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= 040990
(133 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2OJZ|L Chain L, Anti-Dna Antibody Ed10
pdb|2OJZ|M Chain M, Anti-Dna Antibody Ed10
pdb|2OK0|L Chain L, Fab Ed10-Dna Complex
Length = 219
Score = 27.7 bits (60), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 35/77 (45%), Gaps = 13/77 (16%)
Query: 59 FHGTGWAFTYLIKVSREEHHELITHGVHRFASHPSYC--GFHIP-SVGTQTMLCNPMSTI 115
F G+G + +K+SR E +L GV+ YC G HIP + G T L S
Sbjct: 67 FSGSGSGTDFTLKISRVEAEDL---GVY-------YCFQGSHIPLTFGAGTKLEVKRSDA 116
Query: 116 GPAIVVCHSFADMITHG 132
P + + ++ +T G
Sbjct: 117 APTVSIFPPSSEQLTSG 133
>pdb|1ZEA|L Chain L, Structure Of The Anti-Cholera Toxin Antibody Fab Fragment
Te33 In Complex With A D-Peptide
Length = 216
Score = 26.9 bits (58), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 36/77 (46%), Gaps = 13/77 (16%)
Query: 59 FHGTGWAFTYLIKVSREEHHELITHGVHRFASHPSYC--GFHIP-SVGTQTMLCNPMSTI 115
F G+G + +K+SR E +L GV+ YC G HIP + G+ T L +
Sbjct: 67 FSGSGSGTDFTLKISRVEAEDL---GVY-------YCFQGSHIPFTFGSGTKLEIKRADA 116
Query: 116 GPAIVVCHSFADMITHG 132
P + + ++ +T G
Sbjct: 117 APTVSIFPPSSEQLTSG 133
>pdb|1M71|A Chain A, Crystal Structure Of A Monoclonal Fab Specific For
Shigella Flexneri Y Lipopolysaccharide
pdb|1M7D|A Chain A, Crystal Structure Of A Monoclonal Fab Specific For
Shigella Flexneri Y Lipopolysaccharide Complexed With A
Trisaccharide
pdb|1M7I|A Chain A, Crystal Structure Of A Monoclonal Fab Specific For
Shigella Flexneri Y Lipopolysaccharide Complexed With A
Pentasaccharide
pdb|1PZ5|A Chain A, Structural Basis Of Peptide-Carbohydrate Mimicry In An
Antibody Combining Site
Length = 215
Score = 26.9 bits (58), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 8/74 (10%)
Query: 59 FHGTGWAFTYLIKVSREEHHELITHGVHRFASHPSYCGFHIPSVGTQTMLCNPMSTIGPA 118
F G+G + +K+SR E +L GV+ F S + H+P+ G T L + P
Sbjct: 67 FSGSGSGTDFTLKISRVEAEDL---GVY-FCSQTT----HVPTFGGGTKLEIKRADAAPT 118
Query: 119 IVVCHSFADMITHG 132
+ + ++ +T G
Sbjct: 119 VSIFPPSSEQLTSG 132
>pdb|3UO1|L Chain L, Structure Of A Monoclonal Antibody Complexed With Its
Mhc-I Antigen
pdb|3UYR|L Chain L, Structure Of A Monoclonal Antibody Complexed With Its
Mhc-I Antigen
pdb|3V4U|L Chain L, Structure Of A Monoclonal Antibody Complexed With Its
Mhc-I Antigen
pdb|3V52|L Chain L, Structure Of A Monoclonal Antibody Complexed With Its
Mhc-I Antigen
Length = 218
Score = 26.9 bits (58), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 8/74 (10%)
Query: 59 FHGTGWAFTYLIKVSREEHHELITHGVHRFASHPSYCGFHIPSVGTQTMLCNPMSTIGPA 118
F G+G + +K+SR E +L GV+ F S + H+P+ G T L + P
Sbjct: 67 FSGSGSGTDFTLKISRVEAEDL---GVY-FCSQST----HVPTFGGGTKLEIKRADAAPT 118
