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= 003111
(846 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 = 71.2 bits (173), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 49/156 (31%), Positives = 81/156 (51%), Gaps = 9/156 (5%)
Query: 154 RKVILATNIAESSVTIPKVAYVIDSCRSLQVFWDVNRKIDSAELVWVSQSQAEQRRGRTG 213
RKV+++TNIAE+S+TI + YV+D S Q ++ +++S + +S++ A+QR GR G
Sbjct: 370 RKVVISTNIAETSLTIDGIVYVVDPGFSKQKVYNPRIRVESLLVSPISKASAQQRAGRAG 429
Query: 214 RTCDGQVYRLVT-KSFFGTLEDHECPAIXXXXXXXXXXXICCAESKAISDPKVLLQKALD 272
RT G+ +RL T ++F L + P I E K + ++ +D
Sbjct: 430 RTRPGKCFRLYTEEAFQKELIEQSYPEILRSNLSS-----TVLELKKLGIDDLVHFDFMD 484
Query: 273 PPYPEVVGDALDLLDHKRALQ---KISPRGRYEPTF 305
PP PE + AL+ L++ L ++P GR F
Sbjct: 485 PPAPETMMRALEELNYLACLDDEGNLTPLGRLASQF 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 = 71.2 bits (173), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 49/156 (31%), Positives = 81/156 (51%), Gaps = 9/156 (5%)
Query: 154 RKVILATNIAESSVTIPKVAYVIDSCRSLQVFWDVNRKIDSAELVWVSQSQAEQRRGRTG 213
RKV+++TNIAE+S+TI + YV+D S Q ++ +++S + +S++ A+QR GR G
Sbjct: 370 RKVVISTNIAETSLTIDGIVYVVDPGFSKQKVYNPRIRVESLLVSPISKASAQQRAGRAG 429
Query: 214 RTCDGQVYRLVT-KSFFGTLEDHECPAIXXXXXXXXXXXICCAESKAISDPKVLLQKALD 272
RT G+ +RL T ++F L + P I E K + ++ +D
Sbjct: 430 RTRPGKCFRLYTEEAFQKELIEQSYPEILRSNLSS-----TVLELKKLGIDDLVHFDFMD 484
Query: 273 PPYPEVVGDALDLLDHKRALQ---KISPRGRYEPTF 305
PP PE + AL+ L++ L ++P GR F
Sbjct: 485 PPAPETMMRALEELNYLACLDDEGNLTPLGRLASQF 520
>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 = 23/57 (40%), Positives = 31/57 (54%), Gaps = 4/57 (7%)
Query: 557 SETPGEAPLCVYFINGSCNRGTGCPFSHSLQAKRPACKFFYSLQGCRNGDSCIFSHD 613
E P + LC ++I G C R CP+ H P CK +++ C NGD C+FSHD
Sbjct: 7 GELPKKRELCKFYITGFCARAENCPYMH---GDFP-CKLYHTTGNCINGDDCMFSHD 59
>pdb|1YMF|A Chain A, Crystal Structure Of Yellow Fever Virus Ns3 Helicase
Complexed With Adp
Length = 440
Score = 35.4 bits (80), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 29/69 (42%), Positives = 36/69 (52%), Gaps = 6/69 (8%)
Query: 157 ILATNIAESSVTIPKVAYVIDSCRSL--QVFWDVNRKIDSAELVWVSQSQAEQRRGRTGR 214
ILAT+IAE + V V+D CR+ V D RK+ + +S S A QRRGR GR
Sbjct: 227 ILATDIAEXGANL-CVERVLD-CRTAFKPVLVDEGRKVAIKGPLRISASSAAQRRGRIGR 284
Query: 215 TC--DGQVY 221
DG Y
Sbjct: 285 NPNRDGDSY 293
>pdb|1YKS|A Chain A, Crystal Structure Of Yellow Fever Virus Ns3 Helicase
Length = 440
Score = 35.0 bits (79), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 29/69 (42%), Positives = 36/69 (52%), Gaps = 6/69 (8%)
Query: 157 ILATNIAESSVTIPKVAYVIDSCRSL--QVFWDVNRKIDSAELVWVSQSQAEQRRGRTGR 214
ILAT+IAE + V V+D CR+ V D RK+ + +S S A QRRGR GR
Sbjct: 227 ILATDIAEMGANL-CVERVLD-CRTAFKPVLVDEGRKVAIKGPLRISASSAAQRRGRIGR 284
Query: 215 TC--DGQVY 221
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 = 0.59, Method: Compositional matrix adjust.
