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= psy11633
(127 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1KHU|A Chain A, Smad1 Crystal Structure Reveals The Details Of Bmp
Signaling Pathway
pdb|1KHU|B Chain B, Smad1 Crystal Structure Reveals The Details Of Bmp
Signaling Pathway
pdb|1KHU|C Chain C, Smad1 Crystal Structure Reveals The Details Of Bmp
Signaling Pathway
pdb|1KHU|D Chain D, Smad1 Crystal Structure Reveals The Details Of Bmp
Signaling Pathway
Length = 218
Score = 115 bits (289), Expect = 5e-27, Method: Compositional matrix adjust.
Identities = 51/53 (96%), Positives = 51/53 (96%)
Query: 75 RMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLIQMGSPHQPISSVS 127
RMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVL QMGSPH PISSVS
Sbjct: 166 RMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLTQMGSPHNPISSVS 218
>pdb|3GMJ|D Chain D, Crystal Structure Of Mad Mh2 Domain
pdb|3GMJ|B Chain B, Crystal Structure Of Mad Mh2 Domain
pdb|3GMJ|A Chain A, Crystal Structure Of Mad Mh2 Domain
pdb|3GMJ|C Chain C, Crystal Structure Of Mad Mh2 Domain
Length = 245
Score = 113 bits (283), Expect = 3e-26, Method: Compositional matrix adjust.
Identities = 50/53 (94%), Positives = 50/53 (94%)
Query: 75 RMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLIQMGSPHQPISSVS 127
RMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVL QMGSPH ISSVS
Sbjct: 193 RMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLTQMGSPHNAISSVS 245
>pdb|3DIT|A Chain A, Crystal Structure Of Mad Mh2 Domain
pdb|3DIT|B Chain B, Crystal Structure Of Mad Mh2 Domain
pdb|3DIT|C Chain C, Crystal Structure Of Mad Mh2 Domain
Length = 188
Score = 100 bits (249), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 43/44 (97%), Positives = 43/44 (97%)
Query: 75 RMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLIQMGS 118
RMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVL QMGS
Sbjct: 145 RMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLTQMGS 188
>pdb|1MK2|A Chain A, Smad3 Sbd Complex
Length = 206
Score = 96.7 bits (239), Expect = 3e-21, Method: Compositional matrix adjust.
Identities = 44/53 (83%), Positives = 46/53 (86%)
Query: 75 RMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLIQMGSPHQPISSVS 127
RMSFVKGWGAEY RQ VTSTPCWIE+HL+GPLQWLDKVL QMGSP SSVS
Sbjct: 154 RMSFVKGWGAEYRRQTVTSTPCWIELHLNGPLQWLDKVLTQMGSPSIRCSSVS 206
>pdb|1MJS|A Chain A, Mh2 Domain Of Transcriptional Factor Smad3
Length = 197
Score = 96.7 bits (239), Expect = 3e-21, Method: Compositional matrix adjust.
Identities = 44/53 (83%), Positives = 46/53 (86%)
Query: 75 RMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLIQMGSPHQPISSVS 127
RMSFVKGWGAEY RQ VTSTPCWIE+HL+GPLQWLDKVL QMGSP SSVS
Sbjct: 145 RMSFVKGWGAEYRRQTVTSTPCWIELHLNGPLQWLDKVLTQMGSPSIRCSSVS 197
>pdb|1KHX|A Chain A, Crystal Structure Of A Phosphorylated Smad2
Length = 227
Score = 93.6 bits (231), Expect = 3e-20, Method: Compositional matrix adjust.
Identities = 40/45 (88%), Positives = 42/45 (93%)
Query: 75 RMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLIQMGSP 119
RMSFVKGWGAEY RQ VTSTPCWIE+HL+GPLQWLDKVL QMGSP
Sbjct: 175 RMSFVKGWGAEYRRQTVTSTPCWIELHLNGPLQWLDKVLTQMGSP 219
>pdb|1U7F|A Chain A, Crystal Structure Of The Phosphorylated Smad3SMAD4
Heterotrimeric Complex
pdb|1U7F|C Chain C, Crystal Structure Of The Phosphorylated Smad3SMAD4
Heterotrimeric Complex
Length = 198
Score = 93.6 bits (231), Expect = 3e-20, Method: Compositional matrix adjust.
