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= psy6030
(118 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IZR|BB Chain b, Localization Of The Large Subunit Ribosomal Proteins
Into A 5.5 A Cryo-Em Map Of Triticum Aestivum
Translating 80s Ribosome
Length = 147
Score = 60.8 bits (146), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 35/83 (42%), Positives = 47/83 (56%), Gaps = 3/83 (3%)
Query: 2 VSSHLIWNIVKNNNAYLMKA---DNIKKWFSKEPGNLPNLASFKYSGLIHSKTIHIQPTA 58
V LIW IVK NN +L+K N K F+KEP NL N+ S+K+SGL + KT+ IQP+
Sbjct: 4 VPEPLIWEIVKKNNCFLVKQFGNSNAKVQFTKEPNNLYNVHSYKHSGLANKKTVTIQPSG 63
Query: 59 DNKGFACVTKRATKKPTADNKGF 81
++ TKK A K +
Sbjct: 64 VKDAAVVLSTTKTKKQNAPAKLY 86
>pdb|4A18|O Chain O, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 1
pdb|4A1B|O Chain O, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 3.
pdb|4A1D|O Chain O, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 4.
pdb|4A19|O Chain O, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 2
Length = 134
Score = 33.9 bits (76), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 14/29 (48%), Positives = 21/29 (72%), Gaps = 2/29 (6%)
Query: 4 SHLIWNIVKNNNAYLMKADNIKKWFSKEP 32
S L+W IVKNNNA+L+K + + F+ +P
Sbjct: 2 SQLVWEIVKNNNAFLVKNNGV--AFTTDP 28
>pdb|3V0V|L Chain L, Fab Wn1 222-5 Unliganded
pdb|3V0V|B Chain B, Fab Wn1 222-5 Unliganded
pdb|3V0W|L Chain L, Crystal Structure Of Fab Wn1 222-5 In Complex With Lps
Length = 212
Score = 28.1 bits (61), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 18/80 (22%), Positives = 34/80 (42%), Gaps = 3/80 (3%)
Query: 27 WFSKEPGNLPNLASFKYSGLIHSKTIHIQPTADNKGFACVTKRATKKPTADNKGFACVTK 86
W+ ++PGN+P L +K S L + F + ++ +P D + C+
Sbjct: 35 WYQQKPGNVPKLLIYKASNLHTGVPSRFSGSGSGTDFTLII--SSLQP-EDIATYYCLQG 91
Query: 87 RATKKTLSGHVDIGSARMDA 106
++ +T G + R DA
Sbjct: 92 QSYPRTFGGGTKLEIKRGDA 111
>pdb|2LY4|B Chain B, Hmgb1-Facilitated P53 Dna Binding Occurs Via Hmg-BoxP53
Transactivation Domain Interaction And Is Regulated By
The Acidic Tail
Length = 93
Score = 27.7 bits (60), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 9/38 (23%), Positives = 20/38 (52%), Gaps = 11/38 (28%)
Query: 7 IWNIVKNNNAY-----------LMKADNIKKWFSKEPG 33
+W ++ NN ++ D+I++WF+++PG
Sbjct: 22 LWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPG 59
>pdb|2GS0|B Chain B, Nmr Structure Of The Complex Between The Ph Domain Of
The Tfb1 Subunit From Tfiih And The Activation Domain
Of P53
Length = 54
Score = 27.7 bits (60), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 9/38 (23%), Positives = 20/38 (52%), Gaps = 11/38 (28%)
Query: 7 IWNIVKNNNAY-----------LMKADNIKKWFSKEPG 33
+W ++ NN ++ D+I++WF+++PG
Sbjct: 3 LWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPG 40
>pdb|2L14|B Chain B, Structure Of Cbp Nuclear Coactivator Binding Domain In
Complex With P53 Tad
Length = 49
Score = 27.7 bits (60), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 9/38 (23%), Positives = 20/38 (52%), Gaps = 11/38 (28%)
Query: 7 IWNIVKNNNAY-----------LMKADNIKKWFSKEPG 33
+W ++ NN ++ D+I++WF+++PG
Sbjct: 10 LWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPG 47
>pdb|1YJD|L Chain L, Crystal Structure Of Human Cd28 In Complex With The Fab
Fragment Of A Mitogenic Antibody (5.11a1)
Length = 212
Score = 27.3 bits (59), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 19/80 (23%), Positives = 31/80 (38%), Gaps = 3/80 (3%)
Query: 27 WFSKEPGNLPNLASFKYSGLIHSKTIHIQPTADNKGFACVTKRATKKPTADNKGFACVTK 86
W+ ++PGN+P L +K S L + GF ++ +P D + C
Sbjct: 35 WYQQKPGNIPKLLIYKASNLHTGVPSRFSGSGSGTGFTLTI--SSLQP-EDIATYYCQQG 91
Query: 87 RATKKTLSGHVDIGSARMDA 106
+ T G + R DA
Sbjct: 92 QTYPYTFGGGTKLEIKRADA 111
>pdb|3BJS|A Chain A, Crystal Structure Of A Member Of Enolase Superfamily From
Polaromonas Sp. Js666
pdb|3BJS|B Chain B, Crystal Structure Of A Member Of Enolase Superfamily From
Polaromonas Sp. Js666
Length = 428
Score = 27.3 bits (59), Expect = 2.0, Method: Composition-based stats.