Identities = 26/87 (29%), Positives = 43/87 (49%), Gaps = 18/87 (20%)
Query: 141 EQALMAMKICKSHRKVILATNIAESSVTIPKVAYVIDSCRSLQVFWDVNRKIDSAELVWV 200
EQ L+ + + V++AT++ E + +P+V L VF++ + SA
Sbjct: 407 EQKLILDEFARGEFNVLVATSVGEEGLDVPEV--------DLVVFYE---PVPSA----- 450
Query: 201 SQSQAEQRRGRTGRTCDGQVYRLVTKS 227
++ QRRGRTGR G+V L+ K
Sbjct: 451 --IRSIQRRGRTGRHMPGRVIILMAKG 475
>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 = 1.4, Method: Compositional matrix adjust.
Identities = 41/201 (20%), Positives = 84/201 (41%), Gaps = 17/201 (8%)
Query: 8 TKYRDYFRDLGRGERVEVLAIPSTNQRTIFQRRVSYLEQ-----VTELLGVDHGMTSELS 62
T+ D F +G+G+R ++A P + TI + + + + + +L +D E++
Sbjct: 163 TRLIDLFAPIGKGQRGMIVAPPKAGKTTILKEIANGIAENHPDTIRIILLIDE-RPEEVT 221
Query: 63 SLRYCSGPSPSMANAEIKPEVHKLIHDLVLHIHKNESDIEKSILVFLPTYYALEQQWHLM 122
+R + A ++ P+ + +L L + K + +++ L + L + ++++
Sbjct: 222 DIRESTNAIVIAAPFDMPPDKQVKVAELTLEMAKRLVEFNYDVVILLDSLTRLARVYNIV 281
Query: 123 KPLSSFFKVHILHSSVDTEQALMAMKICKSHRKVILATNIAE-SSVTIPKVAYVIDSCRS 181
P S +L VD + K R A N E S+TI A V +
Sbjct: 282 VPPSG----KLLTGGVD------PAALYKPKRFFGAARNTREGGSLTIIATALVETGSKM 331
Query: 182 LQVFWDVNRKIDSAELVWVSQ 202
+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 = 31.2 bits (69), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 34/60 (56%), Gaps = 3/60 (5%)
Query: 157 ILATNIAESSVTIPKVAYVIDSCRSLQ--VFWDVNRKIDSAELVWVSQSQAEQRRGRTGR 214
++ T+I+E K + VIDS +S++ + + ++ E V+ + A QRRGRTGR
Sbjct: 221 VVTTDISEMGANF-KASRVIDSRKSVKPTIITEGEGRVILGEPSAVTAASAAQRRGRTGR 279
>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 = 7.5, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 23/49 (46%), Gaps = 2/49 (4%)
Query: 565 LCVYFINGSCNRGTGCPFSHSLQ-AKRPACKFFYSLQGCRNGDSCIFSH 612
+C +++ G C +G C F H K P C F+ C N + C F H
Sbjct: 12 VCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSKFGECSNKE-CPFLH 59
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 0.137 0.418
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 24,476,928
Number of Sequences: 62578
Number of extensions: 988684
Number of successful extensions: 1959
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1944
Number of HSP's gapped (non-prelim): 20
length of query: 846
length of database: 14,973,337
effective HSP length: 107
effective length of query: 739
effective length of database: 8,277,491
effective search space: 6117065849
effective search space used: 6117065849
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)