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= 041499
(512 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3VNY|A Chain A, Crystal Structure Of Beta-Glucuronidase From
Acidobacterium Capsulatum
pdb|3VNZ|A Chain A, Crystal Structure Of Beta-Glucuronidase From
Acidobacterium Capsulatum In Complex With D-Glucuronic
Acid
pdb|3VO0|A Chain A, Crystal Structure Of Beta-Glucuronidase From
Acidobacterium Capsulatum Covalent-Bonded With
2-Deoxy-2-Fluoro-D-Glucuronic Acid
Length = 488
Score = 52.4 bits (124), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 77/344 (22%), Positives = 131/344 (38%), Gaps = 61/344 (17%)
Query: 80 IRVGGSLQDQVLY-KVGNSAKKCPHFKLRKD-GLFGFSKGCLSMNRWDEINDLFNQTGAM 137
+R+GG+ + + + H D G ++ ++ + +++ ++TG
Sbjct: 75 LRIGGNTSEYTFWNRHAKPTAADEHLAAGPDKGHHAAAREVITPEAVNNLSEFLDKTGWK 134
Query: 138 MTFGLNALIGRKKSKTDDTLWEGDWNAQNARDLMKYTISK--GYKIESYELGNE---LCA 192
+ +GLN G +NA D Y + ++ +++LGNE
Sbjct: 135 LIYGLNL---------------GKGTPENAADEAAYVMETIGADRLLAFQLGNEPDLFYR 179
Query: 193 SGVS-AKVSAEQYAKDIVALKNLVREMYPDATTQPKVLGPAGFFDKQWFNTFLEKSGQDV 251
+G+ A YA D +R+ P+A GP ++ +W F +K DV
Sbjct: 180 NGIRPASYDFAAYAGDWQRFFTAIRKRVPNA----PFAGPDTAYNTKWLVPFADKFKHDV 235
Query: 252 VDGLTHHIYNLGPGNDPEL-INRIQ--DPYYLDQIAQTYKDISETVKEFGPWSGAWVGEA 308
++ H Y GP DP + I R+ +P L + A + ++T F + E
Sbjct: 236 -KFISSHYYAEGPPTDPSMTIERLMKPNPRLLGETAGLKQVEADTGLPF------RLTET 288
Query: 309 GGAFNSGGKYVSHTFADGFWFLDQL------GMTSTFNHKVFCRQALIGGNYALLNTTT- 361
+ G + VS TFA W D + G T H GG Y
Sbjct: 289 NSCYQGGKQGVSDTFAAALWAGDLMYQQAAAGSTGINFH---------GGGYGWYTPVAG 339
Query: 362 -----FIPNPDYYGSLLWHRLMGKNVLA---TTQNASPYLRVYS 397
FI P+YYG LL+ + +L T +A+P L Y+
Sbjct: 340 TPEDGFIARPEYYGMLLFAQAGAGQLLGAKLTDNSAAPLLTAYA 383
>pdb|4ERH|A Chain A, The Crystal Structure Of Ompa Domain Of Ompa From
Salmonella Enterica Subsp. Enterica Serovar Typhimurium
Str. 14028s
pdb|4ERH|B Chain B, The Crystal Structure Of Ompa Domain Of Ompa From
Salmonella Enterica Subsp. Enterica Serovar Typhimurium
Str. 14028s
Length = 148
Score = 32.7 bits (73), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 38/83 (45%), Gaps = 14/83 (16%)
Query: 103 HFKLRKDGLFGFSKGCLSMNRWDEINDLFNQ-------TGAMMTFGLNALIGRKKSKTDD 155
HF L+ D LF F+K L ++ L++Q G+++ G IG D
Sbjct: 17 HFTLKSDVLFNFNKSTLKPEGQQALDQLYSQLSNLDPKDGSVVVLGFTDRIG------SD 70
Query: 156 TLWEGDWNAQNARDLMKYTISKG 178
+G + + A+ ++ Y ISKG
Sbjct: 71 AYNQG-LSEKRAQSVVDYLISKG 92
>pdb|4ATW|A Chain A, The Crystal Structure Of Arabinofuranosidase
pdb|4ATW|B Chain B, The Crystal Structure Of Arabinofuranosidase
pdb|4ATW|C Chain C, The Crystal Structure Of Arabinofuranosidase
pdb|4ATW|D Chain D, The Crystal Structure Of Arabinofuranosidase
pdb|4ATW|E Chain E, The Crystal Structure Of Arabinofuranosidase
pdb|4ATW|F Chain F, The Crystal Structure Of Arabinofuranosidase
