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= 001729
(1020 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 = 151 bits (381), Expect = 2e-36, Method: Compositional matrix adjust.
Identities = 130/470 (27%), Positives = 209/470 (44%), Gaps = 62/470 (13%)
Query: 28 VMSLREKIVEKVLENRVTLIVGETGCGKSSQVPQFLLAENM-----EPILCTQPRRFXXX 82
V + R++ ++ N++ + VGETG GK++Q+PQF+L + M + CTQPRR
Sbjct: 95 VHAQRDEFLKLYQNNQIMVFVGETGSGKTTQIPQFVLFDEMPHLENTQVACTQPRRVAAM 154
Query: 83 XXXXXXXXGRNCELGGEVGYHIGHSKHLSERSKIVFKTAGVLLDE-MRDRGLNALKYKVI 141
+ +LG EVGY I S ++ + + T G+LL E M D L+ +Y I
Sbjct: 155 SVAQRVAEEMDVKLGEEVGYSIRFENKTSNKTILKYMTDGMLLREAMEDHDLS--RYSCI 212
Query: 142 ILDEVHERSVESDXXXXXXXXXXXXXNDLRVVLMSATADITKYRDYFRDL------GRGE 195
ILDE HER++ +D DL++++MSAT D K++ YF D GR
Sbjct: 213 ILDEAHERTLATDILMGLLKQVVKRRPDLKIIIMSATLDAEKFQRYFNDAPLLAVPGRTY 272
Query: 196 RVEVLAIPSTNQRTIFQRRVSYLEQVTELLGVDHGMTSELSSLRYCSGPSPSMANAEIKP 255
VE+ P FQR YL+ + H L + +G +
Sbjct: 273 PVELYYTPE------FQR--DYLDSAIRTVLQIHATEEAGDILLFLTG----------ED 314
Query: 256 EVHKLIHDLVLHIHKNESDIEKSILVFLPTYYAL--EQQWHLMKPLSSFFKVHILHSSVD 313
E+ + + L + + L P Y +L QQ + +P
Sbjct: 315 EIEDAVRKISLEGDQLVREEGCGPLSVYPLYGSLPPHQQQRIFEPAPESHN--------- 365
Query: 314 TEQALMAMKICKSHRKVILATNIAESSVTIPKVAYVIDSCRSLQVFWDVNRKIDSAELVW 373
+ RKV+++TNIAE+S+TI + YV+D S Q ++ +++S +
Sbjct: 366 ----------GRPGRKVVISTNIAETSLTIDGIVYVVDPGFSKQKVYNPRIRVESLLVSP 415
Query: 374 VSQSQAEQRRGRTGRTCDGQVYRLVT-KSFFGTLEDHECPAIXXXXXXXXXXXICCAESK 432
+S++ A+QR GR GRT G+ +RL T ++F L + P I E K
Sbjct: 416 ISKASAQQRAGRAGRTRPGKCFRLYTEEAFQKELIEQSYPEILRSNLSS-----TVLELK 470
Query: 433 AISDPKVLLQKALDPPYPEVVGDALDLLDHKRALQ---KISPRGRYEPTF 479
+ ++ +DPP PE + AL+ L++ L ++P GR F
Sbjct: 471 KLGIDDLVHFDFMDPPAPETMMRALEELNYLACLDDEGNLTPLGRLASQF 520
>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 = 151 bits (381), Expect = 2e-36, Method: Compositional matrix adjust.
