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= 006476
(643 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2EYQ|A Chain A, Crystal Structure Of Escherichia Coli Transcription-Repair
Coupling Factor
pdb|2EYQ|B Chain B, Crystal Structure Of Escherichia Coli Transcription-Repair
Coupling Factor
Length = 1151
Score = 373 bits (957), Expect = e-103, Method: Compositional matrix adjust.
Identities = 198/539 (36%), Positives = 311/539 (57%), Gaps = 8/539 (1%)
Query: 39 AWERRKTKGKVAIQKMVVDLMELYLHRLKQKRPPYPKNPAIAE-FAAQFPYEPTPDQKKA 97
AW R + K ++ + +L+++Y R ++ + + + F FP+E TPDQ +A
Sbjct: 552 AWSRARQKAAEKVRDVAAELLDIYAQRAAKEGFAFKHDREQYQLFCDSFPFETTPDQAQA 611
Query: 98 FLDVERDLTERETPMDRLICGDVGFGKTEVALRAIFCVVSAGKQAMVLAPTIVLAKQHFD 157
V D+ + MDRL+CGDVGFGKTEVA+RA F V KQ VL PT +LA+QH+D
Sbjct: 612 INAVLSDMCQ-PLAMDRLVCGDVGFGKTEVAMRAAFLAVDNHKQVAVLVPTTLLAQQHYD 670
Query: 158 VVSERFSKYPDIKVGLLSRFQSKAEKEEHLDMIKHGHLNIIVGTHSLLGSRVVYNNLGLL 217
+RF+ +P +++ ++SRF+S E+ + L + G ++I++GTH LL S V + +LGLL
Sbjct: 671 NFRDRFANWP-VRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQSDVKFKDLGLL 729
Query: 218 VVDEEQRFGVKQKEKIASFKISVDVLTLSATPIPRTLYLALTGFRDASLISTPPPERLPI 277
+VDEE RFGV+ KE+I + + +VD+LTL+ATPIPRTL +A++G RD S+I+TPP RL +
Sbjct: 730 IVDEEHRFGVRHKERIKAMRANVDILTLTATPIPRTLNMAMSGMRDLSIIATPPARRLAV 789
Query: 278 KTHLSAFSKEKVISAIKYELDRGGQVFYVLPRIKGLEEPMDFLQQAFPGVDIAIAHGQQY 337
KT + + V AI E+ RGGQV+Y+ ++ +++ + L + P IAI HGQ
Sbjct: 790 KTFVREYDSMVVREAILREILRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMR 849
Query: 338 SRQLEETMEKFAQGAIKILICTNIVESGLDIQNANTIIVQDVQQFGLAQLYQLRGRVGRA 397
R+LE M F +L+CT I+E+G+DI ANTII++ FGLAQL+QLRGRVGR+
Sbjct: 850 ERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQLHQLRGRVGRS 909
Query: 398 DKEAHAYLFYPDKSLLSDQXXXXXXXXXXXXXXGQGFQLAEKDMGIRGFGTIFGEQQTGD 457
+A+A+L P ++ G GF LA D+ IRG G + GE+Q+G
Sbjct: 910 HHQAYAWLLTPHPKAMTTDAQKRLEAIASLEDLGAGFALATHDLEIRGAGELLGEEQSGS 969
Query: 458 VGNVGVDLFFEML---FESLSKVDEHCVISVPYKSVQIDININPRLPSEYINHLENPMEM 514
+ +G L+ E+L ++L E + + + ++++ + LP ++I + +
Sbjct: 970 METIGFSLYMELLENAVDALKAGREPSLEDLTSQQTEVELRMPSLLPDDFIPDVNTRLSF 1029
Query: 515 VNEAEKAAEQDIWCLMQFTESLRRQYGKEPYSMEILLKKLYVRRMAADIGITKIYASGK 573
A ++ L + L ++G P LL +R+ A +GI K+ + K
Sbjct: 1030 YKRIASAKTEN--ELEEIKVELIDRFGLLPDPARTLLDIARLRQQAQKLGIRKLEGNEK 1086
>pdb|1GM5|A Chain A, Structure Of Recg Bound To Three-Way Dna Junction
Length = 780
Score = 252 bits (643), Expect = 5e-67, Method: Compositional matrix adjust.
Identities = 151/448 (33%), Positives = 249/448 (55%), Gaps = 26/448 (5%)
Query: 38 TAWERRKTKGKVAIQKMVVDLMELYLHRLKQKRPPYPKNPA------IAEFAAQFPYEPT 91
T + K + ++A +++ V ++L +++++R + P EF P++ T
Sbjct: 313 TFYHLEKARERLAYEELFV--LQLAFQKIRKEREKHGGIPKKIEGKLAEEFIKSLPFKLT 370
Query: 92 PDQKKAFLDVERDLTERETPMDRLICGDVGFGKTEVALRAIFCVVSAGKQAMVLAPTIVL 151
QK+A ++ D+ E PM+RL+ GDVG GKT VA AI AG Q + PT +L
Sbjct: 371 NAQKRAHQEIRNDMIS-EKPMNRLLQGDVGSGKTVVAQLAILDNYEAGFQTAFMVPTSIL 429
Query: 152 AKQHFDVVSERFSKYPDIKVGLLSRFQSKAEKEEHLDMIKHGHLNIIVGTHSLLGSRVVY 211
A QH+ E FSK+ +I V LL + +EKE+ +++G +++++GTH+L+ V +
Sbjct: 430 AIQHYRRTVESFSKF-NIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQEDVHF 488
Query: 212 NNLGLLVVDEEQRFGVKQKEKIASFKISVDVLTLSATPIPRTLYLALTGFRDASLISTPP 271
NLGL+++DE+ RFGVKQ+E + + VD L +SATPIPR++ LA G D ++I P
Sbjct: 489 KNLGLVIIDEQHRFGVKQREALMNKGKMVDTLVMSATPIPRSMALAFYGDLDVTVIDEMP 548
Query: 272 PERLPIKTHLSAFSK-EKVISAIKYELDRGGQVFYVLP--------RIKGLEEPMDFL-Q 321
P R ++T L + +V ++ E+ RGGQ F V P +K E ++L +
Sbjct: 549 PGRKEVQTMLVPMDRVNEVYEFVRQEVMRGGQAFIVYPLIEESDKLNVKSAVEMYEYLSK 608
Query: 322 QAFPGVDIAIAHGQQYSRQLEETMEKFAQGAIKILICTNIVESGLDIQNANTIIVQDVQQ 381
+ FP + + HG+ + + M +FA+G IL+ T ++E G+D+ AN +++++ ++
Sbjct: 609 EVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVGIDVPRANVMVIENPER 668
Query: 382 FGLAQLYQLRGRVGRADKEAHAYLFYPDKSLLSDQXXXXXXXXXXXXXXGQGFQLAEKDM 441
FGLAQL+QLRGRVGR +EA+ +L ++ D GF++AE D+
Sbjct: 669 FGLAQLHQLRGRVGRGGQEAYCFL------VVGDVGEEAMERLRFFTLNTDGFKIAEYDL 722
Query: 442 GIRGFGTIFGEQQTGDVGNVGVDLFFEM 469
RG G FG +Q G G DL+ ++
Sbjct: 723 KTRGPGEFFGVKQHGLSGFKVADLYRDL 750
>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 = 48.9 bits (115), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 36/134 (26%), Positives = 67/134 (50%), Gaps = 11/134 (8%)
Query: 286 KEKVISAIKYELDRGGQVFYVLPRIKGLEEPMDFL-QQAFPGVDIAIAHGQQYSRQLEET 344
+ K+I + + D G + +V + +G + FL ++ FP I HG + Q E+
Sbjct: 289 RSKLIEILSEQAD--GTIVFVETK-RGADFLASFLSEKEFPTTSI---HGDRLQSQREQA 342
Query: 345 MEKFAQGAIKILICTNIVESGLDIQNANTIIVQDVQQFGLAQLYQLRGRVGRADKEAHAY 404
+ F G++K+LI T++ GLDI+N +I D+ ++++ GR GR A
Sbjct: 343 LRDFKNGSMKVLIATSVASRGLDIKNIKHVINYDMPSKIDDYVHRI-GRTGRVGNNGRAT 401
Query: 405 LFY---PDKSLLSD 415
F+ D+++ +D
Sbjct: 402 SFFDPEKDRAIAAD 415
>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3
Length = 395
Score = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 71/326 (21%), Positives = 131/326 (40%), Gaps = 37/326 (11%)
Query: 111 PMDRLICGDVGFGKTEVALRAIFCVVS---AGKQAMVLAPTIVLAKQHFDVVSERFSKYP 167
P + + G GKT + V+ A QA+ LAP+ LA+Q +VV E
Sbjct: 44 PRNMIAQSQSGTGKTAAFSLTMLTRVNPEDASPQAICLAPSRELARQTLEVVQE------ 97
Query: 168 DIKVGLLSRFQSKAEKEEHLDMIKHGHLNIIVGTHSLLGSRVVYNNLGLLVVDEEQRFGV 227
+G ++ S+ + + K + +IVGT G+ + L+ + + + F +
Sbjct: 98 ---MGKFTKITSQLIVPDSFEKNKQINAQVIVGTP---GTVLDLMRRKLMQLQKIKIFVL 151
Query: 228 KQKEKIASFKISVDVLTLSATPIPRTLYLALTGFRDASLISTPPPERLPIKTHLSAFSKE 287
+ + + + D +P+ L L A + + +P L + E
Sbjct: 152 DEADNMLDQQGLGDQCIRVKRFLPKDTQLVLFSATFADAVRQYAKKIVPNANTLELQTNE 211
Query: 288 KVISAIK---YELDRGGQVFYVLPRIKGL------------EEPMDFLQQAFP--GVDIA 330
+ AIK + F VL + GL ++ + L G +++
Sbjct: 212 VNVDAIKQLYMDCKNEADKFDVLTELYGLMTIGSSIIFVATKKTANVLYGKLKSEGHEVS 271
Query: 331 IAHGQQYSRQLEETMEKFAQGAIKILICTNIVESGLDIQNANTIIVQDVQQFGLAQ---- 386
I HG +++ + ++ F +G K+LI TN++ G+DI + ++ D+ Q
