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= psy1679
(250 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3O4N|A Chain A, Crystal Structure Of The Rous Associated Virus Integrase
Catalytic Domain In Mes Buffer Ph 6.0
pdb|3O4N|B Chain B, Crystal Structure Of The Rous Associated Virus Integrase
Catalytic Domain In Mes Buffer Ph 6.0
Length = 150
Score = 33.5 bits (75), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 30/71 (42%), Gaps = 6/71 (8%)
Query: 24 ENFYNRWKLKHSQIVMENEIGEAKEEKLNHLYDELESDLDLVGVTAIEDKLQDDVPKTIA 83
+ RW + H+ + N G+A E+ N L D + V A D +P +
Sbjct: 83 REWLARWGIAHTTGIPGNSQGQAMVERANRLLK------DKIRVLAEGDGFMKRIPASKQ 136
Query: 84 NLLLAVTLYAL 94
LLA +YAL
Sbjct: 137 GELLAKAMYAL 147
>pdb|1VSL|A Chain A, Asv Integrase Core Domain D64n Mutation With Zinc Cation
pdb|1VSK|A Chain A, Asv Integrase Core Domain D64n Mutation In Citrate Buffer
Ph 6.0
Length = 146
Score = 33.1 bits (74), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 30/71 (42%), Gaps = 6/71 (8%)
Query: 24 ENFYNRWKLKHSQIVMENEIGEAKEEKLNHLYDELESDLDLVGVTAIEDKLQDDVPKTIA 83
+ RW + H+ + N G+A E+ N L D + V A D +P +
Sbjct: 79 REWLARWGIAHTTGIPGNSQGQAMVERANRLLK------DKIRVLAEGDGFMKRIPTSKQ 132
Query: 84 NLLLAVTLYAL 94
LLA +YAL
Sbjct: 133 GELLAKAMYAL 143
>pdb|3O4Q|A Chain A, Crystal Structure Of The Rous Associated Virus Integrase
Catalytic Domain A182t In Citrate Buffer Ph 6.2
Length = 150
Score = 33.1 bits (74), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 30/71 (42%), Gaps = 6/71 (8%)
Query: 24 ENFYNRWKLKHSQIVMENEIGEAKEEKLNHLYDELESDLDLVGVTAIEDKLQDDVPKTIA 83
+ RW + H+ + N G+A E+ N L D + V A D +P +
Sbjct: 83 REWLARWGIAHTTGIPGNSQGQAMVERANRLLK------DKIRVLAEGDGFMKRIPTSKQ 136
Query: 84 NLLLAVTLYAL 94
LLA +YAL
Sbjct: 137 GELLAKAMYAL 147
>pdb|1VSM|A Chain A, Asv Integrase Core Domain In Citrate Buffer Ph 5.0
Length = 146
Score = 33.1 bits (74), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 30/71 (42%), Gaps = 6/71 (8%)
Query: 24 ENFYNRWKLKHSQIVMENEIGEAKEEKLNHLYDELESDLDLVGVTAIEDKLQDDVPKTIA 83
+ RW + H+ + N G+A E+ N L D + V A D +P +
Sbjct: 79 REWLARWGIAHTTGIPGNSQGQAMVERANRLLK------DKIRVLAEGDGFMKRIPTSKQ 132
Query: 84 NLLLAVTLYAL 94
LLA +YAL
Sbjct: 133 GELLAKAMYAL 143
>pdb|1VSE|A Chain A, Asv Integrase Core Domain With Mg(Ii) Cofactor And Hepes
Ligand, Low Mg Concentration Form
pdb|1VSF|A Chain A, Asv Integrase Core Domain With Mn(Ii) Cofactor And Hepes
Ligand, High Mg Concentration Form
Length = 152
Score = 32.7 bits (73), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 30/71 (42%), Gaps = 6/71 (8%)
Query: 24 ENFYNRWKLKHSQIVMENEIGEAKEEKLNHLYDELESDLDLVGVTAIEDKLQDDVPKTIA 83
+ RW + H+ + N G+A E+ N L D + V A D +P +
Sbjct: 83 REWLARWGIAHTTGIPGNSQGQAMVERANRLLK------DKIRVLAEGDGFMKRIPTSKQ 136
Query: 84 NLLLAVTLYAL 94
LLA +YAL
Sbjct: 137 GELLAKAMYAL 147
>pdb|1VSH|A Chain A, Asv Integrase Core Domain With Zn(ii) Cofactors
