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= 000621
(1387 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 = 337 bits (864), Expect = 3e-92, Method: Compositional matrix adjust.
Identities = 234/698 (33%), Positives = 353/698 (50%), Gaps = 56/698 (8%)
Query: 127 EDCQRFDWSRIQAFIVRECK-------RLEDGLPIYMYRQDILRRIYGEQILVLIGETGC 179
E+ Q+ + +I F RE ++ LP++ R + L+ QI+V +GETG
Sbjct: 61 EEAQKLEDGKINPFTGREFTPKYVDILKIRRELPVHAQRDEFLKLYQNNQIMVFVGETGS 120
Query: 180 GKSTQLVQF-LADSGIAAEQS-IVCTQPRKIAAISLAQRVREESRGCYEDDSVICYPSFS 237
GK+TQ+ QF L D E + + CTQPR++AA+S+AQRV EE + V F
Sbjct: 121 GKTTQIPQFVLFDEMPHLENTQVACTQPRRVAAMSVAQRVAEEM-DVKLGEEVGYSIRFE 179
Query: 238 SAQHFDSKVIYMTDHCLLQHFMNDRDLSRISCIIVDEAHERSXXXXXXXXXXXXXXCRRF 297
+ + + YMTD LL+ M D DLSR SCII+DEAHER+ RR
Sbjct: 180 NKTSNKTILKYMTDGMLLREAMEDHDLSRYSCIILDEAHERTLATDILMGLLKQVVKRRP 239
Query: 298 DLRLVIMSATADAHQLSKYFYDCGISHVVGRNFPVDVRYVPCATAGTSAVASYVSDVVRM 357
DL+++IMSAT DA + +YF D + V GR +PV++ Y P Y+ +R
Sbjct: 240 DLKIIIMSATLDAEKFQRYFNDAPLLAVPGRTYPVELYYTP------EFQRDYLDSAIRT 293
Query: 358 VGEVHTTEKEGTILAFLTSKMEVEWACEKFD------------APSAVALPFHGQLSFDE 405
V ++H TE+ G IL FLT + E+E A K P +V P +G L +
Sbjct: 294 VLQIHATEEAGDILLFLTGEDEIEDAVRKISLEGDQLVREEGCGPLSV-YPLYGSLPPHQ 352
Query: 406 QFCVFKSYP----GR--RKVIFATNVAETSLTIPGVKFVIDSGMVKESYFEPGTGMNVLR 459
Q +F+ P GR RKV+ +TN+AETSLTI G+ +V+D G K+ + P + L
Sbjct: 353 QQRIFEPAPESHNGRPGRKVVISTNIAETSLTIDGIVYVVDPGFSKQKVYNPRIRVESLL 412
Query: 460 VCRVSQSSANQRAGRAGRTEPGRCYRLYSKSDFETRPLNQE-PEIHRVHLGIAVLRILAL 518
V +S++SA QRAGRAGRT PG+C+RLY++ F+ + Q PEI R +L VL + L
Sbjct: 413 VSPISKASAQQRAGRAGRTRPGKCFRLYTEEAFQKELIEQSYPEILRSNLSSTVLELKKL 472
Query: 519 GIRDVQGFDFIDAPSAKAIEMAIRNLVQLGAIKLNNGVFELTEEGKFLVKLGIEPRLGKL 578
GI D+ FDF+D P A E +R L +L + + LT G+ + ++P L +
Sbjct: 473 GIDDLVHFDFMDPP---APETMMRALEELNYLACLDDEGNLTPLGRLASQFPLDPMLAVM 529
Query: 579 ILSCFRRRLGREGLVLAAVMANASSIFCRVGSDDEKIKADCLKVQFCHRNGDLFTLLSVY 638
++ F + +E L + A M + ++F R D K +AD K F H +GD TLL+VY
Sbjct: 530 LIGSFEFQCSQEILTIVA-MLSVPNVFIRPTKD--KKRADDAKNIFAHPDGDHITLLNVY 586
Query: 639 REWDSLPREER--NKWCWENSVNAKSLRRCQDTIKELETCLEK-ELAIIIPSYWLWNPHK 695
+ S E +KWC ++ +N +SL + +LE + + L + Y K
Sbjct: 587 HAFKSDEAYEYGIHKWCRDHYLNYRSLSAADNIRSQLERLMNRYNLELNTTDY---ESPK 643
Query: 696 YTEYDKWLKEIILSALAENVAMFSGYDQLGYEVAMTGQHVQLHPSCSLLIFGQKPTWVVF 755
Y +D K + + SG GY Q V +HPS + G WV++
Sbjct: 644 Y--FDNIRKALASGFFMQVAKKRSGAK--GYITVKDNQDVLIHPST---VLGHDAEWVIY 696
Query: 756 GELLSVNNQYLVCVTAFDFDSLSTLCPSPLFDVSMMER 793
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 = 337 bits (864), Expect = 3e-92, Method: Compositional matrix adjust.