Query: 119 IVVCHSFADMITHG 132
+ + ++ +T G
Sbjct: 119 VSIFPPSSEQLTSG 132
>pdb|3EAY|A Chain A, Crystal Structure Of The Human Senp7 Catalytic Domain
Length = 323
Score = 26.9 bits (58), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 13/44 (29%), Positives = 20/44 (45%)
Query: 38 LYQTSFTAFFFQVPEYILAIAFHGTGWAFTYLIKVSREEHHELI 81
+Y + FF+ P + H W ++IK RE+ ELI
Sbjct: 267 VYLLQYVESFFKDPIVNFELPIHLEKWFPRHVIKTKREDIRELI 310
>pdb|1TET|L Chain L, Crystal Structure Of An Anticholera Toxin Peptide Complex
At 2.3 Angstroms
Length = 216
Score = 26.9 bits (58), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 36/77 (46%), Gaps = 13/77 (16%)
Query: 59 FHGTGWAFTYLIKVSREEHHELITHGVHRFASHPSYC--GFHIP-SVGTQTMLCNPMSTI 115
F G+G + +K+SR E +L GV+ YC G HIP + G+ T L +
Sbjct: 67 FSGSGSGTDFTLKISRVEAEDL---GVY-------YCFQGSHIPFTFGSGTKLEIKRADA 116
Query: 116 GPAIVVCHSFADMITHG 132
P + + ++ +T G
Sbjct: 117 APTVSIFPPSSEQLTSG 133
>pdb|3NZ8|B Chain B, Crystal Structure Of The Hiv-2 Neutralizing Fab Fragment
7c8
pdb|3NZ8|L Chain L, Crystal Structure Of The Hiv-2 Neutralizing Fab Fragment
7c8
Length = 218
Score = 26.6 bits (57), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 36/77 (46%), Gaps = 13/77 (16%)
Query: 59 FHGTGWAFTYLIKVSREEHHELITHGVHRFASHPSYC--GFHIP-SVGTQTMLCNPMSTI 115
F G+G + +K+SR E +L GV+ YC G H+P + G+ T L +
Sbjct: 67 FSGSGSGTDFTLKISRVEAEDL---GVY-------YCFQGSHVPFTFGSGTKLEIKRADA 116
Query: 116 GPAIVVCHSFADMITHG 132
P + + ++ +T G
Sbjct: 117 APTVSIFPPSSEQLTSG 133
>pdb|1CLZ|L Chain L, Igg Fab (Igg3, Kappa) Fragment (Mbr96) Complexed With
Lewis Y Nonoate Methyl Ester
Length = 219
Score = 26.2 bits (56), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 36/77 (46%), Gaps = 13/77 (16%)
Query: 59 FHGTGWAFTYLIKVSREEHHELITHGVHRFASHPSYC--GFHIP-SVGTQTMLCNPMSTI 115
F G+G + +K+SR E +L GV+ YC G H+P + G+ T L +
Sbjct: 67 FSGSGSGTDFTLKISRVEAEDL---GVY-------YCFQGSHVPFTFGSGTKLEIKRADA 116
Query: 116 GPAIVVCHSFADMITHG 132
P + + ++ +T G
Sbjct: 117 APTVSIFPPSSEQLTSG 133
>pdb|1Z3G|L Chain L, Crystal Structure Of Complex Between Pvs25 And Fab
Fragment Of Malaria Transmission Blocking Antibody 2a8
pdb|1Z3G|M Chain M, Crystal Structure Of Complex Between Pvs25 And Fab
Fragment Of Malaria Transmission Blocking Antibody 2a8
Length = 213
Score = 26.2 bits (56), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 16/74 (21%), Positives = 34/74 (45%), Gaps = 7/74 (9%)
Query: 59 FHGTGWAFTYLIKVSREEHHELITHGVHRFASHPSYCGFHIPSVGTQTMLCNPMSTIGPA 118
F G+G +Y + +S E + T+ +++S+P P+ G+ T L + P
Sbjct: 61 FRGSGSGTSYSLTISGMEAEDAATYYCQQWSSNP-------PTFGSGTKLEINRADTAPT 113
Query: 119 IVVCHSFADMITHG 132
+ + ++ +T G
Sbjct: 114 VSIFPPSSEQLTSG 127
>pdb|2R0Z|L Chain L, Pfa1 Fab Complexed With Gripi Peptide Fragment
