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= 011016
(495 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3BGF|H Chain H, X-Ray Crystal Structure Of The Sars Coronavirus Spike
Receptor Binding Domain In Complex With F26g19 Fab
pdb|3BGF|B Chain B, X-Ray Crystal Structure Of The Sars Coronavirus Spike
Receptor Binding Domain In Complex With F26g19 Fab
Length = 220
Score = 31.6 bits (70), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 32/106 (30%), Positives = 42/106 (39%), Gaps = 16/106 (15%)
Query: 243 SVLNIADKTMRNCTRNGFHKPEELRIRLTYRGGENGDNYAHGSPVTVSNSKDEAGKTTSQ 302
S L D + CTR G P+ LR D + G+ VTVS++K A
Sbjct: 84 SSLTNEDSAVYFCTREGI--PQLLRTL---------DYWGQGTSVTVSSAKTTAPSVYPL 132
Query: 303 EAVVQNCQGFPPHVACFPGAPWPYP----WNSAQWSPPV-TPPAIL 343
V + G + C +P P WNS S V T PA+L
Sbjct: 133 APVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVL 178
>pdb|1YEC|H Chain H, Structure Of A Catalytic Antibody Igg2a Fab Fragment
(D2.3)
pdb|1YEF|H Chain H, Structure Of Igg2a Fab Fragment (D2.3) Complexed With
Substrate Analogue
pdb|1YEG|H Chain H, Structure Of Igg2a Fab Fragment (D2.3) Complexed With
Reaction Product
pdb|1YEH|H Chain H, Structure Of Igg2a Fab Fragment
pdb|1YEI|H Chain H, Catalytic Antibody D2.3 Complex
pdb|1YEK|H Chain H, Catalytic Antibody D2.3 Complex
pdb|1YEJ|H Chain H, Catalytic Antibody Complex
pdb|1KN2|H Chain H, Catalytic Antibody D2.3 Complex
pdb|1KN4|H Chain H, Catalytic Antibody D2.3 Complex
Length = 222
Score = 31.6 bits (70), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 31/106 (29%), Positives = 41/106 (38%), Gaps = 14/106 (13%)
Query: 243 SVLNIADKTMRNCTRNGFHKPEELRIRLTYRGGENGDNYAHGSPVTVSNSKDEAGKTTSQ 302
S L D + CTR GF E + D + G+ VTVS++K A
Sbjct: 84 STLKSEDSAVYFCTRWGFIPVREDYVM---------DYWGQGTLVTVSSAKTTAPSVYPL 134
Query: 303 EAVVQNCQGFPPHVACFPGAPWPYP----WNSAQWSPPV-TPPAIL 343
V + G + C +P P WNS S V T PA+L
Sbjct: 135 APVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVL 180
>pdb|1IGI|H Chain H, 26-10 Fab:digoxin Complex-Affinity And Specificity Due To
Surface Complementarity
pdb|1IGJ|B Chain B, 26-10 Fab:digoxin Complex-Affinity And Specificity Due To
Surface Complementarity
pdb|1IGJ|D Chain D, 26-10 Fab:digoxin Complex-Affinity And Specificity Due To
Surface Complementarity
Length = 218
Score = 28.9 bits (63), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 26/84 (30%), Positives = 36/84 (42%), Gaps = 10/84 (11%)
Query: 270 LTYRGGENG-----DNYAHGSPVTVSNSKDEAGKTTSQEAVVQNCQGFPPHVACFPGAPW 324
+ Y G +G D + HG+ VTVS++K A V + G + C +
Sbjct: 93 VYYCAGSSGNKWAMDYWGHGASVTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYF 152
Query: 325 PYP----WNSAQWSPPV-TPPAIL 343
P P WNS S V T PA+L
Sbjct: 153 PEPVTLTWNSGSLSSGVHTFPAVL 176
>pdb|1KEG|H Chain H, Antibody 64m-2 Fab Complexed With Dtt(6-4)tt
Length = 220
Score = 28.9 bits (63), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 33/120 (27%), Positives = 44/120 (36%), Gaps = 17/120 (14%)
Query: 229 LTFGSDAPLCESMASVLNIADKTMRNCTRNGFHKPEELRIRLTYRGGENGDNYAHGSPVT 288
LT + A S L D + CTR +K L D + G+ VT
Sbjct: 70 LTAVTSASTAYMEVSSLTNEDSAVYYCTRRSGYKYYAL------------DYWGQGTSVT 117
Query: 289 VSNSKDEAGKTTSQEAVVQNCQGFPPHVACFPGAPWPYP----WNSAQWSPPV-TPPAIL 343
VS++K A V + G + C +P P WNS S V T PA+L
Sbjct: 118 VSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVL 177
>pdb|1PLG|H Chain H, Evidence For The Extended Helical Nature Of Polysaccharide
