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= 000380
(1601 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3C4T|A Chain A, Structure Of Rnaseiiib And Dsrna Binding Domains Of Mouse
Dicer
Length = 265
Score = 135 bits (340), Expect = 2e-31, Method: Compositional matrix adjust.
Identities = 77/193 (39%), Positives = 113/193 (58%), Gaps = 17/193 (8%)
Query: 1214 TLEILLGHQFLHRGLLLQAFVHPSF--NRLGGCYQRLEFLGDAVLDYLITSYLYSVYPKL 1271
T E + ++F ++ LLQAF H S+ N + YQRLEFLGDA+LDYLIT +LY +
Sbjct: 17 TFEKKINYRFKNKAYLLQAFTHASYHYNTITDXYQRLEFLGDAILDYLITKHLYEDPRQH 76
Query: 1272 KPGQLTDLRSMLVNNQAFANVAVDQSFYKFLIFDSNVLSETINNYVDYMITPSSTREVKE 1331
PG LTDLRS LVNN FA++AV ++K+ S L I+++V + + + + +
Sbjct: 77 SPGVLTDLRSALVNNTIFASLAVKYDYHKYFKAVSPELFHVIDDFVKFQLEKNEMQGMDS 136
Query: 1332 GPR-------------CPKVLGDLVESSLGAILLDSGFNLNTVWKIMLSFLDPIL-KFS- 1376
R PK +GD+ ES GAI +DSG +L VW++ + P++ KFS
Sbjct: 137 ELRRSEEDEEKEEDIEVPKAMGDIFESLAGAIYMDSGMSLEVVWQVYYPMMQPLIEKFSA 196
Query: 1377 NLQLNPIRELLEL 1389
N+ +P+RELLE+
Sbjct: 197 NVPRSPVRELLEM 209
Score = 41.6 bits (96), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 37/137 (27%), Positives = 58/137 (42%), Gaps = 19/137 (13%)
Query: 1040 ERLEILGDAFLKYAVGRHLFLLHDTVDEGELTRRRSNAVNNSNLLKLAARNNLQVYIRDQ 1099
+RLE LGDA L Y + +HL+ G LT RS VNN+ LA + + Y +
Sbjct: 51 QRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTIFASLAVKYDYHKYFK-- 108
Query: 1100 PFDPCQFFALGRRCPRICSKETERTIHSQYDGRAPDDLNAEVRCSKGHHWLHK-----KT 1154
P F + + + Q + +++E+R S+ + K
Sbjct: 109 AVSPELFHVI------------DDFVKFQLEKNEMQGMDSELRRSEEDEEKEEDIEVPKA 156
Query: 1155 IADVVEALVGAFIDDSG 1171
+ D+ E+L GA DSG
Sbjct: 157 MGDIFESLAGAIYMDSG 173
>pdb|3C4B|A Chain A, Structure Of Rnaseiiib And Dsrna Binding Domains Of Mouse
Dicer
Length = 265
Score = 129 bits (323), Expect = 2e-29, Method: Compositional matrix adjust.
Identities = 77/192 (40%), Positives = 108/192 (56%), Gaps = 17/192 (8%)
Query: 1214 TLEILLGHQFLHRGLLLQAFVHPSF--NRLGGCYQRLEFLGDAVLDYLITSYLYSVYPKL 1271
T E + ++F ++ LLQAF H S+ N + YQRLEFLGDA+LDYLIT +LY +
Sbjct: 17 TFEKKINYRFKNKAYLLQAFTHASYHYNTITDXYQRLEFLGDAILDYLITKHLYEDPRQH 76
Query: 1272 KPGQLTDLRSMLVNNQAFANVAVDQSFYKFLIFDSNVLSETINNYVDYMITPSSTREVKE 1331
PG LTDLRS LVNN FA++AV ++K+ S L I+++V + + + +
Sbjct: 77 SPGVLTDLRSALVNNTIFASLAVKYDYHKYFKAVSPELFHVIDDFVKFQLEKNEXQGXDS 136
Query: 1332 GPR-------------CPKVLGDLVESSLGAILLDSGFNLNTVWKIMLSFLDPIL-KFS- 1376
R PK GD+ ES GAI DSG +L VW++ P++ KFS
Sbjct: 137 ELRRSEEDEEKEEDIEVPKAXGDIFESLAGAIYXDSGXSLEVVWQVYYPXXQPLIEKFSA 196
Query: 1377 NLQLNPIRELLE 1388
N+ +P+RELLE
Sbjct: 197 NVPRSPVRELLE 208
Score = 39.7 bits (91), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 37/137 (27%), Positives = 56/137 (40%), Gaps = 19/137 (13%)
Query: 1040 ERLEILGDAFLKYAVGRHLFLLHDTVDEGELTRRRSNAVNNSNLLKLAARNNLQVYIRDQ 1099
+RLE LGDA L Y + +HL+ G LT RS VNN+ LA + + Y +
Sbjct: 51 QRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTIFASLAVKYDYHKYFK-- 108
Query: 1100 PFDPCQFFALGRRCPRICSKETERTIHSQYDGRAPDDLNAEVRCSKGHHWLHK-----KT 1154
P F + + + Q + ++E+R S+ + K
Sbjct: 109 AVSPELFHVI------------DDFVKFQLEKNEXQGXDSELRRSEEDEEKEEDIEVPKA 156
Query: 1155 IADVVEALVGAFIDDSG 1171
D+ E+L GA DSG
Sbjct: 157 XGDIFESLAGAIYXDSG 173
>pdb|2KOU|A Chain A, Dicer Like Protein
Length = 102
Score = 126 bits (316), Expect = 1e-28, Method: Compositional matrix adjust.
Identities = 58/99 (58%), Positives = 73/99 (73%), Gaps = 2/99 (2%)
Query: 587 ISAGYGVSLLHRYCSKLPHDEFFNPKPKFYY--FDDLGGTICHIILPANAPIHQIVGTPQ 644
IS G +S++++YCS+LPHDEFF PKP+F + D+ GGTIC I LPANAPI +I +
Sbjct: 1 ISGGSSISMMYKYCSRLPHDEFFQPKPEFQFKPVDEFGGTICRITLPANAPISEIESSLL 60
Query: 645 SSMEAAKKDACLKAIEDLHKLGALNDYLLPQEDNATEDE 683
S EAAKKDACLKA+ +LH LG LND+LLP + EDE
Sbjct: 61 PSTEAAKKDACLKAVHELHNLGVLNDFLLPDSKDEIEDE 99
>pdb|2EB1|A Chain A, Crystal Structure Of The C-Terminal Rnase Iii Domain Of
Human Dicer
pdb|2EB1|B Chain B, Crystal Structure Of The C-Terminal Rnase Iii Domain Of
Human Dicer
pdb|2EB1|C Chain C, Crystal Structure Of The C-Terminal Rnase Iii Domain Of
Human Dicer
Length = 200
Score = 125 bits (315), Expect = 2e-28, Method: Compositional matrix adjust.
Identities = 71/179 (39%), Positives = 103/179 (57%), Gaps = 16/179 (8%)
Query: 1214 TLEILLGHQFLHRGLLLQAFVHPSF--NRLGGCYQRLEFLGDAVLDYLITSYLYSVYPKL 1271
E + ++F ++ LLQAF H S+ N + CYQRLEFLGDA+LDYLIT +LY +
Sbjct: 10 NFEKKINYRFKNKAYLLQAFTHASYHYNTITDCYQRLEFLGDAILDYLITKHLYEDPRQH 69
Query: 1272 KPGQLTDLRSMLVNNQAFANVAVDQSFYKFLIFDSNVLSETINNYVDYMITPSSTREVKE 1331
PG LTDLRS LVNN FA++AV ++K+ S L I+++V + + + + +
Sbjct: 70 SPGVLTDLRSALVNNTIFASLAVKYDYHKYFKAVSPELFHVIDDFVQFQLEKNEMQGMDS 129
Query: 1332 GPR-------------CPKVLGDLVESSLGAILLDSGFNLNTVWKIMLSFLDPIL-KFS 1376
R PK +GD+ ES GAI +DSG +L TVW++ + P++ KFS
Sbjct: 130 ELRRSEEDEEKEEDIEVPKAMGDIFESLAGAIYMDSGMSLETVWQVYYPMMRPLIEKFS 188
Score = 43.1 bits (100), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 38/144 (26%), Positives = 60/144 (41%), Gaps = 19/144 (13%)
Query: 1040 ERLEILGDAFLKYAVGRHLFLLHDTVDEGELTRRRSNAVNNSNLLKLAARNNLQVYIRDQ 1099
+RLE LGDA L Y + +HL+ G LT RS VNN+ LA + + Y +
Sbjct: 44 QRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTIFASLAVKYDYHKYFK-- 101
Query: 1100 PFDPCQFFALGRRCPRICSKETERTIHSQYDGRAPDDLNAEVRCSKGHHWLHK-----KT 1154
P F + + + Q + +++E+R S+ + K
Sbjct: 102 AVSPELFHVI------------DDFVQFQLEKNEMQGMDSELRRSEEDEEKEEDIEVPKA 149
Query: 1155 IADVVEALVGAFIDDSGFKAATAF 1178
+ D+ E+L GA DSG T +
Sbjct: 150 MGDIFESLAGAIYMDSGMSLETVW 173
>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 = 125 bits (313), Expect = 3e-28, Method: Compositional matrix adjust.
Identities = 143/540 (26%), Positives = 250/540 (46%), Gaps = 87/540 (16%)
Query: 60 RKYQLELCKKAME-ENIIVYLGTGCGKTHIAVLLIYELAHLIRKPQKS---ICIFLAPTV 115
R YQ+E+ + A+E +NII+ L TGCGKT +AV + + HL +K + S I L V
Sbjct: 9 RPYQMEVAQPALEGKNIIICLPTGCGKTRVAVYIAKD--HLDKKKKASEPGKVIVLVNKV 66
Query: 116 ALVQQQAKVIEESIGFKVRTFCGGSKRLKSHCDWEKEIDQYEVLVMIPQILLYCLYH--- 172
LV+Q + + K G S + + + + ++++ QIL L +
Sbjct: 67 LLVEQLFRKEFQPFLKKWYRVIGLSGDTQLKISFPEVVKSCDIIISTAQILENSLLNLEN 126
Query: 173 ---RFIKMELIALLIFDECHHAQVKSNHPYAKIMKDFY-------------KPDIMKVPR 216
+++ +L+I DECHH ++ Y IM+ + KP ++ +P+
Sbjct: 127 GEDAGVQLSDFSLIIIDECHHTNKEA--VYNNIMRHYLMQKLKNNRLKKENKP-VIPLPQ 183
Query: 217 IFGMTASPVVG---KGASAQANLPK--------SINSLENLLD---------AKVYSVED 256
I G+TASP VG K A A+ ++ K +I +++ LD K +++ D
Sbjct: 184 ILGLTASPGVGGATKQAKAEEHILKLCANLDAFTIKTVKENLDQLKNQIQEPCKKFAIAD 243
Query: 257 AEDLESF------VSSPVVRVYQYGPVINDTSSSYVTCSEQLAEIKREQYISALSRKLHD 310
A + F + + + Q P+ + + Y + Q+ E K + + R +
Sbjct: 244 ATREDPFKEKLLEIMTRIQTYCQMSPMSDFGTQPYEQWAIQM-EKKAAKEGNRKERVCAE 302
Query: 311 HQSLRNTTKQLNRLHDSMKFCLENLGVCGALHASYILLSGDETMRNELIEAEGNTIDDSL 370
H N Q+N D+++ +Y L ET NE + + I+D L
Sbjct: 303 HLRKYNEALQIN---DTIRMI-----------DAYTHL---ETFYNEEKDKKFAVIEDDL 345
Query: 371 ---CRFASQASEVFAAICRRDGIASDLSCIEVLKEPFF-SKKLLRLIG-ILSTF-RLQQH 424
+ + + + L+ + P + ++KL +L I+ + R ++
Sbjct: 346 KKPLKLDETDRFLMTLFFENNKMLKRLA-----ENPEYENEKLTKLRNTIMEQYTRTEES 400
Query: 425 MKCIVFVNRIVTARALS-YILQNLKFL-ASWRCHFLVGV--NAGLKSMSRNAMKSILEKF 480
+ I+F +A ALS +I +N KF + H L+G ++ K M++N K ++ KF
Sbjct: 401 ARGIIFTKTRQSAYALSQWITENEKFAEVGVKAHHLIGAGHSSEFKPMTQNEQKEVISKF 460
Query: 481 RSGELNLLVATKVGEEGLDIQTCCLVIRFDLPETVASFIQSRGRARMPQSEYAFLVDSGN 540
R+G++NLL+AT V EEGLDI+ C +VIR+ L + +Q+RGRAR +S Y + SG+
Sbjct: 461 RTGKINLLIATTVAEEGLDIKECNIVIRYGLVTNEIAMVQARGRARADESTYVLVAHSGS 520
>pdb|4A2W|A Chain A, Structure Of Full-Length Duck Rig-I
pdb|4A2W|B Chain B, Structure Of Full-Length Duck Rig-I
Length = 936
Score = 119 bits (298), Expect = 1e-26, Method: Compositional matrix adjust.
Identities = 143/542 (26%), Positives = 251/542 (46%), Gaps = 60/542 (11%)
Query: 59 ARKYQLELCKKAME-ENIIVYLGTGCGKTHIAVLLIYELAHLIRKPQKSICIFLAPTVAL 117
AR YQ+EL + A+ +N ++ TG GKT +++L+ + +K+ +FLA V +
Sbjct: 249 ARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPV 308
Query: 118 VQQQAKVIE---ESIGFKVRTFCGGSKRLKSHCDWEKEIDQYEVLVMIPQILLYCLYH-R 173
+QQ V + E G+ V+ G + S+ EK I+ +++V+ PQIL+
Sbjct: 309 YEQQKNVFKHHFERQGYSVQGISGEN---FSNVSVEKVIEDSDIIVVTPQILVNSFEDGT 365
Query: 174 FIKMELIALLIFDECHHAQVKSNHPYAKIMKDFYKPDI---MKVPRIFGMTASPVVGKGA 230
+ + L+IFDECH+ NHPY +M + + ++P+I G+TAS VG
Sbjct: 366 LTSLSIFTLMIFDECHN--TTGNHPYNVLMTRYLEQKFNSASQLPQILGLTASVGVGNAK 423
Query: 231 SAQANLPKSINSLENLLDAKVYSV--EDAEDLESFVSSPVVRVYQYGPVINDTSSSYVT- 287
+ + + + I SL + LD + S E+ ++L+ F++ P + V I++ ++ ++
Sbjct: 424 NIEETI-EHICSLCSYLDIQAISTVRENIQELQRFMNKPEIDVRLVKRRIHNPFAAIISN 482
Query: 288 -CSEQLAEIKREQYISALSR--------KLHDHQSLRNTTK-QLNRLHDSMKFCLENLGV 337
SE A ++ Y+ LS+ + ++H + K +L +L D E +
Sbjct: 483 LMSETEALMRTIAYVDTLSQNSKKDFGTQNYEHWIVVTQRKCRLLQLEDKE----EESRI 538
Query: 338 CGALHASYILLSGDETMRNELIEAEGNTIDDSLCRFASQASEVFAAICRRDG----IASD 393
C AL +I + LI +E I D+L S +E F + ++G +
Sbjct: 539 CRAL---FICTEHLRKYNDALIISEDARIIDAL----SYLTEFFTNV--KNGPYTELEQH 589
Query: 394 LSCIEVLKEPFF----------SKKLLRLIGIL-STFRLQQHMKCIVFVNRIVTARALSY 442
L+ KEP + KL L+ IL +R + ++F AL
Sbjct: 590 LTAKFQEKEPELIALSKDETNENPKLEELVCILDDAYRYNPQTRTLLFAKTRALVSALKK 649
Query: 443 ILQNLKFLASWRCHFLVGVNAGLKS--MSRNAMKSILEKFRSGELN-LLVATKVGEEGLD 499
++ L + L+G ++ M+ + K +L+ F++ + N LL+AT V +EG+D
Sbjct: 650 CMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGID 709
Query: 500 IQTCCLVIRFDLPETVASFIQSRGRARMPQSEYAFLVDSGNQRELDLIKNFSKEEDRMNR 559
I C LV+ ++ V IQ RGR R S+ LV S + + N KEE MN+
Sbjct: 710 IVQCNLVVLYEYSGNVTKMIQVRGRGRAAGSK-CILVTSKTEVVENEKCNRYKEE-MMNK 767
Query: 560 EI 561
+
Sbjct: 768 AV 769
>pdb|3TMI|A Chain A, Structural Basis For Rna Recognition And Activation Of
Rig-I
Length = 695
Score = 119 bits (297), Expect = 2e-26, Method: Compositional matrix adjust.
