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= psy3528
(218 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2OQ4|A Chain A, Crystal Structure Of The Dna Repair Enzyme Endonuclease-
Viii (Nei) From E. Coli (E2q) In Complex With Ap-Site
Containing Dna Substrate
pdb|2OQ4|B Chain B, Crystal Structure Of The Dna Repair Enzyme Endonuclease-
Viii (Nei) From E. Coli (E2q) In Complex With Ap-Site
Containing Dna Substrate
Length = 262
Score = 27.7 bits (60), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 31/68 (45%), Gaps = 5/68 (7%)
Query: 63 GKYDVDVSIEAPTKEIIYRQVKSQFDTHQFVTLVEGTYVVCFSNEFSTYSHKVVYMDFQV 122
GK DV P + Q+ Q TH V + FSN+ + YSH +Y ++V
Sbjct: 19 GKPLTDVWFAFPQLKTYQSQLIGQHVTH--VETRGKALLTHFSNDLTLYSHNQLYGVWRV 76
Query: 123 ---GDEPQ 127
G+EPQ
Sbjct: 77 VDTGEEPQ 84
>pdb|1Q3C|A Chain A, Crystal Structure Of The Dna Repair Enzyme
Endonuclease-Viii (Nei) From E. Coli: The E2a Mutant At
2.3 Resolution
Length = 262
Score = 27.7 bits (60), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 31/68 (45%), Gaps = 5/68 (7%)
Query: 63 GKYDVDVSIEAPTKEIIYRQVKSQFDTHQFVTLVEGTYVVCFSNEFSTYSHKVVYMDFQV 122
GK DV P + Q+ Q TH V + FSN+ + YSH +Y ++V
Sbjct: 19 GKPLTDVWFAFPQLKTYQSQLIGQHVTH--VETRGKALLTHFSNDLTLYSHNQLYGVWRV 76
Query: 123 ---GDEPQ 127
G+EPQ
Sbjct: 77 VDTGEEPQ 84
>pdb|1Q3B|A Chain A, Crystal Structure Of The Dna Repair Enzyme
Endonuclease-Viii (Nei) From E. Coli: The R252a Mutant
At 2.05 Resolution.
pdb|2OPF|A Chain A, Crystal Structure Of The Dna Repair Enzyme
Endonuclease-Viii (Nei) From E. Coli (R252a) In Complex
With Ap-Site Containing Dna Substrate
Length = 262
Score = 27.7 bits (60), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 31/68 (45%), Gaps = 5/68 (7%)
Query: 63 GKYDVDVSIEAPTKEIIYRQVKSQFDTHQFVTLVEGTYVVCFSNEFSTYSHKVVYMDFQV 122
GK DV P + Q+ Q TH V + FSN+ + YSH +Y ++V
Sbjct: 19 GKPLTDVWFAFPQLKTYQSQLIGQHVTH--VETRGKALLTHFSNDLTLYSHNQLYGVWRV 76
Query: 123 ---GDEPQ 127
G+EPQ
Sbjct: 77 VDTGEEPQ 84
>pdb|1K3W|A Chain A, Crystal Structure Of A Trapped Reaction Intermediate Of
The Dna Repair Enzyme Endonuclease Viii With Dna
pdb|1K3X|A Chain A, Crystal Structure Of A Trapped Reaction Intermediate Of
The Dna Repair Enzyme Endonuclease Viii With
Brominated-Dna
pdb|1Q39|A Chain A, Crystal Structure Of The Dna Repair Enzyme
Endonuclease-Viii (Nei) From E. Coli: The Wt Enzyme At
2.8 Resolution.
pdb|2EA0|A Chain A, Crystal Structure Of The Dna Repair Enzyme
Endonuclease-viii (nei) From E. Coli In Complex With
Ap-site Containing Dna Substrate
Length = 262
Score = 27.7 bits (60), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 31/68 (45%), Gaps = 5/68 (7%)
Query: 63 GKYDVDVSIEAPTKEIIYRQVKSQFDTHQFVTLVEGTYVVCFSNEFSTYSHKVVYMDFQV 122
GK DV P + Q+ Q TH V + FSN+ + YSH +Y ++V
Sbjct: 19 GKPLTDVWFAFPQLKTYQSQLIGQHVTH--VETRGKALLTHFSNDLTLYSHNQLYGVWRV 76
Query: 123 ---GDEPQ 127
G+EPQ
Sbjct: 77 VDTGEEPQ 84
>pdb|1LFO|A Chain A, Liver Fatty Acid Binding Protein-Oleate Complex
Length = 128
Score = 26.9 bits (58), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 23/38 (60%), Gaps = 1/38 (2%)
Query: 110 TYSHKVVYMDFQVGDEPQLPGV-GEHVTVMTQMESSTQ 146
TY KV++ +F +G+E +L + GE V + +ME +
Sbjct: 54 TYGSKVIHNEFTLGEEXELETMTGEKVKAVVKMEGDNK 91
>pdb|2JU3|A Chain A, Solution-State Nmr Structures Of Apo-Lfabp (Liver Fatty
Acid-Binding Protein)
pdb|2JU7|A Chain A, Solution-State Structures Of Oleate-Liganded Lfabp,
Protein Only
pdb|2JU8|A Chain A, Solution-State Structures Of Oleate-Liganded Lfabp, Major
Form Of 1:2 Protein-Ligand Complex
Length = 127
Score = 26.9 bits (58), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 23/38 (60%), Gaps = 1/38 (2%)
Query: 110 TYSHKVVYMDFQVGDEPQLPGV-GEHVTVMTQMESSTQ 146
TY KV++ +F +G+E +L + GE V + +ME +
Sbjct: 53 TYGSKVIHNEFTLGEECELETMTGEKVKAVVKMEGDNK 90
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
0.324 0.136 0.397
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,936,188
Number of Sequences: 62578
Number of extensions: 222050
Number of successful extensions: 568
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 568
Number of HSP's gapped (non-prelim): 6
length of query: 218
length of database: 14,973,337
effective HSP length: 95
effective length of query: 123
effective length of database: 9,028,427
effective search space: 1110496521
effective search space used: 1110496521
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: 49 (23.5 bits)