Length = 482
Score = 30.0 bits (66), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 27/102 (26%), Positives = 48/102 (47%), Gaps = 8/102 (7%)
Query: 160 GDWNAQNARDLMKYTISKGYKIESYELGNELCASGVSAKVSAEQYAKDIVALKNLVREMY 219
G N A+ KY + Y ++ + +GNE+ ++A++YA+ A K + M
Sbjct: 143 GKGNTYYAQLRRKYGHPEPYNVKFWGIGNEMYGEWQVGHMTADEYAR---AAKEYTKWM- 198
Query: 220 PDATTQPKVLGPA-GFFDKQWFNTFLEKSGQDVVDGLTHHIY 260
P + A G D W L+++G DV+D +++H Y
Sbjct: 199 --KVFDPTIKAIAVGCDDPIWNLRVLQEAG-DVIDFISYHFY 237
>pdb|3UG3|A Chain A, Crystal Structure Of Alpha-L-Arabinofuranosidase From
Thermotoga Maritima Ligand Free Form
pdb|3UG3|B Chain B, Crystal Structure Of Alpha-L-Arabinofuranosidase From
Thermotoga Maritima Ligand Free Form
pdb|3UG3|C Chain C, Crystal Structure Of Alpha-L-Arabinofuranosidase From
Thermotoga Maritima Ligand Free Form
pdb|3UG3|D Chain D, Crystal Structure Of Alpha-L-Arabinofuranosidase From
Thermotoga Maritima Ligand Free Form
pdb|3UG3|E Chain E, Crystal Structure Of Alpha-L-Arabinofuranosidase From
Thermotoga Maritima Ligand Free Form
pdb|3UG3|F Chain F, Crystal Structure Of Alpha-L-Arabinofuranosidase From
Thermotoga Maritima Ligand Free Form
pdb|3UG4|A Chain A, Crystal Structure Of Alpha-L-Arabinofuranosidase From
Thermotoga Maritima Arabinose Complex
pdb|3UG4|B Chain B, Crystal Structure Of Alpha-L-Arabinofuranosidase From
Thermotoga Maritima Arabinose Complex
pdb|3UG4|C Chain C, Crystal Structure Of Alpha-L-Arabinofuranosidase From
Thermotoga Maritima Arabinose Complex
pdb|3UG4|D Chain D, Crystal Structure Of Alpha-L-Arabinofuranosidase From
Thermotoga Maritima Arabinose Complex
pdb|3UG4|E Chain E, Crystal Structure Of Alpha-L-Arabinofuranosidase From
Thermotoga Maritima Arabinose Complex
pdb|3UG4|F Chain F, Crystal Structure Of Alpha-L-Arabinofuranosidase From
Thermotoga Maritima Arabinose Complex
pdb|3UG5|A Chain A, Crystal Structure Of Alpha-L-Arabinofuranosidase From
Thermotoga Maritima Xylose Complex
pdb|3UG5|B Chain B, Crystal Structure Of Alpha-L-Arabinofuranosidase From
Thermotoga Maritima Xylose Complex
pdb|3UG5|C Chain C, Crystal Structure Of Alpha-L-Arabinofuranosidase From
Thermotoga Maritima Xylose Complex
pdb|3UG5|D Chain D, Crystal Structure Of Alpha-L-Arabinofuranosidase From
Thermotoga Maritima Xylose Complex
pdb|3UG5|E Chain E, Crystal Structure Of Alpha-L-Arabinofuranosidase From
Thermotoga Maritima Xylose Complex
pdb|3UG5|F Chain F, Crystal Structure Of Alpha-L-Arabinofuranosidase From
Thermotoga Maritima Xylose Complex
Length = 504
Score = 30.0 bits (66), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 27/102 (26%), Positives = 48/102 (47%), Gaps = 8/102 (7%)
Query: 160 GDWNAQNARDLMKYTISKGYKIESYELGNELCASGVSAKVSAEQYAKDIVALKNLVREMY 219
G N A+ KY + Y ++ + +GNE+ ++A++YA+ A K + M
Sbjct: 163 GKGNTYYAQLRRKYGHPEPYNVKFWGIGNEMYGEWQVGHMTADEYAR---AAKEYTKWM- 218
