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= 000854
(1252 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3KX2|B Chain B, Crystal Structure Of Prp43p In Complex With Adp
pdb|3KX2|A Chain A, Crystal Structure Of Prp43p In Complex With Adp
Length = 767
Score = 338 bits (866), Expect = 2e-92, Method: Compositional matrix adjust.
Identities = 234/698 (33%), Positives = 353/698 (50%), Gaps = 56/698 (8%)
Query: 140 EDCQRFDWSRIQAFIVRECK-------RLEDGLPIYMYRQDILRRIYGEQILVLIGETGC 192
E+ Q+ + +I F RE ++ LP++ R + L+ QI+V +GETG
Sbjct: 61 EEAQKLEDGKINPFTGREFTPKYVDILKIRRELPVHAQRDEFLKLYQNNQIMVFVGETGS 120
Query: 193 GKSTQLVQF-LADSGIAAEQS-IVCTQPRKIAAISLAQRVREESRGCYEDDSVICYPSFS 250
GK+TQ+ QF L D E + + CTQPR++AA+S+AQRV EE + V F
Sbjct: 121 GKTTQIPQFVLFDEMPHLENTQVACTQPRRVAAMSVAQRVAEEM-DVKLGEEVGYSIRFE 179
Query: 251 SAQHFDSKVIYMTDHCLLQHFMNDRDLSRISCIIVDEAHERSXXXXXXXXXXXXXXCRRF 310
+ + + YMTD LL+ M D DLSR SCII+DEAHER+ RR
Sbjct: 180 NKTSNKTILKYMTDGMLLREAMEDHDLSRYSCIILDEAHERTLATDILMGLLKQVVKRRP 239
Query: 311 DLRLVIMSATADAHQLSKYFYDCGISHVVGRNFPVDVRYVPCATAGTSAVASYVSDVVRM 370
DL+++IMSAT DA + +YF D + V GR +PV++ Y P Y+ +R
Sbjct: 240 DLKIIIMSATLDAEKFQRYFNDAPLLAVPGRTYPVELYYTP------EFQRDYLDSAIRT 293
Query: 371 VGEVHTTEKEGTILAFLTSKMEVEWACEKFD------------APSAVALPFHGQLSFDE 418
V ++H TE+ G IL FLT + E+E A K P +V P +G L +
Sbjct: 294 VLQIHATEEAGDILLFLTGEDEIEDAVRKISLEGDQLVREEGCGPLSV-YPLYGSLPPHQ 352
Query: 419 QFCVFKSYP----GR--RKVIFATNVAETSLTIPGVKFVIDSGMVKESYFEPGTGMNVLR 472
Q +F+ P GR RKV+ +TN+AETSLTI G+ +V+D G K+ + P + L
Sbjct: 353 QQRIFEPAPESHNGRPGRKVVISTNIAETSLTIDGIVYVVDPGFSKQKVYNPRIRVESLL 412
Query: 473 VCRVSQSSANQRAGRAGRTEPGRCYRLYSKSDFETRPLNQE-PEIHRVHLGIAVLRILAL 531
V +S++SA QRAGRAGRT PG+C+RLY++ F+ + Q PEI R +L VL + L
Sbjct: 413 VSPISKASAQQRAGRAGRTRPGKCFRLYTEEAFQKELIEQSYPEILRSNLSSTVLELKKL 472
Query: 532 GIRDVQGFDFIDAPSAKAIEMAIRNLVQLGAIKLNNGVFELTEEGKFLVKLGIEPRLGKL 591
GI D+ FDF+D P A E +R L +L + + LT G+ + ++P L +
Sbjct: 473 GIDDLVHFDFMDPP---APETMMRALEELNYLACLDDEGNLTPLGRLASQFPLDPMLAVM 529
Query: 592 ILSCFRRRLGREGLVLAAVMANASSIFCRVGSDDEKIKADCLKVQFCHRNGDLFTLLSVY 651
++ F + +E L + A M + ++F R D K +AD K F H +GD TLL+VY
Sbjct: 530 LIGSFEFQCSQEILTIVA-MLSVPNVFIRPTKD--KKRADDAKNIFAHPDGDHITLLNVY 586
Query: 652 REWDSLPREER--NKWCWENSVNAKSLRRCQDTIKELETCLEK-ELAIIIPSYWLWNPHK 708
+ S E +KWC ++ +N +SL + +LE + + L + Y K
Sbjct: 587 HAFKSDEAYEYGIHKWCRDHYLNYRSLSAADNIRSQLERLMNRYNLELNTTDY---ESPK 643
Query: 709 YTEYDKWLKEIILSALAENVAMFSGYDQLGYEVAMTGQHVQLHPSCSLLIFGQKPTWVVF 768
Y +D K + + SG GY Q V +HPS + G WV++
Sbjct: 644 Y--FDNIRKALASGFFMQVAKKRSGAK--GYITVKDNQDVLIHPST---VLGHDAEWVIY 696
Query: 769 GELLSVNNQYLVCVTAFDFDSLSTLCPSPLFDVSMMER 806
E + + Y+ VT+ + L + P+ +D+S ++
Sbjct: 697 NEFVLTSKNYIRTVTSVRPEWLIEIAPA-YYDLSNFQK 733
>pdb|2XAU|A Chain A, Crystal Structure Of The Prp43p Deah-Box Rna Helicase In
Complex With Adp
pdb|2XAU|B Chain B, Crystal Structure Of The Prp43p Deah-Box Rna Helicase In
Complex With Adp
Length = 773
Score = 338 bits (866), Expect = 2e-92, Method: Compositional matrix adjust.
