.9 bits (63), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 29/119 (24%), Positives = 51/119 (42%), Gaps = 11/119 (9%)
Query: 55 DKSTAELDVEGLTIDESKKVNKFLDEAEDSSIKTVTTGDTPYTSATTFEDLNLSPELLKG 114
+K E+ E + +K++ L E + T G P TS E+L L L K
Sbjct: 244 EKKAHEIAGEEFNLSSTKQLQTILFEKQGIKPLKKTPGGAPSTSEEVLEELALDYPLPK- 302
Query: 115 LYVEMKFQKPSKIQAI---SLPMILTPPYRNLIAQARNGSGKTTCFVLGMLSRVDPNLK 170
V ++++ +K+++ LP+++ P + + S G LS DPNL+
Sbjct: 303 --VILEYRGLAKLKSTYTDKLPLMINPKTGRV-----HTSYHQAVTATGRLSSTDPNLQ 354
>pdb|4FYD|A Chain A, Crystal Structure Of Yeast Dna Polymerase Alpha Bound To
Dna/rna And Dgtp
pdb|4FYD|B Chain B, Crystal Structure Of Yeast Dna Polymerase Alpha Bound To
Dna/rna And Dgtp
Length = 910
Score = 28.5 bits (62), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 42/88 (47%), Gaps = 3/88 (3%)
Query: 384 TIQEERD--KIVKEFKDGLTQVLISTDVLARGFDQQQVNLIVNYDPPVKHGKHLEPDCEV 441
TI ++D + ++E D L + I + D+ ++N+ ++ DP G P +V
Sbjct: 744 TILSDKDPEEALQEVYDYLEDIRIKVETNNIRIDKYKINMKLSKDPKAYPGGKNMPAVQV 803
Query: 442 YLHRIGRAGRFGRKGVVFNLLMDGDDMI 469
L R+ +AGR + G V ++ D I
Sbjct: 804 AL-RMRKAGRVVKAGSVITFVITKQDEI 830
>pdb|4FVM|A Chain A, Crystal Structure Of Yeast Dna Polymerase Alpha
pdb|4FXD|A Chain A, Crystal Structure Of Yeast Dna Polymerase Alpha Bound To
Dna/rna
pdb|4FXD|B Chain B, Crystal Structure Of Yeast Dna Polymerase Alpha Bound To
Dna/rna
Length = 910
Score = 28.5 bits (62), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 42/88 (47%), Gaps = 3/88 (3%)
Query: 384 TIQEERD--KIVKEFKDGLTQVLISTDVLARGFDQQQVNLIVNYDPPVKHGKHLEPDCEV 441
TI ++D + ++E D L + I + D+ ++N+ ++ DP G P +V
Sbjct: 744 TILSDKDPEEALQEVYDYLEDIRIKVETNNIRIDKYKINMKLSKDPKAYPGGKNMPAVQV 803
Query: 442 YLHRIGRAGRFGRKGVVFNLLMDGDDMI 469
L R+ +AGR + G V ++ D I
Sbjct: 804 AL-RMRKAGRVVKAGSVITFVITKQDEI 830
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.317 0.134 0.381
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,820,579
Number of Sequences: 62578
Number of extensions: 550486
Number of successful extensions: 1861
Number of sequences better than 100.0: 102
Number of HSP's better than 100.0 without gapping: 76
Number of HSP's successfully gapped in prelim test: 26
Number of HSP's that attempted gapping in prelim test: 1567
Number of HSP's gapped (non-prelim): 120
length of query: 502
length of database: 14,973,337
effective HSP length: 103
effective length of query: 399
effective length of database: 8,527,803
effective search space: 3402593397
effective search space used: 3402593397
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)