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= psy14080
(113 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2QHR|H Chain H, Crystal Structure Of The 13f6-1-2 Fab Fragment Bound To
Its Ebola Virus Glycoprotein Peptide Epitope
Length = 222
Score = 35.0 bits (79), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 30/99 (30%), Positives = 41/99 (41%), Gaps = 9/99 (9%)
Query: 5 PGGILTAFGQISTGFLAVFSYSDKTVRDIVKVRVSWVRRRDWHILTSGVLTYTND---AR 61
PGG L ++GF A SY VR + R+ WV +I G TY D R
Sbjct: 14 PGGSL-KLSCAASGF-AFSSYDMSWVRQTPEKRLEWVA----YISRGGGYTYYPDTVKGR 67
Query: 62 FQVIHTDGSDDWNLQIKFLQKRDNGTYECQAQPYTTTSH 100
F + + + LQ+ L+ D Y C Y +SH
Sbjct: 68 FTISRDNAKNTLYLQMSSLKSEDTAMYYCSRHIYYGSSH 106
>pdb|1NPU|A Chain A, Crystal Structure Of The Extracellular Domain Of Murine
Pd-1
pdb|3BP5|A Chain A, Crystal Structure Of The Mouse Pd-1 And Pd-L2 Complex
Length = 117
Score = 33.5 bits (75), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 29/58 (50%)
Query: 49 LTSGVLTYTNDARFQVIHTDGSDDWNLQIKFLQKRDNGTYECQAQPYTTTSHSQNAPG 106
++G+ DARFQ+I D+++ I ++ D+G Y C A + + +PG
Sbjct: 49 FSNGLSQPVQDARFQIIQLPNRHDFHMNILDTRRNDSGIYLCGAISLHPKAKIEESPG 106
>pdb|3BIK|B Chain B, Crystal Structure Of The Pd-1PD-L1 Complex
pdb|3BIK|C Chain C, Crystal Structure Of The Pd-1PD-L1 Complex
Length = 134
Score = 33.1 bits (74), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 29/58 (50%)
Query: 49 LTSGVLTYTNDARFQVIHTDGSDDWNLQIKFLQKRDNGTYECQAQPYTTTSHSQNAPG 106
++G+ DARFQ+I D+++ I ++ D+G Y C A + + +PG
Sbjct: 59 FSNGLSQPVQDARFQIIQLPNRHDFHMNILDTRRNDSGIYLCGAISLHPKAKIEESPG 116
>pdb|1QFW|I Chain I, Ternary Complex Of Human Chorionic Gonadotropin With Fv
Anti Alpha Subunit And Fv Anti Beta Subunit
Length = 122
Score = 33.1 bits (74), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 29/99 (29%), Positives = 41/99 (41%), Gaps = 14/99 (14%)
Query: 5 PGGILTAFGQISTGFLAVFSYSDKTVRDIVKVRVSWVRRRDWHILTSGVLTY---TNDAR 61
PGG L ++GF A S+ +R + R+ WV I G TY + R
Sbjct: 14 PGGSLK-LSCAASGF-AFSSFDMSWIRQTPEKRLEWVA----SITNVGTYTYYPGSVKGR 67
Query: 62 FQVIHTDGSDDWNLQIKFLQKRDNGTYEC-----QAQPY 95
F + + + NLQ+ L+ D Y C AQPY
Sbjct: 68 FSISRDNARNTLNLQMSSLRSEDTALYFCARQGTAAQPY 106
>pdb|3RNQ|A Chain A, Crystal Structure Of The Complex Between The Extracellular
Domains Of Mouse Pd-1 Mutant And Pd-L2
Length = 117
Score = 33.1 bits (74), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 29/58 (50%)
Query: 49 LTSGVLTYTNDARFQVIHTDGSDDWNLQIKFLQKRDNGTYECQAQPYTTTSHSQNAPG 106
++G+ DARFQ+I D+++ I ++ D+G Y C A + + +PG
Sbjct: 49 FSNGLSQPVQDARFQIIQLPNRHDFHMNILDTRRNDSGIYLCGAISRHPKAKIEESPG 106
>pdb|1QKZ|H Chain H, 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 = 219
Score = 32.7 bits (73), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 34/78 (43%), Gaps = 10/78 (12%)
Query: 23 FSYSDKT---VRDIVKVRVSWVRRRDWHILTSGVLTYTNDA---RFQVIHTDGSDDWNLQ 76
F++SD VR + R+ WV I G TY D+ RF + + ++ LQ
Sbjct: 27 FTFSDYYMFWVRQTPEQRLEWVAT----ISDGGAYTYYPDSVKGRFTISRDNAKNNLYLQ 82
Query: 77 IKFLQKRDNGTYECQAQP 94
+ L+ D G Y C P
Sbjct: 83 MNSLKSEDTGMYYCARDP 100
>pdb|2ZUQ|C Chain C, Crystal Structure Of Dsbb-Fab Complex
pdb|2ZUQ|F Chain F, Crystal Structure Of Dsbb-Fab Complex
pdb|2LTQ|C Chain C, High Resolution Structure Of Dsbb C41s By Joint
Calculation With Solid-state Nmr And X-ray Data
pdb|2LTQ|F Chain F, High Resolution Structure Of Dsbb C41s By Joint
Calculation With Solid-state Nmr And X-ray Data
Length = 221
Score = 32.7 bits (73), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 29/93 (31%), Positives = 41/93 (44%), Gaps = 10/93 (10%)
Query: 5 PGGILTAFGQISTGFLAVFSYSDKTVRDIVKVRVSWVRRRDWHILTSGVLTYTND---AR 61
PGG L ++GF A SY VR + R+ WV +I + G TY D R
Sbjct: 14 PGGSL-KLSCAASGF-AFSSYDMSWVRQTPEKRLEWVA----YISSGGGSTYYPDTVKGR 67
Query: 62 FQVIHTDGSDDWNLQIKFLQKRDNGTYECQAQP 94
F + + + LQ+ L+ D Y C A+P
Sbjct: 68 FTISRDNAKNTLYLQMSSLKSEDTAMYYC-ARP 99
>pdb|3VE0|A Chain A, Crystal Structure Of Sudan Ebolavirus Glycoprotein (Strain
Boniface) Bound To 16f6
Length = 220
Score = 32.7 bits (73), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 30/104 (28%), Positives = 46/104 (44%), Gaps = 15/104 (14%)
Query: 1 MVAAPGGILTAFGQI-----STGFLAVFSYSDKT-VRDIVKVRVSWVRRRDWHILTSGVL 54
+V + GG++T G + ++GF F+Y D VR + R+ WV +I + G
Sbjct: 4 LVESGGGLVTPGGSLKLSCAASGF--AFNYYDMFWVRQNTEKRLEWVA----YINSGGGN 57
Query: 55 TYTND---ARFQVIHTDGSDDWNLQIKFLQKRDNGTYECQAQPY 95
TY D RF + + LQ+ L+ D Y C Q Y
Sbjct: 58 TYYPDTVKGRFTISRDNAKKTLFLQMSSLRSEDTAMYYCARQLY 101
>pdb|3S88|H Chain H, Crystal Structure Of Sudan Ebolavirus Glycoprotein (Strain
Gulu) Bound To 16f6
Length = 220
Score = 32.7 bits (73), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 30/104 (28%), Positives = 46/104 (44%), Gaps = 15/104 (14%)
Query: 1 MVAAPGGILTAFGQI-----STGFLAVFSYSDKT-VRDIVKVRVSWVRRRDWHILTSGVL 54
+V + GG++T G + ++GF F+Y D VR + R+ WV +I + G
Sbjct: 4 LVESGGGLVTPGGSLKLSCAASGF--AFNYYDMFWVRQNTEKRLEWVA----YINSGGGN 57
Query: 55 TYTND---ARFQVIHTDGSDDWNLQIKFLQKRDNGTYECQAQPY 95
TY D RF + + LQ+ L+ D Y C Q Y
Sbjct: 58 TYYPDTVKGRFTISRDNAKKTLFLQMSSLRSEDTAMYYCARQLY 101
>pdb|3BP6|A Chain A, Crystal Structure Of The Mouse Pd-1 Mutant And Pd-L2
Complex
pdb|3RNK|A Chain A, Crystal Structure Of The Complex Between Mouse Pd-1 Mutant
And Pd-L2 Igv Domain
pdb|3SBW|A Chain A, Crystal Structure Of The Complex Between The Extracellular
Domains Of Mouse Pd-1 Mutant And Human Pd-L1
pdb|3SBW|B Chain B, Crystal Structure Of The Complex Between The Extracellular
Domains Of Mouse Pd-1 Mutant And Human Pd-L1
Length = 117
Score = 32.0 bits (71), Expect = 0.077, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 28/58 (48%)