Identities = 152/554 (27%), Positives = 246/554 (44%), Gaps = 70/554 (12%)
Query: 60 RKYQLELCKKAME-ENIIVYLGTGCGKTHIAVLLIYELAHLIRKP--QKSICIFLAPTVA 116
R YQLEL AM+ +N I+ TGCGKT +++L+ HL + P QK +F A +
Sbjct: 14 RNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEH--HLKKFPQGQKGKVVFFANQIP 71
Query: 117 LVQQQAKVIE---ESIGFKVRTFCGGSKRLKSHCDWEKEIDQYEVLVMIPQILLYCLYHR 173
+ +QQ V E G++V G + + E+ ++ +++++ PQIL+ L
Sbjct: 72 VYEQQKSVFSKYFERHGYRVTGISGAT---AENVPVEQIVENNDIIILTPQILVNNLKKG 128
Query: 174 FI-KMELIALLIFDECHHAQVKSNHPYAKIMKDFYKPDI----MKVPRIFGMTASPVVGK 228
I + + L+IFDECH+ HPY IM ++ + +P++ G+TAS VG
Sbjct: 129 TIPSLSIFTLMIFDECHNTS--KQHPYNMIMFNYLDQKLGGSSGPLPQVIGLTASVGVGD 186
Query: 229 GASAQANLPKSINSLENLLDAKVYSV--EDAEDLESFVSSPVVRVYQYGPVINDTSSSYV 286
+ L I L LDA V + + E+LE V P + I+D Y+
Sbjct: 187 AKNTDEAL-DYICKLCASLDASVIATVKHNLEELEQVVYKPQKFFRKVESRISD-KFKYI 244
Query: 287 TCSEQLAEIKREQYISALSRKLHDHQSLRNTTKQLNRLHDSMKF----------CL---- 332
+A++ R+ +L++++ + L N ++ NR + K+ C+
Sbjct: 245 -----IAQLMRD--TESLAKRI--CKDLENLSQIQNREFGTQKYEQWIVTVQKACMVFQM 295
Query: 333 ----ENLGVCGALHASYILLSGDETMRNELIEAEGNTIDDSLCRFASQASEVFAAICRRD 388
E +C AL ++ S + LI +E + D+L S V AA D
Sbjct: 296 PDKDEESRICKAL---FLYTSHLRKYNDALIISEHARMKDALDYLKDFFSNVRAA--GFD 350
Query: 389 GIASDLS---------CIEVLKEPFFSK-KLLRLIGILS-TFRLQQHMKCIVFVNRIVTA 437
I DL+ V ++P KL L IL + L I+FV
Sbjct: 351 EIEQDLTQRFEEKLQELESVSRDPSNENPKLEDLCFILQEEYHLNPETITILFVKTRALV 410
Query: 438 RALSYILQNLKFLASWRCHFLVGVNAGLKS--MSRNAMKSILEKFR-SGELNLLVATKVG 494
AL ++ L+ + L G ++ M+ A K IL+ F+ SG+ N+L+AT V
Sbjct: 411 DALKNWIEGNPKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAFKASGDHNILIATSVA 470
Query: 495 EEGLDIQTCCLVIRFDLPETVASFIQSRGRARMPQSEYAFLVDSGNQRELDLIKNFSKEE 554
+EG+DI C LVI ++ V IQ+RGR R S+ L + E + I + +E
Sbjct: 471 DEGIDIAQCNLVILYEYVGNVIKMIQTRGRGRARGSKCFLLTSNAGVIEKEQINMY--KE 528
Query: 555 DRMNREIMDRTSSD 568
MN I+ + D
Sbjct: 529 KMMNDSILRLQTWD 542
>pdb|2YKG|A Chain A, Structural Insights Into Rna Recognition By Rig-I
Length = 696
Score = 117 bits (292), Expect = 7e-26, Method: Compositional matrix adjust.
Identities = 151/554 (27%), Positives = 245/554 (44%), Gaps = 70/554 (12%)
Query: 60 RKYQLELCKKAME-ENIIVYLGTGCGKTHIAVLLIYELAHLIRKP--QKSICIFLAPTVA 116
R YQLEL AM+ +N I+ TGCGKT +++L+ HL + P QK +F A +
Sbjct: 15 RNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEH--HLKKFPQGQKGKVVFFANQIP 72
Query: 117 LVQQQAKVIE---ESIGFKVRTFCGGSKRLKSHCDWEKEIDQYEVLVMIPQILLYCLYHR 173
+ +Q V E G++V G + + E+ ++ +++++ PQIL+ L
Sbjct: 73 VYEQNKSVFSKYFERHGYRVTGISGAT---AENVPVEQIVENNDIIILTPQILVNNLKKG 129
Query: 174 FI-KMELIALLIFDECHHAQVKSNHPYAKIMKDFYKPDI----MKVPRIFGMTASPVVGK 228
I + + L+IFDECH+ HPY IM ++ + +P++ G+TAS VG
Sbjct: 130 TIPSLSIFTLMIFDECHNTS--KQHPYNMIMFNYLDQKLGGSSGPLPQVIGLTASVGVGD 187
Query: 229 GASAQANLPKSINSLENLLDAKVYSV--EDAEDLESFVSSPVVRVYQYGPVINDTSSSYV 286
+ L I L LDA V + + E+LE V P + I+D Y+
Sbjct: 188 AKTTDEAL-DYICKLCASLDASVIATVKHNLEELEQVVYKPQKFFRKVESRISD-KFKYI 245
Query: 287 TCSEQLAEIKREQYISALSRKLHDHQSLRNTTKQLNRLHDSMKF----------CL---- 332
+A++ R+ +L++++ + L N ++ NR + K+ C+
Sbjct: 246 -----IAQLMRD--TESLAKRI--CKDLENLSQIQNREFGTQKYEQWIVTVQKACMVFQM 296
Query: 333 ----ENLGVCGALHASYILLSGDETMRNELIEAEGNTIDDSLCRFASQASEVFAAICRRD 388
E +C AL ++ S + LI +E + D+L S V AA D
Sbjct: 297 PDKDEESRICKAL---FLYTSHLRKYNDALIISEHARMKDALDYLKDFFSNVRAA--GFD 351
Query: 389 GIASDLS---------CIEVLKEPFFSK-KLLRLIGILS-TFRLQQHMKCIVFVNRIVTA 437
I DL+ V ++P KL L IL + L I+FV
Sbjct: 352 EIEQDLTQRFEEKLQELESVSRDPSNENPKLEDLCFILQEEYHLNPETITILFVKTRALV 411
Query: 438 RALSYILQNLKFLASWRCHFLVGVNAGLKS--MSRNAMKSILEKFR-SGELNLLVATKVG 494
AL ++ L+ + L G ++ M+ A K IL+ F+ SG+ N+L+AT V
Sbjct: 412 DALKNWIEGNPKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAFKASGDHNILIATSVA 471
Query: 495 EEGLDIQTCCLVIRFDLPETVASFIQSRGRARMPQSEYAFLVDSGNQRELDLIKNFSKEE 554
+EG+DI C LVI ++ V IQ+RGR R S+ L + E + I + +E
Sbjct: 472 DEGIDIAQCNLVILYEYVGNVIKMIQTRGRGRARGSKCFLLTSNAGVIEKEQINMY--KE 529
Query: 555 DRMNREIMDRTSSD 568
MN I+ + D
Sbjct: 530 KMMNDSILRLQTWD 543
>pdb|4AY2|A Chain A, Capturing 5' Tri-Phosphorylated Rna Duplex By Rig-I
Length = 687
Score = 116 bits (291), Expect = 8e-26, Method: Compositional matrix adjust.
Identities = 151/554 (27%), Positives = 245/554 (44%), Gaps = 70/554 (12%)
Query: 60 RKYQLELCKKAME-ENIIVYLGTGCGKTHIAVLLIYELAHLIRKP--QKSICIFLAPTVA 116
R YQLEL AM+ +N I+ TGCGKT +++L+ HL + P QK +F A +
Sbjct: 6 RNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEH--HLKKFPQGQKGKVVFFANQIP 63
Query: 117 LVQQQAKVIE---ESIGFKVRTFCGGSKRLKSHCDWEKEIDQYEVLVMIPQILLYCLYHR 173
+ +Q V E G++V G + + E+ ++ +++++ PQIL+ L
Sbjct: 64 VYEQNKSVFSKYFERHGYRVTGISGAT---AENVPVEQIVENNDIIILTPQILVNNLKKG 120
Query: 174 FI-KMELIALLIFDECHHAQVKSNHPYAKIMKDFYKPDI----MKVPRIFGMTASPVVGK 228
I + + L+IFDECH+ HPY IM ++ + +P++ G+TAS VG
Sbjct: 121 TIPSLSIFTLMIFDECHNTS--KQHPYNMIMFNYLDQKLGGSSGPLPQVIGLTASVGVGD 178
Query: 229 GASAQANLPKSINSLENLLDAKVYSV--EDAEDLESFVSSPVVRVYQYGPVINDTSSSYV 286
+ L I L LDA V + + E+LE V P + I+D Y+
Sbjct: 179 AKNTDEAL-DYICKLCASLDASVIATVKHNLEELEQVVYKPQKFFRKVESRISD-KFKYI 236
Query: 287 TCSEQLAEIKREQYISALSRKLHDHQSLRNTTKQLNRLHDSMKF----------CL---- 332
+A++ R+ +L++++ + L N ++ NR + K+ C+
Sbjct: 237 -----IAQLMRD--TESLAKRI--CKDLENLSQIQNREFGTQKYEQWIVTVQKACMVFQM 287
Query: 333 ----ENLGVCGALHASYILLSGDETMRNELIEAEGNTIDDSLCRFASQASEVFAAICRRD 388
E +C AL ++ S + LI +E + D+L S V AA D
Sbjct: 288 PDKDEESRICKAL---FLYTSHLRKYNDALIISEHARMKDALDYLKDFFSNVRAA--GFD 342
Query: 389 GIASDLS---------CIEVLKEPFFSK-KLLRLIGILS-TFRLQQHMKCIVFVNRIVTA 437
I DL+ V ++P KL L IL + L I+FV
Sbjct: 343 EIEQDLTQRFEEKLQELESVSRDPSNENPKLEDLCFILQEEYHLNPETITILFVKTRALV 402
Query: 438 RALSYILQNLKFLASWRCHFLVGVNAGLKS--MSRNAMKSILEKFR-SGELNLLVATKVG 494
AL ++ L+ + L G ++ M+ A K IL+ F+ SG+ N+L+AT V
Sbjct: 403 DALKNWIEGNPKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAFKASGDHNILIATSVA 462
Query: 495 EEGLDIQTCCLVIRFDLPETVASFIQSRGRARMPQSEYAFLVDSGNQRELDLIKNFSKEE 554
+EG+DI C LVI ++ V IQ+RGR R S+ L + E + I + +E
Sbjct: 463 DEGIDIAQCNLVILYEYVGNVIKMIQTRGRGRARGSKCFLLTSNAGVIEKEQINMY--KE 520
Query: 555 DRMNREIMDRTSSD 568
MN I+ + D
Sbjct: 521 KMMNDSILRLQTWD 534
>pdb|3TBK|A Chain A, Mouse Rig-I Atpase Domain
Length = 555
Score = 116 bits (290), Expect = 1e-25, Method: Compositional matrix adjust.
Identities = 140/520 (26%), Positives = 230/520 (44%), Gaps = 56/520 (10%)
Query: 60 RKYQLELCKKAME-ENIIVYLGTGCGKTHIAVLLIYELAHLIRKP--QKSICIFLAPTVA 116
R YQLEL A + +N I+ TGCGKT +++L+ HL + P QK +F A +
Sbjct: 6 RNYQLELALPAKKGKNTIICAPTGCGKTFVSLLICEH--HLKKFPCGQKGKVVFFANQIP 63
Query: 117 LVQQQAKVIE---ESIGFKVRTFCGGSKRLKSHCDWEKEIDQYEVLVMIPQILLYCLYHR 173
+ +QQA V E +G+ + + G + + I+ +++++ PQIL+ L +
Sbjct: 64 VYEQQATVFSRYFERLGYNIASISGAT---SDSVSVQHIIEDNDIIILTPQILVNNLNNG 120
Query: 174 FI-KMELIALLIFDECHHAQVKSNHPYAKIMKDFYKPDIMK----VPRIFGMTASPVVGK 228
I + + L IFDECH+ NHPY +I + + + +P++ G+TAS VG
Sbjct: 121 AIPSLSVFTLXIFDECHNTS--KNHPYNQIXFRYLDHKLGESRDPLPQVVGLTASVGVGD 178
Query: 229 GASAQANLPKSINSLENLLDAKVYSV--EDAEDLESFVSSP--VVRVYQYGPVINDTSSS 284
+A+ + I L LDA V + ++ +LE V P + R V + TS++
Sbjct: 179 AKTAE-EAXQHICKLCAALDASVIATVRDNVAELEQVVYKPQKISR-----KVASRTSNT 232
Query: 285 YVTCSEQLAEIKREQYISALSRKLHDHQSLRN----TTKQLNRLHDSMKFCL-------- 332
+ QL + + E+ +S +L ++N T K + K C
Sbjct: 233 FKCIISQLXK-ETEKLAKDVSEELGKLFQIQNREFGTQKYEQWIVGVHKACSVFQXADKE 291
Query: 333 ENLGVCGALHASYILLSGDETMRNELIEAEGNTIDDSLCRFASQASEVFAAI-------C 385
E VC AL ++ S + LI +E D+L + +V A
Sbjct: 292 EESRVCKAL---FLYTSHLRKYNDALIISEDAQXTDALNYLKAFFHDVREAAFDETEREL 348
Query: 386 RRDGIASDLSCIEVLKEPFFSKKLLRLIGIL--STFRLQQHMKCIVFVNRIVTARALSYI 443
R +V ++P LR + ++ + L+ K I+FV AL
Sbjct: 349 TRRFEEKLEELEKVSRDPSNENPKLRDLYLVLQEEYHLKPETKTILFVKTRALVDALKKW 408
Query: 444 LQNLKFLASWRCHFLVGVNAGLKSMSRN--AMKSILEKFR-SGELNLLVATKVGEEGLDI 500
++ L+ + L G ++ A K +LE FR SG+ N+L+AT V +EG+DI
Sbjct: 409 IEENPALSFLKPGILTGRGRTNRATGXTLPAQKCVLEAFRASGDNNILIATSVADEGIDI 468
Query: 501 QTCCLVIRFDLPETVASFIQSRGRARMPQSEYAFLVDSGN 540
C LVI ++ V IQ+RGR R S+ L S +
Sbjct: 469 AECNLVILYEYVGNVIKXIQTRGRGRARDSKCFLLTSSAD 508
>pdb|4A2Q|A Chain A, Structure Of Duck Rig-I Tandem Cards And Helicase Domain
pdb|4A2Q|B Chain B, Structure Of Duck Rig-I Tandem Cards And Helicase Domain
pdb|4A2Q|D Chain D, Structure Of Duck Rig-I Tandem Cards And Helicase Domain
pdb|4A2Q|E Chain E, Structure Of Duck Rig-I Tandem Cards And Helicase Domain
Length = 797
Score = 115 bits (288), Expect = 2e-25, Method: Compositional matrix adjust.
