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= 002590
(903 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2O0Y|A Chain A, Crystal Structure Of Putative Transcriptional Regulator
Rha1_ro06953 (Iclr-Family) From Rhodococcus Sp.
pdb|2O0Y|B Chain B, Crystal Structure Of Putative Transcriptional Regulator
Rha1_ro06953 (Iclr-Family) From Rhodococcus Sp.
pdb|2O0Y|C Chain C, Crystal Structure Of Putative Transcriptional Regulator
Rha1_ro06953 (Iclr-Family) From Rhodococcus Sp.
pdb|2O0Y|D Chain D, Crystal Structure Of Putative Transcriptional Regulator
Rha1_ro06953 (Iclr-Family) From Rhodococcus Sp
Length = 260
Score = 31.6 bits (70), Expect = 2.3, Method: Composition-based stats.
Identities = 31/91 (34%), Positives = 43/91 (47%), Gaps = 9/91 (9%)
Query: 794 LAVDVGAAMEL-LRRALVGDELTQKEKQALQRTLTDLASVVPIGVLMLLPVTAVGHAAML 852
L+ D G + L +R+ L + Q E A R SV+P+GV L A G +L
Sbjct: 106 LSADTGETVNLYIRQGLSRVVVAQCESTATVR------SVIPLGVPYPLWAGAAGKILLL 159
Query: 853 AAIQRYVPGLIPSTYGPERLDLLRQLEKVKE 883
AA + S +GPE D LR EKV++
Sbjct: 160 AAPELIDDVAADSPHGPEFADQLR--EKVED 188
>pdb|1QQC|A Chain A, Crystal Structure Of An Archaebacterial Dna Polymerase
D.Tok
Length = 773
Score = 31.2 bits (69), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 18/39 (46%), Positives = 22/39 (56%), Gaps = 4/39 (10%)
Query: 860 PGLIPSTYGPERLDLLRQLEKVKEMESSEVDPDENAGLD 898
PG IPS G DLL + +KVK+ + VDP E LD
Sbjct: 446 PGFIPSLLG----DLLEERQKVKKKMKATVDPIERKLLD 480
>pdb|1D5A|A Chain A, Crystal Structure Of An Archaebacterial Dna Polymerase
D.Tok. Deposition Of Second Native Structure At 2.4
Angstrom
Length = 733
Score = 31.2 bits (69), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 18/39 (46%), Positives = 22/39 (56%), Gaps = 4/39 (10%)
Query: 860 PGLIPSTYGPERLDLLRQLEKVKEMESSEVDPDENAGLD 898
PG IPS G DLL + +KVK+ + VDP E LD
Sbjct: 446 PGFIPSLLG----DLLEERQKVKKKMKATVDPIERKLLD 480
>pdb|2VWJ|A Chain A, Uracil Recognition In Archaeal Dna Polymerases Captured By
X-Ray Crystallography
Length = 773
Score = 30.8 bits (68), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 17/39 (43%), Positives = 22/39 (56%), Gaps = 4/39 (10%)
Query: 860 PGLIPSTYGPERLDLLRQLEKVKEMESSEVDPDENAGLD 898
PG IPS G DLL + +KVK+ + +DP E LD
Sbjct: 446 PGFIPSLLG----DLLEERQKVKKKMKATIDPIEKKLLD 480
>pdb|2VWK|A Chain A, Uracil Recognition In Archaeal Dna Polymerases Captured By
X-Ray Crystallography. V93q Polymerase Variant
Length = 773
Score = 30.8 bits (68), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 17/39 (43%), Positives = 22/39 (56%), Gaps = 4/39 (10%)
Query: 860 PGLIPSTYGPERLDLLRQLEKVKEMESSEVDPDENAGLD 898
PG IPS G DLL + +KVK+ + +DP E LD
Sbjct: 446 PGFIPSLLG----DLLEERQKVKKKMKATIDPIEKKLLD 480
>pdb|2XHB|A Chain A, Crystal Structure Of Dna Polymerase From Thermococcus
Gorgonarius In Complex With Hypoxanthine-Containing Dna
Length = 773
Score = 30.8 bits (68), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 17/39 (43%), Positives = 22/39 (56%), Gaps = 4/39 (10%)
Query: 860 PGLIPSTYGPERLDLLRQLEKVKEMESSEVDPDENAGLD 898
PG IPS G DLL + +KVK+ + +DP E LD
Sbjct: 446 PGFIPSLLG----DLLEERQKVKKKMKATIDPIEKKLLD 480
>pdb|1TGO|A Chain A, Thermostable B Type Dna Polymerase From Thermococcus
Gorgonarius
Length = 773