Identities = 234/698 (33%), Positives = 353/698 (50%), Gaps = 56/698 (8%)
Query: 140 EDCQRFDWSRIQAFIVRECK-------RLEDGLPIYMYRQDILRRIYGEQILVLIGETGC 192
E+ Q+ + +I F RE ++ LP++ R + L+ QI+V +GETG
Sbjct: 61 EEAQKLEDGKINPFTGREFTPKYVDILKIRRELPVHAQRDEFLKLYQNNQIMVFVGETGS 120
Query: 193 GKSTQLVQF-LADSGIAAEQS-IVCTQPRKIAAISLAQRVREESRGCYEDDSVICYPSFS 250
GK+TQ+ QF L D E + + CTQPR++AA+S+AQRV EE + V F
Sbjct: 121 GKTTQIPQFVLFDEMPHLENTQVACTQPRRVAAMSVAQRVAEEM-DVKLGEEVGYSIRFE 179
Query: 251 SAQHFDSKVIYMTDHCLLQHFMNDRDLSRISCIIVDEAHERSXXXXXXXXXXXXXXCRRF 310
+ + + YMTD LL+ M D DLSR SCII+DEAHER+ RR
Sbjct: 180 NKTSNKTILKYMTDGMLLREAMEDHDLSRYSCIILDEAHERTLATDILMGLLKQVVKRRP 239
Query: 311 DLRLVIMSATADAHQLSKYFYDCGISHVVGRNFPVDVRYVPCATAGTSAVASYVSDVVRM 370
DL+++IMSAT DA + +YF D + V GR +PV++ Y P Y+ +R
Sbjct: 240 DLKIIIMSATLDAEKFQRYFNDAPLLAVPGRTYPVELYYTP------EFQRDYLDSAIRT 293
Query: 371 VGEVHTTEKEGTILAFLTSKMEVEWACEKFD------------APSAVALPFHGQLSFDE 418
V ++H TE+ G IL FLT + E+E A K P +V P +G L +
Sbjct: 294 VLQIHATEEAGDILLFLTGEDEIEDAVRKISLEGDQLVREEGCGPLSV-YPLYGSLPPHQ 352
Query: 419 QFCVFKSYP----GR--RKVIFATNVAETSLTIPGVKFVIDSGMVKESYFEPGTGMNVLR 472
Q +F+ P GR RKV+ +TN+AETSLTI G+ +V+D G K+ + P + L
Sbjct: 353 QQRIFEPAPESHNGRPGRKVVISTNIAETSLTIDGIVYVVDPGFSKQKVYNPRIRVESLL 412
Query: 473 VCRVSQSSANQRAGRAGRTEPGRCYRLYSKSDFETRPLNQE-PEIHRVHLGIAVLRILAL 531
V +S++SA QRAGRAGRT PG+C+RLY++ F+ + Q PEI R +L VL + L
Sbjct: 413 VSPISKASAQQRAGRAGRTRPGKCFRLYTEEAFQKELIEQSYPEILRSNLSSTVLELKKL 472
Query: 532 GIRDVQGFDFIDAPSAKAIEMAIRNLVQLGAIKLNNGVFELTEEGKFLVKLGIEPRLGKL 591
GI D+ FDF+D P A E +R L +L + + LT G+ + ++P L +
Sbjct: 473 GIDDLVHFDFMDPP---APETMMRALEELNYLACLDDEGNLTPLGRLASQFPLDPMLAVM 529
Query: 592 ILSCFRRRLGREGLVLAAVMANASSIFCRVGSDDEKIKADCLKVQFCHRNGDLFTLLSVY 651
++ F + +E L + A M + ++F R D K +AD K F H +GD TLL+VY
Sbjct: 530 LIGSFEFQCSQEILTIVA-MLSVPNVFIRPTKD--KKRADDAKNIFAHPDGDHITLLNVY 586
Query: 652 REWDSLPREER--NKWCWENSVNAKSLRRCQDTIKELETCLEK-ELAIIIPSYWLWNPHK 708
+ S E +KWC ++ +N +SL + +LE + + L + Y K
Sbjct: 587 HAFKSDEAYEYGIHKWCRDHYLNYRSLSAADNIRSQLERLMNRYNLELNTTDY---ESPK 643
Query: 709 YTEYDKWLKEIILSALAENVAMFSGYDQLGYEVAMTGQHVQLHPSCSLLIFGQKPTWVVF 768
Y +D K + + SG GY Q V +HPS + G WV++
Sbjct: 644 Y--FDNIRKALASGFFMQVAKKRSGAK--GYITVKDNQDVLIHPST---VLGHDAEWVIY 696
Query: 769 GELLSVNNQYLVCVTAFDFDSLSTLCPSPLFDVSMMER 806
E + + Y+ VT+ + L + P+ +D+S ++
Sbjct: 697 NEFVLTSKNYIRTVTSVRPEWLIEIAPA-YYDLSNFQK 733
>pdb|3I4U|A Chain A, Crystal Structure Analysis Of A Helicase Associated Domain
Length = 270
Score = 91.3 bits (225), Expect = 3e-18, Method: Compositional matrix adjust.
Identities = 70/244 (28%), Positives = 116/244 (47%), Gaps = 21/244 (8%)
