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= psy16320
(214 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4AG4|A Chain A, Crystal Structure Of A Ddr1-Fab Complex
Length = 351
Score = 91.3 bits (225), Expect = 3e-19, Method: Compositional matrix adjust.
Identities = 67/184 (36%), Positives = 95/184 (51%), Gaps = 9/184 (4%)
Query: 31 GLVSYTMPQGEVKTFXXXXXXXXXXXXTDKTYDGVVEDGLLSGGLGQLTDGQIGADNFKM 90
GL+SYT P G+ D TYDG GL GGLGQL DG +G D+F+
Sbjct: 165 GLLSYTAPVGQTMYLSEAVYL------NDSTYDGHTVGGLQYGGLGQLADGVVGLDDFRK 218
Query: 91 DAKSRN-KGYEWIGWRNESFPYGKPVEMVFEFDRVRNFTAMHLHINNYYSKDIQVFSHAN 149
+ R GY+++GW N SF G VEM FEFDR+R F AM +H NN ++ ++
Sbjct: 219 SQELRVWPGYDYVGWSNHSFSSGY-VEMEFEFDRLRAFQAMQVHCNNMHTLGARLPGGVE 277
Query: 150 VYLSLG-GRQFSLEPIQFTYMPDTIMEKARNVTIKLHHKQAKYLKLQMYFSNKWLLISEI 208
G + EP++ + +AR V++ L + A++L+ + F+ WLL SEI
Sbjct: 278 CRFRRGPAMAWEGEPMRHNLGGNLGDPRARAVSVPLGGRVARFLQCRFLFAGPWLLFSEI 337
Query: 209 MFQS 212
F S
Sbjct: 338 SFIS 341
>pdb|2ADF|H Chain H, Crystal Structure And Paratope Determination Of 82d6a3, An
Antithrombotic Antibody Directed Against The Von
Willebrand Factor A3-Domain
Length = 218
Score = 32.3 bits (72), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 37/75 (49%), Gaps = 7/75 (9%)
Query: 87 NFKMD--AKSRNKGYEWIGWRNES---FPYGKPVEMVFEFDRVRNFTAMHLHINNYYSKD 141
N+ M+ ++ KG +W+GW+N + YG+ F F + + +L INN ++D
Sbjct: 31 NYGMNWVKQAPGKGLKWMGWKNTNTGETTYGEEFRGRFAFSLETSVSTAYLQINNLKNED 90
Query: 142 IQVFSHA--NVYLSL 154
+ A N Y +L
Sbjct: 91 TATYFCARDNPYYAL 105
>pdb|1NCB|H Chain H, Crystal Structures Of Two Mutant Neuraminidase-Antibody
Complexes With Amino Acid Substitutions In The Interface
pdb|1NCD|H Chain H, Refined Crystal Structure Of The Influenza Virus N9
Neuraminidase-Nc41 Fab Complex
Length = 221
Score = 31.6 bits (70), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 32/64 (50%), Gaps = 5/64 (7%)
Query: 87 NFKMD--AKSRNKGYEWIGWRNESF---PYGKPVEMVFEFDRVRNFTAMHLHINNYYSKD 141
N+ M+ ++ KG EW+GW N + YG+ + F F + + +L INN ++D
Sbjct: 31 NYGMNWVKQAPGKGLEWMGWINTNTGEPTYGEEFKGRFAFSLETSASTANLQINNLKNED 90
Query: 142 IQVF 145
F
Sbjct: 91 KATF 94
>pdb|1NCA|H Chain H, Refined Crystal Structure Of The Influenza Virus N9
Neuraminidase-Nc41 Fab Complex
pdb|1NCC|H Chain H, Crystal Structures Of Two Mutant Neuraminidase-Antibody
Complexes With Amino Acid Substitutions In The Interface
Length = 221
Score = 30.8 bits (68), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 32/64 (50%), Gaps = 5/64 (7%)
Query: 87 NFKMD--AKSRNKGYEWIGWRNESF---PYGKPVEMVFEFDRVRNFTAMHLHINNYYSKD 141
N+ M+ ++ KG +W+GW N + YG+ + F F + + +L INN ++D
Sbjct: 31 NYGMNWVKQAPGKGLKWMGWINTNTGEPTYGEEFKGRFAFSLETSASTANLQINNLKNED 90
Query: 142 IQVF 145
F
Sbjct: 91 TATF 94
>pdb|4DCQ|B Chain B, Crystal Structure Of The Fab Fragment Of 3b5h10, An
Antibody-Specific For Extended Polyglutamine Repeats
(Orthorhombic Form)
Length = 218
Score = 30.8 bits (68), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 33/70 (47%), Gaps = 8/70 (11%)
Query: 93 KSRNKGYEWIGWRN--ESFP-YGKPVEMVFEFDRVRNFTAMHLHINNYYSKDIQVFSHAN 149
++ KG+EW+GW N P Y + F F + + +L INN ++D V+
Sbjct: 39 QAPGKGFEWMGWINTYSGVPTYVDDFKGRFAFSLETSASTAYLQINNLKNEDTAVY---- 94