Score = 30.8 bits (68), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 17/39 (43%), Positives = 22/39 (56%), Gaps = 4/39 (10%)
Query: 860 PGLIPSTYGPERLDLLRQLEKVKEMESSEVDPDENAGLD 898
PG IPS G DLL + +KVK+ + +DP E LD
Sbjct: 446 PGFIPSLLG----DLLEERQKVKKKMKATIDPIEKKLLD 480
>pdb|1WNS|A Chain A, Crystal Structure Of Family B Dna Polymerase From
Hyperthermophilic Archaeon Pyrococcus Kodakaraensis Kod1
Length = 774
Score = 30.4 bits (67), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 22/39 (56%), Gaps = 4/39 (10%)
Query: 860 PGLIPSTYGPERLDLLRQLEKVKEMESSEVDPDENAGLD 898
PG IPS G DLL + +K+K+ + +DP E LD
Sbjct: 446 PGFIPSLLG----DLLEERQKIKKKMKATIDPIERKLLD 480
>pdb|1QHT|A Chain A, Dna Polymerase From Thermococcus Sp. 9on-7 Archaeon
Length = 775
Score = 30.4 bits (67), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 17/39 (43%), Positives = 21/39 (53%), Gaps = 4/39 (10%)
Query: 860 PGLIPSTYGPERLDLLRQLEKVKEMESSEVDPDENAGLD 898
PG IPS G DLL + +K+K + VDP E LD
Sbjct: 446 PGFIPSLLG----DLLEERQKIKRKMKATVDPLEKKLLD 480
>pdb|1WN7|A Chain A, Crystal Structure Of Archaeal Family B Dna Polymerase
Mutant
Length = 774
Score = 30.4 bits (67), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 22/39 (56%), Gaps = 4/39 (10%)
Query: 860 PGLIPSTYGPERLDLLRQLEKVKEMESSEVDPDENAGLD 898
PG IPS G DLL + +K+K+ + +DP E LD
Sbjct: 446 PGFIPSLLG----DLLEERQKIKKKMKATIDPIERKLLD 480
>pdb|4A0P|A Chain A, Crystal Structure Of Lrp6p3e3p4e4
Length = 628
Score = 30.0 bits (66), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 19/39 (48%)
Query: 659 QDRPNEVVCKSRGLFGFFTRPSIRKPKPQVSVADGHESE 697
QDRP VV + +FT R PK + + DG E E
Sbjct: 431 QDRPRAVVVNPEKGYMYFTNLQERSPKIERAALDGTERE 469
>pdb|3S8V|A Chain A, Crystal Structure Of Lrp6-Dkk1 Complex
pdb|3S8V|B Chain B, Crystal Structure Of Lrp6-Dkk1 Complex
pdb|3S8Z|A Chain A, Crystal Structure Of Lrp6-E3e4
Length = 623
Score = 29.6 bits (65), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 24/51 (47%)
Query: 659 QDRPNEVVCKSRGLFGFFTRPSIRKPKPQVSVADGHESEYCEQTGSNIGIA 709
QDRP +V + +FT R PK + + DG E E +G + IA
Sbjct: 436 QDRPRAIVVNPEKGYMYFTNLQERSPKIERAALDGTEREVLFFSGLSKPIA 486
>pdb|3S2K|A Chain A, Structural Basis Of Wnt Signaling Inhibition By Dickkopf
Binding To Lrp56.
pdb|3S2K|B Chain B, Structural Basis Of Wnt Signaling Inhibition By Dickkopf
Binding To Lrp56
Length = 629
Score = 29.6 bits (65), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 24/51 (47%)
Query: 659 QDRPNEVVCKSRGLFGFFTRPSIRKPKPQVSVADGHESEYCEQTGSNIGIA 709
QDRP +V + +FT R PK + + DG E E +G + IA
Sbjct: 429 QDRPRAIVVNPEKGYMYFTNLQERSPKIERAALDGTEREVLFFSGLSKPIA 479
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
0.317 0.131 0.377
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 24,491,290
Number of Sequences: 62578
Number of extensions: 951459
Number of successful extensions: 2527
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 2522
Number of HSP's gapped (non-prelim): 16
length of query: 903
length of database: 14,973,337
effective HSP length: 108
effective length of query: 795
effective length of database: 8,214,913
effective search space: 6530855835
effective search space used: 6530855835
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (26.2 bits)