Query: 553 AIRNLVQLGAIKLNNGVFELTEEGKFLVKLGIEPRLGKLILSCFRRRLGREGLVLAAVMA 612
A+ L LGA+ + G+ LT G+ + + +EP L K+++ E L + + M
Sbjct: 23 AMEQLYTLGALD-DEGL--LTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVS-ML 78
Query: 613 NASSIFCRVGSDDEKIKADCLKVQFCHRNGDLFTLLSVYREWDSLPREERNKWCWENSVN 672
+ ++F R D++ AD K +F GD TLL+VY W + + N WC+EN +
Sbjct: 79 SVQNVFYR--PKDKQALADQKKAKFHQTEGDHLTLLAVYNSWKN--NKFSNPWCYENFIQ 134
Query: 673 AKSLRRCQDTIKELETCLEKELAIIIPSYWLWNPHKYTEYDKWLKEIILSALAENVAMFS 732
A+SLRR QD K++ +++ ++ + +++ I S N A
Sbjct: 135 ARSLRRAQDIRKQMLGIMDRHKLDVVSC---------GKSTVRVQKAICSGFFRNAA--K 183
Query: 733 GYDQLGYEVAMTGQHVQLHPSCSLLIFGQKPTWVVFGELLSVNNQYLVCVTAFDFDSLST 792
Q GY + Q V +HPS +L F ++P WVV+ EL+ +Y+ VT D L
Sbjct: 184 KDPQEGYRTLIDQQVVYIHPSSAL--FNRQPEWVVYHELVLTTKEYMREVTTIDPRWLVE 241
Query: 793 LCPS 796
P+
Sbjct: 242 FAPA 245
>pdb|3LLM|A Chain A, Crystal Structure Analysis Of A Rna Helicase
pdb|3LLM|B Chain B, Crystal Structure Analysis Of A Rna Helicase
Length = 235
Score = 85.1 bits (209), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 62/183 (33%), Positives = 94/183 (51%), Gaps = 16/183 (8%)
Query: 165 LPIYMYRQDILRRIYGEQILVLIGETGCGKSTQLVQFLADSGI----AAEQSIVCTQPRK 220
LP+ + +IL I ++++ G TGCGK+TQ+ QF+ D I AAE +IV TQPR+
Sbjct: 60 LPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDDFIQNDRAAECNIVVTQPRR 119
Query: 221 IAAISLAQRVREESRGCYEDDSVIC-----YPSFSSAQHFDSKVIYMTDHCLLQHFMNDR 275
I+A+S+A+RV E RG E+ C + S H + + + T LL+ +
Sbjct: 120 ISAVSVAERVAFE-RG--EEPGKSCGYSVRFESILPRPH--ASIXFCTVGVLLRKL--EA 172
Query: 276 DLSRISCIIVDEAHERSXXXXXXXXXXXXXXCRRFDLRLVIMSATADAHQLSKYFYDCGI 335
+ IS +IVDE HER ++R+V+ SAT D +YF++C I
Sbjct: 173 GIRGISHVIVDEIHERDINTDFLLVVLRDVVQAYPEVRIVLXSATIDTSXFCEYFFNCPI 232
Query: 336 SHV 338
V
Sbjct: 233 IEV 235
>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 = 35.8 bits (81), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 33/69 (47%), Gaps = 1/69 (1%)
Query: 386 FLTSKMEVEWACEKFDAPSAVALPFHGQLSFDEQFCVFKSY-PGRRKVIFATNVAETSLT 444
F +K +V+W EK + HG + E+ + K + G +V+ +T+V L
Sbjct: 283 FCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLD 342
Query: 445 IPGVKFVID 453
+P V +I+
Sbjct: 343 VPQVSLIIN 351
>pdb|2HYI|C Chain C, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2HYI|I Chain I, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|3EX7|C Chain C, The Crystal Structure Of Ejc In Its Transition State
pdb|3EX7|H Chain H, The Crystal Structure Of Ejc In Its Transition State
Length = 413
Score = 35.8 bits (81), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 33/69 (47%), Gaps = 1/69 (1%)
Query: 386 FLTSKMEVEWACEKFDAPSAVALPFHGQLSFDEQFCVFKSY-PGRRKVIFATNVAETSLT 444
F +K +V+W EK + HG + E+ + K + G +V+ +T+V L
