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= psy16286
(92 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2XZO|A Chain A, Upf1 Helicase - Rna Complex
pdb|2XZP|A Chain A, Upf1 Helicase
Length = 623
Score = 41.6 bits (96), Expect = 1e-04, Method: Composition-based stats.
Identities = 21/47 (44%), Positives = 28/47 (59%), Gaps = 1/47 (2%)
Query: 7 NVHNNVGFLKTVNRVCVALSRAKQGLFIMGNMKCLSADSQLWQEIKN 53
N H +GFL R+ VAL+RA+ G+ I+GN K LS LW + N
Sbjct: 554 NEHQGIGFLNDPRRLNVALTRARYGVIIVGNPKALSKQP-LWNHLLN 599
>pdb|2GJK|A Chain A, Structural And Functional Insights Into The Human Upf1
Helicase Core
pdb|2GK6|A Chain A, Structural And Functional Insights Into The Human Upf1
Helicase Core
pdb|2GK6|B Chain B, Structural And Functional Insights Into The Human Upf1
Helicase Core
pdb|2GK7|A Chain A, Structural And Functional Insights Into The Human Upf1
Helicase Core
Length = 624
Score = 41.6 bits (96), Expect = 1e-04, Method: Composition-based stats.
Identities = 21/47 (44%), Positives = 28/47 (59%), Gaps = 1/47 (2%)
Query: 7 NVHNNVGFLKTVNRVCVALSRAKQGLFIMGNMKCLSADSQLWQEIKN 53
N H +GFL R+ VAL+RA+ G+ I+GN K LS LW + N
Sbjct: 555 NEHQGIGFLNDPRRLNVALTRARYGVIIVGNPKALSKQP-LWNHLLN 600
>pdb|2WJV|A Chain A, Crystal Structure Of The Complex Between Human Nonsense
Mediated Decay Factors Upf1 And Upf2
pdb|2WJV|B Chain B, Crystal Structure Of The Complex Between Human Nonsense
Mediated Decay Factors Upf1 And Upf2
pdb|2WJY|A Chain A, Crystal Structure Of The Complex Between Human Nonsense
Mediated Decay Factors Upf1 And Upf2 Orthorhombic Form
Length = 800
Score = 41.6 bits (96), Expect = 1e-04, Method: Composition-based stats.
Identities = 21/47 (44%), Positives = 28/47 (59%), Gaps = 1/47 (2%)
Query: 7 NVHNNVGFLKTVNRVCVALSRAKQGLFIMGNMKCLSADSQLWQEIKN 53
N H +GFL R+ VAL+RA+ G+ I+GN K LS LW + N
Sbjct: 731 NEHQGIGFLNDPRRLNVALTRARYGVIIVGNPKALSKQP-LWNHLLN 776
>pdb|2XZL|A Chain A, Upf1-Rna Complex
Length = 802
Score = 37.7 bits (86), Expect = 0.002, Method: Composition-based stats.
Identities = 18/45 (40%), Positives = 28/45 (62%), Gaps = 1/45 (2%)
Query: 7 NVHNNVGFLKTVNRVCVALSRAKQGLFIMGNMKCLSADSQLWQEI 51
N +GFL+ R+ V L+RAK GL I+GN + L+ ++ LW +
Sbjct: 733 NEQQAIGFLRDPRRLNVGLTRAKYGLVILGNPRSLARNT-LWNHL 776
>pdb|3U44|A Chain A, Crystal Structure Of Addab-Dna Complex
pdb|3U4Q|A Chain A, Structure Of Addab-Dna Complex At 2.8 Angstroms
Length = 1232
Score = 26.2 bits (56), Expect = 4.5, Method: Composition-based stats.
Identities = 12/27 (44%), Positives = 17/27 (62%)
Query: 23 VALSRAKQGLFIMGNMKCLSADSQLWQ 49
VAL+RAK+ LF++G+ K WQ
Sbjct: 869 VALTRAKEKLFLIGSCKDHQKQLAKWQ 895
>pdb|1A47|A Chain A, Cgtase From Thermoanaerobacterium Thermosulfurigenes Em1
In Complex With A Maltohexaose Inhibitor
pdb|1CIU|A Chain A, Thermostable Cgtase From Thermoanaerobacterium
Thermosulfurigenes Em1 At Ph 8.0
Length = 683
Score = 25.4 bits (54), Expect = 9.0, Method: Composition-based stats.
Identities = 10/22 (45%), Positives = 17/22 (77%), Gaps = 1/22 (4%)
Query: 2 AGSTNNVHNNVGFLKTVNRVCV 23
+G+T+N +NN+ L T N++CV
Sbjct: 566 SGATSNTYNNINIL-TGNQICV 586
>pdb|3BMV|A Chain A, Cyclodextrin Glycosyl Transferase From
Thermoanerobacterium Thermosulfurigenes Em1 Mutant S77p
pdb|3BMW|A Chain A, Cyclodextrin Glycosyl Transferase From
Thermoanerobacterium Thermosulfurigenes Em1 Mutant S77p
Complexed With A Maltoheptaose Inhibitor
Length = 683
Score = 25.4 bits (54), Expect = 9.0, Method: Composition-based stats.
Identities = 10/22 (45%), Positives = 17/22 (77%), Gaps = 1/22 (4%)
Query: 2 AGSTNNVHNNVGFLKTVNRVCV 23
+G+T+N +NN+ L T N++CV
Sbjct: 566 SGATSNTYNNINIL-TGNQICV 586
>pdb|4EFJ|A Chain A, Crystal Structure Of I-Gzemii Laglidadg Homing
Endonuclease In Complex With Dna Target Site
pdb|4EFJ|B Chain B, Crystal Structure Of I-Gzemii Laglidadg Homing
Endonuclease In Complex With Dna Target Site
Length = 300
Score = 25.4 bits (54), Expect = 9.5, Method: Composition-based stats.
Identities = 21/81 (25%), Positives = 40/81 (49%), Gaps = 9/81 (11%)
Query: 7 NVHNNVGFLKTVNRVCVALSRAKQGLFIMGN-------MKCLSADSQLWQEIKNKLVTRR 59
N NN G + T N+ CV R+ + + I+ + + AD +L+++I NKL ++
Sbjct: 56 NYFNNTGSINTSNKECVYKVRSLKDISIIISHFDKYNLITQKKADFELFKKIINKLNSQE 115
Query: 60 SINESFRLQCNKHRAVTIIRA 80
+ S+ + + + IRA
Sbjct: 116 HL--SYEVGATVLQEIISIRA 134
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
0.326 0.133 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,229,759
Number of Sequences: 62578
Number of extensions: 61953
Number of successful extensions: 163
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 154
Number of HSP's gapped (non-prelim): 12
length of query: 92
length of database: 14,973,337
effective HSP length: 59
effective length of query: 33
effective length of database: 11,281,235
effective search space: 372280755
effective search space used: 372280755
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 45 (21.9 bits)