Sbjct: 272 ILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPA 331
Query: 387 LYQLR-GRVGRADKEAHAYLFYPDKS 411
Y R GR GR ++ A F DK+
Sbjct: 332 TYIHRIGRTGRFGRKGVAISFVHDKN 357
>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 = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 26/91 (28%), Positives = 47/91 (51%), Gaps = 5/91 (5%)
Query: 326 GVDIAIAHGQQYSRQLEETMEKFAQGAIKILICTNIVESGLDIQNANTIIVQDVQQFGLA 385
G +++I HG +++ + ++ F +G K+LI TN++ G+DI + ++ D+
Sbjct: 267 GHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANG 326
Query: 386 Q----LYQLR-GRVGRADKEAHAYLFYPDKS 411
Q Y R GR GR ++ A F DK+
Sbjct: 327 QADPATYIHRIGRTGRFGRKGVAISFVHDKN 357
>pdb|3GFP|A Chain A, Structure Of The C-Terminal Domain Of The Dead-Box Protein
Dbp5
Length = 189
Score = 43.9 bits (102), Expect = 3e-04, Method: Composition-based stats.
Identities = 26/91 (28%), Positives = 47/91 (51%), Gaps = 5/91 (5%)
Query: 326 GVDIAIAHGQQYSRQLEETMEKFAQGAIKILICTNIVESGLDIQNANTIIVQDVQQFGLA 385
G +++I HG +++ + ++ F +G K+LI TN++ G+DI + ++ D+
Sbjct: 61 GHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSXVVNYDLPTLANG 120
Query: 386 Q----LYQLR-GRVGRADKEAHAYLFYPDKS 411
Q Y R GR GR ++ A F DK+
Sbjct: 121 QADPATYIHRIGRTGRFGRKGVAISFVHDKN 151
>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 = 43.9 bits (102), Expect = 3e-04, Method: Composition-based stats.
Identities = 26/91 (28%), Positives = 47/91 (51%), Gaps = 5/91 (5%)
Query: 326 GVDIAIAHGQQYSRQLEETMEKFAQGAIKILICTNIVESGLDIQNANTIIVQDVQQFGLA 385
G +++I HG +++ + ++ F +G K+LI TN++ G+DI + ++ D+
Sbjct: 60 GHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSXVVNYDLPTLANG 119
Query: 386 Q----LYQLR-GRVGRADKEAHAYLFYPDKS 411
Q Y R GR GR ++ A F DK+
Sbjct: 120 QADPATYIHRIGRTGRFGRKGVAISFVHDKN 150
>pdb|2KBF|A Chain A, Solution Structure Of Carboxyl-Terminal Domain Of Dbp5p
Length = 187
Score = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 26/91 (28%), Positives = 47/91 (51%), Gaps = 5/91 (5%)
Query: 326 GVDIAIAHGQQYSRQLEETMEKFAQGAIKILICTNIVESGLDIQNANTIIVQDVQQFGLA 385
G +++I HG +++ + ++ F +G K+LI TN++ G+DI + ++ D+
Sbjct: 59 GHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANG 118
Query: 386 Q----LYQLR-GRVGRADKEAHAYLFYPDKS 411
Q Y R GR GR ++ A F DK+
Sbjct: 119 QADPATYIHRIGRTGRFGRKGVAISFVHDKN 149
>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x
Length = 417
Score = 43.5 bits (101), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 29/102 (28%), Positives = 44/102 (43%), Gaps = 3/102 (2%)
Query: 311 KGLEEPMDFLQQAFPGVDIAIAHGQQYSRQLEETMEKFAQGAIKILICTNIVESGLDIQN 370
KG + DFL G HG + R EE + +F G IL+ T + GLDI N
Sbjct: 287 KGADSLEDFLYHE--GYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISN 344
Query: 371 ANTIIVQDVQQFGLAQLYQLRGRVGRADKEAHAYLFYPDKSL 412
+I D+ + + GR GR A F+ ++++
Sbjct: 345 VKHVINFDLPS-DIEEYVHRIGRTGRVGNLGLATSFFNERNI 385
>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 = 43.1 bits (100), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 29/102 (28%), Positives = 44/102 (43%), Gaps = 3/102 (2%)
Query: 311 KGLEEPMDFLQQAFPGVDIAIAHGQQYSRQLEETMEKFAQGAIKILICTNIVESGLDIQN 370
KG + DFL G HG + R EE + +F G IL+ T + GLDI N
Sbjct: 57 KGADSLEDFLYH--EGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISN 114
Query: 371 ANTIIVQDVQQFGLAQLYQLRGRVGRADKEAHAYLFYPDKSL 412
+I D+ + + GR GR A F+ ++++
Sbjct: 115 VKHVINFDLPS-DIEEYVHRIGRTGRVGNLGLATSFFNERNI 155
>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 = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 39/78 (50%), Gaps = 1/78 (1%)
Query: 326 GVDIAIAHGQQYSRQLEETMEKFAQGAIKILICTNIVESGLDIQNANTIIVQDVQQFGLA 385
G HG Q E+ + F Q I+ILI T++ G+D+ + N +I + Q +
Sbjct: 262 GFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVXSRGIDVNDLNCVINYHLPQNPES 321
Query: 386 QLYQLRGRVGRADKEAHA 403
+++ GR GRA K+ A
Sbjct: 322 YXHRI-GRTGRAGKKGKA 338
>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p
Length = 400
Score = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 39/77 (50%), Gaps = 4/77 (5%)
Query: 326 GVDIAIAHGQQYSRQLEETMEKFAQGAIKILICTNIVESGLDIQNANTIIVQDVQQFGLA 385
G +H + ++ + +F QG ++ L+C++++ G+DIQ N +I D +
Sbjct: 282 GYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAET 341
Query: 386 QLYQLRGRVGRADKEAH 402
L+ R+GR+ + H
Sbjct: 342 YLH----RIGRSGRFGH 354
>pdb|4GL2|A Chain A, Structural Basis For Dsrna Duplex Backbone Recognition By
Mda5
pdb|4GL2|B Chain B, Structural Basis For Dsrna Duplex Backbone Recognition By
Mda5
Length = 699
Score = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 26/87 (29%), Positives = 42/87 (48%), Gaps = 14/87 (16%)
Query: 329 IAIAHGQQYS----RQLEETMEKFAQGAIKILICTNIVESGLDIQNANTIIVQDVQQFGL 384
I H ++ + +E + KF G I +LI T + E GLDI+ N +I ++GL
Sbjct: 437 IGAGHSSEFKPMTQNEQKEVISKFRTGKINLLIATTVAEEGLDIKECNIVI-----RYGL 491
Query: 385 AQ----LYQLRGRVGRADKEAHAYLFY 407
+ Q RGR RAD+ + + +
Sbjct: 492 VTNEIAMVQARGR-ARADESTYVLVAH 517
>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 = 38.9 bits (89), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 61/297 (20%), Positives = 112/297 (37%), Gaps = 41/297 (13%)
Query: 109 ETPMDRLICGDVGFGKTEVALRAIFCVVSAGK---QAMVLAPTIVLAKQHFDVVSERFSK 165
E P + + G GKT + A+ V Q + L+PT LA Q V+ +
Sbjct: 62 EPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKF 121
Query: 166 YPDIKVGLLSRFQSKAEKEEHLDMIKHGHLNIIVGTHSLL---GSRVVY---NNLGLLVV 219
YP++K+ R +K E+ + + I++GT + S++ + + + V+
Sbjct: 122 YPELKLAYAVR-GNKLERGQKISE------QIVIGTPGTVLDWCSKLKFIDPKKIKVFVL 174
Query: 220 DEEQRFGVKQKEKIASFKISVDVLTLSATPIPRTLYLAL--TGFRDA----SLISTPPPE 273
DE Q + S +I +PR + L F D+ + P P
Sbjct: 175 DEADVMIATQGHQDQSIRIQ--------RMLPRNCQMLLFSATFEDSVWKFAQKVVPDPN 226
Query: 274 RLPIKTHLSAFSKEKVISAIKYELDRGGQVFYVLPRIKGLEEPMDFLQQ----------- 322
+ +K K + D Q L + + M F
Sbjct: 227 VIKLKREEETLDTIKQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAEL 286
Query: 323 AFPGVDIAIAHGQQYSRQLEETMEKFAQGAIKILICTNIVESGLDIQNANTIIVQDV 379