Identities = 234/698 (33%), Positives = 353/698 (50%), Gaps = 56/698 (8%)
Query: 127 EDCQRFDWSRIQAFIVRECK-------RLEDGLPIYMYRQDILRRIYGEQILVLIGETGC 179
E+ Q+ + +I F RE ++ LP++ R + L+ QI+V +GETG
Sbjct: 61 EEAQKLEDGKINPFTGREFTPKYVDILKIRRELPVHAQRDEFLKLYQNNQIMVFVGETGS 120
Query: 180 GKSTQLVQF-LADSGIAAEQS-IVCTQPRKIAAISLAQRVREESRGCYEDDSVICYPSFS 237
GK+TQ+ QF L D E + + CTQPR++AA+S+AQRV EE + V F
Sbjct: 121 GKTTQIPQFVLFDEMPHLENTQVACTQPRRVAAMSVAQRVAEEM-DVKLGEEVGYSIRFE 179
Query: 238 SAQHFDSKVIYMTDHCLLQHFMNDRDLSRISCIIVDEAHERSXXXXXXXXXXXXXXCRRF 297
+ + + YMTD LL+ M D DLSR SCII+DEAHER+ RR
Sbjct: 180 NKTSNKTILKYMTDGMLLREAMEDHDLSRYSCIILDEAHERTLATDILMGLLKQVVKRRP 239
Query: 298 DLRLVIMSATADAHQLSKYFYDCGISHVVGRNFPVDVRYVPCATAGTSAVASYVSDVVRM 357
DL+++IMSAT DA + +YF D + V GR +PV++ Y P Y+ +R
Sbjct: 240 DLKIIIMSATLDAEKFQRYFNDAPLLAVPGRTYPVELYYTP------EFQRDYLDSAIRT 293
Query: 358 VGEVHTTEKEGTILAFLTSKMEVEWACEKFD------------APSAVALPFHGQLSFDE 405
V ++H TE+ G IL FLT + E+E A K P +V P +G L +
Sbjct: 294 VLQIHATEEAGDILLFLTGEDEIEDAVRKISLEGDQLVREEGCGPLSV-YPLYGSLPPHQ 352
Query: 406 QFCVFKSYP----GR--RKVIFATNVAETSLTIPGVKFVIDSGMVKESYFEPGTGMNVLR 459
Q +F+ P GR RKV+ +TN+AETSLTI G+ +V+D G K+ + P + L
Sbjct: 353 QQRIFEPAPESHNGRPGRKVVISTNIAETSLTIDGIVYVVDPGFSKQKVYNPRIRVESLL 412
Query: 460 VCRVSQSSANQRAGRAGRTEPGRCYRLYSKSDFETRPLNQE-PEIHRVHLGIAVLRILAL 518
V +S++SA QRAGRAGRT PG+C+RLY++ F+ + Q PEI R +L VL + L
Sbjct: 413 VSPISKASAQQRAGRAGRTRPGKCFRLYTEEAFQKELIEQSYPEILRSNLSSTVLELKKL 472
Query: 519 GIRDVQGFDFIDAPSAKAIEMAIRNLVQLGAIKLNNGVFELTEEGKFLVKLGIEPRLGKL 578
GI D+ FDF+D P A E +R L +L + + LT G+ + ++P L +
Sbjct: 473 GIDDLVHFDFMDPP---APETMMRALEELNYLACLDDEGNLTPLGRLASQFPLDPMLAVM 529
Query: 579 ILSCFRRRLGREGLVLAAVMANASSIFCRVGSDDEKIKADCLKVQFCHRNGDLFTLLSVY 638
++ F + +E L + A M + ++F R D K +AD K F H +GD TLL+VY
Sbjct: 530 LIGSFEFQCSQEILTIVA-MLSVPNVFIRPTKD--KKRADDAKNIFAHPDGDHITLLNVY 586
Query: 639 REWDSLPREER--NKWCWENSVNAKSLRRCQDTIKELETCLEK-ELAIIIPSYWLWNPHK 695
+ S E +KWC ++ +N +SL + +LE + + L + Y K
Sbjct: 587 HAFKSDEAYEYGIHKWCRDHYLNYRSLSAADNIRSQLERLMNRYNLELNTTDY---ESPK 643
Query: 696 YTEYDKWLKEIILSALAENVAMFSGYDQLGYEVAMTGQHVQLHPSCSLLIFGQKPTWVVF 755
Y +D K + + SG GY Q V +HPS + G WV++
Sbjct: 644 Y--FDNIRKALASGFFMQVAKKRSGAK--GYITVKDNQDVLIHPST---VLGHDAEWVIY 696