Identities = 14/36 (38%), Positives = 20/36 (55%), Gaps = 2/36 (5%)
Query: 35 LPNLASFKYSGLIHSKTIHIQPTADNKGF--ACVTK 68
+P A +GL H+ TIH +N G+ ACV+K
Sbjct: 333 IPINAHSSATGLNHAATIHFLAATENAGYFEACVSK 368
>pdb|1IGT|A Chain A, Structure Of Immunoglobulin
pdb|1IGT|C Chain C, Structure Of Immunoglobulin
Length = 214
Score = 27.3 bits (59), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 19/80 (23%), Positives = 32/80 (40%), Gaps = 3/80 (3%)
Query: 27 WFSKEPGNLPNLASFKYSGLIHSKTIHIQPTADNKGFACVTKRATKKPTADNKGFACVTK 86
W+ ++PGN+P L +K S L + GF ++ +P D + C
Sbjct: 35 WYQQKPGNIPKLLIYKASNLHTGVPSRFSGSGSGTGFTLTI--SSLQP-EDIATYYCQQG 91
Query: 87 RATKKTLSGHVDIGSARMDA 106
++ T G + R DA
Sbjct: 92 QSYPLTFGGGTKLEIKRADA 111
>pdb|2PSH|A Chain A, Crystal Structures Of The Luciferase And Green Fluorescent
Protein From Renilla Reniformis
pdb|2PSH|B Chain B, Crystal Structures Of The Luciferase And Green Fluorescent
Protein From Renilla Reniformis
Length = 319
Score = 27.3 bits (59), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 23/50 (46%), Gaps = 12/50 (24%)
Query: 9 NIVKNNNAYLMKADNIKKWF-SKEPG-----------NLPNLASFKYSGL 46
IV+N NAYL +D++ K F +PG PN A K GL
Sbjct: 235 QIVRNYNAYLRASDDLPKLFIESDPGFFSNAIVEGAKKFPNTAFVKVKGL 284
>pdb|4H20|L Chain L, Crystal Structure And Computational Modeling Of The Fab
Fragment From The Protective Anti-ricin Monoclonal
Antibody Rac18
Length = 214
Score = 26.9 bits (58), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 10/24 (41%), Positives = 16/24 (66%), Gaps = 4/24 (16%)
Query: 27 WFSKEPGNLPNL----ASFKYSGL 46
WF ++PG P L AS++Y+G+
Sbjct: 35 WFQQKPGQSPKLLIYSASYRYTGV 58
>pdb|3DIF|A Chain A, Crystal Structure Of Fabox117
pdb|3DIF|C Chain C, Crystal Structure Of Fabox117
Length = 214
Score = 26.9 bits (58), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 10/24 (41%), Positives = 16/24 (66%), Gaps = 4/24 (16%)
Query: 27 WFSKEPGNLPNL----ASFKYSGL 46
WF ++PG P L AS++Y+G+
Sbjct: 35 WFQQKPGQSPKLLIYSASYRYTGV 58
>pdb|3IY4|A Chain A, Variable Domains Of The Computer Generated Model (Wam) Of
Fab 15 Fitted Into The Cryoem Reconstruction Of The
Virus- Fab 15 Complex
Length = 111
Score = 26.6 bits (57), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 19/82 (23%), Positives = 30/82 (36%), Gaps = 13/82 (15%)
Query: 20 KADNIKKWFSKEPGNLPNL-------------ASFKYSGLIHSKTIHIQPTADNKGFACV 66
+ D+ W+ ++PG P L A F SG T++I P +
Sbjct: 30 EGDSYMNWYQQKPGQPPKLLIYAASNLESGIPARFSGSGSGTDFTLNIHPVEEEDAATYY 89
Query: 67 TKRATKKPTADNKGFACVTKRA 88
+++ P G TKRA
Sbjct: 90 CQQSNGDPYTFGGGTKLDTKRA 111
>pdb|1V7M|L Chain L, Human Thrombopoietin Functional Domain Complexed To
Neutralizing Antibody Tn1 Fab
pdb|1V7M|M Chain M, Human Thrombopoietin Functional Domain Complexed To
Neutralizing Antibody Tn1 Fab
pdb|1V7N|L Chain L, Human Thrombopoietin Functional Domain Complexed To
Neutralizing Antibody Tn1 Fab