Query: 220 PDATTQPKVLGPA-GFFDKQWFNTFLEKSGQDVVDGLTHHIY 260
P + A G D W L+++G DV+D +++H Y
Sbjct: 219 --KVFDPTIKAIAVGCDDPIWNLRVLQEAG-DVIDFISYHFY 257
>pdb|3S2C|A Chain A, Structure Of The Thermostable Gh51
Alpha-L-Arabinofuranosidase From Thermotoga Petrophila
Rku-1
pdb|3S2C|B Chain B, Structure Of The Thermostable Gh51
Alpha-L-Arabinofuranosidase From Thermotoga Petrophila
Rku-1
pdb|3S2C|C Chain C, Structure Of The Thermostable Gh51
Alpha-L-Arabinofuranosidase From Thermotoga Petrophila
Rku-1
pdb|3S2C|D Chain D, Structure Of The Thermostable Gh51
Alpha-L-Arabinofuranosidase From Thermotoga Petrophila
Rku-1
pdb|3S2C|E Chain E, Structure Of The Thermostable Gh51
Alpha-L-Arabinofuranosidase From Thermotoga Petrophila
Rku-1
pdb|3S2C|F Chain F, Structure Of The Thermostable Gh51
Alpha-L-Arabinofuranosidase From Thermotoga Petrophila
Rku-1
pdb|3S2C|G Chain G, Structure Of The Thermostable Gh51
Alpha-L-Arabinofuranosidase From Thermotoga Petrophila
Rku-1
pdb|3S2C|H Chain H, Structure Of The Thermostable Gh51
Alpha-L-Arabinofuranosidase From Thermotoga Petrophila
Rku-1
pdb|3S2C|I Chain I, Structure Of The Thermostable Gh51
Alpha-L-Arabinofuranosidase From Thermotoga Petrophila
Rku-1
pdb|3S2C|J Chain J, Structure Of The Thermostable Gh51
Alpha-L-Arabinofuranosidase From Thermotoga Petrophila
Rku-1
pdb|3S2C|K Chain K, Structure Of The Thermostable Gh51
Alpha-L-Arabinofuranosidase From Thermotoga Petrophila
Rku-1
pdb|3S2C|L Chain L, Structure Of The Thermostable Gh51
Alpha-L-Arabinofuranosidase From Thermotoga Petrophila
Rku-1
Length = 484
Score = 30.0 bits (66), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 27/102 (26%), Positives = 48/102 (47%), Gaps = 8/102 (7%)
Query: 160 GDWNAQNARDLMKYTISKGYKIESYELGNELCASGVSAKVSAEQYAKDIVALKNLVREMY 219
G N A+ KY + Y ++ + +GNE+ ++A++YA+ A K + M
Sbjct: 143 GKGNTYYAQLRRKYGHPEPYNVKFWGIGNEMYGEWQVGHMTADEYAR---AAKEYTKWM- 198
Query: 220 PDATTQPKVLGPA-GFFDKQWFNTFLEKSGQDVVDGLTHHIY 260
P + A G D W L+++G DV+D +++H Y
Sbjct: 199 --KVFDPTIKAIAVGCDDPIWNLRVLQEAG-DVIDFISYHFY 237
>pdb|3NB3|A Chain A, The Host Outer Membrane Proteins Ompa And Ompc Are Packed
At Specific Sites In The Shigella Phage Sf6 Virion As
Structural Components
pdb|3NB3|B Chain B, The Host Outer Membrane Proteins Ompa And Ompc Are Packed
At Specific Sites In The Shigella Phage Sf6 Virion As
Structural Components
pdb|3NB3|C Chain C, The Host Outer Membrane Proteins Ompa And Ompc Are Packed
At Specific Sites In The Shigella Phage Sf6 Virion As
Structural Components
Length = 346
Score = 29.6 bits (65), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 27/105 (25%), Positives = 46/105 (43%), Gaps = 17/105 (16%)
Query: 100 KCPHFKLRKDGLFGFSKGCLSMNRWDEINDLFNQ-------TGAMMTFGLNALIGRKKSK 152
+ HF L+ D LF F+K L ++ L++Q G+++ G IG
