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= 039593
(144 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3CFD|H Chain H, Purple-fluorescent Antibody Ep2-25c10 In Complex With Its
Stilbene Hapten
pdb|3CFD|B Chain B, Purple-fluorescent Antibody Ep2-25c10 In Complex With Its
Stilbene Hapten
pdb|3CFE|H Chain H, Crystal Structure Of Purple-Fluorescent Antibody Ep2-25c10
pdb|3CFE|B Chain B, Crystal Structure Of Purple-Fluorescent Antibody Ep2-25c10
Length = 220
Score = 31.2 bits (69), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 22/34 (64%), Gaps = 3/34 (8%)
Query: 111 ADLAWDWPRQVVGDLALALSWVFFLVYSWREKYD 144
+D AW+W RQ+ G+ L W+ ++ YS R +Y+
Sbjct: 31 SDYAWNWLRQLPGN---KLEWMGYISYSGRIRYN 61
>pdb|3G5V|B Chain B, Antibodies Specifically Targeting A Locally Misfolded
Region Of Tumor Associated Egfr
Length = 213
Score = 30.0 bits (66), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 20/34 (58%), Gaps = 3/34 (8%)
Query: 111 ADLAWDWPRQVVGDLALALSWVFFLVYSWREKYD 144
+D AW+W RQ G+ L W+ ++ YS +Y+
Sbjct: 31 SDFAWNWIRQFPGN---KLEWMGYISYSGNTRYN 61
>pdb|3G5X|B Chain B, Antibodies Specifically Targeting A Locally Misfolded
Region Of Tumor Associated Egfr
pdb|3G5X|D Chain D, Antibodies Specifically Targeting A Locally Misfolded
Region Of Tumor Associated Egfr
Length = 216
Score = 30.0 bits (66), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 20/34 (58%), Gaps = 3/34 (8%)
Query: 111 ADLAWDWPRQVVGDLALALSWVFFLVYSWREKYD 144
+D AW+W RQ G+ L W+ ++ YS +Y+
Sbjct: 31 SDFAWNWIRQFPGN---KLEWMGYISYSGNTRYN 61
>pdb|3G5Z|B Chain B, Antibodies Specifically Targeting A Locally Misfolded
Region Of Tumor Associated Egfr
Length = 217
Score = 29.6 bits (65), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 20/34 (58%), Gaps = 3/34 (8%)
Query: 111 ADLAWDWPRQVVGDLALALSWVFFLVYSWREKYD 144
+D AW+W RQ G+ L W+ ++ YS +Y+
Sbjct: 31 SDFAWNWIRQFPGN---KLEWMGYISYSGNTRYN 61
>pdb|3G5Y|B Chain B, Antibodies Specifically Targeting A Locally Misfolded
Region Of Tumor Associated Egfr
Length = 216
Score = 28.9 bits (63), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 20/34 (58%), Gaps = 3/34 (8%)
Query: 111 ADLAWDWPRQVVGDLALALSWVFFLVYSWREKYD 144
+D AW+W RQ G+ L W+ ++ YS +Y+
Sbjct: 31 SDYAWNWIRQFPGN---KLEWMGYISYSANTRYN 61
>pdb|1NSN|H Chain H, The Crystal Structure Of Antibody N10-Staphylococcal
Nuclease Complex At 2.9 Angstroms Resolution
Length = 210
Score = 28.9 bits (63), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 19/34 (55%), Gaps = 3/34 (8%)
Query: 111 ADLAWDWPRQVVGDLALALSWVFFLVYSWREKYD 144
+D AW+W RQ G+ L W+ ++ YS Y+
Sbjct: 31 SDYAWNWIRQFPGN---KLEWMGYITYSGTTSYN 61
>pdb|1BAF|H Chain H, 2.9 Angstroms Resolution Structure Of An
Anti-Dinitrophenyl- Spin-Label Monoclonal Antibody Fab
Fragment With Bound Hapten
Length = 217
Score = 28.9 bits (63), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 20/34 (58%), Gaps = 3/34 (8%)
Query: 111 ADLAWDWPRQVVGDLALALSWVFFLVYSWREKYD 144
+D AW+W RQ G+ L W+ ++ YS +Y+
Sbjct: 31 SDYAWNWIRQFPGN---KLEWMGYMSYSGSTRYN 61
>pdb|1KCS|H Chain H, Crystal Structure Of Antibody Pc282 In Complex With Ps1
Peptide
pdb|1KCV|H Chain H, Crystal Structure Of Antibody Pc282
Length = 217
Score = 28.1 bits (61), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 19/34 (55%), Gaps = 3/34 (8%)