+ G +A+ G+ Q +E+F +G K+L+ TN+ G+D++ + +I D+
Sbjct: 287 SKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDL 343
>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 = 38.5 bits (88), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 61/297 (20%), Positives = 112/297 (37%), Gaps = 41/297 (13%)
Query: 109 ETPMDRLICGDVGFGKTEVALRAIFCVVSAGK---QAMVLAPTIVLAKQHFDVVSERFSK 165
E P + + G GKT + A+ V Q + L+PT LA Q V+ +
Sbjct: 99 EPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKF 158
Query: 166 YPDIKVGLLSRFQSKAEKEEHLDMIKHGHLNIIVGTHSLL---GSRVVY---NNLGLLVV 219
YP++K+ R +K E+ + + I++GT + S++ + + + V+
Sbjct: 159 YPELKLAYAVR-GNKLERGQKISE------QIVIGTPGTVLDWCSKLKFIDPKKIKVFVL 211
Query: 220 DEEQRFGVKQKEKIASFKISVDVLTLSATPIPRTLYLAL--TGFRDA----SLISTPPPE 273
DE Q + S +I +PR + L F D+ + P P
Sbjct: 212 DEADVMIATQGHQDQSIRIQ--------RMLPRNCQMLLFSATFEDSVWKFAQKVVPDPN 263
Query: 274 RLPIKTHLSAFSKEKVISAIKYELDRGGQVFYVLPRIKGLEEPMDFLQQ----------- 322
+ +K K + D Q L + + M F
Sbjct: 264 VIKLKREEETLDTIKQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAEL 323
Query: 323 AFPGVDIAIAHGQQYSRQLEETMEKFAQGAIKILICTNIVESGLDIQNANTIIVQDV 379
+ G +A+ G+ Q +E+F +G K+L+ TN+ G+D++ + +I D+
Sbjct: 324 SKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDL 380
>pdb|3G0H|A Chain A, Human Dead-box Rna Helicase Ddx19, In Complex With An
Atp-analogue And Rna
Length = 424
Score = 38.5 bits (88), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 61/297 (20%), Positives = 112/297 (37%), Gaps = 41/297 (13%)
Query: 109 ETPMDRLICGDVGFGKTEVALRAIFCVVSAGK---QAMVLAPTIVLAKQHFDVVSERFSK 165
E P + + G GKT + A+ V Q + L+PT LA Q V+ +
Sbjct: 78 EPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKF 137
Query: 166 YPDIKVGLLSRFQSKAEKEEHLDMIKHGHLNIIVGTHSLL---GSRVVY---NNLGLLVV 219
YP++K+ R +K E+ + + I++GT + S++ + + + V+
Sbjct: 138 YPELKLAYAVR-GNKLERGQKISE------QIVIGTPGTVLDWCSKLKFIDPKKIKVFVL 190
Query: 220 DEEQRFGVKQKEKIASFKISVDVLTLSATPIPRTLYLAL--TGFRDA----SLISTPPPE 273
DE Q + S +I +PR + L F D+ + P P
Sbjct: 191 DEADVMIATQGHQDQSIRIQ--------RMLPRNCQMLLFSATFEDSVWKFAQKVVPDPN 242
Query: 274 RLPIKTHLSAFSKEKVISAIKYELDRGGQVFYVLPRIKGLEEPMDFLQQ----------- 322
+ +K K + D Q L + + M F
Sbjct: 243 VIKLKREEETLDTIKQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAEL 302
Query: 323 AFPGVDIAIAHGQQYSRQLEETMEKFAQGAIKILICTNIVESGLDIQNANTIIVQDV 379
+ G +A+ G+ Q +E+F +G K+L+ TN+ G+D++ + +I D+
Sbjct: 303 SKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDL 359
>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 38.5 bits (88), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 27/99 (27%), Positives = 49/99 (49%), Gaps = 5/99 (5%)
Query: 317 MDFLQQAFPGVDIAIA--HGQQYSRQLEETMEKFAQGAIKILICTNIVESGLDIQNANTI 374
+D+L + + ++ HG ++ E M++F GA ++LI T++ GLD+ + I
Sbjct: 253 VDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLI 312
Query: 375 IVQDVQQFGLAQLYQLR-GRVGRADKEAHAYLFYPDKSL 412
I D+ +LY R GR GR ++ A F + +
Sbjct: 313 INYDLPNN--RELYIHRIGRSGRYGRKGVAVNFVKNDDI 349
>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 = 38.5 bits (88), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 27/99 (27%), Positives = 49/99 (49%), Gaps = 5/99 (5%)
Query: 317 MDFLQQAFPGVDIAIA--HGQQYSRQLEETMEKFAQGAIKILICTNIVESGLDIQNANTI 374
+D+L + + ++ HG ++ E M++F GA ++LI T++ GLD+ + I
Sbjct: 290 VDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLI 349
Query: 375 IVQDVQQFGLAQLYQLR-GRVGRADKEAHAYLFYPDKSL 412
I D+ +LY R GR GR ++ A F + +
Sbjct: 350 INYDLPNN--RELYIHRIGRSGRYGRKGVAINFVKNDDI 386
>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 = 38.5 bits (88), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 27/99 (27%), Positives = 49/99 (49%), Gaps = 5/99 (5%)
Query: 317 MDFLQQAFPGVDIAIA--HGQQYSRQLEETMEKFAQGAIKILICTNIVESGLDIQNANTI 374
+D+L + + ++ HG ++ E M++F GA ++LI T++ GLD+ + I
Sbjct: 290 VDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLI 349
Query: 375 IVQDVQQFGLAQLYQLR-GRVGRADKEAHAYLFYPDKSL 412
I D+ +LY R GR GR ++ A F + +
Sbjct: 350 INYDLPNN--RELYIHRIGRSGRYGRKGVAINFVKNDDI 386
>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 38.5 bits (88), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 27/99 (27%), Positives = 49/99 (49%), Gaps = 5/99 (5%)
Query: 317 MDFLQQAFPGVDIAIA--HGQQYSRQLEETMEKFAQGAIKILICTNIVESGLDIQNANTI 374
+D+L + + ++ HG ++ E M++F GA ++LI T++ GLD+ + I
Sbjct: 253 VDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLI 312
Query: 375 IVQDVQQFGLAQLYQLR-GRVGRADKEAHAYLFYPDKSL 412
I D+ +LY R GR GR ++ A F + +
Sbjct: 313 INYDLPNN--RELYIHRIGRSGRYGRKGVAVNFVKNDDI 349
>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 = 38.5 bits (88), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 27/99 (27%), Positives = 49/99 (49%), Gaps = 5/99 (5%)
Query: 317 MDFLQQAFPGVDIAIA--HGQQYSRQLEETMEKFAQGAIKILICTNIVESGLDIQNANTI 374
+D+L + + ++ HG ++ E M++F GA ++LI T++ GLD+ + I
Sbjct: 289 VDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLI 348
Query: 375 IVQDVQQFGLAQLYQLR-GRVGRADKEAHAYLFYPDKSL 412
I D+ +LY R GR GR ++ A F + +
Sbjct: 349 INYDLPNN--RELYIHRIGRSGRYGRKGVAINFVKNDDI 385
>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 = 38.5 bits (88), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 27/99 (27%), Positives = 49/99 (49%), Gaps = 5/99 (5%)
Query: 317 MDFLQQAFPGVDIAIA--HGQQYSRQLEETMEKFAQGAIKILICTNIVESGLDIQNANTI 374
+D+L + + ++ HG ++ E M++F GA ++LI T++ GLD+ + I
Sbjct: 268 VDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLI 327
Query: 375 IVQDVQQFGLAQLYQLR-GRVGRADKEAHAYLFYPDKSL 412
I D+ +LY R GR GR ++ A F + +
Sbjct: 328 INYDLPNN--RELYIHRIGRSGRYGRKGVAINFVKNDDI 364
>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 = 38.1 bits (87), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 61/297 (20%), Positives = 112/297 (37%), Gaps = 41/297 (13%)
Query: 109 ETPMDRLICGDVGFGKTEVALRAIFCVVSAGK---QAMVLAPTIVLAKQHFDVVSERFSK 165