Query: 756 GELLSVNNQYLVCVTAFDFDSLSTLCPSPLFDVSMMER 793
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 = 90.9 bits (224), Expect = 4e-18, Method: Compositional matrix adjust.
Identities = 70/244 (28%), Positives = 116/244 (47%), Gaps = 21/244 (8%)
Query: 540 AIRNLVQLGAIKLNNGVFELTEEGKFLVKLGIEPRLGKLILSCFRRRLGREGLVLAAVMA 599
A+ L LGA+ + G+ LT G+ + + +EP L K+++ E L + + M
Sbjct: 23 AMEQLYTLGALD-DEGL--LTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVS-ML 78
Query: 600 NASSIFCRVGSDDEKIKADCLKVQFCHRNGDLFTLLSVYREWDSLPREERNKWCWENSVN 659
+ ++F R D++ AD K +F GD TLL+VY W + + N WC+EN +
Sbjct: 79 SVQNVFYR--PKDKQALADQKKAKFHQTEGDHLTLLAVYNSWKN--NKFSNPWCYENFIQ 134
Query: 660 AKSLRRCQDTIKELETCLEKELAIIIPSYWLWNPHKYTEYDKWLKEIILSALAENVAMFS 719
A+SLRR QD K++ +++ ++ + +++ I S N A
Sbjct: 135 ARSLRRAQDIRKQMLGIMDRHKLDVVSC---------GKSTVRVQKAICSGFFRNAA--K 183
Query: 720 GYDQLGYEVAMTGQHVQLHPSCSLLIFGQKPTWVVFGELLSVNNQYLVCVTAFDFDSLST 779
Q GY + Q V +HPS +L F ++P WVV+ EL+ +Y+ VT D L
Sbjct: 184 KDPQEGYRTLIDQQVVYIHPSSAL--FNRQPEWVVYHELVLTTKEYMREVTTIDPRWLVE 241
Query: 780 LCPS 783
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 = 85.5 bits (210), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 62/183 (33%), Positives = 94/183 (51%), Gaps = 16/183 (8%)
Query: 152 LPIYMYRQDILRRIYGEQILVLIGETGCGKSTQLVQFLADSGI----AAEQSIVCTQPRK 207
LP+ + +IL I ++++ G TGCGK+TQ+ QF+ D I AAE +IV TQPR+
Sbjct: 60 LPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDDFIQNDRAAECNIVVTQPRR 119
Query: 208 IAAISLAQRVREESRGCYEDDSVIC-----YPSFSSAQHFDSKVIYMTDHCLLQHFMNDR 262
I+A+S+A+RV E RG E+ C + S H + + + T LL+ +
Sbjct: 120 ISAVSVAERVAFE-RG--EEPGKSCGYSVRFESILPRPH--ASIXFCTVGVLLRKL--EA 172
Query: 263 DLSRISCIIVDEAHERSXXXXXXXXXXXXXXCRRFDLRLVIMSATADAHQLSKYFYDCGI 322
+ IS +IVDE HER ++R+V+ SAT D +YF++C I
Sbjct: 173 GIRGISHVIVDEIHERDINTDFLLVVLRDVVQAYPEVRIVLXSATIDTSXFCEYFFNCPI 232
Query: 323 SHV 325
V
Sbjct: 233 IEV 235
>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 36.2 bits (82), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 33/69 (47%), Gaps = 1/69 (1%)
Query: 373 FLTSKMEVEWACEKFDAPSAVALPFHGQLSFDEQFCVFKSY-PGRRKVIFATNVAETSLT 431
F +K +V+W EK + HG + E+ + K + G +V+ +T+V L