Query: 150 VYLSLGGRQF 159
+ + GG F
Sbjct: 95 -FCARGGNNF 103
>pdb|1JGL|H Chain H, Crystal Structure Of Immunoglobulin Fab Fragment Complexed
With 17-Beta-Estradiol
pdb|1JHK|H Chain H, Crystal Structure Of The Anti-Estradiol Antibody 57-2
Length = 218
Score = 30.0 bits (66), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 26/56 (46%), Gaps = 3/56 (5%)
Query: 97 KGYEWIGWRN--ESFP-YGKPVEMVFEFDRVRNFTAMHLHINNYYSKDIQVFSHAN 149
KG +WIGW N P Y + + F F + T +L INN ++D + A
Sbjct: 43 KGLKWIGWLNTQSGVPEYAEDFKGRFAFSLETSATTAYLQINNLKNEDTATYFCAT 98
>pdb|1UWX|H Chain H, P1.2 Serosubtype Antigen Derived From N. Meningitidis Pora
In Complex With Fab Fragment
pdb|1UWX|M Chain M, P1.2 Serosubtype Antigen Derived From N. Meningitidis Pora
In Complex With Fab Fragment
Length = 225
Score = 29.6 bits (65), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 36/79 (45%), Gaps = 7/79 (8%)
Query: 87 NFKMD--AKSRNKGYEWIGWRN----ESFPYGKPVEMVFEFDRVRNFTAMHLHINNYYSK 140
NF ++ ++ KG +W+GW N ES Y + F F + + +L INN ++
Sbjct: 31 NFGLNWMKQAPGKGLKWMGWINTYTGEST-YADDFKGRFAFSLETSASTAYLQINNVKNE 89
Query: 141 DIQVFSHANVYLSLGGRQF 159
D + A + G R F
Sbjct: 90 DTATYFCARGFYYYGSRYF 108
>pdb|3S96|A Chain A, Crystal Structure Of 3b5h10
pdb|3S96|C Chain C, Crystal Structure Of 3b5h10
Length = 220
Score = 29.3 bits (64), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 29/59 (49%), Gaps = 3/59 (5%)
Query: 93 KSRNKGYEWIGWRN--ESFP-YGKPVEMVFEFDRVRNFTAMHLHINNYYSKDIQVFSHA 148
++ KG+EW+GW N P Y + F F + + +L INN ++D V+ A
Sbjct: 39 QAPGKGFEWMGWINTYSGVPTYVDDFKGRFAFSLETSASTAYLQINNLKNEDTAVYFCA 97
>pdb|1TPX|B Chain B, Ovine Recombinant Prp(114-234), Arq Variant In Complex
With The Fab Of The Vrq14 Antibody
pdb|1TQB|B Chain B, Ovine Recombinant Prp(114-234), Vrq Variant In Complex
With The Fab Of The Vrq14 Antibody
pdb|1TQC|B Chain B, Ovine Recombinant Prp(114-234), Arr Variant In Complex
With The Vrq14 Fab Fragment (Igg2a)
Length = 212
Score = 28.9 bits (63), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 34/68 (50%), Gaps = 13/68 (19%)
Query: 87 NFKMD--AKSRNKGYEWIGWRNESFPYGKPV-------EMVFEFDRVRNFTAMHLHINNY 137
N+ M+ ++ KG+EW+GW N +F G+P VF D + + +L INN
Sbjct: 31 NYGMNLVKQAPGKGFEWMGWIN-TF-TGEPTYADDFKGRFVFSLD--TSASTAYLQINNL 86
Query: 138 YSKDIQVF 145
++D +
Sbjct: 87 KNEDTATY 94
>pdb|4G6F|H Chain H, Crystal Structure Of 10e8 Fab In Complex With An Hiv-1
Gp41 Peptide
pdb|4G6F|B Chain B, Crystal Structure Of 10e8 Fab In Complex With An Hiv-1
Gp41 Peptide
Length = 236
Score = 28.5 bits (62), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 27/60 (45%), Gaps = 11/60 (18%)
Query: 97 KGYEWIG--------WRNESFPYGKPVEMVFEFDRVRNFTAMHLHINNYYSKDIQVFSHA 148
KG EW+G W S Y PVE F R+ + ++L +NN +D ++ A
Sbjct: 43 KGLEWVGRITGPGEGW---SVDYAAPVEGRFTISRLNSINFLYLEMNNLRMEDSGLYFCA 99
>pdb|2BRR|H Chain H, Complex Of The Neisserial Pora P1.4 Epitope Peptide And
Two Fab-Fragments (Antibody Mn20b9.34)
pdb|2BRR|Y Chain Y, Complex Of The Neisserial Pora P1.4 Epitope Peptide And
Two Fab-Fragments (Antibody Mn20b9.34)
Length = 225
Score = 28.5 bits (62), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 9/72 (12%)
Query: 87 NFKMD--AKSRNKGYEWIGWRNESFPYGKPV-----EMVFEFDRVRNFTAMHLHINNYYS 139
N+ M+ ++ KG +W+GW N G+P + F F + +A +L INN +