E P + + G GKT + A+ V Q + L+PT LA Q V+ +
Sbjct: 129 EPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKF 188
Query: 166 YPDIKVGLLSRFQSKAEKEEHLDMIKHGHLNIIVGTHSLL---GSRVVY---NNLGLLVV 219
YP++K+ R +K E+ + + I++GT + S++ + + + V+
Sbjct: 189 YPELKLAYAVR-GNKLERGQKISE------QIVIGTPGTVLDWCSKLKFIDPKKIKVFVL 241
Query: 220 DEEQRFGVKQKEKIASFKISVDVLTLSATPIPRTLYLAL--TGFRDA----SLISTPPPE 273
DE Q + S +I +PR + L F D+ + P P
Sbjct: 242 DEADVMIATQGHQDQSIRIQ--------RMLPRNCQMLLFSATFEDSVWKFAQKVVPDPN 293
Query: 274 RLPIKTHLSAFSKEKVISAIKYELDRGGQVFYVLPRIKGLEEPMDFLQQ----------- 322
+ +K K + D Q L + + M F
Sbjct: 294 VIKLKREEETLDTIKQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAEL 353
Query: 323 AFPGVDIAIAHGQQYSRQLEETMEKFAQGAIKILICTNIVESGLDIQNANTIIVQDV 379
+ G +A+ G+ Q +E+F +G K+L+ TN+ G+D++ + +I D+
Sbjct: 354 SKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDL 410
>pdb|3FHO|A Chain A, Structure Of S. Pombe Dbp5
pdb|3FHO|B Chain B, Structure Of S. Pombe Dbp5
Length = 508
Score = 37.7 bits (86), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 27/90 (30%), Positives = 41/90 (45%), Gaps = 5/90 (5%)
Query: 326 GVDIAIAHGQQYSRQLEETMEKFAQGAIKILICTNIVESGLDIQNANTIIVQD--VQQFG 383
G +A G Q + M+ F G K+L+ TN++ G+D+ N ++ D + Q G
Sbjct: 381 GHTVACLTGNLEGAQRDAIMDSFRVGTSKVLVTTNVIARGIDVSQVNLVVNYDMPLDQAG 440
Query: 384 L--AQLYQLR-GRVGRADKEAHAYLFYPDK 410
Q Y R GR GR + + F DK
Sbjct: 441 RPDPQTYLHRIGRTGRFGRVGVSINFVHDK 470
Score = 30.8 bits (68), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 28/56 (50%), Gaps = 4/56 (7%)
Query: 121 GFGKTEVALRAIFCVVSAG---KQAMVLAPTIVLAKQHFDVVSERFSKYPDIKVGL 173
G GKT + V A QA+ LAP+ LA+Q DVV+E KY ++K
Sbjct: 168 GTGKTAAFALTMLSRVDASVPKPQAICLAPSRELARQIMDVVTE-MGKYTEVKTAF 222
>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 = 37.4 bits (85), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 34/116 (29%), Positives = 55/116 (47%), Gaps = 12/116 (10%)
Query: 115 LICGDVGFGKTEVALR-AIFCVVSAGKQAMVLAPTIVLAKQHFDVVSERFSKYPDIKVGL 173
LI G GKT +A+ A + + G + ++LAPT L QH + F+ P+ K+
Sbjct: 27 LIVLPTGLGKTLIAMMIAEYRLTKYGGKVLMLAPTKPLVLQHAESFRRLFNLPPE-KIVA 85
Query: 174 LSRFQSKAEKEEHLDMIKHGHLNIIVGT-----HSLLGSRVVYNNLGLLVVDEEQR 224
L+ +S E+ + K +IV T + LL R+ ++ L+V DE R
Sbjct: 86 LTGEKSPEERSKAWARAK-----VIVATPQTIENDLLAGRISLEDVSLIVFDEAHR 136
Score = 34.3 bits (77), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 339 RQLEETMEKFAQGAIKILICTNIVESGLDIQNANTIIVQDVQQFGLAQLYQLRGRVGR 396
R+ + +++FA+G +L+ T++ E GLD+ + ++ + + + Q RGR GR
Sbjct: 406 REQKLILDEFARGEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSI-QRRGRTGR 462
>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 = 37.0 bits (84), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 36/78 (46%), Gaps = 9/78 (11%)
Query: 333 HGQQYSRQLEETMEKFAQGAIKILICTNIVESGLDIQNANTIIVQDVQQFG----LAQLY 388
HG+ + +++F + IL+CT++ G+D N V +V Q G LA
Sbjct: 67 HGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPN-----VHEVLQIGVPSELANYI 121
Query: 389 QLRGRVGRADKEAHAYLF 406
GR R+ KE + LF
Sbjct: 122 HRIGRTARSGKEGSSVLF 139
>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 = 37.0 bits (84), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 36/78 (46%), Gaps = 9/78 (11%)
Query: 333 HGQQYSRQLEETMEKFAQGAIKILICTNIVESGLDIQNANTIIVQDVQQFG----LAQLY 388
HG+ + +++F + IL+CT++ G+D N V +V Q G LA
Sbjct: 67 HGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPN-----VHEVLQIGVPSELANYI 121
Query: 389 QLRGRVGRADKEAHAYLF 406
GR R+ KE + LF
Sbjct: 122 HRIGRTARSGKEGSSVLF 139
>pdb|3SQX|A Chain A, Structure Of Mss116p (Nte And C-Tail Double Deletion)
Bound To Ssrna And Amp-Pnp
Length = 512
Score = 37.0 bits (84), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 36/78 (46%), Gaps = 9/78 (11%)
Query: 333 HGQQYSRQLEETMEKFAQGAIKILICTNIVESGLDIQNANTIIVQDVQQFG----LAQLY 388
HG+ + +++F + IL+CT++ G+D N V +V Q G LA
Sbjct: 322 HGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPN-----VHEVLQIGVPSELANYI 376
Query: 389 QLRGRVGRADKEAHAYLF 406
GR R+ KE + LF
Sbjct: 377 HRIGRTARSGKEGSSVLF 394
>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 = 37.0 bits (84), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 36/78 (46%), Gaps = 9/78 (11%)
Query: 333 HGQQYSRQLEETMEKFAQGAIKILICTNIVESGLDIQNANTIIVQDVQQFG----LAQLY 388
HG+ + +++F + IL+CT++ G+D N V +V Q G LA
Sbjct: 67 HGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPN-----VHEVLQIGVPSELANYI 121
Query: 389 QLRGRVGRADKEAHAYLF 406
GR R+ KE + LF
Sbjct: 122 HRIGRTARSGKEGSSVLF 139
>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 = 37.0 bits (84), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 13/43 (30%), Positives = 23/43 (53%)
Query: 333 HGQQYSRQLEETMEKFAQGAIKILICTNIVESGLDIQNANTII 375
HG + E M F QG +++L+ T++ GLDI + ++
Sbjct: 59 HGDMSQGERERVMGAFRQGEVRVLVATDVAARGLDIPQVDLVV 101
>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 = 37.0 bits (84), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 36/78 (46%), Gaps = 9/78 (11%)
Query: 333 HGQQYSRQLEETMEKFAQGAIKILICTNIVESGLDIQNANTIIVQDVQQFG----LAQLY 388
HG+ + +++F + IL+CT++ G+D N V +V Q G LA
Sbjct: 373 HGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPN-----VHEVLQIGVPSELANYI 427
Query: 389 QLRGRVGRADKEAHAYLF 406
GR R+ KE + LF
Sbjct: 428 HRIGRTARSGKEGSSVLF 445
>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And
Amp-Pnp
Length = 579
Score = 37.0 bits (84), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 36/78 (46%), Gaps = 9/78 (11%)
Query: 333 HGQQYSRQLEETMEKFAQGAIKILICTNIVESGLDIQNANTIIVQDVQQFG----LAQLY 388
HG+ + +++F + IL+CT++ G+D N V +V Q G LA
Sbjct: 322 HGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPN-----VHEVLQIGVPSELANYI 376
Query: 389 QLRGRVGRADKEAHAYLF 406
GR R+ KE + LF
Sbjct: 377 HRIGRTARSGKEGSSVLF 394
>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 = 36.6 bits (83), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 23/85 (27%), Positives = 42/85 (49%), Gaps = 3/85 (3%)
