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= 025622
(250 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3MUN|A Chain A, Appep_pepclose Closed State
pdb|3MUO|A Chain A, Appep_pepclose+pp Closed State
Length = 693
Score = 29.6 bits (65), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 11/25 (44%), Positives = 17/25 (68%)
Query: 179 SGTNAAVIRGALRAERPDLLTVILP 203
G+N ++ GA+ +RPDL+ V LP
Sbjct: 539 GGSNGGLLVGAVMTQRPDLMRVALP 563
>pdb|3IUN|A Chain A, Appep_d622n Opened State
pdb|3IUQ|A Chain A, Appep_d622n+pp Closed State
pdb|3IUR|A Chain A, Appep_d266nx+h2h3 Opened State
Length = 693
Score = 29.6 bits (65), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 11/25 (44%), Positives = 17/25 (68%)
Query: 179 SGTNAAVIRGALRAERPDLLTVILP 203
G+N ++ GA+ +RPDL+ V LP
Sbjct: 539 GGSNGGLLVGAVMTQRPDLMRVALP 563
>pdb|2RJK|A Chain A, Crystal Structure Of Human Tl1a Extracellular Domain C95s
Mutant
Length = 184
Score = 28.9 bits (63), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 181 TNAAVIRGALRAERPDLLTVILPQSLKKQPPESQELLAKVKTVIEKPHNDHLPLIEASRY 240
+ ++ IR A R +PD +TV++ + + PE +LL K+V E N P+ + +
Sbjct: 93 SESSEIRQAGRPNKPDSITVVITK-VTDSYPEPTQLLMGTKSVCEVGSNWFQPIYLGAMF 151
Query: 241 TI 242
++
Sbjct: 152 SL 153
>pdb|2RE9|A Chain A, Crystal Structure Of Tl1a At 2.1 A
pdb|2RE9|B Chain B, Crystal Structure Of Tl1a At 2.1 A
pdb|2RE9|C Chain C, Crystal Structure Of Tl1a At 2.1 A
Length = 181
Score = 28.9 bits (63), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 32/62 (51%), Gaps = 1/62 (1%)
Query: 181 TNAAVIRGALRAERPDLLTVILPQSLKKQPPESQELLAKVKTVIEKPHNDHLPLIEASRY 240
+ + IR A R +PD +TV++ + + PE +LL K+V E N P+ + +
Sbjct: 90 SECSEIRQAGRPNKPDSITVVITK-VTDSYPEPTQLLMGTKSVCEVGSNWFQPIYLGAMF 148
Query: 241 TI 242
++
Sbjct: 149 SL 150
>pdb|2QE3|A Chain A, Crystal Structure Of Human Tl1a Extracellular Domain
Length = 184
Score = 28.9 bits (63), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 32/62 (51%), Gaps = 1/62 (1%)
Query: 181 TNAAVIRGALRAERPDLLTVILPQSLKKQPPESQELLAKVKTVIEKPHNDHLPLIEASRY 240
+ + IR A R +PD +TV++ + + PE +LL K+V E N P+ + +
Sbjct: 93 SECSEIRQAGRPNKPDSITVVITK-VTDSYPEPTQLLMGTKSVCEVGSNWFQPIYLGAMF 151
Query: 241 TI 242
++
Sbjct: 152 SL 153
>pdb|2O0O|A Chain A, Crystal Structure Of Tl1a
pdb|2O0O|B Chain B, Crystal Structure Of Tl1a
pdb|2O0O|C Chain C, Crystal Structure Of Tl1a
Length = 180
Score = 28.5 bits (62), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 32/62 (51%), Gaps = 1/62 (1%)
Query: 181 TNAAVIRGALRAERPDLLTVILPQSLKKQPPESQELLAKVKTVIEKPHNDHLPLIEASRY 240
+ + IR A R +PD +TV++ + + PE +LL K+V E N P+ + +
Sbjct: 89 SECSEIRQAGRPNKPDSITVVITK-VTDSYPEPTQLLMGTKSVCEVGSNWFQPIYLGAMF 147
Query: 241 TI 242
++
Sbjct: 148 SL 149
>pdb|3IVM|A Chain A, Appep_wt+pp Closed State
Length = 693
Score = 28.5 bits (62), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 11/25 (44%), Positives = 16/25 (64%)
Query: 179 SGTNAAVIRGALRAERPDLLTVILP 203
G+N ++ GA+ +RPDL V LP
Sbjct: 539 GGSNGGLLVGAVXTQRPDLXRVALP 563
>pdb|3IUJ|A Chain A, Appep_wt2 Opened State
pdb|3IUL|A Chain A, Appep_wt1 Opened State
pdb|3IUM|A Chain A, Appep_wtx Opened State
Length = 693
Score = 28.5 bits (62), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 11/25 (44%), Positives = 16/25 (64%)
Query: 179 SGTNAAVIRGALRAERPDLLTVILP 203
G+N ++ GA+ +RPDL V LP
Sbjct: 539 GGSNGGLLVGAVXTQRPDLXRVALP 563
>pdb|2RJL|A Chain A, Crystal Structure Of Human Tl1a Extracellular Domain
C95sC135S MUTANT
pdb|3K51|A Chain A, Crystal Structure Of Dcr3-Tl1a Complex
Length = 184
Score = 27.7 bits (60), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 181 TNAAVIRGALRAERPDLLTVILPQSLKKQPPESQELLAKVKTVIEKPHNDHLPLIEASRY 240
+ ++ IR A R +PD +TV++ + + PE +LL K+V E N P+ + +
Sbjct: 93 SESSEIRQAGRPNKPDSITVVITK-VTDSYPEPTQLLMGTKSVSEVGSNWFQPIYLGAMF 151
Query: 241 TI 242
++
Sbjct: 152 SL 153
>pdb|3MI8|A Chain A, The Structure Of Tl1a-Dcr3 Complex
Length = 184
Score = 27.7 bits (60), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 32/62 (51%), Gaps = 1/62 (1%)
Query: 181 TNAAVIRGALRAERPDLLTVILPQSLKKQPPESQELLAKVKTVIEKPHNDHLPLIEASRY 240
+ + IR A R +PD +TV++ + + PE +LL K+V E N P+ + +
Sbjct: 93 SECSEIRQAGRPNKPDSITVVITK-VTDSYPEPTQLLMGTKSVSEVGSNWFQPIYLGAMF 151
Query: 241 TI 242
++
Sbjct: 152 SL 153
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 0.133 0.390
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,123,128
Number of Sequences: 62578
Number of extensions: 283984
Number of successful extensions: 562
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 557
Number of HSP's gapped (non-prelim): 11
length of query: 250
length of database: 14,973,337
effective HSP length: 96
effective length of query: 154
effective length of database: 8,965,849
effective search space: 1380740746
effective search space used: 1380740746
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: 50 (23.9 bits)