Sbjct: 246 FCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLD 305
Query: 432 IPGVKFVID 440
+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 = 36.2 bits (82), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 33/69 (47%), Gaps = 1/69 (1%)
Query: 373 FLTSKMEVEWACEKFDAPSAVALPFHGQLSFDEQFCVFKSY-PGRRKVIFATNVAETSLT 431
F +K +V+W EK + HG + E+ + K + G +V+ +T+V L
Sbjct: 246 FCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLD 305
Query: 432 IPGVKFVID 440
+P V +I+
Sbjct: 306 VPQVSLIIN 314
>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 = 36.2 bits (82), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 33/69 (47%), Gaps = 1/69 (1%)
Query: 373 FLTSKMEVEWACEKFDAPSAVALPFHGQLSFDEQFCVFKSY-PGRRKVIFATNVAETSLT 431
F +K +V+W EK + HG + E+ + K + G +V+ +T+V L
Sbjct: 282 FCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLD 341
Query: 432 IPGVKFVID 440
+P V +I+
Sbjct: 342 VPQVSLIIN 350
>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 = 36.2 bits (82), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 33/69 (47%), Gaps = 1/69 (1%)
Query: 373 FLTSKMEVEWACEKFDAPSAVALPFHGQLSFDEQFCVFKSY-PGRRKVIFATNVAETSLT 431
F +K +V+W EK + HG + E+ + K + G +V+ +T+V L
Sbjct: 283 FCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLD 342
Query: 432 IPGVKFVID 440
+P V +I+
Sbjct: 343 VPQVSLIIN 351
>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 = 0.15, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 33/69 (47%), Gaps = 1/69 (1%)
Query: 373 FLTSKMEVEWACEKFDAPSAVALPFHGQLSFDEQFCVFKSY-PGRRKVIFATNVAETSLT 431
F +K +V+W EK + HG + E+ + K + G +V+ +T+V L
Sbjct: 283 FCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLD 342
Query: 432 IPGVKFVID 440
+P V +I+
Sbjct: 343 VPQVSLIIN 351
>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 = 0.16, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 33/69 (47%), Gaps = 1/69 (1%)
Query: 373 FLTSKMEVEWACEKFDAPSAVALPFHGQLSFDEQFCVFKSY-PGRRKVIFATNVAETSLT 431
F +K +V+W EK + HG + E+ + K + G +V+ +T+V L
Sbjct: 261 FCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLD 320
Query: 432 IPGVKFVID 440
+P V +I+
Sbjct: 321 VPQVSLIIN 329
>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 = 0.42, Method: Compositional matrix adjust.