Query: 333 HGQQYSRQLEETMEKFAQGAIKILICTNIVESGLDIQNANTIIVQDVQQFGLAQLYQLRG 392
HG + M +F +G + L+ T++ G+DI+N + +I D+ + +++ G
Sbjct: 66 HGGMIQEDRFDVMNEFKRGEYRYLVATDVAARGIDIENISLVINYDLPLEKESYVHRT-G 124
Query: 393 RVGRADKEAHAYLFYP--DKSLLSD 415
R GRA + A F +K L+D
Sbjct: 125 RTGRAGNKGKAISFVTAFEKRFLAD 149
>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 = 36.6 bits (83), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 31/77 (40%), Gaps = 4/77 (5%)
Query: 326 GVDIAIAHGQQYSRQLEETMEKFAQGAIKILICTNIVESGLDIQNANTIIVQDVQQFGLA 385
G H + F G + L+CT++ G+DIQ N +I D +
Sbjct: 68 GYSCFYIHAKMRQEHRNRVFHDFRNGLCRNLVCTDLFTRGIDIQAVNVVINFDFPKLAET 127
Query: 386 QLYQLRGRVGRADKEAH 402
L+ R+GR+ + H
Sbjct: 128 YLH----RIGRSGRFGH 140
>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a
pdb|3EIQ|D Chain D, Crystal Structure Of Pdcd4-eif4a
Length = 414
Score = 35.8 bits (81), Expect = 0.081, Method: Compositional matrix adjust.
Identities = 16/65 (24%), Positives = 36/65 (55%), Gaps = 2/65 (3%)
Query: 317 MDFLQQAFPGVDIAIA--HGQQYSRQLEETMEKFAQGAIKILICTNIVESGLDIQNANTI 374
+D+L + D ++ HG ++ + M +F G+ ++LI T+++ G+D+Q + +
Sbjct: 293 VDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLV 352
Query: 375 IVQDV 379
I D+
Sbjct: 353 INYDL 357
>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 = 35.4 bits (80), Expect = 0.087, Method: Compositional matrix adjust.
Identities = 16/65 (24%), Positives = 36/65 (55%), Gaps = 2/65 (3%)
Query: 317 MDFLQQAFPGVDIAIA--HGQQYSRQLEETMEKFAQGAIKILICTNIVESGLDIQNANTI 374
+D+L + D ++ HG ++ + M +F G+ ++LI T+++ G+D+Q + +
Sbjct: 267 VDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLV 326
Query: 375 IVQDV 379
I D+
Sbjct: 327 INYDL 331
>pdb|3P56|A Chain A, The Structure Of The Human Rnase H2 Complex Defines Key
Interaction Interfaces Relevant To Enzyme Function And
Human Disease
pdb|3P56|D Chain D, The Structure Of The Human Rnase H2 Complex Defines Key
Interaction Interfaces Relevant To Enzyme Function And
Human Disease
Length = 299
Score = 35.4 bits (80), Expect = 0.096, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 37/68 (54%), Gaps = 3/68 (4%)
Query: 265 SLISTPPPERLPIKTHLSAFSKEKVISAIKYELDRGGQVFYVLPRIKGLEEPMDF-LQQA 323
+LIST R +K +L++ S + I+Y LD+G V V G+ E LQQ+
Sbjct: 99 NLISTSMLGR--VKYNLNSLSHDTATGLIQYALDQGVNVTQVFVDTVGMPETYQARLQQS 156
Query: 324 FPGVDIAI 331
FPG+++ +
Sbjct: 157 FPGIEVTV 164
>pdb|3PUF|A Chain A, Crystal Structure Of Human Rnase H2 Complex
pdb|3PUF|D Chain D, Crystal Structure Of Human Rnase H2 Complex
pdb|3PUF|G Chain G, Crystal Structure Of Human Rnase H2 Complex
pdb|3PUF|J Chain J, Crystal Structure Of Human Rnase H2 Complex
pdb|3PUF|M Chain M, Crystal Structure Of Human Rnase H2 Complex
pdb|3PUF|P Chain P, Crystal Structure Of Human Rnase H2 Complex
Length = 302
Score = 35.4 bits (80), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 277 IKTHLSAFSKEKVISAIKYELDRGGQVFYVLPRIKGLEEPMDF-LQQAFPGVDIAI 331
+K +L++ S + I+Y LD+G V V G+ E LQQ+FPG+++ +
Sbjct: 112 VKYNLNSLSHDTATGLIQYALDQGVNVTQVFVDTVGMPETYQARLQQSFPGIEVTV 167
>pdb|4I1S|A Chain A, Melanoma Differentiation Associated Protein-5 Helicase
Domain Complex With Inhibitor Non-structural Protein V
Length = 243
Score = 35.4 bits (80), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 15/33 (45%), Positives = 20/33 (60%)
Query: 343 ETMEKFAQGAIKILICTNIVESGLDIQNANTII 375
E + KF G I +LI T + E GLDI+ N +I
Sbjct: 205 EVISKFRTGKINLLIATTVAEEGLDIKECNIVI 237
>pdb|1OYW|A Chain A, Structure Of The Recq Catalytic Core
Length = 523
Score = 33.5 bits (75), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 42/168 (25%), Positives = 71/168 (42%), Gaps = 8/168 (4%)
Query: 242 VLTLSATPIPRTLYLALTGFRDASLISTPPPERLPIKTHLSAFSK--EKVISAIKYELDR 299
LT +A R + L G D LI +R I+ L K +++ ++ + +
Sbjct: 179 ALTATADDTTRQDIVRLLGLND-PLIQISSFDRPNIRYXLXEKFKPLDQLXRYVQEQRGK 237
Query: 300 GGQVFYVLPRIKGLEEPMDFLQQAFPGVDIAIAHGQQYSRQLEETMEKFAQGAIKILICT 359
G + Y R K +E+ LQ G+ A H + + EKF + ++I++ T
Sbjct: 238 SG-IIYCNSRAK-VEDTAARLQSK--GISAAAYHAGLENNVRADVQEKFQRDDLQIVVAT 293
Query: 360 NIVESGLDIQNANTIIVQDVQQFGLAQLYQLRGRVGRADKEAHAYLFY 407
G++ N ++ D+ + + YQ GR GR A A LFY
Sbjct: 294 VAFGXGINKPNVRFVVHFDIPR-NIESYYQETGRAGRDGLPAEAXLFY 340
>pdb|1OYY|A Chain A, Structure Of The Recq Catalytic Core Bound To Atp-Gamma-S
Length = 523
Score = 33.5 bits (75), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 42/168 (25%), Positives = 72/168 (42%), Gaps = 8/168 (4%)
Query: 242 VLTLSATPIPRTLYLALTGFRDASLISTPPPERLPIKTHLSAFSK--EKVISAIKYELDR 299
LT +A R + L G D LI +R I+ L K ++++ ++ + +
Sbjct: 179 ALTATADDTTRQDIVRLLGLND-PLIQISSFDRPNIRYMLMEKFKPLDQLMRYVQEQRGK 237
Query: 300 GGQVFYVLPRIKGLEEPMDFLQQAFPGVDIAIAHGQQYSRQLEETMEKFAQGAIKILICT 359
G + Y R K +E+ LQ G+ A H + + EKF + ++I++ T
Sbjct: 238 SG-IIYCNSRAK-VEDTAARLQSK--GISAAAYHAGLENNVRADVQEKFQRDDLQIVVAT 293
Query: 360 NIVESGLDIQNANTIIVQDVQQFGLAQLYQLRGRVGRADKEAHAYLFY 407
G++ N ++ D+ + + YQ GR GR A A LFY
Sbjct: 294 VAFGMGINKPNVRFVVHFDIPR-NIESYYQETGRAGRDGLPAEAMLFY 340
>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp
Length = 386
Score = 32.7 bits (73), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 25/93 (26%), Positives = 43/93 (46%), Gaps = 4/93 (4%)
Query: 319 FLQQAFPGVDIAIAHGQQYSRQLEETMEKFAQGAIKILICTNIVESGLDIQNANTIIVQD 378
++Q FP IAI G +L ++F +IL+ TN+ G+DI+ N D
Sbjct: 270 LVEQNFPA--IAIHRGMPQEERLSR-YQQFKDFQRRILVATNLFGRGMDIERVNIAFNYD 326
Query: 379 VQQFGLAQLYQLRGRVGRADKEAHAYLFYPDKS 411
+ + L+++ R GR + A F D++
Sbjct: 327 MPEDSDTYLHRV-ARAGRFGTKGLAITFVSDEN 358
>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56
Length = 391
Score = 32.7 bits (73), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 25/93 (26%), Positives = 43/93 (46%), Gaps = 4/93 (4%)
Query: 319 FLQQAFPGVDIAIAHGQQYSRQLEETMEKFAQGAIKILICTNIVESGLDIQNANTIIVQD 378
++Q FP IAI G +L ++F +IL+ TN+ G+DI+ N D