Query: 111 ADLAWDWPRQVVGDLALALSWVFFLVYSWREKYD 144
+D AW+W RQ G +L W+ ++ YS Y+
Sbjct: 31 SDYAWNWIRQFAGQ---SLEWMGYISYSGSTSYN 61
>pdb|1S5I|H Chain H, Fab (Lnkb-2) Of Monoclonal Antibody To Human
Interleukin-2, Crystal Structure
Length = 220
Score = 28.1 bits (61), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 19/34 (55%), Gaps = 3/34 (8%)
Query: 111 ADLAWDWPRQVVGDLALALSWVFFLVYSWREKYD 144
+D AW+W RQ G+ L W+ ++ YS Y+
Sbjct: 31 SDYAWNWIRQFPGN---KLEWMGYITYSGSTGYN 61
>pdb|1F90|H Chain H, Fab Fragment Of Monoclonal Antibody (Lnkb-2) Against Human
Interleukin-2 In Complex With Antigenic Peptide
pdb|1F8T|H Chain H, Fab (Lnkb-2) Of Monoclonal Antibody, Crystal Structure
Length = 220
Score = 28.1 bits (61), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 19/34 (55%), Gaps = 3/34 (8%)
Query: 111 ADLAWDWPRQVVGDLALALSWVFFLVYSWREKYD 144
+D AW+W RQ G+ L W+ ++ YS Y+
Sbjct: 31 SDYAWNWIRQFPGN---KLEWMGYITYSGSTGYN 61
>pdb|32C2|B Chain B, Structure Of An Activity Suppressing Fab Fragment To
Cytochrome P450 Aromatase
Length = 218
Score = 28.1 bits (61), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 19/34 (55%), Gaps = 3/34 (8%)
Query: 111 ADLAWDWPRQVVGDLALALSWVFFLVYSWREKYD 144
+D AW+W RQ G+ L W+ ++ YS Y+
Sbjct: 31 SDYAWNWIRQFPGN---KLEWMGYISYSGSTSYN 61
>pdb|1AY1|H Chain H, Anti Taq Fab Tp7
pdb|1BGX|H Chain H, Taq Polymerase In Complex With Tp7, An Inhibitory Fab
Length = 213
Score = 27.7 bits (60), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 19/34 (55%), Gaps = 3/34 (8%)
Query: 111 ADLAWDWPRQVVGDLALALSWVFFLVYSWREKYD 144
+D AW+W RQ G+ L W+ ++ YS Y+
Sbjct: 31 SDYAWNWIRQFPGN---KLEWMGYITYSGTTDYN 61
>pdb|1KCU|H Chain H, Crystal Structure Of Antibody Pc287
pdb|1KC5|H Chain H, Crystal Structure Of Antibody Pc287 In Complex With Ps1
Peptide
Length = 217
Score = 27.7 bits (60), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 19/34 (55%), Gaps = 3/34 (8%)
Query: 111 ADLAWDWPRQVVGDLALALSWVFFLVYSWREKYD 144
+D AW+W RQ G+ L W+ ++ YS Y+
Sbjct: 31 SDYAWNWIRQFPGN---KLEWMAYISYSGSTTYN 61
>pdb|3RVT|D Chain D, Structure Of 4c1 Fab In P212121 Space Group
pdb|3RVU|D Chain D, Structure Of 4c1 Fab In C2221 Space Group
pdb|3RVV|D Chain D, Crystal Structure Of Der F 1 Complexed With Fab 4c1
pdb|3RVW|D Chain D, Crystal Structure Of Der P 1 Complexed With Fab 4c1
pdb|3RVX|D Chain D, Crystal Structure Of Der P 1 Complexed With Fab 4c1
Length = 255
Score = 27.7 bits (60), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 19/34 (55%), Gaps = 3/34 (8%)
Query: 111 ADLAWDWPRQVVGDLALALSWVFFLVYSWREKYD 144
+D AW+W RQ G+ L W+ ++ YS Y+
Sbjct: 31 SDYAWNWIRQFPGN---KLEWMGYISYSGTTSYN 61
>pdb|1C12|B Chain B, Insight In Odorant Perception: The Crystal Structure And
Binding Characteristics Of Antibody Fragments Directed
Against The Musk Odorant Traseolide
Length = 220
Score = 26.9 bits (58), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 18/34 (52%), Gaps = 3/34 (8%)
Query: 111 ADLAWDWPRQVVGDLALALSWVFFLVYSWREKYD 144
+D AW+W RQ G+ L W+ ++ YS Y
Sbjct: 31 SDYAWNWIRQFPGN---KLEWMGYISYSGSTSYS 61
>pdb|3LEY|H Chain H, 2f5 Epitope Scaffold Elicited Anti-Hiv-1 Monoclonal
Antibody 6a7 In Complex With Hiv-1 Gp41
Length = 221