Sbjct: 283 FCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLD 342
Query: 445 IPGVKFVID 453
+P V +I+
Sbjct: 343 VPQVSLIIN 351
>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 35.8 bits (81), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 33/69 (47%), Gaps = 1/69 (1%)
Query: 386 FLTSKMEVEWACEKFDAPSAVALPFHGQLSFDEQFCVFKSY-PGRRKVIFATNVAETSLT 444
F +K +V+W EK + HG + E+ + K + G +V+ +T+V L
Sbjct: 246 FCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLD 305
Query: 445 IPGVKFVID 453
+P V +I+
Sbjct: 306 VPQVSLIIN 314
>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 35.8 bits (81), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 33/69 (47%), Gaps = 1/69 (1%)
Query: 386 FLTSKMEVEWACEKFDAPSAVALPFHGQLSFDEQFCVFKSY-PGRRKVIFATNVAETSLT 444
F +K +V+W EK + HG + E+ + K + G +V+ +T+V L
Sbjct: 246 FCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLD 305
Query: 445 IPGVKFVID 453
+P V +I+
Sbjct: 306 VPQVSLIIN 314
>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 = 35.8 bits (81), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 33/69 (47%), Gaps = 1/69 (1%)
Query: 386 FLTSKMEVEWACEKFDAPSAVALPFHGQLSFDEQFCVFKSY-PGRRKVIFATNVAETSLT 444
F +K +V+W EK + HG + E+ + K + G +V+ +T+V L
Sbjct: 261 FCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLD 320
Query: 445 IPGVKFVID 453
+P V +I+
Sbjct: 321 VPQVSLIIN 329
>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 = 35.8 bits (81), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 33/69 (47%), Gaps = 1/69 (1%)
Query: 386 FLTSKMEVEWACEKFDAPSAVALPFHGQLSFDEQFCVFKSY-PGRRKVIFATNVAETSLT 444
F +K +V+W EK + HG + E+ + K + G +V+ +T+V L
Sbjct: 282 FCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLD 341
Query: 445 IPGVKFVID 453
+P V +I+
Sbjct: 342 VPQVSLIIN 350
>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 = 34.7 bits (78), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 28/90 (31%), Positives = 38/90 (42%), Gaps = 19/90 (21%)
Query: 414 LSFDEQFCVFKSYP-GRRKVIFATNVAETSLTIPGVKFVIDSGMVKESYFEPGTGMNVLR 472
LS EQ + + G V+ AT+V E L +P V V+ ++EP
Sbjct: 403 LSQREQKLILDEFARGEFNVLVATSVGEEGLDVPEVDLVV--------FYEPVP------ 448
Query: 473 VCRVSQSSANQRAGRAGRTEPGRCYRLYSK 502
S + QR GR GR PGR L +K
Sbjct: 449 ----SAIRSIQRRGRTGRHMPGRVIILMAK 474
>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 = 34.3 bits (77), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 66/320 (20%), Positives = 115/320 (35%), Gaps = 33/320 (10%)
Query: 184 LVLIGETGCGKST--QLVQFLADSGIAAEQSIVCTQPRKIAAISLAQRVREESRGCYEDD 241
++ ++G GK+ L + A +C P + A + V+E +
Sbjct: 47 MIAQSQSGTGKTAAFSLTMLTRVNPEDASPQAICLAPSRELARQTLEVVQEMGKFTKITS 106