Identities = 133/512 (25%), Positives = 237/512 (46%), Gaps = 58/512 (11%)
Query: 59 ARKYQLELCKKAME-ENIIVYLGTGCGKTHIAVLLIYELAHLIRKPQKSICIFLAPTVAL 117
AR YQ+EL + A+ +N ++ TG GKT +++L+ + +K+ +FLA V +
Sbjct: 249 ARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPV 308
Query: 118 VQQQAKVIE---ESIGFKVRTFCGGSKRLKSHCDWEKEIDQYEVLVMIPQILLYCLYH-R 173
+QQ V + E G+ V+ G + S+ EK I+ +++V+ PQIL+
Sbjct: 309 YEQQKNVFKHHFERQGYSVQGISGEN---FSNVSVEKVIEDSDIIVVTPQILVNSFEDGT 365
Query: 174 FIKMELIALLIFDECHHAQVKSNHPYAKIMKDFYKPDI---MKVPRIFGMTASPVVGKGA 230
+ + L+IFDECH+ NHPY +M + + ++P+I G+TAS VG
Sbjct: 366 LTSLSIFTLMIFDECHN--TTGNHPYNVLMTRYLEQKFNSASQLPQILGLTASVGVGNAK 423
Query: 231 SAQANLPKSINSLENLLDAKVYSV--EDAEDLESFVSSPVVRVYQYGPVINDTSSSYVT- 287
+ + + + I SL + LD + S E+ ++L+ F++ P + V I++ ++ ++
Sbjct: 424 NIEETI-EHICSLCSYLDIQAISTVRENIQELQRFMNKPEIDVRLVKRRIHNPFAAIISN 482
Query: 288 -CSEQLAEIKREQYISALSR--------KLHDHQSLRNTTK-QLNRLHDSMKFCLENLGV 337
SE A ++ + LS+ + ++H + K +L +L D E +
Sbjct: 483 LMSETEALMRTIYSVDTLSQNSKKDFGTQNYEHWIVVTQRKCRLLQLEDKE----EESRI 538
Query: 338 CGALHASYILLSGDETMRNELIEAEGNTIDDSLCRFASQASEVFAAICRRDG----IASD 393
C AL +I + LI +E I D+L S +E F + ++G +
Sbjct: 539 CRAL---FICTEHLRKYNDALIISEDARIIDAL----SYLTEFFTNV--KNGPYTELEQH 589
Query: 394 LSCIEVLKEPFF----------SKKLLRLIGIL-STFRLQQHMKCIVFVNRIVTARALSY 442
L+ KEP + KL L+ IL +R + ++F AL
Sbjct: 590 LTAKFQEKEPELIALSKDETNENPKLEELVCILDDAYRYNPQTRTLLFAKTRALVSALKK 649
Query: 443 ILQNLKFLASWRCHFLVGVNAGLKS--MSRNAMKSILEKFRSGELN-LLVATKVGEEGLD 499
++ L + L+G ++ M+ + K +L+ F++ + N LL+AT V +EG+D
Sbjct: 650 CMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGID 709
Query: 500 IQTCCLVIRFDLPETVASFIQSRGRARMPQSE 531
I C LV+ ++ V IQ RGR R S+
Sbjct: 710 IVQCNLVVLYEYSGNVTKMIQVRGRGRAAGSK 741
>pdb|4A2P|A Chain A, Structure Of Duck Rig-I Helicase Domain
pdb|4A36|A Chain A, Structure Of Duck Rig-I Helicase Domain Bound To 19-Mer
Dsrna And Atp Transition State Analogue
pdb|4A36|B Chain B, Structure Of Duck Rig-I Helicase Domain Bound To 19-Mer
Dsrna And Atp Transition State Analogue
Length = 556
Score = 115 bits (287), Expect = 3e-25, Method: Compositional matrix adjust.
Identities = 137/524 (26%), Positives = 242/524 (46%), Gaps = 63/524 (12%)
Query: 47 GAQKTDKDPKQIARKYQLELCKKAME-ENIIVYLGTGCGKTHIAVLLIYELAHLIRKPQK 105
GA +T K AR YQ+EL + A+ +N ++ TG GKT +++L+ + +K
Sbjct: 1 GAMETKK-----ARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRK 55
Query: 106 SICIFLAPTVALVQQQAKVIE---ESIGFKVRTFCGGSKRLKSHCDWEKEIDQYEVLVMI 162
+ +FLA V + +QQ V + E G+ V+ G + S+ EK I+ +++V+
Sbjct: 56 AKVVFLATKVPVYEQQKNVFKHHFERQGYSVQGISGEN---FSNVSVEKVIEDSDIIVVT 112
Query: 163 PQILLYCLYH-RFIKMELIALLIFDECHHAQVKSNHPYAKIMKDFYKPDI---MKVPRIF 218
PQIL+ + + L+IFDECH+ NHPY +M + + ++P+I
Sbjct: 113 PQILVNSFEDGTLTSLSIFTLMIFDECHNT--TGNHPYNVLMTRYLEQKFNSASQLPQIL 170
Query: 219 GMTASPVVGKGASAQANLPKSINSLENLLDAKVYSV--EDAEDLESFVSSPVVRVYQYGP 276
G+TAS VG + + + + I SL + LD + S E+ ++L+ F++ P + V
Sbjct: 171 GLTASVGVGNAKNIEETI-EHICSLCSYLDIQAISTVRENIQELQRFMNKPEIDVRLVKR 229
Query: 277 VINDTSSSYVT--CSEQLAEIKREQYISALSR--------KLHDHQSLRNTTK-QLNRLH 325
I++ ++ ++ SE A ++ + LS+ + ++H + K +L +L
Sbjct: 230 RIHNPFAAIISNLMSETEALMRTIYSVDTLSQNSKKDFGTQNYEHWIVVTQRKCRLLQLE 289
Query: 326 DSMKFCLENLGVCGALHASYILLSGDETMRNELIEAEGNTIDDSLCRFASQASEVFAAIC 385
D E +C AL +I + LI +E I D+L S +E F +
Sbjct: 290 DKE----EESRICRAL---FICTEHLRKYNDALIISEDARIIDAL----SYLTEFFTNV- 337
Query: 386 RRDG----IASDLSCIEVLKEPFF----------SKKLLRLIGIL-STFRLQQHMKCIVF 430
++G + L+ KEP + KL L+ IL +R + ++F
Sbjct: 338 -KNGPYTELEQHLTAKFQEKEPELIALSKDETNENPKLEELVCILDDAYRYNPQTRTLLF 396
Query: 431 VNRIVTARALSYILQNLKFLASWRCHFLVGVNAGLKS--MSRNAMKSILEKFRSGELN-L 487
AL ++ L + L+G ++ M+ + K +L+ F++ + N L
Sbjct: 397 AKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRL 456
Query: 488 LVATKVGEEGLDIQTCCLVIRFDLPETVASFIQSRGRARMPQSE 531
L+AT V +EG+DI C LV+ ++ V IQ RGR R S+
Sbjct: 457 LIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGRGRAAGSK 500
>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 = 89.7 bits (221), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 130/486 (26%), Positives = 210/486 (43%), Gaps = 58/486 (11%)
Query: 60 RKYQLELCKKAMEENIIVYLGTGCGKTHIAVLLI-YELAHLIRKPQKSICIFLAPTVALV 118
R YQ + K E N ++ L TG GKT IA+++ Y L K + LAPT LV
Sbjct: 11 RIYQEVIYAKCKETNCLIVLPTGLGKTLIAMMIAEYRLTKYGGK-----VLMLAPTKPLV 65
Query: 119 QQQAKVIEESIGF---KVRTFCGGSKRLKSHCDWEKEIDQYEVLVMIPQILLYCLYHRFI 175
Q A+ K+ G KS + K + +V+V PQ + L I
Sbjct: 66 LQHAESFRRLFNLPPEKIVALTGE----KSPEERSKAWARAKVIVATPQTIENDLLAGRI 121
Query: 176 KMELIALLIFDECHHAQVKSNHPYAKIMKDFYKPDIMKVPRIFGMTASPVVGKGASAQAN 235
+E ++L++FDE H A N+ Y I +++ + K P + G+TASP S
Sbjct: 122 SLEDVSLIVFDEAHRAV--GNYAYVFIAREYKRQ--AKNPLVIGLTASP-----GSTPEK 172
Query: 236 LPKSINSLENLLDAKVYSVEDAEDLESFVSSPVVRVYQYGPVINDTSSSYVTCSEQLAEI 295
+ + IN+L ++ Y E++ D+ P V+ ++ V D Y + L E+
Sbjct: 173 IMEVINNLG--IEHIEYRSENSPDVR-----PYVKGIRFEWVRVDLPEIYKEVRKLLREM 225
Query: 296 KREQYISALSRKLHDHQSLRNTTKQLNR----LHDSMKFCLENLGVCGALHASYILLSGD 351
R+ L + S K++ R +++ M +L HA + L
Sbjct: 226 LRDALKPLAETGLLESSSPDIPKKEVLRAGQIINEEMAKGNHDLRGLLLYHAMALKLHHA 285
Query: 352 ETMRNELIEAEG---------NTIDDSLCRFASQASEVFAAICRRDGIASDLSCIEV-LK 401
EL+E +G +++ + E+F+ + I+ + E+ L
Sbjct: 286 ----IELLETQGLSALRAYIKKLYEEAKAGSTKASKEIFSDKRMKKAISLLVQAKEIGLD 341
Query: 402 EPFFSKKLLRLIGILSTFRLQQHMKCIVFVNRIVTARALSYILQNLKFLASWRCHFLVGV 461
P K L+ I I + +Q+ K IVF N TA+ + N + VG
Sbjct: 342 HPKMDK--LKEI-IREQLQRKQNSKIIVFTNYRETAKKIV----NELVKDGIKAKRFVGQ 394
Query: 462 NA--GLKSMSRNAMKSILEKFRSGELNLLVATKVGEEGLDIQTCCLVIRFD-LPETVASF 518
+ + +S+ K IL++F GE N+LVAT VGEEGLD+ LV+ ++ +P + S
Sbjct: 395 ASKENDRGLSQREQKLILDEFARGEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRS- 453
Query: 519 IQSRGR 524
IQ RGR
Sbjct: 454 IQRRGR 459
>pdb|3O2R|B Chain B, Structural Flexibility In Region Involved In Dimer Formation
Of Nuclease Domain Of Ribonuclase Iii (Rnc) From
Campylobacter Jejuni
pdb|3O2R|D Chain D, Structural Flexibility In Region Involved In Dimer Formation
Of Nuclease Domain Of Ribonuclase Iii (Rnc) From
Campylobacter Jejuni
Length = 144
Score = 81.3 bits (199), Expect = 4e-15, Method: Compositional matrix adjust.
Identities = 51/146 (34%), Positives = 77/146 (52%), Gaps = 19/146 (13%)
Query: 1211 DMATLEILLGHQFLHRGLLLQAFVHPSFNRLGGCYQRLEFLGDAVLDYLITSYLYSVYPK 1270
++ LE L ++F + LL+ A H SF + +RLEFLGDAVLD ++ YL+ + K
Sbjct: 1 NIEKLEQSLTYEFKDKNLLIHALTHKSFXKKSYNNERLEFLGDAVLDLVVGEYLFHKFAK 60
Query: 1271 LKPGQLTDLRSMLVNNQAFANVAVDQSFYKFLIFDSNVLSETINNYVDYMITPSSTREVK 1330
G L+ LR+ LVN ++FA +A N L N D+++ S E
Sbjct: 61 DAEGDLSKLRAALVNEKSFAKIA-------------NSL-----NLGDFILM-SVAEENN 101
Query: 1331 EGPRCPKVLGDLVESSLGAILLDSGF 1356
G P +L D +E+ +GAI L++GF
Sbjct: 102 GGKEKPSILSDALEAIIGAIHLEAGF 127
Score = 43.9 bits (102), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 34/104 (32%), Positives = 51/104 (49%), Gaps = 4/104 (3%)
Query: 1023 MLLKALTTEKCQER-FSLERLEILGDAFLKYAVGRHLFLLHDTVDEGELTRRRSNAVNNS 1081
+L+ ALT + ++ ++ ERLE LGDA L VG +LF EG+L++ R+ VN
Sbjct: 18 LLIHALTHKSFXKKSYNNERLEFLGDAVLDLVVGEYLFHKFAKDAEGDLSKLRAALVNEK 77
Query: 1082 NLLKLAARNNLQVYIRDQPFDPCQFFALGRRCPRICSKETERTI 1125
+ K+A NL +I + G+ P I S E I
Sbjct: 78 SFAKIANSLNLGDFILMSVAEENNG---GKEKPSILSDALEAII 118
>pdb|3N3W|A Chain A, 2.2 Angstrom Resolution Crystal Structure Of Nuclease Domain
Ribonuclase Iii (Rnc) From Campylobacter Jejuni
pdb|3N3W|B Chain B, 2.2 Angstrom Resolution Crystal Structure Of Nuclease Domain
Ribonuclase Iii (Rnc) From Campylobacter Jejuni
Length = 248
Score = 79.0 bits (193), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 53/152 (34%), Positives = 80/152 (52%), Gaps = 24/152 (15%)
Query: 1207 SASLDMATLEILLGHQFLHRGLLLQAFVHPSFNRLGGCY--QRLEFLGDAVLDYLITSYL 1264
+A ++ LE L ++F + LL+ A H SF + Y +RLEFLGDAVLD ++ YL
Sbjct: 23 NAMKNIEKLEQSLTYEFKDKNLLIHALTHKSFKK---SYNNERLEFLGDAVLDLVVGEYL 79
Query: 1265 YSVYPKLKPGQLTDLRSMLVNNQAFANVAVDQSFYKFLIFDSNVLSETINNYVDYMITPS 1324
+ + K G L+ LR+ LVN ++FA +A N L N D+++ S
Sbjct: 80 FHKFAKDAEGDLSKLRAALVNEKSFAKIA-------------NSL-----NLGDFILM-S 120
Query: 1325 STREVKEGPRCPKVLGDLVESSLGAILLDSGF 1356
E G P +L D +E+ +GAI L++GF
Sbjct: 121 VAEENNGGKEKPSILSDALEAIIGAIHLEAGF 152
Score = 47.8 bits (112), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 28/74 (37%), Positives = 43/74 (58%)
Query: 1023 MLLKALTTEKCQERFSLERLEILGDAFLKYAVGRHLFLLHDTVDEGELTRRRSNAVNNSN 1082
+L+ ALT + ++ ++ ERLE LGDA L VG +LF EG+L++ R+ VN +
Sbjct: 44 LLIHALTHKSFKKSYNNERLEFLGDAVLDLVVGEYLFHKFAKDAEGDLSKLRAALVNEKS 103
Query: 1083 LLKLAARNNLQVYI 1096
K+A NL +I
Sbjct: 104 FAKIANSLNLGDFI 117
>pdb|3O2R|A Chain A, Structural Flexibility In Region Involved In Dimer Formation
Of Nuclease Domain Of Ribonuclase Iii (Rnc) From
Campylobacter Jejuni
pdb|3O2R|C Chain C, Structural Flexibility In Region Involved In Dimer Formation
Of Nuclease Domain Of Ribonuclase Iii (Rnc) From
Campylobacter Jejuni
Length = 170
Score = 78.2 bits (191), Expect = 4e-14, Method: Compositional matrix adjust.
Identities = 53/152 (34%), Positives = 80/152 (52%), Gaps = 24/152 (15%)
Query: 1207 SASLDMATLEILLGHQFLHRGLLLQAFVHPSFNRLGGCY--QRLEFLGDAVLDYLITSYL 1264
+A ++ LE L ++F + LL+ A H SF + Y +RLEFLGDAVLD ++ YL
Sbjct: 23 NAMKNIEKLEQSLTYEFKDKNLLIHALTHKSFKK---SYNNERLEFLGDAVLDLVVGEYL 79
Query: 1265 YSVYPKLKPGQLTDLRSMLVNNQAFANVAVDQSFYKFLIFDSNVLSETINNYVDYMITPS 1324
+ + K G L+ LR+ LVN ++FA +A N L N D+++ S
Sbjct: 80 FHKFAKDAEGDLSKLRAALVNEKSFAKIA-------------NSL-----NLGDFILM-S 120
Query: 1325 STREVKEGPRCPKVLGDLVESSLGAILLDSGF 1356
E G P +L D +E+ +GAI L++GF
Sbjct: 121 VAEENNGGKEKPSILSDALEAIIGAIHLEAGF 152
Score = 48.1 bits (113), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 34/103 (33%), Positives = 51/103 (49%), Gaps = 3/103 (2%)
Query: 1023 MLLKALTTEKCQERFSLERLEILGDAFLKYAVGRHLFLLHDTVDEGELTRRRSNAVNNSN 1082
+L+ ALT + ++ ++ ERLE LGDA L VG +LF EG+L++ R+ VN +
Sbjct: 44 LLIHALTHKSFKKSYNNERLEFLGDAVLDLVVGEYLFHKFAKDAEGDLSKLRAALVNEKS 103
Query: 1083 LLKLAARNNLQVYIRDQPFDPCQFFALGRRCPRICSKETERTI 1125
K+A NL +I + G+ P I S E I
Sbjct: 104 FAKIANSLNLGDFILMSVAEENNG---GKEKPSILSDALEAII 143
>pdb|4I1S|A Chain A, Melanoma Differentiation Associated Protein-5 Helicase
Domain Complex With Inhibitor Non-structural Protein V
Length = 243
Score = 66.2 bits (160), Expect = 1e-10, Method: Composition-based stats.