Epitopes. The 2.8 Angstroms Resolution Structure And
Thermodynamics Of Ligand Binding Of An Antigen Binding
Fragment Specific For Alpha-(2->8)- Polysialic Acid
Length = 215
Score = 28.9 bits (63), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 37/86 (43%), Gaps = 6/86 (6%)
Query: 264 EELRIRLTYRGGENG-DNYAHGSPVTVSNSKDEAGKTTSQEAVVQNCQGFPPHVACFPGA 322
E+ + RGG+ D + G+ VTVS++K A V + G + C
Sbjct: 89 EDSAVYFCARGGKFAMDYWGQGTSVTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKG 148
Query: 323 PWPYP----WNSAQWSPPV-TPPAIL 343
+P P WNS S V T PA+L
Sbjct: 149 YFPEPVTLTWNSGSLSSGVHTFPAVL 174
>pdb|3QG6|B Chain B, Structural Basis For Ligand Recognition And Discrimination
Of A Quorum Quenching Antibody
pdb|3QG6|H Chain H, Structural Basis For Ligand Recognition And Discrimination
Of A Quorum Quenching Antibody
pdb|3QG7|H Chain H, Structural Basis For Ligand Recognition And Discrimination
Of A Quorum Quenching Antibody
Length = 213
Score = 28.9 bits (63), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 33/78 (42%), Gaps = 5/78 (6%)
Query: 271 TYRGGENGDNYAHGSPVTVSNSKDEAGKTTSQEAVVQNCQGFPPHVACFPGAPWPYP--- 327
TY GD + G+ +TVS++K A V + G + C +P P
Sbjct: 93 TYFCTREGDYWGQGTTLTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTL 152
Query: 328 -WNSAQWSPPV-TPPAIL 343
WNS S V T PA+L
Sbjct: 153 TWNSGSLSSGVHTFPAVL 170
>pdb|1EHL|H Chain H, 64m-2 Antibody Fab Complexed With D(5ht)(6-4)t
Length = 219
Score = 28.9 bits (63), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 33/120 (27%), Positives = 44/120 (36%), Gaps = 17/120 (14%)
Query: 229 LTFGSDAPLCESMASVLNIADKTMRNCTRNGFHKPEELRIRLTYRGGENGDNYAHGSPVT 288
LT + A S L D + CTR +K L D + G+ VT
Sbjct: 70 LTAVTSASTAYMEVSSLTNEDSAVYYCTRRSGYKYYAL------------DYWGQGTSVT 117
Query: 289 VSNSKDEAGKTTSQEAVVQNCQGFPPHVACFPGAPWPYP----WNSAQWSPPV-TPPAIL 343
VS++K A V + G + C +P P WNS S V T PA+L
Sbjct: 118 VSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVL 177
>pdb|2AEP|H Chain H, An Epidemiologically Significant Epitope Of A 1998
Influenza Virus Neuraminidase Forms A Highly Hydrated
Interface In The Na-Antibody Complex.
pdb|2AEQ|H Chain H, An Epidemiologically Significant Epitope Of A 1998
Influenza Virus Neuraminidase Forms A Highly Hydrated
Interface In The Na-Antibody Complex
Length = 217
Score = 28.5 bits (62), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 32/74 (43%), Gaps = 5/74 (6%)
Query: 275 GENGDNYAHGSPVTVSNSKDEAGKTTSQEAVVQNCQGFPPHVACFPGAPWPYP----WNS 330
G N D + G+ +TVS++K A V + G + C +P P WNS
Sbjct: 104 GTNYDYWGQGTTLTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNS 163
Query: 331 AQWSPPV-TPPAIL 343
S V T PA+L
Sbjct: 164 GSLSSGVHTFPAVL 177
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
0.311 0.128 0.398
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,544,952
Number of Sequences: 62578
Number of extensions: 637093
Number of successful extensions: 1058
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 18
Number of HSP's that attempted gapping in prelim test: 1058
Number of HSP's gapped (non-prelim): 18
length of query: 495
length of database: 14,973,337
effective HSP length: 103
effective length of query: 392
effective length of database: 8,527,803
effective search space: 3342898776
effective search space used: 3342898776
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 53 (25.0 bits)