Query: 242 SVICYPSFSSAQHFDSKVIYMTDHCLLQHFMNDR--DLSRISCIIVDEAHERSXXXXXXX 299
+I SF + +++VI T +L M + L +I ++DEA
Sbjct: 107 QLIVPDSFEKNKQINAQVIVGTPGTVL-DLMRRKLMQLQKIKIFVLDEADN---MLDQQG 162
Query: 300 XXXXXXXCRRF---DLRLVIMSAT-ADA--HQLSKYFYDCGISHVVGRNFPVDV---RYV 350
+RF D +LV+ SAT ADA K + + VD Y+
Sbjct: 163 LGDQCIRVKRFLPKDTQLVLFSATFADAVRQYAKKIVPNANTLELQTNEVNVDAIKQLYM 222
Query: 351 PCATAGTSAVASYVSDVVRMVGEVHTTEKEGTILAFLTSKMEVEWACEKFDAPSAVALPF 410
C +D ++ E++ G+ + F+ +K K +
Sbjct: 223 DCKNE---------ADKFDVLTELYGVMTIGSSIIFVATKKTANVLYGKLKSEGHEVSIL 273
Query: 411 HGQLSFDEQFCVFKSY-PGRRKVIFATNVAETSLTIPGVKFVIDSGMVKESYFEPGTGMN 469
HG L E+ + + GR KV+ TNV + IP V V++ + + +
Sbjct: 274 HGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATY 333
Query: 470 VLRVCRVSQSSANQRAGRAG 489
+ R+ R R GR G
Sbjct: 334 IHRIGRTG------RFGRKG 347
>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3
Length = 395
Score = 34.3 bits (77), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 66/320 (20%), Positives = 115/320 (35%), Gaps = 33/320 (10%)
Query: 184 LVLIGETGCGKST--QLVQFLADSGIAAEQSIVCTQPRKIAAISLAQRVREESRGCYEDD 241
++ ++G GK+ L + A +C P + A + V+E +
Sbjct: 47 MIAQSQSGTGKTAAFSLTMLTRVNPEDASPQAICLAPSRELARQTLEVVQEMGKFTKITS 106
Query: 242 SVICYPSFSSAQHFDSKVIYMTDHCLLQHFMNDR--DLSRISCIIVDEAHERSXXXXXXX 299
+I SF + +++VI T +L M + L +I ++DEA
Sbjct: 107 QLIVPDSFEKNKQINAQVIVGTPGTVL-DLMRRKLMQLQKIKIFVLDEADN---MLDQQG 162
Query: 300 XXXXXXXCRRF---DLRLVIMSAT-ADA--HQLSKYFYDCGISHVVGRNFPVDV---RYV 350
+RF D +LV+ SAT ADA K + + VD Y+
Sbjct: 163 LGDQCIRVKRFLPKDTQLVLFSATFADAVRQYAKKIVPNANTLELQTNEVNVDAIKQLYM 222
Query: 351 PCATAGTSAVASYVSDVVRMVGEVHTTEKEGTILAFLTSKMEVEWACEKFDAPSAVALPF 410
C +D ++ E++ G+ + F+ +K K +
Sbjct: 223 DCKNE---------ADKFDVLTELYGLMTIGSSIIFVATKKTANVLYGKLKSEGHEVSIL 273
Query: 411 HGQLSFDEQFCVFKSY-PGRRKVIFATNVAETSLTIPGVKFVIDSGMVKESYFEPGTGMN 469
HG L E+ + + GR KV+ TNV + IP V V++ + + +
Sbjct: 274 HGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATY 333
Query: 470 VLRVCRVSQSSANQRAGRAG 489
+ R+ R R GR G
Sbjct: 334 IHRIGRTG------RFGRKG 347
>pdb|2X6W|A Chain A, Tailspike Protein Mutant E372q Of E.Coli Bacteriophage
Hk620 In Complex With Hexasaccharide
pdb|4AVZ|A Chain A, Tailspike Protein Mutant E372q Of E. Coli Bacteriophage
Hk620
Length = 600
Score = 33.1 bits (74), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 41/88 (46%), Gaps = 10/88 (11%)
Query: 339 VGRNFPVDVRYVPCATAGTSA--VASYVSDVVRMVGEVHTTEKEGTIL------AFLTSK 390
+ NF D RY+ GT++ V + V D ++G H ++ G L + + S
Sbjct: 405 IANNF--DCRYMVYNAPGTTSPVVQNLVWDKSNVIGGTHANQRAGQNLFDMQFASVVNST 462
Query: 391 MEVEWACEKFDAPSAVALPFHGQLSFDE 418
+EV+ +CE S + P QLS+ +
Sbjct: 463 IEVQLSCEDLSMFSCILFPASCQLSYSK 490