Identities = 130/470 (27%), Positives = 209/470 (44%), Gaps = 62/470 (13%)
Query: 28 VMSLREKIVEKVLENRVTLIVGETGCGKSSQVPQFLLAENM-----EPILCTQPRRFXXX 82
V + R++ ++ N++ + VGETG GK++Q+PQF+L + M + CTQPRR
Sbjct: 95 VHAQRDEFLKLYQNNQIMVFVGETGSGKTTQIPQFVLFDEMPHLENTQVACTQPRRVAAM 154
Query: 83 XXXXXXXXGRNCELGGEVGYHIGHSKHLSERSKIVFKTAGVLLDE-MRDRGLNALKYKVI 141
+ +LG EVGY I S ++ + + T G+LL E M D L+ +Y I
Sbjct: 155 SVAQRVAEEMDVKLGEEVGYSIRFENKTSNKTILKYMTDGMLLREAMEDHDLS--RYSCI 212
Query: 142 ILDEVHERSVESDXXXXXXXXXXXXXNDLRVVLMSATADITKYRDYFRDL------GRGE 195
ILDE HER++ +D DL++++MSAT D K++ YF D GR
Sbjct: 213 ILDEAHERTLATDILMGLLKQVVKRRPDLKIIIMSATLDAEKFQRYFNDAPLLAVPGRTY 272
Query: 196 RVEVLAIPSTNQRTIFQRRVSYLEQVTELLGVDHGMTSELSSLRYCSGPSPSMANAEIKP 255
VE+ P FQR YL+ + H L + +G +
Sbjct: 273 PVELYYTPE------FQR--DYLDSAIRTVLQIHATEEAGDILLFLTG----------ED 314
Query: 256 EVHKLIHDLVLHIHKNESDIEKSILVFLPTYYAL--EQQWHLMKPLSSFFKVHILHSSVD 313
E+ + + L + + L P Y +L QQ + +P
Sbjct: 315 EIEDAVRKISLEGDQLVREEGCGPLSVYPLYGSLPPHQQQRIFEPAPESHN--------- 365
Query: 314 TEQALMAMKICKSHRKVILATNIAESSVTIPKVAYVIDSCRSLQVFWDVNRKIDSAELVW 373
+ RKV+++TNIAE+S+TI + YV+D S Q ++ +++S +
Sbjct: 366 ----------GRPGRKVVISTNIAETSLTIDGIVYVVDPGFSKQKVYNPRIRVESLLVSP 415
Query: 374 VSQSQAEQRRGRTGRTCDGQVYRLVT-KSFFGTLEDHECPAIXXXXXXXXXXXICCAESK 432
+S++ A+QR GR GRT G+ +RL T ++F L + P I E K
Sbjct: 416 ISKASAQQRAGRAGRTRPGKCFRLYTEEAFQKELIEQSYPEILRSNLSS-----TVLELK 470
Query: 433 AISDPKVLLQKALDPPYPEVVGDALDLLDHKRALQ---KISPRGRYEPTF 479
+ ++ +DPP PE + AL+ L++ L ++P GR F
Sbjct: 471 KLGIDDLVHFDFMDPPAPETMMRALEELNYLACLDDEGNLTPLGRLASQF 520
>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 = 87.8 bits (216), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 54/169 (31%), Positives = 85/169 (50%), Gaps = 11/169 (6%)
Query: 28 VMSLREKIVEKVLENRVTLIVGETGCGKSSQVPQFLLAENME-------PILCTQPRRFX 80
V +I+E + +N V +I G TGCGK++QVPQF+L + ++ I+ TQPRR
Sbjct: 62 VKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDDFIQNDRAAECNIVVTQPRRIS 121
Query: 81 XXXXXXXXXXGRNCELGGEVGYHIGHSKHLSE-RSKIVFKTAGVLLDEMRDRGLNALKYK 139
R E G GY + L + I F T GVLL ++ + G+ + +
Sbjct: 122 AVSVAERVAFERGEEPGKSCGYSVRFESILPRPHASIXFCTVGVLLRKL-EAGIRGISH- 179
Query: 140 VIILDEVHERSVESDXXXXXXXXXXXXXNDLRVVLMSATADITKYRDYF 188
+I+DE+HER + +D ++R+VL SAT D + + +YF
Sbjct: 180 -VIVDEIHERDINTDFLLVVLRDVVQAYPEVRIVLXSATIDTSXFCEYF 227
>pdb|2CQE|A Chain A, Solution Structure Of The Zinc-Finger Domain In Kiaa1064
Protein
Length = 98
Score = 48.9 bits (115), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 30/57 (52%), Gaps = 4/57 (7%)
Query: 731 SETPGEAPLCVYFINGSCNRGTGCPFSHSLQAKRPACKFFYSLQGCRNGDSCIFSHD 787
E P + LC ++I G C R CP+ H CK +++ C NGD C+FSHD
Sbjct: 7 GELPKKRELCKFYITGFCARAENCPYMHG----DFPCKLYHTTGNCINGDDCMFSHD 59
>pdb|1YMF|A Chain A, Crystal Structure Of Yellow Fever Virus Ns3 Helicase
Complexed With Adp
Length = 440