Identities = 37/96 (38%), Positives = 59/96 (61%), Gaps = 4/96 (4%)
Query: 420 RLQQHMKCIVFVNRIVTARALS-YILQNLKFL-ASWRCHFLVGV--NAGLKSMSRNAMKS 475
R ++ + I+F +A ALS +I N KF + H L+G ++ K ++N +
Sbjct: 146 RTEESARGIIFTKTRQSAYALSQWITDNKKFAEVGVKAHHLIGAGHSSEFKPXTQNEQRE 205
Query: 476 ILEKFRSGELNLLVATKVGEEGLDIQTCCLVIRFDL 511
++ KFR+G++NLL+AT V EEGLDI+ C +VIR+ L
Sbjct: 206 VISKFRTGKINLLIATTVAEEGLDIKECNIVIRYGL 241
>pdb|1YYK|A Chain A, Crystal Structure Of Rnase Iii From Aquifex Aeolicus
Complexed With Double-Stranded Rna At 2.5-Angstrom
Resolution
pdb|1YYK|B Chain B, Crystal Structure Of Rnase Iii From Aquifex Aeolicus
Complexed With Double-Stranded Rna At 2.5-Angstrom
Resolution
pdb|1YYW|A Chain A, Crystal Structure Of Rnase Iii From Aquifex Aeolicus
Complexed With Double Stranded Rna At 2.8-Angstrom
Resolution
pdb|1YYW|B Chain B, Crystal Structure Of Rnase Iii From Aquifex Aeolicus
Complexed With Double Stranded Rna At 2.8-Angstrom
Resolution
pdb|1YYW|C Chain C, Crystal Structure Of Rnase Iii From Aquifex Aeolicus
Complexed With Double Stranded Rna At 2.8-Angstrom
Resolution
pdb|1YYW|D Chain D, Crystal Structure Of Rnase Iii From Aquifex Aeolicus
Complexed With Double Stranded Rna At 2.8-Angstrom
Resolution
pdb|2NUE|A Chain A, Crystal Structure Of Rnase Iii From Aquifex Aeolicus
Complexed With Ds-Rna At 2.9-Angstrom Resolution
pdb|2NUE|B Chain B, Crystal Structure Of Rnase Iii From Aquifex Aeolicus
Complexed With Ds-Rna At 2.9-Angstrom Resolution
pdb|2NUF|A Chain A, Crystal Structure Of Rnase Iii From Aquifex Aeolicus
Complexed With Ds-Rna At 2.5-Angstrom Resolution
pdb|2NUF|B Chain B, Crystal Structure Of Rnase Iii From Aquifex Aeolicus
Complexed With Ds-Rna At 2.5-Angstrom Resolution
pdb|2NUG|A Chain A, Crystal Structure Of Rnase Iii From Aquifex Aeolicus
Complexed With Ds-Rna At 1.7-Angstrom Resolution
pdb|2NUG|B Chain B, Crystal Structure Of Rnase Iii From Aquifex Aeolicus
Complexed With Ds-Rna At 1.7-Angstrom Resolution
Length = 221
Score = 60.1 bits (144), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 40/148 (27%), Positives = 70/148 (47%), Gaps = 26/148 (17%)
Query: 1212 MATLEILLGHQFLHRGLLLQAFVHPSFNRLGGCYQRLEFLGDAVLDYLITSYLYSVYPKL 1271
+ LE LG+ F + LL +A H S+++ Y+ LEFLGDA++++ I L P
Sbjct: 4 LEQLEKKLGYTFKDKSLLEKALTHVSYSK-KEHYETLEFLGDALVNFFIVDLLVQYSPNK 62
Query: 1272 KPGQLTDLRSMLVNNQAFANVAVDQSFYKFLIFDSNVLSETINNYVDYMITPSSTREVKE 1331
+ G L+ L++ L++ + F +A +KF+ ++ETI
Sbjct: 63 REGFLSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINETI------------------ 104
Query: 1332 GPRCPKVLGDLVESSLGAILLDSGFNLN 1359
+GD+ E+ A+ +DSG + N
Sbjct: 105 -------IGDVFEALWAAVYIDSGRDAN 125
>pdb|1YZ9|A Chain A, Crystal Structure Of Rnase Iii Mutant E110q From Aquifex
Aeolicus Complexed With Double Stranded Rna At 2.1-
Angstrom Resolution
pdb|1YZ9|B Chain B, Crystal Structure Of Rnase Iii Mutant E110q From Aquifex
Aeolicus Complexed With Double Stranded Rna At 2.1-
Angstrom Resolution
Length = 221
Score = 58.9 bits (141), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 39/148 (26%), Positives = 70/148 (47%), Gaps = 26/148 (17%)
Query: 1212 MATLEILLGHQFLHRGLLLQAFVHPSFNRLGGCYQRLEFLGDAVLDYLITSYLYSVYPKL 1271
+ LE LG+ F + LL +A H S+++ Y+ LEFLGDA++++ I L P
Sbjct: 4 LEQLEKKLGYTFKDKSLLEKALTHVSYSK-KEHYETLEFLGDALVNFFIVDLLVQYSPNK 62
Query: 1272 KPGQLTDLRSMLVNNQAFANVAVDQSFYKFLIFDSNVLSETINNYVDYMITPSSTREVKE 1331
+ G L+ L++ L++ + F +A +KF+ ++ETI
Sbjct: 63 REGFLSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINETI------------------ 104
Query: 1332 GPRCPKVLGDLVESSLGAILLDSGFNLN 1359
+GD+ ++ A+ +DSG + N
Sbjct: 105 -------IGDVFQALWAAVYIDSGRDAN 125
>pdb|1YYO|A Chain A, Crystal Structure Of Rnase Iii Mutant E110k From Aquifex
Aeolicus Complexed With Double-stranded Rna At 2.9-
Angstrom Resolution
pdb|1YYO|B Chain B, Crystal Structure Of Rnase Iii Mutant E110k From Aquifex
Aeolicus Complexed With Double-stranded Rna At 2.9-
Angstrom Resolution
Length = 221
Score = 58.5 bits (140), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 39/148 (26%), Positives = 70/148 (47%), Gaps = 26/148 (17%)
Query: 1212 MATLEILLGHQFLHRGLLLQAFVHPSFNRLGGCYQRLEFLGDAVLDYLITSYLYSVYPKL 1271
+ LE LG+ F + LL +A H S+++ Y+ LEFLGDA++++ I L P
Sbjct: 4 LEQLEKKLGYTFKDKSLLEKALTHVSYSK-KEHYETLEFLGDALVNFFIVDLLVQYSPNK 62
Query: 1272 KPGQLTDLRSMLVNNQAFANVAVDQSFYKFLIFDSNVLSETINNYVDYMITPSSTREVKE 1331
+ G L+ L++ L++ + F +A +KF+ ++ETI
Sbjct: 63 REGFLSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINETI------------------ 104
Query: 1332 GPRCPKVLGDLVESSLGAILLDSGFNLN 1359
+GD+ ++ A+ +DSG + N
Sbjct: 105 -------IGDVFKALWAAVYIDSGRDAN 125
>pdb|1RC7|A Chain A, Crystal Structure Of Rnase Iii Mutant E110k From Aquifex
Aeolicus Complexed With Ds-Rna At 2.15 Angstrom
Resolution
Length = 220
Score = 58.5 bits (140), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 39/148 (26%), Positives = 70/148 (47%), Gaps = 26/148 (17%)
Query: 1212 MATLEILLGHQFLHRGLLLQAFVHPSFNRLGGCYQRLEFLGDAVLDYLITSYLYSVYPKL 1271
+ LE LG+ F + LL +A H S+++ Y+ LEFLGDA++++ I L P
Sbjct: 4 LEQLEKKLGYTFKDKSLLEKALTHVSYSK-KEHYETLEFLGDALVNFFIVDLLVQYSPNK 62
Query: 1272 KPGQLTDLRSMLVNNQAFANVAVDQSFYKFLIFDSNVLSETINNYVDYMITPSSTREVKE 1331
+ G L+ L++ L++ + F +A +KF+ ++ETI
Sbjct: 63 REGFLSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINETI------------------ 104
Query: 1332 GPRCPKVLGDLVESSLGAILLDSGFNLN 1359
+GD+ ++ A+ +DSG + N
Sbjct: 105 -------IGDVFKALWAAVYIDSGRDAN 125
>pdb|2EZ6|A Chain A, Crystal Structure Of Aquifex Aeolicus Rnase Iii (d44n)
Complexed With Product Of Double-stranded Rna Processing
pdb|2EZ6|B Chain B, Crystal Structure Of Aquifex Aeolicus Rnase Iii (d44n)
Complexed With Product Of Double-stranded Rna Processing
Length = 221
Score = 58.2 bits (139), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 39/148 (26%), Positives = 70/148 (47%), Gaps = 26/148 (17%)
Query: 1212 MATLEILLGHQFLHRGLLLQAFVHPSFNRLGGCYQRLEFLGDAVLDYLITSYLYSVYPKL 1271
+ LE LG+ F + LL +A H S+++ Y+ LEFLG+A++++ I L P
Sbjct: 4 LEQLEKKLGYTFKDKSLLEKALTHVSYSK-KEHYETLEFLGNALVNFFIVDLLVQYSPNK 62
Query: 1272 KPGQLTDLRSMLVNNQAFANVAVDQSFYKFLIFDSNVLSETINNYVDYMITPSSTREVKE 1331
+ G L+ L++ L++ + F +A +KF+ ++ETI
Sbjct: 63 REGFLSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINETI------------------ 104
Query: 1332 GPRCPKVLGDLVESSLGAILLDSGFNLN 1359
+GD+ E+ A+ +DSG + N
Sbjct: 105 -------IGDVFEALWAAVYIDSGRDAN 125
>pdb|1I4S|A Chain A, Crystal Structure Of Rnase Iii Endonuclease Domain From
Aquifex Aeolicus At 2.15 Angstrom Resolution
pdb|1I4S|B Chain B, Crystal Structure Of Rnase Iii Endonuclease Domain From
Aquifex Aeolicus At 2.15 Angstrom Resolution
Length = 147
Score = 57.0 bits (136), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 39/148 (26%), Positives = 69/148 (46%), Gaps = 26/148 (17%)
Query: 1212 MATLEILLGHQFLHRGLLLQAFVHPSFNRLGGCYQRLEFLGDAVLDYLITSYLYSVYPKL 1271
+ LE LG+ F + LL +A H S+++ Y+ LEFLGDA++++ I L P
Sbjct: 4 LEQLEKKLGYTFKDKSLLEKALTHVSYSK-KEHYETLEFLGDALVNFFIVDLLVQYSPNK 62
Query: 1272 KPGQLTDLRSMLVNNQAFANVAVDQSFYKFLIFDSNVLSETINNYVDYMITPSSTREVKE 1331
+ G L+ L++ L++ + F +A +KF+ +K
Sbjct: 63 REGFLSPLKAYLISEEFFNLLAQKLELHKFI-------------------------RIKR 97
Query: 1332 GPRCPKVLGDLVESSLGAILLDSGFNLN 1359
G ++GD+ E+ A+ +DSG + N
Sbjct: 98 GKINETIIGDVFEALWAAVYIDSGRDAN 125
>pdb|1JFZ|A Chain A, Crystal Structure Of Mn(Ii)-Complex Of Rnase Iii
Endonuclease Domain From Aquifex Aeolicus At 2.10
Angstrom Resolution
pdb|1JFZ|B Chain B, Crystal Structure Of Mn(Ii)-Complex Of Rnase Iii
Endonuclease Domain From Aquifex Aeolicus At 2.10
Angstrom Resolution
pdb|1JFZ|C Chain C, Crystal Structure Of Mn(Ii)-Complex Of Rnase Iii
Endonuclease Domain From Aquifex Aeolicus At 2.10
Angstrom Resolution
pdb|1JFZ|D Chain D, Crystal Structure Of Mn(Ii)-Complex Of Rnase Iii
Endonuclease Domain From Aquifex Aeolicus At 2.10
Angstrom Resolution
pdb|1RC5|A Chain A, Crystal Structure Of Mg(Ii)-Complex Of Rnase Iii
Endonuclease Domain From Aquifex Aeolicus At 2.30
Angstrom Resolution
pdb|1RC5|B Chain B, Crystal Structure Of Mg(Ii)-Complex Of Rnase Iii
Endonuclease Domain From Aquifex Aeolicus At 2.30
Angstrom Resolution
pdb|1RC5|C Chain C, Crystal Structure Of Mg(Ii)-Complex Of Rnase Iii
Endonuclease Domain From Aquifex Aeolicus At 2.30
Angstrom Resolution
pdb|1RC5|D Chain D, Crystal Structure Of Mg(Ii)-Complex Of Rnase Iii
Endonuclease Domain From Aquifex Aeolicus At 2.30
Angstrom Resolution
Length = 154
Score = 57.0 bits (136), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 39/148 (26%), Positives = 69/148 (46%), Gaps = 26/148 (17%)
Query: 1212 MATLEILLGHQFLHRGLLLQAFVHPSFNRLGGCYQRLEFLGDAVLDYLITSYLYSVYPKL 1271
+ LE LG+ F + LL +A H S+++ Y+ LEFLGDA++++ I L P
Sbjct: 5 LEQLEKKLGYTFKDKSLLEKALTHVSYSK-KEHYETLEFLGDALVNFFIVDLLVQYSPNK 63
Query: 1272 KPGQLTDLRSMLVNNQAFANVAVDQSFYKFLIFDSNVLSETINNYVDYMITPSSTREVKE 1331
+ G L+ L++ L++ + F +A +KF+ +K
Sbjct: 64 REGFLSPLKAYLISEEFFNLLAQKLELHKFI-------------------------RIKR 98
Query: 1332 GPRCPKVLGDLVESSLGAILLDSGFNLN 1359
G ++GD+ E+ A+ +DSG + N
Sbjct: 99 GKINETIIGDVFEALWAAVYIDSGRDAN 126
>pdb|3B6E|A Chain A, Crystal Structure Of Human Dech-Box Rna Helicase Mda5
(Melanoma Differentiation-Associated Protein 5),
Dech-Domain
Length = 216
Score = 56.6 bits (135), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 54/199 (27%), Positives = 94/199 (47%), Gaps = 28/199 (14%)
Query: 48 AQKTDKDPKQIARKYQLELCKKAME-ENIIVYLGTGCGKTHIAVLLIYELAHLIRKPQKS 106
A + +P+ R YQ+E+ + A+E +NII+ L TG GKT +AV + + HL +K + S
Sbjct: 23 AARASPEPELQLRPYQMEVAQPALEGKNIIICLPTGSGKTRVAVYIAKD--HLDKKKKAS 80
Query: 107 ---ICIFLAPTVALVQQQAKVIEESIGFKVRTFCGGSKRLKSHCDWEKEIDQYEVLVMIP 163
I L V LV+Q + + K G S + + + + ++++
Sbjct: 81 EPGKVIVLVNKVLLVEQLFRKEFQPFLKKWYRVIGLSGDTQLKISFPEVVKSCDIIISTA 140
Query: 164 QILLYCLYH------RFIKMELIALLIFDECHHAQVKSNHPYAKIMKDFY---------- 207
QIL L + +++ +L+I DECHH ++ Y IM+ +
Sbjct: 141 QILENSLLNLENGEDAGVQLSDFSLIIIDECHHTNKEA--VYNNIMRHYLMQKLKNNRLK 198
Query: 208 ---KPDIMKVPRIFGMTAS 223
KP ++ +P+I G+TAS
Sbjct: 199 KENKP-VIPLPQILGLTAS 216
>pdb|2A11|A Chain A, Crystal Structure Of Nuclease Domain Of Ribonuclase Iii From
Mycobacterium Tuberculosis
Length = 242
Score = 55.5 bits (132), Expect = 2e-07, Method: Composition-based stats.
Identities = 48/149 (32%), Positives = 68/149 (45%), Gaps = 21/149 (14%)
Query: 1228 LLLQAFVHPSFNRLGG---CYQRLEFLGDAVLDYLITSYLYSVYPKLKPGQLTDLRSMLV 1284
LL A H S+ G +RLEFLGDAVL IT L+ +P G L LR+ +V
Sbjct: 22 LLSLALTHRSYAYENGGLPTNERLEFLGDAVLGLTITDALFHRHPDRSEGDLAKLRASVV 81
Query: 1285 NNQAFANVAVDQSFYKFLIFDSNVLSETINNYVDYMITPSSTREVKEGPRCPKVLGDLVE 1344
N QA A+VA + +E + +V ++T G +L D +E
Sbjct: 82 NTQALADVA------------RRLCAEGLGVHVLLGRGEANT----GGADKSSILADGME 125
Query: 1345 SSLGAILLDSGFNLNTVWKIMLSFLDPIL 1373
S LGAI L G + +++L P+L
Sbjct: 126 SLLGAIYLQHG--MEKAREVILRLFGPLL 152
Score = 40.0 bits (92), Expect = 0.009, Method: Composition-based stats.
