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= 019146
(345 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1AVQ|A Chain A, Toroidal Structure Of Lambda Exonuclease Determined At 2.4
Angstroms
pdb|1AVQ|B Chain B, Toroidal Structure Of Lambda Exonuclease Determined At 2.4
Angstroms
pdb|1AVQ|C Chain C, Toroidal Structure Of Lambda Exonuclease Determined At 2.4
Angstroms
Length = 228
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 42/147 (28%), Positives = 59/147 (40%), Gaps = 23/147 (15%)
Query: 105 WQKLRKHKLTASTFAGAIGF------WPRRRVQ----LWLEKIGAIEPFLGNLATCWSNI 154
W KLR +TAS I WP ++ L E + P + A W
Sbjct: 26 WHKLRLGVITASEVHNVIAKPRSGKKWPDMKMSYFHTLLAEVCTGVAPEVNAKALAWGKQ 85
Query: 155 KEEDALERYKLITGNTVYFTEFQVYRDKSRDDDWLAASPDGLVDRFVYDLPSGGVLEIKC 214
E DA ++ +G V + +YRD+S A SPDGL G LE+KC
Sbjct: 86 YENDARTLFEFTSGVNVTESPI-IYRDESMR---TACSPDGLCS-------DGNGLELKC 134
Query: 215 PFFNGELT--RASPWKRIPLYYIPQAQ 239
PF + + R ++ I Y+ Q Q
Sbjct: 135 PFTSRDFMKFRLGGFEAIKSAYMAQVQ 161
>pdb|3SLP|A Chain A, Crystal Structure Of Lambda Exonuclease In Complex With A
12 Bp Symmetric Dna Duplex
pdb|3SLP|B Chain B, Crystal Structure Of Lambda Exonuclease In Complex With A
12 Bp Symmetric Dna Duplex
pdb|3SLP|C Chain C, Crystal Structure Of Lambda Exonuclease In Complex With A
12 Bp Symmetric Dna Duplex
Length = 229
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 42/147 (28%), Positives = 59/147 (40%), Gaps = 23/147 (15%)
Query: 105 WQKLRKHKLTASTFAGAIGF------WPRRRVQ----LWLEKIGAIEPFLGNLATCWSNI 154
W KLR +TAS I WP ++ L E + P + A W
Sbjct: 27 WHKLRLGVITASEVHNVIAKPRSGKKWPDMKMSYFHTLLAEVCTGVAPEVNAKALAWGKQ 86
Query: 155 KEEDALERYKLITGNTVYFTEFQVYRDKSRDDDWLAASPDGLVDRFVYDLPSGGVLEIKC 214
E DA ++ +G V + +YRD+S A SPDGL G LE+KC
Sbjct: 87 YENDARTLFEFTSGVNVTESPI-IYRDESMR---TACSPDGLCS-------DGNGLELKC 135
Query: 215 PFFNGELT--RASPWKRIPLYYIPQAQ 239
PF + + R ++ I Y+ Q Q
Sbjct: 136 PFTSRDFMKFRLGGFEAIKSAYMAQVQ 162
>pdb|3SYY|A Chain A, Crystal Structure Of An Alkaline Exonuclease (Lhk-Exo)
From Laribacter Hongkongensis
pdb|3SZ4|A Chain A, Crystal Structure Of Lhk-Exo In Complex With Damp
pdb|3SZ5|A Chain A, Crystal Structure Of Lhk-Exo In Complex With
5-Phosphorylated Oligothymidine (Dt)4
Length = 216
Score = 37.0 bits (84), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 52/180 (28%), Positives = 70/180 (38%), Gaps = 26/180 (14%)
Query: 103 KNWQKLRKHKLTASTFAGAI-----GFWPRRR---VQLWLEKI-GAIEPFLGNLATCWSN 153
+ W R K+TAS A + G+ R+ +L +++ G E N A
Sbjct: 6 EEWFAARLGKVTASRVADVMTKTKSGYAASRQNYMAELICQRLTGTQEIRFSNAAMQRGT 65
Query: 154 IKEEDALERYKLITGNTVYFTEFQVYRDKSRDDDWLAASPDGLVDRFVYDLPSGGVLEIK 213
E A RY + TG V TE + + ASPDGLV G++EIK
Sbjct: 66 ELEPHARARYIIETGEIV--TEVGLIDHPTIA--GFGASPDGLVG-------DTGLIEIK 114
Query: 214 CPFFNGELTRASPWKRIPLYYIPQAQGLMEILDRDWMDFYVWT---PNGSSLF--RVYRD 268
CP + K P YI Q Q M R W DF + P+ F R+ RD
Sbjct: 115 CPNTWTHIETIKTGKPKP-EYIKQMQTQMACTGRQWCDFVSYDDRLPDDMQYFCTRIERD 173
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
0.322 0.137 0.449
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,024,600
Number of Sequences: 62578
Number of extensions: 402299
Number of successful extensions: 742
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 742
Number of HSP's gapped (non-prelim): 3
length of query: 345
length of database: 14,973,337
effective HSP length: 100
effective length of query: 245
effective length of database: 8,715,537
effective search space: 2135306565
effective search space used: 2135306565
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (24.6 bits)