pdb|1V7N|M Chain M, Human Thrombopoietin Functional Domain Complexed To
Neutralizing Antibody Tn1 Fab
pdb|1V7N|N Chain N, Human Thrombopoietin Functional Domain Complexed To
Neutralizing Antibody Tn1 Fab
pdb|1V7N|O Chain O, Human Thrombopoietin Functional Domain Complexed To
Neutralizing Antibody Tn1 Fab
pdb|2ZKH|L Chain L, Human Thrombopoietin Neutralizing Antibody Tn1 Fab
Length = 213
Score = 26.6 bits (57), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 16/80 (20%), Positives = 28/80 (35%), Gaps = 3/80 (3%)
Query: 27 WFSKEPGNLPNLASFKYSGLIHSKTIHIQPTADNKGFACVTKRATKKPTADNKGFACVTK 86
WF ++PG P L + S L + + ++ R + D + C +
Sbjct: 34 WFQQKPGTSPKLWIYSTSNLASGVPARFRGSGSGTSYSLTISRMEAE---DAATYYCQQR 90
Query: 87 RATKKTLSGHVDIGSARMDA 106
+T G + R DA
Sbjct: 91 SGYPRTFGGGTKLEIKRADA 110
>pdb|2PSF|A Chain A, Crystal Structures Of The Luciferase And Green Fluorescent
Protein From Renilla Reniformis
pdb|2PSF|B Chain B, Crystal Structures Of The Luciferase And Green Fluorescent
Protein From Renilla Reniformis
Length = 310
Score = 26.2 bits (56), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 13/30 (43%), Positives = 18/30 (60%), Gaps = 1/30 (3%)
Query: 9 NIVKNNNAYLMKADNIKKWF-SKEPGNLPN 37
IV+N NAYL +D++ K F +PG N
Sbjct: 234 QIVRNYNAYLRASDDLPKLFIESDPGFFSN 263
>pdb|2PSJ|A Chain A, Crystal Structures Of The Luciferase And Green Fluorescent
Protein From Renilla Reniformis
pdb|2PSJ|B Chain B, Crystal Structures Of The Luciferase And Green Fluorescent
Protein From Renilla Reniformis
Length = 319
Score = 26.2 bits (56), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 13/30 (43%), Positives = 18/30 (60%), Gaps = 1/30 (3%)
Query: 9 NIVKNNNAYLMKADNIKKWF-SKEPGNLPN 37
IV+N NAYL +D++ K F +PG N
Sbjct: 235 QIVRNYNAYLRASDDLPKLFIESDPGFFSN 264
>pdb|3VI3|L Chain L, Crystal Structure Of Alpha5beta1 Integrin Headpiece
(Ligand-Free Form)
pdb|3VI3|E Chain E, Crystal Structure Of Alpha5beta1 Integrin Headpiece
(Ligand-Free Form)
pdb|3VI4|L Chain L, Crystal Structure Of Alpha5beta1 Integrin Headpiece In
Complex With Rgd Peptide
pdb|3VI4|E Chain E, Crystal Structure Of Alpha5beta1 Integrin Headpiece In
Complex With Rgd Peptide
Length = 219
Score = 26.2 bits (56), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 23/94 (24%), Positives = 31/94 (32%), Gaps = 10/94 (10%)
Query: 13 NNNAYLMKADNIKKWFSKEPGNLPNLASFKYSGLIHSKTIHIQPTADNKGFACVTKRATK 72
N N YL WF + PG P L F+ S L + F T R ++
Sbjct: 33 NGNTYLY-------WFLQRPGQSPRLLIFRMSNLASGVPDRFSGSGSGTAF---TLRISR 82
Query: 73 KPTADNKGFACVTKRATKKTLSGHVDIGSARMDA 106
AD + C+ T + R DA
Sbjct: 83 VEAADVGIYFCLQHLEYPFTFGAGTKLELKRADA 116
>pdb|2PSD|A Chain A, Crystal Structures Of The Luciferase And Green Fluorescent
Protein From Renilla Reniformis
pdb|2PSE|A Chain A, Crystal Structures Of The Luciferase And Green Fluorescent
Protein From Renilla Reniformis
Length = 318