Sbjct: 270 LVEQNFPA--IAIHRGMPQEERLSR-YQQFKDFQRRILVATNLFGRGMDIERVNIAFNYD 326
Query: 379 VQQFGLAQLYQLRGRVGRADKEAHAYLFYPDKS 411
+ + L+++ R GR + A F D++
Sbjct: 327 MPEDSDTYLHRV-ARAGRFGTKGLAITFVSDEN 358
>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56
Length = 390
Score = 32.7 bits (73), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 25/93 (26%), Positives = 43/93 (46%), Gaps = 4/93 (4%)
Query: 319 FLQQAFPGVDIAIAHGQQYSRQLEETMEKFAQGAIKILICTNIVESGLDIQNANTIIVQD 378
++Q FP IAI G +L ++F +IL+ TN+ G+DI+ N D
Sbjct: 269 LVEQNFPA--IAIHRGMPQEERLSR-YQQFKDFQRRILVATNLFGRGMDIERVNIAFNYD 325
Query: 379 VQQFGLAQLYQLRGRVGRADKEAHAYLFYPDKS 411
+ + L+++ R GR + A F D++
Sbjct: 326 MPEDSDTYLHRV-ARAGRFGTKGLAITFVSDEN 357
>pdb|3CU7|A Chain A, Human Complement Component 5
pdb|3CU7|B Chain B, Human Complement Component 5
pdb|3KLS|A Chain A, Structure Of Complement C5 In Complex With Ssl7
pdb|3KLS|B Chain B, Structure Of Complement C5 In Complex With Ssl7
pdb|3KM9|A Chain A, Structure Of Complement C5 In Complex With The C-Terminal
Beta-Grasp Domain Of Ssl7
pdb|3KM9|B Chain B, Structure Of Complement C5 In Complex With The C-Terminal
Beta-Grasp Domain Of Ssl7
pdb|4E0S|A Chain A, Crystal Structure Of C5b-6
Length = 1676
Score = 32.3 bits (72), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 26/87 (29%), Positives = 46/87 (52%), Gaps = 3/87 (3%)
Query: 184 EEHLDMIKHGHLNIIVGTHSLLGSRVVYNNLGLLVVDEEQRFGVKQKEKIASFKISVDV- 242
+ H ++ HLNIIV S ++ + N +L + FG ++K AS++ S+++
Sbjct: 471 DNHKALLVGEHLNIIVTPKSPYIDKITHYNYLILSKGKIIHFGTREKFSDASYQ-SINIP 529
Query: 243 LTLSATPIPRTL-YLALTGFRDASLIS 268
+T + P R L Y +TG + A L+S
Sbjct: 530 VTQNMVPSSRLLVYYIVTGEQTAELVS 556
>pdb|3PRX|A Chain A, Structure Of Complement C5 In Complex With Cvf And Ssl7
pdb|3PRX|C Chain C, Structure Of Complement C5 In Complex With Cvf And Ssl7
pdb|3PVM|A Chain A, Structure Of Complement C5 In Complex With Cvf
pdb|3PVM|C Chain C, Structure Of Complement C5 In Complex With Cvf
Length = 1676
Score = 32.3 bits (72), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 26/87 (29%), Positives = 46/87 (52%), Gaps = 3/87 (3%)
Query: 184 EEHLDMIKHGHLNIIVGTHSLLGSRVVYNNLGLLVVDEEQRFGVKQKEKIASFKISVDV- 242
+ H ++ HLNIIV S ++ + N +L + FG ++K AS++ S+++
Sbjct: 471 DNHKALLVGEHLNIIVTPKSPYIDKITHYNYLILSKGKIIHFGTREKFSDASYQ-SINIP 529
Query: 243 LTLSATPIPRTL-YLALTGFRDASLIS 268
+T + P R L Y +TG + A L+S
Sbjct: 530 VTQNMVPSSRLLVYYIVTGEQTAELVS 556
>pdb|4DDT|A Chain A, Thermotoga Maritima Reverse Gyrase, C2 Form 2
pdb|4DDU|A Chain A, Thermotoga Maritima Reverse Gyrase, C2 Form 1
pdb|4DDV|A Chain A, Thermotoga Maritima Reverse Gyrase, Triclinic Form
pdb|4DDV|B Chain B, Thermotoga Maritima Reverse Gyrase, Triclinic Form
pdb|4DDW|A Chain A, Thermotoga Maritima Reverse Gyrase, C-centered
Orthorhombic Form
pdb|4DDX|A Chain A, Thermotoga Maritima Reverse Gyrase, Primitive Monoclinic
Form
pdb|4DDX|B Chain B, Thermotoga Maritima Reverse Gyrase, Primitive Monoclinic
Form
Length = 1104
Score = 32.3 bits (72), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 27/59 (45%), Gaps = 4/59 (6%)
Query: 121 GFGKTEVALRAIFCVVSAGKQAMVLAPTIVLAKQHFDVVSERFSKYPDIKVGLLSRFQS 179
G GKT + + GK++ ++ PT+ L KQ ER K D KV + + S
Sbjct: 103 GVGKTTFGMMTALWLARKGKKSALVFPTVTLVKQTL----ERLQKLADEKVKIFGFYSS 157
>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 = 32.3 bits (72), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 40/79 (50%), Gaps = 4/79 (5%)
Query: 330 AIAHGQQYSRQLEETMEKFAQGAIKILICTNIVESGLDIQNANTIIVQDVQQFGLAQLY- 388
AI H + + EE +E F G + ++ + +++ G+D+ +AN ++ + G A+ Y
Sbjct: 373 AITH-RTSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVI--MSGSGSAREYI 429
Query: 389 QLRGRVGRADKEAHAYLFY 407
Q GR+ R K + Y
Sbjct: 430 QRLGRILRPSKGKKEAVLY 448
>pdb|4A5W|A Chain A, Crystal Structure Of C5b6
Length = 1580
Score = 32.3 bits (72), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 26/87 (29%), Positives = 46/87 (52%), Gaps = 3/87 (3%)
Query: 184 EEHLDMIKHGHLNIIVGTHSLLGSRVVYNNLGLLVVDEEQRFGVKQKEKIASFKISVDV- 242
+ H ++ HLNIIV S ++ + N +L + FG ++K AS++ S+++
Sbjct: 453 DNHKALLVGEHLNIIVTPKSPYIDKITHYNYLILSKGKIIHFGTREKFSDASYQ-SINIP 511
Query: 243 LTLSATPIPRTL-YLALTGFRDASLIS 268
+T + P R L Y +TG + A L+S
Sbjct: 512 VTQNMVPSSRLLVYYIVTGEQTAELVS 538
>pdb|3P4Y|A Chain A, Helicase Domain Of Reverse Gyrase From Thermotoga Maritima
- P2 Form
Length = 415
Score = 32.0 bits (71), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 28/64 (43%), Gaps = 4/64 (6%)
Query: 116 ICGDVGFGKTEVALRAIFCVVSAGKQAMVLAPTIVLAKQHFDVVSERFSKYPDIKVGLLS 175
+ G GKT + + GK++ ++ PT+ L KQ ER K D KV +
Sbjct: 42 MVAPTGVGKTTFGMMTALWLARKGKKSALVFPTVTLVKQTL----ERLQKLADEKVKIFG 97
Query: 176 RFQS 179
+ S
Sbjct: 98 FYSS 101
>pdb|3OIY|A Chain A, Helicase Domain Of Reverse Gyrase From Thermotoga Maritima
pdb|3OIY|B Chain B, Helicase Domain Of Reverse Gyrase From Thermotoga Maritima
Length = 414
Score = 32.0 bits (71), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 28/64 (43%), Gaps = 4/64 (6%)
Query: 116 ICGDVGFGKTEVALRAIFCVVSAGKQAMVLAPTIVLAKQHFDVVSERFSKYPDIKVGLLS 175
+ G GKT + + GK++ ++ PT+ L KQ ER K D KV +
Sbjct: 41 MVAPTGVGKTTFGMMTALWLARKGKKSALVFPTVTLVKQTL----ERLQKLADEKVKIFG 96
Query: 176 RFQS 179
+ S
Sbjct: 97 FYSS 100
>pdb|3P4X|A Chain A, Helicase Domain Of Reverse Gyrase From Thermotoga Maritima
pdb|3P4X|B Chain B, Helicase Domain Of Reverse Gyrase From Thermotoga Maritima
Length = 413
Score = 32.0 bits (71), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 28/64 (43%), Gaps = 4/64 (6%)
Query: 116 ICGDVGFGKTEVALRAIFCVVSAGKQAMVLAPTIVLAKQHFDVVSERFSKYPDIKVGLLS 175
+ G GKT + + GK++ ++ PT+ L KQ ER K D KV +
Sbjct: 40 MVAPTGVGKTTFGMMTALWLARKGKKSALVFPTVTLVKQTL----ERLQKLADEKVKIFG 95
Query: 176 RFQS 179
+ S
Sbjct: 96 FYSS 99
>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 = 32.0 bits (71), Expect = 1.1, Method: Composition-based stats.