Query: 49 LTSGVLTYTNDARFQVIHTDGSDDWNLQIKFLQKRDNGTYECQAQPYTTTSHSQNAPG 106
++G+ DARFQ+I D+++ I ++ D+G Y C A + +PG
Sbjct: 49 FSNGLSQPVQDARFQIIQLPNRHDFHMNILDTRRNDSGIYLCGAISLHPKLKIEESPG 106
>pdb|1YC7|A Chain A, Caban33 Vhh Fragment Against Vsg
pdb|1YC7|B Chain B, Caban33 Vhh Fragment Against Vsg
Length = 124
Score = 31.2 bits (69), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 27/56 (48%), Gaps = 4/56 (7%)
Query: 42 RRRDW--HILTSGVLTYTND--ARFQVIHTDGSDDWNLQIKFLQKRDNGTYECQAQ 93
+ R+W I + G + Y + RF + + + LQ+ LQ+ D G Y CQ Q
Sbjct: 43 KEREWVSSISSPGTIYYQDSVKGRFTISRDNAKNTVYLQMNSLQREDTGMYYCQIQ 98
>pdb|1OPG|H Chain H, Opg2 Fab Fragment
pdb|1BM3|H Chain H, Immunoglobulin Opg2 Fab-Peptide Complex
Length = 227
Score = 31.2 bits (69), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 29/68 (42%), Gaps = 10/68 (14%)
Query: 38 VSWVR-----RRDWHILTSGVLTYTN-----DARFQVIHTDGSDDWNLQIKFLQKRDNGT 87
+SWVR R +W SG TY + RF + + ++ LQ+ L+ D
Sbjct: 34 MSWVRQTPEKRLEWVAAISGGGTYIHYPDSVKGRFTISRDNAKNNLYLQMSSLRSEDTAL 93
Query: 88 YECQAQPY 95
Y C P+
Sbjct: 94 YYCTRHPF 101
>pdb|1F4W|H Chain H, Crystal Structure Of An Anti-Carbohydrate Antibody
Directed Against Vibrio Cholerae O1 In Complex With
Antigen
pdb|1F4X|H Chain H, Crystal Structure Of An Anti-Carbohydrate Antibody
Directed Against Vibrio Cholerae O1 In Complex With
Antigen
pdb|1F4Y|H Chain H, Crystal Structure Of An Anti-Carbohydrate Antibody
Directed Against Vibrio Cholerae O1 In Complex With
Antigen
Length = 216
Score = 30.8 bits (68), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 28/92 (30%), Positives = 38/92 (41%), Gaps = 11/92 (11%)
Query: 6 GGILTAFGQISTGFLA---VFSYSDKT-VRDIVKVRVSWVRRRDWHILTSGVLTYTND-- 59
GG++T G + A VFS D + VR + R+ WV I + G T D
Sbjct: 9 GGLVTPGGSLRLSCAASGYVFSTYDMSWVRQTPEKRLEWVA----FISSGGGRTSYPDTV 64
Query: 60 -ARFQVIHTDGSDDWNLQIKFLQKRDNGTYEC 90
RF + D + LQ+ LQ D Y C
Sbjct: 65 KGRFTISRDDAKNTLYLQMSSLQSEDTAMYYC 96
>pdb|1KFA|H Chain H, Crystal Structure Of Fab Fragment Complexed With
Gibberellin A4
pdb|1KFA|I Chain I, Crystal Structure Of Fab Fragment Complexed With
Gibberellin A4
Length = 221
Score = 30.4 bits (67), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 26/91 (28%), Positives = 38/91 (41%), Gaps = 8/91 (8%)
Query: 5 PGGILTAFGQISTGFLAVFSYSDKTVRDIVKVRVSWVRRRDWHILTSGVLTYTND--ARF 62
PGG L ++GF SY+ VR + R+ WV I T G Y + RF
Sbjct: 14 PGGSL-KLSCAASGF-TFSSYAMSWVRQTPERRLEWVAT----ITTRGYTFYPDSVKGRF 67
Query: 63 QVIHTDGSDDWNLQIKFLQKRDNGTYECQAQ 93
V + + NLQ+ L+ D + C +
Sbjct: 68 TVSRDNARNTLNLQMSSLRSEDTAMFYCTRE 98
>pdb|1BLN|B Chain B, Anti-P-Glycoprotein Fab Mrk-16
pdb|1BLN|D Chain D, Anti-P-Glycoprotein Fab Mrk-16
Length = 218
Score = 30.4 bits (67), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 26/89 (29%), Positives = 39/89 (43%), Gaps = 9/89 (10%)
Query: 5 PGGILTAFGQISTGFLAVFSYSDKTVRDIVKVRVSWVRRRDWHILTSGVLTYTNDA---R 61
PGG L ++GF SY+ VR + R+ WV I + G TY D+ R
Sbjct: 14 PGGSL-KLSCAASGF-TFSSYTMSWVRQTPEKRLEWVAT----ISSGGGNTYYPDSVKGR 67
Query: 62 FQVIHTDGSDDWNLQIKFLQKRDNGTYEC 90
F + + ++ LQ+ L+ D Y C
Sbjct: 68 FTISRDNAKNNLYLQMSSLRSEDTALYYC 96
>pdb|2YWY|A Chain A, Structure Of New Antigen Receptor Variable Domain From
Sharks
pdb|2YWY|B Chain B, Structure Of New Antigen Receptor Variable Domain From
Sharks
pdb|2YWY|C Chain C, Structure Of New Antigen Receptor Variable Domain From
Sharks
pdb|2YWY|D Chain D, Structure Of New Antigen Receptor Variable Domain From
Sharks
Length = 113
Score = 30.0 bits (66), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 32/58 (55%), Gaps = 9/58 (15%)
Query: 41 VRRRDWHILTSGVLTYTNDARFQV----IHT--DGSDDWNLQIKFLQKRDNGTYECQA 92
+ R DW+ T G TN+ + + + T GS ++L+I+ L+ D+GTY+C A
Sbjct: 31 LERTDWYRTTLGS---TNEQKISIGGRYVETVNKGSKSFSLRIRDLRVEDSGTYKCGA 85
>pdb|1YC8|A Chain A, Caban33- Y37vE44GR45L TRIPLE MUTANT
pdb|1YC8|B Chain B, Caban33- Y37vE44GR45L TRIPLE MUTANT
pdb|1YZZ|A Chain A, Humanized Caban33 At Room Temperature
pdb|1YZZ|B Chain B, Humanized Caban33 At Room Temperature
Length = 124
Score = 29.6 bits (65), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 27/99 (27%), Positives = 44/99 (44%), Gaps = 10/99 (10%)
Query: 1 MVAAPGGILTAFGQIS-TGFLAVFSYSDKT---VRDIVKVRVSWVRRRDWHILTSGVLTY 56
+V + GG + A G + + ++ +YS T VR + WV I + G + Y
Sbjct: 4 LVESGGGSVQAGGSLRLSCAVSGSTYSPCTTGWVRQAPGKGLEWVS----SISSPGTIYY 59
Query: 57 TND--ARFQVIHTDGSDDWNLQIKFLQKRDNGTYECQAQ 93
+ RF + + + LQ+ LQ+ D G Y CQ Q
Sbjct: 60 QDSVKGRFTISRDNAKNTVYLQMNSLQREDTGMYYCQIQ 98
>pdb|3MOQ|A Chain A, Amyloid Beta(18-41) Peptide Fusion With New Antigen
Receptor Variable Domain From Sharks
pdb|3MOQ|B Chain B, Amyloid Beta(18-41) Peptide Fusion With New Antigen
Receptor Variable Domain From Sharks
pdb|3MOQ|C Chain C, Amyloid Beta(18-41) Peptide Fusion With New Antigen
Receptor Variable Domain From Sharks
pdb|3MOQ|D Chain D, Amyloid Beta(18-41) Peptide Fusion With New Antigen
Receptor Variable Domain From Sharks
Length = 126
Score = 29.6 bits (65), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 20/33 (60%)
Query: 60 ARFQVIHTDGSDDWNLQIKFLQKRDNGTYECQA 92
R+ GS ++L+I L+ D+GTY+CQA
Sbjct: 53 GRYVETVNKGSKSFSLRISDLRVEDSGTYKCQA 85
>pdb|2YWZ|A Chain A, Structure Of New Antigen Receptor Variable Domain From
Sharks
Length = 111
Score = 29.6 bits (65), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 20/33 (60%)
Query: 60 ARFQVIHTDGSDDWNLQIKFLQKRDNGTYECQA 92
R+ GS ++L+I L+ D+GTY+CQA
Sbjct: 53 GRYDETVDKGSKSFSLRISDLRVEDSGTYKCQA 85
>pdb|1VER|A Chain A, Structure Of New Antigen Receptor Variable Domain From
Sharks
Length = 111
Score = 29.6 bits (65), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 28/56 (50%), Gaps = 4/56 (7%)