Score = 26.2 bits (56), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 13/30 (43%), Positives = 18/30 (60%), Gaps = 1/30 (3%)
Query: 9 NIVKNNNAYLMKADNIKKWF-SKEPGNLPN 37
IV+N NAYL +D++ K F +PG N
Sbjct: 234 QIVRNYNAYLRASDDLPKLFIESDPGFFSN 263
>pdb|1FVC|A Chain A, X-Ray Structures Of The Antigen-Binding Domains From
Three Variants Of Humanized Anti-P185-Her2 Antibody 4d5
And Comparison With Molecular Modeling
pdb|1FVC|C Chain C, X-Ray Structures Of The Antigen-Binding Domains From
Three Variants Of Humanized Anti-P185-Her2 Antibody 4d5
And Comparison With Molecular Modeling
Length = 109
Score = 26.2 bits (56), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 15/24 (62%), Gaps = 4/24 (16%)
Query: 27 WFSKEPGNLPNL----ASFKYSGL 46
W+ ++PG P L ASF YSG+
Sbjct: 35 WYQQKPGKAPKLLIYSASFLYSGV 58
>pdb|2WUB|L Chain L, Crystal Structure Of Hgfa In Complex With The Allosteric
Non-Inhibitory Antibody Fab40.Deltatrp
pdb|2WUB|Q Chain Q, Crystal Structure Of Hgfa In Complex With The Allosteric
Non-Inhibitory Antibody Fab40.Deltatrp
pdb|2WUC|L Chain L, Crystal Structure Of Hgfa In Complex With The Allosteric
Non- Inhibitory Antibody Fab40.Deltatrp And
Ac-Kqlr-Chloromethylketone
pdb|3K2U|L Chain L, Crystal Structure Of Hgfa In Complex With The Allosteric
Inhibitory Antibody Fab40
Length = 214
Score = 26.2 bits (56), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 15/24 (62%), Gaps = 4/24 (16%)
Query: 27 WFSKEPGNLPNL----ASFKYSGL 46
W+ ++PG P L ASF YSG+
Sbjct: 35 WYQQKPGKAPKLLIYSASFLYSGV 58
>pdb|3G6J|E Chain E, C3b In Complex With A C3b Specific Fab
pdb|3G6J|G Chain G, C3b In Complex With A C3b Specific Fab
Length = 214
Score = 26.2 bits (56), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 15/24 (62%), Gaps = 4/24 (16%)
Query: 27 WFSKEPGNLPNL----ASFKYSGL 46
W+ ++PG P L ASF YSG+
Sbjct: 35 WYQQKPGKAPKLLIYSASFLYSGV 58
>pdb|1N8Z|A Chain A, Crystal Structure Of Extracellular Domain Of Human Her2
Complexed With Herceptin Fab
Length = 214
Score = 26.2 bits (56), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 15/24 (62%), Gaps = 4/24 (16%)
Query: 27 WFSKEPGNLPNL----ASFKYSGL 46
W+ ++PG P L ASF YSG+
Sbjct: 35 WYQQKPGKAPKLLIYSASFLYSGV 58
>pdb|2HFF|A Chain A, Crystal Structure Of Cb2 Fab
pdb|2HFF|L Chain L, Crystal Structure Of Cb2 Fab
Length = 214
Score = 26.2 bits (56), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 15/24 (62%), Gaps = 4/24 (16%)
Query: 27 WFSKEPGNLPNL----ASFKYSGL 46
W+ ++PG P L ASF YSG+
Sbjct: 35 WYQQKPGKAPKLLIYSASFLYSGV 58
>pdb|2HFG|L Chain L, Crystal Structure Of Hbr3 Bound To Cb3s-fab
Length = 214
Score = 26.2 bits (56), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 15/24 (62%), Gaps = 4/24 (16%)
Query: 27 WFSKEPGNLPNL----ASFKYSGL 46
W+ ++PG P L ASF YSG+
Sbjct: 35 WYQQKPGKAPKLLIYSASFLYSGV 58
>pdb|2FJF|L Chain L, Structure Of The G6 Fab, A Phage Derived Vegf Binding