>pdb|2X6X|A Chain A, Tailspike Protein Mutant D339n Of E.Coli Bacteriophage
Hk620 In Complex With Hexasaccharide
Length = 600
Score = 33.1 bits (74), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 41/88 (46%), Gaps = 10/88 (11%)
Query: 339 VGRNFPVDVRYVPCATAGTSA--VASYVSDVVRMVGEVHTTEKEGTIL------AFLTSK 390
+ NF D RY+ GT++ V + V D ++G H ++ G L + + S
Sbjct: 405 IANNF--DCRYMVYNAPGTTSPVVQNLVWDKSNVIGGTHANQRAGQNLFDMQFASVVNST 462
Query: 391 MEVEWACEKFDAPSAVALPFHGQLSFDE 418
+EV+ +CE S + P QLS+ +
Sbjct: 463 IEVQLSCEDLSMFSCILFPASCQLSYSK 490
>pdb|2X6Y|A Chain A, Tailspike Protein Mutant D339a Of E.Coli Bacteriophage
Hk620 In Complex With Hexasaccharide
Length = 600
Score = 32.7 bits (73), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 41/88 (46%), Gaps = 10/88 (11%)
Query: 339 VGRNFPVDVRYVPCATAGTSA--VASYVSDVVRMVGEVHTTEKEGTIL------AFLTSK 390
+ NF D RY+ GT++ V + V D ++G H ++ G L + + S
Sbjct: 405 IANNF--DCRYMVYNAPGTTSPVVQNLVWDKSNVIGGTHANQRAGQNLFDMQFASVVNST 462
Query: 391 MEVEWACEKFDAPSAVALPFHGQLSFDE 418
+EV+ +CE S + P QLS+ +
Sbjct: 463 IEVQLSCEDLSMFSCILFPASCQLSYSK 490
>pdb|2VJI|A Chain A, Tailspike Protein Of E.Coli Bacteriophage Hk620
pdb|2VJJ|A Chain A, Tailspike Protein Of E.Coli Bacteriophage Hk620 In Complex
With Hexasaccharide
pdb|2X85|A Chain A, Tailspike Protein Of E. Coli Bacteriophage Hk620 In
Complex With Hexasaccharide
Length = 600
Score = 32.7 bits (73), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 41/88 (46%), Gaps = 10/88 (11%)
Query: 339 VGRNFPVDVRYVPCATAGTSA--VASYVSDVVRMVGEVHTTEKEGTIL------AFLTSK 390
+ NF D RY+ GT++ V + V D ++G H ++ G L + + S
Sbjct: 405 IANNF--DCRYMVYNAPGTTSPVVQNLVWDKSNVIGGTHANQRAGQNLFDMQFASVVNST 462
Query: 391 MEVEWACEKFDAPSAVALPFHGQLSFDE 418
+EV+ +CE S + P QLS+ +
Sbjct: 463 IEVQLSCEDLSMFSCILFPASCQLSYSK 490
>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 = 32.0 bits (71), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 15/69 (21%), Positives = 32/69 (46%), Gaps = 1/69 (1%)
Query: 386 FLTSKMEVEWACEKFDAPSAVALPFHGQLSFDEQFCVFKSY-PGRRKVIFATNVAETSLT 444
F+ ++ +V+W EK A HG + E+ + + + G +V+ T++ +
Sbjct: 260 FINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGID 319
Query: 445 IPGVKFVID 453
+ V VI+
Sbjct: 320 VQQVSLVIN 328
>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a
pdb|3EIQ|D Chain D, Crystal Structure Of Pdcd4-eif4a
Length = 414
Score = 32.0 bits (71), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 15/69 (21%), Positives = 32/69 (46%), Gaps = 1/69 (1%)
Query: 386 FLTSKMEVEWACEKFDAPSAVALPFHGQLSFDEQFCVFKSY-PGRRKVIFATNVAETSLT 444
F+ ++ +V+W EK A HG + E+ + + + G +V+ T++ +
Sbjct: 286 FINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGID 345