Score = 35.0 bits (79), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 29/69 (42%), Positives = 36/69 (52%), Gaps = 6/69 (8%)
Query: 331 ILATNIAESSVTIPKVAYVIDSCRSL--QVFWDVNRKIDSAELVWVSQSQAEQRRGRTGR 388
ILAT+IAE + V V+D CR+ V D RK+ + +S S A QRRGR GR
Sbjct: 227 ILATDIAEXGANL-CVERVLD-CRTAFKPVLVDEGRKVAIKGPLRISASSAAQRRGRIGR 284
Query: 389 TC--DGQVY 395
DG Y
Sbjct: 285 NPNRDGDSY 293
>pdb|1YKS|A Chain A, Crystal Structure Of Yellow Fever Virus Ns3 Helicase
Length = 440
Score = 34.7 bits (78), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 29/69 (42%), Positives = 36/69 (52%), Gaps = 6/69 (8%)
Query: 331 ILATNIAESSVTIPKVAYVIDSCRSL--QVFWDVNRKIDSAELVWVSQSQAEQRRGRTGR 388
ILAT+IAE + V V+D CR+ V D RK+ + +S S A QRRGR GR
Sbjct: 227 ILATDIAEMGANL-CVERVLD-CRTAFKPVLVDEGRKVAIKGPLRISASSAAQRRGRIGR 284
Query: 389 TC--DGQVY 395
DG Y
Sbjct: 285 NPNRDGDSY 293
>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 = 33.1 bits (74), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 43/86 (50%), Gaps = 18/86 (20%)
Query: 315 EQALMAMKICKSHRKVILATNIAESSVTIPKVAYVIDSCRSLQVFWDVNRKIDSAELVWV 374
EQ L+ + + V++AT++ E + +P+V L VF++ + SA
Sbjct: 407 EQKLILDEFARGEFNVLVATSVGEEGLDVPEV--------DLVVFYE---PVPSA----- 450
Query: 375 SQSQAEQRRGRTGRTCDGQVYRLVTK 400
++ QRRGRTGR G+V L+ K
Sbjct: 451 --IRSIQRRGRTGRHMPGRVIILMAK 474
>pdb|3L0O|A Chain A, Structure Of Rna-Free Rho Transcription Termination Factor
From Thermotoga Maritima
pdb|3L0O|B Chain B, Structure Of Rna-Free Rho Transcription Termination Factor
From Thermotoga Maritima
Length = 427
Score = 32.0 bits (71), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 41/201 (20%), Positives = 84/201 (41%), Gaps = 17/201 (8%)
Query: 182 TKYRDYFRDLGRGERVEVLAIPSTNQRTIFQRRVSYLEQ-----VTELLGVDHGMTSELS 236
T+ D F +G+G+R ++A P + TI + + + + + +L +D E++
Sbjct: 163 TRLIDLFAPIGKGQRGMIVAPPKAGKTTILKEIANGIAENHPDTIRIILLIDE-RPEEVT 221
Query: 237 SLRYCSGPSPSMANAEIKPEVHKLIHDLVLHIHKNESDIEKSILVFLPTYYALEQQWHLM 296
+R + A ++ P+ + +L L + K + +++ L + L + ++++
Sbjct: 222 DIRESTNAIVIAAPFDMPPDKQVKVAELTLEMAKRLVEFNYDVVILLDSLTRLARVYNIV 281
Query: 297 KPLSSFFKVHILHSSVDTEQALMAMKICKSHRKVILATNIAE-SSVTIPKVAYVIDSCRS 355
P S +L VD + K R A N E S+TI A V +
Sbjct: 282 VPPSG----KLLTGGVD------PAALYKPKRFFGAARNTREGGSLTIIATALVETGSKM 331
Query: 356 LQVFWDVNRKIDSAELVWVSQ 376
+V ++ + + ELV Q
Sbjct: 332 DEVIFEEFKGTGNMELVLSRQ 352
>pdb|2QEQ|A Chain A, Crystal Structure Of Kunjin Virus Ns3 Helicase
pdb|2QEQ|B Chain B, Crystal Structure Of Kunjin Virus Ns3 Helicase
Length = 434
Score = 30.8 bits (68), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 34/60 (56%), Gaps = 3/60 (5%)
Query: 331 ILATNIAESSVTIPKVAYVIDSCRSLQ--VFWDVNRKIDSAELVWVSQSQAEQRRGRTGR 388
++ T+I+E K + VIDS +S++ + + ++ E V+ + A QRRGRTGR
Sbjct: 221 VVTTDISEMGANF-KASRVIDSRKSVKPTIITEGEGRVILGEPSAVTAASAAQRRGRTGR 279
>pdb|2KBE|A Chain A, Solution Structure Of Amino-Terminal Domain Of Dbp5p
Length = 226
Score = 30.0 bits (66), Expect = 6.4, Method: Composition-based stats.