pdb|3EYS|L Chain L, Pfa1 Fab Fragment Complexed With Pyro-Glu3-A-Beta (3-8)
pdb|3EYU|L Chain L, Pfa1 Fab Fragment Complexed With Ror2(518-525)
Length = 219
Score = 26.2 bits (56), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 35/77 (45%), Gaps = 13/77 (16%)
Query: 59 FHGTGWAFTYLIKVSREEHHELITHGVHRFASHPSYC--GFHIP-SVGTQTMLCNPMSTI 115
F G+G + +K+SR E +L GV+ YC G H+P + G T L +
Sbjct: 67 FSGSGSGTDFTLKISRVEAEDL---GVY-------YCFQGSHVPLTFGAGTKLELKRADA 116
Query: 116 GPAIVVCHSFADMITHG 132
P + + ++ +T G
Sbjct: 117 APTVSIFPPSSEQLTSG 133
>pdb|2R0W|L Chain L, Pfa2 Fab Complexed With Abeta1-8
Length = 219
Score = 26.2 bits (56), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 35/77 (45%), Gaps = 13/77 (16%)
Query: 59 FHGTGWAFTYLIKVSREEHHELITHGVHRFASHPSYC--GFHIP-SVGTQTMLCNPMSTI 115
F G+G + +K+SR E +L GV+ YC G H+P + G T L +
Sbjct: 67 FSGSGSGTDFTLKISRVEAEDL---GVY-------YCFQGSHVPLTFGAGTKLEIKRADA 116
Query: 116 GPAIVVCHSFADMITHG 132
P + + ++ +T G
Sbjct: 117 APTVSIFPPSSEQLTSG 133
>pdb|2DDQ|L Chain L, Crystal Structure Of The Fab Fragment Of A R310 Antibody
Complexed With (R)-Hne-Histidine Adduct
Length = 218
Score = 26.2 bits (56), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 35/77 (45%), Gaps = 13/77 (16%)
Query: 59 FHGTGWAFTYLIKVSREEHHELITHGVHRFASHPSYC--GFHIP-SVGTQTMLCNPMSTI 115
F G+G + +K+SR E +L GV+ YC G H+P + G T L +
Sbjct: 67 FSGSGSGTDFTLKISRVEAEDL---GVY-------YCFQGSHVPLTFGAGTKLELKRADA 116
Query: 116 GPAIVVCHSFADMITHG 132
P + + ++ +T G
Sbjct: 117 APTVSIFPPSSEQLTSG 133
>pdb|3IFP|L Chain L, X-Ray Structure Of Amyloid Beta Peptide:antibody (Abeta1-
7:12b4) Complex
pdb|3IFP|B Chain B, X-Ray Structure Of Amyloid Beta Peptide:antibody (Abeta1-
7:12b4) Complex
pdb|3IFP|D Chain D, X-Ray Structure Of Amyloid Beta Peptide:antibody (Abeta1-
7:12b4) Complex
pdb|3IFP|F Chain F, X-Ray Structure Of Amyloid Beta Peptide:antibody (Abeta1-
7:12b4) Complex
Length = 219
Score = 25.8 bits (55), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 35/77 (45%), Gaps = 13/77 (16%)
Query: 59 FHGTGWAFTYLIKVSREEHHELITHGVHRFASHPSYC--GFHIP-SVGTQTMLCNPMSTI 115
F G+G + +K+SR E +L GV+ YC G H+P + G T L +
Sbjct: 67 FSGSGSGTDFTLKISRVEAEDL---GVY-------YCFQGSHVPLTFGAGTKLELKRADA 116
Query: 116 GPAIVVCHSFADMITHG 132
P + + ++ +T G
Sbjct: 117 APTVSIFPPSSEQLTSG 133
>pdb|2IPU|L Chain L, Pfa1 Fab Fragment Complexed With Abeta 1-8 Peptide
pdb|2IPU|K Chain K, Pfa1 Fab Fragment Complexed With Abeta 1-8 Peptide
pdb|2IQ9|L Chain L, Pfa2 Fab Fragment, Triclinic Apo Form
Length = 219
Score = 25.8 bits (55), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 35/77 (45%), Gaps = 13/77 (16%)
Query: 59 FHGTGWAFTYLIKVSREEHHELITHGVHRFASHPSYC--GFHIP-SVGTQTMLCNPMSTI 115