Identities = 28/90 (31%), Positives = 38/90 (42%), Gaps = 19/90 (21%)
Query: 401 LSFDEQFCVFKSYP-GRRKVIFATNVAETSLTIPGVKFVIDSGMVKESYFEPGTGMNVLR 459
LS EQ + + G V+ AT+V E L +P V V+ ++EP
Sbjct: 403 LSQREQKLILDEFARGEFNVLVATSVGEEGLDVPEVDLVV--------FYEPVP------ 448
Query: 460 VCRVSQSSANQRAGRAGRTEPGRCYRLYSK 489
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 = 33.9 bits (76), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 62/293 (21%), Positives = 105/293 (35%), Gaps = 31/293 (10%)
Query: 196 AEQSIVCTQPRKIAAISLAQRVREESRGCYEDDSVICYPSFSSAQHFDSKVIYMTDHCLL 255
A +C P + A + V+E + +I SF + +++VI T +L
Sbjct: 74 ASPQAICLAPSRELARQTLEVVQEMGKFTKITSQLIVPDSFEKNKQINAQVIVGTPGTVL 133
Query: 256 QHFMNDR--DLSRISCIIVDEAHERSXXXXXXXXXXXXXXCRRF---DLRLVIMSAT-AD 309
M + L +I ++DEA +RF D +LV+ SAT AD
Sbjct: 134 -DLMRRKLMQLQKIKIFVLDEADN---MLDQQGLGDQCIRVKRFLPKDTQLVLFSATFAD 189
Query: 310 A--HQLSKYFYDCGISHVVGRNFPVDV---RYVPCATAGTSAVASYVSDVVRMVGEVHTT 364
A K + + VD Y+ C +D ++ E++
Sbjct: 190 AVRQYAKKIVPNANTLELQTNEVNVDAIKQLYMDCKNE---------ADKFDVLTELYGV 240
Query: 365 EKEGTILAFLTSKMEVEWACEKFDAPSAVALPFHGQLSFDEQFCVFKSY-PGRRKVIFAT 423
G+ + F+ +K K + HG L E+ + + GR KV+ T
Sbjct: 241 MTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITT 300
Query: 424 NVAETSLTIPGVKFVIDSGMVKESYFEPGTGMNVLRVCRVSQSSANQRAGRAG 476
NV + IP V V++ + + + + R+ R R GR G
Sbjct: 301 NVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTG------RFGRKG 347
>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3
Length = 395
Score = 33.5 bits (75), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 62/293 (21%), Positives = 105/293 (35%), Gaps = 31/293 (10%)
Query: 196 AEQSIVCTQPRKIAAISLAQRVREESRGCYEDDSVICYPSFSSAQHFDSKVIYMTDHCLL 255
A +C P + A + V+E + +I SF + +++VI T +L
Sbjct: 74 ASPQAICLAPSRELARQTLEVVQEMGKFTKITSQLIVPDSFEKNKQINAQVIVGTPGTVL 133
Query: 256 QHFMNDR--DLSRISCIIVDEAHERSXXXXXXXXXXXXXXCRRF---DLRLVIMSAT-AD 309
M + L +I ++DEA +RF D +LV+ SAT AD
Sbjct: 134 -DLMRRKLMQLQKIKIFVLDEADN---MLDQQGLGDQCIRVKRFLPKDTQLVLFSATFAD 189
Query: 310 A--HQLSKYFYDCGISHVVGRNFPVDV---RYVPCATAGTSAVASYVSDVVRMVGEVHTT 364
A K + + VD Y+ C +D ++ E++
Sbjct: 190 AVRQYAKKIVPNANTLELQTNEVNVDAIKQLYMDCKNE---------ADKFDVLTELYGL 240
Query: 365 EKEGTILAFLTSKMEVEWACEKFDAPSAVALPFHGQLSFDEQFCVFKSY-PGRRKVIFAT 423
G+ + F+ +K K + HG L E+ + + GR KV+ T
Sbjct: 241 MTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITT 300
Query: 424 NVAETSLTIPGVKFVIDSGMVKESYFEPGTGMNVLRVCRVSQSSANQRAGRAG 476
NV + IP V V++ + + + + R+ R R GR G
Sbjct: 301 NVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTG------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 = 1.0, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 41/88 (46%), Gaps = 10/88 (11%)
Query: 326 VGRNFPVDVRYVPCATAGTSA--VASYVSDVVRMVGEVHTTEKEGTIL------AFLTSK 377
+ NF D RY+ GT++ V + V D ++G H ++ G L + + S
Sbjct: 405 IANNF--DCRYMVYNAPGTTSPVVQNLVWDKSNVIGGTHANQRAGQNLFDMQFASVVNST 462