Identities = 32/156 (20%), Positives = 63/156 (40%), Gaps = 8/156 (5%)
Query: 31 LREKIVEKVLEN--RVTLIVGETGCGKSSQVPQFLLA----ENMEP-ILCTQP-RRFXXX 82
++E+ + +L N R + ++G GK++ +L E+ P +C P R
Sbjct: 48 IQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRVNPEDASPQAICLAPSRELARQ 107
Query: 83 XXXXXXXXGRNCELGGEVGYHIGHSKHLSERSKIVFKTAGVLLDEMRDRGLNALKYKVII 142
G+ ++ ++ K+ ++++ T G +LD MR + + K K+ +
Sbjct: 108 TLEVVQEMGKFTKITSQLIVPDSFEKNKQINAQVIVGTPGTVLDLMRRKLMQLQKIKIFV 167
Query: 143 LDEVHERSVESDXXXXXXXXXXXXXNDLRVVLMSAT 178
LDE + D ++VL SAT
Sbjct: 168 LDEADNMLDQQGLGDQCIRVKRFLPKDTQLVLFSAT 203
>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 = 30.0 bits (66), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 75/378 (19%), Positives = 134/378 (35%), Gaps = 86/378 (22%)
Query: 31 LREKIVEKVLEN--RVTLIVGETGCGKSSQVPQFLLA----ENMEP-ILCTQP-RRFXXX 82
++E+ + +L N R + ++G GK++ +L E+ P +C P R
Sbjct: 31 IQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRVNPEDASPQAICLAPSRELARQ 90
Query: 83 XXXXXXXXGRNCELGGEVGYHIGHSKHLSERSKIVFKTAGVLLDEMRDRGLNALKYKVII 142
G+ ++ ++ K+ ++++ T G +LD MR + + K K+ +
Sbjct: 91 TLEVVQEMGKFTKITSQLIVPDSFEKNKQINAQVIVGTPGTVLDLMRRKLMQLQKIKIFV 150
Query: 143 LDEVHERSVESDXXXXXXXXXXXXXNDLRVVLMSAT-ADITKYRDYFRDLGRGERVEVLA 201
LDE + D ++VL SAT AD R Y + + L
Sbjct: 151 LDEADNMLDQQGLGDQCIRVKRFLPKDTQLVLFSATFADAV--RQYAKKIVPNANTLELQ 208
Query: 202 IPSTNQRTIFQ------RRVSYLEQVTELLGVDHGMTSELSSLRYCSGPSPSMANAEIKP 255
N I Q + +TEL GV MT S + + + ++ ++K
Sbjct: 209 TNEVNVDAIKQLYMDCKNEADKFDVLTELYGV---MTIGSSIIFVATKKTANVLYGKLKS 265
Query: 256 EVHKLIHDLVLHIHKNESDIEKSILVFLPTYYALEQQWHLMKPLSSFFKVHILHSSVDTE 315
E H +V ILH + T+
Sbjct: 266 EGH---------------------------------------------EVSILHGDLQTQ 280
Query: 316 QALMAMKICKSHR-KVILATNIAESSVTIPKVAYVIDSCRSLQVFWDV----NRKIDSAE 370
+ + + R KV++ TN+ + IP V+ V++ +D+ N + D A
Sbjct: 281 ERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVN--------YDLPTLANGQADPAT 332
Query: 371 LVWVSQSQAEQRRGRTGR 388
+ R GRTGR
Sbjct: 333 YI--------HRIGRTGR 342
>pdb|2D9N|A Chain A, Solution Structure Of Ccch Type Zinc-Finger Domain 2 In
Cleavage And Polyadenylation Specificity Factor
Length = 77
Score = 29.6 bits (65), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 23/49 (46%), Gaps = 2/49 (4%)
Query: 739 LCVYFINGSCNRGTGCPFSHSLQ-AKRPACKFFYSLQGCRNGDSCIFSH 786
+C +++ G C +G C F H K P C F+ C N + C F H
Sbjct: 12 VCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSKFGECSNKE-CPFLH 59
>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3
Length = 395
Score = 29.6 bits (65), Expect = 9.7, Method: Compositional matrix adjust.
Identities = 32/156 (20%), Positives = 63/156 (40%), Gaps = 8/156 (5%)
Query: 31 LREKIVEKVLEN--RVTLIVGETGCGKSSQVPQFLLA----ENMEP-ILCTQP-RRFXXX 82
++E+ + +L N R + ++G GK++ +L E+ P +C P R
Sbjct: 31 IQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRVNPEDASPQAICLAPSRELARQ 90
Query: 83 XXXXXXXXGRNCELGGEVGYHIGHSKHLSERSKIVFKTAGVLLDEMRDRGLNALKYKVII 142
G+ ++ ++ K+ ++++ T G +LD MR + + K K+ +
Sbjct: 91 TLEVVQEMGKFTKITSQLIVPDSFEKNKQINAQVIVGTPGTVLDLMRRKLMQLQKIKIFV 150
Query: 143 LDEVHERSVESDXXXXXXXXXXXXXNDLRVVLMSAT 178
LDE + D ++VL SAT
Sbjct: 151 LDEADNMLDQQGLGDQCIRVKRFLPKDTQLVLFSAT 186
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.321 0.137 0.415
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 27,737,825
Number of Sequences: 62578
Number of extensions: 1100580
Number of successful extensions: 2398
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 2374
Number of HSP's gapped (non-prelim): 24
length of query: 1020
length of database: 14,973,337
effective HSP length: 109
effective length of query: 911
effective length of database: 8,152,335
effective search space: 7426777185
effective search space used: 7426777185
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: 56 (26.2 bits)