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= 029818
(187 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1QHT|A Chain A, Dna Polymerase From Thermococcus Sp. 9on-7 Archaeon
Length = 775
Score = 29.6 bits (65), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 25/39 (64%), Gaps = 2/39 (5%)
Query: 57 SSLVGWDQDQLD--VREILDKYGFKSVYAFSTGVGRGVP 93
S+ W ++ ++ +RE+ +K+GFK +YA + G+ +P
Sbjct: 511 ESVTAWGREYIEMVIRELEEKFGFKVLYADTDGLHATIP 549
>pdb|2VWJ|A Chain A, Uracil Recognition In Archaeal Dna Polymerases Captured By
X-Ray Crystallography
Length = 773
Score = 28.1 bits (61), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 23/39 (58%), Gaps = 2/39 (5%)
Query: 57 SSLVGWDQDQLD--VREILDKYGFKSVYAFSTGVGRGVP 93
S+ W + ++ +REI +K+GFK +YA + G +P
Sbjct: 511 ESVTAWGRQYIETTIREIEEKFGFKVLYADTDGFFATIP 549
>pdb|1TGO|A Chain A, Thermostable B Type Dna Polymerase From Thermococcus
Gorgonarius
Length = 773
Score = 28.1 bits (61), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 23/39 (58%), Gaps = 2/39 (5%)
Query: 57 SSLVGWDQDQLD--VREILDKYGFKSVYAFSTGVGRGVP 93
S+ W + ++ +REI +K+GFK +YA + G +P
Sbjct: 511 ESVTAWGRQYIETTIREIEEKFGFKVLYADTDGFFATIP 549
>pdb|2XHB|A Chain A, Crystal Structure Of Dna Polymerase From Thermococcus
Gorgonarius In Complex With Hypoxanthine-Containing Dna
Length = 773
Score = 27.7 bits (60), Expect = 3.6, Method: Composition-based stats.
Identities = 13/38 (34%), Positives = 23/38 (60%), Gaps = 2/38 (5%)
Query: 58 SLVGWDQDQLD--VREILDKYGFKSVYAFSTGVGRGVP 93
S+ W + ++ +REI +K+GFK +YA + G +P
Sbjct: 512 SVTAWGRQYIETTIREIEEKFGFKVLYADTDGFFATIP 549
>pdb|2VWK|A Chain A, Uracil Recognition In Archaeal Dna Polymerases Captured By
X-Ray Crystallography. V93q Polymerase Variant
Length = 773
Score = 27.7 bits (60), Expect = 3.6, Method: Composition-based stats.
Identities = 13/38 (34%), Positives = 23/38 (60%), Gaps = 2/38 (5%)
Query: 58 SLVGWDQDQLD--VREILDKYGFKSVYAFSTGVGRGVP 93
S+ W + ++ +REI +K+GFK +YA + G +P
Sbjct: 512 SVTAWGRQYIETTIREIEEKFGFKVLYADTDGFFATIP 549
>pdb|1WNS|A Chain A, Crystal Structure Of Family B Dna Polymerase From
Hyperthermophilic Archaeon Pyrococcus Kodakaraensis Kod1
Length = 774
Score = 27.7 bits (60), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 23/39 (58%), Gaps = 2/39 (5%)
Query: 57 SSLVGWDQD--QLDVREILDKYGFKSVYAFSTGVGRGVP 93
S+ W ++ + ++EI +KYGFK +Y+ + G +P
Sbjct: 511 ESVTAWGREYITMTIKEIEEKYGFKVIYSDTDGFFATIP 549
>pdb|1WN7|A Chain A, Crystal Structure Of Archaeal Family B Dna Polymerase
Mutant
Length = 774
Score = 27.7 bits (60), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 23/39 (58%), Gaps = 2/39 (5%)
Query: 57 SSLVGWDQD--QLDVREILDKYGFKSVYAFSTGVGRGVP 93
S+ W ++ + ++EI +KYGFK +Y+ + G +P
Sbjct: 511 ESVTAWGREYITMTIKEIEEKYGFKVIYSDTDGFFATIP 549
>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 = 27.3 bits (59), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 23/39 (58%), Gaps = 2/39 (5%)
Query: 57 SSLVGWDQDQLD--VREILDKYGFKSVYAFSTGVGRGVP 93
S+ W + ++ +REI +K+GFK +YA + G +P
Sbjct: 511 ESVTAWGRQYIETTMREIEEKFGFKVLYADTDGFFATIP 549
>pdb|1QQC|A Chain A, Crystal Structure Of An Archaebacterial Dna Polymerase
D.Tok
Length = 773
Score = 27.3 bits (59), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 23/39 (58%), Gaps = 2/39 (5%)
Query: 57 SSLVGWDQDQLD--VREILDKYGFKSVYAFSTGVGRGVP 93
S+ W + ++ +REI +K+GFK +YA + G +P
Sbjct: 511 ESVTAWGRQYIETTMREIEEKFGFKVLYADTDGFFATIP 549
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
0.321 0.140 0.443
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,119,972
Number of Sequences: 62578
Number of extensions: 197973
Number of successful extensions: 379
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 371
Number of HSP's gapped (non-prelim): 13
length of query: 187
length of database: 14,973,337
effective HSP length: 93
effective length of query: 94
effective length of database: 9,153,583
effective search space: 860436802
effective search space used: 860436802
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 bits)