Identities = 40/45 (88%), Positives = 42/45 (93%)
Query: 75 RMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLIQMGSP 119
RMSFVKGWGAEY RQ VTSTPCWIE+HL+GPLQWLDKVL QMGSP
Sbjct: 146 RMSFVKGWGAEYRRQTVTSTPCWIELHLNGPLQWLDKVLTQMGSP 190
>pdb|1U7V|A Chain A, Crystal Structure Of The Phosphorylated Smad2SMAD4
Heterotrimeric Complex
pdb|1U7V|C Chain C, Crystal Structure Of The Phosphorylated Smad2SMAD4
Heterotrimeric Complex
Length = 198
Score = 93.2 bits (230), Expect = 3e-20, Method: Compositional matrix adjust.
Identities = 40/45 (88%), Positives = 42/45 (93%)
Query: 75 RMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLIQMGSP 119
RMSFVKGWGAEY RQ VTSTPCWIE+HL+GPLQWLDKVL QMGSP
Sbjct: 146 RMSFVKGWGAEYRRQTVTSTPCWIELHLNGPLQWLDKVLTQMGSP 190
>pdb|1DEV|A Chain A, Crystal Structure Of Smad2 Mh2 Domain Bound To The Smad-
Binding Domain Of Sara
pdb|1DEV|C Chain C, Crystal Structure Of Smad2 Mh2 Domain Bound To The Smad-
Binding Domain Of Sara
Length = 196
Score = 86.7 bits (213), Expect = 3e-18, Method: Compositional matrix adjust.
Identities = 37/42 (88%), Positives = 39/42 (92%)
Query: 75 RMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLIQM 116
RMSFVKGWGAEY RQ VTSTPCWIE+HL+GPLQWLDKVL QM
Sbjct: 155 RMSFVKGWGAEYRRQTVTSTPCWIELHLNGPLQWLDKVLTQM 196
>pdb|1MR1|A Chain A, Crystal Structure Of A Smad4-Ski Complex
pdb|1MR1|B Chain B, Crystal Structure Of A Smad4-Ski Complex
Length = 235
Score = 65.5 bits (158), Expect = 7e-12, Method: Compositional matrix adjust.
Identities = 30/46 (65%), Positives = 34/46 (73%)
Query: 71 VLISRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLIQM 116
+ I RMSFVKGWG +Y RQ + TPCWIEIHLH LQ LD+VL M
Sbjct: 181 LCILRMSFVKGWGPDYPRQSIKETPCWIEIHLHRALQLLDEVLHTM 226
>pdb|1U7V|B Chain B, Crystal Structure Of The Phosphorylated Smad2SMAD4
Heterotrimeric Complex
Length = 236
Score = 65.5 bits (158), Expect = 7e-12, Method: Compositional matrix adjust.
Identities = 30/46 (65%), Positives = 34/46 (73%)
Query: 71 VLISRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLIQM 116
+ I RMSFVKGWG +Y RQ + TPCWIEIHLH LQ LD+VL M
Sbjct: 185 LCILRMSFVKGWGPDYPRQSIKETPCWIEIHLHRALQLLDEVLHTM 230
>pdb|1U7F|B Chain B, Crystal Structure Of The Phosphorylated Smad3SMAD4
Heterotrimeric Complex
Length = 239
Score = 65.5 bits (158), Expect = 8e-12, Method: Compositional matrix adjust.
Identities = 30/46 (65%), Positives = 34/46 (73%)
Query: 71 VLISRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLIQM 116
+ I RMSFVKGWG +Y RQ + TPCWIEIHLH LQ LD+VL M
Sbjct: 185 LCILRMSFVKGWGPDYPRQSIKETPCWIEIHLHRALQLLDEVLHTM 230
>pdb|1YGS|A Chain A, Crystal Structure Of The Smad4 Tumor Suppressor C-Terminal
Domain
Length = 234
Score = 65.5 bits (158), Expect = 8e-12, Method: Compositional matrix adjust.