Fab
pdb|2FJF|A Chain A, Structure Of The G6 Fab, A Phage Derived Vegf Binding
Fab
pdb|2FJF|C Chain C, Structure Of The G6 Fab, A Phage Derived Vegf Binding
Fab
pdb|2FJF|E Chain E, Structure Of The G6 Fab, A Phage Derived Vegf Binding
Fab
pdb|2FJF|G Chain G, Structure Of The G6 Fab, A Phage Derived Vegf Binding
Fab
pdb|2FJF|J Chain J, Structure Of The G6 Fab, A Phage Derived Vegf Binding
Fab
pdb|2FJF|M Chain M, Structure Of The G6 Fab, A Phage Derived Vegf Binding
Fab
pdb|2FJF|O Chain O, Structure Of The G6 Fab, A Phage Derived Vegf Binding
Fab
pdb|2FJF|Q Chain Q, Structure Of The G6 Fab, A Phage Derived Vegf Binding
Fab
pdb|2FJF|S Chain S, Structure Of The G6 Fab, A Phage Derived Vegf Binding
Fab
pdb|2FJF|U Chain U, Structure Of The G6 Fab, A Phage Derived Vegf Binding
Fab
pdb|2FJF|W Chain W, Structure Of The G6 Fab, A Phage Derived Vegf Binding
Fab
pdb|2FJG|L Chain L, Structure Of The G6 Fab, A Phage Derived Fab Fragment,
In Complex With Vegf
pdb|2FJG|A Chain A, Structure Of The G6 Fab, A Phage Derived Fab Fragment,
In Complex With Vegf
pdb|2H9G|A Chain A, Crystal Structure Of Phage Derived Fab Bdf1 With Human
Death Receptor 5 (dr5)
pdb|2H9G|L Chain L, Crystal Structure Of Phage Derived Fab Bdf1 With Human
Death Receptor 5 (dr5)
pdb|2R0K|L Chain L, Protease Domain Of Hgfa With Inhibitor Fab58
pdb|2R0L|L Chain L, Short Form Hgfa With Inhibitory Fab75
pdb|3GRW|L Chain L, Fgfr3 In Complex With A Fab
Length = 214
Score = 26.2 bits (56), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 15/24 (62%), Gaps = 4/24 (16%)
Query: 27 WFSKEPGNLPNL----ASFKYSGL 46
W+ ++PG P L ASF YSG+
Sbjct: 35 WYQQKPGKAPKLLIYSASFLYSGV 58
>pdb|3L95|A Chain A, Crystal Structure Of The Human Notch1 Negative
Regulatory Region (Nrr) Bound To The Fab Fragment Of An
Antagonist Antibody
pdb|3L95|L Chain L, Crystal Structure Of The Human Notch1 Negative
Regulatory Region (Nrr) Bound To The Fab Fragment Of An
Antagonist Antibody
Length = 214
Score = 26.2 bits (56), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 15/24 (62%), Gaps = 4/24 (16%)
Query: 27 WFSKEPGNLPNL----ASFKYSGL 46
W+ ++PG P L ASF YSG+
Sbjct: 35 WYQQKPGKAPKLLIYSASFLYSGV 58
>pdb|3SOB|L Chain L, The Structure Of The First Ywtd Beta Propeller Domain Of
Lrp6 In Complex With A Fab
Length = 237
Score = 26.2 bits (56), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 15/24 (62%), Gaps = 4/24 (16%)
Query: 27 WFSKEPGNLPNL----ASFKYSGL 46
W+ ++PG P L ASF YSG+
Sbjct: 58 WYQQKPGKAPKLLIYSASFLYSGV 81
>pdb|2QQK|L Chain L, Neuropilin-2 A1a2b1b2 Domains In Complex With A
Semaphorin-Blocking Fab
pdb|2QQL|L Chain L, Neuropilin-2 A1a2b1b2 Domains In Complex With A
Semaphorin-Blocking Fab
Length = 214
Score = 25.8 bits (55), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 15/24 (62%), Gaps = 4/24 (16%)
Query: 27 WFSKEPGNLPNL----ASFKYSGL 46