Query: 60 ARFQVIHTDGSDDWNLQIKFLQKRDNGTYECQA----QPYTTTSHSQNAPGLGDLL 111
R+ GS ++L+I+ L+ D+GTY+C A PY S + G G +L
Sbjct: 53 GRYVETVNKGSKSFSLRIRDLRVEDSGTYKCGAFRFWLPYGYGSLPLSEKGAGTVL 108
>pdb|2KH2|B Chain B, Solution Structure Of A Scfv-Il-1b Complex
Length = 254
Score = 29.6 bits (65), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 31/72 (43%), Gaps = 10/72 (13%)
Query: 32 DIVKVRVSWVR-----RRDW--HILTSGVLTYTND---ARFQVIHTDGSDDWNLQIKFLQ 81
D + +SWVR R +W +I + G TY D RF + + + LQ+ L+
Sbjct: 157 DFSRYDMSWVRQAPGKRLEWVAYISSGGGSTYFPDTVKGRFTISRDNAKNTLYLQMNSLR 216
Query: 82 KRDNGTYECQAQ 93
D Y C Q
Sbjct: 217 AEDTAVYYCARQ 228
>pdb|1AR1|C Chain C, Structure At 2.7 Angstrom Resolution Of The Paracoccus
Denitrificans Two-Subunit Cytochrome C Oxidase Complexed
With An Antibody Fv Fragment
pdb|1MQK|H Chain H, Crystal Structure Of The Unliganded Fv-Fragment Of The
Anti- Cytochrome C Oxidase Antibody 7e2
pdb|3EHB|C Chain C, A D-Pathway Mutation Decouples The Paracoccus
Denitrificans Cytochrome C Oxidase By Altering The Side
Chain Orientation Of A Distant, Conserved Glutamate
pdb|3HB3|C Chain C, High Resolution Crystal Structure Of Paracoccus
Denitrificans Cytochrome C Oxidase
Length = 127
Score = 29.3 bits (64), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 27/94 (28%), Positives = 37/94 (39%), Gaps = 9/94 (9%)
Query: 5 PGGILTAFGQISTGFLAVFSYSDKTVRDIVKVRVSWVRRRDWHILTSGVLTYTND---AR 61
PGG L ++GF SY+ VR + R+ WV I G TY D R
Sbjct: 14 PGGSL-KLSCAASGF-TFSSYTMSWVRQTPEKRLEWVA----SINNGGGRTYYPDTVKGR 67
Query: 62 FQVIHTDGSDDWNLQIKFLQKRDNGTYECQAQPY 95
F + + + LQ+ L+ D Y C Y
Sbjct: 68 FTISRDNAKNTLYLQMSSLKSEDTAMYYCVRHEY 101
>pdb|1QLE|H Chain H, Cryo-structure Of The Paracoccus Denitrificans
Four-subunit Cytochrome C Oxidase In The Completely
Oxidized State Complexed With An Antibody Fv Fragment
Length = 119
Score = 29.3 bits (64), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 27/94 (28%), Positives = 37/94 (39%), Gaps = 9/94 (9%)
Query: 5 PGGILTAFGQISTGFLAVFSYSDKTVRDIVKVRVSWVRRRDWHILTSGVLTYTND---AR 61
PGG L ++GF SY+ VR + R+ WV I G TY D R
Sbjct: 14 PGGSL-KLSCAASGF-TFSSYTMSWVRQTPEKRLEWVA----SINNGGGRTYYPDTVKGR 67
Query: 62 FQVIHTDGSDDWNLQIKFLQKRDNGTYECQAQPY 95
F + + + LQ+ L+ D Y C Y
Sbjct: 68 FTISRDNAKNTLYLQMSSLKSEDTAMYYCVRHEY 101
>pdb|2Z8V|C Chain C, Structure Of An Ignar-Ama1 Complex
pdb|2Z8V|D Chain D, Structure Of An Ignar-Ama1 Complex
Length = 116
Score = 29.3 bits (64), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 20/33 (60%)
Query: 60 ARFQVIHTDGSDDWNLQIKFLQKRDNGTYECQA 92
R+ GS ++L+I L+ D+GTY+CQA
Sbjct: 53 GRYVETVNKGSKSFSLRISDLRVEDSGTYKCQA 85
>pdb|1VES|A Chain A, Structure Of New Antigen Receptor Variable Domain From
Sharks
pdb|1VES|B Chain B, Structure Of New Antigen Receptor Variable Domain From
Sharks
Length = 113
Score = 29.3 bits (64), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 20/33 (60%)
Query: 60 ARFQVIHTDGSDDWNLQIKFLQKRDNGTYECQA 92
R+ GS ++L+I L+ D+GTY+CQA
Sbjct: 53 GRYVETVNKGSKSFSLRISDLRVEDSGTYKCQA 85
>pdb|2Z8W|C Chain C, Structure Of An Ignar-Ama1 Complex
pdb|2Z8W|D Chain D, Structure Of An Ignar-Ama1 Complex
Length = 116
Score = 29.3 bits (64), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 20/33 (60%)
Query: 60 ARFQVIHTDGSDDWNLQIKFLQKRDNGTYECQA 92
R+ GS ++L+I L+ D+GTY+CQA
Sbjct: 53 GRYVETVNKGSKSFSLRISDLRVEDSGTYKCQA 85
>pdb|2COQ|A Chain A, Structure Of New Antigen Receptor Variable Domain From
Sharks
Length = 108
Score = 28.9 bits (63), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 21/33 (63%)
Query: 60 ARFQVIHTDGSDDWNLQIKFLQKRDNGTYECQA 92
R+ +GS+ +L I+ L+ D+GTY+C+A
Sbjct: 53 GRYSETVDEGSNSASLTIRDLRVEDSGTYKCKA 85
>pdb|2XY1|A Chain A, Crystal Structure Of Ncam2 Ig3-4
Length = 192
Score = 28.5 bits (62), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 28/56 (50%), Gaps = 4/56 (7%)
Query: 37 RVSWVRRRDWHILTSGVLTYTNDARFQVIHTDGSDDWNLQIKFLQKRDNGTYECQA 92
++W R D T G + D R +V GS +L IK ++ D+G Y+C+A
Sbjct: 125 EITWKRAVDGFTFTEGDKSL--DGRIEVKGQHGSS--SLHIKDVKLSDSGRYDCEA 176
>pdb|2JLL|A Chain A, Crystal Structure Of Ncam2 Igiv-Fn3ii
Length = 389
Score = 28.5 bits (62), Expect = 1.0, Method: Composition-based stats.
Identities = 18/55 (32%), Positives = 28/55 (50%), Gaps = 4/55 (7%)
Query: 38 VSWVRRRDWHILTSGVLTYTNDARFQVIHTDGSDDWNLQIKFLQKRDNGTYECQA 92
++W R D T G + D R +V GS +L IK ++ D+G Y+C+A
Sbjct: 32 ITWKRAVDGFTFTEG--DKSLDGRIEVKGQHGSS--SLHIKDVKLSDSGRYDCEA 82
>pdb|1I85|A Chain A, Crystal Structure Of The Ctla-4B7-2 Complex
pdb|1I85|B Chain B, Crystal Structure Of The Ctla-4B7-2 Complex
pdb|1NCN|A Chain A, The Receptor-Binding Domain Of Human B7-2
pdb|1NCN|B Chain B, The Receptor-Binding Domain Of Human B7-2
Length = 110
Score = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 13/43 (30%), Positives = 20/43 (46%), Gaps = 7/43 (16%)
Query: 55 TYTNDARFQVIHTD-------GSDDWNLQIKFLQKRDNGTYEC 90
Y +F +H+ SD W L++ LQ +D G Y+C
Sbjct: 44 VYLGKEKFDSVHSKYMGRTSFDSDSWTLRLHNLQIKDKGLYQC 86
>pdb|2YD1|A Chain A, Crystal Structure Of The N-Terminal Ig1-2 Module Of
Drosophila Receptor Protein Tyrosine Phosphatase Dlar
Length = 212
Score = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 13/31 (41%), Positives = 18/31 (58%)
Query: 72 DWNLQIKFLQKRDNGTYECQAQPYTTTSHSQ 102
D LQI+ ++ D G YEC A+ T HS+
Sbjct: 162 DGFLQIENSREEDQGKYECVAENSMGTEHSK 192
>pdb|3PXJ|A Chain A, Tandem Ig Repeats Of Dlar
pdb|3PXJ|B Chain B, Tandem Ig Repeats Of Dlar
pdb|3PXJ|C Chain C, Tandem Ig Repeats Of Dlar
pdb|3PXJ|D Chain D, Tandem Ig Repeats Of Dlar
Length = 210
Score = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 13/31 (41%), Positives = 18/31 (58%)
Query: 72 DWNLQIKFLQKRDNGTYECQAQPYTTTSHSQ 102