Query: 378 MEVEWACEKFDAPSAVALPFHGQLSFDE 405
+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: 326 VGRNFPVDVRYVPCATAGTSA--VASYVSDVVRMVGEVHTTEKEGTIL------AFLTSK 377
+ NF D RY+ GT++ V + V D ++G H ++ G L + + S
Sbjct: 405 IANNF--DCRYMVYNAPGTTSPVVQNLVWDKSNVIGGTHANQRAGQNLFDMQFASVVNST 462
Query: 378 MEVEWACEKFDAPSAVALPFHGQLSFDE 405
+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 = 33.1 bits (74), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 41/88 (46%), Gaps = 10/88 (11%)
Query: 326 VGRNFPVDVRYVPCATAGTSA--VASYVSDVVRMVGEVHTTEKEGTIL------AFLTSK 377
+ NF D RY+ GT++ V + V D ++G H ++ G L + + S
Sbjct: 405 IANNF--DCRYMVYNAPGTTSPVVQNLVWDKSNVIGGTHANQRAGQNLFDMQFASVVNST 462
Query: 378 MEVEWACEKFDAPSAVALPFHGQLSFDE 405
+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 = 33.1 bits (74), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 41/88 (46%), Gaps = 10/88 (11%)
Query: 326 VGRNFPVDVRYVPCATAGTSA--VASYVSDVVRMVGEVHTTEKEGTIL------AFLTSK 377
+ NF D RY+ GT++ V + V D ++G H ++ G L + + S
Sbjct: 405 IANNF--DCRYMVYNAPGTTSPVVQNLVWDKSNVIGGTHANQRAGQNLFDMQFASVVNST 462
Query: 378 MEVEWACEKFDAPSAVALPFHGQLSFDE 405
+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 = 2.4, Method: Compositional matrix adjust.
Identities = 15/69 (21%), Positives = 32/69 (46%), Gaps = 1/69 (1%)
Query: 373 FLTSKMEVEWACEKFDAPSAVALPFHGQLSFDEQFCVFKSY-PGRRKVIFATNVAETSLT 431
F+ ++ +V+W EK A HG + E+ + + + G +V+ T++ +
Sbjct: 260 FINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGID 319
Query: 432 IPGVKFVID 440
+ V VI+
Sbjct: 320 VQQVSLVIN 328
>pdb|1D2M|A Chain A, Uvrb Protein Of Thermus Thermophilus Hb8; A Nucleotide
Excision Repair Enzyme
Length = 665
Score = 31.6 bits (70), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 26/53 (49%), Gaps = 4/53 (7%)
Query: 167 GEQILVLIGETGCGKSTQLVQFLADSGIAAEQSIVCTQPRKIAAISLAQRVRE 219
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 = 2.8, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 26/53 (49%), Gaps = 4/53 (7%)
Query: 167 GEQILVLIGETGCGKSTQLVQFLADSGIAAEQSIVCTQPRKIAAISLAQRVRE 219
GE+ + L+G TG GK+ + + + G A + P KI A LA RE
Sbjct: 27 GERFVTLLGATGTGKTVTMAKVIEALGRPA----LVLAPNKILAAQLAAEFRE 75
>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a
pdb|3EIQ|D Chain D, Crystal Structure Of Pdcd4-eif4a
Length = 414
Score = 31.6 bits (70), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 15/69 (21%), Positives = 32/69 (46%), Gaps = 1/69 (1%)
Query: 373 FLTSKMEVEWACEKFDAPSAVALPFHGQLSFDEQFCVFKSY-PGRRKVIFATNVAETSLT 431
F+ ++ +V+W EK A HG + E+ + + + G +V+ T++ +
Sbjct: 286 FINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGID 345
Query: 432 IPGVKFVID 440
+ V VI+
Sbjct: 346 VQQVSLVIN 354
>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: 1151 LHLEAAKAL-EQLEGKVLPGCGPWQKMKC 1178
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 = 3.2, Method: Compositional matrix adjust.