Sbjct: 211 QTKHFTLKSDVLFNFNKATLKPEGQAALDQLYSQLSNLDPKDGSVVVLGYTDRIG----- 265
Query: 153 TDDTLWEGDWNAQNARDLMKYTISKGY---KIESYELGNELCASG 194
D +G + + A+ ++ Y ISKG KI + +G +G
Sbjct: 266 -SDAYNQG-LSERRAQSVVDYLISKGIPADKISARGMGESNPVTG 308
>pdb|3EXO|A Chain A, Crystal Structure Of Bace1 Bound To Inhibitor
Length = 413
Score = 28.9 bits (63), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 22/33 (66%), Gaps = 3/33 (9%)
Query: 278 YYLDQIAQTYKDISETVKEFGPWS-GAWVGEAG 309
YY Q++ TY+D+ + V + P++ GAW GE G
Sbjct: 71 YYQRQLSSTYRDLRKGV--YVPYTQGAWAGELG 101
>pdb|2QZL|A Chain A, Crystal Structure Of Human Beta Secretase Complexed With
Ixs
Length = 411
Score = 28.9 bits (63), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 22/33 (66%), Gaps = 3/33 (9%)
Query: 278 YYLDQIAQTYKDISETVKEFGPWS-GAWVGEAG 309
YY Q++ TY+D+ + V + P++ GAW GE G
Sbjct: 77 YYQRQLSSTYRDLRKGV--YVPYTQGAWAGELG 107
>pdb|2ZJJ|A Chain A, Crystal Structure Of The Human Bace1 Catalytic Domain In
Complex With 4-(4-Fluoro-Benzyl)-Piperazine-2-Carboxylic
Acid (2-Mercapto-Ethyl)- Amide
Length = 405
Score = 28.9 bits (63), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 22/33 (66%), Gaps = 3/33 (9%)
Query: 278 YYLDQIAQTYKDISETVKEFGPWS-GAWVGEAG 309
YY Q++ TY+D+ + V + P++ GAW GE G
Sbjct: 71 YYQRQLSSTYRDLRKGV--YVPYTQGAWAGELG 101
>pdb|1TQF|A Chain A, Crystal Structure Of Human Beta Secretase Complexed With
Inhibitor
pdb|2B8L|A Chain A, Crystal Structure Of Human Beta Secretase Complexed With
Inhibitor
pdb|2B8V|A Chain A, Crystal Structure Of Human Beta-Secretase Complexed With
L- L000430,469
pdb|2IRZ|A Chain A, Crystal Structure Of Human Beta-Secretase Complexed With
Inhibitor
pdb|2IS0|A Chain A, Crystal Structure Of Human Beta-Secretase Complexed With
Inhibitor
pdb|2PH6|A Chain A, Crystal Structure Of Human Beta Secretase Complexed With
Inhibitor
pdb|2OAH|A Chain A, Crystal Structure Of Human Beta Secretase Complexed With
Inhibitor
pdb|2P8H|A Chain A, Crystal Structure Of Human Beta Secretase Complexed With
Inhibitor
pdb|2NTR|A Chain A, Crystal Structure Of Human Bace-1 Bound To Inhibitor
pdb|2PH8|A Chain A, Crystal Structure Of Human Beta Secretase Complexed With
Inhibitor
pdb|2QZK|A Chain A, Crystal Structure Of Human Beta Secretase Complexed With
I21
pdb|2ZJM|A Chain A, Crystal Structure Of The Human Bace1 Catalytic Domain In
Complex With
N-[1-(5-Chloro-2-Isopropoxy-3-Methoxy-Benzyl)-
Piperidin-4-Yl]-2-(4-Sulfamoyl-Phenoxy)-Acetamide
pdb|3FKT|A Chain A, Crystal Structure Of Human Beta Secretase Complexed With
Spiropiperdine Iminohydantoin Inhibitor
Length = 405
Score = 28.5 bits (62), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 22/33 (66%), Gaps = 3/33 (9%)
Query: 278 YYLDQIAQTYKDISETVKEFGPWS-GAWVGEAG 309
YY Q++ TY+D+ + V + P++ GAW GE G
Sbjct: 71 YYQRQLSSTYRDLRKGV--YVPYTQGAWAGELG 101