D LQI+ ++ D G YEC A+ T HS+
Sbjct: 164 DGFLQIENSREEDQGKYECVAENSMGTEHSK 194
>pdb|2XYC|A Chain A, Crystal Structure Of Ncam2 Igiv-Fn3i
Length = 291
Score = 28.1 bits (61), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 28/56 (50%), Gaps = 4/56 (7%)
Query: 37 RVSWVRRRDWHILTSGVLTYTNDARFQVIHTDGSDDWNLQIKFLQKRDNGTYECQA 92
++W R D T G + D R +V GS +L IK ++ D+G Y+C+A
Sbjct: 31 EITWKRAVDGFTFTEGDKSL--DGRIEVKGQHGSS--SLHIKDVKLSDSGRYDCEA 82
>pdb|3KDM|H Chain H, Crystal Structure Of Human Anti-Steroid Fab 5f2 In Complex
With Testosterone
pdb|3KDM|B Chain B, Crystal Structure Of Human Anti-Steroid Fab 5f2 In Complex
With Testosterone
Length = 225
Score = 28.1 bits (61), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 27/102 (26%), Positives = 42/102 (41%), Gaps = 13/102 (12%)
Query: 1 MVAAPGGILTAFGQI-----STGFLAVFSYSDKTVRDIVKVRVSWVRRRDWHILTSGVLT 55
+V + GG++ G + ++GF SY+ VR + WV I SG T
Sbjct: 4 LVESGGGLVQPGGSLRLSCAASGF-TFSSYAMSWVRQAPGKGLEWVSA----ISGSGGST 58
Query: 56 YTNDA---RFQVIHTDGSDDWNLQIKFLQKRDNGTYECQAQP 94
Y D+ RF + + + LQ+ L+ D Y C P
Sbjct: 59 YYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARDP 100
>pdb|2M2D|A Chain A, Human Programmed Cell Death 1 Receptor
Length = 118
Score = 28.1 bits (61), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 11/34 (32%), Positives = 20/34 (58%)
Query: 59 DARFQVIHTDGSDDWNLQIKFLQKRDNGTYECQA 92
D+RF+V D+++ + ++ D+GTY C A
Sbjct: 60 DSRFRVTQLPNGRDFHMSVVRARRNDSGTYLCGA 93
>pdb|2BDN|L Chain L, Crystal Structure Of Human Mcp-1 Bound To A Blocking
Antibody, 11k2
Length = 214
Score = 27.7 bits (60), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 32/75 (42%), Gaps = 7/75 (9%)
Query: 28 KTVRDIVKVRVSWVRRRDW---HILTSGVLTYTNDARFQVIHTDGSDDWNLQIKFLQKRD 84
K DI R++W +++ +L SG + + + D+ L I LQ D
Sbjct: 24 KATEDIYN-RLAWYQQKPGSAPRLLISGATSLETGVPSRFSGSGSGKDYTLSITSLQTED 82
Query: 85 NGTYECQ---AQPYT 96
TY CQ + PYT
Sbjct: 83 VATYYCQQFWSAPYT 97
>pdb|3RRQ|A Chain A, Crystal Structure Of The Extracellular Domain Of Human
Pd-1
Length = 129
Score = 27.7 bits (60), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 11/34 (32%), Positives = 19/34 (55%)
Query: 59 DARFQVIHTDGSDDWNLQIKFLQKRDNGTYECQA 92
D RF+V D+++ + ++ D+GTY C A
Sbjct: 61 DCRFRVTQLPNGRDFHMSVVRARRNDSGTYLCGA 94
>pdb|1FH5|H Chain H, Crystal Structure Of The Fab Fragment Of The Monoclonal
Antibody Mak33
Length = 198
Score = 27.7 bits (60), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 25/93 (26%), Positives = 38/93 (40%), Gaps = 13/93 (13%)
Query: 6 GGILTAFGQI-----STGFLAVFSYSDKTVRDIVKVRVSWVRRRDWHILTSGVLTYTNDA 60
GG++ G + ++GF SY VR R+ WV I G TY D+
Sbjct: 3 GGLVKPAGSLKLSCAASGF-TFSSYYMYWVRQTPDKRLEWVAT----ISDGGSYTYYPDS 57
Query: 61 ---RFQVIHTDGSDDWNLQIKFLQKRDNGTYEC 90
RF + + ++ LQ+ L+ D Y C
Sbjct: 58 VKGRFTISRDNAKNNLYLQMSSLKSEDTAMYYC 90
>pdb|3K7U|A Chain A, Structure Of Essential Protein From Trypanosoma Brucei
Length = 128
Score = 27.7 bits (60), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 22/47 (46%), Gaps = 2/47 (4%)
Query: 50 TSGVLTYTN--DARFQVIHTDGSDDWNLQIKFLQKRDNGTYECQAQP 94
T G+L Y + + RF + + LQ+ L+ D Y C A+P
Sbjct: 54 TGGLLFYADSVNGRFTISRDNAKRTVTLQMNSLKPEDTAVYYCAARP 100
>pdb|2ID5|A Chain A, Crystal Structure Of The Lingo-1 Ectodomain
pdb|2ID5|B Chain B, Crystal Structure Of The Lingo-1 Ectodomain
pdb|2ID5|C Chain C, Crystal Structure Of The Lingo-1 Ectodomain
pdb|2ID5|D Chain D, Crystal Structure Of The Lingo-1 Ectodomain
Length = 477
Score = 27.3 bits (59), Expect = 2.1, Method: Composition-based stats.
Identities = 10/21 (47%), Positives = 15/21 (71%)
Query: 72 DWNLQIKFLQKRDNGTYECQA 92
D L++++ Q +DNGTY C A
Sbjct: 440 DGTLEVRYAQVQDNGTYLCIA 460
>pdb|3NCM|A Chain A, Neural Cell Adhesion Molecule, Module 2, Nmr, 20
Structures
Length = 92
Score = 27.3 bits (59), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 23/36 (63%), Gaps = 5/36 (13%)
Query: 58 NDARFQVIHTDGSDDWNLQIKFLQKRDNGTYECQAQ 93
D RF V+ S+++ LQI+ ++K D GTY C+ +
Sbjct: 46 KDVRFIVL----SNNY-LQIRGIKKTDEGTYRCEGR 76
>pdb|1JRH|L Chain L, Complex (AntibodyANTIGEN)
Length = 213
Score = 26.9 bits (58), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 30/67 (44%), Gaps = 4/67 (5%)
Query: 28 KTVRDIVKVRVSWVRRRDWH---ILTSGVLTYTNDARFQVIHTDGSDDWNLQIKFLQKRD 84
K DI R++W +++ + +L SG + + + + D+ L I LQ D
Sbjct: 24 KASEDIYN-RLAWYQQKPGNAPRLLISGATSLETEVPSRFSGSGSGKDYTLSITSLQTED 82
Query: 85 NGTYECQ 91
TY CQ
Sbjct: 83 VATYYCQ 89
>pdb|3UBX|L Chain L, Crystal Structure Of The Mouse Cd1d-C20:2-Agalcer-L363
Mab Fab Complex
pdb|3UBX|I Chain I, Crystal Structure Of The Mouse Cd1d-C20:2-Agalcer-L363
Mab Fab Complex
Length = 214
Score = 26.9 bits (58), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 29/67 (43%), Gaps = 4/67 (5%)
Query: 28 KTVRDIVKVRVSWVRRRDWHI---LTSGVLTYTNDARFQVIHTDGSDDWNLQIKFLQKRD 84
K DI R++W +++ ++ L SG + + + D+ L I LQ D
Sbjct: 24 KASEDIYN-RIAWYQQKPGNVPRLLISGATSLETGVPSRFSGSGSGKDYTLSITSLQTED 82
Query: 85 NGTYECQ 91
TY CQ
Sbjct: 83 VATYYCQ 89
>pdb|3SOB|L Chain L, The Structure Of The First Ywtd Beta Propeller Domain Of
Lrp6 In Complex With A Fab
Length = 237
Score = 26.6 bits (57), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 14/26 (53%), Positives = 15/26 (57%), Gaps = 1/26 (3%)
Query: 72 DWNLQIKFLQKRDNGTYECQAQPYTT 97
D+ L I LQ D TY CQ Q YTT
Sbjct: 93 DFTLTISSLQPEDFATYYCQ-QSYTT 117
>pdb|1DR9|A Chain A, Crystal Structure Of A Soluble Form Of B7-1 (Cd80)
Length = 201
Score = 26.6 bits (57), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 16/68 (23%), Positives = 35/68 (51%), Gaps = 2/68 (2%)
Query: 29 TVRDIVKVRVSWVRRRDWHI-LTSGVLTYTNDARFQVIHTDGSDDWNLQIKFLQKRDNGT 87