W+ ++PG P L ASF YSG+
Sbjct: 35 WYQQKPGKAPKLLIYSASFLYSGV 58
>pdb|3P0V|L Chain L, Anti-EgfrHER3 FAB DL11 ALONE
pdb|3P0V|M Chain M, Anti-EgfrHER3 FAB DL11 ALONE
pdb|3P0Y|L Chain L, Anti-EgfrHER3 FAB DL11 IN COMPLEX WITH DOMAIN III OF
EGFR Extracellular Region
pdb|3P11|L Chain L, Anti-EgfrHER3 FAB DL11 IN COMPLEX WITH DOMAINS I-Iii Of
The Her3 Extracellular Region
Length = 214
Score = 25.8 bits (55), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 15/24 (62%), Gaps = 4/24 (16%)
Query: 27 WFSKEPGNLPNL----ASFKYSGL 46
W+ ++PG P L ASF YSG+
Sbjct: 35 WYQQKPGKAPKLLIYSASFLYSGV 58
>pdb|3R1G|L Chain L, Structure Basis Of Allosteric Inhibition Of Bace1 By An
Exosite- Binding Antibody
Length = 214
Score = 25.8 bits (55), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 15/24 (62%), Gaps = 4/24 (16%)
Query: 27 WFSKEPGNLPNL----ASFKYSGL 46
W+ ++PG P L ASF YSG+
Sbjct: 35 WYQQKPGKAPKLLIYSASFLYSGV 58
>pdb|4DKE|L Chain L, Crystal Structure Of Human Interleukin-34 Bound To
Fab1.1
pdb|4DKE|M Chain M, Crystal Structure Of Human Interleukin-34 Bound To
Fab1.1
Length = 214
Score = 25.8 bits (55), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 15/24 (62%), Gaps = 4/24 (16%)
Query: 27 WFSKEPGNLPNL----ASFKYSGL 46
W+ ++PG P L ASF YSG+
Sbjct: 35 WYQQKPGKAPKLLIYSASFLYSGV 58
>pdb|4F9L|D Chain D, Crystal Structure Of The Human Btn3a1 Ectodomain In
Complex With The 20.1 Single Chain Antibody
pdb|4F9L|C Chain C, Crystal Structure Of The Human Btn3a1 Ectodomain In
Complex With The 20.1 Single Chain Antibody
Length = 259
Score = 25.8 bits (55), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 18/80 (22%), Positives = 30/80 (37%), Gaps = 3/80 (3%)
Query: 27 WFSKEPGNLPNLASFKYSGLIHSKTIHIQPTADNKGFACVTKRATKKPTADNKGFACVTK 86
W+ + PGN+P L ++ S L + GF ++ +P D + C
Sbjct: 35 WYQQRPGNIPKLLIYRASNLHTGVPSRFSGSGSATGFTLTI--SSLQP-EDIATYYCQQG 91
Query: 87 RATKKTLSGHVDIGSARMDA 106
+ T G + R DA
Sbjct: 92 HSYPYTFGGGTKLDIKRADA 111
>pdb|2ZCH|L Chain L, Crystal Structure Of Human Prostate Specific Antigen
Complexed With An Activating Antibody
Length = 215
Score = 25.8 bits (55), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 19/83 (22%), Positives = 32/83 (38%), Gaps = 13/83 (15%)
Query: 19 MKADNIKKWFSKEPGNLPNLASFKYSGL---IHSK----------TIHIQPTADNKGFAC 65
D+ W+ ++PG P L F S L I ++ T++IQP +
Sbjct: 31 FDGDSYMNWYQQKPGQPPKLLIFAASNLASGIPARLSGSGSGTDFTLNIQPVEEEDAATY 90
Query: 66 VTKRATKKPTADNKGFACVTKRA 88
+++ + P G KRA
Sbjct: 91 YCQQSNEDPYTFGGGTKLEIKRA 113
>pdb|4HTG|A Chain A, Porphobilinogen Deaminase From Arabidopsis Thaliana
Length = 320
Score = 25.8 bits (55), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 31/75 (41%), Gaps = 13/75 (17%)
Query: 42 KYSGLIHSKTIHIQ---PTADNKGFACVTKRATKKPTADNKGFACVTKRATKKTLSGHVD 98
K+ L+ IHI+ T D + +P AD G TK + ++GH+D
Sbjct: 37 KHPELVEDGAIHIEIIKTTGD---------KILSQPLADIGGKGLFTKEIDEALINGHID 87