pdb|1VSI|A Chain A, Asv Integrase Core Domain With Ca(Ii) Cofactor
pdb|1VSJ|A Chain A, Asv Integrase Core Domain With Cd(Ii) Cofactors
pdb|1VSD|A Chain A, Asv Integrase Core Domain With Mg(Ii) Cofactor And Hepes
Ligand, High Mg Concentration Form
Length = 152
Score = 32.7 bits (73), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 30/71 (42%), Gaps = 6/71 (8%)
Query: 24 ENFYNRWKLKHSQIVMENEIGEAKEEKLNHLYDELESDLDLVGVTAIEDKLQDDVPKTIA 83
+ RW + H+ + N G+A E+ N L D + V A D +P +
Sbjct: 83 REWLARWGIAHTTGIPGNSQGQAMVERANRLLK------DKIRVLAEGDGFMKRIPTSKQ 136
Query: 84 NLLLAVTLYAL 94
LLA +YAL
Sbjct: 137 GELLAKAMYAL 147
>pdb|1A5V|A Chain A, Asv Integrase Core Domain With Hiv-1 Integrase Inhibitor
Y3 And Mn Cation
pdb|1A5W|A Chain A, Asv Integrase Core Domain With Hiv-1 Integrase Inhibitor
Y3
pdb|1A5X|A Chain A, Asv Integrase Core Domain With Hiv-1 Integrase Inhibitor
Y3
Length = 158
Score = 32.7 bits (73), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 30/71 (42%), Gaps = 6/71 (8%)
Query: 24 ENFYNRWKLKHSQIVMENEIGEAKEEKLNHLYDELESDLDLVGVTAIEDKLQDDVPKTIA 83
+ RW + H+ + N G+A E+ N L D + V A D +P +
Sbjct: 81 REWLARWGIAHTTGIPGNSQGQAMVERANRLLK------DKIRVLAEGDGFMKRIPTSKQ 134
Query: 84 NLLLAVTLYAL 94
LLA +YAL
Sbjct: 135 GELLAKAMYAL 145
>pdb|1CXQ|A Chain A, Atomic Resolution Asv Integrase Core Domain From Ammonium
Sulfate
pdb|1CXU|A Chain A, 1.42a Resolution Asv Integrase Core Domain From Citrate
pdb|1CZB|A Chain A, Atomic Resolution Asv Integrase Core Domain From Hepes
Length = 162
Score = 32.3 bits (72), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 30/71 (42%), Gaps = 6/71 (8%)
Query: 24 ENFYNRWKLKHSQIVMENEIGEAKEEKLNHLYDELESDLDLVGVTAIEDKLQDDVPKTIA 83
+ RW + H+ + N G+A E+ N L D + V A D +P +
Sbjct: 85 REWLARWGIAHTTGIPGNSQGQAMVERANRLLK------DKIRVLAEGDGFMKRIPTSKQ 138
Query: 84 NLLLAVTLYAL 94
LLA +YAL
Sbjct: 139 GELLAKAMYAL 149
>pdb|1CZ9|A Chain A, Atomic Resolution Asv Integrase Core Domain (D64n) From
Citrate
Length = 162
Score = 32.3 bits (72), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 30/71 (42%), Gaps = 6/71 (8%)
Query: 24 ENFYNRWKLKHSQIVMENEIGEAKEEKLNHLYDELESDLDLVGVTAIEDKLQDDVPKTIA 83
+ RW + H+ + N G+A E+ N L D + V A D +P +
Sbjct: 85 REWLARWGIAHTTGIPGNSQGQAMVERANRLLK------DKIRVLAEGDGFMKRIPTSKQ 138
Query: 84 NLLLAVTLYAL 94
LLA +YAL
Sbjct: 139 GELLAKAMYAL 149
>pdb|1ASU|A Chain A, Avian Sarcoma Virus Integrase Catalytic Core Domain
Crystallized From 2% Peg 400, 2m Ammonium Sulfate, Hepes
Ph 7.5
Length = 162
Score = 32.3 bits (72), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 30/71 (42%), Gaps = 6/71 (8%)
Query: 24 ENFYNRWKLKHSQIVMENEIGEAKEEKLNHLYDELESDLDLVGVTAIEDKLQDDVPKTIA 83
+ RW + H+ + N G+A E+ N L D + V A D +P +
Sbjct: 85 REWLARWGIAHTTGIPGNSQGQAMVERANRLLK------DKIRVLAEGDGFMKRIPTSKQ 138
Query: 84 NLLLAVTLYAL 94
LLA +YAL
Sbjct: 139 GELLAKAMYAL 149
>pdb|1ASV|A Chain A, Avian Sarcoma Virus Integrase Catalytic Core Domain
Length = 162
