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= 002653
(896 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 = 31.2 bits (69), Expect = 2.3, Method: Composition-based stats.
Identities = 31/91 (34%), Positives = 43/91 (47%), Gaps = 9/91 (9%)
Query: 787 LAVDVGAAMEL-LRRALVGDELTQKEKQALQRTLTDLASVVPIGVLMLLPVTAVGHAAML 845
L+ D G + L +R+ L + Q E A R SV+P+GV L A G +L
Sbjct: 106 LSADTGETVNLYIRQGLSRVVVAQCESTATVR------SVIPLGVPYPLWAGAAGKILLL 159
Query: 846 AAIQRYVPGLIPSTYGPERLDLLRQLEKVKE 876
AA + S +GPE D LR EKV++
Sbjct: 160 AAPELIDDVAADSPHGPEFADQLR--EKVED 188
>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 = 2.9, Method: Compositional matrix adjust.
Identities = 18/39 (46%), Positives = 22/39 (56%), Gaps = 4/39 (10%)
Query: 853 PGLIPSTYGPERLDLLRQLEKVKEMESSEVDPDENAGLD 891
PG IPS G DLL + +KVK+ + VDP E LD
Sbjct: 446 PGFIPSLLG----DLLEERQKVKKKMKATVDPIERKLLD 480
>pdb|1QQC|A Chain A, Crystal Structure Of An Archaebacterial Dna Polymerase
D.Tok
Length = 773
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: 853 PGLIPSTYGPERLDLLRQLEKVKEMESSEVDPDENAGLD 891
PG IPS G DLL + +KVK+ + VDP E LD
Sbjct: 446 PGFIPSLLG----DLLEERQKVKKKMKATVDPIERKLLD 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 = 3.3, Method: Compositional matrix adjust.
Identities = 17/39 (43%), Positives = 22/39 (56%), Gaps = 4/39 (10%)
Query: 853 PGLIPSTYGPERLDLLRQLEKVKEMESSEVDPDENAGLD 891
PG IPS G DLL + +KVK+ + +DP E LD
Sbjct: 446 PGFIPSLLG----DLLEERQKVKKKMKATIDPIEKKLLD 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 = 3.3, Method: Compositional matrix adjust.
Identities = 17/39 (43%), Positives = 22/39 (56%), Gaps = 4/39 (10%)
Query: 853 PGLIPSTYGPERLDLLRQLEKVKEMESSEVDPDENAGLD 891
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 = 3.4, Method: Compositional matrix adjust.
Identities = 17/39 (43%), Positives = 22/39 (56%), Gaps = 4/39 (10%)
Query: 853 PGLIPSTYGPERLDLLRQLEKVKEMESSEVDPDENAGLD 891
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 = 3.5, Method: Compositional matrix adjust.
Identities = 17/39 (43%), Positives = 22/39 (56%), Gaps = 4/39 (10%)
Query: 853 PGLIPSTYGPERLDLLRQLEKVKEMESSEVDPDENAGLD 891
PG IPS G DLL + +KVK+ + +DP E LD
Sbjct: 446 PGFIPSLLG----DLLEERQKVKKKMKATIDPIEKKLLD 480
>pdb|1QHT|A Chain A, Dna Polymerase From Thermococcus Sp. 9on-7 Archaeon
Length = 775
Score = 30.4 bits (67), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 17/39 (43%), Positives = 21/39 (53%), Gaps = 4/39 (10%)
Query: 853 PGLIPSTYGPERLDLLRQLEKVKEMESSEVDPDENAGLD 891
PG IPS G DLL + +K+K + VDP E LD
Sbjct: 446 PGFIPSLLG----DLLEERQKIKRKMKATVDPLEKKLLD 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 = 5.1, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 22/39 (56%), Gaps = 4/39 (10%)
Query: 853 PGLIPSTYGPERLDLLRQLEKVKEMESSEVDPDENAGLD 891
PG IPS G DLL + +K+K+ + +DP E LD
Sbjct: 446 PGFIPSLLG----DLLEERQKIKKKMKATIDPIERKLLD 480
>pdb|1WN7|A Chain A, Crystal Structure Of Archaeal Family B Dna Polymerase
Mutant
Length = 774
Score = 30.0 bits (66), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 22/39 (56%), Gaps = 4/39 (10%)
Query: 853 PGLIPSTYGPERLDLLRQLEKVKEMESSEVDPDENAGLD 891
PG IPS G DLL + +K+K+ + +DP E LD
Sbjct: 446 PGFIPSLLG----DLLEERQKIKKKMKATIDPIERKLLD 480
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: 24,246,892
Number of Sequences: 62578
Number of extensions: 939517
Number of successful extensions: 2483
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 2481
Number of HSP's gapped (non-prelim): 13
length of query: 896
length of database: 14,973,337
effective HSP length: 108
effective length of query: 788
effective length of database: 8,214,913
effective search space: 6473351444
effective search space used: 6473351444
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)