Identities = 29/78 (37%), Positives = 38/78 (48%), Gaps = 4/78 (5%)
Query: 1016 GAEVSAEMLLKALTTEK-CQERFSL---ERLEILGDAFLKYAVGRHLFLLHDTVDEGELT 1071
G ++ E+L ALT E L ERLE LGDA L + LF H EG+L
Sbjct: 15 GVDLPDELLSLALTHRSYAYENGGLPTNERLEFLGDAVLGLTITDALFHRHPDRSEGDLA 74
Query: 1072 RRRSNAVNNSNLLKLAAR 1089
+ R++ VN L +A R
Sbjct: 75 KLRASVVNTQALADVARR 92
>pdb|2FFL|A Chain A, Crystal Structure Of Dicer From Giardia Intestinalis
pdb|2FFL|B Chain B, Crystal Structure Of Dicer From Giardia Intestinalis
pdb|2FFL|C Chain C, Crystal Structure Of Dicer From Giardia Intestinalis
pdb|2FFL|D Chain D, Crystal Structure Of Dicer From Giardia Intestinalis
pdb|2QVW|A Chain A, Structure Of Giardia Dicer Refined Against Twinned Data
pdb|2QVW|B Chain B, Structure Of Giardia Dicer Refined Against Twinned Data
pdb|2QVW|C Chain C, Structure Of Giardia Dicer Refined Against Twinned Data
pdb|2QVW|D Chain D, Structure Of Giardia Dicer Refined Against Twinned Data
Length = 756
Score = 52.4 bits (124), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/50 (52%), Positives = 34/50 (68%)
Query: 1040 ERLEILGDAFLKYAVGRHLFLLHDTVDEGELTRRRSNAVNNSNLLKLAAR 1089
++LE+LGDAFLK ++ HL LH T+ EG LTR R +A NS L +L R
Sbjct: 648 QKLELLGDAFLKCSLALHLHALHPTLTEGALTRMRQSAETNSVLGRLTKR 697
Score = 47.0 bits (110), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 40/68 (58%)
Query: 1245 YQRLEFLGDAVLDYLITSYLYSVYPKLKPGQLTDLRSMLVNNQAFANVAVDQSFYKFLIF 1304
+QRLE LGDAVL +++T+ L ++P G L +L+ LV N+A + + F
Sbjct: 334 FQRLELLGDAVLGFIVTARLLCLFPDASVGTLVELKMELVRNEALNYLVQTLGLPQLAEF 393
Query: 1305 DSNVLSET 1312
+N+++++
Sbjct: 394 SNNLVAKS 401
Score = 40.8 bits (94), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 35/111 (31%), Positives = 48/111 (43%), Gaps = 21/111 (18%)
Query: 1245 YQRLEFLGDAVLDYLITSYLYSVYPKLKPGQLTDLRSMLVNNQAFANVAVDQSFYKFLIF 1304
YQ+LE LGDA L + +L++++P L G LT +R N + +F
Sbjct: 647 YQKLELLGDAFLKCSLALHLHALHPTLTEGALTRMRQSAETNSVLGRLT-----KRFPSV 701
Query: 1305 DSNVLSETINNYVDYMITPSSTREVKEGPRCPKVLGDLVESSLGAILLDSG 1355
S V+ E+ I P S KV GD E+ L AILL G
Sbjct: 702 VSEVIIESHPK-----IQPDS-----------KVYGDTFEAILAAILLACG 736
Score = 30.8 bits (68), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 53/243 (21%), Positives = 95/243 (39%), Gaps = 52/243 (21%)
Query: 875 SDVENSLVYATHKKW-FYLVTNIVFEKNGYSPY-KDSDSSSHVDHLISSYGIHLKHPKQP 932
+ + +V W Y+V I + S + + ++S +++ + +++ IHL+ P
Sbjct: 154 ASLHGRMVATPEISWSLYVVLGIDSTQTSLSYFTRANESITYMRYYATAHNIHLRAADLP 213
Query: 933 LLRAKPLFRLRNLLHNRKLEDSESHELEE--YFDDLPPEL-------CQLKIIGFSKDIG 983
L+ A +L+D + H++ +DDL P+L C L F
Sbjct: 214 LVAAV------------RLDDLKDHQIPAPGSWDDLAPKLRFLPPELCLLLPDEFDLIRV 261
Query: 984 SSLSLLPSIMHR---LENLLVAIELKHLLSASFPEGAEVSAE---MLLKALTTEKCQER- 1036
+L LP I ++N + A++ SFP+ + E + L ++ + R
Sbjct: 262 QALQFLPEIAKHICDIQNTICALD------KSFPDCGRIGGERYFAITAGLRLDQGRGRG 315
Query: 1037 ----------FSL------ERLEILGDAFLKYAVGRHLFLLHDTVDEGELTRRRSNAVNN 1080
F + +RLE+LGDA L + V L L G L + V N
Sbjct: 316 LAGWRTPFGPFGVSHTDVFQRLELLGDAVLGFIVTARLLCLFPDASVGTLVELKMELVRN 375
Query: 1081 SNL 1083
L
Sbjct: 376 EAL 378
>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 = 51.2 bits (121), Expect = 5e-06, Method: Composition-based stats.
Identities = 43/146 (29%), Positives = 62/146 (42%), Gaps = 29/146 (19%)
Query: 1220 GHQFLHRGLLLQAFVHPSF----NRLG----GCYQRLEFLGDAVLDYLITSYLYSVYPKL 1271
G F + LL +A H S+ N+ G ++LEFLGDAVL+ + LY YP+
Sbjct: 29 GINFKNEELLFRALCHSSYANEQNQAGRKDVESNEKLEFLGDAVLELFVCEILYKKYPEA 88
Query: 1272 KPGQLTDLRSMLVNNQAFANVAVDQSFYKFLIFDSNVLSETINNYVDYMITPSSTREVKE 1331
+ G L ++S + + A V+ + KFL E K
Sbjct: 89 EVGDLARVKSAAASEEVLAMVSRKMNLGKFLFLGKG--------------------EEKT 128
Query: 1332 GPR-CPKVLGDLVESSLGAILLDSGF 1356
G R +L D E+ L AI LD G+
Sbjct: 129 GGRDRDSILADAFEALLAAIYLDQGY 154
Score = 31.2 bits (69), Expect = 5.4, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 32/59 (54%)
Query: 1038 SLERLEILGDAFLKYAVGRHLFLLHDTVDEGELTRRRSNAVNNSNLLKLAARNNLQVYI 1096
S E+LE LGDA L+ V L+ + + G+L R +S A + L ++ + NL ++
Sbjct: 61 SNEKLEFLGDAVLELFVCEILYKKYPEAEVGDLARVKSAAASEEVLAMVSRKMNLGKFL 119
>pdb|3RV0|A Chain A, Crystal Structure Of K. Polysporus Dcr1 Without The
C-Terminal Dsrbd
pdb|3RV0|B Chain B, Crystal Structure Of K. Polysporus Dcr1 Without The
C-Terminal Dsrbd
pdb|3RV0|C Chain C, Crystal Structure Of K. Polysporus Dcr1 Without The
C-Terminal Dsrbd
pdb|3RV0|D Chain D, Crystal Structure Of K. Polysporus Dcr1 Without The
C-Terminal Dsrbd
Length = 341
Score = 48.9 bits (115), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 37/132 (28%), Positives = 62/132 (46%), Gaps = 28/132 (21%)
Query: 1232 AFVHPSFNRLGG----------CYQRLEFLGDAVLDYLITSYLYSVYPKLKPGQLTDLRS 1281
AF+H SF + +RLEFLGD+ L L++ +Y+ +P G L+ ++
Sbjct: 106 AFMHKSFPNMNAHLNDAQKTQLSNERLEFLGDSWLGALVSYIVYTRFPSANEGMLSQMKE 165
Query: 1282 MLVNNQAFANVAVDQSFYKFLIFDSNVLSETINNYVDYMITPSSTREVKEGPRCPKVLGD 1341
+VNN + + +F K L + + TP TR VK+ + K D
Sbjct: 166 SIVNNNNLFDWSTKLNFTKRLQGN--------------IATP--TRVVKD--KMSKRYAD 207
Query: 1342 LVESSLGAILLD 1353
VE+ +GA+++D
Sbjct: 208 CVEAYIGALVID 219
Score = 36.6 bits (83), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 46/211 (21%), Positives = 82/211 (38%), Gaps = 54/211 (25%)
Query: 1025 LKALTTEKCQERFSLERLEILGDAFLKYAVGRHLFLLHDTVDEGELTRRRSNAVNNSNLL 1084
+ A + + + S ERLE LGD++L V ++ + +EG L++ + + VNN+NL
Sbjct: 115 MNAHLNDAQKTQLSNERLEFLGDSWLGALVSYIVYTRFPSANEGMLSQMKESIVNNNNLF 174
Query: 1085 KLAARNNLQVYIRDQPFDPCQFFALGRRCPRICSKETERTIHSQYDGRAPDDLNAEVRCS 1144
+ + N ++ P R + + R
Sbjct: 175 DWSTKLNFTKRLQGNIATPT------------------RVVKDKMSKR------------ 204
Query: 1145 KGHHWLHKKTIADVVEALVGAFIDDSGFKAATAFL---KWIGIQVEFEASQVTNICISSK 1201
AD VEA +GA + D + T FL +W+ E + ++ + + I
Sbjct: 205 ----------YADCVEAYIGALVID---RFGTEFLDIKEWLEELSEKKLAKSSQMVIKE- 250
Query: 1202 SFLPLSASLDMATLEIL----LGHQFLHRGL 1228
PL+ + E+L LGH+ +R L
Sbjct: 251 ---PLNKNAKNELAELLQINKLGHKLHYRKL 278
>pdb|3RV1|A Chain A, Crystal Structure Of The N-Terminal And Rnase Iii Domains Of
K. Polysporus Dcr1 E224q Mutant
pdb|3RV1|B Chain B, Crystal Structure Of The N-Terminal And Rnase Iii Domains Of
K. Polysporus Dcr1 E224q Mutant
Length = 246
Score = 47.4 bits (111), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 37/132 (28%), Positives = 62/132 (46%), Gaps = 28/132 (21%)
Query: 1232 AFVHPSFNRLGG----------CYQRLEFLGDAVLDYLITSYLYSVYPKLKPGQLTDLRS 1281
AF+H SF + +RLEFLGD+ L L++ +Y+ +P G L+ ++
Sbjct: 106 AFMHKSFPNMNAHLNDAQKTQLSNERLEFLGDSWLGALVSYIVYTRFPSANEGMLSQMKE 165
Query: 1282 MLVNNQAFANVAVDQSFYKFLIFDSNVLSETINNYVDYMITPSSTREVKEGPRCPKVLGD 1341
+VNN + + +F K L N+ TP TR VK+ + K D
Sbjct: 166 SIVNNNNLFDWSTKLNFTKRL--QGNI------------ATP--TRVVKD--KMSKRYAD 207
Query: 1342 LVESSLGAILLD 1353
V++ +GA+++D
Sbjct: 208 CVQAYIGALVID 219
Score = 36.6 bits (83), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 37/68 (54%)
Query: 1025 LKALTTEKCQERFSLERLEILGDAFLKYAVGRHLFLLHDTVDEGELTRRRSNAVNNSNLL 1084
+ A + + + S ERLE LGD++L V ++ + +EG L++ + + VNN+NL
Sbjct: 115 MNAHLNDAQKTQLSNERLEFLGDSWLGALVSYIVYTRFPSANEGMLSQMKESIVNNNNLF 174
Query: 1085 KLAARNNL 1092
+ + N
Sbjct: 175 DWSTKLNF 182
>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 47.4 bits (111), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 28/100 (28%), Positives = 51/100 (51%), Gaps = 10/100 (10%)
Query: 426 KCIVFVNRIVTARALSYILQNLKFLASWRCHFLVGVNAGLKSMSRNAMKSILEKFRSGEL 485
+ ++F N T R + ++ + ++ +F V G M + +SI+++FRSG
Sbjct: 242 QAVIFCN---TKRKVDWLTEKMR-----EANFTVSSMHG--DMPQKERESIMKEFRSGAS 291
Query: 486 NLLVATKVGEEGLDIQTCCLVIRFDLPETVASFIQSRGRA 525
+L++T V GLD+ L+I +DLP +I GR+
Sbjct: 292 RVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRS 331
>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 = 47.4 bits (111), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 28/100 (28%), Positives = 51/100 (51%), Gaps = 10/100 (10%)
Query: 426 KCIVFVNRIVTARALSYILQNLKFLASWRCHFLVGVNAGLKSMSRNAMKSILEKFRSGEL 485
+ ++F N T R + ++ + ++ +F V G M + +SI+++FRSG
Sbjct: 279 QAVIFCN---TKRKVDWLTEKMR-----EANFTVSSMHG--DMPQKERESIMKEFRSGAS 328
Query: 486 NLLVATKVGEEGLDIQTCCLVIRFDLPETVASFIQSRGRA 525
+L++T V GLD+ L+I +DLP +I GR+
Sbjct: 329 RVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRS 368
>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 = 47.4 bits (111), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 28/100 (28%), Positives = 51/100 (51%), Gaps = 10/100 (10%)
Query: 426 KCIVFVNRIVTARALSYILQNLKFLASWRCHFLVGVNAGLKSMSRNAMKSILEKFRSGEL 485
+ ++F N T R + ++ + ++ +F V G M + +SI+++FRSG
Sbjct: 278 QAVIFCN---TKRKVDWLTEKMR-----EANFTVSSMHG--DMPQKERESIMKEFRSGAS 327
Query: 486 NLLVATKVGEEGLDIQTCCLVIRFDLPETVASFIQSRGRA 525
+L++T V GLD+ L+I +DLP +I GR+
Sbjct: 328 RVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRS 367
>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 = 47.4 bits (111), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 28/100 (28%), Positives = 51/100 (51%), Gaps = 10/100 (10%)
Query: 426 KCIVFVNRIVTARALSYILQNLKFLASWRCHFLVGVNAGLKSMSRNAMKSILEKFRSGEL 485
+ ++F N T R + ++ + ++ +F V G M + +SI+++FRSG
Sbjct: 279 QAVIFCN---TKRKVDWLTEKMR-----EANFTVSSMHG--DMPQKERESIMKEFRSGAS 328
Query: 486 NLLVATKVGEEGLDIQTCCLVIRFDLPETVASFIQSRGRA 525
+L++T V GLD+ L+I +DLP +I GR+
Sbjct: 329 RVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRS 368
>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 = 47.0 bits (110), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 28/100 (28%), Positives = 51/100 (51%), Gaps = 10/100 (10%)
Query: 426 KCIVFVNRIVTARALSYILQNLKFLASWRCHFLVGVNAGLKSMSRNAMKSILEKFRSGEL 485
+ ++F N T R + ++ + ++ +F V G M + +SI+++FRSG
Sbjct: 257 QAVIFCN---TKRKVDWLTEKMR-----EANFTVSSMHG--DMPQKERESIMKEFRSGAS 306
Query: 486 NLLVATKVGEEGLDIQTCCLVIRFDLPETVASFIQSRGRA 525
+L++T V GLD+ L+I +DLP +I GR+
Sbjct: 307 RVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRS 346
>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 47.0 bits (110), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 28/100 (28%), Positives = 51/100 (51%), Gaps = 10/100 (10%)
Query: 426 KCIVFVNRIVTARALSYILQNLKFLASWRCHFLVGVNAGLKSMSRNAMKSILEKFRSGEL 485
+ ++F N T R + ++ + ++ +F V G M + +SI+++FRSG
Sbjct: 242 QAVIFCN---TKRKVDWLTEKMR-----EANFTVSSMHG--DMPQKERESIMKEFRSGAS 291
Query: 486 NLLVATKVGEEGLDIQTCCLVIRFDLPETVASFIQSRGRA 525
+L++T V GLD+ L+I +DLP +I GR+
Sbjct: 292 RVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRS 331
>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 = 46.6 bits (109), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 31/57 (54%)
Query: 469 SRNAMKSILEKFRSGELNLLVATKVGEEGLDIQTCCLVIRFDLPETVASFIQSRGRA 525
S+ + L +FRSG+ +LVAT V GLDI VI FDLP + ++ GR
Sbjct: 81 SQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRT 137
>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p
Length = 400
Score = 46.2 bits (108), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 28/103 (27%), Positives = 51/103 (49%), Gaps = 10/103 (9%)
Query: 423 QHMKCIVFVNRIVTARALSYILQNLKFLASWRCHFLVGVNAGLKSMSRNAMKSILEKFRS 482
Q + I+F N L+ + +L + C++ +A +K RN + +FR
Sbjct: 257 QINQAIIFCNSTNRVELLAKKITDL----GYSCYY---SHARMKQQERN---KVFHEFRQ 306
Query: 483 GELNLLVATKVGEEGLDIQTCCLVIRFDLPETVASFIQSRGRA 525
G++ LV + + G+DIQ +VI FD P+T +++ GR+
Sbjct: 307 GKVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRS 349
>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x
Length = 417
Score = 45.8 bits (107), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 31/57 (54%)
Query: 469 SRNAMKSILEKFRSGELNLLVATKVGEEGLDIQTCCLVIRFDLPETVASFIQSRGRA 525
S+ + L +FRSG+ +LVAT V GLDI VI FDLP + ++ GR
Sbjct: 311 SQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRT 367
>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 = 45.8 bits (107), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 29/51 (56%)
Query: 475 SILEKFRSGELNLLVATKVGEEGLDIQTCCLVIRFDLPETVASFIQSRGRA 525
++ +F+ GE LVAT V G+DI+ LVI +DLP S++ GR
Sbjct: 76 DVMNEFKRGEYRYLVATDVAARGIDIENISLVINYDLPLEKESYVHRTGRT 126
>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 = 45.4 bits (106), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 43/146 (29%), Positives = 65/146 (44%), Gaps = 16/146 (10%)
Query: 380 VFAAICRRDGIASDLSCIEVLKEPFFSKKLLRLIGILSTFRLQQHMKCIVFVNRIVTARA 439
VF AI G SD+ + + E K +LI ILS +Q IVFV A
Sbjct: 262 VFVAIGIVGGACSDVK--QTIYEVNKYAKRSKLIEILS----EQADGTIVFVETKRGADF 315
Query: 440 LSYILQNLKFLASWRCHFLVGVNAGLKSMSRNAMKSILEKFRSGELNLLVATKVGEEGLD 499
L+ L +F + H L+S A++ F++G + +L+AT V GLD
Sbjct: 316 LASFLSEKEF-PTTSIH-----GDRLQSQREQALRD----FKNGSMKVLIATSVASRGLD 365
Query: 500 IQTCCLVIRFDLPETVASFIQSRGRA 525
I+ VI +D+P + ++ GR
Sbjct: 366 IKNIKHVINYDMPSKIDDYVHRIGRT 391
>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 = 45.1 bits (105), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 27/94 (28%), Positives = 48/94 (51%), Gaps = 10/94 (10%)
Query: 426 KCIVFVNRIVTARALSYILQNLKFLASWRCHFLVGVNAGLKSMSRNAMKSILEKFRSGEL 485
+ ++F N L+ L+N KF S + + L R+ +I+++FRSG
Sbjct: 262 QAVIFCNTRRKVEELTTKLRNDKFTVS-------AIYSDLPQQERD---TIMKEFRSGSS 311
Query: 486 NLLVATKVGEEGLDIQTCCLVIRFDLPETVASFI 519
+L++T + G+D+Q LVI +DLP ++I
Sbjct: 312 RILISTDLLARGIDVQQVSLVINYDLPANKENYI 345
>pdb|1FUK|A Chain A, Crystal Structure Of The Carboxy Terminal Domain Of Yeast
Eif4a
Length = 165
Score = 45.1 bits (105), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 27/94 (28%), Positives = 48/94 (51%), Gaps = 10/94 (10%)
Query: 426 KCIVFVNRIVTARALSYILQNLKFLASWRCHFLVGVNAGLKSMSRNAMKSILEKFRSGEL 485
+ ++F N L+ L+N KF S + + L R+ +I+++FRSG
Sbjct: 32 QAVIFCNTRRKVEELTTKLRNDKFTVS-------AIYSDLPQQERD---TIMKEFRSGSS 81
Query: 486 NLLVATKVGEEGLDIQTCCLVIRFDLPETVASFI 519
+L++T + G+D+Q LVI +DLP ++I
Sbjct: 82 RILISTDLLARGIDVQQVSLVINYDLPANKENYI 115
>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 = 44.3 bits (103), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 30/48 (62%)
Query: 477 LEKFRSGELNLLVATKVGEEGLDIQTCCLVIRFDLPETVASFIQSRGR 524
+E FR G+ ++LVAT V +GLD VI +D+PE + +++ GR
Sbjct: 97 IEAFREGKKDVLVATDVASKGLDFPAIQHVINYDMPEEIENYVHRIGR 144
>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a
pdb|1FUU|B Chain B, Yeast Initiation Factor 4a
Length = 394
Score = 43.9 bits (102), Expect = 7e-04, Method: Composition-based stats.
