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= 028143
(213 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 = 30.0 bits (66), Expect = 0.98, Method: Composition-based stats.
Identities = 11/24 (45%), Positives = 17/24 (70%)
Query: 110 GTNAAVIRGALRAERPDLLTVILP 133
G+N ++ GA+ +RPDL+ V LP
Sbjct: 540 GSNGGLLVGAVMTQRPDLMRVALP 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 = 30.0 bits (66), Expect = 1.0, Method: Composition-based stats.
Identities = 11/24 (45%), Positives = 17/24 (70%)
Query: 110 GTNAAVIRGALRAERPDLLTVILP 133
G+N ++ GA+ +RPDL+ V LP
Sbjct: 540 GSNGGLLVGAVMTQRPDLMRVALP 563
>pdb|3IVM|A Chain A, Appep_wt+pp Closed State
Length = 693
Score = 28.9 bits (63), Expect = 2.4, Method: Composition-based stats.
Identities = 11/24 (45%), Positives = 16/24 (66%)
Query: 110 GTNAAVIRGALRAERPDLLTVILP 133
G+N ++ GA+ +RPDL V LP
Sbjct: 540 GSNGGLLVGAVXTQRPDLXRVALP 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 = 28.9 bits (63), Expect = 2.4, Method: Composition-based stats.
Identities = 11/24 (45%), Positives = 16/24 (66%)
Query: 110 GTNAAVIRGALRAERPDLLTVILP 133
G+N ++ GA+ +RPDL V LP
Sbjct: 540 GSNGGLLVGAVXTQRPDLXRVALP 563
>pdb|2RJK|A Chain A, Crystal Structure Of Human Tl1a Extracellular Domain C95s
Mutant
Length = 184
Score = 28.5 bits (62), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 29/54 (53%), Gaps = 1/54 (1%)
Query: 111 TNAAVIRGALRAERPDLLTVILPQSLKKQPPESQELLAKVKTVIEKPHNDHLPL 164
+ ++ IR A R +PD +TV++ + + PE +LL K+V E N P+
Sbjct: 93 SESSEIRQAGRPNKPDSITVVITK-VTDSYPEPTQLLMGTKSVCEVGSNWFQPI 145
>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 = 28.1 bits (61), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 26/49 (53%), Gaps = 1/49 (2%)
Query: 116 IRGALRAERPDLLTVILPQSLKKQPPESQELLAKVKTVIEKPHNDHLPL 164
IR A R +PD +TV++ + + PE +LL K+V E N P+
Sbjct: 95 IRQAGRPNKPDSITVVITK-VTDSYPEPTQLLMGTKSVCEVGSNWFQPI 142
>pdb|2QE3|A Chain A, Crystal Structure Of Human Tl1a Extracellular Domain
Length = 184
Score = 28.1 bits (61), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 26/49 (53%), Gaps = 1/49 (2%)
Query: 116 IRGALRAERPDLLTVILPQSLKKQPPESQELLAKVKTVIEKPHNDHLPL 164
IR A R +PD +TV++ + + PE +LL K+V E N P+
Sbjct: 98 IRQAGRPNKPDSITVVITK-VTDSYPEPTQLLMGTKSVCEVGSNWFQPI 145
>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 = 28.1 bits (61), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 26/49 (53%), Gaps = 1/49 (2%)
Query: 116 IRGALRAERPDLLTVILPQSLKKQPPESQELLAKVKTVIEKPHNDHLPL 164
IR A R +PD +TV++ + + PE +LL K+V E N P+
Sbjct: 94 IRQAGRPNKPDSITVVITK-VTDSYPEPTQLLMGTKSVCEVGSNWFQPI 141
>pdb|3CA8|A Chain A, Crystal Structure Of Escherichia Coli Ydcf, An
S-Adenosyl-L-Methionine Utilizing Enzyme
pdb|3CA8|B Chain B, Crystal Structure Of Escherichia Coli Ydcf, An
S-Adenosyl-L-Methionine Utilizing Enzyme
Length = 266
Score = 28.1 bits (61), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 16 NVIGMFGSDEDVGTQIPTQAQSVVEGSGAVM 46
NVIG + + +D ++P QA V+ AVM
Sbjct: 18 NVIGQWLAQDDFSGEVPYQADCVILAGNAVM 48
>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 = 4.7, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 29/54 (53%), Gaps = 1/54 (1%)
Query: 111 TNAAVIRGALRAERPDLLTVILPQSLKKQPPESQELLAKVKTVIEKPHNDHLPL 164
+ ++ IR A R +PD +TV++ + + PE +LL K+V E N P+
Sbjct: 93 SESSEIRQAGRPNKPDSITVVITK-VTDSYPEPTQLLMGTKSVSEVGSNWFQPI 145
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
0.320 0.136 0.383
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,857,946
Number of Sequences: 62578
Number of extensions: 224646
Number of successful extensions: 462
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 457
Number of HSP's gapped (non-prelim): 10
length of query: 213
length of database: 14,973,337
effective HSP length: 95
effective length of query: 118
effective length of database: 9,028,427
effective search space: 1065354386
effective search space used: 1065354386
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)