+V ++ + R+ W + + + + SG + + + + I D +++ ++ I L+ D GT
Sbjct: 21 SVEELAQTRIYWQKEKKMVLTMMSGDMNIWPEYKNRTIF-DITNNLSIVILALRPSDEGT 79
Query: 88 YECQAQPY 95
YEC Y
Sbjct: 80 YECVVLKY 87
>pdb|3IY2|A Chain A, Variable Domains Of The Computer Generated Model (Wam)
Of Fab 6 Fitted Into The Cryoem Reconstruction Of The
Virus- Fab 6 Complex
Length = 107
Score = 26.6 bits (57), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 13/28 (46%), Positives = 17/28 (60%), Gaps = 3/28 (10%)
Query: 72 DWNLQIKFLQKRDNGTYECQ---AQPYT 96
++L+I LQ D G+Y CQ A PYT
Sbjct: 68 QFSLKINSLQPEDFGSYYCQHHYATPYT 95
>pdb|1EPF|A Chain A, Crystal Structure Of The Two N-Terminal Immunoglobulin
Domains Of The Neural Cell Adhesion Molecule (Ncam)
pdb|1EPF|B Chain B, Crystal Structure Of The Two N-Terminal Immunoglobulin
Domains Of The Neural Cell Adhesion Molecule (Ncam)
pdb|1EPF|C Chain C, Crystal Structure Of The Two N-Terminal Immunoglobulin
Domains Of The Neural Cell Adhesion Molecule (Ncam)
pdb|1EPF|D Chain D, Crystal Structure Of The Two N-Terminal Immunoglobulin
Domains Of The Neural Cell Adhesion Molecule (Ncam)
Length = 191
Score = 26.6 bits (57), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 20/35 (57%), Gaps = 5/35 (14%)
Query: 59 DARFQVIHTDGSDDWNLQIKFLQKRDNGTYECQAQ 93
D RF V+ + LQI+ ++K D GTY C+ +
Sbjct: 146 DVRFIVLSNN-----YLQIRGIKKTDEGTYRCEGR 175
>pdb|4IDL|A Chain A, Low Melting Temperature Anti-cholera Toxin Llama Vhh
Domain
Length = 136
Score = 26.6 bits (57), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 22/91 (24%), Positives = 41/91 (45%), Gaps = 6/91 (6%)
Query: 6 GGILTAFGQISTGFLAVFSYSDKTVRDIVKVRVSWVRRRDW--HILTSGVLTYTN--DAR 61
GG + G + LA S + ++R + R + ++R+W + T+G Y + R
Sbjct: 11 GGAVQTGGSLKLTCLA--SGNTASIRAMGWYRRAPGKQREWVASLTTTGTADYGDFVKGR 68
Query: 62 FQVIHTDGSDDWNLQIKFLQKRDNGTYECQA 92
F + + ++ LQ+ L+ D Y C A
Sbjct: 69 FTISRDNANNAATLQMDSLKPEDTAVYYCNA 99
>pdb|1I8L|A Chain A, Human B7-1CTLA-4 Co-Stimulatory Complex
pdb|1I8L|B Chain B, Human B7-1CTLA-4 Co-Stimulatory Complex
Length = 208
Score = 26.6 bits (57), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 16/68 (23%), Positives = 35/68 (51%), Gaps = 2/68 (2%)
Query: 29 TVRDIVKVRVSWVRRRDWHI-LTSGVLTYTNDARFQVIHTDGSDDWNLQIKFLQKRDNGT 87
+V ++ + R+ W + + + + SG + + + + I D +++ ++ I L+ D GT
Sbjct: 21 SVEELAQTRIYWQKEKKMVLTMMSGDMNIWPEYKNRTIF-DITNNLSIVILALRPSDEGT 79
Query: 88 YECQAQPY 95
YEC Y
Sbjct: 80 YECVVLKY 87
>pdb|1I3U|A Chain A, Three-Dimensional Structure Of A Llama Vhh Domain
Complexed With The Dye Rr1
Length = 127
Score = 26.6 bits (57), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 21/46 (45%), Gaps = 3/46 (6%)
Query: 60 ARFQVIHTDGSDDWNLQIKFLQKRDNGTYECQAQPYTTTSHSQNAP 105
RF V + + NLQ+ L+ D Y C A+ TT+ N P
Sbjct: 71 GRFAVSRDNAKNTVNLQMNSLKPEDTAVYYCAAK---TTTWGGNDP 113
>pdb|1T2J|A Chain A, Crystal Structure Of A Human Vh Domain
Length = 116
Score = 26.6 bits (57), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 29/63 (46%), Gaps = 10/63 (15%)
Query: 38 VSWVRRR-----DW--HILTSGVLTYTNDA---RFQVIHTDGSDDWNLQIKFLQKRDNGT 87
+SWVR+ +W I SG TY+ D+ RF + + + LQ+ L+ D
Sbjct: 34 MSWVRQAPGKGLEWVSSISGSGGNTYSADSVKGRFTISRDNAKNSLYLQMNSLRAEDTAV 93
Query: 88 YEC 90
Y C
Sbjct: 94 YYC 96
>pdb|1OSP|L Chain L, Crystal Structure Of Outer Surface Protein A Of Borrelia
Burgdorferi Complexed With A Murine Monoclonal Antibody
Fab
Length = 214
Score = 26.6 bits (57), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 30/67 (44%), Gaps = 4/67 (5%)
Query: 28 KTVRDIVKVRVSWVRRRDWH---ILTSGVLTYTNDARFQVIHTDGSDDWNLQIKFLQKRD 84
K DI R++W +++ + +L SG + + +D D+ L I LQ D
Sbjct: 24 KASEDIYS-RLAWYQQKPGNAPRLLISGATSLETWVPSRFSGSDSGKDYTLSITSLQTED 82
Query: 85 NGTYECQ 91
TY CQ
Sbjct: 83 VATYFCQ 89
>pdb|3CRV|A Chain A, "xpd_helicase"
pdb|3CRW|1 Chain 1, "xpd_apo"
Length = 551
Score = 26.6 bits (57), Expect = 4.1, Method: Composition-based stats.
Identities = 27/101 (26%), Positives = 37/101 (36%), Gaps = 30/101 (29%)
Query: 6 GGILTAFGQISTGFLAVFSYSDKTVRDIVKVRVSWVRRRDWHILTSGVLTYTNDARFQVI 65
G IL F +S G FSYS + V I +S+ L ND +I
Sbjct: 274 GSILRFFSLLSIGSFIPFSYSKRLV--IKNPEISYY------------LNLLNDNELSII 319
Query: 66 HTDGS--------DDWNLQIKFL--------QKRDNGTYEC 90
G+ W ++ L QKR +G+YEC
Sbjct: 320 LMSGTLPPREYMEKVWGIKRNMLYLDVEREIQKRVSGSYEC 360
>pdb|3KVQ|A Chain A, Crystal Structure Of Vegfr2 Extracellular Domain D7
Length = 108
Score = 26.6 bits (57), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 18/29 (62%), Gaps = 2/29 (6%)
Query: 64 VIHTDGSDDWNLQIKFLQKRDNGTYECQA 92
++ DG + NL I+ ++K D G Y CQA
Sbjct: 57 IVLKDG--NRNLTIRRVRKEDEGLYTCQA 83
>pdb|2J4W|H Chain H, Structure Of A Plasmodium Vivax Apical Membrane Antigen
1- Fab F8.12.19 Complex
pdb|2J5L|C Chain C, Structure Of A Plasmodium Falciparum Apical Membrane
Antigen 1-Fab F8.12.19 Complex
Length = 225
Score = 26.6 bits (57), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 25/97 (25%), Positives = 40/97 (41%), Gaps = 11/97 (11%)
Query: 1 MVAAPGGILTAFGQISTGFLAV-FSYSDKT---VRDIVKVRVSWVRRRDWHILTSGVLTY 56
+V + GG++ G + A F +SD VR + R+ WV I TY
Sbjct: 4 LVESGGGLVKPGGSLKLSCAASGFIFSDYYMYWVRQTPEKRLEWVAT----ISDGNSYTY 59
Query: 57 TNDA---RFQVIHTDGSDDWNLQIKFLQKRDNGTYEC 90
D+ RF + + ++ LQ+ L+ D Y C
Sbjct: 60 YVDSVKGRFTISRDNAKNNLYLQMSSLKSEDTAIYYC 96
>pdb|2BK8|A Chain A, M1 Domain From Titin
Length = 97
Score = 26.6 bits (57), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 22/40 (55%), Gaps = 2/40 (5%)
Query: 52 GVLTYTNDARFQVIHTDGSDDWNLQIKFLQKRDNGTYECQ 91
GV N ++++ + DG L +K + K D+GTY C+
Sbjct: 39 GVRQLENSEKYEITYEDGV--AILYVKDITKLDDGTYRCK 76
>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 = 4.3, Method: Compositional matrix adjust.