Identities = 12/43 (27%), Positives = 23/43 (53%)
Query: 333 HGQQYSRQLEETMEKFAQGAIKILICTNIVESGLDIQNANTII 375
HG + E + F QG +++L+ T++ GLDI + ++
Sbjct: 62 HGDLSQGERERVLGAFRQGEVRVLVATDVAARGLDIPQVDLVV 104
>pdb|2FZL|A Chain A, Structure Of C-Terminal Domain Of Archaeoglobus Fulgidus
Xpb
Length = 219
Score = 32.0 bits (71), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 40/79 (50%), Gaps = 4/79 (5%)
Query: 330 AIAHGQQYSRQLEETMEKFAQGAIKILICTNIVESGLDIQNANTIIVQDVQQFGLAQLY- 388
AI H + + EE +E F G + ++ + +++ G+D+ +AN ++ + G A+ Y
Sbjct: 138 AITH-RTSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVI--MSGSGSAREYI 194
Query: 389 QLRGRVGRADKEAHAYLFY 407
Q GR+ R K + Y
Sbjct: 195 QRLGRILRPSKGKKEAVLY 213
>pdb|1T5I|A Chain A, Crystal Structure Of The C-Terminal Domain Of Uap56
Length = 172
Score = 31.6 bits (70), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 25/93 (26%), Positives = 43/93 (46%), Gaps = 4/93 (4%)
Query: 319 FLQQAFPGVDIAIAHGQQYSRQLEETMEKFAQGAIKILICTNIVESGLDIQNANTIIVQD 378
++Q FP IAI G +L ++F +IL+ TN+ G+DI+ N D
Sbjct: 51 LVEQNFPA--IAIHRGMPQEERLSR-YQQFKDFQRRILVATNLFGRGMDIERVNIAFNYD 107
Query: 379 VQQFGLAQLYQLRGRVGRADKEAHAYLFYPDKS 411
+ + L+++ R GR + A F D++
Sbjct: 108 MPEDSDTYLHRV-ARAGRFGTKGLAITFVSDEN 139
>pdb|3LY5|A Chain A, Ddx18 Dead-Domain
pdb|3LY5|B Chain B, Ddx18 Dead-Domain
Length = 262
Score = 31.6 bits (70), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 36/126 (28%), Positives = 54/126 (42%), Gaps = 18/126 (14%)
Query: 113 DRLICGDVGFGKTEVAL-RAIFCVVS------AGKQAMVLAPTIVLAKQHFDVVSERFSK 165
D L G GKT L A+ +V G ++L+PT LA Q F V+ E +
Sbjct: 93 DLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNGTGVLILSPTRELAMQTFGVLKELMTH 152
Query: 166 YPDIKVGLLSRFQSKAEKEEHLDMIKHGHLNIIVGTHSLLGSRV------VYNNLGLLVV 219
+ GL+ +++ + + L +NIIV T L + +Y NL LV+
Sbjct: 153 HVH-TYGLIMGGSNRSAEAQKLG----NGINIIVATPGRLLDHMQNTPGFMYKNLQCLVI 207
Query: 220 DEEQRF 225
DE R
Sbjct: 208 DEADRI 213
>pdb|3P5J|A Chain A, The Structure Of The Human Rnase H2 Complex Defines Key
Interaction Interfaces Relevant To Enzyme Function And
Human Disease
Length = 301
Score = 31.2 bits (69), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 29/56 (51%), Gaps = 1/56 (1%)
Query: 277 IKTHLSAFSKEKVISAIKYELDRGGQVFYVLPRIKGLEEPMDF-LQQAFPGVDIAI 331
+K +L++ S + I+Y LD+ V V G+ E LQQ FPG+++ +
Sbjct: 110 VKYNLNSLSHDTAAGLIQYALDQNVNVTQVFVDTVGMPETYQARLQQHFPGIEVTV 165
>pdb|2YKG|A Chain A, Structural Insights Into Rna Recognition By Rig-I
Length = 696
Score = 31.2 bits (69), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 28/49 (57%), Gaps = 2/49 (4%)
Query: 349 AQGAIKILICTNIVESGLDIQNANTIIVQDVQQFGLAQLYQLRGRVGRA 397
A G ILI T++ + G+DI N +I+ + + ++ Q RGR GRA
Sbjct: 458 ASGDHNILIATSVADEGIDIAQCNLVILYEYVG-NVIKMIQTRGR-GRA 504
>pdb|3TMI|A Chain A, Structural Basis For Rna Recognition And Activation Of
Rig-I
Length = 695
Score = 31.2 bits (69), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 28/49 (57%), Gaps = 2/49 (4%)
Query: 349 AQGAIKILICTNIVESGLDIQNANTIIVQDVQQFGLAQLYQLRGRVGRA 397
A G ILI T++ + G+DI N +I+ + + ++ Q RGR GRA
Sbjct: 457 ASGDHNILIATSVADEGIDIAQCNLVILYEYVG-NVIKMIQTRGR-GRA 503
>pdb|4AY2|A Chain A, Capturing 5' Tri-Phosphorylated Rna Duplex By Rig-I
Length = 687
Score = 30.8 bits (68), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 28/49 (57%), Gaps = 2/49 (4%)
Query: 349 AQGAIKILICTNIVESGLDIQNANTIIVQDVQQFGLAQLYQLRGRVGRA 397
A G ILI T++ + G+DI N +I+ + + ++ Q RGR GRA
Sbjct: 449 ASGDHNILIATSVADEGIDIAQCNLVILYEYVG-NVIKMIQTRGR-GRA 495
>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 = 30.8 bits (68), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 19/84 (22%), Positives = 38/84 (45%), Gaps = 5/84 (5%)
Query: 326 GVDIAIAHGQQYSRQLEETMEKFAQGAIKILICTNIVESGLDIQNANTII-----VQDVQ 380
G +++ G+ Q +++F G K+LI TN+ G+D++ ++ V+ +
Sbjct: 58 GHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNVCARGIDVKQVTIVVNFDLPVKQGE 117
Query: 381 QFGLAQLYQLRGRVGRADKEAHAY 404
+ GR GR K+ A+
Sbjct: 118 EPDYETYLHRIGRTGRFGKKGLAF 141
>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 = 30.8 bits (68), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 23/93 (24%), Positives = 43/93 (46%), Gaps = 4/93 (4%)
Query: 326 GVDIAIAHGQQYSRQLEETMEKFAQGAIKILICTNIVESGLDIQNANTIIVQDVQQFGLA 385
GV+ HG + + + +E F +G +L+ T++ GLD +I D+ +
Sbjct: 78 GVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVASKGLDFPAIQHVINYDMPEEIEN 137
Query: 386 QLYQLRGRVGRADKEAHAYLFYP---DKSLLSD 415
++++ GR G + A F D+S+L D
Sbjct: 138 YVHRI-GRTGCSGNTGIATTFINKACDESVLMD 169
>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 = 30.8 bits (68), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 24/35 (68%)
Query: 345 MEKFAQGAIKILICTNIVESGLDIQNANTIIVQDV 379
M++F G+ +ILI T+++ G+D+Q + +I D+
Sbjct: 303 MKEFRSGSSRILISTDLLARGIDVQQVSLVINYDL 337
>pdb|2V1X|A Chain A, Crystal Structure Of Human Recq-Like Dna Helicase
pdb|2V1X|B Chain B, Crystal Structure Of Human Recq-Like Dna Helicase
pdb|2WWY|A Chain A, Structure Of Human Recq-Like Helicase In Complex With A
Dna Substrate
pdb|2WWY|B Chain B, Structure Of Human Recq-Like Helicase In Complex With A