Query: 445 IPGVKFVID 453
+ V VI+
Sbjct: 346 VQQVSLVIN 354
>pdb|1D2M|A Chain A, Uvrb Protein Of Thermus Thermophilus Hb8; A Nucleotide
Excision Repair Enzyme
Length = 665
Score = 31.6 bits (70), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 26/53 (49%), Gaps = 4/53 (7%)
Query: 180 GEQILVLIGETGCGKSTQLVQFLADSGIAAEQSIVCTQPRKIAAISLAQRVRE 232
GE+ + L+G TG GK+ + + + G A + P KI A LA RE
Sbjct: 28 GERFVTLLGATGTGKTVTMAKVIEALGRPA----LVLAPNKILAAQLAAEFRE 76
>pdb|1C4O|A Chain A, Crystal Structure Of The Dna Nucleotide Excision Repair
Enzyme Uvrb From Thermus Thermophilus
Length = 664
Score = 31.6 bits (70), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 26/53 (49%), Gaps = 4/53 (7%)
Query: 180 GEQILVLIGETGCGKSTQLVQFLADSGIAAEQSIVCTQPRKIAAISLAQRVRE 232
GE+ + L+G TG GK+ + + + G A + P KI A LA RE
Sbjct: 27 GERFVTLLGATGTGKTVTMAKVIEALGRPA----LVLAPNKILAAQLAAEFRE 75
>pdb|3PI6|A Chain A, Crystal Structure Of The Cftr Inhibitory Factor Cif With The
H177y Mutation
pdb|3PI6|B Chain B, Crystal Structure Of The Cftr Inhibitory Factor Cif With The
H177y Mutation
pdb|3PI6|C Chain C, Crystal Structure Of The Cftr Inhibitory Factor Cif With The
H177y Mutation
pdb|3PI6|D Chain D, Crystal Structure Of The Cftr Inhibitory Factor Cif With The
H177y Mutation
Length = 301
Score = 31.6 bits (70), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 15/29 (51%), Positives = 17/29 (58%), Gaps = 1/29 (3%)
Query: 1164 LHLEAAKAL-EQLEGKVLPGCGPWQKMKC 1191
LE KA E +EG VLPGCG W +C
Sbjct: 251 FQLEQMKAYAEDVEGHVLPGCGHWLPEEC 279
>pdb|3KD2|A Chain A, Crystal Structure Of The Cftr Inhibitory Factor Cif
pdb|3KD2|B Chain B, Crystal Structure Of The Cftr Inhibitory Factor Cif
pdb|3KD2|C Chain C, Crystal Structure Of The Cftr Inhibitory Factor Cif
pdb|3KD2|D Chain D, Crystal Structure Of The Cftr Inhibitory Factor Cif
Length = 301
Score = 31.6 bits (70), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 15/29 (51%), Positives = 17/29 (58%), Gaps = 1/29 (3%)
Query: 1164 LHLEAAKAL-EQLEGKVLPGCGPWQKMKC 1191
LE KA E +EG VLPGCG W +C
Sbjct: 251 FQLEQMKAYAEDVEGHVLPGCGHWLPEEC 279
>pdb|3KDA|A Chain A, Crystal Structure Of The Cftr Inhibitory Factor Cif With The
H269a Mutation
pdb|3KDA|B Chain B, Crystal Structure Of The Cftr Inhibitory Factor Cif With The
H269a Mutation
pdb|3KDA|C Chain C, Crystal Structure Of The Cftr Inhibitory Factor Cif With The
H269a Mutation
pdb|3KDA|D Chain D, Crystal Structure Of The Cftr Inhibitory Factor Cif With The
H269a Mutation
Length = 301
Score = 31.6 bits (70), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 15/29 (51%), Positives = 17/29 (58%), Gaps = 1/29 (3%)
Query: 1164 LHLEAAKAL-EQLEGKVLPGCGPWQKMKC 1191