Identities = 14/26 (53%), Positives = 15/26 (57%), Gaps = 1/26 (3%)
Query: 72 DWNLQIKFLQKRDNGTYECQAQPYTT 97
D+ L I LQ D TY CQ Q YTT
Sbjct: 70 DFTLTISSLQPEDFATYYCQ-QSYTT 94
>pdb|1I3V|A Chain A, Three-Dimensional Structure Of A Lama Vhh Domain
Unliganded
pdb|1I3V|B Chain B, Three-Dimensional Structure Of A Lama Vhh Domain
Unliganded
Length = 129
Score = 26.2 bits (56), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 21/46 (45%), Gaps = 3/46 (6%)
Query: 60 ARFQVIHTDGSDDWNLQIKFLQKRDNGTYECQAQPYTTTSHSQNAP 105
RF V + + NLQ+ L+ D Y C A+ TT+ N P
Sbjct: 71 GRFAVSRDNAKNTVNLQMNSLKPEDTAVYYCAAK---TTTWGGNDP 113
>pdb|3KAA|A Chain A, Structure Of Tim-3 In Complex With Phosphatidylserine
pdb|3KAA|B Chain B, Structure Of Tim-3 In Complex With Phosphatidylserine
Length = 118
Score = 26.2 bits (56), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 22/40 (55%)
Query: 54 LTYTNDARFQVIHTDGSDDWNLQIKFLQKRDNGTYECQAQ 93
+TY +R+Q+ D +L IK + D+GTY C+ Q
Sbjct: 56 VTYQKSSRYQLKGDLNKGDVSLIIKNVTLDDHGTYCCRIQ 95
>pdb|1ZA3|A Chain A, The Crystal Structure Of The Ysd1 Fab Bound To Dr5
pdb|1ZA3|L Chain L, The Crystal Structure Of The Ysd1 Fab Bound To Dr5
Length = 213
Score = 26.2 bits (56), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 13/27 (48%), Positives = 15/27 (55%), Gaps = 2/27 (7%)
Query: 72 DWNLQIKFLQKRDNGTYECQ--AQPYT 96
D+ L I LQ D TY CQ + PYT
Sbjct: 70 DFTLTISSLQPEDFATYYCQSSSSPYT 96
>pdb|1QZ1|A Chain A, Crystal Structure Of The Ig 1-2-3 Fragment Of Ncam
Length = 291
Score = 26.2 bits (56), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 20/35 (57%), Gaps = 5/35 (14%)
Query: 59 DARFQVIHTDGSDDWNLQIKFLQKRDNGTYECQAQ 93
D RF V+ + LQI+ ++K D GTY C+ +
Sbjct: 146 DVRFIVLSNN-----YLQIRGIKKTDEGTYRCEGR 175
>pdb|3U30|B Chain B, Crystal Structure Of A Linear-Specific Ubiquitin Fab
Bound To Linear Ubiquitin
pdb|3U30|E Chain E, Crystal Structure Of A Linear-Specific Ubiquitin Fab
Bound To Linear Ubiquitin
Length = 214
Score = 26.2 bits (56), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 14/26 (53%), Positives = 15/26 (57%), Gaps = 1/26 (3%)
Query: 72 DWNLQIKFLQKRDNGTYECQAQPYTT 97
D+ L I LQ D TY CQ Q YTT
Sbjct: 70 DFTLTISSLQPEDFATYYCQ-QSYTT 94
>pdb|3J1S|L Chain L, Structure Of Adeno-Associated Virus-2 In Complex With
Neutralizing Monoclonal Antibody A20
Length = 214
Score = 26.2 bits (56), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 15/58 (25%), Positives = 26/58 (44%), Gaps = 3/58 (5%)
Query: 37 RVSWVRRRDWH---ILTSGVLTYTNDARFQVIHTDGSDDWNLQIKFLQKRDNGTYECQ 91
R++W +++ + +L SG + + + D+ L I LQ D TY CQ
Sbjct: 32 RLAWYKQKPGNAPRLLISGATSLETGVPSRFSGSGSGKDYTLSITSLQNEDVATYYCQ 89
>pdb|1DSF|H Chain H, The Crystal Structure Of The Disulfide-Stabilized Fv
Fragment Of Anticancer Antibody B1: Conformational
Influence Of An Engineered Disulfide Bond
Length = 119
Score = 26.2 bits (56), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 25/105 (23%), Positives = 41/105 (39%), Gaps = 19/105 (18%)
Query: 1 MVAAPGGILTAFGQISTGFLAV-FSYSDKTVRDIVKVRVSWVRRR-----DWHILTSGVL 54
+V + GG++ G + A F +SD + WVR+ +W S
Sbjct: 2 LVESGGGLVKPGGSLKLSCAASGFIFSDNYMY--------WVRQTPEKCLEWVATISDGG 53
Query: 55 TYTN-----DARFQVIHTDGSDDWNLQIKFLQKRDNGTYECQAQP 94
TY + RF + + ++ LQ+ L+ D G Y C P
Sbjct: 54 TYIDYSDSVKGRFTISRDNAKNNLYLQMSSLRSEDTGMYYCGRSP 98
>pdb|3K80|A Chain A, Structure Of Essential Protein From Trypanosoma Brucei
pdb|3K80|B Chain B, Structure Of Essential Protein From Trypanosoma Brucei
Length = 130
Score = 26.2 bits (56), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 25/59 (42%), Gaps = 3/59 (5%)
Query: 48 ILTSGVLTYTNDA---RFQVIHTDGSDDWNLQIKFLQKRDNGTYECQAQPYTTTSHSQN 103
I SG LT ++ RF + + + LQ+ L+ D Y C Y SH +N
Sbjct: 51 ISRSGGLTQYAESLKGRFAISRDNAKNTVYLQMGSLKPEDTAVYYCAGDLYGLGSHMEN 109
>pdb|3V2A|R Chain R, Vegfr-2VEGF-A Complex Structure
Length = 772
Score = 26.2 bits (56), Expect = 4.8, Method: Composition-based stats.
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 74 NLQIKFLQKRDNGTYECQA 92
NL I+ ++K D G Y CQA
Sbjct: 721 NLTIRRVRKEDEGLYTCQA 739
>pdb|2I24|N Chain N, Crystal Structure Analysis Of The Nurse Shark New
Antigen Receptor Pbla8 Variable Domain
pdb|2I25|N Chain N, Crystal Structure Analysis Of The Nurse Shark New
Antigen Receptor Pbla8 Variable Domain In Complex With
Lysozyme
pdb|2I25|O Chain O, Crystal Structure Analysis Of The Nurse Shark New
Antigen Receptor Pbla8 Variable Domain In Complex With
Lysozyme
Length = 121
Score = 26.2 bits (56), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 10/25 (40%), Positives = 17/25 (68%)
Query: 69 GSDDWNLQIKFLQKRDNGTYECQAQ 93
GS ++L+I L +D+GTY C+ +
Sbjct: 62 GSKSFSLRINDLTVKDSGTYRCKPE 86
>pdb|3QQN|A Chain A, The Retinal Specific Cd147 Ig0 Domain: From Molecular
Structure To Biological Activity
pdb|3QQN|B Chain B, The Retinal Specific Cd147 Ig0 Domain: From Molecular
Structure To Biological Activity
Length = 137
Score = 26.2 bits (56), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 16/31 (51%)
Query: 75 LQIKFLQKRDNGTYECQAQPYTTTSHSQNAP 105
+ I L + D GTYEC+A +H AP
Sbjct: 92 ISIDTLVEEDTGTYECRASNDPDRNHLTRAP 122
>pdb|3HI5|L Chain L, Crystal Structure Of Fab Fragment Of Al-57
pdb|3HI6|L Chain L, Crystal Structure Of Intermediate Affinity I Domain Of
Integrin Lfa-1 With The Fab Fragment Of Its Antibody
Al-57
pdb|3HI6|Y Chain Y, Crystal Structure Of Intermediate Affinity I Domain Of
Integrin Lfa-1 With The Fab Fragment Of Its Antibody
Al-57
Length = 212
Score = 26.2 bits (56), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 15/31 (48%), Positives = 17/31 (54%), Gaps = 1/31 (3%)
Query: 72 DWNLQIKFLQKRDNGTYECQAQPYTTTSHSQ 102
D+ L I LQ D TY CQ Q Y+T S Q
Sbjct: 71 DFTLTISSLQLEDFATYYCQ-QSYSTPSFGQ 100
>pdb|3QR2|A Chain A, Wild Type Cd147 Ig0 Domain
pdb|3QR2|B Chain B, Wild Type Cd147 Ig0 Domain
Length = 137
Score = 26.2 bits (56), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 16/31 (51%)
Query: 75 LQIKFLQKRDNGTYECQAQPYTTTSHSQNAP 105
+ I L + D GTYEC+A +H AP
Sbjct: 92 ISIDTLVEEDTGTYECRASNDPDRNHLTRAP 122
>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 = 5.2, Method: Compositional matrix adjust.
Identities = 15/28 (53%), Positives = 16/28 (57%), Gaps = 1/28 (3%)
Query: 72 DWNLQIKFLQKRDNGTYECQAQPYTTTS 99
D+ L I LQ D TY CQ Q YTT S
Sbjct: 70 DFTLTISSLQPEDFATYYCQ-QFYTTPS 96
>pdb|2OYP|A Chain A, T Cell Immunoglobulin Mucin-3 Crystal Structure Revealed
A Galectin-9-Independent Binding Surface
Length = 109
Score = 25.8 bits (55), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 22/40 (55%)
Query: 54 LTYTNDARFQVIHTDGSDDWNLQIKFLQKRDNGTYECQAQ 93
+TY +R+Q+ D +L IK + D+GTY C+ Q
Sbjct: 53 VTYQKSSRYQLKGDLNKGDVSLIIKNVTLDDHGTYCCRIQ 92
>pdb|2C5D|C Chain C, Structure Of A Minimal Gas6-Axl Complex
pdb|2C5D|D Chain D, Structure Of A Minimal Gas6-Axl Complex
Length = 195
Score = 25.8 bits (55), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 21/43 (48%), Gaps = 5/43 (11%)
Query: 53 VLTYTNDARFQV-IHTDGSDDW----NLQIKFLQKRDNGTYEC 90
+L + + QV + D DDW L+I LQ D G Y+C
Sbjct: 43 ILELADSTQTQVPLGEDEQDDWIVVSQLRITSLQLSDTGQYQC 85
>pdb|3MJ6|A Chain A, Crystal Structure Of The Gammadelta T Cell Costimulatory