F G+G + +K+SR E +L GV+ YC G H+P + G T L +
Sbjct: 67 FSGSGSGTDFTLKISRVEAEDL---GVY-------YCFQGSHVPLTFGAGTKLELKRADA 116
Query: 116 GPAIVVCHSFADMITHG 132
P + + ++ +T G
Sbjct: 117 APTVSIFPPSSEQLTSG 133
>pdb|4AEI|L Chain L, Crystal Structure Of The Aahii-Fab4c1 Complex
pdb|4AEI|M Chain M, Crystal Structure Of The Aahii-Fab4c1 Complex
pdb|4AEI|N Chain N, Crystal Structure Of The Aahii-Fab4c1 Complex
Length = 219
Score = 25.8 bits (55), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 35/77 (45%), Gaps = 13/77 (16%)
Query: 59 FHGTGWAFTYLIKVSREEHHELITHGVHRFASHPSYC--GFHIP-SVGTQTMLCNPMSTI 115
F G+G + +K+SR E +L GV+ YC G H+P + G T L +
Sbjct: 67 FSGSGSGTDFTLKISRVEAEDL---GVY-------YCFQGSHVPLTFGAGTKLELKRADA 116
Query: 116 GPAIVVCHSFADMITHG 132
P + + ++ +T G
Sbjct: 117 APTVSIFPPSSEQLTSG 133
>pdb|2IPT|L Chain L, Pfa1 Fab Fragment
pdb|2IQA|L Chain L, Pfa2 Fab Fragment, Monoclinic Apo Form
pdb|2IQA|A Chain A, Pfa2 Fab Fragment, Monoclinic Apo Form
Length = 219
Score = 25.8 bits (55), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 35/77 (45%), Gaps = 13/77 (16%)
Query: 59 FHGTGWAFTYLIKVSREEHHELITHGVHRFASHPSYC--GFHIP-SVGTQTMLCNPMSTI 115
F G+G + +K+SR E +L GV+ YC G H+P + G T L +
Sbjct: 67 FSGSGSGTDFTLKISRVEAEDL---GVY-------YCFQGSHVPLTFGAGTKLEIKRADA 116
Query: 116 GPAIVVCHSFADMITHG 132
P + + ++ +T G
Sbjct: 117 APTVSIFPPSSEQLTSG 133
>pdb|1QKZ|L Chain L, Fab Fragment (Mn14c11.6) In Complex With A Peptide Antigen
Derived From Neisseria Meningitidis P1.7 Serosubtype
Antigen And Domain Ii From Streptococcal Protein G
Length = 217
Score = 25.4 bits (54), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 34/74 (45%), Gaps = 8/74 (10%)
Query: 59 FHGTGWAFTYLIKVSREEHHELITHGVHRFASHPSYCGFHIPSVGTQTMLCNPMSTIGPA 118
F G+G + +K+SR E +L GV+ F S + H P+ G T L + P
Sbjct: 67 FSGSGSGTDFTLKISRVEAEDL---GVY-FCSQST----HFPTFGGGTKLEIKRADAAPT 118
Query: 119 IVVCHSFADMITHG 132
+ + ++ +T G
Sbjct: 119 VSIFPPSSEQLTSG 132
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
0.328 0.139 0.453
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,132,857
Number of Sequences: 62578
Number of extensions: 157185
Number of successful extensions: 728
Number of sequences better than 100.0: 28
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 20
Number of HSP's that attempted gapping in prelim test: 720
Number of HSP's gapped (non-prelim): 28
length of query: 133
length of database: 14,973,337
effective HSP length: 88
effective length of query: 45
effective length of database: 9,466,473
effective search space: 425991285
effective search space used: 425991285
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 46 (22.3 bits)