Identities = 27/95 (28%), Positives = 47/95 (49%), Gaps = 10/95 (10%)
Query: 426 KCIVFVNRIVTARALSYILQNLKFLASWRCHFLVGVNAGLKSMSRNAMKSILEKFRSGEL 485
+ ++F N L+ L+N KF S + + L R+ +I ++FRSG
Sbjct: 261 QAVIFCNTRRKVEELTTKLRNDKFTVS-------AIYSDLPQQERD---TIXKEFRSGSS 310
Query: 486 NLLVATKVGEEGLDIQTCCLVIRFDLPETVASFIQ 520
+L++T + G+D+Q LVI +DLP ++I
Sbjct: 311 RILISTDLLARGIDVQQVSLVINYDLPANKENYIH 345
>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna
Helicase From Sulfolobus Tokodaii
Length = 337
Score = 43.1 bits (100), Expect = 0.001, Method: Composition-based stats.
Identities = 21/52 (40%), Positives = 30/52 (57%), Gaps = 1/52 (1%)
Query: 477 LEKFRSGELNLLVATKVGEEGLDIQTCCLVIRFDLPETVASFIQSRGR-ARM 527
++ FR GE ++L+ T V GLDI VI FD P+ + ++I GR RM
Sbjct: 259 IDAFREGEYDMLITTDVASRGLDIPLVEKVINFDAPQDLRTYIHRIGRTGRM 310
>pdb|2LRS|A Chain A, The Second Dsrbd Domain From A. Thaliana Dicer-like 1
Length = 71
Score = 42.7 bits (99), Expect = 0.002, Method: Composition-based stats.
Identities = 20/48 (41%), Positives = 25/48 (52%)
Query: 1528 ELCAANCWKPPTFDCCKEEGLSHLKLFTFRVIVEIEAPEKIIECIGEP 1575
++C W P++ C KE G +H K FTF V V ECIGEP
Sbjct: 2 DICLRKNWPMPSYRCVKEGGPAHAKRFTFGVRVNTSDRGWTDECIGEP 49
>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 = 42.4 bits (98), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 28/101 (27%), Positives = 48/101 (47%), Gaps = 12/101 (11%)
Query: 475 SILEKFRSGELNLLVATKVGEEGLDIQTCCLVIRFDLPETVA------SFIQSRGR-ARM 527
SI+++FR G+ +L+ T V G+D++ +V+ FDLP +++ GR R
Sbjct: 75 SIIQRFRDGKEKVLITTNVCARGIDVKQVTIVVNFDLPVKQGEEPDYETYLHRIGRTGRF 134
Query: 528 PQSEYAFLVDSGNQRELDLIKNFSKEEDRMNREIMDRTSSD 568
+ AF N E+D + + K +D N I + D
Sbjct: 135 GKKGLAF-----NMIEVDELPSLMKIQDHFNSSIKQLNAED 170
>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a
pdb|3EIQ|D Chain D, Crystal Structure Of Pdcd4-eif4a
Length = 414
Score = 41.6 bits (96), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 25/94 (26%), Positives = 45/94 (47%), Gaps = 10/94 (10%)
Query: 426 KCIVFVNRIVTARALSYILQNLKFLASWRCHFLVGVNAGLKSMSRNAMKSILEKFRSGEL 485
+ ++F+N T R + ++ + + F V G M + I+ +FRSG
Sbjct: 282 QAVIFIN---TRRKVDWLTEKMH-----ARDFTVSAMHG--DMDQKERDVIMREFRSGSS 331
Query: 486 NLLVATKVGEEGLDIQTCCLVIRFDLPETVASFI 519
+L+ T + G+D+Q LVI +DLP ++I
Sbjct: 332 RVLITTDLLARGIDVQQVSLVINYDLPTNRENYI 365
>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 = 41.2 bits (95), Expect = 0.005, Method: Composition-based stats.
Identities = 18/51 (35%), Positives = 30/51 (58%)
Query: 468 MSRNAMKSILEKFRSGELNLLVATKVGEEGLDIQTCCLVIRFDLPETVASF 518
MS+ + ++ FR GE+ +LVAT V GLDI LV+ + +P+ ++
Sbjct: 62 MSQGERERVMGAFRQGEVRVLVATDVAARGLDIPQVDLVVHYRMPDRAEAY 112
>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 = 41.2 bits (95), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 25/94 (26%), Positives = 45/94 (47%), Gaps = 10/94 (10%)
Query: 426 KCIVFVNRIVTARALSYILQNLKFLASWRCHFLVGVNAGLKSMSRNAMKSILEKFRSGEL 485
+ ++F+N T R + ++ + + F V G M + I+ +FRSG
Sbjct: 256 QAVIFIN---TRRKVDWLTEKMH-----ARDFTVSAMHG--DMDQKERDVIMREFRSGSS 305
Query: 486 NLLVATKVGEEGLDIQTCCLVIRFDLPETVASFI 519
+L+ T + G+D+Q LVI +DLP ++I
Sbjct: 306 RVLITTDLLARGIDVQQVSLVINYDLPTNRENYI 339
>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 = 41.2 bits (95), Expect = 0.005, Method: Composition-based stats.
Identities = 19/51 (37%), Positives = 30/51 (58%)
Query: 468 MSRNAMKSILEKFRSGELNLLVATKVGEEGLDIQTCCLVIRFDLPETVASF 518
+S+ + +L FR GE+ +LVAT V GLDI LV+ + LP+ ++
Sbjct: 65 LSQGERERVLGAFRQGEVRVLVATDVAARGLDIPQVDLVVHYRLPDRAEAY 115
>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 = 41.2 bits (95), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 26/38 (68%)
Query: 475 SILEKFRSGELNLLVATKVGEEGLDIQTCCLVIRFDLP 512
+++E+FR G+ +LV T V G+D++ +VI FDLP
Sbjct: 374 AVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLP 411
Score = 34.7 bits (78), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 33/121 (27%), Positives = 57/121 (47%), Gaps = 13/121 (10%)
Query: 73 ENIIVYLGTGCGKTHIAVL-LIYELAHLIRKPQKSICIFLAPTVALVQQQAKVIEESIGF 131
+N+I +G GKT VL ++ ++ + PQ C+ L+PT L Q KVIE+ F
Sbjct: 132 QNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQ---CLCLSPTYELALQTGKVIEQMGKF 188
Query: 132 ----KVRTFCGGSKRLKSHCDWEKEIDQYEVLVMIPQILLYCLYHRFIKMELIALLIFDE 187
K+ G+K + ++I + V+ +L +C +FI + I + + DE
Sbjct: 189 YPELKLAYAVRGNKLERG-----QKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDE 243
Query: 188 C 188
Sbjct: 244 A 244
>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 = 40.8 bits (94), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 28/98 (28%), Positives = 42/98 (42%), Gaps = 16/98 (16%)
Query: 461 VNAGLKSMSRNAMKSILEKFRSGELNLLVATKVGEEGLDIQTCCLVIRFDLPETVASFIQ 520
++A ++ RN + FR+G LV T + G+DIQ +VI FD P+ +++
Sbjct: 74 IHAKMRQEHRN---RVFHDFRNGLCRNLVCTDLFTRGIDIQAVNVVINFDFPKLAETYLH 130
Query: 521 SRGRARMPQSEYAFLVDSGNQRELDLIKNFSKEEDRMN 558
GR SG L L N +DR N
Sbjct: 131 RIGR-------------SGRFGHLGLAINLITYDDRFN 155
>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 = 40.8 bits (94), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 26/38 (68%)
Query: 475 SILEKFRSGELNLLVATKVGEEGLDIQTCCLVIRFDLP 512
+++E+FR G+ +LV T V G+D++ +VI FDLP
Sbjct: 307 AVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLP 344
Score = 34.3 bits (77), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 33/121 (27%), Positives = 57/121 (47%), Gaps = 13/121 (10%)
Query: 73 ENIIVYLGTGCGKTHIAVL-LIYELAHLIRKPQKSICIFLAPTVALVQQQAKVIEESIGF 131
+N+I +G GKT VL ++ ++ + PQ C+ L+PT L Q KVIE+ F
Sbjct: 65 QNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQ---CLCLSPTYELALQTGKVIEQMGKF 121
Query: 132 ----KVRTFCGGSKRLKSHCDWEKEIDQYEVLVMIPQILLYCLYHRFIKMELIALLIFDE 187
K+ G+K + ++I + V+ +L +C +FI + I + + DE
Sbjct: 122 YPELKLAYAVRGNKLERG-----QKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDE 176
Query: 188 C 188
Sbjct: 177 A 177
>pdb|3G0H|A Chain A, Human Dead-box Rna Helicase Ddx19, In Complex With An
Atp-analogue And Rna
Length = 424
Score = 40.8 bits (94), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 26/38 (68%)
Query: 475 SILEKFRSGELNLLVATKVGEEGLDIQTCCLVIRFDLP 512
+++E+FR G+ +LV T V G+D++ +VI FDLP
Sbjct: 323 AVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLP 360
Score = 34.3 bits (77), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 33/121 (27%), Positives = 57/121 (47%), Gaps = 13/121 (10%)
Query: 73 ENIIVYLGTGCGKTHIAVL-LIYELAHLIRKPQKSICIFLAPTVALVQQQAKVIEESIGF 131
+N+I +G GKT VL ++ ++ + PQ C+ L+PT L Q KVIE+ F
Sbjct: 81 QNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQ---CLCLSPTYELALQTGKVIEQMGKF 137
Query: 132 ----KVRTFCGGSKRLKSHCDWEKEIDQYEVLVMIPQILLYCLYHRFIKMELIALLIFDE 187
K+ G+K + ++I + V+ +L +C +FI + I + + DE
Sbjct: 138 YPELKLAYAVRGNKLERG-----QKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDE 192
Query: 188 C 188
Sbjct: 193 A 193
>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 = 40.8 bits (94), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 26/38 (68%)
Query: 475 SILEKFRSGELNLLVATKVGEEGLDIQTCCLVIRFDLP 512
+++E+FR G+ +LV T V G+D++ +VI FDLP
Sbjct: 344 AVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLP 381
Score = 34.3 bits (77), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 33/121 (27%), Positives = 57/121 (47%), Gaps = 13/121 (10%)
Query: 73 ENIIVYLGTGCGKTHIAVL-LIYELAHLIRKPQKSICIFLAPTVALVQQQAKVIEESIGF 131
+N+I +G GKT VL ++ ++ + PQ C+ L+PT L Q KVIE+ F
Sbjct: 102 QNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQ---CLCLSPTYELALQTGKVIEQMGKF 158
Query: 132 ----KVRTFCGGSKRLKSHCDWEKEIDQYEVLVMIPQILLYCLYHRFIKMELIALLIFDE 187
K+ G+K + ++I + V+ +L +C +FI + I + + DE
Sbjct: 159 YPELKLAYAVRGNKLERG-----QKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDE 213
Query: 188 C 188
Sbjct: 214 A 214
>pdb|1OYW|A Chain A, Structure Of The Recq Catalytic Core
Length = 523
Score = 40.4 bits (93), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 35/64 (54%), Gaps = 3/64 (4%)
Query: 462 NAGLKSMSRNAMKSILEKFRSGELNLLVATKVGEEGLDIQTCCLVIRFDLPETVASFIQS 521
+AGL++ N + EKF+ +L ++VAT G++ V+ FD+P + S+ Q
Sbjct: 267 HAGLEN---NVRADVQEKFQRDDLQIVVATVAFGXGINKPNVRFVVHFDIPRNIESYYQE 323
Query: 522 RGRA 525
GRA
Sbjct: 324 TGRA 327
>pdb|3SQX|A Chain A, Structure Of Mss116p (Nte And C-Tail Double Deletion)
Bound To Ssrna And Amp-Pnp
Length = 512
Score = 40.0 bits (92), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 33/132 (25%), Positives = 66/132 (50%), Gaps = 12/132 (9%)
Query: 468 MSRNAMKSILEKFRSGELNLLVATKVGEEGLDIQTCCLVIRFDLPETVASFIQSRGR-AR 526
+++N S++++F+ E +LV T VG G+D V++ +P +A++I GR AR
Sbjct: 325 ITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTAR 384
Query: 527 MPQSEYAFLVDSGNQ----RELDLIKN--FSKEE-----DRMNREIMDRTSSDAFTCSEE 575
+ + L ++ REL+ KN +K+E + + E+++ + + S+
Sbjct: 385 SGKEGSSVLFICKDELPFVRELEDAKNIVIAKQEKYEPSEEIKSEVLEAVTEEPEDISDI 444
Query: 576 RIYKVDSSGACI 587
I + S +CI
Sbjct: 445 VISLISSYRSCI 456
>pdb|1OYY|A Chain A, Structure Of The Recq Catalytic Core Bound To Atp-Gamma-S
Length = 523
Score = 40.0 bits (92), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 35/64 (54%), Gaps = 3/64 (4%)
Query: 462 NAGLKSMSRNAMKSILEKFRSGELNLLVATKVGEEGLDIQTCCLVIRFDLPETVASFIQS 521
+AGL++ N + EKF+ +L ++VAT G++ V+ FD+P + S+ Q
Sbjct: 267 HAGLEN---NVRADVQEKFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQE 323
Query: 522 RGRA 525
GRA
Sbjct: 324 TGRA 327
>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 = 39.7 bits (91), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 33/132 (25%), Positives = 66/132 (50%), Gaps = 12/132 (9%)
Query: 468 MSRNAMKSILEKFRSGELNLLVATKVGEEGLDIQTCCLVIRFDLPETVASFIQSRGR-AR 526
+++N S++++F+ E +LV T VG G+D V++ +P +A++I GR AR
Sbjct: 70 ITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTAR 129
Query: 527 MPQSEYAFLVDSGNQ----RELDLIKN--FSKEE-----DRMNREIMDRTSSDAFTCSEE 575
+ + L ++ REL+ KN +K+E + + E+++ + + S+
Sbjct: 130 SGKEGSSVLFICKDELPFVRELEDAKNIVIAKQEKYEPSEEIKSEVLEAVTEEPEDISDI 189
Query: 576 RIYKVDSSGACI 587
I + S +CI
Sbjct: 190 VISLISSYRSCI 201
>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 = 39.7 bits (91), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 33/132 (25%), Positives = 66/132 (50%), Gaps = 12/132 (9%)
Query: 468 MSRNAMKSILEKFRSGELNLLVATKVGEEGLDIQTCCLVIRFDLPETVASFIQSRGR-AR 526
+++N S++++F+ E +LV T VG G+D V++ +P +A++I GR AR
Sbjct: 70 ITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTAR 129