Identities = 30/46 (65%), Positives = 34/46 (73%)
Query: 71 VLISRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLIQM 116
+ I RMSFVKGWG +Y RQ + TPCWIEIHLH LQ LD+VL M
Sbjct: 180 LCILRMSFVKGWGPDYPRQSIKETPCWIEIHLHRALQLLDEVLHTM 225
>pdb|1DD1|A Chain A, Crystal Structure Analysis Of The Smad4 Active Fragment
pdb|1DD1|B Chain B, Crystal Structure Analysis Of The Smad4 Active Fragment
pdb|1DD1|C Chain C, Crystal Structure Analysis Of The Smad4 Active Fragment
Length = 268
Score = 65.1 bits (157), Expect = 9e-12, Method: Compositional matrix adjust.
Identities = 30/46 (65%), Positives = 34/46 (73%)
Query: 71 VLISRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLIQM 116
+ I RMSFVKGWG +Y RQ + TPCWIEIHLH LQ LD+VL M
Sbjct: 214 LCILRMSFVKGWGPDYPRQSIKETPCWIEIHLHRALQLLDEVLHTM 259
>pdb|1G88|A Chain A, S4afl3arg515 Mutant
pdb|1G88|B Chain B, S4afl3arg515 Mutant
pdb|1G88|C Chain C, S4afl3arg515 Mutant
Length = 268
Score = 62.8 bits (151), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 29/46 (63%), Positives = 33/46 (71%)
Query: 71 VLISRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLIQM 116
+ I RMSFVKGWG +Y Q + TPCWIEIHLH LQ LD+VL M
Sbjct: 214 LCILRMSFVKGWGPDYPSQSIKETPCWIEIHLHRALQLLDEVLHTM 259
>pdb|2VPW|A Chain A, Polysulfide Reductase With Bound Menaquinone
pdb|2VPW|E Chain E, Polysulfide Reductase With Bound Menaquinone
pdb|2VPX|A Chain A, Polysulfide Reductase With Bound Quinone (uq1)
pdb|2VPX|E Chain E, Polysulfide Reductase With Bound Quinone (uq1)
pdb|2VPY|A Chain A, Polysulfide Reductase With Bound Quinone Inhibitor,
Pentachlorophenol (Pcp)
pdb|2VPY|E Chain E, Polysulfide Reductase With Bound Quinone Inhibitor,
Pentachlorophenol (Pcp)
pdb|2VPZ|A Chain A, Polysulfide Reductase Native Structure
pdb|2VPZ|E Chain E, Polysulfide Reductase Native Structure
Length = 765
Score = 26.6 bits (57), Expect = 4.1, Method: Composition-based stats.
Identities = 20/69 (28%), Positives = 33/69 (47%), Gaps = 12/69 (17%)
Query: 63 SVIILWYFVLISRMSFVKGWGAEY---------HRQDVTSTPCWIEIHLHGPLQWLDKVL 113
++++ W VLI + K + A+Y H +D T P W E H P Q + +V
Sbjct: 259 ALLLAWIHVLIYEDLYDKEYVAKYTVGFEELKAHVKDFT--PEWAEKHTEIPAQVIREVA 316
Query: 114 IQMGSPHQP 122
+M + H+P
Sbjct: 317 REMAA-HKP 324
>pdb|3M07|A Chain A, 1.4 Angstrom Resolution Crystal Structure Of Putative
Alpha Amylase From Salmonella Typhimurium
Length = 618
Score = 25.4 bits (54), Expect = 8.4, Method: Composition-based stats.
Identities = 11/25 (44%), Positives = 12/25 (48%)
Query: 73 ISRMSFVKGWGAEYHRQDVTSTPCW 97
+S F K WGAEY DV W
Sbjct: 25 MSSKIFCKSWGAEYIAADVVRFRLW 49
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
0.329 0.140 0.456
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,477,310
Number of Sequences: 62578
Number of extensions: 113354
Number of successful extensions: 244
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 228
Number of HSP's gapped (non-prelim): 17
length of query: 127
length of database: 14,973,337
effective HSP length: 87
effective length of query: 40
effective length of database: 9,529,051
effective search space: 381162040
effective search space used: 381162040
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 45 (21.9 bits)