Sbjct: 31 NYGMNWVKQAPGKGLKWMGWINTYT--GEPTYADDFKERFAFSLETSASAAYLQINNLKN 88
Query: 140 KDIQVFSHANVY 151
+D + A Y
Sbjct: 89 EDTATYFCARDY 100
>pdb|2ZPK|H Chain H, Crystal Structure Of P20.1 Fab Fragment In Complex With
Its Antigen Peptide
pdb|2ZPK|I Chain I, Crystal Structure Of P20.1 Fab Fragment In Complex With
Its Antigen Peptide
Length = 216
Score = 28.1 bits (61), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 26/56 (46%), Gaps = 3/56 (5%)
Query: 93 KSRNKGYEWIGWRN--ESFP-YGKPVEMVFEFDRVRNFTAMHLHINNYYSKDIQVF 145
K K +WIGW N P Y + + F F + + +LHINN ++D +
Sbjct: 39 KMPGKSLKWIGWINTRSGVPKYAEDFKGRFAFSLETSASIAYLHINNLKNEDTATY 94
>pdb|1TET|H Chain H, Crystal Structure Of An Anticholera Toxin Peptide Complex
At 2.3 Angstroms
Length = 210
Score = 27.3 bits (59), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 28/59 (47%), Gaps = 3/59 (5%)
Query: 93 KSRNKGYEWIGWRN--ESFP-YGKPVEMVFEFDRVRNFTAMHLHINNYYSKDIQVFSHA 148
++ KG++W+GW N P Y + F F + + +L INN ++D + A
Sbjct: 39 QTPGKGFKWMGWINTYSGVPTYADDFKGRFAFSLETSASTAYLQINNLKNEDTATYFCA 97
>pdb|3DSB|A Chain A, The Crystal Structure Of A Possible Acetyltransferase From
Clostridium Difficile 630
pdb|3DSB|B Chain B, The Crystal Structure Of A Possible Acetyltransferase From
Clostridium Difficile 630
Length = 157
Score = 26.9 bits (58), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 22/43 (51%)
Query: 99 YEWIGWRNESFPYGKPVEMVFEFDRVRNFTAMHLHINNYYSKD 141
YEW WRN +F + + V + E+ R F + +I N KD
Sbjct: 74 YEWSDWRNGNFLWIQSVYVDKEYRRKGIFNYLFNYIKNICDKD 116
>pdb|1ZEA|H Chain H, Structure Of The Anti-Cholera Toxin Antibody Fab Fragment
Te33 In Complex With A D-Peptide
Length = 216
Score = 26.9 bits (58), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 28/59 (47%), Gaps = 3/59 (5%)
Query: 93 KSRNKGYEWIGWRN--ESFP-YGKPVEMVFEFDRVRNFTAMHLHINNYYSKDIQVFSHA 148
++ KG++W+GW N P Y + F F + + +L INN ++D + A
Sbjct: 39 QTPGKGFKWMGWINTYSGVPTYADDFKGRFAFSLETSASTAYLQINNLKNEDTATYFCA 97
>pdb|3UBX|H Chain H, Crystal Structure Of The Mouse Cd1d-C20:2-Agalcer-L363 Mab
Fab Complex
pdb|3UBX|G Chain G, Crystal Structure Of The Mouse Cd1d-C20:2-Agalcer-L363 Mab
Fab Complex
Length = 222
Score = 26.9 bits (58), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 16/63 (25%), Positives = 30/63 (47%), Gaps = 7/63 (11%)
Query: 93 KSRNKGYEWIGWRNESFPYGKPV-----EMVFEFDRVRNFTAMHLHINNYYSKDIQVFSH 147
++ KG +W+GW N G+P + F F + + +L INN ++D+ +
Sbjct: 39 QAPGKGLKWVGWINTY--TGEPTYADDFKGRFAFSLETSASTAYLEINNLKNEDMATYLC 96
Query: 148 ANV 150
A+
Sbjct: 97 ASA 99
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
0.319 0.137 0.411
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,647,514
Number of Sequences: 62578
Number of extensions: 267151
Number of successful extensions: 893
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 16
Number of HSP's that attempted gapping in prelim test: 880
Number of HSP's gapped (non-prelim): 18
length of query: 214
length of database: 14,973,337
effective HSP length: 95
effective length of query: 119
effective length of database: 9,028,427
effective search space: 1074382813
effective search space used: 1074382813
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)