Query: 527 MPQSEYAFLVDSGNQ----RELDLIKN--FSKEE-----DRMNREIMDRTSSDAFTCSEE 575
+ + L ++ REL+ KN +K+E + + E+++ + + S+
Sbjct: 130 SGKEGSSVLFICKDELPFVRELEDAKNIVIAKQEKYEPSEEIKSEVLEAVTEEPEDISDI 189
Query: 576 RIYKVDSSGACI 587
I + S +CI
Sbjct: 190 VISLISSYRSCI 201
>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 = 39.7 bits (91), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 33/132 (25%), Positives = 66/132 (50%), Gaps = 12/132 (9%)
Query: 468 MSRNAMKSILEKFRSGELNLLVATKVGEEGLDIQTCCLVIRFDLPETVASFIQSRGR-AR 526
+++N S++++F+ E +LV T VG G+D V++ +P +A++I GR AR
Sbjct: 70 ITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTAR 129
Query: 527 MPQSEYAFLVDSGNQ----RELDLIKN--FSKEE-----DRMNREIMDRTSSDAFTCSEE 575
+ + L ++ REL+ KN +K+E + + E+++ + + S+
Sbjct: 130 SGKEGSSVLFICKDELPFVRELEDAKNIVIAKQEKYEPSEEIKSEVLEAVTEEPEDISDI 189
Query: 576 RIYKVDSSGACI 587
I + S +CI
Sbjct: 190 VISLISSYRSCI 201
>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 = 39.3 bits (90), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 33/132 (25%), Positives = 66/132 (50%), Gaps = 12/132 (9%)
Query: 468 MSRNAMKSILEKFRSGELNLLVATKVGEEGLDIQTCCLVIRFDLPETVASFIQSRGR-AR 526
+++N S++++F+ E +LV T VG G+D V++ +P +A++I GR AR
Sbjct: 376 ITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTAR 435
Query: 527 MPQSEYAFLVDSGNQ----RELDLIKN--FSKEE-----DRMNREIMDRTSSDAFTCSEE 575
+ + L ++ REL+ KN +K+E + + E+++ + + S+
Sbjct: 436 SGKEGSSVLFICKDELPFVRELEDAKNIVIAKQEKYEPSEEIKSEVLEAVTEEPEDISDI 495
Query: 576 RIYKVDSSGACI 587
I + S +CI
Sbjct: 496 VISLISSYRSCI 507
>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And
Amp-Pnp
Length = 579
Score = 39.3 bits (90), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 33/58 (56%)
Query: 468 MSRNAMKSILEKFRSGELNLLVATKVGEEGLDIQTCCLVIRFDLPETVASFIQSRGRA 525
+++N S++++F+ E +LV T VG G+D V++ +P +A++I GR
Sbjct: 325 ITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRT 382
>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 = 39.3 bits (90), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 43/145 (29%), Positives = 66/145 (45%), Gaps = 40/145 (27%)
Query: 60 RKYQLELCKKAMEENII-----VYLGTGCGKTHIAVLLIYELAHLIRKPQKSICIFLAPT 114
R YQ +KA+E ++ + L TG GKTH+A+ I EL+ + + + PT
Sbjct: 95 RDYQ----EKALERWLVDKRGCIVLPTGSGKTHVAMAAINELS--------TPTLIVVPT 142
Query: 115 VALVQQQAKVI----EESIGFKVRTFCGGSKRLKSHCDWEKEIDQYEVLVMIPQILLYCL 170
+AL +Q + + EE +G F G K LK + Y+ + + L
Sbjct: 143 LALAEQWKERLGIFGEEYVG----EFSGRIKELKPLT-----VSTYDSAYVNAE----KL 189
Query: 171 YHRFIKMELIALLIFDECHHAQVKS 195
+RF+ LLIFDE HH +S
Sbjct: 190 GNRFM------LLIFDEVHHLPAES 208
Score = 35.8 bits (81), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 31/60 (51%)
Query: 469 SRNAMKSILEKFRSGELNLLVATKVGEEGLDIQTCCLVIRFDLPETVASFIQSRGRARMP 528
SR + ILE FR+G +V+++V +EG+D+ + + + +IQ GR P
Sbjct: 379 SREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQRLGRILRP 438
>pdb|2FZ4|A Chain A, Crystal Structure Of The N-Terminal Half Of Archaeoglobus
Fulgidus Xpb
Length = 237
Score = 38.9 bits (89), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 43/145 (29%), Positives = 66/145 (45%), Gaps = 40/145 (27%)
Query: 60 RKYQLELCKKAMEENII-----VYLGTGCGKTHIAVLLIYELAHLIRKPQKSICIFLAPT 114
R YQ +KA+E ++ + L TG GKTH+A+ I EL+ + + + PT
Sbjct: 95 RDYQ----EKALERWLVDKRGCIVLPTGSGKTHVAMAAINELS--------TPTLIVVPT 142
Query: 115 VALVQQQAKVI----EESIGFKVRTFCGGSKRLKSHCDWEKEIDQYEVLVMIPQILLYCL 170
+AL +Q + + EE +G F G K LK + Y+ + + L
Sbjct: 143 LALAEQWKERLGIFGEEYVG----EFSGRIKELKPLT-----VSTYDSAYVNAE----KL 189
Query: 171 YHRFIKMELIALLIFDECHHAQVKS 195
+RF+ LLIFDE HH +S
Sbjct: 190 GNRFM------LLIFDEVHHLPAES 208
>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 = 38.1 bits (87), Expect = 0.044, Method: Composition-based stats.
Identities = 17/57 (29%), Positives = 29/57 (50%)
Query: 468 MSRNAMKSILEKFRSGELNLLVATKVGEEGLDIQTCCLVIRFDLPETVASFIQSRGR 524
M + +++ G +N+LVAT V G+DI V FD+P + +++ GR
Sbjct: 64 MVQGKRNEAIKRLTEGRVNVLVATDVAARGIDIPDVSHVFNFDMPRSGDTYLHRIGR 120
>pdb|2KBF|A Chain A, Solution Structure Of Carboxyl-Terminal Domain Of Dbp5p
Length = 187
Score = 37.7 bits (86), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 29/56 (51%), Gaps = 6/56 (10%)
Query: 476 ILEKFRSGELNLLVATKVGEEGLDIQTCCLVIRFDLPETV------ASFIQSRGRA 525
+++ FR G +L+ T V G+DI T +V+ +DLP A++I GR
Sbjct: 77 LIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRT 132
>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3
Length = 395
Score = 37.4 bits (85), Expect = 0.061, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 29/56 (51%), Gaps = 6/56 (10%)
Query: 476 ILEKFRSGELNLLVATKVGEEGLDIQTCCLVIRFDLPETV------ASFIQSRGRA 525
+++ FR G +L+ T V G+DI T +V+ +DLP A++I GR
Sbjct: 285 LIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRT 340
>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 = 37.4 bits (85), Expect = 0.061, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 29/56 (51%), Gaps = 6/56 (10%)
Query: 476 ILEKFRSGELNLLVATKVGEEGLDIQTCCLVIRFDLPETV------ASFIQSRGRA 525
+++ FR G +L+ T V G+DI T +V+ +DLP A++I GR
Sbjct: 285 LIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRT 340
>pdb|1T5I|A Chain A, Crystal Structure Of The C-Terminal Domain Of Uap56
Length = 172
Score = 37.4 bits (85), Expect = 0.066, Method: Compositional matrix adjust.
Identities = 29/126 (23%), Positives = 59/126 (46%), Gaps = 16/126 (12%)
Query: 400 LKEPFFSKKLLRLIGILSTFRLQQHMKCIVFVNRIVTARALSYILQNLKFLASWRCHFLV 459
LK+ ++KL L+ +L + + ++FV + AL+ +L F A +
Sbjct: 13 LKDNEKNRKLFDLLDVL------EFNQVVIFVKSVQRCIALAQLLVEQNFPA-------I 59
Query: 460 GVNAGLKSMSRNAMKSILEKFRSGELNLLVATKVGEEGLDIQTCCLVIRFDLPETVASFI 519
++ G+ R S ++F+ + +LVAT + G+DI+ + +D+PE +++
Sbjct: 60 AIHRGMPQEER---LSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYL 116
Query: 520 QSRGRA 525
RA
Sbjct: 117 HRVARA 122
>pdb|3FHO|A Chain A, Structure Of S. Pombe Dbp5
pdb|3FHO|B Chain B, Structure Of S. Pombe Dbp5
Length = 508
Score = 37.4 bits (85), Expect = 0.071, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 30/57 (52%), Gaps = 3/57 (5%)
Query: 456 HFLVGVNAGLKSMSRNAMKSILEKFRSGELNLLVATKVGEEGLDIQTCCLVIRFDLP 512
H + + L+ R+A I++ FR G +LV T V G+D+ LV+ +D+P
Sbjct: 382 HTVACLTGNLEGAQRDA---IMDSFRVGTSKVLVTTNVIARGIDVSQVNLVVNYDMP 435
>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp
Length = 386
Score = 37.0 bits (84), Expect = 0.087, Method: Compositional matrix adjust.
Identities = 29/126 (23%), Positives = 59/126 (46%), Gaps = 16/126 (12%)
Query: 400 LKEPFFSKKLLRLIGILSTFRLQQHMKCIVFVNRIVTARALSYILQNLKFLASWRCHFLV 459
LK+ ++KL L+ +L + + ++FV + AL+ +L F A +
Sbjct: 232 LKDNEKNRKLFDLLDVL------EFNQVVIFVKSVQRCIALAQLLVEQNFPA-------I 278
Query: 460 GVNAGLKSMSRNAMKSILEKFRSGELNLLVATKVGEEGLDIQTCCLVIRFDLPETVASFI 519
++ G+ R S ++F+ + +LVAT + G+DI+ + +D+PE +++
Sbjct: 279 AIHRGMPQEER---LSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYL 335
Query: 520 QSRGRA 525
RA
Sbjct: 336 HRVARA 341
>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56
Length = 390
Score = 37.0 bits (84), Expect = 0.088, Method: Compositional matrix adjust.
Identities = 29/126 (23%), Positives = 59/126 (46%), Gaps = 16/126 (12%)
Query: 400 LKEPFFSKKLLRLIGILSTFRLQQHMKCIVFVNRIVTARALSYILQNLKFLASWRCHFLV 459
LK+ ++KL L+ +L + + ++FV + AL+ +L F A +
Sbjct: 231 LKDNEKNRKLFDLLDVL------EFNQVVIFVKSVQRCIALAQLLVEQNFPA-------I 277
Query: 460 GVNAGLKSMSRNAMKSILEKFRSGELNLLVATKVGEEGLDIQTCCLVIRFDLPETVASFI 519
++ G+ R S ++F+ + +LVAT + G+DI+ + +D+PE +++
Sbjct: 278 AIHRGMPQEER---LSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYL 334
Query: 520 QSRGRA 525
RA
Sbjct: 335 HRVARA 340
>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56
Length = 391
Score = 37.0 bits (84), Expect = 0.095, Method: Compositional matrix adjust.
Identities = 29/126 (23%), Positives = 59/126 (46%), Gaps = 16/126 (12%)
Query: 400 LKEPFFSKKLLRLIGILSTFRLQQHMKCIVFVNRIVTARALSYILQNLKFLASWRCHFLV 459
LK+ ++KL L+ +L + + ++FV + AL+ +L F A +
Sbjct: 232 LKDNEKNRKLFDLLDVL------EFNQVVIFVKSVQRCIALAQLLVEQNFPA-------I 278
Query: 460 GVNAGLKSMSRNAMKSILEKFRSGELNLLVATKVGEEGLDIQTCCLVIRFDLPETVASFI 519
++ G+ R S ++F+ + +LVAT + G+DI+ + +D+PE +++
Sbjct: 279 AIHRGMPQEER---LSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYL 335
Query: 520 QSRGRA 525
RA
Sbjct: 336 HRVARA 341
>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 = 36.6 bits (83), Expect = 0.13, Method: Composition-based stats.
Identities = 18/68 (26%), Positives = 35/68 (51%), Gaps = 2/68 (2%)
Query: 459 VGVNAGL--KSMSRNAMKSILEKFRSGELNLLVATKVGEEGLDIQTCCLVIRFDLPETVA 516
+G AG +S++ + ++ F+ ++ +L+AT V G+D+ VI + LP+
Sbjct: 261 IGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVXSRGIDVNDLNCVINYHLPQNPE 320
Query: 517 SFIQSRGR 524
S+ GR
Sbjct: 321 SYXHRIGR 328
>pdb|3GFP|A Chain A, Structure Of The C-Terminal Domain Of The Dead-Box Protein
Dbp5
Length = 189
Score = 35.8 bits (81), Expect = 0.22, Method: Composition-based stats.
Identities = 18/55 (32%), Positives = 28/55 (50%), Gaps = 6/55 (10%)
Query: 476 ILEKFRSGELNLLVATKVGEEGLDIQTCCLVIRFDLPETV------ASFIQSRGR 524
+++ FR G +L+ T V G+DI T V+ +DLP A++I GR
Sbjct: 79 LIDDFREGRSKVLITTNVLARGIDIPTVSXVVNYDLPTLANGQADPATYIHRIGR 133
>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 = 35.8 bits (81), Expect = 0.22, Method: Composition-based stats.
Identities = 18/55 (32%), Positives = 28/55 (50%), Gaps = 6/55 (10%)
Query: 476 ILEKFRSGELNLLVATKVGEEGLDIQTCCLVIRFDLPETV------ASFIQSRGR 524
+++ FR G +L+ T V G+DI T V+ +DLP A++I GR
Sbjct: 78 LIDDFREGRSKVLITTNVLARGIDIPTVSXVVNYDLPTLANGQADPATYIHRIGR 132
>pdb|3FMO|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex
With The Dead- Box Helicase Ddx19
Length = 300
Score = 35.4 bits (80), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 33/121 (27%), Positives = 56/121 (46%), Gaps = 13/121 (10%)
Query: 73 ENIIVYLGTGCGKTHIAVL-LIYELAHLIRKPQKSICIFLAPTVALVQQQAKVIEESIGF 131
+N+I +G GKT VL ++ ++ + PQ C+ L+PT L Q KVIE+ F
Sbjct: 132 QNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQ---CLCLSPTYELALQTGKVIEQMGKF 188
Query: 132 ----KVRTFCGGSKRLKSHCDWEKEIDQYEVLVMIPQILLYCLYHRFIKMELIALLIFDE 187
K+ G+K + +I + V+ +L +C +FI + I + + DE
Sbjct: 189 YPELKLAYAVRGNKLERGQ-----KISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDE 243
Query: 188 C 188
Sbjct: 244 A 244
>pdb|2FZL|A Chain A, Structure Of C-Terminal Domain Of Archaeoglobus Fulgidus
Xpb
Length = 219
Score = 35.4 bits (80), Expect = 0.27, Method: Composition-based stats.