>pdb|3TPJ|A Chain A, Apo Structure Of Bace1
pdb|3TPL|A Chain A, Apo Structure Of Bace1
pdb|3TPL|B Chain B, Apo Structure Of Bace1
pdb|3TPL|C Chain C, Apo Structure Of Bace1
pdb|3TPP|A Chain A, Crystal Structure Of Bace1 Complexed With An Inhibitor
pdb|3UQP|A Chain A, Crystal Structure Of Bace1 With Its Inhibitor
pdb|3UQU|A Chain A, Crystal Structure Of Bace1 With Its Inhibitor
pdb|3UQW|A Chain A, Crystal Structure Of Bace1 With Its Inhibitor
pdb|3UQX|A Chain A, Crystal Structure Of Bace1 With Its Inhibitor
pdb|4DV9|A Chain A, Crystal Structure Of Bace1 With Its Inhibitor
pdb|4DVF|A Chain A, Crystal Structure Of Bace1 With Its Inhibitor
pdb|4DVF|B Chain B, Crystal Structure Of Bace1 With Its Inhibitor
pdb|4FGX|A Chain A, Crystal Structure Of Bace1 With Novel Inhibitor
Length = 433
Score = 28.5 bits (62), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 22/33 (66%), Gaps = 3/33 (9%)
Query: 278 YYLDQIAQTYKDISETVKEFGPWS-GAWVGEAG 309
YY Q++ TY+D+ + V + P++ GAW GE G
Sbjct: 91 YYQRQLSSTYRDLRKGV--YVPYTQGAWAGELG 121
>pdb|3QI1|A Chain A, Design And Synthesis Of Hydroxyethylamine (Hea) Bace-1
Inhibitors: Prime Side Chromane-Containing Inhibitors
Length = 408
Score = 28.5 bits (62), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 22/33 (66%), Gaps = 3/33 (9%)
Query: 278 YYLDQIAQTYKDISETVKEFGPWS-GAWVGEAG 309
YY Q++ TY+D+ + V + P++ GAW GE G
Sbjct: 67 YYQRQLSSTYRDLRKGV--YVPYTQGAWAGELG 97
>pdb|1TUX|A Chain A, High Resolution Crystal Structure Of A Thermostable
Xylanase From Thermoascus Aurantiacus
Length = 301
Score = 28.5 bits (62), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 30/121 (24%), Positives = 49/121 (40%), Gaps = 12/121 (9%)
Query: 121 MNRWDEINDLFNQTGAMMTFGLNALIGR----------KKSKTDDTLWEGDWNAQNARDL 170
+ WD +N+ FN+ G++ N +IG + + + L+ D+N +A
Sbjct: 123 IRAWDVVNEAFNEDGSLRQTVFNNVIGEDYIPIAFRTARAADPNAKLYINDYNLDSASKP 182
Query: 171 MKYTISKGYKIESYELGNELCASGVSAKVSAEQYAKDIVALKNLVREMYPD-ATTQPKVL 229
I K K + G + G +SA Q A AL NL P+ A T+ +
Sbjct: 183 KTSAIVKRVK-KWRAAGVPIDGIGSQTHLSAGQGASIDAALPNLASAGTPEVAITELDIA 241
Query: 230 G 230
G
Sbjct: 242 G 242
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 0.135 0.421
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,590,863
Number of Sequences: 62578
Number of extensions: 744655
Number of successful extensions: 1823
Number of sequences better than 100.0: 28
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 28
Number of HSP's that attempted gapping in prelim test: 1814
Number of HSP's gapped (non-prelim): 34
length of query: 512
length of database: 14,973,337
effective HSP length: 103
effective length of query: 409
effective length of database: 8,527,803
effective search space: 3487871427
effective search space used: 3487871427
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)