Identities = 15/29 (51%), Positives = 17/29 (58%), Gaps = 1/29 (3%)
Query: 1151 LHLEAAKAL-EQLEGKVLPGCGPWQKMKC 1178
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 = 3.2, Method: Compositional matrix adjust.
Identities = 15/29 (51%), Positives = 17/29 (58%), Gaps = 1/29 (3%)
Query: 1151 LHLEAAKAL-EQLEGKVLPGCGPWQKMKC 1178
LE KA E +EG VLPGCG W +C
Sbjct: 251 FQLEQMKAYAEDVEGHVLPGCGHWLPEEC 279
>pdb|2KBF|A Chain A, Solution Structure Of Carboxyl-Terminal Domain Of Dbp5p
Length = 187
Score = 30.4 bits (67), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 25/110 (22%), Positives = 42/110 (38%), Gaps = 7/110 (6%)
Query: 368 GTILAFLTSKMEVEWACEKFDAPSAVALPFHGQLSFDEQFCVFKSY-PGRRKVIFATNVA 426
G+ + F+ +K K + HG L E+ + + GR KV+ TNV
Sbjct: 36 GSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVL 95
Query: 427 ETSLTIPGVKFVIDSGMVKESYFEPGTGMNVLRVCRVSQSSANQRAGRAG 476
+ IP V V++ + + + + R+ R R GR G
Sbjct: 96 ARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTG------RFGRKG 139
>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 = 30.4 bits (67), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 27/126 (21%), Positives = 49/126 (38%), Gaps = 7/126 (5%)
Query: 352 SDVVRMVGEVHTTEKEGTILAFLTSKMEVEWACEKFDAPSAVALPFHGQLSFDEQFCVFK 411
+D ++ E++ G+ + F+ +K K + HG L E+ +
Sbjct: 21 ADKFDVLTELYGVXTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLID 80
Query: 412 SY-PGRRKVIFATNVAETSLTIPGVKFVIDSGMVKESYFEPGTGMNVLRVCRVSQSSANQ 470
+ GR KV+ TNV + IP V V++ + + + + R+ R
Sbjct: 81 DFREGRSKVLITTNVLARGIDIPTVSXVVNYDLPTLANGQADPATYIHRIGRTG------ 134
Query: 471 RAGRAG 476
R GR G
Sbjct: 135 RFGRKG 140
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
0.322 0.138 0.413
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 39,266,235
Number of Sequences: 62578
Number of extensions: 1618749
Number of successful extensions: 3956
Number of sequences better than 100.0: 28
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 21
Number of HSP's that attempted gapping in prelim test: 3926
Number of HSP's gapped (non-prelim): 29
length of query: 1387
length of database: 14,973,337
effective HSP length: 111
effective length of query: 1276
effective length of database: 8,027,179
effective search space: 10242680404
effective search space used: 10242680404
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 58 (26.9 bits)