Identities = 18/60 (30%), Positives = 31/60 (51%)
Query: 469 SRNAMKSILEKFRSGELNLLVATKVGEEGLDIQTCCLVIRFDLPETVASFIQSRGRARMP 528
SR + ILE FR+G +V+++V +EG+D+ + + + +IQ GR P
Sbjct: 144 SREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQRLGRILRP 203
>pdb|3FHC|B Chain B, Crystal Structure Of Human Dbp5 In Complex With Nup214
Length = 235
Score = 34.3 bits (77), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 33/121 (27%), Positives = 56/121 (46%), Gaps = 13/121 (10%)
Query: 73 ENIIVYLGTGCGKTHIAVL-LIYELAHLIRKPQKSICIFLAPTVALVQQQAKVIEESIGF 131
+N+I +G GKT VL ++ ++ + PQ C+ L+PT L Q KVIE+ F
Sbjct: 65 QNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQ---CLCLSPTYELALQTGKVIEQMGKF 121
Query: 132 ----KVRTFCGGSKRLKSHCDWEKEIDQYEVLVMIPQILLYCLYHRFIKMELIALLIFDE 187
K+ G+K + +I + V+ +L +C +FI + I + + DE
Sbjct: 122 YPELKLAYAVRGNKLERGQ-----KISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDE 176
Query: 188 C 188
Sbjct: 177 A 177
>pdb|4A4D|A Chain A, Crystal Structure Of The N-Terminal Domain Of The Human
Dead-Box Rna Helicase Ddx5 (P68)
Length = 253
Score = 33.5 bits (75), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 35/138 (25%), Positives = 57/138 (41%), Gaps = 13/138 (9%)
Query: 81 TGCGKTHIAVLLIYELAHLIRKP-----QKSICIFLAPTVALVQQQAKVIEESI-GFKVR 134
TG GKT L+ + H+ +P IC+ LAPT L QQ +V E +++
Sbjct: 89 TGSGKT--LSYLLPAIVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLK 146
Query: 135 TFC--GGSKRLKSHCDWEKEIDQYEVLVMIPQILLYCLYHRFIKMELIALLIFDECHHAQ 192
+ C GG+ + D E+ + E+ + P L+ L + L+ DE
Sbjct: 147 STCIYGGAPKGPQIRDLERGV---EICIATPGRLIDFLECGKTNLRRTTYLVLDEADRML 203
Query: 193 VKSNHPYAKIMKDFYKPD 210
P + + D +PD
Sbjct: 204 DMGFEPQIRKIVDQIRPD 221
>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 = 33.5 bits (75), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 35/138 (25%), Positives = 57/138 (41%), Gaps = 13/138 (9%)
Query: 81 TGCGKTHIAVLLIYELAHLIRKP-----QKSICIFLAPTVALVQQQAKVIEESI-GFKVR 134
TG GKT L+ + H+ +P IC+ LAPT L QQ +V E +++
Sbjct: 75 TGSGKT--LSYLLPAIVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLK 132
Query: 135 TFC--GGSKRLKSHCDWEKEIDQYEVLVMIPQILLYCLYHRFIKMELIALLIFDECHHAQ 192
+ C GG+ + D E+ + E+ + P L+ L + L+ DE
Sbjct: 133 STCIYGGAPKGPQIRDLERGV---EICIATPGRLIDFLECGKTNLRRTTYLVLDEADRML 189
Query: 193 VKSNHPYAKIMKDFYKPD 210
P + + D +PD
Sbjct: 190 DMGFEPQIRKIVDQIRPD 207
>pdb|3D2E|A Chain A, Crystal Structure Of A Complex Of Sse1p And Hsp70,
Selenomethionine- Labeled Crystals
pdb|3D2E|C Chain C, Crystal Structure Of A Complex Of Sse1p And Hsp70,
Selenomethionine- Labeled Crystals
Length = 675
Score = 32.3 bits (72), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 29/94 (30%), Positives = 45/94 (47%), Gaps = 6/94 (6%)
Query: 199 YAKIMKDFYKPDIMKVPRIFG--MTASPVVGKGASAQANLPKSINSLENLLDAKVYSVED 256
+A K YK DI + P+ + +TA+ + K SA N P S+ S+ N D V S
Sbjct: 245 FADEFKTKYKIDIRENPKAYNRILTAAEKLKKVLSANTNAPFSVESVXN--DVDVSSQLS 302
Query: 257 AEDLESFVSSPVVRVYQYGPVINDTSSSYVTCSE 290
E+LE V + RV + PV + + ++ E
Sbjct: 303 REELEELVKPLLERVTE--PVTKALAQAKLSAEE 334
>pdb|2F7M|F Chain F, Crystal Structure Of Unliganded Human Fpps
pdb|2F89|F Chain F, Crystal Structure Of Human Fpps In Complex With Pamidronate
pdb|2F8C|F Chain F, Crystal Structure Of Fpps In Complex With Zoledronate
pdb|2F8Z|F Chain F, Crystal Structure Of Human Fpps In Complex With Zoledronate
And Isopentenyl Diphosphate
pdb|2F92|F Chain F, Crystal Structure Of Human Fpps In Complex With Alendronate
pdb|2F94|F Chain F, Crystal Structure Of Human Fpps In Complex With Ibandronate
pdb|2F9K|F Chain F, Crystal Structure Of Human Fpps In Complex With Zoledronate
And Zn2+
pdb|3N1V|F Chain F, Human Fpps Complex With Fbs_01
pdb|3N1W|F Chain F, Human Fpps Complex With Fbs_02
pdb|3N3L|F Chain F, Human Fpps Complex With Fbs_03
pdb|3N49|F Chain F, Human Fpps Complex With Nov_292
pdb|3N5H|F Chain F, Human Fpps Complex With Nov_304
pdb|3N5J|F Chain F, Human Fpps Complex With Nov_311
pdb|3N6K|F Chain F, Human Fpps Complex With Nov_823
pdb|3N45|F Chain F, Human Fpps Complex With Fbs_04 And Zoledronic AcidMG2+
pdb|3N46|F Chain F, Human Fpps Complex With Nov_980 And Zoledronic AcidMG2+
Length = 350
Score = 32.0 bits (71), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 29/55 (52%), Gaps = 11/55 (20%)
Query: 1058 LFLLHDTVDEGELTRRRS-----------NAVNNSNLLKLAARNNLQVYIRDQPF 1101
FL+ D + + LTRR +A+N++NLL+ L++Y R+QP+
Sbjct: 95 FFLVADDIMDSSLTRRGQICWYQKPGVGLDAINDANLLEACIYRLLKLYCREQPY 149
>pdb|3RYE|A Chain A, Human Fdps Synthase In Complex With A N-Methyl Pyridinum
Bisphosphonate
pdb|3S4J|A Chain A, Human Fdps Synthase In Complex With A Rigid Analog Of
Risedronate
Length = 349
Score = 32.0 bits (71), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 29/55 (52%), Gaps = 11/55 (20%)
Query: 1058 LFLLHDTVDEGELTRRRS-----------NAVNNSNLLKLAARNNLQVYIRDQPF 1101
FL+ D + + LTRR +A+N++NLL+ L++Y R+QP+
Sbjct: 94 FFLVADDIMDSSLTRRGQICWYQKPGVGLDAINDANLLEACIYRLLKLYCREQPY 148
>pdb|1ZW5|A Chain A, X-Ray Structure Of Farnesyl Diphosphate Synthase Protein
Length = 355
Score = 31.6 bits (70), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 29/55 (52%), Gaps = 11/55 (20%)
Query: 1058 LFLLHDTVDEGELTRRRS-----------NAVNNSNLLKLAARNNLQVYIRDQPF 1101
FL+ D + + LTRR +A+N++NLL+ L++Y R+QP+
Sbjct: 100 FFLVADDIMDSSLTRRGQICWYQKPGVGLDAINDANLLEACIYRLLKLYCREQPY 154
>pdb|3D2F|A Chain A, Crystal Structure Of A Complex Of Sse1p And Hsp70
pdb|3D2F|C Chain C, Crystal Structure Of A Complex Of Sse1p And Hsp70
Length = 675
Score = 31.6 bits (70), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 29/94 (30%), Positives = 45/94 (47%), Gaps = 6/94 (6%)
Query: 199 YAKIMKDFYKPDIMKVPRIFG--MTASPVVGKGASAQANLPKSINSLENLLDAKVYSVED 256
+A K YK DI + P+ + +TA+ + K SA N P S+ S+ N D V S
Sbjct: 245 FADEFKTKYKIDIRENPKAYNRILTAAEKLKKVLSANTNAPFSVESVMN--DVDVSSQLS 302
Query: 257 AEDLESFVSSPVVRVYQYGPVINDTSSSYVTCSE 290
E+LE V + RV + PV + + ++ E
Sbjct: 303 REELEELVKPLLERVTE--PVTKALAQAKLSAEE 334
>pdb|3B7L|A Chain A, Human Farnesyl Diphosphate Synthase Complexed With Mg And
Minodronate
Length = 356
Score = 31.6 bits (70), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 29/55 (52%), Gaps = 11/55 (20%)
Query: 1058 LFLLHDTVDEGELTRRRS-----------NAVNNSNLLKLAARNNLQVYIRDQPF 1101
FL+ D + + LTRR +A+N++NLL+ L++Y R+QP+
Sbjct: 101 FFLVADDIMDSSLTRRGQICWYQKPGVGLDAINDANLLEACIYRLLKLYCREQPY 155
>pdb|2QXL|A Chain A, Crystal Structure Analysis Of Sse1, A Yeast Hsp110
pdb|2QXL|B Chain B, Crystal Structure Analysis Of Sse1, A Yeast Hsp110
Length = 658
Score = 31.6 bits (70), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 29/94 (30%), Positives = 45/94 (47%), Gaps = 6/94 (6%)
Query: 199 YAKIMKDFYKPDIMKVPRIFG--MTASPVVGKGASAQANLPKSINSLENLLDAKVYSVED 256
+A K YK DI + P+ + +TA+ + K SA N P S+ S+ N D V S
Sbjct: 244 FADEFKTKYKIDIRENPKAYNRILTAAEKLKKVLSANTNAPFSVESVMN--DVDVSSQLS 301
Query: 257 AEDLESFVSSPVVRVYQYGPVINDTSSSYVTCSE 290
E+LE V + RV + PV + + ++ E
Sbjct: 302 REELEELVKPLLERVTE--PVTKALAQAKLSAEE 333
>pdb|3CP6|A Chain A, Crystal Structure Of Human Farnesyl Diphosphate Synthase
(T201a Mutant) Complexed With Mg And Biphosphonate
Inhibitor
Length = 376
Score = 31.6 bits (70), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 29/55 (52%), Gaps = 11/55 (20%)
Query: 1058 LFLLHDTVDEGELTRRRS-----------NAVNNSNLLKLAARNNLQVYIRDQPF 1101
FL+ D + + LTRR +A+N++NLL+ L++Y R+QP+
Sbjct: 121 FFLVADDIMDSSLTRRGQICWYQKPGVGLDAINDANLLEACIYRLLKLYCREQPY 175
>pdb|3C7N|A Chain A, Structure Of The Hsp110:hsc70 Nucleotide Exchange Complex
Length = 668
Score = 31.6 bits (70), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 29/94 (30%), Positives = 45/94 (47%), Gaps = 6/94 (6%)
Query: 199 YAKIMKDFYKPDIMKVPRIFG--MTASPVVGKGASAQANLPKSINSLENLLDAKVYSVED 256
+A K YK DI + P+ + +TA+ + K SA N P S+ S+ N D V S
Sbjct: 247 FADEFKTKYKIDIRENPKAYNRILTAAEKLKKVLSANTNAPFSVESVMN--DVDVSSQLS 304
Query: 257 AEDLESFVSSPVVRVYQYGPVINDTSSSYVTCSE 290
E+LE V + RV + PV + + ++ E
Sbjct: 305 REELEELVKPLLERVTE--PVTKALAQAKLSAEE 336
>pdb|4DEM|F Chain F, Crystal Structure Of Human Fpps In Complex With Ys_04_70
pdb|4H5D|F Chain F, Crystal Structure Of Human Fpps In Ternary Complex With
Ys0470 And Inorganic Pyrophosphate
pdb|4H5E|F Chain F, Crystal Structure Of Human Fpps In Ternary Complex With
Ys0470 And Isopentenyl Pyrophosphate
pdb|4H5C|F Chain F, Crystal Structure Of Human Fpps In Ternary Complex With
Ys0470 And Inorganic Phosphate
Length = 375
Score = 31.6 bits (70), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 29/55 (52%), Gaps = 11/55 (20%)
Query: 1058 LFLLHDTVDEGELTRRRS-----------NAVNNSNLLKLAARNNLQVYIRDQPF 1101
FL+ D + + LTRR +A+N++NLL+ L++Y R+QP+
Sbjct: 120 FFLVADDIMDSSLTRRGQICWYQKPGVGLDAINDANLLEACIYRLLKLYCREQPY 174
>pdb|2RAH|A Chain A, Human Fdps Synthase In Complex With Novel Inhibitor
pdb|2VF6|A Chain A, Human Fdps Synthase In Complex With Minodronate
Length = 378
Score = 31.6 bits (70), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 29/55 (52%), Gaps = 11/55 (20%)
Query: 1058 LFLLHDTVDEGELTRRRS-----------NAVNNSNLLKLAARNNLQVYIRDQPF 1101
FL+ D + + LTRR +A+N++NLL+ L++Y R+QP+
Sbjct: 123 FFLVADDIMDSSLTRRGQICWYQKPGVGLDAINDANLLEACIYRLLKLYCREQPY 177
>pdb|2QIS|A Chain A, Crystal Structure Of Human Farnesyl Pyrophosphate Synthase
T210s Mutant Bound To Risedronate
Length = 374
Score = 31.6 bits (70), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 29/55 (52%), Gaps = 11/55 (20%)
Query: 1058 LFLLHDTVDEGELTRRRS-----------NAVNNSNLLKLAARNNLQVYIRDQPF 1101
FL+ D + + LTRR +A+N++NLL+ L++Y R+QP+
Sbjct: 119 FFLVADDIMDSSLTRRGQICWYQKPGVGLDAINDANLLEACIYRLLKLYCREQPY 173
>pdb|1YQ7|A Chain A, Human Farnesyl Diphosphate Synthase Complexed With
Risedronate
pdb|1YV5|A Chain A, Human Farnesyl Diphosphate Synthase Complexed With Mg And
Risedronate
pdb|2OPN|A Chain A, Human Farnesyl Diphosphate Synthase Complexed With
Bisphosphonate Bph- 527
pdb|2OPM|A Chain A, Human Farnesyl Diphosphate Synthase Complexed With
Bisphosphonate Bph- 461
Length = 374
Score = 31.6 bits (70), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 29/55 (52%), Gaps = 11/55 (20%)
Query: 1058 LFLLHDTVDEGELTRRRS-----------NAVNNSNLLKLAARNNLQVYIRDQPF 1101
FL+ D + + LTRR +A+N++NLL+ L++Y R+QP+
Sbjct: 119 FFLVADDIMDSSLTRRGQICWYQKPGVGLDAINDANLLEACIYRLLKLYCREQPY 173
>pdb|4F91|B Chain B, Brr2 Helicase Region
Length = 1724
Score = 31.2 bits (69), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 37/141 (26%), Positives = 71/141 (50%), Gaps = 17/141 (12%)
Query: 61 KYQLELCKKAME--ENIIVYLGTGCGKTHIAVL-LIYELA-HLIRKPQKSI----CIFLA 112
+ Q +L + A+E EN+++ TG GKT++A++ ++ E+ H+ ++ I++A
Sbjct: 82 RIQSKLYRAALETDENLLLCAPTGAGKTNVALMCMLREIGKHINMDGTINVDDFKIIYIA 141
Query: 113 PTVALVQQQAKVIEESIGFKVRTFCGGSKRLKS-HCDWEKEIDQYEVLVMIPQ---ILLY 168
P +LVQ+ S G ++ T+ L H ++EI +++V P+ I+
Sbjct: 142 PMRSLVQEMVG----SFGKRLATYGITVAELTGDHQLCKEEISATQIIVCTPEKWDIITR 197
Query: 169 CLYHRFIKMELIALLIFDECH 189
R +L+ L+I DE H
Sbjct: 198 KGGER-TYTQLVRLIILDEIH 217
>pdb|4F92|B Chain B, Brr2 Helicase Region S1087l
pdb|4F93|B Chain B, Brr2 Helicase Region S1087l, Mg-Atp
Length = 1724
Score = 31.2 bits (69), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 37/141 (26%), Positives = 71/141 (50%), Gaps = 17/141 (12%)
Query: 61 KYQLELCKKAME--ENIIVYLGTGCGKTHIAVL-LIYELA-HLIRKPQKSI----CIFLA 112
+ Q +L + A+E EN+++ TG GKT++A++ ++ E+ H+ ++ I++A
Sbjct: 82 RIQSKLYRAALETDENLLLCAPTGAGKTNVALMCMLREIGKHINMDGTINVDDFKIIYIA 141
Query: 113 PTVALVQQQAKVIEESIGFKVRTFCGGSKRLKS-HCDWEKEIDQYEVLVMIPQ---ILLY 168
P +LVQ+ S G ++ T+ L H ++EI +++V P+ I+
Sbjct: 142 PMRSLVQEMVG----SFGKRLATYGITVAELTGDHQLCKEEISATQIIVCTPEKWDIITR 197
Query: 169 CLYHRFIKMELIALLIFDECH 189
R +L+ L+I DE H
Sbjct: 198 KGGER-TYTQLVRLIILDEIH 217
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 0.136 0.403
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 45,099,043
Number of Sequences: 62578
Number of extensions: 1835955
Number of successful extensions: 4072
Number of sequences better than 100.0: 102
Number of HSP's better than 100.0 without gapping: 78
Number of HSP's successfully gapped in prelim test: 24
Number of HSP's that attempted gapping in prelim test: 3902
Number of HSP's gapped (non-prelim): 152
length of query: 1601
length of database: 14,973,337
effective HSP length: 112
effective length of query: 1489
effective length of database: 7,964,601
effective search space: 11859290889
effective search space used: 11859290889
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 58 (26.9 bits)