LE KA E +EG VLPGCG W +C
Sbjct: 251 FQLEQMKAYAEDVEGHVLPGCGHWLPEEC 279
>pdb|2K52|A Chain A, Structure Of Uncharacterized Protein Mj1198 From
Methanocaldococcus Jannaschii. Northeast Structural
Genomics Target Mjr117b
Length = 80
Score = 31.2 bits (69), Expect = 3.7, Method: Composition-based stats.
Identities = 13/40 (32%), Positives = 22/40 (55%)
Query: 80 YAVFCELNERKKGLFKEREMIMRRVREFKNGMHCVLKYLD 119
Y F LNE+ +GL + R+MI R+ G +++ +D
Sbjct: 19 YGAFINLNEQVRGLLRPRDMISLRLENLNVGDEIIVQAID 58
>pdb|2KBF|A Chain A, Solution Structure Of Carboxyl-Terminal Domain Of Dbp5p
Length = 187
Score = 30.8 bits (68), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 25/110 (22%), Positives = 42/110 (38%), Gaps = 7/110 (6%)
Query: 381 GTILAFLTSKMEVEWACEKFDAPSAVALPFHGQLSFDEQFCVFKSY-PGRRKVIFATNVA 439
G+ + F+ +K K + HG L E+ + + GR KV+ TNV
Sbjct: 36 GSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVL 95
Query: 440 ETSLTIPGVKFVIDSGMVKESYFEPGTGMNVLRVCRVSQSSANQRAGRAG 489
+ IP V V++ + + + + R+ R R GR G
Sbjct: 96 ARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTG------RFGRKG 139
>pdb|1CK0|H Chain H, Anti-Anti-Idiotypic Antibody Against Human Angiotensin Ii,
Unliganded Form
pdb|2CK0|H Chain H, Anti-Anti-Idiotypic Antibody Against Human Angiotensin Ii,
Complex With A Synthetic Cyclic Peptide
pdb|3CK0|H Chain H, Anti-Anti-Idiotypic Antibody Against Human Angiotensin Ii,
Complex With Human Angiotensin Ii
Length = 219
Score = 30.0 bits (66), Expect = 9.5, Method: Composition-based stats.
Identities = 27/102 (26%), Positives = 44/102 (43%), Gaps = 19/102 (18%)
Query: 938 DDKELLMFLE-KNASGSICSIHKFAVGQDSDEKDKWGRVTFLT------------PDTAG 984
DD + +++L+ N I+ G+D + D WG+ T LT P G
Sbjct: 75 DDSQSMLYLQMNNLKTEDTGIYYCVRGRDGEAMDYWGQGTTLTVSSAKTTPPSVYPLAPG 134
Query: 985 KATELNGVEYNGSLLK-VVPSRATLGGD-----NKMYTFPAV 1020
A + N + G L+K P T+ + + ++TFPAV
Sbjct: 135 SAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAV 176
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
0.323 0.138 0.418
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 34,641,964
Number of Sequences: 62578
Number of extensions: 1420626
Number of successful extensions: 3538
Number of sequences better than 100.0: 29
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 21
Number of HSP's that attempted gapping in prelim test: 3507
Number of HSP's gapped (non-prelim): 30
length of query: 1252
length of database: 14,973,337
effective HSP length: 110
effective length of query: 1142
effective length of database: 8,089,757
effective search space: 9238502494
effective search space used: 9238502494
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 57 (26.6 bits)