Score = 32.3 bits (72), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 30/71 (42%), Gaps = 6/71 (8%)
Query: 24 ENFYNRWKLKHSQIVMENEIGEAKEEKLNHLYDELESDLDLVGVTAIEDKLQDDVPKTIA 83
+ RW + H+ + N G+A E+ N L D + V A D +P +
Sbjct: 85 REWLARWGIAHTTGIPGNSQGQAMVERANRLLK------DKIRVLAEGDGFMKRIPTSKQ 138
Query: 84 NLLLAVTLYAL 94
LLA +YAL
Sbjct: 139 GELLAKAMYAL 149
>pdb|1ASW|A Chain A, Avian Sarcoma Virus Integrase Catalytic Core Domain
Crystallized From 20% Peg 4000, 10% Isopropanol, Hepes
Ph 7.5 Using Selenomethionine Substituted Protein; Data
Collected At-165 Degrees C
Length = 162
Score = 32.0 bits (71), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 29/71 (40%), Gaps = 6/71 (8%)
Query: 24 ENFYNRWKLKHSQIVMENEIGEAKEEKLNHLYDELESDLDLVGVTAIEDKLQDDVPKTIA 83
+ RW + H+ + N G+A E+ N L D + V A D +P +
Sbjct: 85 REWLARWGIAHTTGIPGNSQGQAXVERANRLLK------DKIRVLAEGDGFXKRIPTSKQ 138
Query: 84 NLLLAVTLYAL 94
LLA YAL
Sbjct: 139 GELLAKAXYAL 149
>pdb|1C0M|A Chain A, Crystal Structure Of Rsv Two-Domain Integrase
pdb|1C0M|B Chain B, Crystal Structure Of Rsv Two-Domain Integrase
pdb|1C0M|C Chain C, Crystal Structure Of Rsv Two-Domain Integrase
pdb|1C0M|D Chain D, Crystal Structure Of Rsv Two-Domain Integrase
pdb|1C1A|A Chain A, Crystal Structure Of Rsv Two-Domain Integrase
pdb|1C1A|B Chain B, Crystal Structure Of Rsv Two-Domain Integrase
Length = 238
Score = 31.6 bits (70), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 30/71 (42%), Gaps = 6/71 (8%)
Query: 24 ENFYNRWKLKHSQIVMENEIGEAKEEKLNHLYDELESDLDLVGVTAIEDKLQDDVPKTIA 83
+ RW + H+ + N G+A E+ N L D + V A D +P +
Sbjct: 84 REWLARWGIAHTTGIPGNSQGQAMVERANRLLK------DRIRVLAEGDGFMKRIPTSKQ 137
Query: 84 NLLLAVTLYAL 94
LLA +YAL
Sbjct: 138 GELLAKAMYAL 148
>pdb|2NN6|E Chain E, Structure Of The Human Rna Exosome Composed Of Rrp41,
Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, And Rrp40
Length = 305
Score = 29.6 bits (65), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 32/69 (46%), Gaps = 7/69 (10%)
Query: 29 RWKLKHSQIVM--ENEIGEAKEEKLNHLYDELESDLDLVGVTAIEDKLQDDVPKTIANLL 86
R KL H+ I++ + E+G K EK N Y E D E + DD+ IAN
Sbjct: 64 RVKLGHTDILVGVKAEMGTPKLEKPNEGYLEFFVDCSASATPEFEGRGGDDLGTEIAN-- 121
Query: 87 LAVTLYALF 95
TLY +F
Sbjct: 122 ---TLYRIF 127
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
0.325 0.139 0.410
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,920,544
Number of Sequences: 62578
Number of extensions: 264941
Number of successful extensions: 813
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 20
Number of HSP's that attempted gapping in prelim test: 813
Number of HSP's gapped (non-prelim): 20
length of query: 250
length of database: 14,973,337
effective HSP length: 96
effective length of query: 154
effective length of database: 8,965,849
effective search space: 1380740746
effective search space used: 1380740746
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 50 (23.9 bits)