Receptor Junctional Adhesion Molecule-Like Protein, Jaml
pdb|3MJ7|A Chain A, Crystal Structure Of The Complex Of Jaml And Coxsackie And
Adenovirus Receptor, Car
pdb|3MJ9|A Chain A, Crystal Structure Of Jaml In Complex With The Stimulatory
Antibody Hl4e10
Length = 268
Score = 25.8 bits (55), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 30/68 (44%), Gaps = 17/68 (25%)
Query: 37 RVSWVRRRDWHILTSGVLTYTND-----ARFQ--------VIHTDGSDDWNLQIKFLQKR 83
RV W+ +D + VL Y ++ RFQ H DGS L ++ +QK
Sbjct: 39 RVDWLFSKDKDDASEYVLFYYSNLSVPTGRFQNRSHLVGDTFHNDGS----LLLQDVQKA 94
Query: 84 DNGTYECQ 91
D G Y C+
Sbjct: 95 DEGIYTCE 102
>pdb|1MAM|H Chain H, Crystal Structure To 2.45 A Resolution Of A Monoclonal Fab
Specific For The Brucella A Cell Wall Polysaccharide
Antigen
Length = 217
Score = 25.8 bits (55), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 11/36 (30%), Positives = 16/36 (44%)
Query: 60 ARFQVIHTDGSDDWNLQIKFLQKRDNGTYECQAQPY 95
RF + + LQ+ L+ D+ TY C PY
Sbjct: 68 GRFTISRDNSQSILYLQMNTLRAEDSATYYCTRDPY 103
>pdb|3RAJ|L Chain L, Crystal Structure Of Human Cd38 In Complex With The Fab
Fragment Of Antibody Hb7
Length = 211
Score = 25.8 bits (55), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 29/67 (43%), Gaps = 4/67 (5%)
Query: 28 KTVRDIVKVRVSWVRRRDWH---ILTSGVLTYTNDARFQVIHTDGSDDWNLQIKFLQKRD 84
K DI R++W +++ + +L SG + + + D+ L I LQ D
Sbjct: 23 KASEDIYN-RLAWYQQKPGNAPRLLISGATSLETGVPSRFSGSGSGKDYTLSITSLQTED 81
Query: 85 NGTYECQ 91
TY CQ
Sbjct: 82 VATYYCQ 88
>pdb|3QYC|A Chain A, Structure Of A Dimeric Anti-Her2 Single Domain Antibody
pdb|3QYC|B Chain B, Structure Of A Dimeric Anti-Her2 Single Domain Antibody
Length = 146
Score = 25.8 bits (55), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 25/101 (24%), Positives = 40/101 (39%), Gaps = 11/101 (10%)
Query: 1 MVAAPGGILTAFGQISTGFLA----VFSYSDKTVRDIVKVRVSWVRRRDWHILTSGVLTY 56
+V + GG++ G + A + +Y VR + WV I +SG TY
Sbjct: 6 LVESGGGLIKPGGSLRLSCAASGVRLSAYDMAWVRQAPGKGLEWVS----AISSSGGSTY 61
Query: 57 TNDA---RFQVIHTDGSDDWNLQIKFLQKRDNGTYECQAQP 94
D+ RF + + + LQ+ L+ D Y C P
Sbjct: 62 YADSVKGRFTISRDNSKNTVYLQMNSLRAEDTAVYYCVTLP 102
>pdb|2ZJS|H Chain H, Crystal Structure Of Secye Translocon From Thermus
Thermophilus With A Fab Fragment
Length = 221
Score = 25.8 bits (55), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 17/68 (25%), Positives = 27/68 (39%), Gaps = 10/68 (14%)
Query: 38 VSWVRRRDWHILT--------SGVLTYTNDARFQVIHT--DGSDDWNLQIKFLQKRDNGT 87
++WV++R H L SG Y + + T S+ +Q+ L D+
Sbjct: 34 IAWVKQRPGHGLEWIGEILPGSGSTNYNEKFKGKATFTADTSSNTAYMQLSSLTSEDSAV 93
Query: 88 YECQAQPY 95
Y C PY
Sbjct: 94 YYCARSPY 101
>pdb|1IND|H Chain H, How The Anti-(Metal Chelate) Antibody Cha255 Is Specific
For The Metal Ion Of Its Antigen: X-Ray Structures For
Two Fab'(Slash)hapten Complexes With Different Metals
In The Chelate
pdb|1INE|H Chain H, How The Anti-(Metal Chelate) Antibody Cha255 Is Specific
For The Metal Ion Of Its Antigen: X-Ray Structures For
Two Fab'(Slash)hapten Complexes With Different Metals
In The Chelate
Length = 226
Score = 25.8 bits (55), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 33/77 (42%), Gaps = 10/77 (12%)
Query: 23 FSYSDKT---VRDIVKVRVSWVRRRDWHILTSGVLTYTN---DARFQVIHTDGSDDWNLQ 76
F+ S +T VR + R+ WV L+ G T+ + RF + + ++ LQ
Sbjct: 27 FTLSGETMSWVRQTPEKRLEWVAT----TLSGGGFTFYSASVKGRFTISRDNAQNNLYLQ 82
Query: 77 IKFLQKRDNGTYECQAQ 93
+ L+ D Y C +
Sbjct: 83 LNSLRSEDTALYFCASH 99
>pdb|2OM5|A Chain A, N-Terminal Fragment Of Human Tax1
Length = 381
Score = 25.8 bits (55), Expect = 6.6, Method: Composition-based stats.
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 75 LQIKFLQKRDNGTYECQAQ 93
LQI + D GTYEC+A+
Sbjct: 258 LQIPSVSFEDEGTYECEAE 276
>pdb|3PEH|A Chain A, Crystal Structure Of The N-Terminal Domain Of An Hsp90
From Plasmodium Falciparum, Pfl1070c In The Presence Of
A Thienopyrimidine Derivative
pdb|3PEH|B Chain B, Crystal Structure Of The N-Terminal Domain Of An Hsp90
From Plasmodium Falciparum, Pfl1070c In The Presence Of
A Thienopyrimidine Derivative
pdb|3PEJ|A Chain A, Crystal Structure Of The N-Terminal Domain Of An Hsp90
From Plasmodium Falciparum, Pfl1070c In The Presence Of
Macbecin
pdb|3PEJ|B Chain B, Crystal Structure Of The N-Terminal Domain Of An Hsp90
From Plasmodium Falciparum, Pfl1070c In The Presence Of
Macbecin
Length = 281
Score = 25.8 bits (55), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 9/29 (31%), Positives = 16/29 (55%)
Query: 2 VAAPGGILTAFGQISTGFLAVFSYSDKTV 30
++ GG ++ GQ GF + F +DK +
Sbjct: 128 ISKSGGDMSLIGQFGVGFYSAFLVADKVI 156
>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 = 25.8 bits (55), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 14/26 (53%), Positives = 15/26 (57%), Gaps = 1/26 (3%)
Query: 72 DWNLQIKFLQKRDNGTYECQAQPYTT 97
D+ L I LQ D TY CQ Q YTT
Sbjct: 70 DFTLTISSLQPEDFATYYCQ-QHYTT 94
>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 = 25.4 bits (54), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 14/26 (53%), Positives = 15/26 (57%), Gaps = 1/26 (3%)
Query: 72 DWNLQIKFLQKRDNGTYECQAQPYTT 97
D+ L I LQ D TY CQ Q YTT
Sbjct: 81 DFTLTISSLQPEDFATYYCQ-QHYTT 105
>pdb|2P49|B Chain B, Complex Of A Camelid Single-Domain Vhh Antibody Fragment
With Rnase A At 1.4a Resolution: Native Mono_1 Crystal
Form
Length = 123
Score = 25.4 bits (54), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 16/36 (44%)
Query: 60 ARFQVIHTDGSDDWNLQIKFLQKRDNGTYECQAQPY 95
RF + G + LQ+ L+ D TY C A Y
Sbjct: 68 GRFTISRDKGKNTVYLQMDSLKPEDTATYYCAAGGY 103
>pdb|2B2X|H Chain H, Vla1 Rdeltah I-Domain Complexed With A Quadruple Mutant
Of The Aqc2 Fab
pdb|2B2X|I Chain I, Vla1 Rdeltah I-Domain Complexed With A Quadruple Mutant
Of The Aqc2 Fab
Length = 226
Score = 25.4 bits (54), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 25/100 (25%), Positives = 44/100 (44%), Gaps = 18/100 (18%)
Query: 1 MVAAPGGILTAFGQISTGFLAV-FSYSDKTVRDIVKVRVSWVRRR-----DW-HILTSGV 53
+V + GG++ G + A F++S T+ SWVR+ +W +++ G
Sbjct: 4 LVESGGGLVQPGGSLRLSCAASGFTFSRYTM--------SWVRQAPGKGLEWVAVISGGG 55
Query: 54 LTYTNDA---RFQVIHTDGSDDWNLQIKFLQKRDNGTYEC 90
TY D+ RF + + + LQ+ L+ D Y C
Sbjct: 56 HTYYLDSVEGRFTISRDNSKNTLYLQMNSLRAEDTAVYYC 95
>pdb|3G9A|B Chain B, Green Fluorescent Protein Bound To Minimizer Nanobody
Length = 139
Score = 25.4 bits (54), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 21/52 (40%), Gaps = 2/52 (3%)
Query: 47 HILTSGVLTYTND--ARFQVIHTDGSDDWNLQIKFLQKRDNGTYECQAQPYT 96
+IL G TY RF + D + LQ+ L+ D Y C A T
Sbjct: 52 NILRDGTTTYAGSVKGRFTISRDDAKNTVYLQMVNLKSEDTARYYCAADSGT 103
>pdb|1BZQ|K Chain K, Complex Of A Dromedary Single-Domain Vhh Antibody Fragment
With Rnase A
pdb|1BZQ|L Chain L, Complex Of A Dromedary Single-Domain Vhh Antibody Fragment
With Rnase A
pdb|1BZQ|M Chain M, Complex Of A Dromedary Single-Domain Vhh Antibody Fragment
With Rnase A
pdb|1BZQ|N Chain N, Complex Of A Dromedary Single-Domain Vhh Antibody Fragment
With Rnase A
Length = 124
Score = 25.4 bits (54), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 16/36 (44%)
Query: 60 ARFQVIHTDGSDDWNLQIKFLQKRDNGTYECQAQPY 95
RF + G + LQ+ L+ D TY C A Y