Dna Substrate
Length = 591
Score = 30.4 bits (67), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 20/80 (25%), Positives = 34/80 (42%), Gaps = 6/80 (7%)
Query: 333 HGQQYSRQLE-----ETMEKFAQGAIKILICTNIVESGLDIQNANTIIVQDVQQFGLAQL 387
H Y LE K++ I++++ T G+D + +I + + +
Sbjct: 293 HAGAYHANLEPEDKTTVHRKWSANEIQVVVATVAFGMGIDKPDVRFVIHHSMSK-SMENY 351
Query: 388 YQLRGRVGRADKEAHAYLFY 407
YQ GR GR D +A L+Y
Sbjct: 352 YQESGRAGRDDMKADCILYY 371
>pdb|3OT5|A Chain A, 2.2 Angstrom Resolution Crystal Structure Of Putative
Udp-N- Acetylglucosamine 2-Epimerase From Listeria
Monocytogenes
pdb|3OT5|B Chain B, 2.2 Angstrom Resolution Crystal Structure Of Putative
Udp-N- Acetylglucosamine 2-Epimerase From Listeria
Monocytogenes
pdb|3OT5|C Chain C, 2.2 Angstrom Resolution Crystal Structure Of Putative
Udp-N- Acetylglucosamine 2-Epimerase From Listeria
Monocytogenes
pdb|3OT5|D Chain D, 2.2 Angstrom Resolution Crystal Structure Of Putative
Udp-N- Acetylglucosamine 2-Epimerase From Listeria
Monocytogenes
Length = 403
Score = 30.4 bits (67), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 31/64 (48%), Gaps = 3/64 (4%)
Query: 122 FGKTEVALRAIFCVVSAGKQAMVLAPTIVLAKQH---FDVVSERFSKYPDIKVGLLSRFQ 178
FG A++ V++ K+ T+V+ QH D V E F PDI + ++ + Q
Sbjct: 34 FGTRPEAIKMAPLVLALEKEPETFESTVVITAQHREMLDQVLEIFDIKPDIDLDIMKKGQ 93
Query: 179 SKAE 182
+ AE
Sbjct: 94 TLAE 97
>pdb|1FUK|A Chain A, Crystal Structure Of The Carboxy Terminal Domain Of Yeast
Eif4a
Length = 165
Score = 30.4 bits (67), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 24/35 (68%)
Query: 345 MEKFAQGAIKILICTNIVESGLDIQNANTIIVQDV 379
M++F G+ +ILI T+++ G+D+Q + +I D+
Sbjct: 73 MKEFRSGSSRILISTDLLARGIDVQQVSLVINYDL 107
>pdb|3KIO|A Chain A, Mouse Rnase H2 Complex
Length = 301
Score = 30.0 bits (66), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 34/68 (50%), Gaps = 3/68 (4%)
Query: 265 SLISTPPPERLPIKTHLSAFSKEKVISAIKYELDRGGQVFYVLPRIKGLEEPMDF-LQQA 323
+LIST R +K +L++ S + I+Y LD+ V V G E LQQ
Sbjct: 100 NLISTSXLGR--VKYNLNSLSHDTAAGLIQYALDQNVNVTQVFVDTVGXPETYQARLQQH 157
Query: 324 FPGVDIAI 331
FPG+++ +
Sbjct: 158 FPGIEVTV 165
>pdb|2EL7|A Chain A, Crystal Structure Of Tryptophanyl-Trna Synthetase From
Thermus Thermophilus
pdb|2EL7|B Chain B, Crystal Structure Of Tryptophanyl-Trna Synthetase From
Thermus Thermophilus
Length = 337
Score = 29.6 bits (65), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 24/39 (61%)
Query: 272 PERLPIKTHLSAFSKEKVISAIKYELDRGGQVFYVLPRI 310
PER + T+LS F+ + ++ A+K E + G YV+ RI
Sbjct: 235 PERTILFTYLSYFAPKDLVEALKEEYRKAGVGTYVVKRI 273
>pdb|3TBK|A Chain A, Mouse Rig-I Atpase Domain
Length = 555
Score = 29.6 bits (65), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 4/63 (6%)
Query: 345 MEKF-AQGAIKILICTNIVESGLDIQNANTIIVQDVQQFGLAQLYQLRGRVGRADKEAHA 403
+E F A G ILI T++ + G+DI N +I+ + + + Q RGR GRA +++
Sbjct: 444 LEAFRASGDNNILIATSVADEGIDIAECNLVILYEYVG-NVIKXIQTRGR-GRA-RDSKC 500
Query: 404 YLF 406
+L
Sbjct: 501 FLL 503
>pdb|3FHC|B Chain B, Crystal Structure Of Human Dbp5 In Complex With Nup214
Length = 235
Score = 29.6 bits (65), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 31/71 (43%), Gaps = 3/71 (4%)
Query: 109 ETPMDRLICGDVGFGKTEVALRAIFCVVSAGK---QAMVLAPTIVLAKQHFDVVSERFSK 165
E P + + G GKT + A+ V Q + L+PT LA Q V+ +
Sbjct: 62 EPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKF 121
Query: 166 YPDIKVGLLSR 176
YP++K+ R
Sbjct: 122 YPELKLAYAVR 132
>pdb|3FMO|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex
With The Dead- Box Helicase Ddx19
Length = 300
Score = 29.3 bits (64), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 31/71 (43%), Gaps = 3/71 (4%)
Query: 109 ETPMDRLICGDVGFGKTEVALRAIFCVVSAGK---QAMVLAPTIVLAKQHFDVVSERFSK 165
E P + + G GKT + A+ V Q + L+PT LA Q V+ +
Sbjct: 129 EPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKF 188
Query: 166 YPDIKVGLLSR 176
YP++K+ R
Sbjct: 189 YPELKLAYAVR 199
>pdb|1O0W|A Chain A, Crystal Structure Of Ribonuclease Iii (Tm1102) From
Thermotoga Maritima At 2.0 A Resolution
pdb|1O0W|B Chain B, Crystal Structure Of Ribonuclease Iii (Tm1102) From
Thermotoga Maritima At 2.0 A Resolution
Length = 252
Score = 28.9 bits (63), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 13/28 (46%), Positives = 19/28 (67%)
Query: 163 FSKYPDIKVGLLSRFQSKAEKEEHLDMI 190
+ KYP+ +VG L+R +S A EE L M+
Sbjct: 82 YKKYPEAEVGDLARVKSAAASEEVLAMV 109
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.321 0.137 0.397
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,392,052
Number of Sequences: 62578
Number of extensions: 689844
Number of successful extensions: 1708
Number of sequences better than 100.0: 79
Number of HSP's better than 100.0 without gapping: 41
Number of HSP's successfully gapped in prelim test: 38
Number of HSP's that attempted gapping in prelim test: 1638
Number of HSP's gapped (non-prelim): 95
length of query: 643
length of database: 14,973,337
effective HSP length: 105
effective length of query: 538
effective length of database: 8,402,647
effective search space: 4520624086
effective search space used: 4520624086
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 55 (25.8 bits)