Score = 26.2 bits (56), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 18/34 (52%), Gaps = 3/34 (8%)
Query: 111 ADLAWDWPRQVVGDLALALSWVFFLVYSWREKYD 144
D AW+W RQ G+ L W+ ++ YS Y+
Sbjct: 31 TDYAWNWIRQFPGN---KLEWMGYISYSGFTSYN 61
>pdb|3LEX|H Chain H, 2f5 Epitope Scaffold Elicited Anti-Hiv-1 Monoclonal
Antibody 11f10 In Complex With Hiv-1 Gp41
pdb|3LEX|A Chain A, 2f5 Epitope Scaffold Elicited Anti-Hiv-1 Monoclonal
Antibody 11f10 In Complex With Hiv-1 Gp41
Length = 221
Score = 26.2 bits (56), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 18/34 (52%), Gaps = 3/34 (8%)
Query: 111 ADLAWDWPRQVVGDLALALSWVFFLVYSWREKYD 144
+D AW W RQ G+ L W+ ++ YS Y+
Sbjct: 31 SDYAWSWIRQFPGN---KLEWMGYINYSGYTSYN 61
>pdb|1RU9|H Chain H, Crystal Structure (A) Of U.V.-Irradiated Cationic
Cyclization Antibody 4c6 Fab At Ph 4.6 With A Data Set
Collected In-House.
pdb|1RUA|H Chain H, Crystal Structure (b) Of U.v.-irradiated Cationic
Cyclization Antibody 4c6 Fab At Ph 4.6 With A Data Set
Collected At Ssrl Beamline 11-1.
pdb|1RUL|H Chain H, Crystal Structure (d) Of U.v.-irradiated Cationic
Cyclization Antibody 4c6 Fab At Ph 5.6 With A Data Set
Collected At Ssrl Beamline 11-1
Length = 222
Score = 25.8 bits (55), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 11/28 (39%), Positives = 17/28 (60%), Gaps = 3/28 (10%)
Query: 111 ADLAWDWPRQVVGDLALALSWVFFLVYS 138
+D AW+W RQ G+ L W+ ++ YS
Sbjct: 31 SDFAWNWIRQFPGN---KLEWMGYINYS 55
>pdb|1NCW|H Chain H, Cationic Cyclization Antibody 4c6 In Complex With Benzoic
Acid
pdb|1ND0|B Chain B, Cationic Cyclization Antibody 4c6 Complex With Transition
State Analog
pdb|1ND0|D Chain D, Cationic Cyclization Antibody 4c6 Complex With Transition
State Analog
pdb|1ND0|F Chain F, Cationic Cyclization Antibody 4c6 Complex With Transition
State Analog
pdb|1ND0|H Chain H, Cationic Cyclization Antibody 4c6 Complex With Transition
State Analog
pdb|1RUK|H Chain H, Crystal Structure (C) Of Native Cationic Cyclization
Antibody 4c6 Fab At Ph 4.6 With A Data Set Collected At
Ssrl Beamline 9-1
pdb|1RUM|H Chain H, Crystal Structure (F) Of H2o2-Soaked Cationic Cyclization
Antibody 4c6 Fab At Ph 8.5 With A Data Set Collected At
Ssrl Beamline 9-1.
pdb|1RUP|H Chain H, Crystal Structure (g) Of Native Cationic Cyclization
Antibody 4c6 Fab At Ph 8.5 With A Data Set Collected At
Aps Beamline 19-id
Length = 222
Score = 25.8 bits (55), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 11/28 (39%), Positives = 17/28 (60%), Gaps = 3/28 (10%)
Query: 111 ADLAWDWPRQVVGDLALALSWVFFLVYS 138
+D AW+W RQ G+ L W+ ++ YS
Sbjct: 31 SDFAWNWIRQFPGN---KLEWMGYINYS 55
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
0.329 0.140 0.459
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,467,319
Number of Sequences: 62578
Number of extensions: 95149
Number of successful extensions: 225
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 19
Number of HSP's that attempted gapping in prelim test: 225
Number of HSP's gapped (non-prelim): 19
length of query: 144
length of database: 14,973,337
effective HSP length: 89
effective length of query: 55
effective length of database: 9,403,895
effective search space: 517214225
effective search space used: 517214225
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 46 (22.3 bits)