Sbjct: 66 GRFTISRDKGKNTVYLQMDSLKPEDTATYYCAAGGY 101
>pdb|1C7N|A Chain A, Crystal Structure Of Cystalysin From Treponema Denticola
Contains A Pyridoxal 5'-Phosphate Cofactor
pdb|1C7N|B Chain B, Crystal Structure Of Cystalysin From Treponema Denticola
Contains A Pyridoxal 5'-Phosphate Cofactor
pdb|1C7N|C Chain C, Crystal Structure Of Cystalysin From Treponema Denticola
Contains A Pyridoxal 5'-Phosphate Cofactor
pdb|1C7N|D Chain D, Crystal Structure Of Cystalysin From Treponema Denticola
Contains A Pyridoxal 5'-Phosphate Cofactor
pdb|1C7N|E Chain E, Crystal Structure Of Cystalysin From Treponema Denticola
Contains A Pyridoxal 5'-Phosphate Cofactor
pdb|1C7N|F Chain F, Crystal Structure Of Cystalysin From Treponema Denticola
Contains A Pyridoxal 5'-Phosphate Cofactor
pdb|1C7N|G Chain G, Crystal Structure Of Cystalysin From Treponema Denticola
Contains A Pyridoxal 5'-Phosphate Cofactor
pdb|1C7N|H Chain H, Crystal Structure Of Cystalysin From Treponema Denticola
Contains A Pyridoxal 5'-Phosphate Cofactor
pdb|1C7O|A Chain A, Crystal Structure Of Cystalysin From Treponema Denticola
Contains A Pyridoxal
5'-Phosphate-L-Aminoethoxyvinylglycine Complex
pdb|1C7O|B Chain B, Crystal Structure Of Cystalysin From Treponema Denticola
Contains A Pyridoxal
5'-Phosphate-L-Aminoethoxyvinylglycine Complex
pdb|1C7O|C Chain C, Crystal Structure Of Cystalysin From Treponema Denticola
Contains A Pyridoxal
5'-Phosphate-L-Aminoethoxyvinylglycine Complex
pdb|1C7O|D Chain D, Crystal Structure Of Cystalysin From Treponema Denticola
Contains A Pyridoxal
5'-Phosphate-L-Aminoethoxyvinylglycine Complex
pdb|1C7O|E Chain E, Crystal Structure Of Cystalysin From Treponema Denticola
Contains A Pyridoxal
5'-Phosphate-L-Aminoethoxyvinylglycine Complex
pdb|1C7O|F Chain F, Crystal Structure Of Cystalysin From Treponema Denticola
Contains A Pyridoxal
5'-Phosphate-L-Aminoethoxyvinylglycine Complex
pdb|1C7O|G Chain G, Crystal Structure Of Cystalysin From Treponema Denticola
Contains A Pyridoxal
5'-Phosphate-L-Aminoethoxyvinylglycine Complex
pdb|1C7O|H Chain H, Crystal Structure Of Cystalysin From Treponema Denticola
Contains A Pyridoxal
5'-Phosphate-L-Aminoethoxyvinylglycine Complex
Length = 399
Score = 25.4 bits (54), Expect = 7.8, Method: Composition-based stats.
Identities = 12/27 (44%), Positives = 17/27 (62%)
Query: 28 KTVRDIVKVRVSWVRRRDWHILTSGVL 54
KTV+ +K R W + DW I T+GV+
Sbjct: 73 KTVKKWMKDRHQWDIQTDWIINTAGVV 99
>pdb|1N8Z|A Chain A, Crystal Structure Of Extracellular Domain Of Human Her2
Complexed With Herceptin Fab
Length = 214
Score = 25.4 bits (54), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 14/26 (53%), Positives = 15/26 (57%), Gaps = 1/26 (3%)
Query: 72 DWNLQIKFLQKRDNGTYECQAQPYTT 97
D+ L I LQ D TY CQ Q YTT
Sbjct: 70 DFTLTISSLQPEDFATYYCQ-QHYTT 94
>pdb|4DKA|A Chain A, Structure Of Editosome Protein
pdb|4DKA|B Chain B, Structure Of Editosome Protein
Length = 127
Score = 25.4 bits (54), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 23/53 (43%), Gaps = 3/53 (5%)
Query: 48 ILTSGVLTYTNDA---RFQVIHTDGSDDWNLQIKFLQKRDNGTYECQAQPYTT 97
I +G TY D+ RF + + + LQ+ L+ D Y C A + T
Sbjct: 51 ISRNGANTYYTDSVKGRFTISRDNAKNTVELQMNSLKPEDTAVYYCAADRFPT 103
>pdb|4DK3|A Chain A, Structure Of Editosome Protein
pdb|4DK3|B Chain B, Structure Of Editosome Protein
pdb|4DK6|A Chain A, Structure Of Editosome Protein
pdb|4DK6|B Chain B, Structure Of Editosome Protein
Length = 133
Score = 25.4 bits (54), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 23/53 (43%), Gaps = 3/53 (5%)
Query: 48 ILTSGVLTYTNDA---RFQVIHTDGSDDWNLQIKFLQKRDNGTYECQAQPYTT 97
I +G TY D+ RF + + + LQ+ L+ D Y C A + T
Sbjct: 51 ISRNGANTYYTDSVKGRFTISRDNAKNTVELQMNSLKPEDTAVYYCAADRFPT 103
>pdb|1FVD|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|1FVD|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
pdb|1FVE|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|1FVE|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 = 214
Score = 25.4 bits (54), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 14/26 (53%), Positives = 15/26 (57%), Gaps = 1/26 (3%)
Query: 72 DWNLQIKFLQKRDNGTYECQAQPYTT 97
D+ L I LQ D TY CQ Q YTT
Sbjct: 70 DFTLTISSLQPEDFATYYCQ-QHYTT 94
>pdb|2I26|N Chain N, Crystal Structure Analysis Of The Nurse Shark New
Antigen Receptor Ancestral Variable Domain In Complex
With Lysozyme
pdb|2I26|O Chain O, Crystal Structure Analysis Of The Nurse Shark New
Antigen Receptor Ancestral Variable Domain In Complex
With Lysozyme
pdb|2I26|P Chain P, Crystal Structure Analysis Of The Nurse Shark New
Antigen Receptor Ancestral Variable Domain In Complex
With Lysozyme
pdb|2I27|N Chain N, Crystal Structure Analysis Of The Nurse Shark New
Antigen Receptor Ancestral Variable Domain
pdb|2I27|O Chain O, Crystal Structure Analysis Of The Nurse Shark New
Antigen Receptor Ancestral Variable Domain
Length = 121
Score = 25.4 bits (54), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 13/54 (24%), Positives = 24/54 (44%), Gaps = 3/54 (5%)
Query: 40 WVRRRDWHILTSGVLTYTNDARFQVIHTDGSDDWNLQIKFLQKRDNGTYECQAQ 93
W R++ + + R+ GS ++L+I L D+GTY C+ +
Sbjct: 36 WYRKKSGSTNEESI---SKGGRYVETVNSGSKSFSLRINDLTVEDSGTYRCKPE 86
>pdb|3PGF|L Chain L, Crystal Structure Of Maltose Bound Mbp With A
Conformationally Specific Synthetic Antigen Binder
(Sab)
Length = 215
Score = 25.0 bits (53), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 12/24 (50%)
Query: 72 DWNLQIKFLQKRDNGTYECQAQPY 95
D+ L I LQ D TY CQ Y
Sbjct: 71 DFTLTISSLQPEDFATYYCQQSSY 94
>pdb|3BDY|L Chain L, Dual Specific Bh1 Fab In Complex With Vegf
pdb|3BE1|L Chain L, Dual Specific Bh1 Fab In Complex With The Extracellular
Domain Of Her2ERBB-2
Length = 218
Score = 25.0 bits (53), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 14/26 (53%), Positives = 15/26 (57%), Gaps = 1/26 (3%)
Query: 72 DWNLQIKFLQKRDNGTYECQAQPYTT 97
D+ L I LQ D TY CQ Q YTT
Sbjct: 74 DFTLTISSLQPEDFATYYCQ-QHYTT 98
>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 = 25.0 bits (53), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 18/76 (23%), Positives = 32/76 (42%), Gaps = 6/76 (7%)
Query: 17 TGFLAVFSYSDKTVRDIVKVRVSWVRRRDWHILTSGVLTYTND--ARFQVIHTDGSDDWN 74
TG+ +Y+ +R ++ W+ I + G TY +RF + + +
Sbjct: 25 TGYSITSNYAWNWIRQFPGNKLEWMG----FISSYGTTTYNPSLKSRFSITRDTSKNQFF 80
Query: 75 LQIKFLQKRDNGTYEC 90
LQ+ + D GTY C
Sbjct: 81 LQLHSVTIEDTGTYFC 96
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
0.321 0.135 0.421
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,704,744
Number of Sequences: 62578
Number of extensions: 141767
Number of successful extensions: 705
Number of sequences better than 100.0: 112
Number of HSP's better than 100.0 without gapping: 49
Number of HSP's successfully gapped in prelim test: 63
Number of HSP's that attempted gapping in prelim test: 655
Number of HSP's gapped (non-prelim): 113
length of query: 113
length of database: 14,973,337
effective HSP length: 77
effective length of query: 36
effective length of database: 10,154,831
effective search space: 365573916
effective search space used: 365573916
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 45 (21.9 bits)