Query: 99 IGSARM-DARLYIFE 112
I M D Y+ E
Sbjct: 88 IAVHSMKDVPTYLPE 102
>pdb|3AUV|A Chain A, Predicting Amino Acid Preferences In The Complementarity
Determining Regions Of An Antibody-Antigen Recognition
Interface
pdb|3AUV|B Chain B, Predicting Amino Acid Preferences In The Complementarity
Determining Regions Of An Antibody-Antigen Recognition
Interface
pdb|3AUV|C Chain C, Predicting Amino Acid Preferences In The Complementarity
Determining Regions Of An Antibody-Antigen Recognition
Interface
pdb|3AUV|D Chain D, Predicting Amino Acid Preferences In The Complementarity
Determining Regions Of An Antibody-Antigen Recognition
Interface
pdb|3AUV|E Chain E, Predicting Amino Acid Preferences In The Complementarity
Determining Regions Of An Antibody-Antigen Recognition
Interface
pdb|3AUV|F Chain F, Predicting Amino Acid Preferences In The Complementarity
Determining Regions Of An Antibody-Antigen Recognition
Interface
Length = 276
Score = 25.8 bits (55), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 15/24 (62%), Gaps = 4/24 (16%)
Query: 27 WFSKEPGNLPNL----ASFKYSGL 46
W+ ++PG P L ASF YSG+
Sbjct: 46 WYQQKPGKAPKLLIYSASFLYSGV 69
>pdb|2ZCK|L Chain L, Crystal Structure Of A Ternary Complex Between Psa, A
Substrat-Acyl Intermediate And An Activating Antibody
pdb|2ZCL|L Chain L, Crystal Structure Of Human Prostate Specific Antigen
Complexed With An Activating Antibody
Length = 218
Score = 25.8 bits (55), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 19/83 (22%), Positives = 32/83 (38%), Gaps = 13/83 (15%)
Query: 19 MKADNIKKWFSKEPGNLPNLASFKYSGL---IHSK----------TIHIQPTADNKGFAC 65
D+ W+ ++PG P L F S L I ++ T++IQP +
Sbjct: 31 FDGDSYMNWYQQKPGQPPKLLIFAASNLASGIPARLSGSGSGTDFTLNIQPVEEEDAATY 90
Query: 66 VTKRATKKPTADNKGFACVTKRA 88
+++ + P G KRA
Sbjct: 91 YCQQSNEDPYTFGGGTKLEIKRA 113
>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 = 25.4 bits (54), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 17/32 (53%), Gaps = 7/32 (21%)
Query: 13 NNNAYLMKADNIKKWFSKEPGNLPNLASFKYS 44
N N YL +W+ ++PG PNL +K S
Sbjct: 33 NGNTYL-------EWYLQKPGQSPNLLIYKVS 57
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
0.318 0.130 0.391
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,550,336
Number of Sequences: 62578
Number of extensions: 133382
Number of successful extensions: 600
Number of sequences better than 100.0: 51
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 43
Number of HSP's that attempted gapping in prelim test: 591
Number of HSP's gapped (non-prelim): 51
length of query: 118
length of database: 14,973,337
effective HSP length: 81
effective length of query: 37
effective length of database: 9,904,519
effective search space: 366467203
effective search space used: 366467203
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 45 (21.9 bits)